commit b53f4c1f72de6e20f319042baeef52d923db39ea Merge: 626474a 220e5ec Author: Jim Kent Date: Tue Aug 24 18:31:03 2010 -0700 Merge branch 'master' of kent@hgwdev.cse.ucsc.edu:/data/git/kent commit 626474af02e164b0841f341366cda37f24e183ef Author: Jim Kent Date: Tue Aug 24 18:26:14 2010 -0700 Taking this out of main branch. ENCODE Portal changes should now just be on purplePortal local branch. Revert "Starting on an ENCODE specific style sheet." This reverts commit 327e6f818033d8bc0114d944a7b4e2433bc9c79b. commit 220e5ec076e79432d366b3a2a2bb560b8683112a Merge: f83fca9 d0e33a1 Author: vanessa Date: Tue Aug 24 17:18:23 2010 -0700 Merge branch 'master' of vanessa@hgwdev.cse.ucsc.edu:/data/git/kent commit f83fca90454f76b1a74f9366f1b4efbb62d3ff27 Author: vanessa Date: Tue Aug 24 17:15:37 2010 -0700 centered the image and added a border using css commit d0e33a1190c4693ae8bba022312dd8a81e7302cb Author: Tim Dreszer Date: Tue Aug 24 16:13:38 2010 -0700 Added to the suggested improvements list the white-listing of mdb vars. commit 879ac97e46be414bc2357ee01e977a0a05c765d0 Author: Tim Dreszer Date: Tue Aug 24 16:04:44 2010 -0700 Removed comment about broken val drop-down update. commit c05dc3339f0114c3580e856c6d120898e31fba81 Author: Tim Dreszer Date: Tue Aug 24 15:57:10 2010 -0700 Newly populated val dropdowns should enable searching commit aba9ee18d932daaa659dc3298c0ea4db250fc704 Author: Tim Dreszer Date: Tue Aug 24 15:47:41 2010 -0700 Added clear button and fixed bombing simple search, among other things commit 4a137c940e730eeddf1fd887dd56c101ba0bb2f8 Author: katrina Date: Tue Aug 24 15:10:21 2010 -0700 added Donna's regulation track announcement, minimized the most recentannouncement and removed the oldest announcement commit 4536943a3de0910405482fe418e4772a8449ef93 Merge: b85e290 63daf44 Author: katrina Date: Tue Aug 24 14:28:27 2010 -0700 Merge branch 'master' of hgwdev:/data/git/kent commit b85e2907ca92487ff22d8bbea4a3e616da5c9ea0 Author: katrina Date: Tue Aug 24 14:28:19 2010 -0700 Added 18 August 2010 - Cat Genome Browser Available and removed a dash in a comment to make the colors in my browser appear commit 63daf44e237ff298a94dd9ac0c89911ca418c359 Merge: 468048a 23ee025 Author: Hiram Clawson Date: Tue Aug 24 14:19:28 2010 -0700 Merge branch 'master' of hiram@hgwdev.cse.ucsc.edu:/data/git/kent commit 468048aa6d5b9103831b05ddb9fc87d81fb5c59b Author: Hiram Clawson Date: Tue Aug 24 14:19:17 2010 -0700 do not check for base coloring if itemRgb is on commit 23ee02565d5ee5aba67c9e43f87c65db34a6f899 Author: Brian Raney Date: Tue Aug 24 13:21:18 2010 -0700 fix a bug where if Jim's regulation multi-wiggles were selected, core was dumped commit 1d26595eb7df0cd4feb9f792fde0a0af25f783eb Author: katrina Date: Tue Aug 24 12:29:30 2010 -0700 adding image to use in the ENCODE Regulation track announcement commit 19addf2d748df25a3ea1937eea0cc46c72903dc7 Merge: d3b4766 7dbe705 Author: Brian Raney Date: Tue Aug 24 11:29:38 2010 -0700 Merge branch 'master' of braney@hgwdev.cse.ucsc.edu:/data/git/kent commit 7dbe705372d9a9cedb67942f3d6bce431e2fbb40 Author: Hiram Clawson Date: Tue Aug 24 11:29:15 2010 -0700 bed 9 . will turn on score filters and add scoreFilterByRange commit d3b4766537ad22870759479c5560b9f141971779 Author: Brian Raney Date: Tue Aug 24 11:29:11 2010 -0700 fix problem with mouse cell types not getting the org right commit 12b24720f1b1a857eb5ea2db69218111a4f886df Author: Hiram Clawson Date: Tue Aug 24 09:46:08 2010 -0700 do not use expr, use awk instead commit fe6ffc7a7e8badf24041927468086f699927c855 Merge: de8a126 334f608 Author: Hiram Clawson Date: Tue Aug 24 09:41:21 2010 -0700 Merge branch 'master' of hiram@hgwdev.cse.ucsc.edu:/data/git/kent commit de8a1261ff603848a8611203458d7a01c52b8187 Author: Hiram Clawson Date: Tue Aug 24 09:41:15 2010 -0700 do not use expr, use awk instead commit 334f6082eb4f20c25fb8d912097503981e6a41e2 Author: Galt Barber Date: Tue Aug 24 08:00:09 2010 -0700 "Encode release log update" commit e99ce51ced2d461f2901dbbc6bd62683156abfd7 Author: Galt Barber Date: Tue Aug 24 08:00:08 2010 -0700 "Release log update" commit f94cab12bf79de588cdd7682ce24a7afbf62db66 Merge: d03112c 9d16050 Author: Angie Hinrichs Date: Mon Aug 23 19:25:34 2010 -0700 Merge branch 'master' of angie@hgwdev.cse.ucsc.edu:/data/git/kent commit d03112c5eda04bf13ece1613bd57be9ad593c5d6 Author: Angie Hinrichs Date: Mon Aug 23 19:25:13 2010 -0700 [MLQ #763 inconsistency with Neandertal Selection Sweep Scan display]: user found that ntSss description had Papuan and Han in the wrong order, confirmed by Ed Green. Swapped them back and also put the modern human BAM in the same order as the ntSss codes. commit 9d1605021fb725871d7daa82c22f3ee1c402b6d6 Merge: d637d73 662c142 Author: Brian Raney Date: Mon Aug 23 17:27:41 2010 -0700 Merge branch 'master' of hgwdev:/data/git/kent commit d637d73e3c34de9ed4adfc782b389164e4129bfa Author: Brian Raney Date: Mon Aug 23 17:27:34 2010 -0700 v239 preview commit 662c142fd7755be0eadbdfa5391b9548bc7f4ccd Author: Tim Dreszer Date: Mon Aug 23 16:32:11 2010 -0700 Got popup box for descrition in findTracks working properly commit 327e6f818033d8bc0114d944a7b4e2433bc9c79b Author: Jim Kent Date: Mon Aug 23 14:14:39 2010 -0700 Starting on an ENCODE specific style sheet. commit 914f65b1c0fce017682fa7b0e0407d94aa8a2f21 Author: Brian Raney Date: Mon Aug 23 13:36:32 2010 -0700 add a few missing variables commit 2be1929850e0eaa0450ba72536abb923cd4a0f02 Merge: 6cd3bfc 59cc4a1 Author: Brian Raney Date: Mon Aug 23 13:31:13 2010 -0700 Merge branch 'master' of braney@hgwdev.cse.ucsc.edu:/data/git/kent commit 6cd3bfc4dddd1faae0f85770efc301cc54aca3ac Author: Brian Raney Date: Mon Aug 23 13:30:52 2010 -0700 fix up label for the 2way commit 59cc4a1f35ad0ec3a34a762ed8eeabff9db61283 Merge: 7512717 e9adb40 Author: Chin Li Date: Mon Aug 23 10:32:52 2010 -0700 Merge branch 'master' of chinhli@hgwdev.cse.ucsc.edu:/data/git/kent commit 7512717591fbfe6886fcfdf7371a8d1c8be6184d Author: Chin Li Date: Mon Aug 23 10:32:45 2010 -0700 liftOver to felCat3 commit 6e5ec48c37a4d5785b474b93822e4c41ad844662 Author: Chin Li Date: Mon Aug 23 10:31:03 2010 -0700 NumtS tracks commit 7f5736452e11aa082b17c1b0e7e3a59c1b6d8624 Author: Chin Li Date: Mon Aug 23 08:32:22 2010 -0700 felCat3 liftOver to felCat4 commit e9adb40c8a7e046b153e39efa7948ebca76b669b Author: Galt Barber Date: Mon Aug 23 08:00:04 2010 -0700 "Encode release log update" commit 571b4253413b9e1f4927d066d1754e590cd80949 Author: Galt Barber Date: Mon Aug 23 08:00:04 2010 -0700 "Release log update" commit 63d12ea027dad24fd23bd141aefb740413399ba9 Author: Galt Barber Date: Sun Aug 22 08:00:08 2010 -0700 "Encode release log update" commit d155710eafcef8485ae3bb8ea0ee97a57c27bb66 Author: Galt Barber Date: Sun Aug 22 08:00:07 2010 -0700 "Release log update" commit 0c0cedbb6e3cb4d28ef2a5dc7cbad2a1a67afa09 Author: Larry Meyer Date: Sat Aug 21 18:00:24 2010 -0700 loading image used when loading tracks (copied from CB) commit 7fb1a50f661c0dcfa647f99d372328d493376040 Merge: 0f2388a 8ef284e Author: Larry Meyer Date: Sat Aug 21 17:59:18 2010 -0700 Merge branch 'master' of larrym@hgwdev.cse.ucsc.edu:/data/git/kent into mutationClassifier commit 0f2388a167a1ea5f0371ace772bb57840aaa2e84 Author: Larry Meyer Date: Sat Aug 21 17:59:14 2010 -0700 add showLoadingImage commit 8ef284effa3a0d6117d1f6608621149945c09b49 Merge: c48749a b6dd63d Author: Brian Raney Date: Sat Aug 21 12:14:07 2010 -0700 Merge branch 'master' of braney@hgwdev.cse.ucsc.edu:/data/git/kent commit c48749af2f808cb0ac8589270053aaeb9ea55f14 Author: Brian Raney Date: Sat Aug 21 12:13:48 2010 -0700 re-did Human Proteins. commit b6dd63df52aa458131dc37ab729c761a3106fdcc Author: Galt Barber Date: Sat Aug 21 08:01:23 2010 -0700 "Encode release log update" commit 6c697d02493cf68cbc0b67916d7ad0ad580f19e4 Author: Galt Barber Date: Sat Aug 21 08:01:22 2010 -0700 "Release log update" commit 5502bafda708e2d084b1a569e492b73150db8638 Merge: 7abdd38 7fee54a Author: Brian Raney Date: Fri Aug 20 17:53:27 2010 -0700 Merge branch 'master' of braney@hgwdev.cse.ucsc.edu:/data/git/kent commit 7abdd38f20cf638c7cea57c0830ad38977e0e1f2 Author: Brian Raney Date: Fri Aug 20 17:52:42 2010 -0700 get wgEncodeGencode into it's own include file commit 7fee54adcd12c86c24e6656bc32631b4d61a3b88 Merge: 3e02042 8a5a8d5 Author: Brooke Rhead Date: Fri Aug 20 16:58:07 2010 -0700 Merge branch 'master' of rhead@hgwdev.cse.ucsc.edu:/data/git/kent commit 3e02042292c7078b61936410f57eb73fcf0f8fb2 Author: Brooke Rhead Date: Fri Aug 20 16:58:02 2010 -0700 Changed broken link yeastgfp.ucsf.edu to working link yeastgfp.yeastgenome.org. commit 8a5a8d5faea9657f93764d93a6a88da82b6f5ea3 Merge: 5542f25 e6fec86 Author: katrina Date: Fri Aug 20 16:27:36 2010 -0700 Merge branch 'master' of hgwdev:/data/git/kent commit 5542f259c1532e3b8cf0de02345693781edde21a Author: katrina Date: Fri Aug 20 16:27:09 2010 -0700 enabling metadata on Gencode Genes V4 to complete staging on beta commit e6fec862fb2acd1f43983d1dbe639ecb68385222 Merge: 93af650 b6f725d Author: Cricket Sloan Date: Fri Aug 20 16:24:06 2010 -0700 Merge branch 'master' of cricket@hgwdev.cse.ucsc.edu:/data/git/kent commit 93af6502d2e3921d5af64e1a031abd38a33a3f20 Author: Cricket Sloan Date: Fri Aug 20 16:21:13 2010 -0700 Changed short labels to add sh for short commit 6577bce7e86f4f849a74ac9f685cf183e313b675 Author: Cricket Sloan Date: Fri Aug 20 16:15:01 2010 -0700 Changed short labels to match DNA PET and added settings for bam files commit b6f725d47d7e538003b47402b47b4b3cc4f457fe Merge: de1c86c 89a7912 Author: Hiram Clawson Date: Fri Aug 20 16:12:22 2010 -0700 Merge branch 'master' of hiram@hgwdev.cse.ucsc.edu:/data/git/kent commit de1c86c039f0a86655d9347fcb1da7c8a8c0738f Author: Hiram Clawson Date: Fri Aug 20 16:10:04 2010 -0700 changing haplotypeLocations track to altSequence commit 89a7912271fbe67c1b5a8bebdabdde03c6e64b2f Merge: 2b8eef8 3bc38d5 Author: Angie Hinrichs Date: Fri Aug 20 12:02:55 2010 -0700 Merge branch 'master' of angie@hgwdev.cse.ucsc.edu:/data/git/kent commit 2b8eef88acb4dacd494319e2078b5d5981b80cf8 Author: Angie Hinrichs Date: Fri Aug 20 12:02:11 2010 -0700 [Genome Browser - Feature #559] Mary-Claire King's wish list: split hg19.snp131 into two tracks, one with only the SNPs marked as clinically associated by dbSNP, and the other with everything else. At Jim's request, making the clinical SNPs hidden by default, and the non-clinical visible by default to give a picture of typical human variation. commit 8f10629a2eef66ca9076ba84ed43e4de2cc4420e Author: Angie Hinrichs Date: Fri Aug 20 11:22:09 2010 -0700 In overrideField, ignore release tag because it has already been processed and removed from overTd->settingsHash. Now we can have release-specific overrides. commit 3bc38d53aa847acd0915b4c5cf84b5a84795643a Merge: d55a3d6 aa987b1 Author: Hiram Clawson Date: Fri Aug 20 10:40:03 2010 -0700 Merge branch 'master' of hiram@hgwdev.cse.ucsc.edu:/data/git/kent commit d55a3d6c6eb62b0605560fa076b6468c2812d90f Author: Hiram Clawson Date: Fri Aug 20 10:39:54 2010 -0700 adding patch2Chain and patch2Psl tracks commit aa987b131b0cb3d445717b9ab2f3b735f117f2fc Merge: 97373a6 0c29ac6 Author: Cricket Sloan Date: Fri Aug 20 10:16:06 2010 -0700 Merge branch 'master' of cricket@hgwdev.cse.ucsc.edu:/data/git/kent commit 97373a630b9a64ab9d7398eca8b1617d76a87e9e Author: Cricket Sloan Date: Fri Aug 20 10:15:52 2010 -0700 Comments in Fields.ra commit 0c29ac691f9b0cb892698f2c9487e68dffb84212 Author: Venkat Malladi Date: Fri Aug 20 09:57:06 2010 -0700 Uptaded revision of DAF commit d03eb6606f84eb114b762605d6ca4a58dc23d9a5 Author: Venkat Malladi Date: Fri Aug 20 09:52:17 2010 -0700 Uptaded versions, that I forgot in last commit commit e063ff5d360b684b222d0baa0c52b3ffbf4e679c Author: Venkat Malladi Date: Fri Aug 20 09:46:27 2010 -0700 Updated daf's for the Ren lab to not require Signal, as they are having trouble generating bigWig files. commit 205c7c4f5f22f8d427509274d90e22cd6d318c65 Author: Fan Hsu Date: Fri Aug 20 09:16:33 2010 -0700 Updated decipherRaw.sql commit ad2c935d316d1424a247b0bc4910a22eee14db52 Author: Galt Barber Date: Fri Aug 20 08:00:10 2010 -0700 "Encode release log update" commit cf0ee00e1ab399d11508334db24f8d129e611a3d Author: Galt Barber Date: Fri Aug 20 08:00:09 2010 -0700 "Release log update" commit 0f8e5b6b2d898a7622e8dd410ceac60bfa1ee606 Merge: c846960 c4d3d53 Author: Brian Raney Date: Thu Aug 19 17:44:23 2010 -0700 Merge branch 'master' of braney@hgwdev.cse.ucsc.edu:/data/git/kent commit c846960a5d16d7840db474804cfc766e9ca63040 Author: Brian Raney Date: Thu Aug 19 17:44:01 2010 -0700 take out flags that were preventing the most recent copy from being installed commit c4d3d535999da33f254cb75b98f8a7083dd09f0b Author: Fan Hsu Date: Thu Aug 19 17:03:33 2010 -0700 Updated to implement changes suggested by data provider of R-DMR track. commit 9139601297a75309903c4e687cf6102eca1d1aee Author: katrina Date: Thu Aug 19 16:36:31 2010 -0700 one of the labs was missing credis and so I changed credits per Kate's request commit f74d7d37d4aec889550ff38d8f2a625f8af54559 Author: Cricket Sloan Date: Thu Aug 19 15:53:46 2010 -0700 this has the ripChip Antibodies as Antibodies but commented out until we are ready to make the change commit a9012ce00c706264f546e5a12c22d40a19a9902c Author: Hiram Clawson Date: Thu Aug 19 15:25:29 2010 -0700 indicated lifted from Ensembl Sscrofa9 for ensGene commit 1d45056963cb34f49bfd891afc94cb332aa38a26 Merge: c01bbd9 da96f32 Author: Hiram Clawson Date: Thu Aug 19 14:54:55 2010 -0700 Merge branch 'master' of hiram@hgwdev.cse.ucsc.edu:/data/git/kent commit c01bbd9ec093e5d23acd2c6f704737e0653541e8 Author: Hiram Clawson Date: Thu Aug 19 14:54:38 2010 -0700 indicate lifting ensGene from EF 2 commit da96f329a18ab10cd760880d6a598bdc65eecfa7 Merge: 4eadce2 2787b7a Author: Chin Li Date: Thu Aug 19 13:27:19 2010 -0700 Merge branch 'master' of chinhli@hgwdev.cse.ucsc.edu:/data/git/kent commit 4eadce282499415cdaf474e05f28f6380256a49c Author: Chin Li Date: Thu Aug 19 13:26:00 2010 -0700 override dataVersion commit 2787b7ad61ac7a74f4e4774a9645306a81644b40 Author: Brian Raney Date: Thu Aug 19 13:06:20 2010 -0700 add usage message (woooo!) commit 8e921e0dfab12148aaac5817af2a5dd1295b7600 Merge: 51501b0 dc9d0a9 Author: Brian Raney Date: Thu Aug 19 12:57:24 2010 -0700 Merge branch 'master' of braney@hgwdev.cse.ucsc.edu:/data/git/kent commit 51501b0fd9f9e6a693f35e5e507e577bbadfe4b0 Author: Brian Raney Date: Thu Aug 19 12:56:21 2010 -0700 shell of a program to validate cv.ra and make sure metadata is compliant commit b573ffc5957acbcfaac503c0eb8ef38a9606b3ad Author: Chin Li Date: Thu Aug 19 11:50:13 2010 -0700 DONE Sestan Brain commit dc9d0a98e491fef4009f3708a79c4b22cb0b0b15 Merge: 4c90616 2eb57e3 Author: vanessa Date: Thu Aug 19 11:49:17 2010 -0700 Merge branch 'master' of vanessa@hgwdev.cse.ucsc.edu:/data/git/kent commit 4c90616a0ebf03fa2e7c8c709ccf132f29119bd5 Author: vanessa Date: Thu Aug 19 11:49:04 2010 -0700 changed the cell protocols link reflect the new directory structure and made a grammar change commit 2eb57e3799bcc78e08e4a2ae281f2ed5b7888131 Merge: cba344a 6bf2679 Author: Cricket Sloan Date: Thu Aug 19 11:48:41 2010 -0700 Merge branch 'master' of cricket@hgwdev.cse.ucsc.edu:/data/git/kent commit cba344a00772ea57f1cda3d0b8c372f136764b88 Merge: 38ea9b6 3eeb362 Author: Cricket Sloan Date: Thu Aug 19 11:48:26 2010 -0700 The first draft of merging pi.ra with cv.ra Merge branch 'UCV' commit 3eeb3621896644d37660aa63afad2e3277d09138 Author: Cricket Sloan Date: Thu Aug 19 11:45:52 2010 -0700 First draft of adding pi.ra to the cv.ra commit 6bf26795981fdaff4c236d1967c504a929a92fb0 Merge: 7814c41 b732734 Author: Hiram Clawson Date: Thu Aug 19 11:20:31 2010 -0700 Merge branch 'master' of hiram@hgwdev.cse.ucsc.edu:/data/git/kent commit 7814c4182c058508ab8031c28848c01419c2fa35 Author: Hiram Clawson Date: Thu Aug 19 11:20:23 2010 -0700 adding danRer6 recip best commit b732734c3e562bbc9d9d552607866dc527ba376e Merge: 080bf99 38ea9b6 Author: vanessa Date: Thu Aug 19 10:59:04 2010 -0700 Merge branch 'master' of vanessa@hgwdev.cse.ucsc.edu:/data/git/kent commit 080bf99488f4c812b6922aba61c5fb3a241fe29b Author: vanessa Date: Thu Aug 19 10:58:05 2010 -0700 changed the cell protocols link reflect the new directory structure and made a grammar change commit 38ea9b6bc2016c49a9fb37faed06e316a8ffd66e Author: Cricket Sloan Date: Thu Aug 19 10:28:37 2010 -0700 Edit the track description according to POH and change some labels to be consistent commit af0b390d34252236368ca18434503acef4ad2ad8 Author: Cricket Sloan Date: Thu Aug 19 10:27:37 2010 -0700 Start the GIS RNA PET track commit 7c7edada7790f36d554bbd2ead80bebec5f71cd5 Merge: 8b6c084 2143293 Author: Cricket Sloan Date: Thu Aug 19 10:25:33 2010 -0700 Merge branch 'master' of cricket@hgwdev.cse.ucsc.edu:/data/git/kent commit 2143293ec35e9fa71b6ad01afec02b7108d9c8bd Merge: 63b61fa c29bfd2 Author: Hiram Clawson Date: Thu Aug 19 10:03:28 2010 -0700 Merge branch 'master' of hiram@hgwdev.cse.ucsc.edu:/data/git/kent commit 63b61fab9ce085cc5efc329ace160f2c9f19c921 Author: Hiram Clawson Date: Thu Aug 19 10:01:07 2010 -0700 updated with ce6 sacCer2 and dm3 recipBest commit c29bfd2003f6c941391df8f6492fc5c15d9fd2cf Author: Galt Barber Date: Thu Aug 19 08:00:10 2010 -0700 "Encode release log update" commit a9b00684b03c3e467eaf386ad04e301e55f9be8b Author: Galt Barber Date: Thu Aug 19 08:00:08 2010 -0700 "Release log update" commit d6c87e17146315847190867988ac319d86b1e446 Author: Galt Barber Date: Wed Aug 18 18:07:06 2010 -0700 Revert "making sure validate and load links are available in advancedView, basically admins" This reverts commit afd44e0061f2a607e027ef321dc54bdcb6d11849. This turns out to need corresponding changes in the controller, and now it seems like not that safe to do anyway. commit c382998acd182aba13582933c51cf09c450c107c Author: Galt Barber Date: Wed Aug 18 18:06:11 2010 -0700 Revert "oops" This reverts commit 3c39fe091da71c3e024ebb6fc0a4dc55cabf6da4. commit 3c39fe091da71c3e024ebb6fc0a4dc55cabf6da4 Author: Galt Barber Date: Wed Aug 18 17:29:49 2010 -0700 oops commit f801af06653e63b9341379a2d8a479cf661132e4 Merge: 559ccfa5 acf8c0d Author: Galt Barber Date: Wed Aug 18 17:25:22 2010 -0700 Merge branch 'master' of galt@hgwdev.cse.ucsc.edu:/data/git/kent commit 559ccfa54cc6166c771e3df52aab1266392d06e9 Author: Galt Barber Date: Wed Aug 18 17:25:07 2010 -0700 making sure the order of the archives in a project is preserved commit acf8c0d0bf8a322ce4d2b89e3157ee0e97fce546 Merge: 2ed1e07 943541f Author: Mark Diekhans Date: Wed Aug 18 17:03:54 2010 -0700 Merge branch 'master' of markd@hgwdev.cse.ucsc.edu:/data/git/kent commit 2ed1e073d8a216cb15990b3aeac7bb0b3fa324b6 Merge: acf663f 915f551 Author: Mark Diekhans Date: Wed Aug 18 17:03:17 2010 -0700 Merge branch 'master' of markd@hgwdev.cse.ucsc.edu:/data/git/kent commit 943541ffcb387bedd6fdfd295fe13778d085568d Author: Hiram Clawson Date: Wed Aug 18 17:03:06 2010 -0700 more chromosomes available for haplotypeLocations track commit acf663f4471a47ddfdacbef117cb8a832124b6f9 Merge: 4690c81 f24fa3f Author: Mark Diekhans Date: Wed Aug 18 17:02:26 2010 -0700 Merge branch 'master' of markd@hgwdev.cse.ucsc.edu:/data/git/kent commit 915f5513c508cea551a80be6f55efb5d96c40047 Merge: 3028da6 f24fa3f Author: Hiram Clawson Date: Wed Aug 18 17:02:01 2010 -0700 Merge branch 'master' of hiram@hgwdev.cse.ucsc.edu:/data/git/kent commit 3028da66ab25614595b76599c385ae262bb70848 Author: Hiram Clawson Date: Wed Aug 18 17:01:58 2010 -0700 documenting patch2 update procedure commit 4690c819e89c7f5f70ed91da46fb2843e78f043c Author: Mark Diekhans Date: Wed Aug 18 17:01:54 2010 -0700 add CCDS public notes to the CCDS details page commit f24fa3f7b20fcbda646fa5562ec8d807f4ce8038 Author: Tim Dreszer Date: Wed Aug 18 16:56:18 2010 -0700 Something strange happened to last checkin. Also changed popup title. commit 5f34fcb6c09f10a806d853f83d9e18af5914d32e Merge: 304f368 c1b2356 Author: Tim Dreszer Date: Wed Aug 18 16:50:33 2010 -0700 Merge branch 'master' of tdreszer@hgwdev.cse.ucsc.edu:/data/git/kent commit 304f3686ff1f77fb5793cd941ca3420a8903545a Author: Tim Dreszer Date: Wed Aug 18 16:50:30 2010 -0700 Find Tracks now has a description only popup commit c1b23567b2124e334af96580496b98f814480004 Merge: afd44e0 3ac5ebf Author: Galt Barber Date: Wed Aug 18 16:45:59 2010 -0700 Merge branch 'master' of galt@hgwdev.cse.ucsc.edu:/data/git/kent commit afd44e0061f2a607e027ef321dc54bdcb6d11849 Author: Galt Barber Date: Wed Aug 18 16:45:54 2010 -0700 making sure validate and load links are available in advancedView, basically admins commit 3ac5ebf2b625f3bea6037e634bece583e6d97d9f Merge: 30d1ed6 9be0d4e Author: Mark Diekhans Date: Wed Aug 18 16:11:16 2010 -0700 Merge branch 'master' of markd@hgwdev.cse.ucsc.edu:/data/git/kent commit 30d1ed6f9506d32f5f29705df41d0cbe00886b4f Author: Mark Diekhans Date: Wed Aug 18 16:06:51 2010 -0700 fixed bugs in ccdsNotes load commit 9be0d4e97bf4bcfc9bb345d5764c47f4b2ae9517 Author: Tim Dreszer Date: Wed Aug 18 15:10:44 2010 -0700 Fixed off by one bug seen in ie. commit c2eae99cd697a47305633721c6ac6a23e8b277b8 Author: Tim Dreszer Date: Wed Aug 18 14:49:12 2010 -0700 Screwed this up again. Limiting vis from composite parent should only be done by searchTracks, not normal image generation commit d4de265588c9c593e1a4e572b9cb328fcb2df208 Merge: 8595456 3d67229 Author: Mark Diekhans Date: Wed Aug 18 13:20:15 2010 -0700 Merge branch 'master' of markd@hgwdev.cse.ucsc.edu:/data/git/kent commit 859545663a448275431bed3a72ccd4596b6d1963 Author: Mark Diekhans Date: Wed Aug 18 13:19:35 2010 -0700 added support for importing CCDS public notes into a table commit 3d67229a58edd2f055e91b1919e0e1aca9666b94 Merge: eb712f3 8c47d0d Author: Angie Hinrichs Date: Wed Aug 18 13:17:19 2010 -0700 Merge branch 'master' of angie@hgwdev.cse.ucsc.edu:/data/git/kent commit eb712f3c5bc68c3875bebcd554ea523c26461c82 Author: Angie Hinrichs Date: Wed Aug 18 13:17:15 2010 -0700 Added support for new trackDb setting 'tableBrowser off' which prevents hgTables from displaying a track (if related tables need to be excluded from All Tables, they go after 'off', space-sep. commit 8c47d0d9c58b50b378c653b361cc734d4e1fe230 Merge: f5f49de cfd34db Author: vanessa Date: Wed Aug 18 12:57:28 2010 -0700 Merge branch 'master' of vanessa@hgwdev.cse.ucsc.edu:/data/git/kent commit cfd34db2ec47c15e518e3b7f7d76772b22fe03e0 Merge: b159bd2 7b03a2b Author: Brian Raney Date: Wed Aug 18 11:52:28 2010 -0700 Merge branch 'master' of braney@hgwdev.cse.ucsc.edu:/data/git/kent commit b159bd25b28bf1945b751cf752edc49f677d6af3 Author: Brian Raney Date: Wed Aug 18 11:52:12 2010 -0700 update subId to hg19 submission id commit 7b03a2b42f924654bf8e64c675842526f37515a0 Merge: 247b364 d6bce4a Author: Hiram Clawson Date: Wed Aug 18 11:27:53 2010 -0700 Merge branch 'master' of hiram@hgwdev.cse.ucsc.edu:/data/git/kent commit 247b364d70c2a002ae5e0ac8e710ce4b1d26febc Author: Hiram Clawson Date: Wed Aug 18 11:27:47 2010 -0700 add not about scripts to run everything commit e8131103f54045f7f9207b6c4709e460f819de48 Author: Hiram Clawson Date: Wed Aug 18 11:26:28 2010 -0700 rebuilding all blast tabs on account of new Ensembl v59 genes commit d6bce4aa10cf2f9a4234d542d5bd2f2aeb123526 Merge: abc4ef6 8a6bb2e Author: Venkat Malladi Date: Wed Aug 18 10:40:38 2010 -0700 Merge branch 'master' of vsmalladi@hgwdev.cse.ucsc.edu:/data/git/kent commit abc4ef6425b7db399f164c29981bf77be489eaeb Author: Venkat Malladi Date: Wed Aug 18 10:40:29 2010 -0700 Updated all Mouse DAFs to include an explanation of the DDF line commit f5f49debb867bbdf86f5fffb7b699f093d1ca27b Author: vanessa Date: Wed Aug 18 10:33:16 2010 -0700 staging metaDb for GIS PET DNA on hgwbeta commit 8a6bb2e6cddb4cb68db30209656186532ff53f3d Author: Galt Barber Date: Wed Aug 18 08:00:16 2010 -0700 "Encode release log update" commit 0f7e2f2323650e300fc96dc8ecaf87352ad811dd Author: Galt Barber Date: Wed Aug 18 08:00:14 2010 -0700 "Release log update" commit 96b0dc9826d589e09daf2bd1a36ef513c91255b1 Author: Brian Raney Date: Wed Aug 18 07:44:58 2010 -0700 fix another bonehead move (left out a '/') commit 170c44b6f3a9a8fdd67693fe8c1f6116d8d8a7ef Author: Tim Dreszer Date: Tue Aug 17 17:44:32 2010 -0700 Adding support for popup cfg even though there is currently some duplicated code commit bf8b08e446899dc9ce85b6a44fea4d02331512a5 Author: Tim Dreszer Date: Tue Aug 17 17:37:57 2010 -0700 Fixed json to find the composite parent commit fecae123222005ec28e9a9d66ad1c865da79fcbe Author: Tim Dreszer Date: Tue Aug 17 17:36:29 2010 -0700 Removed call to trackHash for parentTdb, since composite parent should only be necessary for foundTracks and foundTracks has incomplete trackHash built commit d91b224fcd76dabff7321290cf435477bd00b09e Author: Tim Dreszer Date: Tue Aug 17 17:34:25 2010 -0700 Changed the rightClick menu and prepared the ground for common hgTrackUi popup for findTracks commit 47c1c3508ce7d717ce0a3fdd4ffeb9cf20feb146 Author: Tim Dreszer Date: Tue Aug 17 17:32:03 2010 -0700 Added some protection for strange interactions between DnD and contextMenu commit d9059b90539b183bcdf43c896890d8d0cca60b39 Author: Tim Dreszer Date: Tue Aug 17 17:30:32 2010 -0700 Changes for ajax=1 version of cfg dialog commit 1253e33baa47f7e97f5768a120af789e3b86becc Merge: 4c94e67 d20058e Author: Tim Dreszer Date: Tue Aug 17 17:27:41 2010 -0700 Merge branch 'master' of tdreszer@hgwdev.cse.ucsc.edu:/data/git/kent commit 4c94e6750582ff70fe72b8d48309504134f37ae1 Author: Tim Dreszer Date: Tue Aug 17 17:27:32 2010 -0700 Make the cfg popup a bit more recognizable commit d20058ee23a8ae826a9c2ce7c47ed474fdf16f28 Merge: d4eb3f7 af7ad6c Author: Brian Raney Date: Tue Aug 17 17:25:59 2010 -0700 Merge branch 'master' of braney@hgwdev.cse.ucsc.edu:/data/git/kent commit d4eb3f7ada9aa9b71466b8398eda0e084e7f9ade Author: Brian Raney Date: Tue Aug 17 17:25:35 2010 -0700 oops, meant to use needLargeMem to avoid the memsettomg tp - commit af7ad6ce035771ccf2a4baae797eba61ea21d354 Merge: 09a423f 32e6f06 Author: Venkat Malladi Date: Tue Aug 17 17:10:12 2010 -0700 Merge branch 'master' of vsmalladi@hgwdev.cse.ucsc.edu:/data/git/kent commit 09a423f7693fb2871e99c3194730821758158813 Author: Venkat Malladi Date: Tue Aug 17 17:09:50 2010 -0700 Updated Human DAFs for tracks that I own, to include a explanation of the DDF line commit 32e6f06a36a70994554082d2c7fd6e83c5cbb7f9 Author: mary Date: Tue Aug 17 16:26:10 2010 -0700 putting the cat in the news, archiving old stories commit 5cc797a7d7058d8b96f35314a3be5c13f94644c0 Author: Hiram Clawson Date: Tue Aug 17 15:03:54 2010 -0700 MYSQLLIBS should be on the L += line, not the MYLIBS line commit 1a5e0a7e7a9ae9ba3cc35b10cb31575b6e77a0a2 Merge: 1a5d46b fb5ce3f Author: Hiram Clawson Date: Tue Aug 17 14:58:50 2010 -0700 Merge branch 'master' of hiram@hgwdev.cse.ucsc.edu:/data/git/kent commit 1a5d46be6bb79ffcf940b30d47f6a63ed6042697 Author: Hiram Clawson Date: Tue Aug 17 14:57:59 2010 -0700 watch out for MYSQLIBS to have other stuff there than just library names commit fb5ce3f8486e2644bdfc66a13f1c60e20eefb5be Author: Galt Barber Date: Tue Aug 17 14:53:51 2010 -0700 keeping the kent/ prefix in zip paths as requested by Hiram commit 24538e73e4fb60e646eece0c1b125c9b0ebc84d2 Author: Galt Barber Date: Tue Aug 17 14:49:30 2010 -0700 Revert "fixing zip paths" This reverts commit 6b74a7dc215a8af4fe906c5101cf1b70cd65877e. Hiram requested we keep the old kent/prefix on the zip paths. commit 999d6eb77e3dc31ec1ce3726945b1fd7d336247e Merge: 41438a0 6fdc36c Author: Brian Raney Date: Tue Aug 17 12:57:32 2010 -0700 Merge branch 'master' of braney@hgwdev.cse.ucsc.edu:/data/git/kent commit 41438a0bfd68335a15a262cf54ff49e32ea0e4a1 Author: Brian Raney Date: Tue Aug 17 12:56:43 2010 -0700 change code that was allocating a 13mb array on the stack to use a scratch area instead commit 6fdc36c27097d226983badf25df7ab1224b2274e Merge: 494ca2a dbd76c3 Author: Venkat Malladi Date: Tue Aug 17 11:52:47 2010 -0700 Merge branch 'master' of vsmalladi@hgwdev.cse.ucsc.edu:/data/git/kent commit 494ca2acd0b47fd026e02814fc13da51c4e55624 Author: Venkat Malladi Date: Tue Aug 17 11:52:40 2010 -0700 Added data from subId=1848. commit dbd76c3af1c65d24c2bdbec34bf15d2367fbe1a5 Author: katrina Date: Tue Aug 17 11:44:31 2010 -0700 creating new makefiles and folders for switching hg19 Mapability track to using metaDb commit 9ed96ae78e3bda7f3c79aa3194033a614735181c Merge: 6e48800 fd0000d Author: Brian Raney Date: Tue Aug 17 11:09:14 2010 -0700 Merge branch 'master' of braney@hgwdev.cse.ucsc.edu:/data/git/kent commit 6e48800949f2bdab20d8bb24bb4b761a05b8461b Author: Brian Raney Date: Tue Aug 17 11:08:50 2010 -0700 remove metadata from Mapabililty composite commit fd0000dd4b6e8cb46287fa5c7ee29bc572f36047 Merge: 8f216c3 cbc0e78 Author: vanessa Date: Tue Aug 17 10:57:58 2010 -0700 Merge branch 'master' of vanessa@hgwdev.cse.ucsc.edu:/data/git/kent commit 8f216c35a6c00022cc814a132ff4766b11588347 Author: vanessa Date: Tue Aug 17 10:57:49 2010 -0700 alphabetized the tracks in the regulatation super track commit cbc0e7804c1ae50d6e182d63ac7e92ba3a774ff4 Merge: d4fc0bc 884a3db Author: Venkat Malladi Date: Tue Aug 17 10:33:12 2010 -0700 Merge branch 'master' of vsmalladi@hgwdev.cse.ucsc.edu:/data/git/kent commit d4fc0bcb95cca6f8f29daa263f8da88e129f1469 Author: Venkat Malladi Date: Tue Aug 17 10:31:52 2010 -0700 Updated Description page with blank document. Add default tracks to be viewd ( Brain tissue, Mel, ES and B Cell) commit 8b6c08405bf45647c5ef533c7b10f023b69fa56b Author: Cricket Sloan Date: Tue Aug 17 09:44:46 2010 -0700 The release notes commit 884a3db6cd049bcb4288b1cfa0b596003dbaa135 Merge: d5e5a80 aa8bf3f Author: Brian Raney Date: Tue Aug 17 09:22:55 2010 -0700 Merge branch 'master' of braney@hgwdev.cse.ucsc.edu:/data/git/kent commit d5e5a8061c0e4cb48c46172d50ef1e531a73cc40 Author: Brian Raney Date: Tue Aug 17 09:22:38 2010 -0700 change the filenames to be *.bigWig commit aa8bf3f23d6c57c260793a9bc68ea2498fdd9f7e Author: Galt Barber Date: Tue Aug 17 08:00:10 2010 -0700 "Encode release log update" commit 5114e984327c628d6a0f7987c0e1062ca2d0eb05 Author: Galt Barber Date: Tue Aug 17 08:00:09 2010 -0700 "Release log update" commit 10831f8ba6f61b235f8400fe4fe269a8eccb20f9 Merge: eeb6e13 59d9ae3 Author: Mark Diekhans Date: Mon Aug 16 23:42:43 2010 -0700 Merge branch 'master' of markd@hgwdev.cse.ucsc.edu:/data/git/kent commit eeb6e13f3c9d1f3e9883b76498f5cb1a80463531 Author: Mark Diekhans Date: Mon Aug 16 23:41:36 2010 -0700 fix bug where insertions between multiple bases of stop codon generated incorrect frame. Provide explicit control over use of gene_id or gene_name for name2 column commit 59d9ae3b183823302b596c958cee9be7d2591b92 Author: Tim Dreszer Date: Mon Aug 16 19:20:32 2010 -0700 Fixed table in row bug commit 43f41483c221b47089a679246f190f547312a781 Author: Brian Raney Date: Mon Aug 16 17:34:55 2010 -0700 "New version number v238" commit 0d84ff7a5e7388469fbcad9e39fdd0cd176f8c3c Author: Brian Raney Date: Mon Aug 16 17:33:09 2010 -0700 v237 final build (for reals this time ;-) commit 72ff794791d307fa6c0def8b4e40a8abd47c885c Merge: 5118cb5 0273a11 Author: Brian Raney Date: Mon Aug 16 17:29:28 2010 -0700 Merge branch 'master' of hgwdev:/data/git/kent commit 5118cb5d38ca6c629540c667b3ce3745f83b43f7 Author: Brian Raney Date: Mon Aug 16 17:29:11 2010 -0700 v237 final build commit 0273a11f1d5fd47b383fbf73ec4119216c92acb4 Merge: de9d43c 7f69638 Author: Angie Hinrichs Date: Mon Aug 16 16:34:37 2010 -0700 Merge branch 'snpCodonBug100816' commit 44e273db21f688f36025ab8c2d6f0c83d63a9af5 Merge: c6c23ed 84e2e5f Author: Venkat Malladi Date: Mon Aug 16 16:34:14 2010 -0700 Merge branch 'master' into Development-Mouse commit 7f69638af183d23eda5fe9f767135a8f3966ebd3 Author: Angie Hinrichs Date: Mon Aug 16 16:33:40 2010 -0700 Fixing off-by-one bug in snp's UCSC predicted function (when - strand last base of codon is on a different exon) reported by user Ivan Adzhubey [Mail Lists - ML - MLQ #650]. commit de9d43cf6f3e2685b22d9e20cd07d111e2b1e35c Author: Tim Dreszer Date: Mon Aug 16 16:32:44 2010 -0700 Hidden vs. seen controls, id should not equal name commit a424349f5b611e235efaae817550a8d51604a1cd Author: Tim Dreszer Date: Mon Aug 16 16:29:39 2010 -0700 Fixed missing ENCODE Gencode bug by using trackHash instead of tdbExtras commit e1c8c74868828f7077d13a32e18a15f00d793393 Merge: e826c3a 36950db Author: Tim Dreszer Date: Mon Aug 16 16:28:08 2010 -0700 Merge branch 'master' of tdreszer@hgwdev.cse.ucsc.edu:/data/git/kent commit 36950db842ea4534a1aa9a8ca0fb86ba10ab163a Author: Hiram Clawson Date: Mon Aug 16 16:00:55 2010 -0700 properly clean everything during clean target commit 2306f5a093f08c8e110eb1eb2d3965469270375d Merge: 108a1b8 64321cc Author: Hiram Clawson Date: Mon Aug 16 15:56:26 2010 -0700 Merge branch 'master' of hiram@hgwdev.cse.ucsc.edu:/data/git/kent commit 108a1b8f542bf258aa2917d34e3ec6936fb7c0b0 Author: Hiram Clawson Date: Mon Aug 16 15:56:11 2010 -0700 properly use ../testBinary in test makefiles commit 7741801d6cb7872801c3066068287e3e99040ebc Author: Hiram Clawson Date: Mon Aug 16 15:55:32 2010 -0700 fixup test target to use compile and to clean up after test commit 64321ccd0efafcd25dc3ef2c3e8165c818859765 Merge: 0251b6b b0a9aa2 Author: vanessa Date: Mon Aug 16 15:51:53 2010 -0700 Merge branch 'master' of vanessa@hgwdev.cse.ucsc.edu:/data/git/kent commit 0251b6b0821f934b21e50a461774a0c29d61d733 Author: vanessa Date: Mon Aug 16 15:51:40 2010 -0700 added release alpha,beta tags commit b0a9aa2e3b77c70d5e489b8d624db1dae65b00b9 Merge: b40a7e5 84e2e5f Author: b0b Date: Mon Aug 16 15:38:35 2010 -0700 Merge branch 'master' of kuhn@hgwdev.cse.ucsc.edu:/data/git/kent commit b40a7e5ae9e72257e0c76bbe8124171b7dd97a35 Author: b0b Date: Mon Aug 16 15:38:25 2010 -0700 removed older items commit 84e2e5ff20522049c13626a852522341dc4573a4 Merge: cbacbe8 951ba89 Author: Venkat Malladi Date: Mon Aug 16 15:38:16 2010 -0700 Merge branch 'master' of vsmalladi@hgwdev.cse.ucsc.edu:/data/git/kent commit cbacbe8b91fe8a410bdd2b7fd05a774db61664ef Author: Venkat Malladi Date: Mon Aug 16 15:38:02 2010 -0700 Added subId=2108 for SYDH Histone data commit 951ba89fb2437d01717074a31266540baba13949 Author: Hiram Clawson Date: Mon Aug 16 15:36:15 2010 -0700 can remove fetchUrlTest at end of tests and during clean commit f6bf286c688942d0b17165340f86ea4f6580ab22 Merge: 6673bfb 897745c Author: Hiram Clawson Date: Mon Aug 16 15:31:26 2010 -0700 Merge branch 'master' of hiram@hgwdev.cse.ucsc.edu:/data/git/kent commit 6673bfb26613129b4eade6b485fcbc12439350aa Author: Hiram Clawson Date: Mon Aug 16 15:31:18 2010 -0700 properly compile target for test target and cleanup after commit 36dec98dae493fd5d63aebf3ba35b2376a256ffd Author: Hiram Clawson Date: Mon Aug 16 15:30:49 2010 -0700 point to updateHtml.sh instead of the rsync to fetch htdocs commit 897745c271ce3df87a2b6aaf2c2ab7c24aef6b67 Merge: 557627e 976c529 Author: Venkat Malladi Date: Mon Aug 16 15:19:14 2010 -0700 Merge branch 'master' of vsmalladi@hgwdev.cse.ucsc.edu:/data/git/kent commit 557627ecce61f1bbf9fb9acc57d45a0f2ae8cb3e Author: Venkat Malladi Date: Mon Aug 16 15:19:07 2010 -0700 Corrected Typo of labExpId as labExpIdn commit 976c52931b48ad54b4779612da208c494118dff4 Author: Hiram Clawson Date: Mon Aug 16 15:15:33 2010 -0700 no need to mention a version or date stamp commit 41242dd1af6d664051cb5415c557d8ae2edbf5ac Author: Hiram Clawson Date: Mon Aug 16 15:12:33 2010 -0700 remove references to CVS commands commit 6486dd4e3e58902f15027ce5f8a806d7d41d1879 Author: Hiram Clawson Date: Mon Aug 16 15:11:46 2010 -0700 no longer required in git world commit 285f4210ccff1709789c97b10571d823c6c2d410 Author: Hiram Clawson Date: Mon Aug 16 15:09:41 2010 -0700 update to git commands commit 355626a17b6a6c26b9e00923ccab854d3c0768f6 Author: Hiram Clawson Date: Mon Aug 16 15:01:45 2010 -0700 irrelevant files since changing to git commit cbde5322da72fb98ff020ce03cae209edb086357 Author: Hiram Clawson Date: Mon Aug 16 15:00:35 2010 -0700 irrelevant file since git introduction commit 0dc2916f48f6f9529b8c5f0da846d96b6ee8a1f9 Author: Hiram Clawson Date: Mon Aug 16 14:59:41 2010 -0700 irrelevant file since removal of makefile commit 172cad048d86c135aa670c1c5f625b099bdb2d4c Merge: 0f8aade 7428ef9 Author: Hiram Clawson Date: Mon Aug 16 14:57:07 2010 -0700 Merge branch 'master' of hiram@hgwdev.cse.ucsc.edu:/data/git/kent commit 0f8aadea917165515c1c8e42814424b829aa3ef6 Author: Hiram Clawson Date: Mon Aug 16 14:56:59 2010 -0700 can remove the loader symlink after the custom track test is done to keep source tree cleaner commit 7428ef9bad01f0004682f90ddba661120e244dc4 Merge: af5d583 9382bae Author: Brian Raney Date: Mon Aug 16 14:46:24 2010 -0700 Merge branch 'master' of braney@hgwdev.cse.ucsc.edu:/data/git/kent commit af5d583c40a211e8d63f5ac636b80b0a54bc8e34 Author: Brian Raney Date: Mon Aug 16 14:46:04 2010 -0700 notes for hg19 release1 of Gis DNA=-pet commit 9382baea01d250ba2d6858a12921565e8933ef67 Author: Hiram Clawson Date: Mon Aug 16 14:44:36 2010 -0700 fixup gbdb no longer relevant in 2010 commit 9faa28bca19e6f5efdd0151bd0489803637dd2dd Author: Hiram Clawson Date: Mon Aug 16 14:43:34 2010 -0700 updated to eliminate references to a CDROM commit 7c409a54fbcf6c209c319d95c9f93df95dbcc305 Author: Hiram Clawson Date: Mon Aug 16 14:43:06 2010 -0700 the makefile and ex.InstallExample are no longer relevant commit 4970ba0d244b066e9b417d9e6b750a7ebe1f9598 Author: Hiram Clawson Date: Mon Aug 16 14:28:18 2010 -0700 contents have been subsumed into trashCleaner.csh commit 3e0403305b213a4261a6734edcb273f328b15485 Merge: 4f6f8af d1e53ae Author: Hiram Clawson Date: Mon Aug 16 13:56:03 2010 -0700 Merge branch 'master' of hiram@hgwdev.cse.ucsc.edu:/data/git/kent commit 4f6f8af73e1f81eef2b7802f45e2c99f8179318e Author: Hiram Clawson Date: Mon Aug 16 13:55:49 2010 -0700 adding -lcrypto to -lssl commit d1e53ae338785f69acd9181a017768139a206986 Merge: 659c8a9 77e3fa6 Author: vanessa Date: Mon Aug 16 11:22:56 2010 -0700 Merge branch 'master' of vanessa@hgwdev.cse.ucsc.edu:/data/git/kent commit 659c8a9f10127a58272cdfcdd205be0ae708a5af Author: vanessa Date: Mon Aug 16 11:22:44 2010 -0700 fixed the ordering of regulation track downloads to be in alphabetical order commit 90dc3124cd13690530f76f6af874071e0918ac36 Author: vanessa Date: Mon Aug 16 10:56:31 2010 -0700 added new section for the regulation super-track hg18 release commit e826c3a1fbfc64c882bb8a20446e7ce9d593e5db Author: Tim Dreszer Date: Mon Aug 16 10:39:19 2010 -0700 If dragReordered, successive newly visible tracks should appear below others commit c6c23ed7b354b5d84274e83aa251ea9e5926a64f Merge: 7febeaa 77e3fa6 Author: Venkat Malladi Date: Mon Aug 16 09:53:07 2010 -0700 Merge branch 'master' into Development-Mouse commit 77e3fa694e960f4777766b3e2152cf6dc103c354 Author: Venkat Malladi Date: Mon Aug 16 09:52:41 2010 -0700 Cleaned up inputType from metaDb for mouse commit d6b355d5cd642d3de8e0dd74db7ba3804c2731aa Merge: 186f984 1c89dc0 Author: Venkat Malladi Date: Mon Aug 16 09:43:32 2010 -0700 Merge branch 'master' of vsmalladi@hgwdev.cse.ucsc.edu:/data/git/kent commit 186f9849b979b0c4c0f4505b5c3d5c9033486b5b Author: Venkat Malladi Date: Mon Aug 16 09:43:18 2010 -0700 Cleaned up inputType from metaDb commit 1c89dc09dec55124f29799e30ae3c184f7e09af7 Author: katrina Date: Mon Aug 16 09:27:42 2010 -0700 changed Top link double arrow to single arrow to match Tim's composite navigation links commit e95cc7ed861c02f6dd2db4c290ebbc600b3f0ecb Author: Galt Barber Date: Mon Aug 16 08:00:09 2010 -0700 "Encode release log update" commit f4610d5a0d2c1c8f9751ea05ce329bacdf3ce34c Author: Galt Barber Date: Mon Aug 16 08:00:08 2010 -0700 "Release log update" commit 73ea423591e96a807bd38b2637ff7587f89c9fe3 Merge: 8b9c96b efbade3 Author: Galt Barber Date: Sun Aug 15 10:48:11 2010 -0700 Merge branch 'master' of galt@hgwdev.cse.ucsc.edu:/data/git/kent commit 8b9c96b39b5b934d37db000da4e736e1cf4b94a8 Author: Galt Barber Date: Sun Aug 15 10:48:06 2010 -0700 fixing path to old sandbox that no longer exists commit efbade3751c5b7c3121a0a655d74810db279e8d6 Author: Galt Barber Date: Sun Aug 15 08:00:17 2010 -0700 "Encode release log update" commit 89e8b9eef9847ab54d4e9c79684abbbd46e38977 Author: Galt Barber Date: Sun Aug 15 08:00:10 2010 -0700 "Release log update" commit c499259638048cc4eefc481d38a8790692c5766b Author: Galt Barber Date: Sat Aug 14 08:00:12 2010 -0700 "Encode release log update" commit 521605ee118de154c4d9a3ee882763a7a51252d9 Author: Galt Barber Date: Sat Aug 14 08:00:10 2010 -0700 "Release log update" commit e25c7abccb447457901e310c382939a73460bd41 Author: Mark Diekhans Date: Fri Aug 13 23:12:08 2010 -0700 reenable cavPor3 commit 292537484e7efd55c600ad4cb6da8a88b0264244 Merge: 0284b76 8d8135f Author: Tim Dreszer Date: Fri Aug 13 19:25:06 2010 -0700 Merge branch 'master' of tdreszer@hgwdev.cse.ucsc.edu:/data/git/kent commit 0284b76bceb901ab77a2ccd87639a7722ff39966 Author: Tim Dreszer Date: Fri Aug 13 19:25:01 2010 -0700 Removed unneeded links from blubar for PDF/PS page and left justified the links commit 8d8135f19d48e6cf315fd8033987f69d73c3af7f Merge: a91f263 f813b5f Author: vanessa Date: Fri Aug 13 16:24:04 2010 -0700 Merge branch 'master' of vanessa@hgwdev.cse.ucsc.edu:/data/git/kent commit f813b5fc8721ce6d53680f668a38df4a46e28e31 Author: Tim Dreszer Date: Fri Aug 13 15:26:26 2010 -0700 Added Bluebar of links to top of PS/PDF page and 'Return to Browser' button. This is because returning from ps/pdf page to image using back button erases dragReorder changes. commit 40dde80b1af335732763a142dda83202a0eb2cdb Author: Tim Dreszer Date: Fri Aug 13 14:36:04 2010 -0700 Changed tooltip for sideButton to make sure shortLabel is seen first, as per QA request commit 33abad99d0c7ed899ba48acaef47d3358a9d214e Author: Galt Barber Date: Fri Aug 13 14:14:13 2010 -0700 trying it without -q so people are aware of the updates happening commit cbcc5d1255988eb2f6c4d7619793e3465928412f Author: Galt Barber Date: Fri Aug 13 14:04:40 2010 -0700 trying it without -q so people are aware of the updates happening commit 471e108b8fefb287396d0aa1c68360eef3f50094 Merge: ec5710c 1042bfd Author: Galt Barber Date: Fri Aug 13 13:53:12 2010 -0700 Merge branch 'master' of galt@hgwdev.cse.ucsc.edu:/data/git/kent commit ec5710cac015e92742bc1559f84f1fc488f6937d Author: Galt Barber Date: Fri Aug 13 13:52:48 2010 -0700 trying it without -q so people are aware of the updates happening commit 1042bfd6f732c0bb181bfbbeb7396225c9537845 Merge: 94c22fc 5dd7ffc Author: Venkat Malladi Date: Fri Aug 13 13:36:26 2010 -0700 Merge branch 'master' of vsmalladi@hgwdev.cse.ucsc.edu:/data/git/kent commit a91f2639bfd2087c280d64da7b14fe4430497bf3 Merge: 9b5303d 5dd7ffc Author: vanessa Date: Fri Aug 13 13:36:21 2010 -0700 Merge branch 'master' of vanessa@hgwdev.cse.ucsc.edu:/data/git/kent commit 94c22fcf2e0957c7af3f506dd797cf637265e559 Author: Venkat Malladi Date: Fri Aug 13 13:36:13 2010 -0700 Updated Treatment Androgen and Estrogen with appropriate description. Changed display matrix labels of treatments for tracks. commit 5dd7ffceca82b6ac503959c67c43f27546b0db40 Author: Mark Diekhans Date: Fri Aug 13 13:30:31 2010 -0700 reenable cavPor3 alignments commit e6eb1b242153ed0dbbb2f4c2f2bbf442d2deb5b6 Merge: 047094c b0b51e8 Author: Mark Diekhans Date: Fri Aug 13 12:58:07 2010 -0700 Merge branch 'master' of markd@hgwdev.cse.ucsc.edu:/data/git/kent commit b0b51e8cb7f7549ba9889231a4a5e2765c77d696 Author: Hiram Clawson Date: Fri Aug 13 12:01:23 2010 -0700 fixing test target in fixed makefiles commit 9b5303da2be8ba513e235ba0ca61a86e45e7ab68 Merge: 5d38806 f543f46 Author: vanessa Date: Fri Aug 13 11:11:34 2010 -0700 Merge branch 'master' of vanessa@hgwdev.cse.ucsc.edu:/data/git/kent commit f543f4621a23ae2252f9c4c87cc4a0951e630ccb Merge: aa2322f 6b34e88 Author: Venkat Malladi Date: Fri Aug 13 11:03:33 2010 -0700 Merge branch 'master' of vsmalladi@hgwdev.cse.ucsc.edu:/data/git/kent commit aa2322fa906d36491804b43e43122f7c2d722575 Author: Venkat Malladi Date: Fri Aug 13 11:03:27 2010 -0700 Added additional celltype Melano that was previosuly missing commit 6b34e88106577bfd828c8dc515d441082982a339 Merge: 0892f86 554ef77 Author: Brian Raney Date: Fri Aug 13 10:43:05 2010 -0700 Merge branch 'master' of braney@hgwdev.cse.ucsc.edu:/data/git/kent commit 0892f861cb9f708d720040d6bc497212897ce19f Author: Brian Raney Date: Fri Aug 13 10:42:51 2010 -0700 change tooltip for file downloads commit df65c9b81396d379c5757f026893575843c90a71 Author: Brian Raney Date: Fri Aug 13 10:41:30 2010 -0700 add solexa pair fastq views commit 554ef77344352b4f8609d01345286b232f317c75 Merge: fc9d050 2e42578 Author: Hiram Clawson Date: Fri Aug 13 10:12:03 2010 -0700 Merge branch 'master' of hiram@hgwdev.cse.ucsc.edu:/data/git/kent commit fc9d050e371bc33467855c54920d640409244f5a Author: Hiram Clawson Date: Fri Aug 13 10:11:53 2010 -0700 fixup permission grant statements to use FILE properly commit 5d388063f0b7f3fc7d595f18f81774ccfe0652e8 Author: vanessa Date: Fri Aug 13 09:29:03 2010 -0700 updated the text so that it had the meaning that Jim wanted commit 2e42578149158eece3eaf224bc6eb336cfd1e513 Author: Galt Barber Date: Fri Aug 13 08:00:11 2010 -0700 "Encode release log update" commit ac9ba5d08b0808579eeb6855a50c2de3fccd4f80 Author: Galt Barber Date: Fri Aug 13 08:00:09 2010 -0700 "Release log update" commit 96bb082b01866c65273531541c20204851c47380 Author: Larry Meyer Date: Fri Aug 13 00:30:54 2010 -0700 move trackDbJson code into imageV2.c and print it out from w/n imageBoxDraw to fix problems with subtracks commit 2880986ea32758d5e840dea6a691bb9b5606abd7 Merge: 80b2452 1532a57 Author: Larry Meyer Date: Fri Aug 13 00:18:56 2010 -0700 Merge branch 'master' of larrym@hgwdev.cse.ucsc.edu:/data/git/kent into mutationClassifier commit 80b2452df24da8a148ea3bd9ceafe8dd0cdc6e74 Author: Larry Meyer Date: Fri Aug 13 00:16:19 2010 -0700 changes to make changing visibility work for subtracks commit 17860a93603acfbdb5aa0b19d889e3fd7d3582f8 Author: Jim Kent Date: Thu Aug 12 19:11:46 2010 -0700 Editing text on DNAse track to be a little more precise. commit 1532a574862e1387be36237b6ef227ba6751fd1b Merge: a9d9e14 44ff0f1 Author: Tim Dreszer Date: Thu Aug 12 17:19:50 2010 -0700 Merge branch 'master' of tdreszer@hgwdev.cse.ucsc.edu:/data/git/kent commit a9d9e14bc6e3d70d01824d06e0d0c1730306155e Author: Tim Dreszer Date: Thu Aug 12 17:17:40 2010 -0700 Needed to change 'sel' and 'vis' logic extensively to make findTracks play nice with composites and non-subtracks commit ac96ec4ed3d2e088a485dd54ffb89cddcbbbe3c3 Author: Tim Dreszer Date: Thu Aug 12 17:15:27 2010 -0700 Extended limitedVisFromComposite() because findTracks calls it when composite itself is hidden commit f4acf7053a5964e984fd0d466446848a8808a892 Author: Tim Dreszer Date: Thu Aug 12 17:11:54 2010 -0700 Now that CART_VAR_EMPTY exists, cartDump should accept it just like it accepts 'n/a' commit db78bd4ad3426168586dd823d1b7f3a121172808 Author: Tim Dreszer Date: Thu Aug 12 17:10:20 2010 -0700 Needed to make subtrack four state CB logic available to hgTracks commit 52a4d1626cac96ed654c5f09b9d6ab60ed9581b5 Author: Tim Dreszer Date: Thu Aug 12 17:08:17 2010 -0700 Keeping track of vars chasnged by cgi requires the concept of CART_VAR_EMPTY commit 44ff0f111ad57f23f19ac5c12fcb59548f7a446d Merge: 37af42d 8f518c6 Author: Brian Raney Date: Thu Aug 12 17:05:55 2010 -0700 Merge branch 'master' of braney@hgwdev.cse.ucsc.edu:/data/git/kent commit 37af42d4a42b62f12f1419f1239faa22cb5ec954 Author: Brian Raney Date: Thu Aug 12 17:05:45 2010 -0700 change dataVersion commit 8f518c6f823ad54d85e8ab1023319b4f98f5eb0e Merge: 5efdd19 7066d6a Author: Hiram Clawson Date: Thu Aug 12 16:48:33 2010 -0700 Merge branch 'master' of hiram@hgwdev.cse.ucsc.edu:/data/git/kent commit 5efdd19750401f1974166e4a0615a4fbdcefe811 Author: Hiram Clawson Date: Thu Aug 12 16:48:26 2010 -0700 fixing makefiles to not leave garbage around commit 00d2e768ef6b7a5f87f3c030ca0382cc67e46e2b Author: Hiram Clawson Date: Thu Aug 12 16:48:25 2010 -0700 fixing makefiles to not leave garbage around commit 8e5bc4c4e9df48ec8bc2cf9ae676200939f56b57 Author: Hiram Clawson Date: Thu Aug 12 16:48:25 2010 -0700 fixing makefiles to not leave garbage around commit 4a3af39fdcba982a24d520245ed4dfd2382e5f0f Author: Hiram Clawson Date: Thu Aug 12 16:48:25 2010 -0700 fixing makefiles to not leave garbage around commit 832c1faa1c12e4f1c634cfab1d8af77c3b8e094d Author: Hiram Clawson Date: Thu Aug 12 16:48:24 2010 -0700 fixing makefiles to not leave garbage around commit deacc7d56f06433fc16d33942516b8216c806e4d Author: Hiram Clawson Date: Thu Aug 12 16:48:24 2010 -0700 fixing makefiles to not leave garbage around commit 4f1dd9a14d4a79224e1907c85b9b194718c8127e Author: Hiram Clawson Date: Thu Aug 12 16:48:24 2010 -0700 fixing makefiles to not leave garbage around commit 92357388384e6be4dea918901e99439eaf4ea3bd Author: Hiram Clawson Date: Thu Aug 12 16:48:23 2010 -0700 fixing makefiles to not leave garbage around commit fc403d2d57434bb2525d5709fd2b09e4f7bb0ba7 Author: Hiram Clawson Date: Thu Aug 12 16:48:23 2010 -0700 fixing makefiles to not leave garbage around commit 0414136b8086100dc8c26df842d737b8c72c6dfc Author: Hiram Clawson Date: Thu Aug 12 16:48:22 2010 -0700 fixing makefiles to not leave garbage around commit 9a4f972116f9d8da08e648761e9469865180d1fa Author: Hiram Clawson Date: Thu Aug 12 16:48:22 2010 -0700 fixing makefiles to not leave garbage around commit 578aee8ebc394149aa84ee888dc257757378e559 Author: Hiram Clawson Date: Thu Aug 12 16:48:22 2010 -0700 fixing makefiles to not leave garbage around commit 6e0630d7df69cc54e95caaf29ab8ef7187355079 Author: Hiram Clawson Date: Thu Aug 12 16:48:21 2010 -0700 fixing makefiles to not leave garbage around commit 82c5d03f02356f578d110eddfb69b4576791ab3b Author: Hiram Clawson Date: Thu Aug 12 16:48:21 2010 -0700 fixing makefiles to not leave garbage around commit 6e7e1c2341bad07e6bea3455718fe71f995400bb Author: Hiram Clawson Date: Thu Aug 12 16:48:21 2010 -0700 fixing makefiles to not leave garbage around commit 8424b4fccfb78219defff8f2f7d87e5435f6b985 Author: Hiram Clawson Date: Thu Aug 12 16:48:20 2010 -0700 fixing makefiles to not leave garbage around commit 73879581d650eb3076dc9c925c3baa671953313f Author: Hiram Clawson Date: Thu Aug 12 16:48:20 2010 -0700 fixing makefiles to not leave garbage around commit f6c2369ff38c88c88c144f2ab8571c0f35b6e2fe Author: Hiram Clawson Date: Thu Aug 12 16:48:19 2010 -0700 fixing makefiles to not leave garbage around commit a810ef606f8ccbf62d97c62982f755a3b827e362 Author: Hiram Clawson Date: Thu Aug 12 16:48:19 2010 -0700 fixing makefiles to not leave garbage around commit a82d0a440b948e4da0d37c3814e9b8f9ba9fe163 Author: Hiram Clawson Date: Thu Aug 12 16:48:19 2010 -0700 fixing makefiles to not leave garbage around commit e3abba0f1de7c11f7a8f8a901868396d3b7e5378 Author: Hiram Clawson Date: Thu Aug 12 16:48:18 2010 -0700 fixing makefiles to not leave garbage around commit 879c0e2198c5a5329357849ded16e1c5354e75b0 Author: Hiram Clawson Date: Thu Aug 12 16:48:18 2010 -0700 fixing makefiles to not leave garbage around commit b2869d61d22733ddc33e66d08ce804de47f3c3a1 Author: Hiram Clawson Date: Thu Aug 12 16:48:18 2010 -0700 fixing makefiles to not leave garbage around commit 7066d6adea5f4489a59050d5e251b513ded488c7 Author: Venkat Malladi Date: Thu Aug 12 16:36:11 2010 -0700 Reverted some changes to metaData protocol lines that were put in by accident commit 33ea6c67c83003de260550555708f7d4d8653304 Author: Tim Dreszer Date: Thu Aug 12 16:33:23 2010 -0700 Name is now optional on drop down select. This was necessary to make findTracks behave commit 0d886980a658f85ecfe23d0a8e71c73bb9692119 Author: Hiram Clawson Date: Thu Aug 12 16:28:37 2010 -0700 use hAllocConn instead of sqlConnect commit 0721db3d53815cd3b7113d0ccb526299bd267f0b Merge: f65eb93 083f2ea Author: Chin Li Date: Thu Aug 12 16:14:34 2010 -0700 Merge branch 'master' of chinhli@hgwdev.cse.ucsc.edu:/data/git/kent commit f65eb9358f891debe18ff23b86d795e9d7b4eb2a Author: Chin Li Date: Thu Aug 12 15:08:45 2010 -0700 phastCons 13-way DONE commit b3a67997d3c4d5ff84676f999214e7a343a77c49 Author: Hiram Clawson Date: Thu Aug 12 15:05:35 2010 -0700 update note about lifting Ensembl EF2 sequence to sacCer2 coordinates commit 083f2eadf934d2c9ac4ca5010465a90e238dcd07 Merge: 64dd1bb 1b06b5d Author: Venkat Malladi Date: Thu Aug 12 14:30:53 2010 -0700 Merge branch 'master' of vsmalladi@hgwdev.cse.ucsc.edu:/data/git/kent commit 64dd1bbaeaef9e5b7203e0bdd7630db4174a2101 Author: Venkat Malladi Date: Thu Aug 12 14:30:45 2010 -0700 Updated metadata that was incorrect and previously looked over. commit 1b06b5dd477dc28112cd6e6aa82ef46abd8de33a Author: katrina Date: Thu Aug 12 14:17:27 2010 -0700 copying metDb .ra files into beta and public so these tracks will use metaDb on beta and the RR commit d622875f5b1531f4cd094ba18c6563dcc0ce884f Author: katrina Date: Thu Aug 12 14:15:43 2010 -0700 adding wgEncodeUwAffyExonArray.ra to make files of beta and public so it will use metaDB commit ef9b00dfacd61c2dc7275dd6c0ad5aa091017030 Merge: 275040a 216f238 Author: Brian Raney Date: Thu Aug 12 12:00:59 2010 -0700 Merge branch 'master' of braney@hgwdev.cse.ucsc.edu:/data/git/kent commit 275040ac865d0e0b47e91affd1f309428947f88a Author: Brian Raney Date: Thu Aug 12 12:00:35 2010 -0700 move UwAffyExonArray metadata to metadb from trackDb commit 216f238cda2196cccaa01c8cd3bfb26934b951fe Merge: fd4d72c 496d852 Author: Venkat Malladi Date: Thu Aug 12 11:10:39 2010 -0700 Merge branch 'master' of vsmalladi@hgwdev.cse.ucsc.edu:/data/git/kent commit fd4d72cdbae30e67234814ce0d77a28edf948565 Author: Venkat Malladi Date: Thu Aug 12 11:10:23 2010 -0700 Updated the registered variables page to include seqPlatform. commit 496d8529a6419c5816f2c43b29e22690535f2fbf Author: vanessa Date: Thu Aug 12 10:39:17 2010 -0700 removed release tags for the release of the regulatory track commit 684de1557b1e16ed830222f760150bcbbf884d72 Author: katrina Date: Thu Aug 12 09:24:05 2010 -0700 adding metaDb for ENCODE Regulation Track to beta and public commit ddbcbaa44a40f0554bd7099d30c91efd55a1f264 Merge: f45bce4 a0e61e7 Author: Brian Raney Date: Thu Aug 12 08:29:29 2010 -0700 Merge branch 'master' of braney@hgwdev.cse.ucsc.edu:/data/git/kent commit f45bce446bb53fc56e100ef27dea7f137caf9b51 Author: Brian Raney Date: Thu Aug 12 08:29:16 2010 -0700 back out my changes from yesterday commit a0e61e7068e931c30a4b0cb62b89b2930bca420f Author: Galt Barber Date: Thu Aug 12 08:00:28 2010 -0700 "Encode release log update" commit 2fbe6aa0a95fbb7f7b9aff796547b18dee4c0cd1 Author: Galt Barber Date: Thu Aug 12 08:00:26 2010 -0700 "Release log update" commit 7febeaa0761ddf86d1dc678b47cfb13afe05e849 Merge: dfdde1a d6cae02 Author: Venkat Malladi Date: Wed Aug 11 23:03:02 2010 -0700 Merge branch 'master' into Development-Mouse commit d6cae025a852fb70f4a0ec4b2bd6b42866c4a3ac Author: Venkat Malladi Date: Wed Aug 11 23:02:26 2010 -0700 Update Mouse metaData to remove human data cell types commit 2466fa633233d31c98f77080f570f4d6588530e6 Merge: 8c2a631 efa7ce6 Author: Brian Raney Date: Wed Aug 11 14:29:26 2010 -0700 Merge branch 'master' of braney@hgwdev.cse.ucsc.edu:/data/git/kent commit 8c2a6312dd08ea398bdffac19d42b534d236dc14 Author: Brian Raney Date: Wed Aug 11 14:28:44 2010 -0700 remove arguments to pass in organism since these are specified in the cv.ra commit efa7ce68ba997f1c4281b8556e9f07132542c761 Merge: e552d8e d615fd9 Author: Cricket Sloan Date: Wed Aug 11 12:53:36 2010 -0700 Merge branch 'master' of cricket@hgwdev.cse.ucsc.edu:/data/git/kent commit e552d8ea891a793ce8e031528fbceed0a3569f38 Author: Cricket Sloan Date: Wed Aug 11 12:53:31 2010 -0700 revoked submissions 1803, 1798, 1809 commit d615fd98c042a93df431f8d4d81ea5f9fab604cb Merge: c62062a 833a570 Author: Hiram Clawson Date: Wed Aug 11 11:51:55 2010 -0700 Merge branch 'master' of hiram@hgwdev.cse.ucsc.edu:/data/git/kent commit c62062a161d1ea955ce28ca89a5c8105c25e9201 Author: Hiram Clawson Date: Wed Aug 11 11:51:46 2010 -0700 done with all organisms for v59 commit 833a570cce0a4cab8e82f0492396b5a9dbe7b637 Author: katrina Date: Wed Aug 11 10:33:39 2010 -0700 removed extra

that was breaking up a paragraph commit 6a7ab9a23932a28dc78e5f4ec8ee67e345ce8d00 Merge: c189b4c b581593 Author: Tim Dreszer Date: Wed Aug 11 09:41:07 2010 -0700 Merge branch 'master' of tdreszer@hgwdev.cse.ucsc.edu:/data/git/kent commit c189b4c3d1229098a814b713977208e2e8775502 Author: Tim Dreszer Date: Wed Aug 11 09:41:04 2010 -0700 Missed sheltering the include execinfo.h within BACKTRACE_EXISTS define commit b581593986a8db2cea3dc5855f629cc37117123d Author: Galt Barber Date: Wed Aug 11 08:00:37 2010 -0700 "Encode release log update" commit e48080b9e2621fe8ff970ab5d59f6b7ec1d5dfab Author: Galt Barber Date: Wed Aug 11 08:00:36 2010 -0700 "Release log update" commit 4b03a52588a9bf903da81c65f9fb6fecd6f5917b Merge: 87fb111 b7bc07f Author: Cricket Sloan Date: Tue Aug 10 22:37:41 2010 -0700 Merge branch 'master' of cricket@hgwdev.cse.ucsc.edu:/data/git/kent commit 87fb111ef6cc787a5aec5261c8acdeab7099b371 Author: Cricket Sloan Date: Tue Aug 10 22:37:31 2010 -0700 Updated track description and track names, tried to make sort work commit 76b730eceab7e4a23e6149e0e20563c5aece67fe Author: Cricket Sloan Date: Tue Aug 10 22:15:33 2010 -0700 release notes for wgEncodeAffyRnaLoc commit b7bc07f37d1c490d724cf931abb4414348c2f34a Merge: 7e836b1 17d1bcf Author: Krishna Roskin Date: Tue Aug 10 19:52:13 2010 -0700 Merge branch 'master' of krish@hgwdev.cse.ucsc.edu:/data/git/kent commit 7e836b1bd064252bc91391297bb64ed655d44311 Author: Krishna Roskin Date: Tue Aug 10 19:50:10 2010 -0700 added paraMd5sum to the makefile commit e54123f3fbd6a3a818eb410447157d73326a74ce Author: Krishna Roskin Date: Tue Aug 10 19:49:24 2010 -0700 parasolized version of md5sum commit 047094cf4ae471ced5b99e19994105e012dbe2b3 Author: Mark Diekhans Date: Tue Aug 10 18:01:31 2010 -0700 prevent opening an sql connection for each sequence retrieved by the table browser commit 17d1bcfd6a902fc1255cd05bc2d03630b23929f9 Author: Hiram Clawson Date: Tue Aug 10 17:58:37 2010 -0700 finished the ce9 ensGenes commit 1d22d6dfe1abfb0357c5f128f219b1a80272361f Merge: af0537c dd36e6e Author: Hiram Clawson Date: Tue Aug 10 17:55:37 2010 -0700 Merge branch 'master' of hiram@hgwdev.cse.ucsc.edu:/data/git/kent commit af0537c1e3d12e96ea7613f20f512e4ec026d97d Author: Hiram Clawson Date: Tue Aug 10 17:54:03 2010 -0700 finished with the broken bits commit dd36e6e94a90e766b49de539ed127934f20f8255 Merge: 0a12de8 2d66644 Author: Tim Dreszer Date: Tue Aug 10 17:33:17 2010 -0700 Merge branch 'master' of tdreszer@hgwdev.cse.ucsc.edu:/data/git/kent commit 0a12de844fc0cdc4ef285366a650aee2d4c6da51 Author: Tim Dreszer Date: Tue Aug 10 17:33:12 2010 -0700 Made subtrack DnD a little more consistent with imageV2 DnD commit 2d66644db0a6f7f522929cbae575a3ae24146101 Merge: 24342a0 9cc3b2f Author: Hiram Clawson Date: Tue Aug 10 17:29:49 2010 -0700 Merge branch 'master' of hiram@hgwdev.cse.ucsc.edu:/data/git/kent commit 24342a0c36a848250497ed9b55ae7fe4404f82aa Author: Hiram Clawson Date: Tue Aug 10 17:29:44 2010 -0700 allow scaffold names of ^Scaffold for macEug1 commit 9cc3b2f13d316e768a4fc1095fb0ae4baa9ecb87 Author: Tim Dreszer Date: Tue Aug 10 17:13:38 2010 -0700 Fixed bug affecting subtrack list DnD but not trackImage DnD commit dfdde1a49743d4dd74aeb9a15cb7cf0173ec141e Merge: e50b4e5 c79b956 Author: Venkat Malladi Date: Tue Aug 10 17:07:47 2010 -0700 Merge branch 'master' into Development-Mouse commit c79b9568b37a81473b8d568c24b72e5c9b8c15bb Author: Tim Dreszer Date: Tue Aug 10 16:54:12 2010 -0700 Fixed a few comments commit 9730805c9805ae4c0ec3821db2243184d4ceae05 Merge: 384ae44 97ee437 Author: Tim Dreszer Date: Tue Aug 10 16:53:05 2010 -0700 Merge branch 'master' of tdreszer@hgwdev.cse.ucsc.edu:/data/git/kent commit 384ae448bc70c1452db276f10369dd2938e1098d Author: Tim Dreszer Date: Tue Aug 10 16:52:55 2010 -0700 Further tweaks in the mysterious black arts of css commit d020e91bb412e58f4456f560a0ea5fadb7c2ab9e Author: Tim Dreszer Date: Tue Aug 10 16:49:45 2010 -0700 Tabs were shown as divs before being set up. Now they are hidden until set up commit eea5c3f688ba673e4a7af3d3a9441690aaaeeb2e Author: Tim Dreszer Date: Tue Aug 10 16:43:07 2010 -0700 Removed the CB_SELECTION ifndefs commit 28fcb140db85344bc22ba86c662c44db4c05ce35 Author: Tim Dreszer Date: Tue Aug 10 16:41:01 2010 -0700 Moved some style settings to cheapcgi.c commit db2405f972ffdd9a183d1b1708c4aaf6fb6804bf Author: Tim Dreszer Date: Tue Aug 10 16:39:16 2010 -0700 Fixed bug when SUBTRACKS_HAVE_VIS was on and wigMafs triggered infinite loop commit 021aee9e624dac151ccab845b23458c99be10b48 Author: Tim Dreszer Date: Tue Aug 10 16:30:51 2010 -0700 Added cartTdbTreeCleanupOverrides to cleanup subtrack settings when composite/view settings change commit 97ee4375847b6f1dfc540c0158cd3d0169cd1550 Merge: 6eaa46e a43f0db Author: Brian Raney Date: Tue Aug 10 16:26:03 2010 -0700 Merge branch 'master' of braney@hgwdev.cse.ucsc.edu:/data/git/kent commit 6eaa46e89f8b865f96169e44ccaffe5c8bc3387e Author: Brian Raney Date: Tue Aug 10 16:25:43 2010 -0700 make link in ENCODE ... metadata section go straight to the file commit a43f0db807237b980027fade3c8dd25adf9e6692 Author: mary Date: Tue Aug 10 16:01:46 2010 -0700 making felCat3 chain/Nets for hg19 and mm9 have o_db rather than o_organism commit e50b4e5ac71c72241de37491b06eb775a6438aac Merge: 4a132d4 e9cf58b Author: Venkat Malladi Date: Tue Aug 10 15:56:10 2010 -0700 Merge branch 'master' into Development-Mouse commit f4d16c968e8bb273b564253341a690ee824d203c Author: Tim Dreszer Date: Tue Aug 10 15:55:50 2010 -0700 Extended commonCssStyles and made amenable to printf/hgPrintf commit 1c1807f693e7a202703ad53b37c933ccf2bfc03c Author: mary Date: Tue Aug 10 15:45:57 2010 -0700 putting felCat4 chain/net in human placental track as well as making the short label for all chain/nets be 'cat' instead of 'felCat4' commit 27f23332a191aeb37b075723b873ad4d14a5ad7f Merge: f328064 e9cf58b Author: Cricket Sloan Date: Tue Aug 10 15:30:36 2010 -0700 Merge branch 'master' of cricket@hgwdev.cse.ucsc.edu:/data/git/kent commit e9cf58be11323d6ff8332adcb91bf37322274935 Merge: 3acd706 5b022ff Author: Brian Raney Date: Tue Aug 10 14:03:13 2010 -0700 Merge branch 'master' of braney@hgwdev.cse.ucsc.edu:/data/git/kent commit 3acd7064c1169e9ef6d6ccaacec88259daa6ece6 Author: Brian Raney Date: Tue Aug 10 14:02:43 2010 -0700 add some release notes declaring that these results were lifted up from hg18 commit f328064ab884a0dc2634e70d9ac3286f487ef2d9 Author: Cricket Sloan Date: Tue Aug 10 12:57:22 2010 -0700 fixed html missing end tag commit 5b022ffbfa6a8ce23d4826750c6833e24f27fe2e Merge: bfd8102 68abe82 Author: Cricket Sloan Date: Tue Aug 10 12:38:21 2010 -0700 Merge branch 'master' of cricket@hgwdev.cse.ucsc.edu:/data/git/kent commit bfd8102039dac663bae007cfd9d2330def627ead Author: Cricket Sloan Date: Tue Aug 10 12:38:12 2010 -0700 Added verbage to say that we did not lift over the signals commit 68abe82cc0553b1456e9ced91c226f2bceef2c97 Merge: 8009c4f 03e5891 Author: Brian Raney Date: Tue Aug 10 12:08:01 2010 -0700 Merge branch 'master' of braney@hgwdev.cse.ucsc.edu:/data/git/kent commit 8009c4fa78ad633256e4d7339d2f99909ae96d4b Author: Brian Raney Date: Tue Aug 10 12:07:30 2010 -0700 build some metadata commit 03e5891eb389aab694e8b63f766b116973d60a14 Author: Hiram Clawson Date: Tue Aug 10 12:07:12 2010 -0700 need 24 characters not just 23 for other name commit 1cbbe2bc44e14c56c1ce0d9a350e1fc921e32af7 Merge: 0839f22 5af4bf8 Author: Hiram Clawson Date: Tue Aug 10 12:02:02 2010 -0700 Merge branch 'master' of hiram@hgwdev.cse.ucsc.edu:/data/git/kent commit 0839f22588fac15d105e88503902d57298fc77a9 Author: Hiram Clawson Date: Tue Aug 10 12:01:56 2010 -0700 longer names for ensembl proteins first seen in mm9 commit 4a132d47ffdc450fa8035b1122f3a9e40b9bc3ee Merge: e16fdd3 5af4bf8 Author: Venkat Malladi Date: Tue Aug 10 11:44:54 2010 -0700 Merge branch 'master' into Development-Mouse commit 5af4bf8145315d9cf3ab45117a854a81726558ad Merge: 610c14a 9f2b7be Author: Venkat Malladi Date: Tue Aug 10 11:43:27 2010 -0700 Merge branch 'master' of vsmalladi@hgwdev.cse.ucsc.edu:/data/git/kent commit 610c14a886417476efde70b530485cc85776a244 Author: Venkat Malladi Date: Tue Aug 10 11:43:19 2010 -0700 Updated metaData with missing data commit 9f2b7be05f19abcf2274bf31c4f7a592d931e1a7 Author: Fan Hsu Date: Tue Aug 10 11:18:19 2010 -0700 Updated otherOrgs.ra for hg19, mm9, rn4, ce6, dm3, and sacCer2 to bring them to the latest state to match the xxBlastTab tables rebuilt for those 6 genomes. commit 57ea41097786723bd1adf4e5559e999220c9a4c7 Author: Hiram Clawson Date: Tue Aug 10 10:32:07 2010 -0700 starting ensembl v59 update commit 603e372fc8a0e876bc75eccc25e2e1e8495cee66 Merge: 44effd7 e9195c0 Author: Jim Kent Date: Tue Aug 10 09:37:35 2010 -0700 Merge branch 'master' of kent@hgwdev.cse.ucsc.edu:/data/git/kent commit 44effd7c3ce78861e3ee110f30bdfcb97bd151df Author: Jim Kent Date: Tue Aug 10 09:37:29 2010 -0700 Adding trackHash parameter to some new code. commit e9195c0b6d8ce9c28ca7491961881b9747e7739e Author: Brian Raney Date: Tue Aug 10 09:33:13 2010 -0700 metadata for regulation rainbow clusters commit e16fdd3d0848b1d9518a5570f1c01594a81b34b5 Merge: 1f7a968 b874dfc Author: Venkat Malladi Date: Tue Aug 10 09:14:12 2010 -0700 Merge branch 'master' into Development-Mouse commit b874dfce8d34de6b7c3fac0a4bf13168881b61c2 Author: Galt Barber Date: Tue Aug 10 08:00:44 2010 -0700 "Encode release log update" commit ea13ce85f76e9138feb19ec25d7d800e126681ae Author: Galt Barber Date: Tue Aug 10 08:00:09 2010 -0700 "Release log update" commit 4baf029a1b32232aa25dcc980dc8cd463d1bee8f Author: Larry Meyer Date: Tue Aug 10 02:57:29 2010 -0700 clicks in menu bar now work commit cf48faf079847e8225889d1f0da7063cfdcd3f61 Author: Larry Meyer Date: Tue Aug 10 02:55:53 2010 -0700 disable postToSaveSettings in search form page (fixes problem where top menu bar didn't work commit 97ad384bacb0c211a2f18ef7563b14f8f5faa520 Author: Larry Meyer Date: Tue Aug 10 02:32:41 2010 -0700 add delSearchSelect and addSearchSelect commit ffab511db81c6c65b22fe49700225b15e105cb21 Author: Larry Meyer Date: Tue Aug 10 02:31:58 2010 -0700 implement -/+ buttons commit fea757a9133c529541ec925a96730d6730c21a9f Author: Larry Meyer Date: Tue Aug 10 02:15:09 2010 -0700 add some items to excludeVars commit 33e8bd7e55e793eeedc522f787b962632a2df0b5 Merge: cda63b5 309bbed Author: Larry Meyer Date: Mon Aug 9 23:08:25 2010 -0700 Merge branch 'master' of larrym@hgwdev.cse.ucsc.edu:/data/git/kent into mutationClassifier commit cda63b561b5ad44c13531c15ff544632696e0f7d Author: Larry Meyer Date: Mon Aug 9 23:06:47 2010 -0700 support -bindingSites option commit 309bbedd27744ac1d557a21e0bbe244ef5bb208a Merge: 11dd820 84202b4 Author: Galt Barber Date: Mon Aug 9 18:55:06 2010 -0700 Merge branch 'master' of galt@hgwdev.cse.ucsc.edu:/data/git/kent commit 11dd82091e4deee2069eaaf4d7cd7922d05a914f Author: Galt Barber Date: Mon Aug 9 18:55:01 2010 -0700 re-running mm8->mm9 liftover with improved process commit 84202b4a607ea21c6aa8acdf378fb69f572829d3 Merge: 5e378d6 55885de Author: Brian Raney Date: Mon Aug 9 17:43:25 2010 -0700 Merge branch 'master' of hgwdev:/data/git/kent commit 5e378d6d1e6b42b49a38cd360ed83f70e5a9281a Author: Brian Raney Date: Mon Aug 9 17:43:14 2010 -0700 v238 preview commit 1f7a9688acc16492253d2bc996157d8b30085c5f Author: Venkat Malladi Date: Mon Aug 9 16:40:48 2010 -0700 Added metaData for Uw Dnase-Seq submissions commit 55885de56a4fa8468f96d28fd5de9bb692b7320e Author: Venkat Malladi Date: Mon Aug 9 16:16:48 2010 -0700 Upated metaData with origAssembly variable. commit 447135ebb7e175f8bf04e28c98376a7be73a9f1e Merge: e4de79d 93f4d41 Author: Hiram Clawson Date: Mon Aug 9 15:46:33 2010 -0700 Merge branch 'master' of hiram@hgwdev.cse.ucsc.edu:/data/git/kent commit e4de79df304a57f9ced1af0737ad420d77cc859b Author: Hiram Clawson Date: Mon Aug 9 15:46:26 2010 -0700 updated with v59 definitions commit 93f4d4114a0f6a8a4857044c3cae299d1d49bba6 Merge: 8d2bb5e 561d608 Author: Jim Kent Date: Mon Aug 9 15:37:41 2010 -0700 Merge branch 'master' of kent@hgwdev.cse.ucsc.edu:/data/git/kent commit 561d6085aead67048e051fb60c4af697b9d4a2c2 Merge: 9c8afc2 742889d Author: vanessa Date: Mon Aug 9 15:29:19 2010 -0700 Merge branch 'master' of vanessa@hgwdev.cse.ucsc.edu:/data/git/kent commit 8d2bb5ed5f45a73862212a7e8ec9c1063425620d Merge: 4a234f0 742889d Author: Jim Kent Date: Mon Aug 9 15:01:13 2010 -0700 Fixed merge conflict commit 4a234f089be336a40604bf7002b3811dc3dad308 Author: Jim Kent Date: Mon Aug 9 14:58:47 2010 -0700 Adding a trackHash parameter to a bunch of metadata routines so that they could find the track associated with a table. Fixing clipping bug in hgTracks.c for multiWig labels when in non-overlay mode due to a special case that seems to be obsolete (did fair bit of testing to make sure it's not used.) commit 9c8afc23fd041cc6cfe501ecf31574053d19b492 Author: vanessa Date: Mon Aug 9 14:54:02 2010 -0700 added the function for hgdownloads commit 742889d80c7d057543636784ba7e4c8a628f374a Merge: 3521370 8e79ba3 Author: Venkat Malladi Date: Mon Aug 9 14:50:31 2010 -0700 Merge branch 'master' of vsmalladi@hgwdev.cse.ucsc.edu:/data/git/kent commit 3521370914197fa7fe08ffbbd07d698697e5cc33 Author: Venkat Malladi Date: Mon Aug 9 14:50:25 2010 -0700 Updated SeqPlatform descriptions commit 8e79ba3505c5e62a41627cf609971f1f9d36c145 Author: Tim Dreszer Date: Mon Aug 9 14:30:37 2010 -0700 Turning on dragReorder in genome-test. commit 310048824102a69526ec655195c65ba5d2559121 Author: Krishna Roskin Date: Mon Aug 9 14:19:05 2010 -0700 fix raw/supp file calling, added fields requested by NCBI, added support for replicate commit afac1155bb0d03cf5f3229b2db99567ad561aa12 Author: Tim Dreszer Date: Mon Aug 9 14:05:15 2010 -0700 cgiClientBrowser() macro checked in commit 7bdd2fca98cde202ee169f599928bf8ffe3ca354 Author: Hiram Clawson Date: Mon Aug 9 13:56:53 2010 -0700 removed older trashCleaning.sh script commit 209345a2fed48b1cc3a8dac176ee3ea64f74e7b5 Author: Tim Dreszer Date: Mon Aug 9 13:39:44 2010 -0700 Adding Nav links to composites with matrix commit f9c027995c634e33c3f68a7b7853aa2c94d6fc2e Author: Jim Kent Date: Mon Aug 9 12:37:49 2010 -0700 Making score an int rather than floating point in regCluster bed output. commit bdf747984907ee1cd61f608e766c9415eb08c3dc Merge: 67b1bb0 016c3ec Author: Hiram Clawson Date: Mon Aug 9 12:34:51 2010 -0700 Merge branch 'master' of hiram@hgwdev.cse.ucsc.edu:/data/git/kent commit 67b1bb0f3d60039ac5744c3829a9e57be5eaa414 Author: Hiram Clawson Date: Mon Aug 9 12:34:23 2010 -0700 remove the safety exit 0, this is now live commit 016c3ec8ccf82fdc3729fbe37b4ff5a0b41fd7f4 Merge: cd89a2b 5111018 Author: Brian Raney Date: Mon Aug 9 12:07:18 2010 -0700 Merge branch 'master' of braney@hgwdev.cse.ucsc.edu:/data/git/kent commit cd89a2b3f7b9bcf966cc9adffa2882d4692747e0 Author: Brian Raney Date: Mon Aug 9 12:06:12 2010 -0700 draw in MG_BLACK, not 1 (which is white in 32-bit) commit 5111018fbad0a74a3039cd7539c2ecae7fb56aa7 Merge: 69b3f11 9cf3425 Author: mary Date: Mon Aug 9 12:03:41 2010 -0700 Merge branch 'master' of mary@hgwdev.cse.ucsc.edu:/data/git/kent commit 69b3f115cf095a06cf9c4c9d4941a062359b99cf Author: mary Date: Mon Aug 9 12:03:36 2010 -0700 removing felCat4 image due to copyright commit 9cf3425051bc1c8d4bd2c7f3afd371cd6b21e71d Author: ann Date: Mon Aug 9 11:52:45 2010 -0700 removed bad link commit 827195cb57696408996558a788c875e514da42fc Merge: 82b7086 1d06b2e Author: Tim Dreszer Date: Mon Aug 9 10:33:07 2010 -0700 Merge branch 'master' of tdreszer@hgwdev.cse.ucsc.edu:/data/git/kent commit 82b708668f8be81961f2eda11562f3318f4359fc Author: Tim Dreszer Date: Mon Aug 9 10:33:02 2010 -0700 Added checkboxes to searchTracks commit 1d06b2e66cd8770d3457b7dbf709327b6bef793c Merge: 0ded825 de95271 Author: Brian Raney Date: Mon Aug 9 10:22:55 2010 -0700 Merge branch 'master' of braney@hgwdev.cse.ucsc.edu:/data/git/kent commit 0ded825547c8c3b3f7fda710cd789baace238b61 Author: Brian Raney Date: Mon Aug 9 10:22:37 2010 -0700 add submission id for gencode commit de95271152122c1e79f59bd208e9dac81368687d Merge: 8a16b33 b4d879a Author: Hiram Clawson Date: Mon Aug 9 09:55:02 2010 -0700 Merge branch 'master' of hiram@hgwdev.cse.ucsc.edu:/data/git/kent commit 8a16b33e9c0108456af046610d4be6ebc75ba7a0 Author: Hiram Clawson Date: Mon Aug 9 09:54:49 2010 -0700 finalized versions ready to go commit 0ad5d0e6ef35b7c69e57d06308a8d83c64aa4655 Merge: d42729e b4d879a Author: Venkat Malladi Date: Mon Aug 9 09:14:44 2010 -0700 Merge branch 'master' into Development-Mouse commit b4d879a4c1655376b3f43e6309294d599052d433 Author: Fan Hsu Date: Mon Aug 9 08:30:40 2010 -0700 Rebuilt xxBlastTab tables for hg19, mm9, rn4, ce6, sacCer2, and dm3 using blast-2.2.11. commit 015ef7e26f1ba2e3e4155309721c27c5a44dc2b7 Author: Galt Barber Date: Mon Aug 9 08:00:32 2010 -0700 "Encode release log update" commit fa494ba39e0de6c19bdb8cae226cf3fbc1702a6d Author: Galt Barber Date: Mon Aug 9 08:00:08 2010 -0700 "Release log update" commit db53dff4c2f7f953ed1b4364e1dca89aab886bc7 Author: Galt Barber Date: Sun Aug 8 08:00:13 2010 -0700 "Encode release log update" commit b9c72771cda7a32bb4deeeee87973adc0086e2e2 Author: Galt Barber Date: Sun Aug 8 08:00:09 2010 -0700 "Release log update" commit a07d549387df3cca0bd648538eeb5134f3625fba Author: Venkat Malladi Date: Sat Aug 7 16:41:01 2010 -0700 Standardized dataType ChIP-seq in the metadata commit e7e530cfc2752ebe3b43d0b59ff635793e048570 Author: Galt Barber Date: Sat Aug 7 08:00:10 2010 -0700 "Encode release log update" commit e40553ed65442e7b8624145f69076c404d7572a3 Author: Galt Barber Date: Sat Aug 7 08:00:09 2010 -0700 "Release log update" commit 74d62ae482ae201092890651e89f69f0940596ba Author: Hiram Clawson Date: Sat Aug 7 06:32:15 2010 -0700 omit reference to my location commit ecf3d1a2f597613814aa005573f71fd957676e5f Author: Hiram Clawson Date: Sat Aug 7 06:26:52 2010 -0700 trash cleaner now in two parts to verify OK commit 5e81abcae4551561d014fa22214a2a4febbf165f Merge: 725d8cc 6d09ea8 Author: Krishna Roskin Date: Fri Aug 6 15:52:17 2010 -0700 Merge branch 'master' of krish@hgwdev.cse.ucsc.edu:/data/git/kent commit 725d8ccfe9dfbd8b7bfd52ff89b77a16c3767384 Author: Krishna Roskin Date: Fri Aug 6 15:52:01 2010 -0700 updated to deal with the fact tha we don't have gbdb directories in the download directories any more and to deal with non-gz files commit d42729e7eccf3fd1d8b63abb415c7055fc6f8ed8 Merge: 1f9c62e cac277c Author: Venkat Malladi Date: Fri Aug 6 15:10:24 2010 -0700 Merge branch 'master' into Development-Mouse commit 6d09ea81e03833f6b070ea24b2b5906eff1113f5 Merge: e29ef5f cac277c Author: katrina Date: Fri Aug 6 15:06:29 2010 -0700 Merge branch 'master' of hgwdev:/data/git/kent commit e29ef5fb1ece4f2eb354ac6c4f6a7d4403cf47a4 Author: katrina Date: Fri Aug 6 15:06:20 2010 -0700 made tier three frame bigger commit cac277cdefdf7c5af13fbe1599d34f6c98c59fde Merge: c8c9b2f 4f2b8c1 Author: Venkat Malladi Date: Fri Aug 6 15:02:51 2010 -0700 Merge branch 'master' of vsmalladi@hgwdev.cse.ucsc.edu:/data/git/kent commit c8c9b2f2a4207288812c502a58f070193465e57c Author: Venkat Malladi Date: Fri Aug 6 15:02:40 2010 -0700 Missed spelled display of factor ZNF274 as ZNF27 in composite subGroup, corrected error. commit 4f2b8c1b855cb51b5323bbab248f0b26b28a0080 Merge: 7bd5f20 10e281c Author: katrina Date: Fri Aug 6 14:57:03 2010 -0700 Merge branch 'master' of hgwdev:/data/git/kent commit 7bd5f20ca85ab82ab80325a8fcb9fde8bccbd10d Author: katrina Date: Fri Aug 6 14:56:55 2010 -0700 added link location that I had forgotten commit 10e281c1c03f9574e0c3551250af66467faffe33 Merge: 89ef435 b72936b Author: Venkat Malladi Date: Fri Aug 6 14:50:00 2010 -0700 Merge branch 'master' of vsmalladi@hgwdev.cse.ucsc.edu:/data/git/kent commit 89ef435e631db9659d9ece4dfdfa720580094d71 Author: Venkat Malladi Date: Fri Aug 6 14:49:41 2010 -0700 Commented out documents, so that mouse cv can be released while documents can be released when a standard can be determined or mouse tracks are released. commit b72936b14b0ef83eb5c0c8f8cf00d30d346e090a Merge: c5fb582 9199607 Author: katrina Date: Fri Aug 6 14:39:31 2010 -0700 Merge branch 'master' of hgwdev:/data/git/kent commit c5fb58278ee5f237602da42585e68297e459f9d7 Author: katrina Date: Fri Aug 6 14:39:24 2010 -0700 additional portal modifications in prep for release commit 9199607ee913f40144efb542e158ccfd9675e862 Author: b0b Date: Fri Aug 6 14:38:03 2010 -0700 mostly shortened run-on lines. added one EM tag pair around et al. commit 52b7f853d6ce308ded69b00c536dd0c55ba468cf Merge: c71c9c2 3ff5072 Author: b0b Date: Fri Aug 6 14:32:45 2010 -0700 Merge branch 'master' of kuhn@hgwdev.cse.ucsc.edu:/data/git/kent commit 3ff5072d9fecd4f85fe5af75e66181f6908b5520 Author: Cricket Sloan Date: Fri Aug 6 13:41:09 2010 -0700 Changed RipChip to RIP-chip commit 6a7d985cfd376f0af507e5654629305ff414db41 Author: Cricket Sloan Date: Fri Aug 6 13:38:15 2010 -0700 changed the RipChip to RIP-chip commit 92a2b1ef7e04a1c74d23eded604d75d3fa123899 Author: Cricket Sloan Date: Fri Aug 6 13:33:05 2010 -0700 Added first draft of pi.ra and cleaned up DataType commit f8f11fe5a89d5161a2db2353741ed05eadf70140 Author: Fan Hsu Date: Fri Aug 6 12:25:00 2010 -0700 Re-built hg19 uniGene_3 track. commit 7cb35b2cc656bca1d5824e8588f3847c4bfd54e2 Author: Brian Raney Date: Fri Aug 6 11:33:20 2010 -0700 fix link out for Gencode V3 commit a7622621a5e071f085ef4906aaaafc2a83738060 Author: Brian Raney Date: Fri Aug 6 11:29:45 2010 -0700 take out metadata for hg19 wgEncodeGencode commit af988f63cb1773dea5c656ae6721127a5789a0be Merge: 9979d1b c93c3a2 Author: Brian Raney Date: Fri Aug 6 11:28:35 2010 -0700 Merge branch 'master' of braney@hgwdev.cse.ucsc.edu:/data/git/kent commit 9979d1beac1326e4cb2e164ea6e94f9e7bf32af1 Author: Brian Raney Date: Fri Aug 6 11:28:21 2010 -0700 metadata for hg19 gencodeV4 commit c93c3a28a5c9c9dae0d4cdc9d30c354fb52f4b1b Merge: 23d9b73 d745f03 Author: Angie Hinrichs Date: Fri Aug 6 11:05:29 2010 -0700 Merge branch 'master' of angie@hgwdev.cse.ucsc.edu:/data/git/kent commit 23d9b73e0a3663f921ffecf76ae1855a7003d018 Author: Angie Hinrichs Date: Fri Aug 6 11:05:18 2010 -0700 Changed blastPath to point to /scratch/data/blast which is now a symlink to the preferred version of blast. commit d745f03636a906cb16c13898fc51ea10812f76e2 Author: Brian Raney Date: Fri Aug 6 11:01:48 2010 -0700 drop alignments from UCSF Brain Methyl since they aren't correct commit 6e22076f8aad294b4cb002ac15a49a5742f0db1a Merge: f7cc53f faebe04 Author: Hiram Clawson Date: Fri Aug 6 10:45:54 2010 -0700 Merge branch 'master' of hiram@hgwdev.cse.ucsc.edu:/data/git/kent commit f7cc53fb3c6c0579fe6823d427bd06fd7e78e8a7 Author: Hiram Clawson Date: Fri Aug 6 10:45:08 2010 -0700 add db setting to table browser custom tracks commit faebe04639085a5f8d0b74825e66e7fb9bdba1ba Author: Brian Raney Date: Fri Aug 6 10:43:47 2010 -0700 take out spurious url variable commit 6dcf2febe1ff55213becd8fe3e69fae3a8cc4df1 Merge: b0efe0c 9a78459 Author: Brian Raney Date: Fri Aug 6 10:30:04 2010 -0700 Merge branch 'master' of braney@hgwdev.cse.ucsc.edu:/data/git/kent commit b0efe0c93185837d0d486ea66fd176a79d9abe9d Author: Brian Raney Date: Fri Aug 6 10:29:44 2010 -0700 fix up some gencode table naming inconsistencies commit 9a78459b434cd040d037289ad1f1e663ee2ab520 Author: mary Date: Fri Aug 6 10:24:59 2010 -0700 felCat4 chain/nets are not quite right. Adding a release alpha, beta tag so don't go out to the RR in their current state. Also added a release alpha to felCatVIe so that these chain/nets never go out to beta or the RR commit ce2cf21f4700f0ce33b9d032c2cd057afbd0435b Merge: 62e3c0c 398fa78 Author: Hiram Clawson Date: Fri Aug 6 10:23:15 2010 -0700 Merge branch 'master' of hiram@hgwdev.cse.ucsc.edu:/data/git/kent commit 62e3c0cf0af74ff7ed6bd9c113632e4843796e67 Author: Hiram Clawson Date: Fri Aug 6 10:23:06 2010 -0700 was missing wibFile setting on track line for cts from table browser commit 398fa7825a52374b2e570818caacaf60a90cce58 Author: Venkat Malladi Date: Fri Aug 6 09:28:41 2010 -0700 Added metaData for submission 1848, such that downloads page has correct metaData. Updted 3 files with incorrect protocol metaData commit 1f9c62e91835fa98fc29cdabfbff31ca6c2f994e Merge: 9edcadc b36594e Author: Venkat Malladi Date: Fri Aug 6 09:10:07 2010 -0700 Merge branch 'master' into Development-Mouse commit b36594e7f80b9c5ab7bdb6cfa688aba316d30a5e Author: Galt Barber Date: Fri Aug 6 08:00:54 2010 -0700 "Encode release log update" commit a87e64fc58975b93d5b5b128f61ef7cfc2bb6249 Author: Galt Barber Date: Fri Aug 6 08:00:19 2010 -0700 "Release log update" commit d2157513e4d5d87120bb42eaf4626261697bb241 Merge: 42864b1 34bdfb3 Author: Brian Raney Date: Thu Aug 5 17:40:50 2010 -0700 Merge branch 'master' of braney@hgwdev.cse.ucsc.edu:/data/git/kent commit 42864b16a6b10ab3084cebca1636336c6fecb2ae Author: Brian Raney Date: Thu Aug 5 17:40:27 2010 -0700 add association between hg19 Gencode class and GTF tables commit 34bdfb36b8a6a9ac026bc5cee1a693b1641dde40 Merge: 504b416 757fadd Author: Angie Hinrichs Date: Thu Aug 5 16:04:23 2010 -0700 Merge branch 'master' of angie@hgwdev.cse.ucsc.edu:/data/git/kent commit 757fadd0d323179d745c45ccb7ddefa4f634869b Merge: c1cd725 34e489f Author: Cricket Sloan Date: Thu Aug 5 15:50:33 2010 -0700 Merge branch 'master' of cricket@hgwdev.cse.ucsc.edu:/data/git/kent commit c1cd7257df9a7c0368111ff29b5ce3143a0edcd2 Author: Cricket Sloan Date: Thu Aug 5 15:50:09 2010 -0700 Fixed the check boxes, set default tracks on, changed the matrix to have 400 and 200 included commit 34e489faa50516ab83f78c869442e28a7d23b9d1 Merge: 03887c3 3a08c57 Author: Chin Li Date: Thu Aug 5 15:48:18 2010 -0700 Merge branch 'master' of chinhli@hgwdev.cse.ucsc.edu:/data/git/kent commit 03887c3ca0bbb48433e37fe3f04ef7e6308d1cdd Author: Chin Li Date: Thu Aug 5 15:48:03 2010 -0700 fixed checkTableCoords error commit 3a08c57eaaacd0af6fb7ed8f987c5472c304e276 Merge: c4af768 a068e76 Author: Hiram Clawson Date: Thu Aug 5 15:35:12 2010 -0700 Merge branch 'master' of hiram@hgwdev.cse.ucsc.edu:/data/git/kent commit c4af768fa06a5d92cc02a41e34d7ec858b9153ad Author: Hiram Clawson Date: Thu Aug 5 15:35:04 2010 -0700 initial contents of single trash cleaner all in one commit a068e7653dfde1cd3423dabe660af7a1112552ee Author: mary Date: Thu Aug 5 15:23:55 2010 -0700 making visibilities hide by default and removing code to make short label be for mm9, since it doesn't seem to have any purpose commit c8f063bce408a7d493cd11674461ed998eadfa86 Author: mary Date: Thu Aug 5 14:52:10 2010 -0700 changing to reference old cat photo because not sure of copyright status of the new photo commit a2e1735a6b12bd6531d6d904ae07f003f4d67b04 Author: Chin Li Date: Thu Aug 5 14:21:25 2010 -0700 Put chain/net in phylogenetic order commit cfba59ec0e8762f674bb690a8fdced0c6d651d4d Author: Hiram Clawson Date: Thu Aug 5 13:31:58 2010 -0700 adding the two chrM sequences to haplotype track commit 44bd2f57090b2a693901fd828a8bb83fc20fa35a Merge: c5942da 6fd9b7a Author: Galt Barber Date: Thu Aug 5 12:56:42 2010 -0700 Merge branch 'master' of galt@hgwdev.cse.ucsc.edu:/data/git/kent commit c5942dacd2055a559d10e824136f312559b6fe01 Author: Galt Barber Date: Thu Aug 5 12:56:06 2010 -0700 fixing code again for overlap commit 6fd9b7a754aadddb0bb28518efbcf87e3c63e9e5 Merge: bc6a462 4443148 Author: Cricket Sloan Date: Thu Aug 5 12:43:42 2010 -0700 Merge branch 'master' of cricket@hgwdev.cse.ucsc.edu:/data/git/kent commit bc6a46217a2a39dc92649f8c39ab4f1d98dfcc21 Author: Cricket Sloan Date: Thu Aug 5 12:43:34 2010 -0700 renamed to accomodate Katrina and tried to fix the matrix issue commit 504b41690e349ac10ce6b4d430fbe9004846ee82 Author: Angie Hinrichs Date: Thu Aug 5 12:18:56 2010 -0700 Error out if a string value is empty instead of one of the join-codes for missing. An empty func value from a script loophole caused a SNP to be invisible from hgTracks display (GB - Bug #75). commit 4443148991d260c388184518dfe804751ba7a734 Merge: 2465f7d a7deae9 Author: Galt Barber Date: Thu Aug 5 12:18:19 2010 -0700 Merge branch 'master' of galt@hgwdev.cse.ucsc.edu:/data/git/kent commit 2465f7d9a627c511d06ebb4f93c102f61d6077cb Author: Galt Barber Date: Thu Aug 5 12:18:06 2010 -0700 fixing code for overlap commit a7deae9f4ffaf37989387d10bd0c671e201ffd90 Merge: 82a705a 2d6239a Author: Cricket Sloan Date: Thu Aug 5 12:16:42 2010 -0700 Merge branch 'master' of cricket@hgwdev.cse.ucsc.edu:/data/git/kent commit 82a705a6ac9f154174913f9dad102c27585dfda6 Author: Cricket Sloan Date: Thu Aug 5 12:16:34 2010 -0700 Changed the matrix, the short label, a typo commit 784e01ae3ad029fbf01baf61667103375d45d46c Author: Galt Barber Date: Thu Aug 5 12:03:20 2010 -0700 correcting overlap so that blat chunk will not exceed 5000 commit 2d6239a0705f6b12d1c6ff08461bbf9ae53bd8a4 Merge: 6e676ff 65e109b Author: Venkat Malladi Date: Thu Aug 5 11:57:10 2010 -0700 Merge branch 'master' of vsmalladi@hgwdev.cse.ucsc.edu:/data/git/kent commit 6e676ff5d36262e8c1a0b966e9311d78cd922ab5 Author: Venkat Malladi Date: Thu Aug 5 11:57:05 2010 -0700 Added subId:1978 bam file metadata so that it can become available for AWG group as a control commit 65e109b1570e90dadb4642db599c3f54db67c905 Author: Brian Raney Date: Thu Aug 5 11:24:19 2010 -0700 put gencode ensembl transcript id link in trackDb instead of hard-coding it commit 9b3836e4edf8d74e176bdcbcd14967f0484126ed Merge: 54925fc c6c3d97 Author: Hiram Clawson Date: Thu Aug 5 10:09:11 2010 -0700 Merge branch 'master' of hiram@hgwdev.cse.ucsc.edu:/data/git/kent commit 54925fc1b3c9737ec25b19bcc0dd629680763cdc Author: Hiram Clawson Date: Thu Aug 5 10:09:01 2010 -0700 should be oviAri not oviAra on newAssembliesList commit bab6a231238ca9673b48b46816f47da4de2c3184 Author: Cricket Sloan Date: Thu Aug 5 09:42:21 2010 -0700 Changed the prostate experiment to be short not total and have correct magic number commit 4a78401d18ccb59ddf4d1e789b8ae2e781f098bd Author: Cricket Sloan Date: Thu Aug 5 09:39:47 2010 -0700 Changed the prostate experiment to be short not total commit c6c3d97e32d8bdf476e5db264eadebeb99baffd3 Author: Cricket Sloan Date: Thu Aug 5 09:12:07 2010 -0700 I am hoping to resolve a weird merge problem, I dont think there are changes commit dd9e56b2be53173be89d12e9bf943f705e415447 Merge: b6d91a9 2c32b1e Author: Cricket Sloan Date: Thu Aug 5 08:47:03 2010 -0700 Merge branch 'master' of cricket@hgwdev.cse.ucsc.edu:/data/git/kent commit 2c32b1e73da1f2d7862c86a34f3c49bc91a530d9 Author: Galt Barber Date: Thu Aug 5 08:00:10 2010 -0700 "Encode release log update" commit e82e20232924fefe921334fee97521296dedee7f Author: Galt Barber Date: Thu Aug 5 08:00:08 2010 -0700 "Release log update" commit 5a4fc100630d6a2fb75bca681b8359aa3226fc76 Merge: 2173d33 23cef54 Author: Venkat Malladi Date: Wed Aug 4 18:04:41 2010 -0700 Merge branch 'master' of vsmalladi@hgwdev.cse.ucsc.edu:/data/git/kent commit 2173d33549b2e8f76bc7d4d1227b28562f8bbb6e Author: Venkat Malladi Date: Wed Aug 4 18:04:33 2010 -0700 Updated Description typo in Fibroblast and termId and termUrl for WholeBrain commit 23cef5432d81381532634095c4886e29942bb00a Author: mary Date: Wed Aug 4 17:29:06 2010 -0700 adding better comments to the script commit b6d91a9a3b9e1d79af6d1e7b0c5cfb5dd1e5e71d Merge: e3a0c9e 5f084b4 Author: Cricket Sloan Date: Wed Aug 4 16:57:53 2010 -0700 Merge branch 'master' of cricket@hgwdev.cse.ucsc.edu:/data/git/kent commit e3a0c9e08c29a83a03d3fa10b9acee2534a829be Author: Cricket Sloan Date: Wed Aug 4 16:57:48 2010 -0700 first draft of adding pi.ra to cv.ra commit 5f084b4bde6c24d9ad988190cf64ded18941a653 Merge: 797ac7e 62414dc Author: Jim Kent Date: Wed Aug 4 16:48:31 2010 -0700 Fixing merge conflicts. commit 797ac7e0b2e66cdfc46abeb801baa4da0e9aac92 Author: Jim Kent Date: Wed Aug 4 16:45:35 2010 -0700 Reworking a little how cell line abbreviation table appears, and moving some of the code for it to the library. commit 4fb800778f956dd3ce1c17fb3e0e0efd1633a13e Author: Jim Kent Date: Wed Aug 4 16:44:19 2010 -0700 Adding cell abbreviation table to factorSource tracks. commit f307d65144ee95bd8afcfd61ca437b6f3fb1c0aa Author: Jim Kent Date: Wed Aug 4 16:43:01 2010 -0700 Adding hPrintAbbreviationTable to library so can use it in both hgc and hgTrackUi. commit bc6a5dbf2f31c929fd1b40324371dc80e19e444a Author: Jim Kent Date: Wed Aug 4 16:21:14 2010 -0700 Making rainbow wigs packable. commit 62414dc2c0cb4c0e80bb269dd25f879367a08319 Merge: 93b4c0d e188b4f Author: Chin Li Date: Wed Aug 4 15:57:59 2010 -0700 Merge branch 'master' of chinhli@hgwdev.cse.ucsc.edu:/data/git/kent commit 93b4c0dac05f43c4dad68e096de79267dc74f49b Author: Chin Li Date: Wed Aug 4 15:57:51 2010 -0700 sestanBrainAtlas commit 3b9a3565f27e423a97c3f160a9f610dc57da24f3 Author: Cricket Sloan Date: Wed Aug 4 15:44:02 2010 -0700 These are changed to accomodate ripTgtProtiens while we still have them and to make sure that there is a vendorId for every vendoerName in the cv.ra commit e188b4fc8829f0bb68f28a1853b961873aca7021 Merge: 8ea6a11 79e18f9 Author: Larry Meyer Date: Wed Aug 4 14:56:36 2010 -0700 Merge branch 'master' of larrym@hgwdev.cse.ucsc.edu:/data/git/kent into mutationClassifier commit 8ea6a116c3ab9e358286ee66c2c1f72d19ac6a8a Author: Larry Meyer Date: Wed Aug 4 14:56:10 2010 -0700 add TXCLUSTER_MOTIFS_TABLE define commit 774607e5a94be3e216a1f2015037cf7c593bf078 Author: Larry Meyer Date: Wed Aug 4 14:54:57 2010 -0700 show motif info only if TXCLUSTER_MOTIFS_TABLE is defined commit e3d6337f9da4e2e0694cdcb31ab049a80d3f98ae Author: Larry Meyer Date: Wed Aug 4 14:53:47 2010 -0700 show motif info if TXCLUSTER_MOTIFS_TABLE is defined commit 79e18f938c9edfe0aafd53c2c2e4fb37b596c66b Merge: b78fee6 33389f8 Author: Angie Hinrichs Date: Wed Aug 4 14:51:58 2010 -0700 Merge branch 'master' of angie@hgwdev.cse.ucsc.edu:/data/git/kent commit b78fee6735fda56a59d42392a98611ee4b8a1116 Author: Angie Hinrichs Date: Wed Aug 4 14:49:12 2010 -0700 snp131: fixed script loophole that allowed a function value to be empty instead of unknown. commit 33389f8d568477ea15fc88afe275c476cd42e463 Merge: 948ec39 969e4ad Author: Mark Diekhans Date: Wed Aug 4 14:14:26 2010 -0700 Merge branch 'master' of hgwdev.cse.ucsc.edu:/data/git/kent commit 948ec3974265b6527f4e6383f0f8e06d3d2dfd2f Author: Mark Diekhans Date: Wed Aug 4 14:13:48 2010 -0700 fixed bug were attempt to allocated a connection cache entry with no-abort for a non-existant database would go very wrong commit 9edcadc10b07f4b3d6c5f61bf2c9ec0946d73fc4 Merge: ab67416 969e4ad Author: Venkat Malladi Date: Wed Aug 4 13:18:22 2010 -0700 Merge branch 'master' into Development-Mouse commit 969e4ad48839b0635fca9c9bf108e5f0f7bdc27b Merge: 9eba28f 57f2dac Author: Venkat Malladi Date: Wed Aug 4 12:57:04 2010 -0700 Merge branch 'master' of vsmalladi@hgwdev.cse.ucsc.edu:/data/git/kent commit 9eba28f1cf01590350ca690b258b4734916b0c40 Author: Venkat Malladi Date: Wed Aug 4 12:56:55 2010 -0700 Added rought descriptions for seqPlatforms, need to verify exact descriptions. commit 57f2dacfa66a2dc253cd03917f0ae028417eec18 Merge: 988074e 2298be9 Author: Brooke Rhead Date: Wed Aug 4 12:38:29 2010 -0700 Merge branch 'master' of rhead@hgwdev.cse.ucsc.edu:/data/git/kent commit 988074e0387accf182917e21f0b75da979d7afa7 Author: Brooke Rhead Date: Wed Aug 4 12:38:00 2010 -0700 Reverting otherOrgs.ra files so that they match current values on RR one more time. blastTabs getting rebuilt once more. commit 2298be902a0487d36edaf0ccb79aa939340f3d16 Author: mary Date: Wed Aug 4 12:04:03 2010 -0700 editing the default tracks to be pleasing to the eye commit 64d5828a97143de2ab05ff8e3bc0acefa4830256 Merge: b5a58c9 066185d Author: Larry Meyer Date: Wed Aug 4 11:51:00 2010 -0700 Merge branch 'master' of larrym@hgwdev.cse.ucsc.edu:/data/git/kent into mutationClassifier commit b5a58c9d7c2147f05ac85188479aea873f200142 Author: Larry Meyer Date: Wed Aug 4 11:50:51 2010 -0700 remove an alert that accidently got checked in commit d4403c36b8505c05fe642294f3a0eb5c36f36e58 Author: Larry Meyer Date: Wed Aug 4 11:46:30 2010 -0700 include imageV2.h commit 515b0b20ea8069cc1892817c3a82aacbe9db9c68 Author: Larry Meyer Date: Wed Aug 4 11:27:59 2010 -0700 add support for ajax option (serves up stripped down html) commit 066185d3592da1471d9b01b1c4012c8a5bb1156c Merge: f361fad 1e4fc3c Author: Hiram Clawson Date: Wed Aug 4 11:19:24 2010 -0700 Merge branch 'master' of hiram@hgwdev.cse.ucsc.edu:/data/git/kent commit f361fadcb33cb336400ff3c2356175b8f0d8fbcb Author: Hiram Clawson Date: Wed Aug 4 11:19:19 2010 -0700 checking incoming bed files for legal coordinates commit d75f5d99fe907dcf158ca0939d8a1a149ed82af1 Merge: e055832 1e4fc3c Author: Larry Meyer Date: Wed Aug 4 11:04:56 2010 -0700 Merge branch 'master' of larrym@hgwdev.cse.ucsc.edu:/data/git/kent into mutationClassifier commit 1e4fc3cbdb938f3270318a241f38f68742e4a340 Merge: b6613b2 522f287 Author: katrina Date: Wed Aug 4 09:47:02 2010 -0700 Merge branch 'master' of hgwdev:/data/git/kent commit b6613b273f0f26c82576e381bcbc4c89f0a432ae Author: katrina Date: Wed Aug 4 09:46:51 2010 -0700 added Overlay method and Transform function; consolidtaed 'y=0.0' and 'Draw indicator line at y' commit 522f287cf142878d4f41b24f6bec796e11c174e2 Author: Brian Raney Date: Wed Aug 4 09:09:16 2010 -0700 added wgEncodeMapability commit c0dbaed5fa5f9d400d45c2c7816602bf2e6cfc00 Merge: 7b220d7 c3516de Author: Brian Raney Date: Wed Aug 4 09:08:43 2010 -0700 Merge branch 'master' of braney@hgwdev.cse.ucsc.edu:/data/git/kent commit 7b220d7d440f888f3ecc869d5611d8822583239d Author: Brian Raney Date: Wed Aug 4 09:08:23 2010 -0700 put this in metaDb commit c3516def1b8452011e323be6bf281b58e991512d Author: Galt Barber Date: Wed Aug 4 08:00:12 2010 -0700 "Encode release log update" commit 387f8d17d43b69f7c2d92696def82988229eb47a Author: Galt Barber Date: Wed Aug 4 08:00:10 2010 -0700 "Release log update" commit 1481da615b3b7bd07e237e859d94134bb916ecba Author: Donna Karolchik Date: Tue Aug 3 22:18:30 2010 -0700 Oops, munged image commit ebf2bff9214b77f262704ceef9bc5fa4f2e1a5d6 Author: Donna Karolchik Date: Tue Aug 3 22:07:41 2010 -0700 Edited the content for accuracy and readability. commit 9b17e2b1f69242284177c231b79093ffed3d1c3f Merge: 45c7edc bcfdab0 Author: Donna Karolchik Date: Tue Aug 3 21:07:38 2010 -0700 Merge branch 'master' of donnak@hgwdev.cse.ucsc.edu:/data/git/kent commit 45c7edc5a191da8b2406db3c2c76b2928902c17e Author: Donna Karolchik Date: Tue Aug 3 21:07:32 2010 -0700 Redid cat credits and added felCat4. commit bcfdab023e0a4d02a159cdf38231d3454633d945 Author: Mark Diekhans Date: Tue Aug 3 20:52:35 2010 -0700 added ignore entry commit 9567358ad30438a51bd2cfb0411ac4c7cf8dc7d6 Author: Cricket Sloan Date: Tue Aug 3 18:50:22 2010 -0700 changed the short labels, fixed some typos, changed the matrix commit d0981371b71c3aed597500b3422f5b0989d9087a Author: Brian Raney Date: Tue Aug 3 18:28:59 2010 -0700 change .bw to .bigWig commit 8c6b90140c10eaeacd425b67b932e1e9a3e2a3de Author: Brian Raney Date: Tue Aug 3 18:28:40 2010 -0700 change .bw to .bigWig commit e7c2342b4455ad13d73e39ca5a95918195dda6ca Author: Brian Raney Date: Tue Aug 3 18:06:44 2010 -0700 fix typos in preamble commit 96e4b3957b1002b7820b80428a93b3d962c1b6d8 Merge: 2149711 77ab117 Author: Brian Raney Date: Tue Aug 3 17:50:51 2010 -0700 Merge branch 'master' of braney@hgwdev.cse.ucsc.edu:/data/git/kent commit 2149711ebfe6640252d1eefaf2e4413d24d912e7 Author: Brian Raney Date: Tue Aug 3 17:50:26 2010 -0700 change Myers to HudsonAlpha commit 77ab117fbcc2ecbccc69d13317095c5b1ae23d1a Merge: 7b8797b 44df4c7 Author: Hiram Clawson Date: Tue Aug 3 17:19:52 2010 -0700 Merge branch 'master' of hiram@hgwdev.cse.ucsc.edu:/data/git/kent commit 7b8797bc71a7dbf88e30425ebf4a2213ab54f899 Author: Hiram Clawson Date: Tue Aug 3 17:19:43 2010 -0700 using an overlap of 500 bases during the 5K split commit 44df4c78189910028264cb4f739f59afc9e950f5 Author: Galt Barber Date: Tue Aug 3 17:18:12 2010 -0700 adding note about search robot commit bd76e5fd64e1adb78ecc0d029ad8a067ab2b57b6 Merge: 870dd7b e305ed2 Author: Galt Barber Date: Tue Aug 3 17:13:58 2010 -0700 Merge branch 'master' of hgwdev:/data/git/kent commit 870dd7b6c9fed79adde5b9644d461782bd247bc5 Author: Galt Barber Date: Tue Aug 3 17:13:52 2010 -0700 adding chmod g+w for build scripts that clone kent dirs commit e981b44e8072941e2f26fce1638f6b78da131511 Author: Galt Barber Date: Tue Aug 3 17:09:39 2010 -0700 trying to speed up 32bit utils build commit e305ed2e1fb71e777a455b91f01b0eee492fa859 Merge: 9de25a8 53c6dd0 Author: Hiram Clawson Date: Tue Aug 3 17:08:28 2010 -0700 Merge branch 'master' of hiram@hgwdev.cse.ucsc.edu:/data/git/kent commit 9de25a8d18743b046a430a119b9d8430cea59e17 Author: Hiram Clawson Date: Tue Aug 3 16:57:30 2010 -0700 adding haplotype position tracks to hg19 and hg18 and lift over chain experiments commit 83492c52001b8f6498c0da87731e511b621217c2 Author: Hiram Clawson Date: Tue Aug 3 16:52:34 2010 -0700 use proper dateTime result string commit 53c6dd04996a7f1352666774aa41a0632078268b Merge: dedaa21 b79bf4b Author: katrina Date: Tue Aug 3 16:09:54 2010 -0700 Merge branch 'master' of hgwdev:/data/git/kent commit dedaa21698ea28eef2b8d976baee38911248426c Author: katrina Date: Tue Aug 3 16:09:47 2010 -0700 expanding on the descriptions of the histone mark tracks commit b79bf4be62062e42fc3428915b128eb3ef15d139 Author: mary Date: Tue Aug 3 15:49:52 2010 -0700 new cat image for felCat4 commit df12c41173ca93da1076693b597e3e0f97023edd Author: Chin Li Date: Tue Aug 3 15:38:10 2010 -0700 stalled by phlopP bug commit 0b3ba2bfd0d53a142bc483ebcd1b835c16f8e5f9 Merge: cacb4ed d6f4b19 Author: Chin Li Date: Tue Aug 3 15:36:05 2010 -0700 Merge branch 'master' of chinhli@hgwdev.cse.ucsc.edu:/data/git/kent commit cacb4ed3716781f6d11c7ae1b78a8d3ba53414a7 Author: Chin Li Date: Tue Aug 3 15:35:55 2010 -0700 complete sno/miRNA track commit d6f4b196601124de1779c0bc1be192fa26aef5a7 Merge: 9ed7823 f5a6adb Author: Hiram Clawson Date: Tue Aug 3 14:49:03 2010 -0700 Merge branch 'master' of hiram@hgwdev.cse.ucsc.edu:/data/git/kent commit 9ed7823da019c78cfcb38869c9c010e5a0d145f5 Author: Hiram Clawson Date: Tue Aug 3 14:48:51 2010 -0700 adding difference tracks hg18 to hg19 to hg18 commit ab674165223a474e0c4869148e46301086e5901e Author: Venkat Malladi Date: Tue Aug 3 13:35:49 2010 -0700 Added prelimary loaded data for UW Dnase data (Mouse) commit f5a6adb169db1fa43c40b94e45190ed8552a0e0a Author: katrina Date: Tue Aug 3 12:43:13 2010 -0700 further clarifications commit c51fd731147e3b3deba2037a81a1ddfa828a118a Author: katrina Date: Tue Aug 3 11:59:57 2010 -0700 moved last sentence to the second sentence; removed repeated sentence; broke into multiple lines commit 732a65ebc126c2d20d21ad48b5f0d2c0ab59026d Author: katrina Date: Tue Aug 3 10:51:33 2010 -0700 changed DNAse to DNase commit 4d272c9d2d6706dc3ddf0441a19885120592ffea Merge: 34a0872 9cd2a06 Author: katrina Date: Tue Aug 3 10:47:43 2010 -0700 Merge branch 'master' of hgwdev:/data/git/kent commit 34a0872ccf0262a80bfa9373cd7e598b26391385 Author: katrina Date: Tue Aug 3 10:47:36 2010 -0700 edited for clarity and added data release policy commit 9cd2a06356fbd0c9aa5555a8a298563dd43fed73 Merge: 781d589 174772e Author: Jim Kent Date: Tue Aug 3 09:44:51 2010 -0700 Merge branch 'master' of kent@hgwdev.cse.ucsc.edu:/data/git/kent commit 174772ef1008f0e0fd1f43c67e10c753dbb05cde Author: Fan Hsu Date: Tue Aug 3 09:41:02 2010 -0700 Added rdmr track. commit 8565386fb39d3201abca057842eb0c2b3975a34d Author: Fan Hsu Date: Tue Aug 3 09:38:40 2010 -0700 Added rdmr track. commit 781d589a5a402c180deb3bd244ffdfdd3434e35e Merge: f1ffaeb 69dca80 Author: Jim Kent Date: Tue Aug 3 09:14:28 2010 -0700 Merge branch 'master' of kent@hgwdev.cse.ucsc.edu:/data/git/kent commit f1ffaeb9bc31d1d94e115dfc2b9db8e29a3fb929 Author: Jim Kent Date: Tue Aug 3 09:14:17 2010 -0700 Updated comment to avoid advising people to generate a compiler error. commit cbadb869693dad2000b128100515a38886517b59 Author: Jim Kent Date: Tue Aug 3 09:12:51 2010 -0700 Making it so reset to defaults option appears in hgTrackUi page for container wigs. commit 69dca805d87617dac046a6e68806c896bb5ac170 Merge: 13f30bb 9e06c9c Author: Fan Hsu Date: Tue Aug 3 08:16:16 2010 -0700 Merge branch 'master' of fanhsu@hgwdev.cse.ucsc.edu:/data/git/kent commit 13f30bb1c479b5d42e7abd8dad7d4fcf4d3919f1 Author: Fan Hsu Date: Tue Aug 3 08:15:31 2010 -0700 Updated genscan track build section to reflect corrections to .lft files. commit 9e06c9c6f223b8708625c88e1a8a622c489d9986 Author: Galt Barber Date: Tue Aug 3 08:00:58 2010 -0700 "Encode release log update" commit 0cc0c8e0f476f9134a657b79cd5efa7d048d9ea2 Author: Galt Barber Date: Tue Aug 3 08:00:35 2010 -0700 "Release log update" commit 939efba7e06f701e3d77a5da542da188ff96ecd1 Merge: 862564e 48a1b19 Author: katrina Date: Mon Aug 2 21:48:51 2010 -0700 Merge branch 'master' of hgwdev:/data/git/kent commit 862564e41f7958166bcdc417e914096ea923828e Author: katrina Date: Mon Aug 2 21:48:32 2010 -0700 making a clarification in the description commit 48a1b194304a752be39073981ab383e2b6f32c49 Author: Brian Raney Date: Mon Aug 2 17:46:26 2010 -0700 change back to old code commit 08edc4e0e8900497ceeba90b103d30c680494b87 Author: Brian Raney Date: Mon Aug 2 16:44:26 2010 -0700 "New version number v237" commit 5bc436f2505affd069002805a844a9560ac21537 Merge: e0c594d 718e2fc Author: Brian Raney Date: Mon Aug 2 16:37:11 2010 -0700 Merge branch 'master' of hgwdev:/data/git/kent commit e0c594de8307f298dedb4a93f68d56684f443cc8 Author: Brian Raney Date: Mon Aug 2 16:36:53 2010 -0700 v237 final build commit 718e2fc49fbdfc662832df25f1b1f197ddac36cb Author: vanessa Date: Mon Aug 2 16:29:10 2010 -0700 moved file to be friends with the other js files commit 9a38351e73716a3ac592c9b1f66707f99906d18b Merge: e6a7edc d524592 Author: Venkat Malladi Date: Mon Aug 2 15:41:57 2010 -0700 Merge branch 'master' of vsmalladi@hgwdev.cse.ucsc.edu:/data/git/kent commit e6a7edca9e36f50b749db48dcf663c422c4ae46c Author: Venkat Malladi Date: Mon Aug 2 15:40:33 2010 -0700 Fixed two typos in terms for mouse cell lines (3143 should be 3134 and Cerebrumm should be Cerebrum). commit d5245921f8b1932510a725c5a32d5e58a4c5e87f Merge: 580c63d 9c85018 Author: Brian Raney Date: Mon Aug 2 15:23:13 2010 -0700 Merge branch 'master' of braney@hgwdev.cse.ucsc.edu:/data/git/kent commit 580c63d8b045f6c067446566868fccd4d8a350c2 Author: Brian Raney Date: Mon Aug 2 15:22:58 2010 -0700 first pass at modifying load scripts commit 9c85018a62c015518178b5e95edbc9983efb4764 Merge: 898ae18 1f1cd26 Author: Cricket Sloan Date: Mon Aug 2 15:00:07 2010 -0700 Merge branch 'master' of cricket@hgwdev.cse.ucsc.edu:/data/git/kent commit 1f1cd266c15b0eead17bbafede72fde53366cc41 Merge: 80b82e3 b9a8e83 Author: Venkat Malladi Date: Mon Aug 2 14:51:29 2010 -0700 Merge branch 'master' of vsmalladi@hgwdev.cse.ucsc.edu:/data/git/kent commit 80b82e3e26a2f12c3d314d1f076a8796ccbac5e0 Author: Venkat Malladi Date: Mon Aug 2 14:51:22 2010 -0700 Updated Methyl Data to be in one composite commit b9a8e8351c8302931db4ca92ab2920d52b17c6fa Author: mary Date: Mon Aug 2 14:32:42 2010 -0700 adding checkGenomeMysql to the makefile commit ac34c6868645641b93cbfb8cf8f82e9505a38f08 Merge: 391ae4d df06923 Author: Krishna Roskin Date: Mon Aug 2 14:16:37 2010 -0700 Merge branch 'master' of krish@hgwdev.cse.ucsc.edu:/data/git/kent commit 391ae4dcf2c93d520623a3ecb119e352ade64421 Author: Krishna Roskin Date: Mon Aug 2 14:16:33 2010 -0700 added die statement to check if there is no matching composite expVars.ra commit 898ae180fdf6f741e7c39b16b8293edfaa71f36b Author: Cricket Sloan Date: Mon Aug 2 14:16:10 2010 -0700 Added the methods changes from Atif Shahab commit df0692357aba040004b4685111e26d5c1ef74892 Merge: bd6c2a9 764dc6d Author: Cricket Sloan Date: Mon Aug 2 13:41:37 2010 -0700 Merge branch 'master' of cricket@hgwdev.cse.ucsc.edu:/data/git/kent commit bd6c2a98c06742568391aad239029245ac2730c8 Author: Cricket Sloan Date: Mon Aug 2 13:41:28 2010 -0700 removed the reference to all raw signal commit 764dc6d3d54fb3e5fb51366f9451a46d5771ef03 Author: katrina Date: Mon Aug 2 13:40:13 2010 -0700 standardized longLabels (super, track & subtrack) for ENCODE Regulation track; made one fix, changed 8 to 9 in one track longLabel; removed confusing parentheses from another track longLabel commit 3011d1325c060577ed2bb254b9361e4a0ae5d1d3 Author: Cricket Sloan Date: Mon Aug 2 13:32:34 2010 -0700 removed the reference to split alignments commit 90420685513fbaf35eeeb4e4cd5673db9c708b8d Author: Cricket Sloan Date: Mon Aug 2 13:03:46 2010 -0700 The correct magic number commit 721f03fc5cc8894afc9cf07e2cdc3122b6e49db9 Author: Brooke Rhead Date: Mon Aug 2 12:12:01 2010 -0700 Removed note about scheduled maintenance. commit 8277bea9573023115c82b05fdde8a54e8369c07a Merge: 4d6db46 b54d45a Author: Venkat Malladi Date: Mon Aug 2 12:02:05 2010 -0700 Merge branch 'master' of vsmalladi@hgwdev.cse.ucsc.edu:/data/git/kent commit 4d6db46e77a709cf1f3cb559ef239b48eefad8fe Author: Venkat Malladi Date: Mon Aug 2 12:01:12 2010 -0700 Split up Stan/Yale TFBS data and Histone data into own trackDb's. Update encode trackDb to have only include statements of the encode composites commit b54d45a869253fbb1ef666428f40054cfbb1ba2b Merge: 984ebab c424622 Author: Angie Hinrichs Date: Mon Aug 2 11:05:13 2010 -0700 Merge branch 'master' of angie@hgwdev.cse.ucsc.edu:/data/git/kent commit 984ebab61320ff4820f634b24a002f9876a8efc3 Author: Angie Hinrichs Date: Mon Aug 2 11:05:04 2010 -0700 Updated NHGRI's GWAS Catalog. commit c424622cc1d45fbd6a1e0a873df2fd6d848d93af Merge: 2940449 8f064fa Author: Venkat Malladi Date: Mon Aug 2 10:48:43 2010 -0700 Merge branch 'master' of vsmalladi@hgwdev.cse.ucsc.edu:/data/git/kent commit 2940449767e9a1f8fcd6a80c0522d986c6dc3a83 Author: Venkat Malladi Date: Mon Aug 2 10:48:25 2010 -0700 Added 4 new submissions. 2087-2090 commit 8f064fa3a514c2cb3fbcfc87e65853e0cd7ea2e6 Merge: 80c48b2 238496d Author: katrina Date: Mon Aug 2 09:42:16 2010 -0700 Merge branch 'master' of hgwdev:/data/git/kent commit 80c48b266e58c46b302fa2a71f2e6dda27793867 Author: katrina Date: Mon Aug 2 09:42:09 2010 -0700 fixed typo Brooke found in code review commit 238496d2a8c43dc274897e6acdaa3fd990b64cc8 Author: Galt Barber Date: Mon Aug 2 08:00:57 2010 -0700 "Encode release log update" commit 604d96585f4766d6d41044ea8fbbdc582bc7e301 Author: Galt Barber Date: Mon Aug 2 08:00:18 2010 -0700 "Release log update" commit 8be1cb4b1261ef8e304f15b8c024bfcb20989976 Author: Galt Barber Date: Sun Aug 1 08:00:08 2010 -0700 "Encode release log update" commit 8ae5d8cc3319e93355fcc26811d111334ac404dd Author: Galt Barber Date: Sun Aug 1 08:00:07 2010 -0700 "Release log update" commit ccc4b05112fb3e6439f71164b83e4d586774dd79 Author: Galt Barber Date: Sat Jul 31 08:00:11 2010 -0700 "Encode release log update" commit 67b7bc2e625dfa4639f79a73c9beb46201c102a2 Author: Galt Barber Date: Sat Jul 31 08:00:09 2010 -0700 "Release log update" commit b89a0f612e03a14dd85aa14da7ac665e19fa9ec5 Author: Tim Dreszer Date: Fri Jul 30 17:13:43 2010 -0700 Hiram noticed this code broke cygwin build, so I ifdef'd it out. It is a rarely handy tool to peak at the stack in a cgi without aborting commit d962b767912e749bf9bdcb19f31754c2acc80e26 Merge: 6f8a76e c6fe28d Author: Tim Dreszer Date: Fri Jul 30 16:26:03 2010 -0700 Merge branch 'master' of tdreszer@hgwdev.cse.ucsc.edu:/data/git/kent commit 6f8a76ebe32d5277740f3e91c3b675ea53b55e51 Author: Tim Dreszer Date: Fri Jul 30 16:25:57 2010 -0700 The 'top link at the top of the subtrack list needed more adjustment commit c6fe28df7e12388285377d018f34ad11a569b6bb Author: katrina Date: Fri Jul 30 15:51:13 2010 -0700 made Encode Regulation track first in Regulation group; enabled subTrack drag/reorder commit 6958dbed7d6ba090bf49ec2a0b501dda4785d9f8 Author: Tim Dreszer Date: Fri Jul 30 15:30:55 2010 -0700 Typo commit 715dcbc5fa4b4cb5f247f310f6e17b3743c0fa80 Merge: f7b21a2 cc2fdb4 Author: Tim Dreszer Date: Fri Jul 30 15:30:01 2010 -0700 Merge branch 'master' of tdreszer@hgwdev.cse.ucsc.edu:/data/git/kent commit f7b21a2f869b468b9a332107839bb2180015f57e Author: Tim Dreszer Date: Fri Jul 30 15:29:48 2010 -0700 Minor tweak to the sideButton toolTip commit cc2fdb4c428a8f78e59bbfecd6235a51ab0fd9b2 Merge: e4f8263 6b73c80 Author: Fan Hsu Date: Fri Jul 30 15:26:19 2010 -0700 Merge branch 'master' of fanhsu@hgwdev.cse.ucsc.edu:/data/git/kent commit e4f8263b0a799237f72994fe39c3e56d04df5c97 Merge: 3e39a9f a31a314 Author: Fan Hsu Date: Fri Jul 30 15:24:41 2010 -0700 Merge branch 'master' of fanhsu@hgwdev.cse.ucsc.edu:/data/git/kent commit 6b73c801c3d197ec01796cb56e2fb78457bff7cc Merge: d7ab952 a31a314 Author: Antonio Coelho Date: Fri Jul 30 15:24:26 2010 -0700 Merge branch 'master' of antonio@hgwdev.cse.ucsc.edu:/data/git/kent commit d7ab952cdde40ec438aaa2e853723adbbf2f4bd2 Author: Antonio Coelho Date: Fri Jul 30 15:23:52 2010 -0700 adding felCat4 commit 3e39a9f2197ff2325de0ac024c98806c6df77929 Author: Fan Hsu Date: Fri Jul 30 15:22:54 2010 -0700 Corrected a comment for hgIkmc track processing. commit a31a314f5067139e6119948b58d60519eaf1d4d3 Merge: 5fb4b59 172a8ea Author: Tim Dreszer Date: Fri Jul 30 15:14:52 2010 -0700 Merge branch 'master' of tdreszer@hgwdev.cse.ucsc.edu:/data/git/kent commit 5fb4b59b7c358560c21a4ac877cada918dcc959e Author: Tim Dreszer Date: Fri Jul 30 15:14:48 2010 -0700 Hopefully smoothing the dragging of tall tracks commit 172a8ea6f6a1715e53141d13699741288a1fc62f Author: Fan Hsu Date: Fri Jul 30 15:05:55 2010 -0700 Built genscan track for hg19. commit c319ae84bb21d5887105b478dc246c514dea2fa3 Author: Tim Dreszer Date: Fri Jul 30 14:59:14 2010 -0700 More tweeking. Make it stop. commit 685ada7e473292096b9bb7a13b309be1ab4f9552 Merge: fbb8320 6a44f6f Author: Cricket Sloan Date: Fri Jul 30 13:53:33 2010 -0700 Merge branch 'master' of cricket@hgwdev.cse.ucsc.edu:/data/git/kent commit fbb832054bdd0b4a5b22054f82c523585c00cb88 Author: Cricket Sloan Date: Fri Jul 30 13:53:08 2010 -0700 added origAssembly and corrected dates commit 6a44f6fedc3aeb82f12233eda6953198f2016bb6 Merge: 87cbf3b ef9ebf9 Author: Antonio Coelho Date: Fri Jul 30 13:47:37 2010 -0700 Merge branch 'master' of antonio@hgwdev.cse.ucsc.edu:/data/git/kent commit 87cbf3b6a74e2fc87bec6846c1b3692b49786ed5 Author: Antonio Coelho Date: Fri Jul 30 13:47:27 2010 -0700 adding HA RNA-seq to downloads commit ef9ebf9f02316937a3c5a803344e7ad5fcddeb07 Author: Tim Dreszer Date: Fri Jul 30 13:25:36 2010 -0700 Minor tweek to make sure resizing doesn't obscure page border commit c9670ae6174f484e9d1816a809fb006e276c2e63 Author: Cricket Sloan Date: Fri Jul 30 13:17:22 2010 -0700 The meta data is changed to reflect the orig assembly and the correct dates. commit 0ba51b411ba447ad5fd0757e6a8c4b3b50b6f92f Author: Tim Dreszer Date: Fri Jul 30 13:07:57 2010 -0700 Something was corrupted in this file. Hopefully it is fixed. Git??? commit 0ec3e50a4167defcbafda094da9a39ca011bf63e Merge: 33b21a1 3cb80a5 Author: Tim Dreszer Date: Fri Jul 30 13:02:52 2010 -0700 Merge branch 'master' of tdreszer@hgwdev.cse.ucsc.edu:/data/git/kent commit 33b21a1f81a7f5cc388f780fabdf48d315014ea9 Author: Tim Dreszer Date: Fri Jul 30 13:02:38 2010 -0700 Checked in Kate's navigation links, slightly modified. Feature is ifdef'd out currently commit 3cb80a531d9fcd88a0fb9752cbc4d2b45ff09192 Merge: ef22189 87dc9d2 Author: Cricket Sloan Date: Fri Jul 30 12:03:17 2010 -0700 Merge branch 'master' of cricket@hgwdev.cse.ucsc.edu:/data/git/kent commit ef22189153b93c7f1dfba9a455374b2552eb70dd Author: Cricket Sloan Date: Fri Jul 30 12:01:18 2010 -0700 Revert "These files have all had origAssembly added, but they will need to have the release date modified" The CshlShort had affy informaiton in it. I need to start this over. This reverts commit 196e751a37514efca4687d4d0e50fb4ca8e71a8e. Conflicts: src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisRnaSeq.ra commit 87dc9d2927796cc73ae947bafb0a1359b7bc7a3a Merge: 93c5ad7 4d200fc Author: Brooke Rhead Date: Fri Jul 30 11:27:46 2010 -0700 Merge branch 'master' of rhead@hgwdev.cse.ucsc.edu:/data/git/kent commit 93c5ad708c458b8611882e3e169190743af7b620 Author: Brooke Rhead Date: Fri Jul 30 11:27:41 2010 -0700 Changed link to NHGRI.gif to nhgriLogo.gif, as the filename of the image was changed. commit 3dbc6545876cd1d726b6cd213461cdd8a15d9351 Author: Brooke Rhead Date: Fri Jul 30 11:23:45 2010 -0700 Renamed NHGRI.gif to nhgriLogo.gif because it was conflicting on filesystems that are not case-sensitive with the file nhgri.gif, also in this directory. commit 4d200fc8c6934220a6a8b4c1b3a4a7e22567a1d0 Merge: 7a2cbd7 7ddd311 Author: Cricket Sloan Date: Fri Jul 30 11:23:18 2010 -0700 Merge branch 'master' of cricket@hgwdev.cse.ucsc.edu:/data/git/kent commit 7a2cbd75b9b48ca7b45d8ea1818c20177e4c30cb Author: Cricket Sloan Date: Fri Jul 30 11:21:05 2010 -0700 Changed this file to be lowercase name. commit 7ddd31168eb48c4d99d3c80a7ca8908742334be0 Author: vanessa Date: Fri Jul 30 11:07:09 2010 -0700 these files were changed to use the js file that changes the url to reflect what server you are on commit 07fdbb984ad58be4bedf55ad60f8f70ee817ae7a Author: Brian Raney Date: Fri Jul 30 11:00:14 2010 -0700 add 2waypseudocons to gencode track commit 2f1d5805cfb69ee15aaf70b6bee55088b81db7ad Merge: 6ef5c98 5dcf458 Author: Brian Raney Date: Fri Jul 30 10:59:32 2010 -0700 Merge branch 'master' of braney@hgwdev.cse.ucsc.edu:/data/git/kent commit 6ef5c9817fed38bd054930f7e47d99e8231d42cc Author: Brian Raney Date: Fri Jul 30 10:59:13 2010 -0700 add 2waypseudocons commit 5dcf458213d7d090770ede36eada321ab1dde06b Author: vanessa Date: Fri Jul 30 10:49:09 2010 -0700 created a js directory for static docs, new js file that changes the url relative to the server you are on for testing purposes commit 6f47e83a850b56d785763922bc5a66c372e28995 Merge: 147cd85 87334ea Author: vanessa Date: Fri Jul 30 10:45:28 2010 -0700 Merge branch 'master' of vanessa@hgwdev.cse.ucsc.edu:/data/git/kent commit 87334eaca30c21b8177a98e467ae1b6d1fb5b082 Author: Antonio Coelho Date: Fri Jul 30 10:31:46 2010 -0700 changing RPKM description commit 147cd854c798bac3c33e26d98285634ac4700211 Merge: 44e813c a971317 Author: vanessa Date: Fri Jul 30 10:04:03 2010 -0700 Merge branch 'master' of vanessa@hgwdev.cse.ucsc.edu:/data/git/kent commit a97131793765d11e55261703485ff74ee771c976 Author: Venkat Malladi Date: Fri Jul 30 09:51:42 2010 -0700 Updated the unit test for ChipSeq. Previously was not working. Also added ability to test BAM file validation and mouse with new daf and ddf combo commit 5d02e9a3c2b9a9d941d22de5575901b646014a39 Author: Galt Barber Date: Fri Jul 30 08:00:31 2010 -0700 "Encode release log update" commit 7072067934fa8a9616f49fc7fc6200117552b50c Author: Galt Barber Date: Fri Jul 30 08:00:29 2010 -0700 "Release log update" commit e0558328fb0d0730ee1f3ec67c57ebbc2d6b8c55 Merge: 25cd5d4 133ec7b Author: Larry Meyer Date: Fri Jul 30 01:18:30 2010 -0700 Merge branch 'master' of larrym@hgwdev.cse.ucsc.edu:/data/git/kent into mutationClassifier commit 25cd5d48ddc5d394053478299e53966b5f5075ab Author: Larry Meyer Date: Fri Jul 30 01:17:29 2010 -0700 add prior and priorBackoff command line parameters commit 133ec7b73d9036e96aeb93b8439c93a9a3f35cbd Author: Brian Raney Date: Thu Jul 29 22:52:57 2010 -0700 reload with v4fix and load Yale pseudo gene table commit d71b2b0a670643c9befb77b300c1d380d6d0288e Merge: 8032497 7617312 Author: Brian Raney Date: Thu Jul 29 17:47:42 2010 -0700 Merge branch 'master' of braney@hgwdev.cse.ucsc.edu:/data/git/kent commit 803249702b823d3b4dc9dbab500cb4640de479b0 Author: Brian Raney Date: Thu Jul 29 17:47:19 2010 -0700 add yale pseudoGene track for gencode v4 commit 76173128fdad9b38ba5c432540a6c371076b488f Author: Venkat Malladi Date: Thu Jul 29 16:38:23 2010 -0700 Updated Hardison Grant labs bam validation (for DNA) and commented out Revision History line/ commit 4d81970927dd299e74d00b755606738725f2e734 Merge: 2b86b26 1fe1e0d Author: Venkat Malladi Date: Thu Jul 29 16:20:56 2010 -0700 Merge branch 'master' of vsmalladi@hgwdev.cse.ucsc.edu:/data/git/kent commit 2b86b26a74c1bffac0f3b25b2706048c998a3d61 Author: Venkat Malladi Date: Thu Jul 29 16:20:50 2010 -0700 Added nMatch and commented out revisions line commit 1fe1e0d7b7aa6f61e9aa50bafaacec2f6de52c35 Merge: 57037fb 364bbd8 Author: Brian Raney Date: Thu Jul 29 16:12:44 2010 -0700 Merge branch 'master' of braney@hgwdev.cse.ucsc.edu:/data/git/kent commit 57037fb652b39cda9184b8d82d0f421c5bf00903 Author: Brian Raney Date: Thu Jul 29 16:12:35 2010 -0700 changes from Felix commit 364bbd848ecad782b910bcfe2aa2f10460ee885f Merge: 40465cc d68d1d1 Author: Venkat Malladi Date: Thu Jul 29 15:45:01 2010 -0700 Merge branch 'master' of vsmalladi@hgwdev.cse.ucsc.edu:/data/git/kent commit 40465cc3528575d717d0ff4549baeb1872475cf5 Author: Venkat Malladi Date: Thu Jul 29 15:44:51 2010 -0700 Updated Dafs to include updated bam validation lines, and replicates required for Peaks and Signals. commit d68d1d134bb434212493a3224fc9c590cb323fc3 Merge: 2368b2e 3cdb4ba Author: Chin Li Date: Thu Jul 29 15:34:41 2010 -0700 Merge branch 'master' of chinhli@hgwdev.cse.ucsc.edu:/data/git/kent commit 2368b2e8349a3d7eb82f70dc6b2031e2a3f1ff74 Author: Chin Li Date: Thu Jul 29 15:34:21 2010 -0700 missing self frames on multiz NwayFrames tables commit 35f0a89503ade5b220675d354ed374493b9222d3 Author: Cricket Sloan Date: Thu Jul 29 15:12:30 2010 -0700 Changed the metadata and the short labels for GisRnaSeq commit 3cdb4baec389bf1b0468a5a02cf7a9ea6a8c210e Merge: 6228c18 9a3d986 Author: Brian Raney Date: Thu Jul 29 14:48:12 2010 -0700 Merge branch 'master' of braney@hgwdev.cse.ucsc.edu:/data/git/kent commit 6228c18018f332bf666a8071b3e9a840153aa14a Author: Brian Raney Date: Thu Jul 29 14:47:49 2010 -0700 add optional quality checks commit 9a3d986aab05e3632d35fa0367c287a6ce5ce5c9 Author: Venkat Malladi Date: Thu Jul 29 14:35:53 2010 -0700 Updated Track matrix and metadata commit 85c7fa5ddf4eba9c163678fb546c8eb7033235bb Merge: c0a8ede ea46012 Author: Venkat Malladi Date: Thu Jul 29 14:30:43 2010 -0700 Merge branch 'master' of vsmalladi@hgwdev.cse.ucsc.edu:/data/git/kent commit c0a8ede95b9a3361c4ee12a66603996720156718 Author: Venkat Malladi Date: Thu Jul 29 14:29:46 2010 -0700 Updated Short and long lables to be consistent with the TFBS tracks. Moved data from Dnase supertrack to TFBS supertrack commit 0322fcb932dd7c46124121c1d5f1bcc9d9c10675 Author: Venkat Malladi Date: Thu Jul 29 14:25:07 2010 -0700 Added Notes section to provide information on track specifications commit ea4601223b66d7534edb2dcee7095444ab87a2ad Merge: 7406011 29edb6a Author: Brooke Rhead Date: Thu Jul 29 14:06:37 2010 -0700 Merge branch 'master' of rhead@hgwdev.cse.ucsc.edu:/data/git/kent commit 740601185d2d9e515cb2b7cea63f4c89e0f1594b Author: Brooke Rhead Date: Thu Jul 29 14:06:21 2010 -0700 Updated git instructions: added links for installation and configuration, removed the gitroot directory reference, and removed instructions for customizing until we have decided what the best practice would be (or maybe this will go in genomewiki). commit 29edb6aa2705610c7723f609c018e35785a05c9d Merge: 0d20f9a 5a99cc5 Author: Hiram Clawson Date: Thu Jul 29 14:01:44 2010 -0700 Merge branch 'master' of hiram@hgwdev.cse.ucsc.edu:/data/git/kent commit 5a99cc5e1091df81782066d940621ad28dc2b5a6 Merge: 611fee4 81504f5 Author: Chin Li Date: Thu Jul 29 13:51:49 2010 -0700 Merge branch 'master' of chinhli@hgwdev.cse.ucsc.edu:/data/git/kent commit 611fee4b048888f0449d8a310429fad2dd1d18e9 Author: Chin Li Date: Thu Jul 29 13:50:40 2010 -0700 missing self frames on multiz NwayFrames tables commit 81504f578fd097ab894513d2b68bb6c63d84258d Author: Brooke Rhead Date: Thu Jul 29 12:00:18 2010 -0700 Added a temporary note about upcoming schedule maintenance. commit 196e751a37514efca4687d4d0e50fb4ca8e71a8e Author: Cricket Sloan Date: Thu Jul 29 11:21:46 2010 -0700 These files have all had origAssembly added, but they will need to have the release date modified commit 2ea86470d103e43aabf6f0bad7ee6d79819da7f0 Author: Venkat Malladi Date: Thu Jul 29 10:55:03 2010 -0700 Removed all metadata for 2 submission: 2041,2042 as advised from lab commit 2f2948605aef286accd85a8b16bfb173bda92335 Author: Venkat Malladi Date: Thu Jul 29 10:24:50 2010 -0700 Removed submission 2041 and 2042 as advised by the lab commit 0d20f9a066b92a4eb795293562642eb71fb236d5 Author: Hiram Clawson Date: Thu Jul 29 09:58:04 2010 -0700 the create statement for useCount table used by useCount CGI commit 57871f0b0276d30232affc3693a49f11281dd088 Merge: 3c5fde6 a6a923c Author: Hiram Clawson Date: Thu Jul 29 09:57:07 2010 -0700 Merge branch 'master' of hiram@hgwdev.cse.ucsc.edu:/data/git/kent commit 3c5fde6715d52701afb7b4ac0c84dd4e596f6e7a Author: Hiram Clawson Date: Thu Jul 29 09:57:02 2010 -0700 do not need to have useCount on the list of browser bins, make it when desired, it is a one-off commit 91209f49b6fe1eb4173a55193e476f55198953d1 Merge: 4ff07a5 a6a923c Author: Cricket Sloan Date: Thu Jul 29 09:31:01 2010 -0700 Merge branch 'master' of cricket@hgwdev.cse.ucsc.edu:/data/git/kent commit a6a923cabe04b268bf49c1a7232bf7da9b784dd1 Author: Galt Barber Date: Thu Jul 29 08:00:10 2010 -0700 "Encode release log update" commit cbaf012699df030c12aa54ebaf5fb35505eb500a Author: Galt Barber Date: Thu Jul 29 08:00:08 2010 -0700 "Release log update" commit 9c122e823e4adcfa155b4925725a03a95828bb29 Author: Galt Barber Date: Wed Jul 28 21:39:02 2010 -0700 handling uniProt connection properly for hgNear GO column so we do not use up thousands of connections unnecessarily commit 89818632e9105a3eaafacdd0dcb5143013e1a3a6 Author: Galt Barber Date: Wed Jul 28 19:52:47 2010 -0700 fixing perms on mgCircle.c commit 7ba6a2e0005fc56dc9e7968fd44accca5d910446 Merge: 93db694 a1aabc0 Author: Jim Kent Date: Wed Jul 28 17:25:47 2010 -0700 Merge branch 'master' of kent@hgwdev.cse.ucsc.edu:/data/git/kent commit 93db69419bb83dea3206ee54df9db4f1872364b7 Merge: e9c37d6 bdb2717 Author: Jim Kent Date: Wed Jul 28 17:25:32 2010 -0700 Fixing merge conflicts. commit a1aabc0dccc0334ce1e73103a0c18e9648ea2ccd Author: Brian Raney Date: Wed Jul 28 16:51:34 2010 -0700 set Brain Methyl to show mismatches, discover all the alignments are off by one commit 594a6ceab960e133969a4fe7f68666225bf532ec Merge: 24c7fbb 4e41264 Author: Brian Raney Date: Wed Jul 28 16:42:07 2010 -0700 Merge branch 'master' of braney@hgwdev.cse.ucsc.edu:/data/git/kent commit 24c7fbb8097bb8946741d2890b51081afe187b67 Author: Brian Raney Date: Wed Jul 28 16:41:46 2010 -0700 set BAM options to show mismatches etc commit 4e41264e732a341aea48ac462e25a459c854219c Merge: fa89b4d 8476a18 Author: Venkat Malladi Date: Wed Jul 28 16:29:59 2010 -0700 Merge branch 'master' of vsmalladi@hgwdev.cse.ucsc.edu:/data/git/kent commit fa89b4d1b722602ae850962e8699ceb4b258673f Author: Venkat Malladi Date: Wed Jul 28 16:29:53 2010 -0700 Added age E0 to the age for embryonic stem cell age commit 8476a18fad60d3db6e783250b403395aed8d677f Author: Brian Raney Date: Wed Jul 28 15:54:59 2010 -0700 fix labels and defaults commit 99cd024be682cd5a0a22c61c7cbd4e1ede38f7ea Author: Brian Raney Date: Wed Jul 28 15:46:04 2010 -0700 take out some spaces in Brain Methyl short labels (per Mary) commit e9c37d6891701339e293d4cb57da547b7ae3d410 Author: Jim Kent Date: Wed Jul 28 15:40:55 2010 -0700 Making little logo show up to left of encode regulatory track and fixing long label on one component. commit bdb271771613baa654f71b4b6f02a3b955ee0397 Merge: 3905606 569fd53 Author: Venkat Malladi Date: Wed Jul 28 15:25:11 2010 -0700 Merge branch 'master' of vsmalladi@hgwdev.cse.ucsc.edu:/data/git/kent commit 3905606cbb38a0960c2e59fd07c6b3a501c51a6e Author: Venkat Malladi Date: Wed Jul 28 15:25:01 2010 -0700 Updated mouse registered Cell lines registered by UW lab commit 569fd536ded830a7595a235dd6705bed25148b1b Author: mary Date: Wed Jul 28 15:13:05 2010 -0700 changing description of how alignments are colored commit 083ecc5217b08a32fb878700d0c71aa5691c9ded Author: Tim Dreszer Date: Wed Jul 28 14:46:42 2010 -0700 Fixed missing fileName link in ... and changed tdb v. mdb metadata hint commit 44e813c7831b70811e23bdc83858e3d4f8016cd0 Merge: bacd068 8de492a Author: vanessa Date: Wed Jul 28 14:29:31 2010 -0700 Merge branch 'master' of vanessa@hgwdev.cse.ucsc.edu:/data/git/kent commit bacd068c74b556331193939f19341c8fd5db67ec Author: vanessa Date: Wed Jul 28 14:28:01 2010 -0700 incorporating changes to the short and long labels for yale rna-seq track commit 8de492a6060531d2006a54055ccd32ecbd4ee1aa Merge: 74c7b78 704ab00 Author: Brian Raney Date: Wed Jul 28 14:06:37 2010 -0700 Merge branch 'master' of braney@hgwdev.cse.ucsc.edu:/data/git/kent commit 74c7b78d1f54b8e545ce4e909b956c117c2700ab Author: Brian Raney Date: Wed Jul 28 14:06:11 2010 -0700 add some d's onto the 1x75 sets commit 704ab00f73055e9fa9d51c6e2db4f50bac94fa58 Merge: 3fc4985 454059c Author: Tim Dreszer Date: Wed Jul 28 14:00:02 2010 -0700 Merge branch 'master' of tdreszer@hgwdev.cse.ucsc.edu:/data/git/kent commit 3fc4985e0565e8d601746484ed273cf353467a60 Author: Tim Dreszer Date: Wed Jul 28 13:59:53 2010 -0700 Finally got dragReorder row highlighting working commit 454059cc0fb8d0750b0fa6d1352b5206f428db3f Merge: 8813598 25978c3 Author: Angie Hinrichs Date: Wed Jul 28 13:55:38 2010 -0700 Merge branch 'master' of angie@hgwdev.cse.ucsc.edu:/data/git/kent commit 25978c3ffeead5c1dd66da41e3ec8e7f9beccdd3 Author: Tim Dreszer Date: Wed Jul 28 13:45:30 2010 -0700 Minor fix to skipBeyondDelimit commit c00a10e001902cc8e28cfe09e909fab970bf8d26 Author: Tim Dreszer Date: Wed Jul 28 13:43:28 2010 -0700 Minor adjustments to client resolution code commit 8813598cdb641218534a48d3fd5c55e9fa42ed95 Merge: 4683b4d ae829e3 Author: Angie Hinrichs Date: Wed Jul 28 13:35:06 2010 -0700 Merge branch 'master' of angie@hgwdev.cse.ucsc.edu:/data/git/kent commit 4683b4d7108b748cb41e5c79a744079e6b55ef52 Author: Angie Hinrichs Date: Wed Jul 28 13:34:56 2010 -0700 User John Hayward reported a sqlConnect without matching disconnect in doMiddle (genome, 6/16/10). Turns out the connection is used only in doDv() -- moved it there and converted sqlConnect to hAllocConn+hFreeConn. I don't think the dvBed track is live in any database now, so doDv is probably dead code anyway. commit ae829e37f6256cc2a3d93be4a65a9fa9ad1c6439 Author: Brian Raney Date: Wed Jul 28 12:36:21 2010 -0700 add gffToPsl commit 08310d1d9e259c91d4db4e022376d66c23675f7d Author: Brian Raney Date: Wed Jul 28 12:29:48 2010 -0700 add transparency for 32-bit PNG. Tim needs it for drag scroll commit d80ad4d0851cb51c2372eed4a346039a44c70da8 Author: Brian Raney Date: Wed Jul 28 12:12:29 2010 -0700 add a verbose statement telling user what chrom is being looked at commit 199ab98fd484893e9f13678550d9c9e2a2bf5447 Author: Brian Raney Date: Wed Jul 28 11:48:05 2010 -0700 add origAssembly, and get submission and restriction end dates from hg18 commit 7b863cba81942ccdd021a398ac79775c6afa3bd9 Merge: f6d0557 0202314 Author: Brian Raney Date: Wed Jul 28 11:33:52 2010 -0700 Merge branch 'master' of braney@hgwdev.cse.ucsc.edu:/data/git/kent commit f6d0557a006c92052c1afc1dc309b205ee8b2a49 Author: Brian Raney Date: Wed Jul 28 11:33:25 2010 -0700 take out tim and brian commit 02023149c1b8387f58044f183e4cebf8a6fca341 Author: katrina Date: Wed Jul 28 11:30:25 2010 -0700 made some edits to the first sentence of description to improve clarity commit 52e5b9bd34d6d645f0b9a0b43e1f62b30de3b194 Merge: 11112de 347a6ef Author: Hiram Clawson Date: Wed Jul 28 11:20:07 2010 -0700 Merge branch 'master' of hiram@hgwdev.cse.ucsc.edu:/data/git/kent commit 347a6ef246da141f4c0820beaf4b24dac035fbf0 Merge: 4c863e0 9d44809 Author: katrina Date: Wed Jul 28 11:19:32 2010 -0700 Merge branch 'master' of hgwdev:/data/git/kent commit 4c863e0e1f8259670cb59314bb0fe4856cfa3d0d Author: katrina Date: Wed Jul 28 11:19:19 2010 -0700 added ENCODE Data Release policy commit 11112dedcf44fbe58a37ee041ca605ae039d22dc Author: Hiram Clawson Date: Wed Jul 28 11:17:07 2010 -0700 adding useCount to BROWSER_BINS commit 9d44809de04fcc5046701f08acc6277a4237f743 Merge: 06038bf 47c692b Author: Hiram Clawson Date: Wed Jul 28 11:14:39 2010 -0700 Merge branch 'master' of hiram@hgwdev.cse.ucsc.edu:/data/git/kent commit 06038bf2b21046d17e6f1fced3648fd686609e1b Author: Hiram Clawson Date: Wed Jul 28 11:14:27 2010 -0700 initial contents for useCount commit 47c692bfdf0e132f92ef238a9386acc949fde5fe Merge: 2cc17e9 0f54361 Author: Brian Raney Date: Wed Jul 28 11:06:33 2010 -0700 Merge branch 'master' of braney@hgwdev.cse.ucsc.edu:/data/git/kent commit 2cc17e9f5c5cb19aa6352be6d7b585777d253958 Author: Brian Raney Date: Wed Jul 28 11:06:14 2010 -0700 changed title to match file name commit 0f543615fccfe42671db8941a7eec15f26dddd8a Merge: f933912 cfa110d Author: Antonio Coelho Date: Wed Jul 28 10:40:55 2010 -0700 Merge branch 'master' of antonio@hgwdev.cse.ucsc.edu:/data/git/kent commit f9339129c8ecee986d31b6370aab8798c623ec5f Author: Antonio Coelho Date: Wed Jul 28 10:40:43 2010 -0700 adding felCat4 chain/net track commit cfa110dd262bf81497ee05aa23d858920f17cb90 Merge: 0b4afb8 d849e42 Author: Venkat Malladi Date: Wed Jul 28 10:26:32 2010 -0700 Merge branch 'master' of vsmalladi@hgwdev.cse.ucsc.edu:/data/git/kent commit 0b4afb82f3c665317ee68ae9442a17cccd6c7b0f Author: Venkat Malladi Date: Wed Jul 28 10:26:18 2010 -0700 Updated each track description with feedback provided by the UW lab commit d849e42e83b8a2bb5283bd7775fb8380b46fdac3 Merge: 7e2c2cc 2d42d7d Author: vanessa Date: Wed Jul 28 09:38:42 2010 -0700 Merge branch 'master' of vanessa@hgwdev.cse.ucsc.edu:/data/git/kent commit 7e2c2ccd254b587c788c91b59c36f19c00d31280 Author: vanessa Date: Wed Jul 28 09:38:24 2010 -0700 rechecking this in with the new link commit 2d42d7d6d9ab52eb9dcc33712db47b7c8586eb35 Author: Antonio Coelho Date: Wed Jul 28 09:34:21 2010 -0700 fixing up description page commit b072f769c61ff69d8cc324c9fea977634ea3720b Author: Galt Barber Date: Wed Jul 28 08:00:20 2010 -0700 "Encode release log update" commit 42c6f85e40360ae9243c753799502ca7a7832a29 Author: Galt Barber Date: Wed Jul 28 08:00:18 2010 -0700 "Release log update" commit c71c9c20d27fb310a8ede62d3f70148931d4c10d Merge: 62a2fa6 9e106fc Author: b0b Date: Tue Jul 27 18:28:38 2010 -0700 Merge branch 'master' of kuhn@hgwdev.cse.ucsc.edu:/data/git/kent commit 9e106fc21503f2b4ae11f71bd50ec2d32e9fa371 Merge: c4c99bd 46edaa9 Author: Venkat Malladi Date: Tue Jul 27 17:36:02 2010 -0700 Merge branch 'master' of vsmalladi@hgwdev.cse.ucsc.edu:/data/git/kent commit 4ff07a51d53013a9980cd54aac0d4e310080dce0 Author: Cricket Sloan Date: Tue Jul 27 17:25:08 2010 -0700 Added line break for viewing of vendorIds commit 46edaa9dd2305a60b772abbd9aa701cf96eace92 Merge: adf3d76 52f2c96 Author: Cricket Sloan Date: Tue Jul 27 17:12:22 2010 -0700 Merge branch 'master' of cricket@hgwdev.cse.ucsc.edu:/data/git/kent commit adf3d76304b46705e4bda7d67d41ef736e6e2e85 Author: Cricket Sloan Date: Tue Jul 27 17:12:01 2010 -0700 added a space commit 1093216b253167149a65ba8bf36f36a45779d46a Author: Cricket Sloan Date: Tue Jul 27 17:07:32 2010 -0700 Changed the long and short labels to include antibody commit 52f2c96a03d05e3ef6075fac37187572e2cf4904 Author: vanessa Date: Tue Jul 27 17:04:44 2010 -0700 fixed the wording on the descriptions for the regulatory track on hg18 commit 559a124b7e0b63df037553fc0dd2312dfad9a95d Merge: 0ff55f9 afbb1d5 Author: mary Date: Tue Jul 27 16:33:26 2010 -0700 Merge branch 'master' of mary@hgwdev.cse.ucsc.edu:/data/git/kent commit 0ff55f935245a0d6422ece154dfd9f1696da16a6 Author: mary Date: Tue Jul 27 16:32:34 2010 -0700 adding script to check functionality of genome-mysql commit afbb1d5bdabf09e0bde0864e1788b5124a5c2354 Merge: 18ca529 1258beb Author: Cricket Sloan Date: Tue Jul 27 16:29:14 2010 -0700 Merge branch 'master' of cricket@hgwdev.cse.ucsc.edu:/data/git/kent commit 18ca52930e377eb3a2bd128a7f23e7d91a2cf03f Author: Cricket Sloan Date: Tue Jul 27 16:28:32 2010 -0700 File made on accident commit 00326e97065f4d47751f431021282971fc578f1c Author: Cricket Sloan Date: Tue Jul 27 16:26:41 2010 -0700 Changed the antibody from upper case to lower case. commit c4c99bdd2721a73e1dfc8d297801b50ca4f604ed Merge: 825199e 1258beb Author: Venkat Malladi Date: Tue Jul 27 16:24:41 2010 -0700 Merge branch 'master' of vsmalladi@hgwdev.cse.ucsc.edu:/data/git/kent commit 825199e5e81120da3c971cb74fd4e7bea43d5559 Author: Venkat Malladi Date: Tue Jul 27 16:20:39 2010 -0700 Added 38 new submissions. Updated short labels to be consistent with previous data. commit 35715b69a35352647e69d95450631f527833e1d2 Author: Cricket Sloan Date: Tue Jul 27 16:13:34 2010 -0700 This commit really has the metaDb changes for SunyAlbanyTiling. With the addition of antibody as well as ripTgtProtien. commit 1258beb280a34bf3d3fca7c55013222a38b03cdb Merge: 48d8f8e 5d200e4 Author: Fan Hsu Date: Tue Jul 27 15:31:44 2010 -0700 Merge branch 'master' of fanhsu@hgwdev.cse.ucsc.edu:/data/git/kent commit 5d200e48ab46ac1ddc089098defedae030e6a6bf Author: Tim Dreszer Date: Tue Jul 27 15:18:33 2010 -0700 Slight improvements to dragReorder: toolTips and hover highlighting commit 1259dfea0041943936efe6831bbcf716c6b0cf4b Author: Tim Dreszer Date: Tue Jul 27 15:13:50 2010 -0700 htmlEncode has been imprived with a newline char. However, FF does not support it commit 5f4e9eadcba8a9ee8b3f89bbe873caec478013ec Author: Tim Dreszer Date: Tue Jul 27 15:10:43 2010 -0700 Added cgiClientBrowser() routine to determine browser from HTTP_USER_AGENT commit fb0e6ff7decbf069aaf16a9ae9702176e414a9cf Author: Brian Raney Date: Tue Jul 27 15:03:42 2010 -0700 copy over from hg18 commit f2939a072013564caeb8a56c26db44da0daf5781 Author: Brian Raney Date: Tue Jul 27 15:00:48 2010 -0700 add transfrags commit e39879143fed2e35fee39b749b3267154756858a Merge: 47e335e e5b2792 Author: Brian Raney Date: Tue Jul 27 14:58:57 2010 -0700 Merge branch 'master' of braney@hgwdev.cse.ucsc.edu:/data/git/kent commit 47e335e437d794c372db6b05cde4e95822989bab Author: Brian Raney Date: Tue Jul 27 14:58:46 2010 -0700 add transfrags commit e5b279265f22dcc1918edd1af318f8db7d9a6309 Merge: f4624fb 3496006 Author: katrina Date: Tue Jul 27 14:50:32 2010 -0700 Merge branch 'master' of hgwdev:/data/git/kent commit f4624fb0e076500caf817c3d6b210b198fc90f13 Author: katrina Date: Tue Jul 27 14:50:25 2010 -0700 prepping to release Tim's metaDb change of inputType to controlId commit 3496006164b5410703377e3259bf184c1e57e265 Merge: 851f0ae 20408d4 Author: Angie Hinrichs Date: Tue Jul 27 14:41:56 2010 -0700 Merge branch 'master' of angie@hgwdev.cse.ucsc.edu:/data/git/kent commit 20408d431a5e38f2f4e469b8a6e73927cf09ab23 Merge: d6c2003 171c836 Author: katrina Date: Tue Jul 27 14:41:03 2010 -0700 Merge branch 'master' of hgwdev:/data/git/kent commit d6c2003319ab618ef2a8eef0af98a2babe395438 Author: katrina Date: Tue Jul 27 14:40:56 2010 -0700 staging Tim's metaDb change of inputType to controlId on hgwbeta commit 851f0ae8b2b90ae8f70171474a862c485e788059 Author: Angie Hinrichs Date: Tue Jul 27 14:38:13 2010 -0700 Removed unused identifiers (thanks Brooke). commit 62a2fa6f27b598320e11440dc54b12bcc9569eb0 Merge: 7a18c8c 171c836 Author: b0b Date: Tue Jul 27 14:28:16 2010 -0700 Merge branch 'master' of kuhn@hgwdev.cse.ucsc.edu:/data/git/kent commit 7a18c8c8eff23c56352b3fd1f67bd70d90f928bc Author: b0b Date: Tue Jul 27 14:27:34 2010 -0700 added omitted 'of' commit 171c8361ea2ddac144e5fe83153789b3f5a20b47 Merge: b756205 b55ad63 Author: Brian Raney Date: Tue Jul 27 14:27:30 2010 -0700 Merge branch 'master' of braney@hgwdev.cse.ucsc.edu:/data/git/kent commit b7562051cc3b1abc9747905f25f419a3b2b91764 Author: Brian Raney Date: Tue Jul 27 14:26:02 2010 -0700 some changes to support CSHL short transfrags commit b55ad63d8e1ca2588a2670d3da35752e0f2b2141 Merge: 2d315f0 8baa66f Author: Hiram Clawson Date: Tue Jul 27 14:18:49 2010 -0700 Merge branch 'master' of hiram@hgwdev.cse.ucsc.edu:/data/git/kent commit 2d315f0d60f44125bc880aba4e17f322284394d2 Author: Hiram Clawson Date: Tue Jul 27 14:18:30 2010 -0700 done with hg18 to hg19 liftOver analysis commit 8baa66f25684cff188005f50d573e98d19cd9179 Author: katrina Date: Tue Jul 27 14:09:21 2010 -0700 added 6 tracks for which we are switching to using metaDb commit e08075bc87ab38d289f85dd8fc0f5e04d3101675 Author: katrina Date: Tue Jul 27 14:08:53 2010 -0700 adding files for tracks that we are switching to using metaDb for the metadata commit 0566459a5da454963b731e38ecf1d52c34b606ee Author: Venkat Malladi Date: Tue Jul 27 13:52:44 2010 -0700 Added 7 new submissions. Still prelimary display, needs clean up. commit 2eb7b49589a7a27f7df71133d4f246e116863a61 Author: katrina Date: Tue Jul 27 13:48:03 2010 -0700 added 6 tracks for which we are switching to using metaDb commit af8ad54d478d1f8ede8abffe4868880a028cbecd Author: katrina Date: Tue Jul 27 13:47:19 2010 -0700 adding files for tracks that we are switching to using metaDb for the metadata commit a618a595337a82eb6065e270e4b3f95334c6fd84 Author: katrina Date: Tue Jul 27 13:37:56 2010 -0700 changing *.new.ra to .ra for 5 tracks for which we are switching to using the metaDb table, techincally already on RR, since release tags weren't used commit 48d8f8e68239259092fd4870bc152b1b919a9dd2 Author: Fan Hsu Date: Tue Jul 27 13:37:44 2010 -0700 Reverse the selfBlastTab table name change. commit 17aa61e72920031385fbc05921d6487dc7fc89b7 Author: Venkat Malladi Date: Tue Jul 27 13:34:46 2010 -0700 Add 8 new submissions and accompanying metaData for UW Histone Track commit 38c043f61a33b5d1c7bf611084d16aaf40fd7ccf Merge: 535e5d7 20fca17 Author: katrina Date: Tue Jul 27 13:32:31 2010 -0700 Merge branch 'master' of hgwdev:/data/git/kent commit 535e5d7c1a564a0429265474b86bc821df736aa3 Author: katrina Date: Tue Jul 27 13:32:24 2010 -0700 copying *.ra over *.new.ra because Brian accidentally made the changes to *.ra instead of *.new.ra; getting *.ra & *.new.ra are back in sync as they should be when releasing new changes (even though this was accidentally already released because release tags weren't used commit 20fca177b6534a4420839f467cbf1972c3f9f722 Merge: c85030a f85139b Author: Fan Hsu Date: Tue Jul 27 13:31:14 2010 -0700 Merge branch 'master' of fanhsu@hgwdev.cse.ucsc.edu:/data/git/kent commit f85139b013318bb76a8df810fcd423b09077145c Merge: e02c399 c4ae98a Author: katrina Date: Tue Jul 27 13:29:10 2010 -0700 Merge branch 'master' of hgwdev:/data/git/kent commit e02c3996099c7f2370002d82ff68fd9feb55b4e6 Author: katrina Date: Tue Jul 27 13:29:01 2010 -0700 copied the *.new.ra over the .ra; would normally be prep for release, but trackDb.wgEncode.ra had include lines for the *new.ra without any release tags, so already on rr commit c85030a4f9fedfce2b6311674c666b07aaaf7459 Author: Fan Hsu Date: Tue Jul 27 13:25:36 2010 -0700 Update the selfBlastTab table name. commit 4e973e2ce1c5be0924bc0379f4c7004f6dbfd62e Author: Fan Hsu Date: Tue Jul 27 13:24:24 2010 -0700 Update the selfBlastTab table name. commit dbab7ebc87dc46cc5a68d35c88fbdea6f5fc3ed3 Merge: c91ccef c4ae98a Author: Hiram Clawson Date: Tue Jul 27 13:17:45 2010 -0700 Merge branch 'master' of hiram@hgwdev.cse.ucsc.edu:/data/git/kent commit c91ccef7e18cf45723079ac4a48ba8158287f09b Merge: f52eabd 6f76af9 Author: Hiram Clawson Date: Tue Jul 27 13:17:40 2010 -0700 finishing merge commit c4ae98ac3023b6120cc359c69710db4c02eaf78b Merge: 61872d2 4b114fe Author: Brian Raney Date: Tue Jul 27 12:57:51 2010 -0700 Merge branch 'master' of braney@hgwdev.cse.ucsc.edu:/data/git/kent commit 61872d2470a3ede22b393eecdb33c6005bfcfc8d Author: Brian Raney Date: Tue Jul 27 12:55:07 2010 -0700 cshl small rna clusters commit 4b114fe198f0dbd27d2eaaf8b447dfeb09426251 Author: b0b Date: Tue Jul 27 11:20:43 2010 -0700 added back edit that got stomped commit f52eabdd5fd5e6268496a7a8b980a483ae4a8176 Author: Hiram Clawson Date: Tue Jul 27 11:20:24 2010 -0700 trying liftOver experiments commit 6f76af9f4f207f66d7794265b9d98180f16c3168 Merge: 71d658f a7dc337 Author: Antonio Coelho Date: Tue Jul 27 11:20:00 2010 -0700 Merge branch 'master' of antonio@hgwdev.cse.ucsc.edu:/data/git/kent commit 71d658f7fe3bf0deab6e383eedac75cbce19f01d Author: Antonio Coelho Date: Tue Jul 27 11:19:54 2010 -0700 changing example searches for felCat4 commit 497f936dcc263f71f0be1f2f12b0d3bfcbb23663 Author: Cricket Sloan Date: Tue Jul 27 11:11:26 2010 -0700 This has the ripTgtProtien added as the antibody as well. Then It can be used either way we decide to go with the cv.ra commit a7dc3377e96263b506d193e4d9618dde89e23064 Author: Cricket Sloan Date: Tue Jul 27 11:02:16 2010 -0700 This is the metadata for Suny updated with the antibody, the ripTgtProtien has not been removed commit 82b716e2d849385829517984beb8b8e93af36dbf Author: Cricket Sloan Date: Tue Jul 27 10:56:58 2010 -0700 Checking in the most recent fiddles with these DAFs commit 398dd54c8bee8c6be0c06798288a02df15593b93 Author: Cricket Sloan Date: Tue Jul 27 10:37:32 2010 -0700 I have changed the names of the include files to match the standard. I also have been working on the short labels for the Suny tracks. commit 009618d09e2cacb1340963a6365af72ce690ddec Merge: 0893b34 8ec2ac1 Author: Cricket Sloan Date: Tue Jul 27 10:27:07 2010 -0700 Merge branch 'master' of cricket@hgwdev.cse.ucsc.edu:/data/git/kent commit 0893b348c02b5af52e230534f8bb5d10139e480f Author: Cricket Sloan Date: Tue Jul 27 10:26:37 2010 -0700 Changed the antibody display to accept semi-colon separated lists for the vendorName, vendorId, and orderUrl. commit ceb7210adf1e288f7c8aed6af4d243d0fa4af732 Merge: 03cd4fe 8ec2ac1 Author: Antonio Coelho Date: Tue Jul 27 09:14:12 2010 -0700 Merge branch 'master' of antonio@hgwdev.cse.ucsc.edu:/data/git/kent commit 8ec2ac1107ee4b7cdbb30526a75d1aa300685b6e Merge: 7fe80d3 a79974a Author: Mark Diekhans Date: Mon Jul 26 23:51:48 2010 -0700 Merge branch 'master' of hgwdev.cse.ucsc.edu:/data/git/kent commit 7fe80d37afd296f8db0058f3e444737ff88ff80e Author: Mark Diekhans Date: Mon Jul 26 23:50:19 2010 -0700 address problem of hgTables consuming all available sockets before TIME_WAIT period by using the connection cache. Have hgTable log connection usage information to help ensure this is fixed commit a79974a5596fc8e8ae1ffd77d1f1d01dccd9b8d4 Merge: 2452c53 7d22534 Author: Galt Barber Date: Mon Jul 26 20:35:22 2010 -0700 Merge branch 'master' of hgwdev:/data/git/kent commit 2452c53353dd7ef242a787c05b5076d437d1f122 Author: Galt Barber Date: Mon Jul 26 20:35:11 2010 -0700 v237 preview commit 7d22534c23380e21685eaf9f62fd88244dbce92f Merge: 351bd76 0f9cc23 Author: Mark Diekhans Date: Mon Jul 26 17:56:43 2010 -0700 Merge branch 'master' of hgwdev.cse.ucsc.edu:/data/git/kent commit 0f9cc2363d28dcf460a7497370b50440dc1ed834 Merge: 68d5d5c a171ba6 Author: Brian Raney Date: Mon Jul 26 17:55:06 2010 -0700 Merge branch 'master' of braney@hgwdev.cse.ucsc.edu:/data/git/kent commit 351bd760c2a6486ac1d2192acd5f1088d768eaae Author: Mark Diekhans Date: Mon Jul 26 17:53:46 2010 -0700 added sqlDump to assist in debuging connection cache/profile problems commit 68d5d5c7a102ee9dc59270f157bc5709f1a43b3d Author: Brian Raney Date: Mon Jul 26 17:51:07 2010 -0700 add tiny piece of information about UCSF Brain Methyl since we don't have Ting's load info commit a171ba6342141dbe5195c5d52cd6f2864ede9e34 Author: Venkat Malladi Date: Mon Jul 26 16:30:16 2010 -0700 Updated compsites to be default dense while supertrack is hide commit f6aef6bb39fe77d083ee6b7141ca4b2d32a25fe6 Merge: 18dd566 e8942fa Author: Venkat Malladi Date: Mon Jul 26 16:19:35 2010 -0700 Merge branch 'master' of vsmalladi@hgwdev.cse.ucsc.edu:/data/git/kent commit 18dd5663e1c89ae76e01f1c52bd52059c39505ab Author: Venkat Malladi Date: Mon Jul 26 16:09:14 2010 -0700 Updated the defaults for the tracks to be default, as the composite is set to default hide. commit e8942fa92b98a9289f30911b8aef8fab80ceb2b8 Author: Brian Raney Date: Mon Jul 26 16:07:36 2010 -0700 change UCSF Brain Methyl table names commit 210e6ce1035fb41e79792b1bd1b80b28c8547d75 Author: katrina Date: Mon Jul 26 15:39:52 2010 -0700 removing release tags to include lines because I forgot that this functionality doesn't exist yet ;) commit 03b0470fb2cebec1be5231a345c3076ee70fdd75 Merge: c39b3b6 e2b7a49 Author: Tim Dreszer Date: Mon Jul 26 15:35:50 2010 -0700 Merge branch 'master' of tdreszer@hgwdev.cse.ucsc.edu:/data/git/kent commit c39b3b69150c8b64cdcd785fd0824e3af7938df7 Author: Tim Dreszer Date: Mon Jul 26 15:35:44 2010 -0700 Changed inputType to controlId commit e2b7a492e95f6a7b379dbf60697d17d66e11adbb Merge: 497bf04 b1293e4 Author: Venkat Malladi Date: Mon Jul 26 15:16:59 2010 -0700 Merge branch 'master' of vsmalladi@hgwdev.cse.ucsc.edu:/data/git/kent commit 497bf04c8861d732400d88b16c9652126ab31a61 Author: Venkat Malladi Date: Mon Jul 26 15:16:47 2010 -0700 Updated Validtor to check assembly and if hg19 and 3 composites require inputType commit b1293e4dfed7dd8d68a0449b130ecac7cb04ded1 Merge: 82ed734 bb0809b Author: katrina Date: Mon Jul 26 15:12:19 2010 -0700 Merge branch 'master' of hgwdev:/data/git/kent commit 82ed734ed1cc37d1ffdb56826acf7a2494162f5b Author: katrina Date: Mon Jul 26 15:12:09 2010 -0700 added release tags to include statements for Yale RNA-seq commit 20d7b2f7fe2707a9aa185186817d79941dccc50d Author: Tim Dreszer Date: Mon Jul 26 15:09:19 2010 -0700 Corrected 40 metadata settings commit bb0809bd58d79cc4b8821f31604b2eff411a9cb7 Merge: 461eebb 5deb247 Author: Cricket Sloan Date: Mon Jul 26 15:05:54 2010 -0700 Merge branch 'master' of cricket@hgwdev.cse.ucsc.edu:/data/git/kent commit 461eebb5fd90f014e07e14428721538972c35b1c Author: Cricket Sloan Date: Mon Jul 26 15:04:00 2010 -0700 This is part of the change to add release tags to the YaleRnaSeq track commit 5deb2474dd499614f8e14e186ce81d7ae536cb90 Merge: dfc6c9e 8d65562 Author: Venkat Malladi Date: Mon Jul 26 15:01:46 2010 -0700 Merge branch 'master' of vsmalladi@hgwdev.cse.ucsc.edu:/data/git/kent commit dfc6c9e30aac71d0b166d4f3300f8eeea8fe4baf Author: Venkat Malladi Date: Mon Jul 26 15:01:39 2010 -0700 Updated type of termP to term commit 8d655627333c9126befddf3520a65b79237001df Merge: 196080d 664b681 Author: Cricket Sloan Date: Mon Jul 26 15:01:05 2010 -0700 Merge branch 'master' of cricket@hgwdev.cse.ucsc.edu:/data/git/kent commit 196080d8e5b2fc360ea05b14a93bff717955e92d Author: Cricket Sloan Date: Mon Jul 26 14:59:58 2010 -0700 Stephen from the lab says that one of the tracks should have a + afterall commit 664b681fe669114d524c2bc5467787746f99c786 Merge: 540d4e2 512b8ba Author: Brian Raney Date: Mon Jul 26 14:56:51 2010 -0700 Merge branch 'master' of braney@hgwdev.cse.ucsc.edu:/data/git/kent commit 540d4e2ecab0216d87ce5ff3c601872aa1cac53e Author: Brian Raney Date: Mon Jul 26 14:56:29 2010 -0700 look for *.bigWig instead of *.bw commit 5ad542555547973fdf90fbce8c628c7b8400a469 Author: Cricket Sloan Date: Mon Jul 26 14:48:25 2010 -0700 Added release tags for the YaleRnaSeq Track and pulled out the track into two files commit c80a9404405d8e4236ff51f4c0da16db5e93e0bd Merge: 68fac08 512b8ba Author: Venkat Malladi Date: Mon Jul 26 14:41:36 2010 -0700 Merge branch 'master' of vsmalladi@hgwdev.cse.ucsc.edu:/data/git/kent commit 68fac088bffa52f7e3217f2790df4feff9bbebac Author: Venkat Malladi Date: Mon Jul 26 14:41:05 2010 -0700 Added 22 cell lines from UW. commit 512b8bac84a86028cad80d5776328cc3d96e443b Merge: 6de7c7b 69e8a1d Author: Angie Hinrichs Date: Mon Jul 26 13:37:29 2010 -0700 Merge branch 'master' of angie@hgwdev.cse.ucsc.edu:/data/git/kent commit 6de7c7b893ad3bd445fef2449dc975270666dc95 Author: Angie Hinrichs Date: Mon Jul 26 13:35:48 2010 -0700 Changes to default wiggle settings requested by Ed Green. commit 69e8a1da6c5c641511e72488efaf47f72c3a7598 Merge: ba92a8c e6136db Author: Cricket Sloan Date: Mon Jul 26 13:08:26 2010 -0700 Merge branch 'master' of cricket@hgwdev.cse.ucsc.edu:/data/git/kent commit e6136db549c606746751e529a431d0f911469edd Author: Tim Dreszer Date: Mon Jul 26 12:49:20 2010 -0700 Changed inputType to controlId and added labExpId commit ba92a8c74f69ded4ac1a40278c8f9892ffa8578c Author: Cricket Sloan Date: Mon Jul 26 12:36:14 2010 -0700 Final changes for the Yale labels to make the long labels have full words commit 3132ab0f9dd0492a4678da8b20a3fd1772faddaf Author: Tim Dreszer Date: Mon Jul 26 12:14:16 2010 -0700 Changed inputType to controlId and added labExpId as optional field commit df7e29302045d83aed9e97575f519684c869127d Author: Brian Raney Date: Mon Jul 26 11:42:33 2010 -0700 add fileIndex for BAM files commit e6849f5893c01253a53fdab8141a06af4740c1db Merge: 68a4335 c67f374 Author: Brian Raney Date: Mon Jul 26 11:41:28 2010 -0700 Merge branch 'master' of braney@hgwdev.cse.ucsc.edu:/data/git/kent commit 68a4335143a390c4f3fad977be5dd5ecb7aa91ad Author: Brian Raney Date: Mon Jul 26 11:40:55 2010 -0700 add fileIndex for BAM files commit c67f3745398271e83f76f5454f4d9009186e30fb Author: Venkat Malladi Date: Mon Jul 26 09:45:41 2010 -0700 Fixed description for TAM treamtent for quantity of 2uM to 1 uM. commit 7d82d8442e76b62887b6fce76a6d6e2f0bc1024b Author: Venkat Malladi Date: Mon Jul 26 09:17:43 2010 -0700 Added 1 new treatment tamoxifen for Myers lab commit c7b0e51932e047193782162e35fbc5e9798a9c3f Author: Venkat Malladi Date: Mon Jul 26 09:10:30 2010 -0700 Remvoed orderUrl for GM12878 registered cell lines, not applicable commit 050b5102f6e0405d7f5119b4f86b0c30728c380d Merge: 23af99a 5476125 Author: Venkat Malladi Date: Mon Jul 26 09:05:04 2010 -0700 Merge branch 'master' of vsmalladi@hgwdev.cse.ucsc.edu:/data/git/kent commit 23af99a04dc22f839894dd47bddcd255b5038244 Author: Venkat Malladi Date: Mon Jul 26 09:04:54 2010 -0700 Added 4 new cell lines for X-inactivation in GM12878 cell lines registered by the Myers lab commit 03cd4fe809c10a1eac15da0bbccfac3ff2e7f7d7 Merge: 8d95a8a 5476125 Author: Antonio Coelho Date: Mon Jul 26 09:00:18 2010 -0700 Merge branch 'master' of antonio@hgwdev.cse.ucsc.edu:/data/git/kent commit 5476125b08a0d9c67cf2f33039578d3ba2987e16 Merge: f7b5155 2bd825b Author: Fan Hsu Date: Mon Jul 26 08:58:37 2010 -0700 Merge branch 'master' of fanhsu@hgwdev.cse.ucsc.edu:/data/git/kent commit f7b5155acd753432890cbf5dac31b2fae0778ed1 Author: Fan Hsu Date: Mon Jul 26 08:57:53 2010 -0700 Added uniGene for hg19. commit 2bd825bae342eaad0445c8d52d674307c22e41b7 Author: Galt Barber Date: Mon Jul 26 08:00:12 2010 -0700 "Encode release log update" commit 26cd76fd36d13ae4c2953e81da865e9667ab8ebb Author: Galt Barber Date: Mon Jul 26 08:00:10 2010 -0700 "Release log update" commit c24dcfabebf6713dcb756ab19b785cf1f7908f79 Author: Krishna Roskin Date: Mon Jul 26 07:32:09 2010 -0700 added missing insertLength values commit 2cdce8fb2ffaf3e92783dcc7bb87841a50b56e12 Author: Krishna Roskin Date: Mon Jul 26 07:27:57 2010 -0700 added makefile commit 01dc993c6f3883d876a51960271e4cc8caede98a Author: Galt Barber Date: Sun Jul 25 08:00:12 2010 -0700 "Encode release log update" commit c01a8ac98f6ecf5bc71a50c564f6070fcfb234d1 Author: Galt Barber Date: Sun Jul 25 08:00:11 2010 -0700 "Release log update" commit 3284c83505c820a010ebf4c92810c6dc17a53554 Author: Brian Raney Date: Sat Jul 24 18:48:15 2010 -0700 special case type for bam index file commit 5ccea53ce950c060b6931c43c7f7a6c0d79e8330 Author: Brian Raney Date: Sat Jul 24 18:13:46 2010 -0700 don't output a separate metadata line for bam index files commit 2d69231f52d0064ae18a41e6dea43e0abaec82a6 Author: Brian Raney Date: Sat Jul 24 17:32:05 2010 -0700 add .bai files to those included in the output files commit dd8c414c1aa8853c4bbc7a4bf571465c28189b7e Author: Brian Raney Date: Sat Jul 24 15:04:52 2010 -0700 take .gz off bigWig and BAM files commit 03138d995c27405a3a4b628a10d42ceec354c1a2 Merge: 18d152c df58b91 Author: Galt Barber Date: Sat Jul 24 14:54:41 2010 -0700 Merge branch 'master' of galt@hgwdev.cse.ucsc.edu:/data/git/kent commit 18d152cdd9a3b14969ea4e3cb0d7d1c0edf4da93 Author: Galt Barber Date: Sat Jul 24 14:54:32 2010 -0700 fixing bug in doSameSpeciesLiftOver - redid mm8->mm9 liftOver commit df58b910a14c6a4d5b83c9dfbb06af0ab0695e48 Merge: 984c26a 7c29b2d Author: Mark Diekhans Date: Sat Jul 24 14:11:09 2010 -0700 Merge branch 'master' of hgwdev.cse.ucsc.edu:/data/git/kent commit 984c26a2f1a75871f48f0ef2a28d34f08787ec5e Author: Mark Diekhans Date: Sat Jul 24 14:10:13 2010 -0700 fixed documentation error commit 7c29b2d48a215909910bb16bf5b3fd2130419b59 Author: Brian Raney Date: Sat Jul 24 14:07:48 2010 -0700 copy from hg18 commit d7e9dc95adee3e7ddc5bf779ffe5325d9b057407 Author: Brian Raney Date: Sat Jul 24 13:57:41 2010 -0700 change the fileName for BAMs and bigWigs to take out the .gz commit d5f5eb2f2427b50d0537ce9649e122fe60ed979e Merge: 4b629f5 c0d0e56 Author: Brian Raney Date: Sat Jul 24 13:34:10 2010 -0700 Merge branch 'master' of braney@hgwdev.cse.ucsc.edu:/data/git/kent commit 4b629f596c7ad456010e6d4d8b9f5716aadb002f Author: Brian Raney Date: Sat Jul 24 13:33:33 2010 -0700 don't gzip BAM or bigWigs commit c0d0e56c0eecb2b66353e5028268cd7848732e9c Author: Galt Barber Date: Sat Jul 24 08:00:15 2010 -0700 "Encode release log update" commit cf3b2724fa480520f2949f98b2dc7a4e36fd5f9b Author: Galt Barber Date: Sat Jul 24 08:00:13 2010 -0700 "Release log update" commit 7216fc2a845ced85598782565ccd42073f2a88e1 Merge: 6debe41 b939d9a Author: Galt Barber Date: Sat Jul 24 01:35:35 2010 -0700 Merge branch 'blatFixFastMap' commit 6debe4124dfe63cf89d5179363e9264e35efe98e Author: Galt Barber Date: Sat Jul 24 01:31:49 2010 -0700 fixing splitSize for doSameSpeciesLiftOver.pl - chunk size cannot exceed 5000 for blat -fastMap commit b939d9a5fefdf1b23173bd7e9003fd08fed13ba1 Author: Galt Barber Date: Sat Jul 24 01:02:50 2010 -0700 adding max query size limit to help commit aadf67fad3561419d2e33a16adba76d969a19b73 Author: Galt Barber Date: Sat Jul 24 00:58:50 2010 -0700 adding needed checks on query sizes against the maximum single piece size for use with -fastMap commit 01ff85fbef6491c888d4dbe5f5c9a91e350b10c1 Merge: 9cb07b8 143ec00 Author: Hiram Clawson Date: Fri Jul 23 16:35:35 2010 -0700 Merge branch 'master' of hiram@hgwdev.cse.ucsc.edu:/data/git/kent commit 9cb07b82197a9701accb2f7fa9ccabb5d7a42522 Author: Hiram Clawson Date: Fri Jul 23 16:35:23 2010 -0700 adding patch1 sequence to hg19 commit 143ec0059a5e598c588d34c8bb66c9e04d2409de Author: Krishna Roskin Date: Fri Jul 23 16:26:02 2010 -0700 fixed URLs for hgEncodeVocab so that they can use the sandbox commit 35faeebf7d8d562f2119b8dad867b1d4eff269a7 Merge: 1aaca9c fd3c3d5 Author: Krishna Roskin Date: Fri Jul 23 15:37:16 2010 -0700 Merge branch 'master' of krish@hgwdev.cse.ucsc.edu:/data/git/kent commit 1aaca9ca5e43d4b9765626a5a072ceb693f8377c Author: Krishna Roskin Date: Fri Jul 23 15:36:49 2010 -0700 added hgsqlTableDate and hgsqlSwapTables to the make file commit 710353ec8861ef4388c6b9fc47b743235309e07a Author: Hiram Clawson Date: Fri Jul 23 15:30:28 2010 -0700 bare .out from RepeatMasker has extra space in header compared to liftUp .out file commit fd3c3d5db81266107e4058143ad9ef17ac1cfd0a Merge: 9eaa176 45f040e Author: Venkat Malladi Date: Fri Jul 23 15:27:38 2010 -0700 Merge branch 'master' of vsmalladi@hgwdev.cse.ucsc.edu:/data/git/kent commit 9eaa176f771dbfda1750e5cee34e11f73fb28403 Author: Venkat Malladi Date: Fri Jul 23 15:27:30 2010 -0700 Updated all Histone tracks to be consistent within the given super track. Short Labels and matrix display( factor and cell type order) commit 45f040e594ebb09ff40717a5b5961f5430926820 Author: mary Date: Fri Jul 23 15:11:04 2010 -0700 updating link to source downloads to include executables in the language as well commit 533544206cd68045dd9d1dfdacc8e9ecb43d4176 Merge: 115531f 12b6e59 Author: ann Date: Fri Jul 23 15:09:09 2010 -0700 Merge branch 'master' of ann@hgwdev.cse.ucsc.edu:/data/git/kent commit 115531fa6aef4ce1e677bc81bf55c907102deb70 Author: ann Date: Fri Jul 23 15:08:32 2010 -0700 added blurb about big paper commit 12b6e595c4f67c8aac534a15d362adcf49627358 Merge: 3f678dc 712b8fa Author: Fan Hsu Date: Fri Jul 23 14:46:36 2010 -0700 Updated for xxBlastpTab tables rebuild using danRer6. commit 3f678dc55082ace72a058fbc4fc662ea146fadea Author: Fan Hsu Date: Fri Jul 23 14:40:54 2010 -0700 Updated for xxBlastpTab tables rebuild using danRer6. commit 712b8fac3c797b50ab0ad7d1f3fd56bc9e1c6ae3 Author: Venkat Malladi Date: Fri Jul 23 13:33:05 2010 -0700 Updated long label for track commit 9794c54fabda37ab9ddb05a794078e0cdf05b172 Author: Venkat Malladi Date: Fri Jul 23 11:56:02 2010 -0700 Updated the order of the cell types in the matrix display. commit c4b9a456ee9c7f1b10afbe52cd90291cba678f39 Merge: 6278805 4266b26 Author: Venkat Malladi Date: Fri Jul 23 11:34:34 2010 -0700 Merge branch 'master' of vsmalladi@hgwdev.cse.ucsc.edu:/data/git/kent commit 627880548b672e4fa14a041ec9625bbfe33ae976 Author: Venkat Malladi Date: Fri Jul 23 11:33:45 2010 -0700 Updated Open Chrom FAIRE-seq track short labels to match DNase-Seq. Also standardized treatment display headers between the two tracks commit 4266b26d500b1945e8f71f5ac0561f362d144317 Merge: 1d76194 3bb97cf Author: Hiram Clawson Date: Fri Jul 23 11:20:44 2010 -0700 Merge branch 'master' of hiram@hgwdev.cse.ucsc.edu:/data/git/kent commit 1d7619462b125e798154077cee64c62c3532a3b9 Author: Hiram Clawson Date: Fri Jul 23 11:20:37 2010 -0700 bare output file from RepeatMasker has different header spacing compared to liftUp produced header commit 3bb97cf66edf80cb10acc05c52205438851c3a3f Merge: e6ae9c5 85c7330 Author: mary Date: Fri Jul 23 10:59:19 2010 -0700 Merge branch 'master' of mary@hgwdev.cse.ucsc.edu:/data/git/kent commit e6ae9c5e2e793dc42890ada2658663e226163396 Author: mary Date: Fri Jul 23 10:59:16 2010 -0700 completely re-doing the description page so that more detailed and accurate commit 86d8755419409fdfe641666bba63dfcd7279dd0d Author: mary Date: Fri Jul 23 10:58:01 2010 -0700 adding link to our source tree downloads so it is easier to find commit 85c7330f9cd3d19393afd98af096b51d779e6b15 Merge: ff576f3 330d9bb Author: Tim Dreszer Date: Fri Jul 23 10:57:16 2010 -0700 Merge branch 'master' of tdreszer@hgwdev.cse.ucsc.edu:/data/git/kent commit ff576f39728b6e487cf5cea4d8e9d35affc76aa9 Author: Tim Dreszer Date: Fri Jul 23 10:57:10 2010 -0700 Added special case restriction to avoid HAIB TFBS ever submitting again without inputType commit fa64dafeef44fb525fdd39410f662c1b8fb17c75 Author: Tim Dreszer Date: Fri Jul 23 10:56:04 2010 -0700 Fixed cells marked as BJ-tert but supposed to be BJ commit 330d9bbc3c4b702428d2412035d1e3001b6615cc Author: ann Date: Fri Jul 23 10:14:58 2010 -0700 fixing broken link commit 1c5fc180ed557a1c5c5a8ca8738c260dc014293b Merge: 0a8848d 44a5465 Author: Venkat Malladi Date: Fri Jul 23 09:21:31 2010 -0700 Merge branch 'master' of vsmalladi@hgwdev.cse.ucsc.edu:/data/git/kent commit 0a8848da22f94c3a62fc234763acd566f7205fea Author: Venkat Malladi Date: Fri Jul 23 09:21:09 2010 -0700 Updated the check for Mouse Tissue category to spell out Tissue to match cv.ra, previously T was used. commit 44a5465af242bdccd0a63a3f3a2a8ce25f0d79c6 Author: Galt Barber Date: Fri Jul 23 08:00:24 2010 -0700 "Encode release log update" commit ad5b4c9357f9c9136cab7394deb2be5da71c7b1c Author: Galt Barber Date: Fri Jul 23 08:00:22 2010 -0700 "Release log update" commit bfc85572419ab0c4752e94821445a1ba44813d0e Author: Brooke Rhead Date: Thu Jul 22 18:47:14 2010 -0700 Temporarily changing the otherOrg databases that go with the blastTab tables rebuild back to their values at the v234 CGI release. Leaving out zebrafish archive.ensembl otherUrl links because Fan, Hiram and I think that these should go to the latest ensembl page. commit 13c9a36e8f347125b8a28d0f21cda0ffab399caf Merge: aace413 6c99517 Author: Brooke Rhead Date: Thu Jul 22 18:38:30 2010 -0700 Merge branch 'master' of rhead@hgwdev.cse.ucsc.edu:/data/git/kent commit aace413b5bb2ec344eae976efb995820b796d6c4 Author: Brooke Rhead Date: Thu Jul 22 18:19:29 2010 -0700 Setting rat mrnas to dense, since pack is huge at the default position for rn4. This may have turned from dense to pack when visibility.ra got folded back into trackDb.ra last December. commit 6c995178b5e539d64f15d1c699de62a5e55ccac1 Author: Venkat Malladi Date: Thu Jul 22 16:33:19 2010 -0700 Updated the short lables and consistency notes. commit 5359e43978c34a46b7090d28c14526d6cd5d0455 Author: Cricket Sloan Date: Thu Jul 22 16:21:35 2010 -0700 This is the draft of how I think the rip Antibody cv should look. This will hopefully become part of cv.ra after approval. commit fcb019c5f37a7304f2d296ad184cad144fd1d20c Author: Cricket Sloan Date: Thu Jul 22 16:11:08 2010 -0700 This is a DAF for the YaleRNA-Seq. I think that it will change a lot from here. commit 1ca62b02c2e76670f1269b078146682085080a0b Merge: 884cd81 4d096d6 Author: Venkat Malladi Date: Thu Jul 22 15:43:56 2010 -0700 Merge branch 'master' of vsmalladi@hgwdev.cse.ucsc.edu:/data/git/kent commit 884cd81092a5947230ece8368adb5e40c4afabce Author: Venkat Malladi Date: Thu Jul 22 15:43:44 2010 -0700 Updated the metaData to be compliant with Hudson Alpha Expectations commit 5898fb31bbc5c0abf9fc0225bb001558c01024ab Author: Cricket Sloan Date: Thu Jul 22 15:34:52 2010 -0700 Changed the short labels to show the treatment as well. commit 3b8f15aa0d55ba6566f008329683ad563698a710 Author: Cricket Sloan Date: Thu Jul 22 15:03:19 2010 -0700 Changed the short labels from PolyA to PolyA- commit bbfb220fa89d9bca2f0f63d51f6cfee9fcd6921b Author: Cricket Sloan Date: Thu Jul 22 14:59:36 2010 -0700 I changed the long labels to PolyA- from Poly A commit 4d096d69d6f22fa2d747819138267f4469783231 Merge: 1d12df4 65e382f Author: Brian Raney Date: Thu Jul 22 14:19:52 2010 -0700 Merge branch 'master' of braney@hgwdev.cse.ucsc.edu:/data/git/kent commit 1d12df49f4ed0a8d8e8d19f5f8657664a1e0d0e1 Author: Brian Raney Date: Thu Jul 22 14:19:30 2010 -0700 edits from Mary commit 8d95a8a9dda88e6d66fe93e4f610fdb91aebc052 Merge: 8fd0703 65e382f Author: Antonio Coelho Date: Thu Jul 22 13:45:56 2010 -0700 Merge branch 'master' of antonio@hgwdev.cse.ucsc.edu:/data/git/kent commit 65e382f9741bb86495cf0877fdecb0024e9791c5 Author: Tim Dreszer Date: Thu Jul 22 13:11:54 2010 -0700 Made dragReorder action which causes whole page scroll, scroll a bit faster. commit 125869e92d119f879af846ea84acaf076284a415 Author: Tim Dreszer Date: Thu Jul 22 13:03:21 2010 -0700 Replaced clenseQuotes with htmlEncode as suggested by Brian commit f60abda45cb49359266843c7bbfbafe2a2bf2051 Author: Tim Dreszer Date: Thu Jul 22 13:02:08 2010 -0700 Extended htmlEncode to handle single quotes properly commit dc9e2d26233a14b14771430de665ff684978fbb9 Author: Tim Dreszer Date: Thu Jul 22 12:58:06 2010 -0700 Fixed redmine 385 where Changing view affected unchecked ABC dimensions. commit d6b52e1b976146d1289002b2216d736ad77e79c2 Merge: bfdbfd1 93542ae Author: Tim Dreszer Date: Thu Jul 22 12:17:02 2010 -0700 Merge branch 'master' of tdreszer@hgwdev.cse.ucsc.edu:/data/git/kent commit 93542ae168ec85faeef48f69cbea46efdc5163ec Merge: bebc45b 2b4db3f Author: Chin Li Date: Thu Jul 22 11:59:30 2010 -0700 Merge branch 'master' of chinhli@hgwdev.cse.ucsc.edu:/data/git/kent commit bebc45b2271bf3fd06d85ecb270db4ec53c7ea53 Author: Chin Li Date: Thu Jul 22 11:59:23 2010 -0700 fix duplicat EST track problem commit 2b4db3fe9f6b6ec57b5e00b5dfdeca144e0d6312 Author: b0b Date: Thu Jul 22 11:17:22 2010 -0700 tweaked news item about workshops commit d1954c4e49b263246aa322bdd3099d59fba437d8 Merge: c589913 c0c1767 Author: b0b Date: Thu Jul 22 10:55:04 2010 -0700 Merge branch 'master' of kuhn@hgwdev.cse.ucsc.edu:/data/git/kent commit c0c1767c13b30e64ea3fa9a816ca5b5058aa8579 Author: Hiram Clawson Date: Thu Jul 22 10:49:46 2010 -0700 adding release tags to separate out different 30way multiz commit 8fd07035d064ddf89fb9930a519d334d59907dfb Merge: 18ee3a9 6c52d02 Author: Antonio Coelho Date: Thu Jul 22 10:38:20 2010 -0700 Merge branch 'master' of antonio@hgwdev.cse.ucsc.edu:/data/git/kent commit bfdbfd1988da3b5de45cc2448d924d8d6d8d7d9d Author: Tim Dreszer Date: Thu Jul 22 09:55:29 2010 -0700 Removed metadata lines from 5 ENCODE DNA tracks so that metaDb is the unambiguous metadata source. commit 6c52d024c2e56f24471309d4db7622dd950f2e92 Author: Fan Hsu Date: Thu Jul 22 08:43:48 2010 -0700 added lines for Decipher track. commit 8d9f30eb029399d4a691134ee4ddd1a2215d8aa4 Merge: 157333b f58e605 Author: Chin Li Date: Thu Jul 22 08:20:44 2010 -0700 Merge branch 'master' of chinhli@hgwdev.cse.ucsc.edu:/data/git/kent commit 157333b61b7cc92ff8180c79fb3ca8f91f755175 Author: Chin Li Date: Thu Jul 22 08:20:28 2010 -0700 Use ensGene to annotate calJac3 commit f58e60524afb20b74c1d4d5920360cffb23b1637 Author: Galt Barber Date: Thu Jul 22 08:00:35 2010 -0700 "Encode release log update" commit efc008e101954214f9998c0ff74cf74896ee72f4 Author: Galt Barber Date: Thu Jul 22 08:00:33 2010 -0700 "Release log update" commit 89772ab1643706903eaa3ceaa5c01f944dc6029b Author: Brian Raney Date: Wed Jul 21 17:27:14 2010 -0700 add some options to let some errors pass through commit a54067938d136b18c46dc6a1d6ad2643a58d686a Merge: 208d932 830a7f4 Author: Brian Raney Date: Wed Jul 21 17:05:24 2010 -0700 Merge branch 'master' of braney@hgwdev.cse.ucsc.edu:/data/git/kent commit 208d93223911df7d3a1e796aab4e4222b5ee333e Author: Brian Raney Date: Wed Jul 21 17:05:09 2010 -0700 transfer hg18 page over to hg19 commit 830a7f44507e5cea5699fdb4851c99f5db3d584a Merge: 2ea60a7 7bf7dd2 Author: Venkat Malladi Date: Wed Jul 21 16:47:28 2010 -0700 Merge branch 'master' of vsmalladi@hgwdev.cse.ucsc.edu:/data/git/kent commit 2ea60a7afe2d248c88df3fd880ff90d7362825ba Author: Venkat Malladi Date: Wed Jul 21 16:47:18 2010 -0700 Removed old track for HAIB Methyl RRBS labeled encHaibRrbs from trackDb.wgEncode.ra commit 7bf7dd239d20b85a9237233582fcc6c6cb9b388b Merge: edf22f0 eefb0fe Author: Brian Raney Date: Wed Jul 21 16:40:45 2010 -0700 Merge branch 'master' of braney@hgwdev.cse.ucsc.edu:/data/git/kent commit edf22f0db87da4fe79fbe24fa4383b9cf9104cf7 Author: Brian Raney Date: Wed Jul 21 16:40:29 2010 -0700 take metadata out of trackDb commit eefb0fe22f35cd405a5c8a68f3a698687c807f17 Merge: a5c0bbc 45cec41 Author: Cricket Sloan Date: Wed Jul 21 16:29:13 2010 -0700 Merge branch 'master' of cricket@hgwdev.cse.ucsc.edu:/data/git/kent commit 45cec414575c42aca7e20797683c654b55ec6994 Merge: c80635f 9307d76 Author: Brian Raney Date: Wed Jul 21 16:13:26 2010 -0700 Merge branch 'master' of braney@hgwdev.cse.ucsc.edu:/data/git/kent commit 9307d7694a025376207749bc97934eaabb8cc634 Merge: cd8eec9 e052c53 Author: Krishna Roskin Date: Wed Jul 21 16:12:14 2010 -0700 Merge branch 'master' of krish@hgwdev.cse.ucsc.edu:/data/git/kent commit cd8eec9311376979c05cbb87040b0cef331a2908 Author: Krishna Roskin Date: Wed Jul 21 16:11:55 2010 -0700 .gz exntensions are now removed from the files commit c80635f67a8272ddd0be2bc3276886213815af79 Author: Brian Raney Date: Wed Jul 21 16:11:32 2010 -0700 transfer hg18 page over to hg19... commit c58991387555b4571aab3fb8673f27c8d9ee04d8 Merge: f9c2ccd e052c53 Author: b0b Date: Wed Jul 21 16:04:59 2010 -0700 Merge branch 'master' of kuhn@hgwdev.cse.ucsc.edu:/data/git/kent commit f9c2ccd0c9ba80d55466c5957dd05caccce38d5a Author: b0b Date: Wed Jul 21 16:02:46 2010 -0700 added announcement of free workshops and archived that and happy birthday genome message commit e052c53ea0a5d238f2dc78ccba13d890d2d16952 Author: Brian Raney Date: Wed Jul 21 16:02:18 2010 -0700 oops, this was supposed to be in there a while ago commit 06045567d5fab0b276e28beeb213746cfabdcc1e Author: Brian Raney Date: Wed Jul 21 15:43:15 2010 -0700 take out spurious comment commit 08e781b35179f4c238b17e235823dae484a42e39 Merge: 128c324 d665577 Author: Brian Raney Date: Wed Jul 21 15:32:00 2010 -0700 Merge branch 'master' of braney@hgwdev.cse.ucsc.edu:/data/git/kent commit 128c324d41b1457ac967d1dccc35449880420f91 Author: Brian Raney Date: Wed Jul 21 15:31:16 2010 -0700 fix gff3ToPsl and add some test files commit a5c0bbc4fe14f0c5d7e40ee2d1d5d2389667c479 Merge: fcb17d7 d665577 Author: Cricket Sloan Date: Wed Jul 21 14:45:47 2010 -0700 Merge branch 'master' of cricket@hgwdev.cse.ucsc.edu:/data/git/kent commit d6655777544400ed0e0bafb38f94a16622b63e9b Author: Krishna Roskin Date: Wed Jul 21 14:39:40 2010 -0700 added missing makefile commit c2d7c4879a2014f50809be0c336fbe9d18141083 Merge: 446e8d4 c2e00c9 Author: Krishna Roskin Date: Wed Jul 21 14:29:07 2010 -0700 Merge branch 'master' of krish@hgwdev.cse.ucsc.edu:/data/git/kent commit 446e8d4a5847b0938992ddc0d75ffb3b4e3bd457 Author: Krishna Roskin Date: Wed Jul 21 14:26:54 2010 -0700 program to make a DDF given a composite name and a list of metadata vars commit c2e00c9fac1df5cb61c6b1a0bac2d55c383b95c2 Merge: 095dd63 e8d600b Author: Chin Li Date: Wed Jul 21 14:17:43 2010 -0700 Merge branch 'master' of chinhli@hgwdev.cse.ucsc.edu:/data/git/kent commit 095dd630bc6630ad9f757ac267012de9b6aa187b Author: Chin Li Date: Wed Jul 21 14:17:20 2010 -0700 start Phylogenetic commit e8d600bee9243c136ebb4d9069345d0c4191a10e Author: Hiram Clawson Date: Wed Jul 21 14:15:00 2010 -0700 masked sequence available commit 7d08d6f78713d0dfeb42eaf15d48fdb331f44304 Merge: 1a26cc0 1f8e628 Author: Hiram Clawson Date: Wed Jul 21 14:14:20 2010 -0700 Merge branch 'master' of hiram@hgwdev.cse.ucsc.edu:/data/git/kent commit 1a26cc04a12ca65478d3a1051ea88d34c766f183 Author: Hiram Clawson Date: Wed Jul 21 14:14:13 2010 -0700 adding Ensembl genes v58 to calJac3 and phyloP30way to mm9 commit 1f8e628c442970dd1bc9243dff920a7319a2ebeb Author: Venkat Malladi Date: Wed Jul 21 13:56:23 2010 -0700 Commented out the Revision history line that was causing problems commit 86bb4b8c094deac6c74f0dd95f0e25095456ee7e Merge: ba2dfbd 4bf4bac Author: Venkat Malladi Date: Wed Jul 21 13:28:10 2010 -0700 Merge branch 'master' of vsmalladi@hgwdev.cse.ucsc.edu:/data/git/kent commit ba2dfbd7c08beffefb53e600c3c842e0f239336f Author: Venkat Malladi Date: Wed Jul 21 13:28:00 2010 -0700 Updated the validateFiles for fastq to check 1 in 1000 rather than the first 1000 lines, which was breaking (refer to Bug:390) commit 4bf4bacbf0cb55ee5fbb87dd808a0b8bfd2bb492 Author: vanessa Date: Wed Jul 21 10:25:24 2010 -0700 reworded some sentences on the regulation track description pages and fixed the redirected link to standford commit f803ec71fde5bf88f73d9bbc7a6b134ec14705a5 Author: katrina Date: Wed Jul 21 09:52:48 2010 -0700 added html line to wgEncodeRegMarkPromoter block of Regulation Super Track because html desc is not equal to track line of trackDb block commit b8a467492b8cd2a8a36de9574af2cc9a925f4fc6 Author: Chin Li Date: Wed Jul 21 09:20:41 2010 -0700 Done gene annotation to multiz6way commit 18ee3a9593c56fe9974802508660e21baa756d0d Merge: 0a1c46f 27aa0ce Author: Antonio Coelho Date: Wed Jul 21 09:18:56 2010 -0700 Merge branch 'master' of antonio@hgwdev.cse.ucsc.edu:/data/git/kent commit 27aa0cea2771c2119b9ebd37f728daf87848aef8 Author: Galt Barber Date: Wed Jul 21 08:00:32 2010 -0700 "Encode release log update" commit 5dbabd0ab6d124f462b4426d402da60d8a7fdc93 Author: Galt Barber Date: Wed Jul 21 08:00:15 2010 -0700 "Release log update" commit abb70518541bd3084c8e1d2479fdb1f6161e5a33 Author: Brian Raney Date: Tue Jul 20 16:37:54 2010 -0700 fix up some of the metadata commit d0182967c95f7e475882824e2fd4c7b1adb50f60 Merge: 3229b0c 32277ce Author: Brian Raney Date: Tue Jul 20 16:24:33 2010 -0700 Merge branch 'master' of braney@hgwdev.cse.ucsc.edu:/data/git/kent commit 3229b0cd5c76cbcc27facec5c8f05a337a943495 Author: Brian Raney Date: Tue Jul 20 16:23:39 2010 -0700 add new utility, gff3ToPsl that converts GFF3 files with CIGARs in GAP attributes commit fcb17d754d6847700698f567d6344e8b06676347 Author: Cricket Sloan Date: Tue Jul 20 15:55:45 2010 -0700 This was really just a rename that should have been a git mv. commit 0a1c46f50dfe9a8ac0dc5b278c50319c2091eea0 Merge: b74f1cb 32277ce Author: Antonio Coelho Date: Tue Jul 20 15:51:15 2010 -0700 Merge branch 'master' of antonio@hgwdev.cse.ucsc.edu:/data/git/kent commit b74f1cb585a540786d5cf4c88c19cb51a0dc530e Author: Antonio Coelho Date: Tue Jul 20 15:51:09 2010 -0700 adding some info to the description commit 32277ce6f460242fe54dd251d13e0029c5ac5ceb Author: katrina Date: Tue Jul 20 15:47:35 2010 -0700 fixed typo, a period mid-sentence commit fb784806fcee0e9116005018d0fe61b098a815b4 Author: Cricket Sloan Date: Tue Jul 20 15:09:33 2010 -0700 The RRBS tracks were in an enc file instead of a wgEncodefile. I moved them from one to the other. There is one more file that should be in this commit which is the newly labeled wgEncodeHaibMethylRrbs.html. There are new tracks in the RRBS trackDb.ra and there is a new include statement in the main trackDb. commit e2fe3fac2d080c5c6a4bdc6e08b1cbfc3e99ffef Merge: f8108e4 57cd640 Author: katrina Date: Tue Jul 20 15:07:28 2010 -0700 Merge branch 'master' of hgwdev:/data/git/kent commit f8108e4585dfb8f97bdbc91e770df53dea8c849a Author: katrina Date: Tue Jul 20 15:07:15 2010 -0700 udpated news: +2 items to 3/18 post, +2 new posts, -2 posts from index.html one had be added to newsarch.html, collapsed 2 posts & added full posts to newsarch.html commit 57cd640db17c4b3999b14802942a04d40501a4ac Merge: aa751f5 6d2e60d Author: Venkat Malladi Date: Tue Jul 20 15:05:27 2010 -0700 Merge branch 'master' of vsmalladi@hgwdev.cse.ucsc.edu:/data/git/kent commit aa751f5d30d4fb72690cd26c6e4fa3e3ed5e69c1 Author: Venkat Malladi Date: Tue Jul 20 15:05:14 2010 -0700 Updated the Mouse cell type controlled vocabulary to be consistent with what was registered as well as update the CGIs to display the correct headers for mouse Cell Type commit 6d2e60dbe6cc688f3585a769d0fb54fdbfe16f14 Merge: 48ed828 93f1455 Author: Cricket Sloan Date: Tue Jul 20 15:05:10 2010 -0700 Merge branch 'master' of cricket@hgwdev.cse.ucsc.edu:/data/git/kent commit 48ed828b9cc272fca5355b120e777925c1cba398 Author: Cricket Sloan Date: Tue Jul 20 15:03:34 2010 -0700 This is a modern daf for the Yale RNA seq data that includes a description of the ddf and updates for hg19 (bam, bigwig) and the addition of rnaExtract and treatment commit 93f14558741adbb5dcd7097b81763de4b613eef3 Author: Chin Li Date: Tue Jul 20 15:01:17 2010 -0700 bosTau4 LIFTOVER to bosTau5 commit 68e1c536e9f1e324e0348aa75ddb827965ad74f6 Author: Venkat Malladi Date: Tue Jul 20 14:01:24 2010 -0700 Changed OpenChromFaire to OpenChromDnase and visversa to be consistent with the data that is within each ra file commit fabdd17d8d99160198dd721325c0ae916094ba54 Author: Donna Karolchik Date: Tue Jul 20 12:51:21 2010 -0700 Added bigwig pub. Updated Epub refs that now have print versions. commit 9d0b2cc7631ccd1128112a22598942692a8d1427 Merge: fd18cae 1f92e5a Author: Galt Barber Date: Tue Jul 20 11:12:53 2010 -0700 Merge branch 'master' of galt@hgwdev.cse.ucsc.edu:/data/git/kent commit fd18caed1c611d3359b9de19a886cb5af758818b Author: Galt Barber Date: Tue Jul 20 11:12:38 2010 -0700 fixing cross-post bug in show-sizes for add (edit already worked) commit 1f92e5a503ef6f6fe09ac7bf5551919ee53ba92d Author: Venkat Malladi Date: Tue Jul 20 09:10:11 2010 -0700 Updated short labels and display standards for the UW DNaseI track commit 2a39f0b18c5015e667881db9a5efebcd8948f96e Author: Galt Barber Date: Tue Jul 20 08:00:13 2010 -0700 "Encode release log update" commit b2977c43e09dba6f48691f049be71573d4950f63 Author: Galt Barber Date: Tue Jul 20 08:00:11 2010 -0700 "Release log update" commit 9cb7b50e7cbd19989774b04e5f8b6c0332939be5 Merge: 8167ab9 480ef94 Author: Cricket Sloan Date: Tue Jul 20 06:41:48 2010 -0700 Merge branch 'master' of cricket@hgwdev.cse.ucsc.edu:/data/git/kent commit 8167ab9b390b7c4af61af1c357859fb7470a0fa0 Author: Cricket Sloan Date: Tue Jul 20 06:40:43 2010 -0700 This DAF is updated to look like what we have actually been using with Colin and to add the Transfrags view. commit 480ef9433b12d277fd3b2e4cfcf02742c49095e3 Author: Galt Barber Date: Mon Jul 19 18:13:29 2010 -0700 "New version number v236" commit 0b5a8f8bdc602e8767732f76bc6a55910590e70f Merge: ce2478a 8f4902e Author: Galt Barber Date: Mon Jul 19 18:12:49 2010 -0700 Merge branch 'master' of hgwdev:/data/git/kent commit ce2478a10c5b9696651c3083c7f5e6cf55c56869 Author: Galt Barber Date: Mon Jul 19 18:12:44 2010 -0700 v236 final build commit 8f4902e5671ff9bf23d8c8b8c05acf462b6c63e2 Merge: fc1ae7b b354a5b Author: Chin Li Date: Mon Jul 19 16:13:25 2010 -0700 Merge branch 'master' of chinhli@hgwdev.cse.ucsc.edu:/data/git/kent commit fc1ae7b5f87c611bf489b210d10de7f54863eeac Author: Chin Li Date: Mon Jul 19 16:13:17 2010 -0700 bosTau4 to bosTau5 liftOver commit b354a5beaf3ba50a7a5109d20d53fd3905ca0eaf Merge: b12b453 90bfd66 Author: Larry Meyer Date: Mon Jul 19 15:44:08 2010 -0700 Merge branch 'master' of larrym@hgwdev.cse.ucsc.edu:/data/git/kent commit b12b4534d4ee7f453368d4ad7426192bab5dfd5d Author: Larry Meyer Date: Mon Jul 19 15:43:41 2010 -0700 fix spacing in find tracks commit b654366a009176d5cc97bf8867f8a31b080af20f Author: Larry Meyer Date: Mon Jul 19 15:42:46 2010 -0700 move TRACK_SEARCH #define to inc/searchTracks.h commit 4b1d961ff5f4f12b43fa09bb5f046b71c8849362 Merge: 460b705 90bfd66 Author: Chin Li Date: Mon Jul 19 15:28:34 2010 -0700 Merge branch 'master' of chinhli@hgwdev.cse.ucsc.edu:/data/git/kent commit 90bfd66fd7a68312ec257cc4c18634d7a4a5d045 Merge: 42b3507 0be6b80 Author: Venkat Malladi Date: Mon Jul 19 12:00:22 2010 -0700 Merge branch 'master' of vsmalladi@hgwdev.cse.ucsc.edu:/data/git/kent commit 42b3507a4fe55102b22fb38cf2b4390c888f8bb1 Author: Venkat Malladi Date: Mon Jul 19 12:00:09 2010 -0700 Updated UW Histone, labels and display to be more standardized across supertrack and ENCODE tracks commit 0be6b805ddd3d6bc44a14a84a2466f65a2207de4 Author: Tim Dreszer Date: Mon Jul 19 11:06:32 2010 -0700 Added beginning of common poupBox and working embedBox for ajax retreived cfg dialogs. commit 1d117a71a704be36027f6781fc393f0f0d2b2c0b Author: Tim Dreszer Date: Mon Jul 19 10:50:56 2010 -0700 Fixed dimZ bug that Jim noticed. Also cleand up failed nesting commit 4685cf6ff5f446bf4c46f72973a6337b958a70bb Author: Galt Barber Date: Mon Jul 19 08:00:12 2010 -0700 "Encode release log update" commit e60cb8d07a78aefd47d104743221c1d1d4d65072 Author: Galt Barber Date: Mon Jul 19 08:00:10 2010 -0700 "Release log update" commit afe39cd4f55dad8db737277a925def827d1ac061 Author: Larry Meyer Date: Mon Jul 19 01:51:49 2010 -0700 oops; I checked in previous copy with TRACK_SEARCH turned on commit cce01e654ee537c366412b2778f6e5bf9e0a1935 Author: Larry Meyer Date: Mon Jul 19 01:43:31 2010 -0700 modify temporary comments list commit 797ca805eed66de60efa2ed7131e4ae36e021608 Author: Larry Meyer Date: Mon Jul 19 01:15:05 2010 -0700 move #define searchTracks to searchTracks.h commit 1167175c82cbc78603658dfb292159b442e4efdf Author: Larry Meyer Date: Mon Jul 19 01:14:14 2010 -0700 add searchTracks.o commit e303a64fd3635a40f19404d99d0a0ceb7af5a352 Author: Larry Meyer Date: Mon Jul 19 01:13:46 2010 -0700 add #define searchTracks commit 65b9478517a5e4746f85c4ff7843bf67891d1580 Author: Larry Meyer Date: Mon Jul 19 01:12:38 2010 -0700 add #include searchTracks.h commit 2aba522ac4e2ab69f305741ec4901a8446957fa9 Author: Larry Meyer Date: Mon Jul 19 01:11:42 2010 -0700 add find tracks button commit c92348fec33dbaaa69db44584a6105ddee6d97bb Author: Larry Meyer Date: Mon Jul 19 01:11:05 2010 -0700 add find tracks button commit c58425da751d6b3bfc23fd8de04f4e24187f2f63 Author: Larry Meyer Date: Mon Jul 19 00:56:00 2010 -0700 searchTracks routines which are shared b/n CGIs commit bba925c6dddbab2de7a7c6a2c073ebb8ffc70ebc Author: Larry Meyer Date: Mon Jul 19 00:55:09 2010 -0700 refactor some code into lib/searchTracks.c and some code-review changes commit 75334660cbef10d907d38cc402e5e2c2502bc759 Author: Larry Meyer Date: Mon Jul 19 00:54:29 2010 -0700 move find tracks to the left and only shown when functionality is supported for this db commit dd950b24f294de251620f159358b1fdf593147d0 Merge: 425fe0a 1e47b8a Author: Larry Meyer Date: Mon Jul 19 00:28:04 2010 -0700 Merge branch 'master' of larrym@hgwdev.cse.ucsc.edu:/data/git/kent into mutationClassifier commit 425fe0ac9cdc7f91527b942b83d51fda439dcde5 Author: Larry Meyer Date: Mon Jul 19 00:27:41 2010 -0700 add dnaMotifBitScoreWithMark0Bg commit 06a402de4866b1a6190865851284edcda6cab3be Author: Larry Meyer Date: Mon Jul 19 00:26:21 2010 -0700 default to mark0 for background commit 7cc2ad1ed09ac992db9cd5d783e871cbdba4dba3 Author: Larry Meyer Date: Mon Jul 19 00:25:27 2010 -0700 add dnaMotifBitScoreWithMark0Bg commit 6352cbdc4cd4e1b2585243f0eb315e376daa7069 Author: Larry Meyer Date: Mon Jul 19 00:23:49 2010 -0700 default to markov0 for background commit 1e47b8a3ccdb322e1da667fe3b6d168f83f183e2 Author: Galt Barber Date: Sun Jul 18 08:00:21 2010 -0700 "Encode release log update" commit a5a8bed22345a1b0ba8c31e81d6e56ef97f12502 Author: Galt Barber Date: Sun Jul 18 08:00:19 2010 -0700 "Release log update" commit 081d9191cc522c84e7798568839f1482ee58469a Merge: cfa0444 e7ffa0b Author: Mark Diekhans Date: Sat Jul 17 15:05:02 2010 -0700 Merge branch 'master' of hgwdev.cse.ucsc.edu:/data/git/kent commit cfa04440936a420d04f03ee5a6ea1db483dcc950 Author: Mark Diekhans Date: Sat Jul 17 15:01:01 2010 -0700 added test case from Sanger bug report commit e7ffa0be3549d200bf1192d8250c05100699e15b Author: Galt Barber Date: Sat Jul 17 08:00:23 2010 -0700 "Encode release log update" commit 6ba7288c7c5a9aacbb4636cf2fbdff4b431d17a9 Author: Galt Barber Date: Sat Jul 17 08:00:21 2010 -0700 "Release log update" commit 989fb68507ab39a21bbc2d1292cf654c841c55ee Merge: af5373e 3ea99d8 Author: Brian Raney Date: Fri Jul 16 17:20:30 2010 -0700 Merge branch 'master' of braney@hgwdev.cse.ucsc.edu:/data/git/kent commit af5373e00b567548eb2f85f0ccb75041a3a67064 Author: Brian Raney Date: Fri Jul 16 17:19:55 2010 -0700 add new datasets to HaibMethylSeq commit 3ea99d8f4e1adf1721bf383deddb4ce6d86cf7a2 Author: Tim Dreszer Date: Fri Jul 16 16:49:25 2010 -0700 Chagning dimZ to dimA to avoid bug in 3-state code commit 2c51828e984b15350188d75e9dbabb2025ca2af0 Author: Tim Dreszer Date: Fri Jul 16 15:01:19 2010 -0700 Fix obscure bug where apostophe in title was interpreted as close quote - thus screwing up html interpretation commit fb9c616d72acdfd0c401ac9cf6fca5b908e9e084 Author: Galt Barber Date: Fri Jul 16 12:30:37 2010 -0700 fixing path for hgcentral.sql push commit 6b91abc699a37a9e09a5d4a8f8b67c9b97d9c784 Author: katrina Date: Fri Jul 16 10:33:03 2010 -0700 changed URL from hard-coded to relative link commit e414939fa196e675d407a6ad0577462a7f269372 Merge: 7597da3 cfac70b Author: Cricket Sloan Date: Fri Jul 16 09:57:11 2010 -0700 Merge branch 'master' of cricket@hgwdev.cse.ucsc.edu:/data/git/kent commit 7597da39b16483a73d8800cc0ac394f16bf81091 Author: Cricket Sloan Date: Fri Jul 16 09:55:59 2010 -0700 Adding the new caltech-RNA seq tracks and fixing cv.ra to comment out ripTgtProtiens until we are ready commit cfac70b29081d35f28828f305877728020d16062 Author: Galt Barber Date: Fri Jul 16 08:00:24 2010 -0700 "Encode release log update" commit bc2e1eef3392c9dea552e777eca862aeaf81c1ff Author: Galt Barber Date: Fri Jul 16 08:00:23 2010 -0700 "Release log update" commit 8c2c46095f296f26417e04556cf09d821a84f165 Author: mary Date: Thu Jul 15 17:42:31 2010 -0700 adding conservation track for danRer6 to the front page as a small bit (that's why edited newsarch too) commit 362d963dde5012d44e844fdd96464c85e51e0b43 Author: Fan Hsu Date: Thu Jul 15 16:09:14 2010 -0700 Refined hgIkmc processing to deal with some troublesome records. commit 460b7054e4e637916bd1a50ccc1a782488d16519 Merge: 6031775 0d33ef0 Author: Chin Li Date: Thu Jul 15 15:33:41 2010 -0700 Merge branch 'master' of chinhli@hgwdev.cse.ucsc.edu:/data/git/kent commit 60317759f66962c36b912a9d747527287cd34d26 Author: Chin Li Date: Thu Jul 15 15:28:44 2010 -0700 Initial setup for bosTau5. commit 0d33ef0196db23c9da713b0747c649dfa81250ee Merge: c5fafbf 4678e13 Author: Hiram Clawson Date: Thu Jul 15 15:27:24 2010 -0700 Merge branch 'master' of hiram@hgwdev.cse.ucsc.edu:/data/git/kent commit c5fafbf3212296260bff443a8c0346e4b4cbab2b Author: Hiram Clawson Date: Thu Jul 15 15:27:21 2010 -0700 adding phyloP tracks to cons30way composite commit fe8ca958dc8ebb9485128dac46179fe79a59c22d Author: Chin Li Date: Thu Jul 15 15:26:52 2010 -0700 Initial descriptions for bosTau5. commit eddfa467e0fe5dce19171b128203ec065eee3759 Author: Hiram Clawson Date: Thu Jul 15 15:25:49 2010 -0700 initial content from existing multiz30way html and hg19 cons46way html commit 7cf67d16e3b64e9bd2205be9ce991789f95a3c94 Author: Chin Li Date: Thu Jul 15 15:23:09 2010 -0700 Added bosTau5 to DBS. commit 4678e136a80897bb0e5496f733340a4ddd7eb5b3 Merge: 7f4efe6 4cfed73 Author: Brooke Rhead Date: Thu Jul 15 15:11:44 2010 -0700 Merge branch 'master' of rhead@hgwdev.cse.ucsc.edu:/data/git/kent commit 7f4efe66d14a1b90228b22c8fb4cc17c8c6b678d Author: Brooke Rhead Date: Thu Jul 15 15:10:54 2010 -0700 Reworded slightly. commit 4cfed7352ab1194ab2a7a4119317e9582e2041a8 Author: Brian Raney Date: Thu Jul 15 12:35:01 2010 -0700 add -f option to rm command for metaDb file commit 92ee29404f955215a689e56a9bde863fa21caf30 Merge: 622adde 51ef15e Author: Hiram Clawson Date: Thu Jul 15 12:07:14 2010 -0700 Merge branch 'master' of hiram@hgwdev.cse.ucsc.edu:/data/git/kent commit 622adde3bd4ed6ad0be3cb67f429caf02ee20cfd Author: Hiram Clawson Date: Thu Jul 15 12:06:38 2010 -0700 add comment about install of hgRenderTracks commit 51ef15e04750c1d6e184e6fd7d12986f0e151967 Author: Fan Hsu Date: Thu Jul 15 11:49:57 2010 -0700 Remove upper case of the warning message. commit 6cfcc3d4ab7c018edeccb3919625f8aa313bc046 Merge: 03ff907 e988041 Author: Hiram Clawson Date: Thu Jul 15 11:35:14 2010 -0700 Merge branch 'master' of hiram@hgwdev.cse.ucsc.edu:/data/git/kent commit 03ff9079c7c8418edd2db605d825968977b74c05 Author: Hiram Clawson Date: Thu Jul 15 11:35:05 2010 -0700 working on phyloP for 30way commit 9f2575b4b5d3c6e2b02f6860a1a062188d4fa2b8 Author: Hiram Clawson Date: Thu Jul 15 11:31:38 2010 -0700 adding quality track as a bigWig commit ed1762344308f294f60ae7253f8ac95af191490d Author: Hiram Clawson Date: Thu Jul 15 11:30:56 2010 -0700 adding quality track commit e988041a8e3237bd2c3e0f41dce2788d29a03090 Author: vanessa Date: Thu Jul 15 09:47:40 2010 -0700 change tags to release alpha,beta for regulation track commit 9de16e0d7a43e7f24a5c62249895bb38d904b690 Merge: d129374 fc3735d Author: katrina Date: Thu Jul 15 09:06:00 2010 -0700 Merge branch 'master' of hgwdev:/data/git/kent commit d129374bd2b405ead3d3640f98166a26142c03fa Author: katrina Date: Thu Jul 15 09:05:42 2010 -0700 changed title, moved links to other cv pages to top, added mouse strains, lessened right margin, increased height of some frames commit fc3735d3cde3de46b03380d4f7f5ccd1af5477d6 Author: Fan Hsu Date: Thu Jul 15 08:28:56 2010 -0700 Made the warning message to UPPER case. commit 6366d3cd535389a174ce4f0af97d31f112567b4a Author: Galt Barber Date: Thu Jul 15 08:01:16 2010 -0700 "Encode release log update" commit e9bd744f18615923a58c9e6202b525afec45bac8 Author: Galt Barber Date: Thu Jul 15 08:00:55 2010 -0700 "Release log update" commit 42ea3c7b968339da8f4cf865740b71507c0ab4c5 Author: Tim Dreszer Date: Wed Jul 14 18:05:11 2010 -0700 Oops. These new things should be marked 'post' freeze commit 0f6da468f6e3a42085003b10e41a0ea2f2fb699a Author: Tim Dreszer Date: Wed Jul 14 17:51:55 2010 -0700 Left a in Mark's Dink buttons commit ded0a6cec652f9504929ba6be3ed9733423bff36 Merge: a98b397 af1d888 Author: Larry Meyer Date: Wed Jul 14 16:23:00 2010 -0700 Merge branch 'master' of larrym@hgwdev.cse.ucsc.edu:/data/git/kent into mutationClassifier commit a98b3972005cbad559f6351b7f5d1b6ae4bdd87f Author: Larry Meyer Date: Wed Jul 14 16:21:04 2010 -0700 check for existence of wgEncodeRegTfbsClusteredMotifs commit af1d888aa9bcc9578c720d78438b792e63a5d39a Merge: 3e07228 07ed898 Author: Brian Raney Date: Wed Jul 14 16:14:07 2010 -0700 Merge branch 'master' of braney@hgwdev.cse.ucsc.edu:/data/git/kent commit 3e07228efbe0c79c7eb4b7ba3ec217ca3b18ddfe Author: Brian Raney Date: Wed Jul 14 16:13:41 2010 -0700 add new tracks commit 07ed8984aac5f2eb4f508b6e0b56a1864e540534 Merge: 52481d9 5632522 Author: Larry Meyer Date: Wed Jul 14 16:02:14 2010 -0700 Merge branch 'master' of larrym@hgwdev.cse.ucsc.edu:/data/git/kent into mutationClassifier commit 563252294bfa6e33c1b7a301488717a901bd36ac Merge: 2b72eba 548c993 Author: katrina Date: Wed Jul 14 15:59:04 2010 -0700 Merge branch 'master' of hgwdev:/data/git/kent commit 52481d9245e86f7eb9c4531d8d5f8b49761ff9c4 Author: Larry Meyer Date: Wed Jul 14 15:59:02 2010 -0700 ui tweaking commit a90a62f73156e667a51fc2c9766eac876ec3a457 Author: Larry Meyer Date: Wed Jul 14 15:57:32 2010 -0700 look for high-confidence motifs in wgEncodeRegTfbsClusteredMotifs commit 548c993e5f6abbe7304867bacee362a4cfb35b2e Author: Tim Dreszer Date: Wed Jul 14 15:57:08 2010 -0700 Added 2 more cell lines for Broad commit 09d2601a9c72f43c32a33a76bd981c8d5099699e Author: Tim Dreszer Date: Wed Jul 14 15:55:04 2010 -0700 Metadata update for resubmitted BAMs and 2 more cell lines commit 2b72ebace320cd497b57755bd0572aa2195e0618 Merge: 5d4ca56 6cd3616 Author: katrina Date: Wed Jul 14 15:52:56 2010 -0700 Merge branch 'master' of hgwdev:/data/git/kent commit 1af29ab7bc8edee6acae40155a29fc1cf03b15f8 Author: Larry Meyer Date: Wed Jul 14 15:41:00 2010 -0700 changeSearchVisibilityPopups commit 6cd361609bc30bedb1f66895e74b508778433ce4 Merge: cce0c4a f6c6fa4 Author: Krishna Roskin Date: Wed Jul 14 15:24:14 2010 -0700 Merge branch 'master' of krish@hgwdev.cse.ucsc.edu:/data/git/kent commit ff9ceeb569c6600937f29fa839da70d06bf904bc Author: Larry Meyer Date: Wed Jul 14 15:12:50 2010 -0700 change cgiMakeDropListClassWithStyleAndJavascript to tolerate all permuations of NULL for parameters commit b821b7df6dab3601709da49c089e08d41961e7e8 Author: Larry Meyer Date: Wed Jul 14 15:09:07 2010 -0700 add motifMultipleHitsSection commit f6c6fa4f9495c62d270299d1bdfa1b8abe750dea Merge: 08b0320 3612642 Author: Brian Raney Date: Wed Jul 14 15:08:53 2010 -0700 Merge branch 'master' of braney@hgwdev.cse.ucsc.edu:/data/git/kent commit 08b0320012cb02af455d1fcf1ff925e521570af6 Author: Brian Raney Date: Wed Jul 14 15:08:37 2010 -0700 add gisDnaPet commit cce0c4afed80cf9b9fb6a21298a86031f2244eb5 Author: Krishna Roskin Date: Wed Jul 14 14:57:40 2010 -0700 added wgEncodeYaleRNAseq exp vars commit 36126428b0627699dec4dc5e118c612c03aa78f7 Merge: cfeb576 e62e33a Author: Antonio Coelho Date: Wed Jul 14 14:26:29 2010 -0700 Merge branch 'master' of antonio@hgwdev.cse.ucsc.edu:/data/git/kent commit e62e33a8e95e5861de156718a4fff29f98548731 Author: Brian Raney Date: Wed Jul 14 14:21:36 2010 -0700 get rid of hgLoadMafSummary during cgi build commit cfeb576ee9d055f09bdf9306623870d5b0ea60e9 Author: Antonio Coelho Date: Wed Jul 14 14:17:42 2010 -0700 aesthetic changes to decipher description commit d118f49cb908b0a85ca89d5095f78b729f011998 Author: Brian Raney Date: Wed Jul 14 13:01:45 2010 -0700 rm metaDb file commit 01d297fb10a969d33064c2d1bdc4fed7f734a256 Author: Brian Raney Date: Wed Jul 14 12:56:40 2010 -0700 rm metaDb file after building metaDb commit 6b895733f51587a510d5e89c9e77c1c7d98635a3 Merge: e3fc14d 70294a0 Author: Brian Raney Date: Wed Jul 14 12:50:21 2010 -0700 Merge branch 'master' of braney@hgwdev.cse.ucsc.edu:/data/git/kent commit e3fc14d1474260fc65cd43777d4dce602b7c07d7 Author: Brian Raney Date: Wed Jul 14 12:48:04 2010 -0700 add wgEncodeGisDnaPet commit 70294a048f471b3ee53f63789b02322596197ea0 Author: Tim Dreszer Date: Wed Jul 14 11:41:35 2010 -0700 NH-A is no longer provisional commit 996620d1eca2cf45f6498241431aab88f4bd627e Merge: 8acc348 70afe44 Author: Hiram Clawson Date: Wed Jul 14 10:54:36 2010 -0700 Merge branch 'master' of hiram@hgwdev.cse.ucsc.edu:/data/git/kent commit 8acc348768346ca798890c1fc88c7ecc0b1045e4 Author: Hiram Clawson Date: Wed Jul 14 10:53:32 2010 -0700 stray ce9 left in where db should be, code review wins commit 70afe44f10846a45c177878ae9e880612d122030 Author: Galt Barber Date: Wed Jul 14 10:36:05 2010 -0700 making sure that jobs waiting longest get first chance to run commit 5d4ca56b94dcaa6a806eebbbd80cda3d541401c3 Author: katrina Date: Wed Jul 14 08:50:20 2010 -0700 modifying page to reflect Mouse cell types (no tiers), add link to controlled vocab, link to strain info commit f4a27f273893d9fe4e4a835590a57b74183ad32a Author: katrina Date: Wed Jul 14 08:32:30 2010 -0700 split ENCODE portal leftbar into 3 sections & added links to ENCODE Mouse pages, Session Gallery, Registered Variables & Data Standards commit 630cc19823f1cf87389f809d6793bcacbef8e799 Author: Galt Barber Date: Wed Jul 14 08:01:46 2010 -0700 "Encode release log update" commit e02b9bdfd0981adf1c5082264bdf1a8b858cc161 Author: Galt Barber Date: Wed Jul 14 08:01:19 2010 -0700 "Release log update" commit daa9de4508d639a5b33a7b1c937d44e2f3aa9f68 Merge: 8189370 c2a73d1 Author: Galt Barber Date: Tue Jul 13 21:14:35 2010 -0700 Merge branch 'master' of /data/git/kent commit 818937065ab17eb5dc945c8bdd75a8a5b9920f87 Author: Galt Barber Date: Tue Jul 13 21:11:15 2010 -0700 increased expansion timeout by a factor of 10 and added better reporting of timeouts commit c2a73d1ce6542bf51b1d651458b9c340f84b06a5 Merge: 22b1c40 0655b69 Author: Fan Hsu Date: Tue Jul 13 17:20:03 2010 -0700 Merge branch 'master' of fanhsu@hgwdev.cse.ucsc.edu:/data/git/kent commit 0655b69609088a6fd7cb5cc39f78813bc2c525ec Author: Cricket Sloan Date: Tue Jul 13 16:52:17 2010 -0700 Changed all references to Yale_TFSB to Yale_TFBS commit b1813d80821643305b62b0604c479a22fb1f85ee Merge: df462dc 072e436 Author: Cricket Sloan Date: Tue Jul 13 16:47:21 2010 -0700 Merge branch 'master' of cricket@hgwdev.cse.ucsc.edu:/data/git/kent commit 072e436dfd1e645c2c5034ad2668a22836d4132c Merge: 489f78a a44aafc Author: Venkat Malladi Date: Tue Jul 13 16:34:51 2010 -0700 Merge branch 'master' of vsmalladi@hgwdev.cse.ucsc.edu:/data/git/kent commit 489f78ad80117570c6ebf6fa3ce7388f3b717925 Author: Venkat Malladi Date: Tue Jul 13 16:33:02 2010 -0700 Added 1 submission 1623 to SYDH TFBS Track commit a44aafc5bb8a589da9ce854101515dbe2ccebb1d Author: Tim Dreszer Date: Tue Jul 13 16:06:21 2010 -0700 Fix table name lookup so that it isn't too smart by half commit 22b1c405be8123c10a8a300ebe1c871d79a5ac56 Merge: e861142 3aacc72 Author: Fan Hsu Date: Tue Jul 13 16:02:33 2010 -0700 Merge branch 'master' of fanhsu@hgwdev.cse.ucsc.edu:/data/git/kent commit e861142f5417024b3b752d6a053d4a92ba817fed Author: Fan Hsu Date: Tue Jul 13 15:28:13 2010 -0700 Refined DECIPHER detailed page. commit 3aacc7236bfa46294d0609cc7b2bc1fbf0d10b51 Merge: 24381de c6f0ca5 Author: mary Date: Tue Jul 13 15:24:57 2010 -0700 Merge branch 'master' of mary@hgwdev.cse.ucsc.edu:/data/git/kent commit df462dcce8efb18a1448f417522404d81d54ed5c Merge: 43e8ca8 c6f0ca5 Author: Cricket Sloan Date: Tue Jul 13 15:21:12 2010 -0700 Merge branch 'master' of cricket@hgwdev.cse.ucsc.edu:/data/git/kent commit 43e8ca8865f0316e629c3c8f1d7cf74e3cdf329b Author: Cricket Sloan Date: Tue Jul 13 15:11:30 2010 -0700 Added growth protocol to protocols commit c6f0ca59304ac032d3012af017f97cb0b34e3de6 Merge: 7566afa 28eec44 Author: Venkat Malladi Date: Tue Jul 13 15:01:02 2010 -0700 Merge branch 'master' of vsmalladi@hgwdev.cse.ucsc.edu:/data/git/kent commit 24381debc6d1a06cdeabd0d468abc9e8035bb8aa Author: mary Date: Tue Jul 13 14:36:10 2010 -0700 removing references to conserved elements, tidying up spacing and other general edits commit 7566afaf50dd1026e8115d3c7fd5fb0e7e59fe84 Author: Venkat Malladi Date: Tue Jul 13 14:21:39 2010 -0700 Added 1 submission for Stanford/Yale Mouse Histone. Also updated all metaData and short and long labels commit 28eec44f8a2a10b85c4aa8dfd8df93372fba9c09 Author: Tim Dreszer Date: Tue Jul 13 14:17:48 2010 -0700 Non-ideal special case code to force replicate to 1 when no replicate entered for pooled data commit cc675c7d55041d7ddc40665e8d6231328c68876c Author: Tim Dreszer Date: Tue Jul 13 14:13:40 2010 -0700 Provisionally added NH-A to finish Broad's pre-AWG meeting submissions commit b0f37152b459c2c796016947ab47eb26826ba916 Merge: 33f79bf b4d86bc Author: Venkat Malladi Date: Tue Jul 13 13:32:13 2010 -0700 Merge branch 'master' of vsmalladi@hgwdev.cse.ucsc.edu:/data/git/kent commit 33f79bf97eab0a270a511b4edcd88b8f2561cd26 Author: Venkat Malladi Date: Tue Jul 13 13:29:57 2010 -0700 Added 10 new Mouse Stan/Yale TFBS Submissions. Fixed metadata for update bam files commit b4d86bcdb8b9b552036d876405eb4624dcf53bc5 Author: Galt Barber Date: Tue Jul 13 12:40:09 2010 -0700 more darned changes requested by sponsor commit 62f796e85264d98c51c9804d7e09f20e18f26e3d Merge: 227c726 e2665e9 Author: Antonio Coelho Date: Tue Jul 13 11:18:24 2010 -0700 Merge branch 'master' of antonio@hgwdev.cse.ucsc.edu:/data/git/kent commit 227c7260618149d29db282e474093de2aba7f8e4 Author: Antonio Coelho Date: Tue Jul 13 11:15:05 2010 -0700 adding felCat4 to beta genBank ups commit e2665e9d9495df973e8086baad5703e382103864 Author: Hiram Clawson Date: Tue Jul 13 11:04:05 2010 -0700 add search spec for bacEndSingles commit b28f7a4c01d9796f4432385e326201fd022b9721 Author: Hiram Clawson Date: Tue Jul 13 10:57:45 2010 -0700 fixup bare use of make instead use MAKE commit 2dd8d47846f8c7cf1d971af5d990573d08701b69 Author: Hiram Clawson Date: Tue Jul 13 10:54:44 2010 -0700 adding marmoset bac ends commit 486d980cfb2ead6665e798b55fe7233be303235a Author: Galt Barber Date: Tue Jul 13 10:30:22 2010 -0700 updating DARNED rna editing trackDb.ra and descr html as requested by sponsor commit 3172eaf836b75c94590766066d99afe3bb14fc4e Merge: 6ad69ec 1a76f44 Author: Mark Diekhans Date: Tue Jul 13 08:14:28 2010 -0700 Merge branch 'master' of hgwdev.cse.ucsc.edu:/data/git/kent commit 1a76f445633c8bcddf5d2c652d61803f09adc129 Author: Galt Barber Date: Tue Jul 13 08:00:58 2010 -0700 "Encode release log update" commit 00c5bcd1a837b4e8da1653499f7f55d714d5f6d0 Author: Galt Barber Date: Tue Jul 13 08:00:55 2010 -0700 "Release log update" commit 102a696b543c1a2b08401895aea767b6113449b7 Merge: 3f1db6a 7b514b8 Author: Galt Barber Date: Mon Jul 12 17:43:46 2010 -0700 Merge branch 'master' of hgwdev:/data/git/kent commit 3f1db6a6f457afbb0126aa8bae2062898ec3d130 Author: Galt Barber Date: Mon Jul 12 17:43:31 2010 -0700 v236 preview commit 7b514b86ee40f5d2ad82e4e1cc38409f5de61cdb Merge: f4efca5 0acbbdc Author: Cricket Sloan Date: Mon Jul 12 15:49:53 2010 -0700 Merge branch 'master' of cricket@hgwdev.cse.ucsc.edu:/data/git/kent commit f4efca59ccc56508de96b1053ace7a145bb93267 Author: Cricket Sloan Date: Mon Jul 12 15:48:09 2010 -0700 Made the changes for the long labels for this track LongPolyA to PolyA+ commit 0acbbdce85b900731876343409c968957eac3ba6 Author: Kate Rosenbloom Date: Mon Jul 12 15:37:03 2010 -0700 Adding geo terms for seqPlatform entries and making the term tag more concise commit 1a2c8727a9ada3805939a7d35a544906d56ad51a Merge: 0f712b5 e70cc36 Author: Larry Meyer Date: Mon Jul 12 15:30:38 2010 -0700 Merge branch 'master' of larrym@hgwdev.cse.ucsc.edu:/data/git/kent into mutationClassifier commit 7c7998863cad5b7c8943c41198479bfab14c8788 Merge: 5b20446 e70cc36 Author: Jim Kent Date: Mon Jul 12 15:17:56 2010 -0700 Merge branch 'master' of kent@hgwdev.cse.ucsc.edu:/data/git/kent commit 5b204465085990ada8139c651688ac2bd215f4bf Author: Jim Kent Date: Mon Jul 12 15:13:27 2010 -0700 Taking some small steps towards implementing import of tracks from a data hub. Made trackDbFromRa take a url rather than a file as input by swapping in netLineFileOpen for lineFileOpen. Have a bunch of code that is compiled but not called (the call is ifdef'd out) that is starting to do some of the work, but that currently is crashing if ifdef'd back in. Just committing at this point so that I can do a git pull and grab everyone elses changes. I'm still learning how to work with half-baked things in git. ;-) commit e70cc369d11b4081652625730d7be64ef68890f6 Author: Galt Barber Date: Mon Jul 12 15:00:40 2010 -0700 adding DARNED the DAtabase of RNa EDiting commit 76f8c0f0652b55bceb998c71aa15b952b2e16126 Author: Jim Kent Date: Mon Jul 12 14:58:05 2010 -0700 Fixed indentation. commit faa2aeb92c59aba0eac7af7c0855ee0b2a364be7 Author: Galt Barber Date: Mon Jul 12 14:36:37 2010 -0700 making the ftp list be sorted as requested commit 19dddcc066867b1b67e5f32973f38a5fefd32497 Merge: 24c7771 c969178 Author: Galt Barber Date: Mon Jul 12 14:10:25 2010 -0700 Merge branch 'master' of galt@hgwdev.cse.ucsc.edu:/data/git/kent commit c9691789f140b589774def065b70335fb265cf9e Merge: 9c5e28a 4477a31 Author: Hiram Clawson Date: Mon Jul 12 14:06:50 2010 -0700 Merge branch 'master' of hiram@hgwdev.cse.ucsc.edu:/data/git/kent commit 9c5e28afc537d29b604665fbb098b7a868aad0aa Author: Hiram Clawson Date: Mon Jul 12 14:06:35 2010 -0700 starting ce9, fixing up phyloP run for hg19 and running phyloP for mm9 commit 9b1f6ace8cc2ca1bfd6a9027ed34c12bce8ff371 Author: Hiram Clawson Date: Mon Jul 12 14:05:19 2010 -0700 adding bacEndCalJac3Singles commit 4477a31918b15e0e1a094c0838629f35d83f8470 Author: Larry Meyer Date: Mon Jul 12 14:03:22 2010 -0700 fix 'trackDbJson' is undefined' message reported by mary commit 0f712b5fcd72a4e55037ebcb0f7c232cdfee15ea Merge: c6faed0 c50cec1 Author: Larry Meyer Date: Mon Jul 12 13:47:33 2010 -0700 Merge branch 'master' of larrym@hgwdev.cse.ucsc.edu:/data/git/kent into mutationClassifier commit c6faed054b45f2724071c0bab32009cdabd7182b Author: Larry Meyer Date: Mon Jul 12 13:45:50 2010 -0700 pick hight scoring hit within sets of overlapping hits commit c50cec1e6860bdfb30e91f717f617e29f8452d82 Author: vanessa Date: Mon Jul 12 13:29:57 2010 -0700 fixed typo and link commit 24c77719af63cd1e6db74d965617b03a2a40c72d Author: Galt Barber Date: Mon Jul 12 13:11:00 2010 -0700 fixing help message for twoBitInfo commit e798f4d41093621881ffe875b94f90714987174e Author: Galt Barber Date: Mon Jul 12 12:12:08 2010 -0700 darned - the database of rna-editing commit 8c9b81403ce01e06b59ec7b25381cd746d416312 Merge: 43c82a4 e01835f Author: Venkat Malladi Date: Mon Jul 12 10:57:23 2010 -0700 Merge branch 'master' of vsmalladi@hgwdev.cse.ucsc.edu:/data/git/kent commit 43c82a41f810b135233d32f003ec256e20e11ca9 Author: Venkat Malladi Date: Mon Jul 12 10:57:11 2010 -0700 Tim noticed that my added category code had a hole in it and stopped some human submissions. To fix I check if category is defined. commit e01835fd92ec63ec9c210eab94acf5179e75a878 Author: vanessa Date: Mon Jul 12 10:53:03 2010 -0700 changed the longlabel for Yale RNA-seq commit a560e18dd3e95ec51419e55f300fa8d7b50237cb Merge: 1866ac8 655df2c Author: Venkat Malladi Date: Mon Jul 12 09:37:11 2010 -0700 Merge branch 'master' of vsmalladi@hgwdev.cse.ucsc.edu:/data/git/kent commit 1866ac887f70657d908b91f5936d42a07cecef52 Author: Venkat Malladi Date: Mon Jul 12 09:37:00 2010 -0700 Fixed typo in code that printed Human Cell Line column names the same as mouse. commit 655df2c16217ebd5bfe462fb88bc7d0d716ade87 Author: Galt Barber Date: Mon Jul 12 08:00:37 2010 -0700 "Encode release log update" commit e45788c36212f9f00d81ad6f66d6281ccfee1c79 Author: Galt Barber Date: Mon Jul 12 08:00:17 2010 -0700 "Release log update" commit 4962fb784599feaa4e3d52c3331a09c21d65ec60 Merge: 48cb71a a8c04b6 Author: Larry Meyer Date: Sun Jul 11 13:26:05 2010 -0700 Merge branch 'master' of larrym@hgwdev.cse.ucsc.edu:/data/git/kent into mutationClassifier commit 48cb71a2a23892700364d8cdb9e35186c016f231 Author: Larry Meyer Date: Sun Jul 11 13:25:51 2010 -0700 add update and insert methods commit 4a7eebb9d8733d4a4bfa36196e0461c3b45f235b Author: Larry Meyer Date: Sun Jul 11 13:24:16 2010 -0700 change 'multiple hits in a peak' algo to use exponential backoff of the prior commit d198a0cb03e1b0420a384edf934c5aceff785459 Author: Larry Meyer Date: Sun Jul 11 13:19:31 2010 -0700 replace mysql order by with in memory sort to get a big speedup commit a8c04b6b6540210bd7ad8be97a03e7ba4bf4419c Author: Galt Barber Date: Sun Jul 11 08:00:11 2010 -0700 "Encode release log update" commit 39c2e08726d05e36ffd3cc267f93bc0de7c48945 Author: Galt Barber Date: Sun Jul 11 08:00:09 2010 -0700 "Release log update" commit cfddca29fac8512308dddafe7dd7fc361b5a3170 Author: Larry Meyer Date: Sun Jul 11 00:59:50 2010 -0700 start adding code to look for multiple binding sites in the same peak commit ed56f1e50df82806dabc4dc9d295bf9be68ed6e0 Author: Larry Meyer Date: Sat Jul 10 14:25:37 2010 -0700 find largest scoring motif(s) in bed items commit dba61e1ddd53125ebd489db99308d00bed39697e Author: Galt Barber Date: Sat Jul 10 08:00:23 2010 -0700 "Encode release log update" commit 7b5ebc3e32454d99cb9d77bfdd85d90a0995da67 Author: Galt Barber Date: Sat Jul 10 08:00:21 2010 -0700 "Release log update" commit 4cb26a6b37d6fb9b3387967d8770fe5f4592a07b Author: Galt Barber Date: Fri Jul 9 18:16:34 2010 -0700 remove unneeded flush commit 8a6ebed93d422f9c92c8f58089c30fd585376181 Merge: 54d193c 9789889 Author: Galt Barber Date: Fri Jul 9 18:04:52 2010 -0700 Merge branch 'master' of galt@hgwdev.cse.ucsc.edu:/data/git/kent commit 9789889065a07ff41bfe48362fde4ca9f3f0f9a2 Author: Brian Raney Date: Fri Jul 9 17:02:19 2010 -0700 fix problem caused by the fact that now colors have the top bit set so they're negative in an int. commit ea6b66a7802145f90c5c6b201573cd39c6c121c1 Merge: 63df25e 48e38ea Author: Venkat Malladi Date: Fri Jul 9 17:01:21 2010 -0700 Merge branch 'master' of vsmalladi@hgwdev.cse.ucsc.edu:/data/git/kent commit 63df25e7b355baffc31d951420985dba55252640 Author: Venkat Malladi Date: Fri Jul 9 17:00:26 2010 -0700 Sample DDF for UW Mouse Samples commit ad53819c0962511b762bfccd0c25c52c8b3b14a6 Author: Cricket Sloan Date: Fri Jul 9 16:48:27 2010 -0700 This is the fix so that the SUNY track reads the Antibody table not the antibody table in cv.ra. Other changes will need to happen with this. commit b7252bad5dcd59f5b9f9b3f6d2ce1c1cced2db1d Author: Cricket Sloan Date: Fri Jul 9 16:35:07 2010 -0700 Adding the word growthProtocol to fields.ra and HAIB RRBS. I would like to validate this using the esisting growth protocol names in the cell line CV. Currently I am not validating. commit c420f6f7f9a39fb75374d772945a9e1fbc707988 Merge: 6ba5b86 48e38ea Author: Larry Meyer Date: Fri Jul 9 15:36:00 2010 -0700 Merge branch 'master' of larrym@hgwdev.cse.ucsc.edu:/data/git/kent into mutationClassifier commit 6ba5b86a404f1e76e016b5620ada9a329b638b64 Author: Larry Meyer Date: Fri Jul 9 15:33:16 2010 -0700 add pos w/n motif and distance to nearest gene to output commit 48e38ea12d1c1856cc6102a877f5952e63d01d81 Author: Fan Hsu Date: Fri Jul 9 14:59:13 2010 -0700 Added identifier hgIkmcName commit ade6e601d20a8a0c32c654f4325b9c7586e13db3 Author: katrina Date: Fri Jul 9 14:56:59 2010 -0700 added two missing tracks: Mapability and NHGRI Bi-Pro commit fd800dd36c3d6ce4b795d1379db4db0594ba6166 Merge: 8d76283 52711e1 Author: katrina Date: Fri Jul 9 14:54:09 2010 -0700 Merge branch 'master' of hgwdev:/data/git/kent commit 8d76283be0e127db88407aee091ae581f24f3821 Author: katrina Date: Fri Jul 9 14:52:19 2010 -0700 corrected cell culture protocol info, increased frame height, decreased right margins, added top button to each frame commit 52711e1c2b6cbb78fc36c3fc228248ca71d67061 Author: vanessa Date: Fri Jul 9 14:50:33 2010 -0700 added Yale RNA-Seq commit 05ee11b3f58d44989976cb4af145d9ab00037c60 Merge: 54c54f3 f6ce1cf Author: katrina Date: Fri Jul 9 14:45:05 2010 -0700 Merge branch 'master' of hgwdev:/data/git/kent commit 54c54f3fea4ae739d4fd670c1356d280a8f2b254 Author: katrina Date: Fri Jul 9 14:44:52 2010 -0700 increased the height of the frame, decreased size of margin on right side to match left side, added top button at bottom commit f6ce1cf6d37d687b582f2f0afabfe2ddc027e57c Merge: a829b23 cda2f38 Author: Venkat Malladi Date: Fri Jul 9 14:24:25 2010 -0700 Merge branch 'master' of vsmalladi@hgwdev.cse.ucsc.edu:/data/git/kent commit a829b239f7e0d4b067bde58a2ca3a0ba4289ec7b Author: Venkat Malladi Date: Fri Jul 9 14:24:14 2010 -0700 Updated hgEncodeVocab to build Mouse Cell Line table according to Mouse specifications. Also made updated links for cell protocols to be ENCODE/protocols/cell/(ogranism) as Melissa. Help from Krish. commit cda2f383c501d3aae1d5c784da4b41ed9716d48c Merge: b480954 8d22c4d Author: Chin Li Date: Fri Jul 9 14:13:55 2010 -0700 Merge branch 'master' of chinhli@hgwdev.cse.ucsc.edu:/data/git/kent commit b480954beef5a2febc79844a12c388fdd49f2d5c Author: Chin Li Date: Fri Jul 9 14:13:24 2010 -0700 remove redundant Cat mRNAs track commit 8d22c4d2db944547e37c53dc9afb6d38a99dde1e Merge: eca5894 b2e7635 Author: Krishna Roskin Date: Fri Jul 9 14:11:21 2010 -0700 Merge branch 'master' of krish@hgwdev.cse.ucsc.edu:/data/git/kent commit eca58948c9a3c86275b384e22bf093c8b8217f43 Author: Krishna Roskin Date: Fri Jul 9 14:11:00 2010 -0700 adder placeholder for the series SORT commit b2e76357f3d6894bd189ea99790bf922cde244d8 Merge: 98c96a7 94afe4f Author: vanessa Date: Fri Jul 9 13:53:51 2010 -0700 Merge branch 'master' of vanessa@hgwdev.cse.ucsc.edu:/data/git/kent commit 98c96a749525b046fa04a132b961c7d7318b42ae Author: vanessa Date: Fri Jul 9 13:53:33 2010 -0700 removed release alpha, beta tags for yaleRnaSeq track commit 94afe4f10bd42725f51a18fdfa66cfc3c683471d Author: Fan Hsu Date: Fri Jul 9 13:12:03 2010 -0700 Added sorting for DECIPHER phenotype list. commit 86ee84df975ad9009f2a093789097e12cf0d76b4 Author: vanessa Date: Fri Jul 9 12:30:49 2010 -0700 fixed typos commit d7f23ba2d5782485e5449bb8f69b78f5ddf7a1b4 Merge: 7522df2 76e41fc Author: Cricket Sloan Date: Fri Jul 9 11:44:25 2010 -0700 Merge branch 'master' of cricket@hgwdev.cse.ucsc.edu:/data/git/kent commit 76e41fc7171c93234a6a7107e0797ffa623ddd4e Merge: f0cbbf8 8fdd534 Author: Krishna Roskin Date: Fri Jul 9 11:36:03 2010 -0700 Merge branch 'master' of krish@hgwdev.cse.ucsc.edu:/data/git/kent commit f0cbbf89fa571e28d1c7e90594def479d2644ec6 Author: Krishna Roskin Date: Fri Jul 9 11:33:37 2010 -0700 change absolute paths to cv.ra to relative paths so they work with the sandboxs commit 8fdd534818443a0c4c83ed4666a94af5266c93db Author: Venkat Malladi Date: Fri Jul 9 11:26:42 2010 -0700 Add category =L cell Line for mouse cell MEL commit 49d98b88d0226e4512d30496bcb7bb095c573925 Author: Venkat Malladi Date: Fri Jul 9 11:23:50 2010 -0700 Accidently used number 0 instead of O when registering DMSO_2.0pct commit 8737c9eae9d9885d32a3fe8db52c2df768d2d6ec Merge: 37fd014 1c305db Author: Venkat Malladi Date: Fri Jul 9 11:12:40 2010 -0700 Merge branch 'master' of vsmalladi@hgwdev.cse.ucsc.edu:/data/git/kent commit 37fd0144527e818297f9c81e429ab728b0aadb2b Author: Venkat Malladi Date: Fri Jul 9 11:12:31 2010 -0700 Updated DAFs, added input instead of control commit 1c305db2cfe39b01fbd6209e880b80deb885a047 Author: Brian Raney Date: Fri Jul 9 11:10:34 2010 -0700 oops, need to add this as it is referenced in trackDb.wgEncode.ra now commit 06ac3ff49cbddffc2ebbbb727e190a25695b14d6 Merge: 978a24f d9c1706 Author: Brian Raney Date: Fri Jul 9 11:08:48 2010 -0700 Merge branch 'master' of braney@hgwdev.cse.ucsc.edu:/data/git/kent commit 978a24f6af5ffc632caafac4c5e6127d5f27a241 Author: Brian Raney Date: Fri Jul 9 11:08:19 2010 -0700 liftOver AffyRnaChip from hg18 to hg19 commit d9c1706a521bf90ad3f4043b9f36d344a685cea7 Merge: 39a5238 5815b57 Author: vanessa Date: Fri Jul 9 11:05:10 2010 -0700 Merge branch 'master' of vanessa@hgwdev.cse.ucsc.edu:/data/git/kent commit 5815b5734b896fae011c1a38db21112282983bba Merge: 77d12bf 312156a Author: Kate Rosenbloom Date: Fri Jul 9 10:56:40 2010 -0700 Merge branch 'master' of kate@hgwdev.cse.ucsc.edu:/data/git/kent commit 77d12bf57d54c79071d1d12776e91900a12e2899 Author: Kate Rosenbloom Date: Fri Jul 9 10:55:46 2010 -0700 Support for Nucleosome submissions. commit 312156a742ae9cbb1dbc0bc9a8848d6420b2fc2c Author: Hiram Clawson Date: Fri Jul 9 10:35:13 2010 -0700 n need to echo commands in csh scripts commit b88f77928b4d228f365195965d6f0b860804436f Author: Hiram Clawson Date: Fri Jul 9 10:33:12 2010 -0700 transition cvs to git commands for trackDb build commit 39a5238a08763dabb145f5d3d71871f290d10073 Merge: d56bb86 877fb91 Author: vanessa Date: Fri Jul 9 10:07:17 2010 -0700 Merge branch 'master' of vanessa@hgwdev.cse.ucsc.edu:/data/git/kent commit 877fb9114fd1662e37f5149a8b58ceaf842b4bf5 Merge: 2245f7d bf617d0 Author: Hiram Clawson Date: Fri Jul 9 09:56:14 2010 -0700 Merge branch 'master' of hiram@hgwdev.cse.ucsc.edu:/data/git/kent commit 2245f7d0f8334d5b346dc5158ae3a01446df9734 Author: Hiram Clawson Date: Fri Jul 9 09:55:54 2010 -0700 adding ce9 to the build commit bf617d0582d59f9982391cbb12eb096b4f69dada Merge: d5600e7 a2670c0 Author: Venkat Malladi Date: Fri Jul 9 09:52:31 2010 -0700 Merge branch 'master' of vsmalladi@hgwdev.cse.ucsc.edu:/data/git/kent commit d5600e701fe1594c869232db7e46c4966cd94f26 Author: Venkat Malladi Date: Fri Jul 9 09:51:44 2010 -0700 Updated 5 cell lines that were missing tier designations commit a2670c038feb26e5449520bc0f8418ca8545b4f8 Author: Galt Barber Date: Fri Jul 9 08:00:21 2010 -0700 "Encode release log update" commit b05b36850c03a60e94aedeed212cc23e6898e5c2 Author: Galt Barber Date: Fri Jul 9 08:00:19 2010 -0700 "Release log update" commit 54d193c97a70c4176b077cf8b6eb5dfbe85dae70 Merge: d7eaef5 114a165 Author: Galt Barber Date: Fri Jul 9 00:00:10 2010 -0700 Merge branch 'master' of galt@hgwdev.cse.ucsc.edu:/data/git/kent commit 114a165787b3f4ae60fba28d9475499014ef3658 Merge: 2b2a4a0 21c1648 Author: Brian Raney Date: Thu Jul 8 18:13:24 2010 -0700 Merge branch 'master' of braney@hgwdev.cse.ucsc.edu:/data/git/kent commit 2b2a4a001b9fa95ae2d09f665e77d006f8dbe655 Author: Brian Raney Date: Thu Jul 8 18:12:06 2010 -0700 add pack to the options for YaleRnaSeq commit 7522df2c65cb1d8c52ba7f6ed29f164e8f6ff1fb Author: Cricket Sloan Date: Thu Jul 8 17:44:45 2010 -0700 This is the attempt at replacing ripTgtProtien with Antibody. I have most of the work done, but it doesn't work with encodeVocab commit 2b579f0fc6bbb10f1a77f332b2d8577ef03fb93c Author: Cricket Sloan Date: Thu Jul 8 17:42:16 2010 -0700 have made the changes that Antonio wants, maybe so that longPolyA+ is polyA+ commit 21c1648d0b25c5ac58acf78d4903e373243412e7 Merge: 9b56aec a2389e6 Author: Cricket Sloan Date: Thu Jul 8 17:09:13 2010 -0700 Merge branch 'master' of cricket@hgwdev.cse.ucsc.edu:/data/git/kent commit 9b56aec9a07e5561384f435b4258074020d2c6c6 Author: Cricket Sloan Date: Thu Jul 8 17:08:04 2010 -0700 Moved all the old DAfs to 1.0 commit a2389e65d7ada0953788da7ef82ea632fc1ed05c Merge: 3a70aa5 7d4662d Author: Hiram Clawson Date: Thu Jul 8 16:55:38 2010 -0700 Merge branch 'master' of hiram@hgwdev.cse.ucsc.edu:/data/git/kent commit 3a70aa57e6700d40d8306e77f5c4ad7a0f87f3f7 Author: Hiram Clawson Date: Thu Jul 8 16:55:32 2010 -0700 adding gc5BaseBw track type commit 63bb67045d33f4f1b368bb732f29407be3025e2e Merge: d5fa465 cf9161c Author: Cricket Sloan Date: Thu Jul 8 16:31:57 2010 -0700 Merge branch 'master' of cricket@hgwdev.cse.ucsc.edu:/data/git/kent commit 7d4662de50de760ec19aa6b5d0cae52cf9487311 Author: Venkat Malladi Date: Thu Jul 8 16:31:16 2010 -0700 Fully updated all mouse DAFs commit 1f480886f1ab120976c3846c78b45eee92831962 Author: Hiram Clawson Date: Thu Jul 8 16:27:09 2010 -0700 turning gc5Base into a bigWig commit cf9161c74c63e3864cd2bc0f30bbf5bb3d985e94 Author: Venkat Malladi Date: Thu Jul 8 16:19:27 2010 -0700 Added new treatment DMSO_2.0pct commit 2d93c908206647a7546d181be8d19e9815fcc22b Merge: 5014a88 7f5630d Author: Venkat Malladi Date: Thu Jul 8 15:45:59 2010 -0700 Merge branch 'master' of vsmalladi@hgwdev.cse.ucsc.edu:/data/git/kent commit 5014a888cbbbf5bbc27083a40c2eba46ad9bf1b5 Author: Venkat Malladi Date: Thu Jul 8 15:43:59 2010 -0700 Changed sextype to cellLineSex upon Krishs recomendation commit 7f5630db497349549deabe027094c4863a375e6b Author: Fan Hsu Date: Thu Jul 8 15:05:27 2010 -0700 updated hgIkmc.html commit 9e1f3b4f9e6c1c28dbd458b06ecc66c6e3f2100c Author: Fan Hsu Date: Thu Jul 8 15:03:42 2010 -0700 Built hgIkmc track for hg19 (IKMC track mapped to human genome). commit ca8d142dc346906220151aca8bfe7ce70201abe5 Author: Fan Hsu Date: Thu Jul 8 15:00:44 2010 -0700 Built hgIkmc track for hg19 (IKMC track mapped to human genome). commit c5d4303120891ad38c855d560c94b1db76d5f038 Author: Tim Dreszer Date: Thu Jul 8 14:50:16 2010 -0700 Remove subtrack level vis override when composite or view vis comes in. commit d7eaef592c17b7731665b72d4341aba0ccef202e Author: Galt Barber Date: Thu Jul 8 14:33:04 2010 -0700 little bit more cleanup on danRer6 conservation descr page commit f88382ceb8d6bb80f6702330966ea2e95a788516 Author: Venkat Malladi Date: Thu Jul 8 14:29:33 2010 -0700 Updated doEncodeValidate to take Sex from DDF for tissue samples. Currently will be used for mouse tissues commit 09ed8bfa0f203ecb818143c81c1f1bf997a4ddb1 Author: Venkat Malladi Date: Thu Jul 8 14:29:03 2010 -0700 Added new seqPlatform variable to cv.ra and fields.ra to check seqencing platform information for GEO submissions commit 3f95eaa01c0fc04abbd7f85f9cf01f2f88888630 Author: Venkat Malladi Date: Thu Jul 8 14:27:36 2010 -0700 Updated hgEncodeVocab to find path for the valdiation documents for the antibodies now mentioned in cv.ra commit b07a05e09e5b7db252ee50d3e6554dd8bffed399 Merge: 96e834a 286bc14 Author: Galt Barber Date: Thu Jul 8 14:25:44 2010 -0700 Merge branch 'master' of galt@hgwdev.cse.ucsc.edu:/data/git/kent commit 286bc14180e3b5c30fcdc9a9276e1734ef7021d6 Merge: 6caab0a a71a7e5 Author: Chin Li Date: Thu Jul 8 14:24:47 2010 -0700 Merge branch 'master' of chinhli@hgwdev.cse.ucsc.edu:/data/git/kent commit 6caab0ae2d525e7c526b599fcda0e2f25624ee0e Author: Chin Li Date: Thu Jul 8 14:24:36 2010 -0700 add CREATE TEMPORARY TABLES permission to readonly@localhost commit 96e834ad724ba16442c7aea220b6a2a96e40a0fa Merge: 5856a80 a71a7e5 Author: Galt Barber Date: Thu Jul 8 14:11:17 2010 -0700 Merge branch 'master' of galt@hgwdev.cse.ucsc.edu:/data/git/kent commit 5856a80a20d2bf9eb16f91eb1e14f54e66536a9e Author: Galt Barber Date: Thu Jul 8 14:10:11 2010 -0700 re-doing danRer6 description page using hg19.cons46way.html as the model commit a71a7e56693144e78f7a4aeae5611244375f468f Author: Hiram Clawson Date: Thu Jul 8 14:08:15 2010 -0700 starting ce9 WS210 commit dc0ad3210615f366da74d321c5a4ff50870ccd49 Author: Hiram Clawson Date: Thu Jul 8 14:04:00 2010 -0700 starting ce9 WS210 commit 764f07d94ce63f0546a5cec1785829eca07fdc87 Author: Brian Craft Date: Thu Jul 8 12:32:31 2010 -0700 Fixed handling of lstring. commit fa2e40f3c9db15fb13434762fd618b354a73a0b1 Merge: 0fbd76c a0a4b8d Author: Chin Li Date: Thu Jul 8 12:14:35 2010 -0700 Merge branch 'master' of chinhli@hgwdev.cse.ucsc.edu:/data/git/kent commit 0fbd76c813fb4f24463825feb7a8d639d9be6de1 Author: Chin Li Date: Thu Jul 8 12:13:49 2010 -0700 remove felCat4 and felCatV17e from transMap section commit d56bb86ed80ef903c5e91f2163e26733649279b5 Merge: 8e43149 a0a4b8d Author: vanessa Date: Thu Jul 8 11:36:37 2010 -0700 Merge branch 'master' of vanessa@hgwdev.cse.ucsc.edu:/data/git/kent commit d5fa465e98f33820fe2210ce5d4f3fb2bd99b86e Merge: 729f949 a0a4b8d Author: Cricket Sloan Date: Thu Jul 8 11:17:34 2010 -0700 Merge branch 'master' of cricket@hgwdev.cse.ucsc.edu:/data/git/kent commit a0a4b8da0f9b067d5aeff3d05959001d6c0f3608 Author: Tim Dreszer Date: Thu Jul 8 10:44:48 2010 -0700 mdbUpdate no longer uses .sql file for table definition. Also tightened usage print. As per Hiram's requests. commit 55bc94a627e1b9a72bc5be19c6100f757905b4de Author: Donna Karolchik Date: Thu Jul 8 09:10:39 2010 -0700 Committed changes for Bob -- updates to birthday news item, new graphic. commit aa4fbc9b6c2613dedfa7259e9a9e642008efa460 Author: Galt Barber Date: Thu Jul 8 08:00:34 2010 -0700 "Encode release log update" commit 4e7e8acd813109838e764a7f36667e5263a896c3 Author: Galt Barber Date: Thu Jul 8 08:00:20 2010 -0700 "Release log update" commit 71bb0dfe42094ceb2a4e04d321b5d418b6edae28 Author: Galt Barber Date: Wed Jul 7 17:11:04 2010 -0700 more tweaks to cherry-picking commit 727d262e81b1d6da3bc17a66a4d4ee14f390c610 Author: Galt Barber Date: Wed Jul 7 17:04:17 2010 -0700 more fixes and tweaks commit e3861829a351797b2d7749ee88bb19bf48f510e4 Merge: 9d7a57b 9919786 Author: Galt Barber Date: Wed Jul 7 16:35:29 2010 -0700 Merge branch 'master' of hgwdev:/data/git/kent commit 9d7a57b76759167e21ec2f7c381ad69c62585a0e Author: Galt Barber Date: Wed Jul 7 16:33:35 2010 -0700 include more detail in the notification about the cherry-picked commit commit 9919786d1958aa8cb1f76d628b303143348b05a2 Merge: f41e418 d3dc118 Author: Brian Raney Date: Wed Jul 7 16:20:46 2010 -0700 Merge branch 'master' of braney@hgwdev.cse.ucsc.edu:/data/git/kent commit f41e418c2b0ec9dc178a972193d8480643d53dd8 Author: Brian Raney Date: Wed Jul 7 16:14:40 2010 -0700 write out PNGs with .png suffix (duh) commit d3dc11866d3d7607a9a6d1dc77f0341cc8dad0a0 Author: Tim Dreszer Date: Wed Jul 7 16:11:15 2010 -0700 SUBTRACKS_HAVE_VIS is dependent upon FLAT_TRACK_LIST which depands upon DRAG_REORDER commit 8dd73a28471214e23f3f875cdb823e3727ae5da0 Author: Tim Dreszer Date: Wed Jul 7 15:58:49 2010 -0700 Make sure the ifdef for SUBTRACKS_HAVE_VIS is seen in imageV2.h commit e7e1a79e109a908d13228907729ef8c71ea3bf4f Author: Tim Dreszer Date: Wed Jul 7 15:56:05 2010 -0700 Minor cleanup that should have been checked in already commit f775312d85bfd7f6d718a0b996c5cee58b49edec Author: Tim Dreszer Date: Wed Jul 7 15:54:48 2010 -0700 Initial support of subtrack vis override of composite->view vis using ifdefs commit 0df7dbe1a4e586b745ea3dffd3d50f29f8f745eb Merge: c93908b 1c232cf Author: Galt Barber Date: Wed Jul 7 13:38:15 2010 -0700 Merge branch 'master' of galt@hgwdev.cse.ucsc.edu:/data/git/kent commit c93908b84f69ca14d4ec949fd8e8dae6110ce1f3 Author: Galt Barber Date: Wed Jul 7 13:38:04 2010 -0700 typo commit 8e43149ebecf3da555fb306317e760342b071d20 Merge: 314db93 1c232cf Author: vanessa Date: Wed Jul 7 13:27:05 2010 -0700 Merge branch 'master' of vanessa@hgwdev.cse.ucsc.edu:/data/git/kent commit 1c232cf435b6001dd59a4b266130fc59aea1215d Author: Tim Dreszer Date: Wed Jul 7 13:21:09 2010 -0700 Fixed side button chrome bug where hgTrackUi wasn't called because of drag reorder commit 5ef132d4939628369285b1dc8baa0e2fc62439da Author: Tim Dreszer Date: Wed Jul 7 13:18:53 2010 -0700 Sorting table rows takes time and needs wait masking commit 314db93b0677e46d9f0a2b9ee2862ce7eefd2eae Merge: c79b644 6ae1c8c Author: vanessa Date: Wed Jul 7 13:11:13 2010 -0700 Merge branch 'master' of vanessa@hgwdev.cse.ucsc.edu:/data/git/kent commit 6ae1c8c4d1aa4ddb5063e76b1055259d572367a1 Author: Tim Dreszer Date: Wed Jul 7 13:08:23 2010 -0700 Added warnWithBackTrace() to aid simple detective work. commit c79b644a406a99b5eff21da479d56806e677f6f8 Author: vanessa Date: Wed Jul 7 10:40:24 2010 -0700 added new publication and organized pubs by year commit 70c9ac948c08a1780149e0b9ce25cf9c85ecd84a Merge: 3e3ece3 b127d8b Author: vanessa Date: Wed Jul 7 09:21:26 2010 -0700 Merge branch 'master' of vanessa@hgwdev.cse.ucsc.edu:/data/git/kent commit b127d8b615f19b6f7668d72c106399530348695d Author: Galt Barber Date: Wed Jul 7 08:00:32 2010 -0700 "Encode release log update" commit 066a5946412d2375c56506c2ebf11901fea38a19 Author: Galt Barber Date: Wed Jul 7 08:00:13 2010 -0700 "Release log update" commit f8d3476f038e91f93e1097731aa49bd04c7fc711 Author: Donna Karolchik Date: Wed Jul 7 01:01:00 2010 -0700 Added news item about 10-yr anniversary; archived a news item. commit c882970cd63441344d6dfa1fb37391b1e9cfcc04 Author: Galt Barber Date: Wed Jul 7 00:48:21 2010 -0700 oops 64 bit has precedence commit 6ba3f402b832648fae93e9c37ecccb8ab415bffb Author: Galt Barber Date: Wed Jul 7 00:30:10 2010 -0700 oops backwards commit 4d9599f7bd0e6fe91bbecc5163de54b2967221e2 Author: Galt Barber Date: Wed Jul 7 00:26:10 2010 -0700 sometimes the working dirs do not exist yet when cherrypicking commit cb9af621d9a6ff805af9da38b3948ab393eec580 Author: Galt Barber Date: Tue Jul 6 23:37:03 2010 -0700 convert to git commit a281acfcec0ebff1f84189fdfda14406a502b492 Author: Galt Barber Date: Tue Jul 6 23:33:45 2010 -0700 static things do not need to be turned off for downloadable utils build commit a9607384ba79fafcca8d7785aa89c9241b389235 Merge: a99c486 b91ca69 Author: Galt Barber Date: Tue Jul 6 23:20:53 2010 -0700 Merge branch 'master' of hgwdev:/data/git/kent commit a99c486e0379b468c76e38d2a87ddb506bfbd85e Author: Galt Barber Date: Tue Jul 6 23:20:36 2010 -0700 try removing the USE_X settings, should not need them now that autodection is in commit b91ca69539448968037e81d3ce82b372e274bc88 Author: Galt Barber Date: Tue Jul 6 23:18:32 2010 -0700 oops support for PNG path for 32-bit systems commit b3d8bf0f8db07a9ed4e414a233f01044506e8db9 Author: Galt Barber Date: Tue Jul 6 22:58:11 2010 -0700 trying to autodetect PNG,SSL,BAM; also trying to use PNG statically linked commit 9195ab92eeb3fa7ef0f5313a122ae741d73833b2 Merge: 72dc952 bd0bd77 Author: Galt Barber Date: Tue Jul 6 22:52:09 2010 -0700 Merge branch 'master' of galt@hgwdev.cse.ucsc.edu:/data/git/kent commit 72dc9523c9541db8122538fac57a87c13d00f2c1 Author: Galt Barber Date: Tue Jul 6 22:52:01 2010 -0700 added paraFetch commit 729f9498ad1bd9ffcb1bbbea3dd37d2d0b7cb850 Merge: 17f05c5 bd0bd77 Author: Cricket Sloan Date: Tue Jul 6 21:30:37 2010 -0700 Merge branch 'master' of cricket@hgwdev.cse.ucsc.edu:/data/git/kent commit 17f05c5270dad15a91d5ce12df67609a79b165aa Author: Cricket Sloan Date: Tue Jul 6 21:29:48 2010 -0700 Suny GeneST tracks have added more cell lines` commit bd0bd77f3dd23f67d49be53ec2b1b8e73201c7a7 Merge: e69d891 cb42630 Author: Brian Raney Date: Tue Jul 6 17:40:19 2010 -0700 Merge branch 'master' of braney@hgwdev.cse.ucsc.edu:/data/git/kent commit e69d891986c6b44ef8e698de27aa96581e7370d0 Author: Brian Raney Date: Tue Jul 6 17:39:37 2010 -0700 some trackDb entries and metaData for two tables missing from the methylSeq submission commit cb426300ba81e1f76359b0348564f47c4f6bfdc5 Merge: 2f22010 a3c2879 Author: Venkat Malladi Date: Tue Jul 6 15:07:06 2010 -0700 Merge branch 'master' of vsmalladi@hgwdev.cse.ucsc.edu:/data/git/kent commit 2f22010006239682ab132797f024ba8fe800bdaf Author: Venkat Malladi Date: Tue Jul 6 15:06:55 2010 -0700 Commented out the validation lines that include file names for 2 antibodies commit a3c28790ecc80ba05124bded602215c76e8c7bf7 Author: Fan Hsu Date: Tue Jul 6 13:58:28 2010 -0700 Built CGAP tables for mm9. commit 885ef3ef10db0338dafbae90199f5cf20575f09e Author: Larry Meyer Date: Tue Jul 6 13:39:43 2010 -0700 code cleanup commit 7db6a6a3e6ed6b45d9025dfe6759977d4c831303 Author: Larry Meyer Date: Tue Jul 6 13:38:33 2010 -0700 code cleanup commit 30e1e6c35782a53df364b48e8cfd3c44a06aec6f Merge: 237f697 194e141 Author: Larry Meyer Date: Tue Jul 6 13:38:04 2010 -0700 Merge branch 'master' of larrym@hgwdev.cse.ucsc.edu:/data/git/kent into mutationClassifier commit 194e141b249f30fc484c7f348d06c15ee47d32dc Merge: d76d306 ca3bf2b Author: Galt Barber Date: Tue Jul 6 13:23:46 2010 -0700 Merge branch 'master' of hgwdev:/data/git/kent commit d76d3065e189c943d748911135b6081c2168ec8f Author: Galt Barber Date: Tue Jul 6 13:23:30 2010 -0700 adding PNG commit ca3bf2b1108946ed3c50befb887515d622c62c83 Author: Fan Hsu Date: Tue Jul 6 11:38:13 2010 -0700 Added lines for knownToKeggEntrez table columns. commit 4f85a4c363d94bc1498b52aec2731d8a3f7fb0d9 Author: Galt Barber Date: Tue Jul 6 10:51:00 2010 -0700 oops, only need to re-open unfinished parts commit b8878d5c1860069439529c84e8f446d01428b37c Author: Venkat Malladi Date: Tue Jul 6 10:12:32 2010 -0700 Add age variable that will be submitted by UW Mouse commit 5021ddb8da73d7059edc3c86660841ddbc27027c Author: Venkat Malladi Date: Tue Jul 6 10:02:24 2010 -0700 Added Mouse labs for Hardison and Stam grants commit fdf3047df4051c6b6fc73a3e84775469e6f4361a Merge: 500c55d 0d02ce3 Author: Venkat Malladi Date: Tue Jul 6 09:48:06 2010 -0700 Merge branch 'master' of vsmalladi@hgwdev.cse.ucsc.edu:/data/git/kent commit 500c55d2593c7afadbb23c00375ddc64c894101e Author: Venkat Malladi Date: Tue Jul 6 09:47:52 2010 -0700 Updated mouse daf variables to include stain and sex where appropriate commit 0d02ce3395f153e69312dbf916b606b27fe77e1e Merge: 4881d8d 61c0574 Author: Fan Hsu Date: Tue Jul 6 09:27:56 2010 -0700 Merge branch 'master' of fanhsu@hgwdev.cse.ucsc.edu:/data/git/kent commit 61c05741c196e815555941e1fb80e93e055762f7 Author: Venkat Malladi Date: Tue Jul 6 09:18:28 2010 -0700 Updated Mouse Dafs to match controlled vocabulary commit 4881d8d0d4a8f2b598a6e5ba9811176b10a957d3 Merge: 13201cf 0b4ea82 Author: Fan Hsu Date: Tue Jul 6 08:06:16 2010 -0700 Merge branch 'master' of fanhsu@hgwdev.cse.ucsc.edu:/data/git/kent commit 0b4ea825ef629faaec269040a084c2dacf69fb5f Author: Galt Barber Date: Tue Jul 6 08:00:12 2010 -0700 "Encode release log update" commit 2b2b7c284504a0bcdcef0580768d8ebf51a1d577 Author: Galt Barber Date: Tue Jul 6 08:00:10 2010 -0700 "Release log update" commit 237f6975130b5c4ac2d5dc83aecf29216b55d265 Author: Larry Meyer Date: Tue Jul 6 00:54:30 2010 -0700 add dnaMarkovSql.o commit 73a4e893adad5f2b60b08044c9e211290c76409f Author: Galt Barber Date: Mon Jul 5 23:26:52 2010 -0700 adding retries to paraFetch for greater reliability to finish unattended. sleeps 30 seconds between retries commit b9969215da1532441c40c4ca26b9095a74f52c0a Merge: 641727d 96b4628 Author: Galt Barber Date: Mon Jul 5 23:24:11 2010 -0700 Merge branch 'master' of galt@hgwdev.cse.ucsc.edu:/data/git/kent commit 641727d6ff71482877716d038a16a629b38523dc Author: Galt Barber Date: Mon Jul 5 23:24:00 2010 -0700 adding retries to paraFetch for greater reliability to finish unattended. sleeps 30 seconds between retries commit 96b46285e85a683fbb0a2a14ddc0cf07eb64e7fa Author: Galt Barber Date: Mon Jul 5 22:52:00 2010 -0700 adding switch for PNG libraries dependency commit 41a6e05f94c43bc100fdb3c726c1f4fc0b1c4408 Author: Galt Barber Date: Mon Jul 5 22:48:08 2010 -0700 cannot yet have png libraries dependency required for default build commit d5fa6d218148a864cc923396169730aacee86f8c Merge: 2386fb7 328cb5e Author: Galt Barber Date: Mon Jul 5 22:46:39 2010 -0700 Merge branch 'master' of galt@hgwdev.cse.ucsc.edu:/data/git/kent commit 328cb5e6e9080f4530caf3ba9d0169bfe1ce082d Author: Larry Meyer Date: Mon Jul 5 20:44:06 2010 -0700 fprintf => verbose commit afbe9e91a8f837a63978e78e9765ba3e039491ad Author: Larry Meyer Date: Mon Jul 5 20:14:58 2010 -0700 add dnaMotifBitScoreWithMarkovBg commit 32d7f059cbf363cf6b98a6139ad1e7975b59e116 Author: Larry Meyer Date: Mon Jul 5 20:12:09 2010 -0700 add dnaMotifBitScoreWithMarkovBg commit bfe161aa0369995852953b6c15d284265c97d750 Author: Larry Meyer Date: Mon Jul 5 20:09:36 2010 -0700 add dnaMarkSql commit fdb7fe01db836e4e26f8a4d8c7b9dfc5e3ff5b67 Merge: 95bd0e2 7f54170 Author: Larry Meyer Date: Mon Jul 5 20:06:06 2010 -0700 Merge branch 'master' of larrym@hgwdev.cse.ucsc.edu:/data/git/kent into mutationClassifier Conflicts: src/hg/utils/mutationClassifier/mutationClassifier.c commit 2386fb722ae61c3c45d721b546b6ae9feb441bf1 Merge: ac03cdc 7f54170 Author: Galt Barber Date: Mon Jul 5 19:24:48 2010 -0700 Merge branch 'master' of galt@hgwdev.cse.ucsc.edu:/data/git/kent commit 95bd0e2cd1b498ac48a41734e3e416ae0442166b Author: Larry Meyer Date: Mon Jul 5 19:17:13 2010 -0700 refactor code into loadMark2 commit 7f54170a118d7d344b624bc826dfecef3e839beb Author: Galt Barber Date: Mon Jul 5 19:15:27 2010 -0700 more convert to git doNewBranch.csh commit d4cd4249b3ac72a4b488741bc56ff4e70188be0f Author: Galt Barber Date: Mon Jul 5 19:11:50 2010 -0700 oops need to change $dir to $branch throughout commit 29b380a5a0ac7fbfc6064e3d89da23d37d9e13a1 Author: Galt Barber Date: Mon Jul 5 18:54:30 2010 -0700 "New version number v235" commit 2b3033e4daf4fce3d53fdc540f234d0b476b7561 Merge: 0b27009 4ee62e4 Author: Galt Barber Date: Mon Jul 5 18:51:54 2010 -0700 Merge branch 'master' of hgwdev:/data/git/kent commit 0b2700970eda2ac7aeb6b23acb3026f78cd7d1a1 Author: Galt Barber Date: Mon Jul 5 18:50:45 2010 -0700 v235 final build commit 082a56ea972fe729c02680809614c895bc3ef4a2 Author: Larry Meyer Date: Mon Jul 5 18:42:00 2010 -0700 look for regulatory mutations w/n introns commit ac03cdc901fa1666e8ee0c635616550a5b89a8fb Author: Galt Barber Date: Mon Jul 5 13:35:46 2010 -0700 add paraFetchStatus monitoring commit a6961d05c989e09848d43e23f72cb0537d53de71 Author: Galt Barber Date: Mon Jul 5 13:34:44 2010 -0700 convert to using paraFetch instead of wget, fix to allow for mixed-case extension, added function for displaying greek disk-size suffixes for human-friendly display commit 4ee62e49c3fa653878bf74d707330914535ccdbd Merge: a95adb6 3521cf5 Author: John Sanborn Date: Mon Jul 5 12:32:59 2010 -0700 added TCGA-related codes commit 3521cf5953a30a9d45165932863f01474eea4b96 Author: John Sanborn Date: Mon Jul 5 12:03:38 2010 -0700 adding changes to tmp branch for merge commit a95adb602d71bf218eccda7e1b6881e49f345ef8 Merge: 1b319b6 a73a1de Author: Galt Barber Date: Mon Jul 5 12:00:54 2010 -0700 Merge branch 'master' of galt@hgwdev.cse.ucsc.edu:/data/git/kent commit 1b319b6b3dfb34f77f15fb81682b23612fc35896 Author: Galt Barber Date: Mon Jul 5 12:00:46 2010 -0700 create paraFetchStatus right away for monitoring programs commit aaa6491e3fb50b62e01c772f564b1ac9bb7963b6 Author: Galt Barber Date: Mon Jul 5 11:25:03 2010 -0700 swapping order so that background runs after foreground seems to work better commit a73a1de082386f6ab8e11b7c0c4a758055ac4030 Author: Galt Barber Date: Mon Jul 5 08:00:11 2010 -0700 "Encode release log update" commit 5b595cf25e8a4a415e19547204a19bb9601c6208 Author: Galt Barber Date: Mon Jul 5 08:00:10 2010 -0700 "Release log update" commit 545cd09e17cd9deb60f513d8d65a86c6dc491897 Merge: 282664c 588d2b1 Author: Larry Meyer Date: Mon Jul 5 01:35:20 2010 -0700 Merge branch 'master' of larrym@hgwdev.cse.ucsc.edu:/data/git/kent into mutationClassifier commit 282664cbfc251776e3b0f751d8f105b114f3e6f7 Author: Larry Meyer Date: Mon Jul 5 01:22:58 2010 -0700 add skipGeneModel option; support 2nd-order markov background model commit 588d2b1ec3dcf81522adf3791d4fa286d9e70c83 Merge: 8578465 26b91ba Author: Galt Barber Date: Sun Jul 4 13:56:02 2010 -0700 Merge branch 'master' of galt@hgwdev.cse.ucsc.edu:/data/git/kent commit 8578465061855052437a62e681327ef4495927d8 Author: Galt Barber Date: Sun Jul 4 13:55:55 2010 -0700 only want to check FD_ISSET for real open descriptors >= 0 commit 26b91ba14a4161e3138cafd0e55c5d9917fa77bd Author: Brian Raney Date: Sun Jul 4 13:00:32 2010 -0700 more GIF to PNG changes commit 07460f6d3812cc695a5b855c4c66b60ca9277351 Author: Galt Barber Date: Sun Jul 4 10:49:38 2010 -0700 removing debugging commit c1b1498696a7c7229bc659c062449b77e731272a Author: Galt Barber Date: Sun Jul 4 10:31:21 2010 -0700 return FALSE instead of errAbort; if downloaded size not equal to fileSize, return FALSE commit 9b06140060969e00200760cda5e406fd646b4841 Author: Galt Barber Date: Sun Jul 4 10:25:46 2010 -0700 fixed bug in doubly-freeing hash when size not returned from server. cleaned up verbose messages. fixed minor sign-related numeric issues commit 90e6bf913b6e17057a36ccd4c7acf16d4f1f30b7 Author: Galt Barber Date: Sun Jul 4 08:00:12 2010 -0700 "Encode release log update" commit 333f6503d565313e22ca6e2fe452b6a68a15daef Author: Galt Barber Date: Sun Jul 4 08:00:10 2010 -0700 "Release log update" commit 79723dd7593d5698258510f20faaf8b83b63ac88 Author: Larry Meyer Date: Sat Jul 3 18:02:32 2010 -0700 free seq after use commit 10a0c9d60db42c7f6c9e3dcc14af5d5fd6ce6c05 Author: Brian Raney Date: Sat Jul 3 15:40:47 2010 -0700 add GIS RNA-seq data commit c74427398368412a927ee3cfc9a602b69fe460a0 Author: Brian Raney Date: Sat Jul 3 14:53:45 2010 -0700 add to RNA-seq supertrack commit 91909bba85e47e299372142efdd4b4647ef42cdf Author: Brian Raney Date: Sat Jul 3 12:57:06 2010 -0700 forgot to commit this commit d3e0333a30a1ff436dbdb1eea88ae3c4f23d0049 Author: Brian Raney Date: Sat Jul 3 12:52:06 2010 -0700 add wgEncodeHaibMethylSeq.ra commit 1b2c101a43b104743d8e58584dbce5c2887f97af Author: Brian Raney Date: Sat Jul 3 12:51:28 2010 -0700 add Haib MethylSeq to hg19 commit 9ed3129560638b05d20558ebfae0e001a1bac9e0 Author: Brian Raney Date: Sat Jul 3 11:40:06 2010 -0700 add some riken tracks commit 216cd7a63714aadff7566e31a7e4dee5baee1ff8 Merge: 9ba8698 73b754e Author: Brian Raney Date: Sat Jul 3 08:04:22 2010 -0700 Merge branch 'master' of braney@hgwdev.cse.ucsc.edu:/data/git/kent commit 9ba8698f67fc6506664bd0584298110b2c991cc9 Author: Brian Raney Date: Sat Jul 3 08:04:07 2010 -0700 use PNG if USE_PNG commit 73b754ec41e94bd5aa288e7e1052139ca7e42fdf Author: Galt Barber Date: Sat Jul 3 08:00:16 2010 -0700 "Encode release log update" commit 2e141e0859d80328b510d84c1b0472dfbf0e23a0 Author: Galt Barber Date: Sat Jul 3 08:00:14 2010 -0700 "Release log update" commit e5c553fdc023741b0d533119468a4b79ebadc00a Merge: 88842bb cfa5485 Author: Larry Meyer Date: Fri Jul 2 21:55:34 2010 -0700 Merge branch 'master' of larrym@hgwdev.cse.ucsc.edu:/data/git/kent into remoteTracks commit cfa548511f7acf2b162e3b0b6d219b1731ba3520 Merge: 7e8df95 365ccf4 Author: Jim Kent Date: Fri Jul 2 18:58:07 2010 -0700 Merge branch 'master' of kent@hgwdev.cse.ucsc.edu:/data/git/kent commit 7e8df95df033889c06bb3e6818621ebd3529f2be Author: Jim Kent Date: Fri Jul 2 18:57:49 2010 -0700 Improving grammar in description. commit f4424a364948c3f69cf55d42ea04ae15eb71e476 Author: Jim Kent Date: Fri Jul 2 18:56:59 2010 -0700 Removing unused routine. commit 78b1d164fe87484978b6475cd271e3d44a08ec39 Author: Jim Kent Date: Fri Jul 2 18:51:46 2010 -0700 Eliminating inputTracks and inputTrackSelGroup tags, which have been replaced with the inputTrackTable tag. commit 88842bb22ac98aedaaae336395747d73699f05d2 Merge: c6096d8 365ccf4 Author: Larry Meyer Date: Fri Jul 2 18:10:01 2010 -0700 Merge branch 'master' of larrym@hgwdev.cse.ucsc.edu:/data/git/kent into remoteTracks commit 6e13a6bf4d25d0584103a547985fbeb3f84ec1c0 Author: Jim Kent Date: Fri Jul 2 16:40:02 2010 -0700 Updating comment that had grown stale. commit 227c3056820bc13eed27f2757739f4b0d62a3dbb Author: Jim Kent Date: Fri Jul 2 16:39:15 2010 -0700 Fixing typo in comment. commit 6516b39007d2885ba9ee03b69f078b8c21e4cd31 Author: Jim Kent Date: Fri Jul 2 16:37:52 2010 -0700 Making it so that a missing 'from' clause in a rql select statement triggers an error message instead of just causing empty output. commit 365ccf4a2d163bddffa0f0ebd58770740f9e810a Author: Chin Li Date: Fri Jul 2 16:21:04 2010 -0700 Finished up felCat4 commit 340bbd479223a0a844183f9f1d13e7e6c39f4193 Merge: 37677bc bfa0ea2 Author: Chin Li Date: Fri Jul 2 16:10:51 2010 -0700 Merge branch 'master' of chinhli@hgwdev.cse.ucsc.edu:/data/git/kent commit 37677bce59ce9f2badf24fbea4dd9b3636efb348 Author: Chin Li Date: Fri Jul 2 16:10:23 2010 -0700 Change download url from http://hgwdev.cse.ucsc.edu/goldenPath/ to http://hgdownload-test.cse.ucsc.edu/goldenPath/ commit bfa0ea2eb3cab487b8cbf2c17fec77f1a4e1a7ee Merge: f3f779d 599124a Author: Tim Dreszer Date: Fri Jul 2 16:02:47 2010 -0700 Merge branch 'master' of tdreszer@hgwdev.cse.ucsc.edu:/data/git/kent commit f3f779decbe9ff02915ee8f972f851756d8b1a9b Author: Tim Dreszer Date: Fri Jul 2 16:01:05 2010 -0700 Fixed Raw Signal view commit 599124a2c5484e7bdb06f47a25dc70607c275142 Merge: 5ef308c b85300c Author: Galt Barber Date: Fri Jul 2 15:33:50 2010 -0700 Merge branch 'master' of galt@hgwdev.cse.ucsc.edu:/data/git/kent commit 5ef308cfcb9f1b43ac47df10f63abc8b3e18c147 Author: Galt Barber Date: Fri Jul 2 15:33:05 2010 -0700 explain to user if requests too many connections commit b85300cf2aa6014a0a223dbfd8ca1f8877d3d734 Author: Galt Barber Date: Fri Jul 2 15:23:25 2010 -0700 oops should say git not cvs in error messages commit 15bd148d08d1656b8de69fbcd53902ba1294149b Author: Galt Barber Date: Fri Jul 2 15:20:15 2010 -0700 removing automatic-merges from the commit-list, by request commit a273d80e7d9747a56dc8106243bdc9eef5b5c06b Author: Venkat Malladi Date: Fri Jul 2 15:12:14 2010 -0700 Changed nm to nM for 2 treatments Estradiol_10nm and Genistein_100nm to register them correctly. commit 5e375a483f1d60c4b4f413bc756db64e87dabc40 Merge: 1f96bdb 3173169 Author: Venkat Malladi Date: Fri Jul 2 15:08:32 2010 -0700 Merge branch 'master' of vsmalladi@hgwdev.cse.ucsc.edu:/data/git/kent commit 1f96bdb38f1aa982a2356b4a8f4036d47edc9ee8 Author: Venkat Malladi Date: Fri Jul 2 15:08:23 2010 -0700 Added 7 treatments registered by the Hudson Alpha (Myers) lab commit 31731692e0d777fb73bd61dcd8f33697564e215d Author: Brian Raney Date: Fri Jul 2 14:44:37 2010 -0700 UCSF Brain Methyl: take out Brain from individual tracks long and short labels, change RNAseq to RNA-seq commit 39c659035c3e6ddbbd81acad02cee68d9474c498 Author: Brian Raney Date: Fri Jul 2 14:08:55 2010 -0700 change some stuff that Mary wanted commit f54f526071669fd7d44e52871eb7ba48ebbaa7df Author: Tim Dreszer Date: Fri Jul 2 13:23:49 2010 -0700 Rearranged code and comments as per Jims suggestion. Made selection by var=val pairs more full proof commit 9c8b6f4047511f8a093952702231e17e4d43b239 Author: Venkat Malladi Date: Fri Jul 2 12:42:20 2010 -0700 Added document names for the validation documents provided for Antibodies commit d440db0fef55419e6fad3f26f46fecdf176c33ac Merge: b801caa e91aaf4 Author: Venkat Malladi Date: Fri Jul 2 12:15:29 2010 -0700 Merge branch 'master' of vsmalladi@hgwdev.cse.ucsc.edu:/data/git/kent commit b801caac44e463c8edbaf9200f8f858b9987d286 Author: Venkat Malladi Date: Fri Jul 2 12:15:14 2010 -0700 Added 3 new antibodies, 2 with validation documents. Antibodies added: Pol2(phosphoS2),ETS1,MEF2A commit c6096d88b54c8e3b7d55cb90b138fd0cdf27a057 Merge: bd2e327 e91aaf4 Author: Larry Meyer Date: Fri Jul 2 11:40:18 2010 -0700 Merge branch 'master' of larrym@hgwdev.cse.ucsc.edu:/data/git/kent into remoteTracks commit e91aaf418973e4061287e39bb8decfac57ac694e Author: Melissa Cline Date: Fri Jul 2 11:38:21 2010 -0700 Added the temporary rfamHuman table commit 83fb1e59777832b547489717aede4c4d1c004a88 Merge: 2c3a31a b58ba48 Author: Brian Raney Date: Fri Jul 2 11:33:18 2010 -0700 Merge branch 'master' of braney@hgwdev.cse.ucsc.edu:/data/git/kent commit 2c3a31aaa0145a1899909a53802f2b9f91905ceb Author: Brian Raney Date: Fri Jul 2 11:32:52 2010 -0700 download new gtf files from FelixK. Need to re-load and change release notes commit b58ba4822dba71c108aeefeaa92670e95b3551dc Author: Tim Dreszer Date: Fri Jul 2 10:47:42 2010 -0700 Removed ifdefs which were past their expiration date commit 4cbe2d63e6da573644b3fba11392daca912665e0 Author: Hiram Clawson Date: Fri Jul 2 08:59:04 2010 -0700 correcly symlink 2bit file for chrom based assembly commit ed20bc30aeddc98f6521b59a90fdeb77d8d0ca76 Merge: a32808f be30e5d Author: Hiram Clawson Date: Fri Jul 2 08:46:01 2010 -0700 Merge branch 'master' of hiram@hgwdev.cse.ucsc.edu:/data/git/kent commit a32808ff286d68e1a6d36c06a0793ac6b30d306a Author: Hiram Clawson Date: Fri Jul 2 08:45:31 2010 -0700 no need to copy README.txt when symlink is good commit be30e5d1e3c03f44d79187f593d5895b83e5b442 Author: Galt Barber Date: Fri Jul 2 08:00:30 2010 -0700 "Encode release log update" commit e9da1dbe9eaf15e803e35f6f6d6f82a393a78029 Author: Galt Barber Date: Fri Jul 2 08:00:28 2010 -0700 "Release log update" commit 6475c808a386fed860a44e16941580d4e2b493aa Merge: ab558bd 0adec95 Author: Brian Raney Date: Fri Jul 2 07:49:03 2010 -0700 Merge branch 'master' of braney@hgwdev.cse.ucsc.edu:/data/git/kent commit ab558bd30d088b3490661c98ce6fb665fd00e076 Author: Brian Raney Date: Fri Jul 2 07:48:40 2010 -0700 switch to using PNG commit 0adec95098c5ba81e9512ff5a45943fd57ae8a65 Merge: da60ae4 0ba2992 Author: Jim Kent Date: Thu Jul 1 23:37:39 2010 -0700 Merge branch 'master' of kent@hgwdev.cse.ucsc.edu:/data/git/kent commit da60ae499fc8c96645ab68a614da11bc83acf58c Author: Jim Kent Date: Thu Jul 1 23:37:25 2010 -0700 Doing another pass at the integrated regulatory track .html pages. commit 0ba29921c5e8000856408b479acd67e6256142cd Merge: b921705 f283327 Author: Chin Li Date: Thu Jul 1 22:00:34 2010 -0700 Merge branch 'master' of chinhli@hgwdev.cse.ucsc.edu:/data/git/kent commit b921705d19b854d7fdea093f673da1f2cba7df92 Author: Chin Li Date: Thu Jul 1 22:00:19 2010 -0700 Put html head back in commit f2833275fbaba79838e25fa392519f2f72375d2f Merge: fd821e1 a3281f4 Author: Brooke Rhead Date: Thu Jul 1 17:12:22 2010 -0700 Merge branch 'master' of rhead@hgwdev.cse.ucsc.edu:/data/git/kent commit fd821e1536794dbb9c82f7bdce512aeaa8d43902 Author: Brooke Rhead Date: Thu Jul 1 17:12:02 2010 -0700 Added a period. commit a3281f499e2cf150e5dbebbc7c1aadb2742b0333 Author: Brian Raney Date: Thu Jul 1 17:11:17 2010 -0700 set up HTML to have the right file type commit 513317814c4a9950efd22d122cf336a35000efc8 Author: Brian Raney Date: Thu Jul 1 17:01:03 2010 -0700 don't fiddle with palette transparency if we're 32-bit commit 8dbf47bf422d211ec80bd5ad352a02d61529ae47 Author: Jim Kent Date: Thu Jul 1 17:00:32 2010 -0700 Renaming .html file to correspond to track name. commit c0cda20c11189b40e01b5753af188b1006933d53 Merge: a79abcd c6652cc Author: Chin Li Date: Thu Jul 1 16:36:45 2010 -0700 Merge branch 'master' of chinhli@hgwdev.cse.ucsc.edu:/data/git/kent commit a79abcd19eaf57c4ff724f7404170092515496d4 Author: Chin Li Date: Thu Jul 1 16:34:37 2010 -0700 put git pull in commit c6652cc836cabcae708c08fdf7d4be90bf136f9b Author: Brooke Rhead Date: Thu Jul 1 16:26:38 2010 -0700 Added execute permission to html files that include the topbar. commit 13201cf37a2c29114e33e1fee5941c270f6aaddb Merge: 7f8a18a 2b211e2 Author: Fan Hsu Date: Thu Jul 1 15:27:33 2010 -0700 Merge branch 'master' of fanhsu@hgwdev.cse.ucsc.edu:/data/git/kent commit 2b211e25eb6dbe0a55690c87d2bccf83a34f1e1f Author: Brian Raney Date: Thu Jul 1 15:18:45 2010 -0700 fix phyloGif to write out PNG, and make sure no one can write out GIF if USE_PNG is set commit bd2e3278946affb61ad8c10190ea124f89518cb9 Merge: d099b15 4b112d9 Author: Larry Meyer Date: Thu Jul 1 15:07:51 2010 -0700 Merge branch 'master' of larrym@hgwdev.cse.ucsc.edu:/data/git/kent into remote commit 7f8a18a14aa40121a14ea46e7e2423f990c655e3 Merge: 6edf70a 4b112d9 Author: Fan Hsu Date: Thu Jul 1 14:58:14 2010 -0700 Merge branch 'master' of fanhsu@hgwdev.cse.ucsc.edu:/data/git/kent commit 6edf70a130a3821393c1d9d332d0160a1223710c Author: Fan Hsu Date: Thu Jul 1 14:57:03 2010 -0700 updated for xxBlastMat tables rebuilds for dm3, sacCer2, and mm9. commit 4b112d95a8ed3f10d24a63750933c64f83a6597d Merge: 69dbdc0 e58a31f Author: Melissa Cline Date: Thu Jul 1 14:53:37 2010 -0700 Merge branch 'master' of hgwdev.cse.ucsc.edu:/data/git/kent commit e58a31fc4204222393f4b27a894ec6a4bc79264f Merge: 6aff409 56c6617 Author: Brian Raney Date: Thu Jul 1 14:35:44 2010 -0700 Merge branch 'master' of braney@hgwdev.cse.ucsc.edu:/data/git/kent commit 3e11deb846a0d41e3d751ecc4088d4dd1607b99f Author: Fan Hsu Date: Thu Jul 1 14:34:42 2010 -0700 Created kegg.html, description of the KEGG column. commit 6aff4099034ccd36edc3f56358b844011f1429f1 Author: Brian Raney Date: Thu Jul 1 14:34:11 2010 -0700 use png instead of gif if USE_PNG is set commit b47767f996cf722b3a4764216279fbb3bac1c167 Merge: 6d0516c 56c6617 Author: Jim Kent Date: Thu Jul 1 13:59:24 2010 -0700 Merge branch 'master' of kent@hgwdev.cse.ucsc.edu:/data/git/kent commit 6d0516cde8c7ac4966dd45ffbd8e2794a4f8fa4b Author: Jim Kent Date: Thu Jul 1 13:58:59 2010 -0700 Restoring about 600 lines deleted mysteriously in 3 different places. I sure don't remember doing this and wander what sort of editor typo I could have made. Any way the code review caught it at least! commit d099b1552b722626b6858c124b33a662a7812019 Merge: 17aefdf 56c6617 Author: Larry Meyer Date: Thu Jul 1 13:33:59 2010 -0700 Merge branch 'master' of larrym@hgwdev.cse.ucsc.edu:/data/git/kent into remote commit 56c6617883481e1d13022ece973205373e7573ff Author: Melissa Cline Date: Thu Jul 1 13:33:07 2010 -0700 Adding the RfamExactMatch track commit f396983d2dca15c4632b3a399828f13b28356bd2 Merge: 38cea64 73d979c Author: Melissa Cline Date: Thu Jul 1 13:17:54 2010 -0700 Merge branch 'master' of cline@hgwdev.cse.ucsc.edu:/data/git/kent commit 17aefdfab8dced56f38962bd31c7d1355d7ea00a Merge: 17b97cd 73d979c Author: Larry Meyer Date: Thu Jul 1 13:10:27 2010 -0700 Merge branch 'master' of larrym@hgwdev.cse.ucsc.edu:/data/git/kent into remote commit 17b97cd028ac6a6cc8d293ea767dfa752a9bc528 Merge: ac6ca1e 9a5ce2c Author: Larry Meyer Date: Thu Jul 1 13:08:07 2010 -0700 Merge branch 'master' of larrym@hgwdev.cse.ucsc.edu:/data/git/kent into remote commit 73d979c4e947b8457f63fb004a12e70215b09e31 Merge: 2677855 9a5ce2c Author: Jim Kent Date: Thu Jul 1 12:56:13 2010 -0700 Merge branch 'master' of kent@hgwdev.cse.ucsc.edu:/data/git/kent commit 26778550a1eddeaeb607e4e1de117a796c526006 Author: Jim Kent Date: Thu Jul 1 12:55:44 2010 -0700 Improving usage statement and a comment. commit 9a5ce2c6c62a3287d1ec1e65f2adb23c4fc33178 Author: Bernard Suh Date: Thu Jul 1 12:48:51 2010 -0700 Changed URL to genecats server commit 38cea64eeed63d77ff2d66058528a46d9291da0c Author: Brian Raney Date: Thu Jul 1 12:34:24 2010 -0700 add some ra files to the makefile commit e5e3fc3f12813ad6532ab1327797059f2b86f0ae Merge: b5c5cc1 60c67c1 Author: Jim Kent Date: Thu Jul 1 12:33:21 2010 -0700 Merge branch 'master' of kent@hgwdev.cse.ucsc.edu:/data/git/kent commit b5c5cc1d7c611d91d6382c7f28ab1d599ac4536b Author: Jim Kent Date: Thu Jul 1 12:32:59 2010 -0700 Adding more common things for git to ignore. commit 60c67c16ca3cb8160a35b558bcf5c29d24ae3de8 Merge: 77d86b6 afceeb6 Author: Brian Raney Date: Thu Jul 1 12:28:47 2010 -0700 Merge branch 'master' of braney@hgwdev.cse.ucsc.edu:/data/git/kent commit 77d86b63bf6524d75f016871533be79c37540cb5 Author: Brian Raney Date: Thu Jul 1 12:28:19 2010 -0700 metadata for CSHL Small RNA-seq commit afceeb6f2da665b063f873ae2c3e61ae6f37bcfb Author: Bernard Suh Date: Thu Jul 1 12:26:58 2010 -0700 Improved report file finding function, added new function for dealing with colors and freeze labels with the keyword "post" commit ff93307ea0860bface5798073d62c153ce1e2969 Author: Bernard Suh Date: Thu Jul 1 12:25:21 2010 -0700 Now uses new freeze label and color functions commit d7bec6a418699c829eb94903e4757572b897c6b1 Author: Bernard Suh Date: Thu Jul 1 12:25:08 2010 -0700 Now uses new freeze label and color functions commit ac6ca1ee18a533a0d99d2412c7589c10a2fa3b61 Merge: 65ad23a 3b651c9 Author: Larry Meyer Date: Thu Jul 1 12:24:54 2010 -0700 Merge branch 'master' of larrym@hgwdev.cse.ucsc.edu:/data/git/kent into remote commit dee2b8b95b6b1a35cd36db01c381ae95c4e594be Author: Bernard Suh Date: Thu Jul 1 12:24:50 2010 -0700 Now uses new freeze label and color functions commit 16ebc8ddd70ab5e6319194e4b6b57206f05fedd3 Author: Bernard Suh Date: Thu Jul 1 12:23:46 2010 -0700 More robustly handle freeze labels with "post" keyword commit 65ad23ade04b4c9314953d5295dc91619bbf49eb Author: Larry Meyer Date: Thu Jul 1 12:23:39 2010 -0700 fix off-by-one error when setting end during selection; more remote renderer work (dead code in non-dev trees) commit 2b878fd16c5ed0b860a0e3712ab4de7b9b48da31 Author: Bernard Suh Date: Thu Jul 1 12:22:40 2010 -0700 Fixed incorrect make variables commit 569497164feafff78ac4d639d0cc1f12e5268917 Author: Larry Meyer Date: Thu Jul 1 12:19:08 2010 -0700 add parsePosition commit 3b651c95632101fe2f7a4f61d909662ea3925196 Merge: ad8891a bf15557 Author: Brian Raney Date: Thu Jul 1 12:01:16 2010 -0700 Merge branch 'master' of braney@hgwdev.cse.ucsc.edu:/data/git/kent commit ad8891ab3211769040d30ed1c68583cb46d7ab8a Author: Brian Raney Date: Thu Jul 1 12:00:48 2010 -0700 make 32-bit PNG the default, use painter's algorithm for mRNA track commit bf15557c175b84b0338ff5b15aac634b8d128d40 Author: Chin Li Date: Thu Jul 1 11:46:23 2010 -0700 Change CVS to Git commit 50c35878a76e00338885ddb4784162ef4bbef356 Author: Larry Meyer Date: Thu Jul 1 11:45:25 2010 -0700 scoreDelta -> minDelta commit 1660f29098379b7846f4213241d211258d320d2b Author: Chin Li Date: Thu Jul 1 10:16:01 2010 -0700 complete LASTZ Panda Swap commit 2c12c3c0307f3bf6306a917524147a0b018a523a Author: Chin Li Date: Thu Jul 1 10:13:21 2010 -0700 complete LASTZ Panda Swap commit d887fd456d54ca826a8a63d6b20acb0943d6609d Merge: 33aa87e ca12a64 Author: Chin Li Date: Thu Jul 1 09:11:53 2010 -0700 Merge branch 'master' of chinhli@hgwdev.cse.ucsc.edu:/data/git/kent commit 33aa87e4513362e08e45251e63a1aa87849cff4f Author: Chin Li Date: Thu Jul 1 09:11:36 2010 -0700 Add felCat4 commit 5c92c24cebbf7ab2cfb34a118c73401a577aa42d Author: Chin Li Date: Thu Jul 1 08:49:00 2010 -0700 rm obsolete sentence about 'cvs update' make stmt commit c700f63613a0c661c1f3fe7a0683c64e3dff7df1 Author: Chin Li Date: Thu Jul 1 08:46:52 2010 -0700 change CVS to Git commit ca12a6449aefe65ac150467f07f6040acc0c979c Author: Galt Barber Date: Thu Jul 1 08:00:11 2010 -0700 "Encode release log update" commit a7858641cd83d15c39166cb1d25340ecd7fcd7ff Author: Galt Barber Date: Thu Jul 1 08:00:10 2010 -0700 "Release log update" commit aa90bf4cb47af0436e2e3f9fd076f7562baa9894 Author: Galt Barber Date: Wed Jun 30 19:37:13 2010 -0700 backing off on the pathspec limitation of staged stuff, since it is fast for git to generate and it is important to know what would get committed commit ae51d63289bc7b17ed4d3adae792ebfbb01474bd Author: Galt Barber Date: Wed Jun 30 19:23:32 2010 -0700 handling programs versus scripts better in gitTools makefile commit be3ca74be95c4f6ae48f211f102a968415edb84e Author: Galt Barber Date: Wed Jun 30 19:14:00 2010 -0700 handling plurals for gilt commit c2ba320f1359455d3f8748d0a6c09cbabaf17dd7 Author: Galt Barber Date: Wed Jun 30 19:10:45 2010 -0700 more bugfixes for gilt commit 69b68588045127b4894a4c4198c3199bd96cec88 Merge: 696638c 3062199 Author: Galt Barber Date: Wed Jun 30 19:03:01 2010 -0700 Merge branch 'master' of galt@hgwdev.cse.ucsc.edu:/data/git/kent commit 696638c18597eda756f88864ffabc4588ee6ebec Author: Galt Barber Date: Wed Jun 30 19:02:44 2010 -0700 bugfixes on gilt commit a1e90d9ea969682e3e6f9a708330e53bfe5e48c8 Author: Galt Barber Date: Wed Jun 30 18:57:39 2010 -0700 initial commit of gilt git status tool commit 3062199bb22656ad9eb55d2cd543cf4c7a6f70a4 Author: Bernard Suh Date: Wed Jun 30 17:52:07 2010 -0700 Updated with new file info and build instructions commit ef0f8b2f474329c11858d73d687756beca8b69bd Author: Bernard Suh Date: Wed Jun 30 17:49:41 2010 -0700 Initial checkin - places files in proper location commit 20b8323d6dc63d5e82249954574233b31d0c40c8 Merge: 89dbf0a 5748a1d Author: Galt Barber Date: Wed Jun 30 17:43:56 2010 -0700 Merge branch 'master' of galt@hgwdev.cse.ucsc.edu:/data/git/kent commit 89dbf0a640c5d0c72bc4611eecd5ef16ed52e309 Author: Galt Barber Date: Wed Jun 30 17:43:50 2010 -0700 adding changes for danRer6 makedoc relating to downloads commit 5748a1d9ef3f4a3dc87eb262c07e02c3004af070 Author: Brooke Rhead Date: Wed Jun 30 17:11:28 2010 -0700 Fixing permissions on html files. commit 98f525277a842f6f8a79257de94f697ff1410540 Merge: 3ba06b7 2a08fe2 Author: Kate Rosenbloom Date: Wed Jun 30 16:50:51 2010 -0700 Merge branch 'master' of kate@hgwdev.cse.ucsc.edu:/data/git/kent commit 3ba06b788f1010f80ae6e51b5326d5f794f93656 Author: Kate Rosenbloom Date: Wed Jun 30 16:49:29 2010 -0700 Remove special chars from tags. Minor tweaks for consistency (e.g. caps) commit c897b686f8b2f0c0248f271a41ba8d59bbde9135 Author: Chin Li Date: Wed Jun 30 16:31:10 2010 -0700 Fix left margin for the Obsolete message commit 2a08fe2b8e491aba0432e9db7c414f9d3fe9e921 Author: Bernard Suh Date: Wed Jun 30 16:30:14 2010 -0700 Updated URL to genecats server. Added changes requested by Kate commit a6c0fcf0f519adc11235b083aa1ec531665946e0 Author: Bernard Suh Date: Wed Jun 30 16:29:12 2010 -0700 Added the "downloads" status commit 3e3ece35e291b2419d9253f7438b6500edd3af72 Merge: de9b481 6b38209 Author: vanessa Date: Wed Jun 30 16:07:23 2010 -0700 Merge branch 'master' of vanessa@hgwdev.cse.ucsc.edu:/data/git/kent commit 6b382090aac369b1271289f0edd98ee89f41ec99 Merge: 6e25502 7bb1cbd Author: Brian Raney Date: Wed Jun 30 14:57:31 2010 -0700 Merge branch 'master' of braney@hgwdev.cse.ucsc.edu:/data/git/kent commit 6e255027f275eb44fd456d70bc031a85096143cc Author: Brian Raney Date: Wed Jun 30 14:57:05 2010 -0700 first pass at CSHL short RNA commit 7bb1cbd1886acafaa02418b816e11e4053a14bb8 Author: mary Date: Wed Jun 30 11:45:17 2010 -0700 another minor edit commit b6e3401f355a255983452f6a82c46ccd83cf4e72 Author: mary Date: Wed Jun 30 11:44:09 2010 -0700 little minor edit to book chapter reference commit 719661cff7cbcaf85954003fbb88ecbf749fcca7 Merge: d8a8841 c5dfe0d Author: mary Date: Wed Jun 30 11:42:55 2010 -0700 Merge branch 'master' of mary@hgwdev.cse.ucsc.edu:/data/git/kent commit d8a884166b080366fad66736fc16922ab30a0b38 Author: mary Date: Wed Jun 30 11:39:48 2010 -0700 formatting book chapter commit c5dfe0dcabe838e6d3b56a4b28386b9484c26e3d Merge: e6a4330 7dac8fe Author: Galt Barber Date: Wed Jun 30 11:21:02 2010 -0700 Merge branch 'master' of galt@hgwdev.cse.ucsc.edu:/data/git/kent commit e6a4330186fa00d90d6e24cc3f9b2fae99ae620b Author: Galt Barber Date: Wed Jun 30 11:20:52 2010 -0700 added git-reports and gitTools to makefile commit 9ec6031e6424f74c97708735c7713a17152627be Author: mary Date: Wed Jun 30 11:18:40 2010 -0700 small edit plus references commit df3efc7afb54cc1ef19460953fe2e9517f238c96 Merge: 6cbaefe 7dac8fe Author: mary Date: Wed Jun 30 11:15:18 2010 -0700 Merge branch 'master' of mary@hgwdev.cse.ucsc.edu:/data/git/kent commit 7dac8fe373f8cf6c576279daef1f05afeb7f060a Author: Galt Barber Date: Wed Jun 30 08:00:21 2010 -0700 "Encode release log update" commit c52c58d818284386ee821bb25c7d9a196d232caa Author: Galt Barber Date: Wed Jun 30 08:00:20 2010 -0700 "Release log update" commit 695646305b7abca4bc1f0592ce59acfe917ed0fc Author: Hiram Clawson Date: Wed Jun 30 06:19:14 2010 -0700 correct comment on retroRefGene commit b7ecf2ea27745d2b875787d2b298e1b97b1b6255 Author: Hiram Clawson Date: Wed Jun 30 06:12:09 2010 -0700 adding refGene name to ucscRetroInfo refSeq relation and inverse commit 6cbaefe40c8913c2099c6890802c90ea27104e1f Author: mary Date: Tue Jun 29 18:22:07 2010 -0700 more edits commit 268c44baf0e4bd1d8dabb29b0a397ae5e2db9b38 Merge: e8f942b 9dd8489 Author: mary Date: Tue Jun 29 18:17:46 2010 -0700 Merge branch 'master' of mary@hgwdev.cse.ucsc.edu:/data/git/kent commit 9dd848915dd2751ceb8061860f35144c65a4fe3f Author: Galt Barber Date: Tue Jun 29 18:11:19 2010 -0700 fixing order of species in danRer6 commit 89e1458440261c2460fdeb11fa2ebf9918d7f8f6 Author: Brian Raney Date: Tue Jun 29 17:21:00 2010 -0700 add noInherit on commit 18e1f3186b428f08781c98d316fe3b78ed0021b2 Author: Cricket Sloan Date: Tue Jun 29 17:14:48 2010 -0700 Added noInherit on commit d8ac6df67490ac593fdebdc84b52358e1b9ae03b Author: Larry Meyer Date: Tue Jun 29 16:31:06 2010 -0700 print out nearest gene for regulatory mutations commit 0a5a014c6fba09e2774878e2deee41cd87e2e12f Merge: 3800d46 25c9567 Author: Brian Raney Date: Tue Jun 29 16:15:55 2010 -0700 Merge branch 'master' of braney@hgwdev.cse.ucsc.edu:/data/git/kent commit 25c95673ce064e897e6bca8092acdd41ffcca3e5 Merge: 6c92669 1e6ea3e Author: Cricket Sloan Date: Tue Jun 29 16:13:52 2010 -0700 Merge branch 'master' of cricket@hgwdev.cse.ucsc.edu:/data/git/kent commit 6c926692ced4c4d2e64e350b32562d389f474f0b Author: Cricket Sloan Date: Tue Jun 29 16:13:05 2010 -0700 Added a super track and removed bad subtrack GM12878 2x75 commit 1e6ea3ebb56bf3e31a4d8070f872d1eb45195cc3 Author: Brian Craft Date: Tue Jun 29 15:07:34 2010 -0700 Moved gitFiles to a makefile variable in htdocs, to allow an override. Builds off a tag must not reference the repository. This change allows an override, e.g. make FIND=find, for such builds. commit 9f02c3611bf7f621928d8dbcc6f6967c61888b51 Author: Larry Meyer Date: Tue Jun 29 14:20:40 2010 -0700 prototype code to support 'remote' tracks commit a6fb0bf99d8733eb30b80d8261240a6f5a9c95b4 Merge: 35a6506 fe5c9a0 Author: Cricket Sloan Date: Tue Jun 29 14:08:28 2010 -0700 Merge branch 'master' of cricket@hgwdev.cse.ucsc.edu:/data/git/kent commit 35a650672bbc2698ebe9286796c75685121063f6 Author: Cricket Sloan Date: Tue Jun 29 14:07:09 2010 -0700 CSHL Long RNA Track improvements in the display commit fe5c9a0b0980a1893d6bbf70ebdc0f53edc79e55 Author: Venkat Malladi Date: Tue Jun 29 14:05:52 2010 -0700 Updated the sex of MEL (mouse) to U, unidentified as we do not know this sex at the moment. commit f766bdab232b2e18279d1b3a68ca5d4af9188b0a Merge: 60b24b5 246e4b4 Author: Venkat Malladi Date: Tue Jun 29 14:03:29 2010 -0700 Merge branch 'master' of vsmalladi@hgwdev.cse.ucsc.edu:/data/git/kent commit 3800d4603e327d831d226399563a796ec93d5afe Author: Brian Raney Date: Tue Jun 29 14:02:22 2010 -0700 fix totally brain dead bug that my code buddy should have caught (take that anonymous buddy!). Also add option for testing commit 246e4b463920a8d71562b29bcb390237cf3b7d0f Author: Cricket Sloan Date: Tue Jun 29 14:01:53 2010 -0700 New DAF's for the June 21st 2010 freeze commit fea3a088aa6b28b8402a5c162ffcf852eeb20381 Author: Cricket Sloan Date: Tue Jun 29 13:50:01 2010 -0700 Improvements on meta data and on display for CaltechRNA seq commit 1b2118ba583fb5a5b3ee7474f9f7833bafd123f6 Merge: 0eb640f 5e0a83e Author: Cricket Sloan Date: Tue Jun 29 13:47:59 2010 -0700 Merge branch 'master' of cricket@hgwdev.cse.ucsc.edu:/data/git/kent commit e8f942bda28dea6dbd52c4540b48401c2a7d6099 Author: mary Date: Tue Jun 29 13:06:05 2010 -0700 some html edits - fairly minor commit 5e0a83e12a1478f59e08c99045cab0cf2faf5450 Merge: 1f53205 bd22a9a Author: katrina Date: Tue Jun 29 12:19:50 2010 -0700 Merge branch 'master' of katrina@hgwdev.cse.ucsc.edu:/data/git/kent commit 1f53205cfcb04c23323637a42166c814de927bf4 Author: katrina Date: Tue Jun 29 12:19:37 2010 -0700 removed this file because it will not be needed after all commit bd22a9a2a5bb9d840ec76b6a4da5d9f2f95748cb Author: Hiram Clawson Date: Tue Jun 29 11:57:36 2010 -0700 limit haplotypeLocations to the three chromosomes it is on commit de9b481d03b897b35a2d0f78e1c27524677594ed Merge: 9590679 fceee73 Author: vanessa Date: Tue Jun 29 11:51:56 2010 -0700 Merge branch 'master' of vanessa@hgwdev.cse.ucsc.edu:/data/git/kent commit fceee730b2cf724296e40212a97d9fbe124a191d Merge: d36b120 75ef1a6 Author: Hiram Clawson Date: Tue Jun 29 11:49:46 2010 -0700 Merge branch 'master' of hiram@hgwdev.cse.ucsc.edu:/data/git/kent commit d36b120b53efde8f3495ac0e3b9b94c41c0d9eaa Author: Hiram Clawson Date: Tue Jun 29 11:49:31 2010 -0700 adding haplotypeLocations track on hg19 commit 95906792fe6ba5f3fb99f234b424e5c09e0d30ea Merge: b26d4be 75ef1a6 Author: vanessa Date: Tue Jun 29 10:17:25 2010 -0700 Merge branch 'master' of vanessa@hgwdev.cse.ucsc.edu:/data/git/kent commit 75ef1a656ec2ed6ef2a7d487892e9b1dab348694 Author: ann Date: Tue Jun 29 10:16:13 2010 -0700 adding release alpha blocks for polyA tracks commit 5416fd2211e6fa65270c066788fcab8854abde7c Merge: 205d90e 046e3d2 Author: Larry Meyer Date: Tue Jun 29 08:55:27 2010 -0700 Merge branch 'master' of larrym@hgwdev.cse.ucsc.edu:/data/git/kent into remote commit eb219acbbf7f769f81a9c0da783815a28f685b15 Author: Larry Meyer Date: Tue Jun 29 08:45:20 2010 -0700 add scoreDelta option commit 60b24b54742fb69112a1050f8b56c9a5c3c3b34c Merge: b5e60a8 046e3d2 Author: Venkat Malladi Date: Tue Jun 29 08:16:10 2010 -0700 Merge branch 'master' of vsmalladi@hgwdev.cse.ucsc.edu:/data/git/kent commit 046e3d2b5a44c41578e5f87c92838a53b5bf862e Author: Galt Barber Date: Tue Jun 29 08:00:12 2010 -0700 "Encode release log update" commit 93bcbf1bd2440692cfaffcf594672d64e32a65d9 Author: Galt Barber Date: Tue Jun 29 08:00:11 2010 -0700 "Release log update" commit 6048cccec48f570db9e32132eb29778a2cd18028 Merge: 0ae681c e698094 Author: Galt Barber Date: Mon Jun 28 22:42:41 2010 -0700 Merge branch 'master' of hgwdev:/data/git/kent commit 0ae681c4fd4582d12d83ca76e3cdd85b7fbefbaa Author: Galt Barber Date: Mon Jun 28 22:42:28 2010 -0700 v235 preview commit e698094f3540a5139db24a31c3184ede3819162c Author: Melissa Cline Date: Mon Jun 28 18:58:44 2010 -0700 Cleaned up some wording commit d8f6123849dfc023b84b5d1867ef668e71024d2e Author: Galt Barber Date: Mon Jun 28 18:05:50 2010 -0700 more path oddness commit f9a8911d062201553005c32260baba16f3fb4bfb Merge: 379d82b 0166664 Author: Galt Barber Date: Mon Jun 28 17:18:59 2010 -0700 Merge branch 'master' of hgwdev:/data/git/kent commit 379d82bbc499f29fd71e76e141f899837a4b504e Author: Galt Barber Date: Mon Jun 28 17:18:51 2010 -0700 error message belows with git show not git cherry-pick commit 01666645a85151abf8dc08a147ea64486c8b27d5 Author: Galt Barber Date: Mon Jun 28 17:15:17 2010 -0700 fixing zlib dependencies in makefile commit a8f415597aaa623278800264671ea383b9df4ef5 Author: Melissa Cline Date: Mon Jun 28 17:11:26 2010 -0700 Adding the Affy Exon track commit fb7634382ada69fab419508a30e1f054adc35d4e Author: Melissa Cline Date: Mon Jun 28 17:09:59 2010 -0700 Typo fix commit c4aa436727a39e1a0bc2d3e36a6e79eaae6ac09a Merge: f9a1474 68268d7 Author: Melissa Cline Date: Mon Jun 28 17:02:46 2010 -0700 Merge branch 'master' of cline@hgwdev.cse.ucsc.edu:/data/git/kent commit f9a1474c86694fdf56781f79eaf934be3f339205 Author: Melissa Cline Date: Mon Jun 28 17:02:12 2010 -0700 Adding an HTML page for the Affy Exon track commit 68268d7f643b42b78521c7b94fefcc2bde80defa Merge: fa9a405 22fec17 Author: Tim Dreszer Date: Mon Jun 28 16:15:48 2010 -0700 Merge branch 'master' of tdreszer@hgwdev.cse.ucsc.edu:/data/git/kent commit fa9a4052cbc6e42d290560755e5f8302c267ce7e Author: Tim Dreszer Date: Mon Jun 28 16:15:42 2010 -0700 Added special features to mdbPrint to print SQL insert statements for expTable and spacial case extension for adding expIds to exisiting mdb objects. commit 22fec17e67abe7195233c1a1eca59493fff51783 Author: Galt Barber Date: Mon Jun 28 16:12:42 2010 -0700 faster, pussycat commit 9d9482c1bc0bbcaa2b8fcf60f34a9de760ddda72 Merge: 6b74a7d 6fcf91b Author: Galt Barber Date: Mon Jun 28 16:10:57 2010 -0700 Merge branch 'master' of hgwdev:/data/git/kent commit 6b74a7dc215a8af4fe906c5101cf1b70cd65877e Author: Galt Barber Date: Mon Jun 28 16:10:48 2010 -0700 fixing zip paths commit 6fcf91bcff9fde5a79907ca84b82532615826075 Merge: fed204c d63b0d9 Author: Fan Hsu Date: Mon Jun 28 16:06:36 2010 -0700 Merge branch 'master' of fanhsu@hgwdev.cse.ucsc.edu:/data/git/kent commit fed204c6a1f677f1c06ab0ee93d48ed7fa113a9e Author: Fan Hsu Date: Mon Jun 28 16:00:01 2010 -0700 Fixed a bug. commit d63b0d99529aec8b5041921fcf2b9cc2c40bacc4 Author: katrina Date: Mon Jun 28 15:58:50 2010 -0700 added display color information to description page commit 205d90e0d50519f0ed06213fd7e1fc62b92b6196 Author: Larry Meyer Date: Mon Jun 28 14:51:02 2010 -0700 remote track work commit 290bed0188b25d96661c246e40d8ae525a1c95ff Author: Larry Meyer Date: Mon Jun 28 14:49:07 2010 -0700 remote track work commit d9043ae1436bf052090bcf525e2f9084208e99b1 Merge: facb9b7 d7e6275 Author: Larry Meyer Date: Mon Jun 28 14:32:38 2010 -0700 Merge branch 'master' of larrym@hgwdev.cse.ucsc.edu:/data/git/kent into remote commit d7e62753f4baddfa7f96aed882a5c28864b34bee Author: Galt Barber Date: Mon Jun 28 14:12:03 2010 -0700 adding another common error condition commit 56048d2c1182d45b6d81269bee032d0b252be1ee Author: Tim Dreszer Date: Mon Jun 28 13:50:42 2010 -0700 Mark incoming ENCODE submissions as 'post' JUne 2010 freeze commit d8f5df8aae554c2a69447de22e092eea33bab558 Author: Tim Dreszer Date: Mon Jun 28 13:05:10 2010 -0700 ignore ~ files created by gedit and other programs commit facb9b72b1e2ee45cf72dbbeee545855409aa060 Merge: 6eab325 c275f4b Author: Larry Meyer Date: Mon Jun 28 12:16:40 2010 -0700 Merge branch 'master' of larrym@hgwdev.cse.ucsc.edu:/data/git/kent into remote commit c275f4b639d2e9189e22b05a40cf0b31f09b4ff0 Merge: 2be79e7 cbced21 Author: Chin Li Date: Mon Jun 28 11:31:45 2010 -0700 Merge branch 'master' of chinhli@hgwdev.cse.ucsc.edu:/data/git/kent commit 2be79e7720a5303411d9f5e747010e6ac744fa00 Author: Chin Li Date: Mon Jun 28 11:28:28 2010 -0700 chmod -x and file name correction to README.local.git.source commit 0eb640f2d3c14b218226019dfbea2e13ab226ff0 Merge: 98f65a8 cbced21 Author: Cricket Sloan Date: Mon Jun 28 09:07:16 2010 -0700 Merge branch 'master' of cricket@hgwdev.cse.ucsc.edu:/data/git/kent commit b5e60a8d61b28eb5427ae20232bc8aa3d9767403 Merge: e51d318 cbced21 Author: Venkat Malladi Date: Mon Jun 28 08:54:18 2010 -0700 Merge branch 'master' of vsmalladi@hgwdev.cse.ucsc.edu:/data/git/kent commit cbced21ffca086247e19ec50783c731af9137194 Author: Fan Hsu Date: Mon Jun 28 08:34:45 2010 -0700 Correct a typo. commit 8af41f8826ce562a068155aae549e8ac075b261e Author: Galt Barber Date: Mon Jun 28 08:00:12 2010 -0700 "Encode release log update" commit 253f793d62f15380bb8d90e2caff5eacb16be363 Author: Galt Barber Date: Mon Jun 28 08:00:10 2010 -0700 "Release log update" commit e5313e9ee01239600d8c4bc22a4aaa274365e843 Author: Galt Barber Date: Sun Jun 27 21:48:16 2010 -0700 little fix commit 593a497b4ff91b88de1ce0ac1748e69aa40f9103 Author: Galt Barber Date: Sun Jun 27 21:41:26 2010 -0700 check if we are on the master branch before running commit 7590361cb4a70ad564d40564a909a88789964889 Author: Galt Barber Date: Sun Jun 27 21:39:35 2010 -0700 minor tweaks commit 8d4a96c72d2dd93c20bb346539c7c15b73055537 Author: Galt Barber Date: Sun Jun 27 21:37:03 2010 -0700 first attempt at git automated patching using the cherry-pick method commit 36a3fe3b8c59a6ba0140b1747661466438f5064e Merge: d7e7d89 f2c2eee Author: Galt Barber Date: Sun Jun 27 21:35:51 2010 -0700 Merge branch 'master' of hgwdev:/data/git/kent commit d7e7d8996dc3031acd0d35d3e5bdde2ce6dc0300 Author: Galt Barber Date: Sun Jun 27 21:35:41 2010 -0700 fix path to full.props commit f2c2eee265ac9b2a4e45f13e5ed9e0b433c41b8d Author: Galt Barber Date: Sun Jun 27 08:00:12 2010 -0700 "Encode release log update" commit 2bb638ed68de10cfee154ff0338eb0c0de4f491d Author: Galt Barber Date: Sun Jun 27 08:00:10 2010 -0700 "Release log update" commit 925d6225005cbc7c4f927ebd1d54b95596c6203c Author: Galt Barber Date: Sat Jun 26 09:13:05 2010 -0700 removing unneeded single quotes around email subject in several build scripts commit 1666d231e1b32b0073e8541aa07ff61681f791cd Merge: 098021ae 7973939 Author: Galt Barber Date: Sat Jun 26 08:31:47 2010 -0700 Merge branch 'master' of hgwdev:/data/git/kent commit 098021ae5b50a637fab23d09fb859082c90f8ddf Author: Galt Barber Date: Sat Jun 26 08:31:40 2010 -0700 little path fixes to these due to modifying JAVABUILD setting earlier commit 79739397d3ac0938847c4b2ba207821c66393e38 Author: Galt Barber Date: Sat Jun 26 08:00:18 2010 -0700 "Encode release log update" commit 2fc82a51019fa00f99d2b0167c7830acbbff8b29 Author: Galt Barber Date: Sat Jun 26 08:00:16 2010 -0700 "Release log update" commit eb8abcf2f67ae470ace8e253e7a33d8d51898031 Author: Jim Kent Date: Sat Jun 26 00:19:22 2010 -0700 Adding HepG2 cell line to wgEncodeReg tracks. Making room for this in the rainbow color scheme. commit 94af166bd687a96c8f7059c67d7568c1ff4b9d0a Author: Jim Kent Date: Sat Jun 26 00:18:16 2010 -0700 Freen does some colorful stuff. commit cb746da657a6e54cf46c1e8793b2d6ced2afdd5e Author: Jim Kent Date: Sat Jun 26 00:17:47 2010 -0700 Making it so that subtracks of composites without priorities are sorted by a case-insensitive comparision rather than a case sensitive comparison of label, which is consistent to how tracks are sorted elsewhere. commit 5de03f14d87642aac601987e63f3f70eb199567c Author: Jim Kent Date: Sat Jun 26 00:15:54 2010 -0700 Fixing order of subtracks of supertracks in hgTrackUi so works for both wgEncodeReg and for wgEncodeHistone.... commit c7e7830ee726192a4e75c8e807a5b7f68c8ce1bb Merge: b2defaa 3c386b8 Author: Jim Kent Date: Fri Jun 25 23:56:21 2010 -0700 Merge branch 'master' of kent@hgwdev.cse.ucsc.edu:/data/git/kent commit 3c386b88dfcb64ab673c9f9e50beefcb5fc658a2 Merge: 5e16f52 1dd3274 Author: Galt Barber Date: Fri Jun 25 23:23:00 2010 -0700 Merge branch 'master' of hgwdev:/data/git/kent commit 5e16f52391a935da9174bc8bd0404b3b6505b782 Author: Galt Barber Date: Fri Jun 25 23:22:53 2010 -0700 fix typo in doJavaUtilBuild.csh commit ede3ab5e8311d7ce3036e7afbfe520c0f5dd6965 Author: Galt Barber Date: Fri Jun 25 23:13:29 2010 -0700 fixing build scripts to not use confusing var $dir commit 1dd3274609a365617b24ebe59439addab618663b Author: Melissa Cline Date: Fri Jun 25 17:56:54 2010 -0700 A few more minor fixes from Katrina commit e51d318c806cd02e37b3d115a385e417cf770483 Author: Venkat Malladi Date: Fri Jun 25 17:03:46 2010 -0700 Added comments for aditional Lab Yale in both Dafs commit f8a9291a2ccfc60dfb0a7e28e544357a5c45527a Merge: f115237 c57a23e Author: katrina Date: Fri Jun 25 17:02:20 2010 -0700 Merge branch 'master' of katrina@hgwdev.cse.ucsc.edu:/data/git/kent commit c57a23e7a56ec8c640ca5e354cc61a720e062625 Author: Venkat Malladi Date: Fri Jun 25 17:00:56 2010 -0700 Initial drafts of MM9, Haridson grant (PSU) Dafs (4 DataType, 5 Dafs) commit f11523786abb963f6509431d8b5fa0a02f2375ba Author: katrina Date: Fri Jun 25 17:00:43 2010 -0700 refining new ENCODE portal pages commit 76c114b52fc861d838bb123f060ae2309777d1e2 Author: katrina Date: Fri Jun 25 16:59:23 2010 -0700 adding new mouse ENCODE specific pages that will be part of the ENCODE portal commit d6abe6e4fdb7907a4bb2d0f8e11293d7908a959d Author: Venkat Malladi Date: Fri Jun 25 16:58:56 2010 -0700 Updated Stanfor/Yale MM9 Dafs to be consistent with other mouse DAFS commit f2e68208e13e633f486a43d87a3ce38370b54d7d Merge: f9910fb 6843085 Author: Venkat Malladi Date: Fri Jun 25 16:57:55 2010 -0700 Merge branch 'master' of vsmalladi@hgwdev.cse.ucsc.edu:/data/git/kent commit f9910fb92b16ea673bf6b5254f5a81653d16ab45 Author: Venkat Malladi Date: Fri Jun 25 16:57:41 2010 -0700 Updated LICR MM9 Dafs to be consistent with other mouse DAFS commit 7054e0143df8c0af9574d843b84d729a128d9c2d Merge: 9934e36 6843085 Author: katrina Date: Fri Jun 25 15:58:51 2010 -0700 Merge branch 'master' of katrina@hgwdev.cse.ucsc.edu:/data/git/kent commit 6843085cc1df8ab1de4efdb3ba02842ae07e2d45 Merge: 69756c2 d23e8e4 Author: Tim Dreszer Date: Fri Jun 25 15:58:19 2010 -0700 Merge branch 'master' of tdreszer@hgwdev.cse.ucsc.edu:/data/git/kent commit 69756c21f8f67dc25eee507c1e399e6e58b558f4 Author: Tim Dreszer Date: Fri Jun 25 15:58:07 2010 -0700 Changes to allow viewInTheMiddle template trackDb files to be patched in properly commit 9934e36b1bbef9d5c0d62e9627c5a5d29bb118cb Merge: 58bec02 d23e8e4 Author: katrina Date: Fri Jun 25 15:57:39 2010 -0700 Merge branch 'master' of katrina@hgwdev.cse.ucsc.edu:/data/git/kent commit d23e8e43c841b0d1f89f6bc52a28d339baeacde3 Merge: 6cf6c10 8728bc5 Author: Chin Li Date: Fri Jun 25 15:56:31 2010 -0700 Merge branch 'master' of chinhli@hgwdev.cse.ucsc.edu:/data/git/kent commit 6cf6c104ca6925c2eec1ad2d7da1f2048b61b1a0 Author: Chin Li Date: Fri Jun 25 15:56:07 2010 -0700 Initial Git Instruction commit 6ad69ec74e88b0093d979b3854ce48e2dab7b3a3 Merge: f556cd0 8728bc5 Author: Mark Diekhans Date: Fri Jun 25 15:40:05 2010 -0700 Merge branch 'master' of hgwdev.cse.ucsc.edu:/data/git/kent commit 58bec024f037ffc4b46ae8c436091d5f53373cdc Author: katrina Date: Fri Jun 25 15:37:47 2010 -0700 adding new cell types controlled vocab page for mouse ENCODE commit b2defaa9c9852f66ab439d1e681205851bf2b164 Merge: 40304e7 99d5d10 Author: Jim Kent Date: Fri Jun 25 14:26:19 2010 -0700 Merge branch 'master' of kent@hgwdev.cse.ucsc.edu:/data/git/kent commit 8728bc595eb1e87284ff88d0dbe2cf2595c995cd Merge: 299cf26 99d5d10 Author: katrina Date: Fri Jun 25 14:04:33 2010 -0700 Merge branch 'master' of katrina@hgwdev.cse.ucsc.edu:/data/git/kent commit 40304e719f6daf3414709747d700a6b7690db240 Author: Jim Kent Date: Fri Jun 25 13:58:41 2010 -0700 Adding inputTrackList build, and removing some old no longer used steps from the part on the wgEncodeReg clusters. commit c6a44344a510f89ba239d63173141f8b4d119560 Author: Jim Kent Date: Fri Jun 25 13:57:08 2010 -0700 Making log transform for wig more apparent in graph, and clarifying it's really ln(x+1) rather than the log(x) you might expect. commit 99d5d105233792fac67ec15464bd0384aa8594ed Merge: 09fb64c 7a56fc7 Author: Tim Dreszer Date: Fri Jun 25 13:54:00 2010 -0700 Merge branch 'master' of tdreszer@hgwdev.cse.ucsc.edu:/data/git/kent commit 09fb64c9161415d91151414ce8ac86404773ff4f Author: Tim Dreszer Date: Fri Jun 25 13:53:52 2010 -0700 Link to composite should be db aware commit 7a56fc7060d2ac3569e8e9dd49176fed353c1558 Merge: b67f28c d326753 Author: Galt Barber Date: Fri Jun 25 12:47:49 2010 -0700 Merge branch 'master' of galt@hgwdev.cse.ucsc.edu:/data/git/kent into paraFetch commit d326753da0ec1050ceb49db6ed12dda49a3a1ab7 Author: Fan Hsu Date: Fri Jun 25 11:58:32 2010 -0700 Rebuilt BlastTab tables of rn4 and ce6 to correct hgGene other org problems. commit 299cf26bd926711786e12224c7048eda126f6031 Author: katrina Date: Fri Jun 25 11:11:42 2010 -0700 adding specific mouse downloads page in prepartion for mouse ENCODE commit 4365874d3eda066fcba6f06a379fd9bad84b0d43 Merge: f100fbd aeee482 Author: Tim Dreszer Date: Fri Jun 25 11:08:48 2010 -0700 Merge branch 'master' of tdreszer@hgwdev.cse.ucsc.edu:/data/git/kent commit f100fbda35af6537ce9341c00fb34d51dcd29acf Author: Tim Dreszer Date: Fri Jun 25 11:08:42 2010 -0700 SuperTracks needed to be slReversed before displaying. Took opportunity to add warnBox to top of hgTrackUi as it should be. commit aeee4826207e8965f1fd2c2994f313108e5bd6e3 Author: Galt Barber Date: Fri Jun 25 08:00:14 2010 -0700 "Encode release log update" commit befed392f5a8daa0fe7a7c525d5a71bae08d5f94 Author: Galt Barber Date: Fri Jun 25 08:00:12 2010 -0700 "Release log update" commit b67f28c479b6780e07033d2259d9592e7441db76 Author: Galt Barber Date: Fri Jun 25 04:19:56 2010 -0700 fixed minor bug needing to check eof right away; also added restartTotalDownloaded so that totalDownloaded gets tracked properly on auto-restart commit 0fb02363d1aa5e7d1138fcbea8c9419a830dbd82 Author: Galt Barber Date: Fri Jun 25 04:09:07 2010 -0700 adding auto-restart commit 7de00abf02bf2410c560355bb66210c6716a6a81 Author: Galt Barber Date: Fri Jun 25 03:02:34 2010 -0700 adding date so that restarts can compare to help confirm that the file has not changed commit c9bc300d2996bdc4bda8808204bad58192ba4893 Author: Larry Meyer Date: Fri Jun 25 02:45:11 2010 -0700 make SNPs zero length commit 45ee17f357279f8cbb3526ea58ff6f94bea22285 Author: Larry Meyer Date: Fri Jun 25 02:43:26 2010 -0700 fix bug in handling of multiple files caused by failing to re-initialize lists commit 3de64c0de4d01cd22d1c4543f0a16e9d89ca91e5 Author: Galt Barber Date: Fri Jun 25 02:19:31 2010 -0700 adding URL and fileSize to status file for verification in future restarts commit b2b50f0a315ff87d6178a8eaf0dab797cfcb745c Author: Galt Barber Date: Fri Jun 25 02:08:51 2010 -0700 adding more triggers to write status file whenever 100MB of data are downloaded commit 3be77b98b5dfdd47cb8a82cb9541a199b2a7516e Author: Galt Barber Date: Fri Jun 25 01:55:35 2010 -0700 added writeParaFetchStatus for both restarting failed downloads and reporting progress commit 643a6966571ee0909811e953d4e1a6a196a5a276 Author: Galt Barber Date: Fri Jun 25 01:18:53 2010 -0700 more re-arranging to support retrying unfinished parts commit 1f20d0bf98e50192fcc35ede31890ca7485c4a29 Author: Galt Barber Date: Fri Jun 25 00:48:21 2010 -0700 re-arranging to support retrying unfinished parts commit 40b3cc4018b542f5cc7637992f4b85632f626306 Author: Galt Barber Date: Thu Jun 24 21:23:46 2010 -0700 paraFetch utility should exit 1 on failure to let caller know commit 8a3a7de94e1769a0c30a7b49ec650793c760df79 Author: Galt Barber Date: Thu Jun 24 21:19:51 2010 -0700 using tempname equal to output name with ".paraFetch" extension until download is complete, then rename the tempfile to the real name when all done commit aaed41015d80e317616ea229e1d4a286249102f2 Author: Courtney Onodera Date: Thu Jun 24 20:54:09 2010 -0700 Edited short labels for Scripture tracks. commit 28b08f12af18947d7a71b0b688e37a59ee026aed Author: Courtney Onodera Date: Thu Jun 24 19:17:09 2010 -0700 Changed visibility for scripture tracks to "hide". commit 655d4160a768912677ee2b37a4dfe47398112995 Author: Courtney Onodera Date: Thu Jun 24 19:10:04 2010 -0700 Changed settings for scripture tracks to bed 12. commit 13d0e077b86f6de8a0df79761656a5839decf6cf Merge: b4d5ea8 006b1a3 Author: Galt Barber Date: Thu Jun 24 19:09:46 2010 -0700 Merge branch 'master' of galt@hgwdev.cse.ucsc.edu:/data/git/kent into paraFetch commit b4d5ea80f4b08957ab253ea9f2d647a7687968f2 Author: Galt Barber Date: Thu Jun 24 19:09:06 2010 -0700 initial paraFetch utility checkin commit 006b1a3b32e42d5bb02a1ae07634034fd7d56097 Author: Courtney Onodera Date: Thu Jun 24 19:02:16 2010 -0700 Added stuff for scripture tracks (scripture_ES, scripture_MLF, scripture_NPC). commit 116110057141c2a380728aa22eda85f03748272a Merge: b3dbed7 66b332c Author: Jim Kent Date: Thu Jun 24 18:27:32 2010 -0700 Merge branch 'master' of kent@hgwdev.cse.ucsc.edu:/data/git/kent commit b3dbed770983d0b61bbb6fd12735e38a10cd7166 Author: Jim Kent Date: Thu Jun 24 18:26:57 2010 -0700 Getting list of tracks that are being clustered from a database table (defined by an inputTrackTable trackDb tag) rather than trying to figure them out from the trackDb subGroup data. This fixes a problem that sometimes caused tracks that should have appeared in the details page to be missed after the HudsonAlpha data integration into the wgEncodeRegTfbs track. commit fc90d3cca06195620fb9ed500a2d998223eb9beb Author: Jim Kent Date: Thu Jun 24 18:23:11 2010 -0700 Adding inputTrackTable tags to wgEncodeReg subtracks that need it. commit 0c62f6d479e117500acbd816649798846fceca97 Author: Jim Kent Date: Thu Jun 24 18:22:00 2010 -0700 Adding inputTrackTable tag to trackDb, which is used by details page of factorSource type tracks. commit c2c88ddf9457758a7460f963bd9a28f50bcf9e17 Author: Jim Kent Date: Thu Jun 24 18:18:55 2010 -0700 Making it so that in dense mode the darker, higher scoring, items are drawn on top of lighter items. commit 81111ee2131f947635ecb4b6a83674e4fb85d61b Author: Jim Kent Date: Thu Jun 24 18:17:35 2010 -0700 Defining a new table type for benefit of factorSource type tracks. commit f556cd021e4cc665a70b98e43e462da244995979 Author: Mark Diekhans Date: Thu Jun 24 17:35:30 2010 -0700 update suppressions due to code changes commit 98f65a835690a67a05ef3b33e94d22c6fe17d6e7 Author: Cricket Sloan Date: Thu Jun 24 17:01:26 2010 -0700 The meta data for CHSL Long RNA Seq commit 66b332c662225a6785e48430d92dd10d309e6514 Merge: 586a85d 0b88330 Author: Cricket Sloan Date: Thu Jun 24 16:58:50 2010 -0700 Merge branch 'master' of cricket@hgwdev.cse.ucsc.edu:/data/git/kent commit 586a85da31276e05767f765daeba06a472dc552c Author: Cricket Sloan Date: Thu Jun 24 16:58:25 2010 -0700 Adding Caltech track description commit 1a5d14f881ea034b776a7dc59f243a283ca98b3a Author: Cricket Sloan Date: Thu Jun 24 16:57:37 2010 -0700 Adding the new Caltech RNA-seq track commit 5d356eade55aee7e480a01e3fda4931c6edd4354 Author: Mark Diekhans Date: Thu Jun 24 16:01:05 2010 -0700 don't do git update except on beta install commit 0b8833078e1bfc453a7ecae80166d4d41a4f52c9 Merge: 8677790 454a9f4 Author: Galt Barber Date: Thu Jun 24 15:46:42 2010 -0700 Merge branch 'master' of hgwdev:/data/git/kent commit 867779070a1256d3e30e18e95663d91eaf920746 Author: Galt Barber Date: Thu Jun 24 15:45:48 2010 -0700 convert to git - uses special merge -s ours commit 454a9f4e1ce6a26b46baa037d0590fccf5713e95 Author: Tim Dreszer Date: Thu Jun 24 15:05:20 2010 -0700 Metadata for UNC OpenChromatin UNC FAIRE June 2010 freeze commit 3902e4fe196165a7358fb55cedcafba452f5165a Merge: 37e74ca 2313d20 Author: Tim Dreszer Date: Thu Jun 24 14:54:32 2010 -0700 Merge branch 'master' of tdreszer@hgwdev.cse.ucsc.edu:/data/git/kent commit 37e74cad7b978cbdb3a39428156c6e555ebb2f03 Author: Tim Dreszer Date: Thu Jun 24 14:54:22 2010 -0700 Adding UNC FAIRE June 2010 freeze data to hg19 and updated Open Chrom descriptions commit 2313d20b658099d6f9e3341b9e31b8280d6ea881 Author: Venkat Malladi Date: Thu Jun 24 14:32:31 2010 -0700 Updated short lables to 17 character length commit eaeeb9cfcb95806de34f52d54cb9ae177d25cfc4 Author: Tim Dreszer Date: Thu Jun 24 13:49:45 2010 -0700 Metadata for Duke Open Chrom DNase June 2010 freeze commit b26d4be30a339f69108f81b838da2538af3ffde2 Merge: 5fa72a9 2856bfe Author: vanessa Date: Thu Jun 24 13:32:02 2010 -0700 Merge branch 'master' of vanessa@hgwdev.cse.ucsc.edu:/data/git/kent commit 2856bfee16596385d79440be5008ec8e5919d4f6 Author: Tim Dreszer Date: Thu Jun 24 13:28:08 2010 -0700 Adding Duke DNase June 2010 freeze data to hg19 and moving composites to supertracks commit f3118c8813dc8b3807deaca80edc14aba48d3969 Merge: b08d6b7 15a0f05 Author: Tim Dreszer Date: Thu Jun 24 12:33:10 2010 -0700 Merge branch 'master' of tdreszer@hgwdev.cse.ucsc.edu:/data/git/kent commit b08d6b782b728cd6c31f28398e7a3674cb29280c Author: Tim Dreszer Date: Thu Jun 24 12:31:59 2010 -0700 Fixed treatment!= to be interpreted as treatment NOT EXISTS commit 4af4d9809ca679c39dd1cbf0d95a46c810bf8fcf Author: Jim Kent Date: Thu Jun 24 12:03:18 2010 -0700 Adding clusterInputTrackTable.as and sql file to support regulatory cluster tracks. commit 15a0f05819e273c0b717fe1ae51f1633a3c9ce23 Author: Cricket Sloan Date: Thu Jun 24 11:57:35 2010 -0700 Adding the CSHL Long and Caltech RNA tracks commit c35fe57588f0bf9a857cf0ecd5fae1c25fd95466 Merge: 131ddc7 ebaf963 Author: Venkat Malladi Date: Thu Jun 24 11:42:42 2010 -0700 Merge branch 'master' of vsmalladi@hgwdev.cse.ucsc.edu:/data/git/kent commit 131ddc79dedf4b4de2acbe4c9d1a105c4ca45228 Author: Venkat Malladi Date: Thu Jun 24 11:41:57 2010 -0700 Updated short labels to 17 characters. Add track to Composite: ENCODE Transcription Factor Binding commit ebaf963b00f18b2569459f446ed9ea4593c823f9 Author: Fan Hsu Date: Thu Jun 24 11:34:25 2010 -0700 Added logic so that mapBoxHc() not be called in dense mode. This enable clicking on dense mode to switch to pack mode. commit c23cbdc571e3e1486137b4cc1ebe455d1618f1aa Merge: 1f28ae4 2d0f692 Author: Fan Hsu Date: Thu Jun 24 11:28:21 2010 -0700 Merge branch 'master' of fanhsu@hgwdev.cse.ucsc.edu:/data/git/kent commit 2d0f6926d9158d93624626048c91d80ec36e35d6 Merge: 31422f5 e6c346e Author: katrina Date: Thu Jun 24 11:09:08 2010 -0700 Merge branch 'master' of katrina@hgwdev.cse.ucsc.edu:/data/git/kent commit 31422f5d22dc4bb0ac1f8998d30b0344adb7daf8 Author: katrina Date: Thu Jun 24 11:08:26 2010 -0700 changed 'Terms' in topbar of ENCODE portal to 'Data Policy' commit e6c346ef43b2d6993f4f8b163bed75ae2293d1ae Author: Venkat Malladi Date: Thu Jun 24 10:54:55 2010 -0700 Added new submissions from data freeze. Add track to Composite: ENCODE Transcription Factor Binding commit 84fa2774c456e5265ded4e1e6c65d418d7ed517e Merge: 97f832d 75aa350 Author: katrina Date: Thu Jun 24 08:39:27 2010 -0700 Merge branch 'master' of katrina@hgwdev.cse.ucsc.edu:/data/git/kent commit 75aa35001e765ff23ec9a5578559ef321ca22cd0 Author: Galt Barber Date: Thu Jun 24 08:00:42 2010 -0700 "Encode release log update" commit 1b21dabd72ebbc0af41d0ef5670d0b57d999a427 Author: Galt Barber Date: Thu Jun 24 08:00:16 2010 -0700 "Release log update" commit 1f28ae43a618f5b557efd311c8f12bbdb4332011 Merge: 590c3bc bbb812e Author: Fan Hsu Date: Thu Jun 24 07:59:57 2010 -0700 Merge branch 'master' of fanhsu@hgwdev.cse.ucsc.edu:/data/git/kent commit 97f832dc2536b40d54f12583c009004cc9c05999 Merge: 9a28248 bbb812e Author: katrina Date: Thu Jun 24 04:38:21 2010 -0700 Merge branch 'master' of katrina@hgwdev.cse.ucsc.edu:/data/git/kent commit 3f201b1198fe2ba6ade9a6dc39b36adf95e18980 Merge: 1438fb8 bbb812e Author: Galt Barber Date: Thu Jun 24 04:07:38 2010 -0700 Merge branch 'master' of galt@hgwdev.cse.ucsc.edu:/data/git/kent into paraFetch commit 1438fb82056f2d3626472057bef4502438b3f985 Author: Galt Barber Date: Thu Jun 24 04:06:38 2010 -0700 initial paraFetch work - the fast multiple connection parallel downloader commit bbb812ef6b5a49857bea32aa946324306ff2c26e Merge: 13ca45a 87bdcb6 Author: Jim Kent Date: Thu Jun 24 02:40:23 2010 -0700 Merge branch 'master' of kent@hgwdev.cse.ucsc.edu:/data/git/kent commit 13ca45a2eaac86644ff1411cc20b2a3bf25136bc Author: Jim Kent Date: Thu Jun 24 02:39:44 2010 -0700 Second pass through wgEncodeReg build doc. commit 21c64045c2cdc23aba0388558fff4748dd706bfc Author: Jim Kent Date: Thu Jun 24 02:38:22 2010 -0700 Adding -dupeLetterOk option. Closing a file left dangling open. commit 5489188ece3be4e5d3bfc88304dd169ff09c06af Author: Jim Kent Date: Thu Jun 24 02:36:19 2010 -0700 Improving readability by adding comments and moving a few lines around in response to Brian's review. commit 832683e00d142ae2543545a9d717fbf40ab41a1b Author: Jim Kent Date: Thu Jun 24 02:33:10 2010 -0700 Adding tabList and cellLetter options. Mistakenly checked in test case for cellLetter with previous commit. commit a2c687b6f1096a46d154a1a0941de0faf2dc8b80 Author: Jim Kent Date: Thu Jun 24 02:29:59 2010 -0700 Improved comment. commit 6eab325c404dbfb5a28d5409f7956bb45d0d1d54 Author: Larry Meyer Date: Thu Jun 24 00:15:04 2010 -0700 fix bug which was causing us to miss exonica mutations in SNPs in N:NN>NN format; use existing dnaMotifBitScore library routine commit 44470302224f0128244554f7b4cb8ea22ce58aa2 Author: Larry Meyer Date: Wed Jun 23 23:05:26 2010 -0700 start adding mapability support commit 2462c2ac30d1f31f8bac9ee400c8d3bd25093cf2 Author: Larry Meyer Date: Wed Jun 23 21:01:50 2010 -0700 -lazyLoading; support regulatory classification commit 87bdcb6bc2b60db900f18fa1e1a3187274340690 Merge: e0b8f4c d93f289 Author: Brooke Rhead Date: Wed Jun 23 18:52:28 2010 -0700 Merge branch 'master' of rhead@hgwdev.cse.ucsc.edu:/data/git/kent commit e0b8f4cc8f57eff9924bae95185b46d96b21dced Author: Brooke Rhead Date: Wed Jun 23 18:48:52 2010 -0700 Changed the copy step at the end to a move, to keep files from accumulating in the qateam home directory. commit d93f2897cdecdf2a0c4db88e33ee3973f510312e Author: Galt Barber Date: Wed Jun 23 18:48:21 2010 -0700 adding capability to grab a url without the http response header embedded commit d2be05c0eb7e7b18d8203a7261a0ce49932070b5 Author: Galt Barber Date: Wed Jun 23 18:45:49 2010 -0700 https should have been there long ago commit 1a08642045d6a9dfdc0e96ebecb94cfab41b6176 Author: Antonio Coelho Date: Wed Jun 23 17:10:46 2010 -0700 Removing broken link commit 9f24d308d3e8400d3f740a59ad3daf42f7bdf26a Merge: d3b3078 32bcc73 Author: Antonio Coelho Date: Wed Jun 23 17:09:37 2010 -0700 Merge branch 'master' of antonio@hgwdev.cse.ucsc.edu:/data/git/kent commit d3b3078c5cf8ba618112aac30ead1c475a22b47b Author: Antonio Coelho Date: Wed Jun 23 17:09:18 2010 -0700 Removing broken link commit 32bcc737a84aefbd6cdb3eff82985ea826775575 Merge: 8da41a4 ad67ae6 Author: Tim Dreszer Date: Wed Jun 23 17:08:36 2010 -0700 Merge branch 'master' of tdreszer@hgwdev.cse.ucsc.edu:/data/git/kent commit 8da41a403e0931c1fcd3ef7e68672ea15e1e3b5c Author: Tim Dreszer Date: Wed Jun 23 17:08:26 2010 -0700 One more fileName error that Jim caught commit ad67ae6e69fc045c2ec5921a974e1ce9500129ab Merge: 264574d b9b3a58 Author: Melissa Cline Date: Wed Jun 23 16:50:35 2010 -0700 Merge branch 'master' of hgwdev.cse.ucsc.edu:/data/git/kent commit 264574d592b9f116fb965beea81e8285baaf772a Author: Melissa Cline Date: Wed Jun 23 16:50:10 2010 -0700 incorporating feedback from Katrina and from review commit b9b3a58715b7d2a1a7afb7587b663d77c79fc440 Merge: b464a39 f2d1ec4 Author: Galt Barber Date: Wed Jun 23 16:40:10 2010 -0700 Merge branch 'master' of galt@hgwdev.cse.ucsc.edu:/data/git/kent commit b464a39d28049a0e07f2a1bda5efdef91d4d0fbb Author: Galt Barber Date: Wed Jun 23 16:26:59 2010 -0700 doubling download timeout to 20 hours commit f2d1ec42733ce448701396e5f269037960dfbf2b Author: Tim Dreszer Date: Wed Jun 23 16:05:24 2010 -0700 Removeing Cshl include as Cricket says it is not ready commit 9a28248a37fbc1e6a5663787b2999c4985c6b3e5 Merge: 6b5679c b7fe3ce Author: katrina Date: Wed Jun 23 15:48:42 2010 -0700 Merge branch 'master' of katrina@hgwdev.cse.ucsc.edu:/data/git/kent commit b7fe3ce56d1a412d4437dda7cf801b38cb538e66 Merge: eaae21b 65b80cd Author: Jim Kent Date: Wed Jun 23 14:53:46 2010 -0700 Merge branch 'master' of kent@hgwdev.cse.ucsc.edu:/data/git/kent commit 65b80cdc795b3d8eb15a328ec557b6fa59d7a828 Merge: db11d2c cdec89b Author: Tim Dreszer Date: Wed Jun 23 14:02:20 2010 -0700 Merge branch 'master' of tdreszer@hgwdev.cse.ucsc.edu:/data/git/kent commit db11d2c66046b7d6c7c80781a70f5e1972abc098 Author: Tim Dreszer Date: Wed Jun 23 14:02:12 2010 -0700 Metadata for UTA Open Chrom ChIPseq June 2010 freeze commit 6b5679c3d4fd261ab1b24d00315db61e15bae22c Merge: 85778cc cdec89b Author: katrina Date: Wed Jun 23 13:54:23 2010 -0700 Merge branch 'master' of katrina@hgwdev.cse.ucsc.edu:/data/git/kent commit cdec89b6c3451e205b7e4fa20f9ab8746dc8723b Merge: e4f6998 30fd5fa Author: Brian Raney Date: Wed Jun 23 13:27:09 2010 -0700 Merge branch 'master' of braney@hgwdev.cse.ucsc.edu:/data/git/kent commit e4f69983f8a0676fe1b62fa156b12b4c623070bc Author: Brian Raney Date: Wed Jun 23 13:25:41 2010 -0700 move CSHL short to its own include file commit 3db407121d432403ad87f9fe833fd3b59b8ebc8c Author: Brian Raney Date: Wed Jun 23 13:24:01 2010 -0700 tweak ucsfBrainMethylation commit 30fd5fadb94625067af1eab51e564aaac1124b64 Author: Tim Dreszer Date: Wed Jun 23 12:09:20 2010 -0700 Adding UTA ChIP data for June Freeze to hg19 commit 20d9c95c018b002523cc9ed44e98e20117e022cb Merge: 12ab67d 98eff92 Author: Tim Dreszer Date: Wed Jun 23 11:59:26 2010 -0700 Merge branch 'master' of tdreszer@hgwdev.cse.ucsc.edu:/data/git/kent commit 12ab67d97bba2947802db91fdeb400acd2ad4bfd Author: Tim Dreszer Date: Wed Jun 23 11:59:19 2010 -0700 Changed some file names that Jim noticed were inaccurate commit eaae21b0e0074a997845d42d92e7631743c6a280 Author: Jim Kent Date: Wed Jun 23 11:25:37 2010 -0700 Working on program that will set up batch file to merge replicates. commit 98eff92a48562ea55e861593d3c4411ea187ad47 Author: mary Date: Wed Jun 23 09:50:37 2010 -0700 making refSeq (and other tracks for cavPor3) on hide by default since there is nothing in them for the default position commit 85778ccf42c22b88a48bd2c36e0d35c56a6df531 Merge: 77695df 35e46f8 Author: katrina Date: Wed Jun 23 09:30:52 2010 -0700 Merge branch 'master' of katrina@hgwdev.cse.ucsc.edu:/data/git/kent commit 35e46f8d67dccb347b53186b2129f920ac5e93a7 Author: Galt Barber Date: Wed Jun 23 08:00:41 2010 -0700 "Encode release log update" commit a70f806877423cd09a3dc47363e070530e91a72c Author: Galt Barber Date: Wed Jun 23 08:00:19 2010 -0700 "Release log update" commit 77695dfffd691b85737dc1110d797c30057b8f3d Merge: cb905c0 109a6f5 Author: katrina Date: Wed Jun 23 04:38:29 2010 -0700 Merge branch 'master' of katrina@hgwdev.cse.ucsc.edu:/data/git/kent commit 109a6f5fca18d8fc9666ed5fe6f4d0789a107fb3 Author: Venkat Malladi Date: Tue Jun 22 19:47:17 2010 -0700 Updated all metadata for HAIB TFBS for June 22 freeze commit 590c3bc5ace4eb1842112a451a88cd3d6e574e26 Author: Fan Hsu Date: Tue Jun 22 16:47:55 2010 -0700 Updated Reactome tables. commit 2bac0833ee1ef9e2d0a1eefcfea33f4f55fd6873 Author: Tim Dreszer Date: Tue Jun 22 16:27:30 2010 -0700 Removed some erroneous dateResubmitteds commit 06f8b84f330d8f59fb764a0d1f9b3c2f7b83dd6f Merge: a0ef1d2 d52d91e Author: Tim Dreszer Date: Tue Jun 22 16:16:31 2010 -0700 Merge branch 'master' of tdreszer@hgwdev.cse.ucsc.edu:/data/git/kent commit a0ef1d2bba0b2b3f0e2960029bfca2bcb00080ca Author: Tim Dreszer Date: Tue Jun 22 16:16:23 2010 -0700 Metadata for Broad Histone June 2010 freeze commit d52d91ee09056f8c7ea54ec68205a944e77a99c7 Merge: 70efeb3 f0901e3 Author: Galt Barber Date: Tue Jun 22 16:15:52 2010 -0700 Merge branch 'master' of galt@hgwdev.cse.ucsc.edu:/data/git/kent commit f0901e37fda7fd51ac842bf73dd1de4129146aea Merge: 8da6fac b6481c9 Author: Donna Karolchik Date: Tue Jun 22 15:54:35 2010 -0700 Merge branch 'master' of donnak@hgwdev.cse.ucsc.edu:/data/git/kent commit 8da6fac0ddf533a4c99253834395e9239da939c7 Author: Donna Karolchik Date: Tue Jun 22 15:54:04 2010 -0700 Fixed typo. commit b6481c9d84740820c6b59d1180e84d39572620a1 Merge: bf3ace3 06be10d Author: Tim Dreszer Date: Tue Jun 22 15:53:46 2010 -0700 Merge branch 'master' of tdreszer@hgwdev.cse.ucsc.edu:/data/git/kent commit bf3ace3b6ee1b89278df2317c7c58ad248d0db34 Author: Tim Dreszer Date: Tue Jun 22 15:53:35 2010 -0700 Adding Broad Histone June 2010 freeze tracks commit 06be10dc9a809e92d82e2be00e58df79b6407670 Merge: 85546fa 7fd9ee9 Author: Brian Raney Date: Tue Jun 22 15:48:45 2010 -0700 Merge branch 'master' of braney@hgwdev.cse.ucsc.edu:/data/git/kent commit 85546fab9cc44b7f715330d90cd6cd490fe33d99 Author: Brian Raney Date: Tue Jun 22 15:48:28 2010 -0700 add RikenCage commit c65ee6c705a6bfa03c5acf5a529ef2a04abea24b Author: Brian Raney Date: Tue Jun 22 15:34:41 2010 -0700 fix typo commit 70efeb35ac5f886374d21c301c507bf83af9d077 Merge: 2ceb783 7fd9ee9 Author: Galt Barber Date: Tue Jun 22 15:11:16 2010 -0700 Merge branch 'master' of galt@hgwdev.cse.ucsc.edu:/data/git/kent commit cb905c0031d1a46b5ddaa6fe92e05c2cbea5a8dc Merge: b7831c6 7fd9ee9 Author: katrina Date: Tue Jun 22 14:14:22 2010 -0700 Merge branch 'master' of katrina@hgwdev.cse.ucsc.edu:/data/git/kent commit 7fd9ee974697f6b9b7c063894c6b5d6c15bc14e4 Merge: fea2362 e70d875 Author: Antonio Coelho Date: Tue Jun 22 14:12:19 2010 -0700 Merge branch 'master' of antonio@hgwdev.cse.ucsc.edu:/data/git/kent commit fea2362764c623358ff34cfafab2fa6305f60f19 Author: Antonio Coelho Date: Tue Jun 22 14:12:01 2010 -0700 adding affyDrosDev tables to tablesIgnored commit b7831c6341c54af4f55f8fbda4b1fa197f459611 Author: katrina Date: Tue Jun 22 13:48:16 2010 -0700 adding new page for other controlled vocabulary terms commit e70d875394eb54eea462aebd1d6b9a8224995333 Author: Venkat Malladi Date: Tue Jun 22 13:41:25 2010 -0700 Added new metaData and updated orginal dates of resubmitted data commit aaf0930b481cf2b5575c82f5403f033028f208de Merge: 89ddf16 f1610bc Author: Venkat Malladi Date: Tue Jun 22 13:40:14 2010 -0700 Merge branch 'master' of vsmalladi@hgwdev.cse.ucsc.edu:/data/git/kent commit 89ddf161dd722432ab523af1cc54516fa4eb9093 Author: Venkat Malladi Date: Tue Jun 22 13:39:13 2010 -0700 Updated metaData to include new submissions and consolidated lab name commit f1610bcea9db115a9c9e0eb0a2c1e4e063ba9fc2 Author: Steve Benz Date: Tue Jun 22 13:33:33 2010 -0700 Added hgsqlProfile to support connecting to dbs using the profile name commit 2ceb78320106255544886ff36b62665b14dd0b62 Author: Galt Barber Date: Tue Jun 22 13:28:32 2010 -0700 all the way out to one million matches old cvs reports commit 745daa8a24998eb92f4d4a07b1f9ad859d0f9144 Author: Galt Barber Date: Tue Jun 22 13:25:50 2010 -0700 adding more context for some big files commit 242f111202bb197770e774741c03dd38b17e107c Author: Galt Barber Date: Tue Jun 22 13:01:22 2010 -0700 allow to get arguments from parent make commands commit c5178873640424d1194963dc697eedc9eede67de Merge: fd327e7 5fcbb05 Author: Galt Barber Date: Tue Jun 22 12:59:44 2010 -0700 Merge branch 'master' of galt@hgwdev.cse.ucsc.edu:/data/git/kent commit c506e8d71956280a330b9ed178c141d35547b5e5 Author: Jim Kent Date: Tue Jun 22 12:43:32 2010 -0700 Turning 3col to 4col output. commit b5900359e90c6d0284ddc8eb9c7dc28fc7b153e4 Author: Jim Kent Date: Tue Jun 22 12:37:55 2010 -0700 Making metaObject be a synonym for obj in selects. commit 9ac75aded11668fb0735ab03c1c7e8b9c9a62285 Author: Jim Kent Date: Tue Jun 22 12:35:13 2010 -0700 Making ra output use metaObject rather than obj. commit 5fcbb051bdabc40345fbffd5e13d8483f523570b Merge: bb5fe7e 6802c6c Author: Tim Dreszer Date: Tue Jun 22 11:56:39 2010 -0700 Merge branch 'master' of tdreszer@hgwdev.cse.ucsc.edu:/data/git/kent commit bb5fe7eb32b2230f201902f950cf524e216aaf53 Author: Tim Dreszer Date: Tue Jun 22 11:56:30 2010 -0700 Filled out details for 2 antibodies for Broad commit 0bbf49e532a555ea527d7f552d6614c511406d80 Author: Jim Kent Date: Tue Jun 22 11:12:11 2010 -0700 Improving some comments and a function name. commit 6802c6c22127d933cf03e74e8dfa75305049be87 Merge: ae19e29 139ad5d Author: Venkat Malladi Date: Tue Jun 22 10:13:34 2010 -0700 Merge branch 'master' of vsmalladi@hgwdev.cse.ucsc.edu:/data/git/kent commit ae19e2955285144130c197ce85a614923af5cdbe Author: Venkat Malladi Date: Tue Jun 22 10:10:20 2010 -0700 Added 2 new submissions to track. Changed tagAligns to Bam files; updated metaData and index.html commit 139ad5d08bcc5a4fef642b306054395aa57e5ecd Merge: acc667d 387f548 Author: Hiram Clawson Date: Tue Jun 22 09:38:18 2010 -0700 Merge branch 'master' of hiram@hgwdev.cse.ucsc.edu:/data/git/kent commit acc667dc7a13505b978804ad99fe6295656b6fc6 Author: Hiram Clawson Date: Tue Jun 22 09:38:07 2010 -0700 proper parallel list makefile commit 387f5481dc5479c50c2fd99dc9b4957d6eeeebca Author: katrina Date: Tue Jun 22 08:24:29 2010 -0700 Placing 'Loc' tracks to new grouping and Genecode Genes to new Genes group commit e9eb375b9b403defb4fe8b0e2e7d9c16f2ccb6e6 Merge: 614cd91 4417ac2 Author: katrina Date: Tue Jun 22 08:15:04 2010 -0700 Merge branch 'master' of katrina@hgwdev.cse.ucsc.edu:/data/git/kent commit 4417ac2825d968442823f69f0f858cf9423f4403 Author: Galt Barber Date: Tue Jun 22 08:00:27 2010 -0700 "Encode release log update" commit 235446a662fc6de03ad422de186dd1a29f3fa867 Author: Galt Barber Date: Tue Jun 22 08:00:12 2010 -0700 "Release log update" commit 614cd91be9005e32a9d984e34496976b0f0132dd Merge: 6f516a5 d3cef4d Author: katrina Date: Tue Jun 22 04:38:37 2010 -0700 Merge branch 'master' of katrina@hgwdev.cse.ucsc.edu:/data/git/kent commit d3cef4d13572d039c8d3c4f230fff3b5579a7483 Author: Galt Barber Date: Tue Jun 22 03:30:22 2010 -0700 fixing typo commit fd327e7b2b86caee9338f8a384ef95b79a83e824 Author: Galt Barber Date: Tue Jun 22 03:23:46 2010 -0700 temporary workaround for an initial commit which has no parent commit 555f105e9d96705ee0c672287c01c29731bda137 Author: Jim Kent Date: Tue Jun 22 02:14:25 2010 -0700 Adding error message when no from clause. commit bce6fc8dcc1d3fee1705faf8ddfb72dfe447772e Author: Galt Barber Date: Tue Jun 22 01:59:02 2010 -0700 fixing branch report commit f22bc99478476c2c72bb4add462bfd9a69241839 Author: Galt Barber Date: Tue Jun 22 01:56:46 2010 -0700 fixing branch report commit bd2d24747d0255e0aa46daffd6e9fbca0a28b5b8 Merge: 93b06c4 53a4f6d Author: Galt Barber Date: Tue Jun 22 01:21:16 2010 -0700 Merge branch 'master' of hgwdev:/data/git/kent commit 93b06c4501318c8a54a3511e920ce83055c65335 Author: Galt Barber Date: Tue Jun 22 01:21:11 2010 -0700 "New version number v234" commit 742b8ed9a2054c706e8f93689757cf0f0ef46796 Author: Galt Barber Date: Tue Jun 22 01:19:37 2010 -0700 some reports commit 9c06bdd27010aed09a6994e1e6ba9aa95689227a Author: Galt Barber Date: Tue Jun 22 01:15:25 2010 -0700 convert to git commit 53a4f6db9c408258c0c8048f29ad93bd861f02e7 Author: Jim Kent Date: Tue Jun 22 01:09:47 2010 -0700 Adding -out=tab option and renaming old out=table to out=3col. commit 3e13983eba7056bc8434a62dbe0c957b1f66c144 Author: Galt Barber Date: Tue Jun 22 01:08:44 2010 -0700 v234 final build commit f4b9b0f019b1ce806da918f81b3d8707395ce78d Author: Jim Kent Date: Tue Jun 22 00:02:53 2010 -0700 Implemented count(*) commit 7ee5c0b4773d6ac8f80ebc8417cc44c682810f50 Author: Jim Kent Date: Mon Jun 21 23:45:05 2010 -0700 First cut of mdbQuery utility. commit be46098becc324ea7350fc40869033ef32bcae80 Merge: 9f05077 cb65e5a Author: Jim Kent Date: Mon Jun 21 22:45:03 2010 -0700 Merge branch 'master' of kent@hgwdev.cse.ucsc.edu:/data/git/kent commit 9f05077cf93a6e7a926efcdf2d771c0896f20abf Author: Jim Kent Date: Mon Jun 21 22:44:35 2010 -0700 Making hgRenderTracks look up default track settings before layering on stuff passed in . commit bbc500cc6664ee209a44d671d0230bd15aa2fe6c Author: Jim Kent Date: Mon Jun 21 22:43:48 2010 -0700 adding hTrackDbForTrackAndAncestors commit 995e0b7572bfbebc0969a14fb4ce0d42c1b981b4 Author: Jim Kent Date: Mon Jun 21 22:41:40 2010 -0700 Propagating rename to makefile. commit cb65e5aa495ea0cb5bbfeb1e816a7684cef0682b Author: Venkat Malladi Date: Mon Jun 21 21:59:49 2010 -0700 Validated all changes in daf commit dd7c7bad65965b637f010cbd280c77d2431ba03b Author: Venkat Malladi Date: Mon Jun 21 20:00:26 2010 -0700 Appended daf, as validating setting got placed on an extra line commit 8afaf0b192b466e1d60d16e796b87dbafc34a904 Author: Antonio Coelho Date: Mon Jun 21 17:49:24 2010 -0700 re-enabling cavPor3 commit 634d097bcde98f8a100d0ce41e77b8265b50d252 Author: Antonio Coelho Date: Mon Jun 21 17:35:31 2010 -0700 re-enabling cavPor3 commit 69dbdc01df173f00faf08ffe4b8279a447ace387 Merge: c522511 d172034 Author: Melissa Cline Date: Mon Jun 21 17:13:10 2010 -0700 Merge branch 'master' of hgwdev.cse.ucsc.edu:/data/git/kent commit c522511d920a2633d4a254a411acf9411d760d2e Author: Melissa Cline Date: Mon Jun 21 17:12:20 2010 -0700 Added new mouse cell types commit d172034dc53750eff4052083b2cf9ff7747b48ba Merge: 3aba302 381f3c9 Author: Antonio Coelho Date: Mon Jun 21 16:22:42 2010 -0700 Merge branch 'master' of antonio@hgwdev.cse.ucsc.edu:/data/git/kent commit 3aba302c83e05f93861ad389d5d521f1db013d8c Author: Antonio Coelho Date: Mon Jun 21 16:21:27 2010 -0700 typo commit 381f3c9c5db1465b662fa548866b57e5139b47b6 Author: Tim Dreszer Date: Mon Jun 21 16:14:31 2010 -0700 UW DGF metadata for June 2010 freeze commit 5fa72a9dff267e65df63ac12a3119a96fe0ab702 Author: vanessa Date: Mon Jun 21 16:14:26 2010 -0700 changed links to reflect examples directory commit 68c0bf90d844f2471cb628421a87bc278e37ba09 Merge: 1cae4e6 6f0bfa0 Author: Tim Dreszer Date: Mon Jun 21 15:51:32 2010 -0700 Merge branch 'master' of tdreszer@hgwdev.cse.ucsc.edu:/data/git/kent commit 1cae4e69c3cdfec236f4b70ef3bf7d415b072fd3 Author: Tim Dreszer Date: Mon Jun 21 15:47:07 2010 -0700 Adding UW DGF after Jun 2010 freeze. Reordered UW Histine and Uw Dnase commit 6f0bfa00fc9175e0574c8f86efc1a241d1a1f415 Author: Venkat Malladi Date: Mon Jun 21 15:43:40 2010 -0700 Renamed file to follow pattern of lab name first in daf instead of pi commit 6f516a5dc27da6eba824f11525d55653cc59c126 Merge: 5565061 9d1eeeb Author: katrina Date: Mon Jun 21 15:19:55 2010 -0700 Merge branch 'master' of katrina@hgwdev.cse.ucsc.edu:/data/git/kent commit 9d1eeebbcf6c800b1cbf007a6017d1ef26e1b4ce Author: Venkat Malladi Date: Mon Jun 21 15:13:55 2010 -0700 Renamed file to follow pattern of lab name first in daf instead of pi commit 943b18db94bbb2937548439de376ca54e8ed195e Author: Venkat Malladi Date: Mon Jun 21 14:52:06 2010 -0700 Added new submission data to composite, previously available as downloads only commit b6d9c5553c65101fa48660b5197d3eedd66d2499 Author: Tim Dreszer Date: Mon Jun 21 14:36:57 2010 -0700 Preliminary descrition page from hg18 commit a0be35952cb34207f3be8a39e261c4ae9df22de7 Merge: ad12f27 7906060 Author: Tim Dreszer Date: Mon Jun 21 14:01:14 2010 -0700 Merge branch 'master' of tdreszer@hgwdev.cse.ucsc.edu:/data/git/kent commit ad12f27f2fc4501969504c1b0a3ddb1675d3c95f Author: Tim Dreszer Date: Mon Jun 21 14:01:05 2010 -0700 blank in wrong spot screwed this one up commit 790606040de93d79f310410092650ebce5305cd4 Author: Venkat Malladi Date: Mon Jun 21 13:58:45 2010 -0700 Added new submissions for SYDH Histone commit 45c3260db573f1abf44a382a681aadcae39c3e68 Merge: 84b01dd 8d61f52 Author: Venkat Malladi Date: Mon Jun 21 13:56:17 2010 -0700 Merge branch 'master' of vsmalladi@hgwdev.cse.ucsc.edu:/data/git/kent commit 5ed6f58758a7fb141dc03b270b7c36e2dbac4ca9 Author: Jim Kent Date: Mon Jun 21 13:53:41 2010 -0700 MOved a function up a bit. commit 8d61f5272792867fdb1841a11b9c58b9ed7a30e2 Merge: f0101a7 7f67786 Author: Cricket Sloan Date: Mon Jun 21 13:51:45 2010 -0700 Merge branch 'master' of cricket@hgwdev.cse.ucsc.edu:/data/git/kent commit f0101a7f05f25d0a5c42fc28b3094c2e95dbf3e4 Author: Cricket Sloan Date: Mon Jun 21 13:50:32 2010 -0700 Adding protocolID commit 7f677860800da3a3e44d057f9e4b17532f9a38e0 Merge: 0d14470 2b5f60a Author: Tim Dreszer Date: Mon Jun 21 13:50:12 2010 -0700 Merge branch 'master' of tdreszer@hgwdev.cse.ucsc.edu:/data/git/kent commit 0d14470fa9b658c27da85d9b4e455e5c32d3f573 Author: Tim Dreszer Date: Mon Jun 21 13:49:57 2010 -0700 Displaying UW DNase submissions for Jun 2010 freeze commit 7451d36950210fb0e91f5983eb98effbf63d519c Author: Jim Kent Date: Mon Jun 21 13:47:22 2010 -0700 Merged two files. commit 2b5f60a1af580952c40d1168b7dd663bc6ea4eaf Author: Hiram Clawson Date: Mon Jun 21 13:40:58 2010 -0700 need to have -lz on this link commit e845ff42eafc8bdbc0850e9f8bddd86eddc51f47 Merge: 665eb45 b69b309 Author: Hiram Clawson Date: Mon Jun 21 13:39:53 2010 -0700 Merge branch 'master' of hiram@hgwdev.cse.ucsc.edu:/data/git/kent commit 665eb45768d21f4e2bd40afc09c031a05df595ad Author: Hiram Clawson Date: Mon Jun 21 13:38:56 2010 -0700 reload genomicSuperDups; commit 18cad7657899363769f7dc179754ad45e99cb46b Author: Jim Kent Date: Mon Jun 21 13:38:48 2010 -0700 Renaming function and putting prototype for it in a shared header file. Again this is all part of testing renaming/splitting/merging functions. commit b5950f513efc3c640aabad95854bb95f004aabf5 Author: Jim Kent Date: Mon Jun 21 13:33:20 2010 -0700 Split testGitRename into two modules. commit de53cfc4fa09c4fbdacd35296bb4820017a46d92 Author: Jim Kent Date: Mon Jun 21 13:32:40 2010 -0700 Split testGitRename into two modules. commit bd66bb1c2162c7b152fa7527c257d629ce105145 Author: Jim Kent Date: Mon Jun 21 13:31:22 2010 -0700 Split testGitRename into two modules. commit b69b3099c094db621f13bc1457d7f6e0ae4b14f7 Author: Tim Dreszer Date: Mon Jun 21 13:03:17 2010 -0700 Did I say 76. No it is H3K479me2 commit 35a5fee74af45029dd70860e0701a39cf4063c50 Merge: 360b7d4 ad53958 Author: Tim Dreszer Date: Mon Jun 21 13:00:27 2010 -0700 Merge branch 'master' of tdreszer@hgwdev.cse.ucsc.edu:/data/git/kent commit 360b7d4071aff38581b547414fa88d288f5f523e Author: Tim Dreszer Date: Mon Jun 21 13:00:19 2010 -0700 Added 2 antibodies provisionally commit 2f00749820941d8e75780fc442bf9c19acc2f053 Author: Jim Kent Date: Mon Jun 21 12:20:34 2010 -0700 Checking in a little something just to work with renaming and merging in a safe place. commit 55650612e742bdd00e5badb0a8b3711c4b9686ae Merge: 06e3115 ad53958 Author: katrina Date: Mon Jun 21 12:15:21 2010 -0700 Merge branch 'master' of katrina@hgwdev.cse.ucsc.edu:/data/git/kent commit ad5395890bfa5b0c4d36398ea34d1ea714ca6d4f Merge: 8f6ebef 5c0a383 Author: Cricket Sloan Date: Mon Jun 21 12:13:09 2010 -0700 Merge branch 'master' of cricket@hgwdev.cse.ucsc.edu:/data/git/kent commit 8f6ebef677519caf494be870c23767dc4b521968 Author: Cricket Sloan Date: Mon Jun 21 12:12:18 2010 -0700 New dafs for HAIB project commit 84b01dd8cea8bf2c0b5b0fd9194e5c40c9c10c34 Merge: 12002a1 5c0a383 Author: Venkat Malladi Date: Mon Jun 21 11:54:25 2010 -0700 Merge branch 'master' of vsmalladi@hgwdev.cse.ucsc.edu:/data/git/kent commit 5c0a3836d994943592859bed5d64c14b7f9a5a33 Merge: f18afe8 e7059e1 Author: Larry Meyer Date: Mon Jun 21 10:39:46 2010 -0700 Merge branch 'master' of larrym@hgwdev.cse.ucsc.edu:/data/git/kent commit f18afe8c824a4a4fa7574840d4c283a25a0517bf Author: Larry Meyer Date: Mon Jun 21 10:31:43 2010 -0700 fix error message which occurrs when the search tabs aren't defined commit 12002a1daf3eed6a3825904e386f47b3fe8ea6ff Merge: 883d4b4 e7059e1 Author: Venkat Malladi Date: Mon Jun 21 10:21:20 2010 -0700 Merge branch 'master' of vsmalladi@hgwdev.cse.ucsc.edu:/data/git/kent commit 06e3115f7ace4d22de6153f021a972aa2a256fb4 Author: katrina Date: Mon Jun 21 08:46:51 2010 -0700 adding two new pages to the ENCODE portal commit e7059e189adc46343dc30517f3f602a78d584d3b Author: Galt Barber Date: Mon Jun 21 08:00:06 2010 -0700 "Encode release log update" commit 4d0ff1dadaf2218a4f4b5b2e7bd9e9716c94fb28 Author: Galt Barber Date: Mon Jun 21 08:00:05 2010 -0700 "Release log update" commit 821af59af8e30f9bfa197ee9aaf83c8a9f9fee3c Author: Galt Barber Date: Sun Jun 20 08:00:16 2010 -0700 "Encode release log update" commit 9d5bfbba4b880c97cb2aee8bf4a17d49de49ecc7 Author: Galt Barber Date: Sun Jun 20 08:00:12 2010 -0700 "Release log update" commit cba9720b3e479224b8e0ce8acce176fa0499907b Author: Galt Barber Date: Sat Jun 19 08:00:15 2010 -0700 "Encode release log update" commit d6f0db205a77491b6cc6b9d11af39670327383bf Author: Galt Barber Date: Sat Jun 19 08:00:13 2010 -0700 "Release log update" commit 82b6ed58d1d8c74bf92220a62ffa3380f679d488 Author: Mark Diekhans Date: Fri Jun 18 22:53:08 2010 -0700 reenable panTro1/2 on rr commit dcaba4f621fa3d6317245c30e8a0b0ce5c027858 Merge: 627ea9c adaefb4 Author: Brooke Rhead Date: Fri Jun 18 22:17:00 2010 -0700 Merge branch 'master' of rhead@hgwdev.cse.ucsc.edu:/data/git/kent commit 627ea9c607ddf6769f7b83aa0110ca1f8944829d Author: Brooke Rhead Date: Fri Jun 18 22:07:39 2010 -0700 Removed quotes from rm *.out, since they were causing those files to be retained. Added process ID variable to files that are created and subsequently removed, so that we can more assured that no innocent bystander files with similar names are discarded. Collapsed 'rm *Only' line into 'rm *out$$*' line. commit adaefb41c47c8ed44b75ad2793770bae5070e71b Author: Hiram Clawson Date: Fri Jun 18 20:36:26 2010 -0700 last bunch of makefiles that need a clean target commit 990ff386fbbd185aad226f6b8dfc0d4eb290d395 Author: Brian Raney Date: Fri Jun 18 17:35:16 2010 -0700 change a 1 to MG_BLACK, shame on me for having done this in the first place commit 883d4b478987921e057d8ed718a3f8e3b25ef0fc Merge: 171d9c2 bd68c5e Author: Venkat Malladi Date: Fri Jun 18 16:37:52 2010 -0700 Merge branch 'master' of vsmalladi@hgwdev.cse.ucsc.edu:/data/git/kent commit bd68c5eb728c4568874b0a2e4a277bb9e53d471d Merge: f3cffc7 98cb5d2 Author: Tim Dreszer Date: Fri Jun 18 16:07:46 2010 -0700 Merge branch 'master' of tdreszer@hgwdev.cse.ucsc.edu:/data/git/kent commit f3cffc7917dd3e275cb4aed10a121929bdc9072e Author: Tim Dreszer Date: Fri Jun 18 16:07:24 2010 -0700 CKM is male, not female commit 98cb5d214226bd5540e7424b4e73788f71627bd2 Merge: 54782f5 46f3fa3 Author: Antonio Coelho Date: Fri Jun 18 16:01:25 2010 -0700 Merge branch 'master' of antonio@hgwdev.cse.ucsc.edu:/data/git/kent commit 54782f54e8010fe01641fd06a0149b7044b3c264 Author: Antonio Coelho Date: Fri Jun 18 16:01:12 2010 -0700 adding the new encode data wranglers commit 46f3fa357941ceb35c7b3fa1fdd60bbfd4a14b6b Author: Brooke Rhead Date: Fri Jun 18 15:51:03 2010 -0700 Removed tip-of-tree cvs checkout of all.joiner file (after switch to git), collapsed joinerPath and joinerFile variables into just joinerFile variable, and updated and clarified usage statement. commit 04bf7f11a88efe09eb1131d924823ec8909de4b7 Merge: 37885ae 16d7cb1 Author: Antonio Coelho Date: Fri Jun 18 15:42:57 2010 -0700 Merge branch 'master' of antonio@hgwdev.cse.ucsc.edu:/data/git/kent commit 171d9c2a3243bedbdc4c4e0b36571f9359a5cdf1 Author: Venkat Malladi Date: Fri Jun 18 15:29:15 2010 -0700 Seperated Ren Lab Chip-Seq daf into TFBS and Histone Dafs. Added preliminary BAM validation commit 16d7cb1acbd50ff9d0f97fd4d9e7f130680698c7 Author: Venkat Malladi Date: Fri Jun 18 15:05:34 2010 -0700 Updated DAF for SYDH Histone to the one they have been using as well as updating a line to the lab names that they may use. commit 0120049e1af065ba852c2fabb1fa27417ff1f617 Author: Hiram Clawson Date: Fri Jun 18 13:51:57 2010 -0700 adding clean targets to makefiles reached via clean_utils commit 2bb11e279db8b3f64fd929319944219f6a8695c0 Author: Brian Raney Date: Fri Jun 18 11:52:35 2010 -0700 try this again, add ilNA field commit 377b5bcb24a157093ac26c0b643eb65143be30c0 Author: Brian Raney Date: Fri Jun 18 11:35:22 2010 -0700 take out NA for insert length since it was interfering with NA for mapAlgorithm commit 3c80cb672d5302e27ca6281e5845ee26f9e49ad8 Author: Brian Raney Date: Fri Jun 18 11:25:10 2010 -0700 fix up a few problems commit 6dda8104b05e000c3385b82844044f92785b945c Author: Brian Raney Date: Fri Jun 18 10:53:17 2010 -0700 add junction type that isn't validate (yet) for Caltech junction beds. commit 0452a5007a316c52c56eae2c186e8357835cc580 Merge: d529b9b 090962f Author: Brian Raney Date: Fri Jun 18 10:24:47 2010 -0700 Merge branch 'master' of braney@hgwdev.cse.ucsc.edu:/data/git/kent commit d529b9b02f39043997b2b72c81347f4b786dcfdb Author: Brian Raney Date: Fri Jun 18 10:23:35 2010 -0700 add view range commit 090962fe5e830398681cb2ef3855c171df2fa0b7 Author: Fan Hsu Date: Fri Jun 18 10:14:29 2010 -0700 Updated KEGG tables (fixed a processing logic error) and rebuilt knownToKeggEntrez tables for hg19, hg18, hg17, mm9, mm8, mm7, rn4). commit 37885ae9a7ed5eb30e426e6c37d4896b5a4d9c13 Merge: 16d85fa d532db8 Author: Antonio Coelho Date: Fri Jun 18 09:24:09 2010 -0700 Merge branch 'master' of antonio@hgwdev.cse.ucsc.edu:/data/git/kent commit d532db8d6e7d66733e91e3e4e605e8b026b14426 Author: Galt Barber Date: Fri Jun 18 08:00:43 2010 -0700 "Encode release log update" commit 74be3a87d04036b13e9e6e44d58995f920658bc9 Author: Galt Barber Date: Fri Jun 18 08:00:41 2010 -0700 "Release log update" commit a87ee673be0b1e9cfc582560d49ed87496b33aca Merge: 8afeab8 dc51591 Author: Galt Barber Date: Fri Jun 18 00:56:09 2010 -0700 Merge commit 'origin/master' into fix commit 8afeab82f52b6c977394509cb98eb94026963fe4 Author: Galt Barber Date: Fri Jun 18 00:50:25 2010 -0700 combining Jims 2 commits into one. Making hgTrackRender and Rearranging things commit f2abaff335ed7b33c465e7eaddc64ae01574cefd Author: Brian Raney Date: Thu Jun 17 17:22:25 2010 -0700 make mismatches 7 commit b1e568a8fe771d2498352d73f7bbc0a971a4f6e3 Author: Tim Dreszer Date: Thu Jun 17 16:57:54 2010 -0700 No more fileDb.ra, stopped obsolete RawSignals generation, made trackDb templates children of views commit 47ea306c424d4b800a1d6fea2cef10547bbaba62 Author: Hiram Clawson Date: Thu Jun 17 15:37:36 2010 -0700 fixup makefiles to have clean targets commit 45da70eea1cd1503f73c3cc0ad5e8a578f430dca Author: Venkat Malladi Date: Thu Jun 17 15:26:50 2010 -0700 Add comments to code as per Cricket in doEncodeValidate.pl. Code commented out is better explained. commit 00c71efb64cfab9e7f77f030724df1b161e5b6b3 Author: Donna Karolchik Date: Thu Jun 17 14:40:52 2010 -0700 Added link to Grisham tutorial, fixed some capitalization for consistency. commit 8b21985212adb48c9821ffe5d70fd0b616ed9bb8 Author: Jim Kent Date: Thu Jun 17 14:26:15 2010 -0700 Renaming cartNewEmpty to cartFromCgiOnly. commit e87a5a48e160352d00b33be48abef65b46dc55ff Author: Jim Kent Date: Thu Jun 17 14:23:40 2010 -0700 Adding a few functions to cart and trackDb to make it easier to build carts and trackDbs out of an existing string-valued hash. commit dc51591db423d074c6e3a4ce50c165f64b6427c9 Merge: 2b91184 03b22de Author: Brian Raney Date: Thu Jun 17 17:22:50 2010 -0700 Merge branch 'master' of braney@hgwdev.cse.ucsc.edu:/data/git/kent commit 2b911844457d3bc27b13835478f0851b8063ab97 Author: Brian Raney Date: Thu Jun 17 17:22:25 2010 -0700 make mismatches 7 commit 03b22de165e2dfbd3353ea5b734a39332b82afb0 Merge: 3a4000b 086c7aa Author: Tim Dreszer Date: Thu Jun 17 17:01:53 2010 -0700 Merge branch 'master' of tdreszer@hgwdev.cse.ucsc.edu:/data/git/kent commit 3a4000b290b59cacead61d2db1e8cc7d93055248 Author: Tim Dreszer Date: Thu Jun 17 16:57:54 2010 -0700 No more fileDb.ra, stopped obsolete RawSignals generation, made trackDb templates children of views commit 086c7aad9a51288e4428886af40b78f82d5a615c Merge: 5aa41d8 38785bd Author: Jim Kent Date: Thu Jun 17 16:48:56 2010 -0700 Merge branch 'master' of kent@hgwdev.cse.ucsc.edu:/data/git/kent commit 5aa41d849c2e4e5c42e9c949e1b6743148905f81 Author: Jim Kent Date: Thu Jun 17 16:46:30 2010 -0700 Rearranging things so that hgTracks.c module is not so severely changed by the web service stuff. commit 38785bd54a6b4f7c5f13bc7a4b6666d69a2a422c Author: Hiram Clawson Date: Thu Jun 17 15:37:36 2010 -0700 fixup makefiles to have clean targets commit e37b69a0b92cc022d17ff1fa0fd305d70d39fe90 Author: Venkat Malladi Date: Thu Jun 17 15:26:50 2010 -0700 Add comments to code as per Cricket in doEncodeValidate.pl. Code commented out is better explained. commit ca68bbcce4b1f466e9e87b56e52ae9f08d13ec83 Author: Donna Karolchik Date: Thu Jun 17 14:40:52 2010 -0700 Added link to Grisham tutorial, fixed some capitalization for consistency. commit 70d181fe8c0667fce247e4436d81322c50112d22 Author: Jim Kent Date: Thu Jun 17 14:30:17 2010 -0700 Making hgTrackRender - a program that renders one track quickly - currently from the command line in postscript only. commit 9d4bdaa271bf85e2f520e900f329f74348caeb2d Author: Jim Kent Date: Thu Jun 17 14:26:15 2010 -0700 Renaming cartNewEmpty to cartFromCgiOnly. commit 72e0ce1046d3a1839e66dd6dc196d734f24a445d Author: Jim Kent Date: Thu Jun 17 14:23:40 2010 -0700 Adding a few functions to cart and trackDb to make it easier to build carts and trackDbs out of an existing string-valued hash. commit 77dee9cfe03d810f8245998b4e6aa9f155a92a14 Merge: 4b2d9ad 54c106e Author: Donna Karolchik Date: Thu Jun 17 14:17:34 2010 -0700 Merge branch 'master' of donnak@hgwdev.cse.ucsc.edu:/data/git/kent commit 54c106e18918600173e0ee158577f6b1ca0258fa Author: Chin Li Date: Thu Jun 17 13:42:21 2010 -0700 felCat4 vs monDom5 swap commit 3a2a03b585dd67591b59896e2964c6eae6bffa97 Merge: d9b2ddf b443875 Author: Chin Li Date: Thu Jun 17 13:32:33 2010 -0700 Merge branch 'master' of chinhli@hgwdev.cse.ucsc.edu:/data/git/kent commit b44387500934bc4668db1c745455f68621959d8e Author: Brian Raney Date: Thu Jun 17 13:28:00 2010 -0700 change spelling of "into" to "in to" commit d9b2ddf8a70c1699ef741e375f85fa8bb7bdb268 Author: Chin Li Date: Thu Jun 17 13:07:37 2010 -0700 complete LASTZ with felCat4 commit dd1e84e843c4da5886865d7276c287c9e7419e32 Merge: 5d892e3 5a8d349 Author: Brian Raney Date: Thu Jun 17 12:31:21 2010 -0700 Merge branch 'master' of braney@hgwdev.cse.ucsc.edu:/data/git/kent commit 5d892e3d5768a275b61a1cdcf31ebfe2bc142220 Author: Brian Raney Date: Thu Jun 17 12:31:01 2010 -0700 change usage message to be more clear commit 5a8d349227e411a4bc34160b7e93b42d6ccb847b Merge: 8a2c6cc 462eb21 Author: katrina Date: Thu Jun 17 12:25:31 2010 -0700 Merge branch 'master' of katrina@hgwdev.cse.ucsc.edu:/data/git/kent commit 462eb21f608d2f2e2866eea2a222669c628a2f9c Author: Galt Barber Date: Thu Jun 17 12:24:05 2010 -0700 "Encode release log update" commit f06d94fe7dba63e4fc8ab2a227b357ea3f6ca03e Author: Galt Barber Date: Thu Jun 17 12:24:03 2010 -0700 "Release log update" commit 8a2c6cc38eb21d35ad6e00e9883cef1b3335cd0f Author: katrina Date: Thu Jun 17 12:23:30 2010 -0700 removing release tags commit 62682e0bacc181a72a09ef034f2270269e98aee1 Merge: 992f8d0 c63dc81 Author: Brian Raney Date: Thu Jun 17 12:09:50 2010 -0700 Merge branch 'master' of braney@hgwdev.cse.ucsc.edu:/data/git/kent commit 992f8d0b6f2cb9f2916864782af2a30d66c5e6c9 Author: Brian Raney Date: Thu Jun 17 12:09:23 2010 -0700 add 32-bit color and write mode support to postscript driver commit c63dc8138bf33f2edcfe4f22272177227d97db81 Merge: dcf874a 74af149 Author: Jim Kent Date: Thu Jun 17 11:23:32 2010 -0700 Merge branch 'master' of kent@hgwdev.cse.ucsc.edu:/data/git/kent commit 74af14908bcda068d39c7861846ad6ad4c216231 Merge: 8fc8c50 3e588fc Author: Brian Raney Date: Thu Jun 17 10:57:11 2010 -0700 Merge branch 'master' of braney@hgwdev.cse.ucsc.edu:/data/git/kent commit 8fc8c50cb3d8996e586fa3a178c086a7e0c51f0f Author: Brian Raney Date: Thu Jun 17 10:56:26 2010 -0700 fix bug in 32-bit land where 0 was being used as MG_WHITE commit 3e588fcca1bfd1e6e4fa24f1ba6588e339684a7d Merge: 7646c69 f0208f3 Author: Tim Dreszer Date: Thu Jun 17 10:50:57 2010 -0700 Merge branch 'master' of tdreszer@hgwdev.cse.ucsc.edu:/data/git/kent commit 7646c691249fae7922f9efbbdf9eceaf064415a1 Author: Tim Dreszer Date: Thu Jun 17 10:50:35 2010 -0700 FDR 1percent not 0.5 percent for peaks commit f0208f31cb6904d68e2eed30da7be65280864800 Author: vanessa Date: Thu Jun 17 10:48:44 2010 -0700 removed release alpha tags and added release alpha,beta tags to stage yaleRna-seq commit 65b7172fccbb69e9eaccfe9cf0a5402389bb04b6 Merge: 5a0ac20 be88301 Author: Venkat Malladi Date: Thu Jun 17 10:12:18 2010 -0700 Merge branch 'master' of vsmalladi@hgwdev.cse.ucsc.edu:/data/git/kent commit 5a0ac2018b73e594f5140f5b3463333fff073209 Author: Venkat Malladi Date: Thu Jun 17 10:11:48 2010 -0700 Changed Sex of LHSR cell line from F to M to be accurate according to OpenChrom Labs commit be8830134576d34e2617858c4a838183a989c28f Author: vanessa Date: Thu Jun 17 09:48:40 2010 -0700 change the link so it does not reference hgwdev to the public commit 16d85fa36fca8c69abac05dd1f0f7625b3d9e25d Merge: ed444aa c1cc70c Author: Antonio Coelho Date: Thu Jun 17 09:26:22 2010 -0700 Merge branch 'master' of antonio@hgwdev.cse.ucsc.edu:/data/git/kent commit dcf874a04b308e082c3cfa6f4fe37334d3bf0ff2 Merge: 24dfdda c1cc70c Author: Jim Kent Date: Wed Jun 16 21:44:14 2010 -0700 Merge branch 'master' of kent@hgwdev.cse.ucsc.edu:/data/git/kent commit 24dfddad4518a489c327f702f6a5b770dbb9a579 Author: Jim Kent Date: Wed Jun 16 21:40:58 2010 -0700 Changing score column from 7 to 6 and #defining it as a constant. commit 43ca9c32c4f2db4a6d1c75326167cb3f934c0c47 Author: Jim Kent Date: Wed Jun 16 21:36:12 2010 -0700 Starting to work on integrating Hudsonalpha ChIP data. Describing how to call encodeMergeReplicates and convert from broad to narrow peak. commit c1cc70cd12d5bf2723feffa4ad45262749145dec Author: Brian Raney Date: Wed Jun 16 19:33:10 2010 -0700 add maxWindowToQuery setting for bigWigs. commit 9c8043c25e4c856dda5a5785e4ba5730e12a2841 Merge: 3f09d93 d291546 Author: Brian Raney Date: Wed Jun 16 17:38:20 2010 -0700 Merge branch 'master' of braney@hgwdev.cse.ucsc.edu:/data/git/kent commit 3f09d93c1f72ec9cb1b60d6c721464d6fcaf0f51 Author: Brian Raney Date: Wed Jun 16 17:37:33 2010 -0700 notes for release1 commit d291546669260b092f68854edef746a106bfe3a3 Merge: 56c78aa 9d8b9db Author: vanessa Date: Wed Jun 16 16:54:29 2010 -0700 Merge branch 'master' of vanessa@hgwdev.cse.ucsc.edu:/data/git/kent commit 9d8b9db37f8d695e5fd3bf8d5df2ba985f93c0d0 Merge: e9bd2ed 7a841e9 Author: Tim Dreszer Date: Wed Jun 16 16:33:55 2010 -0700 Merge branch 'master' of tdreszer@hgwdev.cse.ucsc.edu:/data/git/kent commit e9bd2ed7685217ebe05aa402612ff9d0d4f2a7d9 Author: Tim Dreszer Date: Wed Jun 16 16:33:26 2010 -0700 Minor update commit 56c78aa3131da396383833a0866bf2bd70e5e73f Merge: 50d9bd6 7a841e9 Author: vanessa Date: Wed Jun 16 16:27:29 2010 -0700 Merge branch 'master' of vanessa@hgwdev.cse.ucsc.edu:/data/git/kent commit 7a841e95df3c43f5ced85f63968e289d847d49fc Merge: ff5bd7b 17f0276 Author: Brian Raney Date: Wed Jun 16 16:19:02 2010 -0700 Merge branch 'master' of braney@hgwdev.cse.ucsc.edu:/data/git/kent commit ff5bd7b8ddcaa73d2ef565f97a11e84f93491cef Author: Brian Raney Date: Wed Jun 16 16:18:26 2010 -0700 added some words for Wold. New insert lengths and a code for TopHat as aligner commit 17f027692f02eeaef278aa9cdf08e395f474b3b6 Merge: 22f2c32 51db9ac Author: Cricket Sloan Date: Wed Jun 16 16:14:59 2010 -0700 Merge branch 'master' of cricket@hgwdev.cse.ucsc.edu:/data/git/kent commit 22f2c3272b758bc5c9d351d5aa691eb37b5e09ba Author: Cricket Sloan Date: Wed Jun 16 16:06:51 2010 -0700 Fixed the mapAlgorithm TopHat to be TH1014 commit 51db9ac03d68b2cccba6b43ce299d3705e252c99 Merge: fda7614 3f6151e Author: Brian Raney Date: Wed Jun 16 16:01:23 2010 -0700 Merge branch 'master' of braney@hgwdev.cse.ucsc.edu:/data/git/kent commit fda76149e0833f380565bfc070f8f803ddba8283 Author: Brian Raney Date: Wed Jun 16 15:59:51 2010 -0700 added new file types for Caltech FPKM and insert distribution. At this point these file types are *not* validated commit 3f6151e74ce40850dbe2b92f0f4f5322b6c772a3 Author: Galt Barber Date: Wed Jun 16 15:58:19 2010 -0700 adding bigWigToWig and wigCorrelate to the utils built for hgdownload commit 50d9bd668ab6c22b4ee4c805fd5004bba40beff2 Author: vanessa Date: Wed Jun 16 15:51:27 2010 -0700 allowed the w3c link checker commit 384122128ff2bce52cd9a79dc155c8e67c1f4c40 Author: Melissa Cline Date: Wed Jun 16 15:05:36 2010 -0700 Incorporating feedback from Jim commit 04518890ee9351a5f809736569372ea182422f2d Author: Jim Kent Date: Wed Jun 16 14:16:26 2010 -0700 Improving usage statement. commit a3ee36266acbd5e53c16a818e09360a2911a3859 Merge: 965ed90 75ddc66 Author: Cricket Sloan Date: Wed Jun 16 13:31:21 2010 -0700 Merge branch 'master' of cricket@hgwdev.cse.ucsc.edu:/data/git/kent commit 965ed90c2f84dcc7e1ca5d144384d4c862856efe Author: Cricket Sloan Date: Wed Jun 16 13:28:44 2010 -0700 Added more insertLenth Information for the WOld Lab and added a mapAlgorithm calll TopHat that needs a description commit 75ddc66c532db7ffafa77bd241bfb0a1afdb36cf Author: Tim Dreszer Date: Wed Jun 16 13:28:01 2010 -0700 Adding wgEncodeUwHistone to hg19 commit 16d39bcf7510338903af4793863ac3d7e80ff62e Merge: 25ce7e4 5666464 Author: Chin Li Date: Wed Jun 16 12:31:27 2010 -0700 Merge branch 'master' of chinhli@hgwdev.cse.ucsc.edu:/data/git/kent commit 25ce7e47f9c4a5e97a566db9be0883e4be5c699d Author: Chin Li Date: Wed Jun 16 12:02:20 2010 -0700 fixed /home/gbadmin/kent/src/lib/zlibFace.c:67: undefined reference to uncompress error commit 6dfa1e44feac34d4ac31d06840073fd03d0800e5 Author: Chin Li Date: Wed Jun 16 11:47:06 2010 -0700 Testing git commit 56664642a8d4f4d6fd6fdf352aad442ea4cdbb70 Merge: 550c961 5278a48 Author: Hiram Clawson Date: Wed Jun 16 11:31:37 2010 -0700 Merge branch 'master' of hiram@hgwdev.cse.ucsc.edu:/data/git/kent commit 550c9617043c7cad11dc03dd194a358e6583d40f Author: Hiram Clawson Date: Wed Jun 16 11:31:07 2010 -0700 fixup bedToBigBed usage message -k2,2n commit 5278a484569b67b1f374ba9a54cc3c614da70658 Merge: 58f8997 1808a63 Author: katrina Date: Wed Jun 16 10:38:54 2010 -0700 Merge branch 'master' of katrina@hgwdev.cse.ucsc.edu:/data/git/kent commit 58f8997b76e26868ae198908e39642e73e893074 Author: katrina Date: Wed Jun 16 10:38:49 2010 -0700 Prep to release update of track: removed release tags, cp *.new.ra to *.ra, removed include line for *.new.ra commit 949d61d8ea414ae84136d2af2c7a464d6de66509 Author: katrina Date: Wed Jun 16 10:30:41 2010 -0700 Prep to release update of track: removed release tags, cp *.new.ra to *.ra, removed include line for *.new.ra commit 1808a63e758c94c52c7c7d66e59dfb4b1950afea Author: ann Date: Wed Jun 16 10:20:20 2010 -0700 added info about bigWigToWig utilities commit c40820696fe1482fff21f4aa2807b33d8fd3ca4d Merge: 27ad723 e3d0600 Author: ann Date: Wed Jun 16 10:00:48 2010 -0700 Merge branch 'master' of ann@hgwdev.cse.ucsc.edu:/data/git/kent commit ed444aa1a3bc5a5e6b5483d8a029822e6756ef06 Merge: 7b095d2 e3d0600 Author: Antonio Coelho Date: Wed Jun 16 09:59:16 2010 -0700 Merge branch 'master' of antonio@hgwdev.cse.ucsc.edu:/data/git/kent commit e3d06001db8777add0871b072c89064cde43ade1 Author: Jim Kent Date: Wed Jun 16 09:47:35 2010 -0700 Improving comment. commit ea715e74b80c6a9878899134a6169759d10de694 Merge: a9ba368 5851236 Author: Jim Kent Date: Wed Jun 16 09:39:29 2010 -0700 Merge branch 'master' of kent@hgwdev.cse.ucsc.edu:/data/git/kent commit a9ba3688207718359f7ef75f6d54940afd3942da Author: Jim Kent Date: Wed Jun 16 09:37:12 2010 -0700 Improving some comments. commit 27ad72314583dad3c47f198422d1c4f6748a5220 Merge: 3a69ff5 5851236 Author: ann Date: Wed Jun 16 07:30:21 2010 -0700 Merge branch 'master' of ann@hgwdev.cse.ucsc.edu:/data/git/kent commit 58512368b0f4eeb6e94c4ec0a8961c0c6ca501ac Merge: 64ee275 412651c Author: Galt Barber Date: Wed Jun 16 00:03:52 2010 -0700 Merge branch 'master' of galt@hgwdev.cse.ucsc.edu:/data/git/kent commit 64ee27549c6ce3f5b7d47750be021a7b6ee3bcd6 Author: Galt Barber Date: Wed Jun 16 00:02:48 2010 -0700 adding install target commit e17db54ee6da970811c15ea6361641d08e2f4b3d Merge: 28fd81f bcf2385 Author: Galt Barber Date: Tue Jun 15 23:50:04 2010 -0700 Merge /cluster/home/galt/git-reports-integrate commit bcf2385e0d128af41b2c21c2ffb1a7793b405c12 Author: Galt Barber Date: Tue Jun 15 23:39:48 2010 -0700 moving files to new home under kent commit 7ea14ae657406499ad32f63df7f7267448a840c2 Author: Galt Barber Date: Tue Jun 15 23:28:30 2010 -0700 fix relative path in makefile for integration commit df35108f40d4f3297394bd747cc3ad099e756033 Author: Galt Barber Date: Tue Jun 15 23:25:59 2010 -0700 getting ready to integrate into kent source commit 6f529dfc7d66de9ab6bae6bdf9193b953781bc52 Author: Galt Barber Date: Tue Jun 15 22:55:46 2010 -0700 making author use email account name by request commit 412651ccfe83f6373a744f03c335edd1a51fb8b4 Merge: 2bdf45e 28fd81f Author: Jim Kent Date: Tue Jun 15 21:25:54 2010 -0700 Merge branch 'master' of kent@hgwdev.cse.ucsc.edu:/data/git/kent commit 2bdf45e54df5b8c45b1d5dd055c66c251767e83d Author: Jim Kent Date: Tue Jun 15 21:24:02 2010 -0700 Adding uniqueName option. commit 3ae988930de1fc180e9bcb517e552d7ac1301708 Author: Jim Kent Date: Tue Jun 15 19:59:54 2010 -0700 Adding another test case commit 28fd81f9c6c9004f22ea05a448b35acfc3c5fb10 Author: Galt Barber Date: Tue Jun 15 19:54:30 2010 -0700 adding phastConsElements html description page commit bc54280039f7d95ea93710739f2336605357a1ce Author: Jim Kent Date: Tue Jun 15 19:51:02 2010 -0700 Adding threshold, maxMin, and addMin options. commit aac7791e2bb646de48318a33e1ab5f62985d0ed2 Author: Galt Barber Date: Tue Jun 15 19:49:05 2010 -0700 adding description page for danRer6 phastCons6way commit 6e387483a1eb0407548e354a9f1a1b93007c7e92 Merge: d5e90ee 0a1177a Author: Mark Diekhans Date: Tue Jun 15 18:40:01 2010 -0700 Merge branch 'master' of hgwdev.cse.ucsc.edu:/data/git/kent commit 0a1177a35a3a3563427039abb194f341f51cc2a8 Author: Brian Raney Date: Tue Jun 15 18:17:24 2010 -0700 removed Smear8 in favor of making Smears always take Colors. There are still some problems with 32 bit smears not getting the same colors as it's 8bit analog. I'm thinking this is something to do with the 0 and 1 being white and black in eight bit commit d5e90eea0cd09519de40b9a1022a31a066ff6191 Author: Mark Diekhans Date: Tue Jun 15 17:55:35 2010 -0700 fix rsync for installing etc targets commit f9a24141dd766b4a8425f47548fd3a789cbc2d0f Author: Jim Kent Date: Tue Jun 15 17:38:57 2010 -0700 Adding -add option to add signal column rather than average within a cluster. commit 04be92551d92263c352afb7ebaaac71b2641e7c7 Merge: ab9bd51 b7a3fac Author: Brian Raney Date: Tue Jun 15 16:28:12 2010 -0700 Merge branch 'master' of braney@hgwdev.cse.ucsc.edu:/data/git/kent commit ab9bd511501348a8acc859d710b282c812a02ccb Author: Brian Raney Date: Tue Jun 15 16:27:35 2010 -0700 update makefile to make metaDb_public at make public time commit b7a3facc4d2a0e93fd12895da102428be8902f73 Author: Fan Hsu Date: Tue Jun 15 16:21:30 2010 -0700 added KEGG column for Gene Sorter for hg19, hg18, hg17, mm8, mm7, and rn4 commit 28546e7493908f1b6c40053003126e4de59c298b Author: Mark Diekhans Date: Tue Jun 15 16:18:43 2010 -0700 add native refseqs to cavPor3 commit 67d782cbc5043872ed36fb4f298c8802c7cb7242 Author: Venkat Malladi Date: Tue Jun 15 16:14:22 2010 -0700 Removed metaData for Histone submissions commit 6bd7fcce1885d42d08f90c4877a7e1ff4f39732f Merge: 9008517 453daaa Author: Mark Diekhans Date: Tue Jun 15 16:05:25 2010 -0700 Merge branch 'master' of hgwdev.cse.ucsc.edu:/data/git/kent commit 9008517764dadf5444dbcb62a905c70069dc7148 Author: Mark Diekhans Date: Tue Jun 15 16:01:16 2010 -0700 git conversion, manage etc dir with rsync install commit 7b095d2c890d02282dc0512d1f05d81cf32ab8a7 Author: Antonio Coelho Date: Tue Jun 15 15:40:40 2010 -0700 added a link, changed capitalization commit 3a69ff58cac9d5dc38eda08053702296abdb480d Merge: 74624de 453daaa Author: ann Date: Tue Jun 15 15:21:47 2010 -0700 Merge branch 'master' of ann@hgwdev.cse.ucsc.edu:/data/git/kent commit f3407fa635eeac0c4079ce91444a920e7595a1e2 Author: Antonio Coelho Date: Tue Jun 15 15:19:48 2010 -0700 added a link, changed capitalization commit 453daaaa34148334ec3c1507583e678bfea479b9 Merge: c66a112 2439d4f Author: Brian Raney Date: Tue Jun 15 14:49:22 2010 -0700 Merge branch 'master' of braney@hgwdev.cse.ucsc.edu:/data/git/kent commit c66a112b1730eca815fbfb603e374682f3ab9a78 Author: Brian Raney Date: Tue Jun 15 14:48:57 2010 -0700 add CSHL RNA short commit 01d7002cb7948b46182883f48e0ff2c64b1c22f9 Author: Brian Raney Date: Tue Jun 15 14:38:10 2010 -0700 don't check for mismatches in unmapped reads, put number of alignments on positive and negative strands out to stdout for BAM's with verbose >=2. commit 2439d4f0549590bc55af714882a311b03fe960f9 Author: Venkat Malladi Date: Tue Jun 15 14:04:17 2010 -0700 Removed submission 1144, revoked submission, Lab has provided replacement commit 74624de9ad0ab079d8bb6e3bf1b651d5bbb2a65d Author: ann Date: Tue Jun 15 13:41:47 2010 -0700 backing out last change that I made on aamp's behalf -- the data is incorrect commit 4756cb3c3a2bdc62b9f40cb6cc1f3ae909a2b5b0 Merge: 763ab05 73a0877 Author: Jim Kent Date: Tue Jun 15 13:31:46 2010 -0700 Merge branch 'master' of kent@hgwdev.cse.ucsc.edu:/data/git/kent commit 763ab05a3e411cabc39958b254d342c3f07b3dd2 Author: Jim Kent Date: Tue Jun 15 13:30:38 2010 -0700 Adding peakCluster to library. commit 79899a25a53f001ee967a41a68461550ae364cff Author: Jim Kent Date: Tue Jun 15 13:27:02 2010 -0700 Making item variable a bit more local. commit 4a86b8d1102921df9af22e1e1463b4e008164fda Author: Jim Kent Date: Tue Jun 15 13:25:53 2010 -0700 Polishing names and labels for enhancer subtracks of wgEncodeReg. commit b44bc6693648f9b3a2d1f47683f7a2aa4ed258ed Author: Jim Kent Date: Tue Jun 15 13:23:17 2010 -0700 Adding some test cases commit 0eafc939e842b39786dc377b8025d96cdc67812c Author: Jim Kent Date: Tue Jun 15 13:20:35 2010 -0700 Starting work on replicate merger. Works on narrowPeak files so far with a few options. commit 73a0877eaa87611b825910db599ec267ac123d21 Author: katrina Date: Tue Jun 15 11:34:49 2010 -0700 pointed Bernstein lab link to website w/o login requirement; changed contact link to name commit 3b7f8fa06b5e27de0e5c89e90687d69212229c38 Author: Venkat Malladi Date: Tue Jun 15 11:03:53 2010 -0700 Seperated out the Encode compsite tracks, SYDH Tfbs, SYDH Histone and HAIB Tfbs into 3 seperate trackDb files. Added include statements to trackDb.wgEncode.ra to accomadate the newly generated trackDb files. commit bf0978f646fdf46e2588df4d56cbad31d9312eaf Merge: 500c2cd df544e8 Author: Galt Barber Date: Tue Jun 15 10:47:33 2010 -0700 Merge branch 'master' of hgwdev:/data/git/kent commit 500c2cd74c29e4560896adfa4b297636219bacae Author: Galt Barber Date: Tue Jun 15 10:47:29 2010 -0700 fix hardwired old test symbol commit 4b2d9addf12f50c9be883fda4c73044f4af3228e Merge: 19c0006 df544e8 Author: Donna Karolchik Date: Tue Jun 15 10:45:00 2010 -0700 Merge branch 'master' of donnak@hgwdev.cse.ucsc.edu:/data/git/kent commit df544e8cff773c960ed9ff61d5d9ea41246216f7 Merge: be6b6de b9ce527 Author: Galt Barber Date: Tue Jun 15 10:22:09 2010 -0700 Merge branch 'master' of galt@hgwdev.cse.ucsc.edu:/data/git/kent commit be6b6de7a8e09565f80da913f615700aa01a2f1e Author: Galt Barber Date: Tue Jun 15 10:22:01 2010 -0700 removing mistaken file, Cricket confirms is just a dupe anyway commit b9ce527996a38dca9249dbab7d07b68e8c5b2dba Merge: 27d5d44 cf14990 Author: Brian Raney Date: Tue Jun 15 10:20:20 2010 -0700 Merge branch 'master' of braney@hgwdev.cse.ucsc.edu:/data/git/kent commit 27d5d44ec5acfc27dd7ce94ba69ba5f941cd4338 Author: Brian Raney Date: Tue Jun 15 10:19:39 2010 -0700 fix up to handle BAM files and to remove bigWig downloads commit cf149901695e56c690f70938884d678ec5f7d645 Author: mary Date: Tue Jun 15 10:08:04 2010 -0700 fixing broken link commit b2b0871ccd3d225cbd886ef18c6916a7478d6c66 Author: katrina Date: Tue Jun 15 09:31:13 2010 -0700 adding update to release 3 to release notes section commit b0a1e876536a472f80a4508d6869cec5268d489a Author: Galt Barber Date: Tue Jun 15 02:33:15 2010 -0700 convert to git commit d37ad4a3afa93baffb47e7a68a7a639e4ffc2c7c Author: Galt Barber Date: Tue Jun 15 02:02:34 2010 -0700 getting rid of the last of cvs in paths commit 133d90dc3a927e08b6ec1be214b8a8e36f343f53 Author: Galt Barber Date: Tue Jun 15 01:53:44 2010 -0700 oops need root in path commit 787d4722f2284d136d45299bd2e3107a92f77ac3 Author: Galt Barber Date: Tue Jun 15 01:39:42 2010 -0700 tags are global so do not get automatic origin/ prefix commit d73844eaa70d076b95b631a3be58c31cdae7e217 Author: Galt Barber Date: Tue Jun 15 01:31:33 2010 -0700 making buildGitReports.csh shell to setup and run git-reports commit 4fb0a6719e3b98876a2bf5dd8e0940cf7290553f Author: Galt Barber Date: Tue Jun 15 01:12:02 2010 -0700 do not need CVS_REPORTS_WORKDIR variable commit 885851e262f6434c18ee47675a5fe897fa1b70e9 Author: Galt Barber Date: Tue Jun 15 00:27:08 2010 -0700 v234 preview commit 731e16a7d584c84b711f255aa5b5ef7abcdaddf3 Author: Galt Barber Date: Tue Jun 15 00:16:56 2010 -0700 convert to git commit fd06cbc61eea0e44bead43ccb3dbc6136bf0d030 Merge: 179c634 8e2a590 Author: Galt Barber Date: Tue Jun 15 00:11:05 2010 -0700 Merge branch 'master' of hgwdev:/data/git/kent commit 179c6345943f7ebf7d4c40be83af782805a1c437 Author: Galt Barber Date: Tue Jun 15 00:01:43 2010 -0700 removing test area GBUILDDIR commit 8e2a590605117317833aacf99b50e00e7fd8fb5c Merge: 0470248 cba0c82 Author: Galt Barber Date: Mon Jun 14 22:50:22 2010 -0700 Merge branch 'master' of galt@hgwdev.cse.ucsc.edu:/data/git/kent commit 0470248675c66e5de709b0d0fbf17e40ff2d42ef Author: Galt Barber Date: Mon Jun 14 22:50:16 2010 -0700 restoring some old test file in non-huge form commit 8b476495fdcb4a6483579fc024b02e21065f0ec1 Author: Galt Barber Date: Mon Jun 14 22:48:38 2010 -0700 restoring some old test file in non-huge form commit 8f45bb3988b7548987178934a02fc3e6e3ecea97 Author: Jim Kent Date: Mon Jun 14 18:43:58 2010 -0700 Moving clustering to library. commit cba0c82945d97634dced46db20028f0f31099ab6 Merge: 24babbb 79b1e67 Author: Melissa Cline Date: Mon Jun 14 17:49:31 2010 -0700 Merge branch 'master' of cline@hgwdev.cse.ucsc.edu:/data/git/kent commit 24babbb660402caa1322291bf0b48c46845fa9cf Author: Melissa Cline Date: Mon Jun 14 17:48:49 2010 -0700 Documented most stanza types commit 79b1e675be3fde4061042fe188c77484e09bc1d9 Author: Galt Barber Date: Mon Jun 14 17:35:53 2010 -0700 adding needed downloads for phastCons6way commit db3f43de73f206fe042664992d9fb7045d07b427 Author: Galt Barber Date: Mon Jun 14 17:06:44 2010 -0700 fixing GeneTrack list commit f4cfeb888502a94b2b353c8ccb9a1a6ada859eae Author: Galt Barber Date: Mon Jun 14 16:59:17 2010 -0700 adding track description page commit 19c0006950b4489f0e4a14ab475b7e4591a59ffc Author: Donna Karolchik Date: Mon Jun 14 16:36:31 2010 -0700 Added Vaske pub commit 1445ebfbc9708123867889a93212b63d1c80703d Merge: 2aea14a 2980f39 Author: Melissa Cline Date: Mon Jun 14 16:26:33 2010 -0700 Merge branch 'master' of cline@hgwdev.cse.ucsc.edu:/data/git/kent commit 2aea14a34a4a05cea79501352bc11c949c23c087 Author: Melissa Cline Date: Mon Jun 14 16:26:08 2010 -0700 Executing a bit further... commit 2980f3973bb11d9c9b9fb596765527fc711bdec7 Author: Venkat Malladi Date: Mon Jun 14 16:25:23 2010 -0700 Added new metaData from 58 new submissions commit 6a86bba4c73d23871b547c41c0ebfea954b29340 Author: katrina Date: Mon Jun 14 14:39:34 2010 -0700 added html line pointing to Release3 original html commit ea6f6189d61796f8184fa46dce28374572d7d162 Author: katrina Date: Mon Jun 14 14:34:15 2010 -0700 html page for RR so I can modify the html page for the release3 display update commit ec0aa6abd2a794563b29cd2ff8b54ca905ba0de4 Author: Bernard Suh Date: Mon Jun 14 14:14:27 2010 -0700 Initial checkin. Scripts produces the ENCODE report file as a JSON object to be consumed by the June2010-Freeze.html webpage commit 449aad825ee2124f7a9738dbb285fca172619225 Author: katrina Date: Mon Jun 14 14:01:23 2010 -0700 fixed typo in include line just added commit f1d48a2085d129a94c9efde405856c18e6991aa8 Author: katrina Date: Mon Jun 14 13:59:52 2010 -0700 added include line for wgEncodeBroadChipSeq.new.ra commit 69a23714bc9200c4a77b461e167e878c46d4437f Author: katrina Date: Mon Jun 14 13:58:08 2010 -0700 added release alpha,beta liness commit 1f25365741f38f679fa9284ecbd71ad8842e9230 Author: katrina Date: Mon Jun 14 13:36:20 2010 -0700 added release public tags commit 22bd1a900202a28eb5983bf4df81f6e6d004fc77 Merge: 2b44648 9f3b2f0 Author: Melissa Cline Date: Mon Jun 14 12:33:08 2010 -0700 Merge branch 'master' of cline@hgwdev.cse.ucsc.edu:/data/git/kent commit 2b446481045ab61911b109b9ad038d9c103d887e Author: Melissa Cline Date: Mon Jun 14 12:24:56 2010 -0700 Added a header comment block describing the tissue type section commit 9f3b2f053f8f2b5fb8f752cc79ccca29885e9e5d Author: Venkat Malladi Date: Mon Jun 14 12:19:33 2010 -0700 Added line validatio missing to cv.ra commit a84fc94d26f7b05a41e61a3e90b824b8701f1096 Merge: 6b10e99 728ad85 Author: Venkat Malladi Date: Mon Jun 14 12:11:37 2010 -0700 Merge branch 'master' of vsmalladi@hgwdev.cse.ucsc.edu:/data/git/kent commit 6b10e99653778d257c704c09a567c6c211ffab60 Author: Venkat Malladi Date: Mon Jun 14 12:09:23 2010 -0700 Added Antibody STAT3 from Snyder lab to cv.ra commit 728ad857a3cc710648b666c2b3c83038481538dc Merge: 587c41d 7316ad4 Author: Hiram Clawson Date: Mon Jun 14 11:55:05 2010 -0700 Merge branch 'master' of hiram@hgwdev.cse.ucsc.edu:/data/git/kent commit 587c41dd36fc2d0909e78e213d5119374d1426d4 Author: Hiram Clawson Date: Mon Jun 14 11:54:54 2010 -0700 fixup makefiles to be OK with parallel make commit 7316ad4bd064fe3f68a936e4b4b34ab9f3216166 Merge: 3a4c0cd 20b2e1f Author: Galt Barber Date: Mon Jun 14 11:53:48 2010 -0700 Merge branch 'master' of galt@hgwdev.cse.ucsc.edu:/data/git/kent commit 3a4c0cd9ff60dc2912fbf181806cb1f237dcc639 Author: Galt Barber Date: Mon Jun 14 11:53:43 2010 -0700 adding .gitignore to itself at the highest level commit 20b2e1f46345b9f63de2a5a864393fed55db0af3 Merge: 46f508a d326b6e Author: katrina Date: Mon Jun 14 11:45:10 2010 -0700 Merge branch 'master' of katrina@hgwdev.cse.ucsc.edu:/data/git/kent commit 46f508ae3410dbac18e9e77ad421d22ac9525ade Author: katrina Date: Mon Jun 14 11:44:53 2010 -0700 modified all Signal track spanList to spanList first, via the View level, and changed the view limit to 1:50 as Jim requested commit d326b6ec9eb1c75cabba71d0b90e8e7a8b466ac9 Merge: 9bfcf5e 197e715 Author: Hiram Clawson Date: Mon Jun 14 11:42:59 2010 -0700 Merge branch 'master' of hiram@hgwdev.cse.ucsc.edu:/data/git/kent commit 9bfcf5e486d3ff0032e427a6ccf478fb776f5e0f Author: Hiram Clawson Date: Mon Jun 14 11:42:27 2010 -0700 fixing makefiles to have clean targets commit 197e715c99c028b2ce607c044f91766096772708 Merge: 5bc3cf6 d96d9d2 Author: katrina Date: Mon Jun 14 11:24:01 2010 -0700 Merge branch 'master' of katrina@hgwdev.cse.ucsc.edu:/data/git/kent commit 5bc3cf6f5e34109066a7ecd02f8ed8ef6acdcb0b Author: katrina Date: Mon Jun 14 11:18:33 2010 -0700 creating a .new.ra file for use with release 3 display update commit d96d9d2e1da2b5b7133b8c417d101db158f9c495 Author: Hiram Clawson Date: Mon Jun 14 11:11:14 2010 -0700 do not have all:: target making the test target commit 4420652d50fa93a035709536800dd85a88075557 Merge: d530277 b017815 Author: Galt Barber Date: Sun Jun 13 23:29:17 2010 -0700 Merge branch 'master' of hgwdev:/data/git/kent commit b017815e13ca069236f6005d81ecd4685860f83e Author: Galt Barber Date: Sun Jun 13 23:00:12 2010 -0700 adding FTP notes commit 060e780caa3288678e2b0cefb2dbd9650f5a8aef Merge: 6381d84 cb8c1ce Author: Galt Barber Date: Sun Jun 13 22:06:11 2010 -0700 Merge branch 'master' of galt@hgwdev.cse.ucsc.edu:/data/git/kent commit cb8c1ceab258cb57928a2816cca2c97df472c209 Author: Galt Barber Date: Sun Jun 13 16:30:24 2010 -0700 trying to commit these files with 755 perms that they actually have so they dont appear in the sandbox as dirty commit 6381d8491bbc3c33a7fbfb11fe2a0d8c56c4b06d Author: Galt Barber Date: Sun Jun 13 14:57:13 2010 -0700 tweaking git pull to be safer commit dfdaf96b8dd83314303a7df5a19fcd18909ae9ee Author: Galt Barber Date: Sun Jun 13 14:48:41 2010 -0700 tweaking git pull to be safer, fixing checkbeta target commit d5302770ea6d4fb0d6314af96b1416b20b235128 Author: Galt Barber Date: Sun Jun 13 14:28:10 2010 -0700 added check for being on master branch since we should always be there in the build-kent repo, and also added necessary git push commit e2e6bc456d6349c29c922c0cc40f6da54aef3bb7 Author: Galt Barber Date: Sun Jun 13 14:10:21 2010 -0700 safer to be agnostic about the git pull for now commit 929e29c0efafb2f97840f7fda5f6c6cae02e31cd Author: Galt Barber Date: Sun Jun 13 08:00:10 2010 -0700 "Encode release log update" commit 44a5b97d389a2618b5cddc366102dca17836bf17 Author: Galt Barber Date: Sun Jun 13 08:00:08 2010 -0700 "Release log update" commit 8d2db30d5431ac03f93088cb63ce1ca04e6a84ef Merge: c670592 4bb01fe Author: Galt Barber Date: Sun Jun 13 04:07:09 2010 -0700 Merge branch 'master' of galt@hgwdev.cse.ucsc.edu:/data/git/kent commit 4bb01fe181c3b93b7dcf49d4ed580d5a29356509 Author: Galt Barber Date: Sat Jun 12 23:55:04 2010 -0700 git convert, rename review to preview as that is more common usage now commit c4723b00608c1471ee636bd4193b62360d228e72 Merge: 4547334 f9e6204 Author: Galt Barber Date: Sat Jun 12 23:23:30 2010 -0700 Merge branch 'master' of hgwdev:/data/git/kent commit 45473342de73baa734ce54c7af483ef205adb697 Author: Galt Barber Date: Sat Jun 12 23:23:23 2010 -0700 convert to git commit f9e6204c6ddaa811774c2752c989781db1cd59b2 Merge: 6b66802 b30f9e9 Author: Jim Kent Date: Sat Jun 12 22:50:57 2010 -0700 Merge branch 'master' of kent@hgwdev.cse.ucsc.edu:/data/git/kent commit 6b66802e4a900fb25d4d55c86b2625662f390021 Author: Jim Kent Date: Sat Jun 12 22:49:27 2010 -0700 Improved a few more comments. commit e2c17c7cb8551a267d9cc735cfbf0af393253da3 Author: Jim Kent Date: Sat Jun 12 22:44:11 2010 -0700 Improved header comment. commit b30f9e95ea8b6f579f12999b477eeeb0398bcf37 Merge: e9fd095 21d84be Author: Galt Barber Date: Sat Jun 12 22:29:07 2010 -0700 Merge branch 'master' of galt@hgwdev.cse.ucsc.edu:/data/git/kent commit e9fd0958d39c0510ea968c57b5c3b2114d5f30f1 Author: Galt Barber Date: Sat Jun 12 22:28:18 2010 -0700 moving this to hgdownload repo where it belongs commit 21d84beb3bb3c6fb06235b96d0202826fcb207e6 Author: Galt Barber Date: Sat Jun 12 19:50:16 2010 -0700 convert to git commit c83c6db31acb7c449f79beb977977f3c35501a5c Author: Galt Barber Date: Sat Jun 12 19:35:04 2010 -0700 convert to git commit 6a8fa0f30a7661b52ebd4b0e2f4a01b545093f10 Author: Galt Barber Date: Sat Jun 12 19:19:17 2010 -0700 convert to git commit 29b7abd47a5c331302926cbc57d38d78246e3db8 Author: Galt Barber Date: Sat Jun 12 19:10:09 2010 -0700 print working dir before exit 1 for additional troubleshooting info commit 0e508f214d63fd9d485727882dd0a0a0db3aed29 Author: Galt Barber Date: Sat Jun 12 19:06:14 2010 -0700 converting to git commit da79ee07352af5ba6354b001e644fbed19e8b4ac Author: Galt Barber Date: Sat Jun 12 18:50:04 2010 -0700 conversion of buildUtils.csh to using git commit e84c0e3ec1e01f2d0ddc14a8589db4bffec4a1da Author: Galt Barber Date: Sat Jun 12 18:27:20 2010 -0700 creating BUILDHOME variable commit 60f83276c6b5dd6e55abb9c659deab2e1cf95adc Merge: 70536fa f9a0da6 Author: Galt Barber Date: Sat Jun 12 18:21:25 2010 -0700 Merge commit 'origin/master' commit 70536fa58a3878f6c1211926b97273da7078f05a Author: Galt Barber Date: Sat Jun 12 18:17:38 2010 -0700 hgcentral.sql is in new hgdownload git build repo commit c6705929cd8c7f80e1ad07fd7d05b7bb127302ef Merge: a4373d1 f9a0da6 Author: Galt Barber Date: Sat Jun 12 12:58:23 2010 -0700 Merge branch 'master' of galt@hgwdev.cse.ucsc.edu:/data/git/kent commit f9a0da6dd3257386738f00d4da7ac37de9d6de15 Author: Galt Barber Date: Sat Jun 12 12:17:22 2010 -0700 converted to git using gitFiles the script that checks for CRLF line terminators commit ba1686a387eec113ad8ca33b4955a70a2fdaa841 Author: Galt Barber Date: Sat Jun 12 11:43:15 2010 -0700 conversion to git commit a4373d11f3b7dcb9f68dde03cc689e10e1b30053 Author: Galt Barber Date: Sat Jun 12 08:00:17 2010 -0700 "Encode release log update" commit a19bba22d9b7d6a1005d2bc6839b899cb1863ae8 Author: Galt Barber Date: Sat Jun 12 08:00:16 2010 -0700 "Release log update" commit dd3ab0cc7e5cbdd9c477e5526f3fe4379afbdd46 Author: Galt Barber Date: Sat Jun 12 03:26:37 2010 -0700 adding big test data back smaller commit cf62400a40304c866349d90c56cef7003d2f930f Author: Galt Barber Date: Sat Jun 12 03:22:18 2010 -0700 trying to fix the compiler warnings commit d16c1f4e8cbe2cec382e85235d61fd2f4de3ed90 Author: Galt Barber Date: Sat Jun 12 02:44:41 2010 -0700 do not want to see .a files either commit 0437428aa06121d4ced2d64bb0fd96831a20b6fb Author: Galt Barber Date: Sat Jun 12 02:40:24 2010 -0700 restoring some large files that had already become small enough to add back commit eb6a6e7d6fd23965c7ab5bd2d4a45270f71f2c1e Author: Galt Barber Date: Sat Jun 12 01:59:51 2010 -0700 new location for things under git build - no partial sandbox checkouts available commit 11226e4955f8b24ae9943fde6f34403975832d8c Author: Galt Barber Date: Sat Jun 12 00:04:58 2010 -0700 "Encode release log update" commit 275d9d764f7b9e2e5869310c4248d0e62b266175 Author: Galt Barber Date: Sat Jun 12 00:04:57 2010 -0700 "Release log update" commit ba58dfdc4976da495a35f9a7a0d609de5bc1b1b4 Author: Galt Barber Date: Fri Jun 11 23:41:32 2010 -0700 first quick attempt to change major makefiles from cvs to git. commit 77290fec1ab791320a23aa02e46d3b58b2934029 Author: Galt Barber Date: Fri Jun 11 22:46:51 2010 -0700 renaming .cvsignore files to .gitignore commit 1b02459c298e4c45e686bc43211e21d6664ca052 Author: katrina Date: Fri Jun 11 23:02:53 2010 +0000 adding wgEncodeHudsonalphaChipSeq.ra commit ee1a9045111a6dc00a254836b61917b5a8f44827 Author: galt Date: Fri Jun 11 23:01:40 2010 +0000 updates commit 57fc03f51be1a8ab15cba728e0c82aa05a7a06a9 Author: katrina Date: Fri Jun 11 23:00:28 2010 +0000 creating metaDb for release commit 05c2f7afb66223703534a35fbdac8414d90499c4 Author: tdreszer Date: Fri Jun 11 22:34:53 2010 +0000 Minor change to waitMask CSS definition. Avoids silent warnings in some browsers. commit 4005fd1983a4790669fee3ad8e9f7a7ec3fcd135 Author: tdreszer Date: Fri Jun 11 22:32:01 2010 +0000 Adding longLabelClip now even though the feature is not ready for prime time. Just trying to beat git. commit 981bd43ba649ba35cad7178b96a895095543e4ae Author: katrina Date: Fri Jun 11 22:31:43 2010 +0000 updating metaDb on beta commit 4c8ec0ad21dd6cb61e4e5313144c23b357f33932 Author: tdreszer Date: Fri Jun 11 22:30:32 2010 +0000 These are running docs that I need to check in before git commit 8751c715eef581a22ad2f8aeaea045c35bef6590 Author: chinhli Date: Fri Jun 11 22:24:58 2010 +0000 Initial bosTau4P2 commit 7c0811c89a4290a697f620c0d39f1c1e68d3caf0 Author: mary Date: Fri Jun 11 22:12:18 2010 +0000 hopefully the last time we will have to touch snp131. Making snp131 on by default and hiding snp130 by default commit 41e435aee2922d9af10e49160c5cdf65662b3586 Author: katrina Date: Fri Jun 11 21:13:51 2010 +0000 removed include statement for wgEncodeHudsonalphaChipSeq.new.ra in prep for release on rr commit 7bd2ad504b25b116700bf0ab637f9e28c8aa2c7e Author: katrina Date: Fri Jun 11 21:12:02 2010 +0000 updated to be for release 2, which I am releasing commit 6ed6b50654cdc56da5b3593dd03892ab91c2e863 Author: cricket Date: Fri Jun 11 21:07:19 2010 +0000 Work in progress, trying to get it in boefore the freeze commit 9a72a2450ed509a21c77ecce92e69f9eeebd06b7 Author: katrina Date: Fri Jun 11 21:05:41 2010 +0000 removed release tags to get ready for release commit 4b0977beb594f8206480e084fe1a269d1d114b83 Author: cricket Date: Fri Jun 11 20:27:37 2010 +0000 Changed a bit more of the long label to comply with Katrina requests commit b2a1185d932bcd93210aa0d635080dc93b1e0b96 Author: cricket Date: Fri Jun 11 20:22:54 2010 +0000 Reworded the methods section commit dc2277bfeb22a5bdc6b1f229712eb9162272d775 Author: cricket Date: Fri Jun 11 20:18:40 2010 +0000 Changed long labels to include Boston University commit 6e54527524a9f45e04f1ad8d52741da4a6aab174 Author: tdreszer Date: Fri Jun 11 19:59:00 2010 +0000 Changed the default subtracks and a couple of short labels as well commit f937c5dae3e74cf23ce69c234921cae29d45e7b5 Author: larrym Date: Fri Jun 11 18:21:40 2010 +0000 improve isDescriptionMatch so it finds matches only at the start of words commit 625561a20dd6bfb9de50d1fd4100bacc2a78bd42 Author: larrym Date: Fri Jun 11 18:14:23 2010 +0000 support tabbed ui in searchTracks commit 519b01241eea4c7c667e184993c8dabf69e66f9c Author: larrym Date: Fri Jun 11 17:53:06 2010 +0000 remove searchTracks cartRemove commit 920c230612bf3a9e6e174a5d315cd0ec470d582d Author: tdreszer Date: Fri Jun 11 17:33:57 2010 +0000 Added special option to print mdbUpdate lines to assist in importing vars from one db.mdb to another. commit 7a53ff90a71e2850f1fddd1dc5bdbae7d9948748 Author: vsmalladi Date: Fri Jun 11 17:23:41 2010 +0000 Modifed Lab to LICR and grant to Ren, consistent with pi.ra. Changed compiste suffix to LicrChipSeq(not enought data to support just Tfbs) and changed long labels to Ren -> LICR commit d759b47783f187fefb7eabcf8f76ee646bc1f2f1 Author: chinhli Date: Fri Jun 11 17:12:56 2010 +0000 rework felCat4 commit 2ab93ae51d0915cf8ce7240071b4cf4039eac8c0 Author: tdreszer Date: Fri Jun 11 17:11:50 2010 +0000 Added mdbObjsPrintUpdateLines and mdbObjsSortOnVars to aid special advanced mdbPrint options commit 61c8b03d75b167c358af64b22b855343adf0f5b5 Author: fanhsu Date: Fri Jun 11 16:31:08 2010 +0000 Created rmDupCol1.c, which removes duplicated lines with identical col1. commit 36f3ee85604624e7eb0d23f36686f74e6df6d4f9 Author: fanhsu Date: Fri Jun 11 16:30:27 2010 +0000 Created makefile. commit 2c556079fd955260a51cf42dd00762afd40b42eb Author: markd Date: Fri Jun 11 16:13:38 2010 +0000 remove dos newlines commit feffb9c22bfb4d99d757a7240edbc48e7ada2c44 Author: chinhli Date: Fri Jun 11 16:00:57 2010 +0000 start phyloP commit 6649bd2ed79ec02681512c5c25a7cb963c95d4c3 Author: galt Date: Fri Jun 11 15:00:31 2010 +0000 "Encode release log update" commit c8f5c54bc65d4574cf9f29eab9698ccd91dfd60a Author: galt Date: Fri Jun 11 15:00:07 2010 +0000 "Release log update" commit 4d72a7afe381a23475112c69a5aa8369af79e607 Author: kent Date: Fri Jun 11 11:09:18 2010 +0000 Making it so bot delay is only called every other sequence when user has multiple sequences. commit 14a28c1904c0025f022ae4d82e53d356ab8bc307 Author: kent Date: Fri Jun 11 10:51:19 2010 +0000 Adding another mark to regulatory track and improving a viewLimit. commit d0ad2a430fcd9a67da85d873eb7df06cdb1c3ece Author: kate Date: Fri Jun 11 05:22:01 2010 +0000 Supertrack descriptions from Melissa commit 5e68a0ab322bfc2e562c509410cdb6f5f4fe2643 Author: kate Date: Fri Jun 11 05:17:10 2010 +0000 Restore ENC prefix commit 2e3eae0f15b45d31edec588698c061dc862fef07 Author: vsmalladi Date: Fri Jun 11 04:20:50 2010 +0000 Updated the standardized lab UCD(Farnham) -> UCD commit 95af7260a11c39bc854d0586c1702c2663d225d2 Author: kate Date: Fri Jun 11 04:14:08 2010 +0000 *** empty log message *** commit e94befd7c0434bad1b890b09f1d0bd2159ef8723 Author: kate Date: Fri Jun 11 04:12:25 2010 +0000 More supertrack descriptions from Melissa commit e168f844d7581425ff4e7fe9f6095265bdf42297 Author: kate Date: Fri Jun 11 04:00:09 2010 +0000 Adding supertracks commit a27d8bd8e575cb0d5221f1f42765adda57061b50 Author: kate Date: Fri Jun 11 03:54:03 2010 +0000 More supertrack descriptions, thanks melissa commit c74da2bc3a613d92036c50e01bcea6cd57c9c4fa Author: vsmalladi Date: Fri Jun 11 03:12:51 2010 +0000 Checking in the file with the correct information. revision 1.4 was empty accidently. Updated Lab for submission 1122 and 1123 to UCD. Updated UCDavis -> UCD commit 0781c09876cf7f3a7d4b3f6a62fef7d98d08ebcc Author: galt Date: Fri Jun 11 01:12:40 2010 +0000 adding help for pstat2 commit cda3f3113eef8d5c90e4df3e6dc03a299710791a Author: braney Date: Fri Jun 11 00:16:29 2010 +0000 fix contact email address commit ebb19b374ef4ea44db7175abe109e1e3fc973d21 Author: tdreszer Date: Fri Jun 11 00:13:33 2010 +0000 Fixed RawSignal fileNames which should point to their Alignments parent commit bd09f4dc2e18bde4530dc37ab7666edab2b955cc Author: ann Date: Fri Jun 11 00:03:54 2010 +0000 committing this on aamp's behalf. He altered the hg18 polyaDb table accordingly commit 685713a401f431077593c25e6f28089db5e5c467 Author: katrina Date: Thu Jun 10 23:17:41 2010 +0000 revised # of experiments because it was incorrect commit 538027ec2e5a59942d81c05dbd62d003c571d987 Author: fanhsu Date: Thu Jun 10 22:55:21 2010 +0000 Added AFFYMETRIX TIMECOURSE tracks using the data on dm2. commit 6c35f6dd0bbe20010321628b072d5421a54a7758 Author: galt Date: Thu Jun 10 22:39:27 2010 +0000 "Encode release log update" commit ff3281d8cb3030520bcccb9ed24183015a8fc206 Author: galt Date: Thu Jun 10 22:39:25 2010 +0000 "Release log update" commit 536c0b6b0532863b975967613f9a2f72ab0675e8 Author: cricket Date: Thu Jun 10 20:56:29 2010 +0000 hanged the requirement for the .ddf commit 7a04fb667a40f234c3dd89a72698962edeb3fd7b Author: larrym Date: Thu Jun 10 20:24:01 2010 +0000 use trix search for simple search; style related code review changes per jim commit a037c6306947cede73e872fe1c34aa597a56d7b5 Author: braney Date: Thu Jun 10 20:14:14 2010 +0000 skip browser and track lines at the beginning of a bedGraph. Add better error message commit 80130381d2c180f429661643c0d83bd598791210 Author: braney Date: Thu Jun 10 20:13:29 2010 +0000 skip browser and track lines at the begining of bedGraphs and wigs when creating bigWigs (added function in linefile to do this) commit 6a5809bc45bca8cabb990e16b0128b52d3bec9a3 Author: braney Date: Thu Jun 10 20:12:00 2010 +0000 add a function to remove initial browser and track lines commit 3a01a5b47c7fefb23f57138c9959a4634594e1e1 Author: cricket Date: Thu Jun 10 17:35:44 2010 +0000 Changed the wigs to bigWigs commit 5702e1e606e75e278d158735af88713b7a5d8e43 Author: kate Date: Thu Jun 10 17:01:15 2010 +0000 Add support for new metaDb. Protect against missing data commit 8432619946875fe323d3aff962921db9e99593ac Author: katrina Date: Thu Jun 10 16:56:36 2010 +0000 added commented out heading to make the include statement for BU ORChID easier to find and consistent with other include statements commit 009a175e72b7df3da2671a3bdb55bcfc99a729e4 Author: chinhli Date: Thu Jun 10 16:48:51 2010 +0000 Multiz with felCat4 commit 3cc4c1579fc6f887a3c660b5b640ed3ae46f838f Author: chinhli Date: Thu Jun 10 16:34:40 2010 +0000 Multiz with felCat4 commit c2e1e34dede37cb367fd54ff0d78fb184fecc203 Author: markd Date: Thu Jun 10 05:16:06 2010 +0000 improved dbProfile in trackDb example commit 452cd3078f1e5cc4caf81f067c65b4452e107948 Author: galt Date: Thu Jun 10 00:31:01 2010 +0000 added info about jobtree pstat2 and parahub results fileSize checks commit 5f8543cee85d401a486a61f5f384626134184708 Author: galt Date: Thu Jun 10 00:30:31 2010 +0000 next version increment commit e2d1f03d57e0308194303263d9727d7476ed3d83 Author: bsuh Date: Thu Jun 10 00:26:52 2010 +0000 Initial checkin of html file which generates the ENCODE June 2010 Freeze update chart commit ee10f8a75fdf8b9aa7640e024a937b2382138178 Author: bsuh Date: Thu Jun 10 00:25:35 2010 +0000 Script can now report the latest report file date as json and jsonp objects commit 1859d0e6c6f22360424b154897b9d8fe9da57940 Author: galt Date: Thu Jun 10 00:23:38 2010 +0000 handle -1 fileSize means does not exist so skip output commit b2c4a3a89fa6360a3352c9c13914ae234a22224f Author: bsuh Date: Thu Jun 10 00:17:44 2010 +0000 Improved behavior when key and value are not specified based on suggestion from Krish. Also added freeze=all as option commit af856df1109c32f8633110fe43afe170aec92310 Author: vsmalladi Date: Wed Jun 9 23:52:42 2010 +0000 Commented out the specific check for a lab inorder to write replicate to subgroups. The code has been checked in the unit test and will now write replicate as a subgroup regardless of lab. Have discussed with Brian about changes. commit ea3a780210fbf6ba9d8b634d252d29132bf5ce8d Author: cricket Date: Wed Jun 9 23:52:25 2010 +0000 New daf for remapped from hg18 data commit 60ffdbe81bfe1c292d7d293a9ab140033f5856c9 Author: cricket Date: Wed Jun 9 23:51:33 2010 +0000 Changed -Seq to -seq in all non-conforming files commit c6a33bf97b8f07504f4f1a6a3d77d136828de62a Author: cricket Date: Wed Jun 9 23:49:58 2010 +0000 New daf for remapped hg18 data commit e89b5f7fb2c030c205192bb3a4e0af2481d98a11 Author: cricket Date: Wed Jun 9 23:49:18 2010 +0000 New daf for remapped hg18 commit 79d5428b8d322eec12d86070aabd81288fd24130 Author: cricket Date: Wed Jun 9 23:47:47 2010 +0000 This is redundant with cshlLongRnaSeq.daf commit 338e1af509a4e5a7de51e5e0a1202c5aa3600d98 Author: galt Date: Wed Jun 9 23:09:48 2010 +0000 allowing pstat2 command to optionally use -result=path/results.txt, i.e. for jobTree use commit 95aba86966065fa4c753d7eb796a22e963fc5e61 Author: tdreszer Date: Wed Jun 9 22:44:45 2010 +0000 HudsonAlpha responded that the 2007 paper is the right ref. commit 3207b1049c078ebf6eedd4d2b2625fdbc4702c1d Author: larrym Date: Wed Jun 9 22:26:24 2010 +0000 include long descriptions of metadata; don't propogate html to children commit dbc366d9391d411fb86f9de7bf9ec7eb30fcb736 Author: braney Date: Wed Jun 9 21:56:55 2010 +0000 fix labels commit 8a293d6ed5f7a90ae31312d853ce9ea761e52080 Author: braney Date: Wed Jun 9 21:53:49 2010 +0000 take out wgEncodeBuOrchid commit d9bb7c0a589459573a9ed0e5bb2f6dc116a2e0f7 Author: braney Date: Wed Jun 9 21:52:28 2010 +0000 split out into its own include file commit b9ee449817ac829edcbdfec97b0043f827b49301 Author: kent Date: Wed Jun 9 21:36:11 2010 +0000 Elaborating description just a little. commit 8b61fd496ae666e27641bf98e5a55e7b5d3274e3 Author: kent Date: Wed Jun 9 21:35:00 2010 +0000 Adding a little to doc. commit 91b35b379eed70aa79b099650f02a5103303207c Author: katrina Date: Wed Jun 9 20:50:56 2010 +0000 removed extra . commit 9de1ea1c13096c4f7a7408ff3400dd3036ca6eb3 Author: vsmalladi Date: Wed Jun 9 19:40:15 2010 +0000 Removed ; (semicolns) accidently reintrodcued in labVersion commit b0194c1eabe44cc6f843a70d6b50ff6f5c36abc3 Author: tdreszer Date: Wed Jun 9 19:25:20 2010 +0000 Tiny change commit bbe3ce0cf6c11b0a945ed901172119c78bade5a7 Author: tdreszer Date: Wed Jun 9 19:20:29 2010 +0000 Adjustments/fixes requested by Katrina commit 897a055637b10dfbde2cff573e085e80d67a7fa3 Author: rhead Date: Wed Jun 9 18:38:47 2010 +0000 Added idHitter.csh. commit ce9bf10d5c7cd1abfc426614f1d93c773d2fd5d1 Author: vsmalladi Date: Wed Jun 9 18:03:26 2010 +0000 Made Lab name consistent for all variants of UCD% -> UCD commit 307673f91100ddc1ccf1ffb6761ce6897a7c4208 Author: vsmalladi Date: Wed Jun 9 18:02:17 2010 +0000 Made Lab name consistent for all variants of UCD% -> UCD and Harvard(Weissman) -> Harvard commit 498fd75d8e808776294ba37fe0f2efc9aa783c3d Author: tdreszer Date: Wed Jun 9 17:50:54 2010 +0000 Added missing mdb RA files commit e05e4e59a9b076c7cc92f213cd3b8a87646ebfc4 Author: vanessa Date: Wed Jun 9 17:27:25 2010 +0000 removed include for wgEncodeCaltechRnaSeq.new.ra commit 20ac78587abcf7335dc379957e61a3702f920568 Author: vanessa Date: Wed Jun 9 17:12:38 2010 +0000 copied new trackDb file with no release tags for release to RR commit 7108585f49527e235d203945e2d25da80a34749b Author: vanessa Date: Wed Jun 9 17:08:48 2010 +0000 removed release alpha,beta tags for release commit 3df1afc083e024499d8505a231d7fa634bcf989e Author: katrina Date: Wed Jun 9 16:31:54 2010 +0000 fixed typo commit 8854d7d7cfd6021dbede3a74a9e15b617c4e9902 Author: katrina Date: Wed Jun 9 16:15:56 2010 +0000 fixed typo: changed preditions to predictions commit ca349c11d3dd7446e84b64e8b0422e89c0334c7c Author: katrina Date: Wed Jun 9 15:30:41 2010 +0000 removed extra spaces and fixed several of the citation formats commit 2246704c2c2e0a63e1757861f0c911332016df01 Author: galt Date: Wed Jun 9 15:00:50 2010 +0000 "Encode release log update" commit af36631a599ce03ed0e7f045b5b2b42449219179 Author: galt Date: Wed Jun 9 15:00:17 2010 +0000 "Release log update" commit e48868899fb38912bcc758752f199b0519e5ba63 Author: markd Date: Wed Jun 9 00:37:01 2010 +0000 moved more examples to examples dir commit 77eb31a082db8d3184bd494c633e401c66499404 Author: cricket Date: Wed Jun 9 00:17:23 2010 +0000 Yale Poly A was renamed Yale RNA-seq commit 77b3961b811c0fc211f55feab7781e8f0c27216e Author: tdreszer Date: Wed Jun 9 00:13:45 2010 +0000 More dates have been imported commit 0d921319b8faea872d7afbf02ed845aa9c5b9bae Author: tdreszer Date: Wed Jun 9 00:04:28 2010 +0000 Imported dates from hg18 commit 9cfa8a0e02564852b674a73062fd5ecbca3c0c5f Author: cricket Date: Tue Jun 8 23:58:37 2010 +0000 Took out special character in the long label (-) commit c8960a7c35c4a8e4a04a73f4fa4ee4593a15c28a Author: fanhsu Date: Tue Jun 8 23:41:43 2010 +0000 Added affyDrosDevTransfrags and affyDrosDevSignal tracks with their sub-tracks for dm3. commit 272c68b413466d07615631a78bd352130e601e56 Author: fanhsu Date: Tue Jun 8 23:39:42 2010 +0000 Added affyDrosDevTransfrags.html based on dm2 affyDrosDevTransfrags.html. commit 9d098ce494d60de7087fae03a52a72d6d7b07e2f Author: fanhsu Date: Tue Jun 8 23:38:38 2010 +0000 Added affyDrosDevSignal.html based on dm2 affyDrosDevSignal.html. commit 93e42405b6cf59b3f1f2688c782cb5346cece30f Author: tdreszer Date: Tue Jun 8 23:26:10 2010 +0000 Swap '.' for offending ';' in ddf fields commit d4df33bafebfcff3a59eb844010918c3cc6a5429 Author: cricket Date: Tue Jun 8 23:25:55 2010 +0000 Changed the labels for the BU ORChID tracks commit 58c3c38bdf5b645244a911becf10bfd5b38519d8 Author: vsmalladi Date: Tue Jun 8 23:25:38 2010 +0000 Initial check in of Uw Histone( ChIP-seq) metadata file. commit a3c11478e547dede601f81a97b2c16715a434741 Author: tdreszer Date: Tue Jun 8 23:00:28 2010 +0000 Clensed semicolons from labVersion commit c2ae6243898cca4375cd6f8540252a792e3a3ac2 Author: tdreszer Date: Tue Jun 8 22:41:02 2010 +0000 Imported dateSubmitted from hg18 for one remapped submission commit f6a31beddb093299de47503d102181cc0c8941b7 Author: cricket Date: Tue Jun 8 22:28:56 2010 +0000 Minor typos commit d96522be592bc44f96cc086d15d6fc289ea1c6be Author: cricket Date: Tue Jun 8 22:25:39 2010 +0000 Adding the new meta data file commit c2309487c837e220488ff3f1be7fb8ce657f2529 Author: cricket Date: Tue Jun 8 22:24:11 2010 +0000 Added a new composite for Suny commit b243ce40f8ce3884f0197b7810ba2df7c711d865 Author: vsmalladi Date: Tue Jun 8 22:08:27 2010 +0000 Updated metaData with metaData for bam from sbumission 1246 commit d3b5915c15335d830cf9b96a6751ac7e34fe1420 Author: braney Date: Tue Jun 8 21:58:03 2010 +0000 change validationSettings commit 49123787d08c7cae07d52718abe1f03d28c907fc Author: braney Date: Tue Jun 8 21:43:19 2010 +0000 add treatment and growthProtocol commit 30ca98c2a4ae6a049ebf9349cab1137b9892a503 Author: tdreszer Date: Tue Jun 8 20:55:44 2010 +0000 Initial checkin of Methyl that leaked in during mini-freeze of TFBS commit 148d1abed2f7d43681e524a33e6c81c8d13f480a Author: tdreszer Date: Tue Jun 8 20:54:56 2010 +0000 Post mini-freeze update with wigs removed and dates updated commit a20bb86a2605af63f09abf4888f6d0dec90a61a4 Author: galt Date: Tue Jun 8 19:28:11 2010 +0000 not needed commit 09ab736bf24ee90225b804aaff76f8ed51810365 Author: vsmalladi Date: Tue Jun 8 19:12:58 2010 +0000 Updated metaDb to include new bam and broad peak files from June 7th freeze commit e9abafd89a0c81862c8f068305fc886b2edcbe69 Author: cricket Date: Tue Jun 8 18:46:02 2010 +0000 Track Description for the next Suny Track commit 92318e7e874bf022511f6fc3cd00ad342d03be5d Author: cricket Date: Tue Jun 8 18:45:06 2010 +0000 A new track description as the old one was for Tiling Arrays commit 9d070df39ba06597410b6ae5ed10ff6b181db76f Author: galt Date: Tue Jun 8 18:44:54 2010 +0000 oops commit b7efd84280b2ff546c0544c4084331fa10f71797 Author: cricket Date: Tue Jun 8 18:39:02 2010 +0000 It had the wrong track name commit cf1f4c60a8c4cfc9899a3053835ec080c56a343f Author: cricket Date: Tue Jun 8 18:37:36 2010 +0000 The correct track name for the .html file commit 351a9774974f537cc705ee9771bb61adc61980b6 Author: larrym Date: Tue Jun 8 18:31:13 2010 +0000 make motifHitSection and loadDnaMotif public; use a table for motif section to avoid problem where bases in image and text did not line up; fix typo (occurence => occurrence) commit aee8a9641552fddc8b341d3ad546d5fb1815311e Author: cricket Date: Tue Jun 8 18:30:27 2010 +0000 New Track Description commit 260790239384a19c075f697a126df97a9199d1c7 Author: baertsch Date: Tue Jun 8 17:59:56 2010 +0000 remove old search spec ucscRetroInfo (base table is now ucscRetroAli) commit b0054cf46a38416ea299ba45c0d0dcf428c0853f Author: vanessa Date: Tue Jun 8 17:54:49 2010 +0000 changed the path of data files to be under the examples directory commit 13c4b7164816b5b000eb972e759d1e5175722e4a Author: cricket Date: Tue Jun 8 17:44:53 2010 +0000 I fixed the controlled vocab line to have the right tag and I also removed view from the sort as there is only one view. commit 381267c433f9c479842e2a84baa5da1fc54f208f Author: angie Date: Tue Jun 8 17:39:29 2010 +0000 Use long long not long in getSnpSeqFileOffset, so it will work on 32-bit systems as well. Contributed by John Hayward @ Wheaton. commit 86c58ae558f4a939c9d88d83168733bc6bc0c6d0 Author: katrina Date: Tue Jun 8 17:29:14 2010 +0000 changed links from pointing at inaccessible full text to summary/abstract commit e5290393a051f809c1a8835cde4d9db3dda01c38 Author: cricket Date: Tue Jun 8 16:40:00 2010 +0000 New metadata .ra for the SunyAlbany track commit 97a0416be0368db13aece1e9c50404676acf7efc Author: galt Date: Tue Jun 8 15:00:41 2010 +0000 "Encode release log update" commit bfa809b11e86df231646221add01fc16e6b1d5d0 Author: galt Date: Tue Jun 8 15:00:20 2010 +0000 "Release log update" commit 2da86014d1863bcb56807cd4f3e04224ee21a3b3 Author: braney Date: Tue Jun 8 04:37:31 2010 +0000 some little fixups commit 64927e3dbeb39a7ac51dba28a45c9d3025601396 Author: bsuh Date: Tue Jun 8 04:23:33 2010 +0000 Added output as Google JSON Query Response commit 9f7ca4ce525b8f296030b116130403f0d8f2ed45 Author: cline Date: Tue Jun 8 01:57:08 2010 +0000 Finished one more stage of execution commit 65fe8ffaa75b1ecda607a1f0c4488d232c2bd271 Author: galt Date: Tue Jun 8 00:42:20 2010 +0000 changing qateam to encodeteam commit 6ef784f907116b4310cd7e11ad73c6d8efd4e38e Author: fanhsu Date: Mon Jun 7 23:55:45 2010 +0000 Updated OMIM URL. commit a4b9d1a2f0d120c1fa68717e7b8a8641ae0074a2 Author: braney Date: Mon Jun 7 23:40:58 2010 +0000 fixed problems with different files. Turns out that both of the release2 files were truncated. Hmm... disk exhaustion? commit b56b5feb06354dea7b5843c09645f693679e2e74 Author: cricket Date: Mon Jun 7 23:21:12 2010 +0000 added the field growthProtocol to distinguish which growth protocl is being used commit b4e5c1a18b4b9fe2cca88ad02e2e76f924e819c7 Author: markd Date: Mon Jun 7 23:18:07 2010 +0000 moved some publications, fixed links commit fa13af4f650109cf855e18d981cefb049d8ba64c Author: tdreszer Date: Mon Jun 7 23:08:14 2010 +0000 The new longLabelClip setting is definitely not ready to go out commit 88daeb452323f05dfd273f1fb89a70fadb9c097e Author: tdreszer Date: Mon Jun 7 23:06:13 2010 +0000 Tightened the signal range as per Katrina's request commit 0aa983439a119690b4709e05b7297248537fb78d Author: vsmalladi Date: Mon Jun 7 22:47:41 2010 +0000 Updated the metadata line to include only subId and dateSubmitted. updated track and subtrack names to include wgEncode and appropriate abreviations. Lastly updated type wig line to update to ENC-> WGENCODE commit 7141db48096db23cc1348722835b31db3f221123 Author: bsuh Date: Mon Jun 7 22:46:50 2010 +0000 Updated to latest renderHtml and changed color orange to RGB to fix IE8 problems commit 9491ec6e526b68210e6e82b4a1534a6a601e20c0 Author: bsuh Date: Mon Jun 7 22:46:31 2010 +0000 Fixed bug found by Kate dealing with Jan2010 freeze date commit 32d18e3677b5e2dd58d04e6eff7b75b5669c158f Author: vsmalladi Date: Mon Jun 7 22:46:02 2010 +0000 Upated tablenames to include wgEncode commit f0c643d82724f4cc86c99f79befed532f31c2e33 Author: bsuh Date: Mon Jun 7 22:45:28 2010 +0000 Updated to latest renderHtml commit 46dc43092b6a681b44ba4ba515bced8569be99c3 Author: bsuh Date: Mon Jun 7 22:45:10 2010 +0000 Updated to latest renderHtml and added px to fix IE8 problems commit 52a6a514b41b28e47b9c2c20f10e13079662bfc6 Author: vsmalladi Date: Mon Jun 7 22:45:07 2010 +0000 Updated file names commit 78538b27aaa077fa272e780a5cd3cb70f11ea6ce Author: bsuh Date: Mon Jun 7 22:44:07 2010 +0000 Added another option to renderHtml function and added DOCTYPE tag to fix IE8 problems commit 86048c05bb7c9a1ed8a049f34086bf407abddb7e Author: vsmalladi Date: Mon Jun 7 22:44:03 2010 +0000 Added mdb.txt to check the mdb.txt, might still need to update make file to verify everything in the file commit ea6dc48dfee7b2b5c3c2ecf0f6aab664d8395b2c Author: vsmalladi Date: Mon Jun 7 22:43:05 2010 +0000 Added fileDb.ra as this is generated by the pipeline at the moment commit 7fc546eb32c06898550b750ba3480364decd4e51 Author: vsmalladi Date: Mon Jun 7 22:41:03 2010 +0000 Added mdb.txt and fileDb.ra files to check between expected and actual. Uncommented line to print the file name commit b7cbd7a051df709e5c0d19367c01954ef33f1f21 Author: braney Date: Mon Jun 7 21:57:09 2010 +0000 update for hg19 commit e977b14bd5bf402bbfcebad7b0f741290f2f0111 Author: vsmalladi Date: Mon Jun 7 21:04:57 2010 +0000 Changed fastq format as optional, specified bam files as downloadOnly and standardized compsite name commit ec1ac51d789ba28c1f49fd32de100e4a360f9a7a Author: vsmalladi Date: Mon Jun 7 21:04:19 2010 +0000 Added fastq format as optional, specified bam files as downloadOnly and standardized compsite name commit f88ea54b20d0561a5d89fe8cea1c7dd25ae80921 Author: cline Date: Mon Jun 7 21:02:41 2010 +0000 Fixed the protocol names for ECC1 and T47D commit d17a4c8010caf04e0b70c87c7a55be0a5bd61e8b Author: cline Date: Mon Jun 7 21:00:21 2010 +0000 Added a few more fiends for ECC1 and T47D commit 2bdf94a2c614a5e0214a18ad54ed1cd718f117d4 Author: braney Date: Mon Jun 7 20:40:51 2010 +0000 change default view to include all of the K562 and GM12878 tracks commit f869527bfac5c9ec8dc08f55c43c89e7452700a0 Author: braney Date: Mon Jun 7 20:39:54 2010 +0000 add some text about the Plus and Minus Raw Signal views commit 866f79735a27913d02243928a6a9394c78bdac0a Author: markd Date: Mon Jun 7 20:37:09 2010 +0000 moved training commit 9c351d2d3c21075f3f7a689dbeaa330e14195fa5 Author: mary Date: Mon Jun 7 19:53:26 2010 +0000 making snp131 hidden by default as temp fix for CGI error with new func field commit d76fe2cccb2e5504a420ba197c2e86e9f44e0a1e Author: galt Date: Mon Jun 7 19:37:48 2010 +0000 fixing broken makefile commit b31f9ae12693d9f8c8380c601ddc137240a2a420 Author: vsmalladi Date: Mon Jun 7 19:10:17 2010 +0000 Updated dataType syntax to match what is in cv.ra and lab to match cv.ra commit 26d9b330591022eb354abca292fc0c25f66fffbe Author: vsmalladi Date: Mon Jun 7 19:09:20 2010 +0000 Updated dataType syntax to match what is in cv.ra commit f01130c231fd4a4470a9ddd2a0836c8c87be4db4 Author: kent Date: Mon Jun 7 18:28:31 2010 +0000 Adding description page for wgEncodeRegTxn. commit 3fa077a6d20188227b26bb71a73cf9d724204499 Author: kent Date: Mon Jun 7 17:34:51 2010 +0000 Starting on description page for ENCODE regulatory supertrack. commit 15bcc101c8c489b2ea744ce986109dbe4ae0ad6e Author: galt Date: Mon Jun 7 17:23:35 2010 +0000 "New version number v233" commit 030a6f7ef7caa7ba13d3a256692b6325095024b9 Author: galt Date: Mon Jun 7 17:22:46 2010 +0000 v233 final build commit 72513d33172b23a951a6368149c3345ef91a2836 Author: angie Date: Mon Jun 7 16:57:12 2010 +0000 Regenerated snp131Exceptions, and snp131OrthoPt2Rm2Pa2 which depends on the exceptions. Multiple alignments were flagged even when there were single alignments to a chrom and chrom_hap, which had the effect of excluding haplo regions (even on main chroms) from ortho alignments. commit 32f008c2043ce2e5e5cf388779674b4e90210ec1 Author: angie Date: Mon Jun 7 16:54:21 2010 +0000 Comment tweak. commit 812873b951cf242b7d3f1f008fff8ab4162953dd Author: angie Date: Mon Jun 7 16:53:10 2010 +0000 For bigWig and BAM, provide link to format/info. commit 19be29135a4ad05ee37b9dced0c69d2dbb6a7ac7 Author: chinhli Date: Mon Jun 7 16:30:37 2010 +0000 13-way phastCons commit 19376f5a1f295c700ab9277b220696715a14ed65 Author: chinhli Date: Mon Jun 7 16:25:49 2010 +0000 13-way phastCons commit d66544ac32b73d722a66771dc06cbc8021453e37 Author: chinhli Date: Mon Jun 7 16:23:43 2010 +0000 13-way phastCons commit 54123ab13c24a64c595357f57d2e6781f19a6583 Author: tdreszer Date: Mon Jun 7 16:10:46 2010 +0000 Added rank for UW commit 258e37fa33d8edfbac163f384f258fffa0e0c3e6 Author: vsmalladi Date: Mon Jun 7 15:49:59 2010 +0000 Updated daf to accept new dataTypes bigWig and bam. Updated, by request, Composite Name to seperate indvidual data types submitted by Open Chromati, also changed name from UT -> UT-Austin commit e7bf0b24446c71218b21fd4a2c062fa95343dfb3 Author: vsmalladi Date: Mon Jun 7 15:48:52 2010 +0000 Updated daf to accept new dataTypes bigWig and bam. Updated, by request, Composite Name to seperate indvidual data types submitted by Open Chromatin. commit 4ad590c649c86b6d0cdaabb3b8b3f7da3818402b Author: katrina Date: Mon Jun 7 15:46:17 2010 +0000 added two more /gbdb files to the deprecated files list commit 25de1dd5bdd294a75fe7801ecdccf31a98d0721c Author: tdreszer Date: Mon Jun 7 15:35:56 2010 +0000 Added rank for UW commit 78ddfa655751d381a428b9a32fc1b0dd1c621db0 Author: katrina Date: Mon Jun 7 15:32:42 2010 +0000 added two gbdb files to deprecated list commit 5d5e79bfbddb67b8c299e9eb05faf0f693226296 Author: galt Date: Mon Jun 7 15:00:06 2010 +0000 "Encode release log update" commit e6996b53303cc6aa613160128355bf1d8a479b37 Author: galt Date: Mon Jun 7 15:00:04 2010 +0000 "Release log update" commit 89221057011d0630b7539c76070aaba2f996f751 Author: markd Date: Mon Jun 7 03:48:09 2010 +0000 added import of new tables from ncbi commit 1ecd0c12a766612fbf7959f1448865d0ad3097a0 Author: tdreszer Date: Sun Jun 6 17:45:43 2010 +0000 First version of UW DnaseI HS daf commit 021a792f5e7b395f4a21676f095052f52ec2ecdb Author: galt Date: Sun Jun 6 15:00:06 2010 +0000 "Encode release log update" commit 2e6f4825a528d3c08577a18740416083a76aaeb3 Author: galt Date: Sun Jun 6 15:00:03 2010 +0000 "Release log update" commit 450a4dbaa3762f590f4579d0a4c35e5327361d0e Author: braney Date: Sat Jun 5 19:29:54 2010 +0000 add support for 32-bit color (make USE_PNG have global consequence) commit 57c0a6b04d0637e67506917365cfffef437ed710 Author: galt Date: Sat Jun 5 15:00:07 2010 +0000 "Encode release log update" commit db23d80e2f830784fdf0d9b287d9e7a4e5bfa95c Author: galt Date: Sat Jun 5 15:00:04 2010 +0000 "Release log update" commit 5e0023fd8209063941a5c8798f66eb952c8bff1b Author: galt Date: Sat Jun 5 10:38:57 2010 +0000 adding first gitTools commit f2ede8c0d7043ed6f4f3ca20fd58d3a2c88ebec9 Author: kate Date: Sat Jun 5 05:54:46 2010 +0000 UCD synonym doesn't help reporting so removing commit 646ae425bd6acd5b9c400aa8c91d0c1e42c6ac5f Author: kate Date: Sat Jun 5 05:33:39 2010 +0000 Retiring wrangler emails. Adding synonymous labname for Farnham commit 666750787c029ab1f485398c73a5086d1f7d002d Author: kent Date: Sat Jun 5 00:47:47 2010 +0000 Making wigEncode abort on second track it sees. commit a2027cc190c4a69e6f53de505a3caad7e8bc3cfd Author: chinhli Date: Fri Jun 4 23:32:28 2010 +0000 BLASTZ/CHAIN/NET commit 9b4c70607e97fd3393e9726c4d35c0bbc66ab42b Author: chinhli Date: Fri Jun 4 23:29:32 2010 +0000 phastCons support commit c733e39705d163d63d0dde0b6546a0fe9fc1c411 Author: mary Date: Fri Jun 4 23:24:11 2010 +0000 adding snp131 to news on front page. Pushing older stories to newsarch commit 06eea91d714ba1e19a5e82f6dbaca66d5d60073e Author: katrina Date: Fri Jun 4 22:22:59 2010 +0000 changed max shortLabel to 17 characters commit bc2710ce5fc6a2e6ac22a3a2183ddc34589f3622 Author: angie Date: Fri Jun 4 21:57:00 2010 +0000 loadDgv: don't skip filtering when filterPmIds is NULL -- if the user has deselected everything but wants the filter to be include, we do need to filter. commit 1314f2c6ea2ef02643e0d31269568327d2e08065 Author: angie Date: Fri Jun 4 21:54:56 2010 +0000 DGV: don't second-guess user filtering by include and deselecting all items. commit 457e6e5b23f2ad5596456efcb13a5d2261bc83e9 Author: tdreszer Date: Fri Jun 4 21:54:49 2010 +0000 Not sure if Yale should be in beta since it is identical in public and alpha. HAIB should be in beta. commit 2bc9483dafe790f618f89e27c0555d2aa58b19f7 Author: tdreszer Date: Fri Jun 4 21:52:55 2010 +0000 Establishing the first publicly release mdb RA file commit fc9684ee49a2dec6ff397676699a13064856e975 Author: kent Date: Fri Jun 4 21:37:53 2010 +0000 Adding a few pixels to left label area so that it really does fit the number of characters you select. commit 96f1653c46a9b6e3ac820f4d17f13722ae184c44 Author: kent Date: Fri Jun 4 21:32:32 2010 +0000 Adding wigCorrelate to build. commit a1b1f0e8911211d4ced95d9d3c71316cbecd316e Author: kent Date: Fri Jun 4 21:32:17 2010 +0000 Seems to work. commit 03bd7b9a8d2be0d7b8060206f2c3269b7fc05a96 Author: katrina Date: Fri Jun 4 20:49:52 2010 +0000 changed release beta,public to release public to stage on hgwbeta commit 039cb2aeec561b3f614d91efce33797d079e202e Author: katrina Date: Fri Jun 4 20:49:32 2010 +0000 changed release alpha to release alpha,beta to stage on hgwbeta commit 5f98cdf488799e5f32f1c9a19d5532c18ba52e29 Author: vanessa Date: Fri Jun 4 20:49:06 2010 +0000 corrected some typos commit c7c7cd8297c678ed212489927ec5a21306ccbb30 Author: galt Date: Fri Jun 4 20:46:19 2010 +0000 adding some more search tables before we actually run off the end commit e913bf2cef1202c099c55cc09c0aac78bb45bdef Author: mary Date: Fri Jun 4 18:45:07 2010 +0000 releasing snp131 take 2: removing release tags and changing visibility of snp130 to be hide by default commit 8b1cbf8b944d3ff6a047191e409e399dceca83ac Author: braney Date: Fri Jun 4 18:35:09 2010 +0000 add for mm9 commit 93d0879ee226593a6363acef080452deb620cc20 Author: braney Date: Fri Jun 4 18:33:46 2010 +0000 add makefile commit e017aabd30b494864fe0ef75f6f3abbfbb06a2c9 Author: tdreszer Date: Fri Jun 4 18:09:37 2010 +0000 Put them in order. commit 9ddbd5e66f054169df3946855dbe2f06543d7212 Author: fanhsu Date: Fri Jun 4 18:08:14 2010 +0000 Changed sprintf to safef for DECIPHER track. commit caede43316d216cf8fa58ccf5571486c6d898b7e Author: tdreszer Date: Fri Jun 4 18:08:05 2010 +0000 Added 2 approved cell lines for HAIB commit 65ed0ddd86a42533c4d0fdff8479d51317dc3154 Author: kent Date: Fri Jun 4 17:58:30 2010 +0000 Shortening some long labels commit 3c4152375e4385188ff20de8ab57764f77197b5b Author: tdreszer Date: Fri Jun 4 17:48:05 2010 +0000 Reverting to old matrix as promised commit 303f34c8d2b84e7eac42e7b33af3d43031dafea4 Author: galt Date: Fri Jun 4 15:00:37 2010 +0000 "Encode release log update" commit cd9b4de81520a572d297a1f9f5a2112fc5a72bbe Author: galt Date: Fri Jun 4 15:00:17 2010 +0000 "Release log update" commit ccfa205c88614fd16af9f4c321ee14d7cb27792c Author: angie Date: Fri Jun 4 05:36:03 2010 +0000 Fixed detection of multiple mappings to handle chr*_hap correctly, e.g. if a SNP maps to one chr6 pos and one chr6_cox_hap2 pos it is not multiply mapped. Other misc changes to accomodate human snp131. commit 8e8f7f729b1765a80a99e7f1a7747be5c9dc79ff Author: markd Date: Fri Jun 4 04:40:17 2010 +0000 make more compat symlinks commit 0f2b9897f2019f899cd2d702a0e3b9e8969f797d Author: rhead Date: Fri Jun 4 01:41:19 2010 +0000 Added findBrokenLinks.csh and a comment about how to install in /cluster/bin/scripts since Hiram changed the SCRIPTS defined in common.mk. commit 0fc1c78688ad37df32d45c74cd0273d00a9f5733 Author: mary Date: Fri Jun 4 01:37:23 2010 +0000 adding ability to search genomewiki on contacts page commit 47a6fd6a5cd43a93f3ef3fab0bcfbe79b3a16142 Author: rhead Date: Fri Jun 4 01:36:15 2010 +0000 This has been used in cron jobs run by Angie to find broken links in gbdb and goldenPath for a long time. The jobs are switching to the qateam crontab, and we are finally checking this little script in. commit 67c4a876102fd17df5d38473565b5237a7a3f19b Author: braney Date: Fri Jun 4 00:53:13 2010 +0000 add addresses for rami, flo, and tim commit d978e7a525568435beebcd0f82defc01d5f03d96 Author: larrym Date: Fri Jun 4 00:12:42 2010 +0000 add makeTrackIndex commit c28751374bc6dcf62f02b5d502d4dad4b966f7cf Author: larrym Date: Thu Jun 3 23:41:29 2010 +0000 Make a track ixIxx file for the given to be used in the track search tool commit 4f83634cd2ddc609f88e378c75b54938c5ff6a9d Author: braney Date: Thu Jun 3 23:36:04 2010 +0000 ignore initial browser and track lines commit cf740af4b5d229359f9e00e8d4cf14b074bbedb5 Author: vsmalladi Date: Thu Jun 3 23:30:30 2010 +0000 Updated schema to support types Antibody, protocol, control, treatment commit 16d309e51ab1be228bb1edf8cbf433fed7aca2c2 Author: braney Date: Thu Jun 3 23:25:29 2010 +0000 check dates before rebuilding metaDb commit b82c454e945ee94f776aef514266a03da0e24ca0 Author: braney Date: Thu Jun 3 23:19:48 2010 +0000 utilities to check to see if metaDb needs to be rebuilt, and do so if necessary commit 711a8c4231091efe16333d5cc801ca2089d17d78 Author: braney Date: Thu Jun 3 23:18:41 2010 +0000 a utility to touch a file with the date of an SQL table (for use in a makefile) commit 6f69f837cfa9cd2885a86ad2bb665435d2470215 Author: cricket Date: Thu Jun 3 23:03:06 2010 +0000 include trackDb.wgEncodeSuny.ra commit 44478f372cf75be0401476da88b0d82a040cbddc Author: cricket Date: Thu Jun 3 23:01:08 2010 +0000 Took out ripAntibodies commit 6e90e7c2c1df1b9b65dda88966aef5c035f8c29f Author: mary Date: Thu Jun 3 23:00:29 2010 +0000 changing calJac1 chain/nets so that they are for most dbs and for hg18, ornAna1 and monDom4 commit 32521f546814b9ff3de360364a73a5b7beae2b96 Author: cricket Date: Thu Jun 3 22:59:34 2010 +0000 dded ripInput to the ripTgtProtien table commit 4d11187336c82ec2ef2e7e0400c61d713a5978b9 Author: vsmalladi Date: Thu Jun 3 22:54:57 2010 +0000 Added group type as this was accidently deleted previously. commit ef3b33e566beae330bc64e7ea66110a5c1ccd182 Author: cricket Date: Thu Jun 3 22:49:25 2010 +0000 This is a new track DB to hold the stuff from SunyAlbany commit 6cf4967adebd108b2b35cea45beb290b67f819fd Author: mary Date: Thu Jun 3 21:53:36 2010 +0000 changing the date once again to release the calJac3 - I really am going to release it today commit e127f0989304f725b42b67010388245e3d072de8 Author: tdreszer Date: Thu Jun 3 21:49:54 2010 +0000 Shortened some offending shortLabels and longLabels to make Katrina happy commit accab7b13edc2defbdd65c01ea1577890e5152b1 Author: vanessa Date: Thu Jun 3 20:49:46 2010 +0000 removed release alpha, beta tags and release public block in preparation for the mapability track release commit d54d9d5675d6bcd02272a885e61cf551cd2f2586 Author: tdreszer Date: Thu Jun 3 20:27:26 2010 +0000 Fixed excluded filterComp options bug and made sure subtrack counts are updated with filterComp +/- buttons. commit ab3676bc6ee04ef92fe89969953efdc1ddebdca2 Author: mary Date: Thu Jun 3 20:21:09 2010 +0000 changing trackDb so that primate chain/nets have calJac3 rather than calJac1 commit a655896ea21cfc93a173482cae0f93035ef5a3c7 Author: katrina Date: Thu Jun 3 19:54:34 2010 +0000 removed the last sentence in the 'Select Filter categories' section about holding the cntrl key to select muptiple items since this is no longer the case with filterBy V2 commit 96030cdfc6325d9873bbf760a0ed8c048b7ba889 Author: tdreszer Date: Thu Jun 3 19:39:11 2010 +0000 Removed the duplicate 'None' term from ripTgtProtein commit 595a6fb8c17bbf57d49c3d5d7e1d9be8e4a8cfdf Author: tdreszer Date: Thu Jun 3 19:37:37 2010 +0000 Allow ripTgtProtein to accept control terms, specifically 'None'. commit e1181fb933f985f4db48295f04eca053adba3b67 Author: kent Date: Thu Jun 3 18:54:00 2010 +0000 Fixing symbol conflict with table browser isBigWig function and new library function. commit 1df70d1172d47ebec69b17094b43f60f1c791fca Author: kent Date: Thu Jun 3 18:08:37 2010 +0000 Adding isBigWig function. commit 36c6c8df797aff72db8b36622a14bc5f3acd28d2 Author: braney Date: Thu Jun 3 18:08:27 2010 +0000 move accession's to labVersion commit 3bb732f2e8e74da7d2e8a791f2a185749d80e77e Author: kent Date: Thu Jun 3 18:08:07 2010 +0000 Removing hideFirst option, which no longer does anything. commit dbad8a68fb9ece03d313ba9874adef0cfd2acd8c Author: vsmalladi Date: Thu Jun 3 17:50:46 2010 +0000 For term AP-2gamma: changed santibodyDescription -> antibodyDescription to be consistent with all other entries commit a041cf7d373d8c36b034b9fe40d33f30da44aef3 Author: kent Date: Thu Jun 3 17:09:12 2010 +0000 Removing parameter to metaWigOpen. commit 787413dbfa07436995a3e3da3c23e99e48696983 Author: katrina Date: Thu Jun 3 17:01:33 2010 +0000 adding missing /gbdb files to new files section commit c3659117d94f2716401a4d78fc6b75a28b13fdf5 Author: kent Date: Thu Jun 3 16:57:51 2010 +0000 Removing bbiInternal include. commit 313402ca3bc65a47fcdb22ebde8932e8f5fb882e Author: antonio Date: Thu Jun 3 16:56:11 2010 +0000 removing release tags commit 075d54d3cfa2634206c6ddc6a67b7198d3682094 Author: antonio Date: Thu Jun 3 16:53:38 2010 +0000 typo commit 6ac43dde07b0651c5cf32fbdbdcecba07379baf5 Author: kent Date: Thu Jun 3 16:53:24 2010 +0000 Fixing includes so compiles again. commit 9cf6909037314aa579722de5276236d6624d88ed Author: kent Date: Thu Jun 3 16:51:56 2010 +0000 Moving metaWig stuff from wigCorrelate to library. commit 3c2e35d1a3368a8e0988763519b0a3350886ad48 Author: kent Date: Thu Jun 3 16:48:53 2010 +0000 Adding limit to line size. commit ed622538211342852c92a9ce851dd31f1e4af16b Author: kent Date: Thu Jun 3 16:38:20 2010 +0000 Fixed typo in comment. commit 9f505448d522a6e3c2c2d582cbce4e172c5ff5c0 Author: galt Date: Thu Jun 3 15:00:36 2010 +0000 "Encode release log update" commit d732cc6c9a029eca5b0eb620f862a22c4220765f Author: galt Date: Thu Jun 3 15:00:19 2010 +0000 "Release log update" commit 203046cba8c68875278b9e713563af70c20c3d57 Author: larrym Date: Thu Jun 3 05:52:42 2010 +0000 support simple and advanced tabs commit 5c653787f980af23f82ed3ca644655ff7bdef34f Author: kent Date: Thu Jun 3 05:14:39 2010 +0000 Changing return type of modification-date-ascertaining functions to time_t. commit 523c463c06813b61a747b1d7e7749c39dcd8af35 Author: cline Date: Thu Jun 3 03:18:01 2010 +0000 Added mouse vocabularies including sex and age commit c5acfc9c4110b8887c6fb5d33c14a9c5c33ed7d8 Author: braney Date: Thu Jun 3 01:03:17 2010 +0000 D'oh! check for no metaDb directory commit 31afed3775404f80fe4539bf659a3b91c05bf026 Author: braney Date: Thu Jun 3 00:20:18 2010 +0000 added the build of metaDb commit 6dd27181d672a03dc73e17e72e652f37b8d4cf2d Author: krish Date: Thu Jun 3 00:04:58 2010 +0000 added some tool under dev'ment to deal with exp table commit 96907e96ac2a3fc59bf75df2e65d649a9634b6e9 Author: mary Date: Wed Jun 2 23:52:30 2010 +0000 backing snp131 off the RR to check possibly missing data commit d6a67e15583d2991a34ee71665c2e8f0ea42f800 Author: fanhsu Date: Wed Jun 2 23:04:24 2010 +0000 Added many entries per Antonio's request. commit e4ec016796353f43e5732a3225231d315e81f9bb Author: angie Date: Wed Jun 2 23:01:11 2010 +0000 Updated gwasCatalog: both new catalog data, and use just-released snp131 instead of snp130. commit 617de84b02f5fb0ff64303be3b609b9699dc22f0 Author: angie Date: Wed Jun 2 23:00:02 2010 +0000 Updated gwasCatalog. commit e1b16b02b204f32d73d9d08b1fb02b615492c5b2 Author: mary Date: Wed Jun 2 22:36:10 2010 +0000 making snp130 on hide by default so the coolness of snp131 can show through unhindered commit 59d0907dfda168781f58030715841f4169ee8936 Author: braney Date: Wed Jun 2 21:59:14 2010 +0000 make the metaDb table commit 7a5b6969fe480e1efdd0bd386db9f0547c303e21 Author: tdreszer Date: Wed Jun 2 19:27:51 2010 +0000 Added All plus/minus buttons for filterComposites and added link to cv terms in filterComp box. commit 6114a46eea5410bd32bfe52891ae191726b2ce0a Author: tdreszer Date: Wed Jun 2 19:16:37 2010 +0000 Added support for checkAll/uncheckAll on filterComposites. commit d4a96b9f6a9fa024c35d060c459383ca00835085 Author: tdreszer Date: Wed Jun 2 19:15:10 2010 +0000 Added support for checkAll/uncheckAll commit e1cf6b908ea1b9cf55219c949797148c3f65647c Author: tdreszer Date: Wed Jun 2 19:11:53 2010 +0000 Added useful waitOnFinction() routine that makes sure wait cursor is seen. commit 0b53c466823c1ee24a080ecb647fb6079fcff8d0 Author: tdreszer Date: Wed Jun 2 19:07:02 2010 +0000 Added skipBeyondDelimit() commit 8ba12ccea19a2fa14dd813d698ea61e9e872fbcc Author: tdreszer Date: Wed Jun 2 19:05:51 2010 +0000 Added waitMask and inOutButton css classes commit b5d26470fc4907894aa6b6a6c487a6922d9e7c9c Author: braney Date: Wed Jun 2 18:05:00 2010 +0000 add release notes commit f825caedecc27d70e83ced68d094bc47f8e749ce Author: mary Date: Wed Jun 2 17:47:40 2010 +0000 changing release date to June 2 rather than June1 for marmoset release (lagging a bit due to snp131 track) commit 364dd3ff60de0fdacaab41e470caa54067a3bdf0 Author: braney Date: Wed Jun 2 17:27:55 2010 +0000 take out fastq commit 964d499f769dd8476f54ec272f78192fecf47d3d Author: galt Date: Wed Jun 2 15:00:35 2010 +0000 "Encode release log update" commit f6a84d88f28555b76fb6ded30510726ef21d5e27 Author: galt Date: Wed Jun 2 15:00:16 2010 +0000 "Release log update" commit ed2f711a16fa1b81432e3f87de79f24e2af3d31e Author: markd Date: Wed Jun 2 07:07:45 2010 +0000 added program to lift blat subrange queries commit 0e5874c5ac35842b4887cb687e07508a4037b023 Author: angie Date: Wed Jun 2 04:09:10 2010 +0000 Improvements to SNP controls' explanatory text -- thanks Mary! commit 0040c24ab9ec6e03eb6687c7161b54c581d394ec Author: bsuh Date: Wed Jun 2 00:37:02 2010 +0000 Updated README with latest info commit ea78d766c1f6e8eff66e603d3463f3157c903ebc Author: braney Date: Wed Jun 2 00:29:06 2010 +0000 move HudsonAlphaRnaSeq to correct position commit 2128c3ebee800e326bb0f4a38f7e4f6bca04bb5c Author: bsuh Date: Wed Jun 2 00:18:38 2010 +0000 Initial check-in of ENCODE Report Charts cgis commit f3171664b13f06175152d7411a02df943bed1561 Author: bsuh Date: Wed Jun 2 00:16:52 2010 +0000 Updated June 2010 freeze date commit aa6c488633028876b0ef2f69a508eafa087b8a34 Author: bsuh Date: Wed Jun 2 00:16:27 2010 +0000 Deleted encodeChart.pl commit 9dbfd01681481d8ed6830b9acec5bfcb90b94dc9 Author: braney Date: Wed Jun 2 00:04:20 2010 +0000 moving this track into the proper place commit 5c49fefc53030432407d77f1e6d787f51c5685a0 Author: braney Date: Wed Jun 2 00:03:55 2010 +0000 put this track in its proper place commit 44892ba631c24942ed83ebc44a2fbb8ac4114a9a Author: braney Date: Tue Jun 1 23:47:57 2010 +0000 make a variable bamTypes commit 0fcd4cf4d80e392df18033cb7a49151d37839bf4 Author: katrina Date: Tue Jun 1 23:32:11 2010 +0000 fixing release2 total download file count commit fc8f5f0f7724af330370ab7c286108343820cfd4 Author: angie Date: Tue Jun 1 22:21:38 2010 +0000 Corrected table description (thanks Mary!). commit 6a37e813c02ebe607b39c5217c044d833078a244 Author: pauline Date: Tue Jun 1 21:33:43 2010 +0000 Uncommented dimensions line to fix (null) label on rr commit ddbd57724846898a3435a9b2b9b708207b9e4015 Author: fanhsu Date: Tue Jun 1 21:27:57 2010 +0000 Added search term for DECIPHER. commit d985fc4c3d00859ba602ac4c1ad2552bb3cefd83 Author: katrina Date: Tue Jun 1 21:15:23 2010 +0000 moved 8 tables from new to untouched; moved the associated 8 .wib files from new to untouched; adjusted counts commit f89b9bc5308b6d1cc5cfe209cb65b8c7893a7321 Author: rhead Date: Tue Jun 1 21:09:48 2010 +0000 Removing temporary fix to all_mrna and all_est tracks now that v232 cgis are out on the RR. commit 13b0b2c5e4bcc6c533e219c7a375ed258903c8b1 Author: antonio Date: Tue Jun 1 21:04:52 2010 +0000 releasing public commit 40f4ffb3799905df68f6f9b494fb601a1058f1c9 Author: ann Date: Tue Jun 1 20:56:57 2010 +0000 added info about the timing of the MySQL server sync. commit 8c1c7bfc8e19b86e596c79347e24e7c85a84fd6e Author: fanhsu Date: Tue Jun 1 20:43:58 2010 +0000 Added the section of decipherId. commit 0b894efc62bc3995bbf811785172c19615c26bb8 Author: galt Date: Tue Jun 1 20:38:07 2010 +0000 cannot use char which is 1 byte to represent EOF, must use int commit 212187ed0967d766681e021ea64ae13a86f65384 Author: galt Date: Tue Jun 1 20:35:36 2010 +0000 cannot use char which is 1 byte to represent EOF, must use int commit 8cf77d9dd91fddd5ab12a968ea2323ffc92e1094 Author: galt Date: Tue Jun 1 20:09:36 2010 +0000 stdout stream is not assignable on some operating systems commit 60177f41a0d466d9ec31915d008d88f1481c53bf Author: vsmalladi Date: Tue Jun 1 19:07:35 2010 +0000 Changed DAF to accept Signals of type:wig instead of type:BigWig commit 742b2dcb5bcaa1175bcf6c3a4343ed00738cb3ea Author: fanhsu Date: Tue Jun 1 18:35:32 2010 +0000 Added logic to set a DECIPHER entry's color to gray when its mean_ratio = 0. commit 2e440c2480bf2e7fd80345501a642323fc297e70 Author: katrina Date: Tue Jun 1 18:23:12 2010 +0000 removed 2 deprecated tables because they were not part of release1; two were mis-named release2 tables and one was a release2 experimental table. Tim removed all three from dev. Also added a note to two of the deprecated tables that were part on beta & rr as part of release1 but never had a trackDb entry so didn't display in the track commit 38fead7cf2883ec26446971c68581c75257923b1 Author: fanhsu Date: Tue Jun 1 17:56:24 2010 +0000 Built DECIPHER track. commit 849f0f4f7f491b37a093fdd18475d5ffaa5832d4 Author: katrina Date: Tue Jun 1 17:40:55 2010 +0000 removed two tables that I had listed as deprecated accidently. These tables were listed in the trackDb for release1 but never existed in the database. Since they never existed, they cannot be deprecated commit a5f1711806e3ea7e614a7819a8f570db39e79115 Author: hartera Date: Tue Jun 1 17:40:03 2010 +0000 Removed dateSubmitted from all metadata for Mapability track to remove Restricted Until date on the config page as this does not apply for this track. commit 098a301fd66f9d9f22c3e82a21f9bde89c1c2c69 Author: braney Date: Tue Jun 1 17:25:14 2010 +0000 add parent for public mapability track commit 81fa44492adca2c9d9cf275a47eb3bc622443cea Author: chinhli Date: Tue Jun 1 16:25:53 2010 +0000 Adding felCat4 - Cat - Felis catus commit 23ab58b6776c85a883449716c20907ba96b26668 Author: fanhsu Date: Tue Jun 1 16:12:53 2010 +0000 Added color scheme description and reference. commit 5eac888caa9fabacbc186132f755c283b53b96b7 Author: galt Date: Tue Jun 1 15:00:17 2010 +0000 "Encode release log update" commit dda1d5ac95b7274f4d7b5ac0c001a9dcc3090a35 Author: galt Date: Tue Jun 1 15:00:14 2010 +0000 "Release log update" commit 50647b544e2de606cc00072ea0633a70a9663647 Author: galt Date: Tue Jun 1 05:11:28 2010 +0000 v233 preview commit 39f3ed8bc9e320c0c4da55bd81b5f8d0e7294609 Author: cline Date: Tue Jun 1 02:50:47 2010 +0000 Added U2OS to the Tier 3 human cell types commit 5a948c6d2502d6c19412e03acdd45be2c1fc0c72 Author: baertsch Date: Tue Jun 1 01:22:34 2010 +0000 fixed search problems with ucscRetroAli commit 0feda11fc30699d8c53ced21c5a634fbca3339ac Author: markd Date: Mon May 31 22:42:33 2010 +0000 avoid segv on bad table in search commit 0dd822ed816a10696e40cb676186e2cfd02b164b Author: galt Date: Mon May 31 15:00:06 2010 +0000 "Encode release log update" commit 286db80dd6a65d77cf31fdfd68008946809c4cd6 Author: galt Date: Mon May 31 15:00:03 2010 +0000 "Release log update" commit 98e27624c6ade8cdd503ebec153e0253000d2c93 Author: kate Date: Mon May 31 04:02:04 2010 +0000 Get release date from pushQ commit 960ae3c352f0cd44be8bf23636ad1c1cb3cd11b3 Author: larrym Date: Sun May 30 22:38:13 2010 +0000 trivial changes: metadata is one word commit 0843c62533fc378bca4edf7253560fe54f3f00d2 Author: larrym Date: Sun May 30 21:11:47 2010 +0000 add metaDb command commit 2cecc6f33996aeda8fc28661bb15a07d6429eff1 Author: galt Date: Sun May 30 15:00:06 2010 +0000 "Encode release log update" commit 5ae5b60428017223aa0589cca3cdb04e70d0b667 Author: galt Date: Sun May 30 15:00:03 2010 +0000 "Release log update" commit fc2980197c91b495a194a4b9048f2fd9c97ff1a2 Author: larrym Date: Sun May 30 04:00:39 2010 +0000 refactor code to allow variable number of metadata selects commit 34d6973177bb3d433361242050843ef48940cd4e Author: larrym Date: Sun May 30 01:38:17 2010 +0000 include metadata in description search; make last metadata select variable (with a javascript callback) commit 2ab76b6c374e8b239147af1ae596ab5ff02792e6 Author: kent Date: Sat May 29 22:33:53 2010 +0000 adding test sets commit 381801700b9c1c23bff78f4ce5efc3b495e79525 Author: kent Date: Sat May 29 22:30:47 2010 +0000 Taking out span since it now defaults in one fixedStep line of test. commit c6c2582c3410111015a1d91e96176c693f35f186 Author: kent Date: Sat May 29 22:29:55 2010 +0000 SOme more timing measurements. commit 1bc2b94b32c4e50b6814e924c183df9ae451cb49 Author: kent Date: Sat May 29 22:28:44 2010 +0000 Moving some stuff from bwgCreate to bwgInternal.h where it can be shared a bit more. Tweaking things so first zoom level is a better size, which speeds up 100k views. commit 19ab2411d154230946d5e69c9f0aa89bd27c23f6 Author: kent Date: Sat May 29 22:26:41 2010 +0000 Reducing amount of zoom oversampling, which speeds up 100k views a fair bit. commit 029f63c60748393eceb0c8dea093babd9f7bf03d Author: kent Date: Sat May 29 22:25:51 2010 +0000 Adding correlateNextMulti commit 71299522e6076970029c10903af8ab856d52a15f Author: kent Date: Sat May 29 22:24:53 2010 +0000 Adding some const to string function parameters to better work with C standard library code as callbacks. commit b5eb88a8f8c88b34144af65de2810719c3263fbf Author: kent Date: Sat May 29 22:19:50 2010 +0000 Improving indentation. Improving an error message, and the test that triggers it. commit 82d9b32276db3f7a71bf6140364d48e23f140295 Author: kent Date: Sat May 29 22:18:49 2010 +0000 Renaming wgEncodeRegMarkEnhancer subtracks to have the expected prefix rather than 'jkEnh' commit 49c4cc2e2e7dbcce2ba2a1199bd26ca331a92a18 Author: larrym Date: Sat May 29 20:58:15 2010 +0000 use new metaDb table (if it exists); make description search "google style" (independent of word order); code cleanup commit df64ce324c39cb9286c07a9282b46cb7f826ee6d Author: larrym Date: Sat May 29 20:23:41 2010 +0000 add slNameIntersection commit 4bde5ab7d8255a723cb897b1d360fd92cec52765 Author: galt Date: Sat May 29 15:00:07 2010 +0000 "Encode release log update" commit 50073ded391b4da8656b3ce0bd3be0e54fea090a Author: galt Date: Sat May 29 15:00:04 2010 +0000 "Release log update" commit ae7aaaf66ff4f12026f237981f8a3fecae956e1f Author: markd Date: Sat May 29 06:20:27 2010 +0000 added needed include commit ae99854c6005b32e34d8870937f9957a8244460e Author: markd Date: Sat May 29 05:45:19 2010 +0000 removed felCatV17e commit 4534fd007fb11928429700d17675e8426a98d1fa Author: donnak Date: Sat May 29 04:39:23 2010 +0000 Added Chin Li to calJac3 credits. commit 89ede50f480b6a0d702fbbf2052eaaeec1464934 Author: cricket Date: Sat May 29 02:25:14 2010 +0000 Try that one more time. Removed Input from ripAntibodies and put None in ripProteins. commit 0040a174366a8fc9c317387be004094290295d9f Author: cricket Date: Sat May 29 02:20:57 2010 +0000 Removed the Input in ripAntibodies and was able to do this better commit ecd12c6b1c94cd8e70ff5da68642c623a9010952 Author: cricket Date: Sat May 29 01:49:57 2010 +0000 I entered an Input type for the ripAntibodies, so that we could validate over the weekend. This should be removed and done the same way that Antibodies is. commit 78a576495863f39d9e809ab7e80d8ef63becc953 Author: vsmalladi Date: Fri May 28 23:41:05 2010 +0000 Updated DAF to reflect new bigWig Raw signal format and fix Tfsb->Tfbs format commit 07dfea88f4246a1a6aed1ced6a15f22e5d5af94c Author: cricket Date: Fri May 28 23:37:28 2010 +0000 added more ripAntibodies commit ce5c73b110da2ca56f4407a89a472e792c5910d3 Author: tdreszer Date: Fri May 28 23:28:06 2010 +0000 Oops. Lost them all. commit 9218e7095bed45cb96cba6f604a790055e1ab992 Author: rhead Date: Fri May 28 23:22:56 2010 +0000 Adding dimensions to tracks that were getting a (null) label in hgTrackUi on the sortOrder. According to Brian, this problem is occurring in the v232 CGIs on composits with sortOrders that include things that are not views and that are not included in the dimensions. commit d742eafaf06f3bac486312e32ac848f1d5181635 Author: galt Date: Fri May 28 23:20:25 2010 +0000 override new default SCRIPTS location commit 71abfba4912c7964edcdc34d9ed2d27cca7fe1f6 Author: tdreszer Date: Fri May 28 23:17:01 2010 +0000 Improvements needed for passing list of terms: support control terms mixed with Antibodies commit 18f7c15c66a6ec8f78a19b592e64ef6b066370fb Author: mary Date: Fri May 28 23:06:50 2010 +0000 minor change: fixing name of reference file for SNP track commit 1cb3494c7c134739f0ee6cdd7ba7ef0e9a71bbd7 Author: kuhn Date: Fri May 28 23:04:56 2010 +0000 made bedGraph not ALL CAPS to match usual usage commit 1909fdca92d12b6ee893231cc23b29299cd7f06e Author: vanessa Date: Fri May 28 22:10:07 2010 +0000 fixed a typo commit 2fd4fd899837ddb266c1f5297bace62fb2cc81e5 Author: cricket Date: Fri May 28 22:09:02 2010 +0000 Fixed the .ddf to drop accession and labVersion at Labs request commit 31a69226215473e7e1718074b672a7c1fbffbb66 Author: braney Date: Fri May 28 21:56:46 2010 +0000 take out beta commit 07378c4cf734f71745cbde5f74d3ab0da71322c5 Author: braney Date: Fri May 28 21:53:36 2010 +0000 change wgEncodeGisPet.alpha.ra to wgEncodeGisPet.ra commit 4d347ba17a8b205898bf6ebdb470557eb083dc07 Author: hartera Date: Fri May 28 21:53:30 2010 +0000 Changed colour of CRG Mapability subtracks. commit bf2d50de14ff6be431da03b48ac1b0e5084d3ae4 Author: braney Date: Fri May 28 21:52:37 2010 +0000 moved to wgEncodeGisPet.ra commit b25999a67af80983d3989c6969f001eee805c36a Author: braney Date: Fri May 28 21:52:21 2010 +0000 move this from wgEncodeGisPet.alpha.ra commit b141034d5708caa41ec7e7624562c2b5ded31ba3 Author: hartera Date: Fri May 28 21:47:38 2010 +0000 Changed the colour of CRG Mapability subtracks. commit 2f71b8e1e77a5d4df66a3a24f712f9a923b3e3fe Author: fanhsu Date: Fri May 28 21:32:26 2010 +0000 Changed a compound query of DECIPHER track into two queries to improve performance. commit 39b7cd0a37b642cc50841ea3e9c7835dc0da2175 Author: antonio Date: Fri May 28 21:29:07 2010 +0000 adding gid pet loc to downloads commit 5b4e7eec189a56c09c6d319bae2ebe99149b6e09 Author: hartera Date: Fri May 28 21:25:15 2010 +0000 Changed colour of CRG Mapability subtracks. commit 48564840b0e2fffd1dc0db72edc5da5097bdbc3e Author: katrina Date: Fri May 28 21:24:32 2010 +0000 added 11 tables to the Deprecated list commit b59f34a9c88bbb7039aeb6e408ec41e24937ee20 Author: cricket Date: Fri May 28 21:11:59 2010 +0000 The new dafs for the SUNY lab commit ff24ae7433fb86d133a0b9ec6ccca1bc68242383 Author: katrina Date: Fri May 28 21:04:18 2010 +0000 added two missing tables to New tables list commit 02848847082dd83f87c07589a209139d96c598cf Author: hiram Date: Fri May 28 20:57:07 2010 +0000 update to abstract display to keep in more condensed commit 0058dfb2d3a99393f8bc0e7bb0dcd40a7fc1bfbc Author: cricket Date: Fri May 28 20:51:00 2010 +0000 Moved CELF1 from ripAntibodies table to ripTargetProtien commit 6f6e214d6cee72d15e9d2cddb42a172350638689 Author: vanessa Date: Fri May 28 20:22:54 2010 +0000 fixed grammar issues for CRG Alignability subtrack decscription commit 4fc420a98f28098f49e50dd3d992ededf3dd2f4a Author: krish Date: Fri May 28 20:00:16 2010 +0000 made all warnings fatal commit f206fd8fb2b3345ea5369a91cef9802188fb8077 Author: donnak Date: Fri May 28 19:52:17 2010 +0000 Changed Genome Sequencing Center -> Genome Center. commit 33769e8c329bc054b9af2452cb3576f178633cfa Author: fanhsu Date: Fri May 28 19:50:34 2010 +0000 Added function to set color for DECIPHER entries. commit 8b653f147bdf681da5f77142f7894e39f98c11a2 Author: donnak Date: Fri May 28 19:50:06 2010 +0000 Edited calJac data use section, changed Genome Sequencing Center to Genome Center. commit 7cda11ac72226dd32f0f3ae88cdf73d2fd9eac65 Author: krish Date: Fri May 28 19:43:41 2010 +0000 fixed bug where BAM validator was breaking the cell CV term validator commit 6f66b1ae9bb906767d3a7b0acad012738e06d09d Author: donnak Date: Fri May 28 19:34:32 2010 +0000 Archived a news item. commit a49c99e01f0be8af1ca2b38a2e53d2aed16d3542 Author: donnak Date: Fri May 28 19:34:16 2010 +0000 Added announcement for calJac3, archived a news item. commit ce34d78ef735486e8728c5f80e2baab210312ca3 Author: tdreszer Date: Fri May 28 19:14:31 2010 +0000 Fix for '(null)' showing up in sortColumn header commit 0b4ddf6866a31727676c61352c8ad9b596a7b4f4 Author: hiram Date: Fri May 28 19:09:57 2010 +0000 may as well mkdir on scripts and destdir bindir as we start up commit c127f99178ee48e27e924b9ea407ac708d7f1f6e Author: hiram Date: Fri May 28 19:07:45 2010 +0000 need to mkdir scripts commit e0508ee1c7dcd1fe4c63b6372b85d1211e594b1e Author: hiram Date: Fri May 28 18:53:49 2010 +0000 SCRIPTS is now HOME/bin/scripts not /cluster/bin/scripts commit fec766a10e1e1bef3a77314ce553e47bb11b0e7a Author: donnak Date: Fri May 28 18:53:41 2010 +0000 Added calJac3 credits. commit 8acfcf0077eb32ebedffca59fc0ef55cf51ca790 Author: donnak Date: Fri May 28 18:53:18 2010 +0000 Added calJac3. commit ff61666922fc7a351037dfe7228ba29390f8f73a Author: angie Date: Fri May 28 18:48:07 2010 +0000 Added new func code cds-indel, moved coding-synonymy-unknown from synonymous category (oops) to non-synon category. Thanks Mary! commit a9e51742c412a55324b42c7f57b79af9de9aa093 Author: angie Date: Fri May 28 18:47:08 2010 +0000 Added new functional annotattion codes cds-indel, coding-synonymy-unknown; added 1000Genomes as validation type. Thanks Mary! commit d819e25f986b45366802cd6cbd4b107f0f933e3f Author: braney Date: Fri May 28 18:32:58 2010 +0000 added win to dimensions in mapability track commit e5b10978bf7916373554678f1e45ab0686ee57c2 Author: hiram Date: Fri May 28 18:32:33 2010 +0000 all v58 build sequences done commit ba2d650fb78817a34b3b4c2ca1c0d6b4bd5ea6a2 Author: chinhli Date: Fri May 28 17:59:39 2010 +0000 remove felCatV17e commit 67fbf2912061fe9ffc5e0775a8619ed0d71cd2cc Author: hiram Date: Fri May 28 17:38:44 2010 +0000 add search on bacEnds table commit f066deaabccd00179894ae24c39f23e45e609455 Author: hiram Date: Fri May 28 17:29:47 2010 +0000 adding bac end track commit 63ae8b245325a3256f7f0e1936d8e32c5c985646 Author: fanhsu Date: Fri May 28 17:23:08 2010 +0000 Updated OMIM URL. commit 132efee3f4a38fe89a736e27bc4fee21016fd52e Author: kent Date: Fri May 28 16:00:17 2010 +0000 Putting timing notes under CVS. commit 20271e0b1787535a8c9b60928357a22ac09f39be Author: galt Date: Fri May 28 15:00:22 2010 +0000 "Encode release log update" commit d009c3b9585647b7f5844f9f0815db222cb18c11 Author: galt Date: Fri May 28 15:00:19 2010 +0000 "Release log update" commit 44ea79b5bd13dc6748e11cf803b9d1544f9117aa Author: kate Date: Fri May 28 13:04:05 2010 +0000 Update for newer usage commit e9c2e0159273000418b86899ffc462e5d0075423 Author: kate Date: Fri May 28 04:27:39 2010 +0000 Add Melissa's supertrack descriptions commit e2399de18bfcd49b12ffc864baffbe3923c479d1 Author: tdreszer Date: Fri May 28 00:19:25 2010 +0000 Rearranged some files due to Katrina's careful QA work commit 7868a2264bab570b5da28e9b36b34e354e06daef Author: antonio Date: Fri May 28 00:16:07 2010 +0000 minor grammar updates and display things commit f7feeebe34364665eff43053480dd15496c83d60 Author: vsmalladi Date: Fri May 28 00:08:11 2010 +0000 SYDH TFBS: Add Cell Line Raji subtracks (submissions: 1208 and 1209) commit 9c157a0be27957fafa5480b08b55eb6247c5acdd Author: vsmalladi Date: Fri May 28 00:07:04 2010 +0000 Added metaData from submission 1208, 1209 commit cabbe23fd3bae339db033a646f3e67bf1920faaf Author: angie Date: Thu May 27 23:52:00 2010 +0000 Made snp131-masked genome sequences. commit 71fc3202df5714b26788c60b5ebb78f8ea6513d6 Author: hiram Date: Thu May 27 23:22:21 2010 +0000 bosTau4 and gasAcu1 problems taken care of for v58 update commit 433369f101c2d9119a76357377750007293fcacf Author: hiram Date: Thu May 27 22:53:51 2010 +0000 v58 done for hg19,mm9,rn4 commit 2ea88d44d4b1caa54791053038773b7a641ebdc6 Author: braney Date: Thu May 27 22:22:09 2010 +0000 more load procedures commit f2b035d74027840c9d75f313758510e438ecd150 Author: braney Date: Thu May 27 22:14:37 2010 +0000 first cut at v4 Gencode genes commit 416864796b3dad2a0b647d7e8184f3966f238a48 Author: braney Date: Thu May 27 22:14:08 2010 +0000 first cut at v4 description page commit 0222f842af9305d91d98d0db6d7d855d0c18d737 Author: braney Date: Thu May 27 22:09:32 2010 +0000 move down into hg19 commit e867f4afbf5830d78e1c702b8071ba25cb0556e2 Author: tdreszer Date: Thu May 27 21:50:07 2010 +0000 Split UW Histone, UW DGF and UW DNase out of trackdDb.wgEnocde.ra commit efcb087e8553df857b69cc77b3d34b7fc7394b3d Author: tdreszer Date: Thu May 27 21:39:14 2010 +0000 Split Broad Histone out of trackdDb.wgEnocde.ra commit e1e39e84738485a6aa7dbbd3aab8e6611f5d4dd2 Author: tdreszer Date: Thu May 27 21:34:43 2010 +0000 Split Open Chromatin out of trackdDb.wgEnocde.ra commit 8bec4bbff05ce64339c30a6f509c772dad88ffba Author: tdreszer Date: Thu May 27 21:30:24 2010 +0000 Split Yale TFBS out of trackdDb.wgEnocde.ra commit 63c1932a6b8cbda2d0644962b78141978c93397e Author: chinhli Date: Thu May 27 21:26:41 2010 +0000 adding felCat4 commit ce531c21ed2a42278e96d8e4712757e33167eb51 Author: tdreszer Date: Thu May 27 21:23:55 2010 +0000 Split HAIB TFBS out of trackDb.wgEnocde.ra commit 76816666d18a00537f5ff26d1169f23f6820fe3b Author: rhead Date: Thu May 27 21:15:23 2010 +0000 changed the temporary all_mrna track that angie added to visibility dense. commit a4da44783a95d496984ad0cdaf401490aa4e4fee Author: angie Date: Thu May 27 21:13:24 2010 +0000 When building without USE_BAM=1, install a dummy track handler for bam that prints a message in place of track items, so we don't pop up an annoying 'No track handler' warnbox. commit 774f1e41c081d65c5d13588b07bdd99a1f92bee3 Author: tdreszer Date: Thu May 27 21:07:39 2010 +0000 Fix for memory overrun when many classes are being selected via filterBySet() commit 301965da0111b7490e8bce03a45de80c771d9775 Author: tdreszer Date: Thu May 27 20:46:58 2010 +0000 Fixed bug wherre instance was referenced when it was null commit 4c48468465f71e27c63e9a443ce2f5c81b26a70f Author: tdreszer Date: Thu May 27 19:24:58 2010 +0000 Extended to allow requesting a comma separated list of terms or tags commit c81c7b78b6524747e1cbfdf9e2fbd40a8aaf71c5 Author: hiram Date: Thu May 27 18:26:52 2010 +0000 adding version 58 to the listings commit acb1ebc943c1fdf9eede19439d0f35b99b654a30 Author: hiram Date: Thu May 27 18:24:37 2010 +0000 adding liftUp to the userApps build commit 2f16fc49fc8bb3c56f12003242833d489ad83050 Author: braney Date: Thu May 27 18:19:38 2010 +0000 fix downloads link for Mapability track commit c8c30c9dcdf74fb231d9eeeb5a063b0bc260443c Author: hiram Date: Thu May 27 18:18:39 2010 +0000 allow DESTDIR to be used commit aea41f6ebec9cd7bbd6a4889c692c62a54607846 Author: baertsch Date: Thu May 27 17:18:14 2010 +0000 add search for retrogene track commit fae217d5e4530d00f9f5aa18091370a1821b53c0 Author: vsmalladi Date: Thu May 27 17:15:58 2010 +0000 Registered New Cell Line: Raji with provided protocol from SYDH (Farnham). commit 6135e5958bae10aff26c9c3c7152af406aa5969f Author: larrym Date: Thu May 27 17:14:12 2010 +0000 fix build problem (mapName -> track) commit 08b29ea2d6b81a1bdb0003aae56e2fe2565170c8 Author: tdreszer Date: Thu May 27 16:41:47 2010 +0000 Empty selection is invalid fro filterBy. Force it to 'All' when this case happens. commit f6c4d835f7eec0a2c999fb0bf5fcb8823c1f7402 Author: galt Date: Thu May 27 15:00:23 2010 +0000 "Encode release log update" commit 6f334f8702410a340feef05b9dbd31387e31c482 Author: galt Date: Thu May 27 15:00:14 2010 +0000 "Release log update" commit 298dd6ab80d94b014f638833cfc9c3bbfe710be8 Author: angie Date: Thu May 27 14:45:59 2010 +0000 Adding back all_mrna and all_est with release public for backwards compatibility with CGIs currently on RR. commit bbfc5778c4aeb54026db90f6ae5ed51006f6611f Author: kent Date: Thu May 27 08:24:46 2010 +0000 Adding clampMax option. commit 08fb49bb72c8dc9c6e3731973647483a2d9b5bfc Author: kent Date: Thu May 27 06:44:29 2010 +0000 Seems to work. commit cf0f01c63fc04c212b8adb61dec7783b50edd9b0 Author: kent Date: Thu May 27 05:59:46 2010 +0000 Seems to work. commit f7b69132ea4ccaee172d1ccbe9877dac9a2357b2 Author: bsuh Date: Thu May 27 01:13:19 2010 +0000 Added one more comment commit 6c25e61b373bcf55465bbf3ad1a1a92a1305a825 Author: bsuh Date: Thu May 27 01:06:42 2010 +0000 Added some comments to point to where people can add code to change the MAPQ policy commit f92dca411be829c62d48850db9b91e96c0fb858e Author: bsuh Date: Thu May 27 00:56:17 2010 +0000 After some debate, we now always report MAPQ=255 commit 8600d1a9af3bd8104c81f9488fa43a9a2b484a2f Author: ann Date: Thu May 27 00:25:18 2010 +0000 needed to trap the case of missing entry in trackDb file commit 98ade9313d89b7efdabf48ca0aa412224dd86c74 Author: mary Date: Thu May 27 00:20:25 2010 +0000 turning genbank updates on for calJac3 commit 16fe4e0bdd0b5c9c987004ff2be3f7886ec61049 Author: braney Date: Wed May 26 23:59:24 2010 +0000 very preliminary commit 7451934798c987e3a16c40dccfb5ad6cbf17e8bf Author: vsmalladi Date: Wed May 26 23:46:35 2010 +0000 Updated Description page with preliminary information provided by Stephen Landt commit 2272fc2cad06d20ac0ad9bb7e3a47d5a237ad27b Author: ann Date: Wed May 26 23:42:14 2010 +0000 getting rid of knownGeneLists and references to it. commit 7fef00ac19bb1e2fed11111ddad07e518c6f5b48 Author: bsuh Date: Wed May 26 23:25:37 2010 +0000 Fixed bug identified by Tim Durham @ Broad commit aba1fb9f3d5d6fd2263f51fe42667d5e1148fce9 Author: vanessa Date: Wed May 26 23:18:22 2010 +0000 changed release tags commit 26fcb0f2615b7f6ca5598c408d02794c6044cfed Author: braney Date: Wed May 26 23:08:21 2010 +0000 add canPack to Mapability track commit 0d359708325b0a667e31b24da2845caf18ffbc08 Author: mary Date: Wed May 26 22:55:45 2010 +0000 adding ctgPos2 to trackDb. Copied it exactly from susScr2 commit 65652b6d6c16d8400945d5a70513e7720c1faf82 Author: kent Date: Wed May 26 22:41:32 2010 +0000 Matrix plotter seems to work. commit 6e75b2013728aaa9c6304053e9da038668cd2dbf Author: braney Date: Wed May 26 22:21:32 2010 +0000 fix makeDownloadslink use the current database rather than defaulting to hg18 commit a80856d65d47b4ff855155cfb1615152018d7c22 Author: braney Date: Wed May 26 21:27:53 2010 +0000 moved to official names commit dc64af268570ecb6dd8076b1bcf27923eeed56b8 Author: braney Date: Wed May 26 21:26:31 2010 +0000 make calTech include files follow spec commit ab8e9bd71ddd76a397345e588552a9fee15ca8bc Author: braney Date: Wed May 26 21:25:18 2010 +0000 move to official names commit bb115fe51d0befd4706dd23e8fee1d8fa079b9d4 Author: larrym Date: Wed May 26 20:36:39 2010 +0000 get cell types/antibodies from cv.ra; this is temporary code (will convert to using metaDb in the near future) commit 0435d1914a9229e45b8a00f33b888f72a785c3c9 Author: galt Date: Wed May 26 20:13:48 2010 +0000 added multiz6way and phastCons commit 8636846fdda3f2569e28ff26fd89d64eb4b6e9db Author: tdreszer Date: Wed May 26 20:10:56 2010 +0000 A lot of 'organism Human' lines were missing from cells commit 0d16bf6ff7e61326fd9c7d021d29f9768cce00f3 Author: galt Date: Wed May 26 19:27:52 2010 +0000 multiz6way, annotated, mafSummary, phylotree, phastCons commit d942350ca5c223d4366143e630e9ecbb73c25b27 Author: chinhli Date: Wed May 26 19:10:09 2010 +0000 minor html correction commit 6c0a43e85a1859fcc5745ef4088c379defe3ff5f Author: chinhli Date: Wed May 26 19:03:14 2010 +0000 Initial descriptions for felCat4. commit e1a6e1dc91cf0b9c2c5660796ffbabf14c58437d Author: chinhli Date: Wed May 26 19:03:00 2010 +0000 Added felCat4 to DBS. commit 0c95f269aa6728862368a735c099b14fbdd17258 Author: tdreszer Date: Wed May 26 18:25:20 2010 +0000 At Venkat's urging, added useful comment to trackDb entry with subId commit fec4441959c9edbf4967cad240899e4bb808f530 Author: kent Date: Wed May 26 18:24:20 2010 +0000 Cleaned up a bit and tested more. Fixed a bug that made it hang after about 25 pairwise correlations. commit 68f71c85590d2ab169760315b26550af8204e33c Author: hiram Date: Wed May 26 18:23:47 2010 +0000 new version now with seqIds in t2g.sql commit 6bc1d39603d6fa6f38885036bef84618d7b2669c Author: tdreszer Date: Wed May 26 17:43:18 2010 +0000 Removed an object that didn't belong commit eee9db4ec5ffc5dcadcf68330377ad1d45f4bf09 Author: tdreszer Date: Wed May 26 17:12:20 2010 +0000 Forgot to load Yale PolyA into the mdb earlier commit 9ec3d19170b4e6711414f9cbb5765d0e8c0bd1b4 Author: angie Date: Wed May 26 16:22:55 2010 +0000 Added snp131 & exceptions. commit a6fffa3b64ac63dac4c6a3c972f782f1208178c2 Author: angie Date: Wed May 26 16:17:24 2010 +0000 Rebuilt snp131 and snp131CodingDbSnp with corrected function codes from dbSNP. commit 131dfd99fd7283175bf656b9a83c85ce30a0fa50 Author: chinhli Date: Wed May 26 15:35:31 2010 +0000 htdocs-hgdownload change commit b164149ef227d072f241ac7d2aea5cccb0ff320a Author: katrina Date: Wed May 26 15:21:27 2010 +0000 adding GIS RNA-seq commit bbd34f23c85e7045108ac21c9d60b3605f816f8a Author: galt Date: Wed May 26 15:00:48 2010 +0000 "Encode release log update" commit dbafc8542adfc29d106c0e3dfa0b60dd1576436b Author: galt Date: Wed May 26 15:00:14 2010 +0000 "Release log update" commit dc16ee6be13d38d0d667a209e9240ad2f113e529 Author: braney Date: Wed May 26 13:35:31 2010 +0000 move BAM specific code inside ifdef commit 253bb8fbc4b66347bb2d89c239ebaf9168188a00 Author: kuhn Date: Wed May 26 11:40:04 2010 +0000 sendiing output to stdout instead of to kuhn to make it easier to send to more than one person via cronjob commit 1cd4abba3f8636fb22ec4d98698eccd2ecfa5690 Author: kent Date: Wed May 26 04:43:30 2010 +0000 Still half baked, but it compiles at least. commit eac2c402d37260dd4146d8883ef1dde78b099d95 Author: markd Date: Wed May 26 01:08:55 2010 +0000 added neaded symlink commit 4827cfa216f39ec84a737f06e3112ddddbfa7620 Author: antonio Date: Wed May 26 00:23:50 2010 +0000 grammar fixes and jolly updates commit ce9114a6295bce0490e02c8b52397a881c97e354 Author: hiram Date: Tue May 25 23:53:59 2010 +0000 show wiki track even if not logged in commit 40a3143ccabaaae010dea2e35cac74f98f8b1952 Author: vsmalladi Date: Tue May 25 23:52:32 2010 +0000 Updated metaDb using newly generated,by pipeline, mdb.txt for submission 1210. commit c4fd8a46bb057000a92bbdd7d05806f5a928ee19 Author: vsmalladi Date: Tue May 25 23:51:16 2010 +0000 HAIB TFBS: Added subtracks from submission 1210. commit d9faf0218e2da80ebc8c39f100752851cb0f908e Author: hiram Date: Tue May 25 23:39:07 2010 +0000 fixup target blank for itemUrl om hgc wiki item click URL commit c501ee16e9286ca5ed0a5ff94e45092263e4d3b0 Author: braney Date: Tue May 25 23:08:58 2010 +0000 added release alpha to new calTech tracks in Jims enhancer track commit 00a319631bb63d780ee8486605ffa1345e5a01d1 Author: markd Date: Tue May 25 22:42:22 2010 +0000 removed outdated files commit e3b59abf047be0d071f1d3f233035729590f91a7 Author: katrina Date: Tue May 25 22:35:49 2010 +0000 removed release alpha,beta lines to release Yale TFBS; also removed two ghost sub-block entries for tables that don't exist in the Yale TFBS track commit 470b7c4a0446e83c4232ce7f5413c6f059990c88 Author: katrina Date: Tue May 25 21:52:14 2010 +0000 removed release public trackDb entry of Yale TFBS (release 2) in prep for release 3 of that track commit 90d424cd772ca45e7dada529912602bfdb318a7d Author: krish Date: Tue May 25 21:20:21 2010 +0000 added flag to skip md5 sums for faster run time commit 57bd153ca2a3890cd12fab0fbbf44235cfca004b Author: angie Date: Tue May 25 21:17:28 2010 +0000 Use blatFugu instead of mrna; code now uses all_mrna but that has no bin column in hg15. commit a69c7a8c761b477470d9ceb97d63a853ba049979 Author: tdreszer Date: Tue May 25 21:17:27 2010 +0000 Validate atleast 1000 on fastqs. I am not 'quick' works on fastq. commit c8e5239c4e8a9c3035303f141b307d7085dddef9 Author: vanessa Date: Tue May 25 21:13:26 2010 +0000 changed the mail to to be the name instead commit 095a82892ae592e0e7e00cc552d32c18e9edc850 Author: tdreszer Date: Tue May 25 20:59:44 2010 +0000 Minor touch-ups commit 6b20ea70d8e406ad173fa00e74ba4b8ae868feea Author: tdreszer Date: Tue May 25 20:57:11 2010 +0000 Make sure therre are tabls and dummy up one experiment commit b829fa9d74a30bfdcff7ad6148dbeed72b1ba0a3 Author: braney Date: Tue May 25 20:23:29 2010 +0000 notes! commit bbc48dee28096cf393c8e8a087ebefa8b5cd5292 Author: donnak Date: Tue May 25 20:01:51 2010 +0000 Added Ledbetter article. commit 1164ae6e2a98331207733fc69adecd586e1f4f5f Author: tdreszer Date: Tue May 25 19:46:57 2010 +0000 Added origAssembly metadata term. Moved metadata lines from trackDb.ra and fileDb.ra to mdb.txt commit 4609f6bf156e8e1dba66c7d3035c8ab21540076a Author: kent Date: Tue May 25 19:45:34 2010 +0000 Making wigEncode default the span to the stepSize in fixedStep wigs. commit b402215b3dcb5985cc4e7c59a86c79d526d5f1b8 Author: kent Date: Tue May 25 19:24:16 2010 +0000 Making it so wigToBigWig will default span to step size. commit 006596cf1370c4c2eb76472a4737cb609f3fa563 Author: kent Date: Tue May 25 19:14:04 2010 +0000 Cleaning up the conservation track default settings a little. Commenting out some '_v2' versions of the conservation wiggles that have been up along side the normal one for months now. commit 6d1bf81d3f9c2643c82bba96e549597df997ab5c Author: tdreszer Date: Tue May 25 19:05:01 2010 +0000 Added origAssembly to help distinguish hg18 to hg19 datasets. commit 8554f0e4c4d5acca491f6ba6330d711e94708130 Author: tdreszer Date: Tue May 25 19:02:15 2010 +0000 Added mdb.txt file for metadata lines commit 6fec6c89d652182446d1fc6609d1a6b41e088266 Author: cricket Date: Tue May 25 18:55:17 2010 +0000 A new DAF for the Stanford mm9 Histone Modification Experiments commit 3f8e27a36b710f76858780b5dea46f382a4bf02b Author: kent Date: Tue May 25 18:49:03 2010 +0000 Adding info on showSubtrackColorOnUi commit d7e6c45989b21a14b987383df5144610dfbc16b3 Author: vsmalladi Date: Tue May 25 18:28:25 2010 +0000 Stan/Yale Histone: Shortened Subtrack Long labels to comply with 80 character rule. Modifications -> Mods. commit f19a25b96c1b583359e8907662d5a11e9f605339 Author: vanessa Date: Tue May 25 18:25:39 2010 +0000 fixed table padding, moved some rows, and altered some text commit 6599d8244ece1e6b520072d4ea31ec4f25b338aa Author: kent Date: Tue May 25 17:50:51 2010 +0000 Making log transform work with whiskers. commit aee51615e52f84916b66847c319e06e191a61363 Author: kent Date: Tue May 25 17:22:43 2010 +0000 Adding docs on new tags. commit 64d8ec8b8a49a86dfd951a4af8bb0faced014e60 Author: krish Date: Tue May 25 17:17:29 2010 +0000 change md5 sum calcs to better handle HUGH files, updated paths for htdocs-hgdownload commit c02846b1c842c9337c3b5aee434ed54c6fdb1e39 Author: kent Date: Tue May 25 17:12:30 2010 +0000 Adding transformFunc to wig and bigWig types. commit 53695561ce0c32871a1c30e8d512e4408d7614ae Author: kent Date: Tue May 25 17:11:49 2010 +0000 Improving usage message. commit 22ee6639a274c842426d946d5635c1795dad1ead Author: kent Date: Tue May 25 17:09:24 2010 +0000 Removing stray 'ES' from label of non-ES cells in wgEncodeReg track. commit a65bc60d7b7611bf055731fd447253a8a8c1a4e9 Author: vanessa Date: Tue May 25 16:53:28 2010 +0000 fixed formatting issues, organized the code, and removed extra html code commit 1fcae7370011bb90adc27d0587db69ceb58b25aa Author: angie Date: Tue May 25 16:32:08 2010 +0000 Adding some missing entries found by Antonio. commit c7205b8e86f11a1c8214249e73398553ca07c4cd Author: angie Date: Tue May 25 16:31:12 2010 +0000 Warn, don't die, when there are duplicate .as files, so tableDescriptions tables are still updated. commit 1af7ef31ecdf58710342fe463fa410083597f2cc Author: vsmalladi Date: Tue May 25 16:21:25 2010 +0000 SYDH Histone: Added subtracks from submission 1205 commit 83b67fee2e397c63a5e37c9c5ff43157c5d820d0 Author: vsmalladi Date: Tue May 25 16:20:48 2010 +0000 SYDH Histone: Added meta data from submission 1205 commit 1cab30adc535b8dcd2bd89837501eb152c2bfaf7 Author: galt Date: Tue May 25 15:00:34 2010 +0000 "Encode release log update" commit 1307e1aeb27a2b13e0e4051a1d34d280cfb4e076 Author: galt Date: Tue May 25 15:00:04 2010 +0000 "Release log update" commit 64d599767268a6bc69a8f8d354a27db4316a800f Author: galt Date: Tue May 25 06:44:32 2010 +0000 fixing URL now at genecats commit d6dc59bbe8f99c306b9d0399a2797ffed935a1c6 Author: galt Date: Tue May 25 06:42:17 2010 +0000 pains with utils build commit d7eb249050cc9354fc3b2aff0e1f1ef31f6d35b3 Author: galt Date: Tue May 25 03:47:30 2010 +0000 "New version number v232" commit b0e02a658c582411c1e094edf8506769f06ccde1 Author: galt Date: Tue May 25 03:46:56 2010 +0000 v232 final build commit 4e466458caa41354996e6fe0d3839fc03fc9f516 Author: markd Date: Tue May 25 03:45:04 2010 +0000 add pointer to GFF3 specification to help message commit b55c491e80f0bb9328a63506741858e31e4d4e75 Author: galt Date: Tue May 25 03:23:36 2010 +0000 cvs reports location moved commit 66a0a01659fd9d924adc282fd6fea5c51a2975ba Author: galt Date: Tue May 25 02:52:30 2010 +0000 fixing oops commit b84c6ea78a97f02863b450a23cd9c76fafced6c0 Author: galt Date: Tue May 25 02:48:30 2010 +0000 removing ann commit 95ad94031dc8db32e6af33b74fe838863cd07308 Author: galt Date: Tue May 25 02:38:26 2010 +0000 v232 preview commit d150ba1b072e0daafb1871b4e6b0fe461171b4f2 Author: galt Date: Tue May 25 02:37:50 2010 +0000 v232 preview commit ce35a89677a88680b58a2d6c681c3df477bbd6ba Author: braney Date: Tue May 25 01:19:00 2010 +0000 add release alpha to jim's encode regulation supertrack commit 12dee99d36ec0fac5cc07c84a874dc4e8ea520a2 Author: krish Date: Tue May 25 00:52:56 2010 +0000 added quote function, forwared from DBI commit 82e4896a55f5f5c472940a7850a6051ddfdee4cf Author: galt Date: Tue May 25 00:45:10 2010 +0000 changing of the guard commit a33b29e3d1b8311d4777f77746a0d8990c1cedb0 Author: mary Date: Tue May 25 00:37:28 2010 +0000 adding better examples to description page for calJac3 commit d175ad4da02bacaa260905aaff56b1ae1c003b25 Author: markd Date: Tue May 25 00:14:55 2010 +0000 Made C attribute related names more consistent with GFF3 specification. Fixed bug were bogus quotes were not detected. Fixed bug with empty attribute values. commit a444c0c94d12801a7accbbf582579a01a3ec13d3 Author: vsmalladi Date: Tue May 25 00:07:01 2010 +0000 Add new Sample DDF for Ren Lab submissions commit b7b9cccdcfc5ec5d96d7479617db3b722e6dd732 Author: vsmalladi Date: Tue May 25 00:06:23 2010 +0000 Add new Daf for Ren Lab submissions commit 4c2a41661312974ffda8aac08b496fa2f90181e9 Author: tdreszer Date: Mon May 24 23:10:15 2010 +0000 Undossed that thang commit 08eb00b414300f824f3834941c13744c76d44e60 Author: tdreszer Date: Mon May 24 23:09:11 2010 +0000 Extra pixels for width so that Safari and Chrom don't add scrollbar commit eda41e02ec20f59cb83217c38f7545242aca24f8 Author: tdreszer Date: Mon May 24 23:01:21 2010 +0000 If one filter box is not selected, then other filterboxes exclude nothing commit de15f174220e32dbba51cb9274f64177421e4a81 Author: kate Date: Mon May 24 22:50:46 2010 +0000 First unit test commit 4aadf971b97a34293276bffb42d8aa44438344ec Author: bristor Date: Mon May 24 21:55:07 2010 +0000 Add text describing GREAT usage commit c1e4f8c02e7de87f922d1a126d203633cc6e7742 Author: katrina Date: Mon May 24 21:50:41 2010 +0000 changed excluded color commit c450f01803b7d6ba01e39a56a38fd77bec16271f Author: tdreszer Date: Mon May 24 21:36:40 2010 +0000 Added 'Click to select...' title commit 9b18cbb0fdbeb741172f935553921bd15dc5495c Author: kuhn Date: Mon May 24 21:20:06 2010 +0000 removing old script that won't survive change to git commit 178bfe87a8d216d12fcf5701f9b752b47fb5d0c6 Author: tdreszer Date: Mon May 24 21:12:17 2010 +0000 Make sure to block new 'exclude' options logic from filterBy boxes that are not filtering subtracks commit c931d816acd4437d19bbed6ff214c7d966b4a95e Author: tdreszer Date: Mon May 24 21:08:37 2010 +0000 Made filterBox a little more obvious on hover. commit dd8607e994b139bc77be82eb5420e9f877583fa4 Author: tdreszer Date: Mon May 24 20:51:09 2010 +0000 Minor sort order change to HAIB TFBS commit 55e0f96a65a4477c11c588b9067eff51561908b6 Author: tdreszer Date: Mon May 24 20:43:27 2010 +0000 Make excluded options more obvious commit a25035e47e5af050bc26de69232ec1cf38e2f7a6 Author: tdreszer Date: Mon May 24 20:42:20 2010 +0000 Added support for aryRemoveVals() to subtrack 1 array from another commit d4139c49cbf0af016114890abfb3d9b2935ff0b3 Author: tdreszer Date: Mon May 24 20:40:56 2010 +0000 Support for excluding inappropriate choices from filterComposite boxes, by graying text. commit b4d7c5080238ec923a911ca247ac62949019bbd2 Author: tdreszer Date: Mon May 24 20:34:22 2010 +0000 Back to Filter Composite titles above filter box. commit a82def26dec1cbad645e7c097dfeaf7b5eb1c775 Author: braney Date: Mon May 24 20:33:37 2010 +0000 set visibility modes for UCSF Brain DNA methylation commit d1cfcddcead3985c299a9f914e849249bd7037ba Author: kent Date: Mon May 24 20:19:22 2010 +0000 Cleared up some more track/table mixups in the details pages involving printAlignments in refGene. I tested on quite a number of the details pages that use printAlignments, and made changes to get the transMap and retroGene stuff to work. It looks like some of the retroGene stuff has not worked in some time actually. commit 9f6425d4a9a14c9f2ed93c3386177c308dbd10e5 Author: hiram Date: Mon May 24 19:53:42 2010 +0000 fixup URLs that may have blanks in them, do not quote the whole thing commit c94ecfa8f2a0c9ee46d0e4c2e7f20b8d1dde4c38 Author: tdreszer Date: Mon May 24 19:40:06 2010 +0000 Second attempt to allow 'target=' in URL. commit 097cac5f0b6e0bc0b101007fd06d452835a5e3cf Author: tdreszer Date: Mon May 24 19:24:58 2010 +0000 Fix for Harum's sending a target=blank with his link. commit 7126c052b6f81d1d653ed29651f3af5ea479fa04 Author: braney Date: Mon May 24 19:16:31 2010 +0000 add bedGraph to dividers commit f46f8566957de092e0a5f01b136eeac7f08ca73f Author: mary Date: Mon May 24 18:59:10 2010 +0000 adding overrides so default position looks nice commit 2a658ded03b77332beefbef7c293427f79ae6d57 Author: cline Date: Mon May 24 18:57:44 2010 +0000 Added tissue types for cell types commit 5caf9cd28901854feba15dcd696cad32ddee3128 Author: braney Date: Mon May 24 18:56:59 2010 +0000 description page for Ting's ucsfBrainMethyl track commit 76f51642395572fd7896be09c9a06e3915415dae Author: braney Date: Mon May 24 18:56:19 2010 +0000 add Ting's ucsfBrainMethyl track commit 08f9e926089ed3d771e5f11026a6acfd0aa6bc09 Author: bristor Date: Mon May 24 18:42:37 2010 +0000 Cause Galaxy and GREAT checkboxes to preserve state across filtering, intersecting, etc. commit 475945c9b51671b60b1ca8656508b096b9f7e5d9 Author: kent Date: Mon May 24 18:09:14 2010 +0000 Made utility to fix spans or steps in a wig file. About 100x faster than sed is the motivation.... commit b2d0599d4ff4b5a280892f40d5c4cee5044c91ab Author: angie Date: Mon May 24 17:58:15 2010 +0000 Use blatFugu instead of mrna; code now uses all_mrna but that has no bin column in hg15. commit efa8bd8e770c528499562b7ed2294ff0dd03293d Author: vanessa Date: Mon May 24 17:53:22 2010 +0000 removed release tags for wgEncodeDukeAffyExonArray commit c1db166840ba9d036cf18bdcdcb02b027e5440c1 Author: vsmalladi Date: Mon May 24 17:28:53 2010 +0000 SYDH TFBS:Updated MetaData to include 4 new submissions commit ef693412c1db825a0e4d5c6f5994af2062f28e9e Author: kuhn Date: Mon May 24 17:26:30 2010 +0000 added newline after archived in output to improve the look of forwarded messages in T-bird clients commit 6a3b7758d625038ecc228822a1ea112eef179498 Author: vanessa Date: Mon May 24 17:18:38 2010 +0000 releasing duke affy exon commit 3f461e0c8114c933c334f24cb82985e1cd0586b2 Author: vsmalladi Date: Mon May 24 17:02:58 2010 +0000 SYDH TFBS: Added 4 new submissions to track. (1203,1204,1206,1207). commit 6e169e0b156492a8c2dcdafbc1c0b9b9bc0d9bd6 Author: chinhli Date: Mon May 24 15:41:40 2010 +0000 add a missing mkdir ss commit dcec8bf6b51e9a8721041f695d0bf519cc652b30 Author: galt Date: Mon May 24 15:00:07 2010 +0000 "Encode release log update" commit 9c768cf79dffa2bd94b15aba11aee3c5365d1671 Author: galt Date: Mon May 24 15:00:04 2010 +0000 "Release log update" commit 4b45afb175e68cc9f63800c8e7982d6f950cfd8e Author: tdreszer Date: Mon May 24 14:29:08 2010 +0000 Added class for 'excluded' items commit fde5216e9b230845c953df79ce8402890e89fa0a Author: kent Date: Sun May 23 20:12:32 2010 +0000 Making log transform not crash on negative data values. commit ae62443ca8019d4c7dd8a792cdc0dc8f3fcc5012 Author: donnak Date: Sun May 23 19:57:56 2010 +0000 Added links in text to ENCODE & Neandertal portals. commit 1c6e9163bf1e17bf665905cb202ad816d8fcc8f9 Author: galt Date: Sun May 23 15:00:06 2010 +0000 "Encode release log update" commit 57364a2892edfb4dd1970be1748fb42d642a1825 Author: galt Date: Sun May 23 15:00:03 2010 +0000 "Release log update" commit 8219b97c95f4cec09d93334a57f64206318869ef Author: galt Date: Sun May 23 03:13:53 2010 +0000 nobody wants duplicate smaller than extra overhang commit 61c6da4cade5c62886c6fed71f1dd646c1837e23 Author: galt Date: Sat May 22 18:50:33 2010 +0000 fixing help commit 0ade922dcb5f9ea718635e4703730c0f53bcc7f3 Author: galt Date: Sat May 22 15:00:06 2010 +0000 "Encode release log update" commit dcb92a7f300c8b8fcb33900d7ea98e096b59934a Author: galt Date: Sat May 22 15:00:03 2010 +0000 "Release log update" commit d2da94838f9e80d20d2c8bf688549fb8382ccaf8 Author: braney Date: Sat May 22 02:21:39 2010 +0000 a utility to swap tables with renames while checking for existance commit 0110682a45865f927f65ab9ca4a89b00449d69ff Author: braney Date: Sat May 22 02:18:28 2010 +0000 add sqlRenameTable commit 58b397e8ab8e3e9037b5929a2f6df87fc2ce97e1 Author: vanessa Date: Fri May 21 23:52:35 2010 +0000 changed the path names for the htdoc reorganization to htdoc-genecats and htdoc-hgdownload and changed the appropriate urls commit a2e04049e76f46ad2e6932df73528b4bcc372b27 Author: braney Date: Fri May 21 23:45:38 2010 +0000 only print out the item count on bigBed's after version 2 when the value is valid commit 55edaea03f3620eaa8a55c69b6124dbeae0fc2aa Author: hiram Date: Fri May 21 23:25:39 2010 +0000 fixing error commit 5441a04d3436b756a24ad8ed81c8fa950b1d5884 Author: hiram Date: Fri May 21 23:18:25 2010 +0000 initial text description for text2Genome commit e1c4f6048a77208bd34d968573860f098dea1b14 Author: vsmalladi Date: Fri May 21 22:53:47 2010 +0000 SYDH: I have changed the short and long labels on all Snyder mm9 tracks to refelct that only Stanford and Yale are working on generating data. According the Stephen Landt the new name is Stan/Yale. commit e47df208211f9a1392768892fd6da8b17d2ab75f Author: larrym Date: Fri May 21 22:29:49 2010 +0000 change to returning a list commit eaf48c1299a1a5df944a270ba4f1aac4b13ef6c2 Author: vsmalladi Date: Fri May 21 22:28:51 2010 +0000 SYDH TFBS: Started to add new submssuin id (1203 adn 1204). Still need to clean up commit d0cd282f340ef23062ec8ccf7649f62d29fa1038 Author: ann Date: Fri May 21 22:26:29 2010 +0000 Capitalized BED. Added info about BED file needing to be sorted. commit fddc39f2e8ff65a62de90ab926f4e1278a4e259d Author: pauline Date: Fri May 21 22:17:37 2010 +0000 Removing tags and pointing to new settings for release of this track commit 21c3ce05f40e778b9a07fa124e15c9bca33fd83e Author: braney Date: Fri May 21 22:07:50 2010 +0000 change more tags to alignments commit 6c0d006ea5b82c4301627c0746920e03288194cf Author: vanessa Date: Fri May 21 21:18:32 2010 +0000 fixed release tags for mapability track commit a9d60547e3f6cc394aaa9944151f1e6bdbacd166 Author: vanessa Date: Fri May 21 20:54:12 2010 +0000 updated the description page to be consistant with other encode pages commit 3937cc2c3844da6288e48c3e48fcce3019034c40 Author: braney Date: Fri May 21 20:37:47 2010 +0000 change SplitAligns to Split Alignments commit dc9629316b850b7443f1970a668dd2a2e0668c69 Author: braney Date: Fri May 21 20:37:20 2010 +0000 change Tags to Alignments in GIS RNA-seq, put space in SplitAligns commit 5dbdeaffa7f1c7cdcecf2c93e3127a590cf5dfc9 Author: larrym Date: Fri May 21 20:26:48 2010 +0000 support a JSON based API to the browser commit d9bd8e237698bce755fd68d78fbb78a9dc4bdc46 Author: braney Date: Fri May 21 19:11:40 2010 +0000 add contact commit 8321ac659d73a60e960b66bd940de4cdc157fb77 Author: mary Date: Fri May 21 18:52:23 2010 +0000 changing instances of [0-9]kb to [0-9] kb. Repeated for bp, Mb, Gb, and nts. For every instance that was changed, I made sure that it was changed to be correctly capitalized (bp, kb, Mb, Gb, nts). commit d59f3c73ae754a308371200bc6d0ee3671dba387 Author: braney Date: Fri May 21 18:05:14 2010 +0000 allow N's in both reference and query if nMatch is on. commit f4519ef405e435767912a015803f58bab0c71059 Author: tdreszer Date: Fri May 21 17:42:49 2010 +0000 Changed 'Filter by' to 'Filter items by:' in preparation for distinguishing filterBy from filterComposite commit 66eb59b7cd6107b4512597ed2e4dcea066bc31cd Author: braney Date: Fri May 21 17:38:00 2010 +0000 add checking for sex of cell type for BAM's commit c2765a4108c160fc2c071585d3a34f32a31a3310 Author: fanhsu Date: Fri May 21 16:52:42 2010 +0000 Updated HumanCytoSNP-12 v2.1 section. commit b52191e34a6adf8b1356ae13b116679f4f90c783 Author: angie Date: Fri May 21 16:39:57 2010 +0000 hFindTableInfoWithConn: changed split table logic so that we test mrna/all_mrna and est/all_est before checking whether a chrom has been passed in and split table exists. For mrna and est, now we don't want to know if split tables still exist; it confuses other parts of the code. commit 4430f61d4d9d597506bab41d796aa5f3f24415a8 Author: angie Date: Fri May 21 16:34:26 2010 +0000 In printTrackHtml, we still need hTableForTrack so that we can find a split table given an unsplit table name (to find out update time). commit 7209b2f7f5b2f93fb08e8dac8c9407af283149e2 Author: antonio Date: Fri May 21 16:24:26 2010 +0000 new layout for the new age commit 1a9ca8710c8cffef02b81a2a9f3ea954f1251a79 Author: galt Date: Fri May 21 15:00:06 2010 +0000 "Encode release log update" commit cb27a9145d1fc9a33a3b962dfc2090474b30b0b8 Author: galt Date: Fri May 21 15:00:03 2010 +0000 "Release log update" commit f94ea839e279d5741a7ed35417744a5aa3beb613 Author: markd Date: Fri May 21 06:00:16 2010 +0000 moved more things into cvs commit ca78418deb946a2fc06db772e4a1f7fea56900d7 Author: vanessa Date: Fri May 21 02:48:47 2010 +0000 changed release tags commit d99573e06d107fcae7c17903f0ba8fed854124a9 Author: kent Date: Fri May 21 02:22:58 2010 +0000 Fixing typo of hTableForTrack when I meant hGetTableForTrack. Fixes problem in mrna/est details display on hg19 commit bf3e46ad821beedcf5d0d4f68c2a4dfd82601bb3 Author: markd Date: Fri May 21 01:48:23 2010 +0000 simplified naming and made more consistent with htdocs make commit 8a2a0c195e3a65b388f332dfdaf1b07d38a9095b Author: galt Date: Fri May 21 01:24:24 2010 +0000 adding option to mafSplit to allow it to simply split by chrom/scaffold keeping the target name commit 42f4523cda7e15dd46dff9d9517c12da65f90138 Author: markd Date: Fri May 21 01:22:01 2010 +0000 allow specifying directories commit 1b79130ef54120cdb20394579b833ef8aaf7fdbf Author: hiram Date: Thu May 20 23:25:12 2010 +0000 adding 2bit sequence file to bigZips commit 63024434ba6f8819030874c71e1fb5c39b9609e2 Author: angie Date: Thu May 20 23:23:04 2010 +0000 htcCdnaAliInWindow: hFindSplitTable needs tdb->table, not track name, in order to work for mrna/est. commit 324b7b30c8f3bdd8a94cf543bab09fba4a1f9c02 Author: hiram Date: Thu May 20 23:13:33 2010 +0000 htdocs-download is actually htdocs-hgdownload commit 3e0cb798b34ce20d120c3265a3d3dc3ea06c53c4 Author: angie Date: Thu May 20 23:10:05 2010 +0000 makeDbTableToTrackHash should also use tableName from database (hel->name) and add all_mrna/all_est table if an older trackDb doesn't have that setting. commit 3208c7c4aa859c09d29490f329288a711c9b43ec Author: braney Date: Thu May 20 22:58:58 2010 +0000 change download directory commit e558bb3140e76b1647c58575c57a8321d1f6c2c1 Author: hiram Date: Thu May 20 22:28:05 2010 +0000 better position header information commit c8ddee92fb2cae60e05ea494e0403743860d11ac Author: tdreszer Date: Thu May 20 22:24:28 2010 +0000 Fixed the matrix CB initialization problem seen while QAing v231. Also simplified and cleaned up some code by using fully populated membersForAll struct commit ba9a5d2ff031520b99fd8dab1328dcb58ff5c0ed Author: galt Date: Thu May 20 22:19:17 2010 +0000 updating parasol docs commit a60ad3e437300adb428a02877f73116b2e302cf0 Author: hiram Date: Thu May 20 22:04:15 2010 +0000 correct db spec for t2g tables and minCheck coverage commit 7092fddb255e018cb93b93b2505e1f8f41aeadbb Author: hartera Date: Thu May 20 21:18:14 2010 +0000 Removed subtracks not yet on the RR for Mapability. commit 6439b745df27ed4daf60a82c719dcc3d1ecb355b Author: hiram Date: Thu May 20 21:17:06 2010 +0000 adding text2Genome definitions commit 99077fa19862602c3c739df2fd3cc860c3f3b401 Author: hiram Date: Thu May 20 21:07:27 2010 +0000 using style to set font size for abstract commit cfe97b3674cabe6a8562a8fb3d097f82d0713b34 Author: kent Date: Thu May 20 21:04:36 2010 +0000 Making it so that whiskers mode only sets each pixel once, so it works better in transparent mode. commit cde3796ac978cbc0909edc73b9365c6c259f62cb Author: hiram Date: Thu May 20 20:56:37 2010 +0000 rearrange heading information in t2g printout commit 94ff2b8c955ef251d77405f6e88db116c791d548 Author: kent Date: Thu May 20 19:54:18 2010 +0000 Simplifying wording around transparent overlay in user interface. commit 2479817a6261428b5dec90e43743c540232aedd4 Author: kent Date: Thu May 20 19:53:22 2010 +0000 More track/table changes per Angie's suggestions at code review. commit 8aee40f8b1cbc564f122cbadab94d5fb292f49d1 Author: kent Date: Thu May 20 19:52:32 2010 +0000 Making variable x to hold x1+xOff. commit 5e382f77d3e4f6668f2abb91f03a7bfad36e721a Author: hiram Date: Thu May 20 19:14:15 2010 +0000 Adding version information printout commit f8cc1f23a6adbab59765e57b8042c63ce208ad91 Author: kent Date: Thu May 20 19:03:07 2010 +0000 Making makeTrackSettingsHash use tableName from database rather than track from settings as key, for slightly better backwards compatibility. commit a4865596458827561e3db9888a539d287a114214 Author: hiram Date: Thu May 20 18:43:21 2010 +0000 Adding t2g html page, fix error in gap.html and reset labels for t2g commit 1a007b1496406ae76f2d3a3b9f39036c71a38492 Author: hiram Date: Thu May 20 18:31:05 2010 +0000 initial experiment for text2Genome commit 03261bb4bd0b31fcb32b36a3d4ee99f46cd1bc5f Author: hiram Date: Thu May 20 18:30:00 2010 +0000 initial code for text2Genome details commit 5f6b7cecdb8d3169ce60b4290cc00a5f53d2600b Author: hiram Date: Thu May 20 18:29:08 2010 +0000 initial format of text2Genome data tables commit 6bf83f045a97fb80d37a284c15da0d14fcc98ced Author: hartera Date: Thu May 20 17:46:48 2010 +0000 Added mm9 to ucscRetroInfo rule and removed minCheck as not applicable. commit 5abf322ae6f7d6e566df9752dc6d183cce5c3d71 Author: kent Date: Thu May 20 16:19:43 2010 +0000 Using track in preference to table in a couple of user-visibile strings commit 74a144cc45e976febc076489aebd06f13f45c845 Author: kent Date: Thu May 20 16:18:45 2010 +0000 Making findTdbForTable use hTrackForTable before it searches for track. Fixes missing all_mrna table in table browser correlate page. commit c49fde4114088530f05e3032d97e771e516764a5 Author: galt Date: Thu May 20 15:00:30 2010 +0000 "Encode release log update" commit 419c8e7c85548c79252bda70457d52c2c0cfd5ab Author: galt Date: Thu May 20 15:00:14 2010 +0000 "Release log update" commit 98f563783dbb16fbdb0655dd881788db04bcd1f5 Author: rhead Date: Thu May 20 04:16:15 2010 +0000 Set visibilities and some shortLabels of mrna and est tracks back to what they were before we did away with all_mrna and all_est tracks. commit c4f7d2de9f32be7022315ff8671a8c58553e2885 Author: kent Date: Thu May 20 03:24:11 2010 +0000 Tweaking settings for regulatory track. commit 41ec345e7a7c5afcde9fde88b2de62ce29391742 Author: kent Date: Thu May 20 03:23:08 2010 +0000 Adding showSubtrackColorOnUi commit 4ff808fa5916f7f35b99234dca4e83c4930b54af Author: kent Date: Thu May 20 03:22:12 2010 +0000 Writing out table of cell types and single letter abbreviations on factorSource details page. Removing some debugging. commit b14057d32a3413bf67e2d030292ee83961cd7088 Author: kent Date: Thu May 20 03:21:11 2010 +0000 Making hgc output closing HTML tags that were missing in many cases. Still look to be missing in a few more though. Making a call to printAlignmentsSimple use track rather than table name to keep it like everywhere else. commit 952889f520316a7160527aff757e535f6eb91d94 Author: kent Date: Thu May 20 03:17:21 2010 +0000 Exposing metadataToggle function as compositeMetadataToggle. Adding support for showSubtrackColorOnUi tag. commit 0d20edb99ab0fde041c55062e028397787be0bc7 Author: kent Date: Thu May 20 03:15:51 2010 +0000 Making cartWebStart included jquery.js and utils.js. The function that does this already gaurds against multiple inclusion, so this should work. commit 113b44d5d92549f48667ee022bd9cc3d7262b808 Author: kent Date: Thu May 20 03:14:17 2010 +0000 Fixed indentation a little commit e33cfd728e85f364a06c14f30bcb845d725a4ff4 Author: galt Date: Thu May 20 02:43:31 2010 +0000 adding bedSort commit 3d292a43fb0b5018ee2c8d272b1bd6450f00e271 Author: galt Date: Thu May 20 02:36:56 2010 +0000 adding bedSort commit f5d16f33f7a7018716e62fc0b1da699dc0853a4c Author: rhead Date: Thu May 20 02:26:21 2010 +0000 A floret for hgwbeta-public to keep us from wondering why our trackDb changes are not showing up on the machine we are staring at. Thanks, Venkat. commit 1a33acccd195f96f0d89b7eed1a5d64cef3d9b27 Author: tdreszer Date: Wed May 19 22:49:33 2010 +0000 Undos wiped out file. Now its back commit 9ef9c1377bb58d9807e141dc6228b7e1b7c72976 Author: chinhli Date: Wed May 19 22:27:18 2010 +0000 13-Way multiz gene frames commit 8f798c92f96b20334569103ab1a4a3298fdc3e8e Author: chinhli Date: Wed May 19 22:23:46 2010 +0000 13-Way multiz reading frames commit 4022a55fa05a93f88e4388f7d3af35f2c48b2d42 Author: angie Date: Wed May 19 20:46:09 2010 +0000 addPslResultToHgp: don't trim initial all_ from table name, we need it now. commit f70d9018f2fd7c6cd8729e9267ba50283582a33b Author: vanessa Date: Wed May 19 20:29:41 2010 +0000 changed links to relative links, changed the html formatting, and changed the sentence structure commit 25ed1d3ab9fd608f254aac3c1e68d028848bd698 Author: hiram Date: Wed May 19 19:08:42 2010 +0000 add information about how to sort the input file with sort commit 5b677301d046410089520ffc554dbf67bf1c2a5b Author: hiram Date: Wed May 19 18:51:13 2010 +0000 add unix sort command example commit a48c09076759c385f7772041933227ab3446568e Author: braney Date: Wed May 19 18:47:28 2010 +0000 moved this down to metaDb commit 04c943c18882314ee8a04fb76b2e0ffe94de6944 Author: braney Date: Wed May 19 18:46:50 2010 +0000 moved from above commit b3f1e86e1f6939301799b575089db6c5d9e92aac Author: braney Date: Wed May 19 18:46:04 2010 +0000 this is down in metaDb now commit 58661b3979ea522392693650bba8a7390459927a Author: braney Date: Wed May 19 18:28:37 2010 +0000 moved into alpha commit 62ad33245b596013b854849df80a8a451143f7d8 Author: braney Date: Wed May 19 18:28:18 2010 +0000 moved from above commit de5763392cf9606ff8fb11d5cce2b8c9c4bb59f7 Author: kent Date: Wed May 19 17:11:15 2010 +0000 Fixing typo in comment commit 1b3eb2ac9652270de3a8f7fba142dded7f8a8d0a Author: galt Date: Wed May 19 15:00:08 2010 +0000 "Encode release log update" commit 1b93acd87cf8ca3e5ba8fcd48424cf6cb1fa1655 Author: galt Date: Wed May 19 15:00:06 2010 +0000 "Release log update" commit 067d6878156c64d9d71e4bb6c7f92edaade5c7ef Author: markd Date: Wed May 19 05:33:36 2010 +0000 moved files to genecats modules commit 901103edaeb3e3eb886749413796a44ef228fc54 Author: kent Date: Wed May 19 01:37:13 2010 +0000 Fixing some problems with mrna and est tracks in table browser. commit 73df336821fd54c63b0b9ef29abf4379f1f0fab3 Author: kent Date: Wed May 19 00:52:24 2010 +0000 Fixing crash on regulation group from container track. commit 720f48fa96962358a8a5122243ae108bc4f84b5e Author: mary Date: Tue May 18 23:55:56 2010 +0000 moving chain/net shortLabel override for calJac3 up one level commit 46ca28e87f17f661e6ec2dd4e18dfa34cc779f09 Author: mary Date: Tue May 18 23:52:28 2010 +0000 forgot to update makedoc with the final version of the find command I used to change the date for calJac3 commit a75f0c91c6ed1c5799313c0e051045f24d37c21d Author: cricket Date: Tue May 18 23:46:49 2010 +0000 Added new submissions commit 190ba67563f9064a69c5f896bd48611156387f8b Author: cricket Date: Tue May 18 23:38:16 2010 +0000 Fixed the Signal Tracks failing to scale problem. Added ViewSig on the end of the subtrack names commit 9f7d1f4bd1e5324e39594d7ddfd35c514268937f Author: kent Date: Tue May 18 22:39:08 2010 +0000 Fixing mrna alignment click bug from recent refactoring. Also making listItemsAssayed cgi variable conform with prefix convention. commit c7199511b876293aa6aa33a6104c60df8e2b4bb2 Author: kent Date: Tue May 18 22:37:36 2010 +0000 Exposing trackDbSettingsFromString and using it in place of raFromString. commit 7f9963c191289f468a74e5064adfba7f625a83cf Author: kent Date: Tue May 18 22:36:36 2010 +0000 Adding hGetTableForTrack. Refactoring things so that this and hGetTrackForTable share the same settings hash. commit 16f224c276f091867db357fdfff4ba4223609acf Author: braney Date: Tue May 18 22:14:42 2010 +0000 add primary table and database to schema output commit d886f9bee739417be5fbdda5116bb5df9d0b8edb Author: kent Date: Tue May 18 22:08:25 2010 +0000 Adding end to some peakClusters web pages. commit c3fcdc03108c3800ed1dceabfadb503445a9a803 Author: kent Date: Tue May 18 22:07:52 2010 +0000 Making big hgc track dispatch use table instead of track. commit 919314b39ab4106eea1d9f8809c51b73e9dc522c Author: braney Date: Tue May 18 21:56:26 2010 +0000 make all tier1 cell lines on by default commit 5d3f5178cfd343b74e6584a0c9c293334617e907 Author: braney Date: Tue May 18 21:55:23 2010 +0000 change Tags view back to Alignments, move the Release Notes section commit ce49e8cc133c2e9d2cd76ad386631c21c690ec0a Author: galt Date: Tue May 18 21:27:18 2010 +0000 typo fix in usage help commit 58c3d8d1501fda2d627722db9119f83d5eaa02d8 Author: cricket Date: Tue May 18 21:11:01 2010 +0000 Color changes for MEL cells, and new CH12 tracks added for Histone commit e99cebb42f876f47be081be4166cc28a4fe1c799 Author: kent Date: Tue May 18 20:06:39 2010 +0000 Further work adapting hgFind to separate track and table names. commit 611b97347d6108c675c19e7e72cb9cad19776d4d Author: kent Date: Tue May 18 20:05:59 2010 +0000 Renaming carefulTrackOpenVis to hCarefulTrackUpenVis and making it global. commit 899b384316f633ae04d2dcf6f9d7fe52ff7d1da9 Author: kent Date: Tue May 18 20:05:32 2010 +0000 Adding hGetTrackForTable() commit a815c878bdfbc2e07fcda28cd64ffd0e6918ba30 Author: kent Date: Tue May 18 20:04:52 2010 +0000 Fixing reference to nonexistant function in comment. commit 78eda6b4431e95a263bb23a8643f6e4e7f8907c0 Author: kent Date: Tue May 18 19:01:17 2010 +0000 Adding parent field to struct track, and filling it in for composite and container subtracks. For supertracks, the existing parent finding at the track (as opposed to trackDb) level is buried enough this is difficult, so putting this off until the mythical day when supertracks are refactored out. Making mrna searches open mrna track in hg19, and in general improving search auto-opening when track and table name are different. commit b5e21b76abd15024ac7bca88650fa9078f5fe059 Author: kent Date: Tue May 18 18:58:20 2010 +0000 Renaming carefulTrackOpenVis to hCarefulTrackUpenVis and making it global. commit 8863518643a45762a799993a0f8111ed5ce1101e Author: ann Date: Tue May 18 17:52:41 2010 +0000 bolded statement about track needing to be in non-hide mode in order to see it in this grid. commit 8cc9741b98ce47721484bc5b3ab6059c341c0e11 Author: galt Date: Tue May 18 15:00:32 2010 +0000 "Encode release log update" commit 43e87911d38023d8c2eab30d8c8c73c08d8e43ac Author: galt Date: Tue May 18 15:00:30 2010 +0000 "Release log update" commit c2781a88c421a0f163af120480c546b5f9c037b4 Author: tdreszer Date: Tue May 18 06:31:44 2010 +0000 Removed offending assert commit 3473cd623aa2c13a9c1a6693b5f647f91fff1dbf Author: galt Date: Tue May 18 06:20:55 2010 +0000 fixing for Views, and for case of allTracks with null track commit c1b328975957a746f9aa48de70ce6ef7bfdae953 Author: galt Date: Tue May 18 02:18:14 2010 +0000 "New version number v231" commit acedfe036e9bc91e0c3b3d7fc19e67ab74812d2c Author: galt Date: Tue May 18 02:17:43 2010 +0000 v231 final build commit a20385098e305053cb34f43859d0a833d5d18452 Author: kent Date: Tue May 18 00:04:40 2010 +0000 Putting in page that shows all tracks that could contribute items to a cluster. Link to this page at the end of items in cluster table. commit a2362adf823c0d32b5053f5099b7c2a1d93ddb56 Author: markd Date: Mon May 17 20:39:21 2010 +0000 added symlink building commit 4d0f0758bdc10b4884c81774b1a17bcfa85a3866 Author: hartera Date: Mon May 17 19:09:51 2010 +0000 Changed file names in beta release metadata for CRG Mapability subtracks. commit 5c18c8a148b79f2d839eea8cd269f343ceb4d0e3 Author: hartera Date: Mon May 17 19:04:50 2010 +0000 Changed file names in alpha release metadata for CRG Mapability subtracks. commit 41dd993707b050f2bf70e982b4b13f892454e955 Author: braney Date: Mon May 17 18:42:39 2010 +0000 change alignments view to Tags view commit 01f5ccfb2bb8bea9f298c5618dfbec61d6bbbd31 Author: braney Date: Mon May 17 18:42:16 2010 +0000 change Alignments view to be called Tags commit a7635202d3d00b7b610c4c3686d09454a4b3d98f Author: hiram Date: Mon May 17 18:01:41 2010 +0000 invalid number is actually invalid integer commit d2c51193354f3e8e340ee0fc0b9581ab1d92fc7c Author: galt Date: Mon May 17 15:00:04 2010 +0000 "Encode release log update" commit dca099d1fef29b7aa85cb36afcab93f8f17ddbe0 Author: galt Date: Mon May 17 15:00:02 2010 +0000 "Release log update" commit b0fd78a9a8628c80609bd56f54af6b47bb33c95a Author: jzhu Date: Mon May 17 09:13:35 2010 +0000 remove ispy track from trackDb.cancer2.ra commit 059aa52370775033446262ee72b65dd9a87c36ae Author: rhead Date: Mon May 17 07:10:22 2010 +0000 Removed release restrictions on UW DNase DGF track. commit ba5c7fa9daa8661ef2929abebe39e5bdf8d4292a Author: rhead Date: Mon May 17 06:55:29 2010 +0000 Added link for UW DNase DGF track. commit 2ce4ce390947425c5e24c8f1349ca1b3fb7bbbcb Author: markd Date: Mon May 17 02:37:43 2010 +0000 add building symlink to make commit 4759037cb1898b3431ffdfc3d14d2d97b98dc090 Author: markd Date: Mon May 17 02:33:18 2010 +0000 added missing images commit d32f769392e0e0efb5671c5f4dcb278379905caf Author: kent Date: Mon May 17 02:30:20 2010 +0000 Working on details pages for DNase Clusters and Txn Factor ChIP tracks. commit 83705bdf46d634222cc4a01160d54b6962b33b42 Author: kent Date: Mon May 17 02:28:45 2010 +0000 implementing compositeGroupLabel and compositeGroupId functions, and exposing existing static function as compositeLabelWithVocabLink commit a1b66c901dbd55ad2bc18af1faa97c3d706437df Author: kent Date: Mon May 17 02:25:08 2010 +0000 Adding inputTracks* tags to another wgEncodeReg track. commit 77c5939484a555261bfd87d7c6b3524a89d28722 Author: kent Date: Mon May 17 02:22:49 2010 +0000 Adding factorSource to inputTracks* commit 1adeecad50af1499b12b85732629a6949ea08549 Author: kent Date: Mon May 17 02:21:36 2010 +0000 moving literal 6 to variable scoreColIx commit ebfe98da721fe30cf46aa20573bb7524dc2d08d2 Author: kent Date: Mon May 17 02:18:24 2010 +0000 Fixed small typo in parameter name in function prototype. commit 3cc2f0de0a37b8546f1a16eb23cb044b26268fc6 Author: kent Date: Sun May 16 21:43:14 2010 +0000 Moving wgEncodeReg track and subtracks to hg18/trackDb.wgEncode.ra from hg18/trackDb.ra. Also starting on a couple of the html descriptions - just a bare start. commit 14bc5fc24b98c437467cdbdcde9a578410cf33ac Author: kent Date: Sun May 16 21:41:42 2010 +0000 Putting in something so that multiple peaks in the same cluster from the same source don't get counted twice. commit 08951a8f7c7035d35dcb8f2acac20140012f7dc2 Author: braney Date: Sun May 16 20:52:36 2010 +0000 moving these down to the alpha directory commit 2c28951f453a7d520db7f7741c7cfa8188d76754 Author: braney Date: Sun May 16 20:52:17 2010 +0000 add these in the alpha dir commit 398d9bb526dfa0807874c36999cc446fdda6f859 Author: hartera Date: Sun May 16 20:34:35 2010 +0000 Recreated Signal subtracks for Burge RNA-seq data. Used -bed12 option for bedItemOverlapCount to take the blocks into account. commit 875f34ebdcb17e7234ec7e6c800a81e11892625b Author: galt Date: Sun May 16 15:00:06 2010 +0000 "Encode release log update" commit 83e40b7afa422711ea2d0e7eeea38be64fc320cb Author: galt Date: Sun May 16 15:00:03 2010 +0000 "Release log update" commit 43dc089dbe43614af5f4cb59b1f55531e2cd2c25 Author: braney Date: Sun May 16 01:33:25 2010 +0000 fixed problems with metadata commit e132fe9e8bcd2fa50302e6cb1bf1a9fa68c68ae4 Author: kent Date: Sat May 15 22:08:41 2010 +0000 Adding handler for clustered-peaks like wgEncodeRegDnaseClustered commit cfdcae9e4d10d0b825726ca05b23c8844d4709ff Author: kent Date: Sat May 15 21:03:22 2010 +0000 Adding handler for clustered-peaks like wgEncodeRegDnaseClustered commit 71b55520036efc9a73ece0b6c4aecf77de818295 Author: kent Date: Sat May 15 21:01:54 2010 +0000 Adding inputTracks tags to wgEncodeReg DNAse component commit 602471ee72b3de19136307f275d1bf68eba90ee5 Author: kent Date: Sat May 15 18:50:25 2010 +0000 Adding setting that are used by customTracks to reserve them, and hopefully avoid conflicts in the figure like we had with 'dataUrl' which had to be renamed at some cost to 'bigDataUrl' commit bc02c32bf14e4427e5af8913555c014751d6851e Author: tdreszer Date: Sat May 15 15:45:58 2010 +0000 Un-dos-ed this file commit 77b8d3e09d3d0e58969ebbb0be1a195229eb1b02 Author: galt Date: Sat May 15 15:00:06 2010 +0000 "Encode release log update" commit ffe5c864c7ba8b6160c4d60cf71ecd8e256aed46 Author: galt Date: Sat May 15 15:00:03 2010 +0000 "Release log update" commit 1ad8ebd5fd761f732b47f705c497437500b4689c Author: galt Date: Sat May 15 06:35:45 2010 +0000 Dealing with primers that match but dangle off the ends of the chrom commit ce410320dc61fa43a68724538debb621f7eaa495 Author: tdreszer Date: Sat May 15 02:27:53 2010 +0000 Fix one inputType commit a8c73b41cb4874f27edd0ee2bc06a9db2082caab Author: tdreszer Date: Sat May 15 02:13:16 2010 +0000 Arrival of some missing fastqs for hg18 commit 2d6e337b59e0cb8c01993ce006fe7432a5e92275 Author: braney Date: Sat May 15 00:04:03 2010 +0000 move RikenCage includes to the new policy commit 9cb104e632c67d19b093930faac768217f95f2cb Author: braney Date: Fri May 14 23:52:00 2010 +0000 conform to the threeStateTrackDb naming scheme commit e3b1115f37b227606fb03261637835c848938b62 Author: kent Date: Fri May 14 23:32:00 2010 +0000 Refactoring a bit so can pass a table string rather than a track struct to eliminate a track/table potential blending of things. commit f76279b75dc9a45ece8ed8db232036901a039cba Author: kent Date: Fri May 14 23:31:04 2010 +0000 Fixing a ->table that should be a ->track. Thanks Angie for spotting this. commit ae06369ef5d2f67629f3fccdf8b201f08656a5e3 Author: kent Date: Fri May 14 23:30:24 2010 +0000 Getting rid of some special cases no longer needed for mrna track. commit 986b42bb0d3ede874272ce5ebd84b70037525d12 Author: kent Date: Fri May 14 21:38:54 2010 +0000 Starting a generic click handler for containers. Not really useful now though since decided to just go straight to hgTrackUi for multiWigs. commit 3d5f43aeec9a249448d946a349dfe2cc44a3d06d Author: kent Date: Fri May 14 21:35:37 2010 +0000 Making click on multi-wig bring up trackUi page. commit fcf13b93301629a6bf5df6688c26f6abc2d35fef Author: kent Date: Fri May 14 21:34:15 2010 +0000 improving layout of comment commit f45ca278a51474000aeeaf112d09f5d1a907dbc1 Author: hiram Date: Fri May 14 21:30:00 2010 +0000 maybe is may be commit 0a7a5cf60fd9e5101cf3d4e177cb01776dc15970 Author: angie Date: Fri May 14 20:47:14 2010 +0000 hg18.nt.txt commit 761edea55cc3bd55eac117081966db0bcc77505a Author: cszeto Date: Fri May 14 20:46:15 2010 +0000 Removed broken tracks commit c3418b34dbfc2a61d1209541fcbc2ce1741443c6 Author: cszeto Date: Fri May 14 20:25:11 2010 +0000 Updated tracks and put in dbProfile to get working with the browser again commit fcc5315f48b76b6a2e24618869cce9c90c56cf8f Author: tdreszer Date: Fri May 14 20:22:03 2010 +0000 Added default message when no selection has been made is empty commit 8a56d1f756e48d688cd16eed0d19f35d0a9438d0 Author: tdreszer Date: Fri May 14 20:11:07 2010 +0000 Got rid of unused CSS class that was causing errors. commit 4d2d92504af92602df5746867c8625c5356e0beb Author: cszeto Date: Fri May 14 20:10:40 2010 +0000 Changed from logicalDb to dbProfile flag commit dc958ee00dbd0afc03a9dcfe3a5ff1568ff35f71 Author: cszeto Date: Fri May 14 20:10:00 2010 +0000 Added dbProfile flag commit b69b7260ba8fd994209bbd27e8856df6968d0fb5 Author: markd Date: Fri May 14 19:44:00 2010 +0000 added info on configuring dbProfiles commit acacb7eb680689904369c468595a8e38367b792a Author: tdreszer Date: Fri May 14 19:39:54 2010 +0000 Removed metadata lines from Yale and HAIB. Added filterComposite to HAIB TFBS commit b25c6204cf2ced34ec25ed36994ac8d791553fd4 Author: angie Date: Fri May 14 19:39:04 2010 +0000 Candidate regions for gene flow from Neandertal to non-African modern humans (table 5 of Green et al. 2010). commit 64bee758cb969083de4c022613291eb717c31b72 Author: angie Date: Fri May 14 19:31:33 2010 +0000 Adding bam% to tablesIgnored $gbd and Neandertal tracks to tablesIgnored $hg18. commit 874db7359fe2a5e0629fe154ddbe7ff7d79eae42 Author: tdreszer Date: Fri May 14 18:37:07 2010 +0000 Support for new filterComosite. Rearranged and reworked the mebersForAll struct. Need to redo it as slLists. commit 6180c5e88ca92e161a26701b359fe1db3832cc7e Author: tdreszer Date: Fri May 14 18:35:45 2010 +0000 Supprt for new filterComposite commit da5b6338e01ce1755b823cd60d3bf3e26171ca68 Author: tdreszer Date: Fri May 14 18:33:00 2010 +0000 Modified from plug-in. Style needed for ui.dropdownchecklist.js jquery plug-in to support composites with filter boxes. commit 68c974d194a374e6869feb98c8c4d02765e5ec5f Author: hiram Date: Fri May 14 17:58:29 2010 +0000 add 1.13.0 URL commit 88bbc203c2df239263d577616364ca2f67402427 Author: braney Date: Fri May 14 17:51:56 2010 +0000 add some more text about the alignments to describe their color commit e99edea7f0e0bb6ce41bccc9b90258fc4fa827ac Author: tdreszer Date: Fri May 14 17:44:04 2010 +0000 Added ui.core and ui.dropdownchecklist to support composites with filter boxes commit 60fc5a57336cd58c76312709f7d151979a0fe550 Author: tdreszer Date: Fri May 14 17:43:04 2010 +0000 Initial check-in of modified plug-in needed for filterComposite functionality commit 53350e6f816d88e905adfffc456a66e558c3be92 Author: tdreszer Date: Fri May 14 17:41:44 2010 +0000 Untouched from download. Needed for certain jquery plug-ins commit ccac7df0bf2ec3e5b68c99d9415a1931c4477900 Author: tdreszer Date: Fri May 14 17:33:19 2010 +0000 Got rid of imgOrd hidden inputs. This is set by ajax now. commit 0b10fb5253e90e54edb91765c645cb6e0854c71b Author: tdreszer Date: Fri May 14 17:29:34 2010 +0000 Added setCartVars to set an array of names and values. Needed for inageV2 imgOrd commit 0c2fb0d74e757ea7b65e3e086cf054d7e6a02bf1 Author: braney Date: Fri May 14 16:19:10 2010 +0000 add color to H1hesc for GIS RNA-seq commit b1219b8a6a4d5ae8c7f907785b58045628d22acf Author: braney Date: Fri May 14 16:08:51 2010 +0000 change how the two sequences are printed out for split aligns commit 9ba7f5e58d7393ef0fd242eeb5e3d4443913392c Author: galt Date: Fri May 14 15:00:07 2010 +0000 "Encode release log update" commit f3d1ecc1286b7756dd02d35df6bd54f008643b41 Author: galt Date: Fri May 14 15:00:04 2010 +0000 "Release log update" commit 6a0454d3c3fb9df9678cad146506908bf892baff Author: rhead Date: Fri May 14 02:29:20 2010 +0000 Updated the notes echoed at the end to reflect the automatic copy to hgdownload. commit d3e0122220dc27f2009e83f13ce694e4a614ccb6 Author: kent Date: Fri May 14 01:48:35 2010 +0000 More tinkering on encode regulation track. commit 02f0435560dcd040ac59094d9cbe4bb573d65417 Author: bsuh Date: Thu May 13 21:48:37 2010 +0000 Initial checking of converter script for Philip @ Stanford for ENCODE. Converts from tagAlign to SAM format commit da8500f4228ddb92ab2d565fc9884d9385da03e8 Author: hartera Date: Thu May 13 21:44:19 2010 +0000 Minor edit. commit 2578becff93e5dc1dc6888c5d1b3687523c9e525 Author: kent Date: Thu May 13 21:43:21 2010 +0000 Removing sum and product type aggregates from UI since they aren't implemented now, and may not be soon. commit 68fe0b9af092f8351af99782889ccaa572a72649 Author: kent Date: Thu May 13 21:42:02 2010 +0000 Making it so that multi-wigs can draw without overlay as well. commit 52f84f0790a57606999e7b8065292048a9d20cfb Author: kent Date: Thu May 13 21:39:19 2010 +0000 More noodling getting multiWig UI page to work, mostly by pretending to be composite. commit 441539553925d8bf4ee4c153fea428b580903e38 Author: chinhli Date: Thu May 13 21:38:34 2010 +0000 Conservation track commit 269cb0d10d590512110361e284b276cbbacb5b85 Author: kent Date: Thu May 13 21:38:33 2010 +0000 Adding stuff for aggregate/overlay dropdown. commit 5987d422f494e09445b9effc6cab46fc2377a47d Author: chinhli Date: Thu May 13 21:35:49 2010 +0000 Add gap annotation for multiz13way commit 764ae1357e664a8d19f1e795598b3d4d85221611 Author: katrina Date: Thu May 13 19:06:13 2010 +0000 made cell line in some Yale TFBS shortLables more distinct; shorted a Yale TFBS shortLable commit ad48106d1a8a93dd2b46a4583f1e769deeef6e65 Author: vsmalladi Date: Thu May 13 18:34:52 2010 +0000 HAIB TFBS: Added 5 new tracks from submission 1189 (Control) experiments of cell lines. Updated Data Matrix to include new dimensions. commit b338bdc2a21c7128f6fcdce4f64d1b1fda539342 Author: vsmalladi Date: Thu May 13 18:32:56 2010 +0000 HAIB TFBS: Added Metadata for submission 1189 (Control's for cell lines) commit 46ef901eabeef74e0d3c3449c1c3cbd06ae55676 Author: mary Date: Thu May 13 18:26:59 2010 +0000 editing example to be more pig centric commit cdd4af67c5e6977b93f451e7609388b13541b7a4 Author: chinhli Date: Thu May 13 18:05:27 2010 +0000 Complete Affy_U95 track commit 013b30b7f611be6195a816f1bb30d222fc38e244 Author: kate Date: Thu May 13 17:43:31 2010 +0000 Flip mouse cell color to match human analog (k562) commit 33b682f41aeb516b80088cc14a8f6cc3d3e6f9c2 Author: ann Date: Thu May 13 17:42:00 2010 +0000 removing all links to term.html commit efd694138c2b19deb60052feceb1182d2760d6f1 Author: mary Date: Thu May 13 17:18:14 2010 +0000 adding fixes to dates to the makedoc commit 217479065f38026321398f0dc39c77f17f8b144a Author: galt Date: Thu May 13 15:00:24 2010 +0000 "Encode release log update" commit 482889622ca502ae3dc77be2955f7de6d4abc01e Author: galt Date: Thu May 13 15:00:04 2010 +0000 "Release log update" commit d12a172820c9b998c100ad273d2bf8ee36881485 Author: krish Date: Thu May 13 09:15:46 2010 +0000 files, types, and checksums ooh my commit 37c5acbfa4243525adf2f6884e489f114e4cac77 Author: krish Date: Thu May 13 08:32:16 2010 +0000 more general characteristics system commit 28747db688c1c5ab02d903e493ec5c320832bb55 Author: krish Date: Thu May 13 08:25:11 2010 +0000 more general characteristics system commit daafb0c54c750d69b29b27a12835f009335d25fb Author: kent Date: Thu May 13 01:26:16 2010 +0000 Adjusting some visibilities commit 601377960e7b1a5bac573fef2bd6398f9769561f Author: hartera Date: Thu May 13 01:14:44 2010 +0000 Corrected filename. commit 2b1cc8d1ad727bd49bac2bb9a7866f2eef58d44b Author: hartera Date: Thu May 13 01:07:50 2010 +0000 Changed name of the Mapability track, used to be encMapability. commit ee9521e4f808cddd18ab744c360cf842990a96a5 Author: hartera Date: Thu May 13 01:00:25 2010 +0000 Changed data version for CRG Mapability 36mer track as it was produced in January. commit 266b6336a4841024c5ed992ab43b51932d49cb14 Author: hartera Date: Thu May 13 00:51:18 2010 +0000 Documented adding Mapability 24mer subtrack (CRG) to trackDb entry. Updated downloads for CRG Mapability subtracks. commit 2ce168894b7d967c46521c96a6fd0d5864013f88 Author: hartera Date: Thu May 13 00:13:15 2010 +0000 Updated downloads for new CRG mapability data. commit 06d3c571c66b9dbb954ab5f4660d51c9766e92e8 Author: galt Date: Thu May 13 00:09:58 2010 +0000 dealing with tcsh number handling for leading zeros commit 5489a68cb53e844b038bedc4d889ac3cad83e353 Author: angie Date: Wed May 12 23:46:11 2010 +0000 Updated gwasCatalog. commit 783050c6c5bda2f217d2c1f09ea567368638c91d Author: baertsch Date: Wed May 12 23:34:42 2010 +0000 add ucscRetroAli track for hg19 commit 2d3926cc33777314318ed2f47c9e4f2722e4eded Author: angie Date: Wed May 12 23:24:58 2010 +0000 replSample now needs to be lstring not just string. commit 9923a0e1df2383fe3c381e7c38a5c8c246997dbb Author: baertsch Date: Wed May 12 23:05:01 2010 +0000 add retroGene track on mm9 ucscRetroAli commit 43cb0d73eb54b5465e5afcf826010e97ccf944cd Author: baertsch Date: Wed May 12 22:57:25 2010 +0000 add retrogene track ucscRetroAli commit c9ad382331465654efbcb25456431af7f2e6e118 Author: hartera Date: Wed May 12 22:46:47 2010 +0000 Changed file names back to gzipped version as these refer to downloads. commit 4e92ce026b893b6da1701e8b38ab0954f6440580 Author: hartera Date: Wed May 12 22:40:38 2010 +0000 Added subtrack entry for CRG 24mers in Mapability track. Updated file names in metadata. commit f7774f0911a6cbf3edd98dbd40c4e421bc6d12be Author: chinhli Date: Wed May 12 21:55:45 2010 +0000 Add Affy_U133Plus2 track commit f502ba234f3010a0523d373eb0477c45d4ddb18f Author: vsmalladi Date: Wed May 12 21:38:16 2010 +0000 SYDH TFBS: Added Peak and Signal tracks to include new submission 1190 commit 240b1f0c0e8811cc6816a9b6513662885d23042e Author: vsmalladi Date: Wed May 12 21:35:58 2010 +0000 SYDH TFBS: Updated MetaDb to include information from new submission 1190 commit 7f71f068a36278604602210ecb3481f6d5f990a2 Author: mary Date: Wed May 12 21:35:20 2010 +0000 fixing typo and adding 'thanks' commit 2eeced0d8cdea57e38840178ca78cf435d1c3b8d Author: markd Date: Wed May 12 20:04:40 2010 +0000 explictly ignore read status to keep certain version of GCC happy commit e9692e09bb1f8ed4c4221775b1980042dc0bafce Author: braney Date: Wed May 12 19:02:10 2010 +0000 add information about the clustering process commit 2352a437766c2ee8952fe46d2a6fa36848cd3cf5 Author: braney Date: Wed May 12 17:13:42 2010 +0000 moved trackDb.enc.ra to trackDb.wgEncode.ra commit 8e02b40b2e3d088d5c9464ad176c1f897f467d93 Author: braney Date: Wed May 12 17:13:05 2010 +0000 moved to trackDb.wgEncode.ra commit 8a821f4edaa5d993d65e5ea4414eec65583935e9 Author: braney Date: Wed May 12 17:12:47 2010 +0000 moved from trackDb.enc.ra commit 15d95144db1c84205b54203d47e3bdb8efc3dd4b Author: baertsch Date: Wed May 12 16:52:38 2010 +0000 rename ucscRetroAli4 to ucscRetroAli commit d72c301d5d58be7103273b76a0359531c7cc1c97 Author: mary Date: Wed May 12 16:22:01 2010 +0000 adding comma to pig release commit 1df98f11f2ae85a11e22a89f36476fd55fa5f6ff Author: braney Date: Wed May 12 15:22:55 2010 +0000 new commit ac71db6d9073e3686b4edce2785b8db22f6da546 Author: galt Date: Wed May 12 15:00:42 2010 +0000 "Encode release log update" commit f975e2e31cacdf1c952406421c13e9edbb643de5 Author: galt Date: Wed May 12 15:00:23 2010 +0000 "Release log update" commit 9834d12763230098f985c7d92d1189a13df31748 Author: braney Date: Wed May 12 15:00:05 2010 +0000 add metadata from fileDb.ra in download dirs commit 3059a276bfdecb2c39ccb8df0ac3855722e1700a Author: braney Date: Wed May 12 13:50:17 2010 +0000 new commit 4ac8c67e0cc1788454c8dc698c85b138b6715a18 Author: braney Date: Wed May 12 13:48:59 2010 +0000 hopefully updating to the right value commit 825efa2174c913bd270bc043e006aab98550e28d Author: braney Date: Wed May 12 13:39:33 2010 +0000 moved these down from above commit dd7d3ab6ea6b84cbc90033d65db741f727db55f9 Author: braney Date: Wed May 12 13:38:59 2010 +0000 moved these down into alpha commit 08c3ea162b4015a9d8e00ec1c8801a3fa2ea7666 Author: donnak Date: Wed May 12 07:29:50 2010 +0000 Fixed a typo. commit 782d34ba29ef439ad4d63440b1a7bc67ee1bc282 Author: donnak Date: Wed May 12 07:28:35 2010 +0000 Made a few edits to pig credits. commit d950cd2d6cc0aee47e1cb84de94045f4a9a8f4e3 Author: donnak Date: Wed May 12 07:27:29 2010 +0000 Made a few edits to pig news item. commit a7d261de0761d772c3d6c5d43caedc094c22393f Author: kent Date: Wed May 12 06:52:38 2010 +0000 Fixing composite tag search that should have been compositeTrack search. commit f6c786d25335a92971d15bb7f006c6a84b96d314 Author: mary Date: Wed May 12 01:48:28 2010 +0000 changing shortLabel to be organism for monDom5 commit 5af28ec749c08dd319e1c9ecc9a7460c25df81cb Author: cricket Date: Tue May 11 23:59:23 2010 +0000 Meta data information for Sydh Histone track. commit e62198e5e93f414399c0429dbddfc2f697ed20ce Author: cricket Date: Tue May 11 23:58:21 2010 +0000 The meta data tables for the Sydh Tfbs for mm9 commit ebe4f24fb58bb7fcaf00271698236c25d4ba9a68 Author: cricket Date: Tue May 11 23:56:40 2010 +0000 Track description first draft for mm9 TFBS. commit a8a5c0a2efb8663769e4c7a4587a40851293b02b Author: cricket Date: Tue May 11 23:55:30 2010 +0000 Track descriptions for mm9 SYDH Histones. This is our first draft. commit c71762c577c2a257fa6e4c2bf79e1cd61aee6bae Author: kent Date: Tue May 11 23:46:27 2010 +0000 Making show schema link work when track != table. commit 10302587d6988730d2f405f346c9cc41497bb063 Author: hartera Date: Tue May 11 23:43:07 2010 +0000 Updated names of files and tables as all ENCODE tracks are to have wgEncode prefix. commit f6e12b932191dc07ce04588a92cf404e9762dfdb Author: hartera Date: Tue May 11 23:28:09 2010 +0000 Changed include to new ENCODE trackDb filename. commit 49a5cd680ad6803adcbc9fc352f7be7ebf5391a5 Author: hartera Date: Tue May 11 23:24:37 2010 +0000 Updated Mapability track and subtrack names to have the wgEncode prefix instead of enc. commit 1767ada5026d4136e2b79edb2a87bf54558dbab7 Author: angie Date: Tue May 11 23:03:38 2010 +0000 Mention rsync in Downloads. Not http because it doesn't apply to /gbdb files which are the majority here. commit 52ef99318a4fbb40fcc5b4e8885c7e7456112015 Author: angie Date: Tue May 11 22:47:48 2010 +0000 Added Downloads section. commit a98a5ce8586dc486ec533e5a909fb778ed349fd2 Author: braney Date: Tue May 11 22:36:33 2010 +0000 taking LongPolyA+ out of the sort order and dimensions since it is always set in the data for GIS RNA-seq commit a2cb98c02f34fb30a889ce3c6cb3ec8e692a8113 Author: kent Date: Tue May 11 22:15:41 2010 +0000 Fixing sprung-loose visibilities. commit 9a97023a52d0289c61f91099a2c2e46d957f67c2 Author: katrina Date: Tue May 11 21:38:18 2010 +0000 Edits to method section, mainly punctuation and spacing commit 02e16c8b0f0f532a170464bb02f779cd1b29eb48 Author: braney Date: Tue May 11 21:19:03 2010 +0000 moving this to trackDb.wgEncode.ra commit ad661fec385ab4074a292f2c50b2fd44d36b5b7b Author: braney Date: Tue May 11 21:18:28 2010 +0000 moving trackDb.enc.ra to here commit 47f544648362cd2ab5b3848ee98a2d8ad21b22d5 Author: mary Date: Tue May 11 20:57:48 2010 +0000 fixing broken link (2 anchors called download23) commit 05ed84c9d19b8c955cbbf534541f81644e871ac6 Author: bsuh Date: Tue May 11 20:30:20 2010 +0000 Added info that input can be bzip2/gzip/plain to usage - suggested by Galt commit 4f549b360461c0dcadcda60ef7d1edce20e4dc4b Author: braney Date: Tue May 11 20:25:02 2010 +0000 take out parallel BAM validation path that was broken commit 00aca95fbcdf904612e25228dceb0ec82cd5f84b Author: kent Date: Tue May 11 19:07:47 2010 +0000 Removing old code. commit 2d12bc6d842780e9ae9e4d243da680bdcb87f501 Author: kent Date: Tue May 11 19:07:24 2010 +0000 Making overrides apply to settings rather than fields. Fields are recalculated from settings later by another routine. commit c9cb3decc2ac7e27bf13f5343942d0f9a5323b90 Author: kent Date: Tue May 11 16:59:35 2010 +0000 Making any type take maxItems. commit dcb84e377ce02fe5f412d879b2d5611ead34b0c0 Author: tdreszer Date: Tue May 11 16:03:48 2010 +0000 Improve multi-var query commit c77873e4f39d16318e83ac0273ed57831cf290d9 Author: braney Date: Tue May 11 16:02:41 2010 +0000 add broadPeak to types acceptable to maxItems commit c8489383fe3aeb0c59945d395d1d419e67ebcf7f Author: galt Date: Tue May 11 15:00:06 2010 +0000 "Encode release log update" commit bab3e0f65e95850f5d52d6918b0c1591e63e2226 Author: galt Date: Tue May 11 15:00:03 2010 +0000 "Release log update" commit fbff05918ae0ab5e8d769b0fb2fa0ddf527af520 Author: braney Date: Tue May 11 02:06:22 2010 +0000 handle indels commit 2ff6ba11b286b2aa83bfd18af65ebf378d464433 Author: kent Date: Tue May 11 01:43:30 2010 +0000 Refactoring to split the trackDb.tableName field into separate track and table fields. Similarly track.mapName field goes to the same track and table fields. commit f2f27751b89af4c4130922400bb5ec914e0b3801 Author: kent Date: Tue May 11 01:42:14 2010 +0000 Removing all_mrna and all_est tracks from scaffold databases, since no longer needed, will use mrna and est tracks. commit 245a71976f6b10da03c4388971903468aa0709bb Author: galt Date: Tue May 11 00:39:32 2010 +0000 v231 preview commit 5d770a1150e9f12c34feb8d1a2a33ad947ac885c Author: tdreszer Date: Tue May 11 00:03:06 2010 +0000 Moved to metaDb subdir commit c1d1cf58c2fce562de6fac262f732deb6098e463 Author: tdreszer Date: Tue May 11 00:01:41 2010 +0000 Initial check in of Cricket's SYDH TFBS on mm9 commit 370573ac7ee3621627f53e6ac34a50e9e650819c Author: tdreszer Date: Mon May 10 23:51:59 2010 +0000 Move 3 mdb RA files to metaDb subdir commit 825ae30af8167a13cef4e14b4f73ad48b94cd62d Author: tdreszer Date: Mon May 10 23:46:21 2010 +0000 Magic needed fixing commit b9808fbd9c1e59fb403f16401a787c214d69efc6 Author: tdreszer Date: Mon May 10 23:38:29 2010 +0000 Moved all of this meadata to metaDb subdir and named by composite commit 98bfdb6a772052606cc481c70baee2bfecd85d25 Author: tdreszer Date: Mon May 10 23:32:31 2010 +0000 Moved all of this meadata to metaDb subdir and named by composite commit dd5922ebe2a58cd9bdf7e305deba6fe4a3d8d0c0 Author: hartera Date: Mon May 10 22:15:40 2010 +0000 Fixed probelems with consIndels and danRerBacSangerName rules. For ecores and danRer3 phastConsElements, moved these into the highest level of the hierarchy for the genome in tbalesIgored. commit ce425247e8d9babaea57d85b16d08ff4f3cbc59d Author: kent Date: Mon May 10 21:40:23 2010 +0000 More work on encode regulatory track. commit 1a3f2848686b0566ad4423ddbc662625441e6286 Author: kent Date: Mon May 10 21:39:47 2010 +0000 Adding table tag commit 7080c4e66a771984e4a99a90a3ff609bdea5e1f4 Author: antonio Date: Mon May 10 21:02:06 2010 +0000 added broadStemChip to mouse ignore list commit 11e6e773d3cb534e23da488d1ddfa4fc80c19b67 Author: antonio Date: Mon May 10 20:48:40 2010 +0000 releasing beta commit 5013ea5b343ebff861404154f4c4fd43cbae376a Author: krish Date: Mon May 10 20:24:28 2010 +0000 added missing organisms commit 6f30c7b67b8b11e65a550285fc4b83162ade4254 Author: krish Date: Mon May 10 20:23:30 2010 +0000 added file for experimental variables commit b658c935c215de295d7b0571409cd12a1777194b Author: kuhn Date: Mon May 10 19:57:46 2010 +0000 added decription of ASHG content and added link to ABRF meeting commit d638b4682f05bf1c29524c1802e2e4996a199e84 Author: braney Date: Mon May 10 19:50:30 2010 +0000 set maxItems to 20. This resolves the 32,000 bit image problem commit 97ed3e144beb64b7112e72d42e256adb2117d8b3 Author: hartera Date: Mon May 10 18:46:34 2010 +0000 Changed danRerBacSangerName rule to be specific for danRer3 and danRer4. commit 6d0bddb8c3f83ddf8100a9480e3818496b2c6201 Author: hartera Date: Mon May 10 18:43:35 2010 +0000 Added ecores and phastCons tables to list of tables to be ignored. Added new rules for the consIndels track and the bacCloneAlias tables from danRer. commit d1552b8d2fb269825ebe162c21cf4a594a7e81ef Author: hiram Date: Mon May 10 18:41:34 2010 +0000 Mouse lemur photograph commit 7985a670e11925de5f59a97abd9c583e584acddf Author: mary Date: Mon May 10 17:27:39 2010 +0000 adding Brooke's edits to the codon coloring docs before pushing out commit 2bef621ddc6049deb14de8346686c048db995545 Author: antonio Date: Mon May 10 17:16:44 2010 +0000 adding ctgPos2 to tables ignored commit e41ddf10327ead2c82cae991e8e7479963afedf4 Author: hiram Date: Mon May 10 16:27:46 2010 +0000 correct FTP NCBI address commit 260ad9a5faf83d0ec88ce910c2a93190fba7ce45 Author: galt Date: Mon May 10 15:00:03 2010 +0000 "Encode release log update" commit 944bbd0c76e196b7e64bd5ae602e5e29787ad0c7 Author: galt Date: Mon May 10 15:00:01 2010 +0000 "Release log update" commit 26986fb39846a292dd7d9d79e0d5fb54986e4d86 Author: kent Date: Mon May 10 08:23:35 2010 +0000 Fixing indentation. commit da62efc246020e13f0635d5a8514ba88b0dacd8f Author: kent Date: Sun May 9 17:27:11 2010 +0000 Making calculations that all wigs below share same limits work better. commit 225d8bdb2a284e8c7bf260271308fdaddbdadd2a Author: kent Date: Sun May 9 17:26:29 2010 +0000 Making container code use composite UI code for the moment. commit a99714b0d4a2eaed42d0a1e9516b786bf2f225f3 Author: kent Date: Sun May 9 17:23:57 2010 +0000 Put in commented out line that does not have force-warnings-to-errors compiler flag. commit feba7e5f0634ae3627ac5e998ac420d667bbdff8 Author: kent Date: Sun May 9 17:22:16 2010 +0000 Making usage statement reflect program name. commit ed23bdba1a18fc88258f2789c4315ab8af54d51d Author: kent Date: Sun May 9 17:21:18 2010 +0000 Making subtracks of the regulatory wiggle configurable. commit fca8484058798ea1600148b5bac24248efc179ac Author: kent Date: Sun May 9 17:18:29 2010 +0000 removing commented out testing code. commit ddf52e9bfdf97e52e8453e2221f4e1bff1498925 Author: galt Date: Sun May 9 15:00:02 2010 +0000 "Encode release log update" commit b5a51475d1c6b11c37c3bd0ca236e9b233774114 Author: galt Date: Sun May 9 15:00:01 2010 +0000 "Release log update" commit 5109044c21c7db468eb31ff10547c8e1456f2f2a Author: galt Date: Sat May 8 15:00:05 2010 +0000 "Encode release log update" commit 213d8c83361a098ee8d4e6b63c27518af0bf2144 Author: galt Date: Sat May 8 15:00:03 2010 +0000 "Release log update" commit 3ed87fd29999466ac2de9c5b29c93f8c3e56f329 Author: mary Date: Fri May 7 23:53:55 2010 +0000 turning on genbank updates for susScr2 commit efa68354bb498c665cd224988ea72ea858626f36 Author: kent Date: Fri May 7 23:52:07 2010 +0000 Removing what looks to be an ancient Andy code-in-progress comment and a stray function prototype that went with it. commit a6ca0fdf4045ca1efa6c74bd771178a95250a555 Author: kent Date: Fri May 7 23:50:46 2010 +0000 Simplifying/generalizing code that prints link to parent track's UI page. commit 886f9c2c92f50e22c262623510034511abca685c Author: donnak Date: Fri May 7 23:15:38 2010 +0000 Fixed a few formatting things. commit 4090d911ea81637157effb5338ec3dc22f41c7e1 Author: mary Date: Fri May 7 23:10:15 2010 +0000 moving chain/Net overrides for rheMac2 down one level for calJac3. interferring with calJac1 when on marmoset level commit 57806e31bf920a03da5900b3f3524c8e39e625db Author: mary Date: Fri May 7 22:37:28 2010 +0000 adding pig release to docs commit 0c4eefce7393d2fca715c08bc9e50ca06a7646fa Author: kent Date: Fri May 7 22:30:14 2010 +0000 Separating out multiWigs into a separate module from container. commit d47c666b2bfd5f240e720499767ae1b314c047d3 Author: donnak Date: Fri May 7 21:57:31 2010 +0000 Created a new menu file for the Neandertal portal page. commit 908e493da6736d48584b2208c47e964d7ad31685 Author: donnak Date: Fri May 7 21:57:00 2010 +0000 Added some links. commit 3bb80f2e8cb83944a78502f606675fc944fde928 Author: donnak Date: Fri May 7 21:16:45 2010 +0000 Fixed up a few things in Neandertal announcement. commit 1abec11ec543af7420419d035d143fc316f9927b Author: donnak Date: Fri May 7 21:10:21 2010 +0000 Made a few mods per Ann Pace, fixed up a few other listings. commit de785ca7a67ea7cc5c61732019affac9362532d5 Author: sbenz Date: Fri May 7 20:42:09 2010 +0000 Fixing incorrect sample ordering, and added new gray cell lines names commit f26e83074ab40a0523c2eaa5fb024ce6db2a99f1 Author: kent Date: Fri May 7 20:37:31 2010 +0000 Improving some comments commit 1f9cd3679d5719748579d09574236dd46c28ee07 Author: kent Date: Fri May 7 18:29:15 2010 +0000 Fixing wigMaf tracks by being a little more careful about how the wiggle subtracks are manufactured. commit 8e758ef8084b8ca5dbc2db9cbdc5bec05d745fb1 Author: chinhli Date: Fri May 7 17:20:37 2010 +0000 Complete multiz6way commit 87387c66ca37da597824b7998d42e5b0c7c11e0e Author: angie Date: Fri May 7 17:07:08 2010 +0000 and make that beta,public. commit 80528e3a2f78d4ec0b87ea1b70991cd5aff04561 Author: angie Date: Fri May 7 17:02:36 2010 +0000 Oops, needed to use release public instead of release beta for DGV old label. commit 781dd5f13109c501125526652e3d610295ec4afe Author: chinhli Date: Fri May 7 16:14:23 2010 +0000 Add multiz6way commit 21ebc995ce051b3d918dc845928181e53b482185 Author: cricket Date: Fri May 7 16:04:59 2010 +0000 Change short labels to match human commit 9b86e919944e6981fa3718a65448be628ff489be Author: cricket Date: Fri May 7 15:49:03 2010 +0000 Minor changes in long labels to be consistenet with vsmalladi commit af25b4537b185b04a5e1b31cb117780e32cf58c5 Author: angie Date: Fri May 7 15:16:47 2010 +0000 Better links back to Max Planck Institute. commit 2d50e82b06b560a5ae511500d86ee815f7d17514 Author: galt Date: Fri May 7 15:00:06 2010 +0000 "Encode release log update" commit aeae697e69ac8655b9784009b1d0610b0b5492e1 Author: galt Date: Fri May 7 15:00:04 2010 +0000 "Release log update" commit 5e50ba4c5f2ba28073e77bbf0fe0dd2173cffa42 Author: kent Date: Fri May 7 05:37:08 2010 +0000 Fiddling with spacing. commit bd5d2b025ba214f2b583485fc77922b896b6afcc Author: kent Date: Fri May 7 05:35:53 2010 +0000 Changing subTrack to parent. commit 66f566629a371452d72d8b11d105e2e9d0066268 Author: kent Date: Fri May 7 05:35:26 2010 +0000 Adding regulatory track components. Changing subTrack to parent. commit 5acffa78438b081210dfa3a0e35d6137ae457810 Author: kent Date: Fri May 7 05:32:18 2010 +0000 Adding a few new tags. commit c086c6195c9fc1aaba97ce1117dc0cbf72b678b2 Author: kent Date: Fri May 7 05:31:45 2010 +0000 Adding a few more steps to regulation track. commit 89d2362a3301e38aaf774ae33640d168bd27f0bc Author: kent Date: Fri May 7 05:31:12 2010 +0000 Adding trackDbFieldsFromSettings commit 66bfa3495bf43ed80aeb8309e367fb9259ae4923 Author: kent Date: Fri May 7 05:30:41 2010 +0000 Adding 2.0 versions of gisChaiPet data agreement. commit bd533fd7232519fb7171283eb5ad2b7aeb196ba3 Author: kent Date: Fri May 7 05:07:58 2010 +0000 Removed some debugging statements. commit 435b8ef6c80af4738c24bff740f0f60e46a8c026 Author: kent Date: Fri May 7 05:07:57 2010 +0000 Code to get container multiWig to go. commit 4f374a3b31c1c1eb76f9883abb8a2f716dc8fd57 Author: kuhn Date: Fri May 7 03:46:24 2010 +0000 made link to science direct open new window, fixed stylesheet relative link, added link to ashg2009material commit c8f5f26a90e00f6ae21083201dfecdced4795cd8 Author: galt Date: Fri May 7 03:38:32 2010 +0000 new function hPrintEncodeNonBreak to protect against problems with <>;" in output, problem was recently uncovered by hgNearTest commit 8ed5363f0929a36bc7e20e1ce2c39f6d10f02461 Author: galt Date: Fri May 7 03:37:42 2010 +0000 using htmlEncode via new function hPrintEncodeNonBreak to protect against problems with <>;" in output, problem was recently uncovered by hgNearTest commit a1706f5e9bf609e81d763dc23be542e0da033905 Author: bsuh Date: Fri May 7 02:31:13 2010 +0000 Now optional stdout output or save to gzip-ed file commit 8c94e1d863c39776d6c440116bea89450505ae89 Author: bsuh Date: Fri May 7 02:11:40 2010 +0000 Fixed bugs and added bzip2/gzip file input and gzip file output commit b4f2e7d2958b48c2bd8916010ac0ec9e092cf76b Author: antonio Date: Fri May 7 01:58:42 2010 +0000 fixing credits link commit 23f234d4d366019b4aee4d55aa09506f3451bbb9 Author: antonio Date: Fri May 7 01:53:55 2010 +0000 too many news items commit 48d07608c45218c28a1fac1fb0f2129804f5dedb Author: antonio Date: Fri May 7 01:52:56 2010 +0000 archive link fix commit 3a62986e9df02f5b929d31ecc8d45e95aba78981 Author: donnak Date: Fri May 7 01:05:25 2010 +0000 Flipped the news announcement to the final version. commit d25b00eeadd82d80971e4db3063b04f075ead4b2 Author: vsmalladi Date: Thu May 6 22:40:39 2010 +0000 SYDH Histone: Initial Description page, with place holding values to be filled in once provided. commit 22537ec2574b2fb4d2bd536ae2dce3ae6148136e Author: angie Date: Thu May 6 22:31:59 2010 +0000 Added settings to hgTrackUi links, added ref to the 2008 paper on which ntMito is based, tweaked some track descr's. commit 481cedd62ae63ac9b46732cd30d8f4172c7cfb83 Author: donnak Date: Thu May 6 22:15:19 2010 +0000 A few more mods to Neandertal news. commit 4a23688d29a76e0f1224c9f9f87368f91c92f525 Author: donnak Date: Thu May 6 21:46:55 2010 +0000 Rearranged order of tracks. commit 4141e6a1f2caf3359b1a4889dc17d4943bd2b3e9 Author: donnak Date: Thu May 6 21:37:06 2010 +0000 A few more tweaks to refs. commit ad1f18f21567e499ec924401aed6bae1afb0df47 Author: vsmalladi Date: Thu May 6 21:33:01 2010 +0000 SYDH Histone: Updated Long label of composite track to be consistent with long lable from SYDH TFBS commit 143c707e9a203bd5eeef28c8dfd9cd39886f69b9 Author: mary Date: Thu May 6 21:21:44 2010 +0000 adding matrix and chainMinScore overrides for ponAbe2 in calJac3 commit 922471f5fddc614a66f4b718fa855ef7ba84bcd1 Author: donnak Date: Thu May 6 21:15:21 2010 +0000 Updated refs. commit acd4e3f276f754d1c7558da9d4802fb98ce044a8 Author: donnak Date: Thu May 6 21:06:38 2010 +0000 Updated refs. commit cc38263a87b9eb9e4109f0420caccbf9a45c07a2 Author: donnak Date: Thu May 6 21:00:38 2010 +0000 Updated Green et al. ref. commit c62a6a5ba88fe1a0d8549dc04d2fa7defa22e4c3 Author: angie Date: Thu May 6 20:53:01 2010 +0000 Tweak requested by Ed/b0b: drop 'previous'. commit 4ead58d32f31c8a6f63f69e1be178c9913a2d5ed Author: cricket Date: Thu May 6 20:50:36 2010 +0000 Mostly modifying spelling errors and label changes. The Signal view defaults have been changed. commit c17ba85f75ced14e502e0c08221524a6d8b6d460 Author: tdreszer Date: Thu May 6 20:38:44 2010 +0000 Two files were accidentally listed as deprecated but are actually untouched commit 68eeda57813bd0b6f44839f8deff2582dc0a669e Author: tdreszer Date: Thu May 6 20:23:27 2010 +0000 Added 2 missing fastqs commit ecadd24c750ad4741f9bbc410dc15b67baa8fabe Author: donnak Date: Thu May 6 20:01:20 2010 +0000 Made an interim version of the news announcement until we have everything staged on the RR. commit 0fd84ce3c626236c2f7f4e477a0d514376931b55 Author: angie Date: Thu May 6 19:43:46 2010 +0000 Migrated Neandertal track descriptions from genome-nt. commit 54f9081aa2a83388309bd9407c193b7988595c41 Author: donnak Date: Thu May 6 19:22:42 2010 +0000 Archived an item. commit a5d92b3384e234bef7ad44cfc383009905460aa2 Author: donnak Date: Thu May 6 19:22:28 2010 +0000 Added Neandertal menu link. commit 1f20f84e0ef5522a503429ef22e935e76a4dae01 Author: donnak Date: Thu May 6 19:22:13 2010 +0000 Added Neandertal announcement & link. commit 4f48b4cb720c91637b0b462fd65c2ed94ded1809 Author: angie Date: Thu May 6 19:05:58 2010 +0000 Added various tag types for Neandertal tracks. commit 4f79b6741bb488bf255f1a7eb52c5aada223dc78 Author: angie Date: Thu May 6 19:04:28 2010 +0000 Migrated Neandertal track descriptions from genome-nt. commit 48256d3779adb2c55543f47d8f28bc77622de543 Author: kuhn Date: Thu May 6 19:04:19 2010 +0000 added a little whitespace under image commit 37bb4de05473a69499b854a38dc20d6803ddd898 Author: kuhn Date: Thu May 6 19:01:10 2010 +0000 shruck whitespace around image a little commit cc3249cf98ebf6805a4c20748f6b4b411a9a3243 Author: tdreszer Date: Thu May 6 18:53:34 2010 +0000 Got tired of seeing the error of 'hgTracksInitTracks not defined'. commit 531ff34ede94fba24e39145052f4bc0a8deaf00b Author: angie Date: Thu May 6 18:52:56 2010 +0000 First draft by Ed, Angie, Donna, Pauline, Katrina and b0b. commit 0f942b9ff6cfc0dd2f1d1d33d0b5b9c394e1a1b2 Author: kate Date: Thu May 6 18:49:16 2010 +0000 Corrections, clarifications; this track doesnt yet actually contain footprints commit c1f03eca22e26395699b234541465b97d148a86e Author: hartera Date: Thu May 6 18:24:28 2010 +0000 Removed file as notes for the whole genome ENCODE are in another directory. commit 281ef4737422be4ef990a07fa1148762c335f763 Author: hartera Date: Thu May 6 18:23:10 2010 +0000 Removed documentation about CRG Mapability track as this is from the whole genome ENCODE and this document is for the pilot project. commit ec5c5aef35f1120a10d3ec04422848b28ba6a46e Author: vsmalladi Date: Thu May 6 18:22:04 2010 +0000 SYDH TFBS: Added prelimary default view limits for Signal track. commit afb9e101b14633d24cd08f9082c68c4aab006e9e Author: hartera Date: Thu May 6 18:21:05 2010 +0000 Updated release notes for CRG subtracks of Mapability track. commit 4f5968bbcc7eddd80d415d0612c460e2013b4d1a Author: mary Date: Thu May 6 18:21:03 2010 +0000 adding visibility overrides to make the default position for susScr2. Did affect susSCr1, but figured since it was only on dev this was ok commit 51535f59cde6702e458e942d1fae09332bff89b0 Author: hartera Date: Thu May 6 18:20:12 2010 +0000 Mapabilty track release notes for first release. commit 3f38683719837de3e637a2c27319fd11bb3116fe Author: kent Date: Thu May 6 18:02:38 2010 +0000 Making it so scores go from 0-1000 commit 1fb5e058ec627d9a6b85dccccdde68d911a0605a Author: kent Date: Thu May 6 17:53:41 2010 +0000 Making it so that output scores are integer rather than floating point since they are in 0-1000 range. commit 9930a4c55dcd1ee2bd3b908cb24882ad259781bb Author: mary Date: Thu May 6 17:12:37 2010 +0000 grammar edits and clarification from Brooke commit 54ee74065d524f9e8e3d589420f5f4d3e665a437 Author: mary Date: Thu May 6 17:07:43 2010 +0000 changing green to be a little brighter commit 1e0511ea82be2b7d548530ad1022ac8f2c9cf569 Author: mary Date: Thu May 6 16:57:50 2010 +0000 little changes suggested by brooke: grammar and making colors darker commit b2854476c3d68dbb6ddb670656bc3cf7bf36b1a0 Author: chinhli Date: Thu May 6 16:27:44 2010 +0000 Lastz finished commit 794e0b751e987e4a79465be6212c7bd3b35face2 Author: chinhli Date: Thu May 6 16:05:54 2010 +0000 Correct cases for oviAri1 commit 444d87e76aae37d77cff2e86431661af84fefc4d Author: galt Date: Thu May 6 15:00:07 2010 +0000 "Encode release log update" commit f639ed798d99b6c8170b4fcc06a08b7b35169906 Author: galt Date: Thu May 6 15:00:04 2010 +0000 "Release log update" commit e701fa26de0080e1b937f5f1eb24aaa735024714 Author: markd Date: Thu May 6 02:59:41 2010 +0000 yet another off by one error in my latest stupidity, wish there were unit tests commit a17ab9a81a05557178375ec6c118e76ace2046fe Author: markd Date: Thu May 6 00:04:50 2010 +0000 fixed off-by-one error when have a db.chr commit 800f87569c483cffd2160c5321f8b409d11aa6ac Author: vsmalladi Date: Wed May 5 23:50:06 2010 +0000 SYDH Histone: mdbPrint out file commit b23aea91b42cdb906720b04a0a75ceafbb8dbaae Author: vsmalladi Date: Wed May 5 23:48:06 2010 +0000 SYDH Histone: Changed view limits of signals from devault. Turned Control subtrack off on defult. commit 1ab52d5631c3b954996b37565c663ab792497995 Author: kent Date: Wed May 5 23:34:03 2010 +0000 Getting explicit about not abbreviating 5 letter words. commit 437b5b5aa70754dff4b3df1c9d0620c6242d7163 Author: chinhli Date: Wed May 5 23:33:00 2010 +0000 Add oviAri1 Sheep commit d747d23492dc4eef1ad793d0cda557f3f398f19a Author: ann Date: Wed May 5 23:27:15 2010 +0000 more fine tuning. commit ffcd7dc06710f334396834acd3af3ee4a2b9d59f Author: ann Date: Wed May 5 23:09:44 2010 +0000 updating mirror doc so it does not depend on the most recent version of proteins* and sp* tables, also to include steps to mirror visiGene database. commit 2b3d1ab2433a90b4ababe435bc81e9c99c917133 Author: markd Date: Wed May 5 23:03:39 2010 +0000 strike two at getting name right commit 86c392686202027c9f7e7a87d18d5343b3cb2f6f Author: markd Date: Wed May 5 23:01:59 2010 +0000 come how got function name wrong in header commit 11649aa6c04c5bd733f0665800bd22409042c570 Author: mary Date: Wed May 5 22:26:55 2010 +0000 adding period commit 433af907370ea203de4f0b8002d6e34770dbdce5 Author: chinhli Date: Wed May 5 20:31:40 2010 +0000 remove oviAri1 commit 6985b74f024e38a661edf938e5ffe2f04ede68ca Author: vsmalladi Date: Wed May 5 19:08:44 2010 +0000 Track SYDH TFBS, removed signal filter tags for Signal bigwig files. Track SYDH Histone: Initial checkin of Composite and subtrack. commit 35d79c7878828f74a12748e4d4fa411ea506aa52 Author: cricket Date: Wed May 5 19:00:32 2010 +0000 Now there is a an improved checker for cruff in the Signal Tracks. I have removed the signalFilter line from the Signal tracks and now it should make properly. commit 513aeca1546fbec8db8cea0a8c50729855054747 Author: braney Date: Wed May 5 18:54:20 2010 +0000 add a couple of variables used in the Gencode track commit 25bae505a1192978fa1451ac0a34f02755a8bdd9 Author: mary Date: Wed May 5 18:24:22 2010 +0000 adding search clarification to gene search documentation commit 8c06145ea93478d99da64a3338c37caf54616d3f Author: braney Date: Wed May 5 17:42:49 2010 +0000 take out misspelling commit a2c477dfe41f6e9092d0636bd7f9288c82be8a6c Author: galt Date: Wed May 5 17:41:31 2010 +0000 adding visiGene commit 9595b91a351b03227b2b04fd2878ad0c1613d405 Author: chinhli Date: Wed May 5 17:05:26 2010 +0000 Add Sheep oviAri1 commit a6f8347a3c5d4b947f2caae633d18213c15e0469 Author: hiram Date: Wed May 5 16:23:45 2010 +0000 comment out bottleneck setting and add central.cookie information and udcFuse mountPoint commit 5fff615a6334269a808a0f5408f2d2219c187641 Author: chinhli Date: Wed May 5 16:15:13 2010 +0000 Photo credit commit d1d6fd5735bb56301ba07e1c00be55adae958309 Author: galt Date: Wed May 5 15:00:27 2010 +0000 "Encode release log update" commit 33236192d23bd8700e69d9a3fc833ef69e7969a4 Author: galt Date: Wed May 5 15:00:08 2010 +0000 "Release log update" commit ecf62cee8ed9f30af7013220fd8374997dd6e9f4 Author: braney Date: Wed May 5 14:57:28 2010 +0000 add new cat to human proteins commit c2e69c8199ae9cc13af126638dc0d9f09fc6aeac Author: braney Date: Wed May 5 14:56:10 2010 +0000 human proteins commit 5325c863249bd91a525d89175dbe408f84cdc7ef Author: galt Date: Wed May 5 08:18:42 2010 +0000 fixing error xargs: argument line too long commit b22ca6159d463cc4451a3870e8ce914ca941d8a8 Author: angie Date: Wed May 5 06:47:16 2010 +0000 Obsoleted by Mark's improvements in genbankTables.as. commit feb70ebe5ea46792eb47d7b5520250fa21fef5c0 Author: kent Date: Wed May 5 04:27:06 2010 +0000 Uncommenting tdbQuery -check execution commit d1a997d29fdb0a718545ad1852b81effa1194480 Author: kent Date: Wed May 5 00:50:37 2010 +0000 Doing another pass at the regulatory clustering - this time whole genome rather than just chromosome 22. commit 9cd9342fda0a49be93deca2df1cc7c4cee67d317 Author: kent Date: Wed May 5 00:49:41 2010 +0000 Starting to put in instructions for the encode regulatory track. Will need polishing, but at least this will help me remember what I did..... commit d64ff3af14b494bb3be0123ccebdeeb08b09ae48 Author: braney Date: Tue May 4 23:56:01 2010 +0000 some changes commit c0d1b10283e47aa31340cc0c5e8745841b0faa2b Author: kent Date: Tue May 4 23:55:11 2010 +0000 Removing unused variable. commit 175d6b861bc76077ee90825c1d99e989aecf6220 Author: mary Date: Tue May 4 23:28:17 2010 +0000 changing chainMinScore gap to 3000 for calJac3 as I was told to do by the script commit 8c29532e75582c98b740904ce556aade56949483 Author: chinhli Date: Tue May 4 22:16:27 2010 +0000 correct wrong longLableName commit 29f2a359c705c5df1a626419a0ce82bb2a96eda3 Author: chinhli Date: Tue May 4 22:08:40 2010 +0000 dd image for Sheep commit 2b7bf64f8dbf9585597b1bda3da401af93eb15a7 Author: chinhli Date: Tue May 4 21:42:19 2010 +0000 6 way compare for felCatV17e commit b6dfa0f82d63b5fb905c9eb1f883b162e0d20c1d Author: vsmalladi Date: Tue May 4 21:28:52 2010 +0000 Track SYDH TFBS: Updated shortlabels to be 16 characters long and aligned. commit f66ab90855918492091d27c990b364bab802e53a Author: braney Date: Tue May 4 20:00:08 2010 +0000 some Orchid track changes commit 075501693a12a94a582a2a2499cd2cc3578a4cb5 Author: braney Date: Tue May 4 19:59:27 2010 +0000 track description commit 6c9a9a32fb6ed7a631bc621e823f63ce4a7109d0 Author: mary Date: Tue May 4 18:34:16 2010 +0000 adding include line to include new trackDb.chainNet.ra file commit df206512c0dd11546dbea4bafa6e393fde4198d8 Author: mary Date: Tue May 4 18:33:48 2010 +0000 removing unecessary lines from chainNetPanTro2 override commit f64ea37e3e31d5ae1b640d7448a0dc68726860c3 Author: cricket Date: Tue May 4 18:02:07 2010 +0000 Changing short labels to be more readable commit 1611aeb6c1e119897f4ef4f104de5c103c3d97ee Author: mary Date: Tue May 4 17:55:30 2010 +0000 figured out what I did wrong in the first place with chain/nets for calJac1/3. Am removing unneeded files commit 6d033413d3adccd2174ed4ee6dfad60bd09eb686 Author: vsmalladi Date: Tue May 4 17:48:25 2010 +0000 Updated HAIB TFBS track to include two new submission (1180,1188). Modified Short Labels to 16 chracters. commit 6796ddc7ed064bbb8aabb6d31d9823b09b0f4059 Author: cricket Date: Tue May 4 17:47:56 2010 +0000 Added the inputs with different controls as different factors in the matrix. commit 432931d42a4011ffb61520fa86e23c853774c4ab Author: vsmalladi Date: Tue May 4 17:44:34 2010 +0000 Updated metadata file for HAIB TFBS track to include two new submissions from pipeline (1180,1188) commit e5a3244920cc9b8d231fbc96a3f7a33552ca1a3f Author: vsmalladi Date: Tue May 4 17:42:00 2010 +0000 Added metadata file for SYDH TFBS track commit 9ff071dc3a5949e98f63432381ecdff5681b52b3 Author: mary Date: Tue May 4 17:40:20 2010 +0000 forgot chainMinScore commit 91e04e4f108216ca23b612876f3c61a2896a2d1a Author: mary Date: Tue May 4 17:38:48 2010 +0000 trying other way to make panTro2 chain/nets show up correctly in calJac3 and calJac1 commit a58df6f1f6b660257554280fa79e80ec471a629f Author: mary Date: Tue May 4 17:23:59 2010 +0000 adding a .chainNet.ra file to override chainNets for panTro2 commit 858b78f45b6bc41ddc5e9fb36dd6dd048c732a63 Author: tdreszer Date: Tue May 4 17:08:52 2010 +0000 Added 2 new protocols for HAIB TFBS commit d44399040fc5f2ebf8263311d42829f3b82db74f Author: antonio Date: Tue May 4 16:48:59 2010 +0000 adding scaffold track html commit 983d8d466d012e8fa03c6d07a68431e59faacced Author: antonio Date: Tue May 4 16:32:41 2010 +0000 adding override of scaffold html with correct info commit b7ec3cd8cece6d2aa2d83174a4dcba30ef27fe4a Author: cricket Date: Tue May 4 16:30:16 2010 +0000 Fix the mm9 SYDH encode tracks to show the drop down menus for Peaks and Signal and to hide the UI for Signal and to display all of the signal tracks. commit 9fc5086572a1cf35ce7617ea141f70c307e51b15 Author: braney Date: Tue May 4 15:38:05 2010 +0000 starting human proteins commit 6d10164f6adef0e2b16b79e4fe88d7dd734f1231 Author: galt Date: Tue May 4 15:00:06 2010 +0000 "Encode release log update" commit aa03215272b4992084da0ad91b1a81e7dc8ae15e Author: galt Date: Tue May 4 15:00:04 2010 +0000 "Release log update" commit fc8da9900476d7cb97aff598549c2bdb6ff0fbac Author: markd Date: Tue May 4 06:18:59 2010 +0000 added functions to parse srcDb and src sequence name from mafComp commit 96af23c4d50f88098a0a8778e50a1dc896be444b Author: galt Date: Tue May 4 04:00:10 2010 +0000 "New version number v230" commit 4fe41426ee97af8a87dbdf85538c245ec4caaa20 Author: galt Date: Tue May 4 03:59:27 2010 +0000 v230 final build commit 0e6658b35c4e5310d4f3692cb71d849b495c1bba Author: angie Date: Tue May 4 00:03:28 2010 +0000 bedPrintPos: added setting bedNameLabel in case 'Item: ' doesn't sound right for a track. commit 9a6372297c352f0a3d1f20454b4a909585138dc8 Author: angie Date: Mon May 3 23:56:42 2010 +0000 bamCfgUi: added trackDb setting noColorTag to inhibit the option to color items by user-defined tag (n/a for most tracks including native tracks). commit d93e1104032e8580590480fe86ae9cc58554906d Author: markd Date: Mon May 3 23:47:06 2010 +0000 use bigint for file offsets commit 89876f84f37d8d93558e926a34253de6c0b343e5 Author: markd Date: Mon May 3 23:45:47 2010 +0000 fixed manic editing overwrite of file commit 651a70b187bee9cf7e0eac44b8eb65568ceb0e83 Author: vsmalladi Date: Mon May 3 21:22:32 2010 +0000 Updated SYDH TFBS: Control variable in factors. To make multiple dimesnions matrix 2x2 commit ebddf6b0928f3115e072beb7b16bc11c7341cf62 Author: vsmalladi Date: Mon May 3 21:21:31 2010 +0000 Add prelminary html files for SYDH TFBS track commit 950947d8a3dcfd83fb014b3f8c631a44656fa4f9 Author: vsmalladi Date: Mon May 3 21:20:13 2010 +0000 Add prelminary html files for HAIB TFBS track commit 959de746e8a133b13dcebfaa948c00b2c632cdf6 Author: cricket Date: Mon May 3 20:53:47 2010 +0000 I have added the tracks SYDH_TFBS and SYDH_Hist to the mm9/trackDb.enc.ra. Thedisplay for the Peaks is not working in SYDH_Hist. commit 2638066a1952fc7800706e3a43ffc591b4f4165e Author: chinhli Date: Mon May 3 20:51:20 2010 +0000 maf files done commit fd1c6a2c2c35f99f67d7d62d9bdb520f3ef46031 Author: galt Date: Mon May 3 20:25:57 2010 +0000 allow chainSelf non-split to work for other dbs too - trying to fix danRer6) commit 33232e58c2af7fae80ca08be50310ca48b538669 Author: aamp Date: Mon May 3 18:59:03 2010 +0000 Added MouseAtlas3 stuff. Tissue names will need to be abbreviated because they don't fit well in the browser. commit 96f8168b42d0ecd3b83cfda5a0ad44355f1bd807 Author: galt Date: Mon May 3 18:45:02 2010 +0000 removed duplicate clause commit 3b133da2e37177df5c27cf94e691635123b00a95 Author: tdreszer Date: Mon May 3 18:07:18 2010 +0000 Insignificant change to Yale input titles and commented out settings for filterComposite code commit 34494af6fc4a6191f7a995df87c69f1cb02e68b8 Author: tdreszer Date: Mon May 3 18:02:56 2010 +0000 Flo Pauli updated the methods. commit 2284927efacb63407fd60969f5b273d5dc71ada6 Author: braney Date: Mon May 3 17:22:11 2010 +0000 a little test program to test gif and png timing commit 0e0e14e021746f4daae7f1e3712117c65736a7b3 Author: katrina Date: Mon May 3 17:09:07 2010 +0000 changed link title of contact commit 4ba567684ff44db5ebb0341dbe2ebe7895dc7b31 Author: galt Date: Mon May 3 15:00:07 2010 +0000 "Encode release log update" commit 55f805d9a35887c717573d436b6fe124242b462e Author: galt Date: Mon May 3 15:00:04 2010 +0000 "Release log update" commit a8cf787cf672fbaa645251e5b83af8c3361c226e Author: galt Date: Sun May 2 15:00:07 2010 +0000 "Encode release log update" commit fa950115261fce0ca95d33e5fd8972856d6801f4 Author: galt Date: Sun May 2 15:00:04 2010 +0000 "Release log update" commit cfa00a0a7b7d9993680a93aa94d35b89e58d9e13 Author: hartera Date: Sat May 1 18:42:00 2010 +0000 Added corrected files for crgMapability subtracks of Mapability track. commit 135ffd6ef1280e562830fa0e687c5ab38800b2a4 Author: galt Date: Sat May 1 15:00:06 2010 +0000 "Encode release log update" commit a8b5b90a74493f7fc02af0a8ba2bdcf7d4265246 Author: galt Date: Sat May 1 15:00:04 2010 +0000 "Release log update" commit cf0110841f9fe51a32ac067e084bc0cfd74e0636 Author: markd Date: Sat May 1 04:44:16 2010 +0000 include link back to browser in tables of PSL. also fix corner case on PAR were link to wrong chrom commit 8368d1bb2e10eb2805d5e080305c5658d826ead7 Author: markd Date: Sat May 1 02:11:06 2010 +0000 enabled indel display controls for BAM tracks commit aae983497ffa896aa6216fca0460c699d163b2a1 Author: rhead Date: Fri Apr 30 23:54:51 2010 +0000 Turning on fr1 by default in the conservation track. commit 50fd457a2c6adb583fb0edc3de6b7f5786e96d41 Author: braney Date: Fri Apr 30 21:24:50 2010 +0000 add links out of gencode track to yale pseudogenes commit ad9f1c597b7781ad4fb6ec89aade77a0e1611962 Author: braney Date: Fri Apr 30 21:23:59 2010 +0000 add yaleGencodeAssoc commit e364051fe0f27503a2d8b355c53fe4ce439ff903 Author: braney Date: Fri Apr 30 21:23:38 2010 +0000 files to describe and load table that maps gencode id's to yale pseudogene id's commit d6b4f92964e3523a3bba5125987bf6bede3baa13 Author: braney Date: Fri Apr 30 21:22:31 2010 +0000 yale pseudogene association with gencode ids commit 628940a6b783c3ba853045dff9c269493bb8a132 Author: chinhli Date: Fri Apr 30 21:17:30 2010 +0000 run doRecipBest.pl for felCatV17e commit 56d0669c87a0a13432ed640b164218cacac038ff Author: vsmalladi Date: Fri Apr 30 21:17:11 2010 +0000 Updated HAIB TFBS track with default track view selected. commit 0ecfd34cb28c1c31773f4031b23c947dedb45409 Author: braney Date: Fri Apr 30 20:46:06 2010 +0000 some label changes for RRBS. Some data for link out for Yale pseudo in gencode commit fda30d40ab27bd1de19c7c49ab21941026a3c557 Author: vsmalladi Date: Fri Apr 30 20:37:17 2010 +0000 Intial display of Sydh Chip-seq with default track view selected(Tier 1 cells) commit 5579ce1741c6683223fb45c23f09a6b7a42b097d Author: bsuh Date: Fri Apr 30 19:57:34 2010 +0000 Added -maxRow command line option commit 16c1ddf82b0feb8ddbd0ef1cb06ed6745db8d0ab Author: hartera Date: Fri Apr 30 18:45:00 2010 +0000 Documented adding updated data for CRG Mapability track. commit 96404fb658f7197feaed472bdc626c7e30cd6924 Author: kent Date: Fri Apr 30 17:08:46 2010 +0000 Making it actually render BigWigs commit 40be69015adb9109aa3e56d426855329021c4434 Author: tdreszer Date: Fri Apr 30 15:25:54 2010 +0000 Forgot to check this one in for Farnham commit 3b9895084f5da594b45c8be246a4140c4debd3da Author: galt Date: Fri Apr 30 15:00:06 2010 +0000 "Encode release log update" commit 154df6b4201114e075f5de303c8cf4e9b7c9597c Author: galt Date: Fri Apr 30 15:00:03 2010 +0000 "Release log update" commit ed2220f2bcd73134161d7c8065ededb0e600519c Author: tdreszer Date: Fri Apr 30 00:27:21 2010 +0000 Support for javascript to tie view level and subtrack level controls together in hgTrackUi commit f4c396198f02fe2998c9509b16ff945a553310d6 Author: tdreszer Date: Fri Apr 30 00:24:27 2010 +0000 Added a couple of functions to determine the viewName for a view level track or a subtrack commit c233d655d4ffba9a152a3c368b4d2cbed54f3ead Author: rhead Date: Thu Apr 29 23:49:49 2010 +0000 Turning on K562 cells by default in the UW DNase DGF track. commit ea20ce0eaa8e39af09e8275f19bca35bf4683668 Author: tdreszer Date: Thu Apr 29 23:39:53 2010 +0000 Located bug in freeing memeory never allocated. commit c2e4302110170bc3f895a08105ea7b985e114d6c Author: braney Date: Thu Apr 29 23:38:50 2010 +0000 first pass at BAM sequence validation. Only supports alignments with no indels or trimming. commit 0f41bd9c918d1a1cdf4582e364dee5b9ec8ac59b Author: markd Date: Thu Apr 29 22:57:04 2010 +0000 attempt to preserve modification times on files commit b46d94c4cb3095d3c587157337e9a657cc51b5e0 Author: markd Date: Thu Apr 29 22:55:43 2010 +0000 added file not in CVS commit fe2b692525a1d11b84ea52a0e409af5c0ff150c7 Author: kent Date: Thu Apr 29 22:42:27 2010 +0000 A testing area for rgba graphics stuff. commit e626eee7afc1698cf5fb2e26d9266075fadcdd62 Author: kent Date: Thu Apr 29 20:52:47 2010 +0000 Making a clusterer just for Chromia. commit f1f3b115445d07a8408bade21e03aeecb92be7f7 Author: antonio Date: Thu Apr 29 19:58:44 2010 +0000 adding some things to tablesIgnored and removing redundantentries commit d69394cf3f7e97aa6fddf645c774ff4587014ffb Author: vanessa Date: Thu Apr 29 18:52:39 2010 +0000 replaced released alpha w/ release alpha,beta commit ea5f3f8489b26e77ea7a929601b083e8de04e90f Author: hiram Date: Thu Apr 29 18:11:59 2010 +0000 warn_unused_result mentioned commit 215dc2146246a2e29abdce5d759bec1b6e74d6b0 Author: tdreszer Date: Thu Apr 29 17:44:10 2010 +0000 Extended release notes and changed contact. commit 2d29016dffdb55e69a8cc0757b8119025b45e7b0 Author: antonio Date: Thu Apr 29 17:06:33 2010 +0000 fixing db mistake commit dbb4ef743593d4b80bdc4fecdbdf3139cd0452b4 Author: mary Date: Thu Apr 29 16:42:26 2010 +0000 removing stanzas that put human mRNAs and Ests in native chimp tracks for genbank commit f68400f28af94a9a386cd754f142f84f65753516 Author: galt Date: Thu Apr 29 15:00:07 2010 +0000 "Encode release log update" commit ed9992a474a95d048be8c3d9553e012b7e701173 Author: galt Date: Thu Apr 29 15:00:04 2010 +0000 "Release log update" commit 98e762ead9e13b82738c8b4fd2a499be8c6ff231 Author: markd Date: Thu Apr 29 03:40:22 2010 +0000 fixed invalid autoSql that prevented descriptions from being displayed commit 3960a8edc18269465eb2204edf19caf29d58061a Author: markd Date: Thu Apr 29 03:15:15 2010 +0000 fixed incorrect documentation commit 525e1756d66b1016048e46c8a5da17ca6c8fb6c4 Author: larrym Date: Thu Apr 29 02:56:41 2010 +0000 make gene a link to geneSearchBox.html commit c8a59dec0d112093fdaedb65cb9235c59a8c2599 Author: mary Date: Thu Apr 29 01:23:50 2010 +0000 adjusting message about checking the matrix, chainMinScore and chainLinearGap commit fdc99b088ee5bee2a616e26daa97eb318f0f3add Author: hiram Date: Wed Apr 28 23:16:15 2010 +0000 show how splitMaf is created commit c2cccedd37bca9e5ee190bf2ccd2ce97fdf663e0 Author: braney Date: Wed Apr 28 23:14:08 2010 +0000 add support for bigWig's to put min and max in trackDb file commit ea4fd4c6a8d04dd43f3987a752f40b65615edf75 Author: braney Date: Wed Apr 28 22:56:25 2010 +0000 add minMax option for the ENCODE validator to use commit 52497ccb226912408143782614c9a6a3fc3b420d Author: hartera Date: Wed Apr 28 22:35:21 2010 +0000 Minor edits. commit 35a42f4d7cf038024ce89da055d8d0c60f6ef731 Author: hartera Date: Wed Apr 28 22:32:49 2010 +0000 Documented adding updated data for CRG Mapability track. commit baba5324f48f69698318ad91c5e204983610223d Author: braney Date: Wed Apr 28 22:08:04 2010 +0000 add Tullius commit d3a556bc2f0e5e106d03eb3e6ef4740ee665ef07 Author: bristor Date: Wed Apr 28 22:07:49 2010 +0000 Use 'cartRemove' instead of 'cartSetBoolean' commit d69f8ff55a1d98329530be930a49d852a229e680 Author: larrym Date: Wed Apr 28 21:20:00 2010 +0000 image used for context menus commit 66cc62f44a3b0e55de06de8354f3071a4151f1a3 Author: vsmalladi Date: Wed Apr 28 20:59:18 2010 +0000 IRF-1 to IRF1 commit a38e4fb6a27368f38eb99729dccfdbbcb8b04bb8 Author: krish Date: Wed Apr 28 20:54:07 2010 +0000 updated change notes commit 04880bd4762e79bc8dfff07066b4e70b1980ac64 Author: mary Date: Wed Apr 28 20:37:30 2010 +0000 removing unecessary html files previous used by genbank tracks to have both chimp and human mRNAs be treated as native chimp ones commit f20a76f725262e59970bbe1347bd61d525c2e3ff Author: tdreszer Date: Wed Apr 28 20:32:42 2010 +0000 Removed some misleading 'type' vars from Haib Tfbs commit 744def26ae8fee9fb7ec7228165070123e912632 Author: markd Date: Wed Apr 28 19:55:51 2010 +0000 update schema doc commit f8938c21523034dfe45bcc77703ea68bd59b246f Author: markd Date: Wed Apr 28 19:55:24 2010 +0000 added gbStatus schema doc commit 6b66be4c6f19fca2139f589289f41c796e2e9fa7 Author: markd Date: Wed Apr 28 19:12:17 2010 +0000 bad tandem dup example commit dde55a119524ba35b1e178c5d8f4b827b3fe52c6 Author: rhead Date: Wed Apr 28 18:56:32 2010 +0000 Changed cell culture protocols link. commit 9d30dacbd9bce1596bfcf33da6c76d06884070f4 Author: braney Date: Wed Apr 28 18:28:48 2010 +0000 add oryCun2 to Human Protein tracks commit 1a279e270b71ab31219df559b4bfc64c73ea6e6b Author: braney Date: Wed Apr 28 18:27:40 2010 +0000 Human Proteins commit fb9b37ba6aad3861ea2a3e25af430d9e63a6bb41 Author: cline Date: Wed Apr 28 18:11:11 2010 +0000 Moved the Ccnt2 antibody entry to uppercase (CCNT2) commit 8187e575e2bc7ac5faf852480c1fd90643cc4bc0 Author: antonio Date: Wed Apr 28 18:00:01 2010 +0000 adding felCatV17e to list commit 7a8fa6d9f163041aded39dedd7ad92dd0f933498 Author: galt Date: Wed Apr 28 17:42:53 2010 +0000 solaris patch for problem reported by user - getPid returns pid_t which is defined as long on solaris - but recommended to cast to int for use with printf commit 8f8bffc7cefa9c21a0620b4412edeadf2749aac0 Author: mary Date: Wed Apr 28 17:40:30 2010 +0000 removing stanzas to keep panTro1 genbank tables different on RR from beta (updating panTro1 to not have human RefSeq genes as native chimp) commit 09026b814927a1e5d767251a4f59d1c58c391704 Author: kent Date: Wed Apr 28 16:44:28 2010 +0000 Improving error message when chromosome not in chrom.sizes file. commit dd04d8b952756eb9227d31bf3c7533f9ed0e867e Author: galt Date: Wed Apr 28 15:00:06 2010 +0000 "Encode release log update" commit 8dd789e7eb238a5ab9841d79ee253aa8840ac8cb Author: galt Date: Wed Apr 28 15:00:03 2010 +0000 "Release log update" commit ee82ace220680417d186acf13e3ee621cb3b58e3 Author: markd Date: Wed Apr 28 04:46:37 2010 +0000 Fixed incorrect calculation of CDS refactor commit 76203ef72658486fe9410366cec245749074a175 Author: markd Date: Wed Apr 28 02:06:45 2010 +0000 removed html related to chimp/human hack commit bb2df79942fbe99f5a8fbb8f87cf4c3e8cab32a5 Author: Galt Barber Date: Tue Apr 27 18:43:20 2010 -0700 fixed tiny bug - added check that h output file was actually open commit a99e3221acbfb3202647d31389fb1dabf757f70f Author: cline Date: Wed Apr 28 01:18:47 2010 +0000 Addd the missing targetId and targetUrl for TFIIB. commit e18eab8d2b1bec6af1deef15bda658ef8b8bf8f2 Author: cline Date: Wed Apr 28 01:14:09 2010 +0000 Added antibodies ERalpha(a) and ERalpha(b). Removed some extraneous whitespace on the targetId line for TFIIB. commit 42c7b65c402d5d9f45e8680928d7821502db015a Author: antonio Date: Wed Apr 28 00:52:45 2010 +0000 fixing spacing issues, reinserting makedoc info commit b7740cbaadaac4ccb7df649acb2dd9e0ca59afe2 Author: baertsch Date: Tue Apr 27 23:42:58 2010 +0000 updated description for retro track commit 0859b977c4eca83fb109aaa481e66d444ba8849f Author: braney Date: Tue Apr 27 23:31:41 2010 +0000 first pass at multiWiggle. This shouldn't change existing behavior. Add extTable to your bigWig trackDb to get two tables into one bigWig wiggle track. commit 6dcebd005cdfdb72916b540794e2da825f280021 Author: kate Date: Tue Apr 27 23:29:49 2010 +0000 Set up for use of an automated pipeline (ENCODE-like) for browser tracks commit ce303d4fd214fd7a8fb0ed98968df8d89ba2ea2a Author: kate Date: Tue Apr 27 23:25:21 2010 +0000 ENCODE-related data from Weng lab; trying out loading from a new browser pipeline commit d3b18a464d03d080e115e81a50b8f9bdc254731c Author: baertsch Date: Tue Apr 27 23:14:04 2010 +0000 move ucscRetroAli to top level commit 26e765a6ced84f60e1a1ea58727c020c13f9e2b7 Author: baertsch Date: Tue Apr 27 23:10:29 2010 +0000 move ucscRetroAli.html to top level commit 7fd55124ed236f77e2088d1f069a384471fa3022 Author: baertsch Date: Tue Apr 27 23:07:56 2010 +0000 fix bug with non human retros, reference ucscRetroSeq instead of gbCdnaInfo for sequence data, to handle different versions commit 598d3e37738e8ca8f782a99224cdc656a63f8fa8 Author: tdreszer Date: Tue Apr 27 23:03:07 2010 +0000 Renamed mdb to metaDb commit 9e5192050a46fa4652ab5ef6681c14a280110b62 Author: baertsch Date: Tue Apr 27 23:01:09 2010 +0000 update retro track entry commit f016e450be78188772fe39d2be588e0f5cd74e4b Author: baertsch Date: Tue Apr 27 23:00:34 2010 +0000 add retro track description commit 6e29dda755baf17b52823f5f08b5ee1a40545796 Author: braney Date: Tue Apr 27 22:51:46 2010 +0000 add extTable commit fff58aebef5562d4332b9c8d924aaa393142db22 Author: tdreszer Date: Tue Apr 27 22:40:12 2010 +0000 Renamed mdb to metaDb commit 7287f83f6650101c37aa8011230c1d83d6d64afb Author: markd Date: Tue Apr 27 22:38:17 2010 +0000 removed human-as-chimp xeno refgene hack commit 90b4a73e704164a31b82f18484b9d845e97dee2a Author: tdreszer Date: Tue Apr 27 22:33:22 2010 +0000 Renamed mdb to metaDb commit 238e9081cfd75e745fb23ad06ac80b393430ba62 Author: tdreszer Date: Tue Apr 27 22:26:10 2010 +0000 Renaming mdb to metaDb commit 6a80d0ae5d646acfc3ae41bfa72c7b266814d382 Author: braney Date: Tue Apr 27 21:44:08 2010 +0000 add brTestPlus for test of multiWig commit 6a43c96cfd22b7e2a151887e3fae3d6a84548520 Author: antonio Date: Tue Apr 27 20:40:26 2010 +0000 some usage changes: removed clean, creates a single file. variable name clean up commit 7fb951aae22e8cf8a40778d9d83aee395d24e90d Author: markd Date: Tue Apr 27 20:28:28 2010 +0000 fixed breakage noticed by JK during code review commit ad0faf21f9855820e18d3101fe906f6592713045 Author: chinhli Date: Tue Apr 27 19:30:46 2010 +0000 blatz tasks commit e17a51a6af49aecccc236a04e3b33ad47f914422 Author: chinhli Date: Tue Apr 27 19:20:00 2010 +0000 Add multiz 6 ways support commit 39cba33a09a65e786eb2d88e4aa95b4e0487d7ce Author: tdreszer Date: Tue Apr 27 18:18:38 2010 +0000 Miss changing antibody from Pol2 to Pol2-4H8 commit 44325c32365676772dfcb12aa6187c8fc19c2247 Author: tdreszer Date: Tue Apr 27 18:07:35 2010 +0000 Krish found 2 fastq files conflicting between release1 and release2. The newer had been loaded with the wronng metadata. This is the correction. commit ca3eb86cc4363b7cd5e3fadce49c6c5d08832377 Author: kent Date: Tue Apr 27 17:33:48 2010 +0000 First cut of data agreement for ChIA-PET commit 93b644754571cd9538260fd3a60def3c1edc3abd Author: galt Date: Tue Apr 27 15:00:06 2010 +0000 "Encode release log update" commit 672bca732b0514b9809976ed14495a2ca343e25b Author: galt Date: Tue Apr 27 15:00:04 2010 +0000 "Release log update" commit cf63f68b42a6e31c06ab174c22419fb1db7811c2 Author: braney Date: Tue Apr 27 00:51:51 2010 +0000 starting human proteins commit c7f001ac2ca71bd39701f85b971de900b548fb99 Author: galt Date: Tue Apr 27 00:19:33 2010 +0000 v230 preview commit 0ea17d276d3bc3774cc3f4f7d1ade42a067ae683 Author: tdreszer Date: Tue Apr 27 00:17:23 2010 +0000 Added tooltip for each matrix cell, so moved 3rd state matrix CB hint to CB only. commit b55b75cc787f8b2421b40ebc5fdb2e1cc5ad124f Author: tdreszer Date: Tue Apr 27 00:16:09 2010 +0000 Removed not ready for prime time 'slant titles', 'hint cols and rows' and 'scrolling table'. Added tooltip for each matrix cell. commit 725d3398279dbcc41702bfe8b6159aea776b0118 Author: markd Date: Mon Apr 26 23:17:41 2010 +0000 removed hack put in because panTro2 treated human as native commit d618de3a5134e3321d602a842860de3a6971e15a Author: krish Date: Mon Apr 26 23:14:24 2010 +0000 added minGrayLevel 3 to the WU DGF track so everything isn't white commit 6518bf073ab467c286f76923b6cb6d7a927f90ab Author: antonio Date: Mon Apr 26 22:39:53 2010 +0000 rabbit release commit b0d0c1e9cc78cf14340f070d2bbc16d9103a03c2 Author: rhead Date: Mon Apr 26 22:29:53 2010 +0000 Added cellType=cell to wgEncodeUwDGF and wgEncodeUmasshaTfbsValid tracks to get the cell links on hgTrackUi to work. commit 0e7e52d59fcc3f7b688c8b623d267dffda9a80de Author: vsmalladi Date: Mon Apr 26 22:21:29 2010 +0000 Initial HaibTfbs composite check in commit 4e14545736ca159a0d973daa7fcf8521e564c6ec Author: vsmalladi Date: Mon Apr 26 22:19:36 2010 +0000 Initial Check In of HudsonAlpha commit ad12d744679194005f07fc72a166c4fdfc40609c Author: antonio Date: Mon Apr 26 21:46:19 2010 +0000 adding rabbit to genbank update commit 66a9030ee203696c2d746238b239e40c40d3aae6 Author: cline Date: Mon Apr 26 20:20:17 2010 +0000 Added some new antibodies commit 9dd3addabde6697b13b26187eec3355ac0be450d Author: bsuh Date: Mon Apr 26 19:23:21 2010 +0000 Changed parser so that name doesn't have to start with chr commit f8f7feca6d0b862db7f914c684cde369a10844b5 Author: mary Date: Mon Apr 26 18:24:56 2010 +0000 turning on genbank updates on hgwbeta for panTro1:2 commit fb22b46e7ba8b3db9059fc8349c6cbf2b54eee57 Author: mary Date: Mon Apr 26 18:24:06 2010 +0000 removing release beta for old version of genbank tables so that can stage new genbank tables on beta commit f202f1c3e3f99c6c15dc0ece9e2ebfcd0078bf43 Author: mary Date: Mon Apr 26 17:26:13 2010 +0000 removing release beta for old genbank tables so that can stage new genbank tracks on beta commit 0b27b93abebc24f2fa40a94bdfb8e6793d4b2758 Author: tdreszer Date: Mon Apr 26 17:03:31 2010 +0000 Fixed some minor wording and replaced an unknown with Percent Tags in Hotspots ~40pct commit 2eb848c3567a82c40256263a5c480d7364c0006e Author: vanessa Date: Mon Apr 26 16:31:49 2010 +0000 changed what the tr command was looking for and added warning text alerting the user that the path could be wrong commit d2931023b7f8ee9148d98a2a199c4117cbea7f6d Author: markd Date: Mon Apr 26 16:00:20 2010 +0000 added N-SCAN commit 6d153aa8dc55e15e7313b885eeb216a292152d59 Author: markd Date: Mon Apr 26 15:28:21 2010 +0000 removed stray junk commit 8a9b09ab6fef83820f6bcd93dfa73e6646d6d472 Author: galt Date: Mon Apr 26 15:00:06 2010 +0000 "Encode release log update" commit 8e278ab5155f00ee6d76600fcb5fab30ed48f1a7 Author: galt Date: Mon Apr 26 15:00:04 2010 +0000 "Release log update" commit 306a0414757283a6ecbd6e89d5bbdc3fd5f225ad Author: rhead Date: Mon Apr 26 04:11:58 2010 +0000 Several small wording changes, commented out footprint view, made references conform to PubMed citation format. commit ea60d6b1ca528eb9f725276bafca7ce1aea812e3 Author: markd Date: Sun Apr 25 17:46:51 2010 +0000 removed accidental committed change to label width. (who forgot to keep me honest) commit 7512506fd56e3ed918bcad29c7f8ba80209f5c60 Author: galt Date: Sun Apr 25 15:00:06 2010 +0000 "Encode release log update" commit fb50db642e0fa86d2715c859928aed7a0d3be9a3 Author: galt Date: Sun Apr 25 15:00:04 2010 +0000 "Release log update" commit d7ac993a9813de3bedd52ba9063b8928c1fdb78b Author: bsuh Date: Sat Apr 24 20:29:38 2010 +0000 File was flagged as have DOS carriage returns - filtered out via dos2unix commit acabee6d5c47b8d79a5df3284adbb3b755c9f148 Author: galt Date: Sat Apr 24 15:00:05 2010 +0000 "Encode release log update" commit e967655629f1d71033c8bcf299f17dec10053632 Author: galt Date: Sat Apr 24 15:00:03 2010 +0000 "Release log update" commit 6155f139440f8a3346261f60cf838dcf96509ae7 Author: tdreszer Date: Fri Apr 23 22:33:19 2010 +0000 Show plurals properly commit c19c6e4be4d21e6ef0893fd298eebea366795503 Author: vanessa Date: Fri Apr 23 21:55:57 2010 +0000 updated instructions on matrices commit bff0fd101a569ef27771c93f57de28b476fe645f Author: bsuh Date: Fri Apr 23 21:45:41 2010 +0000 Initial checkin of eland extended to SAM format converter written for Stanford Lab commit 6fc8d9f00b166f35f010257177a8d54d1d95a0ba Author: bsuh Date: Fri Apr 23 21:44:54 2010 +0000 More complicated eland extended data file I found off the web at http://nextgenseq.blogspot.com/2008/10/file-formats.html commit 7b3755d243c20526ded1b75dbda17069a7a4083b Author: bsuh Date: Fri Apr 23 21:43:04 2010 +0000 Sample eland extended file provided by pcayting@stanford.edu commit ff9952b48696204baf0358c5cab4e17b6575dac2 Author: mary Date: Fri Apr 23 20:47:27 2010 +0000 adding explanatory image to page commit 903339726280a5ba4e3e8330f64105ad2de4c6cf Author: sbenz Date: Fri Apr 23 20:46:29 2010 +0000 Added su2c generated data to end commit ec4b834c6d313068a9c5ed00d97c22b34d6b14f0 Author: tdreszer Date: Fri Apr 23 20:29:44 2010 +0000 Fixed labVersions with leading blank that were screwing up MAGIC commit d7c80734c1e9a1ea25b2ff62e54f29388f4729c6 Author: tdreszer Date: Fri Apr 23 19:51:32 2010 +0000 Extended setType and inputType to Open Chromatin commit d81c2e5812bd8565a1f277581d451cfc4748028c Author: tdreszer Date: Fri Apr 23 18:31:56 2010 +0000 Extended setType and inputType to UW Histones commit 7de32f05a08c6d48d4d33792c3fbd83834d31ad9 Author: mary Date: Fri Apr 23 17:54:01 2010 +0000 fixing include errors and improving text flow commit b014149b2dc83f9dfb5ad170ec7d98a61e419c23 Author: tdreszer Date: Fri Apr 23 17:52:28 2010 +0000 Extended setType and inputType to Broad commit d9bde8aaaabaf2ccc6aaa99fd0182627cf313b65 Author: mary Date: Fri Apr 23 17:48:14 2010 +0000 adding documention for new gene search box commit 4debe25dbd6cca808ad1038881c2a4ee60d7c08d Author: mary Date: Fri Apr 23 17:26:20 2010 +0000 changing color of MGC Genes to work with new indel display options commit 5b2fb6b47f5a8739106ba55d51d3b24a958b58a7 Author: tdreszer Date: Fri Apr 23 16:23:27 2010 +0000 Changed labeling of Yale/K562b/MNase/SETDB1 commit fdbc6e54014b41f7122e61cf6c68026e368eadca Author: tdreszer Date: Fri Apr 23 16:01:38 2010 +0000 Straightened out Yale K562/None/SETDB1/MNase at last commit 6101b2e584f4c8e1f696bf97a61af42b9227c73e Author: tdreszer Date: Fri Apr 23 15:58:26 2010 +0000 Making -ra the default resulted in erroneous usage message commit 337abe4f4f51440d3cac6d13a98595fd28cfc325 Author: galt Date: Fri Apr 23 15:00:06 2010 +0000 "Encode release log update" commit 84aa2791638f021cd7a98f591e502badf15f063b Author: galt Date: Fri Apr 23 15:00:03 2010 +0000 "Release log update" commit a163c49f664d346f872ff4fbde01edcaef350359 Author: galt Date: Fri Apr 23 04:20:19 2010 +0000 handling wiggle density better for sparse variableStep wiggles commit 5613cb5d140dc24e34a2a94e5d63c25e70953b01 Author: tdreszer Date: Fri Apr 23 02:56:21 2010 +0000 Made RA style the default output commit 55f6c42475c4541924005e66dd51eb7940074639 Author: tdreszer Date: Fri Apr 23 02:38:36 2010 +0000 Handle '#' comments more gracefully and include quotes in non-RA style printing commit a6df985c6804a5d3dcfb4e9244b7b880361cf3c8 Author: tdreszer Date: Fri Apr 23 00:34:18 2010 +0000 Adding Uw DGF metadata into mdb commit 6339c4ed9348313af1681248595e586c9a9c1400 Author: tdreszer Date: Fri Apr 23 00:30:14 2010 +0000 Adding Uw DNase metadata into mdb commit 1f6a70553153ca4438adb26497a6947e639adeb4 Author: tdreszer Date: Fri Apr 23 00:24:43 2010 +0000 Adding Uw Histone metadata into mdb commit d7bf7cea0e6433da90ceb6aa7f3ddeabec66befa Author: tdreszer Date: Thu Apr 22 23:35:05 2010 +0000 Added control term for Yale because it's experiments must be defined by 4 terms commit 05a21c0dd52883c36f8edeefa738285da322d248 Author: markd Date: Thu Apr 22 22:33:20 2010 +0000 Don't put xeno refseq link up to aligned organism browser if it doesn't have refseq enabled. commit 5c3d2b8dd3b56b39e201edffb5a5f1ca34e36db5 Author: mary Date: Thu Apr 22 22:08:48 2010 +0000 Make blue for query-insertion-at-end purple, so it is more easy to distinguish from green for polyA, essentially reverting back to r1.24 for hgTracks/cds.h commit dd7007d3c1ac6f1f1127edb5b4725a839adbb350 Author: antonio Date: Thu Apr 22 21:32:03 2010 +0000 fixing some spacing issues commit 898f00f81210eed01f2c315fa3b879a48ab64180 Author: tdreszer Date: Thu Apr 22 21:26:51 2010 +0000 Make mdb table queries go to the right db. commit 17d14c8c5fcb71dc7bd61edc08e4326151af7298 Author: ann Date: Thu Apr 22 21:26:46 2010 +0000 fixed typo (thanks Jen!) commit 3fbad17475a46d10d41fa22c5616b195723bd5c4 Author: tdreszer Date: Thu Apr 22 21:01:54 2010 +0000 Unlink bigWig gbdb files as well. commit 0b5f2da7d3b4496719969863a2c6cea2e158bf45 Author: tdreszer Date: Thu Apr 22 20:58:16 2010 +0000 Demoted 'input' to 'control' commit 22ea9e1ef34f1764b475798023e55275d25c8381 Author: tdreszer Date: Thu Apr 22 20:57:07 2010 +0000 Fixed a couple of bugs from the last checkin commit 570e5bffcc688235295cc5c518ab0ac0216962e2 Author: mary Date: Thu Apr 22 20:52:14 2010 +0000 changing documentation, inlcuding BLAT, back to purple commit 2a4d8b1405fa25bdf775c2a5233e135466d3c2f2 Author: antonio Date: Thu Apr 22 20:35:04 2010 +0000 changing searches commit 5e446c64538425db6ea09832a098f7aa8861eb5b Author: antonio Date: Thu Apr 22 20:34:33 2010 +0000 changing which rabbit track is in composite commit 539de61fd0ad08d1743db977ecb5d766dcf2f1ca Author: tdreszer Date: Thu Apr 22 19:56:50 2010 +0000 Added defaulting of setType and inputType which are needed for ChIPseq submissions. commit cd487550e538165e3e1c337dceffd9d35e024e5e Author: braney Date: Thu Apr 22 19:56:01 2010 +0000 fix up some problems commit 1947af9ea5d29d835e65ecd2e23d341e4ed38aba Author: braney Date: Thu Apr 22 19:53:01 2010 +0000 release1 notes commit f122f845a738fa06962ffe68d9b29e51d0617459 Author: kent Date: Thu Apr 22 19:35:38 2010 +0000 Refactoring font-for-size code so that Table Browser can reuse it, and thus not make an error message in correlation page. commit 223e083e6a4497c464164d4e273be150891d7b9d Author: bristor Date: Thu Apr 22 19:25:22 2010 +0000 Added support for integration between the table browser and GREAT. commit f716fc80f1a59cf58e923fd4888734ad9825756c Author: braney Date: Thu Apr 22 18:52:29 2010 +0000 add Clusters, make bam the alignment file type, only include fastq with read 1/2 commit 2543dc769dad10a6716f6e8974a0f185299143b9 Author: angie Date: Thu Apr 22 16:16:57 2010 +0000 Link to hgBaseLabel.html for coloring help for tracks with sequence but no CDS info. commit 2acfcb012363ec25f1b908a2698cab5c2dfcb89a Author: galt Date: Thu Apr 22 15:00:05 2010 +0000 "Encode release log update" commit 5505fd40819b30ae7ad3c9750fc68e7b47f030ad Author: galt Date: Thu Apr 22 15:00:03 2010 +0000 "Release log update" commit 1c1611038c532c8215748d8afc912c0f0302a8d2 Author: cline Date: Thu Apr 22 01:36:35 2010 +0000 removed hg19 from vgTextDbs, for consistency with the comment commit 45e2f9d26e3557b0e986fca2286f6701daf95401 Author: cline Date: Thu Apr 22 00:08:36 2010 +0000 - incremented curVer and lastVer - replaced proteins09(something) with proteins100331 - added hg19 to vgTextDbs - moved the brackets to start executing the first step commit 8e2bd4a9f8a0a8659826a0f64503374966d7f678 Author: cline Date: Wed Apr 21 23:22:12 2010 +0000 First stab at setting up the script to build version 13 of human ucscGenes (on hg19) commit b5710fc0722319486d663b04b6617f576f770948 Author: chinhli Date: Wed Apr 21 20:57:24 2010 +0000 Add sno/,iRNA track commit e3fcd719a34e53a0ac33447a74ff3aeb7ee31d03 Author: tdreszer Date: Wed Apr 21 20:34:31 2010 +0000 Change ENCODCE metdata sort order. Initial check in of both Slant cols and hint cols and rows (both ifdefed out for now). commit 468c08647a7990baa677ceaf59f6159a0e3049ad Author: tdreszer Date: Wed Apr 21 20:29:40 2010 +0000 Initial definition of .slantUp,.slantDn,.hintCol,.hintRow classes commit 569550bc872ea794135a2cf8f8b6df9f90ff93b8 Author: hiram Date: Wed Apr 21 19:32:43 2010 +0000 avoid URL refereces to NCBI for gold and ctgPos2 names they mean nothing there commit 1ac3dc4196cba36bd1a5f7c531f11f16a1e727b1 Author: tdreszer Date: Wed Apr 21 19:31:19 2010 +0000 Changed the sort order once again to handle setType and inputType commit 14ea44d1a602be8660b382fe52bf7e9453c2c473 Author: tdreszer Date: Wed Apr 21 19:28:07 2010 +0000 Added setType and inputType to allowable ddf terms commit c00ecf44aa522a6cad5a39805e9f1f295e83be9c Author: galt Date: Wed Apr 21 19:25:40 2010 +0000 needed to keep setBbiViewLimits() inside the error-trapped block, otherwise get SIGSEGV now if bigDataUrl invalid commit 75046b8e9f695346a3a86675706507772ccae016 Author: galt Date: Wed Apr 21 19:23:47 2010 +0000 Tolerate double-slash in path commit ef3be7fceff3ffdf35787c8fd4194829998e4c1e Author: hiram Date: Wed Apr 21 19:22:27 2010 +0000 adding lastz oryCun2 to monDom5 and cavPor3 and mm9 swap to oryCun2 commit b1ceb979f5f5b402e1f327935cee09b1b5b2ee4a Author: tdreszer Date: Wed Apr 21 19:18:52 2010 +0000 Back to the roundly hated, rudely arcane and vulgarly capitalized wgEncode prefix. commit 10eb59da5fcf6a606824236275dd84feb090ce47 Author: tdreszer Date: Wed Apr 21 19:08:29 2010 +0000 Added setType and inputType ddf fields commit 3dfdc1b73dd8c273c0a3c55540b42c62f176b9d0 Author: tdreszer Date: Wed Apr 21 19:07:09 2010 +0000 Chaged input:yes/no to setType:input/exp commit 50382c709952e09af5a9b39efcd1c40894be74f0 Author: tdreszer Date: Wed Apr 21 18:57:32 2010 +0000 Unloader can now handle bigWigs commit 23bab20aefcfba7f7250ef08aa60333383f8e7c4 Author: tdreszer Date: Wed Apr 21 17:56:36 2010 +0000 First mm9 ENCODE track added and metadata commit 4a0a94e395a35d37567b9467786dff3de607ae2f Author: tdreszer Date: Wed Apr 21 17:55:56 2010 +0000 First mm9 ENCODE track added (included) commit 984f00d01093f0c2eefb8bf26da1724269419f88 Author: tdreszer Date: Wed Apr 21 17:54:43 2010 +0000 First mm9 ENCODE track added commit a96bc352301c3e953c708d2a9bc6681bfd40e7c8 Author: braney Date: Wed Apr 21 17:50:09 2010 +0000 notes for release1 commit 940297125f78f9b22c51ae74b920b877c6fe8261 Author: galt Date: Wed Apr 21 15:00:12 2010 +0000 "Encode release log update" commit 952de40421844a21b5b7a8aeff4049cb75055373 Author: galt Date: Wed Apr 21 15:00:09 2010 +0000 "Release log update" commit 8177c87f3b4af9bb84be110d6e422c5ce8f90651 Author: braney Date: Wed Apr 21 13:15:15 2010 +0000 take out "Map Algorithm" commit f99eb5eac0dc827364858f9619bd924b715e7793 Author: kent Date: Wed Apr 21 11:42:30 2010 +0000 First cut of training sets for k562 enhancer prepared with makeItem track by Jim. commit a7acf9fa3ceb5af2631cd33bf48d9497a72d43b9 Author: tdreszer Date: Tue Apr 20 23:56:29 2010 +0000 added inputType into the sort order commit 511d27ff42fdaa223fc8a419a22ae192f2bb7e31 Author: tdreszer Date: Tue Apr 20 23:40:27 2010 +0000 Fixed Yale Inputs to match the HAIB model allowing pairing of exp.inputType = inp.inputType commit d71283c873c230c5dedcbcc0f9157c5ed7771aef Author: braney Date: Tue Apr 20 23:16:24 2010 +0000 make hudsonalphaRnaSeq a separate include file commit 4e33727b1b13bd512f81c2a6b0097eb89ea078ac Author: braney Date: Tue Apr 20 22:47:56 2010 +0000 changed long labels from "No Treatment" to w/None commit a7a1478745749f11b0be4a43fc58d02a30402c52 Author: vanessa Date: Tue Apr 20 22:42:16 2010 +0000 changed matrix for rheMac2 commit 99152a2f5a33930998d66de119810dd67bb43cb6 Author: braney Date: Tue Apr 20 22:04:21 2010 +0000 add info about files.txt and md5sum to preamble commit c45ee350de5c2370638796b452d67360846c6595 Author: braney Date: Tue Apr 20 21:48:09 2010 +0000 fix long labels commit 1cfe8f1d6297bde7c3352986fcec63835ea1763a Author: rhead Date: Tue Apr 20 21:22:29 2010 +0000 Removing link to ENCODE/modENCODE usability survey. commit 80473c5fad1fba556525cc3cffb05d72ee7be172 Author: tdreszer Date: Tue Apr 20 20:40:04 2010 +0000 Fixed Haib Inputs further by adding inputType variable allowing pairing of exp.inputType = inp.inputType commit ddb4c167563dbf37f421b5d31e9efa85ec078cbb Author: antonio Date: Tue Apr 20 19:29:13 2010 +0000 small change to searches commit 825078357c531620b942e95a8c6637d11d2a258b Author: antonio Date: Tue Apr 20 19:22:35 2010 +0000 small change to searches commit 42853e6eaa297d4b05a539e70e82ae3b3cdadb07 Author: tdreszer Date: Tue Apr 20 18:59:25 2010 +0000 Fixed Haib Inputs (I hope) commit 049bd99b90474875be4f2819a28644bcb9e62c30 Author: braney Date: Tue Apr 20 18:51:10 2010 +0000 small change commit 9c9a61f1bc9ecbe7f021dd4702019791f94f4fd3 Author: braney Date: Tue Apr 20 18:46:38 2010 +0000 make into HTML commit 8713fe3ea1121573fb4a7e27d05c2646d5399a55 Author: braney Date: Tue Apr 20 18:35:45 2010 +0000 first pass commit 078410d985f1c95bb191afd9e5cf7aa2c52bf229 Author: braney Date: Tue Apr 20 18:30:19 2010 +0000 fix up long labels commit 754cc0af401f9e6a1883742ff2f4dbcb9341f875 Author: braney Date: Tue Apr 20 18:14:44 2010 +0000 some edits commit 0acfce655628825e45caf17b13bb3ffc425f4151 Author: braney Date: Tue Apr 20 17:59:29 2010 +0000 use our standard RNA-seq commit 99dc37f37ebcd4c1c1e8119108900752594a1107 Author: braney Date: Tue Apr 20 17:50:44 2010 +0000 make long labels fit in 80 chars commit a9d52526bfcd27e95fa158fdde28c9a258de355e Author: angie Date: Tue Apr 20 17:39:22 2010 +0000 Added codingAnnoLabel_snp131CodingDbSnp (thanks Ann). commit d16848dc1c6bde857ec9fa2edd37dea5f4689ca7 Author: braney Date: Tue Apr 20 17:36:12 2010 +0000 separate it out commit 399ed7c262604d51a37f8ef0073ff45a6922fa08 Author: chinhli Date: Tue Apr 20 17:34:31 2010 +0000 Finished lastz with Sheep oviAri1 commit 8d20147d2737f611bd800959898dee48a58057a3 Author: braney Date: Tue Apr 20 16:58:44 2010 +0000 notes for relase1 commit 4af9e329c008a35de504a286e08c100d8691c0d6 Author: markd Date: Tue Apr 20 15:56:50 2010 +0000 made parameter name C++ friendly commit e36ac1c7cf0e0df348610526dc6f3e3bce7e9316 Author: galt Date: Tue Apr 20 15:00:06 2010 +0000 "Encode release log update" commit daeab575b7e5621624cfd85e690ec57350818351 Author: galt Date: Tue Apr 20 15:00:03 2010 +0000 "Release log update" commit 28dc384905822997aad83f13e40889586027f85d Author: krish Date: Tue Apr 20 08:12:27 2010 +0000 off by one error commit 7f230f2239fb400a6053b7969a872ddc1c3d02ef Author: krish Date: Tue Apr 20 02:43:31 2010 +0000 changed expVar.ra read to get list for given track commit 4fa80b4b23758a7e215c096a3e0376abced46101 Author: krish Date: Tue Apr 20 01:42:20 2010 +0000 added support for expVar.ra file commit d63dce216df252f8607a099ad7af5b55b497e116 Author: galt Date: Tue Apr 20 01:14:44 2010 +0000 "New version number v229" commit 8dac2bb5ff73bcd2a373fa90d0cad04de3ebdd7a Author: galt Date: Tue Apr 20 01:14:14 2010 +0000 v229 final build commit 63c2d61b2fc206030ee429c09883fc4975af4fb9 Author: braney Date: Tue Apr 20 01:06:03 2010 +0000 add Human Proteins to ailMel1 commit ee7a3e1fa425697313ca1a363b4f33426f76a4e3 Author: braney Date: Tue Apr 20 00:06:17 2010 +0000 added Human Proteins commit f5cd1540905330ea47145fcef09ca2261e1b3a05 Author: antonio Date: Mon Apr 19 23:56:04 2010 +0000 adding oryCun2 commit 860070fde589318d9e71f949ea3d49f5a156a2cb Author: markd Date: Mon Apr 19 23:18:40 2010 +0000 fixed bug were target name index was not created if bin was not created commit 9624a534de573913443065b00c7383b83147b89a Author: braney Date: Mon Apr 19 22:04:45 2010 +0000 change labels in response to Flo commit eab5ce6e975cfbfbda89bd9e4f7be577212ad637 Author: hartera Date: Mon Apr 19 21:44:04 2010 +0000 corrected typo. commit ae955a614eef7f570fd9cc3cc290f568a94497eb Author: braney Date: Mon Apr 19 20:59:07 2010 +0000 add 14 Rrbs tracks commit d22fce32137db801555623dd971fcff0ca3e6746 Author: kent Date: Mon Apr 19 20:46:31 2010 +0000 Removed some debugging. commit b2e2a12ab8bf24873188d4e86bae7b1e4d50162e Author: tdreszer Date: Mon Apr 19 20:20:43 2010 +0000 Fixed indent and quotations commit e7bf9d6627cabfc4d245b8d7c331781aed3241d2 Author: tdreszer Date: Mon Apr 19 20:17:34 2010 +0000 Fixed indenting and quotations commit 91deb05cd40288b7d48669ab581bc9681a22cdb1 Author: tdreszer Date: Mon Apr 19 19:03:42 2010 +0000 Fixed ra indenting and quatation marks commit 099b425a32294fb3ba4ceb5bc59b074719fc2bcb Author: tdreszer Date: Mon Apr 19 18:57:45 2010 +0000 Fixed ra file indenting. commit c404e6a5e6099fa0c0927c80abcb2411ab9c22c2 Author: tdreszer Date: Mon Apr 19 18:56:48 2010 +0000 Fix ra file indenting commit fa0c4a92bfe258326b615c595d121a70ed8a243e Author: hiram Date: Mon Apr 19 17:58:34 2010 +0000 add ctgPos2 and intronEst to the tablesIgnored list commit 229502720f22f2b6dae51a2f92174eaad26546c8 Author: braney Date: Mon Apr 19 17:48:35 2010 +0000 set new default visibilities commit cdab80d1239dbf66661bf87449a77b37b6d9a1a8 Author: braney Date: Mon Apr 19 17:36:44 2010 +0000 change tabs to 8 spaces commit 9b779ffe000a1f6908f42e16d2c8de555ab476a0 Author: braney Date: Mon Apr 19 17:23:24 2010 +0000 more metadata and short label fixups. Will I ever be through? commit 31721ef030a51af1d96fb96baf9026e7d4164790 Author: braney Date: Mon Apr 19 17:03:46 2010 +0000 oops added tscan by mistake commit 9af70aecaa6f0f163cbadb5f5f8100e1fdf12e00 Author: braney Date: Mon Apr 19 17:03:05 2010 +0000 starting Human Proteins commit bc9c8ebcf07d814701313651780c260de08accfd Author: braney Date: Mon Apr 19 16:59:08 2010 +0000 change type=wig to type=bedGraph commit 000b7069d7ad4072d4c5375aa864122c4a49f074 Author: tdreszer Date: Mon Apr 19 16:55:52 2010 +0000 Fix names in a reference commit 194ecd855f730c826d97cbe3e5fb1395bdc20474 Author: tdreszer Date: Mon Apr 19 16:24:22 2010 +0000 Limit to 800px, because the massive matrix makes everything too wide. commit 40f5921369110c43894468e4bb70dee666eb6208 Author: tdreszer Date: Mon Apr 19 16:23:28 2010 +0000 Finally have the RNA doc from Yale commit 207ee52b8b91bbef35fd21399a4cda68b821dab0 Author: chinhli Date: Mon Apr 19 16:04:15 2010 +0000 Added oviAri1 - Sheep commit a7ac095c62b2d281e2456d333321edb3c8338c44 Author: galt Date: Mon Apr 19 15:00:06 2010 +0000 "Encode release log update" commit e4d20ed49545693e44eaa4dc4d50a8e85ec8691b Author: galt Date: Mon Apr 19 15:00:04 2010 +0000 "Release log update" commit 036dbcb006f29943a070fdb49fe6d85f06ae05b6 Author: markd Date: Mon Apr 19 04:36:38 2010 +0000 add N-SCAN to susScr2 commit 0a3612c36fdb7ca8aa555be81469e04e50ae8664 Author: galt Date: Sun Apr 18 15:00:02 2010 +0000 "Encode release log update" commit 8ccc0dcbaa385866804ff9993470ad2681bc6277 Author: galt Date: Sun Apr 18 15:00:01 2010 +0000 "Release log update" commit 5e3a2086d7600d35a1e71747e9fc86bc85d53323 Author: krish Date: Sun Apr 18 09:37:14 2010 +0000 more progress commit ccb5556ce6ed70bfa8134c31f9b5e268258dda42 Author: cszeto Date: Sat Apr 17 16:41:39 2010 +0000 Removed conflict markers commit 716101e2a79190897762d6255728c7ea13ce86d8 Author: galt Date: Sat Apr 17 15:00:06 2010 +0000 "Encode release log update" commit f86e2aa5eee2650e90848692b8bb5f5e86f1f5fa Author: galt Date: Sat Apr 17 15:00:03 2010 +0000 "Release log update" commit 141ade57d6e88be8a77a409294b5bc901432f6ad Author: krish Date: Sat Apr 17 04:37:57 2010 +0000 program to make package to send to GEO commit 93cc5a54f1a449cfe03d76938dbe4e17d262170b Author: braney Date: Fri Apr 16 23:27:56 2010 +0000 add a little description for the various views commit fc7ba539dc122d3c89d7e7ea358719b521aa6995 Author: braney Date: Fri Apr 16 23:10:32 2010 +0000 more labels commit e239bbca2c08f827b351d48d5b99e7bb4cde9fdb Author: braney Date: Fri Apr 16 23:02:29 2010 +0000 more labels commit d7a27d092bb3bf53075a509db70f0cc01de1f223 Author: braney Date: Fri Apr 16 22:50:45 2010 +0000 some long labels commit 2cf1d6c1112dc1f3bb9f5227661e54e6f7c34def Author: braney Date: Fri Apr 16 22:13:37 2010 +0000 fix up short labels commit 6dedf4b844acbb7da0ac15219e553a1826bf5447 Author: braney Date: Fri Apr 16 21:44:44 2010 +0000 remove table that doesn't exist commit 5aa49ded997d60bb97b43019f08157b30b46118d Author: angie Date: Fri Apr 16 20:58:58 2010 +0000 Change example file in liftOver/README.txt to be ToHg19 (was ToHg18). commit 9fbb75bdd50c4e083953f40be928011ec0273989 Author: braney Date: Fri Apr 16 20:57:11 2010 +0000 change some metadata from longPolyA+ to total commit c1c748512b544f40aa0afd6c21d94fd810429623 Author: antonio Date: Fri Apr 16 20:05:47 2010 +0000 panda release commit efc7f74629c8104b0c0a9063bd21d96e03be98f0 Author: galt Date: Fri Apr 16 19:05:01 2010 +0000 adding antonio to the list of auto-locking users as requested commit 135bdf85637ba917dffdb9ea05bd8b94e7a3d382 Author: antonio Date: Fri Apr 16 18:18:46 2010 +0000 changing citation commit 29e7dcc755385a6d12dd352d653ce9eccacf43fd Author: braney Date: Fri Apr 16 18:10:36 2010 +0000 fix a long label commit f343ccd6d8c50327784ed293d15b07838f2ddb71 Author: jsanborn Date: Fri Apr 16 17:59:22 2010 +0000 added cancer browser options for other servers commit a2bfc1d9078332d1052ff66f0027ea9dce1ae22c Author: antonio Date: Fri Apr 16 17:56:56 2010 +0000 genbank updates for panda commit a54224f8a74934627a3460717522670a9db2176c Author: cline Date: Fri Apr 16 17:47:11 2010 +0000 Added Terry Furey's email address commit 8a4de687a585772f2ff4017948451738b8840f51 Author: angie Date: Fri Apr 16 17:47:00 2010 +0000 Added snp131OrthoPt2Pa2Rm2 (mappings to other primate reference assemblies). commit 9476c93e9f8d6d385a3e32c38958a80839bdb30b Author: angie Date: Fri Apr 16 17:36:22 2010 +0000 Adding override settings for snp131. commit 6cb4e5b39838a9b05ab6cfa356ce1d2e33780e15 Author: angie Date: Fri Apr 16 17:36:01 2010 +0000 Adding snp131. commit b8b49eb5b82d73e8a8936ad9451adac132a9199a Author: markd Date: Fri Apr 16 17:32:13 2010 +0000 add options to convert TBLASTN to codon nucleotide/nucleotide coordinates, fixed bug with tStart/tEnd extending beyond actual range commit 67c9e277927331463de141d5fca350cc9684c719 Author: hiram Date: Fri Apr 16 17:25:05 2010 +0000 add swap mention for human, dog, rat commit f29dd5593b003ccc1aeeebcb413cbd64ea24b84d Author: markd Date: Fri Apr 16 17:23:43 2010 +0000 have pslCheck catch overall ranges that don't match block ranges commit 893fc88d34dca2c08128b2c765d130c4e4a677fa Author: braney Date: Fri Apr 16 17:16:51 2010 +0000 release1 notes commit 4dfd3624a0e1a2230fb74be057fb44ffb01e8c67 Author: giardine Date: Fri Apr 16 16:58:35 2010 +0000 added new pgSnp tracks from 1000 genomes update commit 788555a63dc3281a260be54cba80d4ad296f53ff Author: braney Date: Fri Apr 16 16:57:18 2010 +0000 fix parentage of subTrack in GIS DNA commit 873d4e3a76101e3c93ce369c1d6e124bf47d209c Author: giardine Date: Fri Apr 16 16:50:59 2010 +0000 updated 1000 genomes data commit f6ab66553551417c4bdbe989f6b7963563ea1411 Author: chinhli Date: Fri Apr 16 15:22:11 2010 +0000 Add Sheep oviAri1 support commit 5c6811ad550b1960767e78196747be153938cff3 Author: chinhli Date: Fri Apr 16 15:19:38 2010 +0000 Finished felCat3 to felCatV17e liftOver commit f8a2e192fd11c034f51fe02ae01b5497fb57a35f Author: galt Date: Fri Apr 16 15:00:22 2010 +0000 "Encode release log update" commit fa9b1ef7a207cc2f8d622b433f60c1fee08619dc Author: galt Date: Fri Apr 16 15:00:19 2010 +0000 "Release log update" commit 66f1601f7ce19c1c90d24811dcf2edf1f9cf0b17 Author: chinhli Date: Thu Apr 15 23:37:48 2010 +0000 re-do the genbank task commit eb30f9e61e7265178e0e5f4724147bc8bc12023d Author: braney Date: Thu Apr 15 23:32:04 2010 +0000 Add a description for some missing views, and little more text commit b6adb489698dc3e5a868e5d001f1b052c7531fa8 Author: hiram Date: Thu Apr 15 23:19:35 2010 +0000 fixup off by one drawing bugs in wiggle graphs commit f62709bf0adfe931b6837359cb01da9cfd3b88b9 Author: braney Date: Thu Apr 15 23:07:20 2010 +0000 add replicate to sortOrder for GIS RnaSeq commit 2f58ddd65f97a2f69d24de4eca09bcc16063c012 Author: braney Date: Thu Apr 15 23:05:59 2010 +0000 just have a couple of the GIS DNA tracks on by default commit d278f8633da4819db704ba1d36d11b45d386d85e Author: angie Date: Thu Apr 15 22:06:57 2010 +0000 Added alternate haplotype contigs to ctgPos. Built snp131. commit ce96da010f7e05f38a85af395a3983dbf2dc5b95 Author: katrina Date: Thu Apr 15 21:19:19 2010 +0000 removed alphas from the ENCODE GIS RNA-Seq track to stage on hgwbeta commit c790f3fc5fc6ff0b8a3fc60c005fb469c220bf5c Author: ann Date: Thu Apr 15 20:24:31 2010 +0000 we changed short and longLabel commit c917c2fafd63d1016e88a81fba6139ddd231eeaf Author: tdreszer Date: Thu Apr 15 19:26:54 2010 +0000 Fix errAbort with too many params commit afa95b42b0653d6b0855716d95dddd68d1cfea2f Author: tdreszer Date: Thu Apr 15 19:25:56 2010 +0000 Strip enclosing quotes before updating a val commit 9a1b1449e212a9aa3f0ffb39ed495b6ae770ff0c Author: tdreszer Date: Thu Apr 15 19:25:12 2010 +0000 Added stripEnclosingQuotes() commit 40c1c80747874d80c10260559696d50cdaead5ef Author: tdreszer Date: Thu Apr 15 19:19:42 2010 +0000 Stripping quotes out of mdb means adding them in here commit 1442b20fa7510ff3e3bb79fd753c309b41edf989 Author: braney Date: Thu Apr 15 18:51:56 2010 +0000 changed long and short labels for GIS DNA PET commit 2bc8dc5be88a4c44e52f4f5e31aaa39e298d912b Author: tdreszer Date: Thu Apr 15 18:46:43 2010 +0000 Fixed one lab that was YaUCDle and stripped out quotes commit d5613703c92d974bd7983b5089fc14ea50cf1163 Author: ann Date: Thu Apr 15 18:16:52 2010 +0000 caltech now released. added GIS DNA PET. commit 64da0c0540221082e10aa80317d8d4d3b6493361 Author: braney Date: Thu Apr 15 18:14:09 2010 +0000 fix GisDnaPet to have the fragment sizes in numerical rather than alphabetical order commit 6f35670fd14e92017785f34ee17028768fac6de3 Author: chinhli Date: Thu Apr 15 18:03:15 2010 +0000 CE6->CE4 LIFTOVER commit d4570c74730df91133451e744fe4514ff35fd561 Author: antonio Date: Thu Apr 15 17:22:34 2010 +0000 typo commit 806cfdcf8cecfb34a4c697f3b0b86aa5dee810b0 Author: antonio Date: Thu Apr 15 17:20:51 2010 +0000 fixing some errors, commenting out features until adjusted commit 09e37acd367b742ffe664fa6f8fe2c4e8319fd9a Author: tdreszer Date: Thu Apr 15 17:18:15 2010 +0000 More Yale Short labels for Katrina commit 0a7596e00e7ee247f3fca4860f4fa93c26979021 Author: kate Date: Thu Apr 15 17:00:22 2010 +0000 Fix cleanup commit 9ecd67277cbc4e76d0135779c4ea193fa071bb78 Author: braney Date: Thu Apr 15 15:50:40 2010 +0000 make H1-hESC into male. Poof! commit f6c75cb9ae790a958755ace9b2de3b8ea38cfadf Author: galt Date: Thu Apr 15 15:00:06 2010 +0000 "Encode release log update" commit e13e364fc022cc16ac4e55437fa52b80e55c8438 Author: galt Date: Thu Apr 15 15:00:03 2010 +0000 "Release log update" commit 12531be34000b4b3b0c6476c3ed1319497bd6fda Author: markd Date: Thu Apr 15 04:59:27 2010 +0000 reenabled chimp alignments commit d51264d59266ab58c5a60943077048e75a1b8e16 Author: markd Date: Thu Apr 15 04:57:53 2010 +0000 forgot to use parameter that was added to get either GTF or GTF (per Hiram) commit 8023eb5af5069e8add1d107ce3aefc52018200f3 Author: angie Date: Thu Apr 15 04:17:08 2010 +0000 Registering snp131. commit e5be126f60175c49c120c6270dc8a8d0192ccfd9 Author: aamp Date: Thu Apr 15 00:05:26 2010 +0000 RT #1632: On the hgGene page, when the user edits the "Microarray Expression Data" to switch it from displaying red/green to displaying yellow-blue and presses the submit button, the page should redraw and remain at the "#microarray" anchor. Instead it pops back up to the top of the page. -- should be fixed. commit 67cb2db88585a91044c12d137fbafb7eea11df9d Author: pchan Date: Thu Apr 15 00:04:22 2010 +0000 created by Andrew H. for autocomplete genome box commit b9d814fcd830d9e420f09076d885ef09e1a0ca13 Author: pchan Date: Thu Apr 15 00:03:33 2010 +0000 fixed tooltip problem by Andrew H. commit 9e339bed5312bf76cf416c86a5eaf33a28de1844 Author: pchan Date: Thu Apr 15 00:01:13 2010 +0000 change code to display tRNA image on detail page commit 7eac1e98291aefdca8f2c094c1d1f87bb72261c7 Author: pchan Date: Thu Apr 15 00:00:32 2010 +0000 move LOWELAB code section close to the top of the if statement in doMiddle() to avoid function calling conflicts commit a833207cbc9d0bdc407a98260e5d3bd0c870cef9 Author: antonio Date: Wed Apr 14 23:56:15 2010 +0000 adding panda and pig to chainnet composite commit 69731afa5e66003fbcf9577ed56692bdc7da4cb0 Author: cline Date: Wed Apr 14 23:36:11 2010 +0000 Added a displayName entry for the cases where there are two or more entities of the same class, and the term field (which has to be unique) cannot represent both entities accurately. commit 39e8e697d75fb572a0d9cf6f7687eabe75536c04 Author: cline Date: Wed Apr 14 23:10:33 2010 +0000 Added antibody H3K9acB commit 28aeaee5ee2ec5b40ffba6519631b3e9a11d9944 Author: hiram Date: Wed Apr 14 22:54:54 2010 +0000 no blue nav bar for susScr2 commit ed6562383becaa5ccabf59765d62549974a0c2f8 Author: mary Date: Wed Apr 14 22:21:21 2010 +0000 changing documentation to be blue rather than purple commit 1de14d878b1ad90ac929dd0fba6d7aadd689e5f0 Author: braney Date: Wed Apr 14 22:11:53 2010 +0000 add colors to cell types for GisDna commit e4c169f0565927a460616b4d00dc5ad0b38feaf8 Author: cline Date: Wed Apr 14 22:09:49 2010 +0000 Cleaned up the HTML to make it nice and pretty... commit d17ff996cc78fd8e0980baf4694da6a899fe77d7 Author: braney Date: Wed Apr 14 22:00:48 2010 +0000 fix a long label commit 36bdd57b74f3d614a20c0ae87080fe7d9eed2f2b Author: braney Date: Wed Apr 14 21:58:05 2010 +0000 make short labels unique commit 170762acc6413a974d950315bbdd168250e72c85 Author: ann Date: Wed Apr 14 21:45:55 2010 +0000 removed alphas for this track; staging on beta commit 64f8eebf3e5059fdd3229bf51e85dfa727609b59 Author: ann Date: Wed Apr 14 21:22:59 2010 +0000 typo commit f16094b9023523980cd0a3cf682db4110f1c3d28 Author: braney Date: Wed Apr 14 20:51:05 2010 +0000 make long labels unique and less than 80 chars commit 9ab4a1dadf56bdf87dfeef3725ac1ffba0e8dd72 Author: cline Date: Wed Apr 14 20:38:02 2010 +0000 Renamed html file for the Duke Affy Exon array. Added text from Terry Furey. commit b3e52fcc81bf3fad92f921a39c704b67de5aeffd Author: cline Date: Wed Apr 14 20:35:42 2010 +0000 Abort, wrong filename... commit b357cd7af19f7700dc432b387cb6371096e1d0df Author: ann Date: Wed Apr 14 18:23:04 2010 +0000 first pass at this release one description page commit abcb16586d28086797fd320d4139437fe2c8e48b Author: hiram Date: Wed Apr 14 17:49:15 2010 +0000 properly draw line at bottom of graph when data point is right on that line commit 19f6285a6e262d87efaca3777853a687ca142929 Author: ann Date: Wed Apr 14 17:11:57 2010 +0000 added support for https commit 57a6eaece44fa4e9c0957494d7449d3f42c18449 Author: galt Date: Wed Apr 14 15:00:07 2010 +0000 "Encode release log update" commit 027c431bb4399b572701069a038b27e270fafaa5 Author: galt Date: Wed Apr 14 15:00:04 2010 +0000 "Release log update" commit e11d4c91e1203c4ed774bd5bef0f17aedf7bd4ae Author: braney Date: Wed Apr 14 13:35:20 2010 +0000 finished Human Proteins commit 7ddb56352b1cd122d95e57d4cd32d7cf78c60429 Author: galt Date: Wed Apr 14 07:56:06 2010 +0000 Adding support for http(s) proxy commit ac1da3ba482643a23067f23160a295ccb512bd61 Author: galt Date: Wed Apr 14 07:42:57 2010 +0000 Adding support for http(s) proxy commit 4e88593028f426f36340d8fe928946c200af8ee3 Author: tdreszer Date: Wed Apr 14 00:50:47 2010 +0000 Initial checkin of mdb style metadata for Broad Histone commit b26536836f0eaa221ffc3ae1f01573fd403d21eb Author: mary Date: Wed Apr 14 00:21:40 2010 +0000 changing sample position queries for susScr2 commit 506abd28e29cb91f19682d35eee174f7ba34fe8a Author: mary Date: Wed Apr 14 00:07:44 2010 +0000 completely changing the codon and base documentation, making it clearer and more accurate commit 39c931a11d4c2bf23edd2d90aae9a833872b8478 Author: hiram Date: Tue Apr 13 23:18:44 2010 +0000 verify no dots in chrom names commit acfd73843489806a76c7de34fbf716199e5f1278 Author: braney Date: Tue Apr 13 23:13:32 2010 +0000 starting human proteins commit edca79bfd11950a79e836a157af2b517ce98f8f6 Author: hiram Date: Tue Apr 13 22:54:59 2010 +0000 sheep is oviAri not oviAra commit 03dc54c8bb4b2a732e1f0cb7d54157066e3368d1 Author: vanessa Date: Tue Apr 13 22:29:29 2010 +0000 added calJac3 for genbank updates commit 1d3cf1564416ab4ddcef1ade4acca68a27dac039 Author: braney Date: Tue Apr 13 21:49:41 2010 +0000 get the number of tables correct commit e7ed0eac7c4721209f1d50f61a2fb2e38fa6dcb9 Author: tdreszer Date: Tue Apr 13 20:38:56 2010 +0000 Removing as part of rename from metaTbl to mdb commit cf84dba527676f517b4d200dbc3d47d09a661771 Author: mary Date: Tue Apr 13 20:33:47 2010 +0000 adding chain and matrix overrides for monDom5 and hg19 commit b3aacb9ff15dc9d8a9494c125d5766174d9490a1 Author: tdreszer Date: Tue Apr 13 20:32:19 2010 +0000 These 3 have been moved from metaTbl to 'mdb'. commit 568ffd6a87f3136f12ae3326badced11de72c314 Author: tdreszer Date: Tue Apr 13 20:30:46 2010 +0000 Removing as part of rename from metaTbl to mdb commit 1413b63eb82fff0a5b7d402abebd5b1c3544d0af Author: tdreszer Date: Tue Apr 13 20:18:51 2010 +0000 Renamed metaTbl to 'mdb'. commit 22f7487c81262d909b2e62bbba1b0da1ebca5372 Author: tdreszer Date: Tue Apr 13 19:59:16 2010 +0000 Renamed metaTbl to 'mdb' and eliminated objType. commit b651ddd526868eb39fde63a61463fb0c119b163b Author: tdreszer Date: Tue Apr 13 19:51:59 2010 +0000 Renamed metaTbl to 'mdb'. commit ebe778293ff43168237d664dbfdbd6a08ecd04f1 Author: tdreszer Date: Tue Apr 13 19:49:20 2010 +0000 Renamed metaTbl to 'mdb' and eliminated objType commit d32f21490812482b315a73e4165a6da0bb7ce57e Author: tdreszer Date: Tue Apr 13 19:48:44 2010 +0000 Removed obsolete old style metadata code commit 5fbc8ee678facb46440892870a4b44e864f07723 Author: tdreszer Date: Tue Apr 13 19:41:38 2010 +0000 The metaTbl is now the 'mdb'. commit 71389a0a19c4386c93000c9745b970605007573e Author: tdreszer Date: Tue Apr 13 19:40:24 2010 +0000 The metaTbl has been renamed 'mdb' and objType has been dropped. commit 1e66d2c90fe48140fbb6602b881160427d14a373 Author: angie Date: Tue Apr 13 17:16:50 2010 +0000 Remove check for canonical db name format -- vestige from when hgwdev had dozens of Lowe lab databases. New db names e.g. felCatV17e don't fit the old regex, but having active=1 in dbDb is good enough. commit ab8b56a185bd6487321993dda99186595bf676e7 Author: tdreszer Date: Tue Apr 13 16:05:50 2010 +0000 Fixed bug in formatted metadata lines requesting a delete commit 2f3745abf47ba234920aaae410822a3eb3afa2f7 Author: tdreszer Date: Tue Apr 13 16:04:13 2010 +0000 Initial check in of Haib metadata commit c62c96146e0a1e3ad886ccf4cc236ff0c8793441 Author: kent Date: Tue Apr 13 08:42:32 2010 +0000 Fixing extra pack-mode labels. commit d59183fe502c82fe3edb1b67b6673c581951d342 Author: galt Date: Tue Apr 13 08:03:26 2010 +0000 hack to keep it afloat, the list was getting too big and I had to fetch 50 record chunks at a time. probably need to be re-designed at some point now that ENCODE and other stuff is creating thousands of tracks where we used to have hundreds commit 72c88f8b9eca4a4b5a817c9ceae48165a9bd13b8 Author: kent Date: Tue Apr 13 07:02:05 2010 +0000 Some work getting makeItems tracks to display better in dense and full mode. commit 08630bf15959e0f34ee90fb790924b036474cb33 Author: baertsch Date: Tue Apr 13 06:23:53 2010 +0000 add track and description for retro track on alpha and beta for push commit b7962a57f03f384cc6771269291a3304a1299345 Author: kent Date: Tue Apr 13 06:14:30 2010 +0000 Adding makeItems to packable types. commit 40c738e9b4629d81634fb0d3f709f9e122165972 Author: kent Date: Tue Apr 13 05:51:25 2010 +0000 Improving BED output for makeItems. commit 711b4304d8599c3ebb30c17f2cdbb5ce3d79872b Author: galt Date: Tue Apr 13 05:50:28 2010 +0000 v229 preview commit 261775428a3db08cd56c4abd5464361ba220cfad Author: kent Date: Tue Apr 13 04:42:01 2010 +0000 Making filter work for makeItems. Hmm, what a complex piece of code! commit 08081398f26db5e7cd8dcac84b28e49debbd4edc Author: tdreszer Date: Mon Apr 12 21:56:28 2010 +0000 Extended special case for ENCODE metadata lines commit 6ba820ddbf99bd36cbf4675523ae2b6f51fc5c3f Author: antonio Date: Mon Apr 12 21:45:12 2010 +0000 turning panda back on commit a0188b8df4ce1274bbd42146ccf2d1a60a2e6f77 Author: antonio Date: Mon Apr 12 21:37:49 2010 +0000 adding html override to vega commit 821cbb07e0ebc329f88396ecfbf0b4a8bd19197b Author: chinhli Date: Mon Apr 12 21:33:00 2010 +0000 Adding oviAri1 lastz swap support commit 2fbe50ff36b21740d412cabd6ea9b43319e795f7 Author: chinhli Date: Mon Apr 12 21:32:38 2010 +0000 Adding oviAri1 lastz support commit ada3b6bd672651b304ad83fe1a9c74fe45a0d3c4 Author: markd Date: Mon Apr 12 21:27:19 2010 +0000 disable native panda refgene, since there are none commit 5d2e4eb1ad5a97cc5b794b674c5be0217ab71da4 Author: antonio Date: Mon Apr 12 21:24:16 2010 +0000 changing searches commit 7ed276474a17e2d7843b64543dcab4b411076408 Author: tdreszer Date: Mon Apr 12 21:22:08 2010 +0000 Initial check-in of metaTbl data from 3 ENCODE labs commit e544c88804d7f27653b3e4f434be0d7658e1e9f4 Author: antonio Date: Mon Apr 12 20:43:31 2010 +0000 removing bad if commit 7178aa5d877557f5b6d8d6ac80200f177dcc1e3c Author: tdreszer Date: Mon Apr 12 19:49:46 2010 +0000 Adjusted short and long labels for Yale TFBS commit 11588874edbcdd02597b33ef6d3c64032162a4b8 Author: hiram Date: Mon Apr 12 19:27:04 2010 +0000 rerun genbank for panda commit 17d49480db41c2f433397ef7b2f8f707470821b2 Author: hiram Date: Mon Apr 12 19:26:00 2010 +0000 reenable panda ailMel1 commit 17e46e84a92335aae00b21525f70e72619b26bab Author: hiram Date: Mon Apr 12 19:23:24 2010 +0000 add HINV-7.0 tables to ignore list for hg19 commit ef962996752dff030d4d46f5d3fb9cf7efe867ed Author: hiram Date: Mon Apr 12 19:17:34 2010 +0000 fixup URL links to HINV db resources commit 82dd79aff88645a6b53fbfb4c5225e551784b400 Author: cline Date: Mon Apr 12 19:15:17 2010 +0000 Added antibodies H3K4me3B, H3K27me3B, H3K36me3B, IRF3, TBP, and USF2 commit 2ea92a888ceb5f41a29d7b7337460814cf3f7885 Author: hiram Date: Mon Apr 12 18:47:02 2010 +0000 missing the root designation on the hgTrackDb command commit 1e03735de9ae5eeda0ec2e8e73feddc23dd26173 Author: krish Date: Mon Apr 12 18:45:53 2010 +0000 fixed double counting bug commit fad19173f8da2b64872ba7f0113aaefad587a61c Author: braney Date: Mon Apr 12 18:33:53 2010 +0000 take out color for GisDnaPet K562 20k track commit bdb1a1850545abf84c21860dc270a7c34b35cd18 Author: kent Date: Mon Apr 12 18:16:48 2010 +0000 Some more progress in making makeItems tracks work in table browser. Selected fields output now works. Filter puts up UI, but filter is still ignored. commit 381d5464bb4a232ef6d8d7aacee04462e8d5fa3f Author: braney Date: Mon Apr 12 17:55:36 2010 +0000 better notes from Krish commit 29f202ea754fd2546ff16b543ad01502aa12ee67 Author: antonio Date: Mon Apr 12 17:50:31 2010 +0000 changing searches commit 4676cf96ab972a0f20af6b251182fb5cba3b8ebb Author: tdreszer Date: Mon Apr 12 17:46:48 2010 +0000 Fixed a bug from cut and pasting commit 09ef37d511d404979a1bfdda01f0c3f5883f1f86 Author: braney Date: Mon Apr 12 17:41:52 2010 +0000 some tiny changes to long labels in GIS RNA-seq track commit cd6807b4543f49e8aad5947e83fe9561e6c2c3e2 Author: krish Date: Mon Apr 12 17:22:43 2010 +0000 now show full filename (not just extention) on warning commit cd42106c8f63871b3a22d0b963946f92a291f8d6 Author: hiram Date: Mon Apr 12 16:33:12 2010 +0000 default big hub is swarm and workhorse is hgwdev commit cc77ffabda57aaed2c62c536da944a6c2859cf1d Author: tdreszer Date: Mon Apr 12 16:22:31 2010 +0000 Got rid of old ifdefs commit bc49c6e679ef9a14cce322ac11afc7c9f1202943 Author: tdreszer Date: Mon Apr 12 16:20:59 2010 +0000 Full support for the new metaTbl based metadata for ENCODE tracks. Uses sandbox table if one is found. commit 138e6b53f6c6727e94a1b85347749fc2c95071b8 Author: tdreszer Date: Mon Apr 12 16:17:22 2010 +0000 Clean up extras hash commit a2b098a544736b475b62dbc31cd09870d0fe3af4 Author: tdreszer Date: Mon Apr 12 16:16:19 2010 +0000 Better cart cleanup for tdb and children commit 955983b53a572807506f30afbb957fad057e6706 Author: tdreszer Date: Mon Apr 12 16:13:39 2010 +0000 Full support for the new metaTbl based metadata for ENCODE tracks. Uses sandbox table if one is found. commit a7ac6e71afe048d29bb146ada1ccec45ba52d6c2 Author: kuhn Date: Mon Apr 12 16:01:09 2010 +0000 modified message commit 7b8624e14c13fb56b5c311b8892c34677b1987ce Author: galt Date: Mon Apr 12 15:00:06 2010 +0000 "Encode release log update" commit c63734afd92aa5e16544ca888e55478af5c13357 Author: galt Date: Mon Apr 12 15:00:03 2010 +0000 "Release log update" commit 7934a03b71bd778f7e3343f533c5fb1f8b5e3e33 Author: kent Date: Mon Apr 12 05:32:51 2010 +0000 Making all fields output work with makeItems. commit 9e749cfc0a63bd1441367b168fc76f4ff56c1d7a Author: kent Date: Sun Apr 11 21:55:27 2010 +0000 Starting to get makeItems custom tracks to work. Schema page is made now, though links in it don't work. commit 291c7359abbf4496e958d3e5d9d64cdd62c93824 Author: kent Date: Sun Apr 11 21:54:51 2010 +0000 Adding makeItemsItemAutoSqlString. commit a82e0dc9352b380561f18f1cf677d0dc8525158c Author: markd Date: Sun Apr 11 16:48:45 2010 +0000 redo chimp genbank to not special case huamn commit c8455123d142837924cba442a4eac5c82d470a56 Author: markd Date: Sun Apr 11 15:08:18 2010 +0000 remove hack to treat human cDNAs and RefSeqs as native chimp commit 789ab2b42dba2959eadc0403df4c6a8040ee8a8b Author: galt Date: Sun Apr 11 15:00:06 2010 +0000 "Encode release log update" commit 36bbf24d744bf4bc3e999d9ff4cf33443ad61460 Author: galt Date: Sun Apr 11 15:00:04 2010 +0000 "Release log update" commit 538d53390aca7de715e53212dd5cc47537b6e2b5 Author: markd Date: Sun Apr 11 07:36:05 2010 +0000 need /cluster/bin/ for making downloads commit 8a7c4e26cd96a4b40f542e1546d670f3db6566df Author: markd Date: Sun Apr 11 06:48:31 2010 +0000 don't include /cluster/bin in PATH when not running on build server to avoid annoy our kind admins by fill up the log with autofs errors commit 6bbd0f1c4e3c58b47b06e01b4592224ba4e0e8ac Author: kent Date: Sat Apr 10 19:05:24 2010 +0000 A little cleanup. commit 4603a736b77268c75313b4580effba8bea43ce7d Author: kent Date: Sat Apr 10 19:01:19 2010 +0000 Removing default values for name and description from makeItems. commit 791bf32cf7cab6fab1ff4e7c3852d9f9a0c45215 Author: kent Date: Sat Apr 10 18:39:53 2010 +0000 Making it so can edit name and description of makeItems item. commit 69cdbc25cb54fb4b5699800a5d7856492697bf03 Author: kent Date: Sat Apr 10 18:39:07 2010 +0000 Adding id column commit 20e558c40307ff859852195202fef900116cfe4f Author: markd Date: Sat Apr 10 18:09:14 2010 +0000 remove hacks to align human as native on chimp commit 41b20a2b225e10b583f993fa68f3211a331be76e Author: markd Date: Sat Apr 10 17:28:38 2010 +0000 disable chimp commit bdda07a486d30f085dae1cddfaf89ec184d253f8 Author: galt Date: Sat Apr 10 15:00:06 2010 +0000 "Encode release log update" commit 72dab6d56e62f35debb906d34a465015298d1e36 Author: galt Date: Sat Apr 10 15:00:03 2010 +0000 "Release log update" commit 20c228c347b964c5c0aceeabed529048ca064a81 Author: kent Date: Sat Apr 10 06:41:03 2010 +0000 Adding some details page handling to makeItems. commit a89fa864bef6f50d1c5dace317ddd981e2c7195e Author: kent Date: Sat Apr 10 06:13:30 2010 +0000 Adding ID to makeItemsItem. commit 4392a5841e73add2c0aa028557a04fd825ec2bbb Author: kent Date: Sat Apr 10 06:11:51 2010 +0000 Adding id field to makeItemsItem. commit 7bce546af97f225a10df4c4da04e909bf304cd93 Author: kent Date: Sat Apr 10 04:11:27 2010 +0000 Replacing dummy first item with something better. Restoring click to details page, which is still sparse. commit 9d4765d7b0f708654517d4700f78059c87fff589 Author: kent Date: Sat Apr 10 01:14:57 2010 +0000 Taking a few more steps towards making the makeItems type custom track. It actually seems to be storing ranges in the customTrash database and displaying them now based on your javascript selections! commit b48763cf6426d34326796ca752dbbbfbe67d5416 Author: antonio Date: Sat Apr 10 00:56:39 2010 +0000 usage statement change commit 9a1758446bc9bddfda441a670d603ae8f5185908 Author: antonio Date: Sat Apr 10 00:24:04 2010 +0000 added cleanup functionality commit 16dd9ea1a179f841106484cf8931b462f026a046 Author: antonio Date: Sat Apr 10 00:20:28 2010 +0000 added cleanup functionality commit 6bbd8154b5377526511ef8958a99fb3ed0c414fd Author: hiram Date: Fri Apr 9 22:32:50 2010 +0000 restart ailMel1 panda to fix up xeno Ref Seqs commit 3b3f2492daa0e3a4276d2b9d67e29a0ba2bfa438 Author: hiram Date: Fri Apr 9 22:31:42 2010 +0000 limit panda to just panda commit b5ef4bc4e751bab99f6ff380e78965d117cbbb0c Author: hiram Date: Fri Apr 9 21:46:01 2010 +0000 working on H-Inv 7.0 and new Ensembl name mapping table commit 4a41a042aab386673122824484067b62db6aff08 Author: antonio Date: Fri Apr 9 21:14:11 2010 +0000 slight interface change commit 971529f49a16091d61752f0efa30ea019f54e0e3 Author: ann Date: Fri Apr 9 20:32:34 2010 +0000 fixed typo in usage statement commit 0fdc6ede1f37e82c0bb20c4e2c3cf29c11017abc Author: kent Date: Fri Apr 9 20:06:59 2010 +0000 Starting to get makeItems to work as a custom track type. commit b2f3decce12a4d75f6f86f53a745ab376c537cdf Author: antonio Date: Fri Apr 9 19:02:56 2010 +0000 slight interface change commit 3f5df8ac6bbecb442104ec61adc41909e4555958 Author: chinhli Date: Fri Apr 9 18:41:24 2010 +0000 put into pushQ commit 059c148b242158f00255f7792844673d06f483ef Author: markd Date: Fri Apr 9 18:41:18 2010 +0000 Switch GTF output to being true GTF commit e57622d506e692e430f6c3a71d45a437d9e8a7ce Author: ann Date: Fri Apr 9 18:31:44 2010 +0000 added 4 new staff members commit 95f2aef27860d7518bdbef730c2d31505061dccb Author: braney Date: Fri Apr 9 18:17:02 2010 +0000 comment out Melissa's recent change. Need to revisit this after some discussion commit 3beb6b1347b93aae5de8ca30d50d733d1d26c02e Author: kent Date: Fri Apr 9 17:45:57 2010 +0000 Updating comment and name. commit d2a8084e8000feb8727957250e09ca15fa9b5ae2 Author: kent Date: Fri Apr 9 17:44:20 2010 +0000 Adding makeItemsItem autoSql object. commit a52fbcd2fc4ad3d6c5bfcf8380a2057d601acf11 Author: mary Date: Fri Apr 9 17:13:35 2010 +0000 moving all shortLabel chainNet overrides for susScr1 to highest level commit 92455b4246d7d38fe4a8c137d4d961d6acc97a7d Author: kent Date: Fri Apr 9 17:08:48 2010 +0000 Refactoring so that ruler and makeItems share code to convert from pixel to chromosome coordinates. commit 65b7471ef0ff7a5ef43bd1bceb7be1ff71ea838a Author: hiram Date: Fri Apr 9 16:59:10 2010 +0000 fixup hg19 references so it is clean on beta commit 38aa24510356e92bc0eca2d685920f65f41016d4 Author: chinhli Date: Fri Apr 9 16:31:19 2010 +0000 Add ctgPos2 for felCatV17e commit 7c76f0c31f5aaa866826e2fb7a51250fbdd6fc35 Author: chinhli Date: Fri Apr 9 15:24:24 2010 +0000 Rerun blastz with felCatV17e commit 51fc969f12a29b6717f667088f852a3ed62cb8ec Author: galt Date: Fri Apr 9 15:00:08 2010 +0000 "Encode release log update" commit 47131ea5466581b7eeb6ec516e6b2bc45e80c77b Author: galt Date: Fri Apr 9 15:00:05 2010 +0000 "Release log update" commit ed4a22c4d6630ded9ffb98fd863c040b541bd90c Author: kent Date: Fri Apr 9 07:48:47 2010 +0000 The makeItems drag now returns a proper track name, chrom, start, end. commit be8982314321f30ced05e63f72c92daeb089649a Author: mary Date: Fri Apr 9 01:23:28 2010 +0000 adding susScr1 chainNet overrides for human commit 1b3ce009c279e7d047f6f59944fdb46310cdd746 Author: mary Date: Fri Apr 9 01:19:00 2010 +0000 adding shortLabel overrides for susScr1 and priority overrides for susScr2 for mouse commit d99feefc0cb347875059674616e30ed5693eca98 Author: antonio Date: Fri Apr 9 00:41:40 2010 +0000 usage statement clean up commit 610de8dab32382c25f3198e5e32d70b3eb9aa1f4 Author: antonio Date: Fri Apr 9 00:33:42 2010 +0000 switching from checkOffend to checkTableCoords commit e26cc2279e1bffadfedc265e3eb1d5ff3767dddd Author: mary Date: Fri Apr 9 00:29:11 2010 +0000 adding shortLabel overrides for susScr1 commit 466bca1f3050bfea6a6ffda1bf654aad2f04637f Author: galt Date: Fri Apr 9 00:25:49 2010 +0000 fixing Stanford SOURCE links commit 687248427a34696ada1bb626ea57f3b26b328cbb Author: mary Date: Fri Apr 9 00:22:42 2010 +0000 adding priority override for susScr2 commit 28d1fad3ebb8f49cbe7cd57dd573b0e9895932ef Author: antonio Date: Fri Apr 9 00:18:06 2010 +0000 spacing fix commit f5083b81ba6646379092857f04d74a55131317e4 Author: antonio Date: Fri Apr 9 00:17:23 2010 +0000 adding qaThis.csh to makefile commit dd5b75106c2e0783ce0d886144b0d851147a9694 Author: antonio Date: Fri Apr 9 00:16:28 2010 +0000 adding this script commit d514dbdf122efeb5c81739333a61f314482e1925 Author: kent Date: Fri Apr 9 00:15:13 2010 +0000 Starting to implement more of the makeItems track javascript/C interface. commit 1ca5d8abf2c7b7a3ee659770137e1b43321c2f70 Author: mary Date: Fri Apr 9 00:12:22 2010 +0000 adding priority override for susScr2 commit ec6e75df75c004ae751a2bb4ca6a495e41927f4c Author: braney Date: Fri Apr 9 00:12:00 2010 +0000 check for an error case that used to core dump commit e3d206390a4f1c4c97685c9c67d53e504c65c094 Author: braney Date: Fri Apr 9 00:11:44 2010 +0000 always check for mafFile in trackDb settings, and if present, use it. commit ab3eaea106b93f7e08cf02cd884888d3cac9b684 Author: mary Date: Fri Apr 9 00:10:19 2010 +0000 taking out unnecessary matrix override for susScr2 commit 4f08ecbc4805a11dfa2ff0ce8b36f5bd1c6f17e7 Author: mary Date: Fri Apr 9 00:03:57 2010 +0000 chainNet overrides for susScr2 commit e73a178a39b5ffdf29b0c934619152c03d144cd3 Author: kent Date: Thu Apr 8 22:31:33 2010 +0000 Making it so that list of makeItems tracks to initialize is determined at run time. Making hgTracks.c generate a javascript function hgTrackInitTracks() that gets called during the javascript init. commit 13794f1310e55ec2d311e8655d6dd5cdedd1cfd8 Author: kent Date: Thu Apr 8 20:36:36 2010 +0000 Starting to work on makeItems type tracks. commit 76274187a075c52f9507a6040e8cfdee49241e20 Author: hiram Date: Thu Apr 8 19:35:11 2010 +0000 adding susScr2 commit 09a2b0dc627c023676a7f97671ee82716c7d9233 Author: cline Date: Thu Apr 8 18:43:21 2010 +0000 Changed the vendor ID and link for the PABP1 rip antibody, due to the vendor discontinuing the old product commit d0260a9af3cc40214301279a77fc552b8dd9ba78 Author: kent Date: Thu Apr 8 18:36:46 2010 +0000 Fixing indentation and putting function comment in right place. Code standards people! commit 06e510de76d6f4e43985590968ddbdab224d0233 Author: galt Date: Thu Apr 8 17:47:50 2010 +0000 adding tablesIgnored clause for aplCal1 commit 2427cf9e29d55052d69879d10a1bd189abcf9d0e Author: antonio Date: Thu Apr 8 17:35:27 2010 +0000 Changing email adress commit c761de9bf150d638931c6ae3aa2ba3d3ad3494a6 Author: vanessa Date: Thu Apr 8 16:54:57 2010 +0000 Redmine issue #11, updated text regarding passwords commit d8f2a760dd2bec0c818d6eae5f01758b6f8a0953 Author: galt Date: Thu Apr 8 15:00:14 2010 +0000 "Encode release log update" commit 581553658085a3a6e9e6dc23edb964332979481c Author: galt Date: Thu Apr 8 15:00:11 2010 +0000 "Release log update" commit aff82264221ac3260a02ddd8134581a2fd90e7fb Author: markd Date: Thu Apr 8 04:39:11 2010 +0000 reload encodeGencodeGeneKnownMar07 commit 9709e83cc3f0cf7d9eea23836ec6ea26d22b2170 Author: bsuh Date: Thu Apr 8 00:29:15 2010 +0000 Updated path to important dates file commit d0a4c66b299d521c5e2db61c97f52e4178e5bb75 Author: krish Date: Thu Apr 8 00:06:54 2010 +0000 support for pairedTagAlign and better addtional files handeling commit 4d46228c5e0a577d3255e7cb3f267e2bb16bbd41 Author: hartera Date: Wed Apr 7 23:32:57 2010 +0000 Added line to list of hg tables ignored so that all Burge RNA-seq tables are ignored. commit cfd4f18b1d834edbabc24c12bf31cd3ba500d5ec Author: cline Date: Wed Apr 7 23:22:08 2010 +0000 Added a whole slew of RIP antibodies commit dafe5f9d11babca4d35c02a453f448c811a8cb5b Author: bsuh Date: Wed Apr 7 23:15:39 2010 +0000 Updated to reflect that encodeTimeline.py is now a cgi-bin script commit 4826da6783a9bc95623defd839bf9b951f221a3f Author: bsuh Date: Wed Apr 7 23:13:58 2010 +0000 Script now specifies path to 2.6 version of Python. Added stuff to make it a cgi-bin script commit 7d1a28fa84b68e2e9437a8352c83fff89be3977a Author: mary Date: Wed Apr 7 23:07:31 2010 +0000 Backing out Angie's change to r1.23 - dark blue not visible when zoomed in commit fe55a72d97c80e4b1b592d1763e16ae2aaba3f1a Author: hiram Date: Wed Apr 7 22:56:00 2010 +0000 adding broken bigWig illustration commit 92e6a76f2135fce19548c2ba15e9384b93640bce Author: hiram Date: Wed Apr 7 22:42:50 2010 +0000 experimental gc5Base track as bigWig commit e590f026aebc74877ed6439dc392a2efbdee554a Author: krish Date: Wed Apr 7 22:08:37 2010 +0000 added support for .bb files commit 92a066e1c9e7375dc28d26f057818d41fd10cf3a Author: braney Date: Wed Apr 7 22:06:53 2010 +0000 change H1hesc cytosol to H1hesc cell commit 79aa00a4b5bbf594723ffe5eb49aff7267a4a7b3 Author: bsuh Date: Wed Apr 7 19:19:26 2010 +0000 Updated file with instructions for new timeline script commit 723ca7b5a096126ec14a8a21c6aa01a9cf406843 Author: bsuh Date: Wed Apr 7 19:10:30 2010 +0000 Initial checking of python script to generate timeline html commit 84767a0fd8d12508b7559de8c4a76a59c50d9b61 Author: bsuh Date: Wed Apr 7 19:07:58 2010 +0000 Google Visualization API python library initial checkin commit 4d6f0f7143bfa38e8c9d824de2d24289f4973c19 Author: hiram Date: Wed Apr 7 18:56:55 2010 +0000 Adding HInv-7.0 gene prediction update commit e1763e6f6055f1aa1d8708c3339a368dad16cb4c Author: chinhli Date: Wed Apr 7 18:14:10 2010 +0000 Yet more minor correction... commit 3693f283a7b429108ff03cb55936586ecd7ea48b Author: hiram Date: Wed Apr 7 17:52:44 2010 +0000 add time from gap finding commit de35755a9f198fafea6a0d9ac47fb260a30a7149 Author: hiram Date: Wed Apr 7 17:43:30 2010 +0000 finished with v57 ensGene update commit 6275e607d2a8098f9720450ef861ceaa280a4508 Author: hiram Date: Wed Apr 7 17:42:44 2010 +0000 vegaGene update to 37 for mouse to 38 for human commit f23768636a7f6d6dd302ca5ac6f0b8df8947b681 Author: hiram Date: Wed Apr 7 17:42:02 2010 +0000 done with all.joiner featureBits downloads and in the pushQ commit dfece5382a9404631ab877af7c4e9ea7348913ac Author: hiram Date: Wed Apr 7 16:02:50 2010 +0000 SusScr2 leaked into chainDest twice commit 7924f29f91d88861d396f762cc562c30e2313405 Author: chinhli Date: Wed Apr 7 15:55:03 2010 +0000 Remove / from end of URL commit a6dfc13d547a756ee62c13d7fb03013758b0e36a Author: chinhli Date: Wed Apr 7 15:40:07 2010 +0000 More minor corrections commit e61099274010d856356b06abce427b45354666f3 Author: galt Date: Wed Apr 7 15:00:06 2010 +0000 "Encode release log update" commit 6352395516807662307ab45289d5ef3c89a32e01 Author: galt Date: Wed Apr 7 15:00:04 2010 +0000 "Release log update" commit c47d4e4a51048968549dd07d887fe73f18828305 Author: chinhli Date: Wed Apr 7 04:19:04 2010 +0000 Add photo credit commit c6955d84d505cae2902748c3fb98c3315b4c77f5 Author: chinhli Date: Wed Apr 7 03:48:49 2010 +0000 Minor correction commit bf1074af9e1dfc106b389476825e9c96174fd107 Author: chinhli Date: Wed Apr 7 03:47:47 2010 +0000 Mirroe correction commit 880bad4d9a2f4ae381a728e412f4a99091033870 Author: markd Date: Wed Apr 7 03:38:15 2010 +0000 Better handling of rounding when capping width of label area to 1/2 of width of size of image commit eaed3acd2f5d7590f463cc2092a9351efc65b5ed Author: chinhli Date: Wed Apr 7 03:05:45 2010 +0000 Add more description to html commit 5253a66f0d6500ddccc8bfb6e02f20d0fd477797 Author: chinhli Date: Wed Apr 7 03:03:05 2010 +0000 Add more descriptions to html commit 4e40f6a26cc76b93aa7198bda3618d300e798c64 Author: rhead Date: Wed Apr 7 01:59:07 2010 +0000 Changed UW DNase DGF track from release alpha to release alpha,beta. commit dc806d5e4c8868ce343111d7e158c700790e35f5 Author: kent Date: Tue Apr 6 23:42:59 2010 +0000 Adding extra sig for detection of truncation at end of file. commit 90f223877eac60e85285016d8203c356fa0fcaed Author: mary Date: Tue Apr 6 23:37:10 2010 +0000 adding susScr2 to Whole Genome Shotgun and chain/net variables commit f6d0a4b6e60e29b1ab4fd39144a81e8c05c88d3b Author: braney Date: Tue Apr 6 23:27:41 2010 +0000 changed some file names so they're consistent with the others commit 71be1895573ce4f98e8d6e9e0fd8fb96f767ac79 Author: braney Date: Tue Apr 6 23:22:24 2010 +0000 changed a table name to look like the others commit be2e056e23bd0f0697a9bec31d824d9432644136 Author: kent Date: Tue Apr 6 23:06:42 2010 +0000 Fixing max field in second and higher level zooms of bedGraphToBigWig and bedToBigBed. commit 209305b151523b9ca86bdc1342f99384b1688121 Author: braney Date: Tue Apr 6 22:57:26 2010 +0000 release1 of wgEncodeGisDnaPet commit df0c83165e90814cb928f0573e5f570755c98342 Author: antonio Date: Tue Apr 6 22:46:47 2010 +0000 panda update commit 8fabe7bdcec926b1f76e3260d160901d786cb231 Author: hiram Date: Tue Apr 6 21:37:43 2010 +0000 adding calJac3 commit 345e4ddcd501d908c4e0ef3a6c8585a0f6ceab4f Author: braney Date: Tue Apr 6 20:48:02 2010 +0000 add K562 with frag size 20k to GisDnaPet commit b7c1351e2190714d59d8bb5ec9feed7895288d6a Author: kent Date: Tue Apr 6 20:12:46 2010 +0000 Adding mgTimes34Font() commit abf1a1739ba564636fcb0f79526e85786a6cc9b3 Author: kent Date: Tue Apr 6 20:12:05 2010 +0000 Expanding bigWig type docs a little. commit 433f0af15ef15f8640f740817cd96aafa4d1c429 Author: kent Date: Tue Apr 6 20:11:30 2010 +0000 Committing changes made a while back for last bits of mm9 known gene rebuild. commit 752c0d7d39246e7dbb4b540cbecd658ea157186f Author: kent Date: Tue Apr 6 19:56:20 2010 +0000 Continued tuning of new font system. commit 775d50e3ece37f74889de7b8f003d60b97036fca Author: galt Date: Tue Apr 6 19:07:27 2010 +0000 adding some ppl to notification commit 549cde4c34b87292dede0f1a0a1223147f310f81 Author: hiram Date: Tue Apr 6 18:39:53 2010 +0000 indicate sequence is masked in chromosomes/README and bigZips/README commit 34b06ca45c39321b4e4e5043f9b856fbc971bc22 Author: hiram Date: Tue Apr 6 18:25:16 2010 +0000 fix a drawing bug in whiskers plot when graphRange is very near zero commit 422aa96e6fc36dbcfc08f4bbb14938be90668cd4 Author: markd Date: Tue Apr 6 17:38:34 2010 +0000 fixed library dependency problems commit 2348c2cc5450edc0367b512cefac284b099b4256 Author: chinhli Date: Tue Apr 6 17:20:07 2010 +0000 Add oviAr1Names entry commit f0e8e2101da56624c1b944ef2dd6fa7239f9b65a Author: galt Date: Tue Apr 6 15:00:07 2010 +0000 "Encode release log update" commit 441a367371c6d16bcedb8905c634fb12ebcc36ef Author: galt Date: Tue Apr 6 15:00:04 2010 +0000 "Release log update" commit ea6b0c17fddc508c028744336d3229b3bd6a3b23 Author: larrym Date: Tue Apr 6 07:36:30 2010 +0000 change minchars to 2 commit 606bc90aaea1494c68998a6dc72683685582448f Author: donnak Date: Tue Apr 6 07:10:45 2010 +0000 Added Craig Lowe pub. commit 939e17036f660bdc64e10630e3dffbec367f1e7e Author: hiram Date: Tue Apr 6 04:30:44 2010 +0000 fixup error in checking argc must be 3 and rework usage message commit ea3d6ea22a966e6c63cf92563882dc1140a0c253 Author: galt Date: Tue Apr 6 02:03:41 2010 +0000 "New version number v228" commit 7cc40227ab7d4247417a67a7ec22082037d74dc3 Author: galt Date: Tue Apr 6 02:03:23 2010 +0000 v228 final build commit 7a1b4f41c01b26fddce36479f9631a10c1345dfb Author: cline Date: Tue Apr 6 01:19:14 2010 +0000 Added stanzas to indicate that the term and tag fields are required in the cv file. commit bb922a437d8625df6d10dbb1d6ddf64240e26803 Author: kent Date: Tue Apr 6 00:58:57 2010 +0000 Adjusting lineHeight of font to be at least two pixels more than pixel height. This gets the chromosome band text to draw again in the ideagram. commit 369061091c2d53daf7895f0328cce303dbe25193 Author: jzhu Date: Tue Apr 6 00:55:43 2010 +0000 cancer browser website update commit 3858205774cc7b3b376d4f459c7fb8347d2183fd Author: mary Date: Tue Apr 6 00:41:09 2010 +0000 fixing tab spacing commit cb5caee2de36c4d5051222f9c9c6db8dfee29659 Author: braney Date: Mon Apr 5 23:39:57 2010 +0000 backing out a change Tim made that breaks tracks without views commit 1e05ce2854fdd498fe168dc6eefeb047f9104943 Author: cline Date: Mon Apr 5 22:05:26 2010 +0000 Added a new DAF for UC Davis, Snyder lab commit b55f006e006b3a39f0a401c8a87e9b6a9e093779 Author: kate Date: Mon Apr 5 21:57:20 2010 +0000 Bogus file commit 140206026030ca040fee2551b8737c7190c5f2a9 Author: chinhli Date: Mon Apr 5 21:46:28 2010 +0000 Added oviAri1 commit 0c2b55ba4fd979341ae18a0a0574060de12bced1 Author: cline Date: Mon Apr 5 21:33:41 2010 +0000 Revised the description of the UC Davis input, according to a request from the UC Davis folks commit f088dcbd2143e9546a2598d9d9c375fd14c923a1 Author: chinhli Date: Mon Apr 5 21:27:30 2010 +0000 Correct project id commit 648746af48297191972afbcfe9bf44c3a3f77130 Author: angie Date: Mon Apr 5 21:06:10 2010 +0000 hgTrackUi.c commit a1a40da281ac35086b6455a81d5f60bf674247d5 Author: angie Date: Mon Apr 5 21:04:43 2010 +0000 Make the blue for query-insertion-at-end darker and bluer, so it is more easy to distinguish from the green for polyA. commit cd2d2bac661e7c19f41d6285e2311a6a4f464892 Author: mary Date: Mon Apr 5 20:42:43 2010 +0000 adding susScr2 to genbank updates on beta commit 8b63e3c313a6822a9ccdf03b4023e5753f9930ba Author: hiram Date: Mon Apr 5 20:31:55 2010 +0000 ftp directories have underscore not period for separator commit e03e47c7a5a892d92892cbb3d0f2b1eb53fd4bde Author: braney Date: Mon Apr 5 20:17:38 2010 +0000 add 20k fragment size commit eefa1e79dea6fdf40234a3a921bb781cc8412465 Author: hiram Date: Mon Apr 5 20:17:13 2010 +0000 first set of v57 done commit 7b228ea6053c69f612d442a386673b3274c4b5bb Author: cline Date: Mon Apr 5 19:24:41 2010 +0000 Added two antibodies: ELK4 and IRF-1. commit 1afa122f9c56e4f9eb8cfc79668a76e8b88c3baa Author: hiram Date: Mon Apr 5 19:09:43 2010 +0000 From NCBI taxonomy viewer, species name lists commit 9a86d9021a1e6c790e24022df6c44fe44d26331a Author: bsuh Date: Mon Apr 5 19:08:34 2010 +0000 Added functionality to include important dates plus added some comments to code commit 3a358871695202e48ec6b91c19a50d2cd861534d Author: bsuh Date: Mon Apr 5 19:07:40 2010 +0000 Tab delimited file of important dates commit e971b386c34ac97cdac0b185b2ce0d31a7188660 Author: bsuh Date: Mon Apr 5 19:07:16 2010 +0000 Brief instructions commit c6c33566483bec5e53b52e00005a420f80ed6309 Author: krish Date: Mon Apr 5 18:47:43 2010 +0000 added UW DGF notes commit 31063af65962f0718965df400a11d7a78dbf7264 Author: braney Date: Mon Apr 5 18:42:21 2010 +0000 notes... thanks Krish! commit ee248312bf7435ca0eaa64db1adf098101a28b99 Author: krish Date: Mon Apr 5 18:37:18 2010 +0000 added pairedTagAlign file type commit ffc5879796b5aceba261ab48841c9418d7211fae Author: krish Date: Mon Apr 5 18:36:16 2010 +0000 added csfasta file type commit 7a27fd9b5c5d18c9b06730f674b7278f3a6a32ad Author: krish Date: Mon Apr 5 18:33:06 2010 +0000 added csqual file type commit 3215406a15acb0f6899a3dee88192af45770397c Author: braney Date: Mon Apr 5 18:24:14 2010 +0000 take out empty sections commit 34fc9df3aace0c5f694e0870b26c7e72c7eae590 Author: braney Date: Mon Apr 5 18:22:33 2010 +0000 some edits from GIS commit dbedbbe2f71c5d0eb658f944c508b76f0b80cfdd Author: galt Date: Mon Apr 5 18:20:01 2010 +0000 added liftoverchain to danRer5 commit 8efd43ca4116df3a4d359ecf0d7af4316f25cfe1 Author: galt Date: Mon Apr 5 15:00:07 2010 +0000 "Encode release log update" commit af97b0e86684ca776a73acaacc855261be4e0377 Author: galt Date: Mon Apr 5 15:00:04 2010 +0000 "Release log update" commit 6837114e5aacc3048a49e205ed5fa9c4359956b3 Author: galt Date: Sun Apr 4 15:00:06 2010 +0000 "Encode release log update" commit c4504d45866b23a7f3041294be8c2a85363c3d8b Author: galt Date: Sun Apr 4 15:00:03 2010 +0000 "Release log update" commit f4466eb41af5144bfbf64025a09439b77806a45e Author: markd Date: Sun Apr 4 00:36:13 2010 +0000 improved description of MGC/RefSeq CDS similarity, fixed percent identity commit 14c1bc9d989d9c2aba80b8917ae958ccbf46f35c Author: kuhn Date: Sat Apr 3 19:30:46 2010 +0000 added graph for users commit 2abdaf51d36e4fdb16a2f3255b6cbbf077fb7ea4 Author: galt Date: Sat Apr 3 15:00:07 2010 +0000 "Encode release log update" commit a303cb5bcc235857d09a348bb034946b7081afb1 Author: galt Date: Sat Apr 3 15:00:04 2010 +0000 "Release log update" commit 5b1f1be4fa22d8a8eb0d596c51cfa432859c5277 Author: chinhli Date: Sat Apr 3 06:17:47 2010 +0000 Initial oviAri1 commit 96edfdf07e2286654e3434eb73ae519b67ecd96d Author: chinhli Date: Sat Apr 3 04:30:48 2010 +0000 Initial oviAri1 support commit 00b34833cb349b3d922fc110682e9c80f937076f Author: larrym Date: Sat Apr 3 01:50:04 2010 +0000 change minchars to 2 commit 2cd5d652dd33d1b765a97b271ef74605f3021a20 Author: rhead Date: Sat Apr 3 00:29:14 2010 +0000 Made TrackCheck output much less verbose, changed links printed to be the same as those that produce the error, added the props file information to the first of the TrackCheck output, and removed some extra commented-out lines. commit 5b0bb50590af2ddb33a372fbd8d0020b68e0380d Author: hartera Date: Sat Apr 3 00:19:07 2010 +0000 Documented replacing a mapability file with new data file due to missing data. commit 70eff017ba270f316a66cf9665ee7c4f77dd73c9 Author: rhead Date: Fri Apr 2 23:59:14 2010 +0000 Added a toString function in order to print target information in TrackCheck output. commit f5ccb37475c3f9ded83e00ce31109f9c861fdd8c Author: ann Date: Fri Apr 2 23:24:08 2010 +0000 adding panda commit 5898eb23db206aa1fc912608f4be551a63cb2c26 Author: tdreszer Date: Fri Apr 2 21:20:58 2010 +0000 Reworked usage(). Support ofr wildcard and NOT in selecting objects commit 618976715ce940efd9e798d9e91f2d8329547de1 Author: tdreszer Date: Fri Apr 2 21:20:36 2010 +0000 Added support for setting multiple vars from command line. Reworked usage(). Support ofr wildcard and NOT in selecting objects commit 8add861b9d7d2dcd6df569e29fdf5f587327ea40 Author: hiram Date: Fri Apr 2 21:15:25 2010 +0000 ensGene v57 added and in the pushQ commit 7fdc1f7d176530485df7147d71af65ad1a4f84e9 Author: tdreszer Date: Fri Apr 2 21:14:38 2010 +0000 Eliminated call to obsolete metadataSetting(). Added support for NOT and wildcard in queries. Added support for setting multiple variables at once. commit 3a61043bcf3450fb3bb4aa3a2daa2d87dcbc2635 Author: katrina Date: Fri Apr 2 20:49:44 2010 +0000 changed release beta,public to release public and release alpha to release alpha,beta for wgEncodeYaleChIPseq commit 2525be61eace6ffcd152cd4a32c17d9d90d25b76 Author: hiram Date: Fri Apr 2 20:38:50 2010 +0000 finalizing gap,gold descriptions commit 3124196e25d064bd03e14c9df9e8112df03f0f80 Author: hiram Date: Fri Apr 2 20:14:15 2010 +0000 allow oryCun2 to find equivalent Ensembl scaffold names for blue bar commit d07cc306c1b6609733b242d6f0a4c9acb305d6a0 Author: krish Date: Fri Apr 2 19:28:23 2010 +0000 added more usage message and README commit d8e853a1190959ff27ca900798fd119e3083f7d8 Author: tdreszer Date: Fri Apr 2 17:59:34 2010 +0000 Added option to specify which metaTbl to use commit 81630c9db0ab7318fa8d0facfb36b30fe0330383 Author: hiram Date: Fri Apr 2 17:53:46 2010 +0000 escaping the dollar signs in the html and the backslashes commit 63b762c9dd0f591996cd4fb8fe6d4887917d2261 Author: hiram Date: Fri Apr 2 17:44:24 2010 +0000 add wiggle and bedGraph formats for comparison commit e26a83a5a6bb5fb612e81c40e85edd51119ba41a Author: braney Date: Fri Apr 2 17:33:35 2010 +0000 make long labels fit 80 char limit commit df486aac31ddcacfc214ad783b83e39e97199d0f Author: angie Date: Fri Apr 2 17:26:05 2010 +0000 Data update for gwasCatalog. commit 0dc74a0f029ecd8b3c295998af8f35c4a4845b00 Author: angie Date: Fri Apr 2 17:25:19 2010 +0000 Regenerated kgTargetAli from knownGene table (instead of wrong build dir), but didn't reload -- Ann and I feel it's not worth the QA effort. commit 01cb3eb9a4bfb980499802ceeb229651726f1cea Author: hiram Date: Fri Apr 2 17:04:43 2010 +0000 can not use shell dollar sign strings in our html files commit 5005841d75efe7d9898b041bc8436f552ba478fc Author: hiram Date: Fri Apr 2 16:59:58 2010 +0000 adding bosTau4ChainPileUp track commit 009d34d2ae68bec0bcc03992f33fed38d6d947e0 Author: hiram Date: Fri Apr 2 16:39:53 2010 +0000 Ensembl calJac3 is not our calJac3 commit 49874f6dcb90152751f74778f5bb730d1e036744 Author: hiram Date: Fri Apr 2 16:34:50 2010 +0000 need quotes around a string in a SQL insert statement commit 5d88463a224d233e42e44b51a05fe537d099c7c4 Author: galt Date: Fri Apr 2 15:00:32 2010 +0000 "Encode release log update" commit d62fd3364707f39fb1ecdd58952f48e46ae8798c Author: galt Date: Fri Apr 2 15:00:04 2010 +0000 "Release log update" commit 29b6861ae966da67988df75d432a2b09ef416de0 Author: kent Date: Fri Apr 2 02:42:54 2010 +0000 Clarifying altPromoter description in response to mailing list query. commit 152cd8c501f59553da183b1c53cb9b27f485df2e Author: tdreszer Date: Thu Apr 1 23:52:17 2010 +0000 Reorganized and filled out metadataForTable routine commit e8e272a928970a83fc9a9ad6c7f19c31a52274ec Author: tdreszer Date: Thu Apr 1 23:51:46 2010 +0000 Added extras hash to the tdb struct and 2 APIs to use it commit 298a47ffe18004d32672763c4e3bc0a42cc93262 Author: mary Date: Thu Apr 1 23:03:38 2010 +0000 removing tag since there was one already there. whoops. commit ec3a2329b6b82dfdbb069347b40a09c8520e307d Author: ann Date: Thu Apr 1 23:03:22 2010 +0000 further drift of the static mrnaID from the updated refLink table commit f05c86832ac23f054a38a2499c2c7d15b1c3d811 Author: mary Date: Thu Apr 1 22:28:07 2010 +0000 fixing old typo commit 96dfc6bfa073a6e99a9211587f48e1b7ef600b9b Author: mary Date: Thu Apr 1 22:24:47 2010 +0000 adding colorByStrand example and tag needed to do the link commit 4b6261088480e68c5362314b7a9ab9a6da061538 Author: hiram Date: Thu Apr 1 21:40:01 2010 +0000 finalizing these document pages commit fd1d8c4f8f54a6ab4eb19dd2565480fc771fd2ac Author: cline Date: Thu Apr 1 21:05:50 2010 +0000 Added a new lightly-edited version of sp090821.txt, for fetching a fresh copy of UniProt and updating the appropriate files & tables. commit 3be0967ed28858791af0d8b534c419d4b45efa8d Author: kuhn Date: Thu Apr 1 21:03:38 2010 +0000 added bar graph for number of sessions commit e68ca1fbc9d72546796892ae0332e820333d76c2 Author: antonio Date: Thu Apr 1 19:01:01 2010 +0000 changing default displays of burge tracks commit 9caaaf494f63fe89d666b48ad9bb4320b921e231 Author: hiram Date: Thu Apr 1 18:56:18 2010 +0000 adding printEnv.pl commit fb4eb57ee74590327c4a099273f2d9eb75a1ec8a Author: hiram Date: Thu Apr 1 18:55:18 2010 +0000 initial source commit 2f35470aa85663da23f67109c385399b5ca903be Author: hiram Date: Thu Apr 1 17:48:38 2010 +0000 adding ctgPos2 track commit 2f4177bfad2815a309c133c1b5bb2a4cab9caff3 Author: hiram Date: Thu Apr 1 17:47:05 2010 +0000 now showing scaffold names commit eab3ec9fffe7990fa8a8cafc6cba919177cb6691 Author: hiram Date: Thu Apr 1 17:34:25 2010 +0000 done with Panda ailMel1 lastz commit 75b65f664833e129000254f4568ce33af5370646 Author: hiram Date: Thu Apr 1 17:33:50 2010 +0000 have blat server and default location commit ebdb14a475961683c8e1802032b1058f2e0ad4f4 Author: hiram Date: Thu Apr 1 17:33:10 2010 +0000 never got susScr1 to work finished with susScr2 lastz commit 0cea3fa8dcd0cb1b8cccc99d481b3ac8eb40baa1 Author: markd Date: Thu Apr 1 17:31:11 2010 +0000 fixed GCC portability issues commit 9b1efa8459e5f0197a20dd19c79a6cc7938fd6bd Author: hiram Date: Thu Apr 1 17:28:00 2010 +0000 done and in the pushQ except for the multiz track commit 6be5d312e1f6be3872483cad411cf334c4490293 Author: hiram Date: Thu Apr 1 17:04:12 2010 +0000 adding Sheep OviAra to a 49-way tree commit 07f912410cdb8dbd11444950204cf9d8a75e3b56 Author: chinhli Date: Thu Apr 1 16:37:15 2010 +0000 Remove grep 829.2 command commit 62fe947023747b15926f5191a86a778d71087116 Author: markd Date: Thu Apr 1 16:35:37 2010 +0000 fixed 3264bit portability issue the right way commit 79f951f86ddcceb366675c1315cd8c76038a3c90 Author: markd Date: Thu Apr 1 16:19:03 2010 +0000 Backed out previous commit, as NULL has special meaning. Need to find a different solution for version of GCC that complain about NULL format string. commit a3fb7ac355a99a72cd05aa1691964b7f26ffbcd5 Author: markd Date: Thu Apr 1 16:02:37 2010 +0000 fixed invalid format in verbose call commit ba8378a069eeb1342f0c9398be77a4af0853edbb Author: galt Date: Thu Apr 1 15:00:06 2010 +0000 "Encode release log update" commit ab50fdeca07baa21cbf957f209f2ce84953885cf Author: galt Date: Thu Apr 1 15:00:03 2010 +0000 "Release log update" commit 05ef1891a4a2518fc00e1fa97c12c615b583c979 Author: markd Date: Thu Apr 1 05:53:37 2010 +0000 Allow empty key to analyticsKey to disable google analytics (for overriding when one hg.conf includes another). commit 900596e85ec5162e76fbc57d7ccc06fe5bd76d92 Author: markd Date: Thu Apr 1 03:19:58 2010 +0000 fix broken indentation that made code hard to read commit f7d9d485ba35368746ffe1703db583b6032feff2 Author: markd Date: Thu Apr 1 03:18:02 2010 +0000 If label area width exceeds 1/2 of image width, set to 1/2 of width instead of default. commit a5ffbc8bcc6b7e6be16c30718570a6fef63c59b0 Author: markd Date: Thu Apr 1 03:12:15 2010 +0000 Fixed segv when an empty search term manages to make it to hgFind commit ea8a7fcd49cc62aae1c4c6763d904ed9451a86d6 Author: antonio Date: Thu Apr 1 00:49:06 2010 +0000 removing unnecessary override commit 33ca8fd323069a2e1ad3411309024e738afa47bc Author: tdreszer Date: Wed Mar 31 23:47:03 2010 +0000 Discover metaTbl name if not provided. Prefer sandBox version. commit a805d0d97081d1fa289c9afcf6e4c258ca66ea5e Author: bsuh Date: Wed Mar 31 23:43:13 2010 +0000 Initial checkin commit 7b707b7b206445370d382ccf015f40c29abf5bec Author: tdreszer Date: Wed Mar 31 23:39:38 2010 +0000 Oops. Changed objName to obj. commit 9a7769431c09f65e4c8feb8b9e5bfcc52323a1f4 Author: tdreszer Date: Wed Mar 31 23:36:08 2010 +0000 Tightening screws. Don't allow shared metaTbl update except from protected file. commit efe911d51777bb0c7a0342fe9ba1c6b7896294b8 Author: krish Date: Wed Mar 31 22:55:51 2010 +0000 incorporated QA suggestions commit 5097e976011ebba2b958645b8266e77b31a9d4bb Author: mary Date: Wed Mar 31 22:52:47 2010 +0000 changing usage statment and redirecting errors to stderr commit abd86d8756bf6434afceb1bb17a8f5d20644a657 Author: braney Date: Wed Mar 31 22:38:33 2010 +0000 some edits from GIS commit 8e5ada08e7f4ae6b95cda0ec5e75860f73ea747a Author: chinhli Date: Wed Mar 31 21:32:36 2010 +0000 Complete ctgPos2 track commit fba2a66bbc33cc9435c52d0c082a7451d0a607ae Author: chinhli Date: Wed Mar 31 21:30:24 2010 +0000 Add Scaffolds ctgPos2 track commit cb4a4655c60d59f8e1d833799088c0d225ff2133 Author: hiram Date: Wed Mar 31 21:13:19 2010 +0000 susScr2 done and in the pushQ commit 4188712dc033d51af5a7f13a4613e68e1d45ed07 Author: hiram Date: Wed Mar 31 21:08:14 2010 +0000 Added susScr2 - Pig commit 230efff0c4cfe7f6ba733d147617f0b167be1a76 Author: braney Date: Wed Mar 31 18:37:19 2010 +0000 oops, remove BAM from the usage message if USE_BAM not defined commit f6c102e6a57b7400f9c494d74ceac5438b5dd672 Author: braney Date: Wed Mar 31 18:35:24 2010 +0000 make BAM testing conditional on USE_BAM commit 72e2696ef801b60dd1dc84ec9d489555b44b2c22 Author: hiram Date: Wed Mar 31 18:18:32 2010 +0000 restoring from a branch commit 60070d1639dfcf22a58a6c13f802b26f4059d7d3 Author: angie Date: Wed Mar 31 17:04:30 2010 +0000 Removed redundant 'ifeq(${VAR},) VAR=0' -- if that evals true then the subsequent 'ifeq(${VAR},1)' would fail anyway. Did a little indenting/nesting of related var checks. commit 6cac98126ba60f4a373fa04f981f56156aceba2e Author: hiram Date: Wed Mar 31 16:29:04 2010 +0000 adding susScr2 ailMel1 and fixing up chain checks commit e2f545c1b74db2b1da767d9f7fc53bbe87dc08af Author: hiram Date: Wed Mar 31 16:27:35 2010 +0000 add verbose output to table check to find out who, what, why, where, when commit 6a5f9198de545e1ccfcb35abecb2bde85e7f7e3a Author: galt Date: Wed Mar 31 15:00:14 2010 +0000 "Encode release log update" commit ab805d501541cc783ebb2c0ad3542e4a8baa021a Author: galt Date: Wed Mar 31 15:00:11 2010 +0000 "Release log update" commit 6b4e25ebcd9e53c0fdef086c64c26b18226aac21 Author: angie Date: Wed Mar 31 14:58:03 2010 +0000 DGV v9 (first time DGV is in hg19). Also a bit more info about how Belinda mapped over the personal genome variants track from hg18. commit b16fcb835abd3c793e1c484349c3793515e03ed7 Author: angie Date: Wed Mar 31 14:55:17 2010 +0000 DGV: data update (v9). commit 0f8c8ff1f03d0c6b98d93d0352ed95ae8c11099b Author: antonio Date: Wed Mar 31 01:04:00 2010 +0000 fixing some release alpha issues commit 5dc54ba83903cf2f26474900a867642f3f02936f Author: rhead Date: Wed Mar 31 01:01:38 2010 +0000 Added release beta,public to chainCb3 and netCb3 to make them work with the non-composite versions at the worm level. commit fd87473673a81329b9785f0d21911465e256d037 Author: kuhn Date: Wed Mar 31 00:46:44 2010 +0000 typo commit d1cb38f1ae1cc6bf7374b4564f688515b3b28307 Author: mary Date: Wed Mar 31 00:45:51 2010 +0000 moving danRer5 shortLabel overrides from trackDb.ra into trackDb.chainNet.ra commit 01512fa7445b03931b473b88f40a703d34cd5ee0 Author: mary Date: Wed Mar 31 00:40:19 2010 +0000 adding chain/net overrides for danRer5 on mouse (only affects mm9) commit 5930a7f132b19b675add8f5d737bdd985894352f Author: mary Date: Wed Mar 31 00:22:32 2010 +0000 added chain/net overrides for shortLabel for tetNig1 and tetNig2 commit d65f1c0fb9c35c41ae4ea77e663ba743cfa3bb8a Author: kent Date: Wed Mar 31 00:07:46 2010 +0000 Adding fixed 34 font. Testing and tweaking for postScript output. commit 3360adfcb1c357e6805d647e5ddd5a904f122cf8 Author: tdreszer Date: Tue Mar 30 23:45:27 2010 +0000 Better handling of RA style files and extension to select by 'vars'. commit 5a80901808ec438a1cd017aaed58fa0b3709cded Author: tdreszer Date: Tue Mar 30 23:35:24 2010 +0000 Better handling of RA style files and extension to selection by 'vars'. commit 414b96bd454923c18728e02116d6d16a77556e3c Author: kate Date: Tue Mar 30 23:25:05 2010 +0000 Add assembly to reports commit 60a870308a4441784ba3d1c605c2f2fe772d60c2 Author: chinhli Date: Tue Mar 30 22:54:33 2010 +0000 Adding LASTZ/Chain/Net support commit 1e543b2f5f7f954aa926ef36e45ba193e0f764a8 Author: rhead Date: Tue Mar 30 22:23:18 2010 +0000 Changing the panTro1 chain and net shortLabel overrides to really match the chainNet override. commit 8cacd11a8b540278d095322c7ea316424df78e1d Author: katrina Date: Tue Mar 30 22:02:51 2010 +0000 changed typo of cap letters to lowercase in table and file for wgEncodeUncFAIREseqZinbaNhek commit e2b50a8fd9d97a89988a7329b94305f75250f407 Author: hiram Date: Tue Mar 30 21:44:53 2010 +0000 Fix one last place where long strings in custom tracks cause problems commit 0b889da2a9fb07ebab276f35f17cad3fb0786868 Author: chinhli Date: Tue Mar 30 21:23:39 2010 +0000 Adding LASTZ Chain/Net support commit 6a1119a3baa2506e3646079d71e2168dfab6438c Author: chinhli Date: Tue Mar 30 21:15:30 2010 +0000 Adding BLASTZ, Chain/Net Support commit fac367d6845932a84ece494c421c484506c9f660 Author: vanessa Date: Tue Mar 30 20:20:11 2010 +0000 updated session example to reflect chain/net merge commit a569652f3ec0aac463eb36eb4cd5a9ad585b6c07 Author: pchan Date: Tue Mar 30 20:18:30 2010 +0000 change description for homologous gene track commit d9246a2d5bb167c1b56b05c03c38238deb857144 Author: katrina Date: Tue Mar 30 20:05:30 2010 +0000 removed the entire release public block/sub-blocks for Open Chromatin and removed the release lines from the release alpha,beta blocks of Open Chromatin in preparation to release Open Chromatin (release 3) to the RR commit 4b104ddf5babe66a449537c4ad9591883072ffe2 Author: katrina Date: Tue Mar 30 19:36:47 2010 +0000 changed default visibility of the Peaks (Zinba) to pack instead of hide. Planning to change back to hide once the v228 CGIs are released with a bug fix commit 18e58d578524b88c0f9bc04ff69cd56c7db5d572 Author: fanhsu Date: Tue Mar 30 17:12:09 2010 +0000 Removed a line commented out. commit b10a4311b72dbddbb72630dc6e4ea36db432f30f Author: fanhsu Date: Tue Mar 30 17:08:49 2010 +0000 Updated snpArrayIllumina HumanCytoSNP-12 SUB-TRACK. commit 83b2d4327a9d22042c60d665ee224ae0a0dc4c45 Author: tdreszer Date: Tue Mar 30 16:56:12 2010 +0000 Spelling mistakes and inconsistencies, oh my. commit e287086cfcab92313c4fdaf33b2156df155887c4 Author: tdreszer Date: Tue Mar 30 16:49:15 2010 +0000 Zinba should also be in the release notes commit a1ab4454c4305492db11915a2eaeaa7346c91824 Author: kuhn Date: Tue Mar 30 16:32:52 2010 +0000 added yellow background to encode survey text commit 20983aab3c08aa66129a91486ed356e99a5b1e42 Author: kuhn Date: Tue Mar 30 16:31:33 2010 +0000 added yellow background to encode survey text commit 12f7cc29a2b1123b0ab741e83f4f8b3eda6c2500 Author: tdreszer Date: Tue Mar 30 16:17:56 2010 +0000 Make that (Zinba) commit f083902b9b54af3ceac63c479e5336f9c9a3dd76 Author: tdreszer Date: Tue Mar 30 16:17:14 2010 +0000 Added description of Zinba peaks commit c386ecd3fa6383178557f5ed379152b2ae41cf01 Author: chinhli Date: Tue Mar 30 16:01:48 2010 +0000 Adding BLASTZ, Chain/Net support commit 601a86c3c2e8aaeddd2aa04022544e1a86600c5e Author: hiram Date: Tue Mar 30 15:10:47 2010 +0000 o_db is sufficient at this time for felCatV17e commit aa5c41e345cbf0054c7b8847dffc9b79bc3ec23b Author: galt Date: Tue Mar 30 15:00:07 2010 +0000 "Encode release log update" commit 31e2b8d58ac089e5be7aba0ee3485d4060445e6f Author: galt Date: Tue Mar 30 15:00:04 2010 +0000 "Release log update" commit bfcba02d9c3320ed3e30ef7b36dee260f774c067 Author: angie Date: Tue Mar 30 14:54:48 2010 +0000 Oops, forgot an #ifdef USE_BAM (thanks Galt). commit 16f33d397272510995880426fd4a83e5dc342889 Author: tdreszer Date: Tue Mar 30 05:33:36 2010 +0000 Round 2 of fixing 4-state checkbox lookup looking at both defaults and cart. commit 2b7f628786aa7ed7802f02c6fe1179da60d6a05b Author: galt Date: Tue Mar 30 01:16:42 2010 +0000 v228 preview commit e1fec27803687c351b9181507d8671b0a1d1d356 Author: antonio Date: Tue Mar 30 00:07:16 2010 +0000 adding colorByStrand documentation commit 7ffcdb52da3b000345a5f2cfb23b739e1d22279d Author: angie Date: Mon Mar 29 23:11:37 2010 +0000 When filling in searchDescription using tdb->longLabel, just omit the table name because it is often more confusing than informative. commit 518eae1f3050506944da09ea20fc735c8358ee0e Author: chinhli Date: Mon Mar 29 22:27:51 2010 +0000 Adding felCatV17e BLASTZ/CHAIN/NET tracks commit 4e9ffece600b224d87f6ea5c521be826c397d0af Author: tdreszer Date: Mon Mar 29 22:19:15 2010 +0000 Initial check in of a subset of the stanford DAFs commit ecf1662d0daa4405790999b3e1b252d044048ca3 Author: chinhli Date: Mon Mar 29 22:12:22 2010 +0000 Adding felCatV17e BLASTZ/CHAIN/NET tracks commit fc924d64a8df630ce9d10befa0d3808c6be08fb2 Author: tdreszer Date: Mon Mar 29 21:09:30 2010 +0000 Added one more Zinba peak commit 540e7f86bd69a759b4a2c01380f142605866466b Author: tdreszer Date: Mon Mar 29 21:07:42 2010 +0000 Added one Zinba peak and changed the view from Zinba Peaks to Peaks Zinba commit 2d228fa7b26f8cc926b8ee41dea8b2a648f852bb Author: braney Date: Mon Mar 29 20:32:38 2010 +0000 add support for BAM download only commit 4da119661cbc2638314ac104c4908ea41191ca77 Author: braney Date: Mon Mar 29 20:25:45 2010 +0000 fix up some printf's and add flag allowing non-native chroms commit 201b0d6581d7ca6ffa12d22e103aa8374db4773c Author: galt Date: Mon Mar 29 18:36:21 2010 +0000 every makefile should have a clean target commit 9d8b1c06d19eb50cf7df67a27a3861d7d90b2cc8 Author: galt Date: Mon Mar 29 18:33:57 2010 +0000 making makefile ready for HG_APPLIST usage commit cf64989c592d8695d7fa07facf9ca970e601af99 Author: antonio Date: Mon Mar 29 18:16:44 2010 +0000 removing redundant stuff commit 747e562b578f1f9918bb07913501e3ae7056e6c6 Author: braney Date: Mon Mar 29 17:26:26 2010 +0000 some small edits, addition of link to protocol commit 26e05309e10c856882096a07be2a463900c6ba65 Author: mary Date: Mon Mar 29 16:46:59 2010 +0000 changing wording so more accurate commit ffcfcfaada51524ddd4a958003364e82791f935a Author: hiram Date: Mon Mar 29 16:11:05 2010 +0000 running a bosTau4 lastz and done with swaps from hg19 mm9 and monDom5 commit bac4c5625446d164bf67b3f853777f8b477ba828 Author: hiram Date: Mon Mar 29 16:01:28 2010 +0000 done with susScr2 lastz and swap commit 3472a2149848536c27693ccf7030c14db7f91a36 Author: galt Date: Mon Mar 29 15:00:03 2010 +0000 "Encode release log update" commit 8d0d723e859b527ff25494601bd80a7f82005713 Author: galt Date: Mon Mar 29 15:00:01 2010 +0000 "Release log update" commit 7d4296b0693310c9953a86f31f7c1b8d2f8fd780 Author: galt Date: Sun Mar 28 15:00:06 2010 +0000 "Encode release log update" commit 08316322a29a82e0fe3421325d5633e0035e5ffb Author: galt Date: Sun Mar 28 15:00:04 2010 +0000 "Release log update" commit 8af6967029a301407d51b95f12e4b0d5d69b3814 Author: kent Date: Sat Mar 27 19:26:07 2010 +0000 Adding 14 point fonts and labeling bold. commit c68d5bef6efc9ef42b4ed15cd3b38e082f320e8c Author: kent Date: Sat Mar 27 19:23:37 2010 +0000 Making freen put up a test image of fonts. commit 5a676938a4249201bd50d2f48185b5e477bdf69d Author: galt Date: Sat Mar 27 15:00:06 2010 +0000 "Encode release log update" commit 3c2a59240a0ee4f1f6909cc4b207cfaff27aad9e Author: galt Date: Sat Mar 27 15:00:04 2010 +0000 "Release log update" commit 901180e211e02b7cd020847409164d5d9f351d09 Author: kent Date: Sat Mar 27 04:27:00 2010 +0000 Adding additional font options to config page. commit 4f3713619274153ef849cbf0434472c951c7e681 Author: kent Date: Sat Mar 27 04:23:15 2010 +0000 Adding a bunch of xfree fonts. Moving fonts themselves to a font subdirectory. Adding explicit lineHeight to font structure rather than just calculating it. commit 50be4df66bafa7759c2ea29f461de3fc6190a3e6 Author: kent Date: Sat Mar 27 04:22:18 2010 +0000 Adding a bunch of xfree fonts. commit 95a3bed4b03646752215960438084ca93a5bdb2c Author: kent Date: Sat Mar 27 01:42:56 2010 +0000 Updating to include lineHeight. commit 0dd771e4414327ea2bab8b95b0196da68b37b2b4 Author: tdreszer Date: Fri Mar 26 23:59:47 2010 +0000 Forgot to set dateResubmitted commit 3bca09bcaf2deb401cc83293144f9ff2e93a75a4 Author: tdreszer Date: Fri Mar 26 23:50:52 2010 +0000 Corrected metadata for 2 HAIB TFBS tracks that needed to be resubmitted commit 8bd6acc5b6eb9cdd1bde96b6009c4183c8b40fd4 Author: tdreszer Date: Fri Mar 26 23:49:58 2010 +0000 Ready for release3 commit fa5c8232f2d32e6790b2e853d5f288423095579b Author: kate Date: Fri Mar 26 23:02:44 2010 +0000 Minor changes commit 35ab7270e04d20e5dcebd99a5849a32a5107d2ac Author: markd Date: Fri Mar 26 22:03:18 2010 +0000 clarified error handling commit 8fa01a0ba8260c964e9b50d565aaca88a7a23903 Author: hiram Date: Fri Mar 26 21:14:55 2010 +0000 adding ctgPos2 track commit 76d58754fd3ff3e6aec0c1d8d2acff717048cec7 Author: markd Date: Fri Mar 26 21:13:29 2010 +0000 readability changes suggest by Tim commit 84d0169de1f3f8ed00f5dbd036bc6068512dfd58 Author: kent Date: Fri Mar 26 19:26:18 2010 +0000 Removing an extra free that was causing crash. Fixing some compiler warnings. commit acc353d33ce7a30e9b9bebd60c5ecd23e1876fe7 Author: hiram Date: Fri Mar 26 19:21:06 2010 +0000 finishing off these description pages commit c64a7e60c29fb70245cdbb6c0d7a5ab76ee650b1 Author: hiram Date: Fri Mar 26 17:24:26 2010 +0000 adding susScr2 - Pig commit 44d71f68823f616e863ef467e74f85f2469f115d Author: angie Date: Fri Mar 26 16:48:49 2010 +0000 DGV: when both thickEnd and thickStart are set to chromStart, as they are since we stopped showing locus whiskers, don't print out separate positions for variant vs. locus because there's only the variant now. commit bcb88e072ab9214c5b2e5bb6fc4bddbaab8ea8cc Author: hiram Date: Fri Mar 26 16:42:01 2010 +0000 add minGap argument commit 04b9e5d1486346b83887aac711cf09f4ad55d4f5 Author: galt Date: Fri Mar 26 15:00:06 2010 +0000 "Encode release log update" commit e617bb17d6f4c2e8e5d44f434e70de89ca2c101b Author: galt Date: Fri Mar 26 15:00:04 2010 +0000 "Release log update" commit 1e36a8ec71f1daa29ec0dda6991732c33030679b Author: cline Date: Fri Mar 26 01:39:35 2010 +0000 Changed the sex of CH12 to U. commit 156f8d2680bcd818b5239bbc707d43f6a3ac9505 Author: tdreszer Date: Thu Mar 25 23:29:21 2010 +0000 Zinba peaks have qValue and no pValue commit 2cf2c9f98f149f945aecb599dd3b247ef8701fdd Author: tdreszer Date: Thu Mar 25 23:27:27 2010 +0000 Fix to evaluating subtrackFourStateChecked checkBox commit af984e2de9fe99ca047c0f4d61ca6402bb59e99b Author: hiram Date: Thu Mar 25 22:46:26 2010 +0000 adding version 57 definitions commit 1fe66149780a8238e780a73db8b41e47c1ae23fb Author: pauline Date: Thu Mar 25 22:34:24 2010 +0000 Fixing server location and dbs checked - an error introduced by me with my last commit. commit d213a83772f1e4c346bc96fdc108b68ba781d2f2 Author: tdreszer Date: Thu Mar 25 21:56:41 2010 +0000 Some adjustments recommended by Mark in code reivew commit ca33b27e436e58e7a5590fec5ee3874ec9dc4ad4 Author: tdreszer Date: Thu Mar 25 21:55:32 2010 +0000 Some adjustments recommened by Mark in code review commit bcfa29e562057616809817af0197689b2267e9be Author: tdreszer Date: Thu Mar 25 21:54:57 2010 +0000 Handle slightly changed metaTbl API commit 0142fca44a9dcc935aefef0b2dfd67b6790402f5 Author: hiram Date: Thu Mar 25 21:43:14 2010 +0000 file allDatabaseUpdate.sh was initially added on branch beta. commit 80f070ff1796be88977d4779dc3d4043e102f5df Author: angie Date: Thu Mar 25 21:35:39 2010 +0000 Some really old changes: snp130 func annotation fixes, hapmap and 1000 genomes experimental work (some interrupted). commit 8febec4c49409cb5caa7d2dec48a8bcd1d2c2caf Author: markd Date: Thu Mar 25 21:16:35 2010 +0000 don't free cached connection with sqlDisconnect commit b4be3162643a098fa62840037715215c9059383f Author: markd Date: Thu Mar 25 21:05:02 2010 +0000 prevent permission errors when installing scripts commit 713100101cdf79286e03b72fa6c2a6ee73d190a6 Author: mary Date: Thu Mar 25 20:48:07 2010 +0000 Took out old reference to mysql version number and replaced with generic text commit cf2ee6b5840d8c070f6eff3110fec8228834744e Author: tdreszer Date: Thu Mar 25 20:09:35 2010 +0000 Last minute addition of Zinba peaks commit 7832aef4a39e78910dafce9f560c810883940821 Author: hiram Date: Thu Mar 25 20:08:11 2010 +0000 initial browser up and running commit 8f90b5b8da81232d2dacb7608de6053ca89de7a4 Author: hiram Date: Thu Mar 25 20:06:23 2010 +0000 adding susScr2 to the build commit 160778424cec45c02f91ee8fc05c768aa5a2b813 Author: hiram Date: Thu Mar 25 20:05:34 2010 +0000 initial files from makeGenomeDb.pl commit cb306459363f1d989a9ba3191df45e16eff02cc8 Author: tdreszer Date: Thu Mar 25 18:59:27 2010 +0000 Fixed bug that prevented non-metaTbl metadata from showing up without special flag commit bda273208f06bfd255d57597fa5e60aaf663d180 Author: angie Date: Thu Mar 25 18:28:56 2010 +0000 Added ikmc (new name of komp). commit 63172c1e0326b11ff50c05cd669d430f8e4f8f47 Author: angie Date: Thu Mar 25 18:24:48 2010 +0000 Renamed komp to ikmc as requested by contributor Carol Bult. commit f1af24c6436dd5411843bf1ea3fd02597674f1a1 Author: tdreszer Date: Thu Mar 25 18:16:58 2010 +0000 Added Zinba peaks to FAIRE portion of Open Chrom commit 2a87806c9a26c1a0ef66604797db0a5db462d087 Author: angie Date: Thu Mar 25 17:53:34 2010 +0000 Hook ikmc into komp code, for table name change requested by contributor Carol Bult. commit fc7c93ff626d2fc9ab11b1e65635aed07bab6b12 Author: angie Date: Thu Mar 25 17:46:01 2010 +0000 Use hAllocConnTrack instead of sqlConnect or hAllocConn to support profiles in hg.conf. commit d5426112769b90d77d216b6563875af74a4729cc Author: angie Date: Thu Mar 25 17:32:12 2010 +0000 Moving bam configuration code from hgTrackUi to hui to support bam in multi-view composites. commit f7e5e65b02fec997235eb404e5a4701ab2742749 Author: angie Date: Thu Mar 25 17:27:26 2010 +0000 Added an eCfgType for bam, to support bam in multi-view composites. (Should eCfgType be in hui instead of here?) commit 24b5a9966703bbf6450d5defbb27cd1526f9d21e Author: angie Date: Thu Mar 25 17:23:14 2010 +0000 Use hAllocConnTrack instead of sqlConnect or hAllocConn to support profiles in hg.conf. commit 8469cd117a81ac7ea80e02c66a71bf606f5405e7 Author: kent Date: Thu Mar 25 17:11:09 2010 +0000 Adding utility functions to get darker colors. Using one of these to darken text when primary color is too light. commit e375ef183408dce709131656f846d54afac90ca4 Author: angie Date: Thu Mar 25 16:56:55 2010 +0000 Copying komp definitions to ikmc to support table rename requested by contributor (Carol Bult). commit 7d484e1dbef793201647f32174177dd688067534 Author: antonio Date: Thu Mar 25 16:36:12 2010 +0000 changing tableCoord info commit 83ad20edafa4ddca88eb764de1bae10ba245c3e2 Author: antonio Date: Thu Mar 25 16:29:55 2010 +0000 adding missing .html extension commit 5b412c4f4e219c45674456d3dfe1a5ea3796c657 Author: markd Date: Thu Mar 25 16:16:22 2010 +0000 fixed stupid bug that caused -idMatch to do the exact opposite of what it was suppose to do commit f0dc185f9923d1afcaa6ae063ae939478284fd39 Author: galt Date: Thu Mar 25 15:00:12 2010 +0000 "Encode release log update" commit 489e94985c8b3e5a6152baf50a4b40847d490918 Author: galt Date: Thu Mar 25 15:00:10 2010 +0000 "Release log update" commit 45ddc8223222071f8d4e86b63b37afe84a87834a Author: cline Date: Thu Mar 25 00:02:35 2010 +0000 Re-added CH12 commit b8bcf6bf9eb48a35b4f2487f6896044cc1fc93f9 Author: braney Date: Thu Mar 25 00:00:09 2010 +0000 add bigWig commit 1a4860868ce74f129361e2c1cfe8263cab94a4b6 Author: cline Date: Wed Mar 24 23:57:47 2010 +0000 Adding CH12, provisionally commit 84e7078088f521777877861dd304c613aeebbca6 Author: kent Date: Wed Mar 24 23:40:11 2010 +0000 Adding info on type factorSource. commit 536b432df9cd3c79677d942592e4bb11bba11f4a Author: antonio Date: Wed Mar 24 22:27:06 2010 +0000 Elephant release commit 0b7c9a9bc56bd3e0893c270aafbc0e37a5ad6365 Author: antonio Date: Wed Mar 24 22:21:26 2010 +0000 Elephant release commit daa6e097d445da2b44ee4293d2e27cf3a53ea580 Author: kate Date: Wed Mar 24 21:39:03 2010 +0000 1. Allow control terms to be used with any variable 2. Add co-PI to lab metadata commit 154ead9a50f458c922ec10dc5468d2c4aca1715d Author: tdreszer Date: Wed Mar 24 21:30:50 2010 +0000 Peaks and Points oh my commit 07a992240ee7186e68b6409e0356e244f1491f71 Author: hiram Date: Wed Mar 24 21:18:33 2010 +0000 it is EXE not EXT commit 0ebbe2fe5cb68bd5226f04e48e51b3c1dd09d87c Author: tdreszer Date: Wed Mar 24 20:37:05 2010 +0000 Added missing JunD description and antibody validation document variable commit a10517526fe09a6d6af40f18f46da9ceaaede248 Author: tdreszer Date: Wed Mar 24 20:35:48 2010 +0000 Added link for antibody validation documents. Now if we can just get some. commit cf28c5a948c32a947431a1b6bef0b3315cc1994a Author: tdreszer Date: Wed Mar 24 19:02:11 2010 +0000 Cleaned up the composite and dataType suffixes commit 77f7d6d241bf844feae53c6cfce0dd3c63b0b4ab Author: kate Date: Wed Mar 24 18:24:31 2010 +0000 Add data agreement suffix commit 38391543c828ab3eae973ee6e69606731c2763ec Author: krish Date: Wed Mar 24 18:08:00 2010 +0000 remove all README stuff commit dfd87f5bb8e68c89e3f9541c82a472490c20a75d Author: tdreszer Date: Wed Mar 24 17:37:12 2010 +0000 Check for metaTbl before querying. commit 69e43d49dcb885f665016d60dbc809c0d45dc915 Author: mary Date: Wed Mar 24 17:18:18 2010 +0000 changed script so that can also check genome-mysql commit 2b837bd6a61620d15a709d76f56b14a61c0eab8f Author: kuhn Date: Wed Mar 24 17:16:58 2010 +0000 moved ailent array lifts (from hg18) back to variation group commit 83fb5e00efdb719f2c84ffef113cba6c5b04d3bd Author: galt Date: Wed Mar 24 15:00:18 2010 +0000 "Encode release log update" commit 4687b9441d27f72ee5661d8a747171b558c579a3 Author: galt Date: Wed Mar 24 15:00:14 2010 +0000 "Release log update" commit f6b7cc868ec08d3f67675dbde50a0f24123e0cd5 Author: kate Date: Wed Mar 24 03:35:36 2010 +0000 Change to file/tablenaming conventions commit 95a8db06ef4b8c263cc5ee7dc3593fcaaa80e16d Author: kate Date: Wed Mar 24 03:16:26 2010 +0000 1. Special handling of 'None' 2. Table/filename gen uses view and replicate last commit 4703d176503313b49ea4142f2cea44be1462e4e3 Author: kate Date: Wed Mar 24 02:50:02 2010 +0000 Proper error if CV term is not registered commit 5dce6669f098683dcab577e79de76740b04df060 Author: tdreszer Date: Wed Mar 24 00:59:42 2010 +0000 Expanded to a near complet sort order list, added noMetaTbl option to compare old and new metadata methods, expanded fileMask to include bigWig, bigBed and BAM. commit 3aa6f9d32b299678aebda5c947012fb20f1f4a21 Author: kate Date: Wed Mar 24 00:13:56 2010 +0000 Add track group commit 8ebe05229894c81d1c85ecb37949ad945729f064 Author: markd Date: Tue Mar 23 23:19:18 2010 +0000 make functionality match usage message by making the database optional on the command line commit 364e0352c49d24d42606e6367cf8adfbae650ed6 Author: tdreszer Date: Tue Mar 23 23:08:30 2010 +0000 Point peaks should be 1 based. commit f355ba0e28d1b6a6bef85065570c699f82c728b1 Author: hiram Date: Tue Mar 23 22:35:57 2010 +0000 proper priorities on chainNetPoodle and RheMac2 and DanRer5 commit f43369b693686ccd81adc2331d664c0707b870a4 Author: braney Date: Tue Mar 23 22:28:52 2010 +0000 add a couple of tests for bigWig and BAM commit c2e5ffd99e1128ed8f3576a4d45bce72085c89c1 Author: braney Date: Tue Mar 23 22:27:59 2010 +0000 a small test for bigWig commit 942478cec0681c310b465a5a4111df5049ac7cc1 Author: braney Date: Tue Mar 23 22:17:48 2010 +0000 a simple BAM test commit 0952617bfb35c43b8642b05e4ac0b2e49e2b9e05 Author: pauline Date: Tue Mar 23 22:17:20 2010 +0000 Enabled genbank updates for elephant on RR. commit d7552c1fa7e7f58124017531b1309fb619850cbc Author: chinhli Date: Tue Mar 23 21:58:10 2010 +0000 Adding felCatV17e trackDb.chainNet commit 08947dfa5f9c4f8756623d1ec971383cf352f35c Author: galt Date: Tue Mar 23 21:51:36 2010 +0000 oops fixes 32bit error gff3ToGenePred.c:58: warning: cast from pointer to integer of different size make[3]: commit 61c0f8f8004ca39f81acb03630eb6f1a913b83fd Author: rhead Date: Tue Mar 23 21:40:03 2010 +0000 Removed alpha and beta,public from vegaGene and vegaPseudoGene tracks, as they contained the same info. commit 09fde0a38b8cca9ff4f59034120017b41a169ee6 Author: cline Date: Tue Mar 23 20:59:09 2010 +0000 Corrected the BTO URL for MDA-MB-231 commit b609a4b94c83519500a67c84e086f356ff4c5999 Author: galt Date: Tue Mar 23 20:41:18 2010 +0000 "New version number v227" commit fba45afba69e14cf388b9587ac977554d3c318b3 Author: galt Date: Tue Mar 23 20:40:50 2010 +0000 v227 final build commit 89c4d6958682a61eb4364b4cda745a4d8e13b243 Author: kate Date: Tue Mar 23 20:22:37 2010 +0000 Add support for DAF dataAgreementSuffix field commit d5210f3ce6bb469ccb7389f2ccd231dd9b0284c1 Author: kate Date: Tue Mar 23 18:28:38 2010 +0000 Restoring input files for chipseq test (removed due to excessive size?) and adjusting output to match commit 934056123051dab783725cc6a3b6ae7bd4a19b7a Author: braney Date: Tue Mar 23 18:19:39 2010 +0000 first round of HAIB Methyl Rrbs track commit 5c3cf31c9abbe611e665958ff3a8a4eb1bcc8090 Author: braney Date: Tue Mar 23 18:18:26 2010 +0000 first round of doc commit ab498a48fc4ca2cc88b9952644ad8ecd33494624 Author: kent Date: Tue Mar 23 18:10:35 2010 +0000 Making some notes on enhancers as called by eye looking at ENCODE tracks on hg18 around some genes. commit 9b9dc292421019933607459d9058c6758f434076 Author: markd Date: Tue Mar 23 17:10:49 2010 +0000 support using twobit as well as nib commit ea22f949bc9d4a594e6264cc11950581e61dc85e Author: markd Date: Tue Mar 23 17:10:32 2010 +0000 fixed broken tests results commit 849334ad4827cf8551d9ab7aa074c0d1958089a8 Author: markd Date: Tue Mar 23 17:09:47 2010 +0000 added function to get sequence size commit 9acd90e560ab6f048ffb9e98494b5995d121bf12 Author: braney Date: Tue Mar 23 16:27:17 2010 +0000 added support for bigWig validation commit 8c509327481478977da93318f03175fc9107269c Author: galt Date: Tue Mar 23 15:00:06 2010 +0000 "Encode release log update" commit 2d9da69689e89a94e8650f2939bd54b5274609da Author: galt Date: Tue Mar 23 15:00:03 2010 +0000 "Release log update" commit c7f8f4320eed6d3843fb8aadf86eda3ec36b2c36 Author: krish Date: Tue Mar 23 03:56:31 2010 +0000 fixed problem with reading config after chdir commit 635d4197b67cb2c36f4e33a75ab3f1cf580b538e Author: braney Date: Tue Mar 23 00:57:01 2010 +0000 third times the charm. hTrackDb now returns list sorted by priority commit b181e5dadfd8cc606c82f3a6a1cdbb2de2dfc36e Author: cline Date: Tue Mar 23 00:11:01 2010 +0000 Added 5 new cell lines to cv.ra. commit 604c4ae693f8e35bc3675de8a5c66d4869610385 Author: krish Date: Mon Mar 22 23:28:22 2010 +0000 added function to get the gbdb store dir commit 595eb4adbe01551c9e8dab9a3ca05bad9dd645cc Author: hiram Date: Mon Mar 22 19:10:07 2010 +0000 file trashCleaning.sh was initially added on branch beta. commit 87ded502afa3260ce355207142ed758996d4d7d5 Author: hiram Date: Mon Mar 22 19:10:06 2010 +0000 add trash file cleaner and TRASHDIR variable to environment fixup readme on the update race condition commit 1964bc3b20918be21e6feb525442d2f549c4f045 Author: ann Date: Mon Mar 22 18:48:07 2010 +0000 removed public stanzas for Broad Chip Seq tracks, and removed alpha,beta lines from the newer tracks commit f516cf9ada0aee298ddc76fa0429b825e265a585 Author: hiram Date: Mon Mar 22 18:32:53 2010 +0000 file dbTrashCleaner.sh was initially added on branch beta. commit 8fecd0280d31e8a6db05ba10bdf4d8cde4ea13cb Author: chinhli Date: Mon Mar 22 16:55:46 2010 +0000 Completed genbank, cgpIslans, BLAT server commit 21efacdca5188ca88dab4ee5c2a77b30a4b3366f Author: katrina Date: Mon Mar 22 15:44:56 2010 +0000 In credits, changed link to email Terry Furey to display his name rather than his email address commit 6e0635f300e370fd76a86d22471a390eb421089c Author: galt Date: Mon Mar 22 15:00:06 2010 +0000 "Encode release log update" commit 81806b2178f5c073d975609aecb037160a098c43 Author: galt Date: Mon Mar 22 15:00:03 2010 +0000 "Release log update" commit 00f25204cf79ce57b14a2797ab83b2470bd76a9d Author: pchan Date: Mon Mar 22 04:18:14 2010 +0000 add selfHomologs track commit 6bfbd9d025a09a302721522bbd928bde4aefd3a8 Author: braney Date: Sun Mar 21 18:03:25 2010 +0000 add support for validating bigWig commit 0b77434053542be2d8bfa7a3c08bddf648c2e4ce Author: braney Date: Sun Mar 21 16:42:12 2010 +0000 some view changes commit 1d6880438a1e07efab25cffacdb976e23a03a8f4 Author: galt Date: Sun Mar 21 15:00:06 2010 +0000 "Encode release log update" commit 0ddbbc832aa8401a0c1635a8c54d7528c0eeb57d Author: galt Date: Sun Mar 21 15:00:03 2010 +0000 "Release log update" commit 5f4a0b24f01d4e65d460a7eb427da95b2cb06f3d Author: markd Date: Sun Mar 21 04:05:28 2010 +0000 fixed incorrect syntax in last change commit 61a923e4dbfecee31a826b62f8f9d37fd010b582 Author: markd Date: Sun Mar 21 03:58:53 2010 +0000 added ignore entries, removed old ones commit 6153447d1d3bad585b28d8b47511541a350a4676 Author: pchan Date: Sun Mar 21 02:53:18 2010 +0000 rearrange refseq detail page section order commit 06d27e4eacf2709413d0ca77fe6856a834523777 Author: pchan Date: Sun Mar 21 01:02:55 2010 +0000 rework refseq track detail page; add gene tree commit 3b8fb9dfd3ed75dc5539c2d8fd694035ce000c6e Author: pchan Date: Sun Mar 21 01:02:15 2010 +0000 add geneTree.c for creating gene tree commit 3a9e490c4d21aa0c3d7e8ca6bb9e9fc0cb93385d Author: pchan Date: Sun Mar 21 01:01:28 2010 +0000 add geneTree table commit 2e5b4c777b7bdaa85bd884f5c14f15f9c52e5345 Author: markd Date: Sat Mar 20 15:43:19 2010 +0000 fixed various issues with error reporting commit 15ae003fd61c36480b756129acdd0c5fd6d51e1d Author: markd Date: Sat Mar 20 15:32:13 2010 +0000 spec unclear where phase is allowed, so don't reject for non-CDS feeatures commit d5d7969ef5af52aaff83f09e8aee60b43ce5c47f Author: galt Date: Sat Mar 20 15:00:07 2010 +0000 "Encode release log update" commit 78460603510e13f428c25aa12c1b552834de5413 Author: galt Date: Sat Mar 20 15:00:03 2010 +0000 "Release log update" commit e42c97249e973d8ed3b26e836d503bf3c5c1a558 Author: markd Date: Sat Mar 20 14:22:17 2010 +0000 wait on process group rather than individual process to prevent deadlocks in certain cases commit 683723f7f63242f373d2a1c2f25d749945cbb9da Author: rhead Date: Sat Mar 20 01:03:04 2010 +0000 Changed the assertion that we synchronize genome-mysql with the main database daily to say that we synch it weekly, which is closer to the truth. commit db0be8f740072ed0c89eb0e075eb3ca1550f839c Author: tdreszer Date: Sat Mar 20 00:15:36 2010 +0000 Preferably use the new metaTbl over the trackDb and fileDb.ra settings. commit fcea5bfb5b428d471a3d2916f51b005ea97ed390 Author: kate Date: Fri Mar 19 23:43:59 2010 +0000 Consistency in layout commit 155367fa64fd70d64f485c5c4b66a484c21ab639 Author: braney Date: Fri Mar 19 23:16:37 2010 +0000 add a check in BAM validation to require that chroms be specified and that they are the correct chroms with the right sizes commit c7c671753fc82d7cd108c1d3866775fbbf845784 Author: hiram Date: Fri Mar 19 23:04:18 2010 +0000 file tagGoldenPath.sh was initially added on branch beta. commit 35b9f94ab2ebfac8bb21e51a06e4c89e1ae4e6a9 Author: hiram Date: Fri Mar 19 22:52:22 2010 +0000 file loadUpdateGoldenPath.sh was initially added on branch beta. commit ae2061aab4848ea0e44e7710c59f792e2cbdf365 Author: hiram Date: Fri Mar 19 22:33:38 2010 +0000 mention order of trackDb tables and what it does commit 71d9cea84c2a911889f98b8e74f060c6be8c0004 Author: fanhsu Date: Fri Mar 19 22:30:03 2010 +0000 Updated Reactome tables in proteom DB using V32 data files from Reactome. commit f1c5fd28d4d38b8fcc4e6574985c1f9caff4e43f Author: krish Date: Fri Mar 19 22:25:00 2010 +0000 fixed some ENCODE Open Chromatin short labels commit be9af294d90165c4f959f7e3d805c637616f3d55 Author: hiram Date: Fri Mar 19 21:33:41 2010 +0000 update to talke about how to use trackDb_localTracks table commit 36dc5b027b515466b54770b2f2512cb548e6593a Author: antonio Date: Fri Mar 19 21:25:37 2010 +0000 aplCal1 release commit 1547fe49b088b03264bb3cc7db81e84eec9ee926 Author: tdreszer Date: Fri Mar 19 21:25:26 2010 +0000 Altered API to put sql connection inside lib API commit 9fcf849dd7312e339241527e93711f8afe5486ab Author: tdreszer Date: Fri Mar 19 21:24:17 2010 +0000 Added support for hgTrackUi to support metadata from metaTbl instead of trackDb commit 4229c2230522085e63a47861dae66031316a6572 Author: tdreszer Date: Fri Mar 19 21:23:14 2010 +0000 Added support routines for hgTrackUi using metaTbl commit 28afc92c8e57a1b73c425b44f8e9d4f78aa8dfd8 Author: antonio Date: Fri Mar 19 21:20:15 2010 +0000 aplCal1 release commit e788b267bb4c9712e0737acb5e792dc3529f0fe9 Author: hiram Date: Fri Mar 19 20:32:17 2010 +0000 file README was initially added on branch beta. commit 49435fc9ed116999a2920afd7ac23e428ca4a20e Author: ann Date: Fri Mar 19 20:30:28 2010 +0000 for wgEncodeBroadChipSeq tracks, enabling new tables on beta commit 70db141fc3d60138035848f8980604326a1fb184 Author: ann Date: Fri Mar 19 19:50:49 2010 +0000 reordernig yeast commit e1947977739a3fb144d85cd09164502761aa2e5e Author: ann Date: Fri Mar 19 19:46:34 2010 +0000 fixing tags commit a4e9369a7a11cb7557f192797f16c7011ae9bcf0 Author: krish Date: Fri Mar 19 19:30:28 2010 +0000 fixed some ENCODE Open Chromatin short labels commit 401172c2adf591e4109796fc9b501378498ee2f8 Author: angie Date: Fri Mar 19 19:16:37 2010 +0000 Grim reaper can take sparseData but not bitmap (esp. when we touch bitmap), so if bitmap exists but sparseData doesn't, get rid of bitmap. To reduce debugging headaches, use maybeTouchFile instead of touchFile. commit 3ea2c0cb21d68873dc59088335fdc1cb2450b21d Author: angie Date: Fri Mar 19 19:11:24 2010 +0000 Converted touchFile to maybeTouchFile because ownership of an existing file (not just permissions) can cause problems. commit e7a2f7fdb7150ffedb607b8170a817b11b8b22b2 Author: ann Date: Fri Mar 19 18:58:14 2010 +0000 stripped white space and new line from tdbQuery output of shortLabel and longLabel commit ab378c0efcfd51f87c4db51c79bee00af848dc0d Author: fanhsu Date: Fri Mar 19 18:38:15 2010 +0000 Updated logic for tRNAs to fix problems with image file names containing '?'. commit b5be087ceaf44f186d1bab2e0eac1e8d312c10b2 Author: antonio Date: Fri Mar 19 18:30:00 2010 +0000 fixing ordering of chain/net commit 1287233ca713e71fb0741a42b267e195a2477c88 Author: antonio Date: Fri Mar 19 18:22:57 2010 +0000 fixing ordering of chain/net commit 37106017726c58367e3d29ec0e9bf87f2a5173d8 Author: braney Date: Fri Mar 19 17:53:10 2010 +0000 fixing my earlier fix. The "right" solution is to make sure that we keep the list in the right order when we return the list. commit 0c14db0eb730456ccd79d0fece7d19be44e7ea09 Author: tdreszer Date: Fri Mar 19 17:38:09 2010 +0000 The most useful query yet: all objs that contain every var=val pair provided. commit 6c8ed0286b418cd760f6d96b24a9db5680564480 Author: tdreszer Date: Fri Mar 19 17:36:50 2010 +0000 This should get undossified. Why isn't it commit 2baa170158e6559da0a51337c10aa626758aa79b Author: katrina Date: Fri Mar 19 17:20:50 2010 +0000 changed release alpha to release alpha,beta and release beta,public to release public for release 3 of the Open Chromatin track commit d07050c4fbc61985177a229856de4b5338392550 Author: hiram Date: Fri Mar 19 16:55:31 2010 +0000 file fetchHgCentral.sh was initially added on branch beta. commit e069c1815706be7f4b18e70cdf204f4897243820 Author: hiram Date: Fri Mar 19 16:50:02 2010 +0000 file updateHtml.sh was initially added on branch beta. commit 9da941c80260069c0f90739a7cac40dfa75c0c84 Author: hiram Date: Fri Mar 19 16:38:10 2010 +0000 file loadDb.sh was initially added on branch beta. commit 392f730c8f4f7a6abbffbe7af9fdf9654e09ed89 Author: cline Date: Fri Mar 19 16:27:58 2010 +0000 Removed a couple of stray HTML brackets. commit 003a356f4ed3d02f40542b88dd7ce768cb643170 Author: cline Date: Fri Mar 19 16:23:44 2010 +0000 Removed a bunch of errant apple span tags from index.html commit 7b5659f6b0c0c47357925d14f97bb0893d8bd437 Author: hiram Date: Fri Mar 19 16:19:34 2010 +0000 rsync command and hgdownload location are parameters commit b67403a113a587f4177e9ba728aeb55140a67344 Author: hiram Date: Fri Mar 19 16:12:01 2010 +0000 only one directory allowed for argument and indicate where this is all taking place commit 4d0e16f69392d633bcfcce7d614f7d49baa079f4 Author: cline Date: Fri Mar 19 16:11:53 2010 +0000 Added a news item for Release 2 of the UW Affy Exon arrays commit 29b35ea7fd26f3276e9b54c042ab0a8bbe681e5d Author: galt Date: Fri Mar 19 15:00:07 2010 +0000 "Encode release log update" commit c6cf1f10fd9deef9cbfb900a743eb166ab4be42f Author: galt Date: Fri Mar 19 15:00:04 2010 +0000 "Release log update" commit 6d98f013f3b6ca278b634429285963757284a199 Author: markd Date: Fri Mar 19 06:04:19 2010 +0000 fixed crash on nodes with no ID or Parent attrs commit 910d4f6fd4c3d3760ec9502f6fe875ebb1395e11 Author: kate Date: Fri Mar 19 04:12:37 2010 +0000 Fix formatting commit 2c1014f0f82c9b7a54a2275d30bce20466b37edc Author: kate Date: Fri Mar 19 03:45:32 2010 +0000 Fix munged URL commit a318cffb531c0c970ae382629e39443ff3405eee Author: kate Date: Fri Mar 19 03:26:10 2010 +0000 Tweaks to ENCODE survey notices commit 014dfa81a15718fa95b0aa32c2db3d403573e3e5 Author: markd Date: Fri Mar 19 02:24:35 2010 +0000 report multiple conversions errors before failing commit b747d13102238189316d11f295632285a5dcac12 Author: hartera Date: Fri Mar 19 00:23:08 2010 +0000 Changed file names to match table names and added downloads and metadata in trackDb for CRG Mapability subtracks. commit 6e7b975cfb1cd6c574e177a35565a1692f93f068 Author: rhead Date: Fri Mar 19 00:15:17 2010 +0000 Fixed the syntax of the release tag setting (thanks, markd) and made a few more small edits. commit 62a81a7ef332cdf5dfa3dd9d21af257e28c17257 Author: braney Date: Thu Mar 18 23:55:31 2010 +0000 remove slReverse to fix problem with menus in hgTables being in the opposite order. Used to be that pruneEmpties ended up flipping the list commit faf88ee97aefb21c0975540772c96051e474f832 Author: hiram Date: Thu Mar 18 23:40:17 2010 +0000 can now fetch all files in goldenPath//database/ commit 18059121161396b0360b87634412d5911ba7fe20 Author: tdreszer Date: Thu Mar 18 23:38:36 2010 +0000 Added metaTblPrint and keeping in one directory for now. commit f15b8ce965083d082483705c7bab07363e8f1e10 Author: tdreszer Date: Thu Mar 18 23:37:51 2010 +0000 Initial print functionality but just starting to test commit aee906a12426162b85a2a9f400cdb9b12dc2685a Author: tdreszer Date: Thu Mar 18 23:37:24 2010 +0000 Undossified and using changed API commit ab250afea44083955b88d407714e12dceae0f8cd Author: tdreszer Date: Thu Mar 18 23:36:18 2010 +0000 Extended API for query and print functions commit 1894183c20a5c1f19d379b346202e812f2fecf5b Author: tdreszer Date: Thu Mar 18 23:35:14 2010 +0000 Undossified commit dcfce7ff421d9de7af2cc3e34ca698227e7e0f10 Author: hiram Date: Thu Mar 18 23:34:09 2010 +0000 this will fetch all files for a given gbdb directory commit ede1ace55ff76cafc234fa23be530a0882812221 Author: chinhli Date: Thu Mar 18 23:24:53 2010 +0000 Adding felCatV17e - Cat - Felis catus commit adba38bb46b561ccfc6704d95cbac7bee03f4959 Author: hiram Date: Thu Mar 18 23:24:18 2010 +0000 can now fetch minimal set of gbdb files commit c9fb04889e7011d6ca78fd513c5f0f723744afd2 Author: hiram Date: Thu Mar 18 23:18:59 2010 +0000 can NOW fetch minimal set of database dumps into goldenPath commit 89180082cfe0cd69cbb19063e3242c122a506a6a Author: hiram Date: Thu Mar 18 23:18:24 2010 +0000 can not fetch minimal set of database dumps into goldenPath commit ec3452a89b39637ca9c440de59ee75eb577a25e0 Author: cline Date: Thu Mar 18 23:12:36 2010 +0000 Fixed a typo, a T with a leading space. commit 1ef77887eb51a15ca400229ade999f919a39c93b Author: cline Date: Thu Mar 18 23:05:52 2010 +0000 Added a missing link for the UW Histone track, under the news. commit 8a107ca72c653aaacc15549efc1ad2508b6d75b5 Author: cline Date: Thu Mar 18 22:55:10 2010 +0000 Added the Feb and March ENCODE news, and a link to the 2010 ENCODE/modENCODE usability survey. commit f7110d6a65d3fc6e9326d026936dd0f65c369620 Author: cline Date: Thu Mar 18 22:54:12 2010 +0000 Added a link to the ENCODE/modENCODE usability survey commit c6a8a2bce90c53825ee9d39413d2013d10cbae9f Author: antonio Date: Thu Mar 18 20:35:15 2010 +0000 even smaller grammatical change commit 57cdff95421cea42facc729d9d01fb5484d4bd92 Author: kuhn Date: Thu Mar 18 18:52:08 2010 +0000 removed rest of files the script makes. thnx, ann commit 7d0e551b0fca0fb22009e0516bcae265eaaf0c8b Author: hiram Date: Thu Mar 18 18:40:13 2010 +0000 initial set of files that can fetch and build kent source tree commit c068f42f775e358691eb9b4956ec1ee7c23e2236 Author: hiram Date: Thu Mar 18 18:34:24 2010 +0000 remove reference to HGCGI in makefile and fix compile warning errors commit c128cc5952496b100e309e32e07656dd1794cfd6 Author: antonio Date: Thu Mar 18 17:59:59 2010 +0000 small grammatical change commit 20ee94d2460af327825626e90cfc5e8b5227485c Author: antonio Date: Thu Mar 18 17:44:30 2010 +0000 Changing session info from 1 year to 4 months commit 549ceda3487405e6575d0162da1bb30dd0cb1215 Author: hiram Date: Thu Mar 18 17:40:50 2010 +0000 adding template file syntax help for the check statement commit 389ba5f7b1d44209b94c8a26c8b323cc252dfd7f Author: hiram Date: Thu Mar 18 17:33:23 2010 +0000 cleaning should do A.EXT instead of just A commit ce5e091443226bd47c038ecb6f19821828834d9d Author: galt Date: Thu Mar 18 15:00:07 2010 +0000 "Encode release log update" commit a8537bbfcd376cb88ba31900da82f5ff63ee6496 Author: galt Date: Thu Mar 18 15:00:04 2010 +0000 "Release log update" commit 44897db2ba438f056d7b10cd2119dcf79ad1e092 Author: giardine Date: Thu Mar 18 13:33:42 2010 +0000 fixed typo commit a10c22585cfeab78595c9825a3da0496193a546f Author: tdreszer Date: Thu Mar 18 01:56:26 2010 +0000 Initial check-in of utility to update/add/remove metaTbl entries. commit 85b7e0e7222317cc51ca9b9c7e5244d63b3cffe4 Author: tdreszer Date: Thu Mar 18 01:53:09 2010 +0000 Needed another flavor of chopByWhite that respects quotes commit 6895df978b106f53a0e23b6426c50f4dc87a94ff Author: tdreszer Date: Thu Mar 18 01:50:56 2010 +0000 Thought this quick lookup of row count would help commit d9e8e8c89e12bbd67b922472ff6979bdb0690af3 Author: tdreszer Date: Thu Mar 18 01:49:29 2010 +0000 Finally making progress on a metadata table. commit 7479340e053e3e8e3993f54823ce168d448cb3ad Author: kate Date: Thu Mar 18 00:51:28 2010 +0000 Generalize survey link commit 48d4311fda99ecce9cc6bc694bea43af8c03b02b Author: rhead Date: Thu Mar 18 00:23:37 2010 +0000 Added a note about how release tags get parsed. Thanks, Brian. commit 9cd13193d8088f1896cb6d17a40e5f51c4cd1057 Author: rhead Date: Wed Mar 17 23:53:21 2010 +0000 b0b hates the labels. Reverting to label only on trackDb_public. commit 9adb1a73b1ded8c38c3eb5bb3f8e96e25c56427d Author: kate Date: Wed Mar 17 21:27:33 2010 +0000 *** empty log message *** commit 42de812ef10d8bfe9f8e27894ed407f3f51e249a Author: kayla Date: Wed Mar 17 20:44:15 2010 +0000 added a link for the UW Affy Exon track commit a077080e019102fcf8e6ddd0c848d30b3ce53c44 Author: rhead Date: Wed Mar 17 19:39:24 2010 +0000 Added labels to the output lines! commit 4f64ae62801d1e10cde6fafb09c9d8c73516d987 Author: hartera Date: Wed Mar 17 18:17:20 2010 +0000 Added metadata information for the CRG Mapability subtracks. commit 415cc5884881943c451a01108c90ede95db3a217 Author: kate Date: Wed Mar 17 16:14:30 2010 +0000 Remove restriction timestamps from ENCODE Mapability as data restriction has been explicitly waiived by the labs (not part of the main production effort). commit ed6a73273067e7e686697bdb9b85a3c640862a39 Author: galt Date: Wed Mar 17 15:00:06 2010 +0000 "Encode release log update" commit 04baeba6bf1556bd1ea54a9c436be1f1d2edb11c Author: galt Date: Wed Mar 17 15:00:04 2010 +0000 "Release log update" commit 3e8cc30c3b38c06961eb6d22bbac3839a7c1a86d Author: donnak Date: Wed Mar 17 01:10:23 2010 +0000 Edited. commit 67c9e02edbffa875aa6f000fa5ce06692cd80863 Author: krish Date: Wed Mar 17 00:49:12 2010 +0000 new types support, warnings now added to notes file commit 2b0abd130c3bf5cfb5476c4d36fc50b6de0e63ed Author: braney Date: Wed Mar 17 00:43:04 2010 +0000 add test. Prolly need to change the target to something other than test? commit 6382291162ab5520ae8869a1d3585798cf803833 Author: braney Date: Wed Mar 17 00:42:39 2010 +0000 fix from adk. MafSplit was clipping off the first base of every split commit d7a8e4201df20c883d2f49eb8c7456ff1334ebd6 Author: braney Date: Wed Mar 17 00:39:47 2010 +0000 add a test to catch a problem with where regions were clipped by one base at the beginning commit 654d70dcf0e0ac3d64fd8bc82c4a57c1aa065d7a Author: galt Date: Tue Mar 16 22:53:08 2010 +0000 typo commit cc6f36055e9a14a95749d99c2a4baeb02fc6e164 Author: vanessa Date: Tue Mar 16 22:26:39 2010 +0000 changed phylo priority commit 03af1bc5ac7a2ad0bba0c7cd4155eacbdc1776b1 Author: chinhli Date: Tue Mar 16 22:10:42 2010 +0000 Adding felCatV17e support commit e79e0dd966dc3a3651f6f8734f5653c99dc7f0f9 Author: hartera Date: Tue Mar 16 21:35:41 2010 +0000 Added missing subTrack label for release alpha version of Mapability track. commit d2611a8bbfc730708339cd24fec68ff81ad8d491 Author: antonio Date: Tue Mar 16 21:33:40 2010 +0000 Reordering chains and nets commit a8f93b94de9c8c2914b97e6d65d64846ac6f5a59 Author: antonio Date: Tue Mar 16 21:27:52 2010 +0000 Reordering chains and nets commit e0a175b95d23090caf3ade99a029751eaa9a2b16 Author: ann Date: Tue Mar 16 20:59:00 2010 +0000 now that we have encode tables on more than hg18, and in more than one kind of trackDb.ra file, I am switching this script to use tdbQuery. commit 152b8f2163355f66f94a3f1dcf4064a3a8f657c0 Author: chinhli Date: Tue Mar 16 19:34:59 2010 +0000 Complete repeat mask, simple repeat, fix gap using comp.gap commit 458530d0800db44fc16890252ea1d88fbba5c9f2 Author: vanessa Date: Tue Mar 16 18:40:30 2010 +0000 changed phylo order commit 2fd1d38d3251c2504e3b56daa7ba51a3363bfb54 Author: kuhn Date: Tue Mar 16 18:38:23 2010 +0000 removed call to updateTimes.csh in localbin dir commit f2b5ed39663662a44105126409e88504e9c15655 Author: kuhn Date: Tue Mar 16 18:22:47 2010 +0000 changed phylo image to match ordering of subtracks commit 964bdf16f63ca55d076e6d81f13bea4dd40117f3 Author: kuhn Date: Tue Mar 16 18:15:12 2010 +0000 reordering chainNets to match phylo tree commit a5acce2769a18d26ac7b82baaddc8b11e12dc029 Author: rhead Date: Tue Mar 16 18:09:02 2010 +0000 Added a check for trackDb_public when the table given is trackDb. commit acc23c93fa816c9c05ddcc5b2469e54b80cc6e72 Author: kuhn Date: Tue Mar 16 17:45:10 2010 +0000 reordering chainNets to match phylo tree commit dedb5d1ef883ae0ae9b5393f2f1d2a5e3df829b8 Author: katrina Date: Tue Mar 16 16:58:16 2010 +0000 made a few minor edits commit 7f9e8b7ee41b6caf8bc00ff50b68cbfb055a2293 Author: katrina Date: Tue Mar 16 15:46:56 2010 +0000 added noScoreFilter line to tRNAs so that the score filter doesn't display in hgTrackUi for that track commit 74d4c0f8c277f3f90c0d33c4be6c66fe58e333ef Author: galt Date: Tue Mar 16 15:00:06 2010 +0000 "Encode release log update" commit e9f14bbfb375dde1358a0e0cb39e62b6a2efbbcf Author: galt Date: Tue Mar 16 15:00:03 2010 +0000 "Release log update" commit e6d9a416b222460ba4659dd1e9c04491bc79cae8 Author: angie Date: Tue Mar 16 06:58:22 2010 +0000 Use knetUdc (put udc underneath samtools' network code) if KNETFILE_HOOKS. commit ae9508d0aefdf1221f69ce3e5d3e4ad66db9fa43 Author: angie Date: Tue Mar 16 05:58:17 2010 +0000 IKMC Genes (komp) update. commit d559baab71ff5a14a70f9f635791c0fe34e3a5d1 Author: galt Date: Tue Mar 16 02:45:37 2010 +0000 begin support for 3way tagging alpha beta public commit 34994945715c3f457e141e738b942928fbfdb39e Author: galt Date: Tue Mar 16 01:48:10 2010 +0000 v227 preview commit f6e3d50b363ff03f890dfb4c8ecda443a5b88385 Author: tdreszer Date: Tue Mar 16 00:42:23 2010 +0000 Fix bug with map area clicking commit dd685860a23100a8f8bc4103c5ec6ae651c4f379 Author: tdreszer Date: Tue Mar 16 00:36:32 2010 +0000 Minor change to clarify, though I don't think postTheForm has ever been called without the href commit 758211399c031723669c6ef9fc8dca552206755f Author: braney Date: Tue Mar 16 00:22:10 2010 +0000 take out colorByStrand on signal tracks which aren't colored by strand commit e0414eeb6b5a9050ecef50b811ed9119ad57ed5b Author: krish Date: Mon Mar 15 23:34:11 2010 +0000 added flag to output lists of files and tables commit 871184a05a4ccad99e2859642d7198a374678724 Author: hartera Date: Mon Mar 15 23:21:45 2010 +0000 Added a restriction for the maximum window size for the alignments tracks of the Burge RNA-seq track. commit 5bfb6822a8ed457d8db82d5716ce9198dbea8954 Author: krish Date: Mon Mar 15 22:58:29 2010 +0000 added script to generate changes notes for ENCODE tracks commit 39c7b7c33bd86ab388624a735d299e0ef2481297 Author: ann Date: Mon Mar 15 22:56:54 2010 +0000 un-hard-coded hg18 from script commit 3893c30cb693dc3e603636d9a9d83a2b550868fb Author: krish Date: Mon Mar 15 22:23:08 2010 +0000 added script to generate changes notes for ENCODE tracks commit c39d0587cdaf5af045c8e677bf2a4c25d0a1277d Author: ann Date: Mon Mar 15 21:42:34 2010 +0000 Massive change of all instances of ($o_date/$o_db) to ($o_date). This is because there was a recent change to hgcentral.dbDb adding much more detail to the description field. That made ($o_date/$o_db) redundant. Found by Ann and sanctioned by Angie. commit fae462ee93ee096b6996834ab05f521082dc2b02 Author: angie Date: Mon Mar 15 21:32:49 2010 +0000 In bamLoader, report any warnings caught by errCatch even if there was no error. commit dd0a20756b21732dbd2a3751c8606269c9bb01b1 Author: fanhsu Date: Mon Mar 15 21:19:29 2010 +0000 Updated the alternate message for tRNAs when image is not available. commit 1f860e22cadafe984163e02024075123c02d7058 Author: kent Date: Mon Mar 15 20:49:42 2010 +0000 Improved an error message. commit 5cd0b45edd3a69e5d92b768643c2a9a142473e4c Author: hartera Date: Mon Mar 15 20:44:38 2010 +0000 Shortened short labels for Mapability subtracks for CRG data. commit 69b7f4cc94271c584df734c6387f16c97c192bbc Author: pauline Date: Mon Mar 15 20:15:46 2010 +0000 Added the other two file formats implied by bbi for clarity. commit 86605308c4a228b82e0a9d90eb73496def77265c Author: tdreszer Date: Mon Mar 15 18:50:53 2010 +0000 Fixed minor css warning commit 510e810cf74f92c9cf2d8fe6ba9a2a6735c2c5c7 Author: rhead Date: Mon Mar 15 18:15:24 2010 +0000 Changing from a 2-state trackDb (alpha,beta), to a 3-state trackDb (alpha,beta,public). commit 53b9037766864272634b38a0401256491d079b70 Author: pauline Date: Mon Mar 15 17:58:44 2010 +0000 Fixed references to old location of tables on beta. commit 70923a396ec59095772d4c85ab577c7b5ffe79d1 Author: kate Date: Mon Mar 15 15:01:46 2010 +0000 Pipeline 2.0 commit 73ac662f221816533eabb31704565c900e4c0364 Author: galt Date: Mon Mar 15 15:00:07 2010 +0000 "Encode release log update" commit 5471b19b7baa7eddf654a5f46bdd5c5b644a0e62 Author: galt Date: Mon Mar 15 15:00:04 2010 +0000 "Release log update" commit e134d449bc1bc4ae4c80afbe3609c7e7e1d8186c Author: kate Date: Mon Mar 15 04:45:46 2010 +0000 Update for pipeline 2.0 commit 423f3e8a940927b844fa5fa4087ebde3a9a0b911 Author: kate Date: Mon Mar 15 04:40:32 2010 +0000 Update for DAF 2.0 commit 43f9e9d4bd98add0da8512dc3ba27749cbc15a6f Author: kate Date: Mon Mar 15 04:33:55 2010 +0000 Tweak error msg commit 523c157512e36400b6200cf2113bea71f7a80b20 Author: kate Date: Mon Mar 15 04:22:23 2010 +0000 Add compositeSuffix. Also some edits for readability. commit f0c070c9f4a2c47672607d90b7d376f979bf52bf Author: kate Date: Mon Mar 15 04:20:12 2010 +0000 Update DAF version to 2.0, freeze to June 2010, assemblies to hg19 and mm9, table/file name prefix to 'enc'. Add warning for beta testing. commit de1a560328bf9f65eb8174fef66fcdffe4f1f2ff Author: kate Date: Mon Mar 15 04:07:21 2010 +0000 Merge in wrangler email (will obsolete labs.ra). Add some new labs and remove some aliases to retire commit d81c308e5fd1bad0abfc41591e08e7406321b1b4 Author: hiram Date: Mon Mar 15 04:07:20 2010 +0000 Well, we need a clean in simpleChain commit 5629b9663b55e9d9b605fc707c0580db53d729e2 Author: markd Date: Mon Mar 15 03:03:52 2010 +0000 fixed clean target to recurse correct, but it doesn't matter, since many sub-makefiles don't have clean commit ef360180044d4217b6be76fb97ec911725f4d811 Author: hiram Date: Sun Mar 14 23:26:20 2010 +0000 need clean targets everywhere here commit 60a28f7d064c5eb68fe98d0cf57f3d3eda802fd4 Author: hiram Date: Sun Mar 14 23:24:43 2010 +0000 need a clean target commit 61cc725388de2b564f4c771901cead8b183c4b8f Author: hiram Date: Sun Mar 14 23:20:59 2010 +0000 add clean target and use curly braces on variables commit 71df7bacfcd869b32911290fe260c69a22a59812 Author: hiram Date: Sun Mar 14 23:16:41 2010 +0000 needed a clean target commit ddb26e6f2e985f0a5c13d31a043dbd319d791ad7 Author: hiram Date: Sun Mar 14 23:14:16 2010 +0000 need to clean algo.msg for clean target commit 383890d301e87b54731d881d8effb4b93c1cacee Author: hiram Date: Sun Mar 14 23:07:24 2010 +0000 need to clean hgTomRough commit ce02343ff839b5ba456d04a4c02edd981c615553 Author: hiram Date: Sun Mar 14 23:04:10 2010 +0000 need to clean in g2cCheck commit 36d679266af4a12f6e3b8858e2b17ee6b4075d5c Author: pauline Date: Sun Mar 14 21:53:47 2010 +0000 Fixing a bug I introduced. Oops! commit bb1b56b9f4b05dfb3239caf98869895e59821855 Author: pauline Date: Sun Mar 14 21:51:16 2010 +0000 Editing usage statement for clarity commit 0bdc3fc78f02982a13867a21d61f797f790d36a9 Author: pauline Date: Sun Mar 14 20:34:00 2010 +0000 Fixed some typos, an unmatched quote and clarified description statement. commit 82c096ad59d06ee4e676126492438d33309f1e70 Author: galt Date: Sun Mar 14 15:00:06 2010 +0000 "Encode release log update" commit 9e5acf968a7f57a40e46cbd700b00a31c67fdf94 Author: galt Date: Sun Mar 14 15:00:04 2010 +0000 "Release log update" commit 62049b4c5d58a517ce220e795a91514cbe6b3674 Author: hiram Date: Sat Mar 13 23:01:50 2010 +0000 fix semiUniqName when host name includes : as in: localhost:8080 (from 41,000 ft) commit d9af92b680372610cb68e66beca94caba3f8e142 Author: kuhn Date: Sat Mar 13 19:14:34 2010 +0000 added support for second trackDb field. settings not yet supported. html will probably never be commit d57b31897877cbe1509fbc578d19302bcd8bdc37 Author: braney Date: Sat Mar 13 17:51:01 2010 +0000 a new function commit 6beeaba0df45b1e6045416e0cf42195e879e1712 Author: galt Date: Sat Mar 13 16:00:06 2010 +0000 "Encode release log update" commit 9f901decf432dcd7597e17a47ddfef71094db194 Author: galt Date: Sat Mar 13 16:00:03 2010 +0000 "Release log update" commit 9990183a15827555b66bd4973fe0919494fe596b Author: donnak Date: Sat Mar 13 02:06:03 2010 +0000 Added tetNig2 announcement, also aplCal1 announcement commented out. commit 3ea04f7429c596101069d1bf909625d945498be6 Author: donnak Date: Sat Mar 13 02:05:15 2010 +0000 Edited. commit c770b81567eaef747a8604c042c8729e4c7bff2e Author: rhead Date: Sat Mar 13 01:35:07 2010 +0000 Added changes to work with updated tdbQuery that recognizes multiple release tags (like beta,public). commit 0450631ec9e1e543f4ee4f23d1dbedcb5f1e79ff Author: donnak Date: Sat Mar 13 01:33:14 2010 +0000 Archived an item, made some edits of existing content. commit 6767db62d243d2776c36dfce2a265c3a112f2d2e Author: donnak Date: Sat Mar 13 01:32:27 2010 +0000 Edited this file. commit 87794c9488bce40cf952144dae058b8ee53de979 Author: rhead Date: Sat Mar 13 01:31:53 2010 +0000 Added notes about release public. commit 81c841d0073c46b6adcd23fa600903570c83f3a2 Author: braney Date: Sat Mar 13 01:29:52 2010 +0000 make it so tdbQuery is called with -release option commit ff95d2f77b19b87772f82ac86220f663be2f73ff Author: braney Date: Sat Mar 13 01:28:10 2010 +0000 update to understand tri-state release mechanims commit 5bd979cab81c2ac7e7d9f29f5d3613479ebeec67 Author: braney Date: Sat Mar 13 01:15:18 2010 +0000 add release policy paragram, and release notes commit b00a0bc080104a534f0e0c043ac5e206f65f70ec Author: braney Date: Sat Mar 13 01:11:13 2010 +0000 fix a missing color for HeLa rep2 in UwAffyExon trakc commit aeace3e09c17f961d81a84091cdba123cbb00cd8 Author: donnak Date: Sat Mar 13 01:06:35 2010 +0000 Initial edit of this file -- still have to fix up a few things. commit a36efdb46259cbb75e70ee6d37e153f4e6be7e52 Author: donnak Date: Fri Mar 12 23:17:51 2010 +0000 Edited aplCal1, added tetNig2. commit 54a93cc1c22bbbde6bc8cbe0303a56501baed27a Author: donnak Date: Fri Mar 12 23:03:54 2010 +0000 Added aplCal1 & tetNig2. commit 08c9a018b41285daa7045afc16000559e3418045 Author: mary Date: Fri Mar 12 22:34:09 2010 +0000 adding shortLabels for stanzas for tetngi1 commit 38a0e2900f04da3039d6fd1032ff728b6bb8d870 Author: pauline Date: Fri Mar 12 19:25:42 2010 +0000 Changing shortLabels to be consistent across a cell line commit db31b89d5d5179ded6cc445cff3ce970bdd0a2bc Author: ann Date: Fri Mar 12 19:22:35 2010 +0000 this is the only way we could get oryLat1 and 2 to place nicely with the new tetNig2 c/n shortLabels. commit a3967747924d86652e5a86b08330667d6c16ca1e Author: mary Date: Fri Mar 12 19:16:50 2010 +0000 removing file because changing at medaka level instead commit e9ecb5ac2e657b40760b650e555fd8e4dafea40f Author: pauline Date: Fri Mar 12 19:07:24 2010 +0000 Forgot to commit this removal of alphas. commit 0c3ba2af3cec6b44eae459188f460d06811703ac Author: mary Date: Fri Mar 12 19:03:50 2010 +0000 trying to fix shortLabel on hgwdev commit e55c76697d7114927d5458b9fd46cc6073541342 Author: fanhsu Date: Fri Mar 12 18:55:07 2010 +0000 Minor cosmetic changes. commit 227ce9b195489b802eb3b88af645d2424c9ed538 Author: ann Date: Fri Mar 12 18:29:02 2010 +0000 overriding old tetNig1 c/n commit 932157a0fe854af4fb50200387da871cdd9418a0 Author: mary Date: Fri Mar 12 18:26:24 2010 +0000 adding chainNet file because needed to add tetNig2 c/n but there was no trackDb.chainNet.ra file available at this level commit f14a17ca180b149618ac5db2a9804c07daee2916 Author: ann Date: Fri Mar 12 18:18:25 2010 +0000 removed -- it already existed at the stickleback level. commit 7bba69253f6b46d0bafd910ee31ef7e820a79504 Author: ann Date: Fri Mar 12 18:15:00 2010 +0000 making chainNet override for gasAcu1 commit b28f77166bebae0a427ef0005d79a4d022ff7213 Author: ann Date: Fri Mar 12 17:38:59 2010 +0000 swapping tetNig1 c/n for tetNig2 c/n. commit 6dc271167028765a54cc2daa6d168318cc50e844 Author: fanhsu Date: Fri Mar 12 17:13:58 2010 +0000 Added search term for rn4 tRNAs track. commit 9dc7a23030cb0b85ad59997c7b619c044da586ff Author: fanhsu Date: Fri Mar 12 17:12:24 2010 +0000 Rebuilt rn4 tRNAs track using updated data files from Todd Lowe. commit de090b4350943e82135db9e775c5780659ac01c7 Author: fanhsu Date: Fri Mar 12 17:04:57 2010 +0000 Added search term for tRNAs track. commit bed731624acb389227ee1e340daa970921e0ae1b Author: fanhsu Date: Fri Mar 12 17:03:25 2010 +0000 Re-built mm9 tRNAs track. commit 76cdf55b5ad6047eea3d36458fd999e1b2898587 Author: fanhsu Date: Fri Mar 12 16:56:50 2010 +0000 Added search term for tRNAs track. commit b7fc8afa2ecebafbf91daac40e45bd2391bd91eb Author: fanhsu Date: Fri Mar 12 16:50:16 2010 +0000 Re-built hg18 tRNAs track using updated source data. commit 59e29b8f4ea8ebb1a3973ac4a3b899644818d2f0 Author: fanhsu Date: Fri Mar 12 16:18:45 2010 +0000 Added search term for tRNAs track. commit cb0b115b28ec9561ea111085fbd0a7f962b2aecf Author: galt Date: Fri Mar 12 16:00:18 2010 +0000 "Encode release log update" commit 129cfab27b4796639646f74266b74843473589b4 Author: galt Date: Fri Mar 12 16:00:09 2010 +0000 "Release log update" commit 003e13067cb44cdbc74bb62a2eda68395b11bb4c Author: giardine Date: Fri Mar 12 13:08:15 2010 +0000 Added tags for additions to genome variants track commit 80f992ea13d88561fd2163e9e8ed402af2f3ecd1 Author: kayla Date: Fri Mar 12 00:52:20 2010 +0000 removed alphas for the wgEncodeUwAffyExonArray track commit 71a20564164639cf6e299f9afcbe4af1c611411f Author: pauline Date: Fri Mar 12 00:41:40 2010 +0000 Finally committing an old ref update change. commit 795e946177b35beb073666641bc8706a01b1a906 Author: katrina Date: Thu Mar 11 22:20:00 2010 +0000 removed release alpha lines for wgEncodeUwDnaseSeq release3 in preparation for release to RR commit 3d5e825d1387606484d1d698363e0aa633c649cf Author: katrina Date: Thu Mar 11 22:12:12 2010 +0000 removed release beta blocks for wgEncodeUwDnaseSeq release3 in preparation for release to RR commit 06845d736074f8590e0925bc226eff8709b806e6 Author: pauline Date: Thu Mar 11 21:53:11 2010 +0000 added link for new ENCODE track commit 2c7102e3738a937cda7b0f027477401232516c29 Author: vanessa Date: Thu Mar 11 19:38:57 2010 +0000 change the mailto: links and removed contact: commit 565a7b6f2f2702deaf58ddbb4c634576448a478b Author: markd Date: Thu Mar 11 19:25:46 2010 +0000 added ignore entry commit 1ffaaa0ca85398e4f827ae6701f15aaf0750dd01 Author: angie Date: Thu Mar 11 17:54:35 2010 +0000 Taking untranslated h_errno out of warning message -- IMO it adds confusion instead of clarification when 99.99999% of the time, the problem is a typo in host name. man h_errno says that herror and hstrerror are obsolete, bummer. commit 9299b199a574504fc513a00f563809321f8af830 Author: galt Date: Thu Mar 11 16:00:06 2010 +0000 "Encode release log update" commit cd6cc7b66ad7be9c0f85af440cfb41e60914d4f6 Author: galt Date: Thu Mar 11 16:00:03 2010 +0000 "Release log update" commit b46689c8767d5923ee3795f221b7ad98c2b70246 Author: donnak Date: Thu Mar 11 07:14:44 2010 +0000 Moved aplCal1 to correct category. commit df5df4dee91272c1e18b2432ff523cc31cc29427 Author: tdreszer Date: Thu Mar 11 04:56:20 2010 +0000 Replaced 2 cgiString calls with cartString calls. commit 8be176bb3888b8cf95dd232b373250d6d0af34c5 Author: tdreszer Date: Thu Mar 11 04:12:44 2010 +0000 halfVis not ready for primetime, because ff and ie can't agree commit ed19481137bb7e4731cbdd5608b35deaaaa4b663 Author: tdreszer Date: Thu Mar 11 03:59:06 2010 +0000 Fixed halfVis style commit 4c982fee0e0eca74698d10791b6b7ce4c26e8a07 Author: kuhn Date: Thu Mar 11 03:52:16 2010 +0000 added support for comparing to trackD on beta, too. still doesn't work for second field commit fb4372fa19e8c7e7d4ad3490907c09ccfb29d0c0 Author: tdreszer Date: Thu Mar 11 02:30:02 2010 +0000 Fixed postToSaveSettings 'this' should have been 'obj' commit 0e7ab8d8041a026bb289325d0622a395644bcd99 Author: fanhsu Date: Thu Mar 11 00:56:00 2010 +0000 Updated the section for tRNA track to accomodate updated tRNA name format and QA feedback. commit db1f1b6d4a0cdf3737a98ceb4bfd8a8bc43a078f Author: fanhsu Date: Thu Mar 11 00:52:22 2010 +0000 Updated tRNAs track build. commit a3928a4aef9aaed688fc27e0c81b4892d73c3519 Author: rhead Date: Thu Mar 11 00:10:36 2010 +0000 Do db check with hgsql instead of tdbQuery, as unrelated errors there will mess with the db check. Also give an error if nothing tdbQuery only gives errors. commit 6eebf1f01ed80f524f2737571af91fb08c670db2 Author: angie Date: Wed Mar 10 23:52:06 2010 +0000 Use udcFileMayOpen and warn if it fails, rather than errAborting in udcFileOpen. commit cbf1d21f94f91e9ad4fd239eb0939204d2981751 Author: angie Date: Wed Mar 10 23:44:05 2010 +0000 Instead of errAborting in low-level net.c routines, pass errors up to higher-level code, most of which already checks for error return values. commit a55fc96c35e34e6a881f784a7735f480201b2621 Author: vanessa Date: Wed Mar 10 23:24:22 2010 +0000 fixed typo and changed the way the mailto:'s were displayed commit b993159a32678280333466650fb9c2f26f72f67d Author: galt Date: Wed Mar 10 22:37:38 2010 +0000 temporarily disabling tests to clean up large wasteful cvs history commit 0f9c76a34cba517bc21a0db1e40b8a113121d4a2 Author: kent Date: Wed Mar 10 22:12:33 2010 +0000 Fixing compile errors under Linux. commit 046bcb30832c06925e46b4be89f321544a7d8930 Author: hartera Date: Wed Mar 10 21:21:36 2010 +0000 added Mapability track with CRG alignability data. commit 6ae5ad06d0a069df13f064ec94ccd5ef86e14dd4 Author: hartera Date: Wed Mar 10 21:18:36 2010 +0000 Added more information about the CRG alignablity subtracks. commit 387454326c08a7041a22aab0264132c10d20625f Author: hartera Date: Wed Mar 10 21:12:24 2010 +0000 added CRG Alignability subtracks to Mapability track. commit 38c036bf93dbdfea84a820c36e700a7d4632aadf Author: hartera Date: Wed Mar 10 21:04:52 2010 +0000 Notes on the new subtracks added to the mapability track. commit 07caa6d1e9a36957a9d09967e5e6f0a541690ea5 Author: hartera Date: Wed Mar 10 21:00:23 2010 +0000 mapability.txt commit beb8d33ab0f17e85d688ed8086f15b65cd9964b8 Author: kent Date: Wed Mar 10 19:46:34 2010 +0000 Removing -two option. commit 3738c923d7681a5dcd2d96d9f04c75e0b9d43c17 Author: kent Date: Wed Mar 10 19:45:19 2010 +0000 Moving doubleBoxWhiskerCalc to library. commit bef8ee2f3e6bd8748c6d7798fb8bc0f162a2e928 Author: kent Date: Wed Mar 10 19:44:59 2010 +0000 Adding doubleBoxWhiskerCalc to library. commit fbd5dc65721342ebcfb1599b8519cfec18ea46eb Author: ann Date: Wed Mar 10 19:44:04 2010 +0000 turning on genbank updates for both aplCal1 and tetNig2 commit c2a7b8f35e06179e4a6195baa175cd4f17d6667b Author: kent Date: Wed Mar 10 19:41:55 2010 +0000 Little program to calculate mean/std and quartile stats for a bunch of bed files. commit 61067b900e89f367c84c9b93b2e2812f2b9d7b7c Author: hartera Date: Wed Mar 10 19:36:10 2010 +0000 Shortened the short label for the CRG Alignability subtrack of the Mapability track. commit aeb8b67df766a27b3ce91f00a68756ab09c1b4c4 Author: kent Date: Wed Mar 10 19:31:20 2010 +0000 Making it so that it will break up clusters that are weakly linked. commit cc7868063c36cb20c6c0fc8afa61da08e9cd8d3f Author: hartera Date: Wed Mar 10 19:29:48 2010 +0000 Shortened the short label for the CRG Alignability subtrack of the Mapability track. commit a1847791867af26a9deca74936bd02b72c95357c Author: galt Date: Wed Mar 10 19:21:46 2010 +0000 fixed typo commit 6fa3a0552fd5aec9970796370386bbcd3835923d Author: katrina Date: Wed Mar 10 18:28:24 2010 +0000 reverted back to version with release alphas and release beta blocks in wgEncodeDnaseSeq track because I am not ready to release as I thought I was commit 0cd200a7db0fe6c1380d72ad2748bb9815b1f5de Author: galt Date: Wed Mar 10 16:00:07 2010 +0000 "Encode release log update" commit 8ed74f034ef7daae5015a4e90f2e4df613c55642 Author: galt Date: Wed Mar 10 16:00:04 2010 +0000 "Release log update" commit cd49bc2766db009db1c4f3a345291fe92316b7e3 Author: angie Date: Wed Mar 10 05:07:57 2010 +0000 When item labels are suppressed, we still need to draw the leftLabel in dense mode (shortLabel). commit 4e0249a0cadefe67c2378873df0198e31701ca3b Author: kuhn Date: Wed Mar 10 00:36:11 2010 +0000 utility to compare trackDb_public on beta to trackDb on RR. first rough cut commit 9ab2f989b3f5dfc53b5e285970f7fdc07b22f1c9 Author: larrym Date: Wed Mar 10 00:19:06 2010 +0000 support "type/paste gene name and click submit without choosing from autosuggest list" commit 5ff39d762007394b4465ea449f085493e38679e8 Author: ann Date: Tue Mar 9 22:52:02 2010 +0000 only for vertebrate assemblies. commit 28b8ed00d7866505dc24d32f5a02258ee3f082e9 Author: mary Date: Tue Mar 9 22:09:36 2010 +0000 Deleting a sample position query that was didn't work commit e35ef62367f8058f3ab614fe0bccdec60faf4b4a Author: ann Date: Tue Mar 9 21:53:54 2010 +0000 added disclaimer about findLevel output since all chainNets now use top-level chainNet.html file commit 0fed46cb27feab8e353e3f2c87bd48a3153d1bb3 Author: kuhn Date: Tue Mar 9 20:39:46 2010 +0000 dropping mid-level html files no longer needed since the consolidation into chainNet composites commit e0d1dd65e06715920288cb03ce722db20cadd175 Author: rhead Date: Tue Mar 9 19:55:05 2010 +0000 Changed beta target to buildBeta in preparation for changing to alpha/beta/public trackDb makes. It does not seem to be used anywhere. commit cc4c06ea86048e2db372f91c05bd9f923f267a70 Author: mary Date: Tue Mar 9 19:46:14 2010 +0000 replacing non-fuctional sample position queries with fuctional ones commit 18c746d9148bf87b0859fb7bc14d166d60ce177e Author: katrina Date: Tue Mar 9 18:21:17 2010 +0000 removed release alphas from wgEncodeDnaseSeq parent, sub-tracks, and view-in-the-middle blocks commit f585704eaf5d43d6a46c4929ecd9ece506eb3eb7 Author: katrina Date: Tue Mar 9 17:23:10 2010 +0000 removed release beta blocks of wgEncodeUwDnaseSeq in preparation to stage and then release release 3 of this track commit 35d1a04638ebcf60700db30bb178cb67170cb604 Author: katrina Date: Tue Mar 9 16:59:23 2010 +0000 changed number of new cell lines in release notes to the correct number, 19 commit 8dc7185b459dd9716926e9902737abf20289cdcf Author: galt Date: Tue Mar 9 16:00:06 2010 +0000 "Encode release log update" commit 8ef4191fc623f178216f17cbd8d3c908101d0534 Author: galt Date: Tue Mar 9 16:00:03 2010 +0000 "Release log update" commit 9fb5e7fb717c3d2e0ae288869ad62e5d5838c7da Author: krish Date: Tue Mar 9 10:36:32 2010 +0000 added notes for wgEncodeYaleChIPseq release 3 commit baa139799d270e2e7b1ba840e70d14b87883f70d Author: angie Date: Tue Mar 9 06:01:18 2010 +0000 Moving the USE_FUSE addition of L += -lfuse to src/fuse only, so execs created in the rest of the tree don't crash on machines that don't have libfuse. commit 58731388eea3d63a5623d99cc5f7597cb343d165 Author: angie Date: Tue Mar 9 05:59:51 2010 +0000 Moving the USE_FUSE addition of L += -lfuse to just this directory, so execs created in the rest of the tree don't crash on machines that don't have libfuse. commit 8d261dca17da48db3d89b2a81c74564e73cf11ca Author: rhead Date: Tue Mar 9 02:51:39 2010 +0000 Changed html file lookup so that it actually starts at the assembly level, like it says it does. Thanks, Ann. commit e88b6e06343ba055ac99ee7c4dc4d9be514f09b8 Author: tdreszer Date: Tue Mar 9 00:22:29 2010 +0000 Move some javascript code into c to speed handling massive images commit ce6abbae5caf03789caf38e24bdb79c275095005 Author: Galt Barber Date: Mon Mar 8 16:21:28 2010 -0800 shorthand git is simpler commit 6a907e6ed9d1335f085d4d8809fd18e316db8f86 Author: tdreszer Date: Tue Mar 9 00:18:37 2010 +0000 Change which is currently ifdeffed out, that avoids warning commit 5af1be08e093460ca82beef13603d12b66ae0c78 Author: tdreszer Date: Tue Mar 9 00:15:35 2010 +0000 utils.js needs to be there whether advancedJavascriptFeatures is on or not commit 2c02e9f146fa5250a360687c5e0d7d93148f18db Author: Galt Barber Date: Mon Mar 8 15:49:30 2010 -0800 fixing end-li tag commit 505671971a17ea59931cc9fa63a490e80d85465a Author: kent Date: Mon Mar 8 23:37:28 2010 +0000 Adding a new experimental track. commit 50e7d4d805dd9a5ca1d874c65d88625495c83b51 Author: kent Date: Mon Mar 8 23:35:38 2010 +0000 Small tweaking to get it to work with real rather than pretend data. commit 944914f8f021e0661977105cfc6294b2386f9347 Author: kent Date: Mon Mar 8 23:35:08 2010 +0000 First cut of some code to combine ENCODE regulatory tracks into a single track done. commit 81d6d3a62c0486e745f8a3717bd6310da16b012c Author: angie Date: Mon Mar 8 23:25:56 2010 +0000 Doh, there was a segv for rest==0x0 as in any bed3 bigBed. commit 0b27db8fb840a73902f762614e71f0bee82034ab Author: Galt Barber Date: Mon Mar 8 15:20:02 2010 -0800 removed redundancy in html generation, and in mkdir, tidied up tags a bit for consistency commit 0bf2a7686adce0bd5f6b580fa68052745c856f3e Author: mary Date: Mon Mar 8 23:13:31 2010 +0000 added shortLabel so that db name rather than org for danRer5 commit 4efcc78713242bcc46720bbf6a4e2aa4c920615d Author: galt Date: Mon Mar 8 22:28:15 2010 +0000 fix paths now heather is gone commit f94227bb6d0baf0e24f3109ed75929ff8a78c2ae Author: galt Date: Mon Mar 8 22:25:17 2010 +0000 fixing java paths now heather is gone commit 1b62b963b4784ea8c1947ec519c3b3b3b8b51fb2 Author: kuhn Date: Mon Mar 8 21:52:27 2010 +0000 dropping bot-level html files no longer needed since the consolidation into chainNet composites commit 923bfe8a6775cefee5204e33760da2e1aa19475d Author: galt Date: Mon Mar 8 21:46:34 2010 +0000 heather is gone, paths old need updating commit 7e0395679cabd3972824e2dfbd0f2da7b47ffd6d Author: kuhn Date: Mon Mar 8 21:42:52 2010 +0000 testing cvs delete to see if hirsotry is retained when replaced commit f1cb1e2b8b8df0bf92868801f1f1311cf989a426 Author: kuhn Date: Mon Mar 8 21:41:56 2010 +0000 testing cvs delete to see if hirsotry is retained when replaced commit d176dd8ba00115be2368db1f6793550da77e1544 Author: donnak Date: Mon Mar 8 21:04:25 2010 +0000 Added Kern pub. commit 2c055f5b9f33ed2028aedf6fe5d1568077913b1b Author: ann Date: Mon Mar 8 20:31:16 2010 +0000 moved sentence. added period. commit fa47fd4867d3707134a08ce08a1af432155913b1 Author: tdreszer Date: Mon Mar 8 19:50:18 2010 +0000 Removed revoked crud and set up html for YDH TFSB release2 so that Release3 can proceed commit 62056cf2405a464f235ff1cc2078e7ca13390c1b Author: tdreszer Date: Mon Mar 8 19:49:03 2010 +0000 Getting ready for Release3 commit 5c349e1658ee1d1b851f8fd3447545e53472f133 Author: angie Date: Mon Mar 8 19:47:41 2010 +0000 Code review: ClosestToHome no longer necessary, and format string was hard to read. (thx Jim) commit af6332d42bca7d3e12efbfbfbdb6675dbf915566 Author: kuhn Date: Mon Mar 8 19:47:36 2010 +0000 dropping mid-level html files no longer needed since the consolidation into chainNet composites commit f5f794843e208d2a1ffdf9eb63af48bfd806de5c Author: angie Date: Mon Mar 8 19:42:31 2010 +0000 Clarifications to comments after user question. commit 5666097ac5be65e879c5d2993bd9a3ec5e576aae Author: tdreszer Date: Mon Mar 8 19:42:02 2010 +0000 Added HeLa/Brg1/IgG-mus as last holdout from Jan 2010 freeze to YDH TFBS commit 000051929861dbc16609052d73f2424d07d9698c Author: Galt Barber Date: Mon Mar 8 11:40:57 2010 -0800 added error checking for system() call, removed some uglyf prints, cleaned up some comments commit c2d43e4ba34bae0c8fc56f4aee7e68ed7e2ddb9c Author: krish Date: Mon Mar 8 19:38:35 2010 +0000 added notes for wgEncodeUwDGF release 2 commit b6014043d6ee1b85df12fe8e1b193b12142380a8 Author: tdreszer Date: Mon Mar 8 19:16:11 2010 +0000 Release 2 should go out in March 2010 hopefully commit 59536705fb306f5d663d60f1a45ac11f376242e0 Author: giardine Date: Mon Mar 8 19:16:10 2010 +0000 Adding phenotype tables for pgSnp track hgc clicks, and new genomes commit bb4a1c0e4a0ca4d28257e5b2ec30029aee83928e Author: tdreszer Date: Mon Mar 8 19:14:46 2010 +0000 Unrevoked HUVEC for YDH TFBS now that input is loaded. commit 2e17e2b41538014a4f03c0f673a2197a4f70eb29 Author: giardine Date: Mon Mar 8 19:09:47 2010 +0000 Add phenotype tables to hg18 pgSnp tracks where available commit c5f94b426c49ed9ed3dd32b57be1a929fdadb0b0 Author: braney Date: Mon Mar 8 18:56:56 2010 +0000 extract GIS RNA-loc to its own file commit d2bb1d962284b54a669bc84085233dbbb6cd582f Author: braney Date: Mon Mar 8 18:55:18 2010 +0000 extract GIS Pet tracks to separte include file commit aed26a2341d9ba110a8bfb47ca5e27aa9378108e Author: tdreszer Date: Mon Mar 8 18:47:53 2010 +0000 Renamed tables and files to match metadata on Yale TFSB commit d2c513efb15bc8800f8541887cdf195cf927bdb7 Author: giardine Date: Mon Mar 8 18:36:51 2010 +0000 Adding new personal genomes to the pgSnp track (Hgwdev only for now) commit ac9a63e5ebf04470f2ccc514e4295b279fefcd54 Author: giardine Date: Mon Mar 8 18:25:40 2010 +0000 This includes all pgSnp tracks so it can be used when updating the pgSnp track to include these additions. commit 589f2e50334ca69419656653286f33685e910bd7 Author: giardine Date: Mon Mar 8 18:18:54 2010 +0000 Adding phenotype tables for pgSnp track hgc clicks commit e3615798f8a36c2b1c48303c29b2428654b657ad Author: giardine Date: Mon Mar 8 18:18:05 2010 +0000 Updated dbPEX links. commit 920d109f1bd9cf824eec3e2431715255c43a89df Author: giardine Date: Mon Mar 8 18:09:20 2010 +0000 Handle empty strings in alleleFreq column of pgSnp tracks commit 86dc689b732cd140697a0c090215c61c26130fae Author: giardine Date: Mon Mar 8 17:52:10 2010 +0000 Adding phenotype tables for pgSnp track hgc clicks commit 84d0cfc28ed3953ae81320cd3b4c7db0e5dff488 Author: giardine Date: Mon Mar 8 17:45:41 2010 +0000 Adding phenotype tables for pgSnp track hgc clicks commit ae05cd53397d5c2fc3797ecef6521e5ac63a9239 Author: galt Date: Mon Mar 8 16:00:07 2010 +0000 "Encode release log update" commit 7fff1f9bb08e7eea129735fa887efab31c590ae7 Author: galt Date: Mon Mar 8 16:00:03 2010 +0000 "Release log update" commit 95196d0b0366e947eb87ed06ef2174b817b46fb3 Author: braney Date: Mon Mar 8 15:12:36 2010 +0000 add gencode commit a157f4fce31b8aee4a230c721624e9f98fd66333 Author: Galt Barber Date: Sun Mar 7 12:07:58 2010 -0800 suppress commitIds as too-much-info, add UL/LI tags to allow text to wrap, htmlEncode the commit-comment, also substitute
for newlines in comment commit 643b47a472e79f63e42aeb075ee02968917eaab6 Author: galt Date: Sun Mar 7 16:00:03 2010 +0000 "Encode release log update" commit 5199912c9842bb27b45d5da783bc85451ad47f0b Author: galt Date: Sun Mar 7 16:00:01 2010 +0000 "Release log update" commit 09987a4e28bd5aaee27e38def6a921c4b66901a8 Author: kent Date: Sun Mar 7 08:05:30 2010 +0000 Getting rid of some records that mix releases at different levels. commit 9eccf9205476ef5be34dc66eaa0a360856a10ce3 Author: kent Date: Sun Mar 7 01:32:42 2010 +0000 Improving handling of release tags. Case where have alpha and beta in composite tracks works better. commit 481bd8279e01efcb2d1ad65a7aaf69815dfc98f6 Author: hiram Date: Sat Mar 6 16:49:58 2010 +0000 adding 13-way definition commit 67a45bcf67d7ea4f33b1288c52fca73a0a514c18 Author: galt Date: Sat Mar 6 16:00:06 2010 +0000 "Encode release log update" commit 56468e5bd8d0ff101c4c400283a24da49aae24b6 Author: galt Date: Sat Mar 6 16:00:03 2010 +0000 "Release log update" commit 61600fe5b6bb05bb7fd77a65835a7426f7a124be Author: tdreszer Date: Sat Mar 6 02:36:28 2010 +0000 Loaded in missing IgG-rab input for Yale TFBS commit 4f0e0177c57277f95e8770d9d910e129cc0e01b0 Author: tdreszer Date: Sat Mar 6 02:05:42 2010 +0000 alpha/beta ize Yale TFBS commit a0ddc7c6be1b680759e6f20c292718bd425eff0a Author: ann Date: Sat Mar 6 00:07:24 2010 +0000 trying to clear this up commit 37442d75350a6efcdea3caa0c286cda4a88c56cf Author: angie Date: Fri Mar 5 22:26:29 2010 +0000 Oops, forgot a cloneString back in Oct. '08 (thx Pauline). commit 862d603bb538d1a38704397c5f45cb9d003f91fe Author: kuhn Date: Fri Mar 5 22:12:32 2010 +0000 dropping top-level html files no longer needed since the consolidation into chainNet composites commit 82256624d7df1796823539f1a190ab560e1e2798 Author: tdreszer Date: Fri Mar 5 22:06:53 2010 +0000 Added 'input' commit dcd9e0740f1377a213d22b34997b489aee8dbc95 Author: tdreszer Date: Fri Mar 5 22:06:39 2010 +0000 Moved certain terms from 'Control' to explicitly 'input' commit 7ce9af81a68d88b0e8be06154e6970faef20c3a9 Author: hiram Date: Fri Mar 5 21:57:14 2010 +0000 add defaultGenome variable discussion, pointer to README.udc and fixup comments for downloadsServer commit eef8a09accaf96008cc2c60fb3984aa0cae72810 Author: hiram Date: Fri Mar 5 21:42:21 2010 +0000 find defaultGenome from hg.conf if present commit 48c764841fe955d738b56e352082ca23dce91c96 Author: Galt Barber Date: Fri Mar 5 13:11:33 2010 -0800 added a copyright and my name and MarkDs name commit 4027e67dd84c4a858e235201a59add8fdd8418e9 Author: tdreszer Date: Fri Mar 5 21:07:54 2010 +0000 Reworked paths - again commit aca6a33817b9af8247abc38ca1bf28012b7dda3b Author: Galt Barber Date: Fri Mar 5 12:52:34 2010 -0800 fixing link formatting regarding position of pre-tag section commit c04adec274538783c357c4f4fd631a7717575b9f Author: tdreszer Date: Fri Mar 5 20:39:32 2010 +0000 Reworked paths and included index.html commit 418a53c019906769fae460d97271268ad520a096 Author: tdreszer Date: Fri Mar 5 20:39:07 2010 +0000 Included index.html and others commit 366dda9766b90a18df3f880b5db3ff111fc7b464 Author: Galt Barber Date: Fri Mar 5 12:24:45 2010 -0800 fixing makefile commit a7ed28dbabf17e5b18b29a3b1bf74a6c9bf25b94 Author: tdreszer Date: Fri Mar 5 19:36:48 2010 +0000 Getting ready for release3 commit 18902c30948eec97d3609357b591ca2cd1da49cb Author: rhead Date: Fri Mar 5 19:05:27 2010 +0000 Changed dependency on symlink in home directory to dependency on the kent source tree in home directory. Also moved this check closer to the top, as tdbQuery run by default also depends on the tree being in the home dir. commit 83d2fcd4e173b9ef8d6d046790afc8f081af2207 Author: chinhli Date: Fri Mar 5 18:47:34 2010 +0000 Initial support for felCatV17e commit 9a104126bf1d7bf94818c81a0d7c962577ef11d4 Author: ann Date: Fri Mar 5 18:47:21 2010 +0000 added missing closing A tag commit 1ea750818a8f9d5cccb9a66217b736eb75331334 Author: chinhli Date: Fri Mar 5 18:37:25 2010 +0000 Initial files for felCatV17e commit cdda5f6fc57ef231aa6efa52c92b6100c506bd0c Author: ann Date: Fri Mar 5 18:29:48 2010 +0000 added error message for non-chrom-based tables commit 7357c7464307f643497d2599c3620da5481ef2e6 Author: chinhli Date: Fri Mar 5 18:26:54 2010 +0000 New support for felCatV17e commit 90e3dab0d7928ca2e0bf22606027e4e189435265 Author: chinhli Date: Fri Mar 5 17:52:06 2010 +0000 Undo Add H-InvDB_7.0 support commit 49ee8100f308c861bc1a4606678c1eb86cce3b6e Author: chinhli Date: Fri Mar 5 17:44:58 2010 +0000 Add H-InvDB_7.0 support commit e217a9018e06f44b98ee3c7224e9b6d8d840863b Author: ann Date: Fri Mar 5 17:35:58 2010 +0000 trying to clarify the release name of this batch commit ed2e94e83ed0842d5395a2f80148673ffeada710 Author: chinhli Date: Fri Mar 5 17:29:13 2010 +0000 Adding URL for H-Inv(V7.0) commit 610efcfb193159206a26f42aa8d915947b16d0b1 Author: galt Date: Fri Mar 5 16:00:10 2010 +0000 "Encode release log update" commit d03a49411ddd14180428faa828046985589dda00 Author: galt Date: Fri Mar 5 16:00:03 2010 +0000 "Release log update" commit ca6c47479b8a4f5034dc1612353f74ab5dba0dd0 Author: krish Date: Fri Mar 5 09:55:38 2010 +0000 added notes for ENCODE Open Chromatin track commit a2ab11beca8f5d958b9a4cd1b2274b3ad8b9337d Author: pauline Date: Fri Mar 5 06:09:46 2010 +0000 Fixed reference to html file to restore description to RR version of track. commit ce60f8edd6c1814b4c9e6b3783c1cfa08cd96412 Author: larrym Date: Fri Mar 5 05:07:55 2010 +0000 comment out the TRACK_SEARCH #define commit a5dda1b5757fd242c21333f2a3eae39c47a64505 Author: Galt Barber Date: Thu Mar 4 20:33:23 2010 -0800 fixed bug with calling makeDiffAndSplit in wrong loop fixed tempfilename in case multiple users run it at same time added main index page made titles and headers consistent removed sed to clean weird unwanted context lines saving 20 seconds commit 5cd40624583fca77b98c145481e02f5ca816a2ed Author: markd Date: Fri Mar 5 03:51:39 2010 +0000 added fogotten build of searchTracks.o commit 0b252f3ca93180c2151ba8df20a564a6a678ab52 Author: markd Date: Fri Mar 5 02:52:17 2010 +0000 fixed incorrect assumption about pthread_t being an int commit ee5e44e2f7aedfd7bd89cc33e3f97185e0b7157e Author: kent Date: Fri Mar 5 00:32:35 2010 +0000 Adding new blat test case. commit 0a70bf39b216c15ef9ec40b3c281115c5afc2956 Author: kent Date: Fri Mar 5 00:31:03 2010 +0000 Describing new input sanity check. commit cb8d935dd625de64bbc7d6e49cbdb597cb3b2a9a Author: kent Date: Fri Mar 5 00:30:41 2010 +0000 Bumping version number. commit 3c15ad961fd7ae582ca4be353710917440674db2 Author: kent Date: Fri Mar 5 00:30:25 2010 +0000 Putting in check for uniqueness of target sequence names. commit 941caf09beedfe082a4d1728dbdc61db097fdd3d Author: pchan Date: Fri Mar 5 00:13:40 2010 +0000 change lowelab wiki path for track access commit 91c5ebde5b8ccf83d2dbe3a705be6d057276aafb Author: tdreszer Date: Fri Mar 5 00:04:16 2010 +0000 Only rep2 for HepG2/SRF so promoting it to rep1 commit 9f2ba8392f53a96d277eadee9b86c5dd4f84d392 Author: tdreszer Date: Thu Mar 4 23:56:03 2010 +0000 Noticed some more discrepencies commit 31219cb61a1d3d3ac433068009ae74bc3dda5f8b Author: tdreszer Date: Thu Mar 4 23:48:29 2010 +0000 Changed a whole lot of Seqs to seqs commit 42cb8af951d55d0871a37d34e7fa2adbe375ca7d Author: pchan Date: Thu Mar 4 23:47:10 2010 +0000 fixed problem of auto-set width button by Andrew H. commit e4bbc11d93a9ebc71ea23106189393e78e8597cb Author: tdreszer Date: Thu Mar 4 23:45:40 2010 +0000 HAIB TFBS HepG2/SRF has only one replicate which has been renamed rep1 commit 4e4c318367c543a43e85f484bbad283d8f7dab98 Author: ann Date: Thu Mar 4 23:06:07 2010 +0000 added BAM to the list of formats that need an embedded URL. commit b11e8e87ac6c7cb9c321a5c3b675097121e30c3a Author: galt Date: Thu Mar 4 21:51:39 2010 +0000 adding some documentation about udc, bbi, bam, udc.cacheDir hg.conf setting commit 7c7fe3756c0edcc6ce5f6982773c05120acab69b Author: braney Date: Thu Mar 4 21:25:20 2010 +0000 RikenCage Loc release notes commit 77941396fc68ed6cd6f776494dad22e121643273 Author: larrym Date: Thu Mar 4 21:24:08 2010 +0000 refactor code into trackUrl; add track search code within TRACK_SEARCH #define; add ruler entry to trackDbJson; clear suggest field when user hits 'clear' button commit 6d7765964527273314c274a12d5230f75b758254 Author: braney Date: Thu Mar 4 20:42:14 2010 +0000 add some release notes commit b862c1b1c6a0c522ab383564fd02dadbb4b6dad2 Author: katrina Date: Thu Mar 4 20:10:32 2010 +0000 fixed totaly of untouched wibs and removed a file from untouched files that is actually being replaced and is already accounted for in the replaced files section. commit 82cf95b43e92425672f75f05bdca679cf5197bec Author: larrym Date: Thu Mar 4 19:53:28 2010 +0000 safef -> safecpy commit 47bcfa24acd56bbcbf291ea191ca2fba7376eb1a Author: ann Date: Thu Mar 4 18:08:37 2010 +0000 reverting Hiram's change. It would have caused tetNig1 chains and nets on the RR to switch from 'Tetraodon' to 'tetNig1'. commit 3df3783da3f8d9f6a1da6e935f4d9fa5dbb58185 Author: ann Date: Thu Mar 4 17:21:37 2010 +0000 backing out Hiram's last change. Mary noticed that if this trackDb was pushed to the RR before the tetNig chain/net tables are released, then the tetNig1 chainNet track would go away. commit 5a3b7e0b8476bca7786ca6c54e60671232791958 Author: galt Date: Thu Mar 4 16:00:21 2010 +0000 "Encode release log update" commit 29fafc7bc0206fb9da4fd40b95b2b4d8ae64a4a0 Author: galt Date: Thu Mar 4 16:00:03 2010 +0000 "Release log update" commit 1191cb012ddd2b8e57a0b8a1686769ffac3422cb Author: Galt Barber Date: Thu Mar 4 03:15:37 2010 -0800 changed from git show to git diff to have more control over output options like suppressing whitespace. Also in order to get the diff for a deleted file, I had to change it to dump the entire diff for the commit and then parse it into parts commit 6c39b88956e6b2b6458c1894066ccf82f1c76765 Author: Galt Barber Date: Wed Mar 3 23:23:02 2010 -0800 getting rid of word Git in title commit 3e56f626ffaea1abffd715356ebacea45c7a1f70 Author: Galt Barber Date: Wed Mar 3 23:16:47 2010 -0800 adding all-files view commit dfbb8f7a87e7c9d74a288e8e34a2c852e9e83622 Author: Galt Barber Date: Wed Mar 3 22:11:03 2010 -0800 added bottom navigation links to files and commits views commit 2631e2da049d64cec05989be115c55159dde6b9b Author: Galt Barber Date: Wed Mar 3 22:07:14 2010 -0800 added navigation links to files and commits views commit ba39e1a14e6dfed2c2bc9352eb76106423a660eb Author: Galt Barber Date: Wed Mar 3 22:00:03 2010 -0800 added files view for user commit e7dba37a20017dc40ddad90aca8c53de7ffd0979 Author: angie Date: Thu Mar 4 05:53:14 2010 +0000 Fixed loadGrps to handle profiles. commit 2aed4724b8d05bfa518f5ea8a4527973b61dcee0 Author: angie Date: Thu Mar 4 05:14:13 2010 +0000 Pass sql conn into bamFileNameFromTable, so we can get it from hAllocConnTrack, to support use of hg.conf profiles. commit 456b70e45495cc9127aa35c329d29e0570d26709 Author: tdreszer Date: Thu Mar 4 02:43:54 2010 +0000 Making sure all of Jurkat files/tables are treated as if new. Thanks Katrina for noticing this problem. commit f67a1a71877a6bee2aba794b03ea281796e1b442 Author: Galt Barber Date: Wed Mar 3 17:37:40 2010 -0800 adding commitNumber for fileview sorting commit 7c6f58351f5c3321627e7c4020b2c5f9d8336c7b Author: Galt Barber Date: Wed Mar 3 17:34:20 2010 -0800 fixed colors, fixed counts on new files when there is no context line to finish the block, fixed bug in output of git show in diff part where odd and variable extra context appeared after @@ .* @@, currently just using sed to trim the diff file so html file inherits automatically commit be742a75ce2a9a99e76ed44cc3510d03029ec12b Author: galt Date: Wed Mar 3 23:52:24 2010 +0000 using a format string is recommended commit ac0ccacc6aba636aee50d5f0f4c491898cb7588b Author: angie Date: Wed Mar 3 23:25:07 2010 +0000 Fix for baseColorDrawItem being called w/drawOpt=off. commit 31650f55b7caaece1b0a4253dfc7ad6d33d9f95a Author: braney Date: Wed Mar 3 23:05:48 2010 +0000 another attempt to capture what's changed between releases. We need a script to make these consistent commit ab381266d86656912f51f23fb27e5eeab19aab72 Author: braney Date: Wed Mar 3 21:52:31 2010 +0000 change default visible tables for MethylSeq commit abc46ae96b981e04fec3503ea230953516fb5a0d Author: braney Date: Wed Mar 3 21:47:43 2010 +0000 fix up some metadata for H9ES cell in MethylSeq commit 2aa7212007b55320035faee5b056f1c368e1444d Author: braney Date: Wed Mar 3 21:22:20 2010 +0000 turn off the nextItem arrows by default for the MethylSeq track commit 2f58f132e99e94394de72f4e1ca32f5270cbb97b Author: hiram Date: Wed Mar 3 20:02:37 2010 +0000 replace tetNig1 with tetNig2 chainNet commit 338a04b857d0e0d0bc5b955e1708f10258b6151a Author: hiram Date: Wed Mar 3 19:58:28 2010 +0000 replace tetNig1 with tetNig2 in vertebrate chainNet commit d9a72fddf935830b4919823eb0e522c917264207 Author: angie Date: Wed Mar 3 19:30:04 2010 +0000 Bam track improvements: 1. Enable indel-coloring. 2. Display soft-clipped sequence instead of pretending it doesn't exist. commit 282dd54a21224701b933df072d8b33541b42f97c Author: galt Date: Wed Mar 3 16:00:08 2010 +0000 "Encode release log update" commit 2ff3d7afa2a6e398848c63d468aa1bfb42f30e44 Author: galt Date: Wed Mar 3 16:00:03 2010 +0000 "Release log update" commit 381e3eb3f51fbf88c9565a575c21fa8297fb93a1 Author: Galt Barber Date: Wed Mar 3 05:04:06 2010 -0800 added users-page commit d78924986222727b233b171259c8a4f557c1eab3 Author: Galt Barber Date: Wed Mar 3 04:10:17 2010 -0800 add counts for lines and files changed for user and grand total commit 636edb07cfa8605de2a53cf51256f65e5930d70c Author: Galt Barber Date: Wed Mar 3 03:55:44 2010 -0800 fixed bugs in output paths, added htmlEncode commit 39363c9d25a55c3bd717b4d1483d895f584d400a Author: Galt Barber Date: Wed Mar 3 02:21:57 2010 -0800 adding linesChanged commit c7d3587df92f36b7d182238cb1d6b8e7dceadbe4 Author: Galt Barber Date: Wed Mar 3 02:10:15 2010 -0800 adding html processing commit acd6dfe3ca9f59cb771de895935f1531916740c2 Author: Galt Barber Date: Wed Mar 3 01:23:43 2010 -0800 fixed bugs, got diffs working commit 79a20d5071a393c46bc3bbcedcf8eaa5b609532c Author: markd Date: Wed Mar 3 07:52:22 2010 +0000 allow bedLoadAll to read from pipe by not closing and reopening commit d136d36062d7c2141f49bad2df0d122daba26771 Author: markd Date: Wed Mar 3 02:53:31 2010 +0000 integrated low lap changes commit f2cc03e19743e8f73885917ac7e605869cdb1d5f Author: galt Date: Wed Mar 3 02:19:44 2010 +0000 fixing compile error warning: cast from pointer to integer of different size commit 2e3bc551d3e73fd77bfcf10b55cab33945c21106 Author: galt Date: Wed Mar 3 01:48:20 2010 +0000 jim added keyword Warning which was triggering as an error, but its not serious enough to stop the build for commit 658519b3f9be6b5a417428d910f949e8b3fb323a Author: galt Date: Wed Mar 3 01:47:03 2010 +0000 adding pauline and ann commit d48b211f8bdd027e3f73383e124de39f43312d9a Author: galt Date: Wed Mar 3 01:45:43 2010 +0000 adding pauline commit 7fe15922ae32275f2798c66ab21a751695889bae Author: galt Date: Wed Mar 3 01:44:51 2010 +0000 updated for bamsam commit dd43fa2d45266868009c5d32f718484b1de81348 Author: galt Date: Wed Mar 3 00:58:05 2010 +0000 trying to get it to run faster commit 8ab909a43a6cbf28d5c7dc9dcfbb768f9cbe2ef9 Author: galt Date: Wed Mar 3 00:08:29 2010 +0000 "New version number v226" commit ca93ba5f27145a5c08e220d38d6aef150ed560a3 Author: galt Date: Wed Mar 3 00:08:04 2010 +0000 v226 final build commit b3d65497825cf1e0a5767b63be30b62149aa0d9e Author: rhead Date: Tue Mar 2 23:45:05 2010 +0000 Removing findLevel.csh. It has been replaced with findLevel. commit fc02d9544ee0b6007b1b8f07c43de8d866f7636b Author: chinhli Date: Tue Mar 2 23:04:52 2010 +0000 Adding H-Inv(7.0) update commit 1037e840f8e714e1f88a1447de3df664cb178755 Author: ann Date: Tue Mar 2 22:36:29 2010 +0000 changed call to the new findLevel script (no .csh extension) commit fcb99b37c724f735b2976caf5345278db85245be Author: tdreszer Date: Tue Mar 2 22:12:27 2010 +0000 Working on release 3 commit 72903f4bc1cd6f7df9b2712900d6d0a96147084a Author: tdreszer Date: Tue Mar 2 21:57:08 2010 +0000 back.gif needed to be a relative path commit 2b7d3399d5925ca952c51f1ff949231cc97db66b Author: tdreszer Date: Tue Mar 2 21:36:08 2010 +0000 Split Broad between alpha and beta commit 4ada17ac22615f43d39337c9f63458ee61603747 Author: tdreszer Date: Tue Mar 2 21:31:59 2010 +0000 Need to save release 1 version while release 2 work is going on commit 764f904edda8f4498067433d33fe9a3f574f4b67 Author: tdreszer Date: Tue Mar 2 21:26:03 2010 +0000 Need to save this release 2 version while working on release 3 commit 462b1b62632ec1405ccc3a40c4ff0e2e3b2d236d Author: kuhn Date: Tue Mar 2 21:24:40 2010 +0000 changed wording slightlyfor clarity commit 70f3ced033d77f38a4ab4176637e3149a5eae825 Author: kuhn Date: Tue Mar 2 21:23:48 2010 +0000 combined chain and netdanRer5 tracks into composite commit f1ae21566a36f6d88b2a4f997529cc47704e19e7 Author: tdreszer Date: Tue Mar 2 20:38:17 2010 +0000 Still flying blind on beta. Thanks Katrina commit e638510359505b69a70e08cad5dc085b48ceaddc Author: tdreszer Date: Tue Mar 2 20:01:16 2010 +0000 Fixing Beta while flying blind commit 76b8c971e371939133bb54364b263df5d3e9429d Author: katrina Date: Tue Mar 2 20:00:48 2010 +0000 lowered flyBase2004IdDm rule against hgBalstTab to 96% as it is getting older and was no longer passing at the previous 99% commit 8e8d001ad1a45c5b8f9ff087098d4ac8ddc58c6f Author: tdreszer Date: Tue Mar 2 19:43:55 2010 +0000 Missed a bunch of alpha flags commit e6e057e0a5fc6249f838eab53bb7e7267fadb871 Author: angie Date: Tue Mar 2 19:13:54 2010 +0000 Enforce capitalization of only the first word in commonName, to match dbDb convention. commit d4df81e5a195becc50413c23e419448b0b1cf1d4 Author: tdreszer Date: Tue Mar 2 19:07:43 2010 +0000 Missed 2 alpha tags commit b7e884f58b7befadd5ff51bf41aac96928bb79c4 Author: katrina Date: Tue Mar 2 18:50:50 2010 +0000 Pointing release beta stanza of wgEncodeUwDnaseSeq to special release 2 html description so that the release 3 desc for the new release doesn't leak back to RR commit a5de36b0be2b525bb690d23e581eca29a46cbee9 Author: katrina Date: Tue Mar 2 18:43:24 2010 +0000 added a release2 html so that the RR won't incorrectly have the release3 info while I am QAing it commit 30071332c5fb57ea175c4714e465ffe75ca33866 Author: tdreszer Date: Tue Mar 2 17:41:48 2010 +0000 Split HAIB TFBS alpha/beta and added 2 tracks commit fb67e4a99ee805358fdeb5424d54dee26b347ca3 Author: tdreszer Date: Tue Mar 2 17:38:25 2010 +0000 Fixed glarring bug in ABC dimension settings persistence commit e298028e2560ca7d1ee1a14587352c802f07001e Author: tdreszer Date: Tue Mar 2 16:38:38 2010 +0000 Had to split UW DNase into alpha/beta commit fb90f11443b07dbc5f1cd2d0887800a5d53fd430 Author: galt Date: Tue Mar 2 16:00:09 2010 +0000 "Encode release log update" commit d38a86ca3fab153006ebbe56bb4c8970276c303a Author: galt Date: Tue Mar 2 16:00:04 2010 +0000 "Release log update" commit 6b7888b32c101165e159a5f84aaff95940915d65 Author: Galt Barber Date: Tue Mar 2 04:43:45 2010 -0800 mkdir more various subdir levels needed commit 1cf2254a64357c73c4fbdc07badb0e2529c18e62 Author: Galt Barber Date: Tue Mar 2 04:31:58 2010 -0800 mkdir various subdir levels needed commit 3689cddf898c0384f276ce9b2e5890cad4090dfe Author: Galt Barber Date: Tue Mar 2 04:24:55 2010 -0800 mkdir outPrefix in case commit 1e8b8614f1e65afd0e9e012925e33babb9f255bb Author: Galt Barber Date: Tue Mar 2 04:13:02 2010 -0800 adding outPrefix to dir or url commit 77f308a1e7b3827d749d6ad10955159dfa3bc4ea Author: Galt Barber Date: Tue Mar 2 04:01:18 2010 -0800 using slNameSort commit 907e51f53079e8d77ae026b7f6dc2e1f25b43608 Author: Galt Barber Date: Tue Mar 2 03:57:16 2010 -0800 adding userHash and users list commit 8d69455e88abc5afe067fbf85d7416969a4e5017 Author: Galt Barber Date: Tue Mar 2 03:42:49 2010 -0800 add parsing for main commits list from startTag to endTag commit dc78303b079985b5a146d093bbb8a5d06489562d Author: Galt Barber Date: Tue Mar 2 02:39:07 2010 -0800 initial commit of git-reports commit 37eabeb672cba560551e384f85aaa1f40c3b39da Author: kate Date: Tue Mar 2 06:19:25 2010 +0000 Report treatment in a separate column instead of as an experimental factor, by request of NHGRI commit dc2d4520c7844b83a528b1b605c038aa547df5b7 Author: kate Date: Tue Mar 2 05:39:28 2010 +0000 Fix mispelling of Tenenbaum commit e8bf14b206619dcaa00a71da1a2155c0f7008507 Author: rhead Date: Tue Mar 2 02:11:52 2010 +0000 Added findLevel. commit 349938a1b2022638687b521595d0d6ff2fac1e5a Author: rhead Date: Tue Mar 2 02:08:44 2010 +0000 Changed findLevel.csh to a bash script to simplify dealing with stderr and stdout. This version throws away errors from tdbQuery (whose errors should be addressed, but not here). Also, this version is not restricted to running from hgwdev. commit e09a37e83d88726cc76e58ff551f5fd7a6704f58 Author: cline Date: Tue Mar 2 00:13:41 2010 +0000 Removed an erranr % sign, changed the RNA type for HepG2 nlos + from pA- to tot, as for consistent with the metadata commit fdec084041d86c3dcffaf8f6fb690f62e7ebcad3 Author: tdreszer Date: Mon Mar 1 23:58:00 2010 +0000 Getting ready to put Broad into the pushQ commit 582edac72aee56b77bbf800ee83433aa44f2493a Author: donnak Date: Mon Mar 1 23:42:47 2010 +0000 Fixed a typo. commit 19e96e9d46b045757787f54767e2010664cdb8b4 Author: angie Date: Mon Mar 1 21:05:26 2010 +0000 gwasCatalog update commit 49dd31f0fe134de9ed4e7fd4b9d37ee16a2ebf72 Author: tdreszer Date: Mon Mar 1 19:51:41 2010 +0000 More ugly unscrambling. And it is not done yet. commit 131f031641ac7833a0b2dc68549e3ed7ba7d390e Author: tdreszer Date: Mon Mar 1 19:21:32 2010 +0000 Straightened out mislabeled replicate. commit 6d83152794360ca49da36dcd985fa53d9b041768 Author: tdreszer Date: Mon Mar 1 19:10:01 2010 +0000 Fix a mislabeled replicate for HAIB TFBS. But there is more unscrambling to come commit 2dd55fcfd22ab76847f48f13c621bb20f94c4605 Author: cline Date: Mon Mar 1 19:08:18 2010 +0000 Cleaned up the long labels commit ca4016b72b97dd771e6d70e6d1c609d0aad1c066 Author: ann Date: Mon Mar 1 18:59:23 2010 +0000 Fixed broken logic for finding out if the chrom list is too long to be useful commit b108c323b27855803b6ac6e7654618e4083824e6 Author: katrina Date: Mon Mar 1 18:51:46 2010 +0000 changed human db from hg18 to hg19 commit 7801fd6e9bbdb337c0d5b3f8c27990ec82e2394c Author: galt Date: Mon Mar 1 16:00:07 2010 +0000 "Encode release log update" commit f719ecb5a6e814c6b5a90c59b13a462cef2e6816 Author: galt Date: Mon Mar 1 16:00:04 2010 +0000 "Release log update" commit 43aeb9b8048e9148160b12bf0935c52d0640f581 Author: braney Date: Mon Mar 1 01:04:54 2010 +0000 allow release tags to be comma separated lists with alpha, beta, and public commit 0c0077a6cd7bb6ff6ffc4422a37c95b1e18e5c8d Author: galt Date: Sun Feb 28 16:00:06 2010 +0000 "Encode release log update" commit c1bb47cb0c1f7f8966328a362937debd4d92708b Author: galt Date: Sun Feb 28 16:00:03 2010 +0000 "Release log update" commit e87c1fd8ed95995f043ae07ba04248dd624ea42d Author: larrym Date: Sun Feb 28 00:11:07 2010 +0000 safari/chrome tweaks commit 75142d5c4f531c3ec247f46e108086e23694b7df Author: larrym Date: Sun Feb 28 00:08:14 2010 +0000 make local links in destDir to avoid problems for mirrors who rsync --links and have a different htdocs path than we do commit 9deb3461cdd36f6ea8cf544044aebf4151837027 Author: cline Date: Sun Feb 28 00:04:21 2010 +0000 Cleaned up the colors and the short labels commit b51ad11815233fd641addc98ab31fc439a7f220d Author: galt Date: Sat Feb 27 16:00:06 2010 +0000 "Encode release log update" commit ac9bd10b0a7bdb72074c763495a9f875327523ee Author: galt Date: Sat Feb 27 16:00:03 2010 +0000 "Release log update" commit fe110c1aaf1e8064f01a3e92d41cda17351b22c8 Author: galt Date: Sat Feb 27 00:57:47 2010 +0000 adding table and file counts as requested commit 140d45158a4bd7e7e192b28c01d68ed674bbf2c4 Author: tdreszer Date: Sat Feb 27 00:57:23 2010 +0000 Needed to include files.txt and md5sum.txt commit c32c165ce8897658298bd1808e0a82d02ea8e1c4 Author: tdreszer Date: Sat Feb 27 00:56:34 2010 +0000 Old stuff that needs to be checked in commit 2b14215b5347768e415fe5268d6cabe18dd1019c Author: tdreszer Date: Sat Feb 27 00:55:54 2010 +0000 Working through a lot of messy issues in order to get this ready for release 2 commit 0794a329f4890b5e8d249b8683d91f16e5f16c23 Author: tdreszer Date: Sat Feb 27 00:53:13 2010 +0000 Straightened out the GM12878/Taf mess, I hope. commit 5841a0f35971b942f4970a781f262f373feaaae8 Author: galt Date: Sat Feb 27 00:39:58 2010 +0000 enabling mary to auto-lock as she reqested commit f0c55ceda066329c15919b2698c7ebc8974700c3 Author: cline Date: Sat Feb 27 00:35:33 2010 +0000 Cleaned up an un-needed and broken link on the ref for the news item of the January NAR paper. commit 2048cf913607c261e47d39da4b3e9eec9029951f Author: tdreszer Date: Sat Feb 27 00:23:14 2010 +0000 Hopefully straightened out the GM12878/TAF mess for HAIN TFBS commit f54ec477f81f1fd245ed62bcf67b1470d264dd81 Author: angie Date: Sat Feb 27 00:12:36 2010 +0000 Adding dependencies to install targets to avoid race conditions when using make -j (parallel). commit bd64452e821235427fd618b0fc7066ae008763af Author: katrina Date: Fri Feb 26 23:46:50 2010 +0000 changed human db from hg18 to hg19 commit 5b5a4274038d7ba414e3959d282cda08aadd743b Author: ann Date: Fri Feb 26 23:40:47 2010 +0000 getting rid of extra space commit 174711209cb8756e8fd2172588fe0ccf0de95297 Author: tdreszer Date: Fri Feb 26 23:14:02 2010 +0000 Removed 2 duplicated and obsolete tracks from HAIB TFSB commit b565767bc4c67ee380d65103f120f73fa6d40f7d Author: cline Date: Fri Feb 26 22:53:36 2010 +0000 Rearranged some wording to emphasize the whole-genome aspect of ENCODE. Added a news item on the Jan. NAR paper. commit 4d2e2fe08c9892989b7db8a02aa97c00d2369887 Author: braney Date: Fri Feb 26 22:41:50 2010 +0000 add ensGene searchs *without shortCircuit* to human so that Gencode releases with the same id's are searched too! commit 5882badbbf642e5df630e0ee7bf8d072f96c7e46 Author: tdreszer Date: Fri Feb 26 21:42:35 2010 +0000 Release 2 is just about ready for QA commit ca79593b6998db20a39bb08198ebccd6876ff6a9 Author: tdreszer Date: Fri Feb 26 21:23:28 2010 +0000 Updated HAIB TFSB data version in preparation for release2 commit 0e5dcb287be096bfe01b97195db65ca8bdb56eea Author: tdreszer Date: Fri Feb 26 21:22:39 2010 +0000 Added a release note in preparation for release2 commit 9393932f477c112db11c7e483789296ef3bccd69 Author: tdreszer Date: Fri Feb 26 21:21:55 2010 +0000 Fixed a link commit 5134737d480ead1f7468297b040d4f21d5ca5587 Author: kent Date: Fri Feb 26 20:20:45 2010 +0000 Adding kgTargetAli to all.joiner. commit 889d3c4e8a24325f2e4b3d623f6200865e0797fc Author: ann Date: Fri Feb 26 18:25:12 2010 +0000 removed beta stanzas and release alpha lines to stage wgEncodeGencode tracks commit 6a82f84d0aa2dd43d68a2bb5126d3f72a943fda1 Author: galt Date: Fri Feb 26 16:00:06 2010 +0000 "Encode release log update" commit bbdc1927f3553bba7751b04f1e50c28ad08a46f1 Author: galt Date: Fri Feb 26 16:00:03 2010 +0000 "Release log update" commit babcc1b34833b99223805cc7ef972592922a6684 Author: katrina Date: Fri Feb 26 15:27:22 2010 +0000 added CSHL Sm RNA-seq commit cf1905a9f4c305743271f62235d0bad74255e1f6 Author: larrym Date: Fri Feb 26 07:51:07 2010 +0000 turn off cache in hgTrackUi call commit 8870f15e7cbc41e26f042b74628dd68cc7308607 Author: larrym Date: Fri Feb 26 07:34:01 2010 +0000 POST => GET to fix problem on chrom with settings dialog; cleanup getDb code; handle IMAGEv2_DRAG_REORDER == false commit 4740248ef32c18e0256a4c1ef1c81f00e8a0db41 Author: angie Date: Fri Feb 26 06:54:57 2010 +0000 Added option to (not) display item names in bam tracks. Also, when coloring by alignment qual and not pairing, sort by score. commit d5cae4de6eb1c92b4de87d66d2edeb3265a0bcb3 Author: rhead Date: Fri Feb 26 03:12:28 2010 +0000 Added more settings that will keep things from failing silently. commit 90b8ea4f406b397c13b175dba62aa158539cc9ca Author: tdreszer Date: Fri Feb 26 01:00:25 2010 +0000 Fixed one more metadata problem for HAIB TFBS commit 91399600f471a2f2b3c9cd53fe57200486c31d4e Author: antonio Date: Fri Feb 26 00:45:43 2010 +0000 made individual chain and net tracks use same html as composite track commit 43cee48d44bbe600b99f00276f20ad864d1777c3 Author: kent Date: Thu Feb 25 23:47:50 2010 +0000 Adding UCSC Genes as a target for In Silico PCR on hg19 commit 001943925373cb1bacd37856193b0de3a193f9e5 Author: kent Date: Thu Feb 25 23:34:02 2010 +0000 Adding some business to help finish up lingering issues. commit 7b3b3c8637409522e8c981e8eaf13e617b861827 Author: tdreszer Date: Thu Feb 25 23:32:08 2010 +0000 Fixed a couple of metadata problems for HAIB TFBS commit 66b14953b9a42065a5063e9d026c543f55721eab Author: angie Date: Thu Feb 25 22:55:55 2010 +0000 No need to use sparseFile in addition to bitmap file for cache age/timeout, and it causes trouble when bitmap exists but sparseData doesn't (yet). Also, moved verbose() up to where it wouldn't cause segv. commit 750b599ab05c55a69052d1a34f1b1e8cae67d0eb Author: angie Date: Thu Feb 25 22:05:02 2010 +0000 If compiling with KNETFILE_HOOKS (samtools extension that lets us hook in udc for URL I/O), don't cd to trash while loading the index -- if udc.cacheDir is a relative path, then that breaks, and if using udc we don't need samtools' index-caching. commit f8ad4acda38e2b375ebb22588fd3e23f26172fed Author: kuhn Date: Thu Feb 25 20:10:54 2010 +0000 removed a print of a variable not used commit 547428d7877427d66840281100d7f100ccce41fd Author: markd Date: Thu Feb 25 05:18:35 2010 +0000 don't let PAR track hide PAR1 genes commit b32993d78289f3cfde9b188fb059fd188582f36f Author: hiram Date: Thu Feb 25 05:03:51 2010 +0000 adding all the chain net overrides for calJac3 commit 138cbedc0306942194cf7862661fa05729af162c Author: markd Date: Thu Feb 25 04:08:52 2010 +0000 fixed backwards logic on including pid in tmp file name commit c5c0c53713b222819b99029ac59e5e22eed72452 Author: hiram Date: Thu Feb 25 01:01:25 2010 +0000 adding cvs ident strings commit c80605350446f867037b13925235e4c0ecbf2549 Author: antonio Date: Thu Feb 25 01:00:32 2010 +0000 overrode chainGasAcu1 parameters due to chainNetTrio results commit 9b5450526780e4da077fc981529d3d4cf77d5a61 Author: hiram Date: Thu Feb 25 00:29:05 2010 +0000 adding definition for calJac3 chain net commit e4a6a4fd86bc7d98e4958aee352a735f4a11c116 Author: hiram Date: Thu Feb 25 00:27:10 2010 +0000 adding cvs ident strings commit 5db4cd48e88acfc9380302725b70f851258a1c3c Author: hiram Date: Thu Feb 25 00:25:29 2010 +0000 adding calJac3 and ailMel1 chain net definitions commit 48a8152d6c2912ff411c7954d659990ab6016192 Author: hiram Date: Thu Feb 25 00:23:18 2010 +0000 adding definition for calJac3 chain net commit 0fc70d218b94c43a8e1782030647858c7923613a Author: hiram Date: Thu Feb 25 00:21:49 2010 +0000 adding calJac3 and oryCun2 chain net definition commit 5d10e9d8a33b784df82b8cd5c8ffcc36e994c08c Author: hiram Date: Thu Feb 25 00:19:39 2010 +0000 adding definitions for calJac3 chain net commit 9cb4883e2b3c786c5f40971f86201f8672473051 Author: hiram Date: Thu Feb 25 00:18:27 2010 +0000 adding calJac3 chain net commit 1abbb8283a040948b03c490d69ab218ab6692fa6 Author: hiram Date: Thu Feb 25 00:10:00 2010 +0000 adding definition for calJac3 commit c145a93732aecec5bec26b72b2756b3ff7000897 Author: hiram Date: Thu Feb 25 00:08:54 2010 +0000 adding calJac3 ailMel1 and susScr1 chain and net definitions commit cdc085bc21971acd436ac03f5ebdababf096a674 Author: hiram Date: Thu Feb 25 00:06:46 2010 +0000 adding calJac3 definition commit 372507fb55ed0aff820da26b8b7312585f4d14b8 Author: hiram Date: Thu Feb 25 00:01:55 2010 +0000 adding calJac3 chain net definition commit 9ed37af35353e5bc0e93ba42ec637f7b025d94d8 Author: hiram Date: Wed Feb 24 23:58:23 2010 +0000 Adding calJac3 chain net commit 64245bf7d6d7c753a3173f233b86803b657cd769 Author: hiram Date: Wed Feb 24 23:52:23 2010 +0000 adding chain net definitions for marmoset calJac3 commit c89f4ad61e85c031076fd3153d9b80b7ff49d046 Author: hiram Date: Wed Feb 24 23:49:35 2010 +0000 adding the new ones for calJac3 13-way commit 6bc09e681dc9ce2f65416d510889e473c0cedafe Author: larrym Date: Wed Feb 24 22:10:04 2010 +0000 turn on autowidth so strings don't get squashed in pulldown commit efd1a4b32c7e803e41997379e0307f37437e8567 Author: ann Date: Wed Feb 24 21:35:28 2010 +0000 clarifying how to get to your gene commit bea51ca7858a2357f66effd43e55547d8dd54962 Author: ann Date: Wed Feb 24 19:57:18 2010 +0000 gene search functionality commit 635a36a3f688cef7bee2e0752fc498bfe242e27e Author: larrym Date: Wed Feb 24 19:54:21 2010 +0000 remove white-space at the bottom commit 7639c366771f33eabf4e94b25fef833ee300826b Author: ann Date: Wed Feb 24 19:20:54 2010 +0000 added informational statement about what to do when the script finishes commit ae6e5da4a10de1038cfa85b493e27d23e0b05044 Author: katrina Date: Wed Feb 24 18:56:33 2010 +0000 removed release alphas from the rest of the ENCODE CSHL Sm RNA-Seq table blocks commit 4fa19ccb5d73f9600d07e8bc4ffeaaf96c9de4ff Author: angie Date: Wed Feb 24 18:55:08 2010 +0000 fixed a couple typos. commit 9c2494b197a85d8d9c5d9845600b8d4cd8c4e840 Author: pauline Date: Wed Feb 24 18:52:27 2010 +0000 Removing alphas in preparation for staging track on beta. commit 7f4078446b63d97ec2e939173569c3941c2bddc4 Author: ann Date: Wed Feb 24 18:18:02 2010 +0000 image showing gene auto complete commit db7f6ff39e561bd9bc92a94092071514a12cfb0a Author: galt Date: Wed Feb 24 16:00:11 2010 +0000 "Encode release log update" commit 27e981e39377473452141dfb5cd2b11db4f5cfd7 Author: galt Date: Wed Feb 24 16:00:07 2010 +0000 "Release log update" commit 6d741b987c6e18eee05a2bd99db0131af7536e62 Author: angie Date: Wed Feb 24 01:10:25 2010 +0000 I have added some hooks into knetfile.c in our local copy of samtools, so that knetfile can serve as a wrapper on udc (or any other suitable code). If KNETFILE_HOOKS=1 (in addition to USE_BAM=1) this will bring the benefits of udc to bam tracks. commit a894f20ee76c0d6a10bc2c74717a69615d33f2e6 Author: angie Date: Wed Feb 24 00:55:09 2010 +0000 Another tweak required to make the cache timeout work: when we do fetch info, update the cache file mod times to reset the cache timeout clock. commit 102fddeaedd9c2b33d30e0b533c4251c99dded8d Author: angie Date: Wed Feb 24 00:51:00 2010 +0000 Added touchFile (like touch command). commit 6d829be8c0cd2168830b975406efd62dbe90a4e3 Author: hiram Date: Tue Feb 23 23:41:38 2010 +0000 initial tree for 13-way on Marmoset commit 56537c9baee51a7b08c350bd0c2109cbef4cdc8f Author: kent Date: Tue Feb 23 23:03:37 2010 +0000 Removing another dependency on hgg_gene for a purely informational page. commit 734cf2928e806bce47ea6f7e953210d199180363 Author: braney Date: Tue Feb 23 22:51:10 2010 +0000 a file I need to create to get this track through QA commit b9edeff980001a7f84b48e11677414e5bdf72826 Author: braney Date: Tue Feb 23 22:25:08 2010 +0000 add some release notes commit dca8dbe893a8e7e8ec0925403662ffa8a41680af Author: angie Date: Tue Feb 23 22:04:07 2010 +0000 When getting updateTime and size from the cache bitmap file, get the real remote update time from the bitmap file contents, not the bitmap fileModTime. commit ea282bdcb0adce507ac12782b67a1708fd24c0a4 Author: vanessa Date: Tue Feb 23 21:38:53 2010 +0000 fixed typo commit 6c545ff23e6c1adbf49274a09b452434597987c7 Author: kent Date: Tue Feb 23 20:35:37 2010 +0000 Making it so can bring up the methods page without a gene specified. commit 5f06fe644d7e0ccded3da909e654701acf1487aa Author: galt Date: Tue Feb 23 19:02:33 2010 +0000 not doing allow reloads automatically for admins because its unneeded commit 73a1eb802b1a2922b164e49049111d5781ff81d0 Author: galt Date: Tue Feb 23 18:12:54 2010 +0000 v226 preview commit 9bbbca1e30d173c278e0c4186728a920b92f05b7 Author: tdreszer Date: Tue Feb 23 17:49:43 2010 +0000 Back to the release 3 version of UW DNaseI HS commit 97e95b91ebe44eedc0faeb09c75c443ebed4edc4 Author: tdreszer Date: Tue Feb 23 17:46:59 2010 +0000 Back to the release 3 version commit 58ebb3959e66ec0f9c53fc9a3a0c518683fae223 Author: galt Date: Tue Feb 23 16:59:20 2010 +0000 removing automatic -allowReloads that got added due to some misunderstanding long ago commit f115f16c42dc29b9517f398c7c62460c9c1e93aa Author: hartera Date: Tue Feb 23 16:48:18 2010 +0000 Removed duplicated subTrack lines from mapability track entry. commit 1e1dbd27ee2131d8206baa16784bb9ec17273382 Author: galt Date: Tue Feb 23 16:00:07 2010 +0000 "Encode release log update" commit 3e5f0a195ab378977dd8ba0dbbfd79578b0fa7d1 Author: galt Date: Tue Feb 23 16:00:04 2010 +0000 "Release log update" commit 04f81c6474fc43c928149248a3d6045dcc81df7c Author: hiram Date: Tue Feb 23 04:34:14 2010 +0000 some better defaults on initial track visibilities commit 78356a2277b95e462b8720d45e89c987f5ae8f87 Author: rhead Date: Tue Feb 23 03:37:21 2010 +0000 Added note for next time about NIAGene track. commit c315047f0806ac9b1b2169ec241e386b43c5cc78 Author: hiram Date: Tue Feb 23 03:29:14 2010 +0000 done with genbank run commit 2287b742c9ad79513ad66fa6ecfd76234309472a Author: hiram Date: Tue Feb 23 03:28:23 2010 +0000 Added gorGor2 - Gorilla Gorilla commit d92023b0a35e0ada4a7dcce876d84f05a0b872a7 Author: braney Date: Tue Feb 23 01:28:08 2010 +0000 extract RikenCage to include files commit 0455c9f37c59901a38a6cd890227d1c5ab2980b2 Author: braney Date: Tue Feb 23 01:27:52 2010 +0000 extract RikenCage track to its own include commit 942514905aa68834655c24149bd97fe3f441a0e8 Author: fanhsu Date: Mon Feb 22 23:28:29 2010 +0000 Added section to process rgdGene2 track. commit e1677cf9f859e8d1b936e2fc77015c65e3c4ea0f Author: tdreszer Date: Mon Feb 22 23:24:38 2010 +0000 Changed the names of 4 HAIB Chip tracks because they should have been versioned commit 2e369fe0aae61a17c27705abed757e01950fb0d0 Author: braney Date: Mon Feb 22 21:01:42 2010 +0000 fiddle with the wiggle dialog a little to get the YLineOff drop down in the right place commit 2f583a20e0f8a35a37bced673f398f3cd5b47172 Author: katrina Date: Mon Feb 22 18:08:21 2010 +0000 fixed typos in newly added Release Notes section commit 5cfea7915af602228baa978978895ba0e89fc772 Author: kate Date: Mon Feb 22 18:04:19 2010 +0000 Add execute bit so Apache correctly handles SSI (server-side include) adjustment of hgTrackUi relative path commit 66cd82e9e1ae6011e1821dec9c00159cb458d9db Author: braney Date: Mon Feb 22 16:45:38 2010 +0000 take out cartSaveSession which ends up swallowing our output commit 4227364269dbea9b7b1ccb464f2ed22746186e9d Author: hiram Date: Mon Feb 22 16:26:57 2010 +0000 adding names for gorilla species commit cae2991394719207343d0bd9b31b939d9d9d5b71 Author: hiram Date: Mon Feb 22 16:22:20 2010 +0000 adding gorilla gorGor2 commit 16dc16926b5be4b7a4f50e6014f2f2d5eb5fb1e0 Author: galt Date: Mon Feb 22 16:00:06 2010 +0000 "Encode release log update" commit 94d004587dfb840f588f894d307778ee3991a466 Author: galt Date: Mon Feb 22 16:00:03 2010 +0000 "Release log update" commit cdbaaf3f86c62a718a155918abee95aaa9784695 Author: hiram Date: Mon Feb 22 04:45:10 2010 +0000 Adding an 8-way conservation commit 72135ea7b004b68dd3b68b23631bf03cb3bf0fb2 Author: galt Date: Sun Feb 21 16:00:07 2010 +0000 "Encode release log update" commit 34f88f924cd9cd9f7ec5af2736a78c20d795920c Author: galt Date: Sun Feb 21 16:00:04 2010 +0000 "Release log update" commit 511822a9d5091a2c0c5bb61377de1fd81c6b086d Author: hiram Date: Sun Feb 21 04:25:25 2010 +0000 adding other gaps and ready for kluster scratch/data rsync commit 70f1b45746c0e80acfb0a9d0a94c0f22f0c9b4cb Author: hiram Date: Sat Feb 20 22:39:43 2010 +0000 initial assembly build and done with repeatMasker and simpleRepeats commit 9e08dfc25f76f19ae6b2644f9630100d8662606f Author: galt Date: Sat Feb 20 16:00:07 2010 +0000 "Encode release log update" commit dfbd141c2fdb3c59c982c8d085f2083c20c37133 Author: galt Date: Sat Feb 20 16:00:04 2010 +0000 "Release log update" commit c34122fd9bee1a52ea9f077b9dd7482b321ed29f Author: markd Date: Sat Feb 20 07:12:50 2010 +0000 check that all config files starting with dot are only readable by the owner commit c4051e4764bb86ef4253d72d56400eb30e0b20bc Author: fanhsu Date: Sat Feb 20 00:59:22 2010 +0000 Created hgRgdParsePathwayObo.c commit ef10dead7ee10d489c354c94c334e7d06cdff841 Author: tdreszer Date: Sat Feb 20 00:10:54 2010 +0000 Reverted UW DNaseI HS to release 2 temprarily for a minor texting change on the RR commit 26b98499fb5d15f539b6166a96723f213c7a5452 Author: tdreszer Date: Sat Feb 20 00:03:11 2010 +0000 Setting this back to a release 3 version. commit 4f8eaf552eb1143d89ce358fc1d0939941b3bba9 Author: ann Date: Fri Feb 19 23:37:18 2010 +0000 fix a typo and long line commit 7df759d1548c7bc6331921fed5b7382913e4fb2e Author: braney Date: Fri Feb 19 23:25:16 2010 +0000 replaced with human/wgEncodeGencode.html commit b5afb3cafbd672aab3cc4e7809c653ab4d686e75 Author: katrina Date: Fri Feb 19 23:25:09 2010 +0000 edited name of Broad Istitute and added link to Broad Institute commit bbd10f142ba2b6ec1b0f7dd98d1e9c6316e48bb7 Author: angie Date: Fri Feb 19 23:24:34 2010 +0000 Instead of dumping out the full BED+ record when there are more than 6 BED fields (we don't subject our users to that on plain BED track details pages), display non-BED fields if there are any. commit ce00ea0ef87566cb281433173e572d2f54740eeb Author: angie Date: Fri Feb 19 23:15:51 2010 +0000 Added new required setting assemblyShortLabel, an abbreviated form of the sequencing center's ID for the assembly (which is often more familiar to users), e.g. NCBI36 for hg18. commit 8d98af66c84cd281eb590455200b1eeeda91389b Author: fanhsu Date: Fri Feb 19 22:31:46 2010 +0000 Created makefile. commit 61a07952f4f7c50da123f08a6be6fcc6dca39cc7 Author: hartera Date: Fri Feb 19 22:14:31 2010 +0000 Changed value in genomicSuperDups table for segmental duplications track. commit 1b36ef7b175a6cd875c335c7c73f7114d78afad8 Author: cszeto Date: Fri Feb 19 21:30:27 2010 +0000 UPdated track names commit c9c801501a579c93734e9f252db9480685d3c214 Author: tdreszer Date: Fri Feb 19 21:15:21 2010 +0000 Neglected to make replaced tables release beta commit 3872012c07ca2b79d5b7386e030367ec98934164 Author: tdreszer Date: Fri Feb 19 21:05:47 2010 +0000 Minor clarification commit b1eb090d0189d1cb8561fe71aef2d75d4cde43ec Author: tdreszer Date: Fri Feb 19 20:48:38 2010 +0000 Files list for release 3 commit da4f1884a3a408a26b35ffc1b5b92f8f67079f5e Author: kuhn Date: Fri Feb 19 18:44:16 2010 +0000 print a manual of all csh files usage statements commit c3a48814f55368240678532758c3e0cbaec1ac16 Author: tdreszer Date: Fri Feb 19 18:41:17 2010 +0000 Getting ready for UW DNase release 3 commit 1bed81917f0fe2f054e3f12f9ae14597b9338b1a Author: hartera Date: Fri Feb 19 18:23:41 2010 +0000 Removed duplicate subTrack line. commit 984980c6564d4c86e13c040a50be63cf7246b172 Author: hartera Date: Fri Feb 19 17:15:48 2010 +0000 Added release alpha/beta versions for the Mapability track. The beta version uses an older description html that omits description for the new CRG subtracks. commit bcbd38ef4dbab24f5a83a260b69567cdc157f0ea Author: galt Date: Fri Feb 19 16:00:07 2010 +0000 "Encode release log update" commit da26662511581a3639e6c4c4f9056f2eaebb10c1 Author: galt Date: Fri Feb 19 16:00:04 2010 +0000 "Release log update" commit 816882dbeb1a92d388309bb6067ddfa271d9343f Author: galt Date: Fri Feb 19 07:17:10 2010 +0000 fixing the cut-paste problem with the warnbox on non-warning plain text messages commit 2c8caa57269aff9b1a1b09f00f7a1ee396a98110 Author: hartera Date: Fri Feb 19 04:50:55 2010 +0000 Older version of Mapability track description before CRG data added. This is for the release beta version. commit 13b50b8dde7afc214f911ef531257a97bca20270 Author: larrym Date: Fri Feb 19 02:22:41 2010 +0000 give the suggest input a name to make a robot happy commit 8a035bb0a1e5540afa87a9ac5741895b10eb297b Author: angie Date: Fri Feb 19 00:22:30 2010 +0000 Added printCustomUrl -- user noticed its absence. commit d96eb56749c127e93d21ac8b08ef3a1936b54ab2 Author: tdreszer Date: Fri Feb 19 00:05:12 2010 +0000 Final touchup before unbouncing to pushQ A commit 62bb3e4c5597f6067e58552663fcae00fa630384 Author: tdreszer Date: Thu Feb 18 23:49:37 2010 +0000 Added 23 tagAligns which are the missing inputs commit ab05635d94304fc18c811d41768f4177b4301b6e Author: hartera Date: Thu Feb 18 22:58:28 2010 +0000 Updated description based on that provided by the data providers. commit 28a3554a14c8701d5ab4c06df847ddcce75e6e50 Author: hartera Date: Thu Feb 18 22:22:02 2010 +0000 Added more method details and information about track configuration. commit b41ccb7b4ee768326506b44b3de2e1cf6527dbbe Author: hiram Date: Thu Feb 18 22:15:04 2010 +0000 trying to lastz papHam1 ogoGar1 micMur1 and tarSyr1 with difficulty commit 740e10eae769f970a4c24502421416931e64129e Author: hartera Date: Thu Feb 18 22:03:53 2010 +0000 Changed Vega Genes so that the genes and pseudogenes subtracks have different colours. commit c2ee7a42bf393fc01996491a86b179a3aa5042d8 Author: hartera Date: Thu Feb 18 21:59:44 2010 +0000 Changed the colour for vegaGenes release beta to the same as for release alpha. commit 1ed9f23908ca8cbfe3d73fa81626c51794938ed1 Author: braney Date: Thu Feb 18 21:55:50 2010 +0000 splitting Orchid and Chai tracks into two separate entities commit d4325b60b1dc61de7f5879844cff79a40bfbfe46 Author: ann Date: Thu Feb 18 21:37:53 2010 +0000 fixed typo commit 4ebccdc7b955e4584c7ebe64a4c2cabb715a3cb4 Author: galt Date: Thu Feb 18 21:11:07 2010 +0000 undoing 1.65, returning to same contents as 1.64 commit 7929dbaf0c97be39e0690082695522e78e126396 Author: braney Date: Thu Feb 18 20:52:39 2010 +0000 fix link to ENSEMBL commit 100652b5849f660e3e45e3b73a4f1258d26fb4b0 Author: hartera Date: Thu Feb 18 20:29:50 2010 +0000 Added a Signal track for the Burge RNA-seq data. Updated trackDb entry for this track to include views. commit 7d11ea7ca9473e4f2a7d2b25417cca26b629fd88 Author: braney Date: Thu Feb 18 20:17:15 2010 +0000 keep using wgEncodeSangerGencode commit efdd2e1ea500699dba6c680afe2ee77c1eb27d5c Author: braney Date: Thu Feb 18 20:16:43 2010 +0000 take out some periods (per Ann) commit da6afa478eb0b3801d87ccd41ec912f15252c516 Author: angie Date: Thu Feb 18 19:59:02 2010 +0000 Added clarifications/corrections to #PSLDisplay about how the direction of the arrows is determined (splice site deduction is only for ESTs) and double-sided gaps. commit a0c3920851468832c4b95d215bb3faca411cae63 Author: kuhn Date: Thu Feb 18 19:52:27 2010 +0000 moved all danRer4 chains and nets to composite and dropped individual tracks commit 2e5768d07c5389557bed894504fbcb0ee758426e Author: larrym Date: Thu Feb 18 19:27:54 2010 +0000 add hgSuggest commit 303c25d4c2be904ded41e37eaf19f2427d6359af Author: markd Date: Thu Feb 18 18:53:47 2010 +0000 removed stray space commit 53cffe39bd3a6fb20de404b73dcd257643abeb8f Author: markd Date: Thu Feb 18 18:53:25 2010 +0000 added PAR tracks commit 8a2accbd6f3cc6cb1996e160072d322c91dcc9b7 Author: markd Date: Thu Feb 18 18:45:25 2010 +0000 added PAR tracks commit f936a432e7bd92412b605a290eaa2267c7326462 Author: angie Date: Thu Feb 18 18:31:08 2010 +0000 Added missing tags, found by hgTablesTest on the description page. commit bc5a3010feb36200fb61dc98b5d3d687f181063c Author: markd Date: Thu Feb 18 18:16:08 2010 +0000 fixed bug when clicking on one par when both are displayed commit e4544665d12392118e01e8025c700e95e03368c0 Author: galt Date: Thu Feb 18 16:00:06 2010 +0000 "Encode release log update" commit 9753cf5185438f369811bd7d0aab408dfc36ad87 Author: galt Date: Thu Feb 18 16:00:03 2010 +0000 "Release log update" commit ea4c8eab9ddd16dd44b91943c55024f847070db5 Author: markd Date: Thu Feb 18 07:12:11 2010 +0000 Added option to not give bonus score for apparent introns. Fix test naming inconsitency commit 2c4a1707b858eb302fb8355e8c437f36d92f1c77 Author: markd Date: Thu Feb 18 06:03:08 2010 +0000 used BED format for PAR commit 543047daf848fa1fdedf1f240d36420bfabece5b Author: markd Date: Thu Feb 18 06:02:29 2010 +0000 added some examples to look at commit 81ed2cbb151b03c735c46b20e49a8781c3d2933c Author: markd Date: Thu Feb 18 06:01:45 2010 +0000 added details page for PAR tracks commit 5a4a3a72e231b4ca2f1b855b47c473c56227d0f4 Author: hartera Date: Thu Feb 18 00:15:26 2010 +0000 For Burge RNA-seq track, made all subtracks on by default and changed the upper view limit to be 1000. commit 24b20e6f0c3c6f7439fcd5f41efd6c69594bad9b Author: tdreszer Date: Thu Feb 18 00:01:36 2010 +0000 Backlog of notes from freeze work commit aa8f9009a8d59b8d84e8e29ee0d6fd1ceba40266 Author: tdreszer Date: Thu Feb 18 00:00:29 2010 +0000 Updated files list for Jan 2010 freeze commit c5cfc159ed29e734171bd205df771ec9efd8f803 Author: hiram Date: Wed Feb 17 21:55:58 2010 +0000 adding an elapsed time calculation when successful completion commit 338594685f38d21f89fdb0876d4d03912d6c7c2b Author: tdreszer Date: Wed Feb 17 21:49:21 2010 +0000 Fixed the filterBy settings for UW Chip commit 5dd7159c42b45ab0093adfded772d0b3fee91a56 Author: tdreszer Date: Wed Feb 17 21:40:26 2010 +0000 Fixed tiny bug that prevented hgTracks cfg page to work. commit 1f8b4d78602ef4a7693dc4e3fb8ea67d737d5b36 Author: tdreszer Date: Wed Feb 17 21:39:16 2010 +0000 Fixed obscure bug that was evident during composite reset to defaults commit f5b7f82ad631ca889f57a050b5e2ca02d5684b07 Author: tdreszer Date: Wed Feb 17 20:20:36 2010 +0000 Larry pointed out tool tips that were wrong. commit c7f782d1e2c5a73ef22d0d78231f5a936b24f0a2 Author: kent Date: Wed Feb 17 20:16:44 2010 +0000 Fixing so it doesn't get misdirected by critically placed comments. commit 52824a23ea0a7a0e1b40418b7e4978336d43f368 Author: angie Date: Wed Feb 17 20:07:46 2010 +0000 Removing stray character that made make barf. commit 0b5917b8839c138c252270d909a74d2c9e03caeb Author: angie Date: Wed Feb 17 19:54:06 2010 +0000 Removing since we no longer have any hgwdev databases with jaxQTL tables (just jaxQtl now), and MarkD found CVS error on Mac's default-case-insensitive filesystem. commit a643d38f54ca4d786719a42937893433f1375de3 Author: angie Date: Wed Feb 17 19:50:58 2010 +0000 Removed vestigial searchSpec. commit 36e27b4f5479a80363f99d22e0578d13dcfa319f Author: angie Date: Wed Feb 17 19:50:24 2010 +0000 Corrected setting for jaxQtlMapped (mm8 table name changed a long time ago). commit a4a21603cc8f33a572f166865f5d1454eeb61897 Author: angie Date: Wed Feb 17 19:43:25 2010 +0000 Removed to avoid clash with jaxQtl.sql (QA's preferred name). hgc still uses jaxQTL.[ch]. commit e409903f0c940390737204b51dfca944b533bd72 Author: angie Date: Wed Feb 17 19:35:49 2010 +0000 Make the link to hgTrackUi for all custom tracks (except those that exit hgCustom() early). commit 08df1e75c7af5174ad175e966cc90c9b964738de Author: rhead Date: Wed Feb 17 19:19:41 2010 +0000 Changed strPur2 nets and chains to composites. commit 08dc6e3237362f755977c085a2808b0134ce8840 Author: tdreszer Date: Wed Feb 17 19:13:53 2010 +0000 Dinks to the navigation links, by request commit 46f1a5eaeddbee40cfa0fa3af997f08421c7bbc3 Author: hartera Date: Wed Feb 17 18:21:58 2010 +0000 Added subtracks and views for the Burge RNA-seq track. commit e1871a0c80a5d38b0b78dfe168ca235097291804 Author: rhead Date: Wed Feb 17 18:04:51 2010 +0000 Changed monDom4 chain and net shortLabels to match chainNet shortLabel. commit 495b5fbe10f8597de5778749e1bbdd78475fa3ef Author: galt Date: Wed Feb 17 16:00:07 2010 +0000 "Encode release log update" commit 3d4bc0d2bfd158b989991e8530d649843ddf93d5 Author: galt Date: Wed Feb 17 16:00:04 2010 +0000 "Release log update" commit 3ff1559dc34d72bbf1a0f56b99449792b184693d Author: markd Date: Wed Feb 17 08:54:22 2010 +0000 added hgPar to load PSL table describing PARs commit 3b4ace777e4af99a0e5581ec0fe93aeb211800e0 Author: markd Date: Wed Feb 17 08:53:20 2010 +0000 allow defaulting to TMPDIR directory commit fc493811bb96b50865ae6b81f62bc067f7e031a3 Author: hiram Date: Wed Feb 17 07:01:29 2010 +0000 Correct text commit 0ee86c795721ac376fa9f8a023103876b7c6259b Author: hiram Date: Wed Feb 17 06:48:42 2010 +0000 working even if contig names are identical and ignoring extra columns on input commit 37026798faf700bd38bf3c9008e4d004ce029bde Author: hiram Date: Wed Feb 17 05:32:58 2010 +0000 cleaned up gap types to cover all included in this assembly commit 069b1d7eea9286563e32df29084f42afcb50392d Author: hiram Date: Wed Feb 17 05:17:49 2010 +0000 cleaned up discussion and references, ready to go commit bda79c4fe347fde331e6333ddf92cb8af96b87d4 Author: braney Date: Wed Feb 17 03:08:39 2010 +0000 do some release tag checking commit 89aa56928037e5cbda1e8d2a4fa1143d3428046d Author: braney Date: Wed Feb 17 01:51:31 2010 +0000 add release alpha and beta to subTracks commit 30b78db06a521e675694dcbb156251a568332486 Author: hartera Date: Wed Feb 17 00:34:03 2010 +0000 Adding single subtracks to test views for Burge RNA-seq data track. commit e1a0f0664014e80bdc7f31822b9226f9f8699267 Author: rhead Date: Wed Feb 17 00:28:07 2010 +0000 Removed an old comment. commit 02e5cf7ae9edc6548ea8d3a5f43ea263736cf96b Author: braney Date: Tue Feb 16 23:55:41 2010 +0000 take out insertLength which isn't in release1 commit 880acaec61b66a511947aecfbea0df48aeeeb8a1 Author: braney Date: Tue Feb 16 23:47:20 2010 +0000 add insertLength variables for those tracks who didn't specify it commit b9d424ebed9a6be24c0b2e0b8621107d9a7d1f70 Author: galt Date: Tue Feb 16 23:42:14 2010 +0000 multiz6way, annotated mafs, annotated and upstream downloads, frames commit 9ebefeec9658c16dc91ef49abfa67ef03d3ca3d4 Author: galt Date: Tue Feb 16 23:40:22 2010 +0000 organism tree for danRer6 6way commit 1235c8a53547eb80e302c156cc06c85196af10c8 Author: kent Date: Tue Feb 16 23:39:41 2010 +0000 Backing out again (via CVS commands) to get rid of some comment munging from the trackDb rewriter. commit 3c5f69452628a547125328aff484c177a420abec Author: braney Date: Tue Feb 16 23:37:32 2010 +0000 fix the code to check that subGroups have the predefined attributes from the composite. This got broken in Jim's trackDb overhaul. commit 49d068fb2220d66440771ddf0bad42d0f0272ef4 Author: ann Date: Tue Feb 16 22:29:28 2010 +0000 undoing change commit b7ace7441cc05747b6ddcd7dcba28f51b56780d8 Author: hartera Date: Tue Feb 16 22:25:24 2010 +0000 Minor edit. commit 9ebaf93bb38b1690859fde0ca85192d7f780cc53 Author: ann Date: Tue Feb 16 22:24:35 2010 +0000 showing browser tree to V & M commit bffafc2fb224789ab7bf2b99e54e10fe3dc65085 Author: hartera Date: Tue Feb 16 22:23:53 2010 +0000 Description for Mapability track. commit f7eb3c96d8f809776b2b77ce3d05e8a7c1bba78c Author: hartera Date: Tue Feb 16 22:20:35 2010 +0000 Adding HTML encoding. commit 657243ddde7f05dddd5926af42823ab698a8247b Author: angie Date: Tue Feb 16 22:18:39 2010 +0000 Added printTrackUiLink in doBamDetails. commit 825acb4d4d0f2c5093f73182cc76620bd7a28e47 Author: galt Date: Tue Feb 16 22:11:59 2010 +0000 "New version number v225" commit fa05f1a87b9dba44f6e1947d0bcd485f613bf949 Author: galt Date: Tue Feb 16 22:11:28 2010 +0000 v225 final build commit 76694a5a8118ba1130537c023c192ed14b515f5c Author: hartera Date: Tue Feb 16 22:08:43 2010 +0000 Updated CRG Mapability track description with text from data providers. commit 7a0e96e9f61e9d20b83161ff01cbe5cc84a5a1a5 Author: angie Date: Tue Feb 16 21:16:53 2010 +0000 In searchKnownCanonical, no need to include knownGene in the query because kgXref and knownCanonical can be joined directly - thanks for catching that Tim. commit f2c472faeb356bc37a2d423fb0759337dd4930cf Author: larrym Date: Tue Feb 16 21:15:44 2010 +0000 move ajax.js include into dragZooming block commit 796cc63e0356c1b295c4522999e269dc69488f76 Author: kent Date: Tue Feb 16 21:10:26 2010 +0000 Backing out subTrack->parent for a few more days waiting for CGIs on RR to catch up. commit 4e9b314fa427f0551dff340a59a253ab258dc099 Author: larrym Date: Tue Feb 16 21:04:20 2010 +0000 add gene autosuggest field commit 0b76ad910aeec5a52cda813ccd903f0e5533c22a Author: kent Date: Tue Feb 16 20:23:54 2010 +0000 Replacing subTrack with parent commit ee478ac0f900e8410bdaa5590dcbe7a9e1986993 Author: kent Date: Tue Feb 16 20:19:50 2010 +0000 Changing subTrack to parent. commit d0346333b24a385874df56a3fa8e10c3eb85c4ce Author: kent Date: Tue Feb 16 20:02:14 2010 +0000 Utility to replace subTrack with parent seems to work. commit 6305be47372c8043a14e16c728117b0da282f627 Author: galt Date: Tue Feb 16 19:07:46 2010 +0000 adding image for Aplysia commit b44ec42c50665c36fa23d6a2b2f7051e7be94a43 Author: galt Date: Tue Feb 16 19:07:00 2010 +0000 organism image for Aplysia commit 06b02989bfa5a1b9bef0837e29066f89b6685018 Author: galt Date: Tue Feb 16 16:00:06 2010 +0000 "Encode release log update" commit d8306b3bdb3dd537e611a1334816c293a868d2c9 Author: galt Date: Tue Feb 16 16:00:03 2010 +0000 "Release log update" commit fa08c7038c19c422a691d8e6ffa0f2257df674c1 Author: donnak Date: Tue Feb 16 09:52:22 2010 +0000 Added Sea Hare. commit 0e1b04926af6eefad88e915e607b612f8c9dacc8 Author: hiram Date: Tue Feb 16 04:55:56 2010 +0000 all.joiner done and pushQ entries commit 1070fc6500ab2af6824d3f1025680e654635de41 Author: hiram Date: Tue Feb 16 04:54:18 2010 +0000 done with a number of lastz runs commit b284e99aff96f4a5efdb918e5466f506a22b5f36 Author: hiram Date: Tue Feb 16 04:47:43 2010 +0000 completed calJac3 lastz alignment commit eb4dbfd4b6fe29e48aab2ad009f3a1c0cdecfd50 Author: larrym Date: Tue Feb 16 02:43:50 2010 +0000 add gene autosuggestion commit 840258c9f6ab548641e7e61fa720d49633882ce6 Author: larrym Date: Tue Feb 16 01:28:58 2010 +0000 add autocomplete files commit 458455c6861519962e8042c5ec61b124c119f8c9 Author: larrym Date: Tue Feb 16 01:28:14 2010 +0000 add autocomplete code; add getDna support commit 51a41c52635ffda7a4ddb7bf70efcb584946fcb8 Author: larrym Date: Tue Feb 16 01:27:05 2010 +0000 add lookupGene commit 26701157630dddeb6e9356f457ef1d9afa1cfa35 Author: larrym Date: Tue Feb 16 01:26:45 2010 +0000 move some code here from hgTracks.js commit 6e71df0eb6ec80662e58ae6721742dcda2c2e9cb Author: braney Date: Mon Feb 15 18:08:23 2010 +0000 started Human proteins commit 01f30f462440cf3c031cad72db31c766809d76e3 Author: galt Date: Mon Feb 15 16:00:06 2010 +0000 "Encode release log update" commit d08533c97d1c5fade74bb0d962361a65d72e87f0 Author: galt Date: Mon Feb 15 16:00:03 2010 +0000 "Release log update" commit 8e38f9b2b77a54b2dc58bf85ffffe7747d68ffd5 Author: hiram Date: Mon Feb 15 02:56:39 2010 +0000 Add monDom5 for calJac3 commit 47cf1b677f1f43c41a9484980776f82e87f3a31d Author: galt Date: Sun Feb 14 16:00:06 2010 +0000 "Encode release log update" commit 9dddff52ea9869da9cf6fd304b528c19f6b4695b Author: galt Date: Sun Feb 14 16:00:03 2010 +0000 "Release log update" commit 407dbbffac7b86690ea69c11dc25dc927b10fb56 Author: galt Date: Sat Feb 13 16:00:07 2010 +0000 "Encode release log update" commit fbe222bb3836159b9315047e8c7b7d4e7adbb7d1 Author: galt Date: Sat Feb 13 16:00:04 2010 +0000 "Release log update" commit c91dcdeab9533f5cb409b4ee2bc0190b0df734cf Author: jzhu Date: Sat Feb 13 11:05:28 2010 +0000 *** empty log message *** commit 4de6632ef83bd39a1ccf363f298b497ad1a0dc03 Author: tdreszer Date: Sat Feb 13 01:27:58 2010 +0000 One more minor adjustment to navagation links commit af6c85ca12d0d3bf1196c21d3f4f2b67b077621f Author: tdreszer Date: Sat Feb 13 00:43:25 2010 +0000 This work allows separate image fro sideLabels which is necessary for dragScroll off end of an image. commit 89ff575220f22a9fe2afc4dc0e243e2183be9040 Author: angie Date: Sat Feb 13 00:18:39 2010 +0000 Fix: handle soft-clipping when fetching query sequence. commit fce8621315b11e1bf1a57f0700d0a8bf607b6740 Author: hiram Date: Fri Feb 12 23:57:29 2010 +0000 rebuild Panda sequence with official genbank release commit 306188616f75acbda7faefee61d654730885b1b1 Author: hiram Date: Fri Feb 12 23:51:36 2010 +0000 last runs to Marmoset calJac3 commit 9a470f6236a8f841561645c9f31484ed062c07cb Author: hiram Date: Fri Feb 12 23:44:52 2010 +0000 rerun the panda alignment, and starting the calJac3 marmoset commit 481dca8a36eb554b3eb9df8530050f195bcbf964 Author: hiram Date: Fri Feb 12 23:43:45 2010 +0000 rerun the Panda lastz, and the calJac3 commit d16bc34ea84d34261e530b18a0d381d21092e6db Author: hiram Date: Fri Feb 12 23:42:33 2010 +0000 liftOver to calJac3 completed commit c9a21e6ad37328954a3eed161c5ee8c5a416854c Author: cline Date: Fri Feb 12 23:08:31 2010 +0000 Temporarily commented out MCF-10A. commit fadfd827823735a33cfc6e5ff4d7ed4e537ce600 Author: galt Date: Fri Feb 12 21:42:24 2010 +0000 keep more debugging info in output about commandline commit 976e4d6e5acf5434f425baebe7a4b132444e0ef4 Author: galt Date: Fri Feb 12 21:27:38 2010 +0000 removing BASE for now, caused problems with but ran without on review reports 2/11/2010 commit 001304b5c6372d96f4c8c01477b32b015478eb40 Author: tdreszer Date: Fri Feb 12 21:15:41 2010 +0000 Good work on dragScroll. Ajax refresh of whole image not yet working but form.submit() works. commit dfe90265cfd10d7b53150b00526994f70f910c69 Author: tdreszer Date: Fri Feb 12 21:12:07 2010 +0000 Removed ifdef IMAGE_V2. This is now permenant. Also worked on dragScroll size 1x. commit c84245ac52864ac114d349aad378f968320cde8d Author: tdreszer Date: Fri Feb 12 21:10:03 2010 +0000 Removed ifdef IMAGE_V2. Work to move style to common classes. Work for dragScroll. commit 609e215aa56cd4bcd9202dc5d208ab88317781e1 Author: tdreszer Date: Fri Feb 12 21:07:35 2010 +0000 Removed ifdef IMAGE_V2. This is now permenant. Also rearranged optional navigation links commit af9f0ce43ab497baade950107dab3e745ac99db3 Author: fanhsu Date: Fri Feb 12 20:40:05 2010 +0000 Added RGD Genes build pipeline. commit 116f6bcbfb58a8342caca21777e90369f5467fc8 Author: ann Date: Fri Feb 12 19:00:50 2010 +0000 a few small typos, and shortening lines to 80 commit 28bf13940e6618b0d337c6b21eeeeee23235a7dd Author: cline Date: Fri Feb 12 18:58:19 2010 +0000 Added the MCF-10A cll type commit e0275cb7819ab5223bcd2701612a74d65781ff34 Author: braney Date: Fri Feb 12 18:54:48 2010 +0000 extract CalTech RNA-seq to its own set of files commit dff9179bb0d588f49bbd8f4c47648c04f3287022 Author: braney Date: Fri Feb 12 18:52:47 2010 +0000 extracting Caltech RNA-seq track to its own set of files commit 0c9564f062d56d7875fd98989c41fbb3b38c510a Author: fanhsu Date: Fri Feb 12 18:26:21 2010 +0000 Created rgdGeneRaw2.sql, an interium table used for RGD Genes build. commit a4e0e016254176301cbae8d99c41151c975b761a Author: fanhsu Date: Fri Feb 12 18:26:07 2010 +0000 Created rgdGeneRaw3.sql, an interium table used for RGD Genes build. commit 01729037f3a16c14262a47aa0836d162424a3413 Author: markd Date: Fri Feb 12 18:03:11 2010 +0000 integrated archae tool tip changes from Andrew Holmes commit 0047123d794de8c7b81e39e7baf5be6a26c05031 Author: angie Date: Fri Feb 12 18:02:33 2010 +0000 Removing - Chris says they are not needed here. commit 89ad3f2e56f900a94e1b0e47cefea4d62a8b5426 Author: angie Date: Fri Feb 12 17:56:12 2010 +0000 Added cgiSpoof so the new cgiOptionalString in hgFind.c doesn't make cgiInit freak out. commit c461522d8e870157fec9f0635f54b5e13f87241c Author: fanhsu Date: Fri Feb 12 16:50:24 2010 +0000 Created rgdGeneRaw0.sql, an interim table for rgdGene build. commit c00921118847f0231ca456de3c69a10e5be5fc42 Author: galt Date: Fri Feb 12 16:00:07 2010 +0000 "Encode release log update" commit 4af65a3d23a5c07bf62273907ba9df36537960e7 Author: galt Date: Fri Feb 12 16:00:04 2010 +0000 "Release log update" commit cf39bb61da2f27b469d9ba511276d78f97c3e52a Author: hiram Date: Thu Feb 11 23:49:36 2010 +0000 check source input for enough valid bases before running cpglh.exe commit 406aef865e676e0018c3d9d97f5b7e4803a94f54 Author: hiram Date: Thu Feb 11 23:48:34 2010 +0000 now adding dateReference to the trackVersion table entry commit 1a6ce5ae85cfcbac2f02f4d70393767e6a1eb91c Author: hiram Date: Thu Feb 11 23:47:51 2010 +0000 not loading split table is now the default commit 5a4c835fe719257c5a754125d20b08bd6cc2c65a Author: hiram Date: Thu Feb 11 23:43:29 2010 +0000 add cpgIslandExt track commit d18f6e21e33660e1318ed87aca86258bf82aebc9 Author: hiram Date: Thu Feb 11 19:12:11 2010 +0000 Adding calJac3 - Marmoset - Callithrix jacchus commit b8dcfeb7600eda6da6a8d8064123f4204ed1210b Author: kuhn Date: Thu Feb 11 18:46:00 2010 +0000 moved all danRer4 chains and nets to composite and dropped individual tracks commit 0fb5b737bb3a991888d9503ab4a6b02af5864ba2 Author: tdreszer Date: Thu Feb 11 18:27:04 2010 +0000 Fixed an onerouus bug in last ci that Angie and Brian both found. commit d60d2aefdacdeb6fee8098a51b3de05907343c50 Author: angie Date: Thu Feb 11 17:21:04 2010 +0000 kent/src/lib is 2, not 3 directory levels above. commit dcd59b73ae7a3c3ca6bfcf008f20d79d4c4b45d8 Author: galt Date: Thu Feb 11 16:00:07 2010 +0000 "Encode release log update" commit cdb73cabbf2f9c9c265fd8d8feb182a4f7ae9607 Author: galt Date: Thu Feb 11 16:00:04 2010 +0000 "Release log update" commit 6384aa51d76a307802f067467c662b34408f2ba5 Author: galt Date: Thu Feb 11 07:40:46 2010 +0000 v225 preview commit bb11c221efc2136c11eae474568c8659b0cc3d40 Author: jsanborn Date: Thu Feb 11 05:30:24 2010 +0000 fixed samples in grayCelllineSNPSeg commit 8b00bb2c441ceb0b32b450725bc86ad80250fedd Author: angie Date: Thu Feb 11 00:42:12 2010 +0000 Suppress the '[db]' if db is contained in assembly label (dbDb.description). (Thx Ann!) commit 9c199642f60e74de34f1534c51459f66ff92063d Author: katrina Date: Wed Feb 10 23:49:46 2010 +0000 Edited the credits & references to fit the pubMed format commit 25e521b3b6bd34083a6728141ec09558575ee936 Author: angie Date: Wed Feb 10 22:54:25 2010 +0000 Added hook for specifying a search type: CGI var (not cart) singleSearch=knownCanonical (and maybe other types someday). This will support stable links to hgTracks views of gene symbols short-circuited to knownCanonical locations. commit 67a9e01044cc8811520d004879e744a32861ad50 Author: hiram Date: Wed Feb 10 21:41:36 2010 +0000 do not error out just because the wiki WEB site has disappeared commit f10c301583f6312727493cfc3637fdc14085d416 Author: tdreszer Date: Wed Feb 10 20:52:05 2010 +0000 And one more time commit 4115d49463ca9053964ac70575bdd695c1d9af64 Author: tdreszer Date: Wed Feb 10 20:49:47 2010 +0000 More protocol naming adjustments commit b7a189c1198c35216403ad522b3ce88596aeeabf Author: tdreszer Date: Wed Feb 10 20:43:55 2010 +0000 Made protocols more specific to groups. This is the only identification of a cell line to a praticular group commit b491fffd38d4aa77b59763dd8fdad96db46fa76f Author: hiram Date: Wed Feb 10 20:28:05 2010 +0000 limit custom tracks short label to 128 characters to avoid buffer overflow elsewhere commit 5d0865790ea3ef0fd026d77ee137095c0b2a2d19 Author: tdreszer Date: Wed Feb 10 20:18:09 2010 +0000 Marking prostate cell line as provisional since we have no approved protocol commit 2af3784511609ddd7e1ba5b073e0121b054222a5 Author: tdreszer Date: Wed Feb 10 20:11:13 2010 +0000 Three cell lines for Crawford's group are no longer provisional. commit b61039e8a32756f1293e9682bcc74d81974eb0ee Author: tdreszer Date: Wed Feb 10 20:03:57 2010 +0000 Show sex for cells commit 559cb2420ca846a58823956cf38b1bde0e80275e Author: galt Date: Wed Feb 10 19:55:21 2010 +0000 re-arranging to run utils early commit c0f1fe605b1a20674a0bf90f7b43219588d65938 Author: katrina Date: Wed Feb 10 19:28:22 2010 +0000 Added dupeOk to tRNAs identifier since, per Fan, it is known & OK for the name to be duplicated commit f8f35af891f3b6cf59f3d6dd3f836bd5dbc0f5a4 Author: katrina Date: Wed Feb 10 19:26:51 2010 +0000 Moved set for tRNAs and CGAP SAGE tracks from being above their identifier to the location with all the other set information commit 21d07d3b4a262468f4ab086b91782ef1a871f23d Author: cszeto Date: Wed Feb 10 19:26:40 2010 +0000 hgMicroscope stuff commit eccace5cab0144d4be9b6d8458a566982cc13fa8 Author: cszeto Date: Wed Feb 10 19:26:03 2010 +0000 hgMicroscope dir commit f86661ee5cba55b6c6ebba50a99dd9a931344877 Author: markd Date: Wed Feb 10 18:57:14 2010 +0000 try number tree to get link rules to behave commit 2fb35bbabfb83863339e001ff62076ce67bf7747 Author: ann Date: Wed Feb 10 18:47:46 2010 +0000 The Lowe lab has added more microbes, and renamed their browser and moved their portal commit e3992f44fa778a2c5ecb6761675ceeb5eff6762e Author: hiram Date: Wed Feb 10 17:12:31 2010 +0000 turning ailMel1 back on after reload commit f5fcf35f3ebb402066bde7a5d86ed834b5c5e1ba Author: hiram Date: Wed Feb 10 17:10:17 2010 +0000 adding marmoset calJac3 commit 2ddbdc6e3522a31c4fa5d18507ccddea906fdda6 Author: galt Date: Wed Feb 10 16:00:07 2010 +0000 "Encode release log update" commit 02d067d6b2ba3362e858a8c9c40e1177934a54c9 Author: galt Date: Wed Feb 10 16:00:04 2010 +0000 "Release log update" commit 129e975148d1dc48f5bc7288fd7e9ef34065eea1 Author: larrym Date: Wed Feb 10 06:23:00 2010 +0000 support exact matches; fix indentation commit 2af9485e6264dc1ea2671a8cab6bb76b1d3eaa34 Author: kent Date: Wed Feb 10 05:16:14 2010 +0000 Making hgTracks be backwards compatible with older trackDb tables in case they didn't run hgTrackDb. commit df85cdba703a3c69b0d3093350127c67f967558c Author: kuhn Date: Wed Feb 10 03:13:03 2010 +0000 moved all fr1chains and nets to composite and dropped individual tracks commit c86ea350c5103b579338b1ddcae07bdf70397532 Author: kent Date: Wed Feb 10 01:51:16 2010 +0000 Hopefully fixing bigBed so that it works in dense mode on a clean cart _and_ it works with custom tracks. Have tested these two anyway. commit 60a1f245d786f0f378e9b2052066ae0ed249af0c Author: tdreszer Date: Wed Feb 10 00:37:57 2010 +0000 Safegaurds against empty tracks which can legitimately happen when there is no centerLabel commit 5f4f15cbce99b78b91351db3fd778d2f3fa7400f Author: donnak Date: Wed Feb 10 00:20:03 2010 +0000 Added aplCal1. commit 2194ebec55d42927dc0a7922e91c0bdcfbd42d41 Author: fanhsu Date: Wed Feb 10 00:01:17 2010 +0000 Fixed a typo. commit 80ac488833d3f0d99c52997ace69d73a1b00f2f0 Author: angie Date: Tue Feb 9 23:27:22 2010 +0000 If the result of 'hFreezeName' (dbDb.description) contains the database name, as I intend to make happen, don't also show the database name in parens. commit 2ffe5d1b6c59ca5b247d116e5f544a3c1f50937b Author: fanhsu Date: Tue Feb 9 23:17:59 2010 +0000 Added tRNAs track section. commit 7a74b28eb6fa452ed57d79cdf1939ebb15f60a9d Author: galt Date: Tue Feb 9 22:37:20 2010 +0000 adding multiz6way to genbank danRer6 commit b60b1f52027b46af70e9663e98e8d1f5f5e1edf8 Author: galt Date: Tue Feb 9 22:24:57 2010 +0000 adding multiz6way to genbank danRer6 commit afb4acfc29a43c5ebda5c80620dc7a9b0f29f4a1 Author: fanhsu Date: Tue Feb 9 21:47:46 2010 +0000 Added section for tRNA tracks. commit 46ac14536d1ce15eef32a30860305e0d94b2ccee Author: markd Date: Tue Feb 9 20:58:51 2010 +0000 even more dependency issues commit 11255f85354af0488bb930d6746496caa607913a Author: markd Date: Tue Feb 9 20:56:39 2010 +0000 fixed dependency problem commit 22460c6ac236cc0b19f4aefa2da6ac4c1e0042f5 Author: larrym Date: Tue Feb 9 20:28:01 2010 +0000 style used by jquery.autocomplete.js commit 1fe2119f99575796bd35a04bb827f7494f68ed94 Author: kuhn Date: Tue Feb 9 19:40:21 2010 +0000 moved all danRer3 chains and nets to composite and dropped individual tracks commit a4bb086ff761e0efbc160f521e6e86943e68df88 Author: hartera Date: Tue Feb 9 19:13:59 2010 +0000 Added crgMapability subtracks to list of tables to be ignored for mm9. commit ac5628b48a3fa1d89c0f20e1f0e946a177da6f35 Author: hartera Date: Tue Feb 9 19:05:39 2010 +0000 Documented adding mapability track. commit 95f929a131a90541e0c90b64c13633181ae6b1a7 Author: tdreszer Date: Tue Feb 9 19:04:45 2010 +0000 Added file count at end of html page, by QA request. commit 525c89a239bccf6d82eeec6fb22e7c23af85d5ea Author: hartera Date: Tue Feb 9 19:03:38 2010 +0000 Changed assembly name. commit 546a468beefe98626481a1c7dddaea107ccade47 Author: hartera Date: Tue Feb 9 19:01:53 2010 +0000 Minor edit of track name. commit 4dcad6e9e803bf03c8a2d3ca23366156405edf6a Author: hartera Date: Tue Feb 9 18:59:57 2010 +0000 Description for mapability track. commit 3feda0e2eac32caa2866e05acd746b6044ffd98a Author: hartera Date: Tue Feb 9 18:58:35 2010 +0000 Minor edit of track name. commit 98cb0bcefcc368491fa97a71e8408bb930d83fd7 Author: hartera Date: Tue Feb 9 18:57:17 2010 +0000 Added Mapability track with subtracks from CRG. commit 420a07bd24cbe440217a741029c2af1cda40bb3a Author: fanhsu Date: Tue Feb 9 18:55:13 2010 +0000 Added rgdGene2.sql. commit f49d6153bc5eccb750d4c9316b9681e72772de88 Author: fanhsu Date: Tue Feb 9 18:15:33 2010 +0000 Created rgdGene2.html. commit 59e51cb1bd094ec14ea4f7a3adc0214536349cb3 Author: tdreszer Date: Tue Feb 9 18:12:13 2010 +0000 Standardized metadata to 'antibody=Input'. commit cd62e667294098f91c7828ee0afb67b3a2b7d567 Author: braney Date: Tue Feb 9 17:58:20 2010 +0000 take out fileName for signals in CSHL short RNA commit 4280cb894e1f06a49af097de80623892113b7381 Author: kuhn Date: Tue Feb 9 17:45:20 2010 +0000 changed spp half of name to lower case commit 6c9d4846a0203bdb7c0146024e32e6d3b5bc39a8 Author: kuhn Date: Tue Feb 9 17:45:08 2010 +0000 changes spp half of name to lower case commit e23c27fc0b892467ff2510c9cc0edf44ee1a3606 Author: hartera Date: Tue Feb 9 16:10:41 2010 +0000 Loaded new data for segmental duplications. commit a22c92e9e83a0cedf5529df50db7d149baa266b6 Author: galt Date: Tue Feb 9 16:00:07 2010 +0000 "Encode release log update" commit f9c7249f7b5c4f33bcb176f232b27a2fb834f375 Author: galt Date: Tue Feb 9 16:00:03 2010 +0000 "Release log update" commit d4bef49efa934bdddc3fba3da8aac25e6178fd52 Author: larrym Date: Tue Feb 9 08:51:30 2010 +0000 ../cgi-bin/suggest => ../cgi-bin/hgSuggest commit 538681bee16cbe8da0c3198b451484377053b8fd Author: larrym Date: Tue Feb 9 08:41:02 2010 +0000 support gene auto-complete commit b5f7ad709b3a8b1cd146202bde151a6f0533ac64 Author: rhead Date: Tue Feb 9 02:16:19 2010 +0000 Changing netHg17 and chainHg17 to chainNetHg17 composite tracks. commit 747b9fa43dd33a06645a410af8737f56876bc09d Author: tdreszer Date: Tue Feb 9 00:12:28 2010 +0000 Changes that I have been sitting on awhile. More info on unexpected errors. Fixes to dragReorder. Support for simpler navigation links. commit 3bf80154ea7eefdd5e83c0061647e16c71827bc1 Author: tdreszer Date: Mon Feb 8 22:11:26 2010 +0000 Big changes to move matrix CB normalizeAll code from js to C. These changes should make the large composites less sluggish commit 041f78fa1873a59e3d8e05d03cb9a2c4e38fafbf Author: tdreszer Date: Mon Feb 8 22:09:22 2010 +0000 Needed to rewrite the 2way CB routines. Now called fourWay commit af305b7edc9ef39522351c37a56d7301f28d12f8 Author: tdreszer Date: Mon Feb 8 22:07:29 2010 +0000 Added some timing routines to help focus on selfish, inefficient code commit d07a09a961da14393d02aa0fb7171c24d7ad9bc0 Author: hartera Date: Mon Feb 8 19:43:43 2010 +0000 Added some missing fields compared tot the sql definition and changed some of the descriptions as suggested by the data provider for this track. commit 86ca6bda4582a3c8412713397bc912bb1254cd29 Author: hartera Date: Mon Feb 8 19:42:34 2010 +0000 Minor edits. commit ea1bb112f28731836489884a2e16c00fe242496a Author: rhead Date: Mon Feb 8 19:28:55 2010 +0000 Changing netHg18 and chainHg18 to composites. commit 194e99c0c1c914b6e051d6654dc5c9a2f657048f Author: kuhn Date: Mon Feb 8 18:18:21 2010 +0000 fixed shortLabel for chainNetDanRer2 for galGal2 commit 5472866dd295584e7bd0ebd23d0cd35fad8e6e3a Author: kuhn Date: Mon Feb 8 17:58:31 2010 +0000 fixed shortLabel for chainNet{mm6,danRer2} for monDom1 commit 6df925fa50a9852fdfb08250f11d21f72dcfcced Author: hiram Date: Mon Feb 8 17:27:24 2010 +0000 have default clade mammal if none found commit 065b3524fe6373e7e766ee79c628b7a219c3fd8d Author: markd Date: Mon Feb 8 16:57:21 2010 +0000 attempt to get autobuild working again by forcing a relink commit 852104c291ab618be91b5b3d315f1390df13b11a Author: galt Date: Mon Feb 8 16:00:06 2010 +0000 "Encode release log update" commit 01323fd52ef28059f39ce48a9b9e50faca212e1c Author: galt Date: Mon Feb 8 16:00:03 2010 +0000 "Release log update" commit ef09e6f2aee8733e9647785b039badf97f2333f6 Author: markd Date: Mon Feb 8 03:14:55 2010 +0000 fixed make issue commit c0e8aa085ab5b55ae2df23873615fcb728d0e730 Author: markd Date: Mon Feb 8 03:13:52 2010 +0000 moved pslUniq out of complelely unrelated directory commit a91656ea523da0dce8b85fa0bdea73fea247d7e8 Author: markd Date: Mon Feb 8 03:05:26 2010 +0000 removed dead programs not being compiled commit 4a136933bed2e2e18670bcf65aaa99b1e2d5d5bf Author: markd Date: Mon Feb 8 03:04:27 2010 +0000 added blastXmlToPsl commit 82cd6dde835e20a0a3905ecb495dbf45e6af0564 Author: kuhn Date: Mon Feb 8 02:50:06 2010 +0000 moved all fr2 chains and nets to composite and dropped individual tracks commit e036b70efa5a86e59456720cff7d3050c3b53ae8 Author: kuhn Date: Mon Feb 8 02:26:03 2010 +0000 moved all danRer1 chains and nets to composite and dropped individual tracks commit d68d282788d17a794d3d49bd2f924a2aa8e317ee Author: larrym Date: Sun Feb 7 19:53:31 2010 +0000 code cleanup per jim's feedback commit 254cfe30947242a0292ea80788b4d374cc89fad4 Author: galt Date: Sun Feb 7 16:00:06 2010 +0000 "Encode release log update" commit de62638eaff99c9316a5b1a75d4949fbe44c07f2 Author: galt Date: Sun Feb 7 16:00:03 2010 +0000 "Release log update" commit 715233352764d55508d3f320ab99571627ad337f Author: kuhn Date: Sun Feb 7 06:50:05 2010 +0000 moved all fr1 chains and nets to composite and dropped individual tracks commit f6c216f7a8ee59183a658269086fe19b64a86860 Author: kuhn Date: Sun Feb 7 05:26:17 2010 +0000 moved all braFlo1 chains and nets to composite and dropped individual tracks commit b940af9efbf2485f5b528528896e8616eee7715e Author: kuhn Date: Sun Feb 7 04:15:30 2010 +0000 moved all petMar1 chains and nets to composite and dropped individual tracks commit 1b92bc62b0eaeb3d4896309274a84e6b0a1a8c21 Author: kuhn Date: Sun Feb 7 03:40:08 2010 +0000 moved all TetNig1 chains and nets to composite and dropped individual tracks commit 020edd022cd3d66bef5386c760ef9f11549761a4 Author: kent Date: Sat Feb 6 21:43:03 2010 +0000 Changing 'subTrack' to 'parent' internally. A backwards compatability routine will make it so either tag can be used in a trackDb file. commit 6318d27ed291fba18e639b24608c3b0f6b80e4c1 Author: kent Date: Sat Feb 6 20:45:12 2010 +0000 Moving bigBedFileOpen to a better place. commit 28e4875ad0b16c5dc0888a26ab8d9eb810579beb Author: kent Date: Sat Feb 6 19:58:52 2010 +0000 Making bigBedCoverageIntervals() static. commit 53ab8e1ca2f6b636f9f3c09b0312edca01b60b55 Author: kent Date: Sat Feb 6 19:58:26 2010 +0000 Removing bigBedFileCreate which is no longer in library. commit b5a7a0bf8486872e959995d84cdd5dc181b1f534 Author: kuhn Date: Sat Feb 6 19:53:14 2010 +0000 adjust column width to allow for Tb-level files commit 8cd81e09a6834698824277cdbc2524304d052d25 Author: galt Date: Sat Feb 6 16:00:08 2010 +0000 "Encode release log update" commit 2d600893c75e46934a25527aa73fe7488bd98db7 Author: galt Date: Sat Feb 6 16:00:05 2010 +0000 "Release log update" commit 2b8a9b86dc33fb995b9b3c4030e432e279c08807 Author: markd Date: Sat Feb 6 08:17:50 2010 +0000 added (disabled) test case for blast+ commit 4c0809bc2dc5079337e253e62b010831c71366ab Author: kuhn Date: Sat Feb 6 06:46:49 2010 +0000 moved all anoCar1 chains and nets to composite and dropped individual tracks commit 994dae41e2e2e95e8b268136ebb2eae2c6fdcc27 Author: kuhn Date: Sat Feb 6 06:39:05 2010 +0000 moved all taeGut1 chains and nets to composite and dropped individual tracks commit bcbb9c3c03db1312b6ec023e1b31eb7dec3d3684 Author: kuhn Date: Sat Feb 6 06:26:51 2010 +0000 moved all taeGut1 chains and nets to composite and dropped individual tracks commit c0eb338a7108e6dcb16d4c6b4f6a488f77012918 Author: kuhn Date: Sat Feb 6 06:18:35 2010 +0000 moved all mm7 chains and nets to composite and dropped individual tracks commit 8e79760108d0402ec2c6a477fe807d64a820cab4 Author: markd Date: Sat Feb 6 05:53:35 2010 +0000 added option to include version in output fasta commit 757c2e850e89d0aef227e9e26e2a58d3edd804b8 Author: larrym Date: Sat Feb 6 03:21:00 2010 +0000 one more try at rcsid commit 35a7ac35547f3e098ffc3c4eb45217a5d44f85e7 Author: larrym Date: Sat Feb 6 03:16:41 2010 +0000 forgot the rcsid commit 1ef29283189f23aa1ec6e0c4386bd786a04147d3 Author: larrym Date: Sat Feb 6 03:15:27 2010 +0000 add suggest.o commit f1ca32ece9014d1727367bff01adc8b2aaa703be Author: larrym Date: Sat Feb 6 03:15:04 2010 +0000 code to support suggesting genes given a prefix typed by the user commit f52e787f3dc5ce79d91262dfaac4d23dbb58c707 Author: hartera Date: Sat Feb 6 02:47:48 2010 +0000 Added a 40mer sequence subtrack to the Mapability track. commit 766e97241290736bf7ca19df8e9d1e41c3c82ff6 Author: larrym Date: Sat Feb 6 01:19:35 2010 +0000 support stuff for auto-complete using jquery.autocomplete.js commit 64dc7e6eed1f9b62e522e96fa96f79397b25931b Author: larrym Date: Sat Feb 6 01:19:17 2010 +0000 javascript for hgGateway CGI commit 2778dfb349469af4e9b42449b4e798c7c23c47e5 Author: braney Date: Sat Feb 6 00:47:50 2010 +0000 get Caltech directional data to be colored by strand commit 06278fc9072d5da8dca6dbdb8008a59c35499a29 Author: hiram Date: Sat Feb 6 00:26:39 2010 +0000 adding calJac3 to the build commit 85dd243824b3631981b0f5de60284c60e140b44b Author: hiram Date: Sat Feb 6 00:25:53 2010 +0000 initial files from makeGenomeDb.pl commit b44c1e27c743de2cca1ec7593f5b7f1ecc824536 Author: hiram Date: Sat Feb 6 00:17:33 2010 +0000 re-run the Panda chain net commit 50804e4c09754d933ff2514116bc492f39e687d0 Author: braney Date: Sat Feb 6 00:05:38 2010 +0000 properly attach directional metadata to mislabeled tables commit e19e13d4cc5670a53b84ad795ec154d86f29af6c Author: hiram Date: Fri Feb 5 23:52:29 2010 +0000 handle chrom names for chromInfo that are longer than 16 chars commit 2036e85fe2021c2617ec790419f4ec5bb4cf472a Author: kuhn Date: Fri Feb 5 23:00:23 2010 +0000 moved all cavPor3 chains and nets to composite and dropped individual tracks commit 1a97bf94dcb47fc745aafb09ff221cba6a893032 Author: fanhsu Date: Fri Feb 5 22:33:20 2010 +0000 Created rgdGeneXref2.c. commit 099e8e04e27319c85338b15bb3588582d4b1208c Author: fanhsu Date: Fri Feb 5 22:32:52 2010 +0000 Created makefile. commit 5c358c0a4495c2955f38da0308f7ff6a824d757b Author: fanhsu Date: Fri Feb 5 22:29:57 2010 +0000 Created rgdGeneXref2.sql commit da9c7c4de38b7189a8eb7a8d52eaed6a530a28a2 Author: rhead Date: Fri Feb 5 20:30:00 2010 +0000 Fixed typo. Thanks, tdbQuery. commit febb4cd1be59a4bb123a87458ef6343f4870684a Author: braney Date: Fri Feb 5 20:08:42 2010 +0000 a little more fix on the items in the conservation dialog to get views commit 50d4db006bb0e8ac06e59253009d376ff0a7d696 Author: kent Date: Fri Feb 5 19:33:43 2010 +0000 Fixed memory leaks. commit b0ac5d08539bf36fda6f1f45c27463d85db93cc9 Author: braney Date: Fri Feb 5 18:55:25 2010 +0000 fix up control in multiz's that changes how codon translation happens commit 4a3dd7387e8727b069273bcbe42f9d3233c30922 Author: angie Date: Fri Feb 5 17:41:02 2010 +0000 Removed stray newline from tx IDs generated for tracks that have no name column. commit f5c2ba76be2c17615f3e8882c43d112bd7c5ad6d Author: galt Date: Fri Feb 5 16:00:07 2010 +0000 "Encode release log update" commit b28eb4c5d5793de1a9d1be67711f9d87e83b1291 Author: galt Date: Fri Feb 5 16:00:04 2010 +0000 "Release log update" commit 8ef4fe68b48377bfb4263964fa149988afeeefdf Author: kuhn Date: Fri Feb 5 07:42:05 2010 +0000 moved all rn4 chains and nets to composite and dropped individual tracks commit 4fe8b186322559a56f4b4d72e0129ade532c622c Author: kuhn Date: Fri Feb 5 07:27:34 2010 +0000 moved chainNet from trackDb.ra to trackDb.chainNet.ra commit 9951798cc1b424ea98d9424c4d331d2d786d5a0c Author: kuhn Date: Fri Feb 5 06:54:06 2010 +0000 grammar commit dadf9d0e5d67f8d5fdd051f281cade68cf38abbf Author: angie Date: Fri Feb 5 06:48:54 2010 +0000 Fixed too-small char[] size, found by Ann w/ENCODE tracks w/giant names, RT 1621. commit 914f27891e7456733c32e33cdb0e97de7de34d2e Author: kuhn Date: Fri Feb 5 05:48:22 2010 +0000 moved all ornAna1 chains and nets to composite and dropped individual tracks commit 90be685b64951ae9a7627776fd14147b08e788e0 Author: angie Date: Fri Feb 5 05:44:53 2010 +0000 pgSnpHeight: if we're in dense mode, no need to double the track height. commit ded97531f6be95ff8d1f60f7efe96bc728004c93 Author: kent Date: Fri Feb 5 01:12:39 2010 +0000 Taking out a half-baked change. commit ad4ceb8d4112b0789f797e0f8fbb7c111495899b Author: kent Date: Fri Feb 5 01:09:43 2010 +0000 Ifdeffing out some of the new code until I finish baking it. commit 0f83c0e4a11b8945c5504f2686c2725204cf08bf Author: kuhn Date: Fri Feb 5 00:14:57 2010 +0000 moved all oryLat2 chains and nets to composite and dropped individual tracks commit dffd284e56e1aa221937b53e1cdd55880ed3b219 Author: kent Date: Fri Feb 5 00:11:18 2010 +0000 Getting to compile in Linux. commit d37ee7091d2af7fd6de7699f0944f5224eb7bb12 Author: markd Date: Fri Feb 5 00:06:41 2010 +0000 enabled xeno refgene commit 1b0d93d2ad00ae904393760426bd0c9e3a3dd1a3 Author: hiram Date: Thu Feb 4 23:49:59 2010 +0000 Downloading new Marmoset assembly commit 513b14995c254fa1ec1f1ac696004a7dcd2ecc24 Author: angie Date: Thu Feb 4 23:31:16 2010 +0000 pgSnpDrawAt: removed the ceiling of 50 items for drawing the cool stacked colored bars -- performance is just fine, and display snaps into squish/dense anyway when there are thousands of items. commit e9eff0e229c318258ed381ae0755077643eed3f9 Author: angie Date: Thu Feb 4 23:13:02 2010 +0000 Added note about why 'my.sorted' instead of 'my.sorted.bam' in the example sort command, as suggested by user. Improved description of both sort and index commands. commit a84d46cab7ff6fb4c46f7bd3a567b0b913ffd61f Author: hartera Date: Thu Feb 4 23:00:22 2010 +0000 Added CRG Alignablity track details. commit d39aa0bd54ca9b6d7b7b4b969f83bc975636d9ac Author: kent Date: Thu Feb 4 22:59:45 2010 +0000 Getting rid of settingsByView stuff. Adding in converter to container/parent syntax. Fix to parent-not-found error message. commit 72403cf4a2b82dec3e707821d0a00380821acd42 Author: kent Date: Thu Feb 4 22:58:17 2010 +0000 Adding trackDbUpdateOldTag function to convert older format trackDb tags to current format. Specifically converting superTrack, compositeTrack, and subTrack tags to use the new container and parent tags instead. commit 7af650ed3353dbf5ae4e7ff626a1135641033e56 Author: larrym Date: Thu Feb 4 22:51:49 2010 +0000 patch which fixes following problem: up/down arrows didn't work on IE, Safari and Chrome; patch downloaded from: http://code.google.com/p/jqac/issues/detail?id=1 commit 41fd0b09ef3dd4fa6ff3738fecbd60732714b760 Author: larrym Date: Thu Feb 4 22:47:57 2010 +0000 version 1.4.2 downloaded from http://code.google.com/p/jqac/ commit 02549631eb9790f8da0d75595964653e4990f518 Author: ann Date: Thu Feb 4 22:26:21 2010 +0000 cheap fix to find more-or-less only the track you're looking for. the better way to fix this would be to figure out the quotes, and include the tableName in the tdbQuery statement. commit 7b5512688ae3d87408b064da5ce857d292108f7a Author: kuhn Date: Thu Feb 4 22:07:28 2010 +0000 moved all gasAcu1 chains and nets to composite and dropped individual tracks commit 304d9931a3b44d8f25dfc0d1ab692a466dee5a09 Author: galt Date: Thu Feb 4 21:22:09 2010 +0000 adding aplCal1 chain/net commit 425054f29a860a017011657d5006b790f1134788 Author: markd Date: Thu Feb 4 21:18:56 2010 +0000 enable xeno refseq on equCab2 commit b5e28caa5188de4f777b4b93cc6551f625e31186 Author: kuhn Date: Thu Feb 4 20:22:37 2010 +0000 grammar tweak commit f98f2545faa1fb92f128cbfb8baf250bd716a6f8 Author: galt Date: Thu Feb 4 19:35:11 2010 +0000 adding trackDb.ra entry for aplCal1 chains/nets commit 4efd9d5e0e789bebe28fbec80e8eaa6d1a4dd9f7 Author: hartera Date: Thu Feb 4 19:25:27 2010 +0000 Loaded corrected data for the Seg Dupes track. commit 86d605a8b198f81ceebf53e50bbc2e38ef2bde07 Author: hartera Date: Thu Feb 4 19:21:58 2010 +0000 Changed descriptions for table columns based on feedback from data provider. commit 48cfff3f65612f6ddd21a0db78437c1b4f0821dd Author: hiram Date: Thu Feb 4 18:33:56 2010 +0000 allow use of lastz or blastz directory commit 4163500bb6dba82e494171f95fabf36c11f17783 Author: hiram Date: Thu Feb 4 18:33:19 2010 +0000 fixup usage of AGP files with comments and FASTA with Genbank ID lines commit 6f62f763f669ef2a99f168b10b37b7d326257331 Author: katrina Date: Thu Feb 4 16:22:58 2010 +0000 added hyphen to Genome-Wide commit 4eb97a129369bf0eec2b700a6ae1ebb12a2937e7 Author: galt Date: Thu Feb 4 16:00:07 2010 +0000 "Encode release log update" commit 9e91a95a2c3357d2a3bb426b7700a9ba2f2bd6a2 Author: galt Date: Thu Feb 4 16:00:03 2010 +0000 "Release log update" commit 3dccd278c8ec515f65b319b79d4a57938d5b7a00 Author: kuhn Date: Thu Feb 4 06:18:24 2010 +0000 moved all ornAna1 chains and nets to composite and dropped individual tracks commit 7d581fde5230c0d86a01fa5fd41868567c4df9c4 Author: kuhn Date: Thu Feb 4 04:30:47 2010 +0000 moved all mm9 chains and nets to composite and dropped individual tracks commit d09b2d90319d1dadac9ea95b18cdbdf356657a63 Author: cline Date: Thu Feb 4 01:48:57 2010 +0000 Changed the sex of the human cell lines from Male to Unknown when there was no obvious gender data available. commit 56929275586782f65ba70303f0de5b3be793f32b Author: kent Date: Thu Feb 4 01:06:13 2010 +0000 Tweaking MATRIX section a bit as per Angie's suggestions. commit 9c9091aa1c72f5ae88ed3ad96cd505264798c603 Author: ann Date: Thu Feb 4 00:05:29 2010 +0000 added explanation about how to properly configure a URL to share your big/BAM data with others commit 736a05f8d9964ae8d30b87bc128217a3542bd02d Author: angie Date: Wed Feb 3 23:41:04 2010 +0000 Long since obsoleted by composite track details (pgSnp.html). thx Pauline! commit 5306c0b201b31ac2855600dcc948c75fcbf8edca Author: kent Date: Wed Feb 3 23:25:31 2010 +0000 Clarifying some view info. commit cdb529c14d08bb8d693c583ee3bc019d9699de81 Author: tdreszer Date: Wed Feb 3 23:16:07 2010 +0000 Fixed the warnbox to make hidden 'OK' not be picked up by select all. commit abfa107b86300438e055710045283ec99e8d3d92 Author: kent Date: Wed Feb 3 22:08:41 2010 +0000 Making a single file rewriter for track in the middle. commit 38595bcb16d1c44de83bc5d53f10d3e6efd09f26 Author: kuhn Date: Wed Feb 3 19:54:54 2010 +0000 moved all mm8 chains and nets to composite and dropped individual tracks commit 9e32302ae63b909a4ca82ee2d2238192dd9b4e13 Author: kuhn Date: Wed Feb 3 19:35:11 2010 +0000 moved all mm8 chains and nets to composite and dropped individual tracks commit 3acaa4e32f4524a6557de850fd703a9d570a9d47 Author: angie Date: Wed Feb 3 18:48:58 2010 +0000 Increased some char[] sizes that caused safef errors with custom track with name longer than 128, and some others that looked like they might. commit 2b3d4183ad449ba561693e7433c8c58063d77fcc Author: angie Date: Wed Feb 3 18:43:38 2010 +0000 Increased some char[] sizes that caused safef errors with custom track with name longer than 128, and some others that looked like they might. commit fe65864aa0be2b957a1c8fc053fd22239bb107a2 Author: kuhn Date: Wed Feb 3 17:58:01 2010 +0000 moved all mm8 chains and nets to composite and dropped individual tracks commit 21b836dc27afa14dfdcb174879cbb5132c64cc46 Author: kuhn Date: Wed Feb 3 17:48:21 2010 +0000 dropped two errant tildes commit d09bbb3cc85ac6522180861f5473e51a4a39a9fb Author: hiram Date: Wed Feb 3 17:19:41 2010 +0000 the extra ; in the comment causes it to be invalid SQL ? commit 35da5886f953b6608f16148755ced4cbb30a28c0 Author: katrina Date: Wed Feb 3 17:13:35 2010 +0000 removed entire blocks for subtracks being dropped from ENCODE UW DNaseI HS track (release 2) rather than my previous change of just removing release beta tag commit 2fe4006dc1c49850f103fbfab4819a97d0a6f0f5 Author: katrina Date: Wed Feb 3 16:45:04 2010 +0000 removed release beta from subtracks being dropped from ENCODE UW DNaseI HS track (release 2) commit 1eacaccbdd7b028df4aec73df51bbcd2b9e61653 Author: galt Date: Wed Feb 3 16:00:07 2010 +0000 "Encode release log update" commit f54a07eb53b8a31ef5cb3a450535658a07358edc Author: galt Date: Wed Feb 3 16:00:03 2010 +0000 "Release log update" commit db91e20d9f8b08e7d3775fe192521331a5b986e7 Author: kuhn Date: Wed Feb 3 07:02:30 2010 +0000 moved all mm8 chains and nets to composite and dropped individual tracks commit 95397c60cee4b154f3808471184d3d30d2a30b15 Author: kuhn Date: Wed Feb 3 05:58:08 2010 +0000 changed animal name to o_Organism for several commit e485f0f3b4f20eb0495b0f164e9a86272db79602 Author: kuhn Date: Wed Feb 3 03:49:35 2010 +0000 changed animal name to o_Organism for several commit 1971f3918cf309073952f0e6c9586ab37b425973 Author: rhead Date: Wed Feb 3 03:19:53 2010 +0000 Removed a stray release alpha from netMm7 track. commit 08d81288144a0ce2f7ed0baacb7d56ef2b5b7257 Author: rhead Date: Wed Feb 3 03:06:57 2010 +0000 Changed xenTro1 chain and net shortLabels to match chainNet shortLabels. commit 2d6e7c5d27f4a3b2ee4e0e02f0aae449ca38a7a5 Author: rhead Date: Wed Feb 3 02:37:07 2010 +0000 Changed bosTau4 chain and net shortLabels to match chainNet shortLabels. commit 9d9f0f9dc763a894204834097e2cb39c1ffc7018 Author: markd Date: Wed Feb 3 00:35:31 2010 +0000 disable ailMel1 (panda), as the genome is starting over commit 47dd8dc1fffb3a59e9e751d0d969bf6158e981a8 Author: galt Date: Wed Feb 3 00:33:03 2010 +0000 "New version number v224" commit f038b91fe292827c178df0184674ca1694cbafe1 Author: galt Date: Wed Feb 3 00:32:28 2010 +0000 v224 final build commit a001a0df5f0c55d1724bffc7b0ab37d7606f7da3 Author: hartera Date: Tue Feb 2 23:46:21 2010 +0000 Added include for new genome-wide ENCODE trackDb.ra file and moved Mapability track to that file. commit b06c6278ba4072767a41b42e6c7509b89036a1f6 Author: hartera Date: Tue Feb 2 23:45:03 2010 +0000 Created new genome-wide ENCODE trackDb.ra for hg19. Added Mapability track. commit 0c03c9ea528b66833324b56672eeaa95a839acfc Author: rhead Date: Tue Feb 2 23:44:11 2010 +0000 Changed bosTau3 chain and net shortLabels to match chainNet shortLabels. commit ecaabd3d4412a636df3ae713e9ae0659fd6407ad Author: rhead Date: Tue Feb 2 21:32:59 2010 +0000 Changed bosTau2 chain and net shortLabels to match chainNet shortLabels. commit b9643489dfffe786a0644bfae86c8c2518793944 Author: rhead Date: Tue Feb 2 20:32:50 2010 +0000 Fixed broken links to wustl. commit c6e18cded968297a74f1dfae281c7dd4f0ec08c0 Author: larrym Date: Tue Feb 2 20:18:47 2010 +0000 support PROFILE option commit c802d829b20bfb5eae4679a7b82038109f385b32 Author: hartera Date: Tue Feb 2 20:11:44 2010 +0000 Re-loading new data for the genomic segmental duplications track - in progress. commit 8bb1336c4cee38fbcdf56cb3724a9b06ba59811a Author: tdreszer Date: Tue Feb 2 19:46:09 2010 +0000 Add rank as separate from replicate to UW commit f92cb9f71ebd33cb91871c8e3852c1d1f6c26c52 Author: hiram Date: Tue Feb 2 18:56:32 2010 +0000 include definition of chain.csh script commit 4497317141c9797006b88d23114291b654a31831 Author: kate Date: Tue Feb 2 18:55:05 2010 +0000 Wrapper for reporting, suitable for cron use, but still has some user-specific stuff commit 1c6c8ff9f8397f0489c22d0de5aa811c1aad47e4 Author: kate Date: Tue Feb 2 18:49:06 2010 +0000 Temp manual report for certain data types commit 47ecf96fd8fa78672df8d83a35f8d98f716bd695 Author: kate Date: Tue Feb 2 18:46:40 2010 +0000 Fixes to lab handling and NHGRI factor reporting commit 6453d2ab9eb2bfca467e4a494531f5d1635841ae Author: kate Date: Tue Feb 2 18:45:47 2010 +0000 Add synonmous entries for labs to accomodate inconsistent DAFs; Distinguish mouse labs commit ca4673e878186d2a82ca5a311498b870f2996bd6 Author: kate Date: Tue Feb 2 18:45:11 2010 +0000 Add label for reporting cosmetics commit 3d48231ce22cc53c05ed4ec97902c6029f3d2162 Author: galt Date: Tue Feb 2 16:00:07 2010 +0000 "Encode release log update" commit 1009bc172d47ae02ae91b59d9a95365b98e38cbb Author: galt Date: Tue Feb 2 16:00:04 2010 +0000 "Release log update" commit f1ffd18f5ff4946987626aa850ca2c8e2b596f6e Author: larrym Date: Tue Feb 2 09:08:36 2010 +0000 remove some cruft in SPLICE_SITE code commit 470622660a1209f4482e4a280c52d0240b6bf261 Author: larrym Date: Tue Feb 2 08:03:09 2010 +0000 use more and longer codes; start working on supporting indels; still not quite done commit c171d909cba120fa029ec130aea83dbe09453ed7 Author: rhead Date: Tue Feb 2 03:34:56 2010 +0000 Changed horse chain and net shortLabels to match chainNet shortLabels. commit 5293c5e4b7784c8170ce880c6e6b8746ee31d376 Author: rhead Date: Tue Feb 2 03:23:42 2010 +0000 Removed trackDb.ra refs to equCab1 net and chain -- these are in composites now. commit bc5704851ac2d1e1049d6a574921876c978f5f6a Author: rhead Date: Tue Feb 2 03:03:15 2010 +0000 Removed redundant shortLabel on chainNetEquCab1. commit 3276e19d7e34efba44bcb9a548a255909f8fc253 Author: rhead Date: Tue Feb 2 02:55:49 2010 +0000 Removing trackDb.ra refs to ponAbe2 nets and chains -- these are in composites now. commit 87387265679c28b970b834dca21e589804ce729e Author: kuhn Date: Tue Feb 2 02:16:40 2010 +0000 moved all mm7 chains and nets to composite and dropped individual tracks commit bf36728877597c015c93766a93e26efd83cdacf3 Author: rhead Date: Tue Feb 2 02:04:50 2010 +0000 Added o_Organism shortLabel override to match the chainNet override. commit 12715d208faf346d0ee4ffa035c52e8495a6a9b2 Author: rhead Date: Tue Feb 2 01:56:48 2010 +0000 Removed release alpha/beta from rheMac1 nets, chains, chainNets and adjusted priority to match rheMac2. commit a750685949b17a405fe81c30932cc6d34f8b4f03 Author: cline Date: Tue Feb 2 01:56:47 2010 +0000 Added sex information for the human cell lines. commit 549856c95d5aea5472880e4e1122fde559e6e579 Author: kuhn Date: Tue Feb 2 01:12:39 2010 +0000 reversed previous commit. not ready to do this and described it wrong commit 21cbce3f3c478b751355caa073260b3e29fae7ec Author: kuhn Date: Tue Feb 2 01:06:02 2010 +0000 changed animal name to o_Organism for several commit 4face4d7f6b728a5acdb6a9b9f3464a4af5b41b7 Author: kuhn Date: Tue Feb 2 00:43:40 2010 +0000 changed animal name to o_Organism for several commit 30462709de9c88098d727368474b0cf3469571a8 Author: pauline Date: Tue Feb 2 00:33:11 2010 +0000 Adding upcoming ENCODE UW histone track. commit 22c558346263fd11d3889263ba922ae01e8b66fd Author: ann Date: Tue Feb 2 00:29:51 2010 +0000 added logic to find all cases of the track in it's different release alpha/beta and staging locations commit 644ddd654219a5cb1e1f33b7d6824cbd44590464 Author: kuhn Date: Tue Feb 2 00:20:27 2010 +0000 changed animal name to o_Organism for several commit b8a5db8f50afb61bd4549f1682f44f796237d3a6 Author: kuhn Date: Tue Feb 2 00:10:59 2010 +0000 changed animal name to o_Organism for several commit 26e970ebe219997bc34f4a31ececb7c7784d150b Author: kuhn Date: Mon Feb 1 23:34:04 2010 +0000 moved all mm6 chains and nets to composite and dropped individual tracks commit 260cfc7379a56c1a3e926076f2e8c0203f6e1670 Author: rhead Date: Mon Feb 1 23:07:46 2010 +0000 Added o_db shortLabels to panTro2 chainNet and chain and net. commit 1123933fee8c5097b138af06ad6fde59405362a2 Author: rhead Date: Mon Feb 1 22:57:55 2010 +0000 Removed lingering release beta on panTro2 chain and net. commit d57f500d841add6d5ca90b0d2f4fef4b55ac4cb3 Author: kuhn Date: Mon Feb 1 22:52:06 2010 +0000 changed animal name to o_Organism for several commit c3471fe79b568b9a77d3b8c8c9ba6c127263f903 Author: rhead Date: Mon Feb 1 22:51:41 2010 +0000 Adding chain and net shortLabel overrides for chimp that match the chainNet overrides. commit f8a1a8ce98655578ede8a9d2fc67410a59e310ca Author: rhead Date: Mon Feb 1 22:35:41 2010 +0000 Removed commented-out lines. commit d429a65a30c3c5e4fe48b781257f18f52a819389 Author: kuhn Date: Mon Feb 1 22:31:40 2010 +0000 changed animal name to o_Organism for several commit 44346ce097f65335daef891b4fd7760bf8904af9 Author: rhead Date: Mon Feb 1 22:25:35 2010 +0000 Adding chain and net shortLabel overrides for opossum to match the chainNet overrides. commit c97a996b4cc38c3e230392d70e67124ceb8d3761 Author: rhead Date: Mon Feb 1 21:54:43 2010 +0000 Removing override for chainNetMonDom4 shortLabel, as this is also done at the dog level. commit e84f077daa36b152f4b1b8a63dfbe40e3c2b45c0 Author: tdreszer Date: Mon Feb 1 21:37:55 2010 +0000 Neglected 4 state subCBs in last check in commit 5055efc0e84f775e2a3f97a21a9d801fb46e0f6f Author: larrym Date: Mon Feb 1 20:23:06 2010 +0000 very rough prototype for search tracks commit bdff5cb7b1057f9e3d1f93d24ed7f0d8cae9849f Author: rhead Date: Mon Feb 1 19:46:27 2010 +0000 Adding chain and net shortLabel overrides to match the chainNet shortLabel overrides. commit f011c3161601c72cdb3265f7e74fc22421ed201b Author: hiram Date: Mon Feb 1 19:43:55 2010 +0000 change Sscrofa8 to Sscrofa9 since it is that commit 3eeb1fe0076a8e06635d154369f6153a778e35ab Author: rhead Date: Mon Feb 1 19:35:49 2010 +0000 Replaced hard-coded galGal2 with o_db variable. commit 0cb02c1f87b98a4d8f8ff1c3a5da2763cccd2a89 Author: galt Date: Mon Feb 1 19:07:46 2010 +0000 gcc34 and some other compilers complained. but we should have the cast around the full expression anyways commit f163b1b6547c64db999ee4431988929e76c4f8d3 Author: katrina Date: Mon Feb 1 19:04:27 2010 +0000 shortened the short label of two subtracks commit 69af26317386304344549cfb8aabc367a5fdb514 Author: tdreszer Date: Mon Feb 1 18:37:32 2010 +0000 Versioned a lot of Open Chromating Peaks and did some reorganization of the deck chairs commit 9360c5685f47c8583559a4fe607a7c8577b063d1 Author: tdreszer Date: Mon Feb 1 18:19:41 2010 +0000 Changes to speed up matrix buttons commit c3e531abe3d4745ff216099bb41352ad63ef43f7 Author: galt Date: Mon Feb 1 16:00:07 2010 +0000 "Encode release log update" commit 333719f1c614677034b74b62b43f523cadc1eca3 Author: galt Date: Mon Feb 1 16:00:03 2010 +0000 "Release log update" commit 0ca92de05c3039e2ec74eb056907cdc9e32f018f Author: kuhn Date: Mon Feb 1 07:34:30 2010 +0000 moved all xenTro2 chains and nets to composite and dropped individual tracks commit fbdc61452cda7b8385be0bbd1856e9424eea33bb Author: kuhn Date: Mon Feb 1 07:08:25 2010 +0000 moved all xenTro1 chains and nets to composite and dropped individual tracks commit cb7df4ced6d1f65442cd348fae3c36cac954e39b Author: kuhn Date: Mon Feb 1 06:27:58 2010 +0000 changed some explicit animal names to o_Organism, including chainNetXenTro1 which should not have said Tetraodon in the first place commit 1ff28deade9b7b3b1faa069073969259bc0f180b Author: kuhn Date: Mon Feb 1 06:19:55 2010 +0000 changed some explicit animal names to 0_Organism, including chainNetXenTro1 which shold not have said Tetraodon in the first place commit 8029e75e26100ff6925b6d66dd8f698a0771f8ca Author: kuhn Date: Mon Feb 1 05:32:42 2010 +0000 reversed previous change. the hap chrom breaks the histogram if two assemblies have different hap sets. fix is too complicated for right now commit 3410200160b2b51a3be6a3aee78336fb078a997f Author: kuhn Date: Mon Feb 1 05:12:48 2010 +0000 added back the haplotype chroms at ann's request commit 3a1e6ce2b1d517bc1e9d8a63a4fac07861b90784 Author: kate Date: Mon Feb 1 02:36:31 2010 +0000 Add support for additional NHGRI reporting fields commit 13060ad04d8fc98049bacaf7fab283ad662016d4 Author: kate Date: Mon Feb 1 01:44:30 2010 +0000 Fix lab and datatype metadata for Hannon lab tracks (short RNA) commit 7c030d5845377b38c63507c27b582c8a045f2fd6 Author: kate Date: Mon Feb 1 01:43:15 2010 +0000 Fix grant metadata in Caltech tracks commit 347e9984d3038e3811d109d48c6f33e35976ac65 Author: pchan Date: Mon Feb 1 00:58:38 2010 +0000 add doCRISPRs() for lowelab CRISPRs track commit 8bbb2c95382e8a2411a3ef6180f8e384b1fb455f Author: pchan Date: Sun Jan 31 17:47:37 2010 +0000 if lowelab is defined, set SCRIPTS to /cse/grads/pchan/scripts since lowelab does not use /cluster/bin commit da38c2804ba22b6dddb3ad2894bf4723183e56a3 Author: galt Date: Sun Jan 31 16:00:04 2010 +0000 "Encode release log update" commit a854dafb13a71cdfc0093bb240ec577fe14fe6f3 Author: galt Date: Sun Jan 31 16:00:02 2010 +0000 "Release log update" commit af835cd4edf90d19e1fe30c5b31f3554334e80ae Author: larrym Date: Sat Jan 30 20:44:10 2010 +0000 first pass; currently only handles coding SNPs; still working on how to output mutation classifications commit 6129f514843b7797a86ddbe24ce6fde8ceb3c803 Author: galt Date: Sat Jan 30 16:00:06 2010 +0000 "Encode release log update" commit d39c6cbcdea87222942a210352a9f4eaf5818b50 Author: galt Date: Sat Jan 30 16:00:03 2010 +0000 "Release log update" commit 8a430468401df9a0a015eb5cbaec2bc7d43f127d Author: kuhn Date: Sat Jan 30 07:08:56 2010 +0000 added support for datasets where the largest data value is smaller than the width of graph. graph then shrinks to width of largest value commit 8ee3afce9f8ad5ff8cb0660c0910ba84b65abce4 Author: kent Date: Sat Jan 30 03:26:32 2010 +0000 Fixing it so that while you have to be sorted within a chromosome, the chromosomes themselves need not be sorted. commit d4d1ff31b34e239c4bbcfeace1d75983ca691f52 Author: markd Date: Sat Jan 30 01:14:01 2010 +0000 allow specifying location of name when specifying column indices so that -statsOutput is useful commit cea62a1974f9a07e19560d04e23b28edfb5deeb1 Author: rhead Date: Sat Jan 30 01:13:44 2010 +0000 Removed individual chain and net settings for chicken, now that they have been moved into composite tracks. commit 8d5ef0712d9ede001d9bade181c8d1d84ca75cd7 Author: kent Date: Sat Jan 30 01:03:33 2010 +0000 Adding more error checking on input. commit fb415b25cf971ee1a17f0948fb6805913c019f06 Author: kent Date: Sat Jan 30 01:03:08 2010 +0000 Adding another error test case. commit 692ae2640a53b2313d91a2f2e308e869bb4eee48 Author: kent Date: Sat Jan 30 01:01:56 2010 +0000 Adding another test case commit 8df244bd4f923563da605b3a0ac7fa708e708170 Author: katrina Date: Fri Jan 29 23:19:12 2010 +0000 removed release alphas from ENCODE UW DNaseI HS release 2 new tables commit ebad406b65a55e86a40ea5d29399f514ab0ab664 Author: braney Date: Fri Jan 29 23:10:13 2010 +0000 fixed some metadata for Caltech GM12878 commit e926b1559136710d289a1b1938eff95483376f9e Author: galt Date: Fri Jan 29 21:49:46 2010 +0000 emergency fix for customTrash db server going offline commit 93e099020183929d90f4d8a03a8c1f68bb86ccb2 Author: angie Date: Fri Jan 29 19:02:59 2010 +0000 Adding correct alignment params for seaHare-human alignments. commit 463d806749f07f22093d79dd966e6af8b42a49de Author: angie Date: Fri Jan 29 19:02:21 2010 +0000 Right now this is only needed for including trackDb.chainNet.ra -- would be cool for hgTrackDb to auto-include some filenames... commit a55ac3ff5672b7984cdeb4647171379352df82f2 Author: tdreszer Date: Fri Jan 29 17:51:41 2010 +0000 Minor adjustments to cell descriptions and officially added UCDavis as control type. This had been implied for some time. commit 0f6bb286140b95039f44f5a5cbdb570e1492155f Author: tdreszer Date: Fri Jan 29 17:30:04 2010 +0000 Added abbreviations to cell line titles in matrix for UW DNase. commit 09980b63c443d9f8e790309e130337c8f5a7e232 Author: galt Date: Fri Jan 29 16:00:07 2010 +0000 "Encode release log update" commit 7bcb309b9be6c060d5a1ea09e07151690e36c365 Author: galt Date: Fri Jan 29 16:00:03 2010 +0000 "Release log update" commit 03c6b92e9ff633b157451333bf9593243d5a811e Author: ann Date: Fri Jan 29 00:24:43 2010 +0000 added a -alpha flag to the tdbQuery call to get tracks that are restricted to alpha. added release to the output, so we can see if they are restricted to one machine or the other. commit 35a8f9ebc55e7d8fce44a6701f158b063278c42f Author: hartera Date: Thu Jan 28 23:49:54 2010 +0000 Renamed tables and added trackDb entry for the CRG mappability tracks as part of an ENCODE Mapability track. commit 768092f6d55285ef79a99945f7c6acb6e2e31471 Author: hartera Date: Thu Jan 28 23:48:44 2010 +0000 Renamed tables and added trackDb entry for the CRG mappability subtracks of the ENCODE Mapability track. commit 34dbe8dd70d2d14b99306b464bdcf48903c951c5 Author: tdreszer Date: Thu Jan 28 23:46:40 2010 +0000 Fix for mapability sort order commit b5c8a122bdf5710d7ffab3a399fb07e39db386e3 Author: tdreszer Date: Thu Jan 28 23:41:30 2010 +0000 Clean up of old crud. UW ChIP to UW Histone. Revoke 1 more for YDH commit fb73a7a35496d4222640cb260ac948716f777a14 Author: hartera Date: Thu Jan 28 23:40:10 2010 +0000 Added an ENCODE Mapability track with data from CRG's GEM Mapper aligner. commit 8205e30e5aeea23b381681ca1aca0ae82d9ed859 Author: hartera Date: Thu Jan 28 23:25:17 2010 +0000 Moved the tag of subGroup1 for the CRG track. commit 927be335f709ac642629d6a21d54c5f10c7453e0 Author: hartera Date: Thu Jan 28 22:59:45 2010 +0000 Added wgEncode prefix to CRG Mapability subtrack table names for consistency. commit be26dad0b192b94146d2765f11eac1353110ec60 Author: donnak Date: Thu Jan 28 22:53:10 2010 +0000 Oops, last version was the .doc file rather than then .pdf...replacing w/correct format. commit bac892c4c8294c5640ed2048e6f0c9d887e6662c Author: donnak Date: Thu Jan 28 22:45:45 2010 +0000 Updated w/new version from Wil. commit 7e6e012233ff9c96d28a9fb6e99cf6bbce4c8ca7 Author: hartera Date: Thu Jan 28 22:27:46 2010 +0000 Added subtracks for CRG's GEM Mapability data to the Mapability track. commit f30c21e85592a02217623dc00dceefd6e47d444b Author: tdreszer Date: Thu Jan 28 18:31:47 2010 +0000 Removed 2 nonexistant tracks and revoked the 3 HUVECs for YDH commit 28d1082ec54cd2a8f1dce21c376b02ace81fc5c0 Author: tdreszer Date: Thu Jan 28 17:35:34 2010 +0000 Re-pair 11 Yale experiments from IgG-rab to IgG-mus (temporary pairing) commit 256a84ab5d2ba415677ac30f1362fa13fab33c5b Author: kuhn Date: Thu Jan 28 16:39:55 2010 +0000 moved diclaimer to top of description section commit 27b2fb4583b7581b411ff1cb39c494a515796124 Author: galt Date: Thu Jan 28 16:00:06 2010 +0000 "Encode release log update" commit 27c14fe37edfc9ca4ec3f92505cba29bb6d52d47 Author: galt Date: Thu Jan 28 16:00:03 2010 +0000 "Release log update" commit 60cc064c113744d8fa45d93f7c4dc3429e53045d Author: kate Date: Thu Jan 28 03:51:03 2010 +0000 Tweak metadata for reporting commit b681fa6e5d9eb55b563b459538bebf5e58488547 Author: kate Date: Thu Jan 28 01:30:21 2010 +0000 Tweak for consistency commit ff0dd3c3b3e7008b65bc70e9c0397ddb28b31470 Author: ann Date: Thu Jan 28 01:27:16 2010 +0000 we don't need that much output in the index check (thanks Brooke) commit 1145a205ee406465f65e26157604d1c0a235c9fb Author: kate Date: Thu Jan 28 01:25:39 2010 +0000 Fix typo in freeze commit 3c0ace1898848b73bfb4343fc1b3193591e20c41 Author: kate Date: Thu Jan 28 01:00:17 2010 +0000 Unify RNA-seq here for reporting -- will do for trackDb when convenient commit c005044e6a9f19ef6b4b29c8b05c4755485aad9b Author: ann Date: Thu Jan 28 00:36:16 2010 +0000 variable needed quoting commit b7dd25c79253db42d703c18b33024442ebae0adb Author: galt Date: Thu Jan 28 00:24:48 2010 +0000 trying to get it to compile, using dynamic libjpeg since static no longer easily available, changing jpeg2000 dependency to default off since most people will not need it, using jpgTilesX.h as a minimal include file removes the conflict over "boolean" between common.h and libjpeg.h commit a42db3ff66da4133f683db2ee0e225e2215e0258 Author: angie Date: Thu Jan 28 00:20:16 2010 +0000 genericChainClick: fixed bug noticed by Katrina: we weren't checking the chainLinearGap trackDb setting, so when recalculating score-in-window, we used incorrect gap penalties unless the default loose penalties were used. Also, recalculating score-in-window had the unexpected side effect of clobbering the original chain's score when the whole chain fit in the window, because chainSubSetOnT was returning the original chain! I took out the score-in-window stuff for chains that fit in the window, and added a position link for the ref. genome (like we have on all of our other pages). commit 5856428f6760b311ec95eb13e3413513e9b961d5 Author: tdreszer Date: Wed Jan 27 22:22:34 2010 +0000 Altered sort order. take only last matching line of metadata from fileDb.ra. Don't show antibody if its eq input commit 65bbe1d7cb2f053a4a5d0cb6882c13602dc75078 Author: tdreszer Date: Wed Jan 27 21:44:12 2010 +0000 Show subId in metadata and hide antibody if it is really input. commit cb2cda66639245a769362df4298acb8b70f4f23e Author: tdreszer Date: Wed Jan 27 21:17:35 2010 +0000 Rearranged a lot of Yale metadata commit 77093a58244243708ccaf86e21ad0d437dac4dca Author: galt Date: Wed Jan 27 21:04:09 2010 +0000 moved new greek byte function to kent/src/lib/obscure.c commit a4e5db9851dd3d4f86a38913e6ba5a062238129c Author: tdreszer Date: Wed Jan 27 19:20:11 2010 +0000 Changed Mouse_IgG to IgG-mus and Rabbit_IgG to IgG-rab commit 6d97bc0d15963f67948bb201363cb8d849aaffa4 Author: galt Date: Wed Jan 27 19:17:32 2010 +0000 adding deadline setting instead of hardwiring it, tolerates missing deadline.yml commit 63f5080756aef7800d9200edff410e2dff1bd796 Author: braney Date: Wed Jan 27 19:16:28 2010 +0000 change all HA methylSeq to PCR1X commit 77241435b33b1308e00adbf0c9eeae847a028df6 Author: galt Date: Wed Jan 27 18:12:32 2010 +0000 activating D-queue link for encode commit 8681abb67fe3c5b101100bc5de8db4cfa4a857f0 Author: braney Date: Wed Jan 27 16:18:30 2010 +0000 fiddle with Credits some more commit dee7ac1f69f4eccf29f1acb43560de639b8e45fb Author: braney Date: Wed Jan 27 16:10:55 2010 +0000 ENCODE Riken Cage NHEK nucleus clusters commit c492ccac66d8e1272b6a530af13bac02075257c3 Author: galt Date: Wed Jan 27 16:00:06 2010 +0000 "Encode release log update" commit ebd5bd5138c7771d0159ca8af70155eb20cc0485 Author: galt Date: Wed Jan 27 16:00:03 2010 +0000 "Release log update" commit 40608f9fff526bc9e376482daf4e47a134b28460 Author: markd Date: Wed Jan 27 07:41:21 2010 +0000 fixed incorrect on-the-fly parse of superTrack setting commit 82c5acc4e85f69a8430c49b6683bf558b141557a Author: tdreszer Date: Wed Jan 27 04:06:19 2010 +0000 minGrayLevel is for narrowPeaks too commit 79261bd3a394aba59f8e59d6465a85cfb7a97321 Author: tdreszer Date: Wed Jan 27 02:51:09 2010 +0000 Added minGrayLevel to HAIB TFSB preaks, since they have scores below 100. commit 0a325669531dadc88b82f5454082d8e9ef9daf26 Author: galt Date: Wed Jan 27 01:35:32 2010 +0000 getting rid of redundant info at top, and adding Greek-Bytes B KB MB GB TB PB to totals displays commit d4e29244ff5cb68a84d05d51e99ede6ac1fb2e4a Author: kate Date: Wed Jan 27 01:32:57 2010 +0000 Tweak around trackDb insconsistencies commit 6859628e6c10f0703aed4b7e22e3ae8f20ac8261 Author: cszeto Date: Wed Jan 27 01:14:49 2010 +0000 Organized some track.ra definitions commit 831d9d195008c0c2c912fbeeb68e79584cb68781 Author: cszeto Date: Wed Jan 27 01:14:22 2010 +0000 Organized some track.ra descriptions commit 4187a8ef10712a86f8996a46ddcff23ed1ea3ec5 Author: tdreszer Date: Wed Jan 27 00:58:20 2010 +0000 Added treatments to long labels of HAIB TFSB commit 4af859f9bd15c5200bc81f23bca55d3b4f7aca67 Author: tdreszer Date: Wed Jan 27 00:48:26 2010 +0000 Fixed a number of experiments which should have hade Rabbit_IgG protocol declared for Yale commit 735ef0b38401e78573579fb6f1c67037b2385e71 Author: galt Date: Tue Jan 26 23:54:07 2010 +0000 adding chromosomes/ download commit c66f00f1d2d7466673ade74a0e62680aa1ed9178 Author: hiram Date: Tue Jan 26 23:24:51 2010 +0000 transMap will not override viz commit 2be22224d3216c400fb053546863d76fa09acbc6 Author: tdreszer Date: Tue Jan 26 23:11:22 2010 +0000 Fixed HepG2/SREBP1 to HepG2/SREBP1/pravastatin for Yale commit d35fb7009cd9df295939c085541fc7e535c93fa5 Author: braney Date: Tue Jan 26 22:41:29 2010 +0000 changes re: Carrie commit 85eab2500831ba462456f60d94eef51f8fda092e Author: hiram Date: Tue Jan 26 22:24:56 2010 +0000 adding definitions for oryCun2 commit 03f5d72fa8cc6216a13a62c31f508e597e506ddf Author: hiram Date: Tue Jan 26 22:22:03 2010 +0000 adjusting some track default visibilities commit 1a19d689557288059b4ce020726bbc398946ec29 Author: galt Date: Tue Jan 26 22:07:00 2010 +0000 v224 preview commit 5ef5b4f0e4936a3464470831b37261a2ea79915d Author: tdreszer Date: Tue Jan 26 22:04:14 2010 +0000 pravastatin treatment illucidated by Yale commit 781ade4d956e16b4fd61083de82c503799025392 Author: hiram Date: Tue Jan 26 22:00:38 2010 +0000 fixup sample searches and finalize assembly description commit f8bfa9ba4699d976bdeac2d20cc0ea9bc2a0e274 Author: rhead Date: Tue Jan 26 21:31:37 2010 +0000 Changed all entries to have a color of black and an altColor of dark brown. The old altColor of tan was showing up on chains within composites and was nearly impossible to see. commit 2eb791877f7b0987bc243b7c436ba27bd7804f33 Author: kent Date: Tue Jan 26 20:55:28 2010 +0000 Removing score filter from bigBed. commit 39793e0ec55a52b8335ba6f9fd48c61929642d5c Author: tdreszer Date: Tue Jan 26 20:48:34 2010 +0000 Fixed SREBP1A to SREBP1 fro Yale and added missing protocol tper for 8 HAIB subtracks commit 2fbdd1fa2bdbf21d4a82d1ad3dec8a6cd824f6e6 Author: tdreszer Date: Tue Jan 26 20:25:28 2010 +0000 Adde pravastatin treatment and renamed SREBP1A to SREBP1 for Yale commit 9a69081c96dfee9f5e2fab8967713704adb395ba Author: kent Date: Tue Jan 26 20:11:27 2010 +0000 Getting rid of special case to allow filtering of bigBed in dense mode. commit 9c89fd4ae994e072b5676c880b548bf05c4c7fda Author: tdreszer Date: Tue Jan 26 20:05:53 2010 +0000 Fix TFIIIC to TFIIIC-110 for Yale commit f16e7b0ed8a0a3aadc71372117c682a1bd47b9fa Author: tdreszer Date: Tue Jan 26 20:00:17 2010 +0000 Some metadata corrections for Yale commit 0abb1f06250532a11707898f38b7bfff0de54694 Author: hartera Date: Tue Jan 26 19:41:22 2010 +0000 Adding a mapability data from CRG. commit 9fa4fde9f29baacdace3491756cd755d23692ee5 Author: ann Date: Tue Jan 26 19:35:53 2010 +0000 add section for creating and sharing direct URLs for remote big tracks commit e2f6b8862a3d22d897469a4113e2926656f4a77c Author: braney Date: Tue Jan 26 18:31:53 2010 +0000 oops one more place commit f878a1ed3ff746f8b08b2ee73b8d135ab788b02d Author: braney Date: Tue Jan 26 18:28:01 2010 +0000 fix up ENCODE Riken to change Hepg2 LongnonPolyA to hepg2 total commit bd5bd4006fcb38a0a6078f4901a61729d64b4ca3 Author: tdreszer Date: Tue Jan 26 17:37:00 2010 +0000 Cleaned up some metadata for HAIB commit 3b497cd45047fe73dcf47a1db6edaf3b91a90672 Author: braney Date: Tue Jan 26 17:32:07 2010 +0000 fix up the ENCODE BU orchid tracks commit 12e190748a6ce6483801ce6b3a68f2c45344c47b Author: tdreszer Date: Tue Jan 26 17:14:21 2010 +0000 HAIB needed Oct-2 changed to POU2F2 commit 21772a45b0965c17a2e663ebc0661dd7aeb94d28 Author: galt Date: Tue Jan 26 16:00:06 2010 +0000 "Encode release log update" commit 252331a85c7ee401e443f6923097b01a56b7781c Author: galt Date: Tue Jan 26 16:00:03 2010 +0000 "Release log update" commit 465058599f333a2087dc78f75f737a741812ea3e Author: kuhn Date: Tue Jan 26 05:19:04 2010 +0000 moved all galGal3 chains and nets to composite and dropped individual tracks commit 5eef84d953fca82147bdf26b8231890e3f1ebdf6 Author: rhead Date: Tue Jan 26 03:34:04 2010 +0000 Changing opossum net and chain tracks to composites. The following assemblies are currently live on the RR: calJac1 canFam2 cavPor3 danRer4 danRer5 galGal2 galGal3 hg17 hg18 hg19 mm8 mm9 ornAna1 panTro2 ponAbe2 rheMac2 rn4 xenTro2. commit 0edd0349a8d0a20df639fb286c1c5dba70c5af28 Author: rhead Date: Tue Jan 26 03:28:45 2010 +0000 Removing release alphas on chainNetMonDom tracks. Also changing color to black, to make the chain longLabels show up against white. commit f9c6a2dc9d69b95472fbadad9f35fc0270cac140 Author: rhead Date: Tue Jan 26 03:11:25 2010 +0000 Removed blocks for chains and nets to monDom2. commit 3cc91746fa684ab95fa673f8d209d61182ff4199 Author: angie Date: Tue Jan 26 00:36:22 2010 +0000 Clarified ENCODE regions label (thanks Kayla/Ann). commit c65afc4aa1d67b7b64420edd5716dee5393c14fd Author: pauline Date: Mon Jan 25 22:57:35 2010 +0000 Removed release alphas to stage UW chip seq track. commit ee357dfcbb9e436dd8fde4945c4922d59e615229 Author: kuhn Date: Mon Jan 25 22:15:52 2010 +0000 moved all galGal22 chains and nets to composite and dropped individual tracks commit a8d8ec60d9b66bdb79061d91af1bfa8ea3a0fc51 Author: kuhn Date: Mon Jan 25 22:10:36 2010 +0000 moved all galGal22 chains and nets to composite and dropped individual tracks commit c11bad40361a2de07ac16e90348445ba8ca9bd23 Author: braney Date: Mon Jan 25 21:36:27 2010 +0000 first cut at Orchid/Chai tracks commit 3b9f039c9666ce0d49ba01ac575a7bc09669c0d2 Author: hiram Date: Mon Jan 25 19:43:27 2010 +0000 genbank done for ailMel1 commit e96a8093de990d9b1d6e25b8c6b14d80329142b8 Author: hiram Date: Mon Jan 25 19:42:34 2010 +0000 no lift file is required for panda commit d262ddb2a8debc8ca67de7919d86aca7f0caab3e Author: kuhn Date: Mon Jan 25 19:34:52 2010 +0000 moved all rheMac2 chains and nets to composite and dropped individual tracks commit e52adce8473af122a936ff25a8412acc2756fe09 Author: ann Date: Mon Jan 25 19:20:31 2010 +0000 https for BAM is not quite ready for prime time commit af14e74b147cad1f921edebd704396e1e1f3799c Author: hiram Date: Mon Jan 25 19:16:14 2010 +0000 panda aligned to dog,rat,mouse,human,opossum pig aligned to mouse,human,opossum,cow bosTau4 to rn4, rabbit to rat,mouse,opossum,guineaPig commit c91c93c2dbb5d711ed37d26dd780c06870d962f1 Author: aamp Date: Mon Jan 25 19:03:31 2010 +0000 Added to expRatio spec the "expColor" trackDb setting. commit 407bf75ddb1a7f093cb0cccbc1e3db5351fcfea6 Author: ann Date: Mon Jan 25 18:53:14 2010 +0000 BAM announcement commit e65f3b2b1d4bf8716b381e7686c82404e0d65dd6 Author: katrina Date: Mon Jan 25 18:52:42 2010 +0000 Edited UCSC Genes ref to current ref standards commit 5e48c8c3233e03b63b61568437734c38c83e8d3b Author: katrina Date: Mon Jan 25 18:33:33 2010 +0000 Edited UCSC Genes ref to current ref standards commit db8b058971f495ca2aa94df682bcb715135be8ec Author: katrina Date: Mon Jan 25 18:21:40 2010 +0000 Edited UCSC Genes ref to current ref standards commit 508e2f385204bc155387c6fd5bcb0759aea4323b Author: katrina Date: Mon Jan 25 18:08:47 2010 +0000 Edited UCSC Genes ref to current ref standards commit ac5d6a1d5be6afaabba5c86c83a05244da3c8623 Author: katrina Date: Mon Jan 25 17:57:38 2010 +0000 Edited UCSC Genes ref to current ref standards commit e16bd7e1403b5a689650b3e6a46b7b796c15090a Author: kuhn Date: Mon Jan 25 17:43:36 2010 +0000 moved all panTro2 chains and nets to composite and dropped individual tracks commit ae40bed390de0961d6938dac8e0edd58c50d91e1 Author: angie Date: Mon Jan 25 16:46:58 2010 +0000 Added template for Genome Variants (pgSnp) liftOver from hg18 by Belinda. commit e77d236507a78b94e9af2d7a17383caa7e452779 Author: angie Date: Mon Jan 25 16:13:46 2010 +0000 Added gwasCatalog. commit 2dbff8b185a89f7922e8c1c618fb6f473eb3e78f Author: galt Date: Mon Jan 25 16:00:07 2010 +0000 "Encode release log update" commit 32234e88eff6253296e1351de95b671af86b4f85 Author: galt Date: Mon Jan 25 16:00:04 2010 +0000 "Release log update" commit fcaeb57b82090b27e8f973a46d4bc128024a9dde Author: kuhn Date: Mon Jan 25 06:15:00 2010 +0000 moved all panTro1 chains and nets to composite and dropped individual tracks. only hg17 and mm7 on RR commit 5274fd63f92796e141b634b1dfb65c968cb4919b Author: kate Date: Mon Jan 25 05:47:07 2010 +0000 Now using submission ID from trackDb to lookup status in projects table, instead of relying on matching metadata. This version only includes latest version (e.g. V2 if any) of experiments commit c6d38e8ae8b06cce2d0da91b13b6494fcd0639f0 Author: kate Date: Mon Jan 25 05:08:33 2010 +0000 Standardize lab name for UT-Austin commit 1e51460066bbef92f83c4bf633fb69d305262f73 Author: kuhn Date: Sun Jan 24 19:45:16 2010 +0000 added support for second set of data in histogram commit f7bbf28e937366e5b235b92bbe2dbf96fa16aa4e Author: kuhn Date: Sun Jan 24 19:42:51 2010 +0000 added formatting for variable first column width commit d06c0238460b74a10ad37e05f6e56952277e2af0 Author: braney Date: Sun Jan 24 18:06:14 2010 +0000 fix up some CSHL small RNA short labels commit c942b9cc0283bcf915586fc374fcad522778540d Author: galt Date: Sun Jan 24 16:00:06 2010 +0000 "Encode release log update" commit fb56c5da5883fa48bdc41ffd2007edb8fc02b1aa Author: galt Date: Sun Jan 24 16:00:03 2010 +0000 "Release log update" commit 7138213a8f884bc82ae890d5d20e0ff1a61099fb Author: kuhn Date: Sun Jan 24 07:01:35 2010 +0000 forgot to implement configurable bar length after adding option in usage statement commit 385efa7705cf809e762cbe0425a09116276253b5 Author: kuhn Date: Sun Jan 24 06:56:41 2010 +0000 made graph.csh to draw a bar graph from a two-column file and added option for countPerChrom.csh to use it commit 0ef4505ee992db042d641e0a6ea59c8f39dee200 Author: braney Date: Sat Jan 23 22:36:41 2010 +0000 shorten up Caltech labels commit ee95cf9e8e73d38aba2f19484c16fe98aab1aa6d Author: fanhsu Date: Sat Jan 23 18:54:07 2010 +0000 Updated one line for tRNAs details page. commit 4181dbf324489ef8d097d277d0fb62f763de5531 Author: galt Date: Sat Jan 23 16:00:06 2010 +0000 "Encode release log update" commit 1f71f6e7cfba108d7a186fc14c625c6d305a4ded Author: galt Date: Sat Jan 23 16:00:03 2010 +0000 "Release log update" commit 023bb58b3ed6d19037f24ee13830b1132c47ad00 Author: rhead Date: Sat Jan 23 01:45:15 2010 +0000 Removing blocks for monDom2 chains and nets. These do not exist anywhere. commit cc2c6342e0039a1b54a3d6139b3049e8bfec0def Author: tdreszer Date: Sat Jan 23 01:12:21 2010 +0000 Fixed a couple of HU TFSB subGroup mistakes commit 2b8dec82cfb97d322f13c6ed7385afefce0afa60 Author: fanhsu Date: Sat Jan 23 01:01:06 2010 +0000 Updated tRNAs track processing per input from Mark and Todd. commit d34f0f7aa5d2ad777fa29dd9474cd5379ac63706 Author: ann Date: Sat Jan 23 00:53:53 2010 +0000 Finally decided to take the plunge and edit the citations for the genbank references. commit 7f491bb739f19900fd4ca9e9e87d3506c9583b63 Author: kuhn Date: Sat Jan 23 00:36:11 2010 +0000 moved all ponAbe2 chains and nets to composite and dropped individual tracks commit 22af7408fb7ac0a5418771933e27dd8ada42f48e Author: lowe Date: Sat Jan 23 00:15:29 2010 +0000 Slightly updated description to include info on what tRNA score means. commit a069e55a15e59175a766f339b9f83af632ae3f50 Author: kuhn Date: Sat Jan 23 00:02:46 2010 +0000 dropped track blocks for chain and netPonAbe1, as no assembly has these tracks commit 7b9682403cb845533d407d054c581c04ec747178 Author: hiram Date: Sat Jan 23 00:02:02 2010 +0000 some border space around the photo commit 66cb042197dd88a6c58c6b9c3a4454ea0b72a55b Author: hiram Date: Sat Jan 23 00:00:29 2010 +0000 fixing up Broad links commit 5928ed331081d2985cb2e78f3e6fe9d8da4ce43a Author: angie Date: Fri Jan 22 23:44:59 2010 +0000 Tweaked label of coding changes. If there are no coding changes, suppress messages about coding changes (confused me a bit). commit f0cb126249bdc17a26688a3a5de928f56cc5f4f8 Author: angie Date: Fri Jan 22 23:43:18 2010 +0000 pgSjk was not hooked up to doPgSnp, oops! Tweaked wording in pgSnp. commit 11c5b34d1cdd4e8a08e512d1bf4dd7ff9866a328 Author: hiram Date: Fri Jan 22 23:21:43 2010 +0000 photos for Pig and Panda commit c911153b1096383787148306cbbc70e537462399 Author: hiram Date: Fri Jan 22 23:15:23 2010 +0000 updated description with appropriate links commit e927a415e25d74dd00684a00b74c73cff690431b Author: rhead Date: Fri Jan 22 23:14:35 2010 +0000 Switching equCab1 and equCab2 chains and nets to composites. EquCab1 is currently on RR for hg18, mm8, panTro2 and rn4. EquCab1 is on RR for canFam2, galGal3, hg19, mm9, monDom5, ornaAna1. commit e225cbc4e61fa46a2c25bd1ddbc9725a10868732 Author: tdreszer Date: Fri Jan 22 22:58:14 2010 +0000 Minor revisions to some long labels commit b08006a5ca6bda7577bcbc3ea0b846d02231c5b5 Author: aamp Date: Fri Jan 22 22:52:04 2010 +0000 Microarray tracks and custom microarray tracks now support the "expColor" trackDb setting which can be "redGreen" (default), "redBlue", "redBlueOnWhite", "yellowBlue", or "redBlueOnYellow". Some things wre changed around so that adding more color options in the future is a cinch. commit f78780231767f006e2253acf9634d562ef530606 Author: angie Date: Fri Jan 22 22:50:14 2010 +0000 Adding snpTable and snpVersion (and url, urlLabel) to gwasCatalog. commit 14201d17faeaa920ce4de098f9b911792d46ed28 Author: cline Date: Fri Jan 22 22:46:43 2010 +0000 Added submission # 1060 commit c322812f87fe80b11c7b7df8415005672604c9a8 Author: ann Date: Fri Jan 22 22:41:19 2010 +0000 italicizing scientific name commit 8b2bf2318bdba220f8bbb62882db07e2329a6860 Author: angie Date: Fri Jan 22 22:23:19 2010 +0000 gwasCatalog: Added links to dbSNP for snp and, if different, the snp with the risk allele. Look up and display the dbSNP observed alleles, and warn if they are complementary (then the risk allele is ambiguous because strand is not noted. commit 8a6fea5acc0ee2953f059048a66791b3a2565046 Author: hiram Date: Fri Jan 22 22:06:04 2010 +0000 liftOver done to oryCun2 commit d392f6639d7b67e9b3c6d3e05c68cef8ed32c5c5 Author: kuhn Date: Fri Jan 22 21:46:10 2010 +0000 removed checking for multiple RR machines since we've gone to single mysql database commit fd3dcbaf1822e73601d1a2035753c9bc7238425e Author: kuhn Date: Fri Jan 22 21:17:19 2010 +0000 fixed getAssemblies.csh to work with RR machines and several other programs that it depends on. it broke when we went to a single mysql machine and genbank dumps only grab from hgnfs1 commit f9e3ad9562f4d4f9a671f8b1b2f4c73651ddfc07 Author: tdreszer Date: Fri Jan 22 20:45:03 2010 +0000 Fixed some shortLabels for Duke commit 0d7916c9b93d8d8be96b5cd2e94dca1b802a9fdc Author: cline Date: Fri Jan 22 20:43:34 2010 +0000 Added one more cell type for Hudson Alpha chipseq commit d974c22aedc6fe8a50f559ff9ee9101540e94cba Author: ann Date: Fri Jan 22 19:50:44 2010 +0000 Edited so that, in general, it only prints output if there is a problem. Removed lots of extra lines. Added a couple of defined values. General clean-up. commit 421d50016f6f9fbe4077c91e44b7da3568458bc8 Author: hiram Date: Fri Jan 22 19:12:39 2010 +0000 adding Panda and Pig chainNet composite tracks commit 1b082a990e54e8d8ae39c2f6e1e82389f9712ca1 Author: hiram Date: Fri Jan 22 18:58:28 2010 +0000 adding chain net priorities for mouse human and opossum commit a8645e9c93445e19cff287829988bb3189992298 Author: hiram Date: Fri Jan 22 18:54:39 2010 +0000 adding priorities for dog, rat, mouse, human chain nets commit 8b3179194b00bb83be82dc2297879d76e315d7f6 Author: hiram Date: Fri Jan 22 18:40:23 2010 +0000 update to a 48-way tree while maintaining same priorities for previous 46-way commit fb83f0295684eecc37cf78186a56df4b13fb2045 Author: tdreszer Date: Fri Jan 22 17:31:41 2010 +0000 Insignificant change. This is not hgEncodeDownloads.pl commit 9d021626f112b9044546cc9c790bf5c64b53ae49 Author: galt Date: Fri Jan 22 16:00:07 2010 +0000 "Encode release log update" commit e874fab0c6bf4b42ba106292db64d2604cbda14c Author: galt Date: Fri Jan 22 16:00:04 2010 +0000 "Release log update" commit 26d1faecc16a2ba67050161847929cc45567a7e5 Author: galt Date: Fri Jan 22 09:09:23 2010 +0000 increased html buffer size for handling huge ENCODE lists commit adcd295c3fcdb7f7f018f06d918adf42b96101a1 Author: angie Date: Fri Jan 22 05:57:54 2010 +0000 Adding -atime=123 option to refreshNamedSessionCustomTracks, so we will no longer refresh files in sessions that have not been accessed in >4 months. commit 2d40685e5214263e92cdefdee83b55ac68b48bb0 Author: kate Date: Fri Jan 22 01:40:56 2010 +0000 Revert to non-debug version commit ba6f6f013b4507d2a397fadc4163bd4137301fd8 Author: kate Date: Fri Jan 22 01:38:14 2010 +0000 1. Add checksum option 2. Add plain text version of index file 3. Fix file perms commit 150b373c1938c8dde24673f9d5ea300136004d30 Author: rhead Date: Fri Jan 22 01:10:34 2010 +0000 Set all of the net tracks within composite chainNet tracks to full. commit 3008c808142435bdba42d6f0a416e9f4a88d245f Author: tdreszer Date: Fri Jan 22 00:57:29 2010 +0000 Jan 2010 freeze notes commit 70dc2cb049b0ada432dedff86f960caa3383be86 Author: tdreszer Date: Fri Jan 22 00:56:04 2010 +0000 Minor change commit c5e7526ddf7ea6e8453f620475ae1304346b649c Author: tdreszer Date: Fri Jan 22 00:55:21 2010 +0000 Older stuff and Jan 2010 freeze notes commit 50d49f3109d09178a8d081811d703829edc1a1a4 Author: krish Date: Fri Jan 22 00:25:57 2010 +0000 added UW DGF tracks commit 7a9b25d2012207b2dd4447ef00736304de3c7289 Author: braney Date: Thu Jan 21 23:59:54 2010 +0000 fix short labels and add some useScores for HA RNA-seq commit 3df62538aad768e15176bfa53c8ef604883897fa Author: tdreszer Date: Thu Jan 21 23:40:52 2010 +0000 Added one last forgotten submission for Yale Jan 2010 freeze commit b78623b2a33b0b0586c779dcf8c0478a83d5151b Author: tdreszer Date: Thu Jan 21 23:29:07 2010 +0000 Fixed some RepK562 to Rep1K562 errors commit d0bea21f3b6d110e57916daeac16ff0033432426 Author: kuhn Date: Thu Jan 21 22:49:29 2010 +0000 moved all calJac1 chains and nets to composite and dropped individual tracks commit 1158461c35aa6877dbdfc266f066de0ea7be7ef7 Author: galt Date: Thu Jan 21 21:58:53 2010 +0000 doing a little lookahead, storing results in boolean vars, eliminating redundancy commit 997f3bf6955466bbc42445b468ea6d0c2626f502 Author: krish Date: Thu Jan 21 21:54:15 2010 +0000 added UW DGF tracks commit b3f9f35c33cab28b9dfa8e67bae6da10a7168088 Author: angie Date: Thu Jan 21 21:46:59 2010 +0000 Adding gwasCatalog (NHGRI's Catalog of Published Genome-Wide Association Studies). commit 32aa23aa75425138e295f1da1377772563a944d4 Author: angie Date: Thu Jan 21 21:46:22 2010 +0000 baseColorDrawOptDropDown: Similarly to the drop-down labels, use 'base' not 'mRNA' in help link label when there is no coding info. commit e700b699c4b81ed784834355c9259209357df48b Author: braney Date: Thu Jan 21 21:12:50 2010 +0000 HudsonAlpha MethylSeq Gm12892 Gm12891 commit 8ad2e7f27032ade0c9204283ad75e99bf8036061 Author: markd Date: Thu Jan 21 20:43:23 2010 +0000 fixed ussage message commit 23e946fd641d9d1f0460565d0f05d9f1bab54144 Author: braney Date: Thu Jan 21 20:24:38 2010 +0000 wgEncodeCaltechRnaSeqPlusRawSignalRep1H1hescCellPapBb2R1x75d commit 8ee30bc9bb72fc9d5e91b4999c09bf3e64507b3f Author: tdreszer Date: Thu Jan 21 19:39:10 2010 +0000 Oops, accidentally swapped the wrong composites' dimensions commit 946f870c0d7d7105d62c87447de7b3e6b0af6c8d Author: tdreszer Date: Thu Jan 21 19:35:20 2010 +0000 Added final 10 UW DnaseI submissions for Jan 2010 freeze commit d0ad376bc5b1f32ceb950c9ee279f2f2aa02c573 Author: angie Date: Thu Jan 21 18:51:13 2010 +0000 Added 'type bam' description. commit 3904c816eb5cdd5b72c467b4af3a53ef2f4545e3 Author: braney Date: Thu Jan 21 16:01:27 2010 +0000 wgEncodeCaltechRnaSeqRawSignalRep2H1hescCellPapBb2R2x75 commit d530eb0f5a33f0f9dce899ab00754ee8e80f8e18 Author: galt Date: Thu Jan 21 16:00:06 2010 +0000 "Encode release log update" commit b13b64cb616bbcfd6a0cf2fc18c2f5be79e4ff2d Author: galt Date: Thu Jan 21 16:00:04 2010 +0000 "Release log update" commit ad7f8ef996eb60f1014ce00b1ec48e3af20b5851 Author: braney Date: Thu Jan 21 04:54:10 2010 +0000 wgEncodeCaltechRnaSeqSplicesRep2Helas3CellPapBlat34R1x75d commit 17f456cffad2f1b9c320d4ff493f609030aec5e0 Author: braney Date: Thu Jan 21 04:27:12 2010 +0000 wgEncodeCaltechRnaSeqSplicesRep1HuvecCellPapBlat34R1x75d commit 5cb5474f939214bb4e4378863815bdecbb9864db Author: braney Date: Thu Jan 21 04:07:29 2010 +0000 wgEncodeCaltechRnaSeqSplicesRep1Helas3CellPapBlat34R1x75d commit 401dfa99fdb18b4e3c3ef4800c451301f49a0d26 Author: braney Date: Thu Jan 21 03:41:50 2010 +0000 wgEncodeCaltechRnaSeqPairedRep1H1hescCellPapErng32aR2x75 commit 0cea08018294e28f319789a8f89305dab21b46cb Author: braney Date: Thu Jan 21 03:20:01 2010 +0000 wgEncodeCaltechRnaSeqRawSignalRep1HuvecCellPapBb2R2x75 commit 9e4fac656c8735668ae1abca89bf9aa0e22bab12 Author: braney Date: Thu Jan 21 03:11:03 2010 +0000 wgEncodeCaltechRnaSeqRawSignalRep2HuvecCellPapBb2R2x75 commit 8c4af8e670a100f63eb45f3ccc9a90236228c7b3 Author: braney Date: Thu Jan 21 03:05:32 2010 +0000 wgEncodeCaltechRnaSeqSplicesRep1NhekCellPapBb2R2x75 commit f2887ca950cdbeebfc312b9f2f02ac95860c3692 Author: braney Date: Thu Jan 21 02:42:56 2010 +0000 wgEncodeCaltechRnaSeqPairedRep2Helas3CellPapErng32aR2x75 commit 8d5c6d515556cfc3b048a45465687bdf38089df9 Author: braney Date: Thu Jan 21 02:29:46 2010 +0000 altechRnaSeqSplicesRep1Helas3CellPapBb2R2x75 commit 62bf8b75cc0b27a8dc3d74b8a8b6cfa57a9557f0 Author: tdreszer Date: Thu Jan 21 01:17:48 2010 +0000 Added 17 more submissions for UW DNaseI Jan 2010 freeze commit 40548e75d494c1d098b15cd115e246876c7759d6 Author: braney Date: Thu Jan 21 01:16:27 2010 +0000 wgEncodeCaltechRnaSeqMinusRawSignalRep1Hepg2CellPapBb2R1x75d commit 141ecfa7c87524eacd7f171db4c261ed7167fff5 Author: angie Date: Thu Jan 21 01:03:28 2010 +0000 Belinda's liftOver'd personal genome variants. commit f84e6221f1c61381a6a992589e1f04fb4053832a Author: braney Date: Thu Jan 21 01:03:25 2010 +0000 wgEncodeCaltechRnaSeqPlusRawSignalRep2Hepg2CellPapBb2R1x75d commit ed17caa4e1458b7c94b2db1dce8023595d2835fa Author: angie Date: Thu Jan 21 00:43:18 2010 +0000 Oops, forgot to use < instead of bare < . commit a64975965c1c702cd18c35cfb5e5c57d669a4043 Author: angie Date: Thu Jan 21 00:35:14 2010 +0000 Corrections: Venter and Illumina's Yoruban variants are not just single-base. Thanks Mark! commit bff4e7b55d8de00d150325aadd934d43026dba48 Author: tdreszer Date: Thu Jan 21 00:00:17 2010 +0000 Added 13 submissions for UW DNaseI Jan 2010 freeze commit 5e457b5c78af2acca2d54fa03836f7d4f036742c Author: braney Date: Wed Jan 20 21:53:40 2010 +0000 wgEncodeCaltechRnaSeqMinusRawSignalRep2HuvecCellPapBb2R1x75d commit b0a456ac313534cf800710a35c00f05a028c1292 Author: braney Date: Wed Jan 20 21:48:13 2010 +0000 wgEncodeCaltechRnaSeqRawSignalRep2Gm12878CellPapBb2R2x75Il400 commit 6cfde533a36817f48e05167a05639eea120d600c Author: braney Date: Wed Jan 20 20:29:40 2010 +0000 wgEncodeCaltechRnaSeqRawSignalRep1H1hescCellPapBb2R2x75Il400 commit 5964106d7036be95fd6cc59565a966cf41c6bc26 Author: braney Date: Wed Jan 20 20:21:06 2010 +0000 wgEncodeCaltechRnaSeqRawSignalRep4H1hescCellPapBb2R2x75 commit 7777ddd59681a6d07c775b8b0a63a21bfb331fb5 Author: braney Date: Wed Jan 20 20:13:36 2010 +0000 Caltech RNA-seq HepG2 rep1 single reads commit 4d9d069c824f14aeb0cf053b11a8e1bef87575e4 Author: braney Date: Wed Jan 20 20:06:48 2010 +0000 wgEncodeCaltechRnaSeqRawSignalRep2Hepg2CellPapBb2R1x32 commit 2d4eeedf1772953d6702ba88e752f1df32b53a00 Author: krish Date: Wed Jan 20 20:03:01 2010 +0000 added UW ChIP tracks commit dddccc81f1d718ad7a6b3007857a33ac6960c0e8 Author: braney Date: Wed Jan 20 19:47:58 2010 +0000 add subbGroup8 commit 950b7abc02fd92f573354954a7ceec951689794f Author: angie Date: Wed Jan 20 19:34:43 2010 +0000 Bumped up gwasCatalog's searchPriority, Jim's request. commit 0d221b39c39f1dca29c8d02a41991f9a30475195 Author: braney Date: Wed Jan 20 19:34:25 2010 +0000 wgEncodeHudsonalphaRnaSeqRPKMRep2JurkatCellPapBow10R1x25 commit 360e43b5c066dcbc17dd1c5d0fb0199d9556ffde Author: tdreszer Date: Wed Jan 20 19:17:35 2010 +0000 Added 4 more submissions for Yale Harvard(Struhl) for Jan 2010 freeze. Could this be it for Yale commit 7af24677f75dd2f6bfc2a9fc872c8d95279aa6fc Author: galt Date: Wed Jan 20 19:11:53 2010 +0000 increasing the sizes of lists commit 45dfd1bf96b7ccc949d71f9b426a283219634fff Author: tdreszer Date: Wed Jan 20 19:04:49 2010 +0000 Added 7 submissions for Yale Harvard(Struhl) for Jan 2010 freeze commit 14029ca4d8625cf5aa347ab2547a49faf3600a68 Author: tdreszer Date: Wed Jan 20 18:41:47 2010 +0000 Four more submissions for Yale Snyder Jan 2010 freeze commit 2aecc3a4bcc8a22372d0480781850aa77fa2ab43 Author: ann Date: Wed Jan 20 18:36:11 2010 +0000 commented out featureBits run commit 4744d1c87d7c5eed124d2a4a98387a9d0d9745b5 Author: tdreszer Date: Wed Jan 20 18:24:06 2010 +0000 Three more Yale, this time IFNs for Jan 2010 commit 35607314d49cc69e1c28f18f62e7af6f7c0a7bc9 Author: tdreszer Date: Wed Jan 20 17:50:51 2010 +0000 Three more Yale IgG submissions for Jan 2010 commit 54b056ecd7a224c0a627a1ca6ead8bb58464dfce Author: angie Date: Wed Jan 20 17:45:58 2010 +0000 Added verbose4 message to add customTrash db tables to the output used by the refresh script. commit 862deff449287de0a1f99aa937f02b2ed5e0e247 Author: tdreszer Date: Wed Jan 20 17:31:20 2010 +0000 Added Yale forskolin and insulin submissions for Jan 2010 freeze commit df556c5f84187b06fbd2ce829f96b5515d2f277c Author: tdreszer Date: Wed Jan 20 17:27:47 2010 +0000 Altered 'notes' to clarify 'protocol' commit 94b943bfbd95e49258c4c3968afefcb809968ab0 Author: tdreszer Date: Wed Jan 20 17:26:19 2010 +0000 Minor correction to 'display conventions' text commit 355b690bb4e0f47e8aa810b0ddd441e3a0d1055d Author: galt Date: Wed Jan 20 16:00:04 2010 +0000 "Encode release log update" commit 4484504a6339e659c0a230111cc09b7a2cfa0ac2 Author: galt Date: Wed Jan 20 16:00:01 2010 +0000 "Release log update" commit 37fa8adeba56d2c87e2aabf0b24077e7ac3c018a Author: markd Date: Wed Jan 20 04:32:17 2010 +0000 disable aplCal1 refseqs, since there are none commit 02db0589a2f3d2ab0024889ce6c4e62dd216b1fc Author: angie Date: Wed Jan 20 00:34:52 2010 +0000 Change gwasCatalog color from blue to green (neighboring tracks are blue). commit 6fd48dc3b206506f90c5adc373c32b6fe4283d91 Author: angie Date: Wed Jan 20 00:29:53 2010 +0000 For snp125+, if there is a gwasCatalog table that also contains the SNP, make a link to open the track in hgTracks (like we do for HapMap). commit 40e4577a717e290a3275841239846847e761b568 Author: tdreszer Date: Wed Jan 20 00:06:57 2010 +0000 Added Yale Stanford(Snyder) Rabbit_IgG submissions for Jan 2010 freeze commit 3678062f2a5c82ae6eb560bbc93e3c4bd97dee82 Author: braney Date: Tue Jan 19 23:31:52 2010 +0000 CSHL short (short in K562 cell) alignments and signals commit f134cfbc2911ce24c819894f0ccf2bc054132ebb Author: tdreszer Date: Tue Jan 19 23:28:52 2010 +0000 Added Yale Stanford(Snyder)s musIgG submissions for Jam 2010 freeze commit 447f436b77abb9d02c6cc45f1aed79dc196d76f5 Author: braney Date: Tue Jan 19 23:22:09 2010 +0000 Riken Cage HepG2 alignments commit 7dd02f596049c1be7d1af94d864815423495487b Author: angie Date: Tue Jan 19 23:13:17 2010 +0000 Adding gwasCatalog (NHGRI's Catalog of Published Genome-Wide Association Studies). commit 179109688f0888b185913260364441edaf8d48b6 Author: braney Date: Tue Jan 19 23:12:26 2010 +0000 RIKEN CAGE HepG2 commit 241d284f29df885cb0c64a56da572d255c46ba41 Author: braney Date: Tue Jan 19 23:02:36 2010 +0000 wgEncodeCshlShortRnaSeqAlignmentsGm12878CellShort commit 0eb5647a4fba59e6ad34f1fd29469c147c994033 Author: angie Date: Tue Jan 19 22:57:12 2010 +0000 Adding gwasCatalog (NHGRI's Catalog of Published Genome-Wide Association Studies). commit d2d7275a1f3d6513c304698c6d2843b4c39e20dc Author: rhead Date: Tue Jan 19 22:54:03 2010 +0000 Got a little overzealous on last commit. Changing this back so felCat3 stays in the placental group. commit d201cf46617c014911376eddf79e193869b447c8 Author: hiram Date: Tue Jan 19 22:24:14 2010 +0000 Adding ailMel1 - Panda - Ailuropoda melanoleuca commit 1a5e42a854411a421fa73d208b4267a97e8849ad Author: rhead Date: Tue Jan 19 21:58:21 2010 +0000 Switched all chainFelCat3 and netFelCat3 tracks to be composite chainNetFelCat3 tracks. commit cc39c3db09df7278c6f36cb28e41e9efcdd29504 Author: angie Date: Tue Jan 19 21:44:30 2010 +0000 Added NHGRI GWAS catalog track. commit 37e25343ed93ada9fc6ae553dec568d28b35818e Author: galt Date: Tue Jan 19 21:07:44 2010 +0000 "New version number v223" commit 456527e1d72e1e8ec97576950741b642cddf25d2 Author: galt Date: Tue Jan 19 21:07:22 2010 +0000 v223 final build commit 8dff5afc42b1c04c1b9bd66d33fa27f165042465 Author: tdreszer Date: Tue Jan 19 21:04:15 2010 +0000 Fixed some UCD(Farnham) metadata commit e138883949bbfb066be5d8aed1ceead9710243d5 Author: braney Date: Tue Jan 19 20:37:24 2010 +0000 forgot the big on the bed again... commit c478cd19c5e6a4872dba47e5381e6db5d71de5d7 Author: braney Date: Tue Jan 19 20:35:44 2010 +0000 ENCODE RIKEN CAGE Tags (longNonPolyA in H1-hESC cell) alignments commit c3864251f632f55f148e0d685e19108bf9ddb958 Author: tdreszer Date: Tue Jan 19 20:35:23 2010 +0000 Added Yale UCD(Farnham)s 3 Jan 2010 submissions commit 59ba8bc660d04d373a19d1916cf0b53d057d4892 Author: braney Date: Tue Jan 19 20:27:56 2010 +0000 oops... need a bigBed on that last commit commit 9c7e4978e02119db58110d4d4d95df1a28c864fa Author: braney Date: Tue Jan 19 20:25:39 2010 +0000 ENCODE RIKEN CAGE Tags (longNonPolyA in NHEK nucleus) commit d7d66c61afe5bdb59ebc543adfc6ec0aec512113 Author: braney Date: Tue Jan 19 20:14:22 2010 +0000 Riken CAGE Gm12878Nucleolus signals commit ad70eab877ebba785c899a0d7de356206fff4e47 Author: hiram Date: Tue Jan 19 20:14:21 2010 +0000 adding algBinding tracks commit dcd190b7149e5a3d0f82abec70733e3da24c5bdf Author: braney Date: Tue Jan 19 19:55:46 2010 +0000 ENCODE Riken CAGE H1hESC commit fea99539cd856eea50891c114076d8249e9835a1 Author: galt Date: Tue Jan 19 19:25:28 2010 +0000 handling blank itemUrl commit 12d651c3ab9ba01ea02a643452c278f527c8e290 Author: galt Date: Tue Jan 19 19:17:06 2010 +0000 handling blank itemUrl commit cfb9d2ad94133a1c7bc8d85e8a871e944049c152 Author: ann Date: Tue Jan 19 19:09:53 2010 +0000 added ALG Binding tables to ce tablesIgnored commit 3476d81f2df1c635798211a1d53b254f888ada52 Author: kuhn Date: Tue Jan 19 07:05:10 2010 +0000 moved all canFam2 chainNets to composite and dropped individual tracks. canFam2 hg18 hg19 mm9 monDom4 ornAna1 panTro2 ponAbe2 rheMac2 are live on RR commit a3bd391f3c036ad50a3aff5a459ea88d22dc52df Author: markd Date: Tue Jan 19 06:22:22 2010 +0000 added note on -env option commit 7ce3c0fd9ab9f4e847d7576728962fe8a5a5eb33 Author: kuhn Date: Tue Jan 19 05:57:37 2010 +0000 moved all bosTau4 chainNets to composite and dropped individual tracks. hg19, hg18, mm9, canFam2, ornAna1 are live on RR commit 521a3a5e40d84a39d63e6fe39349ee0c396b2bff Author: kuhn Date: Tue Jan 19 04:24:17 2010 +0000 moved all bosTau3 chainNets to composite and dropped individual tracks. hg18, mm8 are live on RR commit b99e9cd8f90999cc57d0cdd6f321a1e438010eb6 Author: markd Date: Mon Jan 18 23:52:48 2010 +0000 added to-do case commit 69951f154d2074c0b4f7f5a6d5e1c9a7a22251c8 Author: galt Date: Mon Jan 18 16:00:06 2010 +0000 "Encode release log update" commit b17d07b45f5f84e60eaed43d5684eed03ceb0855 Author: galt Date: Mon Jan 18 16:00:03 2010 +0000 "Release log update" commit f7825f96d828bfeff2afb78338b5d490381fd0d2 Author: kuhn Date: Mon Jan 18 07:31:00 2010 +0000 moved all bosTau1&2 chainNets to composite and dropped individual tracks. hg17, mm7 are live on RR commit 1531f0c693770376d7211f2090738817ab6eb39b Author: galt Date: Sun Jan 17 16:00:07 2010 +0000 "Encode release log update" commit 70af40e92021925d18db395ebc21bfe79a46197f Author: galt Date: Sun Jan 17 16:00:04 2010 +0000 "Release log update" commit 5c1aff0e56b58a930a708df1eb1597fb5c40cc62 Author: galt Date: Sat Jan 16 16:00:07 2010 +0000 "Encode release log update" commit 54b0c7eb74ab368b670c5dcc4fca19d3cf2caffa Author: galt Date: Sat Jan 16 16:00:04 2010 +0000 "Release log update" commit a12d96a24b6f285ca13e5f4237338bfee0a0ad5b Author: kate Date: Sat Jan 16 04:30:37 2010 +0000 Restore hyphen for now, for reporting use commit c5c64240b83bbf7d39a45056d7e3614db7c5eeac Author: kate Date: Sat Jan 16 04:24:50 2010 +0000 Fix hyphen problem commit fb835dd9c7f3a19472a3fe8c68025560decb3bf1 Author: kate Date: Sat Jan 16 04:11:23 2010 +0000 2nd cut of Dekker lab files commit b183e3b41a09f7291a77cb0c90aeb9dd98e16e88 Author: kate Date: Sat Jan 16 04:04:10 2010 +0000 Fix hyphen problem commit 6a698acdbaf7fbcab33c5b54e197ae36f2840176 Author: kate Date: Sat Jan 16 03:56:39 2010 +0000 Adjust Dekker lab entry commit 862830e29b6fc1ff442f98fd210a9775d0086369 Author: kate Date: Sat Jan 16 03:37:42 2010 +0000 First cut DNAse validatation metadata files for UW commit 6198bcb2fc1bc572d973fd0484268cbc4c2afeb2 Author: katrina Date: Sat Jan 16 01:00:27 2010 +0000 add aplCal to the gbd variable commit 94dbe0046ead4fd9e1e9b1b69a702ba9996361d9 Author: katrina Date: Sat Jan 16 00:56:58 2010 +0000 add aplCal to the xrg variable commit 8855eae464d6eaf080334888e07e0dfcdbcf1e67 Author: tdreszer Date: Sat Jan 16 00:41:40 2010 +0000 BRF2 is no longer provisional commit e962ca0827d2df1283a0dc2bfa33f6646c01f51f Author: hiram Date: Sat Jan 16 00:39:10 2010 +0000 liftOver to tetNig2 done commit f442ac8fd5fe7c95b82af0164f01a38b1fd52e2c Author: fanhsu Date: Sat Jan 16 00:35:28 2010 +0000 Removed human/hg18/tRNAs.html. This is moved ../.. as a general description page of tRNAs track for all genomes. commit 8cdfcd984c48332592fde28a361d37043ced498f Author: tdreszer Date: Sat Jan 16 00:17:12 2010 +0000 provisionally added BRF2 for Yale commit 49ba141d4c2ed9ee6e7f5b4e7b0b40a02d261fd0 Author: hiram Date: Sat Jan 16 00:07:09 2010 +0000 Adding chromosome definitions for vegaGene on hg19 commit 677bcebbf8365db4d57dab299d685ee14e1e9fb6 Author: hiram Date: Sat Jan 16 00:06:31 2010 +0000 adding hg19 vegaGeneComposite track; commit 19f6bdb59f531ce4ff809ece96ffe123e5d0477a Author: hiram Date: Fri Jan 15 23:49:38 2010 +0000 vega Gene update done v36 for hg19 v37 for mm9 commit 2f0c058484930e5b293db6a55f5cfeed763dbd38 Author: hiram Date: Fri Jan 15 23:47:36 2010 +0000 proper .ra name for vegaGene commit e081ec2719c520fdd96721228d12c941da28aa8d Author: ann Date: Fri Jan 15 23:44:01 2010 +0000 adding tetNig2 commit 656efce7d9498319da62749c2b7c50cf45471127 Author: hiram Date: Fri Jan 15 23:43:32 2010 +0000 finish doCleanup for vegaGene commit f1a568d5941316aa6437683dffdb3903536b54cb Author: fanhsu Date: Fri Jan 15 23:42:26 2010 +0000 Added tRNAs track. commit b91a634abe43403a0474ee44cf0f46837eddd0b3 Author: ann Date: Fri Jan 15 23:34:57 2010 +0000 added tetNig2 to Human Proteins rules commit 93e74af9e6f6fca39923bc67f3deb1c2f08f922e Author: fanhsu Date: Fri Jan 15 23:30:24 2010 +0000 Added tRNAs track for rn4. commit ddfb3b40e6d13cf07b49e1b017b43b57fae77b2a Author: hiram Date: Fri Jan 15 23:19:01 2010 +0000 adding vega gene version identifier to those gene clicks commit f287a888ac4ee9f02d0df9feecee24f80fbcfb43 Author: donnak Date: Fri Jan 15 23:13:37 2010 +0000 Edited this file for typos & style. commit 3483b7f19be34179aea5cbbb59c623c40a52c869 Author: braney Date: Fri Jan 15 22:47:26 2010 +0000 add 1x25 readType and bow10 mapping method commit 14d9fd2531fdaf1980f015a0d294bdcc7f518038 Author: hiram Date: Fri Jan 15 22:25:55 2010 +0000 adding vegaGene processing option commit fc4ea8741fbe898c017496c3d7d1785c22e4c2c8 Author: hiram Date: Fri Jan 15 22:06:44 2010 +0000 appropriate visibility defaults for algBinding track commit a788797754e8560615296e26f1d7032f1526a682 Author: tdreszer Date: Fri Jan 15 21:17:17 2010 +0000 Added TFIIIC antibody for Struhl commit 19766d6d80369c22a377d7e2301f0736d41152ae Author: tdreszer Date: Fri Jan 15 20:09:36 2010 +0000 Added antibody, fixed antibody tags and spelled insulin correctly commit 2aeec3675d911aef72c5eb97ed84b6759693547c Author: hiram Date: Fri Jan 15 18:47:14 2010 +0000 Adding ALG-1 Argonaute binding sites from the Yeo lab. commit c0ed7b00c4472e0609c13f372f79f58fb1cfdae3 Author: kent Date: Fri Jan 15 18:30:25 2010 +0000 Changing README per view-in-the-middle commit 0263e181a1bbb5dc872df495e66fe4bbe8cbd0f5 Author: braney Date: Fri Jan 15 18:21:54 2010 +0000 add insertLength of 400 commit 0d93c92780a3c5e83b61d0eafc71842c638de488 Author: galt Date: Fri Jan 15 16:00:06 2010 +0000 "Encode release log update" commit aef662a3bdd1af25dd0a95e972e9c576a85ddee3 Author: galt Date: Fri Jan 15 16:00:03 2010 +0000 "Release log update" commit 93efc04cfaa51f720af7ef61d0beaaaffff65cdf Author: fanhsu Date: Fri Jan 15 15:37:58 2010 +0000 Added tRNAs.html from Lowe Lab at the top level (applicable for all genomes). commit 4aa90ed45c98542bb5d33dbe33373efb243cf75c Author: fanhsu Date: Fri Jan 15 15:35:30 2010 +0000 Updated doTrnaGenesGb() per Lowe Lab input. commit 0850fadaae303b16eac7c7c9467591dcd9c04f9e Author: jzhu Date: Fri Jan 15 10:02:41 2010 +0000 *** empty log message *** commit 47a685923e925b9a2c53408f0f51db9856aea18e Author: jzhu Date: Fri Jan 15 01:15:47 2010 +0000 *** empty log message *** commit 937acd0d9d41d4d8005ab5c493b1dd30b04b19c3 Author: braney Date: Fri Jan 15 00:14:05 2010 +0000 CSHL short RNA-seq GM12878 K562 whole cell commit 7c9324a769bf3a095b4784e65d393dac29589531 Author: kuhn Date: Fri Jan 15 00:05:16 2010 +0000 changed shortLabel chain and netBosTau1 o_db as it is only on dev commit f6f408f0cfe4866d359b097845bd223982134d03 Author: tdreszer Date: Thu Jan 14 23:44:30 2010 +0000 Finally got the proper description for Nrf1 antibody commit 35822079b42dfbf91278cf9c435319814e327aad Author: giardine Date: Thu Jan 14 23:28:55 2010 +0000 Added personal genome variants that were lifted from hg18 to hg19. commit e0874bb6b804907e89005b3c3f1c8b88fa19bec9 Author: cline Date: Thu Jan 14 23:26:55 2010 +0000 Updated the link for the data release policy commit cc14cbb1a3d942db1c2b9a68e7a7f59658cc7911 Author: galt Date: Thu Jan 14 23:26:10 2010 +0000 more deadline stuff - do not block out admins commit 0b7b25e18e663ff178423ff787dc08c41c6c82b9 Author: galt Date: Thu Jan 14 23:18:28 2010 +0000 temporary workaround for deadline handling - later do something more complete with freeze-date in yml file and handle security better in controller. we were limited by changes that did not require restarting the server commit 77c23b3bdb86782761c2327467b92287b7f0cc05 Author: braney Date: Thu Jan 14 23:06:32 2010 +0000 add RIKEN CAGE plus and minus clusters for HUVEC cytosol commit f1efc8b7677479c6648d30c56238f060a8120181 Author: kent Date: Thu Jan 14 22:36:31 2010 +0000 Making bigBed code in dense mode bypass the fast summary based method if a score filter is on. commit 6205a5eceabaa74e6927a36aac87c72f5f7bb447 Author: braney Date: Thu Jan 14 22:24:23 2010 +0000 RIKEN Rna-seq GM12878 nucleolus commit fca4516679bf4c26a3346112c25388405dd85bfc Author: tdreszer Date: Thu Jan 14 22:23:17 2010 +0000 Added insolin and forskolin treatments for Snyder commit c7157996577c84a794f933fc07d1c9a42d819bc5 Author: braney Date: Thu Jan 14 22:17:57 2010 +0000 Riken RNA-seq HUVEC alignments commit 20b44f044c69e54fc916d7ac9f8c5bf2d4240d1b Author: hiram Date: Thu Jan 14 22:10:58 2010 +0000 add liftOver to sacCer1 commit 0aaded3c4a005aeb5589c64bbe0eb1ade37d49f2 Author: braney Date: Thu Jan 14 22:06:10 2010 +0000 add CalTech RNA-seq NHEK directional 1x75 commit 5e509774462b7655416378470cc3f764ee670c88 Author: braney Date: Thu Jan 14 21:55:28 2010 +0000 Caltech RNA-seq H1hesc paired end commit 3037066650078e6b4e4b24b345b9d5df30528daa Author: tdreszer Date: Thu Jan 14 21:53:32 2010 +0000 Fix to Open Chromatin setting which had a tag problem commit c7161c7be825c77be3f7d318be4c1e028520bb5e Author: braney Date: Thu Jan 14 21:42:33 2010 +0000 fix silly toed typo commit 621ea69404de06907a8581d49f556e3ae4479bcc Author: braney Date: Thu Jan 14 21:40:30 2010 +0000 adding H1hesc directional to Caltech RNA-seq commit 7b83756473c58c0c182678187255c6ac0436286d Author: tdreszer Date: Thu Jan 14 20:36:20 2010 +0000 Fixed a number of problems with cut and pasted special chars (alpha,gamma,etc.) commit 69e3f9e4e4915315cf42e4c3ad058cc24c3e8a42 Author: tdreszer Date: Thu Jan 14 20:25:40 2010 +0000 Added 2 new cell lines for HudsonAlpha commit 51646baa39648929882c6eddafda9a02e7ad9eba Author: tdreszer Date: Thu Jan 14 20:01:05 2010 +0000 Six cell lines from provisional to approved for Stam lab commit 1af215b45e17badf88d15002fcd26e7ea790134f Author: tdreszer Date: Thu Jan 14 19:36:06 2010 +0000 Added 6 new antibodies for Snyder commit c9ae31d5754ee316612169adc87cee98c133fbda Author: kuhn Date: Thu Jan 14 19:30:39 2010 +0000 removed collorabtors who did not add to this assembly commit ef88a54336bef6c56cc3002718eed2ea68c4c836 Author: hiram Date: Thu Jan 14 19:02:36 2010 +0000 adding susScr - Pig commit b3725adc745226d8459683d9f90cc03149918497 Author: tdreszer Date: Thu Jan 14 18:06:23 2010 +0000 How many changes is this going to take until it is correct? commit 29526ddc93d6f1306817a4c8e7465042f8a80739 Author: galt Date: Thu Jan 14 16:00:06 2010 +0000 "Encode release log update" commit 201726a314697aff81a0337334f0e948ed2fa1df Author: galt Date: Thu Jan 14 16:00:03 2010 +0000 "Release log update" commit bd1f4cf1f6392f23a205da28ee4e1ae3f97b258d Author: donnak Date: Thu Jan 14 07:56:48 2010 +0000 Returned zfish article to full length, since it never saw the light of day on the RR in its entirety; also edited the CT article a bit. commit fcf0c082d31a97d1535499d6cdcd10018856b5fa Author: kent Date: Thu Jan 14 07:39:20 2010 +0000 Moving cartOrTdbClosest to library as cartOrTdbString. Making bigBed pay attention to scoreFilter in case where not using linked features. commit b6fc2afda87098a26e2c65c7db50a8d18f481380 Author: kent Date: Thu Jan 14 07:37:39 2010 +0000 Adding cartOrTdbString and related functions. commit 0a1caf841dbd13c4ba144184374d7b54df1aeea3 Author: braney Date: Thu Jan 14 04:03:50 2010 +0000 add 1x75D commit 3d0523942e96d8e6ff5b6f08ccb6e604679e38fe Author: rhead Date: Thu Jan 14 02:48:58 2010 +0000 Updated encode paper. commit 1bf6f5f0b9d444662c305ef28f9b5291251d5a95 Author: rhead Date: Thu Jan 14 02:12:12 2010 +0000 Added encode paper and removed older reference to update 2010 paper. commit 977e62fe31aa2cc47ba95061f2cd45382ca99eae Author: rhead Date: Thu Jan 14 01:47:08 2010 +0000 Removed block for chainFelCat1. This table does not exist in the hg18 db, and there is no reference to it in the hg18 make doc. commit c579ce065c6dd8c87b18784de4ffb258f1348fda Author: cline Date: Thu Jan 14 01:08:11 2010 +0000 added viewLimits settings for the six new Open Chromatin tracks commit d3d0b712bdccd0016b90f496cb9ca9e99f800834 Author: markd Date: Thu Jan 14 01:07:19 2010 +0000 fix compile when USE_SSL is not set commit ca6b89f1914cddefd1d08dde7e9235ef3d89cbf9 Author: hiram Date: Thu Jan 14 00:40:24 2010 +0000 adding susScr1 Pig commit bff9db551e07a89d27c613e31a5b0785d22fd70a Author: rhead Date: Thu Jan 14 00:10:54 2010 +0000 Added update 2010 paper. commit d8155ecaede1d12d32586495a81874ed8520b9c6 Author: rhead Date: Thu Jan 14 00:10:36 2010 +0000 Updated reference to update 2010 paper now that it has been printed. commit aa4019e4c4fcf6f735e456c81809ead8cd8fdb2c Author: cline Date: Thu Jan 14 00:06:56 2010 +0000 Added one more Open Chromatin track commit 33cc3f1be1bf9c084d25b6f143c0480d7178befb Author: cline Date: Wed Jan 13 23:58:11 2010 +0000 Added 6 new Open Chromatin tracks commit 24f00b8229718b7d58c0e49d7935efb3c38871c6 Author: angie Date: Wed Jan 13 23:45:56 2010 +0000 Fixed another old assumption about cookie format that user's cookie has broken: ';' was assumed to always be followed by ' ', but it might not be. commit 57a7fff58b1ceffce4c03c974ba82a7c8f4ed1a6 Author: galt Date: Wed Jan 13 23:09:32 2010 +0000 trying to avoid erroring on temporary cvs lock commit e6e6e37f265bac5f50e8c430fc616fa0b004957a Author: katrina Date: Wed Jan 13 22:16:36 2010 +0000 changed reference to 'Known Genes track' to 'UCSC Genes track' commit dc518f6f2ea0b02d3ebb2737e72fc3624441f449 Author: ann Date: Wed Jan 13 22:13:37 2010 +0000 bumping Zfish off home page, replacing with CT expiration message commit 15b027fbe1530d33d7984cdc93fe2a9dba165512 Author: angie Date: Wed Jan 13 22:05:53 2010 +0000 parseCookies: fixed bug that caused us to errAbort if cookie string ends with ';'. commit 2a5627f22f86ab200d3009f8a9cd596ad09b8f09 Author: galt Date: Wed Jan 13 21:39:47 2010 +0000 removing status superseded commit c687036353dd5cff3144a63225f122836eef99e9 Author: galt Date: Wed Jan 13 21:37:08 2010 +0000 fixing status to handle more post-"loaded" status values, i.e. to treat them as non-active commit 64b7e883670fd8566653eaf6c93782dd5ba7c580 Author: tdreszer Date: Wed Jan 13 21:34:59 2010 +0000 Nrf1 didn't have a type commit 868d2120021f844024d1a875d1d5ab29456c4cf1 Author: galt Date: Wed Jan 13 21:17:11 2010 +0000 somebody wants showd_af and show_ddf even for loaded status commit 0c0a1bd120c6dbdd7db5cbe4f619eb881f71a898 Author: tdreszer Date: Wed Jan 13 20:50:29 2010 +0000 Added Nrf1 as a provisional antibody so that Mike Wilson can get his data in before the freeze commit 589a950b1a9a89c63acad3008ae4cff3c1861e19 Author: tdreszer Date: Wed Jan 13 20:38:25 2010 +0000 Added 9 more submissions (39 tables) for HAIB TFSB commit f533cc8b54705d85942f047c7f0fbedbf8fe6c24 Author: tdreszer Date: Wed Jan 13 19:59:41 2010 +0000 Added 21 new submissions for HAIB TFSB commit 7422e0c6cf37032ae980fe59140a4c64fa92039b Author: angie Date: Wed Jan 13 19:19:52 2010 +0000 Added link to BAM format (thanks Ann). commit b9f575ea0d894ee51e996c36f038b53723148da9 Author: donnak Date: Wed Jan 13 19:04:32 2010 +0000 Edited assembly credits, per Sanger zfish team. commit f7a0dfb2e793170cbb288fa2ee53887f2e9f58d6 Author: hiram Date: Wed Jan 13 18:39:12 2010 +0000 done with genbank for rabbit commit a02da6533ceb8bc0b602e1508bf74cfb77b6e1c5 Author: hiram Date: Wed Jan 13 18:20:06 2010 +0000 running genbank for Wallaby commit 47d4fb84938c0abf4fc425790b64c4ae418013b9 Author: pchan Date: Wed Jan 13 17:48:47 2010 +0000 add description for tRNA genes track commit c4395dd2677e43c72bdf66a1b1a02d3207fe051b Author: katrina Date: Wed Jan 13 17:29:31 2010 +0000 Added aplCal1 to the blastHg18* identifiers commit f4d8925d1ad7198454098532ce89c8b8bd8e1e18 Author: angie Date: Wed Jan 13 17:27:35 2010 +0000 Added option -atime=N: if a session's lastUsed is older than N days, don't refresh its custom tracks. commit 12f928f4cf1b1d0828d4a211a9e9830a4b596a4a Author: fanhsu Date: Wed Jan 13 16:36:56 2010 +0000 Added tRNAs track from Lowe Lab. commit 84c4db4e993c66b01ea40b6c79beacb6e831cd93 Author: galt Date: Wed Jan 13 16:00:06 2010 +0000 "Encode release log update" commit ced061ecb6013d48e9be17126fcc1fbc86b85d5d Author: galt Date: Wed Jan 13 16:00:03 2010 +0000 "Release log update" commit 9794f176835142dd9382e53d68cb3d4e2adf24f9 Author: donnak Date: Wed Jan 13 07:53:17 2010 +0000 Edited the zv8 assembly description. commit c5e96c8265acef8520b48dd478fc3700902185a7 Author: donnak Date: Wed Jan 13 07:51:32 2010 +0000 Added danRer6 announcement, archived an item. commit 6426d0669f0a2de61d07edb44c051e94af2fc590 Author: pchan Date: Wed Jan 13 04:03:21 2010 +0000 add chrom to select tRNA commit 9fe2171be56d3c526c8f4f7a9bd83f4513904a7e Author: kuhn Date: Wed Jan 13 00:47:23 2010 +0000 added danRer6 links to new browser commit fdae70f5a8126c60a61be016af5fc92f554df685 Author: fanhsu Date: Wed Jan 13 00:45:42 2010 +0000 Created tRNAs.html (using another track as an example). Lowe Lab needs to create correct content of this page. commit 4f87c313fdba66f8a6854df0ebadd2de8cef0f79 Author: tdreszer Date: Wed Jan 13 00:26:32 2010 +0000 Added support for the phase variable commit f8abd6b22a6e2e1623d7ba0d58d6f2a6760c4938 Author: tdreszer Date: Wed Jan 13 00:25:07 2010 +0000 Added G1 phase for Stam lab commit cc23111774541e1f65b1d90eab9216a203b576ce Author: tdreszer Date: Wed Jan 13 00:24:39 2010 +0000 Added phase to ddf commit ed23a79dd92f51cedca7b3728133649f23444f47 Author: galt Date: Wed Jan 13 00:19:18 2010 +0000 v223 preview commit 949cd8fe01f1ac6f9968a42adc2dfff6dcab59e0 Author: kuhn Date: Wed Jan 13 00:16:51 2010 +0000 added danRer6 commit 1839e0357cfafef7cd4fba55ddbbdcea1d7874a0 Author: angie Date: Tue Jan 12 23:36:03 2010 +0000 In bamUi, add baseColor defaults to tdb if this is a custom track, as we do in hgTracks.c. Otherwise baseColor drop-down doesn't appear for BAM custom tracks. commit 8d09ea6807f7b2dfa1dbee4d8c045dcc10d698fd Author: braney Date: Tue Jan 12 23:21:29 2010 +0000 a bunch of UW Affy Exon tables, some HepG2 Caltech RNA-seq commit d7d13c35373ee8e983934c3e8f1777baf6df86e2 Author: galt Date: Tue Jan 12 22:36:05 2010 +0000 fixing score description commit bace4ffb7d5d3febc485293601376e5ab56921a8 Author: fanhsu Date: Tue Jan 12 21:09:19 2010 +0000 dded tRNAs track per request from Todd Lowe. commit 00a909c21f10de24b411ce0708127f1230edcbc5 Author: fanhsu Date: Tue Jan 12 21:07:53 2010 +0000 Added tRNAs track process per request from Todd Lowe. commit e4c87ec57aa6cbd01829505668fd9ab5b5d685ee Author: ann Date: Tue Jan 12 21:01:35 2010 +0000 better wording for what it actally is commit a0b2cfd5852fde61aa2c83ccaa6d6c1694f0f194 Author: tdreszer Date: Tue Jan 12 20:58:45 2010 +0000 Change 10 cell lines from provisional to approved commit 8c67dd7db1972d620664dce4c133708882f9b176 Author: ann Date: Tue Jan 12 20:54:14 2010 +0000 a few more exact details commit d692906eec56c85a2589c8d1e67109e12f9307d4 Author: kuhn Date: Tue Jan 12 20:50:33 2010 +0000 changed output text a bit commit f898d722a50da081c018a1a82ab0cab114d077ad Author: markd Date: Tue Jan 12 20:22:23 2010 +0000 added change descriptions commit a100884146d72c4e332ab18099cf3e5a8a6e4ff8 Author: markd Date: Tue Jan 12 18:56:49 2010 +0000 added include of common.c commit b135bfefd809ba16194174c220249db5a8622fe8 Author: markd Date: Tue Jan 12 18:48:55 2010 +0000 change version number commit 92d7ac486dfd160ee37234f5c34f4cd3790cee20 Author: markd Date: Tue Jan 12 18:48:12 2010 +0000 remove trailing / and /. to fix common problem with -batch option when doing name completion commit 2c17bdb8ccce2576eb5c831188fe862c302f8291 Author: tdreszer Date: Tue Jan 12 18:19:47 2010 +0000 Missed GM12872 in earlier ci fo cells for Stam commit e2bf830ae6a3589f8b5869e31de320ab8ee54a7b Author: markd Date: Tue Jan 12 18:16:27 2010 +0000 added horrible hack so it's possible to distinguish between warning and errors in the warn handler commit 02b22fccadf1c286503dfd893fb1f1c6ea6714f0 Author: kuhn Date: Tue Jan 12 17:28:29 2010 +0000 changed shortLabel for chainNetDanRer6 to o_Organism, as it is the latest and should not use db name commit 026a09a1b4055a014930921e06f654a89dfca30c Author: galt Date: Tue Jan 12 16:00:07 2010 +0000 "Encode release log update" commit 41eeb12b86de27dd4d1413e216343f98044f2cc0 Author: galt Date: Tue Jan 12 16:00:04 2010 +0000 "Release log update" commit 4f6f4cf7ce45961762579baeeb7c39241e456912 Author: markd Date: Tue Jan 12 09:09:15 2010 +0000 add option to set minimum log level, move some logging to debug commit df7b9ac43560dbf1d1e8eca49cde3ceb0cac8886 Author: markd Date: Tue Jan 12 09:06:24 2010 +0000 added support for setting minimum priority to log commit d0f585bdf794ab151a90e0b9e3314502c50e5243 Author: kate Date: Tue Jan 12 03:02:20 2010 +0000 Create md5sum.txt file commit 67b1803e77457f2088a96d6faa4c95a116692eb1 Author: kate Date: Tue Jan 12 01:08:03 2010 +0000 Expand support for versioning. 1. Add V? to metadata column in projects table. 2. Add versioning comment -- newly required field (dataVersionComment) in DAF commit 7e9808a28940cd544943bbd4db915b4cac7f3544 Author: kate Date: Tue Jan 12 01:05:26 2010 +0000 1. Add new field for versioning comment. 2. Fix typo. commit e854351a76ce1e0401757e8471fbbfed751f1a86 Author: ann Date: Tue Jan 12 00:16:00 2010 +0000 adding links to two new pastable examples commit 7ba516cb787e22d33fedb06fbffe81fa366a2c6d Author: donnak Date: Mon Jan 11 23:31:27 2010 +0000 Archived an item, added 2010 link. commit a918d3b266645db4ffdcf0476dfd0a459a9515b7 Author: donnak Date: Mon Jan 11 23:19:32 2010 +0000 Added zv8. commit 1d5d57c57f8ad819611dc93a1080bf5725129b3a Author: aamp Date: Mon Jan 11 23:14:15 2010 +0000 File had weird 775 permissions instead of 664 commit e37627f666a3cb2865900791e9e44443d0c0fcc5 Author: braney Date: Mon Jan 11 22:23:14 2010 +0000 change dimensions back for UwAffyExon commit 2aceccb7d34c1dc6db8308cc2440d789b5c0258f Author: ann Date: Mon Jan 11 19:46:38 2010 +0000 directing users away from our ML, and adding an easier-to-use example. commit 7ebc0b4c9071c84a54e780dbd5f6a77a7a45886f Author: braney Date: Mon Jan 11 19:38:46 2010 +0000 Uw Exons, change dimensions, add Skmc rep 2 commit 396e553fce356351d826649bc77cac1d59d46b2a Author: cline Date: Mon Jan 11 18:54:48 2010 +0000 Added a news item on Release 2 of the Open Chromatin track commit d95070f1c5b4a6b92cbd2513e1a66fe93fb87b69 Author: angie Date: Mon Jan 11 18:34:25 2010 +0000 Added read name (wasn't obvious!). Added overall position & size for paired reads. commit 8a4ec26a72758e52715125125b89bfa97b2bbede Author: kent Date: Mon Jan 11 18:25:47 2010 +0000 Rescuing conservation track and others that have "subTrack parentTrack on" rather than just "subTrack parentTrack" commit 29bc186167f8ba3d6b7962819782c24ec9cee552 Author: ann Date: Mon Jan 11 18:07:13 2010 +0000 just formatting to 80 chars, where possible. Not always possible with the PRE tags. commit 41ae5ee7af2f20668d321d2b1c55b98db9dac305 Author: angie Date: Mon Jan 11 17:52:10 2010 +0000 Changed some errAborts to warns so BAM track connection troubles don't prevent display of other tracks. commit fe1b218ec2886057f0869e242ca8e924bea3dcf4 Author: tdreszer Date: Mon Jan 11 17:45:07 2010 +0000 Inputs have replicates commit 9dbf117e4c72243c3d84bd2d9d95274b9991c977 Author: tdreszer Date: Mon Jan 11 17:30:58 2010 +0000 Added 5 new (provisional) cell lines for Stam and 4 new antibodies for Snyder commit a6a6bee64a340c16aa73363fdb7fec514e8021ec Author: ann Date: Mon Jan 11 17:18:49 2010 +0000 two tweaks commit f244ac7cf0db1d734e5e060be5b22a6ffddc14ee Author: galt Date: Mon Jan 11 16:00:07 2010 +0000 "Encode release log update" commit 2a9bb9a9b12693abad02c35ac3e0e1a76d814ba7 Author: galt Date: Mon Jan 11 16:00:04 2010 +0000 "Release log update" commit 4df4b844db962f468bb5d73595fde622b4e49135 Author: galt Date: Sun Jan 10 16:00:06 2010 +0000 "Encode release log update" commit 09f5a2089071ec60878ccb3ef3f08abe2c02460d Author: galt Date: Sun Jan 10 16:00:04 2010 +0000 "Release log update" commit 377edb72928a5a64a1baf5fab1bfe43a617c6d9b Author: angie Date: Sun Jan 10 07:13:53 2010 +0000 Removed mention of https because udcFuse is not yet ready, and it's time to release BAM with samtools' basic network and index-file-caching code. Also, for example one, use local http file instead of NCBI ftp server (ftp much slower). commit 4e06132a89936484c957e4aa508b589761d2e910 Author: braney Date: Sat Jan 9 21:18:52 2010 +0000 HAIB methylSeq H1hESC submission 887 commit 983a00b71771df9ddc2f6a3116f2bc3255187135 Author: braney Date: Sat Jan 9 21:07:39 2010 +0000 HAIB methyl seq HepG2 and HeLa-S3 commit 9266bf0ced57d15fe52973cd83f819e812fa3d5c Author: galt Date: Sat Jan 9 20:54:15 2010 +0000 release alpha/beta was broken. Now that closest-to-home has gone away, it was very easy to implement very-early release pruning, followed later by pruning of orphans with no parent of the correct release. This keeps the code pretty simple which is nice. commit e2d0f3cd0cbee3e5503c5d0afc71e8a24a166cb6 Author: galt Date: Sat Jan 9 16:00:07 2010 +0000 "Encode release log update" commit 994b42c43fe738cfe9951d108ec9e12bef43a29c Author: galt Date: Sat Jan 9 16:00:04 2010 +0000 "Release log update" commit 6707a21e99639ff6610ba85aa0c584d4995f3356 Author: galt Date: Sat Jan 9 05:40:08 2010 +0000 add clean target commit 6f753f96153a4f8cbeced1f0d2cdd541e3d8a295 Author: galt Date: Sat Jan 9 05:27:58 2010 +0000 add clean target commit 90759b71482fcf7340db204bb2ac20c901832dff Author: tdreszer Date: Sat Jan 9 00:35:58 2010 +0000 Insignificant change to UMass Uniqueness settings commit 3ae07a021e86e94db4fa91f87d5f31a795c25575 Author: tdreszer Date: Sat Jan 9 00:32:56 2010 +0000 Added Rabbit_IgG for Snyder commit 0e3ab18037cb0561420088990fc960a4131c457f Author: hiram Date: Sat Jan 9 00:28:46 2010 +0000 finishing off tetNig2 and into the pushQ commit 87e6f01b5c3893d7b4eba92af5d15c0ff6e832b5 Author: hiram Date: Sat Jan 9 00:07:01 2010 +0000 fix up some chain net confusion and beginning to get ready to use composite settings commit f36aeba74b13976a9d5ff5d377fdd560323feedb Author: markd Date: Fri Jan 8 23:52:49 2010 +0000 fixed use on incorrect variable that caused ideogram to be trancated when label width was increased commit de8dc6549be9ea346ba012dd2f615d86e35a11d7 Author: markd Date: Fri Jan 8 23:50:44 2010 +0000 fixed broken indentation commit 05978a9aabdc046a23ed635f57fe1580d3963184 Author: angie Date: Fri Jan 8 22:57:31 2010 +0000 Example Two refinements. commit 36ece719afdf273d6899ccfc9a94ebe7bd9a12bb Author: braney Date: Fri Jan 8 22:11:25 2010 +0000 check for table existence using tableExists instead of looking in trackDb commit c6efd3aae04f42be6ee13faddb5e6a139858d7be Author: cline Date: Fri Jan 8 20:53:20 2010 +0000 Minor grammatical tweaks commit 4107d0d27ada34fc009ca268d4ded780d8e81050 Author: cline Date: Fri Jan 8 20:35:24 2010 +0000 Cleaned up an over-texty link commit 4f0bb2dd9ac3612af4d214a5995a75fe299f1c20 Author: cline Date: Fri Jan 8 20:28:25 2010 +0000 Added a hard rule to the end of the Jan 6 news item in index.html. Modified terms.html according to the revised data release policy. NOTE that thelinks at the bottom of the page are not current, as the new policy doesn't seem to be up on the pageODE project paqe commit 8012fc6c2e7f8c9ce81e54ce374ecbccabb8c0dd Author: angie Date: Fri Jan 8 20:12:31 2010 +0000 Oops, forgot that SAM generated by aligners may not be sorted -- so sort before indexing. commit d860fae33bf29e8cd9440d97f068cf245fc693c5 Author: ann Date: Fri Jan 8 19:50:27 2010 +0000 Added blurb about label area width. Fixed default image width (620 -> 800). commit 0c498b401c6bdb76f3ce59feab31dcfb03d9d009 Author: rhead Date: Fri Jan 8 19:45:47 2010 +0000 Made UT-Austin STAGE track part of encodeUtexChipSuper per Kate. commit 839160e2c33c6f4cf5ab0b906651d0d8e8c745dd Author: katrina Date: Fri Jan 8 18:52:36 2010 +0000 shortned the short labels for the three recenlty added snpArray tables because they were more than 16 characters commit 9f99b9d39d6829b87bba84d3a6a71880fc4bdf9e Author: tdreszer Date: Fri Jan 8 18:44:59 2010 +0000 Changed name of treatment commit d8aa09d37c18e74390ce0b0b97def99a1ad9aaae Author: tdreszer Date: Fri Jan 8 18:41:05 2010 +0000 Added 5 new cells (3 provisional), 1 new antibody and 1 new treatment commit 2678e8703371c1535c2d1b84d42cb25c4e955d2b Author: fanhsu Date: Fri Jan 8 18:39:37 2010 +0000 Moved 3 new Illumina SNP array entries from snp129 to snp130. commit 3f61c6e7d05784a23cd3fa5479903864b250fca6 Author: rhead Date: Fri Jan 8 18:37:42 2010 +0000 Moved from hg18 level now that the tracks are superTracks on hg16 and hg17. commit 8829034f55b3f49fdb59db87e5cbf9ce0b8afc9a Author: braney Date: Fri Jan 8 18:26:27 2010 +0000 added subGroup7 commit 36559e3d2f1af8fd4625013367dd4dc9daf6af2e Author: braney Date: Fri Jan 8 18:23:23 2010 +0000 remove release alpha from HudsonalphaRnaSeq composite header commit ebee3e5f1d1074013fd6eebba39df80bd979bc26 Author: angie Date: Fri Jan 8 18:13:41 2010 +0000 Removed a little verbosity in BAM section. commit 777eb877822cf33cf451657698e4dc1c05da86a2 Author: angie Date: Fri Jan 8 18:11:02 2010 +0000 Added BAM config help link (if file exists). commit 2cdddcf8daf7777e11ff45b7023d44c924cc95ba Author: angie Date: Fri Jan 8 17:34:04 2010 +0000 Tweaked example one track line for better initial display. commit 08476fc5ffb16d784c944c33f0f4c28b28a1fc3c Author: fanhsu Date: Fri Jan 8 17:27:41 2010 +0000 Added 3 new Illumina SNP array entries. commit d30bfcfc1508cc3b71372ec05bbb5077b1711de4 Author: galt Date: Fri Jan 8 16:00:06 2010 +0000 "Encode release log update" commit b09958694511c7b8fc52ff6851799e46bd706e91 Author: galt Date: Fri Jan 8 16:00:03 2010 +0000 "Release log update" commit 719230f0818b625ed1161f29cd7493d55f36376c Author: markd Date: Fri Jan 8 05:04:56 2010 +0000 added ignored entry commit 3e8805f13cf721af097316e6aeb664ce72204a5b Author: angie Date: Fri Jan 8 00:40:10 2010 +0000 Added section describing BAM format. commit 84a3f4d2c9f82a32052149c0fb81ac6d7768e8a4 Author: angie Date: Fri Jan 8 00:39:44 2010 +0000 Added reference to BAM custom track doc page. commit 1b117c317259b62410815120346033f7ba971ddf Author: angie Date: Fri Jan 8 00:39:01 2010 +0000 Corrected some link targets so redirects aren't necessary. commit dced8e208e83343982a0aa42285f82328a384516 Author: angie Date: Fri Jan 8 00:38:14 2010 +0000 First draft of BAM track doc. commit c7ebb8384a8a1f69df023f6eae2ce914f9d9b9d9 Author: braney Date: Fri Jan 8 00:28:29 2010 +0000 change Caltech signals to use autoScale, per Georgi commit 0c8483c90540156a522731b094b04b8de66aa908 Author: markd Date: Thu Jan 7 23:49:29 2010 +0000 added configuration option for the width of the label area commit 4433d33d9f7db845191bf3e595197924f20d2814 Author: tdreszer Date: Thu Jan 7 23:30:05 2010 +0000 restrictionEnzyme cv term should support control terms commit b8254eaff0506bb9708893d4515aa99e9e9abf5a Author: tdreszer Date: Thu Jan 7 23:29:13 2010 +0000 Removed restrictionEnzyme 'None'. This should be done by controlled vocab commit b6fee8e68a96173dda1ce4b7ac4f3c6c1abbf57e Author: braney Date: Thu Jan 7 23:27:49 2010 +0000 add Myer's lab RNA-seq commit 76aab83a263d03a43a63e34ccfc7507bb71bbe4d Author: larrym Date: Thu Jan 7 22:39:42 2010 +0000 add longLabel tooltips for links in track controls; change order of css includes in CONTEXT_MENU code commit 61cecd7a4b268e366ce3edd0e1b57f5fa093f2aa Author: rhead Date: Thu Jan 7 21:19:24 2010 +0000 Removed alpha/beta block on affyTxnPhase2 that was not doing anything except keeping trackDb from loading correctly on make strict. commit bb4f9c6cf42c119b0d8216782f8dc10c05118341 Author: rhead Date: Thu Jan 7 20:47:49 2010 +0000 Added note about renaming mm8 jaxQTL table to jaxQtl. commit 52075e1f16687289479ecbb354fa7e9ec4fa6bf8 Author: angie Date: Thu Jan 7 20:44:50 2010 +0000 Resolved some strict regex warning from checkHgFindSpec -checkTermRegex mm9. commit f7c0b19446e7d37055fd32f195bcd35496f54dbb Author: tdreszer Date: Thu Jan 7 20:23:43 2010 +0000 Cleaned up some extra tags in Open Chromatin commit 86207eebfeb64516f82a1a9a75831efabf13f997 Author: tdreszer Date: Thu Jan 7 20:06:56 2010 +0000 Reorganized Open Chromatin and Duke Affy Exon commit 4dfbbe56b5200c8a78fc7a6b0303376a5a2f8c23 Author: angie Date: Thu Jan 7 19:53:45 2010 +0000 Fixed comparison edge condition (not a huge problem, it just set tv_{sec,usec} to {0,1000000} not {1,0}). Thx Galt for pointing out that the net.c code was dupl'd from this. commit 50d4c7db73171433b5a4e6c6f088e734b9d6124f Author: markd Date: Thu Jan 7 19:13:44 2010 +0000 make tab file load functions for structs of type object commit db0c9bc663c198b97e4dc4dc9cdf9a81b17c2681 Author: braney Date: Thu Jan 7 19:05:33 2010 +0000 Caltech HepG2 non-directional commit 4fa70554228e9b9cbfe540fa0cc025ee2a931dcc Author: angie Date: Thu Jan 7 18:35:16 2010 +0000 Oops, copy-paste fix. commit 1b292895028a4167f76363a1295efb554a27dc83 Author: braney Date: Thu Jan 7 18:09:46 2010 +0000 calTech RNA-seq GM12878, K562 two replicates, directional commit 8fe9b6b671b62911ca0b70817581b46948a67805 Author: galt Date: Thu Jan 7 16:00:06 2010 +0000 "Encode release log update" commit e9408ef57bb6f9b8076df52b2207197a2e9b1cdd Author: galt Date: Thu Jan 7 16:00:03 2010 +0000 "Release log update" commit 8c6bdc5667f2f7ad4c9d05facaccf77470d6af17 Author: pchan Date: Thu Jan 7 02:56:48 2010 +0000 add code to display GtRNAdb links for tRNAs track commit cba039cefdfd7cb2c4101d672dbd46e739df5538 Author: pchan Date: Thu Jan 7 02:54:53 2010 +0000 add fields for GtRNAdb urls commit f754222905c9cc440f87ced4af07170ff83c31a8 Author: kent Date: Thu Jan 7 01:35:19 2010 +0000 Fixing indentation. Removing an unused define/ifdef. Adding braces for readability in a couple of places. commit 9adf65d50dfdc5eaa6f245559adb35bc15c20f1e Author: cline Date: Thu Jan 7 00:40:56 2010 +0000 Added three January news items commit 9c6f908add47cdf54e0a633967bebfba1d6c2622 Author: tdreszer Date: Thu Jan 7 00:24:05 2010 +0000 Big change to Open Chromatin, due to adding 77 tracks for Jan 2010 freeze. Made alpha and beta versions of entire composite commit 196283e06d9c96b899d237107669b0cdd931778c Author: hiram Date: Thu Jan 7 00:09:35 2010 +0000 tetNig2 now fully enabled commit f656ee0815a8a2d12024c4ffe3f78a2d635ab13c Author: markd Date: Wed Jan 6 23:44:43 2010 +0000 disable tetNig ESTs as there are not any commit c7a3a8a1b419cc2454a3259cdc3a56b6e21b8546 Author: hiram Date: Wed Jan 6 23:21:49 2010 +0000 fixup chainNetDanRer6 for tetNig2 and gaze track for both tetNig1 and 2 commit 0acbbb0b78369eb7755f642646ee1203a2f69922 Author: ann Date: Wed Jan 6 23:20:13 2010 +0000 updated script to use the tdbQuery tool to find the trackDb.ra block(s) in which it is specified commit 0711ec272be47363d2e6cb2ebce9282528b451f1 Author: braney Date: Wed Jan 6 22:56:30 2010 +0000 add some explanatory text commit 1acbc0c1cf65c4767d59b5ac49564947765a6603 Author: angie Date: Wed Jan 6 22:49:11 2010 +0000 search spec for IKMC (komp): made regex a bit shorter, and inclusive of both old and new names. Added a prefix search so the items with new suffixes can still be found by gene name. Thanks to Katrina for finding that this was broken & fixing it for new names! commit 2ee83d860b3b05a87652e34bf9547ae3b5db1e39 Author: braney Date: Wed Jan 6 22:28:29 2010 +0000 list all elements that satisfy the query criteria, not just the first one commit 367c3b23d1a7709692ba6a080bb0275e5bf439e8 Author: angie Date: Wed Jan 6 21:59:47 2010 +0000 Corrections from Katrina. commit 47a93afd7a906cf376e7037502607b817148610b Author: angie Date: Wed Jan 6 21:59:18 2010 +0000 IKMC (komp) update. commit 990e133ed06799b26d3140f6a9b71c3b177f7610 Author: hiram Date: Wed Jan 6 21:48:19 2010 +0000 the track hash was not accumulating track names twice when necessary commit 1422c92f6d872d04ffb5afc6a027ce446f68b343 Author: kate Date: Wed Jan 6 21:45:10 2010 +0000 Add entry for ENCODE reporting commit e3cddd8897ac5928700a44b8f3635644b5877b7a Author: braney Date: Wed Jan 6 21:21:30 2010 +0000 None for restrictionEnzyme. Some new readTypes commit d61a0a95cd507071a0abba2701f3ac07cc98a810 Author: markd Date: Wed Jan 6 21:09:19 2010 +0000 fixed parsing where blastp wraps Identity line commit c439698222a6e0b5b3196b20019f31ec82890423 Author: ann Date: Wed Jan 6 20:12:20 2010 +0000 adding searching for CA Condor track commit 53f5af37fa4de6feb15f0cec2cd05758407dd4e1 Author: braney Date: Wed Jan 6 20:09:19 2010 +0000 add Duke Affy Exon Array composite commit f37c8f29494a871355b7900fea1fca912437c917 Author: hiram Date: Wed Jan 6 19:09:37 2010 +0000 Adding some verbose 3 on the pruning business so it can be watched commit d663d1846924606ba9057c1568ec14d16a4e0854 Author: tdreszer Date: Wed Jan 6 17:45:48 2010 +0000 Added 8 submissions worth for Yale (used new encodePatchTdb) commit ccde7b9c7180142e592aaa7f83825bea379e7652 Author: galt Date: Wed Jan 6 16:00:07 2010 +0000 "Encode release log update" commit 141918a36237c3f667dbd25d896b4820a37a45e2 Author: galt Date: Wed Jan 6 16:00:04 2010 +0000 "Release log update" commit 0b64d3f19cb31baceee42b457823a82ce4284f8d Author: ann Date: Wed Jan 6 01:41:28 2010 +0000 typo (thanks Brooke) commit ff18e1369b46916fb753bcc900fb36f3b35cda94 Author: tdreszer Date: Wed Jan 6 01:02:52 2010 +0000 Added 4 antibodies for Snyder lab commit 32144a2e8787f4e7d47ff602807872eda1c266cc Author: kuhn Date: Wed Jan 6 00:55:50 2010 +0000 turned on danRer6 commit b567ac43fadf37ffd34d81d7710ff386b196ac1c Author: angie Date: Tue Jan 5 23:10:35 2010 +0000 doHapMapSnpsAllPops: don't warn about differering alleles if one is the empty string -- in older hapmapSnps (phase II) tables, allele2 was empty when homoCount2 and heteroCount were both 0. commit 0638b88dbfc13e2edb300d97511925a153adf7f6 Author: kent Date: Tue Jan 5 22:16:44 2010 +0000 Utility to convert wigs to bedGraphs seems to be working in basic tests at least. commit c71ab3e7e69e68f8c4e5e33f23c85077a6bd4b13 Author: kent Date: Tue Jan 5 20:25:37 2010 +0000 Removing some unused code. commit 56f681f6a53d1f007e9b2b2fff081451b9e965ce Author: kent Date: Tue Jan 5 20:20:04 2010 +0000 Adding another test case. commit 58a32990a601b776930c2472d2a58b6c2fdc7ef6 Author: kent Date: Tue Jan 5 20:15:45 2010 +0000 Fixing stanza merge problem when there is no line before stanza in patch file. Fixing replace eating a stanza. Making replace just comment out old stanza by default, but there's a noComment option. Putting in test suite. commit 91142f8017111bc1506ab2898463a0da10de30e0 Author: angie Date: Tue Jan 5 17:32:07 2010 +0000 In debug message, cast pointer to 32-bit unsigned instead of 64-bit so it doesn't break the 32-bit build. commit f745647f15beafe9522524e1350d680b154ad1d7 Author: galt Date: Tue Jan 5 16:00:06 2010 +0000 "Encode release log update" commit 7e15b46b9566d625558e0019d83063728fff7acb Author: galt Date: Tue Jan 5 16:00:03 2010 +0000 "Release log update" commit bff49bfafd220beed431d275a52fa30c59ddc34d Author: kent Date: Tue Jan 5 05:39:14 2010 +0000 Getting rid of unused command line options. commit 7dddd00ab9a17c9e05bc36b59ff33d0a2ad3f305 Author: angie Date: Tue Jan 5 05:36:26 2010 +0000 Oops, don't use global var position -- when we zoom, that is not updated and still has the old pos. Use chromName:winStart-winEnd instead (samtools uses 0-based offsets). commit 636c2a6e5347e509efbc29dd2e8f8880ac46131b Author: kent Date: Tue Jan 5 05:34:27 2010 +0000 Removing unused routine. commit b8ee2baa1158784cf028b69bea2ce3e8c13bda33 Author: kent Date: Tue Jan 5 05:31:25 2010 +0000 Implementing mode=replace commit b01d3efef89934509d8cc47b84ae92a361274f3d Author: kent Date: Tue Jan 5 04:59:58 2010 +0000 Making it ignore parent track in patch.ra. Also making subTrack point to view instead of parent. Making indentation work. commit 81eecf4230202d97df12f2276d131002662e9bdf Author: galt Date: Tue Jan 5 04:49:17 2010 +0000 "New version number v222" commit bc3786041260fc36a071e77d3f7dc7acf559b824 Author: galt Date: Tue Jan 5 04:48:30 2010 +0000 v222 final build commit 22295834f6c498f03fff3bf9a5711441e2c2c700 Author: galt Date: Tue Jan 5 04:15:46 2010 +0000 trying to deal with new cvs version where cvs diff no longer supports non-existent revision 1.0 as a magical previous for a new file commit a9a201897ff7ea045fea8ce8960aff665a3307c7 Author: galt Date: Tue Jan 5 04:13:11 2010 +0000 minor cleanup commit 40f1e9f5a05b48d280c83cff0ff8bf0138c24822 Author: hartera Date: Tue Jan 5 03:04:20 2010 +0000 Changed data for Burge RNA-seq track to BED format. Moved Exoniphy trackDb entry to human level trackDb.ra file. commit 04583b730a193152d2e82d38b30a431c1c9bf2a3 Author: donnak Date: Tue Jan 5 02:37:56 2010 +0000 Removed vacation msg. commit ebbd3a8b9e911ab9d78b83ea8459de6b45de90f4 Author: galt Date: Tue Jan 5 02:34:46 2010 +0000 added output to display command executed commit 75e0d6621157d4e82773f6a36b32d5a560ad8d3a Author: rhead Date: Tue Jan 5 01:37:46 2010 +0000 Quick fix to keep TrackCheck from choking on supertracks. commit 4398e44fc6017f74f7968dc9bf24b7ae99637835 Author: hartera Date: Tue Jan 5 01:16:11 2010 +0000 Changed Burge RNA-seq track data type to bed 12. commit 32a010cca59cc742635b3b1d2e6fa212cc45ea25 Author: hartera Date: Tue Jan 5 01:14:06 2010 +0000 Documented changing Burge RNA-seq data format to BED and re-loading tables. commit d60139a39a23ef23fc1dfd29859030fe177912d0 Author: angie Date: Tue Jan 5 00:39:06 2010 +0000 Make empty directory appear to be non-existent, so udcFuse doesn't get confused by an empty dir becoming a regular file (i.e. udcCache dir with bitmap and sparseData). commit d17e91289f3cd6e69dbffff0ec732b5de69bb1cf Author: angie Date: Tue Jan 5 00:34:49 2010 +0000 pairSearchRange can yield many items that are completely out of the window. Exclude those from tg->items so they don't inflate the item count and scare us off of making map links. commit b6738caf65083655c4ded6008cf0ab15c109c593 Author: tdreszer Date: Tue Jan 5 00:10:21 2010 +0000 Added antibody ZNF274 for Snyder lab and reordered a couple of antibodies commit cd8e4186ca64104336f68fcdc055813032956e11 Author: kent Date: Mon Jan 4 23:54:31 2010 +0000 Removing jaxQTL, which had a name conflict with jaxQtl commit 45487e6460a8838fd68ebdb345cee3329051db91 Author: braney Date: Mon Jan 4 23:44:34 2010 +0000 fix up some GIS Pet tracks that were total not longPolyA. Also remove reference to wig files for signals commit e9655d875a3cf96f4bce939e5f2488bb0d7d651d Author: tdreszer Date: Mon Jan 4 23:43:18 2010 +0000 Altered 'pending' cell lines to put '(provisional)' in description. commit 5d1c8201bf42194f54619e997435966f70d0c1e4 Author: tdreszer Date: Mon Jan 4 23:38:22 2010 +0000 Added 10 provisional cell lines for Stam lab commit 9f778a5a1749486d91ce415c7adb962a26b26813 Author: hartera Date: Mon Jan 4 23:25:10 2010 +0000 Removed exoniphy entry as the exoniphy track has been added to human level as trackDb entry is the same for all human assemblies. commit 7d21098473955e44dbd02f6c21e34e7822f4185f Author: hartera Date: Mon Jan 4 23:22:11 2010 +0000 added exoniphy to human level as trackDb entry is the same for all assemblies. commit 71a04266296cbc60c2f72f1e7266b9dc7473f19a Author: galt Date: Mon Jan 4 22:56:20 2010 +0000 v222 preview commit 995420bf445e8a3ce79db3f7abbdb20dd4f3b650 Author: ann Date: Mon Jan 4 22:39:19 2010 +0000 added table to galGal ignore list commit 0daa910a4809c2bbfa025b3acf95109623e93938 Author: ann Date: Mon Jan 4 22:19:32 2010 +0000 a few more tweaks commit e836565c31b6a9602b850bdb36cdc9be9ae63f35 Author: braney Date: Mon Jan 4 20:27:41 2010 +0000 fix some strings commit c3f39c2dac0148e744deecee20c6ab4fa2518505 Author: hiram Date: Mon Jan 4 20:27:01 2010 +0000 Need release alpha and beta on Mm5 commit c2a8a8d44770e38c45af9530d5849431fb488c68 Author: braney Date: Mon Jan 4 20:12:55 2010 +0000 change tag for longPolyA commit 996b8619c583426adc52500457a17f8a49052bce Author: ann Date: Mon Jan 4 20:02:48 2010 +0000 initial draft of changes commit 155c4e7c4654609db81109e9c6814555d09eb128 Author: hiram Date: Mon Jan 4 19:59:35 2010 +0000 some more edge clean up of chainNet composites for hgwdev commit 1c3118785cdad6ec89a01b00f0a26b5d32e0f2ec Author: tdreszer Date: Mon Jan 4 19:54:11 2010 +0000 Added 14 new tier 3 cell lines for Snyder and Stam labs commit b2c4e9d849cc1f2c2dad662e2f75951bfc7265c1 Author: braney Date: Mon Jan 4 19:52:12 2010 +0000 add 1x75 commit d6a87784d54df6d85aaa55437acc59b0b2898a51 Author: braney Date: Mon Jan 4 19:48:26 2010 +0000 add new maapping protocol commit 54ff0ffb7101bf2dd814df24342a3f765bb14d5b Author: braney Date: Mon Jan 4 19:42:51 2010 +0000 add new mapping algorithm BB2 commit 8761cd9c6e4c076ff5661976ca70a8ee0b34b04e Author: kent Date: Mon Jan 4 19:12:41 2010 +0000 Merging viewInTheMiddle branch. commit 6f94991964bf5b50791df0353e02d1431ec0d332 Author: angie Date: Mon Jan 4 18:24:53 2010 +0000 LiftOver to danRer6 commit 85bb8d9ec121113aeec36bf6dda0223c3785f50f Author: ann Date: Mon Jan 4 17:12:03 2010 +0000 these links require logins -- so, we are removing (ok by Kate) commit 935a3608c49063acc9ae03085721c3eb3555d4e2 Author: galt Date: Mon Jan 4 16:00:06 2010 +0000 "Encode release log update" commit 58577450c9ddf4fe55615b1e3844f90c22ac79c8 Author: galt Date: Mon Jan 4 16:00:03 2010 +0000 "Release log update" commit ed748a308dd44012715c0731a963e6ceb1ff17f8 Author: galt Date: Sun Jan 3 16:00:06 2010 +0000 "Encode release log update" commit e2eb238bcf4aa47f9fb3fa61d98f6d0cf4361e05 Author: galt Date: Sun Jan 3 16:00:03 2010 +0000 "Release log update" commit d730c6aab7c77ad32981db4623b7ffbd3ec283ac Author: markd Date: Sun Jan 3 07:42:33 2010 +0000 change content-type for DAS results to text/xml commit 8fe937ffc625ca3a2224ec85d631e946c060f691 Author: galt Date: Sat Jan 2 16:00:08 2010 +0000 "Encode release log update" commit 8041402d05c4cc10c8669db0c4bca75a664224b4 Author: galt Date: Sat Jan 2 16:00:04 2010 +0000 "Release log update" commit f58759b8accbe081b727ed3b463aef90f67d6152 Author: galt Date: Fri Jan 1 16:00:06 2010 +0000 "Encode release log update" commit 350f12d75f4b33c8f35987272baec8aa654bd331 Author: galt Date: Fri Jan 1 16:00:03 2010 +0000 "Release log update" commit ec106f427b2dd066aee913ab36913e1d3fd30dbc Author: markd Date: Thu Dec 31 20:50:42 2009 +0000 don't align dropped database commit 0b85bba11410dc812f27dba65cd474af9406211a Author: markd Date: Thu Dec 31 20:15:05 2009 +0000 sort to make finding differences easy commit 539d8cfe4ed94fb58869c7e2b0072e4db89a71fa Author: markd Date: Thu Dec 31 19:47:13 2009 +0000 don't align for genomes no longer being updated commit 9ebe13d5a4cbecce7e25a1985c93a6d402052580 Author: markd Date: Thu Dec 31 19:41:23 2009 +0000 don't update danRer1 commit bf43bda87f83bd43b1cb59208d1debee3a0f900e Author: galt Date: Thu Dec 31 16:00:07 2009 +0000 "Encode release log update" commit a5cdd72626cf19f335fc2035e05b81ab5ee86363 Author: galt Date: Thu Dec 31 16:00:04 2009 +0000 "Release log update" commit 32a4c05d5f590a8591c8b8ea12b6e29d575a78c8 Author: markd Date: Thu Dec 31 08:12:53 2009 +0000 added credit commit 61058d943eb97425cbfc6a20508edfa178b08b0a Author: rhead Date: Thu Dec 31 06:31:54 2009 +0000 setting environment variables if they are not already set commit 459e2c59b1965f950b24a719587f6707b03c31ef Author: markd Date: Wed Dec 30 23:13:38 2009 +0000 put database update lists in alphabetical order to make comparisons easy commit 930edbc8053d423101c84a04600d67775dcf4e40 Author: hiram Date: Wed Dec 30 21:33:04 2009 +0000 cleaning rough edges around chain net composite conversion commit 6719b0c158abeca804b1d0a8f74bb534af7b4b4e Author: larrym Date: Wed Dec 30 20:21:17 2009 +0000 add jquery-ui.js and jquery.contextmenu.js commit 011e63cc0fc5b347a72b7d8216cb9504750a7792 Author: larrym Date: Wed Dec 30 20:00:02 2009 +0000 images used by jquery-ui for dialogs commit c2a337f9ebcda5409937d8542d8f10d0dc19de95 Author: hiram Date: Wed Dec 30 19:50:14 2009 +0000 catching up chain and net composites for hgwdev only bosTau1 dasNov1 echTel1 loxAfr1 dasNov2 loxAfr3 commit a0fc9c57c9b3e128d9c16128204335e6fb4ec6ba Author: larrym Date: Wed Dec 30 19:48:20 2009 +0000 use auto for dialog heights and widths; fixes MSIE problems commit 955b37c2e5fe40ad4303fbc84a130b5be905e973 Author: hiram Date: Wed Dec 30 18:49:35 2009 +0000 do not need individual chain net entries for hgwdev specific genomes sorAra1 eriEur1 tupBel1 otoGar1 oryCun1 gorGor1 commit 54960582e27e6ba7d5d4eb29071b9f58c13b9856 Author: galt Date: Wed Dec 30 16:00:06 2009 +0000 "Encode release log update" commit 4eb34611216e5b34185d7260fbd1185f316bb3c6 Author: galt Date: Wed Dec 30 16:00:03 2009 +0000 "Release log update" commit 298505adb99b4424eb8123bac7d7b458eb3f56ee Author: larrym Date: Wed Dec 30 04:14:21 2009 +0000 retrieve new image when user chooses viewImg commit a1aa9bb1bc506b07c4992a6f1bfcc7094ffe0701 Author: hiram Date: Tue Dec 29 23:27:34 2009 +0000 clean up chain net composites for non-released genomes on hg18 commit 93909eed84676c67ed43251f4b5da98e6daa2811 Author: larrym Date: Tue Dec 29 20:24:53 2009 +0000 handle changes to track buttons commit 40edca43fa0ee0cd79e5d0149196020dde10e3f5 Author: galt Date: Tue Dec 29 16:00:06 2009 +0000 "Encode release log update" commit 6c4b3f771239ec82a40f0733a5c45e309d12c471 Author: galt Date: Tue Dec 29 16:00:03 2009 +0000 "Release log update" commit 7644ac2d8f05118de32a82c5fbde8e9ae838b9d3 Author: hiram Date: Mon Dec 28 23:43:29 2009 +0000 all zebrafinch taeGut1 chain net tracks are composite commit d550a9327679dd8cf061821a5fb451b3c2eb403d Author: hiram Date: Mon Dec 28 23:29:10 2009 +0000 all lanclet braFlo1 chain net tracks are composite commit a36109ffa4b9a0d1333294c28c3373af68ee2f9e Author: hiram Date: Mon Dec 28 23:11:38 2009 +0000 all guinea pig cavPor3 and 2 chain net tracks are composite commit 85f6d9aec956f06bf302dfac2da0519eefcb5c51 Author: hiram Date: Mon Dec 28 22:51:29 2009 +0000 all horse equCab1 and 2 chain net tracks are composite commit 971f34e599370f9458c0ecda4fd78cca1f8a30de Author: hiram Date: Mon Dec 28 22:28:21 2009 +0000 all lamprey petMar1 chain and net tracks are composites commit 8186045798c624faa9eb888d51e4d846f53616ba Author: hiram Date: Mon Dec 28 22:07:31 2009 +0000 all lizard anoCar1 chain and net tracks are now composite commit 3656a509649a6511eaa5c8f648eb2386461610bf Author: hiram Date: Mon Dec 28 21:53:10 2009 +0000 all zebrafish chain and net tracks are now composite commit 0319ec90f32b76f8800d80e5f386036265c9abaa Author: hiram Date: Mon Dec 28 21:41:56 2009 +0000 all zebrafish chain and net tracks are now composites commit 44fcbf70103f93a6e80acef2b4f379fdde1216fa Author: larrym Date: Mon Dec 28 21:13:54 2009 +0000 hide menu when user presses the escape key commit 4b12546e64283ba5ac92bccdb90570c7308b95a3 Author: hartera Date: Mon Dec 28 20:13:20 2009 +0000 Added exoniphy to list of tables to be ignored. commit 8bea09660e1dcb392f3f97ae046aae7b41b6e810 Author: hartera Date: Mon Dec 28 20:06:18 2009 +0000 Minor edits. commit 7a1480734a99acbb78bedb4ffad49850fd5e24e9 Author: hartera Date: Mon Dec 28 19:59:10 2009 +0000 Description for hg19 exoniphy predictions track. commit 5ccadd10c8f00df5dec3adc3d03405a29a34d39b Author: hartera Date: Mon Dec 28 19:38:30 2009 +0000 Added track of new Exoniphy predictions. commit fafc71e6170b28ca5c7da0cd28dbfd28c6620c1c Author: hiram Date: Mon Dec 28 17:57:13 2009 +0000 need a cast on a pointer to (int) for compile on MAC commit c382cc662874ef21fe33e31e7edd0bbeedacff5a Author: galt Date: Mon Dec 28 16:00:06 2009 +0000 "Encode release log update" commit e18c64792460748464d6d792631ac2db464952db Author: galt Date: Mon Dec 28 16:00:03 2009 +0000 "Release log update" commit c81bd1c3debc6698078e5d22d1140519765fa691 Author: galt Date: Sun Dec 27 16:00:04 2009 +0000 "Encode release log update" commit 81dc6f6cf4b634745e87e3fd6cd808d5e1fda094 Author: galt Date: Sun Dec 27 16:00:02 2009 +0000 "Release log update" commit eb8ea70bbcf2c9a379ab3cc7ba334b29f737be75 Author: rhead Date: Sun Dec 27 02:40:39 2009 +0000 Moved links to labs to first paragraph, changed paper link to Nature instead of pubmed, small tweaks everywhere. commit fa51c9a011130b26e3ae14dea067a7f4c96667d5 Author: kate Date: Sat Dec 26 20:16:10 2009 +0000 Add datatype for SUNY commit 8353ade58e1986ffac156c5b6ab2721fc20dc4d8 Author: kate Date: Sat Dec 26 19:07:35 2009 +0000 Fix some labels to match metadata and tablenames commit a7703671180328a8e03542571575d8bd7bdffdae Author: kate Date: Sat Dec 26 18:40:22 2009 +0000 Correct some submission IDs so reporting works properly commit bf04c322a3ce4025c6e416f82fe5381f3c9eb944 Author: galt Date: Sat Dec 26 16:00:06 2009 +0000 "Encode release log update" commit 5ea328bd741339f59a3a16489be57d27d10f4677 Author: galt Date: Sat Dec 26 16:00:03 2009 +0000 "Release log update" commit 68d2ff728c91058e0d43e2775220e18b87b90ef7 Author: kate Date: Sat Dec 26 07:09:27 2009 +0000 Remove problem entry for now commit d2a963fbf6a9a3912ba867adade31bf84d4de169 Author: hiram Date: Sat Dec 26 06:09:30 2009 +0000 ready for genbank run commit 03894581b2ab310cb2f58138944ba297596b0bcb Author: markd Date: Sat Dec 26 05:59:23 2009 +0000 added panda commit 85e9f4c9705d2f23b5774e17156762f0cb7f1491 Author: markd Date: Sat Dec 26 04:22:05 2009 +0000 changed panda params commit a0bedd09f80865eabb42f91a2900ddb20ff72c9a Author: markd Date: Sat Dec 26 04:00:52 2009 +0000 fix path for hgnfs1 (fixed premature commit) commit 7fb2a1663436a20cf7130e677a8296ef91005f12 Author: markd Date: Sat Dec 26 03:57:44 2009 +0000 modified extFile updating to match new server configuration commit 5822049bb4400a44d59f80272bce030479695444 Author: markd Date: Sat Dec 26 03:37:14 2009 +0000 modified extFile updating to match new server configuration commit 17c27ad3a79d82b833aac23c83d71b5a8b8a88a3 Author: kate Date: Sat Dec 26 01:17:58 2009 +0000 Roll back default wiggle height for UW tracks for consistency w/ other ENCODE tracks commit 36bdec59615e784405368e467a17d054d9347fe0 Author: kate Date: Sat Dec 26 01:11:57 2009 +0000 Ignore revoked entries commit 0de23d2acf4225783cfec7e84f2a4f15717bed6b Author: kate Date: Sat Dec 26 01:11:08 2009 +0000 Add CV term for submissions versions (used by reporting) commit b51835ce8084fc674c9471a531ddb42477560eae Author: galt Date: Fri Dec 25 16:00:07 2009 +0000 "Encode release log update" commit 87a3e659a22a4392b714aaf67785375221ed7925 Author: galt Date: Fri Dec 25 16:00:04 2009 +0000 "Release log update" commit a47259d014658d15c3a66f17a74924e7bc136397 Author: hiram Date: Thu Dec 24 22:58:53 2009 +0000 need ailMel1.lift = no commit 6aee9f7b560e857a4a9cf23ef326dd9cf71b4329 Author: galt Date: Thu Dec 24 20:30:41 2009 +0000 danRer6/xenTro2 chainswap commit 5c0e5e6c7746b176abc18db8baccc6a95d62abb2 Author: galt Date: Thu Dec 24 16:00:06 2009 +0000 "Encode release log update" commit 83fa8e089b501e7c7c2a355593cef1b85fccbbc9 Author: galt Date: Thu Dec 24 16:00:03 2009 +0000 "Release log update" commit 56b7a9abf6a70be782e98b56ee2327ef8aa04e3f Author: hiram Date: Thu Dec 24 06:29:00 2009 +0000 adding ailMel - Panda with Dog specifications commit e605aade7b809a90f63e71173797582aeca2269e Author: markd Date: Thu Dec 24 05:10:49 2009 +0000 forgot check for fork failure commit 8624958917e8f88d29f7a9ce04ccb9312c460cfa Author: markd Date: Thu Dec 24 04:55:40 2009 +0000 correctly check return status of system; removed confusing function that is no longer used commit 29e2b94454622f3a2873a648de452b8cfa9ce4a7 Author: markd Date: Thu Dec 24 03:59:38 2009 +0000 integrated change from stanford to no print out a error message when trf actually succeeded commit 373e064b091017bbf0af79e46e8d85cabfe71d80 Author: hiram Date: Wed Dec 23 23:58:23 2009 +0000 adding panda ailMel1 commit 5ae48d9d1c0204e2fc8a9f800452bc8d69622e64 Author: hiram Date: Wed Dec 23 23:19:24 2009 +0000 all Medaka oryLat2 chain and net tracks are now composites commit a9626544e235de81fc382e1e9c4345a0d9cbd6b7 Author: hiram Date: Wed Dec 23 22:54:57 2009 +0000 Initial sequence for Panda commit 1cd985d94f58514964cd912670e83ed0a06eaf3d Author: hiram Date: Wed Dec 23 20:40:04 2009 +0000 Marmoset calJac1 chain and net tracks are now all composites commit bffc973b1920668ca0346f837e33b410cc22b7e2 Author: hiram Date: Wed Dec 23 20:09:06 2009 +0000 Fugu fr1 and fr2 chain net tracks are now all composite commit 97a938ba736dd662f271f6affa9d1a1ce8db6d91 Author: galt Date: Wed Dec 23 19:09:24 2009 +0000 fixed typo commit 6d89a39cfe2a584d0b5a5a8ff9b74a2f146a5db6 Author: hiram Date: Wed Dec 23 19:06:36 2009 +0000 rhesus and orangutan chain and net tracks are now all composites commit 7dbcfc8e06fdbf3ef4c63f4d3df8b51bdbd66c2f Author: galt Date: Wed Dec 23 19:02:44 2009 +0000 danRer6 xentro2 chains commit 8c7cad3c1b42179c2ee9aaa6ae26d91fa15fa9b8 Author: hiram Date: Wed Dec 23 17:59:18 2009 +0000 all tetraodon xenTro1 and xenTro2 chain net tracks are now composite commit df5993f1482ec3096ba772b1addd2af127ebc93e Author: galt Date: Wed Dec 23 16:00:07 2009 +0000 "Encode release log update" commit beac173c60bc79790ac597b32eda1073c7b0c3f7 Author: galt Date: Wed Dec 23 16:00:04 2009 +0000 "Release log update" commit 475825ba846488bfef0998c768f4933438d14061 Author: kate Date: Wed Dec 23 06:46:06 2009 +0000 Add some missing protocol metadata commit 57647c8716b54f28cbb1de16dba38b2e8daac25b Author: markd Date: Wed Dec 23 05:47:20 2009 +0000 added transmap build doc commit da603c643dd5f48371a27485845a9de2de187bfc Author: kate Date: Wed Dec 23 05:01:47 2009 +0000 Restore proper lib path commit 4566d0f1cfc040c16e963ecca823db63ae3cd661 Author: kate Date: Wed Dec 23 05:00:53 2009 +0000 Add subroutines for dealing with pipeline statuses commit c16962de909d1fb7294fa4fb989267fe74ec0fcd Author: kate Date: Wed Dec 23 05:00:09 2009 +0000 More successful at sniffing out release date commit 9b5b29fb485bbe8a9f899a20561c43cfcf77c24b Author: kate Date: Wed Dec 23 04:33:09 2009 +0000 Stay with V2 convention commit 702bae785d50f0a5247c08b66c455a27a6c4322f Author: katrina Date: Wed Dec 23 01:41:57 2009 +0000 revised termRegex in komp table search block so that searches of komp.name work commit ea7250f647c40ea984a66200933203767364bd8f Author: kuhn Date: Wed Dec 23 00:42:06 2009 +0000 changed danRer5 chains/nets to db name. now replaced by danRer6 commit 00d6dcadf917b8bdf81d37ae020e4c0d1716936a Author: kuhn Date: Wed Dec 23 00:37:47 2009 +0000 swapped out danRer5 and in danRer6 in vertChainNet composite commit 7b47a30ff2cc29a071a488011f2e645f5b2c5be1 Author: hiram Date: Tue Dec 22 22:48:08 2009 +0000 all stickleback chain and net tracks are now composite commit aaad5d4f64ef70cf9fefac004f88f5b3c6314a92 Author: hiram Date: Tue Dec 22 22:21:31 2009 +0000 all platypus ornAna1 chain and net tracks are composites commit e6cab20c7616ed2727317a364eef1186bdbaa670 Author: hiram Date: Tue Dec 22 21:47:50 2009 +0000 all Tetraodon chain and net tracks are now composites commit 24bd777dd9a11a867c51fb71679ada6df4817ef2 Author: hiram Date: Tue Dec 22 21:14:20 2009 +0000 all chimp chain net tracks are now composites commit a1b035ffae1f1330c3e2174035e662ec4f816d24 Author: hiram Date: Tue Dec 22 20:18:27 2009 +0000 all rat chain and net tracks are now composites commit 3e23d36f71be2e4de4f3248ab19837264e9a945f Author: hiram Date: Tue Dec 22 20:05:10 2009 +0000 Look for older styles, do the reverse lookup automatically if not found and show defaults when not specified commit 0ada101fa829bee4053ad48f5ddd5bd72392d649 Author: galt Date: Tue Dec 22 19:56:42 2009 +0000 danRer6/gas commit 61c85febe7073bd81038788f6294169c25418e01 Author: galt Date: Tue Dec 22 19:49:25 2009 +0000 danRer6 chain swap commit a760a6ba85f2d68ff92f12f9a25680ec92037fc0 Author: hiram Date: Tue Dec 22 19:19:20 2009 +0000 chainNetHg17 is needed for canFam1 and monDom1 to complete human business commit d4109ded3316a83dd874edbf19ad466ff99ab6dc Author: hiram Date: Tue Dec 22 19:00:04 2009 +0000 all mouse human net tracks are now composites commit 0f32139de342d14bcdf0300567035c0868798247 Author: hiram Date: Tue Dec 22 18:58:26 2009 +0000 all mouse chain net tracks are now composites commit aa8390304c021f59991baf4f3a49a22ba193296e Author: kate Date: Tue Dec 22 17:43:28 2009 +0000 Add check for missing DDF file commit 811ee1424fb130d8e9ef8896b085b445e0e1808d Author: galt Date: Tue Dec 22 16:00:06 2009 +0000 "Encode release log update" commit 5552eae23f6191abb0274ede5fb413f8c8db3a43 Author: galt Date: Tue Dec 22 16:00:03 2009 +0000 "Release log update" commit 80182b9ca163ddca661787cd4d6852d79e5ba967 Author: markd Date: Tue Dec 22 08:46:09 2009 +0000 changes to support diff of what happend on a branch commit f92677fb0cdf34ccc72663e02436e7262f82347e Author: kate Date: Tue Dec 22 06:07:07 2009 +0000 Add access for CV rags (used by reporting) commit 49bbc59eb15f7f1e44ecd640e500011da3b75d17 Author: kate Date: Tue Dec 22 06:06:43 2009 +0000 Add labels for automated reporting commit 0eb21e310b22f2c10ff2e6e740a60b56199b7dcc Author: kate Date: Tue Dec 22 06:06:30 2009 +0000 Add labels and CV of data types, for use in automated reporting commit 282cab9b08d56cf361e54a50da41acf1e420ad44 Author: kate Date: Tue Dec 22 06:04:47 2009 +0000 Pretty close to duplicating the manual spreadsheet commit 0616496e039da2483fa73ee13d66c027a54ffe67 Author: hiram Date: Mon Dec 21 23:09:17 2009 +0000 Raising the HUGE_LIMIT to 4280000000 caused a very large slow down in some custom tracks. Doesn't make any sense. commit 58cbc4e3df12daae2a87955a5e0c6bd5f93971db Author: hiram Date: Mon Dec 21 23:02:57 2009 +0000 all hg18 hg19 chain net tracks are now composites commit a6020dfe0afab98338ff4abca3492d44dcfca03b Author: hiram Date: Mon Dec 21 22:56:04 2009 +0000 all hg18 hg19 chain net tracks are now composites commit 499f3d9d7234146bc449bcf90cfe5536d57de84e Author: markd Date: Mon Dec 21 22:43:35 2009 +0000 remove fixed length restrion on size of item names. reduce per-item memory usage by removing unusaed array commit ac72c58e3021d8771f967fe33c5cf663985ecae6 Author: markd Date: Mon Dec 21 21:02:30 2009 +0000 added problem case example commit a8c12383984663fc9db4ef0ee0b7f78bbe591ebf Author: hiram Date: Mon Dec 21 18:37:10 2009 +0000 Raise memory limit for data fetch operations commit 3c107f9c5abee6d72a663701dc8222163756751c Author: galt Date: Mon Dec 21 16:00:04 2009 +0000 "Encode release log update" commit 783605208d183ead767aa7ad8240081e5e567da4 Author: galt Date: Mon Dec 21 16:00:02 2009 +0000 "Release log update" commit c316e50b267f299c2b378e05a270b892a2cd5fe2 Author: galt Date: Sun Dec 20 16:00:04 2009 +0000 "Encode release log update" commit 22defe73bf1f7f237668459b8444e5d1b94529b7 Author: galt Date: Sun Dec 20 16:00:02 2009 +0000 "Release log update" commit 7c413a1134fb05da61539a4f0234b67bf99d57cb Author: galt Date: Sat Dec 19 16:00:06 2009 +0000 "Encode release log update" commit 8c7a8690e30ac50dfeb09cd3c253fd612befcb59 Author: galt Date: Sat Dec 19 16:00:03 2009 +0000 "Release log update" commit 246c0bb122b2175a009d4f9e1e74e3e113209690 Author: angie Date: Sat Dec 19 01:06:27 2009 +0000 Added options -fork (true concurrent access: actually gets no errors unlike the same-process/interleaved-access test!), -seed (try 1261180550 for big failure on empty cache files without -fork), and -protocol (default ftp, can do http instead, boring/no errors). commit e02e55701828ce70180ff56bcd384b01e9cd69f7 Author: galt Date: Sat Dec 19 00:57:58 2009 +0000 danRer6 to mmm9 chains commit 1eefe682e7cd7fe07f73cd32e039181c0e8fab61 Author: angie Date: Sat Dec 19 00:57:09 2009 +0000 Changed all FILE * vars and operations (fopen etc) to integer file descriptors and 'man 2' operations (open etc), for unbuffered I/O which should make it harder for the bitmap file to get out of sync with the sparseData file when there are multiple udcFile*'s accessing the same part of a URL and those files. Unfortunately this doesn't completely prevent udcTest failures (try seed=1261180550), just reduces frequency a bit. Also added a speed optimization: to avoid heavy reconnect penalty when we need to skip a few udc blocks because they have already been cached, just read and discard those blocks' data. commit 0aaf3d56118686b7125511aadf39426d671eec84 Author: tdreszer Date: Sat Dec 19 00:35:56 2009 +0000 Fix dataVersion on Broad during the 13th hour commit 3aeab6ffc5f76df452b4403c3a1f1d4333eeaed8 Author: braney Date: Sat Dec 19 00:32:47 2009 +0000 fix controlled vocabulary links commit f0aef389ef32e9e82dd4994f2f6fab60a45719fc Author: angie Date: Sat Dec 19 00:23:21 2009 +0000 Added must{Open,Read,Write,Close}Fd and mustLseek to common.c, for operations on file descriptors. Some were already in lib/tests/pipelineTester.c - replaced those. commit 1bee2a4b178ff06584714020a81869e44ffa41e9 Author: kate Date: Fri Dec 18 23:41:45 2009 +0000 Add count of sequences to chromInfo page (hg19 has greatly expanded the count over hg18) commit 8807feb4d695c8044d3d449df8cf7c0196439817 Author: hiram Date: Fri Dec 18 23:41:23 2009 +0000 all galGal chain net tracks are now composite commit 663ecaebc39079dc41e783d85a73b509276cf267 Author: angie Date: Fri Dec 18 22:48:27 2009 +0000 Fixed comparison edge condition (not a huge problem, it just set tv_{sec,usec} to {0,1000000} not {1,0}) and more importantly, added a missing EOF check that was allowing unexpected EOF from FTP to result in inf. loop. commit 2b3be99b134f2495f64a523c0aac4541cd2306ed Author: donnak Date: Fri Dec 18 22:31:32 2009 +0000 Added holiday msg. commit 6224806490cc3fbbda89ed365dd346185965fe2e Author: hiram Date: Fri Dec 18 22:27:02 2009 +0000 eliminate duplicate entry for chainNetCanFam2 commit 2dd88ff944cd88bdf9e0c40c915fd9fb02519ade Author: hiram Date: Fri Dec 18 22:21:33 2009 +0000 all canFam chain net tracks are now composites commit d6332865dc0a17553f3a8bfd037b654590a4daff Author: tdreszer Date: Fri Dec 18 22:09:48 2009 +0000 Fix my mistake in 'variables' line commit ae94a8bbf6a09fdc0162e4025ad73f516cc9bdc3 Author: tdreszer Date: Fri Dec 18 21:49:10 2009 +0000 Fix UW ChipSeq settings commit e49982825a09e6c19948f78fc1ff485a9809ab13 Author: tdreszer Date: Fri Dec 18 21:42:26 2009 +0000 Notes for the 2nd release of UW DNase commit 3a7ab2aba0326cbdeed421fa623d7bc3843ffeb0 Author: katrina Date: Fri Dec 18 21:25:42 2009 +0000 correcting minor errors commit afdb60e973333b0808711fe39061543f83e88de4 Author: hiram Date: Fri Dec 18 20:26:51 2009 +0000 eliminate duplicate chainNetMonDom5 override commit b9649a9d2c378f77d1677937950b0505df73ce4f Author: hiram Date: Fri Dec 18 20:24:40 2009 +0000 shorLabel monDom4 for hgwdev commit 1cc3cb8b342b8ef4172290a4546bdd36ca2daae0 Author: hiram Date: Fri Dec 18 20:19:52 2009 +0000 all monDom chain nets are now composites commit 568602ac5e4571c876922a526c2bdb05bd637291 Author: ann Date: Fri Dec 18 18:51:43 2009 +0000 moving ENCODE Gencode so that it doesn't appear first in the genes group commit 0b58bb1c71e08412ae57796297d547d9b885f896 Author: tdreszer Date: Fri Dec 18 18:48:59 2009 +0000 Broads 14 for Jan 2010 commit c380b0b1c864f8ba5d0f2577fe994aa6a03fff4b Author: hiram Date: Fri Dec 18 18:29:31 2009 +0000 It does no good to have a release beta in an override commit 387e9f9f89ccba9603f53574c24a52a35b2a368b Author: galt Date: Fri Dec 18 16:00:06 2009 +0000 "Encode release log update" commit bbf17fe7f645eb4ca96562091dc0c410cffc0e56 Author: galt Date: Fri Dec 18 16:00:03 2009 +0000 "Release log update" commit 8a6dc43e7aa94f85824baab4568e9cf0e88ecdbb Author: hiram Date: Fri Dec 18 00:45:16 2009 +0000 Add ailMel1 panda to the build commit cf6a0a81092307aadfb019d502f3e134bcf0375a Author: hiram Date: Fri Dec 18 00:44:47 2009 +0000 Initial contents from makeGenomeDb.pl commit 00911c1ced4793ac0f5e824e789e721f4c72a4a3 Author: pauline Date: Fri Dec 18 00:25:41 2009 +0000 Fixed matrix parameters for mm9 chain commit a422ed1cf8d857adef129a7a30f8f482eeb15487 Author: katrina Date: Fri Dec 18 00:04:15 2009 +0000 removed release alpha lines for ENCODE CSHL Sm RNA commit 0538464bfd773a998a5fe5794a5e0058dddfacce Author: galt Date: Thu Dec 17 23:54:51 2009 +0000 fix minor timing bug commit 0f4f4c70f1b45b47b80160d89735d47c5b4cb8e6 Author: hiram Date: Thu Dec 17 23:04:35 2009 +0000 Allow whisker plots to show colors in positive and negative tracks commit e53ee6f1797241711354324ad821778ed6d669ce Author: katrina Date: Thu Dec 17 22:12:12 2009 +0000 fixed termRegex of search block for gold so that searching on danRer6 works and so all danRer assemblies now pick up the chrM contig (they were not before) commit a34c5b2f3dde19a946f87c688be29aec22030828 Author: tdreszer Date: Thu Dec 17 19:20:24 2009 +0000 Changed verbose messages from js developers only to hgwdev only commit b514b78bb7954c6ee9e50e0d0eb36a579358f50e Author: tdreszer Date: Thu Dec 17 18:46:57 2009 +0000 Added 'privateData' option and require tab delimit instead of white space delimit commit 78ff25cfed9a487a42a939f653a44df6364851bd Author: ann Date: Thu Dec 17 18:43:38 2009 +0000 removed references to specific assemblies commit 047f950cc1af5a60ec8906c7170885d6a252c693 Author: tdreszer Date: Thu Dec 17 18:16:49 2009 +0000 Special case code for cleaning up tablenames that are too long commit c407a84a0668d2340447d1d046990a9174af204e Author: tdreszer Date: Thu Dec 17 16:58:51 2009 +0000 Fix captitaliZation in paths commit d8081f2d6efc77224a47c3e3c65e3c54d5ac7ef5 Author: hartera Date: Thu Dec 17 16:07:01 2009 +0000 Added track entry for RetroFiner retrogenes, version 2. commit e21de671da1f5534433687a179a288ec9435f01b Author: galt Date: Thu Dec 17 16:00:07 2009 +0000 "Encode release log update" commit 87a85b86b4053f850f11dfa4ed474036d427f850 Author: galt Date: Thu Dec 17 16:00:04 2009 +0000 "Release log update" commit be4dc66c05f95f00c474d4257b78658b646230ff Author: rhead Date: Thu Dec 17 05:52:00 2009 +0000 Removed the priority setting from the rn4, monDom4 and canFam2 chain and net tracks. The settings were formerly overridden by human/priority.ra. commit aa6e0dbdda445ee7d5557cde13f75ad41b68e859 Author: tdreszer Date: Thu Dec 17 00:26:26 2009 +0000 Warning only for javascriipt developers commit a4e5428cf46a764625960843b92b5625fd34a378 Author: kuhn Date: Thu Dec 17 00:15:12 2009 +0000 hiram sez nuke this commit 3e1ef16471a22527f38681512fd22c8a76258457 Author: galt Date: Wed Dec 16 23:43:36 2009 +0000 one more detail commit 194fd725287a1d29a318f2cbb9ed2d0759945658 Author: galt Date: Wed Dec 16 23:16:57 2009 +0000 adding project.id to email as requested by a user commit 432e80b42e75ace1e166d3251c22782ddf9fb364 Author: galt Date: Wed Dec 16 23:02:05 2009 +0000 adding liftover to MD3 commit 95bd96754687d5483afd9cae3398fe2a9185e367 Author: tdreszer Date: Wed Dec 16 17:49:10 2009 +0000 Kayla found some mangled names commit 2d22d26a3368dd3e8cb72dd848f252e494eb3d45 Author: braney Date: Wed Dec 16 16:35:06 2009 +0000 change A+ to tot in Hannon small RNA-seq commit 2bdbd89d5319332834d13a73720160fdb7851849 Author: galt Date: Wed Dec 16 16:00:06 2009 +0000 "Encode release log update" commit 9a422e628ab80148975663dc55d3c8cf4cda5dab Author: galt Date: Wed Dec 16 16:00:03 2009 +0000 "Release log update" commit 6d729d33c53f8f1af8fce2066ba92b6941768b63 Author: donnak Date: Tue Dec 15 23:56:39 2009 +0000 Archived 2 items. commit 857eae9a71b7919ff71f313b36b71eace6edfe72 Author: donnak Date: Tue Dec 15 23:56:30 2009 +0000 Added job announcement. commit 03a19933b55236e5d0e804556905f1f57074b405 Author: tdreszer Date: Tue Dec 15 23:50:33 2009 +0000 Never do in 1 checkin what can be spread out into 2 commit cfa386b8f22c5d6def726f785076c453cd0c8a46 Author: ann Date: Tue Dec 15 23:40:32 2009 +0000 removing alpha from transMapAlnSplicedEst track commit 956d483c4023d90ad7c01677cc04c570216edce8 Author: tdreszer Date: Tue Dec 15 22:59:06 2009 +0000 Exception for chrM should not be an option. If end > chromSize and chrM, then make sure start <= chromSize commit 759e05805e704ecb675e9b6836a04741cf9e580b Author: donnak Date: Tue Dec 15 22:39:53 2009 +0000 Added Rachel's book chapter. commit 7f0d3a25ae24248a2908b170db63a90ca416a15b Author: tdreszer Date: Tue Dec 15 22:24:27 2009 +0000 Fix BTO term for myotubes commit f745ada0bc061e830393cda79560458316b52035 Author: tdreszer Date: Tue Dec 15 22:19:53 2009 +0000 Added 2 cell types for Broad commit 96ca7d0cdf6df8acad978cf6100e466baf794e15 Author: braney Date: Tue Dec 15 20:53:51 2009 +0000 change H1-hESC cell compartment to cell rather than cytosol for GIS RNA tracks commit 718df435822c4db04c186366c729ed8d961cfc4b Author: tdreszer Date: Tue Dec 15 20:25:31 2009 +0000 Simplified controlled vocab validation, tableNames based on cv tags not terms, tag 'None' not included in naem, special case replicate subGroup commit 002c2e7c861eb385a6d83c6bf1adfcf91c863242 Author: tdreszer Date: Tue Dec 15 20:21:06 2009 +0000 Need this to note the obscure hg.conf setting required to test changes commit 3a9ef5e6270875d7b7132a0ff2d0cc2061e81242 Author: tdreszer Date: Tue Dec 15 18:49:34 2009 +0000 Plug up a runtime warning warning commit 07e5713c51813290ba40fa3381a6bc34ebe53fc8 Author: hartera Date: Tue Dec 15 18:48:27 2009 +0000 Changed cdsStart and cdsEnd to be 0 in Burge RNA-seq data and moved track data to directory for hg19 genome assembly. commit db36b01685e80880a95bb183530b03f1b0a67525 Author: hartera Date: Tue Dec 15 18:48:11 2009 +0000 Changed cdsStart and cdsEnd to be 0 in Burge RNA-seq data and moved track data to directory for hg18 genome assembly. commit 58e34b2556dd45f6f10ffcb5c45e4c1a4e094156 Author: fanhsu Date: Tue Dec 15 18:08:28 2009 +0000 Updated search terms for 3 new Illumina SNP arrays. commit 605f713dcc477d912846d00ff673185998a137ed Author: galt Date: Tue Dec 15 16:00:06 2009 +0000 "Encode release log update" commit 4caa24ae56f2c4123fbc91bb85fabf624cef0469 Author: galt Date: Tue Dec 15 16:00:03 2009 +0000 "Release log update" commit 9e346b94853d9015bd09f5df3950dde43d86892c Author: kent Date: Tue Dec 15 05:53:28 2009 +0000 Adding comment as to nature of work-around. commit 0a1fad54ad5f33e3592f2f2990044cad208912a2 Author: kent Date: Tue Dec 15 04:33:32 2009 +0000 Moving encodeAffyChipSuper back down a level in directory to hg18 to serve as a test case that we can have supertracks in levels below their tracks. Have to keep the single child as well as the workaround for over-eager pruning in -strict mode in hgTrackDb. commit 6d6f809e75b463387d9ba48457fe0cc518993559 Author: kent Date: Tue Dec 15 02:53:09 2009 +0000 Moving some supertracks up a dir to live with their component tracks to work around strict mode unbundling of supertracks. commit 29e8e0b0a21ecf259a140d036854b9cf397ef826 Author: tdreszer Date: Tue Dec 15 00:31:30 2009 +0000 Added 4 more HAIB ChIP submissions commit 1526f8802f4d911efea81b49168fb0e2e49ab57a Author: tdreszer Date: Tue Dec 15 00:10:16 2009 +0000 Shortened more tags because tableNames and sorting commit 43a40b372928c86c98afbe20760d54ffaedb54f5 Author: braney Date: Mon Dec 14 23:56:16 2009 +0000 need to bring in some other of the zebrafish trackDb for affyZebrafish commit 7301f3c48ceb24af0a3cea8f31180c719d5ef317 Author: braney Date: Mon Dec 14 23:52:46 2009 +0000 take out override on a track that is composite in danRer5, but not in zebrafish commit 27ad91d2cd64ff0a27552be96c4f8273400f5e9a Author: tdreszer Date: Mon Dec 14 23:41:44 2009 +0000 Shortened some tags because tableNames are over-flowing commit ac889ae4d8fdcf143720d5d941eb94767bdd0f06 Author: katrina Date: Mon Dec 14 23:29:01 2009 +0000 added danRer6 as a database covered by xrg variable; danRer6 is first danRer db to have xenoRefGene commit a51ea7a7d2fb77bd6ced292f2822b21489f9de20 Author: hartera Date: Mon Dec 14 23:23:58 2009 +0000 Added setting for subtracks drag and drop for Burge RNA-seq. commit 2459ffdfae1575d88c1487504421fc8c0c9bb73c Author: angie Date: Mon Dec 14 23:19:57 2009 +0000 For pairSearchRange, don't do two bamFetch's -- very inefficient. Just expand the search range up front. commit 6578864a6de90a60527ad69e434530b138477559 Author: katrina Date: Mon Dec 14 23:01:41 2009 +0000 moved danRer6 from '#transMapDb not public...' to a database covered by transMapDb variable commit b709dec7b7097276de1ebf2e37ea174aa385391d Author: braney Date: Mon Dec 14 22:44:16 2009 +0000 change labels for Cshl Short RNA-seq to Cshl Small Rna-seq commit 7ee5772a5d5248f857f40d98796e467539a0298c Author: braney Date: Mon Dec 14 22:41:34 2009 +0000 add A+ to Transcriptome tracks where polyA+ is the default commit df3d74989ded96e2dce43a2da8a386b231bbbf42 Author: braney Date: Mon Dec 14 21:46:31 2009 +0000 fix big bed filename for Cshl Long tracks commit 26b60e759cb91efd4cfe7aa25bed348cb7cd11fa Author: galt Date: Mon Dec 14 19:23:36 2009 +0000 "New version number v221" commit 12d8f2d68ade64aa8ffb30383b496685a6e29814 Author: galt Date: Mon Dec 14 19:23:08 2009 +0000 v221 final build commit a1780b95a57dea9c32154c8168d4785306f4eb68 Author: galt Date: Mon Dec 14 19:04:29 2009 +0000 no trailing asterix needed commit 9edbfb20eea17b890521f3fbf10aab1a54968c8c Author: galt Date: Mon Dec 14 18:59:52 2009 +0000 fix typo commit 404d1d26e5072fda1fc38946c3d05764fd302292 Author: galt Date: Mon Dec 14 18:56:31 2009 +0000 adding closing tag commit 15c16e1227eb66372ae2b9a8429791e484451f08 Author: ann Date: Mon Dec 14 18:21:44 2009 +0000 mm9 is now based on hg19 for TransMap commit 2db2e8e1b76dd2ecce8de3514fc0ae00c57023b4 Author: fanhsu Date: Mon Dec 14 18:01:46 2009 +0000 Added logic to handle non-dbSnp entries of 3 new Illumina SNP arrays. commit a83988c4d6b12f0d12be56570259948feb70dfda Author: kuhn Date: Mon Dec 14 17:19:13 2009 +0000 fixed so it will not complain about staged encode tracks in B-queue that have no reviewer and have not been in A-queue commit 1f4cee95b09d886d43728c7bf8ff442f0b806776 Author: ann Date: Mon Dec 14 17:08:25 2009 +0000 autoScale is now default on commit d8dcf73ff1624cfa0a9ff44f86a8a61c81afd574 Author: galt Date: Mon Dec 14 16:00:05 2009 +0000 "Encode release log update" commit 81274708365b755242fa18ac68567212498dcac6 Author: galt Date: Mon Dec 14 16:00:04 2009 +0000 "Release log update" commit 3428547044cb04a63b5dd6fac715bf90c00ec629 Author: kent Date: Mon Dec 14 03:14:06 2009 +0000 Tightening up identification of composite tracks with views. Adding in some things from branch. commit dfa6a022d95357a01dbb0fbf8fd8470fe4102f41 Author: angie Date: Sun Dec 13 20:20:46 2009 +0000 'Color by bases' labels: use 'mRNA bases' only when we have coding region info; otherwise, use 'item bases' because items are generally not mRNAs. commit f5256d9f76734f82726ffbe7ce427a187ce0703f Author: galt Date: Sun Dec 13 16:00:06 2009 +0000 "Encode release log update" commit cb5f14e37d5f72c9b6d899db6d98a94467871b60 Author: galt Date: Sun Dec 13 16:00:03 2009 +0000 "Release log update" commit 3e5f80b8f582ca283aca0d028277713f14af20d7 Author: markd Date: Sat Dec 12 23:30:41 2009 +0000 finished condor 454 item base coloring commit 57e32bad98fc443b1b87a0e68f09bc206a302bc6 Author: galt Date: Sat Dec 12 16:00:06 2009 +0000 "Encode release log update" commit cc35ce91afdfa0705437f26d3278646385c8514b Author: galt Date: Sat Dec 12 16:00:03 2009 +0000 "Release log update" commit 9d224c73b4dccd55077d47c4879b26a995241cd5 Author: angie Date: Sat Dec 12 14:50:07 2009 +0000 Removed mention of cds-reference since we no longer include that in the table (thx Katrina!). commit 9bd4810117cfc62ef8a914e8c85c54379e839c54 Author: hartera Date: Sat Dec 12 04:45:10 2009 +0000 Added documentation for making track of Burge lab RNA-seq reads mapped by GEM mapper. commit e03681857523026a2774fa259b8cb0acb5417732 Author: hartera Date: Sat Dec 12 04:39:22 2009 +0000 Added documentation for making track of Burge lab RNA-seq reads mapped by GEM mapper. commit de63e0b776ba1fc159e9232087bbc55fd5272f8c Author: hartera Date: Sat Dec 12 04:34:18 2009 +0000 Editing of description. commit 53ed060ab1d5784db56aa0ae5443370fddeb5d5d Author: hartera Date: Sat Dec 12 03:51:17 2009 +0000 Removed Burge RNA-seq data entry and added it to human trackDb level since the settings are the same for hg18 and hg19. commit 3c0c82ad6f7c5c7612bbe6b617ec7dc656e05af1 Author: hartera Date: Sat Dec 12 03:48:43 2009 +0000 Added Burge RNA-seq data entry to human trackDb level since the settings are the same for hg18 and hg19. commit b3c92f08a3a1cbd339817ed003d5aebfc87e0008 Author: tdreszer Date: Sat Dec 12 01:03:18 2009 +0000 Okay, really fix it. commit 0cb769e86d7a8b5e2a0e78343aadf08548de4e4c Author: tdreszer Date: Sat Dec 12 00:49:04 2009 +0000 Fixed bug in centerLabel toggle seen on mrna track when withNextItemArrows is FALSE commit dab31e8d8480862cc5f13699d76ada4997637791 Author: kuhn Date: Sat Dec 12 00:22:46 2009 +0000 third time's the charm. needed to set to pack. default was dense commit c3b2eb910b026258eae9fc6a65b3fc92c6f6121b Author: kuhn Date: Sat Dec 12 00:20:46 2009 +0000 reset so xenoRefGene is visible. more interesting at new defulat pos commit 939bd695986e8031fa1ca8af40b2b941ca1cd1fa Author: kuhn Date: Sat Dec 12 00:09:59 2009 +0000 set human chain to pack and xenoRefGene to hide as default commit f4c5220ef3fa40c71a34d4ff045383d3da5a7087 Author: ann Date: Sat Dec 12 00:06:45 2009 +0000 cleaning up transMapGeneUcscGenesId (approved by markd) commit 4cd0b270a3f97bf2501b190f4de421f6c1fef52c Author: hiram Date: Fri Dec 11 23:51:26 2009 +0000 felCat3 chain and nets are now composites commit cab5af9f1e31c31ab231d5b746d6e41caf67cfe7 Author: ann Date: Fri Dec 11 23:09:05 2009 +0000 adding hg19 to CGAP rule commit f778cc09ffe74389d3edc85cc1739ae7bd582725 Author: tdreszer Date: Fri Dec 11 23:08:06 2009 +0000 Really fixed. commit 111197c8d13264a76fe1c0df42b81d3563d12f51 Author: ann Date: Fri Dec 11 23:04:02 2009 +0000 added the last two sp databases to databasesIgnored list commit f4c0829fd8703a1d755e6859c1c136607819a435 Author: ann Date: Fri Dec 11 22:58:05 2009 +0000 two new SCOP rules commit 245551d042785c782fc78292a996985ff15ba2c3 Author: tdreszer Date: Fri Dec 11 22:55:27 2009 +0000 Fixed bug in propgating view level radio button cfg to the subtracks commit 1fb6d5d37df0df2e5a67a3a61acef648fb365419 Author: hiram Date: Fri Dec 11 22:22:44 2009 +0000 bosTau4 chain and net is now ready for composite commit fb6d5f8c1c901792ebd835dd50f6efbd6e12e816 Author: hiram Date: Fri Dec 11 22:06:09 2009 +0000 bosTau3 is now ready for chainNet composite commit 312b958858491a48b0c0a27a6a668108179e9869 Author: kuhn Date: Fri Dec 11 22:05:42 2009 +0000 turning on danRer6 commit f88c07d91d6541ea33246cd554607ffdf34b026f Author: hiram Date: Fri Dec 11 21:36:03 2009 +0000 Check chain.csh file in lastz/blastz run for parameters commit 9fd7083a12cf1ca9a9ff6950bb61215d03b5b441 Author: tdreszer Date: Fri Dec 11 21:29:43 2009 +0000 Greg Crawford finds his typo commit 02f5f433c74ebc6c7d0f415c2c0ee57905047c25 Author: tdreszer Date: Fri Dec 11 20:38:46 2009 +0000 Added one more cell line and updated others for Crawford. Fixed INFa4h concentration to what Greg specifically requested. commit de6c202ed96b8360787cbf7d8a27a5a91524e7e2 Author: hiram Date: Fri Dec 11 20:18:31 2009 +0000 Needed some release alpha tags to avoid errors commit 96003f3d620f1e3afdd73fe3f7b9145a2eb280e9 Author: hiram Date: Fri Dec 11 20:12:24 2009 +0000 add chainMinScore to the bosTau2 chain entries commit 7e69ef5c86aea2daa0ba6df1bed97321ae2d0d43 Author: hiram Date: Fri Dec 11 20:01:51 2009 +0000 fixup chainNet priorities for bosTau2 commit d469afd5e366288d053040534fdebaf616050058 Author: hiram Date: Fri Dec 11 19:33:52 2009 +0000 no need to have bosTau2.chainNet here commit e9c4e5247ad88d09cc1d967d4a9b016f4f58b8dd Author: hiram Date: Fri Dec 11 19:26:41 2009 +0000 Eliminate much of the garbage from other chain tables and find appropriate tree in the phylo tree commit 58a88067f2c2a3500955b78e1d3b46d19cf47177 Author: tdreszer Date: Fri Dec 11 19:26:11 2009 +0000 Adding protocol and treatment dimensions to HAIB TFBS commit 9267ad1dea460a025964efb97c79cf707d95aeac Author: hiram Date: Fri Dec 11 18:58:35 2009 +0000 No need to mention the cookie commit 4de04e222c794d885282484777d90df9393734d6 Author: ann Date: Fri Dec 11 18:54:09 2009 +0000 new rule for pfam relationship commit f2d77de0d120b1984eeb5e15c82dcbe3bee3e0e1 Author: tdreszer Date: Fri Dec 11 18:33:48 2009 +0000 Added cell lines and treatments for Crawford. Will need to extend cell line definitions. commit 840cd7e8975a087cd8a9bb90bbdd81cee349d4d6 Author: hiram Date: Fri Dec 11 18:29:00 2009 +0000 Indicate the loading procedure for a bigWig file. commit 9899174fa3b588110b55186bbe6fc3f36d18edbf Author: ann Date: Fri Dec 11 18:16:03 2009 +0000 loosened up allenbrain rule commit e31225792a825340aac90b1df3abed287f4e4798 Author: hiram Date: Fri Dec 11 18:13:16 2009 +0000 Fixup central.domain and central.cookie comments commit d95afb513774ba6475cb9d880425a65ad86a0b01 Author: galt Date: Fri Dec 11 16:00:06 2009 +0000 "Encode release log update" commit 8c2d772fccdc25d8e5e6281a0da5b4bee1fd50a7 Author: galt Date: Fri Dec 11 16:00:03 2009 +0000 "Release log update" commit 87b7958b125e644dcb49479e902320995ea7f894 Author: angie Date: Fri Dec 11 15:32:47 2009 +0000 Null check to prevent segv in command line runs (cgiScriptName returns NULL unless env var SCRIPT_NAME has been set). commit 7db59fe5349c0c89f31f3cd5637d112799b743ce Author: angie Date: Fri Dec 11 15:14:44 2009 +0000 A couple other places where cds-reference needs to be omitted from the list of SNP functions if version >= 130 (Thanks again Katrina!). Also removed an extraneous comment left over from a branch tag move demo (1.429). commit 6f2a5d98fc1afc9d4851a950640f46527c664b01 Author: kayla Date: Fri Dec 11 00:42:35 2009 +0000 removed some "release alpha" lines commit c2aba646f018d934176e4f9254f6134b28ece1d6 Author: ann Date: Thu Dec 10 23:41:43 2009 +0000 added a missing rule for TransMap tables commit 44adc5e1db99fe501e9703da83833c4dac93253e Author: braney Date: Thu Dec 10 23:11:44 2009 +0000 fix short label for GIS RNA-pet prostate commit 17316b24e0d99504ae00a02742630e9ba9ceaa1d Author: ann Date: Thu Dec 10 22:59:16 2009 +0000 oops. joining lines. commit 101a09d1a76b036d1c6d6dbfee1c4eaf8b9928c4 Author: ann Date: Thu Dec 10 22:50:23 2009 +0000 correcting list of dbs for which transMap is built commit 7ff7f46b881aa0c4a8cbc849583c6e44917bacfd Author: ann Date: Thu Dec 10 22:06:52 2009 +0000 removed broken link to danRer6 commit 0d180b66c66206ce2385565833a79c68ef89b1b9 Author: hiram Date: Thu Dec 10 20:02:23 2009 +0000 unlink the custom wia file after it is open so it will disappear if the loader fails commit 7e6ddffb0586ca941431fee3969af1bf5132a439 Author: hiram Date: Thu Dec 10 19:58:49 2009 +0000 backward autoScale default for custom tracks, have autoScale on by default commit c0fd1187a3a4d20abc274b593f6b38635a321cda Author: fanhsu Date: Thu Dec 10 18:15:31 2009 +0000 Updated SNP Arrays description page for new Illumina products and remove their old ones. commit f501e0b526a2434ba5f352a3373fd6c786b9b79c Author: fanhsu Date: Thu Dec 10 18:07:23 2009 +0000 Added search terms for 3 new Illumina SNP array chips. commit efb7ae29be8359ddbb600133e7cdd9e753cd23ae Author: fanhsu Date: Thu Dec 10 17:46:18 2009 +0000 Put back snpArrayIllumina650. commit 2f65d74e64da15afde94e47d7a29456ba14db143 Author: galt Date: Thu Dec 10 16:00:06 2009 +0000 "Encode release log update" commit 96f21f3e6ac4173a7a89a7465268bc3996a4b724 Author: galt Date: Thu Dec 10 16:00:02 2009 +0000 "Release log update" commit fcc7f76b0530f5d7f2873def262c2c2ee1a98e10 Author: angie Date: Thu Dec 10 15:02:12 2009 +0000 Got rid of bogus bamIgnoreStrand() -- make useStrand explicit. Added auto-detect of missing 'chr' in sequence names, so stripPrefix setting is no longer necessary. Better message for samopen failures. commit 1b06faae7ebb6dcc5581d11dddf43016469ff9a8 Author: kent Date: Thu Dec 10 07:13:56 2009 +0000 Improving error message. commit e107cb2746b4318a4ba22183337e9728e284370a Author: kent Date: Thu Dec 10 06:00:04 2009 +0000 A few fixes from release tag being lost in child during override. commit 0032b06eb2c00db40e37ace629b8c7fdff515138 Author: kent Date: Thu Dec 10 05:51:44 2009 +0000 Run of tdbRewriteReduceReplaces. commit 888b61ed865abb1f47a9c351148c1e989d3b9c99 Author: kent Date: Thu Dec 10 04:38:10 2009 +0000 Adding view tag to view. commit 3613f070339e64f18a821337532c2d7e16879941 Author: kent Date: Thu Dec 10 03:06:25 2009 +0000 Adding shortLabel to view. Fixing small indentation problem. commit e9cf17ccc9ed3c7c52fece65efc9e7212993a72e Author: galt Date: Thu Dec 10 00:17:44 2009 +0000 v221 preview commit 29c7bec17e16decead007c0c3c9806ebe0a3da66 Author: hiram Date: Thu Dec 10 00:10:24 2009 +0000 Ancient chain track has no axtChain commit d5b1efa3f064f6cb1372d8ea07b6e3b36a913efd Author: hiram Date: Thu Dec 10 00:09:49 2009 +0000 Ancient chain and net has no axtChain command. commit e299900d461ffa7f49ebd4dcd2308e4970ab620e Author: angie Date: Wed Dec 9 21:57:06 2009 +0000 Omit cds-reference (fortunately the last element of the snp125Func variables) when version is 130 or greater. commit 83ac0bb81c4c7d8778c933e7f7c11a517b03ffb5 Author: angie Date: Wed Dec 9 21:52:19 2009 +0000 Removed mention of cds-reference since we no longer include that in the table (thx Katrina!). commit 86b24c161fe35817955b3b0b8cfd2ba9c674bcad Author: fanhsu Date: Wed Dec 9 20:56:43 2009 +0000 Removed snpArrayIllumina650 per Illumina's request and added 3 new Illumina SNP arrary subtracks. commit ba874b4688b9170ad7c7e303e213517514edc207 Author: fanhsu Date: Wed Dec 9 20:54:34 2009 +0000 Added two more Illumina SNP array subtracks. commit 732ebaa472c329555a4ade0557638fa1f31a2d6a Author: tdreszer Date: Wed Dec 9 20:27:00 2009 +0000 Added protocol and treatment to HAIB TFBS commit 95ef2f333b1aa767d4dff85929d99a4b71fbd26c Author: tdreszer Date: Wed Dec 9 20:09:09 2009 +0000 Added 3 dimensionChecked terms and made subGroup6 allowed on any type commit 58e15caa2078e2fe90aed4f0f323e95669b73d0a Author: tdreszer Date: Wed Dec 9 19:58:17 2009 +0000 Added protocol as another term commit eb7cd5db3bf91ead42c46990ee5dc8238bfd5b0a Author: kent Date: Wed Dec 9 19:53:34 2009 +0000 Removing details page when clicking on RepeatMasker but not on a specific repeat. commit 3d0016b4a49aaea7a56847a4a8ac90ed907b04a7 Author: braney Date: Wed Dec 9 19:33:31 2009 +0000 add stubs for SAM and BAM format checking commit 778dab37aec2ba7d38d2a34b381b4e9b5032304d Author: braney Date: Wed Dec 9 19:32:59 2009 +0000 add support for SAM and BAM files (call validateFiles) commit c5f711a54f065a50ec6b1ff44db97d097061254f Author: hiram Date: Wed Dec 9 19:28:45 2009 +0000 In same order as conservation track commit d15506e5bac6b8817c2adb0edf4d8b7d6a9f4426 Author: galt Date: Wed Dec 9 19:28:10 2009 +0000 Added column to display remote ct errors (big*, bam). Fixed some stray tags. Uses new func javaScriptLiteralEncode(). commit 8ac1606f41322edf764e2afde5e2959565c42d3a Author: galt Date: Wed Dec 9 19:27:06 2009 +0000 splay remote errors if adding new cts. Unless hgCustom, filter out cts with load err (big*, bam) from ctList. Also improved add track list handling using slAddHead and slCat instead of slAddTail. commit 9f7e6c8ec93cf9983c20548dd96bae4b65873126 Author: tdreszer Date: Wed Dec 9 19:26:52 2009 +0000 Example with protocol and treatment commit ed56e481fd58cf895c6eab33fc6862dcb95c135f Author: galt Date: Wed Dec 9 19:26:12 2009 +0000 Added Catch around remote resource (big*, bam) loader when it tries to open the resource commit 0b6ae9753b50e03184fb9d615892d3af071087f3 Author: tdreszer Date: Wed Dec 9 19:26:07 2009 +0000 Added protocol and treatment terms commit c73d6f45535ec0c82c562a58fcbdd23090bdb249 Author: galt Date: Wed Dec 9 19:25:19 2009 +0000 networkErrMsg field added to customTrack struct commit 5bf7f13da604890908b1aafe2cb1310b866724f5 Author: fanhsu Date: Wed Dec 9 19:24:40 2009 +0000 Added snpArrayIlluminaHumanCytoSNP_12 sub-track of SNP arrays track. commit d74dbb85d9099740ffd491e40c13bc70902f3864 Author: galt Date: Wed Dec 9 19:24:35 2009 +0000 added new func javaScriptLiteralEncode commit d10497c8ec58bedb68aec3eadc06a92a307e9ffd Author: braney Date: Wed Dec 9 19:05:28 2009 +0000 when checking fasta sequence names, stop checking at space to allow extra stuff that folks often put after the sequence name commit df5da0082a25e6ed1d0b53a1179e8c11e8309649 Author: braney Date: Wed Dec 9 18:55:26 2009 +0000 add two letter codes to the CalTech RNA-seq short labels commit 24facf1dcee5166bc29163c764d9c04d976c5446 Author: fanhsu Date: Wed Dec 9 18:54:27 2009 +0000 Added 1 table for an Illumina SNP array chip. commit c49dc57dac54430772e438377d14ac0289baefd9 Author: fanhsu Date: Wed Dec 9 18:53:09 2009 +0000 Added 2 new tables for Illumina SNP array chips. commit 85dade0d129c55a3298a66588e5b6abf736699a9 Author: fanhsu Date: Wed Dec 9 18:50:25 2009 +0000 Added table definition for 3 new Illumina SNP array chip raw data. commit ffec847d40e6c2b37db9a2bf7d292bca765c6e9f Author: braney Date: Wed Dec 9 18:44:22 2009 +0000 put cell types in alphabetical order for RNA-seq tracks commit 60bdb0199d1b52bd970b45a043d5d8c3fb1e8cb4 Author: braney Date: Wed Dec 9 18:35:25 2009 +0000 change view terms *RawSig* to *_Raw_Signal commit 2e37e05263ebe08c7b574f7e0f6f394cddc60ac6 Author: hiram Date: Wed Dec 9 18:28:01 2009 +0000 Eliminate confusion from chainSelf tracks commit b3d1ee7e3dcf1a96ca0d535d2ddb48ff2194afad Author: hiram Date: Wed Dec 9 18:26:55 2009 +0000 Initial source appears to work OK commit e414671cf66bd4a1c8fd407f527ab5accfe7a33b Author: braney Date: Wed Dec 9 18:25:17 2009 +0000 RNA-Seq to RNA-seq commit adf70b9294db4c17dda0cd296b0f717b1dbede45 Author: braney Date: Wed Dec 9 18:07:44 2009 +0000 take out unused views from settingsByView and defaults commit 92955fd76ed23ceb7ec8b384cc847e170f1e6fc0 Author: tdreszer Date: Wed Dec 9 18:03:19 2009 +0000 Added some treatments and protocols for HAIB commit ff7f5b13244a0f9b9024fa830c94faa892e625b0 Author: tdreszer Date: Wed Dec 9 18:02:37 2009 +0000 Added protocol for HAIB commit 70d6af93bd5796020119131da69eec5f27ef760b Author: kent Date: Wed Dec 9 17:38:19 2009 +0000 Rewriter to take out views and put in a new layer of hierarchy seems to work. commit e0cee8514378c27618a9c6fb1a162319a9f48f37 Author: hiram Date: Wed Dec 9 17:05:37 2009 +0000 Initial contents commit 4b73e8e7e66d0e1ba5b7158c894f3381fe31e9e7 Author: galt Date: Wed Dec 9 16:00:06 2009 +0000 "Encode release log update" commit 7ae56c3f14bf14c119297dd3bdfb3916b074d84b Author: galt Date: Wed Dec 9 16:00:03 2009 +0000 "Release log update" commit f96d914530e38f6fae662acac929f032d821903f Author: kent Date: Wed Dec 9 10:15:33 2009 +0000 Fixing bug that limited to no more than 4 settings in a settingsByLimit for any view. Sharpening line number reporting in error messages. commit 498bfbbfc6c07af7b03862bc89e9ae8f1692afc4 Author: kent Date: Wed Dec 9 10:14:00 2009 +0000 Fixing bug that limited to no more than 4 settings in a settingsByLimit for any view. commit eed76793c1506309b24de5147c46c37ffb0ddaac Author: markd Date: Wed Dec 9 05:58:28 2009 +0000 added references and credits commit 45ab7fb3cb12d9f8de3b75c96fc2e7b2f0028fee Author: markd Date: Wed Dec 9 05:25:35 2009 +0000 add CA condor 454 commit 7efa046dcf304d3388387b16a82cc308c6ba0eaa Author: tdreszer Date: Wed Dec 9 03:39:48 2009 +0000 Keeping the record up to date commit 71e5ab2fba7b9556715276ef3d738ccd55106930 Author: tdreszer Date: Wed Dec 9 03:36:59 2009 +0000 Added a couple color defines commit 8b11526069b9ddfb59348b77f91b93974bcf32a3 Author: tdreszer Date: Wed Dec 9 03:35:50 2009 +0000 cartJustify has been added to clean up _imgOrd settings superceded by changed priorities commit b92b5722d197252256f196c3b3ace332bf63a03c Author: tdreszer Date: Wed Dec 9 03:31:09 2009 +0000 Checkin for FLAT_TRACKS for dragReorder. Also several other features worked out or cleaned up commit f1ab658faa781366289d812e3b9bb7ab41aba9ab Author: tdreszer Date: Wed Dec 9 03:28:58 2009 +0000 Tie the chrom imnnage drag jump feature to advancedJavascriptFeatures commit 4cacbf242ebb1169b4b2e27c063cd671a2b22692 Author: kent Date: Wed Dec 9 02:28:29 2009 +0000 Rewriter that will convert replacement records to override records when possible, and otherwise add comment that it is a replacement record seems to work. commit e6b50e9c2b6956cd6f2e8aa5a601edfc72d54afc Author: kuhn Date: Wed Dec 9 01:58:17 2009 +0000 added whitespace around image commit 259afeaed8772b5c7efd7c9d38554bc16ea7bb9d Author: braney Date: Wed Dec 9 01:51:41 2009 +0000 change in to on commit 7d95747c47cfb1ab2f3c1642b518eca6dade3c28 Author: kuhn Date: Wed Dec 9 01:38:54 2009 +0000 reversed priorities for chainNets on cow commit 1e0690c28a4a6b77f904ce016adceb5928e793fb Author: kate Date: Wed Dec 9 01:03:41 2009 +0000 Fix bad metadata fields in UW CHIP-seq. Tweak track labels too for consistency commit 2f3dfc5eab40892b5737ab043346c167747d4122 Author: kate Date: Wed Dec 9 00:26:52 2009 +0000 Short label improvements to UW ChIP-seq by Thomas Juettemann commit e2d6a890615863a645c11b778d108aceb570e26d Author: hiram Date: Wed Dec 9 00:26:36 2009 +0000 All chain net tracks in Marmoset are now composite tracks commit 4f4a48bbd67ea5fe56213827fa28584a933627b6 Author: hiram Date: Tue Dec 8 23:44:45 2009 +0000 adding chainNetRn4 and chainNetHg18 for Cow bosTau browsers and setting appropriate release tags to separate from older individual tracks commit dc5f3b6d3e62f82c73d86fc336787fb167ac05ca Author: hiram Date: Tue Dec 8 23:39:35 2009 +0000 all chains and nets on any Cow browser are now composites commit d0a58208d8fc69de553c58fc2694e58e596ecf4b Author: kent Date: Tue Dec 8 23:39:11 2009 +0000 Getting rid of debugging statements. commit c24fe38645d170620dde6941a3096b2fc53f4885 Author: kent Date: Tue Dec 8 23:38:23 2009 +0000 Rewriter that adds 'replace' on track lines in subdirectories where are redefining an old track rather than defining a new track at that level. commit 46751c8a60199b89754bea529e9b32e97155e0a3 Author: fanhsu Date: Tue Dec 8 23:25:59 2009 +0000 Added two more subtracks for Illumina SNP arrays. commit ae5ed0428eb709ab54c36563a690de6e45281734 Author: kent Date: Tue Dec 8 20:42:50 2009 +0000 Making it so that don't lose blank terminating lines in raNextTagVal. Simplifying logic in raSkipLeadingEmptyLines. commit 8811708a7e53a9b368a199cdd1aec856d05a43f4 Author: hiram Date: Tue Dec 8 19:39:22 2009 +0000 ensGene default pack commit fe8f5a5cb7e718c490450c9dec53782ad44a0c3e Author: hiram Date: Tue Dec 8 19:38:59 2009 +0000 Some Fire Lab experiments commit bbf5a826e3a1c4e5cd5b579212e6d4d0850c7558 Author: hiram Date: Tue Dec 8 19:37:37 2009 +0000 Adding link to sequencing center project page commit 59f8cf2ca733416ac560d55ee2b977c4f5481aa8 Author: hiram Date: Tue Dec 8 19:36:27 2009 +0000 Obsolete genome at this time. May reappear sometime in the future commit 8476ea7a56430900c0d1cc3152d14530e630373b Author: tdreszer Date: Tue Dec 8 18:44:27 2009 +0000 Created static variable advancedJsEnabled to avoid excessive calls to look it up commit 59b6e6579dab8319e1e5ffaefa3ecf572c0fdd3c Author: hiram Date: Tue Dec 8 18:40:38 2009 +0000 Adding ctgPos2 track for oryCun2 commit b312b21ba2e7911a5b839ea32bb1be06b41b1a6f Author: tdreszer Date: Tue Dec 8 18:23:59 2009 +0000 Restored viewLimitsCompositeOverride so that minLimit,maxLimit can be used to prompt range in view level cfg commit 9973f086de5aec0cc0d466cbafeddf4b22d6c533 Author: ann Date: Tue Dec 8 16:41:10 2009 +0000 Moving horse c/n up a level. No combo chainNet track. commit c22b313a399dc0f30dfef4223908b1cbcff94583 Author: galt Date: Tue Dec 8 16:00:07 2009 +0000 "Encode release log update" commit b6d78fdb0df7cbfb60c3aedf608e9a2f21ec6a04 Author: galt Date: Tue Dec 8 16:00:03 2009 +0000 "Release log update" commit fe3457d952a0d5154346f1eeeb647c4d9fcb4d2c Author: kent Date: Tue Dec 8 08:48:53 2009 +0000 Rewriter that alphabetizes tags after the first one in a stanza. Not totally sure I like result, but worth bouncing off other people. commit e5319b4516e2855a38d39bdce1b6183fa9a064ba Author: kent Date: Tue Dec 8 01:24:28 2009 +0000 Utility to extract values of tags actually seen seems to work. commit f2e4fa6d015e132c0da0927daeb33de9f6310eb1 Author: donnak Date: Tue Dec 8 00:37:44 2009 +0000 Archived some things. commit 05282a58f68a595392beb4f46ff42d75288737a9 Author: donnak Date: Tue Dec 8 00:37:27 2009 +0000 Added 2 news items, archived some things. commit 2896a83cde59cec91ab7843a5a8b54f56433b1f1 Author: ann Date: Mon Dec 7 23:40:20 2009 +0000 back to separate chain and net (chainNet is still release alpha). commit 7878da7aa605cf3d9484d79a13cd6b892132f6fa Author: katrina Date: Mon Dec 7 22:57:25 2009 +0000 added dragAndDrop subTracks line to parent block of UW Footprints composite track to enable drag & reorder of subtracks commit e9645f97365439be7ae4ec1e75d00cb68d5f1dac Author: ann Date: Mon Dec 7 22:34:06 2009 +0000 using ChainNet instead commit 4bb3b9fd20338aa5fb909cbde47f278309f809fc Author: ann Date: Mon Dec 7 22:33:34 2009 +0000 correctly ordering Opossum. overriding chain vars for Horse. commit fa1b865fe78e776a3dacdb62012b33a9007e9f51 Author: hiram Date: Mon Dec 7 22:00:51 2009 +0000 Move all the chainNet definitions off to their own file commit 5c1549bd8d597b0f008dc27840cea261871b4986 Author: kent Date: Mon Dec 7 20:44:36 2009 +0000 Making trackDb pass tdbQuery -check -alpha commit 17a81dbd94bb83ddd456dde5e34a482dff8ad9cb Author: angie Date: Mon Dec 7 19:44:24 2009 +0000 New test for udc: interleave accesses from two open udcFile * handles to the same part of a URL/file. Fairly reliably fails on hgwdev. I'm not hooking it into makefile until udc passes. commit 056baeb4e41351da752b3054eaa6b4998400d281 Author: tdreszer Date: Mon Dec 7 19:34:20 2009 +0000 Replaced a bunch of viewLimitsMax vars with minLimit and maxLimit. Don't like it but will go along with the current. commit d0397dab3cff78fee31558aa8747d25af5cf6ca7 Author: ann Date: Mon Dec 7 19:28:38 2009 +0000 overrides for chain vars in chainNetOrnana1 track commit 9eed41b5702784f096b40b08b216217bd3529222 Author: tdreszer Date: Mon Dec 7 19:17:09 2009 +0000 Fix for bug Katrina found. All plus/minus buttons were failing when no matrix exists commit 2f815616b0d1b25e8a8815881bf3fae11c17df65 Author: braney Date: Mon Dec 7 19:14:03 2009 +0000 first pass at DAF for Myers RNA-seq commit 9b885325914f5b616cb9d62c69c5f18aa764eef0 Author: galt Date: Mon Dec 7 18:26:37 2009 +0000 fixing neg strand issue reported by user for pcr psl output commit 5f27e1cd0568400b2d27a216393d819cccf3492f Author: kent Date: Mon Dec 7 17:46:29 2009 +0000 Fixed linux-specific compiler warning. commit 9ef4ab853caf7676468b4fb6496c2fe01d0f7ddb Author: kent Date: Mon Dec 7 17:44:25 2009 +0000 Avoiding generating a duplicate record for vis when there is both priority and vis. commit b7bd559b64c4d335b85f9448b9fcd6f5a565783d Author: galt Date: Mon Dec 7 17:43:19 2009 +0000 making it a verb commit b2d29d895af1db578ec38dcbd9b1d07296519a08 Author: kent Date: Mon Dec 7 17:42:39 2009 +0000 Adding a little more comment. commit 87103c8f53a18d1c2876da230a5611c78d5f4f50 Author: hiram Date: Mon Dec 7 17:42:13 2009 +0000 Final loaded phastCons and phyloP for 46-way alignment commit 7ee03afcab9a8eb925d35950c82ededdce92c940 Author: kent Date: Mon Dec 7 17:41:44 2009 +0000 Fixing a few little places where the automatic rewrite left duplicate records. commit c101784ab2232185657d62dea161c7b296fa76a0 Author: tdreszer Date: Mon Dec 7 17:31:38 2009 +0000 Fixed poorly worded release 2 note. commit 6f2bd326b6b9f86e54ec20290bdcc7e3f3faade3 Author: kent Date: Mon Dec 7 17:23:28 2009 +0000 Merging visibility.ra and priority.ra files back into trackDb.ra commit d3bf00280791778fd63ed8691cc18f8fb304adf8 Author: kent Date: Mon Dec 7 17:19:13 2009 +0000 Rewriting to get rid of visibility.ra and priority.ra files. commit a26dcadaba965fb1fe6efb26ca553816555a3665 Author: tdreszer Date: Mon Dec 7 17:08:29 2009 +0000 Switched Gliobla and Medullo commit bc7d1548d1f7af0708a71d8b156807f8c70941dd Author: kent Date: Mon Dec 7 17:00:56 2009 +0000 Moving visibility.ra contents to new trackDb.ra file for rabbit. commit 187f60053573ff9a1ec032a219d67291f45fbb2e Author: kent Date: Mon Dec 7 16:57:36 2009 +0000 Removing empty visibility.ra commit 423a79b9f9b2f58655fc522866cb8c04d812f307 Author: kent Date: Mon Dec 7 16:56:04 2009 +0000 Removing empty visibility.ra file. commit c068d0b92a260f88a65150305d541df90a418b31 Author: braney Date: Mon Dec 7 16:12:07 2009 +0000 change viewLimitsMax to viewLimits commit fa9cb70884b773853c513ce3bd58ddcfec3aad1d Author: galt Date: Mon Dec 7 16:00:06 2009 +0000 "Encode release log update" commit 1532f853f10b43bb61fcd39e84f0d15d4fb01d96 Author: galt Date: Mon Dec 7 16:00:03 2009 +0000 "Release log update" commit fb797411dbcddd237e5ba53f217a6be920b4dea2 Author: kent Date: Mon Dec 7 02:37:39 2009 +0000 Starting to experiment with some rewriting. Not very far along. commit a8eee5668bbd401961ce8fb640256aa63e98ecf4 Author: kent Date: Mon Dec 7 02:37:21 2009 +0000 Fixing some problems with the new dyString parameter to the ra readers. commit 4198daf5c68e3cef37c77bd5aca314b8fe59570a Author: kent Date: Sun Dec 6 20:11:22 2009 +0000 Making tdbRecord have start and end lineIx, and also text representation of stanza. commit 9d0999b901c59d507e5455ff62d6b1b85262bc89 Author: kent Date: Sun Dec 6 20:09:36 2009 +0000 Adding optional dyString parameter. commit a89fb5d03dc63b51039ff3b869dade190f28b615 Author: galt Date: Sun Dec 6 16:00:05 2009 +0000 "Encode release log update" commit 85f2183bed9bfa0df1f5c39130dac353838fb7f1 Author: galt Date: Sun Dec 6 16:00:03 2009 +0000 "Release log update" commit 7443f2805169db0dc18ebd212e0b3343ffa75af0 Author: kent Date: Sat Dec 5 22:47:39 2009 +0000 Adding additional checks on child/parent relationships. Forcing children to be close to parent in file. commit 6d6e6df47e551bc56985cc9ba516e89ac00780e0 Author: kent Date: Sat Dec 5 20:10:39 2009 +0000 Moving around some subtracks that weren't directly under their parents. Adding some indentation to subtracks. commit e8b68690c7b44f530edf22299fa15ff242db4fbb Author: larrym Date: Sat Dec 5 20:01:42 2009 +0000 checkin a minified version, with fixed MS-DOS line ends commit 1f188c7f27b48e3420fd675392349ff25775c947 Author: kent Date: Sat Dec 5 19:30:24 2009 +0000 Making check for tag names in RQL query existing happen even without -check commit 6e2daa5eac04e7509120eaecdc1bd2e073a131c4 Author: braney Date: Sat Dec 5 18:20:25 2009 +0000 fix some short labels commit a2606480c7e978ed7112a7b927635704d5ad13d6 Author: galt Date: Sat Dec 5 16:00:07 2009 +0000 "Encode release log update" commit 4490bced90aea9cb304ff78e1ecd22f86a19a3f7 Author: galt Date: Sat Dec 5 16:00:03 2009 +0000 "Release log update" commit 8630ddbed058a1b45e60e7891db862050248c3b8 Author: kent Date: Sat Dec 5 03:52:19 2009 +0000 When you do a -check also does check of query. commit 55ab31c0a919d307542b61d968bb5d8d5208d9fd Author: kent Date: Sat Dec 5 03:51:36 2009 +0000 Adding in whereVarList to rqlStatement commit 6a746c1e0eb8aa5f6962f5ca4f8dc4228c5f40f0 Author: kent Date: Sat Dec 5 03:51:27 2009 +0000 Adding whereVarList to rqlStatement structure. commit cf0021b5ed8d4d75cfded24b0649960d9f8b9f56 Author: kent Date: Sat Dec 5 02:45:48 2009 +0000 Adding -noBlank option commit db7629f41a56cb575de6c96fa63ff31dd469504f Author: kent Date: Sat Dec 5 02:32:49 2009 +0000 Fixing bug in -strict logic for parent tables. commit 7ac8a4b8285201efeba970bda456af45c01a0157 Author: braney Date: Sat Dec 5 01:37:52 2009 +0000 add some new cell and compartment types to the RNA-pet set commit eb0163a029a107a9f7aa30da0c9b24bddce9c98d Author: larrym Date: Sat Dec 5 01:29:01 2009 +0000 CONTEXT_MENU stuff; mostly turned off, except map area id's are live commit 5f3519ab7e503668844b0e1d7a5bd1f62f3f895d Author: fanhsu Date: Sat Dec 5 00:22:49 2009 +0000 Updated illuminaLookup1M.c to make it work again for newer Illumina SNP array chips. commit 67819a6ffa234dcb50fdaf3650e251ef3ac5461c Author: kate Date: Sat Dec 5 00:21:24 2009 +0000 Update assembly in projects table (support for mouse and hg19) commit 1530a40a5461b3771bbcfb34b099c226cc55d8d4 Author: kate Date: Sat Dec 5 00:20:47 2009 +0000 Add new grants from ARRA (stimulus) and other Mouse ENCODE (LICR) commit 1fcae4ee1bbf4a93a24d1714ba6c9fe4d0d4d981 Author: hiram Date: Sat Dec 5 00:00:22 2009 +0000 Fix usage message for chromSize argument commit 4f5356a81b049abc7328889f7f54712cdfd1cc8b Author: hiram Date: Fri Dec 4 23:56:58 2009 +0000 Really do not contact the database unless it is actually required commit 051c291f62d512ef3d3fd8571662e86900d00704 Author: markd Date: Fri Dec 4 23:50:23 2009 +0000 added -cpu and -ram to the parasol add jobs command commit 0d5016877da697a53d5f8367804931e0964cbae5 Author: braney Date: Fri Dec 4 23:34:37 2009 +0000 move pairedTagAlign to bigBedTypes commit 92f73365cd58945d6c57d6bc589d36b7e7911610 Author: kent Date: Fri Dec 4 22:19:40 2009 +0000 Utility to make first cut of tagTypes.tab seems to work. commit 5320ee2f995c3f4716b030443138e685e7ccb3f7 Author: kent Date: Fri Dec 4 22:15:16 2009 +0000 Making -check do something, specifically look for tagTypes.tab and check tags against it. commit d04e8744fa2eb55f1835c5c4dc13d812f34791af Author: kent Date: Fri Dec 4 22:14:36 2009 +0000 Adding file that list all available tags and the types they can appear in. commit 63d7cea7f707fa4c5e35632bd3ea9ec031276c8e Author: fanhsu Date: Fri Dec 4 22:06:19 2009 +0000 Added one line for Illumina snpArrayIlluminaHumanCytoSNP_12 chip. commit e9a350489de621fd640a67a0e785346304d4aa5c Author: kent Date: Fri Dec 4 21:35:39 2009 +0000 Fixing viewLimts that should be viewLimits commit 277fc61a583ccd73c199d6cec96e6a28e3d737d8 Author: braney Date: Fri Dec 4 21:25:54 2009 +0000 drop entry for wgEncodeGencode2WayV3 which is for hgwdev-gencode only commit e2d2f968c4ab118852b60869595a75319cdb10fd Author: kent Date: Fri Dec 4 21:25:30 2009 +0000 Fixing dataversion that should be dataVersion. commit f817e89ee1794279a8fb4bc30bc13f0e804dd500 Author: kent Date: Fri Dec 4 21:17:51 2009 +0000 removing unused track stanza with weird field. commit 0aac9a5b9a957ae4a69067b4091df5ce0e11641c Author: kent Date: Fri Dec 4 20:43:36 2009 +0000 Fixing visibililty typo commit c0b61bd90fcbd175b63c0e12d5ea1610d64c8740 Author: kent Date: Fri Dec 4 20:37:24 2009 +0000 Removing unused track stanza with unusual tag. commit ee98e96d7e3041290ee6550a665431f0de750fdb Author: kent Date: Fri Dec 4 20:35:00 2009 +0000 correcting altcolor to altColor commit a8934843934b1ea6c67372720aa30945b4c8c227 Author: larrym Date: Fri Dec 4 20:34:22 2009 +0000 contextmenu css commit a1b55320b81df15665b9bef1e1f80779ae4dd086 Author: larrym Date: Fri Dec 4 20:33:53 2009 +0000 jQuery UI CSS Framework commit 358a7b027f559ff8babcb3b0524ac59b1480f12a Author: larrym Date: Fri Dec 4 20:21:37 2009 +0000 jQuery UI 1.7.2 commit afcbab6829e6e64983ae917498fe0eeac906b559 Author: larrym Date: Fri Dec 4 20:18:33 2009 +0000 jStore 1.2.0 commit 5881c7fddee2db946285f64d6b13cdbb0828a3ae Author: braney Date: Fri Dec 4 20:12:12 2009 +0000 add root option to tdbQuery commit 0e4edcfd3d2fd2e98e651a0f0d36c52d166352a0 Author: braney Date: Fri Dec 4 19:34:07 2009 +0000 add release notes for release 3c commit f52635374dff9d65d40de625f9bb2caae18c0228 Author: ann Date: Fri Dec 4 19:01:11 2009 +0000 one was missing from the pushQ entry commit 885d2a03d2ef4697bd2453e98d447e026290feef Author: hiram Date: Fri Dec 4 17:02:25 2009 +0000 Add lowetooltip.js inclusion on behalf of Andrew Holmes commit c2fcb5dc443a82bdc1c86d16612eb71f09d374eb Author: galt Date: Fri Dec 4 16:00:07 2009 +0000 "Encode release log update" commit dbcc4cacf1a15fff1a9c89c705a175da24897fda Author: galt Date: Fri Dec 4 16:00:04 2009 +0000 "Release log update" commit 3909e07e0b6ce73ee96b882406397d2d20025f53 Author: kate Date: Fri Dec 4 01:31:44 2009 +0000 1. Add support for 'organism' option (for mouse) 2. Cleanup (e.g. remove unused ifdef) 3. Add 'tag' option commit 502c353b85587e0b0d7568b5449f5f6cae3484c4 Author: kent Date: Fri Dec 4 00:55:28 2009 +0000 Adding trackDbPatch. commit 2e3a109a4ca64a404d93e581f19d471589e53033 Author: kent Date: Fri Dec 4 00:41:00 2009 +0000 Did some testing, took out debugging statements, and polished interface a little. commit 50055e8a87bc3b305a1d0a2be6231bb0d1f01972 Author: tdreszer Date: Thu Dec 3 23:37:26 2009 +0000 Renamed 6 cell lines by request from Greg Crawford commit 3d753c5b0d910b8e6c4f6214b7143a1593566458 Author: ann Date: Thu Dec 3 23:23:24 2009 +0000 removed alphas from Open Chromatin tracks ready for release commit fa26025b1a12a5456490929e2a3d540b588e918d Author: kate Date: Thu Dec 3 22:19:50 2009 +0000 Add organism setting to Cell Line entries (all existing ones are for Human) commit e0e41be4a8ef91da9f3ab3677c17dc4ecbf09158 Author: kate Date: Thu Dec 3 22:13:22 2009 +0000 Make targetLink handling symmetric with other links (remove special syntax). Splits targetLink setting into two -- targetId and targetUrl commit 49ad9673f082a2011eb54c1051163b40b8ae188c Author: kate Date: Thu Dec 3 22:11:44 2009 +0000 Simplify by: 1) setting link style globally 2) removing special syntax in antibody targets commit 880cccdedc56e0adeedbf08ecc8a9d49a62d9fe2 Author: kent Date: Thu Dec 3 21:51:19 2009 +0000 Improving docs. commit 308be368e316a1ff8246ac52faf8a41400f57bf8 Author: kent Date: Thu Dec 3 21:39:51 2009 +0000 Adding tdbQuery to build. commit 56baf9adb7325c95fc426b30806069bd86ac3ef2 Author: ann Date: Thu Dec 3 21:25:33 2009 +0000 made changes for new wiggle display. cleaned up. commit ed7ed1aa18723b775de0fbbfc5c367c9b5de0e8a Author: kent Date: Thu Dec 3 21:19:21 2009 +0000 Little fixes to trackDb.ra commit 7cf8078d2a32bf509d18714602dd1b849f84dce2 Author: kent Date: Thu Dec 3 21:04:30 2009 +0000 Adding to documentation. commit 63cfb147750c4d16dfe0d5c4ac05175bdd5ebb63 Author: kent Date: Thu Dec 3 20:28:58 2009 +0000 Removing unimplemented 'file' option from usage statement. commit 25d78574afb33a0321adc26d1d977317e9c0084e Author: rhead Date: Thu Dec 3 20:20:07 2009 +0000 Moved the multiz link one directory up. commit 6e8b2ac2e768c91a54fe5fec93ceee8c2a9a5d73 Author: kent Date: Thu Dec 3 20:06:06 2009 +0000 Adding lm parameter to rqlEvalOnRecord since array operation uses memory. commit 90c31700817c9a601805d2155824586e8fbfb7a2 Author: kent Date: Thu Dec 3 20:04:29 2009 +0000 Adding lmCloneSomeWord. commit 75452370c7690c7caf9effb9f79d9da2ab824e24 Author: kent Date: Thu Dec 3 19:26:05 2009 +0000 Making rqlParser handle arrays and field-separating-dots. Evaluation handles arrays but not dots yet. commit 3b2c64820d0a6049d1b527fe4613fe82d4d45cc0 Author: donnak Date: Thu Dec 3 18:53:00 2009 +0000 Updated 10K Genomes pub. commit b923f4de32bd5fe1e28f76e0f9e42804f1c6d5ed Author: kent Date: Thu Dec 3 18:19:29 2009 +0000 Adding integer unary minus. commit 6a4420ae634c64da6db36974ef72d61cc874aeff Author: hiram Date: Thu Dec 3 18:12:12 2009 +0000 remove orphaned overrides for humanChainNet and horseChainNet commit eaa09cf1d8fe754c31d48e052a5257fee81c0c55 Author: kent Date: Thu Dec 3 18:03:09 2009 +0000 Implementing limit clause. commit 7eba2373a4b546b713a6f7748c2f3f270e32168e Author: kent Date: Thu Dec 3 18:00:22 2009 +0000 Adding limit clause to RQL parsing. commit 0952faa5323e0806ff7aa595318a8499ea99aead Author: braney Date: Thu Dec 3 17:59:34 2009 +0000 add restrictionEnzyme to list of non-validated variables commit f34f15466a85146636564fe55515696f8fc6263b Author: braney Date: Thu Dec 3 17:54:13 2009 +0000 add some words to the definition of total commit e3efd64bd485b8711fff0907d527aba5f89d6bb5 Author: galt Date: Thu Dec 3 16:00:06 2009 +0000 "Encode release log update" commit 3a2e87f0272838fad04fbcc18181a936dea69cdb Author: galt Date: Thu Dec 3 16:00:03 2009 +0000 "Release log update" commit 30d0e5a35f02e55127fa51cd371e3e6c7ea59721 Author: kent Date: Thu Dec 3 10:21:39 2009 +0000 Making -strict leave in parents when their children exist. commit 74b5d42a7954d00e79e724ee7a289d21b6bbb6f0 Author: kent Date: Thu Dec 3 08:59:33 2009 +0000 Adding in visibility.ra and priority.ra handling. commit 7af06a915cf4def962b3b7e71ca375173b0ae4ab Author: kent Date: Thu Dec 3 06:03:50 2009 +0000 Freen tests rqlStatementDump commit c266f9d184d60f9b15637a8f5671d42bcb693b19 Author: kent Date: Thu Dec 3 05:59:48 2009 +0000 Fixing more dupes in trackDb. commit 4e371deb9c6cb799adb67917be1f77516ec2871a Author: kent Date: Thu Dec 3 05:17:27 2009 +0000 Fixing some duplicates found by tdbQuery commit 3ff4243b7ac3dc6f4f7ada0ab5e0057fc03642e1 Author: galt Date: Thu Dec 3 04:43:54 2009 +0000 adding feature show_active which filters out the inactive things reaching a completed state commit 8f3368b41f6c8f49623be55b18f3b24df5ed785c Author: kent Date: Thu Dec 3 04:42:28 2009 +0000 Massaging handling of duplicate record detection to handle a tricky case in danRer6 involving inheritence and inherited releases. commit ef3e9750cd102fdf7a49743ea21f4c6e96f02ba5 Author: galt Date: Thu Dec 3 03:56:41 2009 +0000 added db field to show rhtml commit f7d22e45dfda12830aa6e5b5b67a2cabf7913807 Author: galt Date: Thu Dec 3 01:09:24 2009 +0000 adding projects.db field and display, added show_daf and show_ddf commit 16539713a98508d712709d62d0796f8520f20ec3 Author: galt Date: Thu Dec 3 00:28:29 2009 +0000 requested feature quicklinks to jump to sections ABCDL commit 73a5085654b8f05c28624461003a80fb2596c988 Author: hiram Date: Thu Dec 3 00:14:37 2009 +0000 fixup duplicate chainCalJac1 and chainPanTro2 entries commit eb35920907007531271900f2f40551e8655bf755 Author: hiram Date: Wed Dec 2 23:58:50 2009 +0000 Eliminate duplicate definitions of chainHg18 and chainMm9 they are already overridden here commit cb8d9649970e60e9a70562f7b60207465a2dd1e9 Author: hiram Date: Wed Dec 2 23:37:04 2009 +0000 set autoscale to properly read autoscale commit 6b3f51fb36eb8b92ea7b53788101d0db6912b313 Author: hiram Date: Wed Dec 2 23:35:09 2009 +0000 fix autoscale to read properly autoScale commit 45dc870ebe9bc97d26f6a29378835ed0191fac0c Author: braney Date: Wed Dec 2 23:26:23 2009 +0000 show mismatches in GIS Rna-seq alignments commit e8aa0052289eb7324f5b6a242dd061c66028e838 Author: hiram Date: Wed Dec 2 23:11:50 2009 +0000 eliminate duplicate entries for blastzCioSav1 and blastzOikDio0 commit 4c8ce57af6660fa84820d2d381d15453b00e3ef4 Author: hiram Date: Wed Dec 2 23:07:52 2009 +0000 Eliminate duplicate entry for blastzOikDio0 commit f62e9c0398902b56fef54c27c1929da6000a3ed1 Author: hiram Date: Wed Dec 2 23:05:19 2009 +0000 Eliminate a stray track definition line for blastzCioSav1 commit 8e41fb1e69bedb5bd16b7816923a0194eecce0ea Author: hiram Date: Wed Dec 2 23:03:44 2009 +0000 eliminate duplicate definition for axtNetCb1 commit 533141ee782367966d9fbdb79ec4487a8f124b6e Author: hiram Date: Wed Dec 2 23:00:08 2009 +0000 eliminate a duplicate maxHeightPixels definition commit 65813b8d352ae441ed5b59aa2668d6292b8e2edd Author: hiram Date: Wed Dec 2 22:59:03 2009 +0000 Eliminate duplicate spanList definition commit c58909b48847da0bdf36ec2d8a65254db8cbdc58 Author: hiram Date: Wed Dec 2 22:57:52 2009 +0000 eliminate duplicate entry for phastConsElements5way commit 73a6e1a0c39021409505503103d8113796898ccb Author: braney Date: Wed Dec 2 22:36:50 2009 +0000 show different bases in CSHL short RNA-seq track commit c5a81097fbe968ef7f1092639930d0462f8da772 Author: hiram Date: Wed Dec 2 22:29:34 2009 +0000 Eliminate duplicate xenoRefGene entry commit f8af931a17341f1d888112c63e2bff6084c1b5c9 Author: angie Date: Wed Dec 2 22:23:26 2009 +0000 Regenerated qual track to fix omission of chrUn_random. commit 0dbe31da07663132e2e4bac81d31c12dab90e946 Author: donnak Date: Wed Dec 2 21:55:53 2009 +0000 updated MGV pub. commit 15402e79d5949038d2d6f03328fbf84055ae4100 Author: galt Date: Wed Dec 2 21:42:05 2009 +0000 oops get lockuser commit 76846a83bd04c40d426bc4ba93360bb0081ea0de Author: tdreszer Date: Wed Dec 2 21:19:45 2009 +0000 Fix bug in imageV2 maps to make them written in creation order commit 60ce9ec099e7402ec748f648fab571fa6c23a1d6 Author: kent Date: Wed Dec 2 21:02:32 2009 +0000 Improving usage message. commit 623298c78b3fe7ccc5e01383924367ce9b0dfc61 Author: kent Date: Wed Dec 2 21:01:19 2009 +0000 Fixing linux compiler complaints. commit 9211794ef5b10bfc0f71c9c02e0f74bd1e1369d0 Author: kent Date: Wed Dec 2 21:00:09 2009 +0000 Oops, forgot makefile in initial commit off of laptop. commit ef08c3dffdb578f973eed534cb520b44ddea0ca5 Author: kent Date: Wed Dec 2 20:50:17 2009 +0000 Cleaning up debugging statements and also db and filePos pseudo-field handling. commit fa9ad2aa7ddf03f939dc7a1da9ae0c6c21403a49 Author: hartera Date: Wed Dec 2 20:19:56 2009 +0000 Renamed ucscRetroAli description file to have html file name extension instead of hmtl. commit d9abca76da43f88727454c721056fd118d9ef0b4 Author: hartera Date: Wed Dec 2 20:14:33 2009 +0000 Track description for Retroposed genes predicted by RetroFinder. commit cd5512999e306f7614e18d888f94db3319e5daf1 Author: kent Date: Wed Dec 2 20:14:18 2009 +0000 Starting to work. Lots of debugging code still in. commit eca885b37557cfe54a681b538c9ef1ea49cee757 Author: holmes Date: Wed Dec 2 20:02:34 2009 +0000 adding all predictions commit 94c6d279a9762f923d5940c292420d7d087bfc4a Author: holmes Date: Wed Dec 2 20:01:36 2009 +0000 adding gene prediction commit 4791bfb796a2c93851c7cc2066eed12fef30d84e Author: fanhsu Date: Wed Dec 2 19:43:20 2009 +0000 Added GeneNetowrk link for hg19 hgGene page. commit fb10c1432da6822c08e73f7616a6d20cb6a54548 Author: kent Date: Wed Dec 2 19:14:12 2009 +0000 Adding rqlStatementFree. commit 48ec2575dcaa495526ed1415450a7ea784a68f40 Author: kent Date: Wed Dec 2 19:11:55 2009 +0000 Librarifying RQL parser and interpreter. commit 47f4f82c536881cbbf33f7f3dabe084d39fec5ee Author: kent Date: Wed Dec 2 19:10:38 2009 +0000 Fixing bug where options was no longer handling -this=that, just this=that. commit a5a48f1046656e6f792bea11fd84fa9a76428d7a Author: kent Date: Wed Dec 2 19:10:06 2009 +0000 Adding rql parser and evaluator to library. commit 7e2a0dfd7ef2926486bc417ac59f3662beba8a42 Author: braney Date: Wed Dec 2 18:58:42 2009 +0000 don't do LOG transform on RNA-seq or RNA-pet tracks commit e9992a1e5d2fc06c0db92071f9676dfdadc43fd3 Author: hartera Date: Wed Dec 2 18:39:20 2009 +0000 Added entry for RetroFinder Retroposed gene predictions. commit 599828496478c442ef2d28a0539d60a694e0def2 Author: holmes Date: Wed Dec 2 18:31:40 2009 +0000 Adding tooltip CGI in ifdef LOWELAB commit 88ba89d1f3d1b55fe720b1137a1db2433defaeee Author: holmes Date: Wed Dec 2 18:25:33 2009 +0000 adding lowetooltip.js in ifdef lowelab commit 18a0868a1087c49a487ff6ba7778e3c67266042f Author: tdreszer Date: Wed Dec 2 18:20:02 2009 +0000 relabel a couple of Yale tracks that should belong to YCD or Stanford commit f8e80547b4eec0d31dd807143755f7b6c7bf0e34 Author: holmes Date: Wed Dec 2 18:18:22 2009 +0000 Adding lowe tooltip javascript commit c7d6767cbff1cd45fb6eea0cb2bfcdfc1b1f732a Author: galt Date: Wed Dec 2 16:00:07 2009 +0000 "Encode release log update" commit 476b897e2a5470e76d793fb9a55a4eae910cc6b6 Author: galt Date: Wed Dec 2 16:00:04 2009 +0000 "Release log update" commit b5b477706b58da324fb63c296ffb5472ab48df7e Author: kent Date: Wed Dec 2 06:47:27 2009 +0000 Adding check for duplicate records including handling of different records for different releases. Merging together records from root/organism/assembly tree. commit 5095fc549d5b0987ec76ecbf29ab86e18f5ed024 Author: kent Date: Wed Dec 2 06:23:10 2009 +0000 Removing duplicate track records at same level of directory hierarchy, in many cases by adding a missing release tag. commit f0f84fd072996e847246de25e0f0a66548ddcc17 Author: kent Date: Wed Dec 2 05:31:19 2009 +0000 Removing duplicate tags within same stanza. commit 5fe817dac92da3839444f05148bc531d37c2575a Author: kent Date: Wed Dec 2 05:28:46 2009 +0000 Handling include files. CHecking for duplicate tags (in non-include stanzas) commit 84d7e3acdab7fad44ea92ae44dac2a3e0ba1c892 Author: baertsch Date: Wed Dec 2 01:34:47 2009 +0000 change cds from varchar(255) to longtext commit 964fc6f983d1b4be75471182a81a43b3aaf8fb7e Author: baertsch Date: Wed Dec 2 01:34:24 2009 +0000 change cds from varchar(255) to varchar(512) commit 365795a964913fe1991dc1948508dddea7a7b5e9 Author: kent Date: Wed Dec 2 01:29:58 2009 +0000 Initial commit of tdbQuery. Still has clones of some files from raSqlQuery that will eventually end up in library when more stable. commit ba38be6033f47c2aa321de9580942463cf7c11ec Author: kent Date: Wed Dec 2 01:28:29 2009 +0000 Making the this=that option parsing smart about not trying to parse code, filenames, and other things as option. Previously it knew not to treat URLs with = as options. commit d5277212b42294588990973f169d155d4c99d5f1 Author: tdreszer Date: Wed Dec 2 00:57:47 2009 +0000 Removed one file that Richard noticed was replaced with differently named file commit b16e40f0c0894101955f7ab4047de142d2d1c335 Author: baertsch Date: Wed Dec 2 00:46:10 2009 +0000 changed cds from varchar(40) to varchar(255) commit a59d0d625d1e384bea4c55e514194d92596fe814 Author: baertsch Date: Wed Dec 2 00:38:56 2009 +0000 add XX to handle version number commit 9394e9d63bec0083bf006833952641e03a4cfd9f Author: rhead Date: Wed Dec 2 00:24:46 2009 +0000 Turned off tarsier, platypus, lizard, and stickleback in multiz default tracks, and turned on zebrafish. commit 145ea97a36bcacfbdbee2bdef52cd01aafae5b38 Author: kuhn Date: Wed Dec 2 00:13:25 2009 +0000 added star to danRer6, as it's not out yet commit 130c51ed53a65a3a9583b45ba260e7d15ff6e58b Author: kent Date: Tue Dec 1 23:44:25 2009 +0000 Decluttering genes section. Hiding MGC genes by default. Putting hg19's RefSeq Genes back to dense. commit 6abf87f594b1902e158d45dc94b8750082ccbe08 Author: kent Date: Tue Dec 1 23:10:44 2009 +0000 Adding lmCloneFirstWord commit 1568cacdc04295f96f592ff4d4997cb77d19bb0f Author: tdreszer Date: Tue Dec 1 22:47:57 2009 +0000 Backlog of work needing check-in commit abdf28fecd46ccde919fe266737420356e178f3b Author: tdreszer Date: Tue Dec 1 22:47:15 2009 +0000 Finally most of Yale's tagAligns have been corrected. commit 1c69190892531ec9645bbe74956084046bded336 Author: tdreszer Date: Tue Dec 1 22:46:27 2009 +0000 Backlog check-in commit d596b4d4e0e58d65174a2f3e6bb7fd5f91d099a2 Author: tdreszer Date: Tue Dec 1 22:45:33 2009 +0000 Some Rep2 tagAligns were missing. commit 25ba2b3e5bcec8064406afcbf0e0142085719c68 Author: tdreszer Date: Tue Dec 1 22:32:08 2009 +0000 Added in 2 more experiments for HAIB TFSB commit fd61f822c3c139be876c72a34eb78475de0f235f Author: ann Date: Tue Dec 1 21:36:32 2009 +0000 minus quotes commit 039afaa75fde58170186121587ff03d0519f6170 Author: ann Date: Tue Dec 1 21:34:34 2009 +0000 added info about magenta-colored clipping commit f8cdc278c41f031b0211cc077b646dafc067e4f7 Author: ann Date: Tue Dec 1 21:25:42 2009 +0000 added explanation of mean+whiskers commit e046a731cc0e9aa17957e684aa0a2036e9154b93 Author: kate Date: Tue Dec 1 19:59:52 2009 +0000 Allow mouse commit e8f427c05c3e4fdd2df6b953b52ff5eab65fe656 Author: markd Date: Tue Dec 1 19:55:17 2009 +0000 added missing wigBedToStep to make commit 8628254e88df0645fee8d20524ccc57ae143c546 Author: galt Date: Tue Dec 1 19:36:54 2009 +0000 "New version number v220" commit 263a4aa5ef948cb8e866af07598f6008d147b587 Author: galt Date: Tue Dec 1 19:36:12 2009 +0000 v220 final build commit 52600c5e9f7e14372e437cb209e2beceaeefb8e8 Author: rhead Date: Tue Dec 1 19:21:42 2009 +0000 Changed viewLimits for primate phyloP to -4:1, per Hiram, based on http://genomewiki.ucsc.edu/index.php/Hg19_phyloP_histograms. commit e095965d1bc8eaae5675f0956bb2c017867c2303 Author: tdreszer Date: Tue Dec 1 17:15:54 2009 +0000 Added a couple of tagAlign files missing from the versioned files lists commit 183786cf4a3d39d1a794f82b990eda1558302331 Author: tdreszer Date: Tue Dec 1 16:27:44 2009 +0000 Added 2 for Yale and Thomas corrected a DGF setting commit 057e4200e8da31233e69c0e24f447a8c565a9011 Author: galt Date: Tue Dec 1 16:00:07 2009 +0000 "Encode release log update" commit ad1b1be22fbd64749d37ecc7e0a22e701f8fad37 Author: galt Date: Tue Dec 1 16:00:03 2009 +0000 "Release log update" commit 37f264eace12a8d1ba4d1063addb2a77bef48705 Author: baertsch Date: Tue Dec 1 06:53:14 2009 +0000 remove commented code commit b51c230c2e72ab4629c0970e3c5ab1f834f95886 Author: kent Date: Tue Dec 1 06:49:39 2009 +0000 Adding rangeIncludingZero logic to rangeFromMinMaxMeanStd in case when min/max/mean are the same. commit 8de7b017ab6c6a4b2bc04361b80bf158450c177d Author: baertsch Date: Tue Dec 1 06:46:18 2009 +0000 add -notAlignPenalty to reduce score for non-aligning bases. Fix strand bug with -passthru commit e699750a2a80394c875e0f87d0f39787f3967a15 Author: baertsch Date: Tue Dec 1 06:45:23 2009 +0000 remove bad data commit ff48e6e20359b77e102f14dbad7990bf53bd311d Author: baertsch Date: Tue Dec 1 06:45:02 2009 +0000 updated test cases to fix strand[1] and new criteria commit d478b9f3b92140d40931d2657d6d8260497be5f3 Author: kent Date: Tue Dec 1 05:49:36 2009 +0000 Moving a few bigBed-specific functions from bedTrack.c to new modulc bigBedTrack.c Making bigBeds in dense mode do drawing by querying summary rather than going through itemList. Making it so that it only loads maxItems+1 (251 by default) items before flipping to dense. Making it draw density plot in grayscale if denseCoverage is set. Net result should be reduced bigBed i/o when zoomed out. commit 0fde70d129ea75123d504bbd26a35bbe9d8d488e Author: kent Date: Tue Dec 1 05:36:24 2009 +0000 Adding bigBed-specific optional field denseCoverage to trackDb system. One example of it is in wgEncodeGisRnaSeq. commit 092e6862312c46c5e9a8f04918adec92b76c2612 Author: hiram Date: Tue Dec 1 05:36:23 2009 +0000 Update genbank etc/genbank.conf to include upstreamMaf definitions, and phyloP track histograms commit a6f954a845e0197b1ad35dcc034d3ef7a2e30b3e Author: kent Date: Tue Dec 1 05:34:02 2009 +0000 Adding rangeFromMinMaxMeanStd commit 62d105043fdabb9ca28d9ba7dfc20705552938f7 Author: kent Date: Tue Dec 1 05:33:26 2009 +0000 Fixing bug in maxItem handling in bigBedIntervalQuery commit 63830b7af46b5027ea7407daf2f5a88bd0806179 Author: hiram Date: Tue Dec 1 05:32:34 2009 +0000 turn on upstream maf for 46-way conservation on hg19 commit 725cabcef6f9c38c1a6cd36182ab314c64295cd4 Author: sbenz Date: Tue Dec 1 00:31:58 2009 +0000 updated tcga integrated sample ids commit 4c2754db77477083f0fa73fc8e943b18df2c09fb Author: braney Date: Tue Dec 1 00:14:01 2009 +0000 Riken CAGE viewlimits (why?) commit ea06c1afbb89712e77af845762f0609c74769984 Author: angie Date: Mon Nov 30 23:53:28 2009 +0000 Turned bamNA12878 into a subtrack of a new composite track that includes bamNA12891 as well. Adding experimental track phasedGenotypesNA12878 (looks like trivial phasing, but still maybe of interest). commit 9780c475b6ab669e5bd563d11428f80bd0812615 Author: angie Date: Mon Nov 30 23:46:52 2009 +0000 Since samtools' bam_index_load saves .bai files to the current directory, change to a trashDir when calling it (instead of using a locally hacked samtools). commit 3a1f210ac57dcde51710dd3ee954da10d5fe4834 Author: larrym Date: Mon Nov 30 23:31:02 2009 +0000 make -database required if they are using -validateFile; remove "NULL" commit a6d0aa5a89a1e7b82f49f8f14e140044e556fd39 Author: kate Date: Mon Nov 30 23:13:40 2009 +0000 1. Remove hg18 hardcoding 2. Use newly added 'tag' field from CV instead of 'term' commit 1958adabd7bcbc5d29220c83d99b44d307e135f1 Author: kent Date: Mon Nov 30 23:01:32 2009 +0000 Removing whiskers when got more pixels than bases in window. commit d663d531cd2778947aa9f9cd7e5b7eb1965fac3c Author: rhead Date: Mon Nov 30 21:08:39 2009 +0000 Trying out viewLimits of -4:4 for phyloP per Adam. commit 4d2cb8b30d20b44c51ded1e29c2b341e6a59c30c Author: hartera Date: Mon Nov 30 21:06:32 2009 +0000 Corrected typo. commit fe02056397dbea85f7ceeb2805a566329beaec6b Author: hartera Date: Mon Nov 30 21:04:49 2009 +0000 Corrected typos. commit d69111c22465b573b9a6df39b97f1e3199fb0288 Author: ann Date: Mon Nov 30 19:38:25 2009 +0000 actual pub came out commit 0a8f284c4d0b54eb7a957912f36d1cb5bc590a2a Author: braney Date: Mon Nov 30 19:38:01 2009 +0000 a couple of new MethylSeq cell types commit a6419affc1f76097b8b9e692c436343d92b772a8 Author: larrym Date: Mon Nov 30 19:34:05 2009 +0000 add -database option commit fabd250e226d3f9d6939b23849c85ba24f86ad7b Author: angie Date: Mon Nov 30 19:26:51 2009 +0000 Change bam cart variable names and bamTrack code to use Tim's cart and trackDb ClosestToHome API. commit 8d84ae8b6abe81e0a61ad0eb2bc4fc9d31f6e93d Author: galt Date: Mon Nov 30 19:10:04 2009 +0000 finishing touches on MD3 liftover commit 2c6d3889de96b9f378addd04e0624bda03ef8dee Author: ann Date: Mon Nov 30 18:33:42 2009 +0000 pointing Type 3 cells to the relative server commit ee113cd78100384e1b8f22652d46ef80a4eac668 Author: kent Date: Mon Nov 30 17:59:07 2009 +0000 Making autoScale no longer the default for wiggle and related tracks. Making wiggleWindowingWhiskers follow name conventions better. commit 39d31b305cf41e77f3d8d7a0f5b7924202da5a38 Author: kent Date: Mon Nov 30 17:58:11 2009 +0000 Expanding size of buffer that looks like it is too small and may overflow someday. commit 238996a2798efd39ccd2d40608367aeb21c7ff0e Author: kent Date: Mon Nov 30 17:55:07 2009 +0000 Experimental change-a-comment commit because CVS is being quirky. commit 69955c9688bd78f352383671d405960c4f399af2 Author: markd Date: Mon Nov 30 17:54:31 2009 +0000 fixed error detected in optimized compile commit 58699eccf969391ca9451af70550630e3fa2036b Author: galt Date: Mon Nov 30 16:00:06 2009 +0000 "Encode release log update" commit 2be1b90ba5fdd1063ed079feb5d4989e7df82576 Author: galt Date: Mon Nov 30 16:00:03 2009 +0000 "Release log update" commit 5156ccb51184e8bcca00b2b86bd64c1f65c90ccc Author: galt Date: Sun Nov 29 16:00:06 2009 +0000 "Encode release log update" commit 74f798a2f5263f744a8830b8eb298313656b609f Author: galt Date: Sun Nov 29 16:00:03 2009 +0000 "Release log update" commit 689c41c12b11780b5afe287d93ea1c2abc760652 Author: galt Date: Sat Nov 28 16:00:05 2009 +0000 "Encode release log update" commit 0707f5ffc159dba895c30db2e3bae92e5aeaa2bc Author: galt Date: Sat Nov 28 16:00:03 2009 +0000 "Release log update" commit 6645681a1756cb6ceb4fffef5b9c9121a7899e9a Author: galt Date: Fri Nov 27 16:00:07 2009 +0000 "Encode release log update" commit f0b77f9fa36fd8dda365943760146e2b805f8d87 Author: galt Date: Fri Nov 27 16:00:04 2009 +0000 "Release log update" commit 891ef68a1c1ba81cb2994a3be3c1a5de44f7dc6a Author: galt Date: Thu Nov 26 16:00:06 2009 +0000 "Encode release log update" commit 2d5e7db37dcca57ebb9654f40fb572ba5ab85836 Author: galt Date: Thu Nov 26 16:00:03 2009 +0000 "Release log update" commit c58288177907395e4609c146b5031f45a7b418c1 Author: tdreszer Date: Thu Nov 26 02:10:12 2009 +0000 Added 5 more antibodies for Myers commit 2c9b3e758c0455eb0dfea8c6679b939d89f61d69 Author: tdreszer Date: Thu Nov 26 01:33:32 2009 +0000 Added BCL11A, BCL3 and BHLHE40 for Myers commit d4cea26a038789b4335951212c636a64cc821b9e Author: kent Date: Thu Nov 26 00:39:06 2009 +0000 Fixing bug in track replacement by lower level tracks. Downgraded a verbose 2 to a verbose 3. commit dedd128b9558e791be078f3cc0ebff9d2e1e0c6a Author: angie Date: Thu Nov 26 00:35:38 2009 +0000 Add pairSearchRange setting-controlled extra search for improperly paired items' mates that didn't happen to fall in the viewing window, a la hgc/bamClick.c. commit e3312407abeb507155243a57bb47538a7877f335 Author: angie Date: Thu Nov 26 00:29:11 2009 +0000 Refinements to searching for mates out of window: don't do the extra bamFetch unless pairSearchRange > 0; increase default pairSearchRange default; clip start of window at 0; there's only one item name, so don't need to loop on pairHash name. commit 7e0d43bf1a000d144b6b57644107a61bf3710c32 Author: tdreszer Date: Thu Nov 26 00:28:41 2009 +0000 Added missing color for Open Chromatin H1-hESC commit 4be924fbb80682eb701b4ce2cbafbf45c54bfeb9 Author: rhead Date: Wed Nov 25 23:53:34 2009 +0000 Reordered 46-way assemblies to match phylo image. commit db34984c7ba1e3974c96f1ec56214ad2f7d4b8bd Author: kuhn Date: Wed Nov 25 23:29:33 2009 +0000 shortened primates bar so it does not include tree shrew commit 34cb22b858b9a602611692015a3afbb5859cb26c Author: kuhn Date: Wed Nov 25 23:14:10 2009 +0000 shorted primates bar so it does not include tree shrew commit a71770c6d6288adba8a0361a147f412ae544a489 Author: galt Date: Wed Nov 25 22:30:52 2009 +0000 finish load and cleanup; add dbDb row commit c91e977b4d021fe5efcffaabc6615b21e97dc893 Author: ann Date: Wed Nov 25 22:25:48 2009 +0000 shortening shortLabel from 18 to 16 commit ab7365b453f55e67a0db998734a092c9d227cc29 Author: hiram Date: Wed Nov 25 21:55:13 2009 +0000 change autoScaleDefault to autoScale commit 8b7a25b2a873747e68f21ba18c09919b0492c827 Author: markd Date: Wed Nov 25 21:38:05 2009 +0000 converted uwFootprints to composite track commit b94a578e4a4d98618766a4854d87dcd4951d3dd8 Author: tdreszer Date: Wed Nov 25 21:20:53 2009 +0000 Fixed inconsistency in Barski settings caught by Jim commit 8e0f727c20cd71fbc86664d5c8480c0392bc9fc0 Author: kate Date: Wed Nov 25 21:17:41 2009 +0000 Add color (green) to H1 es cells commit 8454dcdaaf9e67b4b0727bd57c55dbf4b5e0e36c Author: kate Date: Wed Nov 25 21:15:22 2009 +0000 Short label consistency for Broad Histones commit 46b68b513d97eb3bebe82e38f2b2de2b326dfc8c Author: markd Date: Wed Nov 25 20:52:35 2009 +0000 added an option to connect to a remote hub (for jobTree) commit 016211e125a342222e71dcabbfc95a988d9b1464 Author: kate Date: Wed Nov 25 20:45:30 2009 +0000 Add color to Broad H1ES tracks commit 7c5e24b3dd330337773cd0ae1d5bf5814905e255 Author: ann Date: Wed Nov 25 20:24:58 2009 +0000 correcting links, cleaning up commit 1c64c8310c6b08b0f0dcf6a411e544aec535d783 Author: tdreszer Date: Wed Nov 25 20:07:51 2009 +0000 Ann noticed missing colors on Open Chromatin tracks commit 4224ee67b7e418d28e158729c820cddca5a040c0 Author: hiram Date: Wed Nov 25 19:55:25 2009 +0000 Allow it to work on multiple tables in a single database commit 13b78e4d13dae23ecb6f1b24cff0ae2c4825b8d8 Author: hiram Date: Wed Nov 25 19:17:10 2009 +0000 Add a viewLimits for stanfordNRSFOverlaps commit 154fd6dac871d405ca78280521f4f19936ed0b4d Author: hiram Date: Wed Nov 25 19:10:44 2009 +0000 Add viewLimits to usage message commit 59712d1ffa2a1e0ba66af05c4db22dfd099a2c27 Author: hiram Date: Wed Nov 25 18:52:08 2009 +0000 change autoScaleDefault to be only autoScale commit 13a60714e303021b75100810212a318c1985740b Author: hiram Date: Wed Nov 25 18:44:41 2009 +0000 premature, need to wait for trackDb to update before eliminating the recognition of defaultViewLimits commit 610cc252a3a3800c9e15ab6786b3588ab5fa1398 Author: hiram Date: Wed Nov 25 18:34:47 2009 +0000 eliminate defaultViewLimits it is all viewLimits now commit 3819b9c538c89699fa2b304503b585aa8c77ad79 Author: hiram Date: Wed Nov 25 18:31:29 2009 +0000 change defaultViewLimits to viewLimits commit de5743dc274e2ae97b0faa758d3aa414bf456b4b Author: hiram Date: Wed Nov 25 18:01:46 2009 +0000 Add viewLimits recommended calculation commit d42f363bc2f9dbdf0848ab55d245e30011babe4e Author: hiram Date: Wed Nov 25 18:01:02 2009 +0000 remove obsolete ponAbe1 and rn5 and add a listDbs target commit 4e3e7067d80065e65df77a206145d0c6a214b0b7 Author: kent Date: Wed Nov 25 17:52:55 2009 +0000 Pulled rangeRoundUp into a new numObscure file so as not to force all obscure users to drag in mlib. commit 6ce6eb288bd11d8aec839426c53e33590f775668 Author: kent Date: Wed Nov 25 17:31:25 2009 +0000 Seems to work. commit 7951819002ae70b65116ecfa3e5775963d172b1c Author: kent Date: Wed Nov 25 17:29:47 2009 +0000 Adding (indirectly) -lm to link. commit 60ea9fc8b7bb3d7b16609ddc9b89d7242b092d13 Author: braney Date: Wed Nov 25 16:29:26 2009 +0000 add settingsByView to GisRnaSeq commit efedd6d44b62c23d45a5068f044811bf9b86ed2d Author: galt Date: Wed Nov 25 16:00:06 2009 +0000 "Encode release log update" commit 4f2eaa9e53e279e1f53192ec1b63b2dada1431b6 Author: galt Date: Wed Nov 25 16:00:03 2009 +0000 "Release log update" commit 548f78fe03b587f9773c305522a6e30d5029a17a Author: kent Date: Wed Nov 25 09:38:06 2009 +0000 Adding a viewLimits commit 0504fada66bf7fd9b98153810b53c3f5deade161 Author: kent Date: Wed Nov 25 09:36:00 2009 +0000 Adding a few viewLimits commit f9e46152c43b93bdd120f4d7edbe370554de6cfb Author: kent Date: Wed Nov 25 09:24:59 2009 +0000 Bumping up recommended view range by another std on each side of mean. commit b303d2951cfb3aa2f4bf018a0463059584eee52c Author: kent Date: Wed Nov 25 07:17:25 2009 +0000 Getting rid of largely redundant bwgSectionWriteUnc commit 8f212221cb22a5ea91a186f1d1d605b25438df6d Author: kent Date: Wed Nov 25 07:16:38 2009 +0000 Adding 'hashThisEqThatLine.' commit 3aa8383a393cfb2fc24ef7ff99c5fc6c25e4a281 Author: kent Date: Wed Nov 25 07:16:03 2009 +0000 Hacking a lot of very trackDb-specific settings parsing into raSqlQuery with db= option on. This enables inherit-by-view. commit 45fc151ab58ff26079e0f9b807b23bfd84b51159 Author: kate Date: Wed Nov 25 01:17:12 2009 +0000 Add tags field (unique, no special chars, alpha start) to each entry commit 7399a6cfa561118073f0f5549a934814c3f9ee28 Author: braney Date: Wed Nov 25 00:58:02 2009 +0000 made subtrack processing check for more errors, fail on errors, and a lot easier to read without all the continues and huge functions. Confirmed that trackDb generated is the same as the old hgTrackDb (after fixing the 8 errors found in existing tracks). All of this is prep for automatically adding prefixes to subGroups for automatic sorting commit 17227de2618fb8ec5f1080881ec231b87ba841fb Author: galt Date: Wed Nov 25 00:29:11 2009 +0000 make liftover commit aff2aac88c9955fed9b6e32207270f6320b37a1c Author: rhead Date: Tue Nov 24 23:22:55 2009 +0000 Turned of stsMap and gap by default, now that release of conservation and knownGene tracks is imminent. commit 9e665adb9bd17c8dccf867f01f00af872eba9572 Author: braney Date: Tue Nov 24 22:52:01 2009 +0000 fix up some problems with some encode yale tracks commit eddc76b3ef01865042ae0b049a7ad3f7be932cc0 Author: braney Date: Tue Nov 24 22:51:30 2009 +0000 fix up tiny non-important error in multiz46way trackDb entry commit 0a0b53973b05420ec6be1d2c42bca951a48ab067 Author: braney Date: Tue Nov 24 22:50:41 2009 +0000 fix up little problem in multiz28way trackDb entry commit a91cba626144a30d9424fb88d34c7631ad74f310 Author: braney Date: Tue Nov 24 22:06:52 2009 +0000 take out pesky ancestors commit 23ac2b6e4e286b1421412743606c00a27c190fdf Author: rhead Date: Tue Nov 24 20:53:27 2009 +0000 Turned on cons46way by default and changed mRNas to dense. Changed speciesCodonDefault to hg19. commit a72a2de57ca2b824568fd47e7196c113fa4da27d Author: rhead Date: Tue Nov 24 20:15:43 2009 +0000 cons46way track: uncommented speciesDefaultOff line and updated assembly names for oryCun2, danRer6, and tetNig2. commit bfbb57f15331218638f5dd3c95f5d2f2e6bb9bed Author: ann Date: Tue Nov 24 17:32:37 2009 +0000 added block for exoniphy commit 39ab5fe717690d3e1b542e81f1f24fe5c46b2c96 Author: galt Date: Tue Nov 24 16:00:06 2009 +0000 "Encode release log update" commit be07c7a2f9f3f59a3583bd7c5f1d8ea9c1345877 Author: galt Date: Tue Nov 24 16:00:03 2009 +0000 "Release log update" commit b3bbc89023adb7adefc3a89c35ffc0492944900a Author: kent Date: Tue Nov 24 15:51:11 2009 +0000 Improving comment. commit 5e5f66a46f0705beb9b6f7aa5fc0345594ec2224 Author: kent Date: Tue Nov 24 15:50:23 2009 +0000 Commenting out some debugging statements. commit 0fed08c1b0543cec3d1f7545fbd4597670911816 Author: kent Date: Tue Nov 24 15:49:14 2009 +0000 Tweaking size check to compile under 32 bit Mac OS. commit fde9457d1ecd38f3feaac26c921696b5a54083c8 Author: kent Date: Tue Nov 24 15:48:52 2009 +0000 Commenting on bananas example. commit e7f238a17cd5679d8d2b45ae5192ee893ad53719 Author: kent Date: Tue Nov 24 15:36:59 2009 +0000 Making a couple of little functions inline. commit 954e8bdef4d99fcd8b24b8f4c348a2a16a161c9b Author: kent Date: Tue Nov 24 15:36:22 2009 +0000 Fixing missing commnt end. commit 53e61edaeee9bdfbb7836e487ddf228cf41fffe7 Author: markd Date: Tue Nov 24 07:06:40 2009 +0000 added CA condor 454 transcript tracks commit 442f8019604391aad397c7678c92e989b1a68041 Author: kent Date: Tue Nov 24 03:58:25 2009 +0000 Polishing routine that rounds ranges. commit a99f81f3c62291df6f8eb3cf2ae43867ea5a3c3a Author: kent Date: Tue Nov 24 01:42:04 2009 +0000 Correcting viewLimit to viewLimits commit 1ddf62fc6e3de01d73e3c702be92bee5b7c5209b Author: larrym Date: Tue Nov 24 01:24:54 2009 +0000 make validationSettings required; fix some typos ("type in" => "type int") commit c7c214b999829afbd680abb818d09e8090db72d8 Author: larrym Date: Tue Nov 24 01:18:39 2009 +0000 add validationSettings commit a65ba50c13288387e05a0346d131c0a7943d91c8 Author: larrym Date: Tue Nov 24 01:15:44 2009 +0000 update expected files to accomodate doEncodeValidate.pl changes commit 80d070548e9e86340db173199142f4ad98066f04 Author: kent Date: Tue Nov 24 00:59:18 2009 +0000 Adding rangeRoundUp to obscure library and testing in freen. commit 64f984d120d1db92d650cbcfe27a97b29c4da6bd Author: rhead Date: Tue Nov 24 00:49:20 2009 +0000 downloadsServer uses personal .hg.conf, not cgi-bin/hg.conf :( :( :( commit e9180813236654a349bc6bda69b39a91062c5754 Author: braney Date: Tue Nov 24 00:46:32 2009 +0000 make viewLimits line into the right format commit dfad470df62d7b3e966d2282b8558f4526c01aed Author: kent Date: Tue Nov 24 00:18:43 2009 +0000 Adding -ignoreStrand to knownToCdsSnp build. commit 2e169ef8a533f9cd0f8a95aa5f0a4fd5a2785f66 Author: kent Date: Mon Nov 23 23:39:44 2009 +0000 Adding ignoreStrand option. commit 0673c2a667249eb199f227be50acef829c708aae Author: angie Date: Mon Nov 23 23:04:22 2009 +0000 Display wigFetchMinMaxYWithCart's warning about missing data range settings only when we're on hgwdev. commit d59d786520dc05412a984e4c738941813bf250be Author: braney Date: Mon Nov 23 19:32:35 2009 +0000 change text describing colors to reflect colors by cell type (in Caltech RNA-seq track) commit 2f50d3df5118958e2f097f192e1727025a905488 Author: braney Date: Mon Nov 23 19:31:04 2009 +0000 go back to color by cell type for Caltech RNA-seq track commit e55f67d453027f6d9d7bb08d5dc86789ef2305ef Author: braney Date: Mon Nov 23 19:02:45 2009 +0000 change CalTech RNA-seq track to color-by-strand commit bbd0b048d159e414ee6827a4d53532f6139a221c Author: hiram Date: Mon Nov 23 18:32:16 2009 +0000 Adding missing type wig min max limits and adding viewLimits to those guys at + or - five stdDev commit 6900f56df28e34ca59ff37060b2bb6073ff6ac38 Author: tdreszer Date: Mon Nov 23 18:02:16 2009 +0000 Tiny bit more protection for findWordByDilimiter() commit f2307eba9a19d1d28f1b4c48a456508d76745ca4 Author: markd Date: Mon Nov 23 17:45:19 2009 +0000 added CDS to meta data commit 28c272bcadc7dc0ffd458453ccaf2b14d3922b4f Author: galt Date: Mon Nov 23 16:00:04 2009 +0000 "Encode release log update" commit a6ae90ca13593a36dcbc4245bb28094a88cca98f Author: galt Date: Mon Nov 23 16:00:02 2009 +0000 "Release log update" commit 8694ca9fa8553493411aa873d5200810a780f695 Author: larrym Date: Mon Nov 23 07:56:56 2009 +0000 some browser specific changes for right-click code (currently dead code) commit d4a8fdd96383b97b1a13d42e038b7841b61e31ba Author: kent Date: Mon Nov 23 07:39:46 2009 +0000 Creating patched files in -test mode now. Works for adding new fields, keeping comments and indentation level. Haven't tested yet for modifying existing fields. commit 9912e74ec2ceddcac4be9915a70a9b4cc9b005da Author: kent Date: Mon Nov 23 07:38:17 2009 +0000 Adding -firstOnly option. commit fc5f861c57dadf33c4374ce896a1bdcf2e4b3891 Author: kent Date: Mon Nov 23 07:33:44 2009 +0000 Adding a few new .ra parsing routines. commit b0c40ee9ad081bbdd4bd714b8ee0aa8b269db9da Author: kent Date: Mon Nov 23 07:32:29 2009 +0000 Moving altEvents up to root level so everyone can use it. SImplifying knownGene priorities. commit 210a9751a47da8c8390132d54137517f6c186290 Author: markd Date: Mon Nov 23 02:56:21 2009 +0000 added program to get consistent versions of refseq data from database commit 34a11314c8704ffbf8cb17a469047903338e9d5f Author: kent Date: Sun Nov 22 23:56:30 2009 +0000 Starting to work on utility to patch trackDb files. Just reads one of two inputs at the moment, no output. commit 171db4e7f26cfd2f41c6a26b7ba71cc8fb92e560 Author: kent Date: Sun Nov 22 23:21:12 2009 +0000 One shot program to help patch viewLimits of bedGraph here. commit 13e49bf965a41418e1010b89706948d814994d3f Author: hiram Date: Sun Nov 22 22:50:02 2009 +0000 Initial contents commit c699b53679c88b382aa8f416251dc3b37ca4a8d1 Author: kent Date: Sun Nov 22 20:08:55 2009 +0000 Adding missing 4 to type bedGraph line. commit f45182bb590a075a995298c05c9d2739829bf24e Author: kent Date: Sun Nov 22 18:37:43 2009 +0000 Utility to figure out missing bedGraph limits seems to work. commit 3aed0b6d124a06eaad6c22f077c0daf7dfd6a429 Author: fanhsu Date: Sun Nov 22 18:02:07 2009 +0000 Removed anyWild(), it was added to common.c. commit 7676824d826c2f953c01174cbd25424beee193ea Author: galt Date: Sun Nov 22 16:00:05 2009 +0000 "Encode release log update" commit aafb076c742d01f2858d602eb62dac063e87e6e8 Author: galt Date: Sun Nov 22 16:00:03 2009 +0000 "Release log update" commit 8f06044d266c28cef731dea6965a0134ff1a7f18 Author: kent Date: Sun Nov 22 05:58:13 2009 +0000 Making count statement work better with db=all and with from clauses. commit cdf916a47fb753d06412b75df03bd67c26022ec6 Author: kent Date: Sun Nov 22 05:28:52 2009 +0000 Implementing from as file list. commit c0e57a2c2c95c3beca397ae72595746551d0ef78 Author: kent Date: Sun Nov 22 03:38:59 2009 +0000 Skipping over things inside parenthesis in count(*). Trimming spaces. commit 4b96f3e2b29a017cced17f5b82555e52c0ee4cf9 Author: kent Date: Sun Nov 22 02:54:37 2009 +0000 Parsing out (and ignoring) optional from clause. commit 0448061e0b1fc983f08f4f325d24d79bfcfd2ccd Author: kent Date: Sun Nov 22 02:45:33 2009 +0000 Letting 'select count(*)' be a synonym for 'count' commit 63d5f25c9a315adda6154061698372755eea0e2f Author: kent Date: Sun Nov 22 02:11:09 2009 +0000 Adding rcsid strings. commit 8d61d7ea8ec87c9088183586067436c995520414 Author: kent Date: Sun Nov 22 02:10:20 2009 +0000 Improving usage statement. commit 9353ae357ba7de051826800500c6769266162acc Author: kent Date: Sun Nov 22 02:06:06 2009 +0000 Adding a little more error checking to command line. commit 40b49ff8d79f338b5f14f03f778cd7678f2e81ea Author: kent Date: Sun Nov 22 02:04:06 2009 +0000 Adding a little more error checking to command line. commit 5cb0be4b72dacacbb7cd443c8da08ae05688f0cc Author: kent Date: Sun Nov 22 02:01:30 2009 +0000 Adding 'strict' option, to only put in ones where database table exists. commit 68d7f69704220314fc6d1808525c1b3525562b34 Author: kent Date: Sun Nov 22 01:37:41 2009 +0000 Implementing arbitrary databases in db= option. Adding db=all option. commit a4b3621becb855b09d56df884b9968b55d12159c Author: kent Date: Sun Nov 22 00:31:01 2009 +0000 Adding bedClip to utilities build. commit cf973ccb123a495c6af98cc91f96e46fd1a1cb51 Author: kent Date: Sun Nov 22 00:30:33 2009 +0000 Adding required -lz to link line. commit e17fbb961f135f19135df89c203f49dd3590bba9 Author: kent Date: Sun Nov 22 00:25:26 2009 +0000 Making it deal with overrides. Making it start to work with our usual trackDb directory structure when using -db= flag. commit 9a8644930b3718a05bddb07034d616f0056ac0ce Author: kent Date: Sun Nov 22 00:18:05 2009 +0000 Adding simplifyPathToDir commit 3b989a772262005a48575685d9f4731746bc4330 Author: braney Date: Sat Nov 21 16:08:19 2009 +0000 make GisDnaPet use bigBeds commit 9e9bd4145b0bd2b7857546c8976303457c3303cb Author: galt Date: Sat Nov 21 16:00:07 2009 +0000 "Encode release log update" commit 522fb88b6a062cce1ba069000b6e870186bae68b Author: galt Date: Sat Nov 21 16:00:03 2009 +0000 "Release log update" commit e393db8a2ea01e9fa2e1479a1d145345dd8297b1 Author: hiram Date: Sat Nov 21 06:02:16 2009 +0000 Proper calculation lodToBedScore for 46-way mostConserved tracks commit 5b96cdcd47eae2770d38e0131398213a51aada55 Author: rhead Date: Sat Nov 21 01:56:27 2009 +0000 Trying to make the downloadsServer variable work. commit 148d212d67e4b15ac719794fe1f6a170e200261e Author: galt Date: Sat Nov 21 01:25:40 2009 +0000 adding MD3 so we can make chains to bosTau4 commit 07f2606b9f3be1ed1c604e4ea896e9fdeda2b296 Author: markd Date: Sat Nov 21 01:07:58 2009 +0000 added option to allow setting arbitrary environment variable for jobs commit 91556e28e737b1b2753cb2d5a3ea7d207986b85f Author: markd Date: Sat Nov 21 01:07:12 2009 +0000 fixed incorrect usage message commit 2e828c2d67e50d8401a934ba5f9241e4095686a9 Author: sbenz Date: Sat Nov 21 00:13:52 2009 +0000 Cleaning up some tracks for the cancer browser commit de0eaf9d9a092ed582e7e38bc8bf27c9a456b161 Author: tdreszer Date: Fri Nov 20 23:51:17 2009 +0000 Added support for calling warnBox insteadf of alert. Now a list of messages can be created, just as from C. commit fda4d3e1c27e373eac62c3a6c5319a64531aac7b Author: tdreszer Date: Fri Nov 20 23:49:42 2009 +0000 Added dragStartIndex to be returned by onDrag() callback. commit 54c57afca18428641540d498127b0bc9ddff07e7 Author: tdreszer Date: Fri Nov 20 23:36:32 2009 +0000 Fix for bug Angie found which sets position to 1bp on hgc click commit 204c806b33809c6c7ee7582eabc66f525666a08f Author: katrina Date: Fri Nov 20 23:33:42 2009 +0000 updated the UniProt data restrictions and copyright commit dd07388d44bfb72b3a5443f1162cf327b0ea0bba Author: ann Date: Fri Nov 20 23:17:09 2009 +0000 new link to new CSHL downloads commit 2d14abad66fbf95f9567299884a5684838af0d35 Author: angie Date: Fri Nov 20 20:45:54 2009 +0000 Needed to be a bit more careful setting both stub coordinates and lfs->end -- was getting lfs->end too short, resulting in too short cachedDna in cds.c in some cases. commit d92e73f4ab3b10e63a346511303647161f03fe16 Author: tdreszer Date: Fri Nov 20 20:43:34 2009 +0000 Minor fix of a referenece to Yale which should have been HudsonAlpha commit 53f42362163eef52e23466ab30c69fcbaac50e61 Author: tdreszer Date: Fri Nov 20 20:40:40 2009 +0000 Checkin for Thomas. Notes for UwChIPseq release1, because there are too many files to be listed in the pushQ. commit fca7f89786012b2a68a87f5c1d22e03359c47b42 Author: kent Date: Fri Nov 20 20:26:27 2009 +0000 Adding lmCloneStringZ commit 40b4bf4a0ee06eaefe05491a48b8e8e782d23166 Author: kent Date: Fri Nov 20 20:25:54 2009 +0000 Doing some stuff to cope with track names having additional fields after the first word. commit 3ff9d2c198383a9b560290e8d47bb06e0d31f0d9 Author: kent Date: Fri Nov 20 20:04:45 2009 +0000 Fixing it so only prints file field once. commit 7b38bd0033225039e054dd362368c6c306354a73 Author: kent Date: Fri Nov 20 20:00:23 2009 +0000 Adding -addFile option. commit 79cfd931f31f4a5d9e62f57be96df664c4d9474d Author: braney Date: Fri Nov 20 19:56:00 2009 +0000 make GIS RNA-PET alignments bigBeds commit 2505ffbc61010b02e941ec08ae5e18ecd6c3e64f Author: angie Date: Fri Nov 20 19:17:35 2009 +0000 Removing duplicate definition of anyWild (use the common.h/wildcmp.c version). commit e8b46b2588d33f36b4b4cbef1e18de288a2f6dbd Author: angie Date: Fri Nov 20 19:11:16 2009 +0000 Adding more const qualifiers because cart.c needs startsWith and wildMatch to have the same signature (thanks Galt!). commit acdd7b26f204022ea37c7d3970388026a58fdb49 Author: angie Date: Fri Nov 20 17:56:35 2009 +0000 Path may now include http auth info (that's the only way of communicating the info to udcFuse) -- if so, strip it out when making the udc cache path. commit 4a7e4ef4b61b7eb9121cac7f2fbdd41b487e92c1 Author: angie Date: Fri Nov 20 17:51:56 2009 +0000 Include http auth string in udcFuse path because udcFuse has no other way to get the auth. commit cdfdf11cf2d389dc469fcaac9120e119cb614282 Author: angie Date: Fri Nov 20 17:45:32 2009 +0000 Added udcParseUrlFull, which returns http auth portion instead of silently skipping it. commit 3d90b994ca069c118800830c4628cc6b17457c2a Author: angie Date: Fri Nov 20 17:44:45 2009 +0000 Added a couple const keywords for smoother interoperation with external code. commit 12bed7476f8bbe059630ea528247b400112620ea Author: tdreszer Date: Fri Nov 20 17:31:31 2009 +0000 Changed Stefan Graf's affiliation by Terry Furey's request commit 7497c149eb85de79950079c1e9ee78e0c44c5b00 Author: kent Date: Fri Nov 20 17:12:17 2009 +0000 Adding bbiSumStandardDeviation to the summary types. commit 14934be796290ed1927c33bc148f9788bf16fea7 Author: galt Date: Fri Nov 20 16:00:07 2009 +0000 "Encode release log update" commit 69720c3933ccb0b13e6da4022d89a30d79bf38f5 Author: galt Date: Fri Nov 20 16:00:03 2009 +0000 "Release log update" commit abaf67649fefc988da9c3c55fa33f73464c70d9c Author: kent Date: Fri Nov 20 09:59:30 2009 +0000 Adding parent,key,noInherit options and implementing inheritance. commit 312f7c9828582044cf499550a8498b6533b76c34 Author: kent Date: Fri Nov 20 08:17:38 2009 +0000 Adding raSqlQuery to makefile of parent. commit 903907d5c2dd795cf1bfbcf78cdf74e49bcf96b1 Author: kent Date: Fri Nov 20 08:12:35 2009 +0000 Adding test set. commit ae092a4d7f60f1538462b0785960f7df8845730e Author: kent Date: Fri Nov 20 08:12:16 2009 +0000 Fixes to get to compile under Linux unstead of my laptop. commit 8e252c531f922f2c9b19fc74602602c7e3322c89 Author: kent Date: Fri Nov 20 08:10:38 2009 +0000 Adding raRecord.h commit e4df1e7a71f5bdae9d2e2685f26c342ad099a801 Author: kent Date: Fri Nov 20 08:08:53 2009 +0000 Adding leadingSpaces field to tokenizer commit 0ab5a1f4dfb0ebf3af907a68760f3c14406790cd Author: kent Date: Fri Nov 20 08:08:26 2009 +0000 Adding sqlMatchLike commit 8b155167a082c08a419fd2a0137831f939580ade Author: kent Date: Fri Nov 20 08:01:12 2009 +0000 Adding logical not commit 40ea9e72bd0cd5f5ffc1522e941af122fb63c463 Author: cszeto Date: Fri Nov 20 07:48:45 2009 +0000 Ovarian cell line data commit 274ae4556e7f685e929edd544aeebae7d8387862 Author: cszeto Date: Fri Nov 20 07:47:46 2009 +0000 Added Ovarian Cell Line data commit d0a9f82fc0b7031098281f6a587e0fb2f6954572 Author: kent Date: Fri Nov 20 07:41:56 2009 +0000 Adding in merge option. Supporting 'not like' operation. Splitting into modules. commit 894a7cbc4b1446ffaae1b54ce3e05f8ca27482f5 Author: kent Date: Fri Nov 20 06:12:40 2009 +0000 Improving usage statement. commit 5b88f9d251e90cf71658f95a71ba206340310c27 Author: kent Date: Fri Nov 20 06:10:04 2009 +0000 Adding parenthesis in expressions. commit 9adb66d9b7fced9e170a919dfc94265272070d00 Author: kent Date: Fri Nov 20 06:00:29 2009 +0000 Adding 'or' and 'and' commit b16f495c65c12b7a8c97d2738a6a4fbe42d0168d Author: kent Date: Fri Nov 20 04:57:14 2009 +0000 Allowing like in where spec. commit 507f0314ab9b48576070710e5e628a8ca3ded59f Author: kent Date: Fri Nov 20 04:39:16 2009 +0000 Making wildcards (other than the single ?) work in field specs. commit c8ff4dc8316f7a4ec58953f41a19e6985d61aa7a Author: kate Date: Fri Nov 20 02:30:03 2009 +0000 Need to force all labs in Snyder project to be the same, for now commit df62578333756b63370917719c262ff59303559a Author: kent Date: Fri Nov 20 01:52:43 2009 +0000 Adding inequalities. Reducing debugging uglies to verboses. commit 2ae1be1d5bd896fc40a86d3c12c67c92436db124 Author: kent Date: Fri Nov 20 01:35:37 2009 +0000 Adding unary minus. commit 8f74be8c2ddc7de4cc1c584eee68e1b5ec4bf573 Author: kent Date: Fri Nov 20 01:18:09 2009 +0000 Adding casts to parse tree and evaluator so can have numeric as well as string types. Making floating point numbers parse. commit b8a7fdb4f94900bf0a15e5486ad4f3ed7a680c44 Author: kent Date: Fri Nov 20 00:24:55 2009 +0000 Starting work on raSqlQuery. commit 50dbb20a79be7f1d67189d435c7704a399ee14b8 Author: galt Date: Fri Nov 20 00:06:49 2009 +0000 adding subsetLittleIds option where agp ok if all its ids in col 6 are found in the fasta files commit 21245513856f156659ee959c2960988dc78383e5 Author: hiram Date: Thu Nov 19 23:35:31 2009 +0000 Bug in determing parent from subTrack variable, may have "off" following name commit c9eb48d201979ef409117aa015ddf3d75edbe724 Author: tdreszer Date: Thu Nov 19 22:43:12 2009 +0000 Loaded several new submissions from HAIB TFSB and corrected a few settings commit 303a22b6df281d843c0a9cfbcfb935b5e90bdb5d Author: hiram Date: Thu Nov 19 22:04:02 2009 +0000 Add some arguments to make it at least a little bit useful commit 5e03ebf4cab8b953cce68f702423c76c586f3dc8 Author: tdreszer Date: Thu Nov 19 21:21:16 2009 +0000 Minor adjustments to UW settingsByView commit 06f6f8853d4d67175a52196d25e758f1eb26cff7 Author: hiram Date: Thu Nov 19 21:05:53 2009 +0000 Initial source of a scanner commit 831a44dae7aaf879fdcd400d1ae7620d8edec4d5 Author: kate Date: Thu Nov 19 20:25:13 2009 +0000 More metadata fixes to GIS commit a2e2a9ab47bb64baf976e35e6bcdfce69f6284cb Author: kate Date: Thu Nov 19 20:14:31 2009 +0000 Fix additional metadata problems in Gis commit df87c4f45f3f9674d8afaa4dd33e188037f0c90a Author: kate Date: Thu Nov 19 19:39:35 2009 +0000 Fix metadata for GIS tracks (subtrack ordering stuff was seeping in) commit 6a5e446e0ff0cbaa0e456cccf8478dfd24319e27 Author: tdreszer Date: Thu Nov 19 19:37:06 2009 +0000 Check-in for Thomas. Added Display Conventions commit cd50b58391ecfe2bb8c4d1b405bcdbbce7c88dbd Author: tdreszer Date: Thu Nov 19 19:34:02 2009 +0000 Check-in for Thomas. Changed UW ChIP_Seq to UW-ChIP-seq commit 9459001d773c58e0f1ace6099bb86436f3b02c81 Author: kate Date: Thu Nov 19 19:23:17 2009 +0000 Save changed experiment commit 3646e4b59a75ac2807bef1b7dbd3fddbc1096840 Author: angie Date: Thu Nov 19 19:11:18 2009 +0000 Adding rcsid for version tracking with ident. commit 585477b61db45bb3dcac3cae4f89bc5581096f91 Author: angie Date: Thu Nov 19 19:10:06 2009 +0000 Fix: remember to close sockets if necessary in udcFileClose. commit e0775b26d6076376d529cba123569fcda559c260 Author: angie Date: Thu Nov 19 19:07:58 2009 +0000 Debug message improvements. commit ab96836935faa0163c88666bbf058774f7c3b6cc Author: rhead Date: Thu Nov 19 18:59:58 2009 +0000 Fixed broken links to WUSTL. commit ccfee66f0b4e101286ea24ad5f5ef230d96bd572 Author: angie Date: Thu Nov 19 18:54:51 2009 +0000 Removed the clipping of viewing range to (optionally expanded) data range at Jim's request. Since that removes the purpose of expanding the data range to viewLimits or settingsByView's viewLimitsMax, I took that out too and those trackDb settings are now ignored & obsolete. commit 952dbac6f19ce5fcab455a9d0be35879860cb204 Author: katrina Date: Thu Nov 19 18:32:07 2009 +0000 changed link so it goes to a page that better describes the gene categories commit 903fac8b46824eff9a56558e73e116ecb74d48bc Author: tdreszer Date: Thu Nov 19 18:05:09 2009 +0000 Fix bug Rachel found with imageV2 framework, where BLAT sequence track was being forced to the bottom. commit 98fc8af057ebf412fd587316dfe95b67a56ca47c Author: galt Date: Thu Nov 19 16:00:07 2009 +0000 "Encode release log update" commit 618974f85cb4898363e98d034d1f26b7858ce587 Author: galt Date: Thu Nov 19 16:00:04 2009 +0000 "Release log update" commit e854ee62569bdcd3e068aa1f2b6dd99c17721bb5 Author: markd Date: Thu Nov 19 05:31:21 2009 +0000 added option to filter mafs by species prefix commit 8d47827af3f16ea4ab2f2d353a7d87a6e980e3e7 Author: markd Date: Thu Nov 19 04:46:19 2009 +0000 added ignore entries commit e3c99dd279f634f88bdc438eb91bedd6c066130f Author: tdreszer Date: Thu Nov 19 01:21:10 2009 +0000 Jim requested no enforcement of view range limits commit b3e9e9974657bd8cf924ad42adf38593dc878c6a Author: braney Date: Wed Nov 18 22:56:01 2009 +0000 some long label changes, add settingsByView to GisPet commit b66c540511e3fdac2c3867c2d85d934ac2f37464 Author: sbenz Date: Wed Nov 18 21:53:41 2009 +0000 Added TCGA Ovarian Integrated datasets commit 48752d26991bd94bbcd4eef4ee546682e9cfcacc Author: kent Date: Wed Nov 18 21:12:55 2009 +0000 Adding allenBrainGene. commit 542e2fe442085b468b36d7e063480321adb0e9fa Author: hiram Date: Wed Nov 18 20:07:23 2009 +0000 Previous standard deviation was incorrect, was not using N-1 commit 59ba6769531ee301ecaf6a6c6419c8f332a4abca Author: braney Date: Wed Nov 18 19:55:18 2009 +0000 add settingsByView to CSHL long rna-seq commit abe5a19758a67b3a82d40886bdaa1dfb6cdbb1b8 Author: tdreszer Date: Wed Nov 18 19:50:53 2009 +0000 Thomas doen not have cvs ci permission yet. He changed UW ChIP-seq to ChIP-Seq commit a87656675d0591ce64abc756fb495e2abeb85eb0 Author: galt Date: Wed Nov 18 19:38:56 2009 +0000 enlarging user field at Bobs request commit 0e8192a955b2fc3d121b6f41e0c6a07ad2bf4685 Author: kate Date: Wed Nov 18 19:30:02 2009 +0000 Minor fix to Broad metadata (for consistency, reporting) commit 168d49f3b32dad044b11bb22d207d159bd88f5d7 Author: hiram Date: Wed Nov 18 18:07:23 2009 +0000 Add -settings option to loadTracks and EXTRA options to your private trackDb commit 85d10fa6fbe429dfc0845729c5e999906f2bbbc2 Author: hiram Date: Wed Nov 18 17:41:23 2009 +0000 Add -settings option for debug scanning of trackDb settings hash variables commit a10aa82648b59bf3fc77d24106a6115306ecf1e1 Author: hiram Date: Wed Nov 18 17:36:52 2009 +0000 adding geographic allele frequency images options commit 9d52ca5b0c81636e60a39b90f1400d2d7b7a0067 Author: braney Date: Wed Nov 18 17:23:25 2009 +0000 duke affy exons commit bf88104c754b1d5f68828b2ea0a3452adf4406e1 Author: braney Date: Wed Nov 18 16:37:42 2009 +0000 Uw Exon arrays commit bb79b36a799d62a5fc58459fea6edf1c816d1ff3 Author: galt Date: Wed Nov 18 16:00:06 2009 +0000 "Encode release log update" commit 133d37c6bf3d75d40bc4016fdbf4fc3334502267 Author: galt Date: Wed Nov 18 16:00:03 2009 +0000 "Release log update" commit a48ba47eecac8dc35e14b0772771f0f4b3807e19 Author: kate Date: Wed Nov 18 07:55:12 2009 +0000 Improved status handling commit 91eec4d7f4bbef37f11ef88238b64d2c27642bfc Author: angie Date: Wed Nov 18 05:45:06 2009 +0000 Oops, logic bug prevented absMin from being set properly for wiggle (thanks again Jim!) commit ce1963afe9c731eea645a6159919701cc76cf2ca Author: markd Date: Wed Nov 18 05:23:33 2009 +0000 allow mafFilter -needComp to work on files produced by mafFrag that have species but not sequence in the name commit de998d78d79c3f73da35714814c8092658103d84 Author: angie Date: Wed Nov 18 05:11:31 2009 +0000 Oops, used double instead of int for abs{Min,Max} -- thanks Jim! commit a1e52d501857e1ec29811152fa33322e662a61e8 Author: rhead Date: Wed Nov 18 02:08:09 2009 +0000 Updated the update paper. commit 99d75a2872ea4f29c7e3a9997405b81d4e260ce6 Author: braney Date: Wed Nov 18 02:00:03 2009 +0000 some defaults for Gis Rna Pet Loc commit 035e91439865ccb18aac88b0dbd960f2eda64f39 Author: braney Date: Wed Nov 18 01:44:33 2009 +0000 turn on some defaults for GIS DNA-pet commit aeec4c218fc592857e876a1e7d1b688a186f9252 Author: rhead Date: Wed Nov 18 01:14:03 2009 +0000 Added phlyoP pub. commit 4dd91e440f3716cba6e9c50a09f5937f265af3cf Author: hiram Date: Wed Nov 18 01:10:54 2009 +0000 Brought up to date on the occassion of losing the copy on genome-test commit 0d310ea59575f1d1ad75e5c49c9f71a85b4d5ab7 Author: braney Date: Wed Nov 18 00:48:14 2009 +0000 add RNA to GIS RnaSeq commit 2cc552e92f42d346d804cb77b9cff5bcf42b0b1b Author: donnak Date: Wed Nov 18 00:21:03 2009 +0000 Added Rochelle & Susan. commit 309af8e1d7c4ecde3c0aaac7f0045b1ac6387651 Author: rhead Date: Wed Nov 18 00:18:47 2009 +0000 Changed wording on description of phastCons and phyloP and trimmed references, per Adam Siepel. commit 4f36a67c66123bb617de10b2a47e1a9ec6398bb9 Author: braney Date: Wed Nov 18 00:17:44 2009 +0000 fix up some stuff with GisRnaSeq, fix clicking on control terms with CshlLongRna commit be06200bdb70e7ed4039ca08bb33d3fe18c0df20 Author: galt Date: Wed Nov 18 00:16:26 2009 +0000 removed temporary variable no longer needed in transtion from name dataUrl to bigDataUrl commit fc4dd503626b62c0f4a37f2695538dcd055ab689 Author: pauline Date: Wed Nov 18 00:16:18 2009 +0000 Removed alphas to stage track on beta. commit 21db21e4fcfe1647aac5206b2b0425c7a3f44f8e Author: donnak Date: Wed Nov 18 00:08:16 2009 +0000 Added Cell pub. commit 749b44374f44ac70b15f7318b64cd941b931298e Author: galt Date: Wed Nov 18 00:05:24 2009 +0000 v220 preview commit ee9611ff637a50b048f9f1dbb46a9076715e5278 Author: hiram Date: Tue Nov 17 23:39:26 2009 +0000 Add -noQuartiles option commit 04e96d215bcdbe4300343609ff86d810cf1c100d Author: kent Date: Tue Nov 17 22:41:59 2009 +0000 Making whiskers take light and medium color from primary color rather than always using grays. commit 8c91dab6f996537defd8e6162c854b0a4fa9fbe2 Author: jzhu Date: Tue Nov 17 22:28:58 2009 +0000 *** empty log message *** commit 1801c9d06908ff740c898bcb83e8c1e8d923427e Author: tdreszer Date: Tue Nov 17 21:12:56 2009 +0000 Background color of image should only be red for debugging commit c7a3d0d9ce1668f2e940a6b94fb31ec18af9f239 Author: galt Date: Tue Nov 17 20:59:32 2009 +0000 using flag to produce separate insert statements in dump commit 50c8d5e60a12d3c96a2e2fc8b38bd9d96af4d728 Author: kent Date: Tue Nov 17 20:47:50 2009 +0000 Adding whisker plots. commit e8ae37c8b91f97c36f8cd73977f313363ffb533c Author: katrina Date: Tue Nov 17 20:21:42 2009 +0000 fixed outdated information about OMIM links on Entrez records commit 3565f279cf9061aa6b4acd1786441e4b1f0b526d Author: angie Date: Tue Nov 17 20:17:57 2009 +0000 bugfix: don't assume we have linkedFeatures in baseColorInitTrack because this is called for linkedFeaturesSeries too. Use tg->drawItems as a proxy for type (lf vs. lfs). Then the proper range is set and we can replace a slow hDnaFromSeq call with getCachedDna. commit 539ebb9f539b8c418bca378f6b36f2e739b0c3b6 Author: markd Date: Tue Nov 17 20:16:44 2009 +0000 fixed incorrect code generation when no SNPs are mapped to structure commit a976dbd5dd836ac96acbf4f779a280e58fced4b1 Author: ann Date: Tue Nov 17 20:08:09 2009 +0000 Rewrote action setion to drop broken link, redirect another link to a better location, and make the section more clear. commit 1dd218912e2d4efd8d11095772735e18c5a18f53 Author: angie Date: Tue Nov 17 18:03:55 2009 +0000 bamDrawAt: Skip zero-length blocks or blocks out of the viewing window. commit 22c3f057c555ba48a28c27c6bf6982398c562eea Author: braney Date: Tue Nov 17 17:09:23 2009 +0000 human proteins commit 0dfb39a7d7d370156d6f8a386f9b1fd1575e286e Author: galt Date: Tue Nov 17 16:00:06 2009 +0000 "Encode release log update" commit c3afbf39cdbc32558d1107df49444412f2398810 Author: galt Date: Tue Nov 17 16:00:03 2009 +0000 "Release log update" commit e9f301706af2fd2428b17d46710e41dc05c38866 Author: angie Date: Tue Nov 17 07:18:01 2009 +0000 Added minLimit, maxLimit to bedGraph subtracks of wgEncodeGisPet from sql min & max queries on bedGraph tables missing those settings. commit c1f334a98213c8dc2bc79938e166f729df072a59 Author: angie Date: Tue Nov 17 06:54:24 2009 +0000 Added missing bedGraph data range settings (minLimit and maxLimit) based on commented-out type bigWig lines that specify range. commit d3f8aa87b4077039c527ff104da2807627bb526f Author: angie Date: Tue Nov 17 06:37:58 2009 +0000 Refactored wigFetchMinMaxYWithCart. It is still quite complex because I kept the old behavior that tolerates missing data range specifications (although it does warn now). When hgTrackDb is enhanced to enforce data range specs, this can become a lot simpler -- but still not simple because we still allow the viewLimits setting (not defaultViewLimits) to push out the data range boundaries. commit 4937d3ec174a8dd7344b956bf9d43ee6da3d734c Author: braney Date: Mon Nov 16 22:48:36 2009 +0000 fix long label and some view setting for CSHL short RNA-seq commit 8fa4684e32c95480cb068aedcba386d2e2d4010b Author: pauline Date: Mon Nov 16 22:31:03 2009 +0000 Fixed typo. commit a43485d99df56beb5a26c91793f2cfde8737ecde Author: kate Date: Mon Nov 16 22:19:21 2009 +0000 Removing PI name from lab in Caltech track commit 9a893dd5c6523e0817b26632218bec48e4c479de Author: katrina Date: Mon Nov 16 22:11:12 2009 +0000 set primate chain/Net to hide commit 4a3b11bc086387975850bd54ba90abbb25f809b2 Author: kate Date: Mon Nov 16 22:08:09 2009 +0000 Correcting ENCODE grant/lab metadata for Caltech RNA commit 05540104d2f83e0bf7fe95d9ad913c6ea7dcb4c1 Author: katrina Date: Mon Nov 16 22:06:31 2009 +0000 added track block for Alt Events commit bde2b1e138f12248c12e870acbcf3584a8b4ac35 Author: braney Date: Mon Nov 16 19:44:04 2009 +0000 started Human Proteins commit a753db9eec37f5505fe7e1617cb47c6167d7c7d3 Author: braney Date: Mon Nov 16 19:42:57 2009 +0000 continue to make Tim do most of the work (Bwahhh haha) commit 26d402d931e7a96271397fa7200b1875e47c4ba2 Author: hiram Date: Mon Nov 16 19:40:42 2009 +0000 Working on the genbank run commit 4207fb7ed9e009b8a0008b8490ea0c6e59595d21 Author: kent Date: Mon Nov 16 18:12:04 2009 +0000 Making compression the default for the bigBed and bigWig creators. commit 8520a52947322b8af03726b375970b6cb8f2bead Author: galt Date: Mon Nov 16 16:00:06 2009 +0000 "Encode release log update" commit 9e9da148873e87d5a2e98bc371c64b071058c251 Author: galt Date: Mon Nov 16 16:00:03 2009 +0000 "Release log update" commit cfcd6fc322f0383c6b502a6a6079bfcb7ae5d307 Author: kent Date: Mon Nov 16 11:01:22 2009 +0000 Improving calculations about initial zoom level in wigToBigWig, especially for compressed files. commit ce3f502417e13c429f26d13beecb3c6ebf781ff5 Author: hartera Date: Sun Nov 15 22:19:08 2009 +0000 added Burge RNA-seq data tables to list of tables to be ignored for hg. commit 452c1d49354ee09a01621dec537b6c819f58f41a Author: hartera Date: Sun Nov 15 22:01:32 2009 +0000 changed Burge RNA-seq data track default visibility to hide. commit a93d1534809f13655e3a054ce74e782cf469d5cb Author: hartera Date: Sun Nov 15 22:00:38 2009 +0000 added Burge lab data mapped using GEM mapper. commit 4a5831a2c714a10ecdfcace7c1b4c824cc6d51be Author: hartera Date: Sun Nov 15 21:57:45 2009 +0000 Description for Burge lab RNA-seq data mapped with GEM mapper. commit e7638a92db81927ed3563d2059dfd6a40f9ae7cb Author: hartera Date: Sun Nov 15 21:49:42 2009 +0000 Description page for Burge RNA-seq data re-mapped with GEM mapper. commit 060fee8fe0788d63ac946652c0013ec7a0552cfc Author: galt Date: Sun Nov 15 16:00:05 2009 +0000 "Encode release log update" commit 1c046e00fcedd5835cedc367c3416babb2283efd Author: galt Date: Sun Nov 15 16:00:03 2009 +0000 "Release log update" commit 73017667f1f1e2dce6760da34472637377f5ed13 Author: galt Date: Sat Nov 14 16:00:06 2009 +0000 "Encode release log update" commit e4cca000d123f6cd1a1986092b03b8c9aa3f4f69 Author: galt Date: Sat Nov 14 16:00:03 2009 +0000 "Release log update" commit 4f2021578639d57aa69d436d9bd3ea57bd75068f Author: galt Date: Sat Nov 14 06:45:31 2009 +0000 TODO note commit 3570f30bf7fc34c995873c04271fa00ac702fa18 Author: braney Date: Sat Nov 14 01:50:19 2009 +0000 fix up prostate signals commit 9ceaa68902371f765b068abd98d0be1cb9947d03 Author: kent Date: Sat Nov 14 00:11:32 2009 +0000 Making assumptions of bbiTotalSummary vs. version numbers a bit more explicit in response to Angie's feedback. commit 5ba2eb9b5b5762517f94e0c89e2b939bb11a8505 Author: kent Date: Fri Nov 13 23:47:02 2009 +0000 Fixed bug in sumSquares. commit 63c9e787cae784a85e0385780ed9bfd50201aac1 Author: braney Date: Fri Nov 13 23:25:03 2009 +0000 fix short labels for GIS RNA Pet commit 4c3161f19a87dfcfb6a41beb7ff4fd2c0494812c Author: markd Date: Fri Nov 13 21:33:25 2009 +0000 use different exit code when differences are detected to make it easy to use in scripts commit 14613015b13730adf0b9b96c58579701e22e6003 Author: braney Date: Fri Nov 13 21:22:57 2009 +0000 add GIS RNA PET back in commit ced62f42269c6413f1066e67b493d82953bbeeef Author: kent Date: Fri Nov 13 19:02:39 2009 +0000 Adding compression to bigBed. Improving bigWigInfo and bigBedInfo a little. commit ec986e842a2b0a192b54cb20f0665af67778938e Author: kent Date: Fri Nov 13 19:01:56 2009 +0000 Adding dyStringWriteOne. commit 7974b713d0ab6c2ed0d0e9ea2caccd53c50e1686 Author: kent Date: Fri Nov 13 18:22:46 2009 +0000 Removing unused library. commit 42b4edc76e9680eddb4e65355d74a43aaa36a19f Author: galt Date: Fri Nov 13 16:00:06 2009 +0000 "Encode release log update" commit 3ac37dd56db7757688e0e75140807cea4ae18c7a Author: galt Date: Fri Nov 13 16:00:03 2009 +0000 "Release log update" commit e94bec1ee811328df42ed11c2170805980d5d554 Author: braney Date: Fri Nov 13 09:34:43 2009 +0000 take out GIS Pet Rna commit 8a8d5700724f370a3c839b4635bd8c053fb84424 Author: angie Date: Fri Nov 13 07:07:36 2009 +0000 Oops, last-minute bug that negated performace gain :). commit ea80264166d6549cb87a5e4f66e9a8102808a926 Author: pauline Date: Fri Nov 13 07:02:09 2009 +0000 Fixed minor typos. commit 944b08a7e858edb671374ec91e524905a319a51c Author: pauline Date: Fri Nov 13 06:46:47 2009 +0000 Fixing file to conform to 80char line limit. commit a528d6266856efcf7adaad8b5b9cf18122f744b2 Author: angie Date: Fri Nov 13 06:42:43 2009 +0000 Use net.c's new support for open-ended byterange and sockets that stay open, so that we can read successive data blocks from the same socket, instead of reconnecting to the remote server for each successive chunk. This dramatically improves the performance of udcFuse on block-compressed data. Refactored to reduce code duplication between ftp and http fetchData methods, and keep private struct & methods out of udc.h. Added checking of return value from fetchData; we were just writing a bunch of 0's to sparseData when fetchData returned fewer bytes than we asked for [error while debugging net.c], which resulted in corrupt sparseData file. commit d9825f1450a6e6d4e713c84fda328fa1ee1ced9b Author: angie Date: Fri Nov 13 06:35:45 2009 +0000 Added netUrlOpenSockets/netGetOpenFtpSockets, which can pass the FTP control socket back to the caller instead of forking for the sake of closing the control socket immediately. This prevents the accumulation of zombie (defunct) child processes forked from the udcFuse daemon, and saves a bit of overhead. netUrl byterange can now be open-ended (only the start offset is specified), which also supports persistent connections in udcFuse. Also did some refactoring (readability & error messages). commit a8e08f61c67080689f132f4dcd87c57692be0396 Author: braney Date: Fri Nov 13 01:14:42 2009 +0000 fix up the long labels for GIS RNA-seq commit 179a2835f3be7c734cd64f358f64a4bb2be39392 Author: kent Date: Fri Nov 13 00:26:29 2009 +0000 Adding new bigWigToWig utility. You won't get _exactly_ the same wig that you gave to wigToBigWig back. It'll omit printing the decimal point in the floating point values when possible, and also it will break up large sections into medium-sized ones. Still at least it keeps fixedStep and varStep rather than converting everything to bedGraph. commit 24ca46334aaea661054fc8adbd702c09f7c28854 Author: tdreszer Date: Fri Nov 13 00:17:59 2009 +0000 Changes to fix no leftLabel bug and changes to support separate button slice (needed for subtracks with separate imgTracks) commit 6f35429f9b1db0667069ee27f9c576b09f5e165f Author: tdreszer Date: Thu Nov 12 23:38:41 2009 +0000 Change to support buttonSlice (code isn't even used without dragScroll which is disabled) commit fe6b431f8bc67ccd4baabe71f0ef8b3f08a9de5c Author: kent Date: Thu Nov 12 23:15:52 2009 +0000 First cut of compressed bigWig/bigBed stuff. So far read side should be complete including Genome Browser, Table Browser, wigToBigWig and bigWig utility functions. Still to do bedGraphToBigWig and bedToBigBed. commit 15cf83e17a6a9ba2030ccd2f723bfed9661c4e5d Author: kent Date: Thu Nov 12 23:11:54 2009 +0000 More zlib testing. commit 5c625b371f2614325b75bf533bdd02cf16c0c9a4 Author: tdreszer Date: Thu Nov 12 20:50:54 2009 +0000 Bob does not want no double negatives so I disabled the disable and instead enabled 'Enable advanced javascript features' commit b66bb8ca860c187db9ba9155dff56d5b5fe42ede Author: tdreszer Date: Thu Nov 12 20:34:36 2009 +0000 Fix uninitialized variables, which hit on matrix X no Y commit a7241d3fe77dca412bc089d796af03d66d36c2fb Author: donnak Date: Thu Nov 12 19:51:37 2009 +0000 Added Brooke's NAR pub. commit afcc6e9b77d4c951bf24bf0120827e910ac0cb9f Author: hiram Date: Thu Nov 12 19:36:21 2009 +0000 Fixed up comment about fixed WEBROOT location commit d6e84d05740655da18f0f000884e0de5a644f705 Author: kent Date: Thu Nov 12 19:34:48 2009 +0000 Removing some commented out debugging statements. commit 676de5edb160c7f941802a86ed232efcd20d606e Author: kent Date: Thu Nov 12 19:33:54 2009 +0000 Adding a few new utilities to common.h/common.c for benefit of bbi compressed encoders. commit 855449499e431d35fb95cb3544f734303ef1890d Author: kent Date: Thu Nov 12 19:31:52 2009 +0000 Changing uglyf to printf since it's not just a temporary thing. commit 8b2ea346af8445d70843618388f45b445fcbc6ed Author: kent Date: Thu Nov 12 19:30:41 2009 +0000 Seems to work. commit e1c57afbd5fe197a0ee13b94cec899140b8bbb02 Author: kent Date: Thu Nov 12 17:46:41 2009 +0000 Updating expected output. commit b88223d728fb26a17a27c588213d9025b938fc95 Author: braney Date: Thu Nov 12 17:36:06 2009 +0000 change Cshl short RNA-seq to use bedGraph instead of bigWig commit c0f07ee72140234e439770bf29f80c8f33c50d37 Author: galt Date: Thu Nov 12 16:00:07 2009 +0000 "Encode release log update" commit fc1b5bf505399986c67c6f75ced6ad83fe2f7626 Author: galt Date: Thu Nov 12 16:00:04 2009 +0000 "Release log update" commit e89b883d0b23abeef7abde18399ede960811fa9b Author: braney Date: Thu Nov 12 03:12:33 2009 +0000 change GIS signal tracks to normal wiggles and make them LOG commit 80954619d5d023354bc57639a214308e5f76c5c7 Author: braney Date: Thu Nov 12 00:23:06 2009 +0000 make LOG the default transform for CSHL long RNA-seq signals commit 9fffc1d06ab70918f95e6ff2d7a62c1defe09cb0 Author: braney Date: Wed Nov 11 23:28:00 2009 +0000 changing CSHL long RNA-seq signal tracks to bedGraph commit 966a6b742ce41995e040c3606bd6aa81b4b34945 Author: tdreszer Date: Wed Nov 11 22:25:31 2009 +0000 Added instructions for the 'ABC' dimensions commit 6b10ee5e78cfc381c9666d35a55cbdd9415a991a Author: tdreszer Date: Wed Nov 11 22:17:22 2009 +0000 Minor change to validationSettings commit a2c7e95a4b2777e75a2849c1bb7dcf50e32d8013 Author: tdreszer Date: Wed Nov 11 22:15:27 2009 +0000 Dribbling in commit 5c36c747093e1fd93336010a40432d6a47cd9d6d Author: tdreszer Date: Wed Nov 11 22:14:22 2009 +0000 Old... Broad into QA for release2 commit 86768c4439d7b938788b2e5804376d82586b1f54 Author: tdreszer Date: Wed Nov 11 22:13:13 2009 +0000 Old stuff needing to be checked in commit 5aa959ce2a7beeef3112b838bea558c6392c8713 Author: tdreszer Date: Wed Nov 11 22:11:43 2009 +0000 Finish with Base overloap and getting release2 into QA commit c7959bfc7050151e8c1b4230dce753fa917e7f34 Author: tdreszer Date: Wed Nov 11 22:11:05 2009 +0000 Loaded version v3c commit cdf623d3c776cb4ff5c3941ecc697fb875ee0322 Author: tdreszer Date: Wed Nov 11 22:06:42 2009 +0000 Changes to allow the 5th dimension commit 375bf87e0afcadcfd4cf38c09e0153f46110068b Author: tdreszer Date: Wed Nov 11 21:55:14 2009 +0000 Added some obvious array functions commit 1e68bfb39114b6e61df54ef0fd5ec463d90d9b1e Author: tdreszer Date: Wed Nov 11 21:14:54 2009 +0000 FINALLY, checkin imageV2 framework without features. commit 7e00ca77d628b9246c2ca48a8a2863d9aa4e1b78 Author: tdreszer Date: Wed Nov 11 21:13:14 2009 +0000 Changed 'Enable drag-zoom' to 'Disable advanced javascript features' in preparation for imageV2 commit a678e29cf7c37c4bb8ba9bf892e0ad79811fe87e Author: tdreszer Date: Wed Nov 11 20:41:30 2009 +0000 Cleanup before checkin of imageV2 framework without features. Also made track toggle work better for composites, but only in imageV2 commit fb9fba604ca1e458a97594c2f1b7241fd9bd4d2a Author: galt Date: Wed Nov 11 16:00:07 2009 +0000 "Encode release log update" commit b7b28c2de079942646302d2d047825c6bf8f82e6 Author: galt Date: Wed Nov 11 16:00:04 2009 +0000 "Release log update" commit 1f3d4f019bcb68bb5c0c5fcfb0a23ed4c913762e Author: cszeto Date: Wed Nov 11 01:40:33 2009 +0000 171819 data commit a7f53736abc7ede7c8e9749f8d4b0d8254428aa3 Author: hiram Date: Wed Nov 11 01:07:36 2009 +0000 done with hg19 46-way track, once again commit f9da62695497ef56a545074efcafb2f788074a87 Author: kate Date: Wed Nov 11 00:16:13 2009 +0000 Mention new ENCODE grants in the news commit 72f140d8d5aa1aae21fbeec1d15c7e1b27ed0b7f Author: hiram Date: Wed Nov 11 00:01:53 2009 +0000 The 46-way phastCons and phyloP tracks turn back to the old style wiggle tracks commit e94c089f5010f2be93529d9ca3cdadbd03dacd2b Author: kuhn Date: Tue Nov 10 23:52:05 2009 +0000 mentioned files in usage statement. removed redundant statement about defaults to beta. removed code that restricts to dev as it runs ok on beta, too. per brooke commit 81ad7a73212047a6860ee9a42a9e582418968967 Author: kate Date: Tue Nov 10 23:50:34 2009 +0000 Add liftover chain tracks for newer assemblies commit 1b6129e90b50949370d496d44f0feaf26dad3139 Author: angie Date: Tue Nov 10 23:23:59 2009 +0000 Force keys to uppercase for netUrlHead's hash, for case-insensitive lookup. Also, in udcInfoViaHttp, accept Date: as a poor substitute for missing Last-Modified:. commit fc30b03da7b7a3febdcb6cf61c575db9b87f9ee7 Author: kent Date: Tue Nov 10 23:05:52 2009 +0000 Adding zlib interface routines. commit 65a051ac8ec17f16cc82d2bbd335d97f7d98e13c Author: tdreszer Date: Tue Nov 10 23:04:03 2009 +0000 Finish (I hope) Base Overlap updates from Open Chromatin release 2 commit 082f65ac18a6997f09c6890d72d10eeb421b6750 Author: angie Date: Tue Nov 10 22:46:19 2009 +0000 Added hashFindValUpperCase (based on hashLookupUpperCase). commit 38117b547f2464c9e998a2f4bacdb9a1fc57d8e1 Author: tdreszer Date: Tue Nov 10 21:52:08 2009 +0000 validateFiles.c commit 51583773b0c28db53bb50d14d8780d4480bd1b13 Author: kent Date: Tue Nov 10 20:52:58 2009 +0000 Testing zlibFace. commit a2b07aa555c1f37da83ef0c4ee929cadc7870b96 Author: rhead Date: Tue Nov 10 20:26:26 2009 +0000 Fixed broken links to Beijing Genomics Institute. commit f59f8f0dc1a4d12f831fe7f7c76fa91d9e850104 Author: galt Date: Tue Nov 10 16:00:07 2009 +0000 "Encode release log update" commit dcd4a38ee6fed6fcae52011ca885ddcfd2e64787 Author: galt Date: Tue Nov 10 16:00:04 2009 +0000 "Release log update" commit 397fbf1b5c1829c3302e60cfef3dcc76c10656ff Author: kent Date: Tue Nov 10 07:53:58 2009 +0000 Initializing some vars to zero to fix compiler warning on older compiler that wasn't quite sophisticated enough to see that these are actually initialized in all paths. commit b411a38a19c1f8d127262551191c268cb14f60f2 Author: angie Date: Tue Nov 10 06:30:03 2009 +0000 Don't add -lfuse here, leave that to common.mk if USE_FUSE==1. commit 6ea3c79d9a9f51a55d6dcd84af421ef7a2bb88d7 Author: galt Date: Tue Nov 10 06:29:19 2009 +0000 rearranging the order of background operations so that utils do not hold up cgi and cvs-reports commit 11a27b48e1e23076f0849cd4a26f89825f6b6541 Author: kent Date: Tue Nov 10 05:48:18 2009 +0000 Changing bbiFileName field in track to bbiFile, so that it is kept open rather than repeatedly opened and closed. This avoids round trips to remote servers. Also starting to put in some stuff for tracks hosted on remote MySQL servers, though this is not complete. commit 748f912f807d2a6b4a062e60b6ac4243b6e8ce8d Author: kent Date: Tue Nov 10 05:47:03 2009 +0000 Changing default blockSize and itemsPerSlot to something more reasonable. commit 52b30eafa34d58089b481149e783f00231e0deea Author: kent Date: Tue Nov 10 05:46:36 2009 +0000 Making bigWigSummary functions take a bbiFile rather than a fileName. commit 29a7e7c0ff1b2900a0ca22d3777a8f4a00ba6a39 Author: kent Date: Tue Nov 10 05:41:56 2009 +0000 Hopefully making wiggle limits behave a little nicer when defaults are not set. Certainly works nicer with bigWig commit 250990418b011056b56c0e7f40317a80b8e7a74b Author: kent Date: Tue Nov 10 05:39:34 2009 +0000 Adding bbiFile field to customTrack to avoid reopening it repeatedly. Setting display limits from bigWig/bigBed files so they don't end up the weird 0-127 defaults. commit b4b2df5864a1d7bf3b8a00fee0cbe352ac367598 Author: kent Date: Tue Nov 10 05:38:02 2009 +0000 Adding bbiFile field to customTrack to avoid reopening it repeatedly. commit 8e0646e163fdc49a7d95a1a52f1bbc05edb9cd15 Author: galt Date: Tue Nov 10 04:57:35 2009 +0000 "New version number v219" commit 876e846d4855103579545b0fe39511de0af591c8 Author: galt Date: Tue Nov 10 04:19:02 2009 +0000 "New version number v217" commit b7f39850fd4031e7bb5e04fab6ffd26cd881ffc4 Author: galt Date: Tue Nov 10 04:18:03 2009 +0000 v219 final build commit ebc85316873e1644b17920cc348c9a82c57f6550 Author: kate Date: Tue Nov 10 01:54:17 2009 +0000 Add jobs info and some formatting commit 231639319b2afe8ecdaa20e6518f184ae0b6b1de Author: kate Date: Tue Nov 10 01:27:22 2009 +0000 Add Oct news commit e01d57e0eb9eddaec909ab8b164b2b90865b3140 Author: kent Date: Tue Nov 10 01:21:14 2009 +0000 Testing zlib compress and uncompress. commit 59d048415bd5f757f0d1f44e09830f866b5551f4 Author: angie Date: Tue Nov 10 00:54:26 2009 +0000 Doh, forgot to leave in a dummy main when USE_FUSE is not defined (thanks Tim!). commit 2837a0d987279bf0d25d8efcd7bb48c80df078a1 Author: braney Date: Mon Nov 9 23:56:25 2009 +0000 initial/current status commit 3e3ec739ce47f239fced34ba0c6efc98c57c6c3b Author: galt Date: Mon Nov 9 23:01:18 2009 +0000 fix beta tag so that it does not move until the cgis are pushed and released to the RR commit aa86621bf3d3309c9862a60950fc7f84cf6ec25a Author: holmes Date: Mon Nov 9 22:35:56 2009 +0000 Adding megablast commit 0970a0c49205c5ed09539ab609835f82e44ff51d Author: angie Date: Mon Nov 9 22:32:18 2009 +0000 Call customFactoryEnableExtraChecking -- initial load is a good time to perform more expensive tests. commit a58b9f5b4487c804eb20cc18ad414cb0c41cc8c6 Author: angie Date: Mon Nov 9 22:31:15 2009 +0000 Added customFactoryEnableExtraChecking, intended to be called only by hgCustom. When the user first loads a custom track, it's a good time for more expensive testing (like opening remote BAM files). However, hgTracks etc. can save time by not duplicating that work every time they parse existing tracks. Currently only bamLoader uses this. commit 407c94c6c5c416be0634ff0e0e019940d3f33edb Author: holmes Date: Mon Nov 9 22:24:55 2009 +0000 Adding megablast track commit f0aca11cd68754c2bee94f4f9255fdbde13f6bf8 Author: ann Date: Mon Nov 9 22:15:16 2009 +0000 added info about new utility commit 6cb03c128cac8fda3e244011abaaf3e1e796d5b3 Author: galt Date: Mon Nov 9 22:07:31 2009 +0000 fixing makefile commit 5188a236bc186732917d6d3fa063505374bc4713 Author: galt Date: Mon Nov 9 22:01:03 2009 +0000 adding bigBedInfo util commit d2cc25986afa063fdeeeeb4a990f2a391c1658e2 Author: hiram Date: Mon Nov 9 21:17:13 2009 +0000 Updated for todays source tree particularies commit c60d9bd78c53fd381dd770b7ecb57c9b9d0459d8 Author: kate Date: Mon Nov 9 19:59:32 2009 +0000 Update archive reference section of News commit 3ccc1a7b12d4295408264de62f80d4962cdbf892 Author: kate Date: Mon Nov 9 19:46:25 2009 +0000 Update Sept. news to include NRE track, add links commit 8eceffbb8f941fc2bc2e7bc490fdb8361da11c81 Author: holmes Date: Mon Nov 9 19:20:29 2009 +0000 Adding vecscreen and orthologs commit e55b753088cf3430a10ea1e0eed4d7d56005a7d0 Author: hartera Date: Mon Nov 9 19:17:24 2009 +0000 Documented the chrom names that were corrected and made a note that the otherSize column could be dropped in future for the seg dupes data. commit 4250d63551714296b7d0869d95ce0f5372fa3bea Author: hartera Date: Mon Nov 9 19:06:29 2009 +0000 Added extra line in seg dupes track documentation. commit 30f093c38055756b07144d24c8d48b3f9f4b22fb Author: angie Date: Mon Nov 9 18:41:56 2009 +0000 Added off-by-default USE_FUSE so udcFuse won't break compiles on machines that don't have fuse installed (thanks Mark!). commit 5d100e0fb86d9f0cf4fb24bd7b527aaf05c4fe49 Author: angie Date: Mon Nov 9 18:41:18 2009 +0000 Added #ifdef USE_FUSE wrapper so this won't break compiles on machines that don't have fuse installed (thanks Mark!). Also, use appropriately sized int for cache file size, and merge adjacent errCatch wrappers. commit 648569e87c5b5d52fa2ac9f5890254cdba87262a Author: braney Date: Mon Nov 9 18:23:58 2009 +0000 initial/current status commit 2e85044ef104ca070af7816039093c91a4b0624e Author: braney Date: Mon Nov 9 18:18:25 2009 +0000 initial/current status commit ef260e69c2a92dd7a2bd56acee6491cac93d7d83 Author: tdreszer Date: Mon Nov 9 18:09:05 2009 +0000 Added subgroup5 for HudsonAlpha... planning for 5 dimensions to come commit cc7cf11ae78895e552816ff2bd1d0abb10d24b38 Author: galt Date: Mon Nov 9 16:00:07 2009 +0000 "Encode release log update" commit 21788ca831fc49d17d171ee5f46027f38f6c15c7 Author: galt Date: Mon Nov 9 16:00:04 2009 +0000 "Release log update" commit ac867fe5627359d724c6b84a83dc0fffe69ce5ca Author: galt Date: Sun Nov 8 16:00:07 2009 +0000 "Encode release log update" commit 6d0a49f5b6f2ef9a194a8cc296a1fec6c6e771f6 Author: galt Date: Sun Nov 8 16:00:03 2009 +0000 "Release log update" commit b31b4cfcbd4f04b0e03f32c6031719263a053233 Author: kent Date: Sat Nov 7 19:31:19 2009 +0000 Adding totalSummary to big files. Should be helpful in quickly calculating ranges to be displayed by default. commit 97078a9ea15e23653ee18e0e1c796f5e28e3ac1b Author: kent Date: Sat Nov 7 19:30:32 2009 +0000 Adding additional information to bigWigInfo output - data and index sizes. commit 40f62b82ab153732790fde13b20cb3ba9ceb3702 Author: kent Date: Sat Nov 7 19:25:54 2009 +0000 Updating bbiOpen to handle totalSummary. commit ac21739e49c47ecbb7b4ffaadab53648374ab104 Author: hartera Date: Sat Nov 7 17:41:04 2009 +0000 File cleanup for seg dupes. commit 681b584ba87112d7d83730843c56aef836d00215 Author: kent Date: Sat Nov 7 17:38:19 2009 +0000 adding bbiSummaryElementWrite commit bc9ba663f8c9925125178646354d883767fee733 Author: hartera Date: Sat Nov 7 17:35:48 2009 +0000 Re-loaded segmental duplications data after correcting chromosome names. commit 7cfe206aaa6ae526dea3bbe5b23bef5f87c85e24 Author: galt Date: Sat Nov 7 16:00:05 2009 +0000 "Encode release log update" commit e47ea3f540595b3d6f61d2b294ed30f518ff70cc Author: galt Date: Sat Nov 7 16:00:03 2009 +0000 "Release log update" commit 8393f1aafdfaa53851a74f1f00b9ba36bbbd42e8 Author: markd Date: Sat Nov 7 06:07:33 2009 +0000 added ignore entries commit 312e7db0bf0fd00c1083585c598d65d1a533acc7 Author: braney Date: Sat Nov 7 01:36:58 2009 +0000 put summary view back to 1000000 commit ec207395b4f0081270965fd8366d7095e110e3e2 Author: ann Date: Sat Nov 7 00:32:49 2009 +0000 more stuff for monDom5 CN override commit f87f2e54cb3a7959e454b1f17585dbb939b804cc Author: braney Date: Fri Nov 6 23:53:13 2009 +0000 add bounds to bigWig commit b31d9889f8ca210b791d6fe57275555622cba50d Author: ann Date: Fri Nov 6 23:38:19 2009 +0000 override for monDom5 ChainNet track commit fec2b696d81058ea63bcd9eaabb6f966eeee5d69 Author: donnak Date: Fri Nov 6 23:37:04 2009 +0000 Updated a few entries. commit ed9ddd26fc5c3cb0243c76b094a280ac9950bc71 Author: fanhsu Date: Fri Nov 6 23:18:06 2009 +0000 Added GeneNetwork ID table to enable hgGene link to GeneNetwork. commit 37a94b2a91dd736692503454fe3db26afa0600b7 Author: fanhsu Date: Fri Nov 6 23:06:53 2009 +0000 Added GeneNetwork ID table for hgGene link to GeneNetwork. commit 1ab6db19b72557c5d0cc337a7ad1abf5c49e1cac Author: donnak Date: Fri Nov 6 23:06:16 2009 +0000 Added Genome 10K pub. commit ff62045423c46f4136a9c808fb40de8d3bfd83cc Author: fanhsu Date: Fri Nov 6 23:05:28 2009 +0000 Added GeneNetwork link. commit 3a6dc1f4fd6a8dc77a348160d9e532adda5b9e48 Author: angie Date: Fri Nov 6 22:42:06 2009 +0000 Oops, forgot that file size really needs to be a long long. commit 94475ea75bcdff3d12f12dbc7fd1ccb638a45c41 Author: fanhsu Date: Fri Nov 6 22:38:30 2009 +0000 Added GeneNetowork ID table for hgGene link to GeneNetwork. commit 52472edcf47aa1e19416ef51072ee8f8ab67e8ef Author: hiram Date: Fri Nov 6 22:38:18 2009 +0000 Adding susScr1 to the build commit 83f7376733a2c8819d3dc9c9f88dcd57a0edfbd4 Author: hiram Date: Fri Nov 6 22:37:23 2009 +0000 Initial contents from makeGenomeDb.pl commit c15260a3cdd2fb766276d795270dbc0bbb9ea8ec Author: braney Date: Fri Nov 6 22:27:12 2009 +0000 add transform function for wiggles commit 41ddbafb40e742489b775a3ce671f822e6038e44 Author: hiram Date: Fri Nov 6 19:57:51 2009 +0000 Fixup some dates on assemblies commit de3bfa45e31c55e740de63ac8957ae28bbbfad31 Author: kent Date: Fri Nov 6 19:46:54 2009 +0000 Adding version number to usage statement. commit 619375f8b0e20006c32440a601945ce2f5ab2704 Author: hiram Date: Fri Nov 6 18:59:39 2009 +0000 Add reference to new paper on phyloP commit 7f7be2d49033fd7a34fe25594f97f6d4cb4536f5 Author: galt Date: Fri Nov 6 18:44:51 2009 +0000 documenting SSL option commit 009654cc9c8ed6b58e112dd37e557f22433564f1 Author: angie Date: Fri Nov 6 18:09:55 2009 +0000 Don't use kentlib free functions on mem returned from samtools, because kentlib functions weren't used to allocate it. commit f4d0bde09b5eee25203ec79b0f582c35c144b342 Author: galt Date: Fri Nov 6 16:00:07 2009 +0000 "Encode release log update" commit efc60966ae97d5af114cb65cbcb02bba0b97878c Author: galt Date: Fri Nov 6 16:00:04 2009 +0000 "Release log update" commit 0edffbce15cd0d06ae691ccba09dcab42b96c97e Author: kate Date: Fri Nov 6 05:35:11 2009 +0000 Fix key for 'pi' file -- should be 'lab' commit 46964ced34d20d254360164cf6e10f80ff428b85 Author: kate Date: Fri Nov 6 05:33:51 2009 +0000 Reorder so lab (which is key) is first commit b88f99fc6e68e7b047618b78af003fed6c9e737b Author: kate Date: Fri Nov 6 05:33:22 2009 +0000 Fix lab to project mapping commit 7ede62b8804d386ce4b8306ee5def8defbcdf5b0 Author: angie Date: Fri Nov 6 05:16:01 2009 +0000 Set the udc cache timeout to an hour [need to add refresh button to hgTrackUi, then can make timeout very large], and if cache files are younger than that, use kernel caching (on top of udc's faster open) for almost-local performance. commit 02c4344858d35ea74ac80d129cd3301d0bd57ee4 Author: angie Date: Fri Nov 6 05:08:02 2009 +0000 More changes motivated by udcFuse performance: added udcCacheAge, udcCacheTimeout and udcSetCacheTimeout. If cache files exist and are younger than the cache timeout threshold, don't fetch info from the remote server when opening, just use size and date from bitmap file. This saves 0.8s per open for ftp to NCBI. By default, cache timeout is 0 (same behavior as before -- always fetch info). commit 539da12ce6a714e86296baceb721b738c1e0a4e7 Author: angie Date: Fri Nov 6 04:50:52 2009 +0000 Yikes! Stray 'else' could have led to mem corruption (use after free). commit e5e358edb3c8383abe0fa2d57644841ca8c575d9 Author: braney Date: Fri Nov 6 02:39:40 2009 +0000 GIS RNA-seq signal tracks commit 1790bd82953935e4250cd7eadb78d48910f2edc2 Author: rhead Date: Fri Nov 6 01:40:21 2009 +0000 Changed this to accept a website and list of files rather than a list of files that includes most of the path and no machine. Also added filename: to output. commit 876b30e945023a82f81fa30f3936153fa0e62e69 Author: kate Date: Fri Nov 6 00:55:56 2009 +0000 Adjust lab name to match projects table commit 1f2329c74e557769034c30cb91f0294e96a2e375 Author: kuhn Date: Fri Nov 6 00:26:04 2009 +0000 added comment about changing colors in dgv commit 9bc273a58154231c9bd0682180fefc8d2baa7164 Author: kuhn Date: Fri Nov 6 00:21:10 2009 +0000 added comment about changing colors in dgv commit 2841f973f501a98b49b6ff24830b37779a8e6bbe Author: ann Date: Fri Nov 6 00:09:52 2009 +0000 putting chicken chain/net in the correct order commit 838d87beb565165808fc61e29baec8a03940606f Author: kuhn Date: Thu Nov 5 23:55:23 2009 +0000 added support for gbdb files and disabled noIndex option. fixed to accomodate MySQL 5 TABLE STATUS dumps commit 7e196c31268e884380e8e3b17fcc9312e4af874b Author: kate Date: Thu Nov 5 23:52:47 2009 +0000 Fix another line format error in UW ChIP seq entry commit 8ed4a83998daa98b9c28a167e8e65143d099764e Author: rhead Date: Thu Nov 5 23:50:51 2009 +0000 Added a wild card to the ends of phastCons tables (in tablesIgnored). commit 83410e9e40ab2d914a4c888d75689c6afe77c8b1 Author: kate Date: Thu Nov 5 23:31:29 2009 +0000 Fix line format error in UW ChIP seq entry commit 7ccb520bf43ecb431382184bf1c1975b3ba0ed6c Author: braney Date: Thu Nov 5 22:28:37 2009 +0000 set correct clipping rectangle commit d4daf23458e0b61bfedf742c9c74847c1c3f1e89 Author: kent Date: Thu Nov 5 20:00:23 2009 +0000 Fixing bug where sumSquares was actually just sum. commit 505d3a52f4a65d6fbfdd4d86ceeda901b8b2ef16 Author: kent Date: Thu Nov 5 19:57:32 2009 +0000 Utility to get information on a bigBed seems to work. commit 4f706cd323fc058bb8c0102539326d5c896bfffd Author: kent Date: Thu Nov 5 19:48:21 2009 +0000 Making listing of chromosomes just an option. Adding info from totalSummary, which some day may be used to set min/max values of bigBed/bigWig wiggle ranges. commit 0442310c3c4c0ca357e5ddc2ebdaaec8799c2c94 Author: kent Date: Thu Nov 5 19:46:58 2009 +0000 Adding bbiTotalSummary. commit eb63d189735f0a17c91cc77b889464c854c3de2e Author: kent Date: Thu Nov 5 19:45:30 2009 +0000 Adding udcReadDouble. commit ca5764a9ec4b4d47a19587d119ad276805db20d2 Author: kent Date: Thu Nov 5 19:35:38 2009 +0000 Bumping version number. Making sectionCount and zoomCount more consistent. Also fixing bug with sumSquares being just sum. commit 0eb447402b37fe32852e1543b3a5469e1684250d Author: kent Date: Thu Nov 5 19:35:01 2009 +0000 Bumping version number. Making sectionCount and zoomCount more consistent. commit f69bf95f72e573380491a66b8f2d15a8ca847af1 Author: kent Date: Thu Nov 5 19:29:31 2009 +0000 Adding bigBedAutoSqlText. commit cd5bc0619ae2fbf5886bd9d17a03ff92af99b581 Author: kent Date: Thu Nov 5 19:28:04 2009 +0000 Adding udcReadFloat function. commit f29adbc676c9f45e33acbb5028ff4e29cf2aeac9 Author: ann Date: Thu Nov 5 19:15:34 2009 +0000 collapsing exactly idential release alpha/beta blocks into one (for chain and net of galGal3) commit 1accbc1b970f3b604a39936b0a56216c5ccc9b7b Author: angie Date: Thu Nov 5 18:48:36 2009 +0000 Handle chromosomes setting in customTrackUpdateFromSettings, to avoid hgTracks loading overhead for a custom track that has no data on the current chrom. commit f21780ac63ee3678dc39e4493d86aeb9b524e1a9 Author: ann Date: Thu Nov 5 18:33:47 2009 +0000 collapsing chainMm9 and chainMm9 override blocks into one block commit 896c1e8e1ee3d01004a85934b2b8d48a44fdb3b2 Author: tdreszer Date: Thu Nov 5 18:08:18 2009 +0000 Added MCF-7 protocol for Farnham and removed the obsolete HA antibody listing commit 46a1485f29c03e96472ea655bbe812b5ba270132 Author: angie Date: Thu Nov 5 17:50:24 2009 +0000 It's not sufficient to test existence of a path in udcFuse, because empty directories are left behind when bitmap and sparseData files are cleaned up, and then udcFuse will show the directory. So test whether a udcFuse path is a regular file (as a dir with bitmap and sparseData files will appear). Also, test existence of index files independently from .bam, and look for both index possibilities as udcFuse paths before attempting the costly udc open. commit 681baf29647c42d853904daec08d0d495dea26a0 Author: galt Date: Thu Nov 5 16:00:06 2009 +0000 "Encode release log update" commit 3104ee200ad3f4cbbfcb7312079e4a0723c4d019 Author: galt Date: Thu Nov 5 16:00:03 2009 +0000 "Release log update" commit 772a73ff76e3a0bc462ba0ee4189c763e768933a Author: hartera Date: Thu Nov 5 00:44:50 2009 +0000 Added text to methods and another reference as requested by Eicher lab. Added data provider for the hg19 data for this track. commit c7f70d342c470076587dc989ef9a219febf1cf62 Author: hartera Date: Thu Nov 5 00:33:06 2009 +0000 Added segmental duplications provided by Eichler lab. commit 9fa3efc94761b1cfec0496232cb7c0d2e3984248 Author: ann Date: Wed Nov 4 23:44:52 2009 +0000 putting the chain and net tracks in phylo order commit 19e20a6b1c9fba60500c66bedb568d212809e753 Author: ann Date: Wed Nov 4 22:32:32 2009 +0000 putting the species in Conservation track in proper phylo-order commit e8ff03c7bc3146b16062639f17008a0f799a1d99 Author: tdreszer Date: Wed Nov 4 19:45:06 2009 +0000 35 of 41 Base Overlap tracks for ChromatinMap were replaced. commit 37f0aed1b22dadafb4b9ada81c2c51e9a617880c Author: kuhn Date: Wed Nov 4 19:15:59 2009 +0000 typo. thnx, ann. commit d54f6f6db1bb402b12b3926b05771da666af50a8 Author: galt Date: Wed Nov 4 16:00:06 2009 +0000 "Encode release log update" commit b914091c9c73e66aaf1975199aa72e99ab02bbf8 Author: galt Date: Wed Nov 4 16:00:03 2009 +0000 "Release log update" commit 250c6210fd13ec32f25c4e674cfe6fe78a8d79ee Author: markd Date: Wed Nov 4 06:42:51 2009 +0000 added ignore entry commit 33a2f26464036e2f2f0d7a8bccf64593fef28ad0 Author: braney Date: Wed Nov 4 04:17:05 2009 +0000 finish up hgPal download commit 2c44bbea1a4f74cd33efccea9c372af37af479d0 Author: kate Date: Wed Nov 4 01:35:16 2009 +0000 Edits for clarity commit 58ee478348006aa50777971454874fa16de81484 Author: tdreszer Date: Wed Nov 4 01:12:18 2009 +0000 Added support in controlled vocabulary link to support suffix that is not pare of the link commit cefe071132975fdad643f4c307b3159ff373eeab Author: rhead Date: Wed Nov 4 01:08:02 2009 +0000 Updated description of display of all tissues vs. display of averages. commit 100fed954d1b77c9a9ef37289bfec11db9318c2b Author: hiram Date: Wed Nov 4 00:20:17 2009 +0000 Fixup chainNet composite Ui commit 378284c3a87859db7333ab85364a2f7ce36a50d1 Author: hiram Date: Tue Nov 3 23:11:01 2009 +0000 blank out some stray periods commit 74e46495de2df2445217a75211b23d4c34cc1f88 Author: hiram Date: Tue Nov 3 23:05:52 2009 +0000 updated image with name labels and three groups marked commit 2eb1343d4e82294e133b99201e68b78fa45aa809 Author: rhead Date: Tue Nov 3 23:02:14 2009 +0000 Restored wormbase links to assembly-specific versions. commit 3b3284f431395bcf225bba6f4822685be1e7f6da Author: rhead Date: Tue Nov 3 22:52:29 2009 +0000 Restored wormbase links to v170 versions. commit 9d143e7e0f4f74d536a48ed14889f7bf43a9dc6c Author: hiram Date: Tue Nov 3 22:01:35 2009 +0000 Copied from the hg18 44way and updated for 46 way specifics commit daa786ba725e9627e8dba526ac3ba929c8c2a3b5 Author: galt Date: Tue Nov 3 21:32:46 2009 +0000 v219 preview commit b1da5773c53c704dd3e4a5d846c18d3faf92871b Author: tdreszer Date: Tue Nov 3 20:04:15 2009 +0000 Added OTTER id search spec for gencode v3c and set gencode freeze to Oct 2009 commit 74927dfe6844e8d8668e8e8c0794ee43f8bd56d2 Author: braney Date: Tue Nov 3 20:00:19 2009 +0000 initialize some variables commit 9524b8a2ceb905c48fba82b9da997fca7dc45705 Author: donnak Date: Tue Nov 3 19:39:06 2009 +0000 Added several new pubs, fixed a few formatting things. commit ffd104c5eab9b7f0e3e8167abd977af7dc5572d0 Author: braney Date: Tue Nov 3 18:43:23 2009 +0000 add some Release Notes commit d714c86319b8ec769d156d987a838353402031b0 Author: donnak Date: Tue Nov 3 18:35:56 2009 +0000 Added MGC pub. commit 4b7bfe80a9c1d379a50bedcc5b86dd287cf4c428 Author: fanhsu Date: Tue Nov 3 16:38:13 2009 +0000 Added logic to take care "N/A", "N/D", and "" for text mode of Table View. commit fb02af3649d30d8528cf13f71cc1cf4e387aaa3b Author: tdreszer Date: Tue Nov 3 16:36:51 2009 +0000 This is Gencode's October 2009 freeze commit 05f59ea059d2a51617d06f1a8d3cab1435e8eb24 Author: galt Date: Tue Nov 3 16:00:07 2009 +0000 "Encode release log update" commit 65266030e2e8f71dae18caefe7d98e9327e7de6d Author: galt Date: Tue Nov 3 16:00:04 2009 +0000 "Release log update" commit 28ddc469d0c700a3302b85a0780ee07b5ab76c4a Author: fanhsu Date: Tue Nov 3 14:08:42 2009 +0000 Updated some labels per GSID's request. commit 8e31150dd85f5c36620bc67670076192e933630a Author: angie Date: Tue Nov 3 01:20:40 2009 +0000 Should have finished writing it first. commit ebdf6573ee1e68e6e438b0079f0e05a1ba00cc64 Author: angie Date: Tue Nov 3 01:18:32 2009 +0000 Hooking udcFuse into top-level build commit 90a90af678de0b83790b224d857312c68dd5f1af Author: braney Date: Tue Nov 3 01:16:30 2009 +0000 add some V2's to the CSHL long RNA-seq K562 cytosol tables commit ed884a8bfafaa6d2c3174dff3c54639f48769f0e Author: angie Date: Tue Nov 3 01:04:20 2009 +0000 First cut, mostly works but performance is not yet satisfactory. commit effbe25b94b852780b651fcd4a28f3a0b367562c Author: angie Date: Tue Nov 3 00:51:53 2009 +0000 Support for udcFuse and apps that will read files from it: plug minor memory leaks, use errAbort not assert, make udcFileMayOpen public, make udcParseUrl public so apps can determine path to file in udcFuse, add udcPathToUrl and udcSizeFromCache so that udcFuse can report the correct total file size. commit 13bf4503113b06dc1f86d44d6dfbe2ba8c691fea Author: angie Date: Tue Nov 3 00:35:53 2009 +0000 Make errCatch POSIX thread (pthread) safe: instead of a single global stack, use per-thread stacks hashed by thread ID. commit 5e1e35857fe63294fb09c06a73db7eb0a22c4efb Author: angie Date: Tue Nov 3 00:33:45 2009 +0000 If udcFuse.mountPoint is set in hg.conf, translate BAM URLs into filenames underneath that mount point, which mirrors the local udc cacheDir's hierarchy. Open the URL for bam and the associated .bai index file using udc, to make sure that the translated filenames will exist. commit 87173e6e530723a4261c448f2ae85c30a80f6312 Author: tdreszer Date: Tue Nov 3 00:31:08 2009 +0000 Getting the url to use the OTT id which is now in the classes table turns out to be easy commit d8cea0966acb04f4fb70d22f8322963de90f0918 Author: angie Date: Tue Nov 3 00:29:08 2009 +0000 Better error message in bamLoader. commit a61e0a840eb907585a0e80272873a24925475680 Author: angie Date: Tue Nov 3 00:26:33 2009 +0000 Gordon Robertson request: make gray lighter for unpaired ends. commit 7c3ac6aeb316b14095283b6f214d672c8b9f3de9 Author: angie Date: Tue Nov 3 00:25:43 2009 +0000 Added setUdcCacheDir() as in hgTracks, hgc etc. Without it, files were being initialized in /tmp/udcCache not our locally configured /data/apache/trash/udcCache. commit 89892c79ecc92a8ec9f9b4e5b56bcde44b844c46 Author: tdreszer Date: Mon Nov 2 23:41:27 2009 +0000 Keeping up with the flood commit ba53ba1bbb0c3ab61aa0d131ab776a9ee5ca9539 Author: tdreszer Date: Mon Nov 2 23:39:44 2009 +0000 Kayla noticed too many tables being eliminated and too few files being added. commit 056f825b92ec8613f01a6688210bfb60a40d2cd5 Author: tdreszer Date: Mon Nov 2 21:58:23 2009 +0000 Gencode v3c with new subtrack 2way consensus psuedogenes commit 21a2e884eda0cf5221c75b5cf5a947eb8cdeca5a Author: tdreszer Date: Mon Nov 2 21:56:50 2009 +0000 New coloring scheme and V3c release commit 3207cbf9e69610e97b8374513d645182b9d929e2 Author: hiram Date: Mon Nov 2 21:40:02 2009 +0000 Fixup crash in mafAddQRows and off-by-one error in qacAddGapIdx commit 653c0e7ac4abdb867af66d9e2c0a9ff0ffce90d9 Author: hiram Date: Mon Nov 2 21:39:51 2009 +0000 Fixup crash in mafAddQRows and off-by-one error in qacAddQRows commit 693f7f53874866b18cb0442cb092377d51c19c7e Author: hiram Date: Mon Nov 2 21:27:50 2009 +0000 Allow maybeSystem() to only warn on system errors. trf always exits with an error commit 592852b379fbdba75f7619c9740d713c283b26bb Author: braney Date: Mon Nov 2 21:27:45 2009 +0000 add some text about the color display commit 5a9b0a2ba40179fb59bafdf7baeebb77b2b5b1ce Author: braney Date: Mon Nov 2 19:48:55 2009 +0000 dereference symbolic links commit 587bfffdbcc1c97a674d5835154cb32edaa06500 Author: tdreszer Date: Mon Nov 2 19:19:25 2009 +0000 Removed wgEncodeHudsonalphaChipSeqProv provisional composite as its entire contents have been superseded by wgEncodeHudsonalphaChipSeq commit 29f68f4376feb6202101c1a544f0ac386f5a10ff Author: braney Date: Mon Nov 2 18:24:53 2009 +0000 started building hgPal downloads commit 08e15d5c6bf68396fe5191fb0ca8b712c498a9f5 Author: hiram Date: Mon Nov 2 18:04:30 2009 +0000 Add install target to get all.joiner done properly on a make install commit 4c76a728d91515f675230aa6ec28b437c2442380 Author: kate Date: Mon Nov 2 17:51:22 2009 +0000 Sep09 freeze is done! commit 8f4f60c3e695a459771664b39da199e2d6b5a266 Author: kent Date: Mon Nov 2 16:20:02 2009 +0000 Removing duplicate lines from knownToPfam.tab commit 2c3ccd2d1d37b4f7f20fb0e7834e9d2395791ac8 Author: galt Date: Mon Nov 2 16:00:07 2009 +0000 "Encode release log update" commit 7649891d4f73ecd266c69c46afa50e74797d4d45 Author: galt Date: Mon Nov 2 16:00:03 2009 +0000 "Release log update" commit 7a2eb7b84eb92cecb69bceb27a6bf5afd43b5770 Author: braney Date: Mon Nov 2 15:55:08 2009 +0000 new Hannon lab short RNA-seq description commit 8e1158293928cd36f1a268a54b7352d6223708ee Author: markd Date: Mon Nov 2 05:17:39 2009 +0000 set t/q insert stats in mapped psl commit 7aa68d774e3074be1c18f576827078692dc02c0a Author: aamp Date: Sun Nov 1 21:24:23 2009 +0000 Enabled trackDb setting "nextItemButton on" (actually the setting will work if it's set to "true" or "enabled" as well). This overrides user settings for a specific track when they don't have next-item button navigation turn on. commit cb7af45e0eebda371282008d2b7a69988c340dd5 Author: aamp Date: Sun Nov 1 20:35:58 2009 +0000 Removed "Sorry, no items found" error. commit 72304bcf75072e64e6e62dc1e1e73ef0eb006ece Author: aamp Date: Sun Nov 1 19:46:05 2009 +0000 Just variable name changes. s/nextPrevItem/nextPrevExon/ and s/labelNextPrevItem/nextPrevItem/. commit 08e20dc69968903aa333aaefeabc3ad0b3720e3b Author: galt Date: Sun Nov 1 16:00:03 2009 +0000 "Encode release log update" commit dacbf5e5c8b88b4c1a5167478f7467660b3fd899 Author: galt Date: Sun Nov 1 16:00:01 2009 +0000 "Release log update" commit 028927fc83fd6ee83bc909af14f6f2eb084f46c5 Author: markd Date: Sun Nov 1 01:11:13 2009 +0000 png portability changes for ubuntu and gcc 4.3.3 commit 2b824eaba5f5a09cca30ec4701a298fce6b2ee6b Author: galt Date: Sat Oct 31 15:00:05 2009 +0000 "Encode release log update" commit c18b3a5945238bfdc7065dd824373c0b6c434976 Author: galt Date: Sat Oct 31 15:00:03 2009 +0000 "Release log update" commit d2ac9ae0b4a2b9f5bd3a41834fcff3d62614ac8a Author: cline Date: Sat Oct 31 01:09:46 2009 +0000 Cut down the Broad ChIP seq long labels to meet the max label length of 65 chars commit 1c4aa6c9756866e32ff45ba760102ec6d92a2d81 Author: tdreszer Date: Fri Oct 30 23:55:53 2009 +0000 Added explanitory note for PCR2x control commit cf50cdf522348353c8bd6f243ee8856510230a8e Author: cline Date: Fri Oct 30 23:39:48 2009 +0000 Shortened the short track names for UwChIPSeq, to try to bring everything down within 16 chars commit e0c6425c14085ab421bb9e75783ae8c8e2d62c4b Author: tdreszer Date: Fri Oct 30 23:16:50 2009 +0000 4 more tracks to haibChip and more work to distinguish PCR2x input commit e8178f44074f7941f4ae5991944694fb69192c0b Author: markd Date: Fri Oct 30 21:58:42 2009 +0000 allow overriding the location of libpng commit d7ef7fbb2703d1f2c70535e8fc11d8de6d826bf2 Author: tdreszer Date: Fri Oct 30 21:41:34 2009 +0000 More attempts to straighten out 2 controls fro Gm12878 and K562 on haibChip commit a00797dfaa830c61d5a7062cceb86bee86d80a54 Author: hiram Date: Fri Oct 30 21:38:14 2009 +0000 Take care of gif_out_line error out warning situation with newer gcc versions commit 828005cda0e237908c131867bb906ee2464a14ba Author: markd Date: Fri Oct 30 21:08:19 2009 +0000 fixed bug computing mean query size commit 2fc18eb38aea84eee2408fdc8e9653cbd3a0d70f Author: braney Date: Fri Oct 30 21:03:23 2009 +0000 fix typo commit af3d168d2a1d97f75f27e50d482890c4e7449cf4 Author: braney Date: Fri Oct 30 20:46:43 2009 +0000 fix sortOrder commit 27c987163c4253b641816ebee5bf38c1f629b2ba Author: tdreszer Date: Fri Oct 30 20:40:33 2009 +0000 Changed GM12878Taf1 to V2 and made Input(PCR2x) visible for haibChip commit 6a62c6148d0fd3425b4174337b9c8186464cd108 Author: tdreszer Date: Fri Oct 30 18:57:46 2009 +0000 Added labVersion=PCR2x to older GM12989 and K562 experiments for haibChip commit fea45bd24f6886f09a44d17727a261005af22e88 Author: tdreszer Date: Fri Oct 30 17:11:10 2009 +0000 Fixed bug that left matCB indeterminate though no subtracks match state. commit 9f8cf0f048cb59e677d868c34d1aff9ff3fa184f Author: galt Date: Fri Oct 30 15:00:06 2009 +0000 "Encode release log update" commit 0d2abac9ffc755562c07f4103bc3db2415d23ce7 Author: galt Date: Fri Oct 30 15:00:03 2009 +0000 "Release log update" commit 463d85d06419fbe8403666df7d4fd3a9a8d3be62 Author: kent Date: Fri Oct 30 00:44:43 2009 +0000 Making mrna links in hgGene work in hg19. commit afd2191b67bb73cb047434d45569c605260ca3c0 Author: braney Date: Fri Oct 30 00:29:05 2009 +0000 new GIS RNA-seq data commit b19313e124547338a978d2309617929a63a681b4 Author: hiram Date: Thu Oct 29 23:32:06 2009 +0000 Turning on the 46 way phyloP tracks commit c9fdeeeb7f3f095e33ab9cfcf557dccc300efbab Author: hiram Date: Thu Oct 29 23:13:02 2009 +0000 Done with phastCons and phyloP for 46-way conservation track commit 51d9a07321926ede369b110ab2534bfc6e243a62 Author: ann Date: Thu Oct 29 19:49:35 2009 +0000 correcting matrix for rat and mouse chains commit 96e36675e2d01b01eb2cbe98f466748e931c5178 Author: tdreszer Date: Thu Oct 29 19:26:15 2009 +0000 New DAF for Rami commit 373cb0215ceaea3ec09c57aa07f6201fde433359 Author: kuhn Date: Thu Oct 29 18:19:27 2009 +0000 capitalized Mendelian twice commit 78940d23a14a7125e8c768e5405970f1e25003ea Author: tdreszer Date: Thu Oct 29 17:55:14 2009 +0000 Initial checking of my clean up of varias issues commit cb02530df0bce20cd187d68bbc9964e93aabcd2f Author: tdreszer Date: Thu Oct 29 17:25:49 2009 +0000 Renamed some HudsonAlpha tables and cleaned up some metadata commit 15edadf0c5691d816c28e8bf44152711a1af57ed Author: tdreszer Date: Thu Oct 29 16:10:17 2009 +0000 Limited the number of tracks shown by detault for Broad commit f7f1c2fe74e5425c3d3bb8ff82abf4416e03dca1 Author: galt Date: Thu Oct 29 15:00:06 2009 +0000 "Encode release log update" commit 2a6e71f6fbdbd799203e5dfea7d289a18ca793d8 Author: galt Date: Thu Oct 29 15:00:03 2009 +0000 "Release log update" commit 592e7b52405215e1f4d387976edbc48727763e48 Author: angie Date: Thu Oct 29 04:19:08 2009 +0000 DGV: Change the default filter to include-all instead of exclude-none -- positive logic is more intuitive. (Thx b0b) commit b49215bae641495a105bfead360e26cd4c5948a7 Author: tdreszer Date: Wed Oct 28 23:14:20 2009 +0000 Straightened out GM12878 Taf1 and K562 Taf1 as per Flo's wishes commit 20fa3281f8f5aa1b9f4973b8b10957e084c8adda Author: hiram Date: Wed Oct 28 23:05:53 2009 +0000 enable gorilla gorGor2 and wallaby macEug1 commit 45663aa98fd572f920601f6d1a2074855cea6bba Author: hiram Date: Wed Oct 28 23:04:58 2009 +0000 Initial files from makeGenomeDb.pl commit 48da867160ef332dc0b657d376d70a9245a4fa34 Author: tdreszer Date: Wed Oct 28 20:29:11 2009 +0000 More cleanup of HAIB TFBS commit be0b7acf716933dbfff59507097fab8b20737719 Author: kuhn Date: Wed Oct 28 18:47:29 2009 +0000 changed bars to blocks in describing the BEDdisplay commit dd600920627764fd2f164157bd2aba4aa6326516 Author: kuhn Date: Wed Oct 28 18:46:01 2009 +0000 changed the way the coloring was described so it matches other places where break it out into a list and highlight the meaning in the actual color. had to pull the link to OMIM out of the Morbid Map text to get it be red commit c7af955bb1347f749f867d1fc6b428e19dde2830 Author: hiram Date: Wed Oct 28 17:58:09 2009 +0000 remove logs before overwriting them to maintain proper ownership commit 801cbefb3f04a9c1286a878a9d0f8f18b30c8ddc Author: hiram Date: Wed Oct 28 17:43:26 2009 +0000 Correct dates for v218 final commit 774d5925ab81dbc66b4f34bc3d53c304fe1ec8e9 Author: galt Date: Wed Oct 28 15:00:07 2009 +0000 "Encode release log update" commit 7b2f5d5be9d299a5720826593b093e19fab4a45d Author: galt Date: Wed Oct 28 15:00:04 2009 +0000 "Release log update" commit f853f96bb860cb1dc74e062ea61e771085c6384d Author: tdreszer Date: Wed Oct 28 00:34:33 2009 +0000 A lot of work on HudsonAlpha TFSB commit 2022845a71a1f68d4a0e293bd254ada75b5bdafa Author: braney Date: Tue Oct 27 22:47:48 2009 +0000 fix up controlledVocabulary trackDb setting for CSHL long rna-seq commit 64eada3d3e25c04581596e9f3fd3f7618eb48302 Author: hiram Date: Tue Oct 27 22:31:17 2009 +0000 "New version number v218" commit 536ea88449ebb12d657c3a008f8f4ac58bf683b9 Author: hiram Date: Tue Oct 27 22:26:49 2009 +0000 Starting build v218 commit 3e2ea3c10ccab65f8ef217de7a240e7a11098311 Author: hiram Date: Tue Oct 27 21:35:59 2009 +0000 Rerun the 4D site predictions with chrX only and non-ChrX others commit d2554203db294bdd818c160698f4fb26a2f271b3 Author: hiram Date: Tue Oct 27 21:32:38 2009 +0000 Rat rn4 v56 update done commit 545c087b9c04cce5941d85f5153e102681ee774c Author: hiram Date: Tue Oct 27 21:26:00 2009 +0000 fixup password string given to FTP server to be correct commit 54e9b85984aff5b589687a2a0dd824e5d4b43156 Author: hiram Date: Tue Oct 27 21:20:10 2009 +0000 Adding version 56 definitions commit 7dececded038e5462d3d456265a35e16af456517 Author: kate Date: Tue Oct 27 20:53:08 2009 +0000 Remove download files for raw signal from metadata (not posting these for download) commit 9c0e0b15bac36f850bb048d6c9095e542f203b53 Author: tdreszer Date: Tue Oct 27 20:46:22 2009 +0000 Added 2 more submissions for UwDnase commit 33e7b6422392962e44d29d4288b342a924cc41f7 Author: kate Date: Tue Oct 27 20:38:57 2009 +0000 Restore +1 too long label, as it was already released commit a94619725f042aaa3040be7490e007b4bf3fa4bd Author: kate Date: Tue Oct 27 20:34:33 2009 +0000 Label consistency and length, sort order consistency for CSHL Long RNA track commit 8747170c4343e03f80271850e706fd8ffa84a958 Author: tdreszer Date: Tue Oct 27 20:12:09 2009 +0000 I guess I was sitting on these changes rather than checking them in commit f9bf60ab1dca0b9adad0f066e9897e518658b604 Author: tdreszer Date: Tue Oct 27 20:09:56 2009 +0000 More submissions for Yale (post release2) commit eadf6246acce4685a2585f0c47fb21445d5369bf Author: tdreszer Date: Tue Oct 27 20:09:05 2009 +0000 Put release2 into the pushQ commit 436b88605d9a2b45cbceacaa50c05e6105dbf158 Author: tdreszer Date: Tue Oct 27 19:05:23 2009 +0000 File list for Open Chromatin release 2 commit 438614a481afcd26a7cd42d819f24b94d445b9cd Author: tdreszer Date: Tue Oct 27 18:40:34 2009 +0000 Don't display parentTable which is actually obsolete commit ca10c270ea719d389ca682846b855630c87e41cb Author: tdreszer Date: Tue Oct 27 18:27:20 2009 +0000 Renamed an additional 28 tables for consistency of Open Chromatin tracks commit e5321bc308f91ebcb0faf3eba16501e4b253dc06 Author: braney Date: Tue Oct 27 15:35:28 2009 +0000 restoring changes I made yesterday commit 901cd70c535ec87b9a4868fad060b5df49a16291 Author: galt Date: Tue Oct 27 15:00:06 2009 +0000 "Encode release log update" commit 93d78bb6758968af7dcdabff66ca46cb87472fd3 Author: galt Date: Tue Oct 27 15:00:03 2009 +0000 "Release log update" commit bd498c863cd9ee398de0333017ad2279404d2313 Author: cline Date: Tue Oct 27 01:01:52 2009 +0000 In UwChIPSeq, replaced entries for 2HepG2 with 2HEPG2. commit a439d28c5f658cd17fdf50cae229cb5eab80375d Author: cline Date: Tue Oct 27 00:41:35 2009 +0000 Reorganized the wording on the page to make the description a bit nicer. commit e177e7828ecc7e39a16271fd2ff2384e70583d78 Author: cline Date: Tue Oct 27 00:29:52 2009 +0000 Added 10 new subtracks under UwChIPSeq commit ec2b36cfd7d2d8eee60951f6476b890c29562ae9 Author: tdreszer Date: Tue Oct 27 00:18:55 2009 +0000 11 more name changes commit 299267a1ac526ca75a7b4dd9372f246941f5355d Author: tdreszer Date: Mon Oct 26 23:55:09 2009 +0000 Renamed 3 tables in Duke commit 753ce28da644ecdff885a04b5cfb26a32b40ee52 Author: tdreszer Date: Mon Oct 26 23:06:11 2009 +0000 Added count of selected subtracks commit 1eb7b561f22af818e5b56106c2e1caac0a4f2ad2 Author: tdreszer Date: Mon Oct 26 22:14:40 2009 +0000 Moved dimension Z outside of matrix. Requested by Pauline and does make things clearer commit 5a9637232b6e2c7881cf0a384875ff0e13606300 Author: hiram Date: Mon Oct 26 20:54:43 2009 +0000 Add the removal of the /err/ parasol directories during cleanUp commit 2ac34fcdfc542969725b2be8c65d6bf63bd447a0 Author: braney Date: Mon Oct 26 20:01:34 2009 +0000 add bounds information to bigWig commit 3d6d75b2f9944becf64b1b6ecffffde79d6b4509 Author: braney Date: Mon Oct 26 19:44:53 2009 +0000 more text commit 899c7eaddf7990483c53e9343db6720617b0d46e Author: braney Date: Mon Oct 26 18:57:35 2009 +0000 more text commit 9d90d2409cb6e3040730f1dfe03484edd02781db Author: braney Date: Mon Oct 26 17:45:36 2009 +0000 some short label edits and defaults for CSHL long RNA-seq commit 9367e5f5bbeef59556f1e04ee7432b8bd9d1aa27 Author: braney Date: Mon Oct 26 17:22:03 2009 +0000 take out old CSHL long RNA-seq track commit 73ef22a787c5d8ede298747dc3cd69301c0b8c2f Author: hiram Date: Mon Oct 26 17:04:20 2009 +0000 Now working on phyloP business commit f99ea57d66bd155a613c551164617b0042c4ede8 Author: aamp Date: Mon Oct 26 15:32:53 2009 +0000 Details stuff for 5C tracks. commit b122b412d47a398f0dc07d3b7363235ed15d00a3 Author: aamp Date: Mon Oct 26 15:31:48 2009 +0000 Added a little converter for 5C data. commit 941247c10b5d59c3aa91f673a238d30ee2a6367c Author: galt Date: Mon Oct 26 15:00:06 2009 +0000 "Encode release log update" commit f29e636722d43057cef0c6ccb1a98ed2cb1364a1 Author: galt Date: Mon Oct 26 15:00:03 2009 +0000 "Release log update" commit 52201dec3cddc9350fe78f1acf6ec8084501a634 Author: galt Date: Sun Oct 25 15:00:06 2009 +0000 "Encode release log update" commit c5b1d2acf24e65586df567c5fb055503db7efc7c Author: galt Date: Sun Oct 25 15:00:03 2009 +0000 "Release log update" commit 19a229a5d60c70c184354b551993265e316ff985 Author: galt Date: Sat Oct 24 15:00:06 2009 +0000 "Encode release log update" commit 3af95fc893c0b7497bc6e0b925c2c8cca956d86a Author: galt Date: Sat Oct 24 15:00:04 2009 +0000 "Release log update" commit 1023eaeaf894298e861cd803171b387a28c77ffb Author: braney Date: Fri Oct 23 23:21:17 2009 +0000 seom fixups for the CSHL long rna track commit 4edfa3f0e883a93dbfe3ebfd2abe889ecfdcea86 Author: cline Date: Fri Oct 23 23:05:53 2009 +0000 Added a bunch of new UW Chip seq tracks commit 1bc5e783ae394ba34a7ea04af78f0e1fccefacb8 Author: kate Date: Fri Oct 23 23:02:19 2009 +0000 Add encode-announce to the About section commit f512c0a853d4b7dcfa3a6a9600026306c957863c Author: kate Date: Fri Oct 23 22:52:38 2009 +0000 Add FTP commit 0af5b61755ba1f4b3bb3c3b8d4967d9090031567 Author: tdreszer Date: Fri Oct 23 20:11:21 2009 +0000 Added V2 notes to Open Chromatin commit 84264f2c2003c4560ff168eaf0a06bbc60b54c2a Author: tdreszer Date: Fri Oct 23 20:10:07 2009 +0000 Added release 2 notes commit ebd901448e880bf21d21d91604dd3ce11e2bbfc4 Author: tdreszer Date: Fri Oct 23 20:09:49 2009 +0000 Added Mapability reference to Broad commit 80028a7dc9f900a79e0c5303b741a6d3c9fe84ba Author: tdreszer Date: Fri Oct 23 16:56:37 2009 +0000 Vendor for H3K4me3 has changed. commit 9f54c72c5822478cd9b8119243dbb0ca65a44e4d Author: kuhn Date: Fri Oct 23 15:28:26 2009 +0000 changed layout of color description to match SNP tracks and added color to the text commit 277538f13758ca764f8323216f65dd025d2976a8 Author: galt Date: Fri Oct 23 15:00:06 2009 +0000 "Encode release log update" commit 90211b87435af23e25e0016913a4ac85b481d815 Author: galt Date: Fri Oct 23 15:00:03 2009 +0000 "Release log update" commit c5dca55d59e7be71e89d79048008d74affaad0c0 Author: braney Date: Fri Oct 23 02:07:41 2009 +0000 add CSHL long rna back in, now with compartment and rnaExtract commit 4d0200b80a444b1a52d804d8118e2e3e30709f63 Author: braney Date: Fri Oct 23 01:42:49 2009 +0000 first pass commit ad52839d2971be9f7dff45dde55a08a78326babf Author: kate Date: Fri Oct 23 01:19:57 2009 +0000 Add functions used by reporting script commit c238c2ba622897a3ac7ace43fb5adb1ce23a6ec1 Author: kate Date: Fri Oct 23 01:17:05 2009 +0000 First cut of reporting script for ENCODE commit 79055bb1daa7719f93bf0d23d568b637151c56c6 Author: kate Date: Fri Oct 23 01:03:44 2009 +0000 Add TFBS validation track from Weng lab, with first dataset commit 53f92e2e8adadc244589037f75d3ed8940168cc3 Author: rhead Date: Fri Oct 23 00:07:58 2009 +0000 Fixed broken links to atcc.org products. commit 017a44060199529ab31e16b00eb42e518c50d6b6 Author: hiram Date: Thu Oct 22 23:17:44 2009 +0000 Get the other phastCons46way tracks set to bigWig commit 8cf5578eeef6a48f08834eeb5542afa36863fe53 Author: braney Date: Thu Oct 22 19:23:11 2009 +0000 remove CSHL long rna commit 86f84d740e8e669d8e58095cc73bcc70c13cc7d9 Author: cszeto Date: Thu Oct 22 18:36:01 2009 +0000 new datasets commit ea9acd158efa0e9b1216850a21f6159cb20ed504 Author: cszeto Date: Thu Oct 22 18:35:41 2009 +0000 New datasets commit d1e47db1cfd05f42606682c6bb9843119eee957c Author: tdreszer Date: Thu Oct 22 17:21:49 2009 +0000 Change BAFT to BATF commit f91c3c5d8d7a19491f97be9bcd37c1a11810d510 Author: tdreszer Date: Thu Oct 22 17:02:23 2009 +0000 Added 10 new antibodies for Myers and one for Farnham and Myers commit 6503140e94259a05bd9f84aa6f46b0ca01078f8a Author: galt Date: Thu Oct 22 16:38:51 2009 +0000 slightly faster commit 80689cd122d6873f36c275b675028a17e3cf212b Author: tdreszer Date: Thu Oct 22 16:12:44 2009 +0000 Added one more for UwDnase commit a3088ec9f2cf1f647f1a5e46e8fd8343623e1661 Author: galt Date: Thu Oct 22 15:00:07 2009 +0000 "Encode release log update" commit 9b8c6afd2a0665eb05d211fd9967e8f9e7725f2e Author: galt Date: Thu Oct 22 15:00:03 2009 +0000 "Release log update" commit 89d5c92ab30864e56aaca7e8aebf72a5d681f1cc Author: kent Date: Thu Oct 22 04:01:17 2009 +0000 New utility to do renaming of all sequences in fasta file seems to work. commit 21963035f2a1df323a0a0c91f98a8e8e54a2eb09 Author: kent Date: Wed Oct 21 23:20:19 2009 +0000 Updating OMIM link to make it faster. commit 81d462063b5b8dd8d5f903f2e96af7b35a2d1f5f Author: tdreszer Date: Wed Oct 21 21:38:56 2009 +0000 Fixed one longLabel commit 55b8a3627d49bcb7bbd2a39b47227f54b2b0f3b3 Author: tdreszer Date: Wed Oct 21 21:33:22 2009 +0000 Added 3 UwDnase sets commit 2e1e063e51f5555af1d861eca2f38792d9944b6a Author: cline Date: Wed Oct 21 21:29:41 2009 +0000 Made the long labels for the Broad Chip Seq controls consistent with each other commit 52919e3232a4a1c028a783b807f6d55bc9bd33a6 Author: hiram Date: Wed Oct 21 19:15:36 2009 +0000 Bring the msa_split procedure up to date commit 5caa9ace198ac42f6fd6f010326334d751a99c22 Author: tdreszer Date: Wed Oct 21 19:14:52 2009 +0000 Made vis changes work on 3-way matCBs commit 593d0e68b47529e2c0f2d9ca8ad45acd5e796c2d Author: hiram Date: Wed Oct 21 18:34:58 2009 +0000 done with phastCons runs for the 46-way commit edbd5f1aa57826ac3058a552822183058c2826ff Author: katrina Date: Wed Oct 21 18:10:31 2009 +0000 fixed typo and added color to the color key commit 5b6bbd879e9f8dd2c6748cb5d67632852ac77a61 Author: tdreszer Date: Wed Oct 21 16:44:43 2009 +0000 Added Yale HeLa E2F6. commit a031043b43bce403a395aec80ace44c1e09c207f Author: tdreszer Date: Wed Oct 21 15:51:47 2009 +0000 Remove hintOverSortableColumnHeader which does nothing commit 5dff8894c608367b865080a9d8b9f984cb8167e8 Author: tdreszer Date: Wed Oct 21 15:48:50 2009 +0000 Temorarily readd hintOverSortableColumnHeader to avoid js errors. commit cf86ac01aae186fa3d9f0c01815cd428b6105abd Author: galt Date: Wed Oct 21 15:00:06 2009 +0000 "Encode release log update" commit 99c4163e1890ce1e70dfec2093f7e6d47b3e4564 Author: galt Date: Wed Oct 21 15:00:03 2009 +0000 "Release log update" commit ba47176109f445b6f84d0f1a64a05cb046c0adeb Author: galt Date: Wed Oct 21 08:49:03 2009 +0000 v218 preview commit 4a1122b42d79db3d43a0201f9da29b70eb89a101 Author: tdreszer Date: Tue Oct 20 23:24:43 2009 +0000 Major changes to support the matrix 3-way CBs. Also some cleanup of old code. commit 43c7533dc9108898f0a25b14dfad96ace552d87b Author: tdreszer Date: Tue Oct 20 23:23:44 2009 +0000 Changes to support the matrix 3-way CBs. Requires hui.js to be uptodate as well. commit 96fe019816b9f866a783531f15d5e4c3b5b77cfe Author: tdreszer Date: Tue Oct 20 22:50:44 2009 +0000 Added halfVis class to support 3-way matrix CBs commit 8382f758947ad890c5248cbab5aae043f3ffa549 Author: galt Date: Tue Oct 20 22:39:47 2009 +0000 keep http request together commit 7fe2ee17d37f081dcd9e4965b833abc58b9e14f5 Author: hiram Date: Tue Oct 20 21:30:18 2009 +0000 Initial picture of 46-way tree diagram commit e3da0406371505e9c36ea9d10b57c035c7b83d63 Author: angie Date: Tue Oct 20 20:25:54 2009 +0000 Updated link to Dan Pollard's matrices and email (thx Brooke). commit 2c72d3b99c92f48bb7cbbfec7debf12b4f92fc0f Author: rhead Date: Tue Oct 20 20:07:43 2009 +0000 Fixed broken link to Burge lab. commit cc0f2fa82b4848ac48dcaeffbebe6df111884c0a Author: tdreszer Date: Tue Oct 20 19:49:24 2009 +0000 Added findWordByDemiliter which allows searching a string for a word, but the word must be set off by a delimiter. commit eee035a58552f26a0c75680b7686bc81e7546379 Author: tdreszer Date: Tue Oct 20 19:46:28 2009 +0000 Added dimensionZchecked for supporting the new 3-way dimension checkboxes commit 67ced192ba16eff99d84710acae4bff276678983 Author: pauline Date: Tue Oct 20 19:24:11 2009 +0000 Fixed typo. commit a505be10e50035a3162ccd6dc931956151455290 Author: pauline Date: Tue Oct 20 19:20:15 2009 +0000 Fixed typo. commit 381cd405c62beb0734d948c274caddf771246236 Author: tdreszer Date: Tue Oct 20 19:17:34 2009 +0000 Added dyStringCreate which will create a new dyString from printf style content. commit 6125ff0a3fd429d8f90d7b4763967f282efd5f33 Author: pauline Date: Tue Oct 20 19:05:52 2009 +0000 Fixed font and date. commit 37c2709e1f4765014c4365ec56d8b99c09a5760b Author: pauline Date: Tue Oct 20 19:00:22 2009 +0000 Added new job posting. commit 984ce007f4ebc13886018e319671f943d87140a3 Author: tdreszer Date: Tue Oct 20 17:38:17 2009 +0000 Cleaned up the release notes a little and removed references to Raw Signals commit 796546c1fd03d632645d1f1afa71191ee7b01061 Author: galt Date: Tue Oct 20 15:00:06 2009 +0000 "Encode release log update" commit 55c55535950b9f45280675b6da72079c45e49d26 Author: galt Date: Tue Oct 20 15:00:03 2009 +0000 "Release log update" commit 811833e08010337aa01ef7ef3207468cc8be92dd Author: fanhsu Date: Tue Oct 20 05:14:33 2009 +0000 Fixed a typo. commit 9bd8f61ed244c0c869f756c0086d9164e071e7d6 Author: fanhsu Date: Tue Oct 20 00:18:43 2009 +0000 Disable danSeqs and aaSeqs as options to filter. commit b1c41b44d8d016e955e0d051fd345c8f769834b8 Author: fanhsu Date: Tue Oct 20 00:09:12 2009 +0000 Reversed the previous change, which was done in error. commit 2810ad7e893818e3f74986a66ea0fe3f4f8c6135 Author: angie Date: Mon Oct 19 23:10:18 2009 +0000 Fixed syntax error in case of multiple previous logfiles. commit 990580a894d63875db24feace3fc062a50e8e9d0 Author: angie Date: Mon Oct 19 22:50:08 2009 +0000 Implemented grayscale for base qualities and coloring by user-specified tag. commit c3bd8651a840ce2ee450d9a865b49f18f0fcaa10 Author: cline Date: Mon Oct 19 22:17:07 2009 +0000 Revised the release notes commit 7e7cb8d149dd34e2d102b773711dc804a3ef9ab2 Author: galt Date: Mon Oct 19 21:15:07 2009 +0000 adding some better error messages commit d4a9e5a5e964cd60c733680048f05497d16052dc Author: cline Date: Mon Oct 19 20:48:58 2009 +0000 Cleaned up the Release Notes sections. commit a48728bfe57d093722bbfd822cd054537040305f Author: cline Date: Mon Oct 19 20:35:19 2009 +0000 Added a Release Notes section. commit 4043c8d9b5163503307e6dd143bf84887c4911dc Author: braney Date: Mon Oct 19 18:41:22 2009 +0000 make display of hgPal link dependent on multiz46way on hg19 commit 599557dfc0cb9c9a926776d9258e2032099516c6 Author: cline Date: Mon Oct 19 18:29:53 2009 +0000 Temporarily commented out the UW DGF footprints subtracks commit 15ec201d4662b4fde202156640886adf4e3dc622 Author: galt Date: Mon Oct 19 15:00:06 2009 +0000 "Encode release log update" commit 10f60dcdba63097b74d85bc8c5564371004874af Author: galt Date: Mon Oct 19 15:00:04 2009 +0000 "Release log update" commit a22c345b883c66982401564bd9a4d24ed1426c8d Author: galt Date: Sun Oct 18 15:00:06 2009 +0000 "Encode release log update" commit e1cbd9b78a3e63481e81f3a919dcfea00734781b Author: galt Date: Sun Oct 18 15:00:03 2009 +0000 "Release log update" commit 568a40e867521f600715f789d00708c919d5c82d Author: larrym Date: Sat Oct 17 22:36:03 2009 +0000 ignore drag activity in gray tab and track title column; fixes "jumping coordinates" bug found by ann commit 7dadc38400ade3c3445d99d7a82ceb2bb9b83a43 Author: kuhn Date: Sat Oct 17 17:22:33 2009 +0000 changed BEDGRAPH to lower case bedGraph commit 804b24a0eeaa8e2f6fc46df27fb2ebdf7429c975 Author: galt Date: Sat Oct 17 15:00:05 2009 +0000 "Encode release log update" commit 0164b6cb97faa4823ffbe192e0f4b32d1d0831c5 Author: galt Date: Sat Oct 17 15:00:03 2009 +0000 "Release log update" commit f188a32a9f5efb9f687da2aadbf93e261aaf8893 Author: markd Date: Fri Oct 16 22:17:04 2009 +0000 added warning that it overwrite input; fixed bug in count commit 4df18be017ed89a6e562f7050a266d0031b0fd2d Author: cline Date: Fri Oct 16 20:27:16 2009 +0000 Update notes for the wgEncodeUwDgf composite track commit f89592c93079d0302162fd9b0c6632e5779a25b3 Author: kuhn Date: Fri Oct 16 20:19:18 2009 +0000 added new Current Protocols pub commit 19bc17123783cb269c9022012ed338cebf6a6cc7 Author: cline Date: Fri Oct 16 19:04:23 2009 +0000 Fixed a typo in the visibilityViewDefaults entry for the visibilityViewDefaults entry for wgEncodeUwDgf (Foorprints -> Footprints). Replaced the longLabel with a more descriptive label commit 1fa0e0da48f2772567c400a903bd7f1b039fd8d9 Author: tdreszer Date: Fri Oct 16 18:45:44 2009 +0000 bedGraph 4 cannot handle viewLimits on same line commit ac867d71d2bb3d89c1913eb3e19f560834efb62b Author: kent Date: Fri Oct 16 17:35:33 2009 +0000 Adding update procedure for hg19 P2P tracks. commit b72ae84d2360fbfdaf9d000a6212c5bb7e2f399f Author: kent Date: Fri Oct 16 17:17:44 2009 +0000 Fixed glitch in knownToHprd table build instructions. commit 9225dd6fe48e2ab151ff5fdd3abd54b0cf92d4ca Author: fanhsu Date: Fri Oct 16 17:16:27 2009 +0000 Updated a section title per GSID request. commit ab94dc540d54ca473949cb4b0f645c9c6f8d6cfe Author: fanhsu Date: Fri Oct 16 17:12:04 2009 +0000 Updated the text of a long label. commit 4abeed259631e355996d3e6da8668f17419e7231 Author: fanhsu Date: Fri Oct 16 17:10:37 2009 +0000 Disable DNA Sequences and Protein Sequences options per GSID request. commit 7c74dbe719ab16aa161f922600b082faeef54919 Author: tdreszer Date: Fri Oct 16 17:09:30 2009 +0000 Changed UwDGF signals settings as per Stam lab. commit 8149c464b8d3f57df96a31fa2025b40801038676 Author: fanhsu Date: Fri Oct 16 16:57:13 2009 +0000 Updated the text of a long label. commit 9ee72c893b41186a74b1435b1ee547cceb510706 Author: kent Date: Fri Oct 16 16:28:29 2009 +0000 Relaxing the minCheck on omimMorbidMap a little. commit 2cf2bc2029df55fdfafabbffaabb741a17ac3ad8 Author: kent Date: Fri Oct 16 16:17:09 2009 +0000 Adding hg19 columns. commit a7099ee0fdb702354a804b1c17e4b73fa260aa96 Author: tdreszer Date: Fri Oct 16 15:54:46 2009 +0000 Fixed Broad metadata, 5 cases of H3K04me1 which should have been H3K4me1 commit 3619c98205de52783ac78df8d415ffae7044d6a2 Author: galt Date: Fri Oct 16 15:00:08 2009 +0000 "Encode release log update" commit ebe5acb5723cbfcd698c429a9fbbbcebf8290832 Author: galt Date: Fri Oct 16 15:00:05 2009 +0000 "Release log update" commit cbe7249b2a64141fda858364d97e85d2a67f19bf Author: kate Date: Fri Oct 16 05:47:27 2009 +0000 Correct typo in lab name commit 81408f3f6285d5e86870ff097252f381bb650ca0 Author: angie Date: Fri Oct 16 00:34:31 2009 +0000 Added enhanced coloring options (user-requested) to hgTrackUi and implemented 3 out of 5 in hgTracks. commit 73d354b57685db0789fb2dd33eefa0f7cd012b67 Author: markd Date: Fri Oct 16 00:07:04 2009 +0000 don't generate warnings on invalid dates; error not if warns occur, also added -drop option commit 365e2ef18a0bfa3610ddda428d5f2874b46ce2b1 Author: markd Date: Fri Oct 16 00:06:02 2009 +0000 deleted forgotten debug commit bd099297343658e9c105d4d242613a6940fbd095 Author: galt Date: Thu Oct 15 23:52:38 2009 +0000 adding warnings to jksql new for mysql5 commit 835704fb344776a0872b2109816386f69e77cea3 Author: galt Date: Thu Oct 15 22:36:03 2009 +0000 updating visiGene for hg19 commit 1d7b0a7753737730156dcd43606c3b281388bab1 Author: tdreszer Date: Thu Oct 15 22:13:47 2009 +0000 Changed Broad link by request of Charles Epstein commit ed278e9bd367809f25150e2a192b0cb274702f46 Author: tdreszer Date: Thu Oct 15 22:08:21 2009 +0000 Metatdata typo commit 462d76fdd80e7e65aaab894971714a51582a9519 Author: tdreszer Date: Thu Oct 15 22:05:06 2009 +0000 No sooner is Yale publicly released than errors are found that need correction. HA to HA-E2F1 and make GM12989 and K562 tracks on by default commit 1f3c526b1d4dde822b9771848c950d4ecf5da770 Author: kent Date: Thu Oct 15 21:58:38 2009 +0000 Utility to convert HPRD interaction html file to tab-separated list of protein/protein interactions seems to work. This is based on an autoXml parser and a snippet of code Galt wrote that now lives in hprdXmlToTab.c. commit adcfb5d34c566776227e9444c29c912442bf743e Author: tdreszer Date: Thu Oct 15 21:55:28 2009 +0000 Don't you know I am just trying to up my total modified lines in cvs-reports. commit 2b7eff469dfe7cf07db6eb41eaafdf2ffd09ac8a Author: tdreszer Date: Thu Oct 15 21:49:48 2009 +0000 Type HA-E2F1 not H1-E2F1 commit c2b57bc4b6feb4fe910db5b5eeb1c87570b6261a Author: tdreszer Date: Thu Oct 15 21:47:58 2009 +0000 Altered E2F1 to HA-E2F1 at Farnham's request commit fb0caa924a18f1474537c43a59daf3eadc4bab8e Author: katrina Date: Thu Oct 15 21:17:32 2009 +0000 Copied hg18 knownGene.html to hg19 so that hg19 description is more up to date. The top level has an old description from hg17 and that is what hg19 UCSC Genes was displaying commit c3d77d10fc6cdbdc88de75e539ff3d3e182bc745 Author: hiram Date: Thu Oct 15 21:17:18 2009 +0000 Now with frames, irows and phastCons46way all bigWig commit 0f9081f33ea3a348d06179cd424b24b72d03145f Author: kent Date: Thu Oct 15 20:14:11 2009 +0000 Getting rid of _1 from hprd ID's. commit 471ee30dc875dc8bde2e3ff561bd3a93e546ea5e Author: hiram Date: Thu Oct 15 19:51:20 2009 +0000 Properly send output to DESTDIR BINDIR commit 434460d51e3ce9adc5572335fd3e5d3dbaf9ad05 Author: hiram Date: Thu Oct 15 19:36:00 2009 +0000 Properly create the destination directory before making a binary there commit bd70244521c6811419b77d0144fbae05d2946ca3 Author: hiram Date: Thu Oct 15 19:31:46 2009 +0000 adding stringify encode/validateFiles ratStuff/mafsInRegion and pslCDnaFilter to the userApps build commit ed2076af38a7e4fced3b90828627840c8a8f63f6 Author: hiram Date: Thu Oct 15 19:29:43 2009 +0000 result properly honoring DESTDIR commit 02ce70735e30d36c16ba091edfb5491f5dab47d0 Author: hiram Date: Thu Oct 15 19:27:05 2009 +0000 binary result to DESTDIR commit e2151a986e0adcf666e6f5f3e578f9e35110054f Author: hiram Date: Thu Oct 15 19:26:36 2009 +0000 STRINGIFY needs to look in DESTDIR commit 198f717ded0d01e5b55f88f3227c8af06b8b04ac Author: hiram Date: Thu Oct 15 19:15:27 2009 +0000 Must use DESTDIR with BINDIR to be sane commit d394e407040451355077e8b23483252ea8ae338d Author: hiram Date: Thu Oct 15 18:51:23 2009 +0000 liftOver out of place on lists, there were duplicates commit d91c9ef15962aa9466170b9451bfd0af98b28964 Author: hiram Date: Thu Oct 15 18:44:19 2009 +0000 fixup the userApps list of build items commit 8d16b32ebfe5545574cf2265227c6fb8c5b42944 Author: rhead Date: Thu Oct 15 18:12:09 2009 +0000 Updated update paper to 2009. commit be4d72793fb6264394ab5307c0ce8f4b20b55faa Author: angie Date: Thu Oct 15 17:05:32 2009 +0000 Fixing another broken link. commit 651ac17d4c39001b92ead1c12252f5cffefa6bf6 Author: tdreszer Date: Thu Oct 15 17:04:09 2009 +0000 Minor edits - no change of table/file lists commit c12715f89b6d1bfde8e701a44c7a1175c94fccd7 Author: galt Date: Thu Oct 15 15:00:06 2009 +0000 "Encode release log update" commit eec8ac6d06ab74fcc97c90ff2e3ba76382e84143 Author: galt Date: Thu Oct 15 15:00:04 2009 +0000 "Release log update" commit d6a3113fb32824f11889e84a8a1d77b804602d94 Author: cline Date: Thu Oct 15 00:39:58 2009 +0000 cleaned up: moved the raw seq files into the deleted files section. In the replaced files section, listed the files that have been replaced. commit bcfd1abbc7592f79b4656ab2271908b009eb0a5f Author: tdreszer Date: Thu Oct 15 00:20:56 2009 +0000 Minor edit commit 1fa8c442302cdcb72cac9191220625ac54ac0be8 Author: tdreszer Date: Thu Oct 15 00:08:26 2009 +0000 Getting things ready for Release2 commit c7e8ed29558d5bf056c9e81e1cc8861899b33935 Author: tdreszer Date: Thu Oct 15 00:07:32 2009 +0000 Release 2 is out the door. commit 26da40a873483b20538be10da4004d982bad6010 Author: cline Date: Wed Oct 14 23:44:55 2009 +0000 Created an update log for the Broad Chip Seq tracks commit 270b0483448366915363024ce16593097758603b Author: tdreszer Date: Wed Oct 14 23:41:49 2009 +0000 Added one last submission for Terry. Fixed some DNCT view limits and colors commit 334e8b9b1c6015ef326f0811296aa0541f249471 Author: galt Date: Wed Oct 14 23:37:40 2009 +0000 tiny update commit fcf4e4a7f3629cfb7473e54c15a476accfcc9460 Author: holmes Date: Wed Oct 14 21:19:30 2009 +0000 Added arcog targets commit 70e7710942b5b70d64c773e38842ed1459fa985a Author: holmes Date: Wed Oct 14 20:28:27 2009 +0000 adding arcog table commit 070becfdd262dcd3d0b05fa0043da1ef987f1a73 Author: holmes Date: Wed Oct 14 20:26:28 2009 +0000 Added arCOG code commit c7d261e444b465b770a11f77e1bbfd99cba78a06 Author: galt Date: Wed Oct 14 19:08:58 2009 +0000 adjustments for mysql5 blob string comparisons commit db54cceeec1b679576b9f9a63c39db9e4da1a9a8 Author: galt Date: Wed Oct 14 19:03:02 2009 +0000 making adjustments for mysql5 blob string compare behavior commit c9ba405f27bcb006d2efff2ca17e4a9919912522 Author: kuhn Date: Wed Oct 14 17:20:03 2009 +0000 added kgTableAll commit d736f6ed5b06e7c47f6db9630df419da81e002c1 Author: katrina Date: Wed Oct 14 17:17:13 2009 +0000 updated some of the script output commit 8ac6fcd84428e7497528b42fadbc848210a7d43d Author: kent Date: Wed Oct 14 15:29:12 2009 +0000 Creating knownToHprd column. commit 9908c333294f88c31413b247cc1e2a09ae7df87e Author: donnak Date: Wed Oct 14 15:28:17 2009 +0000 Changed MKE mirror URL, per Paul. commit 894454dde1110379930d3dbb8001e032d0562223 Author: galt Date: Wed Oct 14 15:00:06 2009 +0000 "Encode release log update" commit 19c879b5852205b52ae2ed4304752b6db0da2ddf Author: galt Date: Wed Oct 14 15:00:03 2009 +0000 "Release log update" commit 1820d4ea3181a41fa6b824b64adb4761e362918a Author: fanhsu Date: Wed Oct 14 13:41:41 2009 +0000 Added logic for special processing of sequencing day. commit 928418baa8012bd0379f74dc14f001472729a7be Author: pchan Date: Wed Oct 14 07:08:13 2009 +0000 add support to annotRev tracks; use annotRev instead of genepred if available for blastp tracks detail page commit 639eec49968d513283cc0219b808cd5c79350e29 Author: ann Date: Wed Oct 14 02:01:36 2009 +0000 last fixes commit d67672dc148189a89f07eb5867d03271874a72a8 Author: ann Date: Wed Oct 14 01:48:39 2009 +0000 prettier commit b10e8ea20082adcd61c27ca00a96a6427b6fb161 Author: kate Date: Wed Oct 14 01:28:33 2009 +0000 Streamline & clarify the Release Notes section commit c6e039b668a45fbeb1d05632812865c14fa2643c Author: rhead Date: Wed Oct 14 01:02:41 2009 +0000 Fixed bug that was causing intronEst to be printed in the list of tracks when no such table exists (thanks, pauline). commit a04d1989d13f0cd80767a1696decdd0aa6c44e21 Author: tdreszer Date: Wed Oct 14 00:06:08 2009 +0000 Cleaned up commented out and replaced tracks commit f3c204d7d52c074e28f7ba8c56c5b29e9f81587c Author: tdreszer Date: Wed Oct 14 00:04:21 2009 +0000 Keeping up to date commit 98f2a583312191f46658932e03f4c59baa253e57 Author: kent Date: Tue Oct 13 23:16:33 2009 +0000 Updating omimGene commit 1afff197baedba9e7d3fd209576be6afb1a32020 Author: kent Date: Tue Oct 13 23:16:22 2009 +0000 Adding omimGene commit 130f25435a7e1ab54e740b999bf5b647b7d12390 Author: markd Date: Tue Oct 13 21:24:49 2009 +0000 backed out previous change, as it was incorrect. Instead improve a more informative diagnostic message commit 3418ca5c9dbf88565e6393c3ffd0d805727e9ddf Author: cline Date: Tue Oct 13 20:26:06 2009 +0000 Put back changes on the UwDGF settings under viewLimitsMax commit 32db163afbb358f5495c6f2aad29fdf5122add57 Author: cline Date: Tue Oct 13 20:21:26 2009 +0000 Fixed a few miscolored font lines commit dcb430b3889b3701d89a2ea9baf22b21ac2aa327 Author: cline Date: Tue Oct 13 20:19:18 2009 +0000 Added html page for DGF commit cbe30c318ad70ee5d71a942d8b830b5f77045e03 Author: kate Date: Tue Oct 13 20:17:31 2009 +0000 Correct a minor setting error (track with table had parentTable setting which is used for downloadables only) commit 9c3750fe5ec22bd842bcc05ef0035d993625eeaa Author: kate Date: Tue Oct 13 19:54:46 2009 +0000 Remove Tier in cell type labels until there can be some review commit 22e1c25b005b5b132b4e091729541850ded4c400 Author: hiram Date: Tue Oct 13 19:26:27 2009 +0000 Add note about chrM being type F finished commit 7629f3ec87fb92baa0f25476d4474af52c3a4e23 Author: ann Date: Tue Oct 13 18:59:33 2009 +0000 hard link to download server commit a74e084455d602192cd7725bfad77bfb1e754bc1 Author: ann Date: Tue Oct 13 18:58:25 2009 +0000 fixed color of HeLa cell line for Yale TFBS tracks commit 5f343ec84abaa3bb9188d1717a29fa25bda56012 Author: braney Date: Tue Oct 13 18:48:48 2009 +0000 added mocked up submission dir 685 to methyl27 tracks commit e783918afe9cb211fb816ca4eed952d64a7cb9e1 Author: tdreszer Date: Tue Oct 13 18:31:31 2009 +0000 Removed 3 tables erroneously listed as new. Thanks Ann commit b1c67a1359e08507db614d1a12ddd4c92d43f411 Author: braney Date: Tue Oct 13 18:06:16 2009 +0000 add submission id for HudsonAlpha CNV commit abe01b4c1c3399543e70d13160204888c9c013ff Author: tdreszer Date: Tue Oct 13 17:39:42 2009 +0000 Nine more UwChIP submissions commit d852900b7b288924bee79e562c1f5e95994074ed Author: kuhn Date: Tue Oct 13 15:48:59 2009 +0000 removing release alpha from chainNetEquCab2 commit 371433bec7e02dd685c65ab8bd0ae02671151a60 Author: galt Date: Tue Oct 13 15:00:07 2009 +0000 "Encode release log update" commit 3c6c3d795f37dca24bb6fc4ee5c445442e8024e4 Author: galt Date: Tue Oct 13 15:00:03 2009 +0000 "Release log update" commit 6dc65a364362afc5e8c5ac9514a3beea71db6cd0 Author: kent Date: Tue Oct 13 07:54:37 2009 +0000 Creating nibbImageProbes table. commit 98b2d90fd357b5e44aa09cf6d811b9933e53fc9d Author: markd Date: Tue Oct 13 05:43:01 2009 +0000 don't skip validate non-coding RNAs commit 281706387acecdf1150a284df9301d76521c9b04 Author: galt Date: Tue Oct 13 05:37:19 2009 +0000 handle 2bit as well as nib commit c26d071ddf1402b79d1e82ed4d8a269e1ef539fc Author: galt Date: Tue Oct 13 05:21:55 2009 +0000 fix misleading name commit 912be5fbd950cca817e4f79d30704bf3bd48e4a0 Author: galt Date: Tue Oct 13 05:09:40 2009 +0000 yay, hgLoadChrom takes db arg now commit e6790b27add8a7b199e008447bf58d315d0d02c0 Author: galt Date: Tue Oct 13 05:03:54 2009 +0000 "New version number v217" commit 0ac5e31bac18e32e6b4fb71666bd1eee727d288a Author: galt Date: Tue Oct 13 05:03:22 2009 +0000 v217 final build commit a57fb1b0dbd9f5cabe2ab4aab253101581a326a9 Author: kuhn Date: Tue Oct 13 00:47:23 2009 +0000 added chain info for dog chain and adjusted priority for mousr chainnets commit 9a3b1c28f85744f16eb33793373fccd53f250a2d Author: tdreszer Date: Mon Oct 12 23:45:03 2009 +0000 Added 14 more Uw ChIP submissions commit aaa2501051dec6f33aa3f800b5bd5a18ebea10c7 Author: cline Date: Mon Oct 12 23:19:19 2009 +0000 Added wgEncodeUwDgf tracks commit 523fc68e86fe35874a0d76d5cbaf67beefb744c8 Author: ann Date: Mon Oct 12 23:16:38 2009 +0000 removed release beta blocks and release alpha lines from Yale TFBS tracks commit 14810174a2ed49e5aec8ef8280cc792ab2d42ba9 Author: galt Date: Mon Oct 12 22:43:34 2009 +0000 getting it to be a little more consistent, better code organization, and fixes problem where custom bedGraph track was not working commit e25c6090c8ae16a125555ce69bf0f57275d1fa7e Author: tdreszer Date: Mon Oct 12 21:56:24 2009 +0000 Left out 2 Duke submissions commit 1b4c6ce52fe42894b963660346f9caa3058db1bc Author: tdreszer Date: Mon Oct 12 18:21:50 2009 +0000 More Duke tracks (added by Tracy) and reordered UW tracks commit 42eb0ef5a03eee8e621be87f41d5e1b390dacbaa Author: ann Date: Mon Oct 12 18:03:08 2009 +0000 added dog chain and net override (because the chainNetCanFam2 at the top level is release alpha) commit ac1a3eb87f239ad6101f49983b4fa633de9a8575 Author: kate Date: Mon Oct 12 17:26:19 2009 +0000 Add new required setting commit 77ccf71fe5ee7fe1fbfdf0d1b9c64a0b216b9ac4 Author: angie Date: Mon Oct 12 16:33:52 2009 +0000 Updated link -- annoying when a working link disappears. commit fe710719b1b33ed6701a51c8cb2ee74106382eea Author: angie Date: Mon Oct 12 16:32:18 2009 +0000 Fixed INDEX. commit aa8ca6f3c36360e3878f47500089f37eef93e8dc Author: galt Date: Mon Oct 12 15:00:07 2009 +0000 "Encode release log update" commit 261bc2d3275e990a4e3426a5c0a7d85b730a1b20 Author: galt Date: Mon Oct 12 15:00:04 2009 +0000 "Release log update" commit 275a92c603297d1ada88492823f3b444e71c3e82 Author: larrym Date: Mon Oct 12 06:50:48 2009 +0000 add disconnect, getChromSizes and DESTROY methods commit 2f5e4d8b6d9263604cdc8b6f142ce1f8f8e151b1 Author: galt Date: Sun Oct 11 15:00:05 2009 +0000 "Encode release log update" commit 680a3da5f684fe07ebaa08fe586068e5f588ec57 Author: galt Date: Sun Oct 11 15:00:03 2009 +0000 "Release log update" commit 7346dbc27981f87e84ec9d5cba22af7cdd77bc99 Author: kuhn Date: Sun Oct 11 06:55:05 2009 +0000 adjusted priority for human and dog chainnets commit 55cc55b8af41853a290bc595bf061000ffec5675 Author: kuhn Date: Sun Oct 11 06:49:25 2009 +0000 moved chainnets for canFam2 from priority.ra to trackDb.ra (override) commit 32dbaf813a1f209d3675a9341d9e9399cdc405bd Author: kuhn Date: Sun Oct 11 06:44:28 2009 +0000 adjusted priorities and set chainnets for equCab1 to o_db commit 9480650559bf7fc2ac3199bd14c084f088f1377e Author: kuhn Date: Sun Oct 11 04:47:31 2009 +0000 checked in script to get list of KG tables for current assembly from master list commit 48a531db7d83c759444e11aeb2e4834d375db073 Author: kuhn Date: Sun Oct 11 04:46:17 2009 +0000 updated to work with new KG. still needs work commit c4e3c339cc2df7806dedd2040fcc1b5959eafe44 Author: kuhn Date: Sun Oct 11 04:42:10 2009 +0000 checked in script to get list of KG tables for current assembly from master list commit 5f75d9e56b8fd73c4c4729f209fc012790438813 Author: kuhn Date: Sun Oct 11 03:03:48 2009 +0000 removed stray comma commit 1420cacedb0ad72649af6028bbeae85924ea7784 Author: braney Date: Sun Oct 11 00:27:06 2009 +0000 put tabs between bed fields commit 8cb776be48eaf592b73706e2c515da94e395a30c Author: cszeto Date: Sat Oct 10 16:56:45 2009 +0000 New cosmic update commit d507ac0a3964d13bf78bb3a845727400c17e4ab3 Author: galt Date: Sat Oct 10 15:00:06 2009 +0000 "Encode release log update" commit 4731a00305744b6ca6eb98422098a7f715cb6a93 Author: galt Date: Sat Oct 10 15:00:03 2009 +0000 "Release log update" commit 01090ebb092a2fc86b00640c569f43e24dd07c59 Author: kate Date: Sat Oct 10 02:31:35 2009 +0000 Replace Andy's entries commit 3fc36881f9076bdbb836d6bb8e073c98036484bd Author: rhead Date: Sat Oct 10 01:59:23 2009 +0000 Updated CCDS paper with actual print date. commit 6caba9771decdfacc0eec1f6efce321781d88813 Author: galt Date: Sat Oct 10 00:29:24 2009 +0000 added support for customtrack to getBedGraphField commit fa7db4007f6117f5f8786a1d36ff964a7db707a0 Author: kate Date: Fri Oct 9 23:12:07 2009 +0000 Add testing of color by cell type from cv.ra commit e61453f62d4c8d5f46469eeb088b9ccb71fe7f73 Author: kate Date: Fri Oct 9 23:10:39 2009 +0000 Add color by cell type (from cv.ra) to trackDb file commit cb360c1983ed3d6256696428f079bdb298639eff Author: galt Date: Fri Oct 9 23:03:52 2009 +0000 local vars are undefined, not nil like $global and @instance commit b39ff34083084e3d8f5aa8eafad577da49cd40a0 Author: angie Date: Fri Oct 9 21:26:01 2009 +0000 Added pgSjk to tablesIgnored (thx Brooke). commit 4781ae3d0fd67aa029b863d5ac9a4eee2e157f3d Author: cszeto Date: Fri Oct 9 20:36:07 2009 +0000 uldated cosmic data commit c57c1732409668d90a1e3a9715d8b86655f4a921 Author: kate Date: Fri Oct 9 20:27:21 2009 +0000 Allow metadata extraction w/o requiring file validation settings, for backwards compatibility commit d98f526197e86ea699abd2062d1262a345c435e9 Author: galt Date: Fri Oct 9 20:26:58 2009 +0000 suggested by qa commit 17cadc2fae4c546d24fe8860577c5f741de1299b Author: tdreszer Date: Fri Oct 9 19:57:57 2009 +0000 Fixed bug that broke IE8 support. Problem was that IE* doesn't support local variable 'class' and instead tries to overwrite obj.class. commit fe46871203ba5f8ec5d3464439e6d2b3d8911836 Author: kent Date: Fri Oct 9 19:36:03 2009 +0000 Trimming a few lines to make it follow same stepSize pattern as blat.c commit 40eecd1abfa55e07cc0fc83de46d4a3192b30627 Author: kent Date: Fri Oct 9 19:35:06 2009 +0000 Making sure stepSize is initialized commit 15a1d6af8902edf9d6a5d599b307a18aa2bbce4f Author: ann Date: Fri Oct 9 19:06:47 2009 +0000 release notes commit d2f18c4845b47f9c12c02337daac2ea66f0d9cbf Author: ann Date: Fri Oct 9 17:41:27 2009 +0000 a few tweaks to the new Notes section for this second release of the data commit 7e1f69b123deaf68bb7248ef1e1c4bb5e0f9fec5 Author: kuhn Date: Fri Oct 9 16:56:35 2009 +0000 added table lists for knownGene.csh script to use and removed some names from existing kgTables list commit d96e5976299f631aaed831792ee69bb4da49ea84 Author: galt Date: Fri Oct 9 15:00:06 2009 +0000 "Encode release log update" commit 24aaf7bd597588ef606a289f780ac478ab7fa4bc Author: galt Date: Fri Oct 9 15:00:03 2009 +0000 "Release log update" commit f0444b1c0597763c213e076232abe74f19d505f6 Author: kuhn Date: Thu Oct 8 22:38:36 2009 +0000 set shortLabel on hg18 chainnet tracks to o_db, set priority of chainNetHg19 and some fish and moved some items from priority.ra commit 5d06162c09dae4cc42debd97e11d890d4b29f6db Author: kuhn Date: Thu Oct 8 22:03:53 2009 +0000 set shortLabel on hg18 chainnet tracks to o_db and set priority of chainNetHg19 commit a6abd7047fd948b73cf791901165fd5316cdfe70 Author: kuhn Date: Thu Oct 8 21:52:55 2009 +0000 set shortLabel on hg18 chainnet tracks to o_db commit cfa6f7df5891a8413f1576d00511971820579de5 Author: ann Date: Thu Oct 8 21:44:46 2009 +0000 adding these to CVS (they had just been in the target directory -- until I got busted by Angie!). part of the bigWig and bigBed help pages. commit ba36282bc2adaf83764a61b0048ba7513a1cc45d Author: kuhn Date: Thu Oct 8 21:20:45 2009 +0000 moved priority.ra into trackDb.ra, adjusted priority on chainNetHg19 and set shortLabel on hg18 chainnet tracks to o_db commit e509ac7e74b8bb13af950e55f3fcc42337040a26 Author: kent Date: Thu Oct 8 18:30:34 2009 +0000 Adding hg19 to set of most recent 'knownGene' format databases. commit 2af038b23047709bb380417e7225741cc0c0f61c Author: galt Date: Thu Oct 8 18:21:15 2009 +0000 help in the concurrency battle with validator or loader mods to projects record commit a7586af3ca1abfc260e08afc28b6a91da42727f9 Author: braney Date: Thu Oct 8 18:14:34 2009 +0000 make validationSettings required commit fabccfb1c79b5395f5b30232659fca0eb82329d7 Author: kent Date: Thu Oct 8 18:09:38 2009 +0000 Moving repMatch calculations from blat to library so can be shared with gfServer. commit 3f2ee13f29347979d199501ed717904bb68ce206 Author: angie Date: Thu Oct 8 17:02:30 2009 +0000 Support inclusion of other hg.conf files. commit e6fb672c8499d4a7a0efad0836584a5292cea918 Author: galt Date: Thu Oct 8 15:00:06 2009 +0000 "Encode release log update" commit 7802b635cb537f44cca7dec155094faf3e7f0c9f Author: galt Date: Thu Oct 8 15:00:03 2009 +0000 "Release log update" commit e2c32813baedab242eeda10cf82b8e97cf8fe53c Author: angie Date: Thu Oct 8 06:38:26 2009 +0000 Added support for bam as a custom track type. commit c7069a92aee13d95db69d4d569ae840b8c82df3c Author: angie Date: Thu Oct 8 06:25:38 2009 +0000 Use of samtools is spreading in the tree, so (if USE_BAM) add SAMLIB to L at the top level (inc/common.mk). commit 607971d618f353a82dff3fc9930279753d9ab3d9 Author: kuhn Date: Thu Oct 8 06:12:51 2009 +0000 changed hg18 chainnets to o_db and set priorities of hg18 and hg19 chainnets commit 58f09511c7ba97e02a3e686515d9e10f5fc60411 Author: angie Date: Thu Oct 8 03:33:26 2009 +0000 A little code cleanup: removed vestigial save/restore of env vars, improved a couple warning messages, replaced dangerous use of stack variable outside its scope w/dyString, removed some unnecessary uses of dyString. commit cba5b6871abab1827c78c20414618be2df5cdc76 Author: kate Date: Wed Oct 7 23:33:21 2009 +0000 Change name of chipseq test so it differs from real track so it can test out composite trackDb output commit 153e4d555514a65827d6c555bec4e40faae2ec4d Author: kate Date: Wed Oct 7 23:29:25 2009 +0000 Add support for specifying track group in DAF commit 7da5250efe8694b0a9292ea7be147a2c84a0847d Author: katrina Date: Wed Oct 7 22:15:14 2009 +0000 added new aplCal1 to list commit d1494f65eec114edf8066f26d2bb293d4f8dd85b Author: tdreszer Date: Wed Oct 7 22:12:45 2009 +0000 Added that olderversions of 'versioned' files are availabel through ftp commit c42d63318bedd0da300edb66fd64b9afddb485c5 Author: tdreszer Date: Wed Oct 7 22:05:48 2009 +0000 Fixed some 3D matrix plus-minus button problems. commit 72b46aa4ba2d3dddf4cc7f9d34d232d61f606979 Author: katrina Date: Wed Oct 7 21:56:19 2009 +0000 adding link to Broad sequencing commit a997957f72a96f8ecad3e7e1310c0ff1f82ea5b9 Author: rhead Date: Wed Oct 7 21:13:10 2009 +0000 Fixed broken link to EGTC. commit f668f4591877a849d657c2ae9bcc21e1d6927c86 Author: tdreszer Date: Wed Oct 7 20:34:34 2009 +0000 Added 5 more submissions included in Sept freeze. Account for 'release2' downloads dir. commit c7ec505e297873cce2321d19402b32d7987a6f24 Author: tdreszer Date: Wed Oct 7 19:39:19 2009 +0000 Fixed 'singals' typo in Yale metadata commit 6d0b13207e982fe3adf22c4169ef4734131d4dbd Author: hiram Date: Wed Oct 7 19:04:01 2009 +0000 use sqlTableExists() in place of hTableExists() to avoid custom track bottleneck commit fd0939bf909ae150321baec7ea2e659a62b5f46a Author: galt Date: Wed Oct 7 18:51:56 2009 +0000 redirect output because 32bit utils build on titan for some reason leaks into the calling terminal output, but not on hgwbeta 64bit for some reason commit 7604c311b73d682198fb699038da8d8a15c2a1de Author: galt Date: Wed Oct 7 18:25:51 2009 +0000 adding missing utils commit 7ea4a56d1857766fe32886b6323a6a04e332e49d Author: galt Date: Wed Oct 7 18:18:38 2009 +0000 since all other dates are changing, this one should too commit 2ddbdb49e5ba5bec8e3373e7fbb8f2c0d68523b2 Author: kuhn Date: Wed Oct 7 18:01:33 2009 +0000 removed in press paper from 2006 as it appears in full in 2007 list commit c3200fd638f7d6228acb67ac934e229962855a09 Author: galt Date: Wed Oct 7 17:49:35 2009 +0000 qa does not want this doc file anymore on hgdownload commit c1fba8b2d2ef893af0f881f5e655c07469368c08 Author: kuhn Date: Wed Oct 7 15:07:30 2009 +0000 removed sessionif from link, as it is probably personal for someone and doesn't work commit d974a76bd33289a2cbc940a834e231b558d21a86 Author: galt Date: Wed Oct 7 15:00:05 2009 +0000 "Encode release log update" commit a8db8417c583407f2a26d80a7590e755606cc853 Author: galt Date: Wed Oct 7 15:00:02 2009 +0000 "Release log update" commit a986c591e5e9b876ea0c25c791c24e77e9687ac9 Author: katrina Date: Wed Oct 7 14:31:56 2009 +0000 corrected alphabetical order of new entry commit 3eb14459bc2b71e3746b1595e1fd3120474968c4 Author: katrina Date: Wed Oct 7 14:21:25 2009 +0000 corrected alphabetical order of new entry commit b7fa51a4b470ce9b566fdcf33ad99b3690315075 Author: braney Date: Wed Oct 7 02:33:19 2009 +0000 use colors in bed rather than cell type color commit 80af2354479f00cdd18f56fbf9e69f05df8732a6 Author: tdreszer Date: Wed Oct 7 02:26:56 2009 +0000 Third time is not yet charmed commit fec88ea56348b867097463f7e0db086d037dd2d8 Author: tdreszer Date: Wed Oct 7 01:58:15 2009 +0000 Once is never enough. More cleanup to Notes commit 429f86c0f1c3b229ce5bbdcedfcaf37ba4fd7fa3 Author: tdreszer Date: Wed Oct 7 00:37:24 2009 +0000 Added notes to Yale desc page commit 4264aa3835dc9b063d90d9ac9dc31f71b4096a43 Author: galt Date: Wed Oct 7 00:34:59 2009 +0000 adding to the pushQ and all.joiner commit 2745994e22febc35cc04472b58ade6b09a2fc1fb Author: kate Date: Wed Oct 7 00:34:53 2009 +0000 Update chipseq tests for latest DAF & label conventions. Assure they fail if expected files differ. Disable methylseq test for now. commit 12ed1c2b10906dd9a4c2f28905a09289fc90e1d4 Author: galt Date: Wed Oct 7 00:34:17 2009 +0000 adding danRer6 commit af31789a5b5d304a98ce3afae429b1b70b3f471a Author: tdreszer Date: Wed Oct 7 00:14:50 2009 +0000 A few more Yale metadata correctioons commit 6a3bd1a8c278a0f8949cccfc96b044f458e73f56 Author: galt Date: Tue Oct 6 23:53:00 2009 +0000 its done commit 09295cb950ae6c3d79048491995344d8a4806e42 Author: braney Date: Tue Oct 6 22:49:30 2009 +0000 defaults for the CSHL short rna track commit 416ad02eda0521c5f36b04338d3c2a67802894ae Author: hiram Date: Tue Oct 6 22:48:51 2009 +0000 fixup install target so files go to correct hgGeneData on 'make install' commit b288bea249392808ebab8aa3ebb3268e21eab9f2 Author: tdreszer Date: Tue Oct 6 22:21:30 2009 +0000 Updating Yale metadata V2 commit 2cfac583aad11449050f5cd269b1dc739b09dbab Author: braney Date: Tue Oct 6 21:37:54 2009 +0000 CSHL short rna-seq: take out log signals, edit short labels, add sorting prefixes commit 635606f4f5d26a682e75a96856d7b1e8d430b655 Author: tdreszer Date: Tue Oct 6 20:39:36 2009 +0000 Added 5 to Yale TFSB commit 832ec6d810fe9f56efb168730423a0a77afa1f16 Author: katrina Date: Tue Oct 6 20:26:33 2009 +0000 updated staff list by removing mike, andy and ruth, adding melissa and making Ann QA team lead commit 160412bccd0d8b4274836a2272cc96eea05854bc Author: tdreszer Date: Tue Oct 6 18:30:00 2009 +0000 Removed H3K4me1 from UwChIP and renamed BJ-tert to BJ by Stam lab request. commit 9c7de315c831e9118e1feda57a2b9361ce097b27 Author: tdreszer Date: Tue Oct 6 18:12:24 2009 +0000 Changed BJ-tert to BJ by Stam lab request. commit 4fac604f2f5d1f87cfff2198d723b358bd7ec5b4 Author: angie Date: Tue Oct 6 17:39:16 2009 +0000 Added refreshNamedSessionCustomTracks to DIRS. commit 85a9b9bff72703913687264ff67517958247ee50 Author: pchan Date: Tue Oct 6 17:11:02 2009 +0000 created by Andrew Holmes for lowelab alignment feature track commit fb16c6cab5691231d82694d8da64e64d660033c5 Author: angie Date: Tue Oct 6 16:51:43 2009 +0000 Don't require user-read-only for included files (just ~/.hg.conf itself). This allows us to include our cgi-bin-\angie/hg.conf files, and simply override the db.user and password in ~/.hg.conf. commit 8c24f213e1cec51f146f50980f97ef9aac3edec7 Author: galt Date: Tue Oct 6 16:36:20 2009 +0000 v217 preview commit 52aaa62c59509aa2f91e0c50b43018fe8a949886 Author: galt Date: Tue Oct 6 15:00:07 2009 +0000 "Encode release log update" commit 7ca325ed49fb99a775dfec40da1e18ab53fccbcc Author: galt Date: Tue Oct 6 15:00:04 2009 +0000 "Release log update" commit ef642bedd962005b7c57ba2ae7d4dcd2e4da0ad6 Author: kate Date: Tue Oct 6 01:07:52 2009 +0000 Add SQL schema commit 698a6b53fed9fc653b7f22520371ef24dfa880b2 Author: cline Date: Tue Oct 6 00:58:27 2009 +0000 Modified the tags for the factors for the Broad tracks so that the subtracks appear in proper alphabetical order. commit 13b994f5edc26e728bb9544b428526161b03f4e1 Author: kate Date: Tue Oct 6 00:53:03 2009 +0000 Add support for 'sql' field in DAF. Allows specifying the schema for a non-standard table. The .sql file needs to be copied to /cluster/bin//sqlCreate commit c05e5705689b5d173c12101f54701cb8405faeea Author: galt Date: Tue Oct 6 00:47:48 2009 +0000 adding work-around to genome graphs import for bedgraph customtracks, also some elimination of unneeded connection variable commit 9695ccd924a683e284d0919ec64e3c5b3abc094c Author: braney Date: Mon Oct 5 19:35:11 2009 +0000 fix up some long labels for AffyRna and other tracks qVS: ---------------------------------------------------------------------- commit 33468e84ed6cf3fe6158af7424b8aebd55dcf8e1 Author: kuhn Date: Mon Oct 5 16:43:59 2009 +0000 checking in script to find out what a heavy hitter is doing commit 8a908b6ba239424a2c2f36dbb0ea1242058de3ff Author: galt Date: Mon Oct 5 15:00:07 2009 +0000 "Encode release log update" commit be5d4cb8b6125a7d22fe434649e4d8bc4371ae85 Author: galt Date: Mon Oct 5 15:00:03 2009 +0000 "Release log update" commit 95da1fd8e40a8577da08c759f4fd28b2fbf82479 Author: kuhn Date: Sun Oct 4 18:38:28 2009 +0000 set hg18 chainnets to o_db and adjusted priority of chainNetHg19 commit a62ff46f503f365da38bacd22cdace9a1cd77f63 Author: kuhn Date: Sun Oct 4 18:24:05 2009 +0000 set hg18 chainnets to o_db commit 4deb87eeb5b1d8d599967f43e3ea72fddaa80917 Author: galt Date: Sun Oct 4 15:00:07 2009 +0000 "Encode release log update" commit bc7d054686e7ac12176fc42cd721063688637cb2 Author: galt Date: Sun Oct 4 15:00:04 2009 +0000 "Release log update" commit 75cece2b65464755a949e90a63aa15b5a973a75d Author: sbenz Date: Sat Oct 3 19:40:55 2009 +0000 Fixed TARGET cnv ids to match exp commit 17429a021024a479cd8e4b990e289712a4627d40 Author: galt Date: Sat Oct 3 15:00:05 2009 +0000 "Encode release log update" commit 08bc82cfa1c1d5e2d5cfe722c592297cea71f2fd Author: galt Date: Sat Oct 3 15:00:03 2009 +0000 "Release log update" commit 209b0836a2d27b748361f54b86aad139942f42e6 Author: kent Date: Sat Oct 3 02:21:19 2009 +0000 Did old to new mapping. commit 6e02d6467d919af0239836571a8ab82357177ea2 Author: kent Date: Sat Oct 3 02:15:22 2009 +0000 Adding -unmapped and -oldAsm options. commit 4cd296a8544f2d52ce74812597a3d10e9d5c955e Author: kent Date: Sat Oct 3 01:28:43 2009 +0000 Utility to add in genes that couldn't be mapped from previous assembly to oldToNew table seems to work. commit 2fe1916d7e34d0df60ff556926204c56c7e17fc8 Author: pauline Date: Sat Oct 3 00:29:34 2009 +0000 Added new elephant. commit 38874b8fd2fecb0b232201efaa024e9226b66169 Author: kate Date: Sat Oct 3 00:07:26 2009 +0000 Add DAF support for listing sql schema for custom bed file commit 17fe5b39c690169fb08df99004fd107aa9be0758 Author: kate Date: Fri Oct 2 23:45:38 2009 +0000 Add custom bed schema for Weng lab commit aae053478af3b42a6c1177d594104e59c010cf66 Author: tdreszer Date: Fri Oct 2 23:17:37 2009 +0000 Finally checking in some antient notes commit 631844091fdd1262d0672e576e0ab46d756fd671 Author: tdreszer Date: Fri Oct 2 23:14:23 2009 +0000 Tim adds some preliminary notes. No activity seen for Sept 2009 freeze commit 321c90a5fe9889921acd37c22e4b6a7520f68938 Author: tdreszer Date: Fri Oct 2 23:13:27 2009 +0000 Thought I should check in old stuff done for Gencode Release 3. Two issues still unresolved, though commit 301c43a737dd1bd411772c465ba17fb63747fc77 Author: tdreszer Date: Fri Oct 2 23:10:47 2009 +0000 Added a lot of ChIPseq and DNase as part of the Sept 2009 freeze. Tracy Ballinger helped with trackDb, fileDb commit f0e8de87e440e93a872bb40958cbf911929d62ca Author: tdreszer Date: Fri Oct 2 23:08:35 2009 +0000 Finished up the Sep 2009 freeze submissions with Melissa's help commit 2f60478b6c79a97990e3d9ff297df620ae5700ed Author: tdreszer Date: Fri Oct 2 22:48:36 2009 +0000 Sorry changing NFkB back to NFKB as this seems to be a valid term in the literature commit d137752e79d1629edb58be1a73318b7d291d5c27 Author: tdreszer Date: Fri Oct 2 22:39:46 2009 +0000 Support bed3s commit 86d33dfae1b996f012782275cecc5ea83b25a743 Author: tdreszer Date: Fri Oct 2 22:35:42 2009 +0000 For Yale added NF-YA and NF-YB and renamed NFKB to NFkB commit b01a09e4264be21ff902e603ad101b31a0b6f8a8 Author: braney Date: Fri Oct 2 22:13:05 2009 +0000 colorByStrand for bed12's commit a0febc074f5531c7d3fded38cecd7dd95066b6f2 Author: tdreszer Date: Fri Oct 2 22:12:54 2009 +0000 Finxed HeLa and HepG2 sort order in UW Dnase and ChIP commit 66ce34d87930e63c0401c7bbfba1eee6ee4a4197 Author: tdreszer Date: Fri Oct 2 22:06:08 2009 +0000 Did some Broad track reordering commit 89d35888d63e14a1841dbfcd8c691c6339f0cea9 Author: angie Date: Fri Oct 2 20:35:50 2009 +0000 Made the color explanation more clear (thx Pauline). commit 12f263794397bf481bb51f1880a9a1543edc8163 Author: fanhsu Date: Fri Oct 2 20:27:39 2009 +0000 Create webUsers.sql to be used by webUserAdmin. commit 4855baea12b897e699d1d13452ac6eb8b9169a9c Author: kate Date: Fri Oct 2 19:20:29 2009 +0000 Weng lab ENCODE data agreement commit e1c0964385edd07733834b27f7f18a891282a49c Author: tdreszer Date: Fri Oct 2 18:00:11 2009 +0000 Left out UW ChIP HUVEC CTCF rep1 from last night's checkins commit 7f5d9a0862c214cbfd47922af920d435ef8dd42d Author: fanhsu Date: Fri Oct 2 17:53:59 2009 +0000 Take out a break. Ann does not like it and Fan forgot why he put it in. commit ae7a45d6354b592e1b4b5b5001c67ac2a298deaa Author: galt Date: Fri Oct 2 17:08:39 2009 +0000 new better location without tmp stigma commit 2b94b07423dc6ebba092c054fd79eb8d030b9dad Author: galt Date: Fri Oct 2 15:00:07 2009 +0000 "Encode release log update" commit 00869dfa6f0ef71036be4f663c2e51110c1eac10 Author: galt Date: Fri Oct 2 15:00:04 2009 +0000 "Release log update" commit 4857991f87075925dd6ffa863dea071dc2c8b6f9 Author: kent Date: Fri Oct 2 05:14:15 2009 +0000 Made it treat 'tmpFoo' as a mammal for updates in place of the database. commit 0cef1aba66d9965ca32187de962e88ed57a2d4b6 Author: tdreszer Date: Fri Oct 2 03:45:44 2009 +0000 Its ChIP-seq not ChIP-Seq commit b5ffc33e2e54091b6a18d5ee33a7d610fffa9a80 Author: tdreszer Date: Fri Oct 2 03:37:09 2009 +0000 Reorganized UW DNase commit fe14aff1f47b7edfc26a5cba7bb0e850ad4cebd8 Author: tdreszer Date: Fri Oct 2 03:15:22 2009 +0000 Removed stray bad line. Changed UW DNase raw sig view range commit f65edb075b9ee2c7c6c30e30c4eb3dc4dc94b478 Author: tdreszer Date: Fri Oct 2 03:09:00 2009 +0000 Added UW ChIPseq nad UW DNase. Reorganized a little commit 33296d09df7b76a8e95f54757a183c54cfb39897 Author: cline Date: Fri Oct 2 00:33:21 2009 +0000 Added new Broad histone chip-seq data commit 860707ba452cbaf0fb63487f10b95fe87d577bce Author: braney Date: Thu Oct 1 23:51:16 2009 +0000 turn on GM12878 nlos by default in Affy RNA loc track commit 65b95324b12a1892c90e2cd6b3c823796d771c02 Author: rhead Date: Thu Oct 1 23:43:19 2009 +0000 Wording improvement in collaboration with braney. commit 751ca44b1a34c80ec400d07bfeca0a42a8600286 Author: kuhn Date: Thu Oct 1 23:41:11 2009 +0000 set override on chain and net hg18 to o_db commit b81a4a6267ccd791a99f2328846c677eb55d93ba Author: braney Date: Thu Oct 1 23:30:34 2009 +0000 small fix, npls to nplm in Affy RNA loc track commit 133a91049c03c1d15a663c9b1cd899a92d618473 Author: kuhn Date: Thu Oct 1 23:27:34 2009 +0000 moved venter and his dog out of the way of the main chainNet tracks commit 6a5ff91d83e01a222501265c57dd0fb0ae503b6d Author: braney Date: Thu Oct 1 23:24:59 2009 +0000 fix up short labels for Affy RNA loc track commit b1462403a3ac940a75936d3cd9bd9108bdde1a30 Author: ann Date: Thu Oct 1 23:08:06 2009 +0000 added two variables commit 55f80c3f40ba4ec867492fd8116747d3d6cd6825 Author: kuhn Date: Thu Oct 1 22:28:57 2009 +0000 moved all the overrides together commit 0b7061cbee2d28352dc62eb18cc95a74c59090c9 Author: kuhn Date: Thu Oct 1 18:39:47 2009 +0000 remade grep table in include new column and split reg from expr commit 8448ec23034a8f09ce4966644aa67c88f200dbdf Author: galt Date: Thu Oct 1 15:00:07 2009 +0000 "Encode release log update" commit d9d54d34ce2baf11ae41eeb7c52374acaa7de1e0 Author: galt Date: Thu Oct 1 15:00:03 2009 +0000 "Release log update" commit ebd4470df32ca3caf37645ac2ec22e12b4448e90 Author: kent Date: Thu Oct 1 10:01:27 2009 +0000 Doing stuff to get gnfAtlas2 data in. commit a986982125ee1f3c41010863eacd04fba25519f2 Author: kent Date: Thu Oct 1 08:43:50 2009 +0000 Making a few more knownTo tables commit 97f49507948cbc92dd8dd574b2f09eedb812e552 Author: kent Date: Thu Oct 1 07:50:03 2009 +0000 Adding a little more detail to history table record of hgLoadSeq. It still is giving warnings, I think maybe because of the missing gbDate field. commit e268e9f20799606ace9e8054ca71c53e16cdc7b5 Author: braney Date: Thu Oct 1 04:50:06 2009 +0000 implement Angie's suggestions to make the code more readable commit 675bdca74ad636717eec0237993b1bfbd6093acb Author: angie Date: Thu Oct 1 03:58:18 2009 +0000 Oops, introduced a new fputs w/no return value -- thanks Brian for catching in review. commit 911b371e6031f8c2ff989526a047651718a1b993 Author: braney Date: Thu Oct 1 01:45:07 2009 +0000 take out commented out old CSHL short RNA-seq entries commit 55d08345c853c23b58c245ce8ef4da520ed48943 Author: braney Date: Thu Oct 1 01:43:08 2009 +0000 add color to CSHL Long RNA-seq track commit 13c4981021b3abbacc5881dd1f261bdf247f0e89 Author: kent Date: Thu Oct 1 00:08:39 2009 +0000 Doing/redoing some knownTo tables and pfam. commit 1b8e950c86dd49dc5bef4303d3b2da6bdd8e3876 Author: pauline Date: Wed Sep 30 23:41:43 2009 +0000 Updated to point to current mysqlbeta. commit 3043c98f084fa341e408ab8e65fc604477f2068f Author: hiram Date: Wed Sep 30 23:17:14 2009 +0000 fixup access to normScore column for tables that have that commit d8195f03e25f0350e20653089c4c67a0622174a7 Author: tdreszer Date: Wed Sep 30 22:11:03 2009 +0000 Reverting Hiram's changes temporarily, since ENCODE pipeline is now failing validation left and right commit c98e2ba79f7287a0891aecab365a3c87a5ece34c Author: braney Date: Wed Sep 30 21:40:00 2009 +0000 fix narrowPeak check to actually use the peak rather than the score commit ca3a38b3037b1ad59321f8c94300b8acc09dbf55 Author: hiram Date: Wed Sep 30 20:29:18 2009 +0000 A bit too agressive on that overlap check, don't do it for position 0 commit b403211c7f490e4ea88edcd015cb3f54b15f9211 Author: kent Date: Wed Sep 30 19:40:49 2009 +0000 Fixed typo in comment commit 024c720ebe3770652298dd39e23904e16c029852 Author: kent Date: Wed Sep 30 19:30:56 2009 +0000 Adding Allen Brain track to hg19. commit ab4ca027edd3f4e9d6a3864f081bd50c9eb1aded Author: hiram Date: Wed Sep 30 17:13:26 2009 +0000 Was missing overlapping data condition on a fixedStep case commit 64769799cb577ba6dec3bf89c6b8255ac30fbb5f Author: galt Date: Wed Sep 30 15:00:07 2009 +0000 "Encode release log update" commit a75b978e74d2dec175e574ac7da61318fd51d39d Author: galt Date: Wed Sep 30 15:00:04 2009 +0000 "Release log update" commit 0e3b125879a5cc23c364178ba7ecab32cfe67687 Author: galt Date: Wed Sep 30 04:34:31 2009 +0000 tidying up commit 4e7665f23fb2a0b68fe23a69991244cad605b571 Author: braney Date: Wed Sep 30 03:26:42 2009 +0000 put X in missing 14th field commit ffe5db1267f623423da1cdb71d845d967dbb34ac Author: braney Date: Wed Sep 30 03:26:06 2009 +0000 add append option to add to, rather than create files commit 2653477f64c734ca783338af8a8bbe2a993c5ebc Author: braney Date: Wed Sep 30 03:19:42 2009 +0000 new CSHL long RNA-seq setup commit 0ce9d2ed07842a62fc430ef527d86c590c501fe6 Author: kent Date: Tue Sep 29 23:19:08 2009 +0000 Improving error message. commit 2cf74a749e6d2dcca19e925a1cce86d72af2194d Author: tdreszer Date: Tue Sep 29 23:15:29 2009 +0000 Added antibody NFKB and treatment TNFa for Yale. commit 0435aa7ef1c618c8ca620404ebb3456d41268963 Author: kuhn Date: Tue Sep 29 23:01:15 2009 +0000 grouping hg18 and hg19 chainnets together commit 6873be8aa8836accdbf1ae458162db6922151bd7 Author: ann Date: Tue Sep 29 22:10:16 2009 +0000 adding some color commit 775d5916a6cbe0eb075eb4da20580ae7890e8be5 Author: ann Date: Tue Sep 29 21:49:04 2009 +0000 removing types that are no longer going to be part of this track commit e345ed9d365716bb70bc027f50994f5e9ac7f274 Author: angie Date: Tue Sep 29 21:47:37 2009 +0000 Make it clear that this is a provisional release, based on the hg18 data files but w/mapping to hg19 coords from dbSNP. commit e620cd215e3ad2e89f85be8edb3083994298ee27 Author: ann Date: Tue Sep 29 21:45:39 2009 +0000 changing dataVersion to include Sep 09 freeze commit 1529159632b3fef4b2581758bc45055bc16af4b3 Author: tdreszer Date: Tue Sep 29 21:41:22 2009 +0000 Initial version of UW Digital Genomic Footprinting DAF commit e58b112a828d7e8997f0aa3b495f70de1c901224 Author: kuhn Date: Tue Sep 29 21:36:32 2009 +0000 fixed chain o_db override in shortLabel to say chain, not net commit 4a4de2925575926688c4b7675622506a4f81eda7 Author: kuhn Date: Tue Sep 29 21:35:36 2009 +0000 fixed chain db override in sortLabel to say chain, not net commit 3bf23e925982852dce9c6897b17f458486c2abb1 Author: galt Date: Tue Sep 29 18:15:31 2009 +0000 fix for 32bit commit 85fd0f03c7add041523303e4317e70edd9e47562 Author: rhead Date: Tue Sep 29 17:48:07 2009 +0000 Fixed date on canFam2. commit dc92ba8743c605dbaa73f5ce9b52415a9d83a5cd Author: galt Date: Tue Sep 29 17:40:36 2009 +0000 cvs reports fixing email msg on cvsreports ready commit 9a4480e5b935ee6aca4b9e190eabaa539c4a3492 Author: fanhsu Date: Tue Sep 29 15:48:30 2009 +0000 Added the section of immuno build. commit fff439d325337f1d73a76e0ee80e3e6eef1f266b Author: fanhsu Date: Tue Sep 29 15:29:51 2009 +0000 Create immunoRaw.sql to be used on building immuno related data for GSID TB. commit 436fda058b80280d29a09abe480ab7d19b457ff9 Author: fanhsu Date: Tue Sep 29 15:28:39 2009 +0000 Created immuno.sql for GSID immuno data. commit 02c05cc6296e8d64ff95f3812cdf6656d84a7d55 Author: galt Date: Tue Sep 29 15:00:07 2009 +0000 "Encode release log update" commit d0e775c90b486350e1ecf2c7525198c4afd700f7 Author: galt Date: Tue Sep 29 15:00:04 2009 +0000 "Release log update" commit 82355fc20008c49e7d314966f94350d773209cd6 Author: kent Date: Tue Sep 29 06:40:00 2009 +0000 Starting new build of mouse UCSC Genes. commit 3194489a0c5ded1bf3d72b0a898841dcfb8e6cc7 Author: galt Date: Tue Sep 29 02:23:50 2009 +0000 "New version number v216" commit 9e1f3d0284f3d7c3a8c26d31178d27aba6fb89bc Author: galt Date: Tue Sep 29 02:23:18 2009 +0000 v216 final build commit 4179afb0e3fd6c484c0fffca8f1f8cbb560b13b7 Author: braney Date: Tue Sep 29 00:54:16 2009 +0000 add a little optimization to avoid hash search on each line commit 20abe8d85c319dca1770eb40cc3ae99b26005b25 Author: braney Date: Tue Sep 29 00:17:04 2009 +0000 added a couple of options to facilitate use in ENCODE pipeline commit a768067ffa0ec969ee62fa8c441a43ead3600fca Author: rhead Date: Tue Sep 29 00:15:34 2009 +0000 Changed codon translation table per andy. commit 818e4ac61a6a1a00277acb2cdfc91c5359d4dca0 Author: aamp Date: Tue Sep 29 00:04:13 2009 +0000 Forgot a period. commit 7a344bd8319b20aac50a3fc859414d2986a6645e Author: aamp Date: Mon Sep 28 23:59:42 2009 +0000 Added phastCons parameters to the description. commit 9c435e77cb17663fd3021d62856898d060f74c2f Author: aamp Date: Mon Sep 28 23:55:54 2009 +0000 Fixed a bad sentence. commit 11e03d6fb0a872e46edf1b2d208d6fdc25c5abe7 Author: aamp Date: Mon Sep 28 23:40:58 2009 +0000 Changed the description for the conservation track to reflect the correct phastCons tree model creation procedure in this case, which was NOT to use 4D sites like in the human conservation track. commit 1370102f53c171938821d2bd742461a59574d27d Author: fanhsu Date: Mon Sep 28 23:25:24 2009 +0000 Fine tuned Table View display. commit cf6490197c17e63ddce65d9e17557b269b904275 Author: fanhsu Date: Mon Sep 28 23:23:08 2009 +0000 Turn off visibility for most of immuno cols per GSID layout design. commit e57d0a8f59e48f06ba70ac63809f3c2a209ca36b Author: tdreszer Date: Mon Sep 28 23:21:45 2009 +0000 Complete lists of files and tables for ENCODE Yale TFSB release 2 which should occur after the 9-30-2009 data freeze. Notes were too long to include directly in pushQ entry. commit 5452e5e1f789c30ccbf9aa2ef52144bcc3810e36 Author: fanhsu Date: Mon Sep 28 23:18:18 2009 +0000 Updated to present precisely like the layout design by GSID. commit d1c78cea89f57bd19425cf32ab629d650f6da110 Author: angie Date: Mon Sep 28 22:50:03 2009 +0000 pgSnp: added pgSjk, moved 1000 Genomes NA* from pgSnpHgwdev to pgSnp. commit 2749e9dc060bcae675da86a2d47bbd0f9ae25b3c Author: rhead Date: Mon Sep 28 22:20:52 2009 +0000 Removed release alpha lines for Affy RNA Loc sep-09 update tables. commit f2f3ff25e5994a44ed3d975897d672709ad11f11 Author: angie Date: Mon Sep 28 22:07:49 2009 +0000 Genome Variants: added Korean (SJK). Added base counts to 1000 Genomes SNPs. commit eecc3b757a79eacd1ff739b328dacb189f8097ca Author: angie Date: Mon Sep 28 21:55:55 2009 +0000 Added description of repetitive sequence highlighting in re-alignment of flanking sequences. commit 840bd8acbb7ad20e6965ad20285e91ac6a3d817a Author: angie Date: Mon Sep 28 21:51:10 2009 +0000 snp125: Add a persistent shadow variable to the list of gene tracks, so we can distinguish between a 'clicked to deselect all' vs. 'hasn't made any selections'. Should cart.c make multshad variables persistent? commit 4a2eb65e666cae861a407ca0d7fc018f767e2653 Author: rhead Date: Mon Sep 28 21:30:33 2009 +0000 Updated species list to reflect make doc. commit 229893bd7bec221acc2e8ce197e72a5d69556eda Author: aamp Date: Mon Sep 28 20:49:09 2009 +0000 Added multiz/phastCons make instructions. commit 1ab45b3138b33cbb03837e252c652009b662891f Author: hiram Date: Mon Sep 28 19:50:28 2009 +0000 Added oryCun2 - Oryctolagus cuniculus - Rabbit commit 4717e76b4aa27db84eb1fbfc40066d4ef08ab677 Author: tdreszer Date: Mon Sep 28 19:36:29 2009 +0000 Added Antibody HA and cell HGF commit 1a60a376642c7587563b7e76a0fe648345b5a959 Author: kent Date: Mon Sep 28 19:00:34 2009 +0000 Patching things to look for all_mrna when chr1_mrna doesn't exist and the like. commit 1ee2fac85b9aeffb1ec25d58105578262f06c26d Author: braney Date: Mon Sep 28 18:52:20 2009 +0000 add bounds output commit bd62e5679970b90cbfd0582a943139c1246133dd Author: kent Date: Mon Sep 28 18:20:28 2009 +0000 Making printf formating agree in signedness to avoid error on different compilers. commit f4ae73ff6cc09f4dedc5f6faabc1f8b9930ae5db Author: kent Date: Mon Sep 28 18:19:31 2009 +0000 Making error message a little more informative, and not an 'internal error' since it is in response to erronious input, not software error. commit e68dfd62802992e4ee3de2594b991b813059f309 Author: hiram Date: Mon Sep 28 17:49:54 2009 +0000 Initial files from makeGenomeDb.pl commit 530fad800c4b2912528d2410100c9078d3403000 Author: kent Date: Mon Sep 28 17:11:01 2009 +0000 Got rid of a test case that depended on a database being constant. commit 276dd3ba140160f87672bb3f63defa3362cf6e5b Author: hiram Date: Mon Sep 28 16:57:57 2009 +0000 Added macEug1 - Macropus eugenii - Wallaby and Papio Hamadryas - Baboon commit f428d2db691b909cedca9b71b71704addb9133c4 Author: galt Date: Mon Sep 28 15:00:06 2009 +0000 "Encode release log update" commit 64be7bad93f25fd883fc366d5f0dc61d573b3226 Author: galt Date: Mon Sep 28 15:00:03 2009 +0000 "Release log update" commit 3b782121e0c1a7f8942e5f16ca12c691bb0a7ee5 Author: galt Date: Sun Sep 27 15:00:03 2009 +0000 "Encode release log update" commit 5833a2972ad5b2df1fb596e2948560e9e4e53d19 Author: galt Date: Sun Sep 27 15:00:01 2009 +0000 "Release log update" commit 2d7ca3ba10000f7d5698eec0d5ccf78e0256e749 Author: kent Date: Sun Sep 27 04:54:50 2009 +0000 Finishing up build and database integration. Will need to add more knownTo and XyzDistance tables as the hg19 database in general is built up. commit 4b8e9d7221c62111d93eff009d67f8978cb6a3c7 Author: kent Date: Sun Sep 27 04:45:41 2009 +0000 Fixed bug in memory management Andy recently introduced where the geneId was freed after the microarray section leaving subsequent sections with garbage geneId. commit dba1386368026a8627240c86357866e3526c54f4 Author: galt Date: Sun Sep 27 03:32:29 2009 +0000 fix based on mysql5 commit e955a0f0a6b8986fd6acb1fd1c9bc87215097e00 Author: kent Date: Sun Sep 27 01:16:28 2009 +0000 Making directory for config files for hg19 commit 1d38f3b78e9d9b72c50cf92bd8408917651f37b7 Author: kent Date: Sat Sep 26 21:22:51 2009 +0000 Working around mysql 5 bug. commit fa2553b83c4cb4035b249fb7f4fd72ef6441c50e Author: kent Date: Sat Sep 26 20:59:31 2009 +0000 Adding some configuration so hg19 known genes details page works. commit 8e56fe8a1426f75e77ba566101eac0e7b35cb277 Author: galt Date: Sat Sep 26 15:00:05 2009 +0000 "Encode release log update" commit d2a68176e2c49a1e6e73c2f25ed85c28d62e608c Author: galt Date: Sat Sep 26 15:00:03 2009 +0000 "Release log update" commit 4fcbc57f4f2483d4c2c3eef8bfcd56bc2a881ed0 Author: kent Date: Sat Sep 26 03:33:52 2009 +0000 Done with first pass of the build. Now for some testing.... commit ef6209c4ed0c4c624a6f889696194325acc48d44 Author: kuhn Date: Sat Sep 26 00:09:06 2009 +0000 combined chainnets for hg18 from priority.ta into trackDb.ra and set shortLabel to o_db commit 9c21e25a60ffe9cc087f6045912e52ffeda59adc Author: braney Date: Sat Sep 26 00:07:12 2009 +0000 add LogSignal tracks for Hannon lab commit 63bb4ddfdd156327ec020e2c772faa610f4100b3 Author: rhead Date: Sat Sep 26 00:07:11 2009 +0000 Archived a bunch of news items. commit 6aed8807b36e86e971bd4193fb9f1735c30ebd50 Author: kuhn Date: Sat Sep 26 00:06:30 2009 +0000 set hg18 chainnets to o_db commit b528023ff5a9124d8747173f2f407b9e28ae021a Author: kuhn Date: Fri Sep 25 23:38:47 2009 +0000 moved possum net back with other mammals commit 1ab0b5ff78a5ac93d582753213d36b5b097db383 Author: braney Date: Fri Sep 25 23:17:20 2009 +0000 oops, default should be to use 32 bits commit e74a4bc075c74d3c657952883dafb8f7023a45b8 Author: braney Date: Fri Sep 25 23:08:41 2009 +0000 added -bed12, -max, and -zero options. Made default counting unit size and unsigned long commit 249508044f63e3247170dcb574cac796ee9fb571 Author: kent Date: Fri Sep 25 22:41:23 2009 +0000 Built new version of proteins database on top of corresponding swissProt database. commit 35968a7250c4e054f5d90e1bd7bcf35726846767 Author: kuhn Date: Fri Sep 25 22:40:07 2009 +0000 combined chainnets for hg18 from priority.ta into trackDb.ra and set shortLabel to o_db commit 1bb23e1d792fcc44f56dcdb58fe72aece48eeedc Author: rhead Date: Fri Sep 25 22:34:58 2009 +0000 Fixed up references section (used text from calJac1 multiz page). commit 80df3ef500c0e5da5dc6a1d060ecb7c412e56147 Author: kent Date: Fri Sep 25 22:01:28 2009 +0000 Adding pbCalResStdGlobal to parent makefile so we'll spot when it doesn't compile sooner. commit 3217a77bac924d1cbdb6838cd1c6410616e66066 Author: kent Date: Fri Sep 25 21:57:47 2009 +0000 Adding database parameter as now required for hAllocConn(). Changing a stderr message to verbose(2 since it was coming up a lot to no bad effect. Bumping up MAXN so can handle 20 million proteins in SwissProt since now up to 9.3 million and previous limit was 10 million. Changing biggest array to be dynamically allocated to avoid linkage error. commit 338248b26382da488ac370e328a085273b3ef5da Author: hiram Date: Fri Sep 25 21:48:34 2009 +0000 Adding rabbit and wallaby oryCun2 and macEug1 commit 60931ee85e26241b6864e5eb63b548db313b8e0a Author: kuhn Date: Fri Sep 25 20:40:04 2009 +0000 set vertChainNet track to go beyond dev and turned on four tracks for default commit c8d8909ec660829559cbd7155a14efa70588e3be Author: hiram Date: Fri Sep 25 20:39:22 2009 +0000 Adding Wallaby Macropus eugenii commit 7ed754a72817de493f98aeb53684a46f91b4b6e0 Author: kuhn Date: Fri Sep 25 20:39:01 2009 +0000 set hg18 chainnets to o_db commit 82b693bf4da84591dbbda02a2b551a8ce6887346 Author: tdreszer Date: Fri Sep 25 19:40:59 2009 +0000 Oops. Turned off some Yale RNAseq tracks commit 9371c460fc4677c8257dede086260ee53bb89c0b Author: galt Date: Fri Sep 25 19:23:05 2009 +0000 allowing renames commit 8cf847aa0e03d7ab2650473237fd2ccb5eab4aa0 Author: tdreszer Date: Fri Sep 25 19:12:40 2009 +0000 Added 5 Yale RNA-seq tracks commit 46bbe3333d062f8c7e8ad3c5e029b1ebb9570935 Author: kent Date: Fri Sep 25 18:55:00 2009 +0000 Reduced a warn to a verbose 2 since it was complaining about 'U' which is common these days. Also took out a system call to speed it up about 2x. commit c631b640e8dc90950b989179041b860c246eb207 Author: hiram Date: Fri Sep 25 18:43:18 2009 +0000 Adding Baboon Papio hamadryas hamadryas commit 2fc5261ee1570f01c11b450252618c6a29847f00 Author: hiram Date: Fri Sep 25 18:39:25 2009 +0000 Adding Baboon papHam1 commit 186dffd6a3a34fbbbeaef5793456cbe35991b3bf Author: kent Date: Fri Sep 25 18:37:59 2009 +0000 Simplified code. Reduced run time from 5 hours to 20 minutes. commit 1804359dc174cea06cc384bbf48f5a4a9ee1c80d Author: aamp Date: Fri Sep 25 18:26:16 2009 +0000 Fixed the problem with the missing Affy Exon data from known genes. The problem stems from the removal of the requirement to have a lookup table in the Gene Sorter. In this case, that table would have been called "knownToKnown" but is simply "null" in the columnDb.ra commit f87790aeafa25d343ad85110eae206205c589667 Author: ann Date: Fri Sep 25 18:22:35 2009 +0000 added chain vars for all orgs commit 39c32a12ba0f0d08a43849f0d7b15b8aa7ce93b9 Author: angie Date: Fri Sep 25 17:48:07 2009 +0000 Adding uptime command after error/warning messages so we can see whether load is high. commit d37b568e12dc279218ab75164d27b1b3b9e81f20 Author: braney Date: Fri Sep 25 17:25:11 2009 +0000 reload wiggles for Hannon lab commit e7c8db7775119cf07226f74afb5ab66fc9d94f85 Author: hiram Date: Fri Sep 25 16:57:31 2009 +0000 Using hTableOrSplitExists() instead of just hTableExists() to get composite tracks to properly work with split tables commit e096d53bb527c3276258f1da6d4057ef36441a73 Author: kuhn Date: Fri Sep 25 15:39:38 2009 +0000 fixed the way GENBANK list is used commit 53e4a974884afc9aa55c5ab61a93f76c513e4807 Author: galt Date: Fri Sep 25 15:00:07 2009 +0000 "Encode release log update" commit 2b68b4a0b78225ba3d81ef76a5fc017f49925bae Author: galt Date: Fri Sep 25 15:00:04 2009 +0000 "Release log update" commit c54318d33375a3675e108714099f708cb9a750ce Author: kent Date: Fri Sep 25 08:52:45 2009 +0000 Sped up 10 or 20x by using a hash table instead of repeated sql queries. commit 33e20bcca028b56a4d178a719e01c5c9bf8a382f Author: kuhn Date: Fri Sep 25 04:08:51 2009 +0000 added some parameters for zfish chain commit 231dfcf692fa458554876e74690c2886aadd6c7b Author: angie Date: Fri Sep 25 02:22:00 2009 +0000 Move aside tmp output after failure; keep a lastLog file with most recent successful log. commit 59b442d33807e5fe315f7e889b82dcc7837403a6 Author: kuhn Date: Fri Sep 25 02:03:42 2009 +0000 added chainnet priority overrides for separate chainnetGalGal3 tracks commit c83e3d113787dc551f780c424f5232859f5b328e Author: kuhn Date: Fri Sep 25 01:31:42 2009 +0000 changed name of chainnets for monDom4 to o_db commit d537b30a0d89fb653c028709166a9a74b93f686b Author: kuhn Date: Fri Sep 25 01:29:15 2009 +0000 reduced size of block for guinea pig chains by using override commit 03fbffa0b01848af151f2836551de1a6b2d62781 Author: angie Date: Fri Sep 25 00:34:31 2009 +0000 Adding refreshSessionCtFiles*csh which have been living in ~qateam/bin/scripts, and souped them up to use tmp file names based on hour, and to watch out for signs of multiple refresh jobs happening at once. makeExclusionList.pl now accepts doNotRmFile as an arg instead of hardcoding it. commit f72129aa5f7ca407d509104160008a75fc9b5bdb Author: galt Date: Fri Sep 25 00:21:40 2009 +0000 close all extra descriptors to fix fork for mysql5 client commit d190530964ec2ece753ada62fc9c5be6f0d91dfb Author: galt Date: Fri Sep 25 00:20:20 2009 +0000 adding missing https commit c063a9f7f18c7df81c0deb46a6f54feeca2f30a9 Author: pauline Date: Thu Sep 24 23:29:23 2009 +0000 Fixed broken link, typo and ref commit b5fc48ccd20ab1bebc4da3423ceed2c9accab49a Author: hiram Date: Thu Sep 24 23:15:47 2009 +0000 Settle on a single function to determine chainNormScoreDb() commit 7bacc3ba5e707c831a8975408be622c66bad9220 Author: hiram Date: Thu Sep 24 23:05:10 2009 +0000 Eliminate use of chainDbNormScoreAvailable() function and use the trackDb variable instead commit c990b8c4b950bd9938398878d477f043d73fa6f2 Author: hiram Date: Thu Sep 24 23:00:47 2009 +0000 Eliminate the call to chainDbNormScoreAvailable() and instead use the trackDb variable commit fd55fcad2fa74a85ea332a8c07fe18d294370b6a Author: hiram Date: Thu Sep 24 22:52:13 2009 +0000 Properly release lable the ornAna1 chain and net composite and separate tracks commit 00473a7aef021a5368b810b056966bbaf3122b0c Author: tdreszer Date: Thu Sep 24 22:27:04 2009 +0000 Added wgEncodeGencode V3 tables commit 099c1c3d458d220c8f5ab942edfceb8b10287f5f Author: tdreszer Date: Thu Sep 24 22:25:17 2009 +0000 autocreated custom trackNames now exclude all special chars and append a uniquifier number commit 1cec6fc5c84d0957c659a126793cd7f152368fb8 Author: tdreszer Date: Thu Sep 24 22:21:42 2009 +0000 Added eraseNonAlphaNum() commit 2953e5f40d1d6e0bcb5c8fd0c95608f04728289f Author: tdreszer Date: Thu Sep 24 22:15:27 2009 +0000 Removed a define dependency commit 51cd749e41dc88894b82916b7796a0cb90d0cdff Author: tdreszer Date: Thu Sep 24 22:14:37 2009 +0000 Bug in imageV2 found by Ann a week ago commit 74aec566e1420332f15bee8d6ccd46a3c1b34daa Author: tdreszer Date: Thu Sep 24 22:13:13 2009 +0000 Cleanup recommended by Angie a week ago. commit 23180fb466aeb78545bdedac90e2c4ac25487dc8 Author: hiram Date: Thu Sep 24 22:06:20 2009 +0000 Finish lastz oryLat2 <-> danRer6 commit 6547b61e0c253ac6bfdb088b04e3388e5901fa4d Author: braney Date: Thu Sep 24 21:27:50 2009 +0000 a program to convert a tagAlign file into a bed12 with a couple of sequences commit c5970fdd14a4a2f8005364a92fb022c28fd12200 Author: braney Date: Thu Sep 24 21:27:43 2009 +0000 a program to convert a pairedTag file into a bed12 with a couple of sequences commit 38e54d2c8393f65ecce18ac22d487e7fcf7d818a Author: braney Date: Thu Sep 24 21:26:52 2009 +0000 bed12 plus a couple of sequences at the end commit ee94305abf793b9409346e869e8bf3b4c457749a Author: braney Date: Thu Sep 24 21:26:17 2009 +0000 a header file for bed12 plus a pair of sequences commit 3a8fa4eba9a2353b6229127bfee5396fcfceaf0b Author: braney Date: Thu Sep 24 21:22:42 2009 +0000 add a few files to the library (yay! it's even bigger now ;-) commit 16155535e258e83ec8ce86feb697b447ab77805f Author: holmes Date: Thu Sep 24 21:16:35 2009 +0000 adding description to cdd commit bc6e7dc9d95eddeccef4f57c610ca416ef6bb777 Author: hiram Date: Thu Sep 24 21:10:38 2009 +0000 add automatic generation of upstream files to genbank conf, and danRer6 swap lastz running and tetNig2 lastz done commit f7b1e2889df2143204d4bb16d5f0baa9c9125fc5 Author: holmes Date: Thu Sep 24 21:01:21 2009 +0000 adding cddDesc.o commit 220ef44cace9b1004ac40d774cfa09c4ae62acb8 Author: hiram Date: Thu Sep 24 21:01:01 2009 +0000 add automatic generation of upstream files to genbank configuration commit c40578e40a059b373c2163c1a74526d22b667a91 Author: hiram Date: Thu Sep 24 20:59:16 2009 +0000 Finish off repeat tracks, lastz run with hg19 commit 59389ac4d831e388d9a7f805d72e756cf23a2cbc Author: hiram Date: Thu Sep 24 20:57:52 2009 +0000 Working on the 46way conservation, oryCun2 lastz chain net cavPor3 synNet and reload cavPor3 extra large chain tables commit 63fd4e5d66c14e5b16b4e644cd16fe41f7db0683 Author: holmes Date: Thu Sep 24 20:57:09 2009 +0000 adding cdd description table commit 63a20f106ad1a9184e025e81421375dea0289f82 Author: hiram Date: Thu Sep 24 20:55:31 2009 +0000 Finish tetNig2 chain/net commit 81ca4d29ae87b9077234233b0543e136c65e3d40 Author: hiram Date: Thu Sep 24 20:54:50 2009 +0000 Reset default position commit 9cab5d5b42e70bb0ca8b67a2614811e8af98ef1f Author: hiram Date: Thu Sep 24 20:54:24 2009 +0000 Tried to get the sanger genes up, not complete commit c56e4ac7dbf6be918eb0196ad12d157a948b5aff Author: tdreszer Date: Thu Sep 24 20:51:45 2009 +0000 Fixed some colors and converted H1_ES to H1-hESC for clarity commit 86be5bfd242e40b8a46a8372055fc265d17e75ea Author: kent Date: Thu Sep 24 20:07:38 2009 +0000 Making wigToBigWig creation check for overlaps in sections for a better error message rather than the internal error message. commit 7cecaa36e927df794001ae45fb4d84a98dcb51bb Author: tdreszer Date: Thu Sep 24 20:03:40 2009 +0000 Changing H1 ES or H1_ES to H1-hESC for clarity commit 80fa6770b962653bfc454c341ab9c91c9865f09d Author: rhead Date: Thu Sep 24 19:28:32 2009 +0000 Added speciesCodonDefault to multiz9way entry. commit 0664a2ca30cedb555ad05a8d8f33fbee653ae7ec Author: ann Date: Thu Sep 24 19:27:39 2009 +0000 added overrides for chain/net monDom4/5 commit 1a70fce811b33ab0e16a93932a94aadf95885571 Author: ann Date: Thu Sep 24 19:26:46 2009 +0000 added details about mm9 chain commit 4a2a74e3363e477dfcb1fb570b51ce93af3d4467 Author: pauline Date: Thu Sep 24 18:25:08 2009 +0000 Added upcoming tracks to list. commit 82a883c4da0925f8c871520a19e29c27d66c2cf4 Author: tdreszer Date: Thu Sep 24 18:06:02 2009 +0000 Three new experiments for YDH-Peggy Farnham commit 6ea5c61c376c27b73ba5c57b35142545e64f447a Author: tdreszer Date: Thu Sep 24 17:45:08 2009 +0000 UW Exon Affy submissions added commit d81d698591c9f78e00e4a472a2b294f8b24575d7 Author: braney Date: Thu Sep 24 17:18:34 2009 +0000 Hannon lab short rna edits commit 37b4df027959547c20d6e6284b246635459527e2 Author: ann Date: Thu Sep 24 17:10:10 2009 +0000 Brooke and Bob want it to be opposite of the Conservation line-up (which I think is incorrect:-) commit c7d2ae407b98a90846835d40612bcea2a6a6f23f Author: angie Date: Thu Sep 24 17:07:44 2009 +0000 Initialize orgForm.clade to empty string instead of NULL (oops!) which causes segfault on solaris. orgForm.clade is overwritten w/selected value when mainForm select is changed, and ignored if genome or db is changed, so initializing to stub value is fine. commit 474bcf71ea0760074fbf759ebec2bc86c3b5c769 Author: fanhsu Date: Thu Sep 24 16:51:44 2009 +0000 Fixed a bug that was hidden for years. commit ccc9604b07ab89d129a4618edfd45589b748f768 Author: holmes Date: Thu Sep 24 16:44:25 2009 +0000 Moved functions to loweutils.c commit 69f7faceae3275783e99fb827744e62f9c84b5a0 Author: kuhn Date: Thu Sep 24 16:27:51 2009 +0000 moved monDom4 chainnet blocks from priority.ra to trackDb.ra and changed shortLabel to o_db commit 423fadccd867b9b54f0542eabf054a1ede293566 Author: holmes Date: Thu Sep 24 16:08:47 2009 +0000 Adding loweutils.o commit 47f665efb73c295dd623b26bd0c7ae8ca236b52f Author: fanhsu Date: Thu Sep 24 16:07:58 2009 +0000 Corrected an early termination bug for AA Anomalies track. commit e9b044335413a106b252bfd8cd03a91b915f273d Author: galt Date: Thu Sep 24 15:00:06 2009 +0000 "Encode release log update" commit 88d7e8000b1d001792c3dd211ce811f54f65c608 Author: galt Date: Thu Sep 24 15:00:03 2009 +0000 "Release log update" commit 0c78820cd48aa88843aaf631335702fe524c53cb Author: angie Date: Thu Sep 24 04:33:50 2009 +0000 Added bamGetQueryQuals for displaying sequence quality scores. commit 4d37118ee98711794abb8b5af9e2b4c2bd691c80 Author: kent Date: Thu Sep 24 03:34:20 2009 +0000 Fixing problem with bptTraverse on larger data sets. Causes problems in bigWig on scaffolded assemblies. commit e78ef24eab7f5c810ae8af9ad2c4c2376a1e58e4 Author: rhead Date: Thu Sep 24 02:11:01 2009 +0000 Removed extra parenthesis. commit e63ab1124561851501f13bf514ab1d0e08bf69c5 Author: rhead Date: Thu Sep 24 02:04:32 2009 +0000 Edits to About section. commit c873bd02a3f0977c5489288a29eabbdc0ce73dd9 Author: kate Date: Thu Sep 24 01:29:32 2009 +0000 Update dataVersion from Fall to Sep 2009 commit 0ffb59b39fe7c1cbfadff2163954451095e22446 Author: kate Date: Thu Sep 24 01:24:57 2009 +0000 Add news item commit 66fa105841b826cf8475e81e93bbac903f0d1541 Author: kate Date: Thu Sep 24 00:57:44 2009 +0000 Add missing logo, fix a kentian path commit 883a12f2639bb9d6e02e5e61d280382af19723a7 Author: tdreszer Date: Thu Sep 24 00:26:23 2009 +0000 Fixed matrix CB normalize to do it's best for dimension Z commit ce7ff32983dfc6eb8dddefb0a0fcc6b1abd4192f Author: braney Date: Thu Sep 24 00:21:46 2009 +0000 shortened and editing some labels for Affy/CSHL exons commit e7b10d64efc59af020457b00b7f15c1de19d8a6f Author: galt Date: Thu Sep 24 00:21:13 2009 +0000 fixing dates to include year commit b283356ac97687741db302fd520411860022a46e Author: kate Date: Thu Sep 24 00:01:26 2009 +0000 Rename freeze commit 833e0ae6105237c1e23faa05014614addc1f3227 Author: angie Date: Wed Sep 23 23:50:30 2009 +0000 Added bamShowFlagsEnglish to explain the flag bits. commit 1f3477880e7098d446860fc98329331128fbce96 Author: braney Date: Wed Sep 23 23:49:28 2009 +0000 new Hannon lab short RNA data commit 151f5be5c0c10b0d989b339a042cd042a1df438c Author: tdreszer Date: Wed Sep 23 22:39:30 2009 +0000 Tracy and Tim have been straightening out UW commit 0fe546ccfbb210724481215ed90a830d0514a759 Author: holmes Date: Wed Sep 23 21:48:55 2009 +0000 moving core functions to lib commit 195cc7dbe02da920d76d3e9b14594c42a018d3f3 Author: ann Date: Wed Sep 23 18:50:09 2009 +0000 ordered chain/net tracks wrt the opossum and each-other. commit 77fd0e3685598a0e467204917bf67d45a8c5dbd9 Author: angie Date: Wed Sep 23 18:42:30 2009 +0000 Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args. commit b72aeb274e349305e4676224a245de6f220e8163 Author: braney Date: Wed Sep 23 18:27:10 2009 +0000 drop all the old Hannon lab stuff so I can start over commit 5856b131a9a5b5afe2dfeefabb569225b57f4a75 Author: ann Date: Wed Sep 23 18:07:56 2009 +0000 added call for new getChainLines script commit a6f32323ccc165fd3b9f87d5df3513facf35721f Author: ann Date: Wed Sep 23 18:01:57 2009 +0000 we do not need the dollar-sign before the variable commit bbb2b436044f8c5f8ea8080dd07f34be48aa31b6 Author: ann Date: Wed Sep 23 17:56:40 2009 +0000 new getChainLines script commit df12c75404f837ae0d1caf0076443791b94aa0fb Author: ann Date: Wed Sep 23 17:55:29 2009 +0000 this script gets the two variables needed for the chain description page ($chainMinScore and $chainLinearGap). similar to the getMatrixLines script which gets the $matrix variable commit 96b75842b62ff54f23290e6bf45ac692e5d2d16c Author: fanhsu Date: Wed Sep 23 17:18:22 2009 +0000 Updated to be the same as last checked in for ART release. commit bb1d7319d180db86a9fd4d83c3f65d015521cd33 Author: hiram Date: Wed Sep 23 17:10:15 2009 +0000 Fixup compile error due to incorrect type from sizeof() in a printf format commit 479bba57a6f9f5b2f8854c5d19837ff292888d6b Author: fanhsu Date: Wed Sep 23 17:04:09 2009 +0000 Turn off sorting for dnaSeqs and aaSeqs. commit ad657766a06acb5c01924473659c242d981f8540 Author: kuhn Date: Wed Sep 23 16:29:02 2009 +0000 changed name of old possum chains to o_db commit fae07dc26553fdaab7f5be3ce333773cab4e1b2a Author: kuhn Date: Wed Sep 23 16:17:27 2009 +0000 moved override block with others commit bfb74aa2fee23b1fa7ff0866e458e7942106974f Author: markd Date: Wed Sep 23 16:08:03 2009 +0000 removed rn5 commit c2ae85b7b7daca75630fed69dab7f13aab3c6cfd Author: galt Date: Wed Sep 23 15:00:07 2009 +0000 "Encode release log update" commit 9857d9fca598fba32b9f642888ca9a71f590a549 Author: galt Date: Wed Sep 23 15:00:04 2009 +0000 "Release log update" commit b146579c47dc327a14714bb160277ac5ac12787c Author: kuhn Date: Wed Sep 23 13:43:59 2009 +0000 added matrix for possum chain commit ed3d4346c3ac8b471ed7e692e6f1620c7b11d761 Author: tdreszer Date: Wed Sep 23 03:58:11 2009 +0000 Tracy Ballinger added new UW Dnase-seq and UW ChIPseq tracks commit 8d8aeaa10d0943fc55813b3919f5fe39bd7f07e1 Author: kuhn Date: Wed Sep 23 02:39:31 2009 +0000 added matrix to possum.chainPonAbe2 track commit 09e38fe0571f02c2e74403171885a3fb94dad951 Author: kuhn Date: Tue Sep 22 23:13:21 2009 +0000 moved override to bottom of track block commit 33c3876ab352cc75dc731a875cf942275f6e6117 Author: kuhn Date: Tue Sep 22 23:01:45 2009 +0000 moved chimp chainnets next to orang commit 7c7341315e8df091391d0bbeb94ba116e7453a87 Author: braney Date: Tue Sep 22 21:49:43 2009 +0000 make barb colors be the same color as the line and box. commit 1cde9b2b86e9fdfafaeaed24668a76d41b2615b7 Author: galt Date: Tue Sep 22 21:03:58 2009 +0000 adding SOCKETLIB back, apparently needed for solaris and other stuff (this is not SSL related) commit 6872e702a4b42f29fc00354b88d084006d870d42 Author: tdreszer Date: Tue Sep 22 20:53:54 2009 +0000 Broad DAFs need to be checked in and need to use dafVersion 1.1 commit 12e67463fa05d4f6929e043f7d0fc0c5737aa69b Author: galt Date: Tue Sep 22 20:01:30 2009 +0000 fixing makefiles; getting rid of unnecessary $SOCKETLIB, adding $DESTDIR and removing an unneeded space-char commit 19e0b2ef9f0650821a21805d4a2ea9c556d3ccbe Author: tdreszer Date: Tue Sep 22 19:44:00 2009 +0000 DukeUNC/UT needs base overlap signal commit b2a4734792f91969a81dd2f9051055bc6a7ea182 Author: galt Date: Tue Sep 22 19:43:29 2009 +0000 adding DESTDIR commit 2e90db519b0651551402cd8ea8526552de0c4644 Author: galt Date: Tue Sep 22 19:39:49 2009 +0000 oops fixed path problem commit aab1e7f2ce7e7c44620194aae7067886cfc498c7 Author: galt Date: Tue Sep 22 19:38:57 2009 +0000 happy fiction that preview is really on next branch already commit 4e132b364334cd7f29609b7fa50f5ba4efcfdbf3 Author: tdreszer Date: Tue Sep 22 19:13:03 2009 +0000 Duke/UNC/UT should be using dafVersion 1.1 now. commit 5d9d88e6708f22be87e2f21e6b605092d4a04590 Author: tdreszer Date: Tue Sep 22 19:11:36 2009 +0000 Yale signal is bedGraph commit a200a2d7f88b3d2deb391ea7b0c34c519e801e2b Author: tdreszer Date: Tue Sep 22 19:03:20 2009 +0000 UW should provide replicates for peaks to be consistent commit 23a29aeae290c1c6cc287018170203d1c3022e78 Author: ann Date: Tue Sep 22 18:46:18 2009 +0000 fixed typo commit 8d8d50f6b856900fe2995c0028ec1e84d6e30872 Author: kuhn Date: Tue Sep 22 16:07:07 2009 +0000 changed netMonDom4 shortLabel to say Net, not Chain commit 78d87d0b9d01d952c1a27735ecc73ad41fc962ca Author: braney Date: Tue Sep 22 15:38:17 2009 +0000 move Gis Pet to variation commit 3773e7808e87b278c0458fb540f8b84964737261 Author: galt Date: Tue Sep 22 15:00:06 2009 +0000 "Encode release log update" commit 04287d6ba45ca25db5c0363ec53dacd3fba15f7a Author: galt Date: Tue Sep 22 15:00:03 2009 +0000 "Release log update" commit 02b4ab2b37389c93b3210f07e4656b9cee91e50b Author: kuhn Date: Tue Sep 22 14:52:04 2009 +0000 tweak to usage commit 23ff8fee9d0d91254e3c4f986cec7bb81c190429 Author: galt Date: Tue Sep 22 03:43:38 2009 +0000 making it a little more friendly commit 797db6163d6139d33b7634ee4545110522368d4b Author: galt Date: Tue Sep 22 03:00:12 2009 +0000 v216 preview commit 845b5d2b6d9cbc621fdc852ff143f56a6e369349 Author: galt Date: Tue Sep 22 02:46:59 2009 +0000 fixing so old gets deleted before copying new to hgdownload commit a38dd76c06dc9ef0b8e3d596fd7d0f579ac08521 Author: galt Date: Tue Sep 22 01:53:06 2009 +0000 fixing more mysql 5 dump problems due to not being line-oriented commit 0cca7f51e83279a0695c48a2275f566f322cfb41 Author: tdreszer Date: Tue Sep 22 00:12:34 2009 +0000 New order of the day. DAFs must have dafVersion 1.1 commit 9667928bb1f2c612f019dc7b523d6f9beca18802 Author: braney Date: Mon Sep 21 23:50:42 2009 +0000 fix memory trashing bug that's been here for ages. Thanks Brooke! commit 8f4284ba5a2c4f57ad1c030dd3626da9d2e0b8a7 Author: ann Date: Mon Sep 21 23:35:17 2009 +0000 small tweak to list commit f95ef385fff3117db1aa263ad040f7576558ac97 Author: ann Date: Mon Sep 21 23:34:59 2009 +0000 fixing up the citations commit 9807138ce2441267b9d8dc48a1c5cdb888d0b09d Author: kuhn Date: Mon Sep 21 22:47:59 2009 +0000 changed short label to o_db for hg18 chainnets commit 06f3741b9fa93f6004e39979828e26ecde7deb9e Author: aamp Date: Mon Sep 21 22:31:32 2009 +0000 phastConsElements html was missing. Using the top-level html. commit 4b7e4d4dc70bbc12b60313ea67bece2234bf2742 Author: kuhn Date: Mon Sep 21 21:29:03 2009 +0000 removing comment about possum release alpha commit 4c5d2a3a24e575cd931fa0d7de39cb37c5aa699a Author: kuhn Date: Mon Sep 21 21:28:22 2009 +0000 combined priority.ra into trackDb.ra commit 97283177346b3f8ff9e39d90e33b37da15fbc73b Author: hiram Date: Mon Sep 21 20:26:39 2009 +0000 Turned on updates for genbank commit ad2a18dee492e8998c324e795b57f6899d701611 Author: hiram Date: Mon Sep 21 20:25:56 2009 +0000 Added caeJap2 - C. japonica commit 176951a4a6024019eea2a6c82e293957cb1990bf Author: tdreszer Date: Mon Sep 21 18:41:03 2009 +0000 New order of the day. DAFs must have dafVersion 1.1 commit 69ecbc088de9d1d66602fbe1d389be1c27cb63ec Author: tdreszer Date: Mon Sep 21 18:39:58 2009 +0000 view RawSignal commit 7e631bf78c34c56b7c8394e4278943fdcfcb05e6 Author: tdreszer Date: Mon Sep 21 18:19:01 2009 +0000 New order of the day. DAFs must have dafVersion 1.1 commit c0f537a2ebc19f2dd309c0ab5218c7515aa82be8 Author: ann Date: Mon Sep 21 17:33:27 2009 +0000 updated MySQL version number (thanks Jen!) commit 10a8d7081e093931881490e50254e7aaf3a1a886 Author: kuhn Date: Mon Sep 21 15:22:27 2009 +0000 reversed change to create_time and added GENBANK filter to grep to properly eliminate genbank tables commit e01e6152b5ce53362fbc1d7206410f195e726c54 Author: galt Date: Mon Sep 21 15:00:06 2009 +0000 "Encode release log update" commit 5752361ef26989668f0d65a275ccaea8739f3cf1 Author: galt Date: Mon Sep 21 15:00:03 2009 +0000 "Release log update" commit ae94d70befe8a1882b0c206e5e8aeb79368e3101 Author: cszeto Date: Mon Sep 21 05:24:00 2009 +0000 New datasets commit cff0060c4723a7f241f9569931441c309e35cfe2 Author: fanhsu Date: Mon Sep 21 03:59:58 2009 +0000 Fixed the base 0 problem for REST track. commit c3416579a641048389db07dc3e7a8f0267fa1d7c Author: pchan Date: Sun Sep 20 23:46:23 2009 +0000 check existence of scaffolds table for metagenome blastx track commit 535c97ed292325baa12cd28a19df9e787f698e46 Author: kuhn Date: Sun Sep 20 18:40:35 2009 +0000 adjusted to use create_time instead of update_time to eliminate genbank from output commit 617051c17a23b1b30e2d076347e799f7fa3fe5f1 Author: kuhn Date: Sun Sep 20 18:32:09 2009 +0000 fixed to deal with MySQL 5.0 status diff commit 7b87cc627d0b883efaf1ddb7214071b3be1292d2 Author: markd Date: Sun Sep 20 17:24:35 2009 +0000 updated transMap doc commit 2156e8077113a7501a36fa5fa47c8a7d3f96f806 Author: markd Date: Sun Sep 20 17:16:47 2009 +0000 transmap build commit 7144ef1c4e3b6089bd9bbd37f3568a00fb21e455 Author: galt Date: Sun Sep 20 15:00:07 2009 +0000 "Encode release log update" commit 32a25cb9da97073b7b65833c25d308ebdd604cf2 Author: galt Date: Sun Sep 20 15:00:04 2009 +0000 "Release log update" commit ae225567f4bc53f0637d4a1ea494c00d24794d60 Author: kuhn Date: Sat Sep 19 17:53:24 2009 +0000 restored org name to longLabel commit e8f0fbce98a70766dbe15ada84763e28c88a62b0 Author: kuhn Date: Sat Sep 19 17:52:42 2009 +0000 moved chimp priority.ra into trackDb.ra commit b7a2dc9b395e7fdd920fb1e2213f30b3c11e1e55 Author: galt Date: Sat Sep 19 15:00:06 2009 +0000 "Encode release log update" commit 5e1a2ae479aeeec068fc0796ca36d31f57ed28bc Author: galt Date: Sat Sep 19 15:00:04 2009 +0000 "Release log update" commit c0085591118d9fa39a5754eea3f3fdda25476d80 Author: tdreszer Date: Sat Sep 19 07:44:15 2009 +0000 Fix a bug when no 'validationSettings' are provided. commit 6d9e7accdd6e9f4dcb593a4ab8a815c8bd98b578 Author: kuhn Date: Sat Sep 19 01:50:36 2009 +0000 changed name to 0_db for hg18 chainnets commit 176b504a65a4f78bb33c95d7ca0f8a7558bdec02 Author: kuhn Date: Sat Sep 19 01:47:17 2009 +0000 fixed accidently breakage of 9way. had interrupted the block when moving nscan override commit 26c01c7ccf8543602344ac1e6a45b67c6371c948 Author: kuhn Date: Sat Sep 19 01:41:02 2009 +0000 moved override block to bottom of track section commit dc70a533d95830e721c45d32a5a45706b32c92a7 Author: kuhn Date: Sat Sep 19 01:35:35 2009 +0000 reordered chainnets (again - how do they keep getting messd up?) and set old monDom4s to o_db shortLabel commit 047e6366dc71ae70fd6b544c86d669fde864428d Author: kuhn Date: Sat Sep 19 00:51:50 2009 +0000 moved override blocks together commit 43b3b9e2d3b76840f558d6c0fad4d2a2e5232258 Author: rhead Date: Fri Sep 18 22:17:45 2009 +0000 Added documentation for new alwaysZero feature Brian added. commit 62e3f2b8d12d64469f5042f80fab7981db59fabf Author: hiram Date: Fri Sep 18 22:15:32 2009 +0000 Completed tetNig2 chains and nets to everything commit fdcf528f8a9da58b27f2c7d8e12799abfda3c3de Author: ann Date: Fri Sep 18 22:13:42 2009 +0000 cleaning up lots of loose references commit 132d8e92fe63b30be2b70242efd14499b860ce7d Author: hiram Date: Fri Sep 18 21:57:39 2009 +0000 Updating chainNet composite tracks for tetNig2, fr2, oryLat2, danRer6, hg19, mm9 commit b883b9c5ad34f5bf0bb7c21929fe7d8a6d2111fa Author: ann Date: Fri Sep 18 21:21:11 2009 +0000 adding some links commit 503e9b70d4a04a96f46323b075023468668b2d7e Author: jsanborn Date: Fri Sep 18 21:19:00 2009 +0000 changed color scaling (expScale) for a few datasets commit 1b03e2b794766b3f985a62a1921e47c2e2298516 Author: ann Date: Fri Sep 18 21:18:48 2009 +0000 just cutting the lines to 80 chars (no changes) commit e907024aee22a6e926fbe53c39b5b1c7c3a9abc8 Author: fanhsu Date: Fri Sep 18 21:11:24 2009 +0000 Renamed into rest.html. commit 5e06312358476823fd05fe3af3fefeed9d332460 Author: ann Date: Fri Sep 18 21:09:04 2009 +0000 added mm9.rest to tablesIgnored commit 2c55c2ff8c5fd7acbffa2a523c7a6480d4f2e719 Author: fanhsu Date: Fri Sep 18 21:05:36 2009 +0000 Renamed REST.html into rest.html. commit e691cd8c9bd59a206acfaba1608399b9445cac68 Author: fanhsu Date: Fri Sep 18 20:55:31 2009 +0000 Changed REST into rest. commit 06b8d8d07a317e93721229779c5e1e36c8ecb4de Author: fanhsu Date: Fri Sep 18 20:53:09 2009 +0000 Changed REST to rest. commit c7929c22b51183933643083b846118f07de5e0c0 Author: ann Date: Fri Sep 18 20:52:59 2009 +0000 shortened l-o-n-g lable commit b9884b8d76cb271d702a2b9832ca328d3e1ed876 Author: braney Date: Fri Sep 18 20:05:16 2009 +0000 allow alwaysZero to be set in trackDb, set to off by default commit 8163f55f79c591f76a65af73061f641da224ac27 Author: kuhn Date: Fri Sep 18 18:50:30 2009 +0000 moved priority.ra content into trackDb.ra as overrides commit 5cb5a9b583626548b27b0004ee8326ceab6ff8e3 Author: kuhn Date: Fri Sep 18 18:29:49 2009 +0000 restoring Human to longLabel on hg18 chain/net tracks commit 3e6c4ee03fa1026c2b5d6bc4cd9290ccb96e15d1 Author: kuhn Date: Fri Sep 18 18:23:52 2009 +0000 restoring Human to longLabel on hg18 chain/net tracks commit bd35f197e60c93f2c2d50e0c2d141a999f9d7f36 Author: kuhn Date: Fri Sep 18 18:17:02 2009 +0000 restoring Human to longLabel on hg18 chain/net tracks commit 88c12fc693c4a36ff6210fb6dc82787b06b3282d Author: braney Date: Fri Sep 18 15:23:40 2009 +0000 add wiggles for CSHL long rna tagAligns commit 81410b71ee24c47cb3d40c0cbf27c99baadfd990 Author: galt Date: Fri Sep 18 15:00:06 2009 +0000 "Encode release log update" commit 44e4eaec7c6b3cb0737ee8d63a6fd670e03a2223 Author: galt Date: Fri Sep 18 15:00:03 2009 +0000 "Release log update" commit 711d2c85542d50a17e1d927014fdd855485fd4d4 Author: markd Date: Fri Sep 18 04:11:43 2009 +0000 added ignore item commit f924ec23f0664eb60a0eb9ea65bde1e71c8b3348 Author: rhead Date: Thu Sep 17 23:09:46 2009 +0000 Added a line describing the Always include zero function that Brian added. commit b493c1aa1a0860f900c7e1e983df2383c95229d1 Author: rhead Date: Thu Sep 17 22:05:17 2009 +0000 Wording tweak to previous change. commit 000e412c53cef013b5275313139cc86d33a5009e Author: hiram Date: Thu Sep 17 21:43:24 2009 +0000 Special link for hg18 ncbi build36 commit f4b33c2a90af8b0e496bf84d872ce82331d3c90c Author: hiram Date: Thu Sep 17 21:43:03 2009 +0000 Special Ensembl link for hg18 ncbi build36 commit 533dba5cbbb0b31d0209112cca7cea07c964c962 Author: tdreszer Date: Thu Sep 17 21:36:52 2009 +0000 Changed antibody TCF4 to TCF7L2 commit 2b3f29ddcec4879a5a22d302a5b46bd58e0349b2 Author: tdreszer Date: Thu Sep 17 21:33:54 2009 +0000 Changed antibody TCF4 to TC7L2 commit ed52a673c88dc37b93f9b00aa2e62f58c126ae06 Author: hiram Date: Thu Sep 17 21:31:46 2009 +0000 Proper NCBI blue bar links for hg18 and hg19 commit f08a0a2db21b1fa8b670f3bf69de74112c564b0d Author: hiram Date: Thu Sep 17 21:25:09 2009 +0000 Properly free the second subChain commit 8529474dd82da06c68f5e3c5b2353f9d21ccf982 Author: hiram Date: Thu Sep 17 21:16:20 2009 +0000 Fix up memory management in the remapRange loop commit 70054f72b6d96c82fc9344ee5af7628b84499a32 Author: fanhsu Date: Thu Sep 17 20:50:31 2009 +0000 Added missing item processing logic for text output. commit 4e3491c3f0cb010f98e1a79ffc44cdad9e3fea49 Author: rhead Date: Thu Sep 17 19:32:31 2009 +0000 Added a description of the new ideogram click or drag functionality (thanks, Tim). commit 88945fa7ad141506aca8b309fc8027c943ce7551 Author: kuhn Date: Thu Sep 17 18:57:28 2009 +0000 returned monDom4 shortLabel back to Opossum, because not pushing monDom5 chainnet set after all commit 640a6915ea79270b80332d99d870c8cebcd3af3a Author: kuhn Date: Thu Sep 17 18:55:58 2009 +0000 returned hg18 longLabel to Human commit 0259ffcc41ba7a26163c8f10cc1a5ee201e13f7a Author: fanhsu Date: Thu Sep 17 18:42:22 2009 +0000 Turn off all new cols except "ART Sequencing". commit 8d88fdd43b7a94fc92435094466de6d97205206b Author: fanhsu Date: Thu Sep 17 18:34:57 2009 +0000 Added logic to check NULL for string cols. commit 65d1c0452861ae6205253b3098fe09ebda4a1966 Author: kuhn Date: Thu Sep 17 18:05:53 2009 +0000 changed shortLabel for old monDom4 chainnets commit 2e90e1bbb807e9d3adccf07c664182a833e91b8e Author: kuhn Date: Thu Sep 17 18:03:51 2009 +0000 dropping release alpha for chainNetMonDom5 so it works on beta commit 3650bbe08f4138eebf96e06418f3d8656ab710ee Author: ann Date: Thu Sep 17 17:54:37 2009 +0000 adding info about bigWigInfo program commit 2447d95fa0f8b50e2470f78a94c4be5def1c66fd Author: ann Date: Thu Sep 17 17:49:31 2009 +0000 added info about new bedClip program commit 804b1d3e8de442a0c8d065f7a20623fc4698cc3e Author: hartera Date: Thu Sep 17 17:35:22 2009 +0000 Edited table name and order of RNA types. commit bb93458cd029fef2e1078af0d88981f0f2707d93 Author: hartera Date: Thu Sep 17 17:29:15 2009 +0000 Created description for the wgRna table for the sno/miRNA track. commit 12570e435ae1a8fbd50846f7c226f5f86987a3c8 Author: jsanborn Date: Thu Sep 17 17:28:37 2009 +0000 added maxItems 2000 to all entries commit adad724e35b5608e6b784fd11fa0a6abea3e83f3 Author: jsanborn Date: Thu Sep 17 17:25:10 2009 +0000 hopefully fixed this by removing CVS conflict lines that were accidentally committed commit 7822e58af95069b971be62e7a440706201225044 Author: ann Date: Thu Sep 17 17:15:44 2009 +0000 added bigWigInfo program to user apps list commit d8054bb0db54f9e4417d1560e33dfff178cbebe8 Author: tdreszer Date: Thu Sep 17 17:14:13 2009 +0000 Oops. YaleRnaSeq no longer has view, but left the subGroup commit 3257e66f6cc1338323007e627ef960bac07117a7 Author: fanhsu Date: Thu Sep 17 17:12:43 2009 +0000 Changed "ESDI Basis" to string intead of integer. commit 35de333258485e416624722487e7be483b39a1a4 Author: fanhsu Date: Thu Sep 17 17:09:24 2009 +0000 Checked in a fix and additional logic to process "N/A". commit bae579f44fa8cfe62644f2c6520ee720651b3438 Author: fanhsu Date: Thu Sep 17 17:05:06 2009 +0000 Checked in ART related new fileds. commit 8b3d289c439e88744be30b312daa97d817ad3b04 Author: kuhn Date: Thu Sep 17 16:34:35 2009 +0000 converted dbChainNet trackNames to chainNetDb to match pattern we've been using commit 9bf2e535c77060035d2ed5c00f043cf02e505918 Author: kuhn Date: Thu Sep 17 16:23:58 2009 +0000 converted dbChainNet trackNames to chainNetDb to match pattern we've been using commit 3856124145962410df34fb570d5cd3ea522cfe6a Author: braney Date: Thu Sep 17 15:49:39 2009 +0000 new CSHL long rnaSeq commit 1e039b04ac8a768637628540d58f602d6024c46c Author: fanhsu Date: Thu Sep 17 15:25:37 2009 +0000 Re-edited the Display section of REST per data provider's request. commit e1499fd6078a9128e700d992600b719864832301 Author: galt Date: Thu Sep 17 15:00:07 2009 +0000 "Encode release log update" commit 5375846d60884fb7ed30f7c014dcba40ab5f70dd Author: galt Date: Thu Sep 17 15:00:03 2009 +0000 "Release log update" commit d897f19e1c47d4f5470339b8f5de68ff1fa78df7 Author: tdreszer Date: Wed Sep 16 23:26:42 2009 +0000 Removed a bunch of RawSignals from Broad and Yale commit d1ff118127011d0b177ee6d550623bac75857f62 Author: kate Date: Wed Sep 16 22:42:26 2009 +0000 Post-release tweak to defaults: more logical view ordering, suppress rep2 by default commit dadbf208234bc1b1035886dfb206c48d810faa76 Author: braney Date: Wed Sep 16 21:31:15 2009 +0000 5C to regulation, CSHL long RNA tables commit af5226788104052767fbf083f571e3477aec6734 Author: kuhn Date: Wed Sep 16 21:24:06 2009 +0000 fixed status dump to work proely for RR commit e96b820804da7f92a1935ca9580b1828137098e3 Author: kuhn Date: Wed Sep 16 21:15:40 2009 +0000 inproved usage and output commit ae6f12edaefe0857f649bde48aaa2df8dd5a9fc3 Author: kuhn Date: Wed Sep 16 21:12:07 2009 +0000 typo commit 3e842fa65a4583b2cdd19565ea219c2e7f32aa48 Author: kuhn Date: Wed Sep 16 21:09:55 2009 +0000 inproved usage and output commit a52e233d371b330d529df7a6840088e02b146753 Author: kuhn Date: Wed Sep 16 21:08:48 2009 +0000 added comment about what GENBANK variable is commit d07aa13783b69485d1e9fe83f9457339d744ac47 Author: aamp Date: Wed Sep 16 20:41:35 2009 +0000 5C test track. commit 8e18c45112ab7fd919811a6f95967cb2236b1f1c Author: kuhn Date: Wed Sep 16 20:29:54 2009 +0000 primate and mammal chain reordering, etc. reduced some influence of stay priority.ra files commit 1d45b83316749ccdd39ba6c303d9a45d71191b13 Author: tdreszer Date: Wed Sep 16 19:52:52 2009 +0000 One last change to make sure chromDrag off right end can still pick up selection commit c19f3a9d2cf3df223cca10eda10950e85457ff32 Author: fanhsu Date: Wed Sep 16 17:41:24 2009 +0000 Added color and altColor for REST. commit 195ce9a69d6d262d500d01b0aaa61394efdd3827 Author: fanhsu Date: Wed Sep 16 17:40:45 2009 +0000 Updated color logic for REST per Andy's suggestion. commit 8a7e475f061774be3cd221dd65b32b5b53bb0e70 Author: tdreszer Date: Wed Sep 16 17:34:00 2009 +0000 A bit more cleanup and make sure that after doing the chromDrag selection no more chromDrag code is called. commit e9b01f0e9308b776431296d3917a6b5e7b007cf4 Author: kuhn Date: Wed Sep 16 17:07:23 2009 +0000 moved priority overrides into trackDb.ra commit 6cadd394d4b1d668aeb81040c71bd19ffefcb777 Author: kuhn Date: Wed Sep 16 16:49:06 2009 +0000 moved override stuff to bottom of track blocks commit 195fa6e4d0c07eee99fd3dc4f0425e878522bdce Author: kuhn Date: Wed Sep 16 16:43:14 2009 +0000 moved override stuff to bottom of track blocks commit fdd2ca6da4fa96c10bbeee8034b700bc06177fb4 Author: fanhsu Date: Wed Sep 16 16:11:58 2009 +0000 Added REST track. commit a30b525cbcf63b62ea9ebf9bfc5166ebdf5014ba Author: fanhsu Date: Wed Sep 16 16:01:30 2009 +0000 Updated the Display section per data provider's request. commit 47b93cb139172cbbede04a24481a538ef1cc5890 Author: galt Date: Wed Sep 16 15:00:06 2009 +0000 "Encode release log update" commit 030042e4721ec339c48ddf00628f02feef20809f Author: galt Date: Wed Sep 16 15:00:03 2009 +0000 "Release log update" commit 7627ce1a0d5019c6644c2bf4b66c8432b2a1180e Author: tdreszer Date: Wed Sep 16 00:40:57 2009 +0000 Fixed... scrolling, reverse, cyto-band coordinates and cleaned up. commit 64ea11cf60e2e011bdc216f5b3a1921dc5c944d3 Author: kent Date: Wed Sep 16 00:39:48 2009 +0000 Far enough into rebuild should save the as ever slightly tweaked instructions. commit 93f4e6546c22c5b44a248074b6e05bc16dce94d2 Author: kuhn Date: Tue Sep 15 23:27:26 2009 +0000 moved override stuff to bottom of track blocks commit acd8453ce1a07f7d56fd39e2ae97c4ac1431fc03 Author: kuhn Date: Tue Sep 15 23:20:27 2009 +0000 moved override stuff to bottom of track blocks commit f81d414a2f0ce4bfb8d2317e683b460494ed601c Author: cszeto Date: Tue Sep 15 22:39:09 2009 +0000 New dataset commit 2c353ba05ada54fe0321fba22743fea374901225 Author: kent Date: Tue Sep 15 22:02:00 2009 +0000 Making sure that bigWig or bigBed file referred to in bigDataUrl actually exists. commit c1e60f7c7aeccfd521fbf0063404de7e426d007d Author: kayla Date: Tue Sep 15 21:20:51 2009 +0000 set visibility to hide for a track commit a0653479a0cb31d88aefa1247f882463a4d3e6bd Author: katrina Date: Tue Sep 15 19:00:22 2009 +0000 Change reference date from ePub info to print info commit c126ad0d0f1e48fcf585a820022e2344c52764e0 Author: kuhn Date: Tue Sep 15 18:52:50 2009 +0000 added the common name of the squirt commit e9ace40c0469fc9fe0a2f51fdab8b8d8d025e058 Author: katrina Date: Tue Sep 15 18:46:44 2009 +0000 Change reference date from ePub info to print info commit edff8a1f64ef64f5e1879dcd04039604707b28d9 Author: katrina Date: Tue Sep 15 18:37:49 2009 +0000 Change reference date from ePub info to print info commit 929785f71bf1e209023946896ef5c2a886a6c4e3 Author: galt Date: Tue Sep 15 15:00:08 2009 +0000 "Encode release log update" commit 4a08ea54522b92f442b7b6aa30d4aec4e058f20f Author: galt Date: Tue Sep 15 15:00:04 2009 +0000 "Release log update" commit 47d3a0579c44f2245adeb7e037be5e93f6f0e1af Author: galt Date: Tue Sep 15 09:36:56 2009 +0000 "New version number v215" commit 1a8666fbad213d3fa9aec198ec1b40292321b48d Author: galt Date: Tue Sep 15 09:35:57 2009 +0000 v215 final build commit 6365c1965d9c4818981486ab86718484cf2db718 Author: galt Date: Tue Sep 15 08:56:23 2009 +0000 fixing cvs-reports with correct by tag sandbox on fast local disk commit 06400d21cdd311e705fad18303dcae1ed0909d1c Author: galt Date: Tue Sep 15 08:55:25 2009 +0000 fixing cvs-reports with fast local disk commit 75ccac89d94fbd01000c11b4f3e9b108088392ff Author: markd Date: Tue Sep 15 06:59:00 2009 +0000 updated lsSnpPdb commit 65d56efd4e751490f019e96a01824d988e049037 Author: markd Date: Tue Sep 15 06:52:29 2009 +0000 added scripts for auto update lsSnpPdb commit 417c6835eefd1a0389caf3cc92e2fde24644cd08 Author: markd Date: Tue Sep 15 06:50:30 2009 +0000 allow loading from compressed files commit 18f8a60ae2ce82e8a564f9905877a717731a11c9 Author: tdreszer Date: Tue Sep 15 00:21:53 2009 +0000 Make the chrom image draggable. Note click gives new position, same window size. Ctrl- gives cytoBand. commit a98a0fcb5de6a6a567405f7e0e229aa524696900 Author: angie Date: Mon Sep 14 23:53:59 2009 +0000 Added chr21 to bamNA12878 -- remote access to 1000Genomes DCC using (for now) samtools' support for FTP. commit a62b9db66681d2ad666fde9d52c76b157f4936b3 Author: angie Date: Mon Sep 14 23:44:25 2009 +0000 Added bamFileNameFromTable to bamFile.h and changed bamFetch to take a filename, not db+table, so it can be used for CT files someday. bamFileNameFromTable supports an optional seqName column in the db table, for per-chrom BAM files (as we get from 1000Genomes). commit f478e18d90ae8b24ec34deaaacda9c30e0fdd97e Author: galt Date: Mon Sep 14 21:30:12 2009 +0000 adding bedClip to user utils commit 07c1cd1456a009ae229cdf8fc7306be0fca4f302 Author: markd Date: Mon Sep 14 20:33:13 2009 +0000 added function to get list of profile names for Fan commit 63e9750853fbfe646b209aad9444dd8fe131c888 Author: kuhn Date: Mon Sep 14 19:35:01 2009 +0000 added a hyphen in All-Exon Array longLabels for UW tracks commit 4e16c3f88ce617caef0923683cf7226d970ce1fb Author: tdreszer Date: Mon Sep 14 18:40:44 2009 +0000 Added 10 resubmissions and 1 new submission for Duke,UNC,UTA commit ff24eb77b94a9af9e65d9068fbb5540a96a12008 Author: kent Date: Mon Sep 14 18:16:26 2009 +0000 Backing out a change I didn't mean to commit. commit 6eb93a1295458583fe12d61d4e119d2e1ce08e78 Author: kent Date: Mon Sep 14 18:14:12 2009 +0000 Adding functions involving timestamps to apacheLog. commit 6b6311d78be32d51b3b605d1eb4e710c921bbf43 Author: kent Date: Mon Sep 14 18:13:15 2009 +0000 Seeing if preinitializing things to zero gets rid of an off-by-one problem. commit 1e5d43c7d17f43619dd2a0e2a5bac1c3fefea4ae Author: fanhsu Date: Mon Sep 14 17:18:52 2009 +0000 Added color methods for the REST track. commit 3a10a5f7bb5359a067ef8bebc4e82cf2ede2c8cb Author: fanhsu Date: Mon Sep 14 17:07:28 2009 +0000 Updated per data provider and added Display Convention section. commit 54950af55f5a2304c5c01fd407bb9f6da54cf9a4 Author: tdreszer Date: Mon Sep 14 15:33:18 2009 +0000 Make chrom ideo map no longer directly clickable, as per Jim's plan. Instead, by setting class=cytoBand, javascript will control clicking. commit 49d8f6a616de249df0b7c27ff04e5ab83d71929c Author: tdreszer Date: Mon Sep 14 15:30:12 2009 +0000 Use imgTrackAddMapItem in case map items need to be split between slices. Experiment with making short map items for full bed. commit 52480f03c9d3520c7974b32258c9565a25ec1b8f Author: tdreszer Date: Mon Sep 14 15:28:25 2009 +0000 Make curImgTrack global to use imgTrackAddMapItem in case map items need to be split between slices commit a129aa79052d757661dcb44b6493dabcd1987f94 Author: tdreszer Date: Mon Sep 14 15:25:46 2009 +0000 Use imgTrackAddMapItem in case map items need to be split between slices commit ac439830e9c1a704217d8c9d173be3670d149df9 Author: tdreszer Date: Mon Sep 14 15:22:39 2009 +0000 Added imgTrackAddMapItem to let the imgTrack divide map items between slices. commit d905b1039a7066d1ddccad2684eae974d3dd7f01 Author: galt Date: Mon Sep 14 15:00:06 2009 +0000 "Encode release log update" commit 747f48c507d2a3d4abd775a4947c334660c7fd43 Author: galt Date: Mon Sep 14 15:00:04 2009 +0000 "Release log update" commit 1d532e4f5de6fea86bb6811e1c17cde567fe0cf8 Author: larrym Date: Sun Sep 13 21:05:49 2009 +0000 use 'not-allowed' cursor when user drags out of image (suggested by braney); add lots of imageV2 specific code (currently only active in larrym's tree) commit b2d30e7ae3e3f9768dde20a76744955de2a7db5a Author: genbank Date: Sun Sep 13 19:27:12 2009 +0000 fixed error in cron date specs (there are *not* 8 days in a week) commit d1f33cda09ae6f9cb03af4d10ce54c8e6da88496 Author: galt Date: Sun Sep 13 15:00:06 2009 +0000 "Encode release log update" commit a14c8ff102bb26eeba3d8e65b4a52eb952e2ffc9 Author: galt Date: Sun Sep 13 15:00:04 2009 +0000 "Release log update" commit 7d73bbae6eefcecb3a9a4dc233744af79830b377 Author: markd Date: Sun Sep 13 06:20:21 2009 +0000 changed frequence of hgdownload rsync to reduce number of email messages commit 2aa664aaec8020ca26c1f3b09179295094f36af8 Author: kuhn Date: Sun Sep 13 01:23:13 2009 +0000 moved all searches to bottom, as per usual practice commit 87179062e8758e3afbb98e18399bc0d9b2609d3f Author: kuhn Date: Sun Sep 13 00:59:27 2009 +0000 changed labels on hg18 chain/nets from orgName db commit 2f544eea16cc1824e2d37198baa3ab287612618d Author: kuhn Date: Sat Sep 12 23:38:13 2009 +0000 moved all searches to bottom, as per usual practice commit 334bfb56f2a4e0e96b91e3a4e79e9b1eec6e82bd Author: kuhn Date: Sat Sep 12 17:57:16 2009 +0000 added donna to email list for monthly reminder commit 9cf44b270ff2e12fd5e576b7c0d3b58effe6905d Author: jsanborn Date: Sat Sep 12 16:18:29 2009 +0000 added gbm vs norm affy commit ec1f971ec635821e955ce411db2ac1147d17c868 Author: galt Date: Sat Sep 12 15:00:05 2009 +0000 "Encode release log update" commit 29c94509f1ecc14b7b98d974411bcd26d9cae9e9 Author: galt Date: Sat Sep 12 15:00:03 2009 +0000 "Release log update" commit e97d8ca033506985c661b2255bab997bdae293da Author: jsanborn Date: Sat Sep 12 05:04:18 2009 +0000 updated harvard cgh dataset commit be8d25218f7023c9ea516d3403726886a18ee7e4 Author: kent Date: Sat Sep 12 02:44:31 2009 +0000 Seems to work. You need to edit source code to change filter parameters though. commit cc0e7ed06f54e3376165b2f48b37c95416133126 Author: jsanborn Date: Sat Sep 12 01:25:05 2009 +0000 added logicalDb line to mskcc1x1m commit bbdcbb7278eac2aac6ba3ac4996ffdfad4a94e98 Author: markd Date: Fri Sep 11 22:49:03 2009 +0000 added refseq problem commit 4c1ffbede8f8f3b94044c2f5461240a01f89f1c1 Author: katrina Date: Fri Sep 11 21:51:30 2009 +0000 added HAIB Methyl27 and HAIB Methyl-seq commit 0ac1f347e0e356217ab95b7de2d1895c7e1adfd4 Author: tdreszer Date: Fri Sep 11 20:30:10 2009 +0000 Handle radio buttons in dependent cfg settings commit 00985dee7c1a6e2918f970ce90d14d3b26e3733e Author: pchan Date: Fri Sep 11 20:14:04 2009 +0000 include lowe lab specific definitions and add LOWELAB_DEFS to gcc statement only when LOWELAB environment variable is defined commit d81698963fba81c1643ca2b359a56fa121cc4a78 Author: pchan Date: Fri Sep 11 20:12:04 2009 +0000 add LOWELAB_DEFS to link with lowe lab specific code only when LOWELAB environment variable is defined commit dce5c4aac1ec8b513d65331294a5c270cef4406d Author: kayla Date: Fri Sep 11 19:30:19 2009 +0000 removed some "release alpha" lines commit 34baac9896a0925b3e61dad672e8357214398168 Author: katrina Date: Fri Sep 11 18:40:14 2009 +0000 removed release alphas from HAIB Methyl-seq track commit e2c03461c2e8457e8405fd113da329e7f0356b44 Author: katrina Date: Fri Sep 11 18:13:08 2009 +0000 removed release alphas from the HAIB Methyl27 track commit dbaf2b01ecdfde5dd7e7ed2d1829fac22350f049 Author: katrina Date: Fri Sep 11 17:21:27 2009 +0000 Added Common Cell CNV commit 504e486bf081eb893bdbca983ef0151a4af5bbcd Author: galt Date: Fri Sep 11 15:00:06 2009 +0000 "Encode release log update" commit 556de224f744b6581912e74b0a9a5d77b9d6c6bf Author: galt Date: Fri Sep 11 15:00:03 2009 +0000 "Release log update" commit 8bece60e2c1cd439dadd5dd1a772e5be1a19a031 Author: genbank Date: Fri Sep 11 06:25:32 2009 +0000 fixed bug where CCDS update failes if UCSC genes doesn't exist. Delete obsolte mgc-related code commit 9f2fec2be95b5ae9b7600a1ca5422b0a4bea8046 Author: markd Date: Fri Sep 11 01:09:05 2009 +0000 added ccds tables to genbank table list (thanks B0b) commit a1dab0638f365ead25c2b2fbfc084d9739d9d5b0 Author: braney Date: Thu Sep 10 23:16:15 2009 +0000 fix validator for pairedTagAlign to catch sequence errors commit f9c8cfc8b130c118ca3690d6e32752c4d332fa43 Author: kuhn Date: Thu Sep 10 22:55:50 2009 +0000 added RR results, though not in real time commit 8feca6fa29d556b427b2aabc5e8226086b9f4432 Author: kuhn Date: Thu Sep 10 22:50:04 2009 +0000 removed some debugging statements commit ab1ebbb8140a6b6ba4bd4db70c662b958e0a1c58 Author: kuhn Date: Thu Sep 10 22:33:57 2009 +0000 adjusted getRR to look in the dumps for dev and beta values, too. fixed getTableSize.csh to use them properly commit 4bc69e9c86742cf00e9c107f0cbfb3e1734a148d Author: kuhn Date: Thu Sep 10 22:30:55 2009 +0000 simplified to remove extra processing, including dependence on writing files. fixed so actual rowcount is printed, instead of message that dev and beta agree commit a7485c3347c296d1a66b9496fe6f9d393ebeabc9 Author: kuhn Date: Thu Sep 10 22:27:24 2009 +0000 put GENBANK variable in central place, to simplify finding the genbank tablelist. changed checkSync.csh to use it commit 5d71af5633f81dba3990cfdf5d604b07108dfe0d Author: katrina Date: Thu Sep 10 21:09:39 2009 +0000 removed release alphas from ENCODE Common Cell CNV track in preparation for release commit 65a2ea6b0f483682a0d8ddfa8c9052ba30a53d03 Author: jzhu Date: Thu Sep 10 20:08:54 2009 +0000 *** empty log message *** commit 605ee3470eefa592093e41498e3c145e0480f4c1 Author: jzhu Date: Thu Sep 10 19:53:15 2009 +0000 update genome browser trackDb file for tcga1 control acccess data commit 3a3b7d9607fec12735e15f9531830a2075a0724b Author: katrina Date: Thu Sep 10 19:47:53 2009 +0000 added UW DNase1 HS to list because I am releasing the track on the RR today commit ff24194f5eb0768d46b4f4c325e82abfa601b45c Author: ann Date: Thu Sep 10 17:51:16 2009 +0000 bumped for addition of big* programs. commit 94a06311f8fb1c9e6bf1bc6a3e755de7f7673b93 Author: ann Date: Thu Sep 10 17:50:55 2009 +0000 added big* program announcement. commit 546e3f6256bd55cfad9f852a3d8f13079f0c1f62 Author: fanhsu Date: Thu Sep 10 17:28:02 2009 +0000 Created REST.html. commit db4402d3d22d4d8a6f55d30e4db576ad368cec5d Author: fanhsu Date: Thu Sep 10 17:27:31 2009 +0000 Added REST track. commit 03d1cd432cc303a2ccb54f70a15fc47de16ad126 Author: hiram Date: Thu Sep 10 16:54:49 2009 +0000 fixup for broken tables that give NULL for every column commit 30e3c8b9e62986d9869aa07d6483d9f09b3ddc67 Author: markd Date: Thu Sep 10 05:52:48 2009 +0000 added to-do item commit f75c52e873bb11d4a462509b4e62ed5a38f32ed9 Author: markd Date: Thu Sep 10 04:59:35 2009 +0000 change maxShrinkage safety net minimum size commit 7710191ca619d62b0ea02f64a4a8e640f9c13b62 Author: tdreszer Date: Thu Sep 10 04:43:10 2009 +0000 Fixed bug which had independent boolshad hidden checkbox support fields erroneously updated by subtrack dependent cfg logic commit e05a323b8dbc72efc75d82707b2a063b31320f8a Author: larrym Date: Thu Sep 10 04:19:26 2009 +0000 make stripRegEx a public function commit 41f19b0040f0dd59b7248d0f61b2b4432ee90cbf Author: kent Date: Thu Sep 10 02:22:28 2009 +0000 The bedClip utility seems to work. commit a1758dd4b4fef3df50274a9bd2c858eb5d079d5b Author: aamp Date: Thu Sep 10 02:02:58 2009 +0000 Added chain/net make quasi-instructions. commit c5e8453232f21b5c9c9a6e024f6054c9a933df0a Author: kent Date: Thu Sep 10 01:50:01 2009 +0000 Checking end coordinate for off-chromosome. commit fbb52a190f9095282e70a2df0992e21a5358dbff Author: kent Date: Thu Sep 10 01:49:38 2009 +0000 Removing nonfunctional clip option. commit 55e19ed37bca902e4fd934b1962cfa1463d139ac Author: galt Date: Thu Sep 10 00:37:05 2009 +0000 v215 preview commit 6dba91aba81b0f53d2ce1374f9c67cc6f4b76278 Author: tdreszer Date: Wed Sep 9 23:52:19 2009 +0000 A bunch of color changes for Gencode. commit bf8cb89a5b964e58ea342b36fa1ade7166991c18 Author: tdreszer Date: Wed Sep 9 23:50:55 2009 +0000 A bunch of color changes. commit f3f3068161c959a695d760d750b1fe9e6bb6a2d8 Author: galt Date: Wed Sep 9 22:51:30 2009 +0000 no need for a push request to hgdownload, we can do it ourselves commit 622643f844f7acbffbdecbe9af02c6ebfe0ae4fb Author: braney Date: Wed Sep 9 22:22:56 2009 +0000 get the right kind of bed in there commit 927a75df031dee49d46b6c26b33701c86057ce21 Author: galt Date: Wed Sep 9 22:09:58 2009 +0000 getting rid of silly hgdownload1 and 2 when we just need one plain instance hgdownload commit c35a4a5987f7571d55b892980d5b50398eb6e93a Author: kent Date: Wed Sep 9 19:11:50 2009 +0000 Removing some debugging code. commit a9b6ca5db58a5688cafd0fcd0785b32e479a38f3 Author: kent Date: Wed Sep 9 19:11:27 2009 +0000 Utility to convert tab-separated files with Unix timestamps and optionally a number to wiggle plots seems to work. commit ddf8809d6e5e7dcf4e9275cf664c943fc2f92cbb Author: fanhsu Date: Wed Sep 9 18:51:40 2009 +0000 Added NIA Gene Index. commit 5f0881bc36263235cb86f4fa9566f5222cc4058a Author: fanhsu Date: Wed Sep 9 18:35:28 2009 +0000 Added NIAGene for mm9. commit fc1d67cae4e9845cdeeb4d0efedc1cc9d8ba8a90 Author: fanhsu Date: Wed Sep 9 18:33:43 2009 +0000 Added NIAGene.html for mm9. commit f8b5dfc0e7a630941ae4d8616b5b63c77ab9b33b Author: hartera Date: Wed Sep 9 18:13:55 2009 +0000 Documented code changes and reloaded vegaPep table with only those proteins whose transcripts are in vegaGtp. commit 1721bd39d8dd4796166db927652aed00e46672cc Author: ann Date: Wed Sep 9 17:46:06 2009 +0000 adding new table: vegaPep commit 5751d9998ab96b949620ed757b45b3cdc3222a50 Author: ann Date: Wed Sep 9 17:04:35 2009 +0000 removing references to zipped files (which are no longer supported by bedToBigBed) commit 118aada25e8af68e0db96600ab9877923afaa2cf Author: markd Date: Wed Sep 9 17:02:02 2009 +0000 integrated carefully reviewed changes from Robert to retro gene details page commit bea61865cb05e9376129a68d6aed2f775df0f2ee Author: ann Date: Wed Sep 9 16:56:23 2009 +0000 adding info about change to bigDataUrl commit 467f11a7228cf660c6178b34503d45a7457680a2 Author: holmes Date: Wed Sep 9 15:41:22 2009 +0000 removing allpredictions.h commit 92d4687a66619d3fcf4bfc9d563d182aef974d09 Author: galt Date: Wed Sep 9 15:00:06 2009 +0000 "Encode release log update" commit 513f2d16d5a3ad93cf32d2d89bf6cd8e63d2ee01 Author: galt Date: Wed Sep 9 15:00:03 2009 +0000 "Release log update" commit 1efbc73c8227054525fdd0aa462b468d05f7d488 Author: kent Date: Wed Sep 9 01:57:56 2009 +0000 Utility to yank out window size and some timing info on logs seems to work. commit 6c6177e4523c23e8363691e67db59ed32fded9fc Author: aamp Date: Wed Sep 9 01:52:24 2009 +0000 Small note about creating monDom5 chains/nets (swapped) on canFam2. commit dd5b5ac152d2ae236c3eb2d6740584f81cc8acab Author: aamp Date: Wed Sep 9 01:46:17 2009 +0000 Unsplit tables for monDom5 chains on canFam2. commit 659a8aa6848ed0b47d03ec88656d5726c87f1e5b Author: holmes Date: Wed Sep 9 00:30:58 2009 +0000 Adding alignment info commit 517cd35a1ee533b9d44fff985df08be65e715fa8 Author: hartera Date: Wed Sep 9 00:19:34 2009 +0000 Changed colour for vega genes to distinguish them more clearly from the pseudogenes subtrack. commit 3d793a1612ebd5e9a614641208c816594311c6c5 Author: kent Date: Tue Sep 8 23:41:06 2009 +0000 Adding a few more troughs to the hog-finder. commit 836cc6378b87ac3ace28e6e1577589d6d74d9e8c Author: hartera Date: Tue Sep 8 23:24:44 2009 +0000 Changed code for Ensembl and Vega message given on details page if there is no protein prediction available. commit 60eca27933635b39d301b383bb2d01e328162785 Author: angie Date: Tue Sep 8 21:39:38 2009 +0000 Added basic filtering on hgTrackUi settings. Make paired-but-not-properly items a lighter shade. commit b982f43943b9a8a996a64114c27c4f6347677a5f Author: tdreszer Date: Tue Sep 8 21:11:48 2009 +0000 Cleaned up more non-jquery syntax and made multi-selects work with subtrack cfg updating commit f36041918c974f506e123d4526872b40a145f79b Author: tdreszer Date: Tue Sep 8 21:09:23 2009 +0000 Fixed configurable subtracks to not depend upon subgroup/view membership commit d3e18e84e6b6213c81417efa1e0d7d17538635b5 Author: kent Date: Tue Sep 8 19:50:25 2009 +0000 Adding udcDir to the command line as an option. commit 625d3a267f3040bcaa2455d41d88826cd8fa44c1 Author: kuhn Date: Tue Sep 8 18:55:20 2009 +0000 added host to get beta result properly commit 4608b29eb5a1e260e132e1d9405f8546c0a7e029 Author: holmes Date: Tue Sep 8 18:44:17 2009 +0000 adding aligned features autosql commit 7a7d724ea057122b4812379a4c7d5e9bae1bb9b1 Author: holmes Date: Tue Sep 8 18:43:35 2009 +0000 adding cdd autosql commit 5c3dc8ac79f616a4750af0d061569699d7f1579d Author: holmes Date: Tue Sep 8 18:43:06 2009 +0000 Adding alignment and domain tracks commit 183bc53a9cbcee7a052d7a9dfacb6958d2827cc1 Author: holmes Date: Tue Sep 8 18:11:19 2009 +0000 Predicted genes commit 607b39140c23f3c9aa283c136b60db9c5abe0ae8 Author: kuhn Date: Tue Sep 8 17:47:26 2009 +0000 fixed updateTimes.csh to work with msyql v5.0 dumps. also simplified the way it works, removing some of the flexibily seldom used. changed call in genbankRun.csh to use new version. commit aaa2e69810bb59f9d343228dd904b16141afe33e Author: galt Date: Tue Sep 8 15:00:04 2009 +0000 "Encode release log update" commit eae9944849e56bf0e3cf7a6b1bc9fba86248519c Author: galt Date: Tue Sep 8 15:00:02 2009 +0000 "Release log update" commit 9ff94b389ce49e063ba4ae431d4a73c69b361296 Author: markd Date: Mon Sep 7 23:40:22 2009 +0000 added option to control minimum height of a sequence logo column commit c978186946b7df50aab639568b8f970d7633c99e Author: galt Date: Mon Sep 7 15:00:06 2009 +0000 "Encode release log update" commit aac59c8427a3d0815b5c19eea3b1d0e043a6f567 Author: galt Date: Mon Sep 7 15:00:03 2009 +0000 "Release log update" commit 59145082df7041e34640d0f6961448c6b8c0af3d Author: galt Date: Sun Sep 6 15:00:03 2009 +0000 "Encode release log update" commit 2d25134ce74f87504736c79c0de5930adc11158b Author: galt Date: Sun Sep 6 15:00:01 2009 +0000 "Release log update" commit 3fd64f7ecae94a8fef94483cd7c239d825cf3cbf Author: galt Date: Sat Sep 5 15:00:06 2009 +0000 "Encode release log update" commit 81d4d44ceb9b0ae46371c9b0777640a2e1e6151f Author: galt Date: Sat Sep 5 15:00:03 2009 +0000 "Release log update" commit 05723023febf33e8ef7d0cf11d8500cec6a0c9d9 Author: kent Date: Sat Sep 5 07:24:17 2009 +0000 Sorter for access logs, currently just by timestamp. commit 5a7c03bfba35d4523124337d7970f07a00a1dd4e Author: tdreszer Date: Sat Sep 5 01:20:14 2009 +0000 Fix for crazy quantum entanglement bug that Brooke found on cons 44-way commit 1546447c87faf449ccaad07fe402aaa8a6d45824 Author: braney Date: Sat Sep 5 00:17:09 2009 +0000 add is alwaysZero commit ce93baa783fd868d54bb2a49ea38e96b870e9987 Author: braney Date: Fri Sep 4 23:45:29 2009 +0000 always include 0 logic commit fc4fd3c18e26fc680103a87e1583e82b4a125039 Author: braney Date: Fri Sep 4 23:42:38 2009 +0000 always include 0 option commit e91119d9cf48296ba6ddd907a581eaabb96e58f3 Author: tdreszer Date: Fri Sep 4 23:13:37 2009 +0000 Splitting out RNA-seq PolyA tails into separate composte in Expression group commit 320aa14f32631b69b3da12e236cbd4ba971975b4 Author: tdreszer Date: Fri Sep 4 21:59:07 2009 +0000 Added K562b/GATA-2 and K562b/YY1 for Yale/UCDavis commit 593046fcbea63a979801b693996454d9565f60ca Author: tdreszer Date: Fri Sep 4 21:19:12 2009 +0000 This is the third release July 2009 commit 7996efaba978b743378ef012481da5f97532dfe1 Author: tdreszer Date: Fri Sep 4 21:14:01 2009 +0000 Cleaned up metadata for wgEncode Gencode commit a47c89f3c705e3a8c2911c92a38fd7f182dee84c Author: tdreszer Date: Fri Sep 4 19:52:49 2009 +0000 Added wgEncodeGencode search specs and fixed some longLabels commit 212d8db19637742cc6b31f5999536955594d71c1 Author: tdreszer Date: Fri Sep 4 18:36:14 2009 +0000 wgEncodeGencode V3 (alpha) and wgEcodeSangerGencode Rel2 (beta) commit 42171685933ef5b395d50b0906a0539929645346 Author: tdreszer Date: Fri Sep 4 18:34:38 2009 +0000 Moved hg18/wgEnoceSangerGencode to human/wgEncodeGencode for V3 and above. (Sanger left at 18 for rel2) commit 7b32f1f9652ab504fff9efa461c6ffa8183bd933 Author: tdreszer Date: Fri Sep 4 18:25:50 2009 +0000 Changes for imgTbl withot dragReorder or dragScroll commit 8b17b92969c57fcb9106758df79b95c2fc8aca13 Author: tdreszer Date: Fri Sep 4 18:05:31 2009 +0000 wgEncodeSangerGencode for Rel2 but wgEncodeGencode for V3 commit 4208c384ad0f0faae13f4d1f1c9b3caf520565c2 Author: tdreszer Date: Fri Sep 4 18:02:33 2009 +0000 Registered wgEncodeGencode composite to use gencodeGeneMethods commit 109008a78ff01e32c14799d84dc452b53b545d06 Author: hiram Date: Fri Sep 4 17:48:18 2009 +0000 How about a generic location ? commit 2039975b04e7760cf7e7705f5797d53cb7c3ff71 Author: hiram Date: Fri Sep 4 17:41:55 2009 +0000 different location for .hg.dev40.conf commit 460586d612928c30f19abf9fbe9075b4860afff0 Author: angie Date: Fri Sep 4 17:23:59 2009 +0000 Swapped order of outputs to reflect mysql 5 index-order vs. mysql 4 table-order. commit 71685a50d5748ed83ebb922612a00a22934cce72 Author: hiram Date: Fri Sep 4 17:17:16 2009 +0000 fix example commit 2c071856dd023b9a57ac047c1e754e7b9e559222 Author: angie Date: Fri Sep 4 17:16:44 2009 +0000 Add to L instead of overwriting -- need common.mk's handling of USE_SSL. commit 48f03a3497790e3c46269737568713d12e6deca6 Author: hiram Date: Fri Sep 4 17:15:23 2009 +0000 Initial sources derived from the beta to beta script commit 151e23244600ea20230d54aefbfe44c82f1d3dac Author: hiram Date: Fri Sep 4 16:53:07 2009 +0000 Initial source derived from dumpBeta40.csh commit f4c49b8511afeb5f354139b1cdd43f7b86b44f27 Author: hartera Date: Fri Sep 4 16:52:27 2009 +0000 Documented creation of vega35 directory. Documented reloading tables after some of them reverted to older versions during mySQL upgrade. commit 1e884da8b3e9b57d9c3aa1c45ab9c4af4dc87c6a Author: hartera Date: Fri Sep 4 16:51:03 2009 +0000 Documented reloading tables after reversion to older data during mySQL upgrade. commit 912d40c27a7f2ed562ee1c54d4a7d672824bc5a7 Author: galt Date: Fri Sep 4 15:00:06 2009 +0000 "Encode release log update" commit 4eb159a77a61a56ec37afefe08332ebcfcc4f506 Author: galt Date: Fri Sep 4 15:00:03 2009 +0000 "Release log update" commit cf7872a19f057367ebec7197344f62e233d40ac6 Author: kuhn Date: Fri Sep 4 07:38:10 2009 +0000 oops. misnamed outPath variable commit 761aacbedd267985562c1b8d8bff0351559cd38f Author: kuhn Date: Fri Sep 4 07:35:51 2009 +0000 added path to filename in chmod statement to stop file-not-found error. reduced size of test for proper input parameters commit 55e34d495bb289570685543fc68ae8862f327be1 Author: braney Date: Fri Sep 4 00:14:26 2009 +0000 add encode/validateFiles to utils. THis probably should be part of something ENCODE specific (or maybe not). commit c61f722a522678efe35e7183277c67fb18ef7501 Author: braney Date: Thu Sep 3 23:12:10 2009 +0000 if there's no wiggle on a chrom, just assume minSpan is 1 since we won't end up using this value anyway. TIME TO GET RID OF THESE WIGGLES!! commit 998c4d1c5b181929e0ad0aa1374fbaa0982af24e Author: braney Date: Thu Sep 3 22:51:06 2009 +0000 ln to right place with bigBed files commit 6051848e5d9d4ac0367804d69b0b4941df47f3fa Author: kuhn Date: Thu Sep 3 22:27:56 2009 +0000 clarified usage statement per Ann commit 2109a23135b18e9592a0786ce0ebe7bdf3de8911 Author: tdreszer Date: Thu Sep 3 22:20:55 2009 +0000 Protection from when no validationSettings have been provided commit 7b6d1024367e5231834d8a8bc91570ea7d8d59f9 Author: ann Date: Thu Sep 3 19:18:13 2009 +0000 changed maintenance hour to something more reasonable (per admins!) commit 5e24a059d7a57f2ab1ae8f7b6229ba3015f2dcff Author: braney Date: Thu Sep 3 19:13:49 2009 +0000 add validateFiles command line commit 98569bbf270dfeb59de9cdfce621bf25c03cd30c Author: tdreszer Date: Thu Sep 3 18:24:34 2009 +0000 Removed hack to default missing RawSignal to on. This has the affect that raw signals are no longer auto-created unless the view is specifically defined in the DAF. commit 7d7e3fbc2d9154bf2408ebcad69a6dbc962fa957 Author: katrina Date: Thu Sep 3 17:57:14 2009 +0000 Made the link to the myers lab open in a new window commit fb70e58d145129b1d49edd295967924cedf01172 Author: tdreszer Date: Thu Sep 3 17:46:51 2009 +0000 Expanded valitationSettings support to handle ignoreAlignment and ignoreChromLen commit e6e135b4a9c102fc88dc1a6320de183e0b85b820 Author: markd Date: Thu Sep 3 16:49:20 2009 +0000 enabled ccds on hg19 commit 88b4894c832f49d41fb904467e0c7b1e7e3f5bf1 Author: hartera Date: Thu Sep 3 15:39:32 2009 +0000 Added a vegaPep table for the Vega Genes update. commit 3b833ee7adaea4d40cc9f4911b55bb8c4e4fed7b Author: hartera Date: Thu Sep 3 15:25:59 2009 +0000 Added vegaPep table to vegaGeneComposite track entry. commit acb0c33df82fc943e22d0cf7abcf1f1a6d624f32 Author: galt Date: Thu Sep 3 15:00:06 2009 +0000 "Encode release log update" commit 2f26fb4473091165eba3df1f0020171dbbccf67f Author: galt Date: Thu Sep 3 15:00:03 2009 +0000 "Release log update" commit 8459f978b4f3f5b89ffbe4bff0671df65f9b38cf Author: galt Date: Thu Sep 3 02:12:57 2009 +0000 fixed db location commit ff5ffb2ac45e9d6efd584d52f85add18bf29f974 Author: holmes Date: Wed Sep 2 23:56:16 2009 +0000 Adding coverage and percent positive commit a17a6cdef1706558e9ca8e0a006419f05c993a20 Author: angie Date: Wed Sep 2 23:22:21 2009 +0000 Basic ui for type bam -- still need to add filtering on BAM flag bits. commit 17a108b0f1b520f3bb585af014bcc2075ff1ffeb Author: braney Date: Wed Sep 2 23:00:46 2009 +0000 wgEncodeGisRnaSeqAlignmentsK562Cytosol commit f527e9b56eb28904c5cde6963a37dc7b103b670a Author: tdreszer Date: Wed Sep 2 22:55:39 2009 +0000 Turns out OK jpg is not needed. Using 'button' tag commit 21abf844c12a9148d0419bbb657799b9bd757cb7 Author: angie Date: Wed Sep 2 22:38:05 2009 +0000 Added bam to packableType(). commit ab2c418833ebde08e8e4b4bf5998fd735dc38a8f Author: braney Date: Wed Sep 2 22:28:11 2009 +0000 fixed bug where replicate 2 was labeled as replicate 1 commit 46c3e77c6256772cc0386b7df7de17ac60d65936 Author: markd Date: Wed Sep 2 21:59:10 2009 +0000 backed out change to use hTableExists in some places, as it attempts to access the cache while it's being build in certain cases commit ba385da6b595c4059b117f88b6d7b4cfcb4c5e6a Author: angie Date: Wed Sep 2 21:47:28 2009 +0000 Added snp130CodingDbSnp (used dbSNP's provisional SNP coord mapping from hg18). commit c1386cbada7dafe4828af461de6a883e9865bb60 Author: hiram Date: Wed Sep 2 18:42:26 2009 +0000 Need to back quote escape table names to avoid problems with tables that are SQL reserved words commit c176388021016bd47907df4e9f3fa4e1d9258a7f Author: galt Date: Wed Sep 2 18:28:36 2009 +0000 "New version number v214" commit 6d145ee8b56fd4cec98b574de6d5dbbb8ccdac88 Author: galt Date: Wed Sep 2 18:27:53 2009 +0000 v214 final build commit bfbcb8af2d24861dcd69b356adcef5a9f69c9491 Author: hartera Date: Wed Sep 2 18:26:39 2009 +0000 Added vegaPep to vegaGeneComposite trackDb entry. commit 8db42543224d8507910ec89041e665a4323d06cf Author: ann Date: Wed Sep 2 18:11:11 2009 +0000 changed contact email address to genome-www commit 23b7d3b9e34d045a691cb9121bcbe60635d92457 Author: galt Date: Wed Sep 2 15:00:07 2009 +0000 "Encode release log update" commit c0fbf66e8e19122c5c48d22002be263556a0f6ae Author: galt Date: Wed Sep 2 15:00:03 2009 +0000 "Release log update" commit 49a1ec50c72b248c392169c012297363dfd33684 Author: hiram Date: Tue Sep 1 21:58:49 2009 +0000 Adding Bing msnbot search engine authentication commit 22c75ceb422145e4a4154867cb88434181387805 Author: rhead Date: Tue Sep 1 17:41:29 2009 +0000 Fixed broken link to wustl. commit a8a49173c8624a4749fb41d2f153724bfe0f1467 Author: galt Date: Tue Sep 1 15:00:05 2009 +0000 "Encode release log update" commit 85b39862dc4d72168d9fed1c3468f07b64524a3b Author: galt Date: Tue Sep 1 15:00:03 2009 +0000 "Release log update" commit 5cd38ba94f38cf9423c66eeec32398f1af78cd36 Author: angie Date: Tue Sep 1 04:54:41 2009 +0000 Adding minCheck to snp130Exceptions.name -- sometimes a snp can trigger an exception before we detect a real error and omit it from snp130. commit 30f830a9daf1e6bb79e50c84eabc1f50f1207f4a Author: angie Date: Tue Sep 1 04:27:30 2009 +0000 Added snp130: dbSNP's provisional mapping from b36 to GRCh37 coords. Also added orthologous allele table for snp130. commit 757e2a011b874499cabaefbb7609cf81777114d6 Author: jsanborn Date: Tue Sep 1 03:59:06 2009 +0000 added leukemia/lymphoma dataset commit 855c9dedd758eb535d95126739fe739496243480 Author: tdreszer Date: Mon Aug 31 23:38:53 2009 +0000 Added support for targetLink, lab and lots in antibodies commit cf114d920064a42313fbb4af65a1edc44f70ff55 Author: angie Date: Mon Aug 31 23:38:46 2009 +0000 If refNCBI is wrong size (or snp coords are wrong), make an error instead of aborting. Don't abort on between+in-del -- between size is 0, min observed size can be 0 (-). commit 2b0244474c1ddbb92a6658aef6a352b8f76b19d8 Author: tdreszer Date: Mon Aug 31 23:21:00 2009 +0000 Added a few antibodies and added targetLink to antibodies commit 5ed64dec391b39e82a3c090d2219134d2f8c9990 Author: braney Date: Mon Aug 31 23:14:42 2009 +0000 adding metadata for Methyl27 commit 57dbea0bb704f8b8671c01a7e7e5031981b87f86 Author: markd Date: Mon Aug 31 21:47:45 2009 +0000 fixed stupid commit commit ea42f54d8593c99de07e6f5918370dd05d9d2bf7 Author: ann Date: Mon Aug 31 21:43:01 2009 +0000 new rules for new-style Vega Gene tracks for hg18 and mm9 (Rachel has blessed) commit f2e5595b6eab4c74cbb5c8697895ad1612e351bf Author: braney Date: Mon Aug 31 21:33:54 2009 +0000 wgEncodeGisRnaSeqSplitAlignH1esCytosolLongpolya commit 58521497953f44b3c1aaaafd402e64cf2210d744 Author: braney Date: Mon Aug 31 20:55:59 2009 +0000 wgEncodeGisPetAlignmentsNhekNucleusLongpolya commit 1eb3fc6d2788d2c69640e9fa0c7e8439ac50b905 Author: markd Date: Mon Aug 31 20:00:36 2009 +0000 switch more sqlTableExists to hTableExists commit 2921b34f9d9a898482154ad2335d8871967e5708 Author: markd Date: Mon Aug 31 19:10:49 2009 +0000 converted gbSeq related sqlTableExists to hTableExists commit 5bcdd07052a80c92b4c85c6314c742e4ecc481bb Author: braney Date: Mon Aug 31 18:48:08 2009 +0000 add AffyRNA GM12878 nucleolus (sub: 452) commit eaa6081f0f7a3bd3875193484a0abb7e6046ac21 Author: angie Date: Mon Aug 31 18:37:53 2009 +0000 Adding local overrides for snp130 (*provisional* b37 coord release by dbSNP). commit 11a522555e6b63ec5ff8d5a6231b0fd0a0d5229b Author: angie Date: Mon Aug 31 18:31:53 2009 +0000 Added check for table existence to printSnp125CodingAnnotations so an extra trackDb setting is ignored instead of errAborting. commit 4838fa77b048dbe913326d8c170c8a4e7367f97c Author: braney Date: Mon Aug 31 18:19:44 2009 +0000 add (help) for tracks without views commit 96f99c3b1c466dbec63b7f4e24438a08b93628ab Author: ann Date: Mon Aug 31 17:59:11 2009 +0000 Making it a bit easier to read. commit f53a347c53176946e46c752ef513eaa689215090 Author: braney Date: Mon Aug 31 17:55:50 2009 +0000 GIS, Affy, and Methyl27 changes/additions commit 161d16ca72765b124d519c8e84dddb2077b262d5 Author: galt Date: Mon Aug 31 15:00:06 2009 +0000 "Encode release log update" commit 41ce10ba48745a2a92955edb92d49bf21df0e108 Author: galt Date: Mon Aug 31 15:00:03 2009 +0000 "Release log update" commit 936af055d84199fc6df642ba5687079f12a79adc Author: galt Date: Sun Aug 30 15:00:04 2009 +0000 "Encode release log update" commit d67c4bf888f10674c377ca6a38c1a2c40dc3cfc1 Author: galt Date: Sun Aug 30 15:00:02 2009 +0000 "Release log update" commit cfb42a4766419076c0bca7774eea6f9b38bbb4d8 Author: galt Date: Sat Aug 29 18:05:22 2009 +0000 fix stray perl -c output commit 217612a9b92ba3e5fb061a0067143eae965d4b03 Author: galt Date: Sat Aug 29 15:00:05 2009 +0000 "Encode release log update" commit f88df9965667134f2add881fe6803bcf09804bdb Author: galt Date: Sat Aug 29 15:00:03 2009 +0000 "Release log update" commit d45c8dd67950aab07b484c669965e2806b9af288 Author: kent Date: Sat Aug 29 02:34:52 2009 +0000 Updating runTime to be milliseconds not seconds in comment. commit 6064a52d05940298e70837ac42bb0037c0b60b61 Author: kent Date: Sat Aug 29 02:33:43 2009 +0000 Making this output log-format instead of tick/time format. commit 1b2239518b4ee6b26a3e3d05305cb1d5839d7013 Author: kent Date: Sat Aug 29 02:33:12 2009 +0000 Committing utility to make wig files from access logs. commit 09d3fd7ffd10d1508bd951c1131ba033eca04fed Author: markd Date: Sat Aug 29 00:55:35 2009 +0000 updated to new machine names commit 50a14165740d881efd730d5699088233849832f7 Author: galt Date: Sat Aug 29 00:30:01 2009 +0000 migrate to new mysqlbeta db server commit 36b71001ce31c80ed2ce0a37db3fd6a973381061 Author: larrym Date: Fri Aug 28 23:33:19 2009 +0000 add in SQL_FETCH monitoring commit b5e09987bc4418003fe3e50560d82d9e0d331b18 Author: galt Date: Fri Aug 28 23:18:46 2009 +0000 trying to get clean commit 8f3a09bba53462ce06e9dc302d7feaf5c1ecc0df Author: tdreszer Date: Fri Aug 28 21:49:23 2009 +0000 Added support for 'validateSettings' in the DAF commit 1a3a62c36e0a3dcbb7fbe2a805af779ff5b9d3ce Author: katrina Date: Fri Aug 28 20:55:31 2009 +0000 changed first paragraph to past tense commit 44909355c3b58320044b8dc21935481122d374a4 Author: katrina Date: Fri Aug 28 19:21:24 2009 +0000 Removed incorrect configuration information about the items being represented by thin blocks commit cb2c6c42d5c0b62e22e60f2d238283b7a7dd177d Author: rhead Date: Fri Aug 28 18:47:45 2009 +0000 Fixed broken links to WUSTL. commit 89b2fef4cd9ab9becc50654f5862a61ff8e8c9b1 Author: tdreszer Date: Fri Aug 28 18:46:11 2009 +0000 Added support for validationSettings commit d6b9b05c5420728742df8ea0557486c5e612d437 Author: katrina Date: Fri Aug 28 18:29:19 2009 +0000 Removed replicate information from metadata of each table of the wgEncodeHudsonalphaCnv composite track because it does not apply; sanctioned by Kate commit 61f628b149d87577c61dfe0c5781101e90fc409a Author: hartera Date: Fri Aug 28 17:47:07 2009 +0000 Removed the hide noncoding genes option. commit 9d6d598e0928cec9c584b94ce870c141d261d8b4 Author: hartera Date: Fri Aug 28 17:40:45 2009 +0000 Added code to geneShowPosAndLinks() to write that there is no protein prediction for Vega gene if it is noncoding instead of having the sequence link. commit 994456ed6f978bc7bc95f92e6cd1346e167ea597 Author: hartera Date: Fri Aug 28 17:30:56 2009 +0000 Added printEnsemblOrVegaCustomUrl() to create URL links like Ensembl for the Vega track details page to link to the Vega gene, transcript and protein reports. Only Vega uses this right now. Need to test for Ensembl. commit c72ba3fd0e5a14d7f09f1cca80a99087485ed76b Author: ann Date: Fri Aug 28 17:21:49 2009 +0000 adding bedGraphToBigWig info commit c6fa7eaaaeb9d57d50fe8f2f3019a8af14b06c5d Author: ann Date: Fri Aug 28 17:21:16 2009 +0000 info about using bigWig commit b3982aa142cfc0e53235a2327c2f82d3c4371bdc Author: hartera Date: Fri Aug 28 17:11:09 2009 +0000 Added code to vegaMethods() that calls loadGenePredWithConfiguredName on loading track items to interpret the radio button selections in the track UI. commit e0c50b11f575560dcb5c9ab14f55b9f47575e2d7 Author: hartera Date: Fri Aug 28 17:09:18 2009 +0000 Added code to call the vegaGeneUI function if the track is vegaGeneComposite. vegaGenUI() creates radio buttons to select accession, gene name, both or none for track item labels. It also adds a check box to select for noncoding genes not to be shown and the base colouring drop down menu. commit 9a68ed9ac4464587e01bdeba795ddfe0c96f91dc Author: ann Date: Fri Aug 28 17:03:06 2009 +0000 added example for bedGraphToBigWig commit eaf2ddcd6922348f95101423fe19ffba335bcfd4 Author: galt Date: Fri Aug 28 16:58:28 2009 +0000 adding bedGraphToBigWig commit 6c836d305584ab1ea3124ba45c406a73df470d0b Author: katrina Date: Fri Aug 28 16:26:08 2009 +0000 Minor edits commit 2cd076ab2abeda80103152fadfa168a93fb1e35c Author: ann Date: Fri Aug 28 16:25:29 2009 +0000 added in 'reverse' utilities commit c6cbaf1dbbf042ea6a86d1ec96743ad9d9174f20 Author: galt Date: Fri Aug 28 15:00:07 2009 +0000 "Encode release log update" commit 55585556469ad5b18eb935a288291fe741b43431 Author: galt Date: Fri Aug 28 15:00:04 2009 +0000 "Release log update" commit 207b864d054129e95a25fbacbda692ad6d7e7155 Author: markd Date: Fri Aug 28 03:49:25 2009 +0000 sqlMustGetResult doesn't actually generate an error commit ed0f4bf60e2cee051fdb638e9ccecefd21167aee Author: kent Date: Fri Aug 28 00:58:08 2009 +0000 Starting work on yet another access log crawler/grapher. commit 8985eca0f9275a390a258f00bb3f954443e8f783 Author: kent Date: Fri Aug 28 00:56:55 2009 +0000 Utility to merge Apache access logs from different servers while preserving ordering by time stamp seems to work. commit 5325c2e639e084c86972790dca491d6d73ada1fc Author: galt Date: Fri Aug 28 00:56:22 2009 +0000 added useful comments, put in fastest method found to determine if a table exists, added extention function sqlGetRestultsExt to help with testing and generally getting better error info out of mysql commit 39f8f7cbb4804e05d1d4c992a796cd8041cfaa87 Author: kent Date: Fri Aug 28 00:56:01 2009 +0000 Making it accept times in seconds or microseconds. commit 8e47b8237c0c344133e1f259b2a47e1a2732ce84 Author: galt Date: Fri Aug 28 00:54:54 2009 +0000 do not need sqlTableOk now that sqlTableExists works right with innodb and myisam both commit ae1aab60813cabbf007dc9419ab4cc135ad4f5a2 Author: galt Date: Fri Aug 28 00:54:01 2009 +0000 adding some handy comments commit d6f5e234d22bfc27ff9b9028fe647bedf2ec9c7b Author: galt Date: Fri Aug 28 00:53:12 2009 +0000 test table exists - which is fastest method on mysql 4/5 mysam/innodb? commit ac6dd7bf3072e613bf43e408a238daa02703c0ed Author: tdreszer Date: Fri Aug 28 00:11:49 2009 +0000 Support for noScoreFilter and bigBed in cfgTypeFromTdb commit 02c81b65ed50af45ca44602349f000e3d33b22e4 Author: markd Date: Thu Aug 27 23:09:51 2009 +0000 added hg.conf directive to delete variables commit 0712a990ceb44595c2fec796f7a8b308942eb117 Author: kent Date: Thu Aug 27 20:52:01 2009 +0000 Adding more time parsing. commit ca7214f852b22dcb276886b1353ef2ed546c985e Author: rhead Date: Thu Aug 27 20:25:47 2009 +0000 changed hqsqlbeta to mysqlbeta. commit 1ab2f1164ae8c35e88dff36981537841e254a6a0 Author: rhead Date: Thu Aug 27 20:18:46 2009 +0000 Removed spaces around variable assignment. This wasn't working! Also changed hgsqlbeta to mysqlbeta. commit dfb5bd4eb4fb5be7bce7fda79f177217e03325ff Author: galt Date: Thu Aug 27 20:17:11 2009 +0000 somebody not me forgot to check in the .h file commit c1975721b4c07fc593545c4561dd295887730083 Author: katrina Date: Thu Aug 27 20:13:36 2009 +0000 moved reference to reference section commit 191128e15087e9ed64677680ea94aef29160c407 Author: markd Date: Thu Aug 27 19:33:07 2009 +0000 don't dereference NULL if an annotation doesn't have an exon' commit b31ddc6af90906d71a4445bf08d8fc65fc4129be Author: braney Date: Thu Aug 27 19:30:58 2009 +0000 bye Mike! commit dee0817ffb76c8a2a008f6cd4ecac65127fa8913 Author: kent Date: Thu Aug 27 18:07:35 2009 +0000 Testing strptime function. commit 665c717e04ac104fa75749e71a419ce27196a18e Author: hiram Date: Thu Aug 27 18:05:07 2009 +0000 lastz alignments done between mouse and elephant commit e1255d36f4993762e01436c7c19460308c71ae23 Author: kuhn Date: Thu Aug 27 17:57:33 2009 +0000 change identifiers on subtracks to match those in container track for reordering fish. thanks, kayla commit 154957cf9f15f4732504977794297ba6a30c8b82 Author: kuhn Date: Thu Aug 27 17:10:01 2009 +0000 dropped unneeded line and dropped # in output commit 20869191c1ec52e3de9dc3096705d2e67e9f4011 Author: kuhn Date: Thu Aug 27 17:05:49 2009 +0000 tweak to usage statement commit 0a18c9a8ed5c0fd59b5a2fa23651ab0580591d83 Author: kuhn Date: Thu Aug 27 17:02:22 2009 +0000 script to generate touch commands for changing table timestamps commit 3a382e64eb6d731656d01218b8d0e239a532c8ea Author: tdreszer Date: Thu Aug 27 16:38:51 2009 +0000 Fixed default order when DRAG_REORDERING is off commit 9ff534819fd698baa029c1f801e6b3b0f0019f8c Author: galt Date: Thu Aug 27 15:00:08 2009 +0000 "Encode release log update" commit 708ec39f4319422f048a071bb2082793327ceb0e Author: galt Date: Thu Aug 27 15:00:04 2009 +0000 "Release log update" commit a5b2484cbe306b6d1730f8306c29a16876b0e532 Author: fanhsu Date: Thu Aug 27 13:50:27 2009 +0000 Point Help on top bar to PB help page instead of GB help page. commit 7cb99177d4c97f94d3005df65fc36d576fcfcea2 Author: kent Date: Thu Aug 27 03:57:12 2009 +0000 Making zero coordinate error message handle negative coords too. commit e081fa10ac228734081476f27f06f89b7fc4c3fc Author: kent Date: Thu Aug 27 03:54:39 2009 +0000 Checking for zero chromosome coordinate (supposed to be 1-based coordinates) commit 75f7274fc37178855a8942d9227a5e7419452a43 Author: tdreszer Date: Thu Aug 27 00:15:30 2009 +0000 removed some commented out garbage that was accidentally checked in commit 64c5ee179054e0246ab99089a8cba777b037ad1a Author: tdreszer Date: Thu Aug 27 00:13:08 2009 +0000 Now dynamically resizes height based up drag-scrolling over map areas (bed items) commit 8d3a6c4c743a63fcbe0db36c92b9ebce7f63fab9 Author: galt Date: Thu Aug 27 00:10:52 2009 +0000 making output more infomative commit 0cbe4ee8546dd4384d92abc90decddf1d6034412 Author: tdreszer Date: Thu Aug 27 00:10:16 2009 +0000 Fixed a couple bugs and ensured ps-pdf code still works with IMAGEv2 commit e479ad6321cb4351c69853d2a2c893b666b94bdb Author: hiram Date: Wed Aug 26 23:20:21 2009 +0000 Remove the separate monDom5 chain and net entry commit c2a2ae7586e251d8cd4b9745319f213436c83a3f Author: rhead Date: Wed Aug 26 21:38:39 2009 +0000 Fixed broken links to WUSTL. commit 59fe2daf3e1f6bce96b6534b3a16de5ef4199a22 Author: braney Date: Wed Aug 26 18:41:29 2009 +0000 add bed12 support commit f2b2096b7546099da6d010306a7f71dc05ec2a37 Author: braney Date: Wed Aug 26 18:34:55 2009 +0000 some methylSeq changes to change the dimensions of the matrix commit 783c4d1b46ca73f5e462e09b5de41fe6ac59fe9f Author: braney Date: Wed Aug 26 18:29:40 2009 +0000 sort files and build index.html for downloads commit 44b22c4b66f4fdb9767b756186b8164c1d53f0e9 Author: braney Date: Wed Aug 26 18:27:10 2009 +0000 let Reset to Defaults button appear on UI pages without views commit 9a62b3fefe4291ca2cb61075bff066934b90230a Author: katrina Date: Wed Aug 26 17:23:45 2009 +0000 minor formatting changes commit 88ff3b09af9fb3655fbfd658be6c0f38d10e7c4d Author: hiram Date: Wed Aug 26 17:20:18 2009 +0000 Turn on chainNormScoreAvailable since that check has disappeared from the code commit c231637e7174102bccf48672798bc71ea8734c95 Author: galt Date: Wed Aug 26 15:00:06 2009 +0000 "Encode release log update" commit 9a81ccfee59b7bd5aa0410658677e155add0db7e Author: galt Date: Wed Aug 26 15:00:03 2009 +0000 "Release log update" commit 30e51dfa8183dbafb7798fbfa2fbd1de39da2c26 Author: kent Date: Wed Aug 26 03:09:14 2009 +0000 Added -bed option commit 8a6a6888ab0669f36b3135801d7b098fecc2edf0 Author: pauline Date: Wed Aug 26 01:16:49 2009 +0000 Removed alphas in prep for staging of encode caltech track. commit a38ef53ec58526666df4b7df138181e8805b3aa9 Author: braney Date: Wed Aug 26 00:37:21 2009 +0000 always print releaseDate commit b03a96dec399ab7a10731cf57b7ec03b0d42ac06 Author: braney Date: Wed Aug 26 00:21:06 2009 +0000 add link to Illumina's site commit 209b22c3528f19e91f85b7e2b34ee9d8ff1ec778 Author: hiram Date: Tue Aug 25 22:58:42 2009 +0000 Turn on chainNormScoreAvailable for all the chainSelf tracks commit 3f5abec016dacbd8a4b0e6c2449a531545ae0fb5 Author: hiram Date: Tue Aug 25 22:55:51 2009 +0000 For the three tracks that need normScoreAvailable detected, look into the trackDb instead of two describe queries to every chain track. commit af35df5174fd3ade93d1474133458da0a43f9602 Author: markd Date: Tue Aug 25 22:49:39 2009 +0000 changed errAbort to hUserAbort to avoid stack dumps commit c0c2cea3bf49406ee397fc1b6222de2731c4f719 Author: braney Date: Tue Aug 25 21:28:40 2009 +0000 a fix to prevent loading of composite subTracks that are set to on in the trackDb but are hidden by the view settings. commit 7c0cfbc54bbe69d756a0203184a030e12d897bb0 Author: galt Date: Tue Aug 25 18:19:54 2009 +0000 moving the bogus preview to a real preview commit f70a0b4a60b0e78f7ab3200201a7287b3a573928 Author: galt Date: Tue Aug 25 15:00:07 2009 +0000 "Encode release log update" commit 4ebcfa2989ab17a29b074efb6fd6c5580655685c Author: galt Date: Tue Aug 25 15:00:04 2009 +0000 "Release log update" commit 0795e614602e30cbb259d0ec321ea747a0d3f534 Author: angie Date: Tue Aug 25 06:04:05 2009 +0000 Ignore strand -- seems to always be + and BAM inherently adjusts sequence and CIGAR to the positive strand when the alignment was -. Probably should test for inversion cases and make those appear minus strand. commit e463f70d1ab671c73fe534aefb698c3cf7e04e18 Author: angie Date: Tue Aug 25 05:58:18 2009 +0000 Fixed maxWindowToDraw-handling to support the setting at both composite track and subtrack level. Unfortunately, view-level does not yet work because limitedVisFromComposite overrides the dense limitedVis, so if view default vis is pack then the message is not displayed (clipped, 0 items = 0 height). commit b60e379ef2768c0aff8a04909d8390296fef7795 Author: larrym Date: Tue Aug 25 00:10:44 2009 +0000 support showTableCache config in sqlListTables commit 8077c39cd807c6ae696f42aefe9c59493f6046c9 Author: angie Date: Mon Aug 24 23:47:56 2009 +0000 Added bamIgnoreStrand, bamIsRc, bamShowCigarEnglish, bamShowTags. In hgc/bamClick.c, also added showOverlap. commit 69cfedbb9017643660ce2e0284d2e5ae3d2e6df4 Author: hiram Date: Mon Aug 24 23:07:54 2009 +0000 Avoid thousands of describe tables on wigMaf summary tables on large chrom views commit 75ae4412619fba4d7145ef5934c62395c6288dfa Author: braney Date: Mon Aug 24 22:46:21 2009 +0000 make min and max on HA CNV track integers commit f862aaad3d157714c1d177fb86c546dd3d472707 Author: braney Date: Mon Aug 24 22:35:51 2009 +0000 a little text that Katrina wanted commit 1bb4a12956d04a4f8c2225b1b13c0591424bcb37 Author: braney Date: Mon Aug 24 22:35:13 2009 +0000 add noScoreFilter to CNV tracks commit d5e69a6855b674e60cb996ccc15d5fd2e14655d2 Author: katrina Date: Mon Aug 24 21:52:12 2009 +0000 added link to cell line information and cell culture procedures commit 8ba37439fe59ac53b7175b40106f9b20981afceb Author: braney Date: Mon Aug 24 20:39:53 2009 +0000 add comment commit 00830d4c4a0499f16433ba12dac7ae879e34e160 Author: braney Date: Mon Aug 24 20:34:32 2009 +0000 take out slow query to find all spans and replace with code to look for first span commit 9eb2d78e0fc87288542a735f5e1549f508fbad6d Author: braney Date: Mon Aug 24 18:56:38 2009 +0000 set minLimit and maxLimit commit 5e0db8f5f9c3ff21d4a5a59e0e394587604493ff Author: rhead Date: Mon Aug 24 18:15:35 2009 +0000 Fixed broken links to wustl. commit 5c52f1f23b066e87ef151a65966dffb0a7ec06ca Author: fanhsu Date: Mon Aug 24 18:02:46 2009 +0000 Added some loginc to display "N/A" when the stored table value of a variable is -1. commit 812383be001a73bfcd9ae08172d2cbe44f705ce3 Author: braney Date: Mon Aug 24 17:21:57 2009 +0000 change back HA CNV to bed 9 to get back colors and labels (D'oh!) commit f3478ac26830f0061315ad817f20a4c0122c544b Author: larrym Date: Mon Aug 24 16:55:02 2009 +0000 move map manipulation code into contextMenu block commit b816f991179e7401b26aed175d96ed83535959ac Author: galt Date: Mon Aug 24 15:00:03 2009 +0000 "Encode release log update" commit 07a04d89cbb6f2b85817726fe4751ad337dbad42 Author: galt Date: Mon Aug 24 15:00:01 2009 +0000 "Release log update" commit 17b25f76b52a23036b9475d68ba3a1c90ef11d2a Author: markd Date: Mon Aug 24 03:06:49 2009 +0000 removed ulimits commit 5b4720ae487b1cb466b142ffad4da8d8c511002c Author: larrym Date: Sun Aug 23 21:35:34 2009 +0000 add contextMenu support (currently dead code if jquery.contextmenu.js hasn't been loaded by hgTracks.c) commit 59f9919dbf7fec2b2ad393c727274adfb6d9fbf6 Author: larrym Date: Sun Aug 23 20:38:06 2009 +0000 add Rectangle class support commit d0bafb0bb9d9795ff45624a449d2bf3412c507bd Author: kent Date: Sun Aug 23 19:51:26 2009 +0000 Coping with addition of sp| at start of fasta protein name in varSplice section of SwissProt. commit c4ba357fe57b333f89a0de2cd4bb82219469119d Author: kent Date: Sun Aug 23 19:50:47 2009 +0000 Creating sp090821 database. commit 6b45381fda206e0eb14effda6e2ff1986ad03f48 Author: markd Date: Sun Aug 23 16:18:36 2009 +0000 DAS wants 0 for unspecified strand commit c8db83b0bae24810f435d52b217892f8b89bb416 Author: galt Date: Sun Aug 23 15:00:06 2009 +0000 "Encode release log update" commit 3a99711339b7cae7051eaf562639044e16b2432e Author: galt Date: Sun Aug 23 15:00:03 2009 +0000 "Release log update" commit 8814d3a025aa30ecbb1eb5f1c85bcf584106a7cc Author: hartera Date: Sun Aug 23 04:14:30 2009 +0000 Documented adding new code to handle Vega Genes track and loaded a vegaGtp table. commit 4627f14d459ca6d33a605fbf6a8619e16bc79513 Author: markd Date: Sat Aug 22 22:16:59 2009 +0000 added to-do commit de29d42c16cce36e7c1ecf221333977c1e0cb8f6 Author: galt Date: Sat Aug 22 15:00:07 2009 +0000 "Encode release log update" commit f145947bc0f434c2505d3998172b5490b7914a90 Author: galt Date: Sat Aug 22 15:00:04 2009 +0000 "Release log update" commit 6d7dd0b5bbd45f93a55f5d43e950689278ccd3d9 Author: angie Date: Sat Aug 22 02:18:35 2009 +0000 Added search for paired ends outside window, +- trackDb setting pairSearchRange. commit 135abe9e15675cd2ae78522e48aa764550737f8e Author: angie Date: Fri Aug 21 22:54:39 2009 +0000 Added pairing for easy cases (both ends in hgTracks window). commit 7dd9eff8b12c8047ff8114f24bedaf857fa948d6 Author: angie Date: Fri Aug 21 22:52:35 2009 +0000 Added bamClone. Fixed bamToFfAli to walk through CIGAR operations backwards when strand is -. commit 3bce320113df6a5dde80ba47a31a324aecdeb20c Author: braney Date: Fri Aug 21 22:15:55 2009 +0000 some fix-ups requested by Katrina commit 305fb06299168becdf4acc48fc7cde4bf829d6c0 Author: braney Date: Fri Aug 21 21:19:36 2009 +0000 take out "first" change cuz I stupid commit 26a94c14fc0fa37782f9dffb10bc5a52d48c055f Author: braney Date: Fri Aug 21 20:36:20 2009 +0000 change HudsonalphaCnv top level to bed3 to disable score filtering commit e3976da58ae04ac8591cfa9df3bb6585aba8bf45 Author: angie Date: Fri Aug 21 18:43:50 2009 +0000 Use the new ffShowSideBySide to display just the side-by-side read alignments, instead of ffShAliPart which expects to fill a page. commit 45d1c17bbf68977505f736505ca25a1917258c72 Author: katrina Date: Fri Aug 21 18:41:38 2009 +0000 Added Display Conventions and Configuration section commit 57df652b12e21c77aae1535b1dfb349efb06b1e7 Author: angie Date: Fri Aug 21 18:41:34 2009 +0000 Factored out the side-by-side part of ffShAliPart into ffShowSideBySide. commit cd2c3b11d1fba18831c035c9ffeb93cac7d7c0a8 Author: angie Date: Fri Aug 21 18:39:59 2009 +0000 Added bafFlushLineNoHr for more compact side-by-side alignment display. commit 8ac318a95c05870aeefeed1c39e7020c434010e5 Author: hiram Date: Fri Aug 21 18:08:53 2009 +0000 Commands to dump and load tables from beta v4.0 server to beta v5.0 server commit 669c7fb1da4f48bc8bb9216d8f1b4b655307f6e1 Author: braney Date: Fri Aug 21 17:21:01 2009 +0000 testing some things commit 060d8678b4553c9173742b31acc0a82ccfbce549 Author: galt Date: Fri Aug 21 15:00:07 2009 +0000 "Encode release log update" commit b1f1060977ba59569cdee6c12f7e808e78cf6969 Author: galt Date: Fri Aug 21 15:00:04 2009 +0000 "Release log update" commit f38f716c2aae3047b4d79f1f1539eaea97ef6c44 Author: markd Date: Fri Aug 21 06:25:21 2009 +0000 re-annotate/reload unrelease maf to fix bug commit 4ba401dee318e37f7010c23f6be262737042370d Author: angie Date: Fri Aug 21 05:27:29 2009 +0000 Use the new bamToFfAli and the old ffShAliPart to display aligned bases. commit e49ca55889bf264a5c3fec77755682ad9bcad301 Author: angie Date: Fri Aug 21 05:22:01 2009 +0000 Added bamToFfAli (for using fuzzyShow display). commit 7d100cebc6e2a6d9a1bff844c17b5f79fe451b1e Author: kuhn Date: Fri Aug 21 00:13:44 2009 +0000 grouped fish in proper near-neighbor order commit 08bf74cedd7a33d7d56a404b78ef958eac72f74b Author: braney Date: Thu Aug 20 23:34:49 2009 +0000 if no spanList is specified in trackDb, build list by choosing first span in the table rather than trying to find all the spans. This is the same behavior as adding "spanList first" to the trackDb for over 500 tables. commit 9b61566f7a9d0e694fde00dd6ceeef69bae9dd1a Author: angie Date: Thu Aug 20 22:51:18 2009 +0000 Updates for MGI: RepTranscript, Allele, Phenotype, and IKMC. commit d939dd63bac679bfe7be54f74770471995453be4 Author: angie Date: Thu Aug 20 22:40:38 2009 +0000 Added link to file referenced in Methods. commit 6ec7be574e159e542c7d928e4820edb2e77e3ed7 Author: kent Date: Thu Aug 20 22:31:46 2009 +0000 Initializing a field to zero which otherwise would be garbage. commit 0506a32b5a4164897cd65f09ae5989ab9320dcc6 Author: kayla Date: Thu Aug 20 22:01:58 2009 +0000 removed maxWindowToDraw 500000 from snpArray for now commit 92bed39a5780747beead615fda73719bc6d60708 Author: hiram Date: Thu Aug 20 21:53:41 2009 +0000 Take care of faAcc strings being (null) commit a9e434eba4b66cb9be97229fbdbc9cd6846c8fad Author: hiram Date: Thu Aug 20 21:52:01 2009 +0000 Add txCdsEvFromBed to the build commit bcf159f467706a8a080cad20786da998b1a1a5ed Author: hiram Date: Thu Aug 20 21:51:19 2009 +0000 Cleaned code and working better May 6th 2009 commit 2d1997277cf3d15e07af8ba81823fa62b6fbc9a8 Author: donnak Date: Thu Aug 20 21:45:10 2009 +0000 Added link to Ensembl/NCBI/UCSC Browser Genome Release Agreement document. commit 6df1068929c3186f05b69162c91058bbb6d76bca Author: hiram Date: Thu Aug 20 21:42:29 2009 +0000 Number of names has increased to 70 commit bacdd4022d5babbb2a1f34ef0decaa81b31bc145 Author: angie Date: Thu Aug 20 21:36:17 2009 +0000 Corrected terminology: PNG palette images do not have an alpha channel, just a parallel map of opacity values. So useAlpha-->useTransparency. commit 1b539505329bbc7871ee11c3f77f9964a6db8c64 Author: kayla Date: Thu Aug 20 21:35:34 2009 +0000 Added maxWindowToDraw 500000 to the snpArray track commit 2f59b7dcaf09f39f5de278d54aa9649d7534afd9 Author: angie Date: Thu Aug 20 21:34:44 2009 +0000 Used more civilized language in comment & errAbort per Larry's code review feedback. Also corrected terminology: PNG palette images do not have an alpha channel, just a parallel map of opacity values. So useAlpha-->useTransparency. commit fa7135e89022a7a45197b3d7db1c1be8f6258c2d Author: angie Date: Thu Aug 20 20:34:57 2009 +0000 Use trackDbSettingClosestToHome (not just trackDbSetting) in getMaxWindowToDraw, so subtracks will display the correct size threshold. commit 4d999bddbd9b61c844bb7b4cb06a458ad3338f0b Author: tdreszer Date: Thu Aug 20 19:29:21 2009 +0000 Fixed bug in my jquery code that threw exception commit 576c69f05630f3e56a15423e473d6f192893392d Author: angie Date: Thu Aug 20 18:40:23 2009 +0000 Handle composite tracks in maxWindowSizeExceeded. (Individual subtracks of a composite track still not supported.) commit b505383ad91e024e0bb736150b14762ddb627372 Author: markd Date: Thu Aug 20 18:22:35 2009 +0000 added spanList to uwNunOcc tracks commit a5fb075a9bd3c7ad262f2c466d87f6d7913a070a Author: larrym Date: Thu Aug 20 18:15:41 2009 +0000 use tableList table (if available) instead of show tables in sqlListTables commit d0184c353826f0ba3f3868ddd7e91a485da7a882 Author: larrym Date: Thu Aug 20 18:11:36 2009 +0000 avoid N^2 list scan in hasTrackDbAlready by using a loaded hash commit 3b7d3349f14e4c196e37303ea35e73847bd29a09 Author: tdreszer Date: Thu Aug 20 17:07:48 2009 +0000 Toggling metadata didn't work on MSIE. Converting contents to comment was the problem. commit e5c58a709f4c13e7e1673f05ef07879f6b3c93c2 Author: braney Date: Thu Aug 20 16:58:41 2009 +0000 change summary view to start after 50K rather than 1mb. commit 9438dd64e95f54059d8d4e36fb74548024c0f478 Author: katrina Date: Thu Aug 20 15:46:50 2009 +0000 Updated and revised out of date description page commit 12fd107fdebd5b50f54e22abc7219e3a1be0d43b Author: galt Date: Thu Aug 20 15:00:06 2009 +0000 "Encode release log update" commit 6d3e1f400a45aa8ae87e9f0d5bf0f67f702d43e7 Author: galt Date: Thu Aug 20 15:00:03 2009 +0000 "Release log update" commit 923f611c017bb4fe6fca98a524bcd39b2f5ba4ae Author: markd Date: Thu Aug 20 06:31:43 2009 +0000 don't display repeat masker when > 10000000 bases window commit 1ae265ac96c048930d4a3e70e03e343febf4d781 Author: angie Date: Wed Aug 19 23:35:58 2009 +0000 Added option to mgSaveToGif and its call stack, to use GIF's Graphic Control Extension to make memgfx's background color (0) transparent. Also corrected terminology for PNG in .h files: useAlpha -> useTransparency. commit 1ae9181ae0ea634c3db5aaf430856ba039ade95c Author: tdreszer Date: Wed Aug 19 23:19:12 2009 +0000 Missing 'else' caused Gencode level filter to duplicate entries. commit a5de86d16bb47f90e537d185fff299e055a9e49c Author: angie Date: Wed Aug 19 23:00:17 2009 +0000 Added option to mgSaveToGif and its call stack, to use GIF's Graphic Control Extension to make memgfx's background color (0) transparent. Also corrected terminology for PNG in .h files: useAlpha -> useTransparency. commit 3bbf6fc12e497bba4ccebc5e5885ba3b343d3db7 Author: angie Date: Wed Aug 19 22:28:37 2009 +0000 Added option to mgSaveToGif and its call stack, to use GIF's Graphic Control Extension to make memgfx's background color (0) transparent. Also corrected terminology for PNG in .h files: useAlpha -> useTransparency. commit c656f8f93a4468720b8cb9cd2b9a5bf6ba21d59d Author: sbenz Date: Wed Aug 19 21:27:10 2009 +0000 Fixed caps issue on one label commit aa25b50b34e1df76ebaf0fcbfb00a7241c1f238d Author: katrina Date: Wed Aug 19 21:20:27 2009 +0000 Made minor edits and fixed a reference format commit d2d595cb724ec486bf0b665c9eeb098329d63719 Author: katrina Date: Wed Aug 19 21:16:10 2009 +0000 Made minor edits and fixed a reference format commit f3ad820fc5e71a57c6680b61a50066ff88d5ad98 Author: katrina Date: Wed Aug 19 20:45:15 2009 +0000 Made minor edits and fixed a reference format commit f1421b49833ae122bfe1715526c5b139d5e3e34a Author: sbenz Date: Wed Aug 19 20:41:32 2009 +0000 Added gray Exon data commit a7302a5a4fc60665b47c768b8369cbd7249c08a5 Author: braney Date: Wed Aug 19 19:32:44 2009 +0000 cgi encode controlled vocabulary terms commit cf0cd29987ce56a52e754e8dd6c73df5f9cd1207 Author: angie Date: Wed Aug 19 18:58:13 2009 +0000 Added errCatch around customTracksParseCartDetailed (similar to that around customTrackUpdateFromConfig) because bad URL in doc input was causing abort. commit 4c86925765ed8a02045e55eaa8f33288debfddc6 Author: katrina Date: Wed Aug 19 18:36:21 2009 +0000 Fixed typo in the longLabel commit ba95548ca0bd7454ab4e71e893fca5eaec0f76bd Author: markd Date: Wed Aug 19 18:16:34 2009 +0000 fixed bogus return of value that compiler didn't detected; correct non-kentian indentation commit e67cea3c2fb0eaa6e83a75db3560c80ca39b1374 Author: braney Date: Wed Aug 19 17:58:00 2009 +0000 add matchFirst argument commit ec521368ae790dbfce372d11d8dcb0ef76c0f1a9 Author: sbenz Date: Wed Aug 19 17:37:52 2009 +0000 Fixed incorrectly named cell lines, added most recent list of gray snp data commit bd9ef9117ae61ff503760ef49624c7046a843c68 Author: katrina Date: Wed Aug 19 15:26:12 2009 +0000 reinstated reference to ORegAnno links since the site and links are now working commit c1bbd016c6101cf5c3da2e16dd73db70e3b3b3e7 Author: galt Date: Wed Aug 19 15:00:07 2009 +0000 "Encode release log update" commit a257baff84d42d3481123ad612f13b8ac353985a Author: galt Date: Wed Aug 19 15:00:04 2009 +0000 "Release log update" commit ceba84500ad37aa6ce1a7a40cab7f7868f56c9a6 Author: kate Date: Wed Aug 19 14:41:19 2009 +0000 Add comment to assist repair when links break commit 12a1bf80d51661f45f554995b52dcd045fddac59 Author: kate Date: Wed Aug 19 14:33:10 2009 +0000 makeg commit 2c610737521871b8ba33c954a548be15798a25a2 Author: jzhu Date: Wed Aug 19 08:13:03 2009 +0000 update microArray ra file for Broad Affy U133A Tumor vs. Normal commit 10f6ce38fd8c645e2a91506c9cf1773f6b737e0e Author: galt Date: Wed Aug 19 06:02:57 2009 +0000 fixing htmlUrl to handle net.c errAbort using errCatch commit e97745f265c23ebdd40c82e1775ccc05aa3c66cf Author: galt Date: Wed Aug 19 03:44:27 2009 +0000 add https support for redirect commit 868a4b8a4348b8ff191d48278b231710797a415b Author: markd Date: Wed Aug 19 03:21:23 2009 +0000 fix problem missing syntentic clones in mgc commit 6f2cdcbd25be1df4cb2e385445d25963c3037960 Author: baertsch Date: Wed Aug 19 00:13:19 2009 +0000 remove commented code commit bf5ffa81e780d31ee5969f9fce6b56cc5c25f565 Author: baertsch Date: Wed Aug 19 00:12:37 2009 +0000 bug in filtering alignments commit b5da9915f64f8102110adacd7187aa2e4fbb1fef Author: angie Date: Tue Aug 18 23:41:23 2009 +0000 Removed the hardcoded BAM_MAX_ZOOM -- using trackDb setting maxWindowToDraw now. commit 726a0c4968c52c087b1b2da63e10fb5baa49b078 Author: angie Date: Tue Aug 18 23:29:27 2009 +0000 Added maxWindowToDraw setting to bamNA12878 so we don't have to rely on hardcoded max in bamTrack.c. commit fd8bd614184de1a9366a0f5cb361453565652c90 Author: baertsch Date: Tue Aug 18 23:24:05 2009 +0000 fix counter commit 1112fb9edd0bcf6a36f91e73ff9a95ff5d1c930a Author: tdreszer Date: Tue Aug 18 23:22:51 2009 +0000 Now composites are automatically made vis=full only when they are vis=hide and a multi-view is made visible. commit 576f90e0bab23c0d15105502fd909f4776ae83c0 Author: angie Date: Tue Aug 18 22:47:49 2009 +0000 Updated snp130 with corrected functional annotations from dbSNP. commit c89a4218287fa52e92d30310276a6bcd1657549e Author: baertsch Date: Tue Aug 18 22:31:32 2009 +0000 fix bug with non pass thru mode. alignments are now removed if there are multiple hits that are less than minDiff cutoff. removed commented code and tweaked logging messages. commit 4264ed5040130d8a0c0caed8aef5d9fb9d40b603 Author: galt Date: Tue Aug 18 22:31:14 2009 +0000 better err handling for URL redirect commit 032e95e7b175bace3da2b5e230d3243cfc6cbc82 Author: kent Date: Tue Aug 18 21:39:57 2009 +0000 Moving this back to bedToBigBed now that it's tested. commit f35063429a67eb18aebac65fb2df8c8f59e9f4c3 Author: kent Date: Tue Aug 18 21:39:13 2009 +0000 Changing to a multi-pass design to conserve memory. commit 2bf573edf1405d5ee330d61d01ace78706534a91 Author: kent Date: Tue Aug 18 21:29:46 2009 +0000 Moving the old one-pass bedToBigBed to the one-shot directory where it need not be maintained. commit e83781025109176d7449697265ce8d9f5b9c51c8 Author: tdreszer Date: Tue Aug 18 21:22:15 2009 +0000 Fixed warnBox to go to prev page when page halted by errorAbort. Restored multiple message suppoprt. Still supports selectAll not selecting empty warnBox. commit ce340568208430429d3985b437ff5beecf596c8b Author: angie Date: Tue Aug 18 20:31:01 2009 +0000 When winEnd-winStart > trackDb setting maxWindowToDraw, inhibit the toggle-link over the message because toggling vis doesn't affect the image. commit 56d777649dfc82bf3e9371e0da36c9d3cb897cbb Author: galt Date: Tue Aug 18 19:48:19 2009 +0000 v214 preview commit 395680ff8e843ac95c07884a1984c9b366b1e6cd Author: markd Date: Tue Aug 18 18:37:24 2009 +0000 added to-do item commit 36fa19c5bd3231c35a4d0df3d5c670868f62c443 Author: tdreszer Date: Tue Aug 18 17:56:52 2009 +0000 Sort of terms should ignore case commit fd23f37707ab8743b333e075bb6eedb28bd8b319 Author: tdreszer Date: Tue Aug 18 17:51:15 2009 +0000 Added two for Duke/UTA commit 1a46dc8fbdcdd6b69e8490f555a9d63feda53019 Author: galt Date: Tue Aug 18 16:20:29 2009 +0000 "New version number v213" commit 34f7f8ae921a94c103a6b37a4b1a12bdfaf15b1c Author: galt Date: Tue Aug 18 16:16:50 2009 +0000 v213 final build commit 97fd8fe5684c313b0d59fe76a04b449026fc742d Author: braney Date: Tue Aug 18 15:02:59 2009 +0000 works with bed3 commit 2cff423701a268787ab07f6858c4e96216434c99 Author: galt Date: Tue Aug 18 15:00:06 2009 +0000 "Encode release log update" commit 94525fb30e523720a32a55b6872952698b2bf3e4 Author: galt Date: Tue Aug 18 15:00:03 2009 +0000 "Release log update" commit e87d1e1ba3fe0d66c9657b01eeb567ca5bf37447 Author: hartera Date: Tue Aug 18 04:15:22 2009 +0000 Added entry for Retroposed Genes version 1. Added search for the track. commit 0a359404b55cdff20f1110da849dcad87946a956 Author: hartera Date: Tue Aug 18 04:08:24 2009 +0000 Draft of details page for UCSC Retrogenes predicted by RetroFinder. commit 3179f293a564ecc901fe894c1785d64f8c8f67de Author: hartera Date: Tue Aug 18 04:07:25 2009 +0000 Updated link and citation for an article. commit 98d6e5c837566507d1e64d784ae2b87e327cf301 Author: tdreszer Date: Tue Aug 18 00:08:45 2009 +0000 Included the protocols commit 291bd3deea2d1d9ca4048be4de50ab1b85bd3ece Author: tdreszer Date: Mon Aug 17 23:56:56 2009 +0000 Four for Myers, two for Stam commit 5cbadbc9232a357ba3bc2f9e202db3e89730a528 Author: rhead Date: Mon Aug 17 21:51:15 2009 +0000 Fixed broken link to ganegoodall.org. commit 96941f195443f8b2665184f1d5ff36545037d6b9 Author: angie Date: Mon Aug 17 21:33:59 2009 +0000 Added new setting maxWindowToDraw. commit 2c557c37c6d56a38389a97e045ba7aad210bc5c0 Author: angie Date: Mon Aug 17 21:30:12 2009 +0000 Added new setting maxWindowToDraw to snp1* tracks, so they don't bog down views that are zoomed out way past the point where item display is meaningful. commit 6a2e30873f58422646a9ba2d94a07981b57d101e Author: angie Date: Mon Aug 17 21:27:43 2009 +0000 Added support for new trackDb setting maxWindowToDraw: if winEnd-winStart>maxWindowToDraw, don't load or draw items, just print out a message telling the user how close they must zoom in to see items. commit 0667b2fdbbaa330d71436181c92c7418fe510c75 Author: tdreszer Date: Mon Aug 17 21:07:50 2009 +0000 Two protocols approved for Bernstein commit 76c9b1d4feb030d3c5b9383b15216341bc0df33c Author: galt Date: Mon Aug 17 15:00:06 2009 +0000 "Encode release log update" commit 743a37bf04530526fc511fe36dae77e37a194344 Author: galt Date: Mon Aug 17 15:00:03 2009 +0000 "Release log update" commit 7c3eb3fce084f8c0de9b04c5a5bd26b79b2def8d Author: galt Date: Sun Aug 16 15:00:05 2009 +0000 "Encode release log update" commit a487c294095fcf130ad303fba9f283ee74f2fa72 Author: galt Date: Sun Aug 16 15:00:03 2009 +0000 "Release log update" commit 59eaaa467257717531933a7c6c4cc91f4955fc89 Author: larrym Date: Sat Aug 15 20:04:03 2009 +0000 restore dynamic creation of javascript symlinks which I deleted in version 1.29; rationale: to handle mirrors who don't preserve mtime's when rsync'ing commit f24f2c752abe82d65ad7dad73900f7a9ca741e13 Author: baertsch Date: Sat Aug 15 17:59:49 2009 +0000 changed assert condition that was too strict (start >=0) instead of start > 0. Fixed compiler warnings. commit 030a3bf34731ccf91a5da042a0f24757c37c31e2 Author: galt Date: Sat Aug 15 15:00:06 2009 +0000 "Encode release log update" commit b353b27f68c1724159e13810cc62c93cbd600db5 Author: galt Date: Sat Aug 15 15:00:03 2009 +0000 "Release log update" commit a610a319fe54372c3eb661915c3f8c1294b24c12 Author: tdreszer Date: Fri Aug 14 21:37:36 2009 +0000 Oops. Last change was tested 1/2 on the wrong browser. This ci is properly tested. commit 57d288010eef7ed56e6251bbdc34de8353baa327 Author: kent Date: Fri Aug 14 21:18:04 2009 +0000 Fixing bug that made b2bb skip lots of data in case where bed just had three columns. commit e68cd696eafbd47ef63c6ba9a86109dc58f81a8c Author: tdreszer Date: Fri Aug 14 21:15:49 2009 +0000 Multi-view settings should not show up in the table browser 'merge' function. commit 4186c8c1645db26df5bd423bb3b9f3b2bb0bb08d Author: kent Date: Fri Aug 14 20:56:48 2009 +0000 Fixing bug in coverage calcs. commit d7d6242fd3ad2b5b4765818b1b66e1c11fb4ed0f Author: kent Date: Fri Aug 14 20:52:35 2009 +0000 Making it handle 3 column beds better. commit d1123c15e11cce7d1097b67fb28f3bda79c2e7a5 Author: tdreszer Date: Fri Aug 14 20:52:04 2009 +0000 Fixed dimension Z to dynamically wrap when dimension X is dynamically reduced. commit 2c99563529e776588b04fe226be4a418f3d205d5 Author: baertsch Date: Fri Aug 14 19:06:45 2009 +0000 initial version commit 92070ce57fb108fbb83b97ebfe9eb0317553169f Author: fanhsu Date: Fri Aug 14 18:36:45 2009 +0000 Consolidated a few statements, cleaned up a little bit. commit 3b829ed638dd4fc61971b1c7055f795568ff1531 Author: rhead Date: Fri Aug 14 18:29:10 2009 +0000 Fixed broken link to WUSTL. commit f5015352a15392449cae2ea0ecc9e16ee0743e20 Author: galt Date: Fri Aug 14 15:00:06 2009 +0000 "Encode release log update" commit 72ea0549acc661d2b1d3bd220530b0e39b57100d Author: galt Date: Fri Aug 14 15:00:04 2009 +0000 "Release log update" commit 4e81e99aac849979c0549bd3e1caf74aba693ef4 Author: aamp Date: Fri Aug 14 07:18:53 2009 +0000 Changes to reflect library changes dealing with the next-item button custom track bug. hGetBedRange wasn't up to the task. commit b8a7ddfc784ee812b274bd79f54a469644bac5b9 Author: aamp Date: Fri Aug 14 07:16:16 2009 +0000 Change to hGetBedRange() for custom tracks. The problem was that hParseTableName expected a database to be passed to it that included a chromInfo table. customTrash isn't one of those databases, so instead we're also including the name of the database being browsed. commit 40cafea6614a269cf90664a62410080e8eec1ea2 Author: hiram Date: Thu Aug 13 23:15:57 2009 +0000 Proper reference to /bin/ls instead of just ls in a system() call to avoid PATH searching commit a2462d790a17f0b6655e32eb08aad1536b565b36 Author: braney Date: Thu Aug 13 21:51:56 2009 +0000 fix up memory leaks commit feca5961445822ee0f50fa013252738c1b932e28 Author: braney Date: Thu Aug 13 21:48:17 2009 +0000 add some memory clean up routines commit 711f0741f15ff012a845c6ddcf410a442ebaa163 Author: galt Date: Thu Aug 13 19:57:52 2009 +0000 temporary workaround to help the keep-alive during transition to new variable name bigDataUrl commit 2801b685dd33bf1555dcd222b7057c1c3267dd88 Author: kate Date: Thu Aug 13 17:23:09 2009 +0000 Correct TAF1 antibody name, by request of Rick Myers commit 786464efbabe2683ada31adb0b4e51df2c4bac7a Author: kate Date: Thu Aug 13 17:20:48 2009 +0000 Correct antibody name, by request of Rick Myers commit c5679ed9d66b556f95dcc6b58f3032a4d79d54a5 Author: larrym Date: Thu Aug 13 17:19:04 2009 +0000 pass event object to beforeShow callback commit 706a3fae631a5d44b6e4782288fddf12addc0dde Author: larrym Date: Thu Aug 13 17:18:16 2009 +0000 Version 1.0 downloaded from: http://www.javascripttoolbox.com/libsource.php/contextmenu/source/jquery.contextmenu.js commit 39a7e57fb429514720cd6cab10998a4d2290ecf3 Author: hiram Date: Thu Aug 13 17:07:56 2009 +0000 Adding automatic upstream file creation for ornAna1, fr2, gasAcu1, oryLat2 commit 82a58cb82e169e4481e16837efea5bf4c608398e Author: markd Date: Thu Aug 13 16:25:31 2009 +0000 always get modification time right commit 71473dfecfb0c09d5c97031cde71e86ce4a1609b Author: galt Date: Thu Aug 13 15:00:07 2009 +0000 "Encode release log update" commit 45f9caf1f19d266f533c6a2f3c5757b0f5424569 Author: galt Date: Thu Aug 13 15:00:04 2009 +0000 "Release log update" commit afcc8b68fd4fab156822451be760a2ce661bf763 Author: fanhsu Date: Thu Aug 13 13:58:15 2009 +0000 Reformated a printf statement and removed a debugging function. commit 8a4e55fd9d4bb3ee8b4f886ce2a9ee2eecf7bad0 Author: larrym Date: Thu Aug 13 07:32:29 2009 +0000 remove code in jsIncludeFile which dynamically creates the versioned softlinks (they have to be created via make install) commit 6cf3966787be54c21cd1d31bcda57ff36a9200de Author: larrym Date: Thu Aug 13 06:51:52 2009 +0000 fix typo of previous checkin (change to use cpJsFiles.pl) commit 55c279edf8662612a3889232655f8f24d4b00fd0 Author: larrym Date: Thu Aug 13 06:49:59 2009 +0000 back out inadvertent checkin of code commit 3c5f3ec367ffbd02c17125d034633cc833bf00a9 Author: larrym Date: Thu Aug 13 06:47:10 2009 +0000 move getHgsid code to utils.js commit e0a3b5cf4251821956a77d5aeb5b4d239efaad6f Author: larrym Date: Thu Aug 13 06:46:23 2009 +0000 add getHgsid commit 09e3db535b89c87ae3160cb70fb98d61db9b788e Author: markd Date: Thu Aug 13 06:27:00 2009 +0000 simplify computer chain normalized score gray scale suggest by jk commit 0c0e4c1bf1b9c4c0a26ab4bbe8f6f34aa3c9959a Author: kent Date: Thu Aug 13 04:48:33 2009 +0000 Reduced memory use a little more. Polishing status reporting as program runs. commit 84aa7c8c83298965489a48350ff5bc63acf1bc43 Author: markd Date: Thu Aug 13 04:15:52 2009 +0000 don't allow chain item to g white with normalize score commit f31cf263400d8e3da57deaba9b08a9c4cfd13e00 Author: markd Date: Thu Aug 13 03:08:30 2009 +0000 fixed misuse of AllocVar macro detected by gcc 4.5 commit 4f6e718bf85438c05e976dbe5890ca0a75e1d3d2 Author: kate Date: Thu Aug 13 00:13:45 2009 +0000 Link out commit aba9145dfe14839c791b20c42f77afaca7a1d39b Author: kate Date: Thu Aug 13 00:05:04 2009 +0000 Usability and consistency changes to UW Affy Exon track commit 83d8b92c00f4d17fe00d99c4d291504a980530c9 Author: kate Date: Thu Aug 13 00:03:14 2009 +0000 Cleanup for consistency commit f0fa68c7d394330d8f780a7074799917c6c7a23c Author: kent Date: Wed Aug 12 23:38:50 2009 +0000 Fixing strict compiler warnings. commit bdc3e7594f36b2402822e94a446217d6481b39ce Author: kent Date: Wed Aug 12 23:38:37 2009 +0000 Adding sizes file for testing. commit 07c5d64263477956ce880ae93f46feb64dc4646e Author: katrina Date: Wed Aug 12 23:35:23 2009 +0000 added release alpha line to wgRnaOld track because it will not be going past dev commit 96168a9578cca298d4d9390f7d9fab9828566eb8 Author: kent Date: Wed Aug 12 23:31:04 2009 +0000 Adding docs on bigBed/bigWig types. commit 8b1b1873bd4ebdb7f3ca62b2df4da0fd092909ab Author: jsanborn Date: Wed Aug 12 22:19:38 2009 +0000 added tcga ovarian RNA seq track commit 63fc2659e354b768c959f9ca03e27c0944eeeaa7 Author: kent Date: Wed Aug 12 21:44:24 2009 +0000 Removing unused include file. commit b6405564a3327dfd16a4130c573850e72e00c3ae Author: kent Date: Wed Aug 12 21:43:40 2009 +0000 Bumping up default itemsPerSlot for better efficiency. commit 5b1b16636fe6f4510fa58feb208de9dbc7bcaa68 Author: kent Date: Wed Aug 12 21:36:26 2009 +0000 Moving some functions from bedGraphToBigBed to library. commit 45853d1c0efd59ea66f9b3bfa35aa202e3073516 Author: galt Date: Wed Aug 12 21:20:26 2009 +0000 handling rename for bigBed and bigWig for dataUrl which was already in use to bigDataUrl commit 50a878c6441600f33e68e82ed02515bca7d25111 Author: kent Date: Wed Aug 12 20:15:21 2009 +0000 This utility is basically bedToBigBed using a multi-pass approach. After some more testing it'll replace bedToBigBed. Seems to work now, but more testing needed. commit e3a0e7c5300c7fc9720e824117940c603652ec2c Author: larrym Date: Wed Aug 12 19:43:47 2009 +0000 escape database name in hDbExists to fix error reported by sysadmin at NIH commit 98e00764d9d4ee6f364ed70022bf8e9d4d718232 Author: hiram Date: Wed Aug 12 19:29:35 2009 +0000 Adding tetNig2 and oryCun2 commit 9357089e4fb0407456208ed53fe5b3f888328601 Author: hiram Date: Wed Aug 12 18:59:37 2009 +0000 Adding oryCun2 to the build commit 16d451429bf9cbc19d99080d9720cc9a76b73d29 Author: hiram Date: Wed Aug 12 18:58:11 2009 +0000 Initial files from makeGenomeDb.pl commit d815bba523a748b47b68053e2d1f66da28036f06 Author: angie Date: Wed Aug 12 18:50:08 2009 +0000 Don't enforce double- or int-checking on numeric sql fields because the filter inputs can be ranges too. commit c51b531c5b73c812c3fe1719316a5bfbaf82063a Author: markd Date: Wed Aug 12 18:13:19 2009 +0000 fix using variable string where a format should be, detected by gcc 4.3.3 commit 6f059cba1eaad0de34064c5beeb46754d7fec806 Author: angie Date: Wed Aug 12 18:12:10 2009 +0000 DGV updated to v8. commit 43c599fa662065b59411ace5c7dba1e34ee96b49 Author: angie Date: Wed Aug 12 18:00:02 2009 +0000 DGV updated to v8; changed color scheme to match their browser's. commit ab359385b60bc7f1846242d212683f809d38b6b7 Author: galt Date: Wed Aug 12 15:00:05 2009 +0000 "Encode release log update" commit a880ae165c788b7f97be6eb343e25e3718971b46 Author: galt Date: Wed Aug 12 15:00:03 2009 +0000 "Release log update" commit 9da02f88deee4b5a6e908aef91d844c3eee8e66e Author: markd Date: Wed Aug 12 08:22:34 2009 +0000 forgot comming of test input commit 111ad25a5941b54aabc62d4121a339a22e870849 Author: markd Date: Wed Aug 12 08:21:38 2009 +0000 added make test, simplify rules commit 9d60a2021f0455f9022a5704f3da5d87b5f09c3f Author: markd Date: Wed Aug 12 07:48:06 2009 +0000 added initial implementation of gff3ToGenePred converter commit 9438dad5c5658063a1fb64f23a0a49c50eb1ee45 Author: jsanborn Date: Wed Aug 12 04:26:57 2009 +0000 updated tcga ovarian cancer datasets commit 8b49b1d3d2388bb2a3bac5163975412c1e9ae776 Author: hiram Date: Tue Aug 11 23:33:10 2009 +0000 Initial browser built, running repeat masker and simple repeats commit 5ee5163cf5bee54d574a8ff1aa07630a4ec04c79 Author: galt Date: Tue Aug 11 23:00:47 2009 +0000 remove now unneeded code - thanks Brian for the review commit 29459afc458e9ca04013c3f2a0db1d24ef2ccd61 Author: ann Date: Tue Aug 11 22:52:15 2009 +0000 adding sort to a sql query so it's easier to find your db commit 6b3246ed3158fff0fa529651ba16d76e588e6373 Author: hiram Date: Tue Aug 11 17:16:53 2009 +0000 done with hg19 tetNig2 chain and net commit 8602218ba9d5488087ad9f0e9d64456846c3fed2 Author: hiram Date: Tue Aug 11 16:58:08 2009 +0000 Added tetNig2 - Tetraodon Nigirividis commit e9761573c1c81e4c96688bd6a95f4d9dbf4187a3 Author: braney Date: Tue Aug 11 16:57:51 2009 +0000 some HA CNV changes commit c6cbbc0eda3dbaf10ec8c80b7788ca0231a9a80e Author: hiram Date: Tue Aug 11 16:53:38 2009 +0000 Adding tetNig2 chain and net composite commit 04a0c81793e5248d71f6fd76ceac8da8489f8a3d Author: galt Date: Tue Aug 11 15:00:06 2009 +0000 "Encode release log update" commit 468c95510cc3ae292e933cf27ba1cc49bd9f2e96 Author: galt Date: Tue Aug 11 15:00:03 2009 +0000 "Release log update" commit 752073adf60f0bc82755492154e7373b37ac4097 Author: kate Date: Tue Aug 11 01:58:58 2009 +0000 Add contacts, and minor corrections commit 6428de980e71757c74d1978fc1a71286ccc5d428 Author: kate Date: Tue Aug 11 01:58:31 2009 +0000 Changes to Caltech configuration and labels for clarity and consistency commit cf03a49e5c376b6b3c0764a4a598d5c1fdb5daaf Author: pauline Date: Tue Aug 11 01:56:55 2009 +0000 Edited to include announcement for new yeast browser. commit d47869581804117e08c7292f305f7229a15483f8 Author: braney Date: Tue Aug 11 01:51:38 2009 +0000 change table names commit f7ac3f97c85a48b9cb29fee7c0183d881c576d4f Author: kate Date: Tue Aug 11 01:32:01 2009 +0000 Adjust display configuration based on input from Ali Mortazavi commit 53da5cb6c99af055e268e84abe178927ab7c85eb Author: braney Date: Tue Aug 11 00:58:00 2009 +0000 more HA CNV fixes commit 1c691bfb2093be4abbe3231a9c0feeca99abd7d4 Author: braney Date: Tue Aug 11 00:44:09 2009 +0000 change some colors and table names for HA CNV track commit 25c0a0c33d8f1c10d35d799119fb2a03d4c83930 Author: rhead Date: Tue Aug 11 00:37:50 2009 +0000 Added CSHL Long RNA-seq, commented out UW DNaseI HS, as it looks like this is not out yet. commit b4b70f4584bf3d795554ac0c7863425f8f570fac Author: galt Date: Tue Aug 11 00:17:23 2009 +0000 fixing 32-bit compatibility commit 161e87fe02e2911ad4400c9b2dbf463d31463783 Author: kate Date: Tue Aug 11 00:04:53 2009 +0000 Add credit to ENCODE track commit 23e82efdf7b6fa10375c0d7b3784bc2aea805e28 Author: kate Date: Tue Aug 11 00:04:14 2009 +0000 Tweak ENCODE track label commit b74b13356ada29fe45982fa1680e13b9ff9d0737 Author: mikep Date: Tue Aug 11 00:03:21 2009 +0000 v213 preview commit 8e0875b99e38bcc695808769454f2322391eb3a1 Author: hiram Date: Mon Aug 10 23:40:02 2009 +0000 Added tetNig2 commit 2389eee97e9ab53260cca38ce4a8ea7de427ad45 Author: mikep Date: Mon Aug 10 22:15:24 2009 +0000 changing download format to bedGraph commit 435fe7955f6e49cc65a44564606bd84dacba5383 Author: larrym Date: Mon Aug 10 21:14:20 2009 +0000 workaround cp -p problem commit 53427b9f7117d5139c498331611bbe90769a3533 Author: braney Date: Mon Aug 10 21:05:29 2009 +0000 change printf to verbose commit 81015a50be7a7e38ec5ea469c85ffb6ef566c579 Author: hiram Date: Mon Aug 10 20:58:59 2009 +0000 Properly output lift and bed lines for chroms that have no gaps commit 694d7ae4f7272c9555b269a0bf8bc1736c45191e Author: larrym Date: Mon Aug 10 20:42:16 2009 +0000 initial checkin commit 415bca0fef171cdcc34bbc4203c0beb5cab3b912 Author: braney Date: Mon Aug 10 18:58:16 2009 +0000 add some tests commit cc261c3850698b61cdb054c5961bba45217103cc Author: braney Date: Mon Aug 10 18:57:18 2009 +0000 more mismatch tweaks commit 170c2199c7ae61fee1a133ebfe3bcb7655f290b8 Author: braney Date: Mon Aug 10 18:56:55 2009 +0000 some unit tests commit acace87eb81336b0da755df9dab7ff7351646ffb Author: kate Date: Mon Aug 10 18:44:09 2009 +0000 July freeze close-out commit 75c4b0821413e7fa7c1e8d7a0b158072120668ac Author: braney Date: Mon Aug 10 17:55:25 2009 +0000 another typo.... darned Mondays commit c92b54149bb8337a6fbd22cb38c6f74dd643d097 Author: braney Date: Mon Aug 10 17:51:09 2009 +0000 oops... fix a typo in dataSubmitted and dataRestricted commit f5a4156ae2248d8c389364dfe6d879c45837f7e5 Author: braney Date: Mon Aug 10 17:32:25 2009 +0000 fix up dates for HudsonalphaCnv track. Also change dataType to CNV commit cb4ab88889c52dad973639ac9a3befc88cf9ea03 Author: braney Date: Mon Aug 10 17:22:49 2009 +0000 add options to ignore N's in mismatching and to deal more efficiently with sorted files (assuming there are a lot of records) commit 38b445150ec2321d56affabf9c3b11de461963ce Author: hartera Date: Mon Aug 10 16:38:35 2009 +0000 Documented production of dog canFam2 chains, nets and downloads. commit 2e8b4f1f4a0a1558f0fbaa3cd4665b2331684b3e Author: hartera Date: Mon Aug 10 16:38:13 2009 +0000 Documented production of zebrafish danRer5 chains, nets and downloads. commit f21d9d9970832ccbd9f7bb1c91fcd9116d392434 Author: galt Date: Mon Aug 10 15:00:06 2009 +0000 "Encode release log update" commit 2752b3050fdd988b852b5b0626a07681d6a31341 Author: galt Date: Mon Aug 10 15:00:03 2009 +0000 "Release log update" commit 83b36ca243869bf206d68bf9005617024ef37fc9 Author: braney Date: Sun Aug 9 21:41:13 2009 +0000 changes from Kate commit b2348262273e338b53b56bbb183fdf6334c71ccf Author: braney Date: Sun Aug 9 21:38:47 2009 +0000 have everything right (methinks) except dates and dataType for HA CNV tracks commit 92992793b0650bf8830a2e7982dcd22739e3a8b3 Author: braney Date: Sun Aug 9 21:10:19 2009 +0000 make downloads commit da624c61ba76519d39db36fffa3dcedf9e120554 Author: braney Date: Sun Aug 9 21:02:48 2009 +0000 added some HudsonAlphaCNV stuff... not quite done but need to test something commit e5816dcbb9e2eac3c92a2f43771d851fa9266c90 Author: galt Date: Sun Aug 9 15:00:05 2009 +0000 "Encode release log update" commit f18fe89858eefc6e8e38bf38bb81791bb71b4a21 Author: galt Date: Sun Aug 9 15:00:03 2009 +0000 "Release log update" commit 9e2b3e401eba697bb57f1abac49eb7173d0b24f7 Author: markd Date: Sun Aug 9 07:29:28 2009 +0000 add JK's explanation of enrichment commit 517039b6d08a8e9ec9e8a18a16a69a7b0c9a7db0 Author: galt Date: Sat Aug 8 15:00:05 2009 +0000 "Encode release log update" commit 7510f534832809949e28816ca3919643ce87345d Author: galt Date: Sat Aug 8 15:00:03 2009 +0000 "Release log update" commit ad2d152d2d9bc84bb150e328c7cb440f3701f129 Author: hiram Date: Fri Aug 7 21:13:12 2009 +0000 Trim down the gold and gap initial trackDb.ra entries commit 7bb384dc258ffc097faafad5ba12f191a5f2b598 Author: hiram Date: Fri Aug 7 21:11:56 2009 +0000 Better pages describing this V8 assembly and trimmed down gold and gap definitions commit 2a68d4f64f4a731119d01bf1aaf8104c6fba0e2e Author: hiram Date: Fri Aug 7 18:16:48 2009 +0000 improved comment, minor change commit 6e3798eb4a2adf9ebef90b091d222583a944fc94 Author: hiram Date: Fri Aug 7 17:50:43 2009 +0000 Calculate N50 values from two column sizes files commit b2548d80ce21314223eb003c3e4535684b735bf6 Author: galt Date: Fri Aug 7 15:00:06 2009 +0000 "Encode release log update" commit cf9bea8adb8ce7f02842d47c323bbe9479e7ac2c Author: galt Date: Fri Aug 7 15:00:04 2009 +0000 "Release log update" commit c6e9016d60655b42aa5525dd00cb152e036cdf3c Author: braney Date: Fri Aug 7 14:42:33 2009 +0000 make Human Proteins track. Needs re-doing to deal with chrUn correctly commit f5af1622e002dff8f792e4a1b907862995d94abf Author: hiram Date: Thu Aug 6 22:59:01 2009 +0000 Set blat server and default position commit 1d9c518bb097eda67db9682be96b852bffab18e3 Author: galt Date: Thu Aug 6 22:13:19 2009 +0000 fixing chainself downloads commit 0cb6ba18828625bc18d31afac7ee7138fa18a69d Author: pauline Date: Thu Aug 6 22:04:34 2009 +0000 Turned on genbank updates for new yeast. commit 9b2a9f5f912b42136ad001915d32bc73c9a722ec Author: galt Date: Thu Aug 6 21:30:46 2009 +0000 chainSelf commit c69efcdc8d303ad45e6e54e7e9589b939a183aee Author: galt Date: Thu Aug 6 21:27:08 2009 +0000 adding chainSelf to danRer6/trackDb.ra commit fcdbff23346f7814c23c2d004b5983da3ea4bc2a Author: kuhn Date: Thu Aug 6 21:02:44 2009 +0000 added loxAfr3 to chain/nets commit 277f6f2a5b741245dc9c629eca3bfb6418a2052f Author: hiram Date: Thu Aug 6 20:57:39 2009 +0000 Through masking and Ensembl v55 genes loaded commit b281720e4d9ab7009d06dcea68062d38f5f504e9 Author: fanhsu Date: Thu Aug 6 19:13:55 2009 +0000 Changed errAbort() to hUserAbort(). commit 8be706ec94033162dd51d8592d779a96af428585 Author: hiram Date: Thu Aug 6 18:25:04 2009 +0000 Adding tetNig2 to the browser build commit 1473c3c7fc2f9fd05f13dd2824a3881a2f5e8b94 Author: hiram Date: Thu Aug 6 18:24:20 2009 +0000 Initial files from makeGenomeDb.pl commit 4aebdacb63672eeccb49ad1a79f6ce81e9d86917 Author: hiram Date: Thu Aug 6 18:22:56 2009 +0000 Add version 54 for hg18 to get it to its last version commit ebcb11d8d8becca70b764ba49f3ee9495247cf90 Author: hiram Date: Thu Aug 6 18:22:31 2009 +0000 Adding chrM entry to the AGP file commit 54b7ec45b39a08e85ffec37f9d19b8d6f1d0f7fe Author: fanhsu Date: Thu Aug 6 17:24:49 2009 +0000 Added logic to handle missing immuno data. commit d01237e59ed93107751c4af811b762ead613bd11 Author: hiram Date: Thu Aug 6 16:44:35 2009 +0000 Download sequence tetNig2 browser build commit ac6c6f8412d967411bb341aff583580623e4429c Author: galt Date: Thu Aug 6 15:00:06 2009 +0000 "Encode release log update" commit bc6c6ff400219adb37ec44de6f1d857b83bbf82e Author: galt Date: Thu Aug 6 15:00:03 2009 +0000 "Release log update" commit 0f333c86e458bcf1a9d862d4012e4f0c61e27d5b Author: galt Date: Thu Aug 6 05:52:27 2009 +0000 fixed problem where warnBox has text with display:none but doing select-all in browser (ctrl-a) selects this extra text even when there is no warning which messes up the clipboard with extra junk commit a69d4d02c322708f78601572acfca0f8b47fb752 Author: pauline Date: Thu Aug 6 01:11:33 2009 +0000 Fixed typo. commit ea8b95cada53bc4f9b94158e36a6cc31da8a6a8d Author: angie Date: Wed Aug 5 23:34:31 2009 +0000 Added conditional use (USE_PNG) of external library libpng (http://libpng.org/pub/png/, sourceforge) to write memgfx images in the PNG format instead of GIF. Currently used (conditionally!) only for hgTracks' main image. This is to support Tim's enhancements for horizontal scrolling of the browser track image. Image file size also appears smaller than GIF but should try more test cases. commit 95e9b18cca990818597843bbecc4bd8f528f2e2d Author: hiram Date: Wed Aug 5 23:29:26 2009 +0000 Update hg18 to v54, and reset hgFixed entries to work properly for v55 commit f13a2ea820fdc620b413f0c68335b6cd6b73c3d9 Author: galt Date: Wed Aug 5 23:28:24 2009 +0000 detect and report apparent sick batch commit b34d6f2a267f23d93a6ad32ae478e40843c64ec9 Author: galt Date: Wed Aug 5 23:19:39 2009 +0000 fix problem addJob with sickBatch leaving batch on curBatches instead of oldBatches commit 4c246b5a5edcadda00ed9f9de3d9a5fc8bd3e203 Author: kent Date: Wed Aug 5 23:06:27 2009 +0000 Fixed integer overflow that was causing right half of display to be empty at some zoom values. Added back a comment that got deleted as well. commit 363455bf0859ad743649076ca4ea224f6606bf61 Author: hiram Date: Wed Aug 5 23:01:08 2009 +0000 Adding loxAfr3 commit e50c379c563eeec7b5790ab73888ac395d712a0e Author: hiram Date: Wed Aug 5 22:58:07 2009 +0000 Avoid Ensembl protein out link when non-coding gene commit c3747fdcde19badc7a913365174a3b81abba816e Author: galt Date: Wed Aug 5 20:51:57 2009 +0000 fixed comment mistake commit 70bfff7ab4babf1532db22eb16ba3ac7282b12d0 Author: galt Date: Wed Aug 5 20:33:50 2009 +0000 use width 60 for protein codons, and 50 for nucleotides commit dcf2f42e763c7f397a2d243c795d8637e7b06c27 Author: katrina Date: Wed Aug 5 20:32:52 2009 +0000 Added UW DNaseI HS to Encode download page commit 099409437da7446d8e6dfb207ccc09e66d9ec4c2 Author: giardine Date: Wed Aug 5 19:50:17 2009 +0000 Put ORegAnno links back in commit e4cda75f0f689dc0d8f0c9b7a84c073ae3c81d30 Author: galt Date: Wed Aug 5 19:40:15 2009 +0000 adding alternate path for minimal utilities commit 55e78de82fdafdf17ba206127adcea145df2e637 Author: rhead Date: Wed Aug 5 18:44:46 2009 +0000 Added a note about putting bigBed and bigWig urls in a track line. commit ad8fa47c85b3d16e0f979c4dfa201f8fb13260c4 Author: ann Date: Wed Aug 5 18:27:23 2009 +0000 added link to track line explanation commit f5b487f4d31c4625f227c13a2a7869821f1af49f Author: hiram Date: Wed Aug 5 17:57:42 2009 +0000 WUSTL has changed their URL locations for assemblies commit e90b13218b49924efbf804eaf1ddb8f3e3a1d6e6 Author: hiram Date: Wed Aug 5 16:56:47 2009 +0000 WUSTL links have changed commit 997094f2f57d777af0d0d6c946fbe4211432c20b Author: galt Date: Wed Aug 5 15:00:06 2009 +0000 "Encode release log update" commit bf2236e2945e0ac09f2f11bf7683e5e95f2a2847 Author: galt Date: Wed Aug 5 15:00:03 2009 +0000 "Release log update" commit 76cff1557da86f06600bf8ec70900ff44fc0ea76 Author: sugnet Date: Wed Aug 5 06:35:30 2009 +0000 Adding level 1-3 cage track data for evaluation commit efb4c95ac7d4ee96d54129a0f45e6717ee4e4f57 Author: braney Date: Wed Aug 5 01:03:16 2009 +0000 changed first person to passive voice. English teachers everywhere feel a tremour in the force. commit cf5d76e09e36e174050fe0ec8bba484e029f43a3 Author: braney Date: Wed Aug 5 00:00:05 2009 +0000 changed red to orange for methyl calls commit 1e4db00e729098ea76819e97f1156316b163a49e Author: braney Date: Tue Aug 4 23:59:37 2009 +0000 changed red to orange for methylated calls commit 8df97b1b9938059be4396707754ac67fc4fa0615 Author: braney Date: Tue Aug 4 23:05:17 2009 +0000 fixed publication date commit 1af4c3d9d8a3f94bcc3a16354d36e3ef27f56149 Author: braney Date: Tue Aug 4 22:43:33 2009 +0000 properly deal with the N word commit b850e0cb0d0954613d88cbb0c9e30c464f00837a Author: mikep Date: Tue Aug 4 22:05:00 2009 +0000 "New version number v212" commit 8fa8e025be6e86351eb531d7b4e82de3c96f24b2 Author: mikep Date: Tue Aug 4 22:04:33 2009 +0000 moved the download commit e1fcc1a2513a74f3d77e2ef2ff703ff38549fc6d Author: mikep Date: Tue Aug 4 22:03:28 2009 +0000 v212 final build commit 58062c2ee2a169f0de6cc91b7db11b7cb9d46269 Author: hartera Date: Tue Aug 4 21:41:12 2009 +0000 Updated Vega Genes track to build 35 to bring it up to the current release. commit 1424b1261ae8adc04e06d1f15a4fc7a01c6c8a84 Author: hartera Date: Tue Aug 4 21:40:18 2009 +0000 Added note about code addition for this track. commit b812aaf58ec0f390fa84a186f31a351452380407 Author: galt Date: Tue Aug 4 18:28:38 2009 +0000 removing unneeded dependency commit 07e6be7a1f673d9a1120e6b61b5952fa330e7a93 Author: hiram Date: Tue Aug 4 16:18:36 2009 +0000 Correct comment about sequencing center commit d23506b6fdb0fc2e0c49e10ee3d598c18a8280f3 Author: hiram Date: Tue Aug 4 16:17:40 2009 +0000 Add links to Broad FTP site, and photo dimensions commit 5a09f467106027808ae58c78bb3b61dede94db12 Author: hiram Date: Tue Aug 4 15:53:49 2009 +0000 loxAfr2 has become loxAfr3 commit 0f1d080f7e33dbc8e4a73edaae20fff50b466b3a Author: galt Date: Tue Aug 4 15:00:05 2009 +0000 "Encode release log update" commit 497d2e34804aa071cae343e8f421b4dd6011f2a6 Author: galt Date: Tue Aug 4 15:00:03 2009 +0000 "Release log update" commit 49e65d344a6ba7958fb41987fca60e83d2365f08 Author: galt Date: Tue Aug 4 00:40:08 2009 +0000 making pslShow and pslGenoShow use the same maxSkip==8 for small block merging that hgBlat htcUserAli uses commit f802bce37950f033ae444c8bb01c9919abc8125b Author: galt Date: Tue Aug 4 00:34:03 2009 +0000 stay clean commit 801651b6ef1fc6af2b7bb2d79ce24637d9c2f448 Author: galt Date: Tue Aug 4 00:30:33 2009 +0000 changing 60 column display to 50 commit a0c863afdbd540bee104049a483ac21b30f702b6 Author: hartera Date: Mon Aug 3 23:11:45 2009 +0000 Added a track handler for the vegaGeneComposite track so that it uses vegaMethods(). Updated a sprintf to safef in vegaGeneName() as suggested by Hiram. commit 218dfcc9e6e829125a0f8aa7f2eef048f111cba8 Author: angie Date: Mon Aug 3 22:41:09 2009 +0000 Fixed our local samtools installation so it's always in samtools/x86_64 (no exception for x86_64) -- thanks Mark. commit 645bfb53ceb617520e94ddbcd5a122a52c043eb0 Author: angie Date: Mon Aug 3 22:14:39 2009 +0000 Oops, silly flag-testing bug (& comment clarification) in bamGetQuerySequence. commit 7f97a53ed35e4eb8cbfa4277969aff6e54b8bb7b Author: angie Date: Mon Aug 3 22:00:24 2009 +0000 Libified more commonly used BAM code from hgc and hgTracks. commit 9e10f80f5c5bb1a06ebf16b27e73015ed0c58a16 Author: katrina Date: Mon Aug 3 21:51:55 2009 +0000 Minor edits to Methods, Verification and References sections commit 8ca7a84da935e133ed76c432e749082adb4e2b74 Author: fanhsu Date: Mon Aug 3 21:49:31 2009 +0000 Created for V3 with new immuno data. commit df608ab4744671acb58a96279be8162557e7483e Author: katrina Date: Mon Aug 3 21:45:59 2009 +0000 shortened short labels commit 54d1c3e5c09ec2f9c7c35fe60f7040eeb58abb9b Author: markd Date: Mon Aug 3 21:11:44 2009 +0000 made several hard-coded parameters into command line options commit 892f8438f9e5221f86ab873eb5c5d9e8a399e404 Author: markd Date: Mon Aug 3 20:05:00 2009 +0000 added comment about how syntenic filtering works commit e5707d394e2e0e4ff708caf10cd374d42f4fe2d0 Author: mikep Date: Mon Aug 3 18:34:16 2009 +0000 no autoscale, limit 1-20 commit b9dd5f2a131ea22ae9a4ac4e02e626c862b3f800 Author: ann Date: Mon Aug 3 17:18:10 2009 +0000 enabled automatic generation of upstream fa files for download server commit d31f7ce02ea5a37f73d1d18492b4d004028f187f Author: ann Date: Mon Aug 3 16:59:57 2009 +0000 fixed logic error commit 9a930660985feb31451c82ed734afe65af70fef9 Author: galt Date: Mon Aug 3 15:00:06 2009 +0000 "Encode release log update" commit 73a53e433f93521277a09e4fe46490a82209dbd9 Author: galt Date: Mon Aug 3 15:00:03 2009 +0000 "Release log update" commit 2022a811ae50c583f1c61f29d701adcd9872e6b7 Author: katrina Date: Mon Aug 3 14:11:27 2009 +0000 removed release alphas from ENCODE UW DNaseI HS subtrack blocks commit e20c356919a955ed9ef293fe0f851211ca749f90 Author: baertsch Date: Sun Aug 2 21:26:10 2009 +0000 type checking and add -l ssl commit b6f1957800cf0e90667ef6ddd4b054dc8bd8cb15 Author: markd Date: Sun Aug 2 20:54:39 2009 +0000 allow disabling gap or repeat spliting, fixed bug creating duplicate output, make -minRepeat actually work commit bf40beb5cbb9268cb2b9079240966d5c3303dc1a Author: markd Date: Sun Aug 2 19:51:20 2009 +0000 Add options for counting di-nucleotide frequencies and looking at both strands of the input sequences. (from stanford) commit d43560f8b1a6f4a26b5e4187b678a92d94a17fba Author: markd Date: Sun Aug 2 19:47:35 2009 +0000 add option to specify mask input format when reading from stdin. check command line options commit 414451f6d6a58447dcaccd241c9dce90d6cf38f0 Author: markd Date: Sun Aug 2 18:57:08 2009 +0000 allow more flexability in find SAMTools commit 5a5c128b8a2aa712c20a033c2d5bef43974a22c9 Author: kuhn Date: Sun Aug 2 17:59:21 2009 +0000 dropped s from Primate chain/net track short label commit 9cb6e4aa62f669918b1d32b2090e4a4d69546290 Author: galt Date: Sun Aug 2 15:00:07 2009 +0000 "Encode release log update" commit d3efe43cbcb2691c296862bee5d752a1251f31d9 Author: galt Date: Sun Aug 2 15:00:04 2009 +0000 "Release log update" commit cc64e5d53e0b6e8e25cbc4b855c5ceace8dae44c Author: kent Date: Sat Aug 1 22:16:27 2009 +0000 Removing these unused modules. Can get them off the web again if need be. commit 3e2d2281bbc1dd91ddeb1a6fa21be21d8a839698 Author: galt Date: Sat Aug 1 15:00:04 2009 +0000 "Encode release log update" commit 033e66c6025fbf4ab29056ba61dc2530ad75f7db Author: galt Date: Sat Aug 1 15:00:03 2009 +0000 "Release log update" commit c021dbad1d6e00fe2376e78e06c5966ca03fceaf Author: galt Date: Sat Aug 1 09:13:16 2009 +0000 fixing padded display coordinate offset and negative strand issues, adjusting pslGenoShow.c to be like fixed pslShow.c commit dfe6c78ef49f0e724010de6554fb0650b4ec7e40 Author: markd Date: Fri Jul 31 21:38:19 2009 +0000 clean up executable commit 484ca69111262223b2cf0cc1425d10b70ac8e967 Author: ann Date: Fri Jul 31 21:14:03 2009 +0000 removed first part of FOOTER file, as we now have proper help files (that are mentioned instead in the README) commit 1b7954123ec0de882f28678583746d96a84d7387 Author: braney Date: Fri Jul 31 21:12:05 2009 +0000 fix up wig limits for Broad TFBS tracks commit c8d4a7863bd61acb58c9f1639a50805cc5e53892 Author: mikep Date: Fri Jul 31 20:06:17 2009 +0000 extra angle commit cacabedb86747e40009832a8ea16c37bc4a37c29 Author: mikep Date: Fri Jul 31 20:03:52 2009 +0000 fixed contacts commit ec7d5fe87b6046abf71552d365eca1fc2678b2ec Author: markd Date: Fri Jul 31 19:51:29 2009 +0000 added new valgrid defs commit 35834251026db19ae80d23878e27dd2644d109ee Author: mikep Date: Fri Jul 31 19:38:53 2009 +0000 show only the encode dir, not full hive path commit 6a56d2711f02222704fc0e1f24e79343796df0be Author: kuhn Date: Fri Jul 31 18:50:35 2009 +0000 added a little prtective logic for when the otherOrg does not have an assembly (chromInfo) commit 810f20ed8b239654053c24bcdeb443c5f4a56b47 Author: ann Date: Fri Jul 31 18:45:18 2009 +0000 a little more information. and a better URL to the userApps. commit b318fea16fb38128fb38158465a28982558f37d3 Author: markd Date: Fri Jul 31 18:27:12 2009 +0000 forgot test file commit 5cf8362094847e1e2e10013a5ee47393608a82a5 Author: kuhn Date: Fri Jul 31 18:17:02 2009 +0000 turned on some tracks be default so it's not blank when users want to see it. changed lonagLabl slightly commit 3aba837bc8c5fc35163e1bd342c7e4d1674b4db7 Author: markd Date: Fri Jul 31 18:09:24 2009 +0000 added rcsids commit 03461fbba7171339074bbab960117b09f9803f20 Author: rhead Date: Fri Jul 31 17:33:43 2009 +0000 Fixed contact name. commit e70026c7aafedb6aceaa6ae96a472720181ab200 Author: galt Date: Fri Jul 31 15:00:06 2009 +0000 "Encode release log update" commit 3374997f8b0f691722f09072160829fd9657200a Author: galt Date: Fri Jul 31 15:00:04 2009 +0000 "Release log update" commit e7c6724450828bb129e32c370edfbbc0443611c9 Author: angie Date: Fri Jul 31 04:47:21 2009 +0000 Backing out previous change -- those tables are on hgwbeta after all, oops. commit f0efb8c994553949cf033f345ca40b0f6b1e059b Author: angie Date: Fri Jul 31 04:36:23 2009 +0000 Workaround for appearance of extra column on hgwbeta which is missing some tables: add "release alpha" to the subtrack defs for hgwdev-only tables and the complete composite track def, and add a "release beta" composite track def which omits the subGroup item for the hgwdev-only tables. commit a501b5a767f84b7dd2a3d24ece571a5336a8b2a4 Author: hartera Date: Fri Jul 31 04:17:56 2009 +0000 Updated Vega Genes track to Build 35 from March 2009. commit d65ebe0bd0a49c9b18bec2b448f99fe5c12225d0 Author: rhead Date: Thu Jul 30 22:51:53 2009 +0000 Mostly wording and punctuation changes. commit f13d68d5a3ede239cdf48ceea3b9846344c22979 Author: hiram Date: Thu Jul 30 22:34:07 2009 +0000 No need to explicitly mention liftOver binary in makeDownloads README business, and better warning messages in makePushQSql.pl and move one genbank to optional list commit f1fed0527102f43681b98def49f0f4b5811e3d9f Author: galt Date: Thu Jul 30 22:21:18 2009 +0000 work-around for collision of two uses of dataUrl commit b0d55d342adc71df8826fd906d20c140001eac44 Author: kayla Date: Thu Jul 30 21:35:02 2009 +0000 removed release alpha commit c210836a26b25bf5240bde52f8d132ac0ff5ccd0 Author: larrym Date: Thu Jul 30 21:09:16 2009 +0000 tweaks commit 198091631f82babf09940fdb091065da06a2486d Author: genbank Date: Thu Jul 30 20:48:44 2009 +0000 make hgdownload contrab solaris comapatible commit de78ed7cd29acb29d2464a656c80ca80fdcbf065 Author: ann Date: Thu Jul 30 19:52:55 2009 +0000 new script commit 48d7e50da3cbc99b75ecd7651ed354ea8b1b20d1 Author: ann Date: Thu Jul 30 19:52:11 2009 +0000 this script checks to see if the file push got to its correct destination commit 48595371ca146913ed3edc71eea0327de924e154 Author: mikep Date: Thu Jul 30 19:27:29 2009 +0000 adding coords to error message commit ca0f7dfdd6615afe2236617c21039871fe28d8fe Author: kayla Date: Thu Jul 30 18:51:45 2009 +0000 removed release alpha commit 96751eacc25e6032190d9afe9d3119e7057a1fc7 Author: kuhn Date: Thu Jul 30 17:36:36 2009 +0000 fixed some capitalization on chain/net composites commit 4ca34911c41904c2d1d666c431e45ef43338ce4f Author: galt Date: Thu Jul 30 15:00:07 2009 +0000 "Encode release log update" commit f497f968a577340eec122d873502e1f9c9b93b13 Author: galt Date: Thu Jul 30 15:00:04 2009 +0000 "Release log update" commit cb63b7be81c583f8a0dcc47647e4d491995aca3b Author: markd Date: Thu Jul 30 09:03:34 2009 +0000 added some test cases around strand commit 88c24c3dbfc7ccab992490cf86b63c7bbd79fa10 Author: markd Date: Thu Jul 30 03:50:51 2009 +0000 fixed time overflow check commit 63f660200357252851b02b0b1e19472152e324f2 Author: markd Date: Thu Jul 30 01:45:05 2009 +0000 added debugging for download build problem commit f1aea861837e013fa2014a5578e89427ab5e9022 Author: genbank Date: Thu Jul 30 01:26:07 2009 +0000 added support for two hgdownload servers commit 6197d9fccb7cf499bb8411ac144d35ec17a46611 Author: aamp Date: Wed Jul 29 23:41:04 2009 +0000 Added a couple lines for genbank zip-file creation on hgdownload. commit 20733f4a86945281a79b9fc115500bc202f65a2d Author: ann Date: Wed Jul 29 20:09:55 2009 +0000 added uname command commit 5752faf467b9a4a0dc12ceb3e61980ed0d15be82 Author: hiram Date: Wed Jul 29 18:59:18 2009 +0000 Add 2bit file to bigZips, and checking bed/repeatMasker/ directory for the fa.out file commit 99015af81613883b6f352a02a7c3292327c01546 Author: rhead Date: Wed Jul 29 18:42:22 2009 +0000 Added note about chrM sequence for next build. commit 74ecc3c3afd8d62fe75c90e4506ce99afd93e731 Author: ann Date: Wed Jul 29 16:28:30 2009 +0000 getting ready for beta commit d0c7e40aa75eb6cea50c2e741c7ae8a05f1d8ca2 Author: kuhn Date: Wed Jul 29 15:50:02 2009 +0000 fixed Capitalization on long labels for chain/net tracks commit 76793f8f14660be1512375b0ed47bc32b0c7b941 Author: galt Date: Wed Jul 29 15:00:05 2009 +0000 "Encode release log update" commit 35f7b8fb1559cfedb6b8c34e6356c955d8cb8805 Author: galt Date: Wed Jul 29 15:00:03 2009 +0000 "Release log update" commit b2ff3ef98db572982ca3d7944d52c7983b24b91f Author: aamp Date: Wed Jul 29 06:51:16 2009 +0000 Added hg19 lifted version of Agilent Probes track. commit 08cb95643d0c496437c4090afdaf5cad57b2c137 Author: aamp Date: Wed Jul 29 06:50:44 2009 +0000 Added lifted version of Agilent Probes track to hg19. track override for group. HTML has an extra methods section explaining the lift along with a downloads link. commit 621473d5e5fbba69178e6301a2d4fd0dcc63dcd6 Author: aamp Date: Wed Jul 29 06:49:25 2009 +0000 Added lifted version of Agilent Probes track to hg19. commit 39781098f753c3d8cac74d1a7fbd95a8e8c5d0ef Author: markd Date: Wed Jul 29 04:24:25 2009 +0000 added RNA Binding proteins track commit cecb2fd7002fa53a1e4d2c5de59b3554a252d504 Author: pauline Date: Wed Jul 29 01:43:14 2009 +0000 One last minor edit. commit 5a160cf0a71fab5d8a9b7245a3623d4e8c68fae1 Author: rhead Date: Wed Jul 29 01:42:35 2009 +0000 Added a note about incorrect chrM sequence. commit f560c2e8a652a704a94d65aca94c30e5916aa74f Author: pauline Date: Wed Jul 29 01:38:53 2009 +0000 Forgot to uncomment changes in last commit. commit acc41a403fc24aed0d2219eaacdc8cc07ef2e056 Author: pauline Date: Wed Jul 29 01:36:02 2009 +0000 Updated reference. commit b9ec52a3cf7c375303f035323f0ce52eeb7c1f1f Author: aamp Date: Wed Jul 29 00:47:06 2009 +0000 Fix to previous two Agilent Arrays track load. Faked two extra columns to make it bed 6. commit f4c432a35b71a8c6497492dcc7d05a420a53d148 Author: aamp Date: Tue Jul 28 23:54:53 2009 +0000 Added a couple rules for Agilent arrays. commit 518d8efad47ab91fae6943789b9d38470f90362e Author: aamp Date: Tue Jul 28 23:38:08 2009 +0000 Added a couple more Agilent arrays to that composite track. commit 8646771e2c6de3e319798d8e91838fe164715a62 Author: hiram Date: Tue Jul 28 22:57:18 2009 +0000 fix spelling error commit a2c5b4ce6ffdbd7640a36a64a8686f6c022c221d Author: hiram Date: Tue Jul 28 22:56:58 2009 +0000 Cleaned up to represent what probably is true. commit 04abbcf3e7c1d2d095c5f4132b932742ed229f53 Author: hiram Date: Tue Jul 28 22:47:07 2009 +0000 Perhaps closer to the truth commit bfd31071a721fbd47b7b9ee8014c43ca24ea8dfa Author: rhead Date: Tue Jul 28 22:39:09 2009 +0000 Added two periods. commit 58a92c00673059fdbbe0bbb6c887172e318809d2 Author: ann Date: Tue Jul 28 22:25:48 2009 +0000 removing prostate cellType commit a8e343876365a45ddcf3f8e4de5b14c9b1ea8985 Author: ann Date: Tue Jul 28 22:11:22 2009 +0000 enabling RikenCage alpha release commit a829ff3f3ea86eac392e65fda1ca5cd3b787c06c Author: hiram Date: Tue Jul 28 22:02:41 2009 +0000 gap track is hidden by default commit 8b4c0dbdf2e75bae6fc41d0ae6730ef9a00e3151 Author: hiram Date: Tue Jul 28 21:59:46 2009 +0000 Combining chains and nets into single composite tracks commit 7efa079db011ae95c3a699c8e82114ba033af415 Author: hiram Date: Tue Jul 28 21:56:20 2009 +0000 Adding 5-way multiz conservation tracks commit ab81bb0dd782acbf6ba60e35ab7511c36cebe04a Author: hiram Date: Tue Jul 28 21:55:26 2009 +0000 5-way alignments done on ce7 and ce8, liftOvers done for ce6 to ce7 and ce7 to ce8 commit 6bd8f14e09f5180e58ff1b46d619468ce742255d Author: hiram Date: Tue Jul 28 21:50:08 2009 +0000 Initial images for ce7 and ce8 5-way alignments commit c4d88cf140477a05ab12b160c63284cd73c89c14 Author: ann Date: Tue Jul 28 21:31:20 2009 +0000 added link for color space commit 5c9c5a92b66a2d21d1b0471e64a20b930a722f8c Author: katrina Date: Tue Jul 28 16:21:30 2009 +0000 changed full+ to full on RawSignal visibilityViewDefaults so that the configuration menu does not display by default commit 992980875e6278c87efec8bf2eedf1b33a761965 Author: ann Date: Tue Jul 28 16:13:59 2009 +0000 can't alphabetize! commit b0560a5dd3d68bfe87f127e395c67e9996ef1929 Author: ann Date: Tue Jul 28 16:13:01 2009 +0000 added line for qaConfig script commit f6d783d727e3cc21c1a356230e920982d1787306 Author: ann Date: Tue Jul 28 16:05:05 2009 +0000 added new qaEncodeTracks script commit 91f40143bb2a1775ee8a99b4db32a1b2f83534ca Author: ann Date: Tue Jul 28 16:04:10 2009 +0000 initial quick version of script for uor use QAing Encode tracks commit dd362cf546f4230f1560d91cb86c2e5adbf92fec Author: angie Date: Tue Jul 28 15:57:40 2009 +0000 Added rudimentary click handler for bam tracks (Heng Li's alignment format). commit 114379bee1236992fd78f7bfb0bb7ba6afb30cf1 Author: fanhsu Date: Tue Jul 28 15:54:21 2009 +0000 Updated help links for GSID stamps. commit ee102402eb36eb71cb276949213aeacc1a117589 Author: fanhsu Date: Tue Jul 28 15:44:16 2009 +0000 Updated PB help links for GSID. commit c638fd34b48e04a6e23e83901960fc8af88c6f3b Author: galt Date: Tue Jul 28 15:00:06 2009 +0000 "Encode release log update" commit 2f52409e3aa148441445400998575a16a397c789 Author: galt Date: Tue Jul 28 15:00:03 2009 +0000 "Release log update" commit 4518ea1c6385e38fb64f3ef5d0f9342abe731168 Author: aamp Date: Tue Jul 28 08:56:27 2009 +0000 Added stuff for first cut of the UW Southerns track. commit 2f70a0f1b8a2308baa0fd85644c96c47b8d53a7d Author: mikep Date: Tue Jul 28 06:14:53 2009 +0000 tweak the text commit 9dcefc8f4a2672a0de293b330036a17baf996645 Author: kent Date: Tue Jul 28 03:06:18 2009 +0000 Including cirTree.h to avoid compiler error in bedToBigBed. commit 7603108eada54791589ef7749857870f5efeb4a6 Author: fanhsu Date: Mon Jul 27 23:55:39 2009 +0000 Updated link to Explanation ... commit e5270bbcb583a370a8fca482a7da5ccaa742e877 Author: ann Date: Mon Jul 27 23:40:11 2009 +0000 added strand info commit c9932be716b1a620bbf1cf3c6ab6e0d48bcb10bf Author: braney Date: Mon Jul 27 23:17:47 2009 +0000 a wee bit of text. commit 5f74cc87ccecf0383778dc81d8148a9ea5f5af3e Author: katrina Date: Mon Jul 27 22:31:58 2009 +0000 added Helicos RNA-seq release to downloads page commit 92f57792da2bb13d7956fb1bf20f1f6ac8a4e472 Author: angie Date: Mon Jul 27 21:52:09 2009 +0000 Libified the code that interfaces directly with libbam to open, fetch, close. commit 2dbffb887c1b24e8f660f6ee210bde28caf29c16 Author: angie Date: Mon Jul 27 21:46:33 2009 +0000 bamNA12878: adding stripPrefix so we don't hardcode stripping of chr from chromName for bam tracks. commit c642173da03e5c45e02c20fc8e19e3a4b8d6768a Author: braney Date: Mon Jul 27 20:22:36 2009 +0000 do downloads commit e875bb30d53d16a25841233522ded797280c2d25 Author: angie Date: Mon Jul 27 19:55:17 2009 +0000 Added include needed by .c's that include this .h only, which should be OK. commit 1135bce6616aa435cff9fde49ce721389d30ae54 Author: kent Date: Mon Jul 27 19:46:58 2009 +0000 Fixing compiler warnings. commit 026a3ea40f934a32f890339a17e32295b73cc47d Author: rhead Date: Mon Jul 27 19:39:29 2009 +0000 Removed release alphas for CSHL Long RNA-seq (Jul-09). commit 912bbab2485d0b712cac0369c00c2603d86cc3ac Author: angie Date: Mon Jul 27 19:32:37 2009 +0000 Added setting pairEndsByName. commit 04824f532e418b34a412964c2feb7a3d548db391 Author: angie Date: Mon Jul 27 19:31:49 2009 +0000 Added option (trackDb setting pairEndsByName) to join separate BAM records for paired ends into linkedFeaturesSeries paired-end items. commit 693715389ea3a3ac9f7c2ccd9c38fb3e5ea4afec Author: rhead Date: Mon Jul 27 19:08:03 2009 +0000 Fixed broken link to WUSTL. commit dc8537086f29c8df5b336bae44099949ddd7ffdc Author: braney Date: Mon Jul 27 18:52:42 2009 +0000 finished I think commit 7574af41712108a2821b0dea11b55b76140a98d6 Author: ann Date: Mon Jul 27 18:19:48 2009 +0000 fixed citation commit 9ee2196dbeaf6be4603b3f85bc52a6f930b637e8 Author: kent Date: Mon Jul 27 18:09:29 2009 +0000 Refactoring bedGraphToBigWig to put more code in libraries for reuse and to clean up some. commit bf087c11bdd4fdf816eb7fca9558127f612254d2 Author: kent Date: Mon Jul 27 18:02:11 2009 +0000 Refactoring bedGraphToBigWig to put more code in libraries for reuse and to clean up some. commit 549d1b4da6dd7fe15dc05890ebe637b7e8ca51ce Author: kent Date: Mon Jul 27 18:00:06 2009 +0000 Adding haval, an md5 alternative. commit f7854fbef8110852a6c223724015f49a54011901 Author: braney Date: Mon Jul 27 17:47:23 2009 +0000 first pass, waiting on doc from ting commit 6134516003f15f98d02650f0f6db869b82dc06e9 Author: fanhsu Date: Mon Jul 27 17:25:46 2009 +0000 Added "target=_blank" for PDF and PS links per GSID's request. commit e36192e95cb1f12ae1f07a8123296d7943180449 Author: galt Date: Mon Jul 27 15:00:06 2009 +0000 "Encode release log update" commit 7632c4f677dbb6bc9386fc9ddf42ffcf0b84bae0 Author: galt Date: Mon Jul 27 15:00:03 2009 +0000 "Release log update" commit 1ef10f3009e37dd753eeadcebe052c060c4bf1bf Author: sugnet Date: Mon Jul 27 06:53:47 2009 +0000 Adding some methods documentation from fantom 4 commit 1835895e50fbefbb6e85b02ff4d23060b4e4c2ce Author: sugnet Date: Mon Jul 27 06:53:08 2009 +0000 Adding a little documentation about the bedFilter flag commit 7e801b94cc94b2018d85364e93acf0b4af95e9bd Author: sugnet Date: Mon Jul 27 06:51:56 2009 +0000 Removing the unused combination logic from bedUi commit 9e5cbbfb1273dcf3990e84e792bfb0b13cf16ddf Author: galt Date: Sun Jul 26 15:00:07 2009 +0000 "Encode release log update" commit 8d13041c1321e5a8ed4f31b35c35f1f19bdf0920 Author: galt Date: Sun Jul 26 15:00:05 2009 +0000 "Release log update" commit 303ca1d2ce09c784b49c64bf145ab71cd25820ec Author: galt Date: Sat Jul 25 15:00:04 2009 +0000 "Encode release log update" commit 9b5047df36bd66c00e7b1ae460308147e3b3160b Author: galt Date: Sat Jul 25 15:00:03 2009 +0000 "Release log update" commit 5ffd49845fd7a443b03bc8d334d0247a722c5497 Author: markd Date: Sat Jul 25 08:32:16 2009 +0000 added option to keep initial/training gaps in alignment' commit 145d94261126e6b784378efd04f9aa9f10fb94b4 Author: mikep Date: Sat Jul 25 06:36:30 2009 +0000 added warning about link commit 35104f161835edd431822675e49ad2acd4ba2530 Author: braney Date: Sat Jul 25 02:59:20 2009 +0000 took out views, and added replicate in matrix for HA Methyl tracks commit d799a3cd3186c3ebc0633d019bda6e02088ee136 Author: kate Date: Sat Jul 25 02:40:16 2009 +0000 44way phyloP update from Adam Siepel commit acdef8f4bb710aa759d54fb43be50b1547b43ee0 Author: braney Date: Sat Jul 25 01:18:12 2009 +0000 add Rami as contact commit 615c9307177c86c99cdf2865426e7cc7855ae84f Author: braney Date: Sat Jul 25 01:17:46 2009 +0000 some rearrangements and track suppression for HA Methyl tracks commit 9cefddf656b54a171a39273ccfa730371775be4c Author: pauline Date: Sat Jul 25 00:08:36 2009 +0000 Updated for new blastTab tables. commit 9fd3cb01ce502cc3748250d6186d54ebf1d85daa Author: katrina Date: Sat Jul 25 00:00:05 2009 +0000 fixed minor formatting commit 7d64484bb1891c5302abd07913a530b3a2d35f31 Author: pauline Date: Fri Jul 24 23:25:47 2009 +0000 Corrected ref format. commit 744e389bb929f033b63ecc6f166b78f1beda8946 Author: donnak Date: Fri Jul 24 22:59:43 2009 +0000 Edited the About section of this page. commit 02b0b91e7145488ec35669d37a0e8b10d955d0dc Author: hiram Date: Fri Jul 24 22:54:44 2009 +0000 Initial build through repeat masking and kluster scratch data populating commit cb7bdd7d35fdc556ccc9e7992d0e019a7001eee1 Author: hiram Date: Fri Jul 24 22:53:13 2009 +0000 Adding ce8 to the build commit fbaad0b4f3e260c9e0925e7316856a6f9c01e7c4 Author: hiram Date: Fri Jul 24 22:52:50 2009 +0000 Initial file contents from makeGenomeDb.pl commit 611ecc64c974f76c585a1c1ce3f6b37d87c034fc Author: braney Date: Fri Jul 24 21:26:38 2009 +0000 Hudsonalpha CNV track commit 759b1027086210e6b12413e1347b7e7e0f9d45e4 Author: braney Date: Fri Jul 24 21:25:36 2009 +0000 change default visibility on HudsonalphaCNV track commit 215c8d3ebbd5758d66b07c8805cfda41999ba75c Author: hiram Date: Fri Jul 24 20:32:52 2009 +0000 lastz runs done for caePb2, caeRem3, cb3, caeJap2 commit 819afaa07eed38430cd93c25c37f13f545e4e98f Author: braney Date: Fri Jul 24 20:29:06 2009 +0000 add wiggles to the CNV track commit 286e0c7c33093674515bfaec7f58ee33653f1d5b Author: pauline Date: Fri Jul 24 20:25:06 2009 +0000 Fixed link. commit 853b3a0c1e0d1eb4851323becfb8b78505c4c6fc Author: hiram Date: Fri Jul 24 20:22:34 2009 +0000 Restore a chainFree() to eliminate a memory leak commit 522f5ec3fbcb2ba7390bf374c720ce987c1b428b Author: rhead Date: Fri Jul 24 19:21:39 2009 +0000 Updated link to reference. Changed credit to reflect the fact that we run Genscan locally. commit 312d322bfde470f00c1de03e8469400de65c9e9a Author: mikep Date: Fri Jul 24 19:00:26 2009 +0000 link to source data on Helicos commit 127a0ebb2839f9b17ef0213761909b8f69505181 Author: katrina Date: Fri Jul 24 18:55:45 2009 +0000 added a comma for clarity commit 3adf44e9c4e149e3a979ce13552ef03cf0835e1d Author: kate Date: Fri Jul 24 18:30:48 2009 +0000 First cut revamp of ENCODE portal overview section commit 27de325b05c73324e5606373b9868d44d3aaa54a Author: angie Date: Fri Jul 24 17:53:28 2009 +0000 Added link to just-published article (not yet in pubmed, but it's open-access). commit 78a0f826fea9f10bacd546d0b1e0fc30fe18fc47 Author: galt Date: Fri Jul 24 15:00:06 2009 +0000 "Encode release log update" commit 351179138d4e2f8590778263c8562aa44a2afddc Author: galt Date: Fri Jul 24 15:00:03 2009 +0000 "Release log update" commit 9a6d4a850bc28c79d866c1574d23c887ede9b955 Author: angie Date: Fri Jul 24 04:20:10 2009 +0000 When htmStart'ing in a subdirectory of trash (showSomeAlignment), call htmStartDirDepth with depth=2 so that htmlWarnBox will generate a correct relative path to images. commit b6be4070f3d98abaf23b66b10c344aac0fb92010 Author: angie Date: Fri Jul 24 04:18:45 2009 +0000 Added htmStartDirDepth, so htmlWarnBox can generate a relative path to images with the correct number of ../'s depending on where the HTML comes from (used only in hgc's alignment index/ and body/ files now). Cleaned up code a bit. commit 22bfc6962c4cf47ee11d2f4dbe9b999fd8a54ba6 Author: pauline Date: Fri Jul 24 00:39:49 2009 +0000 Added paragraph for new yeast. commit 4604477d6b18a9bc93720e28be7aaf95a4246160 Author: pauline Date: Fri Jul 24 00:32:57 2009 +0000 Added new line for new yeast. commit 79d1cd37acae1fee9cbd5e9b7e0cf89db15061c2 Author: aamp Date: Thu Jul 23 23:53:26 2009 +0000 Changes to coloring, hotspot shortLabels, and "DNase-Seq" -> "Digital DNaseI" longLabel changes in UW DNase track that Kate put in and I clobbered later. commit a84a594850afbd07a4073cde9ad566217797faef Author: mikep Date: Thu Jul 23 22:47:53 2009 +0000 free the dna commit dc05b91c65834d036cd544e4ff17b0427dbdea35 Author: mikep Date: Thu Jul 23 22:22:22 2009 +0000 check sequence or seq1/seq2 match the genome for tagAlign and pairedTagAlign files commit b4b856a8e5d9619aa150546fb9c1b5661f351aa5 Author: hiram Date: Thu Jul 23 21:40:01 2009 +0000 Now running genbank commit 0a32777d03c7d7c1bd96dc4919acd2c4b63e8932 Author: hiram Date: Thu Jul 23 21:38:53 2009 +0000 Adding chainNet composite for caePb2 commit b707782e08f02a001e3d656c20ff8379b8766868 Author: hiram Date: Thu Jul 23 21:26:23 2009 +0000 Adding ce7ChainNet commit 1f1aaabdcad42219300c47dda868d485ee6f0588 Author: katrina Date: Thu Jul 23 20:57:42 2009 +0000 removed release alpha line to push table to beta commit ab14a17e93096bb96cf75bb131eec834badfe2e5 Author: hiram Date: Thu Jul 23 20:26:21 2009 +0000 Through genome build and first lastz of caePb2 commit 74f1242e550fcb868620d51703f7d281b492956d Author: braney Date: Thu Jul 23 19:46:46 2009 +0000 fixed HudsonAlpha CNV track commit 3d523d3efaa94b1cc88096841398c004835d920a Author: hiram Date: Thu Jul 23 19:13:08 2009 +0000 Added caeJap2 commit c6e465ee6866a0d1e522d5d9e2837de67900e49e Author: galt Date: Thu Jul 23 19:12:38 2009 +0000 minor correction, thanks Hiram commit ca3b596bab8a2040d3ef16b60967fbe93ec5e066 Author: braney Date: Thu Jul 23 18:36:20 2009 +0000 added new Hudsonalpha cell types and factors for ChIP-seq track commit abfff75dd63ce88b250a0b75bf0323b4a1c46022 Author: larrym Date: Thu Jul 23 18:08:57 2009 +0000 use $submitPath instead of $submitDir when determining the encode pipeline instance commit ae8c7b35a7e6298e8d9a5e92421211e10a38d0ad Author: hiram Date: Thu Jul 23 17:46:02 2009 +0000 Initial sequence through masking commit 5d95e2cfb768a86572c7224b7ff1c5463f74211b Author: mikep Date: Thu Jul 23 17:02:25 2009 +0000 configurable tracks commit 3bef87682ed2fdaf33b0511bad7b6dfce3b26cc6 Author: braney Date: Thu Jul 23 15:14:50 2009 +0000 added human proteins track commit 6fc248d1a54a3e30ecc596b9c8e447d7f15469bb Author: galt Date: Thu Jul 23 15:00:06 2009 +0000 "Encode release log update" commit 4f6f2239dddebc5d115e6f7b66a8027afaeaad58 Author: galt Date: Thu Jul 23 15:00:03 2009 +0000 "Release log update" commit c7f16b06ea4a84a27f990cc5a754ce62bcaaf84b Author: markd Date: Thu Jul 23 04:08:32 2009 +0000 reintroduced silent truncation of chromosome part of split table names as other code relies on the buggy behavior commit f7f434cef7c823a104396d9e255887e590de15e2 Author: mikep Date: Thu Jul 23 01:08:55 2009 +0000 fixing GM colorByStrand on GisPet commit cdd1883d178d5e5936ae37a9e8388e71ed4a0ee0 Author: braney Date: Thu Jul 23 00:53:28 2009 +0000 start human proteins track commit 18b8750d466763c76e2c36c04548f28a73854e98 Author: mikep Date: Wed Jul 22 23:44:50 2009 +0000 color by strand commit fba8dcd9989028a82f585baffe674b744e43e05e Author: kate Date: Wed Jul 22 23:37:20 2009 +0000 Set default wig config for CSHL Long RNA commit d1c18d6d825f95cf1d2e2dc57344c251c390ed53 Author: hiram Date: Wed Jul 22 23:33:33 2009 +0000 Adding caeJap2 to the build commit 644a67a0df1f4027ab367a900d0d5c63b2191ae8 Author: hiram Date: Wed Jul 22 23:33:08 2009 +0000 Original files from makeGenomeDb.pl commit 0ba70003b39c51708593c2002a75c273363fe849 Author: mikep Date: Wed Jul 22 23:26:14 2009 +0000 removed unused subgroups to get rid of trackDb warning commit a10682041ad7db5b05e7a41dad0f69ccef909384 Author: kate Date: Wed Jul 22 23:23:48 2009 +0000 Explain views commit 7c6b64859d5a570259f5bde7e4f8741e74a7f1d0 Author: rhead Date: Wed Jul 22 23:08:43 2009 +0000 Added monDom5 release announcement. commit d231d172461952d1c0d38c0934808b06a399cc8e Author: kayla Date: Wed Jul 22 22:45:51 2009 +0000 removed some "release alpha" lines commit edfbc714935e220a6638f293660938f55a445fc1 Author: larrym Date: Wed Jul 22 22:34:59 2009 +0000 change releaseLogUrl to use ../.. commit 2bad543fdeb27069b2b73abf71afe1a769637453 Author: kate Date: Wed Jul 22 22:33:27 2009 +0000 Remove superfluous matrix from several Transcriptome tracks commit 37a81ca8657f26a4d6969481a2c89c3e6a263127 Author: pauline Date: Wed Jul 22 21:52:11 2009 +0000 Removing release alphas to stage on track on beta. commit 7e221fd035b31696d103755bdc84dcf3514a4f12 Author: kuhn Date: Wed Jul 22 21:24:17 2009 +0000 added disclaimer about chain/nets to assemblies without browsers commit cb68be30f642cb0dc2cab8e5aca9c6d3123bb120 Author: kuhn Date: Wed Jul 22 21:02:30 2009 +0000 adjusted grammar commit 3646c1b75d92cfa7790cac453faf74d7d5277d0a Author: katrina Date: Wed Jul 22 20:42:15 2009 +0000 short label was too long for the Encode Helicos RNA-Seq subtracks and so I shortened them commit ce6acce1d5e1d8ad30bafd7fd54d925608f7fbef Author: kate Date: Wed Jul 22 20:34:38 2009 +0000 Add some ENCODE links. Updaet signal view description for CSHL long rna track commit bd1f7e9b0eb2dfef1ba1b35dc99e9ded628dd973 Author: kate Date: Wed Jul 22 20:33:39 2009 +0000 Label and sort ordering changes to CSHL RNA-seq for consistency commit c8453343f7e123396a842dca59aa99e3ebcda827 Author: markd Date: Wed Jul 22 20:23:27 2009 +0000 fixed major memory leak (from stanford) commit 42aab769a92e4bd12aee837d7352e9f2b43fba66 Author: mikep Date: Wed Jul 22 18:53:41 2009 +0000 adding ranges for CSHL Long RNASEQ wiggles commit 93e4a2809c83e990fec065cd2200f05e35a0374a Author: mikep Date: Wed Jul 22 18:45:53 2009 +0000 added contacts commit da740d134e48f348a3d30bb59d87de9b7da9e7b8 Author: hiram Date: Wed Jul 22 18:40:28 2009 +0000 testing commit from outside UCSC commit 8497dcb7dc050165bd2db264c5dbeb75a4cf3f7a Author: mikep Date: Wed Jul 22 18:37:13 2009 +0000 fixing up controlled vocab so clickable link works in config box commit 1846a9d3a94f468bd6f193275acc05386fa2d3e5 Author: hiram Date: Wed Jul 22 18:29:55 2009 +0000 Initial files from makeGenomeDb.pl commit 409548f6a9fe0dd0e378c5a5f96b6c5ae6b1a636 Author: mikep Date: Wed Jul 22 18:25:10 2009 +0000 user-friendly names in subgroup commit f1733ce9979767f0a40848756a46ae00181f594a Author: mikep Date: Wed Jul 22 18:16:56 2009 +0000 metadata missing from Helicos commit 3069519ece334f4b75193c9b916c3db416c487a2 Author: mikep Date: Wed Jul 22 18:06:45 2009 +0000 adding Plus/Minus Raw Signal Views commit b4bfde309d8eb072ce88bc4f1e98e2d3afaec163 Author: markd Date: Wed Jul 22 18:00:27 2009 +0000 fixed broken indent commit 72c7376402dd4f182abf641c9acbe5b8efd609a7 Author: mikep Date: Wed Jul 22 17:37:31 2009 +0000 shortening name commit 4f83c6e67f1b36be82b45b560aff1915ff0e3f50 Author: markd Date: Wed Jul 22 17:36:22 2009 +0000 changed shuffleArrayOfPointer to produce a truly uniform random permutation of the input elements (from stanford) commit de2b8091407e47a33c757926955165589b95aa80 Author: hiram Date: Wed Jul 22 17:35:50 2009 +0000 Add indexes for chrM_gold and chrM_gap commit cf910834dc3308b9cbbe88b4ee9c2e4c5ba12c09 Author: markd Date: Wed Jul 22 17:28:27 2009 +0000 fixed memoryleak. remove chrom name from component names (from stanford) commit 4540a6025c24544812b58032c33172bcccd510e6 Author: markd Date: Wed Jul 22 17:21:16 2009 +0000 fixed null pointer derefernces on i and e lines (from stanford); fix broken formatting commit dc09b77de99a2630f3d409e10f1e8fb520c9f81e Author: markd Date: Wed Jul 22 16:45:17 2009 +0000 host names should be treated as case-insensitive (fix from stanford) commit a5e22a5e0010b98891c90e6019c52926cec00466 Author: galt Date: Wed Jul 22 15:00:05 2009 +0000 "Encode release log update" commit d0ac2736289969909a3e1c1205f03dd9002ad938 Author: galt Date: Wed Jul 22 15:00:03 2009 +0000 "Release log update" commit 8639b117ea759fb5f17172354260cc5a48b641c1 Author: markd Date: Wed Jul 22 07:01:29 2009 +0000 fixed bug when doing stranded overlap with psls commit c555bdca21157a43cde3711d7f420e27e65938fc Author: kuhn Date: Wed Jul 22 04:52:37 2009 +0000 reordered placental chain/nets and added to the long label: Non-primate mammals and non-mammal verts commit b9c94cdee4c19b29861e1e80c42d68781c2cf2fc Author: kate Date: Wed Jul 22 00:34:35 2009 +0000 Tweak labels on Helicos track so it's easier to interpret in dense commit a916101eec7d2ce5e13e745b7f3c6ea361dc08ac Author: kate Date: Wed Jul 22 00:25:50 2009 +0000 Minor edits to Helicos page commit 82046e7f2aef4532edbb1a85b8435e43c477655f Author: tdreszer Date: Wed Jul 22 00:01:31 2009 +0000 Fix for B0b's toggle problem, but ifdef'd out since I am leaving on vacation. Look for TOGGLE_SUBTRACKS commit 80c04932e81cb59210e966aa1fe3d13699d4ab3c Author: rhead Date: Tue Jul 21 23:53:52 2009 +0000 Removed release alpha from wgEncodeUncFAIREseqPeaksHelas3 subtrack. Data contributor noticed it was missing from RR. commit dd9d60763e5ff23fb50f138440cb38d40b6cbdd8 Author: kuhn Date: Tue Jul 21 23:50:00 2009 +0000 turned off confg boxes for view controls commit 91e7e1fbddd8a0a59c3ca8a0e12d22cf30d210c1 Author: braney Date: Tue Jul 21 22:46:09 2009 +0000 added HudsonAlpha ChIP-seq celltypes U87 and BE2_C vs NRSF commit 142ea7317eaa727f8dae8dd0c40a1722542ceaa1 Author: tdreszer Date: Tue Jul 21 22:29:48 2009 +0000 Neglected to declare these as released. commit f18ac1fba0dad08b1bd4ab4a26a1994d31e6f981 Author: angie Date: Tue Jul 21 22:29:00 2009 +0000 Hide snp129 by default now that snp130 is released. commit 65122c5e2e861448764bfffbe8204853f787873f Author: tdreszer Date: Tue Jul 21 22:28:36 2009 +0000 Mike updated 6 peaks and 8 signals. Only 6 peaks to go. commit 6d4d9368724b4f972004908a394cb520b849d9c4 Author: kate Date: Tue Jul 21 22:25:12 2009 +0000 Add Antibodies page and link in menu bar commit ae751d59f47713e06346007476b37989551bfd48 Author: tdreszer Date: Tue Jul 21 21:50:21 2009 +0000 Yale resubmitted 8 signal tracks as V2s commit b187d5f78c48092f56e7f9a328a2996d4c810cd6 Author: braney Date: Tue Jul 21 21:22:01 2009 +0000 temporarily add U87 and BE2_C to get some HudonAlpha data loaded commit 1ba590a86bacd7bbe634ae7854f426a06397cf9f Author: markd Date: Tue Jul 21 21:01:46 2009 +0000 added transmap update blurb commit 58be38046ec322614d5a8932d661ed3f28226e26 Author: hiram Date: Tue Jul 21 20:52:43 2009 +0000 add to build fastqToFa and faToFastq commit cb01dd492e77fce3c309fffde5ce1480a1e31503 Author: hiram Date: Tue Jul 21 20:42:58 2009 +0000 Initial file, through genbank run commit 912938dc093699ff96eb97b074c7fb27a87f3ac6 Author: hiram Date: Tue Jul 21 20:42:19 2009 +0000 Added loxAfr3 - Loxodonta africana commit a6b1fc0083ca58f9b84d235ef5ea51dc0c06fe1b Author: kuhn Date: Tue Jul 21 20:10:32 2009 +0000 mods for hg19.primateChainNet and reverse tracks on chimp, orang, rhesus and marmoset commit a9e3d40b04c3def1c1a272122e536769fe508690 Author: galt Date: Tue Jul 21 20:02:29 2009 +0000 cleanup commit ef37f0ae367818deaa384131b4957942ac158448 Author: braney Date: Tue Jul 21 19:42:47 2009 +0000 HudsonAlpha GM12878 TAF-II PU.1 Pbx3 Oct-2 commit e85428e35b8df608f9f1a281f214e085ebfb6628 Author: braney Date: Tue Jul 21 19:35:21 2009 +0000 HudsonAlpha ChIP-sec PFSK-1 NRSF commit df6f099c53a60ff446ad9a2a5404fb05650bac25 Author: braney Date: Tue Jul 21 19:32:59 2009 +0000 HudsonAlpha ChIPsec HeLa-S3 Pol2 commit c57a5f6f2575ac6c894278e18c4a227e781255dd Author: braney Date: Tue Jul 21 19:17:05 2009 +0000 added HudsonAlpha ChIP-seq SK-N-SH_RA vs. NRSF commit 1ed90f28ee7636409287beb09ffe6f4ce294d7eb Author: braney Date: Tue Jul 21 19:13:59 2009 +0000 added Hudsonalpha ChIP PANC-1 vs NRSF commit fba1c470a6f44be5957dcacedb61fefe38c1ebd9 Author: galt Date: Tue Jul 21 19:12:13 2009 +0000 adding more info to the commandline and removing some debug output from log commit 23444ab6ae7bb2e0de42f52d86f657e053c360f3 Author: galt Date: Tue Jul 21 18:30:45 2009 +0000 better err reporting commit 4b5dfedc9f936b773bfca1aac4b447d20654cfc6 Author: galt Date: Tue Jul 21 18:26:50 2009 +0000 better err reporting commit dde9a71118401b39f486e56a828d8b09e5cceb3b Author: galt Date: Tue Jul 21 18:25:59 2009 +0000 minor typo commit 3be3f945dde433c137ec0cfea0fa399f2f2a0944 Author: mikep Date: Tue Jul 21 17:39:45 2009 +0000 removing GIS PET Tags views commit c15e979ac339be1b1dab7027000ceb6804cd0818 Author: hiram Date: Tue Jul 21 17:10:16 2009 +0000 Adding loxAfr3 commit 8371a0b4432093c115815c55b73f6c8484568d6f Author: galt Date: Tue Jul 21 15:00:05 2009 +0000 "Encode release log update" commit 2d70bb65b21fe4ef8549565be0e173299ae56849 Author: galt Date: Tue Jul 21 15:00:03 2009 +0000 "Release log update" commit b8d8de46bad6867b4d28e4f98c8aaaa6d65153bc Author: mikep Date: Tue Jul 21 14:53:30 2009 +0000 "New version number v211" commit dce08b587423cea89be2dfe29eae037617a8ad86 Author: mikep Date: Tue Jul 21 14:53:14 2009 +0000 v211 final build commit 9371dcf34a1e9d8558ced72e2a7b05e293e1ebe8 Author: galt Date: Tue Jul 21 04:58:32 2009 +0000 resurrecting the progress bar for uploads commit 7b98985e0b06100b683d7bc3d762c6565d1ea506 Author: galt Date: Tue Jul 21 01:09:20 2009 +0000 New improved background runner with greater concurrency, throttles on validation and loading, nice-ing of process priorities, fork/exec/zombie-handling, some logging for high server load or high number of processes, some admin functions to display or reset the running-lists commit db897f27ff4e5615d5d9a80d996c2799eb6454a4 Author: kate Date: Mon Jul 20 23:45:23 2009 +0000 Adding -g allows ident to work once more. It was optimized out by new C compiler on new hgwdev commit dc3ebb713e6690f6e153a5a3e6038f577d9cf48e Author: angie Date: Mon Jul 20 23:33:13 2009 +0000 In doOutWig, when handling a composite's subtrack table: instead of applying the appropriate subtrack info only to shortLabel and longLabel, keep the whole subtrack tdb. Its type is used below, and we can no longer assume that composite type = subtrack type. commit f88a295dbcad29494a2aefa81051cf7e4c19b20f Author: rhead Date: Mon Jul 20 23:16:33 2009 +0000 Added monDom5 credits. commit 319285296df784e87c7915a9173debdafa4bd7af Author: tdreszer Date: Mon Jul 20 23:00:37 2009 +0000 The other shoe dropped Gm12878/Pol3 peaks reloaded commit b228ebb8e31d2e944d898d4e88c0f28c546d733c Author: rhead Date: Mon Jul 20 22:47:09 2009 +0000 Added monDom5, and also added the Broad release numbers for all of the opossums. commit f73fa9085739b189935f0c3ebde3e8eb9ce00525 Author: tdreszer Date: Mon Jul 20 22:44:45 2009 +0000 Yale updated 5 sets of peaks commit 74d2aa55ca90b2493eb56ee81b773a9c909081fc Author: aamp Date: Mon Jul 20 22:29:38 2009 +0000 More UW DNase changes commit 547b65d16a7f1ae83d7ed25d88ac6e659787abfe Author: ann Date: Mon Jul 20 22:13:54 2009 +0000 shortening some longLabels commit c2384a104ed9648f3c12560382dce4435b30e0a2 Author: galt Date: Mon Jul 20 22:08:16 2009 +0000 cvscheck checks for sandbox changes without updating the sandbox commit 5784365a8c32eb51afb76a18653fb1730c8b4eca Author: tdreszer Date: Mon Jul 20 20:57:18 2009 +0000 Making composite parent abandon kids without tables before building UI commit ac2a1d2e995942e1ba3c73fcd2dd746a6ad2e06b Author: tdreszer Date: Mon Jul 20 20:54:33 2009 +0000 Adding method for parent to abandon kids commit ddf2fbc912ad4ef8a39a6fedab048d2b20fa04b7 Author: rhead Date: Mon Jul 20 20:53:26 2009 +0000 Added note about setting default position. commit 3dbf6d9b159290e0e63c5fc057d8d57fb5d5474a Author: tdreszer Date: Mon Jul 20 20:42:26 2009 +0000 Added some detail about the ClosestToHome paradigm, since this was confusing people commit 146a2eb683962d49b3efac6784adb7c6e9ea9dd0 Author: braney Date: Mon Jul 20 20:28:34 2009 +0000 add Data Restriction Policy commit bbf62ca321462a56faa266926b0d57db60ca8332 Author: rhead Date: Mon Jul 20 19:00:53 2009 +0000 Added monDom5. commit c9566b2180d6af64747128cab6d4dd7f1d92145a Author: angie Date: Mon Jul 20 18:57:13 2009 +0000 bdtnpChipper settingsByView: fixed other part of sloppy copy/paste (thx Ann). commit 953f69cf19ead739003b7982e579e1060bd03912 Author: rhead Date: Mon Jul 20 18:45:22 2009 +0000 Fixed broken links to genome.wustl.edu. commit 25e60ebea8d2b1988d90334f33701ae61fa69b06 Author: ann Date: Mon Jul 20 18:38:53 2009 +0000 fixed typo in configuration of BDTNP track commit 5ba5a2a0296c0a4540c8096d6d684872a760c168 Author: hiram Date: Mon Jul 20 18:30:02 2009 +0000 Version 55 update done commit cf9167c42bec681fd0057f3879bc0cc4a9f4579a Author: katrina Date: Mon Jul 20 17:42:02 2009 +0000 moved Brian R. from grad student list and put him on staff list commit 7dca6a62d5049f38b8815620eb3e768eaf137649 Author: katrina Date: Mon Jul 20 17:03:29 2009 +0000 encrypted two email addresses commit 7a346cd6945136bc8b987ac33e767d874a7e10d3 Author: tdreszer Date: Mon Jul 20 16:41:22 2009 +0000 Fix bug where default view cfg open was remaining closed commit 5ad1649ed6ee410fac5e9af7e87411c2e032878f Author: katrina Date: Mon Jul 20 16:39:55 2009 +0000 added myself to the staff list commit f1dca98f033d27fa25253d8208b85c40e4132728 Author: tdreszer Date: Mon Jul 20 16:37:46 2009 +0000 more trickle from yale commit 608a4a151a9802946fd7ec348fde986051b032a1 Author: tdreszer Date: Mon Jul 20 16:37:02 2009 +0000 Replaced unprintable chars in NRE item names commit 6db6888935195179a140356e6c7f92ca66a21015 Author: tdreszer Date: Mon Jul 20 16:36:21 2009 +0000 Old stuff that should have been checked in long ago commit 347b0b79e3c6d704fb5a73016d8ede4720546de9 Author: galt Date: Mon Jul 20 15:00:04 2009 +0000 "Encode release log update" commit a4b4198c7543f0663b5b601083d87c04f816fb1c Author: galt Date: Mon Jul 20 15:00:03 2009 +0000 "Release log update" commit 9b275306a10c28821387f5a6c0b72b363e51c41a Author: galt Date: Sun Jul 19 15:00:05 2009 +0000 "Encode release log update" commit 3123f20e7983b04371a83d486b59c59b732b09b6 Author: galt Date: Sun Jul 19 15:00:03 2009 +0000 "Release log update" commit 48f8c94e80008fee1318d8e383d813dea933d282 Author: galt Date: Sat Jul 18 15:00:06 2009 +0000 "Encode release log update" commit 832791be680432ffd0f6a5ebb633a041708fd2fa Author: galt Date: Sat Jul 18 15:00:04 2009 +0000 "Release log update" commit 7c14a2bd5faf76d090ff3b91bb88dbf273ca0512 Author: galt Date: Sat Jul 18 10:49:13 2009 +0000 adding ./ for users without . on path commit d4eea32d48b4c96cb1e3e4d5dd5a352178604b54 Author: kuhn Date: Sat Jul 18 00:22:18 2009 +0000 changed some settings. turned multiz off by default for now commit 43453c79712ff731b75a257fc5c265a441c66a92 Author: galt Date: Fri Jul 17 23:26:47 2009 +0000 handle sandbox configuration commit a9b4bfc810a6a19d494497c78fe0cccf6ce71d4c Author: braney Date: Fri Jul 17 22:55:20 2009 +0000 add some new antibodies from wiki: Oct-2 PU.1 Pbx p300 commit 59a5cac4b562ff7c6dd4e85888020c153f0e6104 Author: tdreszer Date: Fri Jul 17 22:28:05 2009 +0000 Cleaned up some metadata mistakes in Yale commit 07ff2c7ed110e9f438b2b055b70c99f10865820b Author: tdreszer Date: Fri Jul 17 22:26:25 2009 +0000 Added data release policy commit e0db365931282cb14bdea4320a433f7979bf5ccf Author: tdreszer Date: Fri Jul 17 22:25:25 2009 +0000 Added Data release policy commit 083701edf95d946ae7c0b760b42bd681fe99ffe4 Author: mikep Date: Fri Jul 17 22:19:57 2009 +0000 Affy data for 431 commit 43a1fda561753f545f72b9eaeaf22dd1e8bd5fdd Author: kuhn Date: Fri Jul 17 22:02:52 2009 +0000 a few typos commit e99e4895cbb72664f74d137086701c155f4cdf78 Author: galt Date: Fri Jul 17 20:32:52 2009 +0000 add settings profiles for SSL and BAM commit 83d2fba7c2a6daba6a91089d9da2de48667d4e7f Author: galt Date: Fri Jul 17 20:31:38 2009 +0000 make util to help configure a sandbox with settings like SSL,BAM commit d65bf638c974c109b84b4a118bd6d574e65e9b05 Author: ann Date: Fri Jul 17 19:07:29 2009 +0000 fixed up references commit 47a35e7656ecc5bcca71b2a256f572fc9081c4ec Author: angie Date: Fri Jul 17 18:57:52 2009 +0000 bugfix for igtcColor: BayGenomics' suffix is BG. commit 0757e7729776e0b82db974414159811ec6b438a0 Author: katrina Date: Fri Jul 17 18:26:33 2009 +0000 reordered the multiz9way so wallaby is at the top commit 8775ca4194b77652d0780011ae394967aa8fdccd Author: tdreszer Date: Fri Jul 17 18:25:41 2009 +0000 Limit portal to chromSize. Fix dragScroll in IE which choked on ondrag event. commit 91163652078c82a93bc706bdbd893833bb5cebe8 Author: tdreszer Date: Fri Jul 17 18:23:05 2009 +0000 imageV2 change to fix position inflation due to portal/dragScrolling commit 41045cd1b73a3d47d14b81f9258038d2f2316b41 Author: tdreszer Date: Fri Jul 17 18:19:22 2009 +0000 Limit GET->PUT logic to when page has a form (CEL search creates 500 links and timeouts). Also played with smothing IE dragScroll. commit 65d0b2f9d8f8a9fec813e7c0355aee684e68157f Author: rhead Date: Fri Jul 17 17:53:14 2009 +0000 Removing link to Mark Fishman at Massachusetts General Hospital. There does not seem to be a suitable replacement link. commit 623bc137dd9a1eaf9f8e95e79e0cf97e7cf9967b Author: kuhn Date: Fri Jul 17 17:38:08 2009 +0000 lower-cased the C in hg19chainNet commit 7c6452aff8622d3bd2a00a8658bd970618f3b9ef Author: angie Date: Fri Jul 17 17:34:17 2009 +0000 Copy-paste error noticed by Brian in code review, thanks! commit 80a00929ac7bf5659b31b0fef5f7a16ffccfdbca Author: sugnet Date: Fri Jul 17 16:08:43 2009 +0000 Adding some additional documentation commit f4916888b0296204e2646882c21cd8e360f9859b Author: mikep Date: Fri Jul 17 15:24:26 2009 +0000 new data from AFfy commit a2619f65f49993f9d47fda52b1cd83f5df958ecf Author: sugnet Date: Fri Jul 17 15:03:31 2009 +0000 Handle bed filter ui in multi-view composites commit 661039d6aeec878175585c7e2ac1e86455c4c759 Author: galt Date: Fri Jul 17 15:00:06 2009 +0000 "Encode release log update" commit e80b6e6c593ae5a675917701597bc188e33a6eb4 Author: galt Date: Fri Jul 17 15:00:04 2009 +0000 "Release log update" commit dfad0cfd197dfa699869918829e57a67a02d5b37 Author: sugnet Date: Fri Jul 17 07:40:40 2009 +0000 Adding additional options to trackDb.ra commit 92edb66c751c7ec5b651051866a3056ad5ee0081 Author: sugnet Date: Fri Jul 17 07:29:27 2009 +0000 Files for CAGE track commit 2704d3480a9ca93710bc319b7d836be77b15fca0 Author: sugnet Date: Fri Jul 17 06:48:58 2009 +0000 Adding docs about generating the cage track. commit 4287ed639b1548f6e7ca40051d52f6a13a860d98 Author: sugnet Date: Fri Jul 17 06:30:37 2009 +0000 Adding support for Fantom CAGE 4 track and filtering beds based on their name. commit f5dfb74014b6e2f2a192364554055056bbce9794 Author: sugnet Date: Fri Jul 17 06:24:58 2009 +0000 Adding support for Fantom CAGE 4 track and filtering beds based on their name. commit eb3e8e0645ccd1c1fc33ad08bd47a246732d8d47 Author: braney Date: Fri Jul 17 01:14:00 2009 +0000 add some Hudsonalpha control information. commit 4fd5921705ede4799ca0b6d9ac2f38635b921c96 Author: aamp Date: Thu Jul 16 23:00:42 2009 +0000 Disable next/previous item on bigBed. commit 62b7332c5a3b0a2bc44a86e6ae60805fe43fe120 Author: mikep Date: Thu Jul 16 19:50:36 2009 +0000 adding fragsize to labels commit 0d8084f1084d09df77c4c3484185520be316c959 Author: rhead Date: Thu Jul 16 18:31:34 2009 +0000 Changed broken link to paper to a DOI link, which should be permanent. commit a0b57f4725ecc57ca5119b65e9514c3901f1e3de Author: ann Date: Thu Jul 16 17:12:09 2009 +0000 removing beta block for snp128 override block. we are hiding snp128 by default now that we have snp130 (so snp130 and snp129 will be on by default) commit 8b84e0634900096e7719a68f525086943ccfd74a Author: angie Date: Thu Jul 16 17:01:21 2009 +0000 Oops, no space or quote characters in ifeq. commit 3d4d1c44bafdc9ad93cc177fe3dd231e5c4d0c61 Author: ann Date: Thu Jul 16 16:39:23 2009 +0000 added paragraph about the new feature of displaying the function and coding differences relative to particular gene sets. commit 5b667d5d2ca8e33fcacf2e7c279c03a48fa99da2 Author: galt Date: Thu Jul 16 15:00:05 2009 +0000 "Encode release log update" commit 15797683a3b1a93bc63f2b4734b7295b4d6a5d4e Author: galt Date: Thu Jul 16 15:00:04 2009 +0000 "Release log update" commit 240482f06688e6fdaa6bb6b5febedd2ad8c9af14 Author: larrym Date: Thu Jul 16 06:32:20 2009 +0000 narrow special cased AppleWebKit versions in dragZoomingConfig commit f888984a4ede10f74295f43ec8b81884878c7146 Author: braney Date: Thu Jul 16 03:25:22 2009 +0000 added K562 C12878 cell lines to Hudsonalpha MethylSeq commit b5cb05cd566f254c447002faf765db758deea78c Author: galt Date: Thu Jul 16 01:09:32 2009 +0000 burned once, trying a helping hack commit 6ae6f61d8aa42dc254d8a9672fb7ae1b400a0ec7 Author: galt Date: Thu Jul 16 00:13:15 2009 +0000 typo fix pine to pipe commit 99e8eebc372cd06a56011a641a43622abdbe1b43 Author: kate Date: Thu Jul 16 00:06:52 2009 +0000 Minor edits commit 7912b09f443d1ff581672336263e16dc274f1e63 Author: aamp Date: Thu Jul 16 00:06:29 2009 +0000 quick bugfix on an undefined variable access. commit dc4f11a2d5ae478c655e3f39751c2ebcae4c47ac Author: kate Date: Wed Jul 15 23:46:17 2009 +0000 Edit label and defaults for consistency commit c16507a11648d3501292feda90140d23cb8f3e72 Author: kate Date: Wed Jul 15 23:34:53 2009 +0000 Minor edits for consistency and clarity commit f58a365ebc9b690e985b8e795b10bec711e07a24 Author: pauline Date: Wed Jul 15 22:35:09 2009 +0000 Fixed reference formats. commit 67a8753b7d3b309e0d484f78d4db2bb2bdba2070 Author: mikep Date: Wed Jul 15 20:46:54 2009 +0000 v211 preview commit 3c164bf292c5aac9f58bc461435105a0417ace84 Author: mikep Date: Wed Jul 15 20:45:18 2009 +0000 different link line with gbWarn in it commit 7a98a2ea539cc2e921006e03f90c17b3d465eb8b Author: hiram Date: Wed Jul 15 20:40:22 2009 +0000 Adding loxAfr3 to the build commit ce782e06ebde5d9fab9aa3bda2b40bb9ffc7b10d Author: hiram Date: Wed Jul 15 20:39:48 2009 +0000 Original files from the makeGenomeDb.pl script commit bf47ddee005893d0b29b759e6007dcc75a0feba9 Author: markd Date: Wed Jul 15 20:29:42 2009 +0000 removed unneeded stackdump commit 400ef3ab01dabf0651a4159fb73ba0a68f610c4f Author: angie Date: Wed Jul 15 20:26:10 2009 +0000 Fix to SAMPATH setting: for MACHTYPE other than x86_64, look for a MACHTYPE subdir lib. Also let user's SAMPATH env variable take preference if set. commit 0e9feed74b8cbd86bdcf7a3bad1399dbf65f8b1b Author: mikep Date: Wed Jul 15 19:43:10 2009 +0000 fixing same problem with g+w, teh fiels are alrady this permission commit e6e437e4d09ac86787647b72c6c25b5ac11204f5 Author: mikep Date: Wed Jul 15 19:37:17 2009 +0000 merging fix for weekly build, stops make failing with error if done sequentially by 2 different people commit 6affc0c36944f6f70d58453ce15ec7881329f064 Author: ann Date: Wed Jul 15 19:10:03 2009 +0000 did not mean to check that in! commit baab29e991b5ab54d4573adb759684238cffaa30 Author: ann Date: Wed Jul 15 18:43:01 2009 +0000 description commit aecd6006c6dbdc0aa8f5ab976ab9751418d46ad2 Author: ann Date: Wed Jul 15 18:42:00 2009 +0000 description commit 6503999825c0394cdf01fbf7b5f0912a7df37353 Author: ann Date: Wed Jul 15 18:34:40 2009 +0000 added borders commit c36a4e7578c72dfb739f2b604ca0095fa6dc221b Author: ann Date: Wed Jul 15 18:24:49 2009 +0000 point to new iupac html page commit bbcd9be66c2c8728b239e529fa42b71004707e3b Author: angie Date: Wed Jul 15 18:22:37 2009 +0000 Updated link to IUPAC codes to Ann's new goldenPath/help page. commit 4570749a7991daef860e8032a60e0cb91be316ac Author: mikep Date: Wed Jul 15 18:17:26 2009 +0000 better errror message commit e93100ec72dc3040fbd880568301e3d3ccfcb96a Author: rhead Date: Wed Jul 15 18:16:10 2009 +0000 Fixed broken links to wustl.edu. commit 3bd337868ba611fcae74c02b685099c48295565f Author: ann Date: Wed Jul 15 18:12:25 2009 +0000 the table commit e75a2da6cc1b308557e4b5d2f326530167b7ab62 Author: ann Date: Wed Jul 15 18:03:22 2009 +0000 point to new iupac.html page commit 50c016169b7259d39bdb6589a7df002f30e909c6 Author: ann Date: Wed Jul 15 16:35:47 2009 +0000 goldenPath/help/iupac.html commit 16bbff70902dc4a9eb9ff156348e7fc5fcd1a35d Author: galt Date: Wed Jul 15 15:00:06 2009 +0000 "Encode release log update" commit 57991510f6a869e396ab960305c41d2da3ed54ab Author: galt Date: Wed Jul 15 15:00:03 2009 +0000 "Release log update" commit 6a8d4c65a98ddc216707689ebd0dbd5217c78557 Author: katrina Date: Wed Jul 15 14:05:50 2009 +0000 made comment in makeDoc about removing sgdToSgd table commit d4de94bdd66529812b6e9a641cb07a200935e03a Author: aamp Date: Wed Jul 15 09:22:53 2009 +0000 Run validator with -allowReloads if (a) the box is checked on the upload page, or (b) user is an admin. commit 5f2047baa7a70dfdd797e6462f02150f693e7b96 Author: mikep Date: Wed Jul 15 05:22:26 2009 +0000 new GIS RnaSeq data commit 03040a598b3e93f2bb2fa0ec06965ee03c7e67d9 Author: markd Date: Wed Jul 15 04:14:50 2009 +0000 don't close files that function didn't open, which lead to double-free crash commit e8165c44d997ebc1b7cc0c13d0cbf1adab56b51c Author: braney Date: Wed Jul 15 03:08:05 2009 +0000 added USF-1 Egr-1 Sin3Ak-20 to HudsonAlpha ChIP-Seq commit 30f5d219fc597389956bc84e3e8ccd0814a9c4fd Author: mikep Date: Wed Jul 15 02:03:48 2009 +0000 dont need comment commit 3f80a244ffc0a954ea12ddb7985c8c72b56a8505 Author: mikep Date: Wed Jul 15 01:42:51 2009 +0000 removed deprecated warning and added check for raw directory commit 04cb838091d81e1b046db941d1c932859ea4722f Author: mikep Date: Wed Jul 15 01:38:57 2009 +0000 GIS PET new tracks loaded commit 142d484747629aca4a4b483ee7fb36765d6c17d1 Author: angie Date: Wed Jul 15 00:55:21 2009 +0000 Moved connection-freeing into the block that originally allocated the connection. commit e621eb6a4b19e9f58c6f1b7010332944ed9c6309 Author: tdreszer Date: Tue Jul 14 22:50:07 2009 +0000 FF 2.0 had problems with inline-box. So the box resizing must be more primative. commit 910d47f44d9f39be8a958679eed79d6396efd36f Author: hiram Date: Tue Jul 14 22:26:08 2009 +0000 Updated with version 55 gene set pointers commit a8d1293fa9d29dcc89a1ee7b6ddf6d87a47e3141 Author: rhead Date: Tue Jul 14 22:13:21 2009 +0000 Fixed broken links to wustl. commit e1fadc2641bab15b9548c5619f7b1652a7cbc752 Author: hiram Date: Tue Jul 14 21:57:04 2009 +0000 Ensembl human release v55 today, no longer need to go to pre.ensembl for hg19 commit f0f3b0a947e8669751cf55d3dc35d22b5ad586f9 Author: markd Date: Tue Jul 14 21:11:48 2009 +0000 don't dump stack on bot trap commit bdf81d358de931f13e0588b7e8334e83c888562f Author: markd Date: Tue Jul 14 20:17:30 2009 +0000 fixed some missing closes noticed while search for a bug commit bdda2f7276978d95b78bcfea1e89b1dd3e265100 Author: markd Date: Tue Jul 14 19:49:29 2009 +0000 generate useful error message when there is a huge chromosome name, most likely caused by an invalid table name commit 81d90b77f49909669c53ac13f4dca743579c1bd6 Author: hiram Date: Tue Jul 14 18:40:25 2009 +0000 Initial source used for the past couple of Ensembl updates commit ed2549d4add90e2695b2373d36eb6138198a90d5 Author: galt Date: Tue Jul 14 18:27:38 2009 +0000 ann requested some fields be enlarged commit cfe666240c00c7544c1025abfe1d004ad5874dda Author: kuhn Date: Tue Jul 14 17:52:24 2009 +0000 dropped mantin of cgdToSgd commit e16c64ef010bd66f6c187debb058b6e4447517ad Author: larrym Date: Tue Jul 14 17:45:55 2009 +0000 re-enable drag-and-droom for AppleWebKit >= 531 commit f1aaddfce2f9782d1d979c194a446844d6256b9f Author: galt Date: Tue Jul 14 15:00:08 2009 +0000 "Encode release log update" commit 40f03fd8da6ce56a78590e498fcc7d11897737b2 Author: galt Date: Tue Jul 14 15:00:04 2009 +0000 "Release log update" commit 2625b92dcebaa680e8a830bf790232b72e0a7e71 Author: aamp Date: Mon Jul 13 23:39:14 2009 +0000 Put UW DNase tracks back into trackDb. Will work around validation stuff another way i.e. adding -allowReloads validate capability in the pipeline. commit f5c9052aa5f26297217796ef19b85494eec0dbb7 Author: kuhn Date: Mon Jul 13 22:59:37 2009 +0000 changed to hgw8 for now, as hgw1 is out for upgrade commit 02ce0e2d67bf0e59512ee726ce81bb2237e21635 Author: mikep Date: Mon Jul 13 22:34:31 2009 +0000 fixed up coloring and track short/long labels to all be standard for CSHL and Affy and fixed up track settings for Transfrags commit b90277f9cb4bf772ec72b2e12192844397d8b426 Author: kate Date: Mon Jul 13 22:34:16 2009 +0000 Change labeling for consistency commit 3643f57b4e2224328b1bb066a7fdc890af0debf6 Author: aamp Date: Mon Jul 13 22:02:47 2009 +0000 Removed UW DNase-seq in prep for reload (to avoid validation errors) commit 0339f15de65872191b5f03c2d6a27c4ec454c292 Author: mikep Date: Mon Jul 13 20:55:44 2009 +0000 updated documentation commit 14638daf0d8c69186b3db9a5cf710b68a83cf5ef Author: hiram Date: Mon Jul 13 20:42:06 2009 +0000 overrides for hg19ChainNet track commit 63f43e7e14dace96b7a656a592a8cb00009f44d9 Author: hiram Date: Mon Jul 13 20:38:13 2009 +0000 Done with enough tables to get full hgGene click through to work commit 4f0255aed6f1f42c919fa283c053d42c38baeda6 Author: hiram Date: Mon Jul 13 20:37:38 2009 +0000 danRer6 lastz done, phylo tree 4d site prediction done for 46 way, biocyc data obtained commit 26f6620ae177fbaffcc4f5c0ec4256e6cffdb47f Author: galt Date: Mon Jul 13 15:00:05 2009 +0000 "Encode release log update" commit d33ef4e4972cd1ab0843165feec837cb557316b0 Author: galt Date: Mon Jul 13 15:00:03 2009 +0000 "Release log update" commit ba04abe9a387bb2f30ec86ea1091105553505d55 Author: galt Date: Sun Jul 12 15:00:05 2009 +0000 "Encode release log update" commit f687fe8948b338a90d5a3ea5065cb186eefa8701 Author: galt Date: Sun Jul 12 15:00:03 2009 +0000 "Release log update" commit 69e8a4424d489e9fc1f7198de46adcb6ecc07245 Author: markd Date: Sat Jul 11 17:30:44 2009 +0000 added option to preserve reference coordinates commit 9af645efdfb1357553a7e7e94f46851a82bb341a Author: galt Date: Sat Jul 11 15:00:06 2009 +0000 "Encode release log update" commit 8b2010d469cb6960604ec7a06a785a5d74b6ccef Author: galt Date: Sat Jul 11 15:00:03 2009 +0000 "Release log update" commit 36041350062ecc21bcb9234a118bd51ae84b7fb3 Author: fanhsu Date: Fri Jul 10 23:37:24 2009 +0000 Updated with actual fields of the latest data from GSID. commit 9dfe3d776d2c2f1b6da3d6f702f3949d0ee3bff1 Author: fanhsu Date: Fri Jul 10 22:58:40 2009 +0000 Minor update. commit 2ce7202d6e489b36c599f70c7114fa6a904a8683 Author: mikep Date: Fri Jul 10 22:21:59 2009 +0000 formatting commit e1d63cf5c3036e919c1f3c992574c5f38d55ccdd Author: mikep Date: Fri Jul 10 22:18:01 2009 +0000 first version of doc for CSHL Long RNA-seq commit 8370ab69a2ee3be4139923cea6c7f3a383af6f6b Author: angie Date: Fri Jul 10 22:17:04 2009 +0000 In printSnpAlleleRows, don't reverse-complement refUCSC if it is like '(1000bp insertion)'. commit a30995aa49b57a15754571aafd780278ab8e084d Author: braney Date: Fri Jul 10 22:16:49 2009 +0000 check trackDb for species that should be off rather than depending on the cart having this. commit 9ebc6ac42da83a5ad7ca0bf08cbbcfa648c95dd4 Author: rhead Date: Fri Jul 10 21:54:36 2009 +0000 Added explanation of chrM and chrUn, and noticed there are 8 autosomal chroms, not 7 commit 489d39874be9727fed0a2387022c1927fbf04f77 Author: hiram Date: Fri Jul 10 21:54:19 2009 +0000 Fixup the multiple lastz and axtChain matrix displays commit 810bc4ee5505af0414ce522b18a7d24978da6c70 Author: hiram Date: Fri Jul 10 21:11:54 2009 +0000 the ChainNet tracks should be specified by their db name commit 62f7961b66f6e36d8fd9c5aa0d83ffcb4360beed Author: katrina Date: Fri Jul 10 20:27:40 2009 +0000 Added info about removing records from sgdToName commit e5dc63193d38bed9f7b2d6351a2906409c026ecc Author: tdreszer Date: Fri Jul 10 20:10:30 2009 +0000 Fixed bug in leftLabel size under imageV2 logic commit 633de1027f28c31d335c4f8247deb241a36a4e0b Author: tdreszer Date: Fri Jul 10 19:49:58 2009 +0000 Next rouund of imageV2 development. dragScroll is working. commit 739dd0955b73a3afc8642e65e1ebae23a6591f05 Author: hiram Date: Fri Jul 10 19:30:37 2009 +0000 Fixup sgdToName table commit 12fd64b4369d3894f14922c0cfa6f2082894265c Author: hiram Date: Fri Jul 10 19:28:24 2009 +0000 Update date/time for fetch of this data commit 1ecc49ea64f8514577dde91f3b366bb5e0aa5dd4 Author: donnak Date: Fri Jul 10 19:26:48 2009 +0000 Added eng job announcement. commit d33beac67dd74f104b20cc983c782106635cca55 Author: donnak Date: Fri Jul 10 19:26:22 2009 +0000 Archived an item. commit cefa21d74fc5c0712b9a763656ecef406679f1d8 Author: mikep Date: Fri Jul 10 19:04:24 2009 +0000 CSHL Long RNA-seq is a new composite type commit 67f178f645179459caa36d6e1dfa01a89909fb1d Author: kuhn Date: Fri Jul 10 19:00:35 2009 +0000 adjusted to only check one RR machine, as they all now share hgsqlrr commit 8ea9beed4908c91af0874a6b4412fdff98328c15 Author: mikep Date: Fri Jul 10 18:51:12 2009 +0000 new datatype as this will be a separate composite track from CshlRnaSeq (short RNA-seq) commit 70ba660fe5b0a0d89e904a150ec7ee1dcc900847 Author: tdreszer Date: Fri Jul 10 18:23:57 2009 +0000 Replaced input type submit with BoB's new OK button image. Removed obsolete, ifdef'd out code for warnBox using real HTML alert() commit 90bda5ce9937e37cd5ff26b8a4f588f37ad18904 Author: markd Date: Fri Jul 10 18:11:57 2009 +0000 added option to output mapping chain that was used commit a67c9b567f4650719c3291dbceb59b27a7485a62 Author: markd Date: Fri Jul 10 17:48:36 2009 +0000 fixed segv when file doesn't exists and no database was supplied commit b16ed39513fd8648b1eb817c16321a022a8f68f1 Author: fanhsu Date: Fri Jul 10 16:09:39 2009 +0000 Minor update. commit c94a6934dc941491833bafca14ad7b686da7a877 Author: galt Date: Fri Jul 10 15:00:06 2009 +0000 "Encode release log update" commit a25629947e5014137b64d0597b69e853c6fdd851 Author: galt Date: Fri Jul 10 15:00:03 2009 +0000 "Release log update" commit 128c2da47fe4a57590ce7fca254d29b535a277c0 Author: markd Date: Fri Jul 10 06:26:56 2009 +0000 updated description commit fcaec6b1729bbf54743a931a2b9119b153a9038a Author: markd Date: Fri Jul 10 06:21:04 2009 +0000 composite track was premature, switch back to super tracks until controls figured out commit af5529afcc801bf70077183f874706914c68d266 Author: markd Date: Fri Jul 10 04:55:15 2009 +0000 convert transMap to composite tracks commit 190dfb485040746ef0970757d4fecd37500cc864 Author: markd Date: Fri Jul 10 04:51:06 2009 +0000 allow transMap tracks to work with composite tracks commit 7afc8fae56149183b62f58ab12f34c13d0083d05 Author: kate Date: Fri Jul 10 03:58:01 2009 +0000 Add July 2009 news item commit 036af53a3e14e54a54f71f8795c5dfd5ee4b2815 Author: kuhn Date: Fri Jul 10 03:21:06 2009 +0000 added release alphas to control push to beta. made new html files for three chain/net sets. reversed order of three chain/net tracks to match order in Conservation track. adjusted order of views on details pages commit d6ab050a82f35ab91617ab5c51e94663dbe03ee1 Author: kuhn Date: Fri Jul 10 03:02:51 2009 +0000 made separate files for the three chain/net tracks commit b1a5628d467a25a13c7e86761bb2a470ab154056 Author: braney Date: Fri Jul 10 02:42:07 2009 +0000 added human proteins track commit 793b0462871419f75010d7625eb863e38c9e94ab Author: kuhn Date: Fri Jul 10 02:10:37 2009 +0000 adding ok button commit af43cd90a0c0eb0af3b3922490d6190d4d6f051d Author: kuhn Date: Fri Jul 10 02:01:12 2009 +0000 added MicMur1 to list of chains commit 1c4581f41a2751908c0ecb626b63bcb91fa971cf Author: kuhn Date: Fri Jul 10 01:53:07 2009 +0000 adjusted BLOCKQUOTE tag to put text over matrix tables commit 7b9f9ed7ca68c88b8a3df02d5451b84008422941 Author: markd Date: Fri Jul 10 01:52:27 2009 +0000 flush stdout before forking commit 27832f881491af4ec303973016f66820831f9a66 Author: markd Date: Fri Jul 10 01:51:23 2009 +0000 fixed comment commit 543342525f8de71c58771aac22c2080bb8f87573 Author: markd Date: Fri Jul 10 01:50:11 2009 +0000 build mafToPsl as part of std make commit 09c4bf229cd79c0f559b155dc3b4078873a79541 Author: markd Date: Fri Jul 10 01:42:22 2009 +0000 use hUserAbort to prevent unneed stack track commit 29389446cbd438813d4eadffbb00a91924b848cd Author: markd Date: Fri Jul 10 01:40:38 2009 +0000 moved stackDump stuff to hCommon; added function for user errAbort commit 8e755215ba8a4978817853d6e95b9c4ef42d366d Author: kuhn Date: Fri Jul 10 01:26:31 2009 +0000 added OtoGar1 to list of chains commit 8c842124c043b3577fb5f582b3ef8126cd1361fd Author: ann Date: Thu Jul 9 23:34:19 2009 +0000 added snp130 (for hg18) commit 4facec6e59c632ede03c5b61cf2ca08ababbbfee Author: angie Date: Thu Jul 9 23:17:51 2009 +0000 Correcting comment. commit 70066d0534b1b4f673827a85d1f67bcbc59df9c8 Author: hiram Date: Thu Jul 9 22:53:08 2009 +0000 Adding the lastz matrices and chain matrices to details page commit 6f3209d39821e02f6f71aac9cbb34d55d4118777 Author: hiram Date: Thu Jul 9 22:44:16 2009 +0000 Properly fill an empty cell in a table with nbsp commit fd8510f0dcb3cfff0dc7bf24497731eedcd249bd Author: angie Date: Thu Jul 9 22:21:24 2009 +0000 Added back the varying blastp -e params that I lost when writing this. Have been using 0.01 for all blastp runs, but the original process used 0.001, 0.005, 0.01 depending on clade distance. Thanks Hiram and b0b! commit ef7019888f558d629540ca1b4fbc366a94b22f6e Author: mikep Date: Thu Jul 9 21:43:24 2009 +0000 Long RNA Seq for CSHL commit 1a7c3f660ff590d62f63900103665f29d0896cf7 Author: kuhn Date: Thu Jul 9 21:29:09 2009 +0000 added TarSyr1 to list of chains commit 9dc94179f7d15f8324fb74be7aed6b3371f512d3 Author: kuhn Date: Thu Jul 9 21:19:55 2009 +0000 dropped exit command that was in there for debugging commit c9ea9b176cd1093a6d8aa641ed07d168bf1cba02 Author: kuhn Date: Thu Jul 9 21:19:54 2009 +0000 added sort check for chain and net tables commit 68dae6982ee67feb9aed2c9f63886e7ec4e1dd0d Author: hiram Date: Thu Jul 9 20:42:30 2009 +0000 Print track description html page for transRegCodeProbe table commit df885cd76072181f73d94599433d48c547b08376 Author: mikep Date: Thu Jul 9 20:10:05 2009 +0000 notify the database being queried unless -quiet commit 7dba997ff6377f0032b2967da6b0bac0642afbec Author: mikep Date: Thu Jul 9 20:06:38 2009 +0000 get default database from default genome instead of hg17 commit ce50c526be083f883764bc27994fd43dff00dbff Author: mikep Date: Thu Jul 9 19:35:23 2009 +0000 allow INPUT tags inside SCRIPT tags for where we have javascript modifying FORM controls commit 9ce334dfcf20cecb8033c70cbf348a2e11c8c775 Author: rhead Date: Thu Jul 9 19:13:56 2009 +0000 Fixed links to wustl. commit fcd015a02f855b7ccc2e9963321b1754db671589 Author: galt Date: Thu Jul 9 15:00:07 2009 +0000 "Encode release log update" commit 998b46a214d44c2d2438be076923900ccdef1f44 Author: galt Date: Thu Jul 9 15:00:05 2009 +0000 "Release log update" commit 20547a704796ccc15582696ecb64877ea490f9df Author: angie Date: Thu Jul 9 04:13:05 2009 +0000 Oops, backing out the previous changes because they trigger both mrna and all_mrna trackDb records to display, and an upstream fix in hgFind.c fixed the original problem. commit 9bea1cbb8c41f0ecdc403fe04d4db39a3508826a Author: kate Date: Thu Jul 9 00:45:52 2009 +0000 Update to display conventions section commit 09b953ec59b3c2c8b3b4aacdb6b255c4a082cfd7 Author: kate Date: Thu Jul 9 00:29:10 2009 +0000 Clarify labels, and used preferred terms of submitting lab, UW Dnase commit 7bf536149ccb39baa515ea1ffd94359d1bdec9c2 Author: angie Date: Thu Jul 9 00:06:02 2009 +0000 When searching all_{mrna,est}, strip off the all_ only if there are split tables; otherwise all_{mrna,est} is the trackDb track name too. commit 3e4a7759fb7c842c22ab25fccee9157d0a54c02f Author: tdreszer Date: Wed Jul 8 23:54:49 2009 +0000 Don't show restriction dates if they are in the past. commit b3cecdca02d3503d8466bf9808a9c1fe3c2b9352 Author: kate Date: Wed Jul 8 23:54:10 2009 +0000 Add subtrack coloring by cell type and set default on for Rep1 of Tier 1 and Tier2 subtracks, UW Dnase track commit c73276fedfef14ec9b93f65ff7dd53baca5157a0 Author: tdreszer Date: Wed Jul 8 23:41:07 2009 +0000 Set dateUnrestricted to dateSubmitted for ENCODE Mapability tracks commit 15d7a23f2e8958ddbc94c03146a497025177c88b Author: galt Date: Wed Jul 8 23:26:32 2009 +0000 genbank, blatserver, downloads commit e26392e8fa31ef5c7a0f5b75d15495fdbdc82891 Author: angie Date: Wed Jul 8 23:18:53 2009 +0000 Fix for corner case in explainIdentifiers: when xrefTable is the selected table, and its idField happens to be the same as its alias field for the main table (e.g. refLink), don't refer to the field twice (thanks Katrina). commit 00ed49f42e889c106070ac3c02e4caa50f0b1848 Author: tdreszer Date: Wed Jul 8 23:10:38 2009 +0000 I surrender. commit d1748858c4d280b3dc266f8da3d6434d478c948d Author: kate Date: Wed Jul 8 22:53:55 2009 +0000 Add lab to mapability subtrack short labels to distinguish methods commit 18d07eec75e07da16e8d182db77df66c0e7628d8 Author: rhead Date: Wed Jul 8 22:48:07 2009 +0000 Edited sample searches so that they are more like monDom4 searches. commit e62dafbcdca3b8071e1b6ff78db814fafec412f5 Author: kate Date: Wed Jul 8 22:43:29 2009 +0000 Clarify some labels, prune others to fit length limits commit 19e3b859ac0f624f9adfbd85b01a05edb916bc41 Author: kate Date: Wed Jul 8 22:42:59 2009 +0000 Add data release blurb. Minor fixes and remove comments commit 0f3d371364b24149622370b040ccf595970dc9d5 Author: tdreszer Date: Wed Jul 8 22:07:12 2009 +0000 No blinking for the warn box title commit abe65fda18a400b294c6f6c82de2af6342be05aa Author: angie Date: Wed Jul 8 21:50:18 2009 +0000 Added some special cases to support tracks all_{mrna,est} in a database that could have split tables. commit 0b3cd0e762536bfb2f36f12128b7c50fdc849a3d Author: larrym Date: Wed Jul 8 19:48:54 2009 +0000 errAbort if we can't create symlinks in js directory commit f6a2fa1fc97c28c77f1c640910b5f10c895c9567 Author: fanhsu Date: Wed Jul 8 19:20:28 2009 +0000 New column.ra for the coming V3 data update. commit c1847438106aabf2e4affd9dbb800018833a1e54 Author: mikep Date: Wed Jul 8 18:42:33 2009 +0000 to build with SSL and BAM commit 3b162ce3519f8bdb0231356624ba50f94365d0ac Author: markd Date: Wed Jul 8 18:42:14 2009 +0000 fixed install rule to preserve permissions commit fa7acb7f0774d47a2f0a24c08ade00c0844a3e59 Author: tdreszer Date: Wed Jul 8 18:40:36 2009 +0000 Added note of caution concerning Gencode, Havana and Ensembl release cycles commit f19a49bea62d17db983631e16e87693074f09e92 Author: mikep Date: Wed Jul 8 18:29:47 2009 +0000 colon after variable is interpreted by CSH, oops commit 7ef643ed4c5125e3dd9a70bbb314e060e072c836 Author: galt Date: Wed Jul 8 17:53:47 2009 +0000 Added danRer6. commit 4d54db547b3770a6e1f58b3e16fb5ff4a2c00123 Author: ann Date: Wed Jul 8 17:46:16 2009 +0000 fixed obfuscated email address (thanks Kayla) commit 90f704980ff4e07d29dc0dcd8d387a96483b86ad Author: larrym Date: Wed Jul 8 17:09:51 2009 +0000 implement javascript versioning with symlinks commit 7ad884c7092c4e66b3736dd4da03837f3d1bd6f1 Author: kuhn Date: Wed Jul 8 16:58:35 2009 +0000 added PapHam1 to chainlist and capitalized AplCal1 commit f2a8f52cc63f1af7d4da812446d808ef9e8a6da8 Author: galt Date: Wed Jul 8 16:52:20 2009 +0000 corrected link library handling commit 0157dd3b7ecbfa69c579d6e7976075eeaf03296e Author: larrym Date: Wed Jul 8 16:24:25 2009 +0000 add listDirRegEx commit 14629634f0700dc4e483b76147f42765f5cf14b9 Author: galt Date: Wed Jul 8 15:00:06 2009 +0000 "Encode release log update" commit 8d64418b7b22bce6921bfe8e450ab94161c5f996 Author: galt Date: Wed Jul 8 15:00:03 2009 +0000 "Release log update" commit 605c42c140ec42f0cdabfd274200d8c8f9f15113 Author: angie Date: Wed Jul 8 04:06:32 2009 +0000 Functional annotations including mapped coords. commit 48b16ee234700825ac12e4e7524e6847c8c65200 Author: galt Date: Wed Jul 8 03:32:16 2009 +0000 fixed wrong path for genbank liftfile commit 3219ca3d27f7cdd3ac1d2f6112e576c794c5fae8 Author: galt Date: Wed Jul 8 03:18:21 2009 +0000 Added danRer6. commit 55bc4f8050dbd788bfbc7bfca02947a2aa2515ad Author: aamp Date: Wed Jul 8 00:43:33 2009 +0000 Made left margin 5% instead of 15%... there was just too much space on the left. commit 8f4ff6bffe228174e29e958ab0332f76332f5b88 Author: aamp Date: Wed Jul 8 00:43:00 2009 +0000 Various changes to sort links, added links to Submitter column, removed "Type" column. commit 7ed2d8eed3282c162f0096b7a8221ec69fdad2fd Author: aamp Date: Wed Jul 8 00:41:29 2009 +0000 Make sure that when viewing list of submissions from a submitter, all three of the main links on the top navbar are clickable. commit 70db6bd00c62805799d097d10a224df32f6b995c Author: aamp Date: Wed Jul 8 00:40:26 2009 +0000 Necessary small extension to helper to add optional params to the sort link i.e. the additional submitter CGI var. commit bcd0d06e0ac45fc7f216833775e94e522250aad1 Author: aamp Date: Wed Jul 8 00:39:20 2009 +0000 Changes to list and show_user action dealing with the submitter CGI var, as well as sort defaults. commit beaa6c0e554dab115875d98748f1feab4b4f0126 Author: kate Date: Wed Jul 8 00:12:09 2009 +0000 Adjust defaults as requested by John Stam at UW commit 962739a0b44a61c6d8269dc5275f7565165e8838 Author: galt Date: Wed Jul 8 00:00:49 2009 +0000 Added danRer6. commit 5581082b7b57e687a0a876342d791fbd491cc448 Author: galt Date: Tue Jul 7 23:28:51 2009 +0000 Added danRer6. commit 0af24e8f8e98ae1ea5fd7e10a90a475680182cb8 Author: rhead Date: Tue Jul 7 23:16:30 2009 +0000 Fixed error in sample position search. commit 9d7e862f727c68c6d48884a363fbbf815efa0ec7 Author: galt Date: Tue Jul 7 22:54:52 2009 +0000 final agp, browser default position, repeat masking, simple repeats, cluster data prep, cpgIsland commit 7ca8124dc9490fd9698aa411fd975bb02efccb38 Author: ann Date: Tue Jul 7 22:05:57 2009 +0000 finished editing example 3 based on the new .as file rules commit 1ed7a22ce055519ef9b9fa425835d4b84d77ae0c Author: markd Date: Tue Jul 7 21:08:38 2009 +0000 use contstant for max file path commit 60f03ba29bd00282a4edd8c85e0831cd322d1447 Author: angie Date: Tue Jul 7 21:07:37 2009 +0000 Adding search on jaxQtl (just like the old one on jaxQTL, thanks Brooke). commit c7efd3153e7b07b8a847f96f7d076213fc6d5441 Author: angie Date: Tue Jul 7 20:46:43 2009 +0000 Shortening shortLabel of jaxRepTranscript to 16 chars. commit 142fd19ab74e68c0f94b1914fd33d0bfc066ee28 Author: angie Date: Tue Jul 7 20:33:39 2009 +0000 Meant to check these in a long time ago (thanks Brooke!). commit 830f7c9dc28a39bdbf9cb0bffb2247e7bdc0db76 Author: hiram Date: Tue Jul 7 19:15:05 2009 +0000 Should be using MAKE, not make in sub-makes commit b9f3e917894cdf258d53a438994c0689f13e371a Author: hiram Date: Tue Jul 7 19:12:08 2009 +0000 Should be using MAKE not make in sub-makes commit 5dacb8af496094c23029753868e87c8be6b0600c Author: hiram Date: Tue Jul 7 18:59:26 2009 +0000 Add SOCKETLIB for Solaris build commit 8b27b252063781577ece444d33b69914f4714c39 Author: hiram Date: Tue Jul 7 18:50:29 2009 +0000 Add SOCKETLIB for Solaris build commit ee0b8621a784426ba3118d8dd85cc6bd7ad200de Author: hiram Date: Tue Jul 7 18:45:02 2009 +0000 Fixup broken build on Solaris commit ba5b77c9bf2f86b62467acb63fe96c16be1fbf48 Author: hiram Date: Tue Jul 7 18:44:48 2009 +0000 Fixup broken build on Solaris, add SOCKETLIB commit 618fbbbd5984b7effc1ee57b7587a02cca821c8f Author: tdreszer Date: Tue Jul 7 18:23:26 2009 +0000 Mary Q. Yang commit 0faac6e4c54f548aa4d04528c7b4e755379a512f Author: markd Date: Tue Jul 7 18:05:11 2009 +0000 removed gbSeq, as it is in it's own file commit c2bb6cc85abfb033f2493377f877bf8bf8ce7bbe Author: hiram Date: Tue Jul 7 17:58:56 2009 +0000 Fixing a gap confusion bug commit 539834b908a94b7a5454523ac53a34b665133ac9 Author: hiram Date: Tue Jul 7 17:58:00 2009 +0000 adding bigWigInfo to the build, and need SOCKETLIB for building on Solaris commit 116a32985072a74f1db8ebb35f4d41d0461c6dbb Author: hiram Date: Tue Jul 7 17:57:39 2009 +0000 dding bigWigInfo to the build, and need SOCKETLIB for building on Solaris commit 0ea2bbdf5151eda886944f18e780d34d88a5096a Author: aamp Date: Tue Jul 7 17:57:27 2009 +0000 "New version number v210" commit 1a886bc58d4e967bb10a6284d2935667e03572c3 Author: tdreszer Date: Tue Jul 7 17:56:53 2009 +0000 Elnitski BiPs have no score filter at all since all scores are 800 for this species commit 664e20b11c773691943e4e84a0949cb685e00b4f Author: aamp Date: Tue Jul 7 17:55:58 2009 +0000 v210 final build commit ebf05fad1062445b192cfc795ff8e74c3e763f5d Author: tdreszer Date: Tue Jul 7 17:39:34 2009 +0000 Cleanup for Mapability. BiPs now use new 'filterBy score'. commit ad6902b782c5c02e3f5b4133b61655919c763f82 Author: tdreszer Date: Tue Jul 7 17:38:04 2009 +0000 Last minute addition of another reference. commit 61dc007be65d1aa49ef4cfcc1c3ae5f3d2ba99f0 Author: tdreszer Date: Tue Jul 7 17:37:05 2009 +0000 Cleaned up. commit 4a9f3a9bbbb122e500ed5efb8f290d4ed824d1c4 Author: hiram Date: Tue Jul 7 17:14:19 2009 +0000 Needs SOCKETLIB for build on solaris commit ae21dc84233db6770d8c23a440a6aba28deae6b2 Author: hiram Date: Tue Jul 7 17:10:20 2009 +0000 Needs SOCKETLIB for build on Solaris commit 225201a75a44ae4965f6d2616b71a4694f3a6a60 Author: hiram Date: Tue Jul 7 17:08:03 2009 +0000 Needs SOCKETLIB for build on solaris commit c6c53285081b040fdf04d5ba8d3b9ef5d791e2f1 Author: tdreszer Date: Tue Jul 7 16:40:46 2009 +0000 Very minor work towards making the imgBox portal. Mostly just want to check in some format changes before too much dust gathers commit a1980868d94aad33db7ee47d58d61f9bfbfeb5bf Author: galt Date: Tue Jul 7 15:00:06 2009 +0000 "Encode release log update" commit 9f3e556d5867e69f897d933d71600e4d4e3ba611 Author: galt Date: Tue Jul 7 15:00:03 2009 +0000 "Release log update" commit a00642db13041382fcb30c69ed973d71d643c1a3 Author: kate Date: Tue Jul 7 01:07:51 2009 +0000 Use new setting to set minimum gray level for Affy RNA transfrags commit 9606dcb6debea96559ffd660ac4fd84897f30ca3 Author: kate Date: Tue Jul 7 01:07:13 2009 +0000 Add trackDb setting for minimum gray level, corresponding to trackUi min gray level dropdown commit cc79bead819b7f63dfc959b1f98d5de1f696d765 Author: rhead Date: Tue Jul 7 00:49:42 2009 +0000 Fixed broken link to Baylor conditions for use page. commit 53c0046a7efc4ce6117deaf3f7f08d0ee6007e9a Author: tdreszer Date: Tue Jul 7 00:10:43 2009 +0000 Removed an extra .. from a help link commit 04626cabf1f52719cc1e6ea4017963ad6c81b1e2 Author: angie Date: Mon Jul 6 23:59:37 2009 +0000 In maybeGetSeqUpper, no need to cloneString the third arg of newDnaSeq (code review - thanks Tim). commit 110e65e3dd2837cb454eb3284006e9ecb68e0834 Author: angie Date: Mon Jul 6 22:56:22 2009 +0000 Don't printf something that might be NULL -- it segv's on Solaris. commit b54ad4e0e1cd923bc1f44aaa471cd73fca3d588f Author: braney Date: Mon Jul 6 21:45:29 2009 +0000 added new field restrictionEnzyme commit 196f3ef5c9d8fd193173e0db0379bc649eb7bfab Author: tdreszer Date: Mon Jul 6 19:00:49 2009 +0000 Added filterBy using 'score' so that ENCODE NHGRI BiPs can filter on annotations commit 6fcef754885c916c2df217dbdef21dc652a7a604 Author: tdreszer Date: Mon Jul 6 18:58:18 2009 +0000 Added value|label to 'filterBy' and allowed filterBy to work with score for ENCODE NHGRI Bips commit 02d33d3125ec3afc2e8667bfb3ceac6523eed591 Author: tdreszer Date: Mon Jul 6 18:57:30 2009 +0000 Added vaule|label to 'filterBy' and allowed filterBy to work with score for ENCODE NHGRI Bips commit c64b2c9aee93c269ea28ab278c884fc833754c2d Author: larrym Date: Mon Jul 6 18:45:59 2009 +0000 change Myers wranglerEmail to braney commit 96defc1983cac45fb615e69cbc4b064145536b26 Author: hiram Date: Mon Jul 6 18:10:32 2009 +0000 EquCab2 track moved up to the composite commit 635e1b973c1a0e0acd1d9aca77087abd2aa16805 Author: rhead Date: Mon Jul 6 18:03:15 2009 +0000 Changed single quotes to double quotes so that sqlbeta variable gets interpreted. commit 2b4c61ecfc7c9f6693a33ade552f785bee3c055b Author: ann Date: Mon Jul 6 17:58:20 2009 +0000 added Affy RNA track commit 54e79d29290281c9d6154689dadfc47b766d5480 Author: hiram Date: Mon Jul 6 17:50:32 2009 +0000 Composite chain/net tracks for equCab2 release, chicken, platypus, opossum, human, mouse, dog commit d2271c9f4f401ee87de37f56f134df678ff1433a Author: braney Date: Mon Jul 6 17:43:08 2009 +0000 make sure hgPal is in sync with composite multiz tracks commit 41a84ec88c6609ffe5c671230a74601c1c6048fe Author: rhead Date: Mon Jul 6 17:28:24 2009 +0000 Fixed link to data use policy. commit 114f41db0a577ceb9da441b80369625f1ebca68a Author: tdreszer Date: Mon Jul 6 16:49:12 2009 +0000 ENCODE NHGRI Bidirectional promoters has no '-'. commit 19f43bef01b9b8ab03ca2c64b332a3742f32e773 Author: galt Date: Mon Jul 6 15:00:05 2009 +0000 "Encode release log update" commit 8441490a88f3e09ee8ae40091c3aecc24923b3ab Author: galt Date: Mon Jul 6 15:00:03 2009 +0000 "Release log update" commit 3aa6322d4b81ff549f92e39c0e423451d41747eb Author: galt Date: Sun Jul 5 15:00:05 2009 +0000 "Encode release log update" commit 40944ddbcb1a8e6c52ff141ab97a43f344e361ca Author: galt Date: Sun Jul 5 15:00:03 2009 +0000 "Release log update" commit 25b0dda3a45ad87cf55a6ef81fc26eee3f87e6a5 Author: markd Date: Sat Jul 4 22:34:33 2009 +0000 don't adjust core limit commit c04b2198d8dfe78bc28b983ee7948e9b4c6899ed Author: markd Date: Sat Jul 4 22:29:23 2009 +0000 fixed typo in help commit f5e99d075662520c4f7dec3a868ec65260694623 Author: markd Date: Sat Jul 4 22:19:02 2009 +0000 added option to drop weird overlapps independent of other filtering commit af20a778d2d56a1e444c456464f82f09a3eaadb0 Author: markd Date: Sat Jul 4 17:06:06 2009 +0000 added program to quickly validate refseq tables commit 48ab5c8a2b89729f27210d794311aa5c34d97be8 Author: galt Date: Sat Jul 4 15:00:05 2009 +0000 "Encode release log update" commit e7989403c4c7e1a0763b51afd91b681b6ba84556 Author: galt Date: Sat Jul 4 15:00:04 2009 +0000 "Release log update" commit 243db6b68753b54112d27c891bc2e9c519960303 Author: markd Date: Sat Jul 4 07:14:20 2009 +0000 added some .h files for genbank tables commit c49667b6df0c37a27e99d5d29a3d6885c674e8da Author: markd Date: Sat Jul 4 07:13:51 2009 +0000 deleted no longer needed function commit d2f15a554700297b4f7bf6a533c62f5418d38f9f Author: markd Date: Sat Jul 4 04:45:29 2009 +0000 adjust enum/set values to be valid C indentifiers commit 105847dba7dfb0d3791ddcd25c4c319558485d71 Author: galt Date: Fri Jul 3 15:00:05 2009 +0000 "Encode release log update" commit 20fefad9f971c74166df7e3873fafb61b853895e Author: galt Date: Fri Jul 3 15:00:03 2009 +0000 "Release log update" commit 1dfb3d8de2e6389e687bee3ebeff6cdf088aa94b Author: markd Date: Fri Jul 3 07:28:09 2009 +0000 clairfed documentation commit f15bbfeeece93f2e1c6121bc92f4b37260776c9f Author: hiram Date: Thu Jul 2 23:23:18 2009 +0000 No longer need the priority here, it is in the trackDb.ra now commit 9fb6b9c6924fcc308420c5104fe88ddf3b9a5b8e Author: hiram Date: Thu Jul 2 23:21:17 2009 +0000 priority for human and horse chainNet composites commit d56e0043892ae87ef6c19c31cf01e353cbc3bd02 Author: hiram Date: Thu Jul 2 23:18:28 2009 +0000 horse and human chainNet overrides commit 51f7c7510090191f36af69bbb7edd70165d0c963 Author: hiram Date: Thu Jul 2 23:15:17 2009 +0000 Fixup equCab2 chain net priorities and overrides for hg19 chain net composite commit c472de5ff2971e989d35ef5329ed079dcd74e01f Author: hiram Date: Thu Jul 2 23:11:59 2009 +0000 Overrides for humanChainNet and horseChainNet commit df90cf5cee7828044188c7926f8eb29f78264e7c Author: hiram Date: Thu Jul 2 22:59:37 2009 +0000 overrides for humanChainNet and horseChainNet commit 4ca87a32d96c789bb0668e11318b240837a95266 Author: tdreszer Date: Thu Jul 2 22:54:46 2009 +0000 Laura Elnotski wishes BiP to be Bi-Pro commit 46a4b89559a9301f5785c760ed6d1b6849b9f9fd Author: hiram Date: Thu Jul 2 22:46:56 2009 +0000 Adding Horse chains and nets as a composite commit 4e6691febb55482f72d635e2ff0bd78010ab9c7c Author: hiram Date: Thu Jul 2 22:25:06 2009 +0000 Making upstream maf files from the 7-way alignment commit 4c30beaadae72c2f93cbe645da0f856f2d494d04 Author: hiram Date: Thu Jul 2 22:21:45 2009 +0000 Rerun all the equCab2 chains and nets to clean up problems commit b778658019392c094d4b8d7940459e04d005b187 Author: ann Date: Thu Jul 2 22:13:43 2009 +0000 fixed citations and typo. commit a1b8fcb3e793c2f9ebe1b2d3b380c3524ac35a9a Author: kate Date: Thu Jul 2 22:11:47 2009 +0000 Add dataVersion to Affy RNA composite commit d4bd9ae180b4f48206d4e4ea117d21ce4ab9a909 Author: kuhn Date: Thu Jul 2 21:40:51 2009 +0000 adding provision html file for a HudsAlpha track commit 8c58563825a55b449fa67afd88dfc4bf5e3c7370 Author: kuhn Date: Thu Jul 2 21:39:28 2009 +0000 changed longlable to provisional release on some HudAlph tracks commit 7055f5189050b2ed72e3c5bfe88559a11d435a4f Author: katrina Date: Thu Jul 2 21:21:46 2009 +0000 Minor reference formatting commit 6b09999664049385ac0ff4df8911b00f3d1f6f3a Author: ann Date: Thu Jul 2 21:10:56 2009 +0000 made wording consistent and correct commit bb1eeb83b169a3b598e42677284b9f4ffdafd519 Author: ann Date: Thu Jul 2 18:47:51 2009 +0000 used removeAlpha to remove release alpha lines as appropriate from Affy RNA tracks (thanks Brooke) commit 5ca530c8ce52186b921b0963c8cd329608086d57 Author: rhead Date: Thu Jul 2 18:41:12 2009 +0000 Added a few more details to the usage statement. commit 832700afd315bc4f861e3f85c2f91e6a35183b68 Author: tdreszer Date: Thu Jul 2 18:33:34 2009 +0000 Snyder wanted some cell line order changes commit fd39c879a450348016a92d29d6f756cff0ac19ae Author: kate Date: Thu Jul 2 18:08:01 2009 +0000 More label fixups for Affy RNA commit c95a6a465d0a2ef04a46a19929382df6a8c548a1 Author: kate Date: Thu Jul 2 18:01:23 2009 +0000 Label fixup commit 68b88c6c7bf37847de32bb62fe2542fe04688fc1 Author: kate Date: Thu Jul 2 17:58:16 2009 +0000 Color up new Affy RNA tracks commit 7aa3f356cf652a49af582cd3a334ea6df3ffdeae Author: kate Date: Thu Jul 2 17:54:42 2009 +0000 Remove obsolete priorities from Affy RNA commit 3b44c3bd94b3a70d4a9df16e00d754a1162cd950 Author: kate Date: Thu Jul 2 17:50:44 2009 +0000 Correct errors in Affy RNA track labels, and update freeze date commit d6670d63d2d727d457e75a4d0eaf1b5a3e7da6d7 Author: angie Date: Thu Jul 2 17:14:39 2009 +0000 When adding libs to L, use += not = so we keep the -lssl from inc/common.mk when USE_SSL=1. commit 6d9f2677044439424365601dfd9031e0e5b340ba Author: angie Date: Thu Jul 2 17:09:28 2009 +0000 When adding -lm to L, use += not = so we keep the -lssl from inc/common.mk when USE_SSL=1. commit 053599794bb334395815f96b9c3646cf285dc73f Author: galt Date: Thu Jul 2 15:00:05 2009 +0000 "Encode release log update" commit 791d1ccc4a0396c749c614a1e23bc19f55c95e5e Author: galt Date: Thu Jul 2 15:00:03 2009 +0000 "Release log update" commit b193166828f93bf818a2042649b4714c39dfe8be Author: aamp Date: Thu Jul 2 13:40:44 2009 +0000 Additions to UW ENCODE tracks. commit bd310b4310d98b4e4725389a35bfc2b87651e125 Author: tdreszer Date: Thu Jul 2 00:15:17 2009 +0000 Rosetta uniqueness should be consistent commit b23764647a63c7478cfc8b554e866836fc731575 Author: tdreszer Date: Thu Jul 2 00:11:05 2009 +0000 Moving Rosetta uniqueness track into Mapability commit 4d3468e7f696e5fc58572be2ea65e7148bc40109 Author: kuhn Date: Wed Jul 1 23:30:16 2009 +0000 corrected some info on usage statement commit ae27c32cc7eed9ef42fe31552f59ae9e010765b4 Author: ann Date: Wed Jul 1 22:44:57 2009 +0000 starting to clean up Example Three (you no longer have to use a .as file just for the color field) commit 2bc55adaae3d44ac5ae3a95a390dbd80083de426 Author: kuhn Date: Wed Jul 1 22:39:45 2009 +0000 oops. munged the rename commit da39c3e8122443e1550d841b5a12c92bed55d76d Author: kuhn Date: Wed Jul 1 20:38:08 2009 +0000 small changes commit 9569c1c3602d38185e1b88e36e6ed8e28a69e4fc Author: tdreszer Date: Wed Jul 1 20:33:34 2009 +0000 submittedDataVersion=Vn needed to be added to metadata commit aab3b4ad2ff50629c66e9b1ce8fdfaf2417007a5 Author: kate Date: Wed Jul 1 20:00:06 2009 +0000 Long RNA metadata files for CSHL commit 1bbf6871c6b384ff58fd42a460c3e1ce8cc38620 Author: ann Date: Wed Jul 1 18:58:49 2009 +0000 a few more tweaks commit 64cdd6daedd7e7e7abade3c9ab2d0c7849188e11 Author: rhead Date: Wed Jul 1 18:58:18 2009 +0000 Fixed broken links to WUSTL. commit 94fc735847e61e30a4789bb82abb8463374edc45 Author: ann Date: Wed Jul 1 18:50:26 2009 +0000 edits based on feedback from Donna and Jim commit 57e493b8e45ec8285421f30727c2011295f5eed2 Author: galt Date: Wed Jul 1 18:31:48 2009 +0000 improving example contig ids commit 28ce6a5762d68e1898f919c3fe9dd7d34a815687 Author: rhead Date: Wed Jul 1 18:31:18 2009 +0000 Changed push request notes. commit 3f3eb3df48da8aa61ec829e8c95d54e395520f77 Author: tdreszer Date: Wed Jul 1 18:22:03 2009 +0000 Also collapsed HepG2 and HepG2b into a single column. commit c60560c96ae5ba4f1cc4deb3e4d1fe9d79388e32 Author: tdreszer Date: Wed Jul 1 18:16:56 2009 +0000 Collapsed K562 and K562b into a single column. Not the best solution, but neither was 2 columns quite right. commit 2ec500be5138debfb1430bcd4b34c077e5d7fe3e Author: tdreszer Date: Wed Jul 1 17:43:05 2009 +0000 Resubmitted Yale/K562 peaks, input. Fixed some metadata, standardized ChIP-seq commit ac250a033113abc4876ddff2971e82e006c5664b Author: kuhn Date: Wed Jul 1 16:39:25 2009 +0000 turned on some primate net defaults so the primate chain/net track is not empty when first turned on commit 10dd124f47bacfa51289ec91e44505489d95ba26 Author: tdreszer Date: Wed Jul 1 16:19:06 2009 +0000 Inital check-in of Encode Gencode Classes table commit b38bdc0a582c4084c62456aca781988d10768d31 Author: galt Date: Wed Jul 1 15:00:06 2009 +0000 "Encode release log update" commit c22cb7f105973d0ee4f6a1773ae39e9160191793 Author: galt Date: Wed Jul 1 15:00:03 2009 +0000 "Release log update" commit 70453bad6551860105ae0cbad3ad5de44f577987 Author: kayla Date: Tue Jun 30 23:46:59 2009 +0000 release alpha/beta cleanup commit 36a08dc9d19736ef8c2839d34ef5b62187e82508 Author: kent Date: Tue Jun 30 22:47:09 2009 +0000 Fixing nearly empty filter page on bigBed custom tracks. commit 938eff32bccf8eaa48609ad49b502f716d570f07 Author: markd Date: Tue Jun 30 20:59:44 2009 +0000 fixed library list so SSL can be included commit ebb58802096bd39be32e0c8b85b87deee872e76b Author: aamp Date: Tue Jun 30 17:32:29 2009 +0000 v210 preview commit 6c43a22a544e8ff74b8e40e25f9d09d9753d845d Author: katrina Date: Tue Jun 30 16:43:22 2009 +0000 added sgdToPfam to all.joiner and removed it from the tables ignored commit ea48c15db6879f641152720c3b1262b62ea80244 Author: galt Date: Tue Jun 30 15:00:06 2009 +0000 "Encode release log update" commit f0d1dd21fa0a20dfca8220e736aba0e6f6fc6ca4 Author: galt Date: Tue Jun 30 15:00:03 2009 +0000 "Release log update" commit a6cd631f144ea2eb65b7d67defaee0320619ecd7 Author: kent Date: Tue Jun 30 00:47:00 2009 +0000 Adding bedGraphToBigWig commit d35c94ce2b1903d9ac0a275e63fc75000fdf1e9f Author: angie Date: Mon Jun 29 23:19:15 2009 +0000 Updated MGI (jax%) tracks. commit 280001f3dc5b4a6c977afa399be6bc984b584045 Author: kent Date: Mon Jun 29 20:29:44 2009 +0000 Changing reserved field to a string so it can handle the various color morphs. commit 8429aa1a1eef46c217b5c5cfa2c0f6d6db3e9353 Author: kent Date: Mon Jun 29 19:52:25 2009 +0000 Removing some unused variables. commit d7e1473fe6ed7d2b160fecc3f4dd90bf4d0e0cb0 Author: kent Date: Mon Jun 29 19:29:33 2009 +0000 Turning some debugging statements (uglyf and uglyTime) to things that are only produced when the verbose flag is on. commit beb262783f1e34f9c7f4e48ed5c05333a503558b Author: tdreszer Date: Mon Jun 29 18:15:03 2009 +0000 imageV2 should now work with reverse. commit b41977a7d5224a430aae42e9cf957119916b621b Author: kent Date: Mon Jun 29 18:04:42 2009 +0000 Adding some time probing. Fixing bug in section sizes. commit 7f610e37c1a1d877e0f8260f273ead771eb30c8d Author: kent Date: Mon Jun 29 17:50:50 2009 +0000 Utility to print out diagnostic information on bigWigs seems to work. commit a0252a5babfa6adc576cec86ed83dfcbe56f8a90 Author: angie Date: Mon Jun 29 17:45:39 2009 +0000 Pass a file pointer to htmlWarnBoxSetup, so when we are creating trash/ html files for a frameset, the script is printed to the files not stdout. commit 4252a0a2a9bb6fbf2c8a92b82e576041c588fff0 Author: tdreszer Date: Mon Jun 29 17:28:18 2009 +0000 Newling also breaks the warnBox code. sway '\n' with '
'. commit 692a3ee4a500cdc7c99ab0bd087d4a02b9fe08f2 Author: fanhsu Date: Mon Jun 29 17:14:37 2009 +0000 Added validate logic for GISAID users (on GISAID server only). commit 3f1a0a6e07f425b08d6ed97d48750301bb71ef41 Author: tdreszer Date: Mon Jun 29 16:31:19 2009 +0000 Two typos commit 2c01865fe66adec9263a77693971861bffb0fa1e Author: tdreszer Date: Mon Jun 29 16:29:57 2009 +0000 Broad alpha tracks had default hide for raw signals which made the matrix checkbox normalize code do strange things commit e81b666ff117ce4cc71027e24dbafa149388c707 Author: tdreszer Date: Mon Jun 29 16:15:14 2009 +0000 Keeping my head above water commit f7d552eae8f2138fa4cbd3b2aa52aaf4b9307185 Author: tdreszer Date: Mon Jun 29 16:14:43 2009 +0000 Keeping up commit 7954568cfd9fab8895d36a37ce660fe527bbca1f Author: tdreszer Date: Mon Jun 29 16:07:34 2009 +0000 Removing not ready for prime time code (debugMsg) which I accidentally checked in commit fcb59caabad392bf5d607a9db6c3eed76c9558f5 Author: galt Date: Mon Jun 29 15:00:05 2009 +0000 "Encode release log update" commit 1de7771f8d390f3332ebec139d245e5856f0515b Author: galt Date: Mon Jun 29 15:00:03 2009 +0000 "Release log update" commit c6017aaa61e12af8d0629ed885f9a140654628c7 Author: markd Date: Mon Jun 29 07:39:49 2009 +0000 don't build genbank as part of standard build, causes grief to mirrors who don't needed it commit b854aaa359c0600894b6339618adfdae5358443c Author: kent Date: Sun Jun 28 00:14:25 2009 +0000 Simplifying logic that double-checks sorting. commit c96b733f3b94ec50ffe81f518808569c4961dace Author: kent Date: Sun Jun 28 00:09:27 2009 +0000 Some testing and instrumenting. It looks like the third level of zoom may be off. commit 82023dbb3f2a66c1bf79252cc64798922be48676 Author: kent Date: Sat Jun 27 22:07:43 2009 +0000 Fixed problem with second zoom level. commit c24384bb854cb0fe34371321b79be1ec8b33778d Author: tdreszer Date: Sat Jun 27 20:13:01 2009 +0000 Drag reorder should now be persistent commit 5a2ab600c67499df2d3f807008e09602f00dbeff Author: tdreszer Date: Sat Jun 27 20:10:53 2009 +0000 Tweeks to get post on click to work in IE commit b69ad82c22a4665573233bb41a7510ad9f5eb47f Author: kent Date: Sat Jun 27 19:22:24 2009 +0000 Writing header. Fixing chrom size/id mixup. On test.bedGraph the loop of bedGraphToBigWig and bigWigToBedGraph yeilds test.bedGraph again, which is a good sign. Still need to test zooms and on larger files. commit 3606037c10d953cb767ea710a3d74212f23b7632 Author: galt Date: Sat Jun 27 15:00:05 2009 +0000 "Encode release log update" commit 05456ee42eb21a928424edb9b8fc30da5b8e31b3 Author: galt Date: Sat Jun 27 15:00:03 2009 +0000 "Release log update" commit a32dffd774b4beadbc8e81afc6ee28b7f61a8a53 Author: mikep Date: Sat Jun 27 10:51:59 2009 +0000 loading CSHL bigbed tagAligns commit db579f15586730790b6519f36532f673395d876f Author: larrym Date: Sat Jun 27 01:21:31 2009 +0000 fix dragZoomingConfig so it works when hgTracks is called from command line commit 198f9147b7c4e6e277dd9fe2456fb5ecb52c3bb4 Author: aamp Date: Sat Jun 27 00:47:00 2009 +0000 Updates to the UW Affy Exon track description including track configuration. commit 185495f7ed718e1f53ad3e000b2464ec1ba77557 Author: kent Date: Sat Jun 27 00:41:57 2009 +0000 Adding in other zoom levels. Still need to rewrite header before can test this. Compiles and runs without crashing at least though. commit d7d773337662a5be978f80e8805d3ba0d46889a2 Author: kent Date: Sat Jun 27 00:02:20 2009 +0000 Adding initial zoom index to file, and some diagnostic messages. commit 7231b783a841774edaed6084e3be5a0baf8a751a Author: tdreszer Date: Fri Jun 26 23:35:15 2009 +0000 Some adjustments to make sure dragZoom still works with imageV2 commit b879a2eb8046061873981f7ca818b69beed365a3 Author: kate Date: Fri Jun 26 23:18:37 2009 +0000 Try raising scoreMin to darken the transfrags commit e4c714ceba90a680c4623bb3b8fdcc7752f4d83b Author: fanhsu Date: Fri Jun 26 22:18:57 2009 +0000 Added logic to validate GISAID user if the server is a GISAID server. commit 2d15e760212393d34f510266e8c149c1e7e8fe04 Author: kuhn Date: Fri Jun 26 22:06:50 2009 +0000 made entry show more clearly what will change when converted to real track - using comments commit 54425cdc9a25b2cb00bbe084c0572b0d10ccf40b Author: kent Date: Fri Jun 26 21:57:27 2009 +0000 Work on zoom arrays, not finished. commit 07d93a6f051fc34d317af0d9db52e4937f6da109 Author: markd Date: Fri Jun 26 21:41:40 2009 +0000 just leave ccds database download as nightly commit 474afdca1439db89765fb28de140215caa0c071b Author: hiram Date: Fri Jun 26 21:28:23 2009 +0000 Talk to the all_mrna table after testing for its existence, not the chr*_mrna table. commit 48f7fc865cb9b605969d2732bf15d46b6c5a1eb4 Author: tdreszer Date: Fri Jun 26 20:53:18 2009 +0000 First baby steps for imageV2 commit ed2a37712487f566738ac14fe97071ce5f2bbf76 Author: mikep Date: Fri Jun 26 20:40:59 2009 +0000 temporary new version until we get CSHL working with bigBed tagAlign commit d154691987174ac1dc02a4e459dae748d606fb5e Author: tdreszer Date: Fri Jun 26 20:24:57 2009 +0000 Inital checkin of imageV2, but ifdef'd out. commit c8a97d60ffff89ad5d742d308c4e1784f6d7c021 Author: tdreszer Date: Fri Jun 26 20:17:51 2009 +0000 Inital checkin of imageV2, but ifdef'd out. commit 0cbf0fa5c45972df63a1ec1c0544b5eda13a1ef6 Author: tdreszer Date: Fri Jun 26 20:04:32 2009 +0000 Adding imageV2.c into build. commit 56f3df4420ca79496c7eaf6e165894fa346dfbbe Author: tdreszer Date: Fri Jun 26 20:02:52 2009 +0000 In warnBox sheild ' with HTML specil char is possible. commit 6741f4bd5d4ec36f28a7c3893f9f3ce80b1e3797 Author: tdreszer Date: Fri Jun 26 19:57:54 2009 +0000 Added strSwapStrs like replaceChrs but swaps in place. commit cd486d54c51d46aa2b3f5fc419eca6d3111030ec Author: mikep Date: Fri Jun 26 19:46:53 2009 +0000 added split tags, and raw data for Solexa commit 5efb8d5a1eb201c48faada92843cd108c5da416c Author: kuhn Date: Fri Jun 26 19:11:39 2009 +0000 typo commit 0840b4275581b9a28617c909fc48a8063768302c Author: mikep Date: Fri Jun 26 19:09:37 2009 +0000 new clone-free method for GIS RNA-PET commit 3db52a3eeff9e43d54c7c964074ffa40adeb44e7 Author: mikep Date: Fri Jun 26 19:09:04 2009 +0000 tweak to UI commit 2b08dc7dacd5c0a659526bd4542bad4d4dd227cb Author: kuhn Date: Fri Jun 26 18:40:23 2009 +0000 moved two subtracks into a new track to test provisional release idea commit d599b375080c95b44817e91b3b90bc6b8d409a91 Author: fanhsu Date: Fri Jun 26 18:17:16 2009 +0000 Added logic to check if the user is a registered GISAID user. commit b2a859a4eb3ec917d17e1357cedf542d1c7a10c4 Author: mikep Date: Fri Jun 26 18:11:34 2009 +0000 added data-release policy dna-pet doco commit a231643bd5fa71b1afe18c3477aab57dd6498bfd Author: mikep Date: Fri Jun 26 18:08:57 2009 +0000 updated version of dna-pet doco commit 0e984ffea49fb410e13838d6a1781d92cf47e981 Author: fanhsu Date: Fri Jun 26 18:04:05 2009 +0000 Added logic to call validGisaidUser(). commit b7cfb9d87dda18191af790b48ea7b88cf06484d5 Author: tdreszer Date: Fri Jun 26 17:49:09 2009 +0000 Initial check-in of new image V2.0 which will allow drag-reorder and drag-scroll. This is a work in progress and ifdef'd out of the build. commit bea7ce3270fd5796fdaaba8a09abdae248deba5b Author: mikep Date: Fri Jun 26 17:49:06 2009 +0000 format tweak commit ca296bd3c5ca9aea014a6b1be81a956bf054b72d Author: hiram Date: Fri Jun 26 17:46:57 2009 +0000 Use new multiz7way.html file for the conservation details page commit 911376908e066bf973bd66c347580ad2ce0a7c20 Author: hiram Date: Fri Jun 26 17:46:31 2009 +0000 Initial file, with bits of hg18 44-way discussion brought over commit f69af8a809e781d172e795bc4317cf258c1e8ae2 Author: tdreszer Date: Fri Jun 26 17:42:15 2009 +0000 Reworked the html warning one more time. Fan complained about lack of html inside warnings and inability to copy/paste from an IE abort box, so I have created a warnBox embedded into the page. Again, no jQuery commit bd2a73b882f934b2158ce58a8800da6840ef223c Author: mikep Date: Fri Jun 26 17:38:07 2009 +0000 Track documentation for GIS RNA-seq commit 7c7005fec57d76c0dee6ee8755456b9854c7b4b2 Author: larrym Date: Fri Jun 26 17:21:47 2009 +0000 add missing metadata for HA MethylSeq commit 5d79c7cea1aa14b1ea76ccf22f982ac39c41f368 Author: larrym Date: Fri Jun 26 17:21:07 2009 +0000 credits commit 7018c6dedab3625adfb183797573a60526c57b31 Author: larrym Date: Fri Jun 26 16:09:18 2009 +0000 fix filename in fileDb.ra so it handles types with spaces commit 06e14e6f29f200bd6aeb65e3f43ea4034f56eb8f Author: larrym Date: Fri Jun 26 15:32:21 2009 +0000 metadata for wgEncodeHudsonalphaMethyl27 commit 5659aaccff0f4ab5d19b0df1b7fc47f9c6bbd67b Author: larrym Date: Fri Jun 26 15:20:54 2009 +0000 minor edits commit cc2dc1f9252738adcc2bc71dbb96490f910c39ef Author: galt Date: Fri Jun 26 15:00:06 2009 +0000 "Encode release log update" commit b4e521b04a766f3091812f4a6b05576cb1eefda8 Author: galt Date: Fri Jun 26 15:00:03 2009 +0000 "Release log update" commit d2bc3da02830344a95f55cd878c3581111e8377c Author: fanhsu Date: Fri Jun 26 15:00:01 2009 +0000 Added validateGisaid.o. commit bf2985ea93e6df332c8f24e4d092c1ce9af37b59 Author: fanhsu Date: Fri Jun 26 14:49:43 2009 +0000 Added logic to check user authentication for the GISAID server. For other servers, a dummy/empty validation function is called, which just pass thru. commit 9b388458c93e5b1900a633bd456e56c4687106a3 Author: fanhsu Date: Fri Jun 26 14:38:57 2009 +0000 Added validateGisaidUser() declaration. commit 927b31c4054eae057dcb9a3aa409b63a8c10ae7a Author: fanhsu Date: Fri Jun 26 14:37:42 2009 +0000 Dummy/empty validateGisaidUser() for non-GISAID servers. The real validateGisaidUser() for GISAID server is confidential and is kept elsewhere. commit 394490266bf5838d1d91e9fbcc3d4fde19598b12 Author: fanhsu Date: Fri Jun 26 14:34:45 2009 +0000 Created validateGisaid.dummy, which should be used as validateGisaid.c for non-GISAID servers. commit a5922e6b2173b0d9b239c135fbb429860ff6c83c Author: pauline Date: Fri Jun 26 01:03:53 2009 +0000 Added italics. commit da3aacb4a9f61da7635d10e01c12a839e17e927b Author: rhead Date: Fri Jun 26 01:03:21 2009 +0000 Added Open Chromatin. commit e6705f5c092a26ebfbf44dd942a9860cf145e3d3 Author: pauline Date: Fri Jun 26 00:51:44 2009 +0000 Added italics and formatting. commit 742ab22aa0d51b97980accc60cf973a4d12ebea1 Author: genbank Date: Thu Jun 25 23:50:40 2009 +0000 allow override of grepIndex location commit dfbb1b2cb3206e2fa8404b91b6938f20438f6005 Author: genbank Date: Thu Jun 25 23:50:26 2009 +0000 moved grepIndex to /gbdb/genbank/grepIndex commit 3e1c855857ae36d85a8bea8c804b4e01d4ac97ea Author: galt Date: Thu Jun 25 23:29:25 2009 +0000 fixed gold elements description commit dbeb889fc0389a880351d1e8582e4737e29ea417 Author: galt Date: Thu Jun 25 23:25:27 2009 +0000 fixed gold elements description commit 4f501b0edbd24ceba26e7ce8d87e1481ddbcbec1 Author: rhead Date: Thu Jun 25 23:02:55 2009 +0000 Changed the error and usage message so that it does not appear that something is assumed about the location of the file specified. commit a93401aba7c9365d0b6a289f6c6cfce4fd766401 Author: genbank Date: Thu Jun 25 22:06:13 2009 +0000 relocate grepIndex on hgnfs1 commit 462b2ccca306f9767dc40be8cdca07d6ce07091e Author: ann Date: Thu Jun 25 21:20:47 2009 +0000 changed to reflect actual contents of this directory commit 76ae247c331cb06265175165b57459949e4ed7d1 Author: cline Date: Thu Jun 25 18:15:15 2009 +0000 Added instructions for making the (35-mer) uniqueness track data commit bb6b58c98e11c79ec55cd67ed850cf29423688f8 Author: ann Date: Thu Jun 25 17:45:13 2009 +0000 typo commit 1fd27c8e5ecb951426f318b34cb9ec81a9ffbb66 Author: ann Date: Thu Jun 25 17:36:44 2009 +0000 added sentence about memory problems commit 02fee72c8823d0c0d7fd43d454abf17f092eb7d6 Author: fanhsu Date: Thu Jun 25 17:08:09 2009 +0000 Added validateGisaidUser() to be used ONLY on the GISAID server. This will be a dummy blank function for other servers. commit 8a7b5a9b3982bca99a7124c0a3dde8701c55c008 Author: galt Date: Thu Jun 25 15:00:06 2009 +0000 "Encode release log update" commit f5aa77e115fe5f379a80b1f6130ad9cb05f18955 Author: galt Date: Thu Jun 25 15:00:03 2009 +0000 "Release log update" commit 4804caada624aeeebf204006cba29544c29a5b1a Author: markd Date: Thu Jun 25 08:43:09 2009 +0000 removed outdated mgc code commit ec7dedf3675e6f662ee67866a9acc224a4e62c3d Author: genbank Date: Thu Jun 25 07:03:52 2009 +0000 running load on hgnfs1 requires a copy of hgsql commit e7c674a8fba69e267d6660e58a34e12b310308d3 Author: genbank Date: Thu Jun 25 07:03:25 2009 +0000 don't try to build grepIndex on hgnfs1 commit 7d9f1a2b29b028a325bb4b7054723ab41b10af81 Author: markd Date: Thu Jun 25 05:34:42 2009 +0000 added suppot for downloadsServer variable in html commit b2720001f8114db1bf041801778a907342c949bf Author: genbank Date: Thu Jun 25 03:40:46 2009 +0000 *** empty log message *** commit 0534834d9f9431fd50ddb157d1bebb998b45fd41 Author: genbank Date: Thu Jun 25 03:23:05 2009 +0000 switch hgsqlrr load host to hgnfs1 commit 1aa941272aa7893876fabdbd5aeb38fd32450244 Author: kate Date: Thu Jun 25 01:26:53 2009 +0000 Fix perms commit 602507f1a99dbb70293e804596463c22b037224e Author: kate Date: Thu Jun 25 01:01:24 2009 +0000 Add execute bit to enable SSI commit 36748888dec684ee20c66d6fbac1daa8360bae29 Author: rhead Date: Thu Jun 25 00:35:47 2009 +0000 Fixed up instructions for editing this file when Mapability is available. commit b912e96ac582d3c49bb3cb34cf5a66eb6f3af545 Author: galt Date: Thu Jun 25 00:29:16 2009 +0000 Initial descriptions for danRer6. commit 8008b41d7b7e0f2eed4405611a72eac1fde1d7a9 Author: galt Date: Thu Jun 25 00:29:06 2009 +0000 Added danRer6 to DBS. commit 66b2e2e54779a21e8ccd965019fcc30751ddb674 Author: angie Date: Thu Jun 25 00:20:02 2009 +0000 Added baseColor settings to bamNA12878. commit 90f9e0ed4750f2ba6fc619f1fa3241035d68b750 Author: angie Date: Thu Jun 25 00:09:32 2009 +0000 In linkedFeaturesDrawAt's hairy if() that decides whether to call baseColorDrawItem, !psl no longer cuts it as a test for whether we are drawing codons. commit 8db7a7d6289b2db8ac00bad3091887640bf698b4 Author: angie Date: Thu Jun 25 00:05:52 2009 +0000 Added new baseColorUseSequence option lfExtra (use sequence in lf->extra). commit f15c58f4ca3f1c1231067db4febafccaa5dcf6bb Author: angie Date: Wed Jun 24 23:57:05 2009 +0000 Oops, reverse-complement BAM query sequence when on - strand. commit e8373cd107ae7d4fea4c02d0fe64fd542e2bb96a Author: ann Date: Wed Jun 24 23:34:06 2009 +0000 hooking into new bigWig/bigBed help docs and utilities commit 9227c52df4ab04ae7f98ab55ce36873362fa47db Author: kate Date: Wed Jun 24 23:31:43 2009 +0000 Clarify views section commit cc4d555722141a495c6aa2b01e11f46f318d248e Author: tdreszer Date: Wed Jun 24 23:23:50 2009 +0000 Fix for matrix 'right buttons' being parially triggered by empty columns commit 9f985cf0ca3761aa86dc268f134dc0bd87a54085 Author: mikep Date: Wed Jun 24 23:20:14 2009 +0000 new process for copying userApps binaries (not just liftOver now) commit 8c418124422129168713477d4c5cc105c5cd9f3d Author: hiram Date: Wed Jun 24 23:14:39 2009 +0000 Add bigBed and bigWig help doc pointers commit cf3cc3232b2e51a8898c20fe53740c9aa783aba9 Author: ann Date: Wed Jun 24 22:38:07 2009 +0000 moved download directory, again commit 7e71c7532404620ec9454677790c3543d20c83b6 Author: angie Date: Wed Jun 24 22:32:24 2009 +0000 bugfix: when using sf->qStart as mrnaS in drawCdsDiffBaseTickmarksOnly, correct for adjustment to target start. commit f4dc14f025b2b3f5d559aa735025ae67a019aaae Author: hiram Date: Wed Jun 24 22:11:38 2009 +0000 Ready to start loading the database commit 93fa9bc069531d4eb66248afef1e4a3dd9ba7e3b Author: rhead Date: Wed Jun 24 22:06:17 2009 +0000 Added a link to downloads. commit fbb7d7ec90291b6e254100ad4ef2f4f8cd65ea2b Author: mikep Date: Wed Jun 24 21:53:03 2009 +0000 liftover is part of larger suite of user apps now commit e3b089c6710d7d4169d6b81df32999730c42941e Author: mikep Date: Wed Jun 24 21:35:36 2009 +0000 adding hg libs for user apps commit d45ee998efc9d569ea1e461db6873fa0bf4a6a54 Author: tdreszer Date: Wed Jun 24 21:12:56 2009 +0000 Added 5 new experiments to Yale alpha, changed tags to ensure sort order, removed empty NT2-D1 cell line from yale beta commit e49d93d734b0d529923b424dcb5bacc053a264e6 Author: angie Date: Wed Jun 24 20:46:13 2009 +0000 Ahem, forgot to fix default visibility before checking in. commit b6b147f632fc786a29057f73e5a90b58398f5380 Author: angie Date: Wed Jun 24 20:44:43 2009 +0000 Adding experimental tracks with a spot of 1000Genomes data for HapMap individual NA12878 on chr22. commit fdbbd819867af4a539a3c44e2524452803a7d77e Author: angie Date: Wed Jun 24 20:33:04 2009 +0000 Adding rudimentary support for BAM (compressed alignments) files as a native track type. commit 15d212e502eea869073556a7c21fc6cd7dc771cf Author: tdreszer Date: Wed Jun 24 19:57:01 2009 +0000 Touch ups getting ready for the pushQ 'D' commit 535e0c10e91aaca13ea1f29a9b2821740821a719 Author: tdreszer Date: Wed Jun 24 19:55:10 2009 +0000 Touch ups getting ready for the pushQ commit 47ea67b09ca1f103d402aab356926268917fa102 Author: ann Date: Wed Jun 24 19:17:48 2009 +0000 example three commit d9250754ffc15948a9ab8f1343fb499cf48044ad Author: angie Date: Wed Jun 24 19:14:27 2009 +0000 Added support for samtools/libbam, disabled by default. commit 2af6fbb73cd8bb58658a9707c9f804342faa4ec8 Author: angie Date: Wed Jun 24 18:53:57 2009 +0000 Make a CGI parameter for measureTiming (not just hardcoded), for convenience and so we don't risk accidentally checking in measureTiming=TRUE. commit 56b54a101dfc1d22fca4a4abd064ede7cea00cc8 Author: angie Date: Wed Jun 24 18:48:00 2009 +0000 Share bbiNameFromTable() between bedTrack.c and bigWigTrack.c. commit 18e156a17e381bccb8d7d79b7d1e32ecec6ae4e5 Author: katrina Date: Wed Jun 24 18:18:42 2009 +0000 changed nucleotoide to nucleotide commit 606ccfde57399a842d522f19863f5606ef5f42ca Author: katrina Date: Wed Jun 24 18:17:02 2009 +0000 fixed some tiny problems in the references commit 94cced64d1755e817e0d5612f34ab37ff253ad2c Author: genbank Date: Wed Jun 24 17:08:16 2009 +0000 move hgsqlrr update to hgw2 to aboid poltergeist commit f34e5fbed3cfca1e1b6074a9424f4c51948ea667 Author: genbank Date: Wed Jun 24 17:00:37 2009 +0000 disabled poltergeist hack commit 525f870e5af5c1c29027659bee8856b93f92c306 Author: galt Date: Wed Jun 24 15:00:05 2009 +0000 "Encode release log update" commit 3e5c37e8ed1b6ebd75ae679f0a3965a617362684 Author: galt Date: Wed Jun 24 15:00:04 2009 +0000 "Release log update" commit f5b150b8a9445a74d51c1aa1708c39eaaa17da2f Author: genbank Date: Wed Jun 24 05:32:59 2009 +0000 output more info when molType corruption is detected commit bf5332a9848b00a62ff4273795dfbff6dbe5bced Author: genbank Date: Wed Jun 24 04:48:43 2009 +0000 attempt to correct very strange corruption reading gbidx files on RR commit f2ce4210c8cb1b54fb09c9938d0ffdf3cb9bc299 Author: galt Date: Wed Jun 24 03:26:11 2009 +0000 making more senseful error messages commit a2a74c482cd32d185068698e75541d9e43ce2338 Author: galt Date: Wed Jun 24 02:19:23 2009 +0000 MSIE is not able to handle long urls in GET forms, so detect and MSIE will just have to miss out on the copy-the-url to generate a tree feature commit 1cb6a10ffccaf53ee5c8acc05ecdbe2efe555122 Author: galt Date: Wed Jun 24 01:48:57 2009 +0000 make sure leafs have labels commit 32ed3f6bb9ebc75e7868933b40585cc110fc3daa Author: genbank Date: Wed Jun 24 01:26:23 2009 +0000 added dumpStack call in attempt to understand intermitent bug commit ab6b105838184444a4eb876927ba3297124d38b5 Author: markd Date: Wed Jun 24 01:22:17 2009 +0000 added n-scan track commit 9100fb647743b6218a9f5c92cc2b2c57277d957d Author: galt Date: Wed Jun 24 01:19:55 2009 +0000 adding more error checking to phyloTree, especially for case of missing subtree (A,); commit 37b64fc857079716178545c336df28e8c346119a Author: kent Date: Wed Jun 24 00:38:35 2009 +0000 Saving data index. Doing some calculations for zoom. commit c338ba5fb5fd19b2ea63092414fb63ed9b63da8f Author: kent Date: Tue Jun 23 23:39:10 2009 +0000 Adding lineFileRewind. commit f08a9e434d54069e8dc64946aec4f5382efed725 Author: markd Date: Tue Jun 23 23:20:21 2009 +0000 loaded monDom5 nscan commit c1431550f21433878d9b7f486b8b6e6fb113837a Author: kent Date: Tue Jun 23 21:29:09 2009 +0000 I've been working on this long enough it's worthwhile to commit to repository. Currently in limited cases it makes two passes through input without crashing. The output is just starting - with the chromosome tree and the raw data output, but still needing the data index and the zoomed views. Not yet worth reviewing. commit f51eec296cabcc66a7a85463e203a84904f82f61 Author: angie Date: Tue Jun 23 21:21:15 2009 +0000 Oops, backing out inadvertently added debugging track. commit 713017cc4bf372b457761511dd6fec5bf8559daa Author: mikep Date: Tue Jun 23 21:20:51 2009 +0000 GIS RnaSeq base coloring commit 00346eb2d10b2bde590c5d5811b8e601264858aa Author: kuhn Date: Tue Jun 23 21:04:04 2009 +0000 changed from CREATE new table to RENAME commit bb374fdcc6851e8ccc9f344a7f24610916709901 Author: tdreszer Date: Tue Jun 23 19:36:11 2009 +0000 Four more antibodies for Yale commit 20730fe3f972bc5d20b4bfcceaec1f5410375b5e Author: ann Date: Tue Jun 23 17:10:05 2009 +0000 moved utilities location on download server commit acdd981d9a987837815429ab05418f90d0faa9c4 Author: hiram Date: Tue Jun 23 16:40:19 2009 +0000 The meFirst stuff was broken when the input maf does not have the separator commit ba5047573c89f8b0fd0e6968fb66c1eb9443446e Author: mikep Date: Tue Jun 23 15:42:45 2009 +0000 "New version number v209" commit b1c7c2f232580456781e0cc51b032a17c4e27c28 Author: mikep Date: Tue Jun 23 15:42:28 2009 +0000 v209 final build commit d170d057d374b41cec7da31559f20056f416b4fb Author: galt Date: Tue Jun 23 15:00:07 2009 +0000 "Encode release log update" commit 86063312af810a8b70acac292cd273e42880e748 Author: galt Date: Tue Jun 23 15:00:03 2009 +0000 "Release log update" commit 923956afcc3ed6e88c5588d4c7b594ec22d98900 Author: galt Date: Tue Jun 23 07:47:22 2009 +0000 utility to patch unfinished contigs in agp for sanger commit 8717c17b3215c6c63c0d845e4d1ee8c6c297e2ab Author: galt Date: Tue Jun 23 07:46:43 2009 +0000 utility to merge chrom and scaff agp for sanger commit 5c32730bd6ae2b510de9a60b0e4a3cca60490e6c Author: galt Date: Tue Jun 23 07:01:08 2009 +0000 start zv8 commit 587e7ecf1d53612652b1ef745ce9fc2ce41b37fc Author: aamp Date: Tue Jun 23 05:52:28 2009 +0000 scale bar defaults to on, just like hgTracks. commit 5028bc985b60e0fa9e261031ece010a82e4288ee Author: mikep Date: Tue Jun 23 04:45:10 2009 +0000 fixed up labels and #75 commit 8379d30388370f23ef51894bac7127c5eb46458a Author: markd Date: Mon Jun 22 23:35:47 2009 +0000 added nscanGene commit 9b3a5d0f42d8b0d500c3460d819b74e1e6cf66f3 Author: cline Date: Mon Jun 22 22:55:26 2009 +0000 Moved the uniqueness track from the variation to the sequencing group commit 5bf57bab8ffd5913e672f9fabe13256546211cb5 Author: ann Date: Mon Jun 22 22:48:59 2009 +0000 finally got the binaries out on the download server commit b8a34310d122f0e51450cbcafbb5df55ed77470e Author: mikep Date: Mon Jun 22 22:26:53 2009 +0000 addign missing Filtered tables due to metadata problem commit 8c90777dd2b4d38d0cea1512a63a16d147be12f5 Author: angie Date: Mon Jun 22 22:25:22 2009 +0000 Added note that HDGP geographical allele images may show alleles from the - strand (thanks David). commit 3f954be61d9d13ddb88674ec9fdb96002f6aba92 Author: ann Date: Mon Jun 22 22:21:21 2009 +0000 starting example three commit 62504ba4a9ed757df29432b76fff2cf0e3ee905c Author: angie Date: Mon Jun 22 21:50:31 2009 +0000 Added new SNP-specific setting defaultGeneTracks, to enable functional annotations of SNPs relative to some gene track(s). commit 22c0fa873d8ddb836de5f56f8fed824437ab0bcd Author: ann Date: Mon Jun 22 21:42:14 2009 +0000 more udpates from old wig origins commit 9dd22971483c9a38a93ca5033c38d487a89d205b Author: mikep Date: Mon Jun 22 21:32:44 2009 +0000 bed files allow comment lines commit 7161bbf5d35cf5e6156a1c5d62f0d7236d411c4c Author: jzhu Date: Mon Jun 22 21:12:36 2009 +0000 fix cell line name commit 83e0abb31396a2367c9fa10dfcb762ad3f626fbf Author: mikep Date: Mon Jun 22 21:10:52 2009 +0000 fixing Gm12878NucleusTotal to be Gm12878NucleusLongpolya And, reloading *Transfrags as the tables were missing commit a6d9492b93f2566e00e5109cb9ec461a585b2f6a Author: kent Date: Mon Jun 22 21:02:36 2009 +0000 Removing some debugging code. commit 03ef84e4998bcf9d0382c151f33da825a0620c1b Author: rhead Date: Mon Jun 22 19:09:17 2009 +0000 Forgot a line break. commit a2ed5dcc7adfd97d089538fc9fbd7fdcb96580ed Author: rhead Date: Mon Jun 22 19:05:25 2009 +0000 More edits after consulting Tim and Kate. Added a reference and links to protocols. commit 3fadf7e17220c2fcc7ab5dcbd9e1e30f276854bd Author: ann Date: Mon Jun 22 18:55:43 2009 +0000 first pass at intro and Example One commit fbda071be983740cd2d4aa1ea1675c9f23e4aaec Author: ann Date: Mon Jun 22 18:55:24 2009 +0000 to bring it in concert with bigBed file. commit 46ec57760a0a276ca72d465345aa5f57f9ecb988 Author: ann Date: Mon Jun 22 18:30:55 2009 +0000 small tweak commit 3e9f89fe065e0f0280802a3f1dddc295c4c9389b Author: rhead Date: Mon Jun 22 18:24:02 2009 +0000 Updated links to WUSTL. commit ee9b0a611709003f1d6ab5490051a7237bb31122 Author: kuhn Date: Mon Jun 22 18:22:13 2009 +0000 added a little whitespace at the bottom commit 76e12428545a9ce6634ce52e9f031399b4e8d8de Author: angie Date: Mon Jun 22 18:02:19 2009 +0000 Added clarification for meaning of cds-reference / "Reference (coding)". commit 243e0eb5eb43d7823779c86f6d964fe2be8760ff Author: ann Date: Mon Jun 22 18:00:31 2009 +0000 initial commit. copied from bigWig file commit 6f1514cb4b7f2448105a8678569485072d5a8758 Author: ann Date: Mon Jun 22 17:58:24 2009 +0000 a little closer to true commit 49f7f17ce351ac716757c5e21c3e992666f1929f Author: kuhn Date: Mon Jun 22 17:57:30 2009 +0000 removed capitals on Single Nuc Polymorphism commit c7884461fb3815e7167af79599238cea7f6f5a63 Author: ann Date: Mon Jun 22 17:56:03 2009 +0000 more polish commit 68ae1101b614da1b56c48106fe575fb710eabef7 Author: kuhn Date: Mon Jun 22 17:55:14 2009 +0000 expanded description of track jsut a little. explaining Simple Nuc Polymorphism commit 1ee63461c397e6d6670ee9b6a6a226b456a56e44 Author: kuhn Date: Mon Jun 22 17:37:12 2009 +0000 removed some comments about comparing to previous versions commit 0541ad970fd5985c1dc10fbf6f2859d3684f49f4 Author: aamp Date: Mon Jun 22 17:33:15 2009 +0000 First draft UW Exon Arrays description. commit e7d39db31153d53e34f7f9d9eb3e9fc3dd94c88f Author: hiram Date: Mon Jun 22 17:27:23 2009 +0000 bedSplitOnChrom should be on the build list, used in UCSC gene production commit b39d6736f237f8485a947c73349ff93bd76035f0 Author: tdreszer Date: Mon Jun 22 17:22:47 2009 +0000 I forgot to check this in earlier. Moved metadataLinesToArrays from encodeDownloadsPage.pl to lib so that it could be called by doEnocodeValidate.pl commit 4a244c609e358206f2a48bed4275346c96e79bb7 Author: hiram Date: Mon Jun 22 17:01:57 2009 +0000 Have proceeded through the first cluster job OK without CCDS genes commit 7625367098a107a44384c40bc1134490afe8f6af Author: mikep Date: Mon Jun 22 17:01:02 2009 +0000 new affy tracks for #375 #376 commit 3e2291bd765e2bfbc780c82c47cb3f23e6a7629b Author: galt Date: Mon Jun 22 15:00:06 2009 +0000 "Encode release log update" commit 0b97fb0f3f4218aadf6f3fffe8ebd368b63206ec Author: galt Date: Mon Jun 22 15:00:03 2009 +0000 "Release log update" commit 92272dba17808fe071fb877b2cfb20f390d9b990 Author: galt Date: Sun Jun 21 15:00:05 2009 +0000 "Encode release log update" commit 14852887a8d2a99df52b1f837a83b81ef8ec778f Author: galt Date: Sun Jun 21 15:00:03 2009 +0000 "Release log update" commit 23743caa6a5cbcafca9ff32de9b87525b0f8ecad Author: kate Date: Sun Jun 21 02:36:14 2009 +0000 Fix label commit 80278f9dd7d8306acb9884db0f6a43a1c0ccdfe2 Author: kate Date: Sat Jun 20 19:59:22 2009 +0000 Changes after feedback from Carrie Davis commit dd87607af9eec9785e7619ebc53c073d9b95bcd1 Author: kate Date: Sat Jun 20 19:58:46 2009 +0000 Reverted to allowing viewing negative signal on Affy RNA as it is explained in the description commit 19e3a613c875bf2feb55c930fa362cedd2b25b38 Author: kate Date: Sat Jun 20 19:38:06 2009 +0000 Add CSHL to long labels of Affy RNA track, by request of submitter commit d447f0cf7104364a71f5fb09d4637c5cec0f8980 Author: kate Date: Sat Jun 20 19:25:22 2009 +0000 Disallow negative signal viewing on Affy RNA , by request of Carrie Davis commit f79e1c6cf4c0eb4537cd61ee6218100dac521122 Author: kate Date: Sat Jun 20 19:06:47 2009 +0000 Tune defaults for Affy RNA commit e8d3d3c1c8c171000f56175f0c564906b04cf26c Author: mikep Date: Sat Jun 20 17:25:10 2009 +0000 remove unnecesary dependence on math:floor() commit c50c880fdf705b4bda1730c18cf82cac57dbbef2 Author: mikep Date: Sat Jun 20 16:08:01 2009 +0000 floor is in math.h, dont know why it builds for me but not the nightly build commit 83f158213829b82442ea625c31d2f624f6c85c71 Author: kate Date: Sat Jun 20 16:05:14 2009 +0000 Respond to request from MarkD to correct hostname commit 75690968b21fb6130e830800021aa961e86a2355 Author: kate Date: Sat Jun 20 16:01:05 2009 +0000 Minor edits to ENCODE pages for consistency commit 073f8cd78dc39358363147d58ee0e70393a65d87 Author: galt Date: Sat Jun 20 15:00:05 2009 +0000 "Encode release log update" commit 687d15c64e62abfe20b0ef0f9b1e2f26132e690a Author: galt Date: Sat Jun 20 15:00:03 2009 +0000 "Release log update" commit f615aa6bee89b083a50558805c69ae999424246a Author: markd Date: Fri Jun 19 23:53:39 2009 +0000 fixed dereference of NULL in error check commit d597a8fe660aa8098e9600554f7c00024fd2cfeb Author: ann Date: Fri Jun 19 23:16:19 2009 +0000 removed the last of the wiggle stuff and added a good bit of the bigWig stuff commit 30ae692c04e4b6b831f78417e3abb73473d5696c Author: aamp Date: Fri Jun 19 23:14:40 2009 +0000 First cut of the UW ChIP-seq description. Missing is the bit about antibodies because the table originally only listed one. Also, no track configuration stuff. And the overview section might be a bit on the technical side... in any case, it's in. commit d2f2c7dad844d873e2e3e30e773bb92da50bdfbc Author: hiram Date: Fri Jun 19 21:54:43 2009 +0000 Need to load exoniphy manually, it seems to have different columns in it ? commit 385bfb85c6282499040394432f6c4016f4740faa Author: hiram Date: Fri Jun 19 21:37:32 2009 +0000 Cytobands done, Venter Poodle chain/net done, starting 46-way conservation, exoniphy lifted from hg18, liftOver to hg18 done. commit 4899a93db711c665857c9f511f7a851be46c6b5d Author: mikep Date: Fri Jun 19 19:14:42 2009 +0000 added RGB->HSL/HSV->RGB conversion and transformation code, plus test cases in colorConv program commit e20e9e07b2fe8da6b359f663bb4ae7c81f450106 Author: rhead Date: Fri Jun 19 19:11:09 2009 +0000 Changed crosslink to cross-link to be consistent everywhere. commit b7142a07a6542c0610363af5d036a7a9068cb672 Author: larrym Date: Fri Jun 19 18:55:03 2009 +0000 add RawData commit 9f5966b95dec3948e63b7105995f7bf510c5e058 Author: kuhn Date: Fri Jun 19 18:40:15 2009 +0000 tweaked pubMed format per ann commit 15f256b09c68a7c969140a79372b29a9ac7deff4 Author: rhead Date: Fri Jun 19 18:38:52 2009 +0000 Edits to References section. commit c065b4460ea05af4805e1029e8e4ce672a0ac6af Author: angie Date: Fri Jun 19 18:05:24 2009 +0000 Yet another duplicate to ignore. commit c7948aa7e40795fa039a123fcd28d6b9c8306f5a Author: hiram Date: Fri Jun 19 18:00:11 2009 +0000 Beginning to work through this script to get it ready for UCSC gene build commit 827eb56f400c124dbeb7e500452cec773e36b234 Author: ann Date: Fri Jun 19 17:44:00 2009 +0000 initial commit (contains lots of junk from wig page) commit 067fff9210f66f36b037dc66c38f349011b6b61f Author: galt Date: Fri Jun 19 15:00:05 2009 +0000 "Encode release log update" commit 36bdbe4b2ce3ebcee594f7ce504614eb6fb0e776 Author: galt Date: Fri Jun 19 15:00:03 2009 +0000 "Release log update" commit a358ef54c72d12993080a426675fa0009221336d Author: kuhn Date: Fri Jun 19 00:21:43 2009 +0000 commented out reference to main GFP site because link is broken commit 754e9f1dd35677e4c87b4c653a061e184ac8aec1 Author: rhead Date: Fri Jun 19 00:19:56 2009 +0000 Lots of minor grammar/punctuation/consistency edits. Put Credits in a list. Made quotes html-friendly. commit 2b1dd589cc164e946648ea165ab2ddd24cdc2901 Author: kuhn Date: Thu Jun 18 22:48:09 2009 +0000 added a bit more explanation of just what this is. and changed broken link to paper. thanks, katrina commit fc2f89609e45ba32a9fa9aea317f02d79c99716f Author: pauline Date: Thu Jun 18 22:23:05 2009 +0000 Changing credits to reflect upcoming publication. commit 250a2da3989a597c4be0dba96ce659718cc91697 Author: kuhn Date: Thu Jun 18 21:59:48 2009 +0000 added record of RENAME of table knownBlastTab to sgdBlastTab so GS can use it. thanks katrina commit b7ee7d9c5eaf161a2bc78c541337eab4d8154d14 Author: rhead Date: Thu Jun 18 21:51:02 2009 +0000 Changed tigem link to location to which it was being redirected. commit cfca91521f16f2b1f67fbfe4dc32b76a7da55b5b Author: hiram Date: Thu Jun 18 20:19:18 2009 +0000 Fixup background color on Links Out table when only one row of links ... commit 19d87309586403a4cf0e35f527ed2674d14febd0 Author: hiram Date: Thu Jun 18 17:59:16 2009 +0000 The spaces need to be tabs since that is what comes out of bigBedToBed commit d67304c591e818addaa3cdd22f5f99997caf4f43 Author: larrym Date: Thu Jun 18 17:57:03 2009 +0000 use dragZoomingConfig; currently defaults to off for safari and chrome b/c drag-and-zoom doesn't work under WebKit; make superTrackHasVisibleMembers non-static commit c990f55aeb126d3bf048358f97d05ad465a5929f Author: larrym Date: Thu Jun 18 17:55:05 2009 +0000 add dragZoomingConfig commit caa103c75ec14d20c25a1f1d7681b15e7d31fbbd Author: larrym Date: Thu Jun 18 17:53:38 2009 +0000 add cgiUserAgent commit 35669ce5e99c5177f5c7a605b235c945f40e4840 Author: hiram Date: Thu Jun 18 17:42:07 2009 +0000 Adding an itemRgb test example commit 4034d901f61b79619372ccfae85e3a5c0f515ea3 Author: tdreszer Date: Thu Jun 18 16:57:09 2009 +0000 Terry had one more adjustment commit e23bf8ee38f8e2a21a52454f08308e71290b3173 Author: tdreszer Date: Thu Jun 18 16:38:16 2009 +0000 That was a stupid error commit 3499aa17180ca94e9fccd5cc17c477c84b29377b Author: markd Date: Thu Jun 18 15:53:00 2009 +0000 don't allow core dumps commit ef77cb1c62b200c9b19fe96e82e980fc9115fe66 Author: galt Date: Thu Jun 18 15:00:07 2009 +0000 "Encode release log update" commit 12d8d33d83794a47be42845d466c99e3ec1a1c7f Author: galt Date: Thu Jun 18 15:00:03 2009 +0000 "Release log update" commit 182bb564946e1d18ad421d2532d49c9f1627917a Author: pauline Date: Thu Jun 18 07:18:10 2009 +0000 Changing credits and refs to reflect upcoming publication. commit de2a02cd3bff3fc11fca0491b876974605904f55 Author: markd Date: Thu Jun 18 06:07:47 2009 +0000 added bug commit 3bba64f60fe3aea9fe5e816f65d5f7973f6b121d Author: markd Date: Thu Jun 18 05:23:10 2009 +0000 added bug commit 3dce81296f7fbc846a29b43721f7ca1694eac051 Author: tdreszer Date: Thu Jun 18 02:36:42 2009 +0000 Added wgEncodeUncFAIREseqBaseOverlapSignalK562 back in commit ea6fa5926868712e80994f141c4d40ec4a5c33cd Author: rhead Date: Thu Jun 18 01:03:31 2009 +0000 Whitespace changes. commit 46a881e3aff081ed7738f1957449ec9bd322e2df Author: kate Date: Thu Jun 18 00:27:26 2009 +0000 Correct whacked cell type from mass edit commit 539a3238285ba576f4e05cb11a4f0d6223bd2130 Author: tdreszer Date: Thu Jun 18 00:26:10 2009 +0000 Moved sub metadataLineToArrays to Encode.pm so that doEncodeValidate.pl can also use it commit e0d88f1341ebb820187e87139c8d75f447207310 Author: tdreszer Date: Thu Jun 18 00:22:27 2009 +0000 Temporarily remove K562/FAIRE/Signal BO to reload it commit 4388b1bd75957d415c25d71cbc9826cf7264c940 Author: kate Date: Thu Jun 18 00:21:38 2009 +0000 Rename cell type for more specificity commit e22cedda108c89acfabef6b3dc67f4939cc78a12 Author: kate Date: Thu Jun 18 00:20:41 2009 +0000 1. Change Keratinocyte term to NHEK. 2. Readability mods to Affy RNA labels commit bc1f97324d20850a741f54ff94e0f14eb1ca7993 Author: tdreszer Date: Thu Jun 18 00:18:14 2009 +0000 Trying to get old metadata for new submissions commit dae34ddde5c8954206c2a4b8152f8b4264f98d0c Author: kate Date: Wed Jun 17 23:46:01 2009 +0000 Updates to track labels commit 64dd5a152be1d129bdd7f192ba1b2c6f69066341 Author: tdreszer Date: Wed Jun 17 22:55:18 2009 +0000 Open Chromatin short labels of GM12878 cannot be abreviated to GM128. commit 8431dd3706d8379ce778a63c8a34d821144a86a4 Author: katrina Date: Wed Jun 17 22:50:30 2009 +0000 Changed priority of SGD Gene and SGD Other so that they are first and second in their track group commit 654b3f2385e02763604ea6d4c014bbde6b3be8a0 Author: tdreszer Date: Wed Jun 17 22:49:39 2009 +0000 Someone finally had the sense to point out that the name 'Excludable regions' was a lemon commit df2ca3f5e28b3e6d46f9837bef650ffca49397c8 Author: tdreszer Date: Wed Jun 17 19:55:36 2009 +0000 Terry finally weighs in on 'Duke Excludable' regions description commit b8339e237279a8dbe7a69e7cc045ba7f81ebe923 Author: tdreszer Date: Wed Jun 17 19:52:00 2009 +0000 More twiddling... Actually fixing some of my mistakes with the last check-in commit 85fb0389f4096ed6de03ffd8f42f06185369b7fc Author: angie Date: Wed Jun 17 19:05:52 2009 +0000 Added new setting defaultLinkedTables. commit c5933ecf9f6467eaec1cb239751e2025f51ad214 Author: tdreszer Date: Wed Jun 17 19:01:27 2009 +0000 More adjustments for Terry's Open Chromatin commit 4e900c4c2d2e2d473f74202cce69f55ea65920bc Author: tdreszer Date: Wed Jun 17 19:00:29 2009 +0000 Renamed Signal tracks on Terry's request commit ceb018d8160eeb6983970bbcd5f60eb2fb4b9b9d Author: angie Date: Wed Jun 17 18:54:50 2009 +0000 Added NULL check -- this can happen when a trackDb setting specifies a table that isn't properly linked in all.joiner. commit f7b723ca01f6c571fd96f85512960ca8828ca99b Author: angie Date: Wed Jun 17 18:53:54 2009 +0000 Added mm6 back to mm -- it is still on hgwdev. commit 577f56f230224e3a1cce524a7bead0ecf26307a2 Author: tdreszer Date: Wed Jun 17 18:22:13 2009 +0000 Terry requested some changes which recommend that the user turns on auto-scale for signals commit 93c27caca9507afa3448aae8883076c7cb9588df Author: tdreszer Date: Wed Jun 17 18:18:16 2009 +0000 Terry's signal viewLimit defaults commit d15393d7ae400387b27ca41cf5c13154a6fca932 Author: angie Date: Wed Jun 17 18:17:47 2009 +0000 Convert knownGene to override, to simplify and to inherit new top-level settings. commit 8582243c0e27ddb02ab2ad4d5b693db29786fcd5 Author: angie Date: Wed Jun 17 18:17:45 2009 +0000 Add override labels for knownGene (now UCSC Genes at top level). commit 207eae552300086823f8838c2f56e001e8fa1e90 Author: angie Date: Wed Jun 17 18:17:44 2009 +0000 Removed local knownGene definition (duplicate of top level now). commit 2fc7ea59fc10d23f1a6f6d35f3439df3dba57411 Author: angie Date: Wed Jun 17 18:17:43 2009 +0000 Make UCSC Genes the default label for knownGene going forward. commit 672d3868012d8e7597457ed42b3e15be5639f204 Author: angie Date: Wed Jun 17 17:15:49 2009 +0000 Added new defaultLinkedTables setting to knownGene so kgXref will appear by default when selecting output fields in hgTables. commit b134bb681b43a8f385066ceffc1a4e5e3367b0be Author: angie Date: Wed Jun 17 17:05:42 2009 +0000 Added new defaultLinkedTables setting to knownGene so kgXref will appear by default when selecting output fields in hgTables. commit 9803dc80f288166826f9722e2526c73b52892b63 Author: angie Date: Wed Jun 17 16:49:03 2009 +0000 When selecting fields for output, automatically include any tables specified in trackDb setting defaultLinkedTables. commit 05eee9446baa7fb33888be04d1cc59f711d7b36e Author: hartera Date: Wed Jun 17 16:16:25 2009 +0000 Added CCDS paper reference. commit 5726fd606bd3f6dc86025dbbba4396b71c2734fe Author: kent Date: Wed Jun 17 15:19:03 2009 +0000 Updating comments to more closely reflect code. commit d498c2069cd0493206f33bd0e8f9a2f275492824 Author: galt Date: Wed Jun 17 15:00:06 2009 +0000 "Encode release log update" commit 64c6758528068f860f3c082dce6df7859948d5aa Author: galt Date: Wed Jun 17 15:00:04 2009 +0000 "Release log update" commit ff19e9c5902d31ecb8cff76b103901f18a87bc8c Author: donnak Date: Wed Jun 17 00:41:52 2009 +0000 Added CCDS paper. commit 47214b51dcec427f2e351be6ab74d636cd987721 Author: rhead Date: Wed Jun 17 00:24:13 2009 +0000 Added release alpha back to Open Chromatin raw signal tracks. commit 6316052a661383164a519affb065b4b3d627507a Author: hiram Date: Tue Jun 16 23:21:08 2009 +0000 Turning on first look at 46-way alignment commit 51438d3921dc997904dc68dc751726803e33ab90 Author: rhead Date: Tue Jun 16 22:20:24 2009 +0000 Removed release alphas for initial release of Open Chromatin track. commit bbf906b0b8cbb7cf3d31c7ea2a15e2c59cdd18e2 Author: rhead Date: Tue Jun 16 21:58:16 2009 +0000 Added removeAlphas. commit 95b8d5eb99483fdf40da62befe1fd8d7f9a26392 Author: rhead Date: Tue Jun 16 21:54:31 2009 +0000 Initial commit. Thanks, markd! commit 5be3c976a89c798aeb2a777879088e08c7a0ec81 Author: tdreszer Date: Tue Jun 16 20:17:31 2009 +0000 Set Vishy Iyer's default viewLimits for ChIP experiments commit ad14b6cfb066d2656916d818fdfbedcd403b1868 Author: galt Date: Tue Jun 16 19:51:17 2009 +0000 getting wider use of sorted genepreds including knownGene commit 5d5bb506e2948aef81ba0b6a5d610092b29f9a39 Author: tdreszer Date: Tue Jun 16 18:34:16 2009 +0000 Added 3 new tier 3s for Stam lab commit 1595eaacebf638095f0fe040ca0bed53bc8968e5 Author: tdreszer Date: Tue Jun 16 18:33:43 2009 +0000 Added dataVersion for the DAF commit be7f18083d4fbf6b43c80e7e0501371752c68707 Author: angie Date: Tue Jun 16 17:04:23 2009 +0000 Fixed termRegex for ctgPos2. commit 73eb1a8276165fc78fd23e823c05c7e659d852cc Author: angie Date: Tue Jun 16 17:04:05 2009 +0000 hgFindSpec tweaks: for the more restrictive stsMapAliasMrnaAcc search, don't require that all aliases match the termRegex. Broaden sgpGene and geneid termRegexes to accomodate hg19. commit 813f0a6dab53056ced71d98ce597e69108dbbe08 Author: fanhsu Date: Tue Jun 16 15:49:53 2009 +0000 Minor edit. commit b240b63dcb3d5ecf83cd1b5274b0d1ee87163669 Author: fanhsu Date: Tue Jun 16 15:48:33 2009 +0000 Added humanHA and swineHA tracks. commit 646975be3ae96e53a7aa93521021f99d3579f919 Author: fanhsu Date: Tue Jun 16 15:48:03 2009 +0000 Created swineHA.html. commit b8bb6ed33e6c4adec3e0def5391e9dbec4d85515 Author: fanhsu Date: Tue Jun 16 15:45:03 2009 +0000 Added humanHA.html. commit 386f0439a09a637090536a30f54c75588e486af5 Author: galt Date: Tue Jun 16 15:00:07 2009 +0000 "Encode release log update" commit c7d8c29b7d2add39e6a75084948eebb90c50a390 Author: galt Date: Tue Jun 16 15:00:03 2009 +0000 "Release log update" commit 542a6f669608b76d11f00b4a87a725fa9eb78240 Author: mikep Date: Tue Jun 16 14:55:56 2009 +0000 v209 preview commit fce41f7cb420f22b75eb2c07dbb0206e5c0127aa Author: markd Date: Tue Jun 16 06:17:38 2009 +0000 avoid pop all warn handles; just hacked around it commit 3a0f7c6b0b489df10eaf7c90cb055b79048751c1 Author: tdreszer Date: Tue Jun 16 01:27:40 2009 +0000 Added Yale/UCD K562b E2F6 and Setdb1 commit 9942bedcf87ba2394bc6b10e2e0fae35bb064a17 Author: tdreszer Date: Tue Jun 16 01:25:46 2009 +0000 Kate didn't like colons, count occupied rows and columns in matrix, composteViewControlNameFromTdb didn't support ClosestToHome. commit 7658324e946ea4bcbbb0851b836f9ee461de9dfd Author: tdreszer Date: Tue Jun 16 00:26:11 2009 +0000 Minor wording change commit c65825e8b98ee894f38a68b824da138c7c614c7c Author: tdreszer Date: Tue Jun 16 00:24:57 2009 +0000 Changed the wording for Duke excludable regions commit 0cc5bd8e1263808fc00d3d358bb128a1c1de02b1 Author: markd Date: Mon Jun 15 23:56:50 2009 +0000 get gisaid locations from hg.conf commit dea9e52fb03e98ef6c80ac415dcb6c42e85512c3 Author: angie Date: Mon Jun 15 23:47:29 2009 +0000 Prevent stack dump in case of stoopid invocation (googlebots). commit b2a6992b0e44f01765aae7c3009c59aa05e7daef Author: angie Date: Mon Jun 15 23:37:20 2009 +0000 Added stderr logging (a la htmlVaWarn) to cartEarlyWarningHandler, so we get an informative message along with the stack dump. commit 2cb34011903dbda6516335d88ff2c6e2c97f5dbf Author: rhead Date: Mon Jun 15 23:30:21 2009 +0000 Fixed broken links to wustl. commit 2506902be4b3acd48a7470ce7b1e22645b5ae8db Author: markd Date: Mon Jun 15 23:00:24 2009 +0000 highlight only specific sequence differences in gene seq display commit 1aa93b30b703b8ff1d7768228fd68cc17bec4910 Author: fanhsu Date: Mon Jun 15 21:56:28 2009 +0000 Added doH1n1Gene(). commit 01fba62fb4e3f76448582208c1b8d6e9e0024dcc Author: fanhsu Date: Mon Jun 15 21:48:03 2009 +0000 Minor update. commit 71d552e22eadf465b9391155e805836cadc40764 Author: fanhsu Date: Mon Jun 15 21:34:49 2009 +0000 Added method of doH1n1Gene(). commit bb076fadbfb836cc7e17ab326bc6678b15500c80 Author: fanhsu Date: Mon Jun 15 21:34:19 2009 +0000 Added details page for h1n1Gene. commit cdc335cde57a0ad4faf1d759f020e0d0a99fed65 Author: aamp Date: Mon Jun 15 21:13:09 2009 +0000 Reverted gold.html to top-level. Used gap.html form monDom4. commit 65390231fb7f1e1406ac25bb2be5bdd267270201 Author: mikep Date: Mon Jun 15 21:05:12 2009 +0000 fixing - strandness problem with paired tag align data commit 43456a31b0a7e75499006f5de3ef201258e484c7 Author: tdreszer Date: Mon Jun 15 20:47:06 2009 +0000 I removed js file versioning by fake get variable, as it has led to some browsers/configurations reacquiring the file from the server every time a function is called. Versioning solution still remains to be done. commit 2bdb419d033830e5885b64f48340746365b0b256 Author: rhead Date: Mon Jun 15 18:52:11 2009 +0000 Fixed the hashpling so that this is run with tcsh. commit ecf319bdbaee12587c339c114ce6929ab028a2b5 Author: angie Date: Mon Jun 15 18:15:53 2009 +0000 Merged some duplicate notification messages about custom tracks and blat results when creating a session -- Thanks Ann. commit 35627dd7a4581afc9fb4ae606251d1173a8bfc94 Author: kate Date: Mon Jun 15 18:06:56 2009 +0000 expand description for NHEK commit ca513876a15f89f6c584bad85d385890d2888ce5 Author: kate Date: Mon Jun 15 17:56:02 2009 +0000 Lonza web site has changed commit 7f4d854f01690f87224b4a2fb0521275ffb67dfa Author: kate Date: Mon Jun 15 17:46:28 2009 +0000 Consistency edits to Affy RNA. Need to get this into validator/loader commit d1c1b2e0615dcab8123391123f331cc9f4bad701 Author: hiram Date: Mon Jun 15 16:37:52 2009 +0000 Adding a generic chain net description page for all the chains and nets commit 8f02281c215e09c83b9f65b3f39861ce5b98bf48 Author: galt Date: Mon Jun 15 15:00:04 2009 +0000 "Encode release log update" commit 3b8180d2b6e5009c8f35ea3a34b5faa2d51c07e2 Author: galt Date: Mon Jun 15 15:00:02 2009 +0000 "Release log update" commit 4e085b303f7b0cad5a0fb0cd34ec837675f0a508 Author: fanhsu Date: Sun Jun 14 23:07:11 2009 +0000 Created h1n1Gene.html. commit aaaed735b1bc6ed1ef42d0e4ddcf22f2d701b81e Author: sbenz Date: Sun Jun 14 22:04:22 2009 +0000 Added gray breast cell line SNP6 segmented data commit d1e7bb73f0f237da87d42bf5767ae2048d405e23 Author: fanhsu Date: Sun Jun 14 21:46:10 2009 +0000 Added search teram for h1n1Gene. commit b06b37733765d9435b40b145dbfe94cc5fc502db Author: fanhsu Date: Sun Jun 14 16:58:02 2009 +0000 Fixed a bug due to sample based instead of subj based. commit 680a6701312e32619bc722d425fec3cf084a0ee5 Author: fanhsu Date: Sun Jun 14 16:52:10 2009 +0000 Added "Select Subjects" to top bar. commit 1244aee198c04661c0c88e5672e0e4a9dc0c2fff Author: fanhsu Date: Sun Jun 14 16:23:17 2009 +0000 Added isolate (sample view) link. commit 30e15e461e1e7c03ff998cc9b07bd005a31f2a82 Author: galt Date: Sun Jun 14 15:00:04 2009 +0000 "Encode release log update" commit d0bc2f62d509a1ed157e6182b84e5b355a52c264 Author: galt Date: Sun Jun 14 15:00:02 2009 +0000 "Release log update" commit cb3c69badedd8b08cbc97c1cd7f78a7ce25209e0 Author: hartera Date: Sat Jun 13 20:48:53 2009 +0000 Changed long label of old wgRna track. commit f8fa9d1cf5208f9a6810c9a61072fb4a079fb633 Author: hartera Date: Sat Jun 13 20:46:12 2009 +0000 Updated short labels on sno/miRNA tracks. commit 9712069b78d19ebb7abaebc3de6625902002d0c1 Author: hartera Date: Sat Jun 13 20:39:58 2009 +0000 Updated the wgRna track with latest miRBase and snoRNABase data. commit cebb1ff01026edbc4f2f93d6978a42178cdbd61b Author: hartera Date: Sat Jun 13 20:28:31 2009 +0000 After updating the wgRna track, renamed the old track to wgOld to keep it around for a while before replacing it with the new track. commit 864664be93f8d71fd73fc382eabdb9ac071ba42c Author: hartera Date: Sat Jun 13 20:27:31 2009 +0000 wgRna track was updated to temporarily renamed old track to keep it around for a while before being replaced by the new track. commit 628ec46ca98f5f2db9f3a50ae02f326b12ed563c Author: hartera Date: Sat Jun 13 20:26:08 2009 +0000 Updated description for updated wgRna track. commit 43d40ca33bf17b583f3bd006f81bf3ad90cc7f3b Author: galt Date: Sat Jun 13 15:00:04 2009 +0000 "Encode release log update" commit d47671c4f0372bd690d1820e8897805fe88fb398 Author: galt Date: Sat Jun 13 15:00:02 2009 +0000 "Release log update" commit 6faa9f1ad0a4e9b776bd4119f37c5fe8f2399d0b Author: markd Date: Sat Jun 13 04:19:39 2009 +0000 extract protein ids for dynamic_highlight script commit 85cc1dc7344b4c349448ba1f74aa200f5a8873f3 Author: tdreszer Date: Sat Jun 13 00:32:40 2009 +0000 Lots o stuff commit 4bba5a9b7dc8635cc55b862708ce8edea440b0fa Author: tdreszer Date: Sat Jun 13 00:32:15 2009 +0000 Pushed so keep this up to date commit edaf42e734c97728e5accfb7967d23e3f7cf2adc Author: tdreszer Date: Sat Jun 13 00:31:33 2009 +0000 Keeping this up to date commit eae46d3b3f3d76990cafc748f5eaa2784212dafe Author: ann Date: Sat Jun 13 00:30:58 2009 +0000 added new block for ENCODE Riken CAGE with release beta to get rid of non-pushed prostate cell line commit cb20035009a8463d387d74e0fd872cc30fe81a25 Author: markd Date: Sat Jun 13 00:15:21 2009 +0000 added makefile for build all subdirectories commit 8224d638d60857867d11db5257b26f37cc7d0e80 Author: hartera Date: Sat Jun 13 00:10:02 2009 +0000 Updated wgRNA track description. hg18 is the only human assembly with the track at the moment. commit 21cecc0463727a9ff8bbf207091316811352dd44 Author: hartera Date: Sat Jun 13 00:01:56 2009 +0000 Added html encoding for correct rendering of URL label for wgRna track. commit 8f923bed188b87fb86a53a1a5e4174687994bd08 Author: hartera Date: Fri Jun 12 23:56:51 2009 +0000 Removed wgRna track entry as duplicated from trackDb.ra at human level. commit 105b4bd008eee8e5c5ee1318bd40fdb47c367cc0 Author: tdreszer Date: Fri Jun 12 23:40:51 2009 +0000 Fixed metadata associated with moving excluded regions from open chramatin to mapability commit b423051ae3e2891bfe95a9842184073c13931f55 Author: angie Date: Fri Jun 12 23:35:24 2009 +0000 Added section describing settings specific to the snp125 (or later) tracks -- Kate's review feedback. commit fe9a7581d9edca41f629d884aba7bb0e5af63a67 Author: tdreszer Date: Fri Jun 12 23:17:36 2009 +0000 Moved Excluded Regions to the Mapability track commit 7a837fdfee0ef1c842c27de837f4c426f5323ee8 Author: hartera Date: Fri Jun 12 23:13:05 2009 +0000 Removed reference to Blat. commit 6990c2b4b5a6b84d257ed671000623eb8690c70d Author: hartera Date: Fri Jun 12 23:12:02 2009 +0000 Track description for the sno/miRNA track update. commit 457eb740256a230fe7bbba6b3a1e5a50046d322d Author: fanhsu Date: Fri Jun 12 22:52:14 2009 +0000 Updated MySQL select logic to accomodate change from subjId to sampleId (on gisaidTable). commit 837783987c6b0ecc24f03b2ef786d05af158deaf Author: hiram Date: Fri Jun 12 22:19:35 2009 +0000 Implement modes squish and pack for net tracks commit e0d8fcecf706811a28744b2d97dc324dce0865f0 Author: hiram Date: Fri Jun 12 21:53:49 2009 +0000 Adding poodle chain/net commit 5c724abf617a7083a110fa3db2bfd3d2f8382a0b Author: hiram Date: Fri Jun 12 21:52:51 2009 +0000 Organizing the big chain net composites into clades commit 59454a6320687f35f3add505e2b927388c545e06 Author: tdreszer Date: Fri Jun 12 21:05:51 2009 +0000 Huge Yale matrix requires right buttons and bottom buttons commit 4f2efe12bbdb42ce446491efded6f7c4428e90c9 Author: tdreszer Date: Fri Jun 12 20:46:26 2009 +0000 Yale is one massive 2D array commit 9131b8af5ac60f106bd13886f3a83c7e2ce05a44 Author: kuhn Date: Fri Jun 12 20:24:07 2009 +0000 added blocks for chimp chain/nets to exist on beta and RR while composites are worked out on dev. removed some override stuff that was in there commit a9aeda207fd7229c2f4b535f20d73ca1dfb1b286 Author: kuhn Date: Fri Jun 12 20:21:14 2009 +0000 changed reference to fit pubmed model commit abd46726585dbb8bc5b097e516c003674ab84223 Author: fanhsu Date: Fri Jun 12 20:01:15 2009 +0000 Moved sequence cols priority up. commit d23d5cf0100640ed5c2ec61581b95e0fc35e24ee Author: tdreszer Date: Fri Jun 12 19:56:17 2009 +0000 More Yale Tables K562b/E2F2 and HepG2b/TR4 commit 0e2f4227117ba6a79e649e3136750597d9ba3184 Author: kuhn Date: Fri Jun 12 18:32:49 2009 +0000 changed reference to fit pubmed model commit a6305b94d999e406bfb56a6ffc9e7658e3dc950d Author: fanhsu Date: Fri Jun 12 18:24:54 2009 +0000 Removed the query lines. commit 72b69998ab71d1b65455bddff871748255de91fb Author: fanhsu Date: Fri Jun 12 18:23:57 2009 +0000 Updated the dnaSeqIds and aaSeqIds cols. commit b5659b25cb66d1dcc90d59db569d5c80de5a1bf8 Author: kuhn Date: Fri Jun 12 18:06:03 2009 +0000 changed reference to fit pubmed model commit 7c87ec6b73b5ba8295e2ce30764fc2194532dc97 Author: kuhn Date: Fri Jun 12 17:14:58 2009 +0000 added comment about viewing mode commit 92f838e662b7d058626a6469dc714618f3e665e0 Author: hartera Date: Fri Jun 12 17:10:13 2009 +0000 Added a note to the miRNA track update section. commit 1f8bcf9548f6b671afb1571a1b3f933696a4897c Author: kuhn Date: Fri Jun 12 17:03:17 2009 +0000 Capitalized sentences commit 850396773c2368ce6d01eed5dc61af75a08c8e6e Author: kuhn Date: Fri Jun 12 17:01:29 2009 +0000 moved hg18ctoBand down to hg19 level and added html page for it commit 3cd9a6e7ed86ba8e078371f7ff6500ecd119e2c9 Author: hiram Date: Fri Jun 12 15:52:24 2009 +0000 Fixup chainCfgUi to work properly on split table names commit 19ed83f47ee84c1635279652c354a0f85aaa768e Author: galt Date: Fri Jun 12 15:00:06 2009 +0000 "Encode release log update" commit 5d28198c91bb09bf38a7dfa13df9243ea10fb7cf Author: galt Date: Fri Jun 12 15:00:03 2009 +0000 "Release log update" commit afd21b3ecf422b433ba203bd3d4565181dc212b7 Author: fanhsu Date: Fri Jun 12 14:18:04 2009 +0000 Enabled doValueRange and doValueHistogram for GSID and GISAID. commit e8a50e5e48cacaf25e384f17c6a028f0418c1d7e Author: markd Date: Fri Jun 12 07:21:30 2009 +0000 added support for chimera in H1N1 prototype; also some refactoring commit 7a278f3489349c1c5f3aff4ad967c12e6ca10362 Author: tdreszer Date: Fri Jun 12 00:11:41 2009 +0000 Typo on of of the billion tablenames commit a9b58fc92fd588ac6cf2cb46bd941ec2566d040a Author: tdreszer Date: Thu Jun 11 23:52:50 2009 +0000 Added E2F6 antibody for Yale commit 6a516a65ac201e3b98a950de811e3a27b879e72e Author: fanhsu Date: Thu Jun 11 23:51:55 2009 +0000 Changed subject view to sample view. commit f504174ebee4a4a0a9b2c0c072e9c2ba577eefd3 Author: fanhsu Date: Thu Jun 11 23:49:10 2009 +0000 Changed "subject view" to "sample view" for gisaid. commit f7fa7fae567d4425f07ef3f137b1aea3675b7703 Author: fanhsu Date: Thu Jun 11 23:44:51 2009 +0000 Updated some logic. commit 4af36e15488c101f9b8c52377d002a1bd4b66577 Author: fanhsu Date: Thu Jun 11 23:42:40 2009 +0000 Added gisaidSample.h commit 1bdba2e678028c5fe5338ca39ed5ecb57dce0857 Author: fanhsu Date: Thu Jun 11 23:29:47 2009 +0000 Turned off sequence cols. commit 4b27936cefd15513826efbf9bc6377230dcb7b25 Author: fanhsu Date: Thu Jun 11 23:28:40 2009 +0000 Switched from subj oriented to sample oriented. commit 81791c3c70bca52bdaa33609819187c8e65b2075 Author: fanhsu Date: Thu Jun 11 23:27:16 2009 +0000 Switched from gisaidSubj to gisaidSample. commit 5036547b78e433cadc81b8b4a927cfa36c53e3df Author: tdreszer Date: Thu Jun 11 23:17:06 2009 +0000 Added new Yale treatments, split out 'b' versions of K562 and HepG2, reworked some metadata commit 0352cfeeba94d915558c6a971c0b8bedc81899cc Author: fanhsu Date: Thu Jun 11 23:17:00 2009 +0000 Created section.ra commit 2c421f97c9008ac6c55f2b76157ec2c7c29573ec Author: fanhsu Date: Thu Jun 11 23:15:46 2009 +0000 Created makefile. commit 61e811b989e3f6ba98fcea97e6c4161ba6ea8175 Author: fanhsu Date: Thu Jun 11 23:15:32 2009 +0000 Created for gisaidSample. commit a8cbbe78c3f426294b88e17659af73a431658ba9 Author: kuhn Date: Thu Jun 11 22:43:44 2009 +0000 enabled hg18ctyoBand track for comparison commit 7ff83d8a2132430c4ba13157c7894f393dc5bc36 Author: hartera Date: Thu Jun 11 22:28:31 2009 +0000 Fixed an off by 1 error in the BED file loaded for miRNA track. commit c13343728ecd38ac1a15dbd702d9c66b66c8f352 Author: hartera Date: Thu Jun 11 21:28:25 2009 +0000 removed html extension for html line for miRNA release beta. commit 50413692d30fc781599c334a43700af3be5a884a Author: tdreszer Date: Thu Jun 11 21:20:59 2009 +0000 Added K562b and HepG2b alternate cell lines because Yale and UCDavis can't agree commit 93e1deaa19e210e2423f2250dd65db28a5d6154e Author: tdreszer Date: Thu Jun 11 19:52:31 2009 +0000 It appears that these changes were committed in January, then stepped on in February commit 2c76d01eb30ae42ccef4656d2e6f1c50ecef79ef Author: fanhsu Date: Thu Jun 11 19:44:05 2009 +0000 Changed "Sequence View Gateway" into "Sequence View" commit 554ceea4682da5f14da321f909c636905e379a9b Author: hartera Date: Thu Jun 11 19:41:14 2009 +0000 Added release alpha and beta versions of miRNA track until the update is released. commit 6b8cc2191ac8c2b5850f2070bc56d7d290c92822 Author: fanhsu Date: Thu Jun 11 19:40:40 2009 +0000 Changed "Sequence View Gateway" to "Sequence View". commit cd13d6035329768ce2cd045ff9e0eb1ff90375b2 Author: hartera Date: Thu Jun 11 19:40:04 2009 +0000 Old version of miRNA track description, use for release beta until new miRNA track released. commit d517c2ad46746b264ebd3c3f755f630478d4b89d Author: angie Date: Thu Jun 11 19:13:10 2009 +0000 wgEncodeGencode names are not specific enough to warrant semiShortCircuit -- that was excluding UCSC Genes and other matches. commit e0fbedf2ac1f2b01c4be61df10f35b50c3bac2d9 Author: hiram Date: Thu Jun 11 18:48:28 2009 +0000 Fixup sgdOther reference to new assembly and turn off the score filter commit f5d14be8e4c078c291de5fd8a4222d9835250851 Author: tdreszer Date: Thu Jun 11 18:45:33 2009 +0000 Bryan updated his uniqueness methods commit 1a88c1a6177ee45a5eeb3791c53cee077ded825d Author: galt Date: Thu Jun 11 18:17:49 2009 +0000 chains to sea hare commit cc90850a7bc3f4ef56944421bc62a15e9a026721 Author: fanhsu Date: Thu Jun 11 17:37:06 2009 +0000 Disable hgGateway top bar link for GISAID. commit 61dcfb1d0624143ac0da2e101af2b953289692bf Author: markd Date: Thu Jun 11 16:43:01 2009 +0000 don't bogusly crash on array or list colomns commit 006e76bffee5c6ec34cd0b5fab6640520a49c138 Author: angie Date: Thu Jun 11 16:36:06 2009 +0000 Added sacCer2 (why was it missing?). commit cb5a055b1260247bf668b0e1bc1081d30f2c30d8 Author: fanhsu Date: Thu Jun 11 16:17:27 2009 +0000 Added logic for GISAID. commit 434bdd02ca9d8eed670c0ea73191858383fe8ba3 Author: fanhsu Date: Thu Jun 11 16:15:14 2009 +0000 Minor updates for GISAID. commit c28761a4029bad9015fff4d3fd595f6c97686b6e Author: fanhsu Date: Thu Jun 11 16:10:37 2009 +0000 Added top bar section for GISAID. commit 285eef8aa3ea3d02c65f4748114e6ff19336a32e Author: hiram Date: Thu Jun 11 16:01:38 2009 +0000 This didn't work when gap and rmsk were not split tables, fix that up with more extensive MySQL queries commit 2bbcc5e71c40fd8a4384d2d29564e5f1b26f7223 Author: galt Date: Thu Jun 11 15:00:06 2009 +0000 "Encode release log update" commit 655a18a8106a81125ec16abf0b555bd1f835c01c Author: galt Date: Thu Jun 11 15:00:03 2009 +0000 "Release log update" commit 76d278a90101de3215145991c23dea5ce5d87dcd Author: hartera Date: Thu Jun 11 00:11:49 2009 +0000 Minor edits and added release date for miRNA data. commit 35001f5bec32b25123a1e3790fa26a6098031635 Author: tdreszer Date: Wed Jun 10 23:27:08 2009 +0000 Yale's many subtracks outgrew the 8 bit counter that I was using commit a3db8e04fe62bb1c45777cc9211eecaaedec4eea Author: tdreszer Date: Wed Jun 10 23:26:02 2009 +0000 Added a bunch of Yale treatments which necessitated breaking the composite between alpha nad beta and creating a 3D matrix for on alpha commit 36317c4701ac9635f6f9d117bee3012ef5eee620 Author: hartera Date: Wed Jun 10 23:12:29 2009 +0000 Re-loaded the miRNA track after adding scores that correspond to whether the sequence is on the + or - strand. commit 4fd941b64c7c8410f9c6648f5745c3272267d1bf Author: hartera Date: Wed Jun 10 23:09:33 2009 +0000 Updated the miRNA track description after updating to Release 13.0 from miRBase. Added another reference. commit 0fae3837b6e971213622f7daad0180dbebed6dfa Author: hartera Date: Wed Jun 10 23:07:54 2009 +0000 Re-enabled use of scoring for miRNA track. commit c2ae489846d6e7e36593498dc3e7ac81441bd01f Author: angie Date: Wed Jun 10 19:46:20 2009 +0000 Some code for codons smaller than 3 bases was erroneously applied to noncoding blocks smaller than 3 bases. commit 1a7d25041cbfab49d9dd0ad8e7965ef4756b7a95 Author: hartera Date: Wed Jun 10 19:16:49 2009 +0000 Updated the miRNA track to miRBase data release 13.0. commit 8552aa7f5b768ee9fffcbd5885c2cbc9c379bcb8 Author: hartera Date: Wed Jun 10 19:15:24 2009 +0000 Added version number for update of miRNA track and removed useScore as there is no score for this track. commit dbe5149168832b49a3a5812bfea3da5614675c9a Author: kuhn Date: Wed Jun 10 18:47:09 2009 +0000 turned on scalebar by default commit 67e50eae9149c50cffa330efe578450d8414fad6 Author: kate Date: Wed Jun 10 16:07:21 2009 +0000 Description for ENCODE variation track from HudsonAlpha commit c83e10362056c152da2ef91ea4d786ff6d5fdfaf Author: kuhn Date: Wed Jun 10 15:33:33 2009 +0000 balanced a quote in a comment commit 9560a8f20c8a1dbf9a2588170261bc3e90f9ea13 Author: galt Date: Wed Jun 10 15:00:06 2009 +0000 "Encode release log update" commit 30d688a64e9f46d2728c54597f9b6aae580ccfa2 Author: galt Date: Wed Jun 10 15:00:03 2009 +0000 "Release log update" commit 6953afe478d0880919a24207a51461ff7b55bee9 Author: tdreszer Date: Wed Jun 10 04:42:29 2009 +0000 Missing Restricted Until link commit e26e56be6260ae01ff7736308040ce6ae9f3a7e4 Author: fanhsu Date: Tue Jun 9 21:45:27 2009 +0000 Added logic to support gisaid. commit 3612120de78e4f2c7838b9138760372cfca8cd03 Author: fanhsu Date: Tue Jun 9 21:21:16 2009 +0000 Added logic to support gisaid. commit 9ee0b748edef042cde940321aac50ad835752121 Author: fanhsu Date: Tue Jun 9 18:02:25 2009 +0000 Cleaned up h1n1/h1n1/trackDb.ra. commit d73cb6b705562c7c87662086be27177eba346786 Author: markd Date: Tue Jun 9 17:56:06 2009 +0000 only build encodeValidate on hgwdev/hgwbeta commit 606d1751ef736c31365c3ed1c33fef54148fd013 Author: markd Date: Tue Jun 9 17:42:33 2009 +0000 fixed non-portable code commit 3bb1f8c1d28df87430d2e321c107dc718636251d Author: markd Date: Tue Jun 9 16:22:18 2009 +0000 removed bash-specific syntax commit 37089b052c86909c3d23ac150b491b0c485c7b6e Author: fanhsu Date: Tue Jun 9 16:05:18 2009 +0000 Added section.ra, work in progress. commit fec9d7c45b5173c5a737c6753286cc931184132e Author: fanhsu Date: Tue Jun 9 16:04:04 2009 +0000 Created makefile. commit 2d5a5883f31ae6c6e8daed7fc7bed1938e491aed Author: fanhsu Date: Tue Jun 9 16:03:45 2009 +0000 Created gisaidSubj.h. commit 611198dab7a72f3a19c0f626e3a190ca59d005d2 Author: fanhsu Date: Tue Jun 9 16:03:26 2009 +0000 Created *.c for gisaidSubj. This is work in progress for GISAID demo site. commit aaf6675d5dad4ddcd3752a04a80933be54071701 Author: fanhsu Date: Tue Jun 9 15:59:02 2009 +0000 Created column.ra commit 778d3f0e3346b63780aeb18b5e230a514f5fe953 Author: fanhsu Date: Tue Jun 9 15:58:26 2009 +0000 Created gsiaidTable.h commit cd8d92f5e9e1a942367724d497f9e5eb1269fd1e Author: fanhsu Date: Tue Jun 9 15:58:07 2009 +0000 Created makefile. commit 2206b1979c45d515bf5ce9158d1b5918aa77918b Author: fanhsu Date: Tue Jun 9 15:57:49 2009 +0000 Created *.c for gisaidTable (based on gsidTable). commit 1a580fde8e4f74e1f69ee256b4ea53a2886cc0b8 Author: fanhsu Date: Tue Jun 9 15:55:39 2009 +0000 Added the hook for Mark to add protein structure display stuff for H1N1. commit f52bdda1e8c575428742f8f42d1c93968463350b Author: fanhsu Date: Tue Jun 9 15:47:45 2009 +0000 Added gisaid selection file option variable names. commit 17ff3f71d1e4ce3a75d034f3ef596d1b7db16ce0 Author: mikep Date: Tue Jun 9 15:30:30 2009 +0000 "New version number v208" commit c2554912d4f100486cb6a4c13abcf439c10fc845 Author: mikep Date: Tue Jun 9 15:30:14 2009 +0000 v208 final build commit 6c4d705eeca56f80eb879c7716952f6fc552d2d5 Author: galt Date: Tue Jun 9 15:00:06 2009 +0000 "Encode release log update" commit cdbde23c519fe4dc593c61e8bf05e67302d49696 Author: galt Date: Tue Jun 9 15:00:03 2009 +0000 "Release log update" commit 06e54d673c089101c71174dfd6e0c69bc400910b Author: galt Date: Tue Jun 9 07:18:22 2009 +0000 adding aplCal1 sea hare commit ed4938fc2833f34257ea33c22b25116424894c58 Author: galt Date: Tue Jun 9 07:15:08 2009 +0000 making pushQ entry commit 7e27f45a198ae3f9ebc20658d3d9e179eff05493 Author: galt Date: Tue Jun 9 07:00:26 2009 +0000 making pushQ entry commit 64870b871564b713668e34e7763803ab78eff045 Author: braney Date: Tue Jun 9 00:45:27 2009 +0000 human proteins commit 01eb296b3e262358f958d7c18a0f8ac3c302607c Author: rhead Date: Tue Jun 9 00:20:15 2009 +0000 Added onintr to remove files when script has been killed. commit e0886748ca9e999c331ecdebbae20f9f4c2f3065 Author: ann Date: Tue Jun 9 00:09:45 2009 +0000 added HAIB commit 9da25c75d9fba2ba54750cf962dbe77e10e1ce5a Author: aamp Date: Mon Jun 8 23:39:54 2009 +0000 one tiny bit about the goldenPath/monDom5/database dir + README. commit cbecb17eb69bddc853a6baea860676b5b5888968 Author: aamp Date: Mon Jun 8 23:35:31 2009 +0000 big zips/downloads commit 49ab76bd053153880d9d49bc6bdd2979e79a4973 Author: kuhn Date: Mon Jun 8 23:21:42 2009 +0000 allowed use of "hgwbeta" as argument commit 2179ded26fe955e2836b89954e99298eaff1613c Author: fanhsu Date: Mon Jun 8 23:07:27 2009 +0000 Added an errAboort. commit 07a4e7001884da8f8141a809146cd3eb335aeba0 Author: kuhn Date: Mon Jun 8 22:58:07 2009 +0000 grammar tweak commit 4789a095829580e08b1c606cfb20f7792286fc24 Author: kuhn Date: Mon Jun 8 22:55:36 2009 +0000 added missinf endquote commit 79e55eeb53b9744ee67f2f404112596deb2a6208 Author: kuhn Date: Mon Jun 8 22:55:03 2009 +0000 droppped a comma from the usage statement commit 2b3142f7709baeaa40977d7faee3bbaaf79d7944 Author: tdreszer Date: Mon Jun 8 22:34:51 2009 +0000 Added tracks for Yale amd cleaned up a lot of obsolete settings commit 0ac8e753d45efd45fbacb043b3fc1b727703b282 Author: aamp Date: Mon Jun 8 21:59:20 2009 +0000 Added unsplit mRNA and EST trackDbs commit 5bd1e81b695400a60f39fd55cc60999ab398d388 Author: angie Date: Mon Jun 8 20:33:42 2009 +0000 Bumped up a buf size -- caught by Mark, checking the error_log for his new pstack dumps. commit 3789d843d89e96314dfe1743467d1a68cf2b5cd7 Author: markd Date: Mon Jun 8 19:16:48 2009 +0000 removed unused hgofbeta stuff commit f236d1462fce78f2ba11a0875a7218575ea33659 Author: tdreszer Date: Mon Jun 8 18:55:21 2009 +0000 Fixed STAT1 url commit 854c1c0f7da8d09b1dbe131f43e337bba730ebee Author: tdreszer Date: Mon Jun 8 18:53:15 2009 +0000 Added STAT2 for Yale commit d9bffe6e7f86b7329d164ec50ae5087fe55f3e94 Author: galt Date: Mon Jun 8 18:50:58 2009 +0000 link to be allowed as requested by Tim D commit 06be6439d24d8665226e8e996db7b1fb78945c85 Author: hiram Date: Mon Jun 8 18:42:40 2009 +0000 Find db name from /scratch/data/ directory name, and generalize the ssh command to avoid questions to the shell for new hosts, and properly verify all DEF variables before they start commit 3abb6e76e6b18b63d2a0d5ad7182ab97ceb21096 Author: hiram Date: Mon Jun 8 18:41:32 2009 +0000 Generalize the ssh command to avoid questions to the shell for new hosts commit dbdfd1e7e0fa435c44cfccc11035e6fc1ea5b077 Author: hiram Date: Mon Jun 8 18:37:16 2009 +0000 hgofbeta is now hgsqlbeta, and generalize the ssh command commit 9796153c5a13d0ff0682405d78e7fe93dc9ab0ed Author: galt Date: Mon Jun 8 18:24:17 2009 +0000 Tim D wants validate link to be available commit 9784f93921f3f3d96d294dafcf49052f9b08b190 Author: tdreszer Date: Mon Jun 8 18:23:21 2009 +0000 Adder controlde vocam term 'treatment' commit 5b7b5597a9e93655d8b7509732fc2e4674db4e3b Author: tdreszer Date: Mon Jun 8 18:21:13 2009 +0000 Added type treatment with 4 treatments for Yale commit 7251ac8970512e23956e61a35a455ead301c8dbd Author: rhead Date: Mon Jun 8 18:00:17 2009 +0000 added whitespace. commit 3eee3a25c670246405e1134763d95c69a6b6c6b2 Author: galt Date: Mon Jun 8 17:29:54 2009 +0000 fixing the search info commit c07439419fb39880677faaa95e5571ac72cb8eb2 Author: galt Date: Mon Jun 8 15:00:06 2009 +0000 "Encode release log update" commit 75fae764c52d1cce9408ef05a2ec29dfa8854b34 Author: galt Date: Mon Jun 8 15:00:03 2009 +0000 "Release log update" commit cdb84789ce61531a049c067c37bf79fad2a0675e Author: aamp Date: Sun Jun 7 23:47:50 2009 +0000 Andy's blastzs to hg19. commit 24c18c691e2fb094964165374983f7603cae47e3 Author: galt Date: Sun Jun 7 15:00:05 2009 +0000 "Encode release log update" commit fc3f127b275427c8c64fa2b37d94e27e371f415b Author: galt Date: Sun Jun 7 15:00:03 2009 +0000 "Release log update" commit 612f6d9b66877aad97bff53c9c187e2fad1cdc84 Author: markd Date: Sun Jun 7 07:13:37 2009 +0000 make stack dump on warn/abort stack under/overlow permanet commit 7d30988708b6fe0bfbb31471707e37aec9ae58d3 Author: markd Date: Sun Jun 7 07:11:55 2009 +0000 make sure dumpStack does end up being recusivel called due to an error commit 0d9b657a2158f3b2c95a8838e8e6a8e0100773bd Author: galt Date: Sat Jun 6 15:00:04 2009 +0000 "Encode release log update" commit 605a380f2f90b86da39180dc68fd13a06ad27c17 Author: galt Date: Sat Jun 6 15:00:03 2009 +0000 "Release log update" commit 98404900aba0110651e54ace1c530daa2b57b77e Author: angie Date: Fri Jun 5 21:59:00 2009 +0000 Restored a line of code inadvertently deleted in 1.38 (green beer ? ;) commit aa76566c3660bae353cb4de5f45f0edd1b2324d9 Author: fanhsu Date: Fri Jun 5 21:23:08 2009 +0000 Added #defines for gisaidTable selection list files commit b5076eb7a3378bdbb5a0c988e8786168ce3d9fef Author: ann Date: Fri Jun 5 21:21:34 2009 +0000 a temporary and quick fix for the fact that the phyloP and phastCons tracks have been accidentally dropped from beta and the RR commit 20c421d36c8536ca56678b3d9102dd22f708f341 Author: hiram Date: Fri Jun 5 21:16:20 2009 +0000 ATCC clone link now taken care of in hgc.c commit dc511424078162395286ee8c5961ae079a04b819 Author: hiram Date: Fri Jun 5 21:14:06 2009 +0000 Proper ATCC URL link for Yeast clones commit fc2e9d3a0d6a49904fab97ebc73a11f55d216ba7 Author: angie Date: Fri Jun 5 20:52:49 2009 +0000 cgiToDoubleFilter wasn't allocating quite enough space for its results, and callers of cgiToDoubleFilter weren't handling NULL results. commit b47960a8f678e403fa1811211f2635e7e1945a77 Author: hiram Date: Fri Jun 5 19:27:44 2009 +0000 Fix error for -strict operation, and properly clean up subTracks that had parents disappear commit f1101a93af71977512b979e58cb6eadfb093dd47 Author: tdreszer Date: Fri Jun 5 18:25:30 2009 +0000 Did I happen to mention how much I hate updating cv.ra? commit e17b75f88dca9a266d3ade54d64969f214719202 Author: tdreszer Date: Fri Jun 5 18:19:08 2009 +0000 Missing orderUrl's commit 71596a93c8796ebb373143d73b21188540e7f112 Author: tdreszer Date: Fri Jun 5 18:14:43 2009 +0000 Missing type commit aad9ba64a24a2e359eb5e47bd4047f40d29000d8 Author: tdreszer Date: Fri Jun 5 18:07:29 2009 +0000 Added a batch of cell lines commit 7998746a8e51c2c437928a32839fde5a0d7f5c03 Author: fanhsu Date: Fri Jun 5 17:16:52 2009 +0000 Added handler for h1n1_0602Seq. commit 6d42e3e633cf9172640e0920935f5bcacc8e5e64 Author: tdreszer Date: Fri Jun 5 17:16:32 2009 +0000 Added a bunch of new antibodies commit ec20c23499b08b53c6fae22a479ecf5dd96e2dc0 Author: fanhsu Date: Fri Jun 5 17:14:02 2009 +0000 Added logic for GISAID project. commit 1af32c41129c1de4dbf43c0178e46c07af79c5b0 Author: fanhsu Date: Fri Jun 5 17:07:27 2009 +0000 Added showProtH1n1() to accomodate Kevin Karplus's new Modeller pipeline. This is work in progress. commit f3e30bb9bf88e12d28052733c46baef9d2f5a111 Author: hiram Date: Fri Jun 5 15:20:04 2009 +0000 Adding canFamPoodle1 to the build, Craig Venter's poodle "Shadow" commit c27eb2a7018bfdffa4cc54d1e71585c4e06f2f31 Author: hiram Date: Fri Jun 5 15:19:34 2009 +0000 Updated initial docs to better represent reality commit e90fddc387718d9dbe604ab1a8e13fe64cef2526 Author: galt Date: Fri Jun 5 15:00:06 2009 +0000 "Encode release log update" commit 371d4d40eec4831b44897e2ce3379c89dd243d6d Author: galt Date: Fri Jun 5 15:00:03 2009 +0000 "Release log update" commit 8cc226ea4407e41b57311b6173af85e229365ce1 Author: fanhsu Date: Fri Jun 5 14:53:32 2009 +0000 Created gisaidXref.sql. commit 82c057017b31b062b5d673452cfc7f4e2b53d0f2 Author: markd Date: Fri Jun 5 08:30:06 2009 +0000 don't webEnd if didn't webStart commit 9fdd88be393ed56411aeb75a7a91242e75305129 Author: rhead Date: Fri Jun 5 02:58:31 2009 +0000 Updated link to wustl. commit 6118726264ce387fb8df55557e559086103ee1ba Author: rhead Date: Fri Jun 5 02:49:52 2009 +0000 Added link to Broad. commit 838b33fb8e4a5f29a8de7b180ae3306d60c431b4 Author: pauline Date: Fri Jun 5 01:40:33 2009 +0000 Added nucleosome occupancy tables. commit 8e9d7096c2776d8308ad62cdef44b75ef4ea8709 Author: hiram Date: Fri Jun 5 00:10:45 2009 +0000 Copyright C. Venter - poodle Shadow commit 8968a3fc98bd220f065befa66d8ffe6a7b5d293e Author: hiram Date: Thu Jun 4 23:53:51 2009 +0000 Initial files from makeGenomeDb.pl commit af01c47b9fd5ee05bd09a8418a1e7b97e6342bcb Author: hiram Date: Thu Jun 4 23:46:51 2009 +0000 Add Tasha's name to the photo caption commit 0f4c286c0f12eeda9f8a14163cbff6a7dc42c65e Author: katrina Date: Thu Jun 4 22:55:11 2009 +0000 Clarified the Repeat Masker track description commit 1cf8986276d79eeacb13c9e9e9532d6d9f91efa5 Author: katrina Date: Thu Jun 4 22:45:58 2009 +0000 Clarified the Repeat Masker track description commit 4c4e7faeaed1f37cda1814a0743e110f9b8f1b87 Author: angie Date: Thu Jun 4 22:36:14 2009 +0000 Added snp130CodingDbSnp to identifier snpName130. Consolidated identifiers for snp*.name. commit 1aa8cad05fc1c374dac84de5eefd2d91805ac887 Author: katrina Date: Thu Jun 4 22:35:56 2009 +0000 Clarified the Repeat Masker track description commit 3273c66b1eabb34b1183d3feab4ee897c6a52bf0 Author: katrina Date: Thu Jun 4 22:18:00 2009 +0000 Clarified the Repeat Masker track description commit 3e44a79ab698e214c35579f31cc8af7786735ea0 Author: katrina Date: Thu Jun 4 22:02:04 2009 +0000 Clarified the Repeat Masker track description commit f254b5afc722efacfd8dd3772b7da005c763b09e Author: fanhsu Date: Thu Jun 4 21:08:30 2009 +0000 Added hIsGisaidServer(). commit 3db2081616a1578f5abac6926f19e580b66fef42 Author: tdreszer Date: Thu Jun 4 21:05:18 2009 +0000 Minor typos commit 0926fe9e491ac959b831f2aad48b27eda3e8b5d9 Author: hiram Date: Thu Jun 4 20:56:23 2009 +0000 Add humanChainNet override variables chainMinScore and chainLinearGap commit 38497243db4b80d82be2c551caaa6387c969b086 Author: tdreszer Date: Thu Jun 4 20:49:57 2009 +0000 Added Bryan Lajoie's uniqueness track commit d588d041710d9a3a43dbbaa8b1bc53fd14dfe0fd Author: pauline Date: Thu Jun 4 20:46:03 2009 +0000 Edited for redundancy. commit 79023ae9cfa03cad434dc8487c68a3f261d517b6 Author: tdreszer Date: Thu Jun 4 20:22:44 2009 +0000 Added Bryal Lajoie's uniqueness track commit 3172b98a6c681237a6e1bcf3314c46bdd2a2da92 Author: angie Date: Thu Jun 4 20:22:16 2009 +0000 Added new setting codingAnnotations to snp130 (for hgc). commit 3cda10d998e0ec0de5862a3c6d6e3295597ebb37 Author: angie Date: Thu Jun 4 20:18:03 2009 +0000 Added snp125CodingCoordless: coding effects of SNPs identified only by ID (no disambiguating coords, tsk tsk dbSNP). commit 25b194c8cd5bb679a3a8bb87d6f753ff3215a315 Author: angie Date: Thu Jun 4 20:15:07 2009 +0000 Added printSnp125CodingAnnotations, to display coding effects of SNPs from a table specified by a new trackDb setting (e.g. dbSNP's annotations). commit ac9c507eb0cff10a2bf2a6322ba0dba6619463c3 Author: kuhn Date: Thu Jun 4 19:14:44 2009 +0000 removed some slashes that were not doing anything and added some whitespace in usage output commit 2a3581a6a2a98bcd15030cc65a6a61750dd95349 Author: hiram Date: Thu Jun 4 19:14:43 2009 +0000 Properly mark composite parents and children so that ClosestToHome settings will function OK commit 02daa116d39aaa085aa3c4af31af7b3bdd980080 Author: hiram Date: Thu Jun 4 19:13:55 2009 +0000 Properly look for ClosestToHome variables during substitution and add chain linearGap matrix variable recognition commit 790f13849b098ef4ab0f2827d7f6b62568ce4622 Author: hiram Date: Thu Jun 4 19:12:16 2009 +0000 Now showing chain minScore and linearGap options commit d1f61b77f45a9a69bd13e7fed956bb55b54a5384 Author: markd Date: Thu Jun 4 17:53:21 2009 +0000 added tmp debugging code track down harmless but annoying warn/abort stack underflows commit feac7b6cd0e04e9248897ffe33ccf680f26b0255 Author: kuhn Date: Thu Jun 4 17:16:15 2009 +0000 new tree for new conservation track commit ddca439c1273812aef46a879988b03ca7b22c762 Author: kuhn Date: Thu Jun 4 16:59:16 2009 +0000 new tree for new conservation track commit 8fb0b07cfdf70c6ba844965d6da596a7032c9cc9 Author: galt Date: Thu Jun 4 15:00:06 2009 +0000 "Encode release log update" commit 4ba9c55d7d528f610ed5210053645a63c456af4b Author: galt Date: Thu Jun 4 15:00:03 2009 +0000 "Release log update" commit 4fc5ac3c94bc5a5c29337e504d4d6072dd16b391 Author: rhead Date: Thu Jun 4 04:48:15 2009 +0000 Removed jsessionid from nature paper link. commit cb2cc62b55f2fa153ed1ba37f85b190916b016c1 Author: rhead Date: Thu Jun 4 04:45:50 2009 +0000 Removed jsessionid from nature paper and linked to abstract instead of full article. commit c89ecbaaee1f7d8ecaa87248acf7907ae3224e09 Author: rhead Date: Thu Jun 4 04:42:36 2009 +0000 Removed jsessionid froom nature paper and linked to abstract instead of full article. commit ca7d9cf347affe22c473f39d3f119b6aa628a9db Author: mikep Date: Thu Jun 4 00:13:04 2009 +0000 url must be a url, move descriptoin to vendor name commit 09dfe1ce802e1585de264d8ae4e542ddf684a319 Author: ann Date: Wed Jun 3 23:15:54 2009 +0000 these are the 40 subtracks that are going to be released initially commit 0f03a9d43b327a25d819f058d3f0d37c176f6272 Author: rhead Date: Wed Jun 3 20:27:31 2009 +0000 Link to american statistical association paper stopped working. Updated link. commit 1bc6dff1f26c6f6dbeffd0dba935327453bc5d18 Author: rhead Date: Wed Jun 3 20:13:18 2009 +0000 Removed session ID from links to nature papers. commit 92b57a817e5c8f4d08e479cdd13790962133f931 Author: rhead Date: Wed Jun 3 20:06:39 2009 +0000 Removed session ID from link to nature paper. commit 38630e7f157f6c43009daae923b087686271d2e2 Author: ann Date: Wed Jun 3 19:22:44 2009 +0000 added Data Release Policy commit 8152e5474dd5a5d77d3d16f88b249a4c4dd7186a Author: tdreszer Date: Wed Jun 3 19:20:03 2009 +0000 Angie's review found
s where there should be
s. I bet this is in other description pages as well. But it is really not a worry. commit 528688c7a09ac7f551acd51b854714e230cce60b Author: ann Date: Wed Jun 3 19:13:17 2009 +0000 corrected date (per Tim) commit 31856e58cd2ad50ac3253c38208e978f94650b93 Author: ann Date: Wed Jun 3 18:45:46 2009 +0000 initial tweaks commit 48b19f3fbe618691f236d677078067941fd448d3 Author: tdreszer Date: Wed Jun 3 18:25:35 2009 +0000 Mark caught my sloppy code. vsprintf replaced with vsnprintf() commit b19565f00091ce931b71acbdf9f0b773c5dd16da Author: galt Date: Wed Jun 3 15:00:06 2009 +0000 "Encode release log update" commit 863851feb3b279d50e5ff77f22734de696137f94 Author: galt Date: Wed Jun 3 15:00:03 2009 +0000 "Release log update" commit ffbdfb1f6ec4ac572ac3a5d808c47e63fdf354f5 Author: markd Date: Wed Jun 3 07:07:51 2009 +0000 removed extra newline that added annoy line to log file commit c76b3b57a80bcdc4c2734de54fbd0d7589828002 Author: aamp Date: Wed Jun 3 06:21:51 2009 +0000 per-chrom = no, and got a lift file for monDom5. commit d2026a95e6987e9f9fa97b688c50f617a80294e2 Author: markd Date: Wed Jun 3 04:30:19 2009 +0000 don't dumps stacks on find errors; doing stack dump in abort handler rather than warn handler simplifies commit b3e023323008458422dff4b738a0651aa077d6ce Author: markd Date: Wed Jun 3 03:50:07 2009 +0000 don't strip binaries to allow stack traces commit 858a0df8cc91d49262552fc116376296b1be1b6a Author: rhead Date: Wed Jun 3 01:56:14 2009 +0000 Added a missing endif. commit cf54d24bdbdd054e2d64d8bc62802ee99aeb3696 Author: markd Date: Wed Jun 3 00:34:11 2009 +0000 added option to generate stack dumps when browser errors occur commit 8f46052b61e957c8f32b86225eda1ccf97c9f69a Author: kate Date: Wed Jun 3 00:15:35 2009 +0000 Complete for release, as per wiki instructions commit 6466534a28db4018c128c1e3abf392109c713ec9 Author: aamp Date: Wed Jun 3 00:05:03 2009 +0000 Some stats filled in. commit fbf95e6cb68943c5676359083421aac52c3bbc3c Author: markd Date: Tue Jun 2 23:50:26 2009 +0000 rebuild incorrect data that was submitted commit 2fd982eb19414774aefae6b11328a8f9b42cd8b3 Author: markd Date: Tue Jun 2 23:49:01 2009 +0000 update nucleosome occupance track due to corrupted data on chr3 commit e107566b9e153bc0eae56af7b309e5de41fd18dd Author: kate Date: Tue Jun 2 23:36:05 2009 +0000 Adhere to Details pages -- conventions commit e0290553353d83f1390ce43523f948e2e99d93a9 Author: kate Date: Tue Jun 2 22:57:12 2009 +0000 Adjust defaults for HudsonAlpha TFBS commit 3e9f5b99d6d55295dcd4df75df9183707c7726e0 Author: tdreszer Date: Tue Jun 2 21:49:55 2009 +0000 Overkill with the drip drip drip of changes commit 8e8868b16186760cd6dc9b9210b52d6d186cf4cf Author: tdreszer Date: Tue Jun 2 21:45:43 2009 +0000 And alignability should be selected by default commit caa38304c195d3f09ccfa000285f0703e3055bab Author: hiram Date: Tue Jun 2 21:43:00 2009 +0000 the swap lastz are done for those genomes that are public on the RR commit 5b368ebfbf13c1ad77989ac9879730ecb5f9b7d4 Author: tdreszer Date: Tue Jun 2 21:40:59 2009 +0000 Tarjei requested windowFunction=mean on his alignability track commit 398b54d25364b2c337c50897d74484b2aaf8fc9a Author: tdreszer Date: Tue Jun 2 21:40:06 2009 +0000 Tarjei requested a credit change commit d2c0519783352de3693e30c0b548bcb8e381a798 Author: hiram Date: Tue Jun 2 21:15:47 2009 +0000 Adding hg19 chain and net composite track commit f0a50e4706e3bf672080944261e5084507c6d8a3 Author: tdreszer Date: Tue Jun 2 20:57:09 2009 +0000 Added Broad's alignability track to the Mapability composite commit dddea346015f092afad0ea52f7253d8db2709fad Author: pauline Date: Tue Jun 2 20:57:02 2009 +0000 Scientific name needed italics. commit ded59d453e1aaf53be67d1379303f3e54fd8154e Author: pauline Date: Tue Jun 2 20:52:01 2009 +0000 Adding page to allow yeast specific italics. commit 464a6df933277c3e64edcabc0a3796440567a61e Author: tdreszer Date: Tue Jun 2 20:40:05 2009 +0000 Added Broad's alignability track commit f0d76052b16fc6e8ee74d6caaf373789ca15d153 Author: kate Date: Tue Jun 2 20:09:01 2009 +0000 Fix label for Open Chromatin subtrack commit b083b035930efe0738136b92a0448195b984a708 Author: tdreszer Date: Tue Jun 2 19:14:49 2009 +0000 Added allButtonPair and hopefully clarified some details commit de8cf22bdc81b0ea48f8acdf73e3795a5e259294 Author: tdreszer Date: Tue Jun 2 19:13:32 2009 +0000 Added support for 'allButtonPair' UI commit 21c382624578db51795bce4b6543a273d927e6cd Author: tdreszer Date: Tue Jun 2 19:12:17 2009 +0000 Rearranged a little and added subtrackCBsSetAll() for 'allButtonPair' tdb setting commit f4e70257403416c9ca1f04e025c79c6a05187107 Author: kate Date: Tue Jun 2 19:10:17 2009 +0000 Adjust default views for Open CHromatin commit 374a8b8b222899b7f5097aac03c5714e8dddcaf0 Author: kate Date: Tue Jun 2 18:59:27 2009 +0000 Edit for spelling and formatting commit f2895d0a5b1f712ccc8aaa5563206c2472ef2a66 Author: hiram Date: Tue Jun 2 18:35:57 2009 +0000 Begin running the swaps commit 459882dd2ab0ea2239dfb575247244028c097c6a Author: ann Date: Tue Jun 2 18:14:58 2009 +0000 italicizing scientific name. commit 46267c3c0c15676280d3887d7c8bfff9670e70d6 Author: ann Date: Tue Jun 2 16:06:26 2009 +0000 two small tweaks based on code review with Bob commit f053c170796a82e9cd78bb480441645f6cb31160 Author: galt Date: Tue Jun 2 15:00:06 2009 +0000 "Encode release log update" commit dd02ed16ae21daaa1b5f329c1544c8ae5e14d585 Author: galt Date: Tue Jun 2 15:00:03 2009 +0000 "Release log update" commit 37138dc4c5d788c1153e29cd053d0938ec3f9a17 Author: mikep Date: Tue Jun 2 14:52:34 2009 +0000 v208 preview commit 1989252de1055a1cacce04368a54aa547db6b8ab Author: markd Date: Tue Jun 2 07:00:25 2009 +0000 added cache to avoid repeated databases queries for organism name for xeno items, 4.28x speedup commit 19d800fbb4a2651eb837ea272be6b3b4bef7ce9a Author: mikep Date: Tue Jun 2 05:36:33 2009 +0000 disable JavaScript on the rest of the pages commit 92302f262dd3bb9ced1ba26d664fd54bd8876845 Author: rhead Date: Tue Jun 2 02:44:18 2009 +0000 Fixed broken link to Bioinformatics Institute of Singapore. commit 2d554718305482ff80575ff282a9257581879864 Author: rhead Date: Tue Jun 2 02:33:20 2009 +0000 Fixed broken Exogean link. commit 9bc7050bb66d804facae68362ca0d1047853fbc7 Author: rhead Date: Mon Jun 1 23:47:17 2009 +0000 Removed session ID from link to Nature Methods, which was causing an html error 404 commit dd48417f81ab9768977276a9c0cc4123caaed3d7 Author: kate Date: Mon Jun 1 23:19:31 2009 +0000 Edit labels for consistency (need to update DAF files) commit b231252fb002d35a187f74f44aa0d6b8bb85b08b Author: tdreszer Date: Mon Jun 1 22:45:49 2009 +0000 Moved mapability track to map group commit 1913df2fe7b2351a19ab5caa16ba1bbfcdb79c7c Author: tdreszer Date: Mon Jun 1 22:21:35 2009 +0000 Reformatting. No wording changes, except adding contact commit a1052e505ea8a0fc6ea6f1d7a80c51cbd8d168e1 Author: tdreszer Date: Mon Jun 1 22:19:33 2009 +0000 Changed some Elnitski labels commit 372123522720ebe5b87f2a4dcb4bfad64c47c4ae Author: tdreszer Date: Mon Jun 1 22:10:15 2009 +0000 Added 'NHGRI' to long label of ENCODE BiP track commit d94909624b565e0334c0cc378c76eb34dd202542 Author: tdreszer Date: Mon Jun 1 21:51:49 2009 +0000 Moved this description page to the root directory because it is needed for hg18, mm9, rn4, panTro2, rheMac2, canFam2 and bosTau4 commit 310f1370026ec12d9bdf242d1185be1f107db2f5 Author: galt Date: Mon Jun 1 15:00:05 2009 +0000 "Encode release log update" commit 0610bf77b2ba07806f453a9f9c41af1cc4925da7 Author: galt Date: Mon Jun 1 15:00:03 2009 +0000 "Release log update" commit c9952c726d9fde53172ff5df8dab8c034bfba3f7 Author: galt Date: Sun May 31 15:00:05 2009 +0000 "Encode release log update" commit 5951810a3222279c17dbc92c76b02ec44d3c2a97 Author: galt Date: Sun May 31 15:00:04 2009 +0000 "Release log update" commit f3ff92e2e7da9deca867bff1204b2d3a036eb730 Author: markd Date: Sun May 31 07:28:33 2009 +0000 don't modify input sequences when converting alignments commit 208894adbed3bff14ce9f4c452bab3f43dbfbe23 Author: kate Date: Sun May 31 02:03:33 2009 +0000 Adding Carrie Davis of CSHL to credits commit 4516fab7b853f07a1104b3c0f3bea7755467a452 Author: galt Date: Sat May 30 15:00:05 2009 +0000 "Encode release log update" commit 5d2341fd20aebd45ee7257f69ce94e185a3dc10d Author: galt Date: Sat May 30 15:00:03 2009 +0000 "Release log update" commit 5b3c863f88cb2a9891f3c0950e9a8dbf4ff089f3 Author: hiram Date: Sat May 30 03:22:22 2009 +0000 lastz run updates, now running the last two, and many are finished commit c0b3ac49993369e25997f88c288d7e7935b76773 Author: kate Date: Sat May 30 01:11:34 2009 +0000 Make signal height consistent for Riken commit 7b0e839fdab32746376e6371433a7f3f5885afdd Author: hiram Date: Fri May 29 23:59:41 2009 +0000 Now with all tracks individually configurable, and species order on Vertebrate group commit eb725eaac1157c178257b9befcba62bdf3e489a5 Author: tdreszer Date: Fri May 29 23:30:51 2009 +0000 Added searching for geneId on ENCODE Gencode tables commit 205ed92e96a350aec43f282436f3378df2bd1364 Author: tdreszer Date: Fri May 29 23:27:57 2009 +0000 Built RawSignal gzs and put them in {downloads}/raw commit 598c967b22de3e0cd756466cd1d9a979a489ea91 Author: tdreszer Date: Fri May 29 23:23:44 2009 +0000 Minor changes to UI links. Ensure two cfg boxes are not opened at the same time commit bb12502d2061ded9694e56bc43e42365db0c7a72 Author: hiram Date: Fri May 29 23:04:21 2009 +0000 Put in the species order list for the Placental chain net composite track commit e4013ee24c2d3f6e7ec746f7fa2cd3ef2b36099a Author: genbank Date: Fri May 29 22:52:46 2009 +0000 fixed for hgsqlrr commit b258d1a4506eb51661953d0e5ee64f5ccfdcbcf1 Author: hiram Date: Fri May 29 22:30:13 2009 +0000 Indicate chain norm score available for the MHC composite of chains and nets commit 05ed3f50e535f4c98cd19ffdf2c0183e396b5e69 Author: hiram Date: Fri May 29 22:29:29 2009 +0000 No species dimension in the venter chain net composite commit 3e5328fa8eb1f0dba30c018430ff3c99806c1256 Author: markd Date: Fri May 29 22:22:34 2009 +0000 enable using hgsqlrr for hgw1 commit 1806415840cc656e008e7903004281f85ed4dd34 Author: hiram Date: Fri May 29 22:19:50 2009 +0000 Fixup chainCfgUi to honor a normScore option from the trackDb composite bucket commit 2d12eb8816bb89fa410aef2b4725838078081f18 Author: mikep Date: Fri May 29 22:07:01 2009 +0000 no, we do not, the type of a track is its type no need to consult parent commit 16ac92765eeaeb3165cc55f13885c2dd359277fb Author: kuhn Date: Fri May 29 21:06:52 2009 +0000 changed to ChIP-chip to match elsewhere commit aed518f0fbd5d350b8aa170c1f4a9fadaf9d8961 Author: tdreszer Date: Fri May 29 21:06:48 2009 +0000 Terry Furey's latest take on this. Not doubt it will be parred down. commit 3ac1a9f5deded709efcb94b454be3b9d8add825b Author: mikep Date: Fri May 29 21:05:06 2009 +0000 adding option to replace default 'red' tickmarks with contrasting or lighter color ones similar to the color in zoomed in base view commit c21180c0ed3c560da1b40ebfa4a16512873f05f8 Author: kuhn Date: Fri May 29 21:00:33 2009 +0000 added assembly name to header commit a19822569b40f9ba457154d2ac6fcb6f773d8809 Author: kuhn Date: Fri May 29 20:38:59 2009 +0000 added range query syntax to searches now that we have STS Markers up commit ca0c4c36e6a98a3c8f510288a0ff4910f0948de3 Author: mikep Date: Fri May 29 19:22:45 2009 +0000 choose a contrasting color for tick marks when drawgin differnt bases commit f1a9a8f0411ab7588dfa28d9d43512eb5144faa8 Author: tdreszer Date: Fri May 29 19:18:12 2009 +0000 One protocol had a broken link commit ef35d500b0e38f29a33917996175dd86ddf5f24c Author: tdreszer Date: Fri May 29 18:52:33 2009 +0000 Added some cell line protocols which had not been checked in before commit 226e514b80c0f9f2229fe5e7e1f37d2054b51b2d Author: galt Date: Fri May 29 18:11:37 2009 +0000 minor tweaks commit c581bba11da6cc876f1bb19e9e7dd740b96b7881 Author: mikep Date: Fri May 29 17:28:25 2009 +0000 make colorByStrand work for ordinary beds (item is a bed) and for sequences where basecoloring is done (item is a linkedFeature) commit ca038dbdf39ff8ef7aaa81b56d968a04ee956f99 Author: hiram Date: Fri May 29 16:27:15 2009 +0000 Put Venter chain and net together into a composite commit 2d8f04808f9bd8a4e5da1e3dfb1eda8d278d75a3 Author: galt Date: Fri May 29 15:00:06 2009 +0000 "Encode release log update" commit e37ab3ce8328ef4607183f9246375fc72a7119b7 Author: galt Date: Fri May 29 15:00:03 2009 +0000 "Release log update" commit 39d12a5302b4bcd33a88329fd93020f657486fef Author: mikep Date: Fri May 29 14:53:35 2009 +0000 make colorByStrand independent of baseColor commit 6477b90865c42523281c0ceba10de7aa92beb31b Author: hiram Date: Fri May 29 06:24:29 2009 +0000 allow the Primates chain and net tracks to sort by specified order commit 96b929561cea3470a444c44cc684114209e5be1e Author: kate Date: Fri May 29 03:53:05 2009 +0000 Finally got mapping parameters from Timo commit 09c0b672b906400be7c05e9025a72eb4d720ef20 Author: kate Date: Fri May 29 03:15:07 2009 +0000 Set colors on Riken to indicate strand commit 5342c42cae68aad91d7928219fe538cb4d0fd976 Author: mikep Date: Fri May 29 01:40:03 2009 +0000 removign /cluster/hive even from comment in case it causes confusion commit 2157df2155aa5395f8e22cf79b76589f553704d7 Author: tdreszer Date: Fri May 29 01:02:18 2009 +0000 Approved cell lines for Myers: BG02ES,H9ES, HAL, HFL11W and HFL24W commit 27862e120bcd1106e703136558d6c5364e6c2343 Author: hiram Date: Thu May 28 23:12:58 2009 +0000 Adding placental and vertebrate Chain/Net composite tracks commit 55bd494f01ecfcc218f58fd87736265e8735e358 Author: tdreszer Date: Thu May 28 22:42:30 2009 +0000 Added description of Base Overlap Signal commit fc7a693431718889f6bdcd3b2a41de7da95ed48f Author: hiram Date: Thu May 28 22:41:19 2009 +0000 Add Primates Chain/Net composite track as an 'alpha' release configuration commit d61294a86c4b4887352fa7559d2eea781e0a5b1e Author: tdreszer Date: Thu May 28 22:17:00 2009 +0000 Load should now make the RawSignals files but put them in 'raw' subdir. Fixed some typos. commit 331869593060ce2b0b747d7c32fe16df28aa915a Author: hiram Date: Thu May 28 21:57:49 2009 +0000 Do not allow ruler chrom name to spill over into buttons on left, truncate chrom name until it fits properly commit 9b3bf03e2c6ae55f68efff04752fd1b92b87ae4e Author: donnak Date: Thu May 28 20:54:11 2009 +0000 Added news item abt Aussie mirror. commit 250e06e71b6c6d1c5761e668b760e0df523535f5 Author: donnak Date: Thu May 28 20:53:53 2009 +0000 Archived an item. commit 6014c8f3ea0b378c1fe6b629625c5d3c602159a4 Author: tdreszer Date: Thu May 28 18:51:39 2009 +0000 Added score to the transRegCode hgc commit 3546a073fc8049dfe5753c01ddafffb0d54b4bec Author: tdreszer Date: Thu May 28 18:30:12 2009 +0000 Kayla didn't like the prev button repeat errors commit deba306710fab6aa7b56a40c7b08050ad0370243 Author: galt Date: Thu May 28 18:21:39 2009 +0000 aplCal1 sea hare progress: genbank blat downloads commit 4d19938e054b35e6b47dbcffc7a78a7ec54c08b7 Author: katrina Date: Thu May 28 18:14:54 2009 +0000 Changed the scoreFilter and scoreFilterLimits for transRegCode commit bb1a31e78db35a3c7e356bd2c3e04a6ed535524c Author: kuhn Date: Thu May 28 17:09:38 2009 +0000 added error-checking for case where 4th parameter is no good. thanks katrina commit b49d46c08d5af58bf5fc853b646b921ec349106c Author: mikep Date: Thu May 28 16:49:28 2009 +0000 show seq1,seq2 columns (non-standard bed cols 7+8) for pairedTagAlign. This is not very nice way to deal with it, asking Jim for other suggestion. commit e609fbef8117a538c27872d9debc8628e1e2b1cb Author: mikep Date: Thu May 28 16:48:30 2009 +0000 show seq1,seq2 columns (non-standard bed cols 7+8) for pairedTagAlign commit 9217645faf641599c86b809bcaf07e8b0db21b0e Author: mikep Date: Thu May 28 15:30:40 2009 +0000 dont print the full record if all the fields are already nicely formatted above commit 3a63f18273a60ef3886ee275898d95b9afdfe0dc Author: galt Date: Thu May 28 15:00:05 2009 +0000 "Encode release log update" commit d02b21d1f85f7bbc0b91c4ad0f89d4b9061225db Author: galt Date: Thu May 28 15:00:03 2009 +0000 "Release log update" commit ecce555968d47fc3c70ab820297133d578312afd Author: galt Date: Thu May 28 07:33:35 2009 +0000 Added aplCal1 commit 168bb9ccfe25a83fd7ef8c2ba93e84d1f1a3bd80 Author: galt Date: Thu May 28 03:07:26 2009 +0000 Added aplCal1. commit 9d4701ef1c18081631d2816651ed2c1462e1ea02 Author: kate Date: Thu May 28 01:34:25 2009 +0000 Show database commit 1fdc33b72ad97ba946afa9ccaa658e90313fb224 Author: galt Date: Thu May 28 00:08:53 2009 +0000 adding aplCal commit 8232c2e21b0fdf8888029f3f7dd0c279cd5690ac Author: galt Date: Thu May 28 00:04:40 2009 +0000 Added aplCal1. commit 0309afe58231c7f9cd1381ba7f88287514d8a600 Author: angie Date: Wed May 27 23:51:55 2009 +0000 More tricks from Tim: use noInherit on and settingsByView so hgTracks doesn't get misled by the composite type of bed3. commit be9ca8ae18d080a1facf7205b722cd4fb5d80008 Author: angie Date: Wed May 27 23:45:41 2009 +0000 Fixing recently introduced bug -- missing left side & assignment. commit f40c3aece8aa56e0a0097c5e6e5a5cd07123bbf8 Author: hiram Date: Wed May 27 23:14:37 2009 +0000 Running Elephant and Tenrec lastz commit 5c425f7be02586557789a3d5d17c79b10e33cc28 Author: galt Date: Wed May 27 23:14:27 2009 +0000 more work on sea hare commit c4356d4175788dab37b07e3a18ede7a7bbfbd3c7 Author: galt Date: Wed May 27 23:11:14 2009 +0000 noting arachne commit ff6baed85b47b1c8a5d72c4b1074dc8e42d82d8e Author: mikep Date: Wed May 27 23:07:54 2009 +0000 adding 4 new AffyRnaChip submissions, removing old duplicated metadata settings, adding a missing metadata line commit 204e6f81e79c9fe5b34683e55610c4f7435af564 Author: galt Date: Wed May 27 23:02:45 2009 +0000 trying to add the hard-to-find Aplcal 2.0 version number for WGS commit 5d467fce32bf35726985fdacbe7c3395805e75b6 Author: angie Date: Wed May 27 22:31:58 2009 +0000 Changing bdntpChipper composite type back to wig instead of bed 3, which caused all subtracks to be drawn as bed3 not wig despite the wig subtrack types. commit 35b0306e8961a32128feeef2d1a611fd55a7b291 Author: tdreszer Date: Wed May 27 21:55:15 2009 +0000 Added searching to ENCODE Gencode and 1D matrix to mapability commit 4c31816b00748bf3461497caa90a33131d631036 Author: mikep Date: Wed May 27 21:37:24 2009 +0000 shortened view names commit e14f871d1c4d8962fdf8d676bc6af371b77284ec Author: tdreszer Date: Wed May 27 21:36:17 2009 +0000 Support for composite level controls to update view and subtrack level. Support for blocking view level controls. Fix for single dimension matrix. commit a83242302352dff93357dedcbd793e7860546116 Author: angie Date: Wed May 27 21:09:15 2009 +0000 Several more suggestions from Tim: get rid of dimZ FDR subgroup (redundant w/view), add sortOrder and dragAndDrop, and move type wig declaration from composite down into subtracks, so the composite-level controls will not be shown and view-level controls will work. Also broke down classes Anterior-posterior early and Dorsal-ventral into more detailed subclasses for proper sort ordering. commit f8e0dda976d87cf0108be85feb89d14d0bf94905 Author: mikep Date: Wed May 27 20:54:42 2009 +0000 fix up FilteredRawSignal View name to be shorter FiltRawSignal for mysql table names commit 6cddc11d01cadccef096ead4c64539bd1f7de7c2 Author: mikep Date: Wed May 27 19:30:10 2009 +0000 rename view to FiltTransfrags to ensure MySQL tablenames shorter than 65 commit a5f68f92c6f3bdb5203646bbaa2d31450bf5a710 Author: rhead Date: Wed May 27 18:58:00 2009 +0000 Simplified getting intronEst table names even further (and logic was backwards in last commit). commit 6a323bc4876ad80f19dd330ebdf671f9052eef67 Author: rhead Date: Wed May 27 18:41:25 2009 +0000 Simplified some if statements. commit ba942792a386def8e5845ef2af5c7fc6cc66d7e6 Author: cline Date: Wed May 27 17:52:42 2009 +0000 Moved the uniqueness track from expression to varRep, to be consistent with the mapability track commit c6376dcaf1968f036f861959a54f4e91039947cd Author: angie Date: Wed May 27 17:17:01 2009 +0000 Added boxedCfg on to bdtnpChipper (thanks Tim!). commit c8db94b1d322dc22e87d97912c9a7283c004e6cf Author: kuhn Date: Wed May 27 16:46:43 2009 +0000 typos and line-length adjustment commit 3144e5b64b7c1b3bcebe1c5a8d32b19c433ab3d2 Author: galt Date: Wed May 27 15:00:06 2009 +0000 "Encode release log update" commit d17b0f69f7e93b10021d8ecadd7423b9b977c0b2 Author: galt Date: Wed May 27 15:00:03 2009 +0000 "Release log update" commit 0bbf4833ac591505f9b35fb2e13aa8e2912fbb6d Author: kuhn Date: Wed May 27 14:52:14 2009 +0000 added australian mirror commit 7a0a9577d0486f1e30cb68c6e5e213b379aa36d6 Author: rhead Date: Wed May 27 03:29:31 2009 +0000 Added special handling for intronEst in split form. Also changed a variable name. commit 9efd20c34bf610c15d52d0edf46149824ef4b84c Author: kate Date: Wed May 27 01:41:27 2009 +0000 Redo cellular localization labels so enforce order requested by Carrie Davis, CSHL commit 52d6db3372e4186d88c5e9db7e35e89ad48e4616 Author: kate Date: Tue May 26 23:46:30 2009 +0000 Next ENCODE data freeze has been set for July 2009 (guessed wrong on May) commit 06e3001373f4f771da6ce84ae55b3d6d01eb03d6 Author: hiram Date: Tue May 26 23:28:38 2009 +0000 Update to the lastz run status, many going at this point commit 215a37fdf8ae6d84b310006076b7e77a29ff7970 Author: rhead Date: Tue May 26 23:21:13 2009 +0000 Removed unused variable, changed date format slightly. commit f3bad26f5d012cb95d94f0abe760a2d8f58b495a Author: kate Date: Tue May 26 23:03:23 2009 +0000 Turn on individual subtrack configurability for Open Chromatin, by request of Terry Furey. Will turn off before release commit 3c572609192989b714eeb039818e395d9e164fb7 Author: angie Date: Tue May 26 22:50:54 2009 +0000 Added snp130. commit 7adf0afe6276210cdd6f7a97198ba1181c845e63 Author: angie Date: Tue May 26 22:13:50 2009 +0000 Added snp130 basic tables. commit d8bb3266823c1fb1291b29e19ba438cc88768295 Author: tdreszer Date: Tue May 26 21:23:31 2009 +0000 ShortLable needs to be short commit 20288a7c809f0fb6d6dc2142a41482039696beca Author: rhead Date: Tue May 26 20:20:43 2009 +0000 Removed broken link to transcriptomes.org, which has not worked for several months. commit 6df6a3b1b8de09e5433941f3329cd119b7de6c37 Author: tdreszer Date: Tue May 26 20:13:47 2009 +0000 Broad's Raw Signals were updated commit dc08e58adf6c91138f9fd2571305836720e482f7 Author: mikep Date: Tue May 26 19:16:45 2009 +0000 turn off the base display until we have a better visualization commit 2d3781931f6ddc1276a1d0fc2d9a53a5d3d4e35d Author: rhead Date: Tue May 26 18:56:35 2009 +0000 Changed links to specific worm data freezes to generic wormbase links, at least temporarily. commit 49462e50ed78636dbce21921965b1d7840f5300a Author: rhead Date: Tue May 26 18:37:50 2009 +0000 Removed broken link to Release 3.2 heterochromatic sequence. commit 6a3c8c5f1c0040c01f72331bd8021f9d60567bf8 Author: mikep Date: Tue May 26 17:02:58 2009 +0000 showing diffBases for Helicos until we can find an alignment format commit 3163758bf9d883d3d3baa6cd7e3eb19afaa9e71d Author: kuhn Date: Tue May 26 16:32:27 2009 +0000 dummy page to silence error during build commit 309fc7cf660bf7a58359e05417418329610342cf Author: mikep Date: Tue May 26 15:20:35 2009 +0000 "New version number v207" commit 277dd58ad6d9c076fda4b9c88daa5367fde45964 Author: mikep Date: Tue May 26 15:20:17 2009 +0000 v207 final build commit 10018d15ccf3644f3f5e9e351ce26538714509f7 Author: galt Date: Tue May 26 15:00:04 2009 +0000 "Encode release log update" commit 18fdc8a6565e943040b73db32d305a5c501282c0 Author: galt Date: Tue May 26 15:00:02 2009 +0000 "Release log update" commit 113b6deecf793196615944dd70215f4568917d3f Author: sbenz Date: Mon May 25 18:54:48 2009 +0000 Added ispy u133a data commit 324d6a1c4ea022074e9c95ca35b5b7b48fe5fcce Author: galt Date: Mon May 25 15:00:03 2009 +0000 "Encode release log update" commit 3894ac1b07bafde0e2c44a238c0b7b3c55be05c3 Author: galt Date: Mon May 25 15:00:01 2009 +0000 "Release log update" commit a47b41b97f09de667e6a1662a793bae656e535ea Author: markd Date: Mon May 25 03:35:26 2009 +0000 added ignore entry commit f337236b69a9d32aeb692c8c63dc797ca1ebce47 Author: mikep Date: Sun May 24 17:00:55 2009 +0000 simplify code and add warning about assuming seq1,seq2 are in row[6] and row[7] respectively commit 9b42467e4038ee5849670caf93c9311fc69d70d9 Author: galt Date: Sun May 24 15:00:03 2009 +0000 "Encode release log update" commit fc2decb7e2c1fcdee40d0bb9b87253f7e8f4b903 Author: galt Date: Sun May 24 15:00:02 2009 +0000 "Release log update" commit 406ded3e7f5e44569876fd861839f7449880451e Author: mikep Date: Sun May 24 09:24:14 2009 +0000 forgot or commit 0a6d608efba7e6dd68d577649937e59200b5e9d5 Author: mikep Date: Sun May 24 09:10:39 2009 +0000 Added pairedTagAlign baseColor option controlled by 'seq1Seq2' option to baseColorUseSequence commit d67ab0ff4f39fc838e57bf5de95a02f0152c31f3 Author: markd Date: Sat May 23 19:53:00 2009 +0000 only rsync download files every 6 hours commit 46ee0dd6a9a55e755ccd7dfd685ce24892ee4554 Author: tdreszer Date: Sat May 23 16:44:52 2009 +0000 Keeping up with the data commit 2b699ba3984f7766801fc5dc839247e6815ba242 Author: tdreszer Date: Sat May 23 16:42:32 2009 +0000 Fix misspelling - Thanks Angie commit 8659ab594721e39ec2598075c6b1ec71f11261a5 Author: galt Date: Sat May 23 15:00:05 2009 +0000 "Encode release log update" commit 2deb6f06d4d7ae53fcfdbccd7a7abde925425f9c Author: galt Date: Sat May 23 15:00:03 2009 +0000 "Release log update" commit 77c40869a3f0ed920610eec0343d723a973767fc Author: tdreszer Date: Sat May 23 00:31:09 2009 +0000 Reregenerated Yale LargeFrag with fragLength=575 commit d9405de64cfee61967c59138473569d8dffbe978 Author: hiram Date: Fri May 22 23:52:09 2009 +0000 Running some recip bests, and started Medaka oryLat2 commit e4d59a98d8ed0708981605881c2064da86ed8c3b Author: ann Date: Fri May 22 23:26:12 2009 +0000 made usage more clear commit 38e76ccae1014ac51755cc8de7a6c8e5edce78e1 Author: tdreszer Date: Fri May 22 23:04:11 2009 +0000 The same NO_VALUE protextion is needed for the float version commit 2668a6932371dc316beed468ffdb8569c00d044a Author: rhead Date: Fri May 22 22:53:26 2009 +0000 Added priorities for monDom5 net and chain. commit a4b6fb426d4fa2eeb340b7e8a61c87122645f8f2 Author: kuhn Date: Fri May 22 22:48:33 2009 +0000 hid decipher track by default commit 5b2573fc500de7694e821692da86b0fcce5b88ca Author: kuhn Date: Fri May 22 22:47:30 2009 +0000 changed to make it more clear where to get info about SV affy chip commit fc57d1d6bb90d747420ee128e5874fba1fc3a1f4 Author: kuhn Date: Fri May 22 22:44:04 2009 +0000 changed 32P-gamma-ATP to gamma-32P-ATP commit ab7b3df03c473bc208ab121c47d0ec68856a6208 Author: rhead Date: Fri May 22 22:42:28 2009 +0000 Added top-level trackDb blocks and html files for monDom5 nets and chains. commit 1926098bbfc760ba5ee5f8f95404fc1156a179b6 Author: tdreszer Date: Fri May 22 22:33:20 2009 +0000 ReRegenerated Open Chromatin Raw Signals and finally got FAIRE HeLa-S3 Peaks which were accidentally missing commit 7bb48d8c104cc2a1b30d811662962bacf230032d Author: hiram Date: Fri May 22 22:26:21 2009 +0000 Added updates to phastCons44way and Elements, six tables updated commit 3a0ad9f22610e25672cc36229c1b5993bc6bb602 Author: hiram Date: Fri May 22 22:10:32 2009 +0000 Updated phastCons44way tables and elements to new version from Adam's lab commit 74999ce7ddc553095161bd68c95f3e37e5b5ef94 Author: kuhn Date: Fri May 22 21:58:32 2009 +0000 removed need/ability to specify beta as second machine. thanks pauline commit c66608c7473f93f24007fda7851d70255780d48e Author: hiram Date: Fri May 22 21:32:06 2009 +0000 Swap to hg19 lastz done commit 3f913223edc6586f7c9722001163000a78bc5012 Author: hiram Date: Fri May 22 21:31:45 2009 +0000 Fugu Fr2, Bushbaby OtoGar1 lastz done, Baboon PapHam1 running, SGP and GeneID Genes loaded. 4-way multiz done for UCSC gene build commit 36ed6218d67e06a9f77ea0d8b587e3bd9ce49f66 Author: rhead Date: Fri May 22 21:31:11 2009 +0000 Switched to a generic link to wormbase instead of the ws190 link until the old one is functioning again. commit 7c71903e93600e3aad3f00d4dc933755205a7ce8 Author: tdreszer Date: Fri May 22 20:40:26 2009 +0000 handle implied 'scoreFilter' setting and assume that filter at limits is the same as no filter commit 132b31a354fc75b6aef4675ef07aa2702e86a0b2 Author: angie Date: Fri May 22 20:24:58 2009 +0000 Added -1000GenomesRsIds for adding our own by-1000genomes validation status using a flatfile of 1000Genomes IDs from dbSNP. Also, treat NULL like MISSING, for input from one big sql query instead of from little queries and join commands. commit fb2288844efa87124c7bf3bc45d5feb48cea013a Author: tdreszer Date: Fri May 22 19:38:12 2009 +0000 Make filterBySetCfgUi() publicly available commit ddb524ec9f6bbb655963f7efdc1e113a146f9ac3 Author: tdreszer Date: Fri May 22 19:37:05 2009 +0000 Need to not limit min/max default score if 'NO_VALUE' was passed in. commit 37a23b5edeae6a24c7b35455acb3ed88bff3d4fc Author: mikep Date: Fri May 22 19:26:08 2009 +0000 get rid of colon between +/- strands and split on space, by popular demand commit eaf915ef74582f16ac95e49e71c4f8205ec79207 Author: mikep Date: Fri May 22 19:22:33 2009 +0000 getting rid of offending colon cancer commit 9d4811fedc7b1773489b83836f5652a1eab40c90 Author: kuhn Date: Fri May 22 18:46:25 2009 +0000 modified usage statement commit 87535a022483be2becf4fcefbda54cdbe991001f Author: kuhn Date: Fri May 22 18:45:20 2009 +0000 added checking to see if track can pack. set to full in those cases commit 2d9a0178557189d59573420387a9748ccd443fbc Author: hiram Date: Fri May 22 18:32:27 2009 +0000 Add multiz4way for UCSC Genes construction commit e0db1e744363ad68d75bec250d32b0a90d0af124 Author: tdreszer Date: Fri May 22 18:30:14 2009 +0000 Angie pointed out that my last ci erroneously presumes oldVars is never NULL commit dcae321c53b17f4d8a214daefb04b659d3a3bb64 Author: ann Date: Fri May 22 18:17:34 2009 +0000 it wanted a tab not spaces commit 847516dd7625e1c0351a63ea1518e8dc4d91734e Author: ann Date: Fri May 22 18:15:06 2009 +0000 added cvsup to makefile so we can be sure we are building the latest and greatest commit 421fecd23e7446efd5baf283ab8782a135227a55 Author: ann Date: Fri May 22 17:57:29 2009 +0000 cleared up two output messages commit 0734a69b5d5a5526d1331f9c05fd4830f9ab67b2 Author: hiram Date: Fri May 22 17:39:55 2009 +0000 Image of 4-way multiple alignment on hg19 for UCSC gene construction commit dd4b4be4ecfbda169b7e0d752a1859aa2a16e028 Author: galt Date: Fri May 22 15:00:04 2009 +0000 "Encode release log update" commit 1164d091b71b75842e91b2cd04a1a25f7a4f2156 Author: galt Date: Fri May 22 15:00:03 2009 +0000 "Release log update" commit b813a0f4a8c21147041b3a7a3393ae951cde1800 Author: mikep Date: Fri May 22 10:30:54 2009 +0000 first cut of RIKEN colorByStrand settings commit c423a9dd6f1cb5647ed745ce582de4e766606f39 Author: mikep Date: Fri May 22 10:11:16 2009 +0000 added 'colorByStrand' option which specifies a + and - strand color to override the main 'color', currently works for bed/bigBed tracks which have base coloring commit 801fcbad9d5ee906c5f0ed964b9d2db682784075 Author: ann Date: Thu May 21 23:41:41 2009 +0000 quieting more egreps commit a7724475c4ab605d8c3c92580ad02756ae4d007b Author: ann Date: Thu May 21 23:18:26 2009 +0000 quiet the egrep. this section also works for symlinks (which was untested until now) commit 417736edfad920c358a56aeec1c6fdfe6d99cdfa Author: ann Date: Thu May 21 22:58:26 2009 +0000 exit at the end of setup run just in case something is wrong and it runs into the real run commit e42f2acb71d177a262099e554121a74592730d6f Author: ann Date: Thu May 21 22:54:35 2009 +0000 used multi-line echo trick commit ed9d37e7ec5d6a03eb88b5782c71f63c1ff9d141 Author: pauline Date: Thu May 21 21:01:49 2009 +0000 Removed duplicated paragraph. commit 2e7477b11ddcb5936897d96325060dbda2db5a32 Author: tdreszer Date: Thu May 21 20:40:11 2009 +0000 Terry provided his methods commit 41661fb9a64c310b6e31fbbc12333566772086db Author: tdreszer Date: Thu May 21 20:35:53 2009 +0000 Cleaned up mapability track commit d63c176dbff3dc614d969833dddf7f1fa670be45 Author: tdreszer Date: Thu May 21 20:32:35 2009 +0000 'Maximum' display mode is needed where there is a mult0view, not when dimensions exist. commit ce215e5a687a30631494fdf007ac3b35b27a213f Author: tdreszer Date: Thu May 21 20:30:50 2009 +0000 Added multiViewCount(), support for boxedCfg setting, moved multiView call up a level. commit 1e0e6ba6967076de621c18b1f1095541853b1238 Author: tdreszer Date: Thu May 21 20:25:35 2009 +0000 Added multiViewCount() commit 73400fdc85980bb13af2fc5470cac10aae741372 Author: fanhsu Date: Thu May 21 19:24:12 2009 +0000 Added decipher section. commit 59a065d760ca97fb681d0f1f164a7a9f3e94494b Author: tdreszer Date: Thu May 21 19:00:00 2009 +0000 Fixed scoreFilter defaults code and matrix rendering when dimension row/column has no accociated subtrack commit a6cbfa1f43b6a2e56d15963f082b5a481cedbc46 Author: markd Date: Thu May 21 18:21:06 2009 +0000 user rsh for download rsync commit 45a8e70df89dd6a5dfb17c8f6f348436c8e050e6 Author: mikep Date: Thu May 21 16:53:27 2009 +0000 error with the Riken Polysome data, should be PolyA- commit 5267af3eb5dc12796980595897272665cdfc5ec3 Author: markd Date: Thu May 21 16:34:01 2009 +0000 fixed bug in passing wrong param commit fb448f3a71d32b2b06846f5a535ecc70459172ef Author: galt Date: Thu May 21 15:00:06 2009 +0000 "Encode release log update" commit 4fc65bce5ad785e1e20b670aa4e137cd041f1341 Author: galt Date: Thu May 21 15:00:03 2009 +0000 "Release log update" commit 1e1fcf10299dfc54665b4047b9a22f8c8fb71f35 Author: markd Date: Thu May 21 07:55:20 2009 +0000 added new script to makefile commit fae7925dcb84b443ccf5f4abee8cf418a3212d56 Author: markd Date: Thu May 21 04:36:27 2009 +0000 fixed typo in previous change commit d366bd9020d33801d34f1e9e87b263cacd6747f9 Author: markd Date: Thu May 21 04:23:12 2009 +0000 modifyied rsync of download to use locking mechanism used by other genbank scripts commit 4f83e4437574d6b4bd4f57222bb569e076307e7b Author: rhead Date: Thu May 21 01:28:08 2009 +0000 Changed getChromlist.csh so that it does not create a file, just prints results. Changed all of the scripts that call it to redirect output to a unique file name, and then remove only that file at the end. Added onintr command that allow for cleanup of files created if scripts are ended prematurely. commit 35e50d7bba6f55af74dd6e80fe7a90758aa06a69 Author: tdreszer Date: Thu May 21 01:05:12 2009 +0000 Added code for a protocol setting in cv.ra which is needed for lab specific protocols on tier 3 cell lines commit 3564b589681f561195e425a0980ac26e2612fba8 Author: tdreszer Date: Thu May 21 01:02:04 2009 +0000 Misnamed a protocol commit e2b5ab832d3d8a86b5bd810cdd34b0d31eb019aa Author: cline Date: Wed May 20 23:17:10 2009 +0000 Reworded to use the passive voice, for consistency with other tracks. commit 6d081ab92cf1b8871ef3bf651468bb6510c677ba Author: cline Date: Wed May 20 23:12:55 2009 +0000 Moved the entry for the uniqueness track farther up the file, with the other track entries. commit 6a333445bb80fb5765b80870f1ebae4f950cb9a7 Author: mikep Date: Wed May 20 22:58:26 2009 +0000 adding new baseColor options to get the sequence from the name field (eg tagAlign tracks), and updated the track type list commit 4b4f9fb83ec54c048c647979d5cb164dad01a32a Author: mikep Date: Wed May 20 22:55:40 2009 +0000 Show bases different to teh genome in the RIKEN tagAligns commit 213162440712759b75ee02193e515bf4c20c58e5 Author: kuhn Date: Wed May 20 21:27:31 2009 +0000 added image size and some whitespace around it commit b0eb2d6367b1bbf6e3940932c83fb50b941f7fd5 Author: tdreszer Date: Wed May 20 21:01:45 2009 +0000 Added approved protocols commit 8f94efbd7627448c666d1eb4feff724cdd8a09ab Author: mikep Date: Wed May 20 20:59:57 2009 +0000 Libified findTdbForTable, findTypeForTable, trackIsType, hIsBigBed from hgTables so that other code can easily determine if a track is a bigBed. commit 74b8645c623b3106f45f70bbecca257b88f47f76 Author: mikep Date: Wed May 20 20:50:52 2009 +0000 display sequence or sequence different to the genome using a bed or bigBed which has the sequence in the name (eg tagAlign) in a similar manner to PSL files (by loading the BED as a linkedFeature like a PSL) commit f3294641fb2ee439e5eed72aeb0327f61d691e37 Author: kuhn Date: Wed May 20 20:48:01 2009 +0000 fixed parsing of IPs. thanks pauline commit a79c797e28973a15f225d59b71d4dd03aab86f10 Author: larrym Date: Wed May 20 20:30:25 2009 +0000 fix missing metadata fields for some HA control tracks commit 7519e6d7bb43fe5897fbc70d30eb451194527c4c Author: ann Date: Wed May 20 18:49:29 2009 +0000 sweet tweaks from Brooke commit 78c01a8919f1ba17a331890c10ca49a67ebc15cc Author: angie Date: Wed May 20 18:08:22 2009 +0000 Increased string size for snp125 observed allele (blob not varchar!). commit 713f7c16c520f5874c78559e4fc83f8b3583406a Author: hiram Date: Wed May 20 17:02:17 2009 +0000 Fixup hg19 so it is much cleaner commit 1ff8bd5d7c74dec54a6a5f83f9dc75fade6b9d9d Author: kuhn Date: Wed May 20 16:55:08 2009 +0000 set 3 snpArray subrtracks to on by default commit 94c996a66ccca16b7462667669e201be66888ce2 Author: fanhsu Date: Wed May 20 16:04:44 2009 +0000 Added decipherRaw.sql. commit a72ed7fd018b782c816e871d525b5d5fc4de368b Author: mikep Date: Wed May 20 16:01:34 2009 +0000 adding a new trackDb.ra option to get the sequence from the name column of a bed file (plus fixing a logic flaw in case an invalid setting was chosen) commit 762b41b81cb1c883c78558932bc25effdedab559 Author: galt Date: Wed May 20 15:00:05 2009 +0000 "Encode release log update" commit 775a8e42ca63f441b64217dcf5afbc0766fce8c3 Author: galt Date: Wed May 20 15:00:03 2009 +0000 "Release log update" commit 36038650af912f3ed2e5851d238b311722955e65 Author: angie Date: Tue May 19 23:54:31 2009 +0000 Instead of processing the hgcentral query of session info row by row, slurp the results into memory and then process. Hopefully this will reduce the frequency of losing the connection to hgcentral (currently 4x/day). commit db4745c3171bf1ddf87b19fd8f032e7c80eb6d27 Author: kuhn Date: Tue May 19 23:30:17 2009 +0000 added info about consent commit bfc1c9669f434ff62502078c215348900eba8ffd Author: kuhn Date: Tue May 19 23:28:49 2009 +0000 adjusted line lenghts to fit on screen commit 53548329f457b8a66133cea7987632207896e64a Author: fanhsu Date: Tue May 19 22:36:48 2009 +0000 Added decipher tracks. commit 4d9e87191c719df75703465234fb05013b153c99 Author: fanhsu Date: Tue May 19 22:22:19 2009 +0000 Added decipher track. commit 26bb410bb63dd5e6edcd7c9f916dfb00e5308ee4 Author: fanhsu Date: Tue May 19 22:21:49 2009 +0000 Added decipher.html. commit 4d0aab45843814e2c48eba97e8d96e299b1d1a16 Author: ann Date: Tue May 19 21:29:15 2009 +0000 added rules for two new UCSC to Ensembl mapping tables for hg18,hg19. commit 6e4f6a59cebaac8d18d7862ca6c06a3dbdeb7f78 Author: angie Date: Tue May 19 20:38:57 2009 +0000 Added by-1000genomes validation string for dbSNP 130. commit 5fb401e2dbd60554245807fb3141323ce7d337e0 Author: ann Date: Tue May 19 18:53:29 2009 +0000 UniProt has decided that they want to connect using 'org' names rather than 'db' names. I have cautioned them. This fixes the script to produce only 'org' names. commit 3fcc1ba234fbe98532c5744721f758f51bbac621 Author: ann Date: Tue May 19 18:51:34 2009 +0000 My preliminary attempt to clean up the 'sqlbeta' substitutions made during the last checkin. It is going to need to be tested during the next run of this script. Most of the variables were not being interpreted. commit a4fb47f0e826a6cdb3efcaa31fe4d3917efe0940 Author: mikep Date: Tue May 19 16:03:52 2009 +0000 v207 preview commit eb67c94341a7ed293204f09d4cceb52d6efc815e Author: galt Date: Tue May 19 15:00:05 2009 +0000 "Encode release log update" commit abec0d972529da71bfdd97d8d87ef5e8c1336b08 Author: galt Date: Tue May 19 15:00:03 2009 +0000 "Release log update" commit 0a06e1e6a29ed4779dc1e8c4ce06608355804ec3 Author: markd Date: Tue May 19 06:04:36 2009 +0000 added mention of gapToLift commit 2f5d9655667c1d876373c984a34ea35c5cda3fc8 Author: markd Date: Tue May 19 06:03:20 2009 +0000 minor refactoring that decided not to use commit 44d3c07a918f6cd93aca620016db6efc6068259b Author: markd Date: Tue May 19 05:40:38 2009 +0000 fixed typo commit 9fc6cec95c57daf71732bc4c7ee613071a9e0d6c Author: angie Date: Tue May 19 04:56:13 2009 +0000 Initial description. commit d22926ff9d87572bd5953f0a45034ad0a4654d06 Author: markd Date: Tue May 19 04:51:00 2009 +0000 change frequence of building download files commit 74560101a68a5f4a60669075467ca4d2afab89e3 Author: angie Date: Tue May 19 04:42:27 2009 +0000 addVersion: when strict-checking existence of xrefTable, use sqlTableExists instead of hTableOrSplitExists because xrefTable might be db.table. commit 720dcb33308a52f4f1455e081c831eae3c0f896e Author: rhead Date: Mon May 18 23:37:15 2009 +0000 Added an onintr trap and label so that temp files will be removed if the script is killed prematurely. commit 1f918d647421b4b2664a803aa30ca7feb96a00d6 Author: galt Date: Mon May 18 23:30:41 2009 +0000 remove what does not work commit 723e6ef8274ff7fa7adfefe663244bb2e7a7f79a Author: galt Date: Mon May 18 23:16:06 2009 +0000 fixed typo commit 02c8fd08819b885cbd701d6732be63b8eeb5173a Author: galt Date: Mon May 18 23:01:52 2009 +0000 Try to deal with lost Mysql connection after long waits for validate or load commit 7ac410b8b17a697d9c768b05b97966bc82b18c26 Author: angie Date: Mon May 18 22:38:22 2009 +0000 Added search def for snp130. commit e4600eb6bcf1b336aef58ced6930be896cf12835 Author: galt Date: Mon May 18 21:47:18 2009 +0000 handling udc cache files touching commit ef5e5f5d51eda4c0d8ecfffc1d2ba2092975821c Author: galt Date: Mon May 18 21:38:07 2009 +0000 tweak to handle udcCache location and process dataUrl setting to touch files in cache and report them for the do-not-kill list commit 6adfde27930a4c44141788c8878e6d9e025967d6 Author: galt Date: Mon May 18 21:36:41 2009 +0000 add touching of udc files in cache and reporting of names for the do-not-kill-list with verbose=4 commit 081ec38638194b1dee014d6ed9d3329f77eb52d6 Author: galt Date: Mon May 18 21:35:20 2009 +0000 refactored to all udcFileCacheFiles to operate without requiring the url to be actually opened commit a75afbf97affeac236c0bd484e1d786bd33d4186 Author: angie Date: Mon May 18 21:18:35 2009 +0000 Added debugging hook for command-line reproduceable forms (&formMethod=GET). commit bce51d4450f63f45af353c49cea74c335c947dc6 Author: angie Date: Mon May 18 21:17:41 2009 +0000 Registered snp130. commit bfc7ebe65a6175549936b7d1e8ca27ba3b7f87a5 Author: angie Date: Mon May 18 20:45:14 2009 +0000 In overrideField, ignore the release setting because it was removed from overTd->settingsHash earlier by pruneRelease. commit dc730913865c5cfd61ef250f6814c860371fd590 Author: fanhsu Date: Mon May 18 20:43:42 2009 +0000 Added dnaSeq table. commit 5ed045e4e58d4fb3e8eb6bfd5a6722e84b469aa7 Author: angie Date: Mon May 18 19:55:09 2009 +0000 Added snp130 and changed snp12*'s to overrides instead of duplicate def's. commit 1209a10ba1de8e0adeb96e2d5809ce7bf36a1215 Author: angie Date: Mon May 18 19:52:40 2009 +0000 Adde snp130. commit a2e7dbe1072449007044188a330edb368571e9f0 Author: ann Date: Mon May 18 18:43:08 2009 +0000 added support for some non-UCSC Gene orgs commit a3d428a9ef16d616a5f1b3ea5e068bb3419063c2 Author: cline Date: Mon May 18 18:26:54 2009 +0000 Added a 35-mer uniqueness track commit d4d7e1188ccafbaf1068d55c5945bf0bbb22d0f2 Author: angie Date: Mon May 18 17:25:09 2009 +0000 Small tweaks for dbSNP 130: broadened some formats, raised MAX_SNPID. commit 1f44dd3b1309f882a8736f4b80c43e552b609b3f Author: galt Date: Mon May 18 15:00:05 2009 +0000 "Encode release log update" commit 88b25c6934f52da40bed5fd8ec638486b4fc5773 Author: galt Date: Mon May 18 15:00:03 2009 +0000 "Release log update" commit 1dcc552ddc03f0c8358eb44c458fc823d2473e92 Author: markd Date: Sun May 17 15:18:03 2009 +0000 fixed use of non-posix include commit 2e721bca09a1cf0401628b0142d6c1fcceb39c9f Author: galt Date: Sun May 17 15:00:05 2009 +0000 "Encode release log update" commit 13175ca968d680a68017af8b1dd9ab3af30a921b Author: galt Date: Sun May 17 15:00:03 2009 +0000 "Release log update" commit 50c5ec2a894ab12fb149aa6ee1cee99f645e4906 Author: markd Date: Sun May 17 02:31:00 2009 +0000 rebuild downloads any day of the week commit 17964b9f672bad43482e0bfda852934d8becac8d Author: markd Date: Sat May 16 23:29:14 2009 +0000 like number of hours download build runs commit 94dc4472dc4b757b0fb3fc5fff87202ebe783711 Author: galt Date: Sat May 16 15:00:05 2009 +0000 "Encode release log update" commit 074eaa97f6f5122c837bef5ef969df3e37342530 Author: galt Date: Sat May 16 15:00:03 2009 +0000 "Release log update" commit 223cfc26807e5e2f217d0fd2150607d7a96df2d1 Author: angie Date: Sat May 16 00:03:05 2009 +0000 Removed an old debugging message that confused the heck out of me when I saw it again today. commit 779f42612eb6847924a44dcf946f4dc6ab77347c Author: fanhsu Date: Fri May 15 22:46:08 2009 +0000 Added the latest h1n1_0514Seq track build process, with good CDS display. commit df83f04e2e8f8061ef088f79a3ac95c81651c9ac Author: fanhsu Date: Fri May 15 22:44:54 2009 +0000 Removed old h1n1 track build processes. commit 75a409916640e46246a01f189969dcae18cb94d7 Author: kuhn Date: Fri May 15 22:39:08 2009 +0000 fixed a parameter to sort that was throwing an error commit 6b815385514ee03179a8a698e4605f8c0211adde Author: donnak Date: Fri May 15 22:29:22 2009 +0000 Synched up Current Protocols entries to latest PubMed style. commit d78e41772e82e7fe215c978023cf57214c4bcf09 Author: tdreszer Date: Fri May 15 20:32:30 2009 +0000 IE turns out to be a pain. Switched from div.innerHTML to textarea.value in order to preserve newlines. commit 4224b5467f373f955d930bda5824c13afc14e77a Author: fanhsu Date: Fri May 15 18:58:25 2009 +0000 Updated h1n1 tracks. commit 54c3aaaee901a6c8e3b89f9883d0b8dfb2b7c525 Author: tdreszer Date: Fri May 15 18:57:17 2009 +0000 Handle html warnings as alerts commit 8e9bd7ddc093dba5eaf93e77e40ad64bfbddefe5 Author: tdreszer Date: Fri May 15 18:23:25 2009 +0000 Sloppy typo commit c318871c266ea993eef4d5d1297c558999dd923d Author: tdreszer Date: Fri May 15 18:21:55 2009 +0000 Added E2F4 fro Yaale/UCD Farnham commit d1b8d42aee4ac968d57a444d046fd9fd3db5cc3b Author: tdreszer Date: Fri May 15 17:02:32 2009 +0000 Restore last position if newly requested position proves invalid. commit 37e5bd056b6f6f1df5ec0adc3fa0d9bdd7c5f125 Author: tdreszer Date: Fri May 15 16:58:10 2009 +0000 Store last position in case new position proves invalid commit f6f2c6e6875d752367ebe5c40d5d0137bba7ffc0 Author: galt Date: Fri May 15 15:00:05 2009 +0000 "Encode release log update" commit b2b754903ee566aae92ed7ba1010cdbfc924562c Author: galt Date: Fri May 15 15:00:03 2009 +0000 "Release log update" commit 6605e10c8b4b2a7e7ee456a814a806a5d1c00582 Author: mikep Date: Fri May 15 09:25:54 2009 +0000 Could not get DNA from bigBed because bigBed table has only a single column 'fileName' and it cannot be range queried (Easier solution than doign custom code for range query) commit 359366847cf94f49db796b9cd17a03d92d1ed8c2 Author: rhead Date: Fri May 15 02:24:02 2009 +0000 Moved gbSanity test to the end, collected table names into variables for each test, clarified error message. commit 285cbdb9aafbe87e28270748267ae0f62fae0c11 Author: katrina Date: Thu May 14 23:53:31 2009 +0000 removed reference to broken links commit ed93420e0ec409b015564789db51ebc25fb820ea Author: hiram Date: Thu May 14 23:44:55 2009 +0000 Additional lastz runs started commit c29ffede3952c0bac956a88c19444e50afc86552 Author: fanhsu Date: Thu May 14 23:31:25 2009 +0000 Replaced multiple sameWord() statements with on startWith() for H1N1 tracks.:wq commit 2e49b1136c4d02c57b4abba7aaa5254e09fc1b47 Author: kuhn Date: Thu May 14 23:17:15 2009 +0000 removed sessionIDs to expose IP itself for getting location of user commit c6350e9ea5e2ea204ae292cb0baff26d3f8717cb Author: cszeto Date: Thu May 14 22:32:17 2009 +0000 Fixed IDs on TCGA mutation data. commit 5101f9f95fef3a03063686ab6417acb143da2d42 Author: kuhn Date: Thu May 14 22:27:41 2009 +0000 improved debugging a little and fixed the case where larrym was being converted to larrymm by adding a space after the substitution commit d990425ac9576dba29aa21b2572d7d86ba397261 Author: hiram Date: Thu May 14 22:23:28 2009 +0000 Adding a supercontigs mapping track commit a4178d21d9c8b2dbb3f122edf80a9ae578cb208f Author: hiram Date: Thu May 14 22:22:29 2009 +0000 Update NCBI link to Build 37 statistics commit 1c244da5ea685c46a371aae212d239457bff4487 Author: kuhn Date: Thu May 14 22:07:33 2009 +0000 put quotes around rm *.out to get rid of annoying error message commit 9a023a4038be9b40c555001c8b26461160b9399e Author: braney Date: Thu May 14 21:45:24 2009 +0000 check for zero size before calling maf score function commit 395c30eeec74b187a7b782276271f25566af784a Author: kuhn Date: Thu May 14 21:44:45 2009 +0000 a few cosmetic or typo changes commit bed62acf2e3a31b3e13044e19e87b00bdebf40b5 Author: ann Date: Thu May 14 19:41:05 2009 +0000 new script commit 3353f9af08523b25597e70e82cadd29942307b51 Author: ann Date: Thu May 14 19:40:48 2009 +0000 a little clean-up with the file names commit 330cec87e7aff9358ebd286d38d7fed2abeee278 Author: tdreszer Date: Thu May 14 19:31:02 2009 +0000 Oops, change for ChkBoxNormalize had one error commit e32c42551e004ba80e5c6526dfa54ae312d0abab Author: hiram Date: Thu May 14 19:00:51 2009 +0000 lastz runs updated commit 9a8c9d864f65e9b5101298fdda176cc8e4e327f9 Author: tdreszer Date: Thu May 14 18:58:08 2009 +0000 Rearranged RIKEN CAGE commit 546985ab2b3b26dc1fe5f994aaaddcf28c6b8851 Author: ann Date: Thu May 14 18:51:15 2009 +0000 this creates a mapping from UniProtIDs to ucscGeneIDs. UniProt uses it to create links from their web site to our KG details pages commit 6aab1d487a6b2e94c9decc4f86e3ac6226c691d7 Author: kuhn Date: Thu May 14 18:10:57 2009 +0000 dropped commas in usage statement to conform to norm commit b8f4523e88d45291d9a8acd473bf5ce0f18db304 Author: kate Date: Thu May 14 17:45:57 2009 +0000 Adjust visibiltiies on transcriptome tracks so views are visible commit 0e7ed7636c8facf646e9781a81bdba17041ff911 Author: hiram Date: Thu May 14 17:37:13 2009 +0000 lastz runs status updated commit 338b899450027aaa65613d4857d9ade5f8df8ed2 Author: tdreszer Date: Thu May 14 17:34:55 2009 +0000 Marked Genoced as released commit 3e7b0977603a515cf9aac99f9bf67deb860b5f86 Author: tdreszer Date: Thu May 14 17:34:21 2009 +0000 Open Chromatin into the Push Q commit 618a04cf784276a8a88f2c9acd252a798ec02f91 Author: galt Date: Thu May 14 15:00:05 2009 +0000 "Encode release log update" commit 4748fca2b24f452d6cdc31c0621a15ca4ea1f9a6 Author: galt Date: Thu May 14 15:00:03 2009 +0000 "Release log update" commit b010113ae515d6f3673561bcedeaaf59996cfa62 Author: hiram Date: Thu May 14 04:56:59 2009 +0000 Had some of the SEQ2_LAP mixed up with SEQ1_LAP commit 29925643a743cffd890fcf62d30a260be8667277 Author: rhead Date: Thu May 14 01:03:15 2009 +0000 Added special logic for getting the shortLabels for est and mrna tracks (which are special cases in trackDb). Changed some whitespace stuff. commit 4130b78f9f06537b6d2f3e028f73e8b9d2abfc34 Author: galt Date: Thu May 14 00:35:33 2009 +0000 Initial Aplysia californica commit a70437b67f174d14d09ad84afc95b5582bd783f8 Author: galt Date: Thu May 14 00:26:13 2009 +0000 Initial Aplysia californica commit 90903c772b7eaf33c1c591ec31b3ec73efecc8d5 Author: katrina Date: Wed May 13 23:52:28 2009 +0000 removed output referring to file that no longer exits commit c3bc644ff63f3a0ba86cf446b2fe85d1664d196b Author: tdreszer Date: Wed May 13 23:16:00 2009 +0000 Fixed downloads link bug in entraUiLinks (as seen in hgc) commit d69fcb0a6453a78922ebad57836b3395fec74f2f Author: galt Date: Wed May 13 20:56:14 2009 +0000 Initial Aplysia californica commit 52b3e651aa13c542c68aac038b855923453825b7 Author: hiram Date: Wed May 13 20:51:33 2009 +0000 Running lastz alignments commit 184eec5eef84ac25444a93d5d40e6d4bf49aeccd Author: galt Date: Wed May 13 20:36:22 2009 +0000 Initial descriptions for aplCal1. commit c41ffbc1a7c701944311fa54d86a60608cf7896e Author: galt Date: Wed May 13 20:36:10 2009 +0000 Added aplCal1 to DBS. commit f1164f793290050b2ef551051b375b99f0f4c562 Author: tdreszer Date: Wed May 13 19:37:01 2009 +0000 Reworkd Matrix to subtrack box checking to solve dimZ commit c5cc083845a6fe45466555caa11496a84ee3fc67 Author: markd Date: Wed May 13 19:05:17 2009 +0000 added prototype support for launching 3D structure browser on H1N1 predicted structures commit f62c75b2e5557561d199a4617c460223517524f6 Author: tdreszer Date: Wed May 13 19:02:49 2009 +0000 Added dimZ class to make javascript handle dimZ properly. commit 16b19d6b4384cdb32a2954e744a4e7257ee62c0b Author: mikep Date: Wed May 13 17:29:21 2009 +0000 adding variable sort fields from RNA projects commit 57058728b7d3ef037813df117a450b3c17091efa Author: kuhn Date: Wed May 13 16:48:38 2009 +0000 dropped ref to page now gone from cbse site commit 8005ac682f3a1fb53c5a2a18e53fb2aba9ee4fc9 Author: fanhsu Date: Wed May 13 16:12:00 2009 +0000 Updated URL to Gene Network web site. commit 1eaf99e308614dc6f618eb60212af464c4226b37 Author: fanhsu Date: Wed May 13 16:09:48 2009 +0000 Updated URL to Gene Network site. commit e7acb0da2f5f850d6ab10fe7f6a6b3cfcdbd826f Author: galt Date: Wed May 13 15:00:06 2009 +0000 "Encode release log update" commit eda1a45be1c900b88cfdb8831d44ac7481211d34 Author: galt Date: Wed May 13 15:00:03 2009 +0000 "Release log update" commit ca35faadb258ea2beb4226ccf84571797856c09f Author: kuhn Date: Wed May 13 01:38:46 2009 +0000 refactored handling of single chrom. removed extra steps in txStart-assignment pipe. put all rm statements together using else clause. thanks, brooke commit 4b2dd724b0d283d928c9c2df2470ba1c13514144 Author: kent Date: Wed May 13 01:13:57 2009 +0000 Adding clip parameter to bigBed creation. Making a few functions static that don't seem to need to be exposed at the moment. commit 18509f3c7d08352151ba4223c5edd04edbcd2c09 Author: hiram Date: Wed May 13 00:04:56 2009 +0000 Tolerate empty results when running lineage specific repeats and tolerate previously existing results commit 7c10a4d95e3ba591e6e1f401cd1f601d20554d80 Author: pauline Date: Wed May 13 00:03:10 2009 +0000 Added Gencode Genes to downloads. commit 81ba7f359972988047a76d4d7d492bdae090ec8d Author: kuhn Date: Wed May 13 00:02:50 2009 +0000 reset to accept hgwbeta as input. dropped machineName checking as redundant. thanks, brooke commit eb295be904fed0782bd1271cee6a0d9a179d3de9 Author: kate Date: Tue May 12 23:55:32 2009 +0000 Changes to HudsonAlpha Chip-seq for consistency commit e7ca09fb7fa7a63f6321cdaac8cc18f7d1b9e5b8 Author: kuhn Date: Tue May 12 23:49:32 2009 +0000 dropped declaration of varialbe no longer used commit ff858807ba9432b1988516319e519932ec7a422e Author: kuhn Date: Tue May 12 23:48:03 2009 +0000 simplified and dropped some variables. caught error state where table does not exist either split or unsplit commit 200d0b27e372172a0f0530b2edb8fa58bf6a6829 Author: tdreszer Date: Tue May 12 23:40:51 2009 +0000 Consistent metadata antibody=Input for Broad commit 709648e429850ba460c9b93e2043ad36d2f3ac3b Author: pauline Date: Tue May 12 23:40:46 2009 +0000 Fixed a typo and added ref hyperlink. commit 9fb928a29ca912ca32428f8e0bddac1be61d4ef4 Author: tdreszer Date: Tue May 12 23:34:50 2009 +0000 Changing Duke and Broad's input/control to Input_Control for consistency commit 929081dfa0aa37faf84ebbde26a51e6113e5c8d0 Author: pauline Date: Tue May 12 23:19:59 2009 +0000 Added subscripts and greek letters to make equations easier to follow. commit 17fa6a631eed23c5e6d7a0489458e8f9545a9b73 Author: hiram Date: Tue May 12 23:14:00 2009 +0000 Adding baboon papHam1 to the build commit ea4a89681e6a2837da7158083663420078c20d2a Author: hiram Date: Tue May 12 23:13:23 2009 +0000 Initial files from makeGenomeDb.pl commit 87e6355c1a59d96973a3fc3caa91d39baaebba40 Author: tdreszer Date: Tue May 12 23:06:47 2009 +0000 Split uniqueness tracks out of Open Chromatin and made new Mapability composite commit 558db96adf5b738340b1d5a4ea4aaf19a2d2dbf1 Author: kuhn Date: Tue May 12 23:00:50 2009 +0000 added exit after error detect. thanks, brooke. commit 1645ad3571a9af63f19b80ba98d6f92be485bbe5 Author: kayla Date: Tue May 12 22:58:11 2009 +0000 added Riken Cage to the downloads commit 27ca7520cdf33dae45872ab4fb67eafbf11b8207 Author: tdreszer Date: Tue May 12 22:50:56 2009 +0000 minor typo commit b5d8cff7389d3911ed213ded9328c365a3b0422d Author: tdreszer Date: Tue May 12 22:50:25 2009 +0000 Initial check-in of mapability which was creating be stripping uniqueness tracks from the Duke/UNC/UTA composite. commit 550c09acc9fc9bc9b4d3b28a706d52133ff2369d Author: kuhn Date: Tue May 12 22:50:05 2009 +0000 made dir group writeable commit 62a246616f4d08970b53625e0214558ad68709ac Author: fanhsu Date: Tue May 12 22:45:10 2009 +0000 Hide two h1n1 tracks. commit 74cb455bee00c7f36683d2d30550419fd73dc451 Author: kate Date: Tue May 12 20:10:30 2009 +0000 Tweak defaults on Riken CAGE commit 190f2178753fe708b1fb3a3735d001c85acab982 Author: kate Date: Tue May 12 19:22:37 2009 +0000 Adjust labels and priorities of Riken CAGE for consistency, length commit 02b61779542ff4e284a34d9f585c56c2545d7e3a Author: tdreszer Date: Tue May 12 18:20:24 2009 +0000 Straightening up before pushing to QA. commit 68d4dc5cd2d0ef04b70b8785f47f0f23ae6a6be2 Author: kuhn Date: Tue May 12 17:10:12 2009 +0000 made it work for RR. allowed optional arguments to be used singly. allowed use of hgwbeta or hgsqlbeta. simplified logic for doing randoms last. removed tableName variable commit 1bd0914a43d11a6696bfde9297b413764f78eb25 Author: mikep Date: Tue May 12 15:25:08 2009 +0000 make sure we wait for any background processes before we exit after an error commit d4d0caacaeee76c2e403dcf8324dbf30bbb5b8f2 Author: galt Date: Tue May 12 15:00:05 2009 +0000 "Encode release log update" commit c2aa3685c9adca5b9b2b55efd6a7ad7bf2976429 Author: galt Date: Tue May 12 15:00:03 2009 +0000 "Release log update" commit d4b5e453d3bff634c58f4cfeaee66a031a978f61 Author: mikep Date: Tue May 12 14:22:31 2009 +0000 "New version number v206" commit edcc60d540f181b86d5d4c1329f3956bcd42be24 Author: mikep Date: Tue May 12 14:22:17 2009 +0000 v206 final build commit 2ca74a149996788544cd9ddb178cd7f2b21a06cc Author: galt Date: Tue May 12 03:16:20 2009 +0000 maybe this is better ncbi url to fetch the chrM seq with commit 7a3f4bc301d37fb3e35ae34c609f690e1820ece9 Author: angie Date: Tue May 12 00:00:37 2009 +0000 Quick fix for an interaction bug before the code release -- I hope a cleaner fix can be implemented afterwards. groupTracks() removes cart vars that are redundant with trackDb settings, which I think is good for reducing cart bloat. Unfortunately, something upstream of trackFromTrackDb, and also trackFromTrackDb itself, overwrite tdb->priority with the cart value, causing false detection of redundancy with trackDb here. commit ff2ed552f76c66f4c028a27a450e88daa9e9c962 Author: kuhn Date: Mon May 11 23:59:13 2009 +0000 changed to accept hgsqlbeta instead of hgwbeta commit f93b3656a6ff16d13ad07a3eca583bd957f379bb Author: fanhsu Date: Mon May 11 23:21:09 2009 +0000 Added h1n1_0511Seq. commit 99b97ed0756eaf9791d6716b3c2e9675b0861890 Author: kuhn Date: Mon May 11 23:16:14 2009 +0000 fixed interaction with split chroms. removed some unused variables. simplified logic and combined some variables. replaced long block with call to getChromFieldName.csh. commit 79165e763e0df77baee7b1a2fc7c67349568bc0d Author: fanhsu Date: Mon May 11 23:15:16 2009 +0000 Added h1n1_0511Seq (last time was h1n1b_0511Seq). commit 5f30b750ff07c7fecd294581bb2e365802403e69 Author: fanhsu Date: Mon May 11 23:13:51 2009 +0000 Added h1n1_0511Seq. commit 214bbddfb496a763da8f5ad240e5cc9411555ea4 Author: tdreszer Date: Mon May 11 22:16:23 2009 +0000 Added a link to help on 'Filter by category' UI commit 335e542d9f959fe59ae1e74d533048430f382a61 Author: aamp Date: Mon May 11 22:01:32 2009 +0000 Added fox2ClipClusters to tables ignored. commit 56249bf9981b9647d3fe1562f0a707818a04073b Author: tdreszer Date: Mon May 11 21:58:45 2009 +0000 Call common API for showing downloads, schema and metadata links commit 1125aa1bc8f0a738bab44a5176a0bd8aae6a21dc Author: tdreszer Date: Mon May 11 21:56:31 2009 +0000 Added API for hgTrackUi and hgc to show schemaLink, Downlaods link and metadata commit 3fd0c51350f4649e47862d58e9f72ba1ad280b90 Author: aamp Date: Mon May 11 21:56:27 2009 +0000 FOX2 clusters track from Gene Yeo commit f77b7118276cf4417914a9b256b903613e8d05eb Author: hiram Date: Mon May 11 20:50:57 2009 +0000 Running Mouse Mm9 and Dog CanFam2 blastz commit 0e68d69e119f5c167fc3992ea33f5efdbf7c21fd Author: ann Date: Mon May 11 18:59:58 2009 +0000 fixed typo commit 8d11a195e2a240921cfce159ba0846ae7f307180 Author: galt Date: Mon May 11 15:00:06 2009 +0000 "Encode release log update" commit 8b11e2d9aac15acbf2d3bc288981aa0a8c0738bd Author: galt Date: Mon May 11 15:00:03 2009 +0000 "Release log update" commit 9f9e55088ae67edf2e3f464c7fae2a62e908433b Author: kuhn Date: Mon May 11 05:29:21 2009 +0000 added support for split tables and added a bit of protective logic commit 6921eba316a9308745f64ea25a9160f70555adfd Author: kuhn Date: Mon May 11 03:44:41 2009 +0000 added support for split tables commit 17ff5ce73be6265486f228525a61dbaed31f21ca Author: kuhn Date: Mon May 11 03:36:47 2009 +0000 adjusted so default is to dev and a few other cosmetic changes commit b430fda9cdc425ad8a2e6e9dead84606f166b2b6 Author: galt Date: Sun May 10 15:00:05 2009 +0000 "Encode release log update" commit 7bd6b94aaf1d29df609a5e1a3a1e533793a45d61 Author: galt Date: Sun May 10 15:00:04 2009 +0000 "Release log update" commit 3d0adfb6811f29b7d9f01555d01c5bf2e19db2a4 Author: markd Date: Sun May 10 02:09:16 2009 +0000 convert slAddHead to an inline function, bitten one too many times by it being a macro commit 0f414fcf4f1151a97678bcbb4d5852ae21c88642 Author: galt Date: Sat May 9 15:00:05 2009 +0000 "Encode release log update" commit 64e0901dc7d160394c189f5cf4d2499003faa0b9 Author: galt Date: Sat May 9 15:00:03 2009 +0000 "Release log update" commit e47bd17b9172ab340330206c8a5b9e7a622dcf79 Author: tdreszer Date: Sat May 9 00:29:56 2009 +0000 Initial checkin of accumualted wrangler logs commit db9bbde62d07241102d100645f7f0520f8f3a0c7 Author: tdreszer Date: Sat May 9 00:24:47 2009 +0000 Added description of scoreFilter and filterBy category commit baa0ba52374af53205409d9baf66d366213def29 Author: tdreszer Date: Sat May 9 00:02:04 2009 +0000 Changed the name of some Yale tables to be consistent commit e6490ee847fdf74a38a51561042854c05ffe981a Author: rhead Date: Fri May 8 23:36:25 2009 +0000 Changed example double-lift from human to mouse, as we now have the direct lifts for the human example mentioned. commit e2bb8b4800103d68a1be58004277382ee5fbc27e Author: hiram Date: Fri May 8 23:05:22 2009 +0000 Do not check swarm for workhorse idle machines, and add orfeomeGenes to genbank list of tables for makePushQSql.pl commit a1a45d868f295c09175554ca3aef3efe70534d70 Author: hiram Date: Fri May 8 22:57:01 2009 +0000 Adding encodek and disable sanvol1 commit 03e285de4ed7a7a759479564cf08a65574f18406 Author: tdreszer Date: Fri May 8 22:43:39 2009 +0000 Had to regen some 1/2 of Yale Raw Signals. Since already release, made alpha/beta tracks. commit 6d25a92e95330f0785b4d75e5d1ddfea51e340bf Author: rhead Date: Fri May 8 22:34:41 2009 +0000 Added monDom5. commit 765df74a60032f9ca1c6cc0b0a5cd2083c799d00 Author: hiram Date: Fri May 8 22:23:22 2009 +0000 Document ctgPos table build, done with STS Markers, BAC Ends, and now working on FISH Clones commit 9760b6153a5483bb5221899cb84f8f35b468ee62 Author: hiram Date: Fri May 8 22:14:01 2009 +0000 Assembly description for hg19 is different commit 3d3780ee760fdff91c964454640a7f1833b54098 Author: angie Date: Fri May 8 21:26:54 2009 +0000 IKMC (komp): data update. commit 27fac0d4246888e9e2e75c86a3f3b21442374a6b Author: pchan Date: Fri May 8 21:15:26 2009 +0000 fix hTableExist call for blastp track; change code to use centraldb name from hg.conf; add code to support blastx track commit cefb125012bd8fc47487843f025def4972abc269 Author: fanhsu Date: Fri May 8 20:55:58 2009 +0000 Added h1n1_0506Seq and h1n1b_0506Seq. commit 1b8161d0a89f7865b41047f18887d5777dfdd06a Author: pauline Date: Fri May 8 19:33:33 2009 +0000 Added new section on filter drop down menus. commit fb560e4c6149f4a6d1fc16406b1a64f31421a197 Author: tdreszer Date: Fri May 8 18:51:15 2009 +0000 Added Duke/Uta/Unc Raw signals back in, now that they have been regenerated. commit 98b60e25933e7f5011a6f4f10a212e2638a741c2 Author: angie Date: Fri May 8 17:59:36 2009 +0000 doKomp: Added explicit inclusion of all targets for given gene, with the Design ID now appended to each gene name. commit 0b005f0a6a1b5121ffe2ed5ed76aae5d62caf1ab Author: hiram Date: Fri May 8 17:39:00 2009 +0000 Add UCSC to Ensembl chrom name translation and haplotype lift tables for Blue Bar Ensembl click through commit 5bc3ea43a34c96a2e61aa572782dd7c16897ad27 Author: hiram Date: Fri May 8 17:36:16 2009 +0000 Properly lift to Ensembl haplotype coordinates for Blue bar click through commit 43c464e36c5c505f997f44241f4502c90695ec00 Author: hiram Date: Fri May 8 16:49:17 2009 +0000 Allow hg19 to click through to pre.ensembl.org with chr name translation commit be30514b21a1349a8fc5a03c1b392b9fc8b9dc18 Author: tdreszer Date: Fri May 8 16:01:57 2009 +0000 Added Display Conventions section commit 32acb52c3aa8ac631db5dc3ebcf989cb9984ad38 Author: ann Date: Thu May 7 20:55:25 2009 +0000 turning off some tracks by default commit c83586da21b64b468463e8178ed6569f627150cd Author: ann Date: Thu May 7 20:49:18 2009 +0000 added monDom5 as appropriate commit 1f92756797f9fa39c228e933fc416e1e7d3758d0 Author: tdreszer Date: Thu May 7 19:46:05 2009 +0000 Fixed -quick, allow fragLength=0, removed obsolete trackDb.ra settings commit 4bc44167607c8fc8f753a5455f28a9b57a16090e Author: tdreszer Date: Thu May 7 19:38:04 2009 +0000 Temprarily comment out Duke/Unc/Uta RawSignals while they are regenerated commit aab22f42e03de0abc3657a8f796f74a25bddc47a Author: hiram Date: Thu May 7 18:05:53 2009 +0000 Allow click through to NCBI entrez search for Contig names on ctgPos tracks commit d5ded27011c5828db2050f4459d7aa06585dc57c Author: galt Date: Thu May 7 15:00:06 2009 +0000 "Encode release log update" commit b0b7ad9911cf7830e9f05239366a508eb4b9540a Author: galt Date: Thu May 7 15:00:03 2009 +0000 "Release log update" commit 046355ec9a8e29c31ac1f427f87399ef62480bd4 Author: tdreszer Date: Thu May 7 00:33:31 2009 +0000 Changed 'Track details..s' to 'Table metadata...' commit aaec3d3c949b84b5255feb593ba3bd0b66fea237 Author: tdreszer Date: Thu May 7 00:12:33 2009 +0000 Now the page will be sorted on the defined sort order fields from the metadata. commit e8de03e8ed161bf73f3495a84c49b4ca65733364 Author: tdreszer Date: Thu May 7 00:09:47 2009 +0000 Removed the Gencode url setting for auto-annotated track. tRNAs have no Ensembl ID so the link was broken. commit 6379a2fcdbd2149f1c5acac1a4dddf0ac7e68a9c Author: tdreszer Date: Thu May 7 00:07:51 2009 +0000 Added the special case Ensembl Transcript Report link back in, due to tRNAs not having Ensembl IDs causing the trackDb.ra url setting to fail commit 72dd9914871f1081035871efd5089d6c584eced4 Author: hiram Date: Wed May 6 23:45:51 2009 +0000 STS Markers track done commit 66f6726864d5ae3e8541c18f1924c7fd5ec643da Author: tdreszer Date: Wed May 6 23:27:09 2009 +0000 Fixed some Yale metadata and make Gencode not a default track (as per Jim) commit 467f4b5b656306c471a310d2c7f6c069888562eb Author: ann Date: Wed May 6 21:39:53 2009 +0000 added image and info about photo from monDom4 commit 4daa6af3a7eeec5cb12c83a03b8cfdd041815656 Author: katrina Date: Wed May 6 21:28:35 2009 +0000 changed the explanation of the type because chrM contains a contig that is type F commit a9b4e8c7085700dd270bafecc4dc00db957c4e0b Author: hiram Date: Wed May 6 21:20:33 2009 +0000 Proper size on target chromosome commit 9323243c5e801c89ecb9fae69cb369f095a2ce55 Author: hiram Date: Wed May 6 21:14:33 2009 +0000 Initial source rescued from /cluster/bin/scripts commit cea1402d2bbdcd9865b2465962ca58f65763a931 Author: hiram Date: Wed May 6 20:55:42 2009 +0000 This functioned OK on hg19 commit 67a79784749b763c1e9a60613b2728dea096f42d Author: fanhsu Date: Wed May 6 19:27:46 2009 +0000 Added h1n1_0506Seq track. commit 32aa9fcbceb2ae5541e449e1ac8f025664d7ce1b Author: fanhsu Date: Wed May 6 19:06:21 2009 +0000 Added more h1n1 tracks. commit 04ce7321edba98aa72b83aaee003c1a9d02ada2c Author: kuhn Date: Wed May 6 17:33:18 2009 +0000 clarified output so it is clear that "not real time" refers only to RR results commit 6305e46a0272b015130a26422620221c4315b89d Author: galt Date: Wed May 6 15:00:06 2009 +0000 "Encode release log update" commit 25a1112d169d5d5771b4187fae2e788015847a09 Author: galt Date: Wed May 6 15:00:03 2009 +0000 "Release log update" commit a778419bfa7380aefab0567823c8d7a65a3e3253 Author: aamp Date: Wed May 6 07:04:02 2009 +0000 Added UW Affy Exon track and UW WERI-Rb-1 ChIP-seq subtrack. commit aa3fbdd2b6104c693e86501884ca042de1209d35 Author: kuhn Date: Wed May 6 03:49:51 2009 +0000 added code to strip out directories a year old commit 56bf7a39a91a802d78a04df041aeece29e5b4bb7 Author: cszeto Date: Wed May 6 02:02:56 2009 +0000 New datasets commit 3260d47e2105a2183296def6086b8695cb8bac11 Author: cszeto Date: Wed May 6 01:58:21 2009 +0000 New Datasets commit 5665fc1c2ead63ab223473088654e1673d8aa540 Author: tdreszer Date: Wed May 6 00:38:50 2009 +0000 Removed a lot of obsolete settings - values now in metadata. Should remove all these obsolete settings from non-released tracks commit 04df0424dafcaaa400769f8a465a4171c044b13e Author: tdreszer Date: Wed May 6 00:27:49 2009 +0000 Added call to show metadata commit 7994c37bab7c5d87fe427f28ab4cfe6fea15e70f Author: tdreszer Date: Wed May 6 00:26:59 2009 +0000 Added call to show metadata if track is not a composite commit a64f01b93dc10e81d86b3dfdeb18366de0f7d27a Author: tdreszer Date: Wed May 6 00:26:06 2009 +0000 Moved metadata display toggle code to utils to be called from hgc and hgTrackUi commit d9cea4b6fa3fc5fec9884eadbc579bb4b648b5dd Author: tdreszer Date: Wed May 6 00:24:36 2009 +0000 Moved metadata display to separate function to be called from hgc and hgTables commit 556226df5a1769193f8ee9ee6c3da0d2556447d7 Author: tdreszer Date: Tue May 5 23:35:07 2009 +0000 Removed NO_VALUE define, as it is defined in the header file. Thanks Hiram commit 83cfb32d19f4969836ca21f7614b18e989a329e6 Author: rhead Date: Tue May 5 23:23:55 2009 +0000 Keeping in sync with qaConfig.tcsh. commit 45194393b26aa3e2af8b890d9f0161e606e9cb36 Author: kuhn Date: Tue May 5 23:13:56 2009 +0000 added sqlrr variable where needed to set up for new machine testing commit 61a03c65e513a59c07ae8a79abc269b36ce2b9db Author: tdreszer Date: Tue May 5 22:48:31 2009 +0000 Removed obsolete special case code for ENCODE Gencode linking to VEGA and Ensembl, because this is now done with trackDB.ra url settin. Also made dataVersion and restriction date use metadata commit 7931a5bf8740b90c54ae52df81b7ad622b1173b4 Author: tdreszer Date: Tue May 5 22:39:41 2009 +0000 Free memory after restrictionDate lookup commit ebdebed8ffd3444dfbf63b925819226ffaf94c7b Author: tdreszer Date: Tue May 5 22:38:51 2009 +0000 Clarified function comment commit 5ec91e7bcc10e37aa60f20b81f701b5e51d6cef3 Author: tdreszer Date: Tue May 5 22:37:28 2009 +0000 Use metadata setting for controlled vocabulary look up and for restriction date lookup commit 6972d391a3581d23cf8e6598ec18e147045f0042 Author: tdreszer Date: Tue May 5 22:33:58 2009 +0000 Added simple routine to find a metadata setting commit 953fbf9b69929e1776936ab91c34f12b34fce208 Author: katrina Date: Tue May 5 22:27:39 2009 +0000 changed the links for the mailing list google searches because google has indexed the new location commit a1ba01b99e45150fef97f13e8771f45e6a4379c6 Author: katrina Date: Tue May 5 22:11:02 2009 +0000 changed the links for the mailing list google searches because google has indexed the new location commit 1cb2b5bd520a601eeb9980d7213ddc6ae5ddb762 Author: katrina Date: Tue May 5 22:05:38 2009 +0000 changed the links for the mailing list google searches because google has indexed the new location commit d935ea7425db323becf21a78f272c88e5b9c3fc2 Author: hiram Date: Tue May 5 22:02:41 2009 +0000 Initial source, worked with the ePCR results for hg19 commit 68c6d355b3fd867c44767927d3495f0e946b2164 Author: katrina Date: Tue May 5 22:00:31 2009 +0000 changed the links for the mailing list google searches because google has indexed the new location commit ac30e70a6e92d7164c745585d24bb4e21dce2f9b Author: rhead Date: Tue May 5 18:56:20 2009 +0000 Blocks that exist solely to pick up local html diffs are no longer needed. commit 41cd0100eea7a81e7efc1b8dd3ccb2fea75e0641 Author: tdreszer Date: Tue May 5 18:06:18 2009 +0000 Marked the metadata of Yale's datasets that still have problems (peaks and signals) commit 0b6e98dd390dd9beb25bc4aa3256c2a2112be58f Author: rhead Date: Tue May 5 18:04:09 2009 +0000 Replaced visibility.ra settings for netPanTro2 and refGene tracks with track override visibility settings, and condensed chainPanTro2 block tojust the matrix and matrixHeader lines. commit 8073d2edcb0df60b46690c7963a69a3e73b75873 Author: rhead Date: Tue May 5 17:55:38 2009 +0000 Removing this file because visibility.ra and priority.ra have been superceded by track override in the regular trackDb.ra file. commit 801ef6b15fa46e71926705365c67bfe0e2e993b4 Author: hiram Date: Tue May 5 17:52:38 2009 +0000 The line files need to be opened with zTerm and the split is on tab commit 4d712d716dd6701946673a9e84014b3caac5f81d Author: ann Date: Tue May 5 17:47:18 2009 +0000 removed all mention of affyHumanExon% tables (they are gone, never to return, says Andy) commit 3dfbaa54eb3ea14f1e25aee0d55ecf6d3e58eb36 Author: ann Date: Tue May 5 17:43:55 2009 +0000 removed affyHumanExon* tables (they are gone sez Andy) commit 03c110a0da06b9a603ab5287bc360b29a18513ff Author: tdreszer Date: Tue May 5 17:41:00 2009 +0000 Added 6 more datasets for Yale and changed the Peak controls commit d1f838a651d33272628bbb5a2988c5b6cdf78518 Author: mikep Date: Tue May 5 15:49:40 2009 +0000 fixing links commit 067cf860357e76da50a210cc26bf94ae84b0de71 Author: mikep Date: Tue May 5 15:08:12 2009 +0000 v206 preview commit da79e57e7dae528e206668d7c6fbbd7064965642 Author: galt Date: Tue May 5 15:00:06 2009 +0000 "Encode release log update" commit 20e3e4c79754017bfe43e59b6eecfbe93e4c1156 Author: galt Date: Tue May 5 15:00:03 2009 +0000 "Release log update" commit c30b762066224a08f4191a83fd2efa6edb9d34b0 Author: aamp Date: Tue May 5 06:42:47 2009 +0000 UW Stam ChIP-seq track with 40 subtracks: 4 views each of 10 different cell/antibody combos. commit c3c314a1ed205ea04d5b89602b95e6fb9924100b Author: markd Date: Tue May 5 06:01:05 2009 +0000 prevent bogus stale lock message by doing one database's downloads at a time commit f9b04f8038de7802340b382eadf91346cc2c05de Author: jsanborn Date: Tue May 5 00:41:30 2009 +0000 added updated version of harvard ovarian CGH array commit 4e55a2d3df10b26dc59e54662b7470210d2ff529 Author: tdreszer Date: Tue May 5 00:19:35 2009 +0000 Fixed a broken link commit 54f53226a962ec9b2133e358dd9920f8af76ae79 Author: tdreszer Date: Mon May 4 23:42:43 2009 +0000 Added Yales resubmitted signals and fixed metadata dates by adding dateResubmitted= value commit 43c1634d5d4ed3446266d609d8899b21257ffb2c Author: aamp Date: Mon May 4 23:23:56 2009 +0000 Added HL-60, Th2, and SKMC cells to UW Stam DNase track. commit 152bb16e6cdc3323c4a8820c9d0a9a72bb60b953 Author: aamp Date: Mon May 4 23:02:14 2009 +0000 Three more cell lines for the UW DNase-seq track. commit 047a38883128142142e6e6447d3c716a8db92fb0 Author: tdreszer Date: Mon May 4 21:42:35 2009 +0000 Removed this empty doc file as all docs are by lab in the encodeDccHg18 subdirectory commit 5f895df3c81ac0f9c77a23381f76c4ff3e85e21e Author: giardine Date: Mon May 4 21:23:24 2009 +0000 Put in IF to skip src links, until ORegAnno is fixed. commit ea3ca6c7d9efd1f5a7b690582288a731c4928d2d Author: rhead Date: Mon May 4 19:38:37 2009 +0000 Typo. commit 5aac0e06331b62c69f0c346958b758694b872278 Author: tdreszer Date: Mon May 4 19:36:03 2009 +0000 fastq sequence names can have # in them. commit 72862882cfa9b9b07517031f7190f210f8c07a01 Author: pauline Date: Mon May 4 19:11:52 2009 +0000 Commented out release alpha to stage on beta. commit 426f8b45bbd518725fefe99427673423d02a2683 Author: angie Date: Mon May 4 19:07:52 2009 +0000 Performance/memory leak fix: move hTrackDbForTrack (and bedItemRgb, thanks Tim) out of the inner loop of doGetBedOrCt. commit f6e50d4958403de9cd0f44a122fd44ff33b6765c Author: tdreszer Date: Mon May 4 18:53:26 2009 +0000 Added resubmitted Yale Peaks, though I may be changing unrestructed date yet. commit 9ffdb4838fa81e46554846eb07055d53dfb6f8d7 Author: fanhsu Date: Mon May 4 18:32:02 2009 +0000 Added h1n1_0504Seq commit d4dd7d193ca704551bc08e04895a7827b1568318 Author: fanhsu Date: Mon May 4 18:16:34 2009 +0000 Added details page for H1N1. commit 3a447c99e41ddfaf28d6676ce31650d08b565138 Author: katrina Date: Mon May 4 18:16:01 2009 +0000 Added color description commit efa2cb9a75d3c9eb948f8c67b1cb5b9342744540 Author: angie Date: Mon May 4 17:44:39 2009 +0000 Remove the working directory after generating images, because the cleaner script does not remove empty dirs (Thx Hiram). commit 35b97994de3120501a941ca8945ef2dca8199090 Author: hiram Date: Mon May 4 17:30:12 2009 +0000 Transitioned and updated file to src/hg/stsMarkers/findAccession.pl commit a0292b77fb3250a54246c50ee91a9f8b84b4aff0 Author: hiram Date: Mon May 4 17:29:29 2009 +0000 Transitioned file to findAccession.pl commit 68f6ac15c077352974723a2983f3c1b8517c428a Author: hiram Date: Mon May 4 17:29:07 2009 +0000 Transition of file from src/utils/findAccession.pl, updated to work with hg19, added strict and warnings and worked out a number of deficiencies commit 4bac1f74158e39361b231bf628fb4115aa44c09a Author: galt Date: Mon May 4 15:00:04 2009 +0000 "Encode release log update" commit 7c25fa70717226d7db807443748b8e8510a064e2 Author: galt Date: Mon May 4 15:00:03 2009 +0000 "Release log update" commit 49b95981e1ce93fab41710702c57acc1608e34be Author: galt Date: Sun May 3 15:00:13 2009 +0000 "Encode release log update" commit 6f4f228dd0ee5a45f179a41d782d6255b6965749 Author: galt Date: Sun May 3 15:00:11 2009 +0000 "Release log update" commit f8950cb00aa20086ad91745d74f3a5df91f26ea6 Author: kuhn Date: Sun May 3 01:54:56 2009 +0000 changed single quotes to double so sqlbeta variable can be interpreted commit 5868a16371c1456b8ceecf8caa0b80e67578d297 Author: tdreszer Date: Sat May 2 19:30:55 2009 +0000 Added Rad21 and XRCC4 antibodies fro Yale commit 5afd4d867248b5864a808a8cecd46a7e4511daf9 Author: tdreszer Date: Sat May 2 19:07:00 2009 +0000 Added Pol3 for Yale commit b7236f88d5edd7b18d186a6e88f412369a96ac50 Author: galt Date: Sat May 2 15:00:15 2009 +0000 "Encode release log update" commit 7870ff6caf9db28be42a186a2c3c65cb46b62da6 Author: galt Date: Sat May 2 15:00:13 2009 +0000 "Release log update" commit e539b263bf3ee84751f7e1c8b2ddcb7001807fb8 Author: markd Date: Sat May 2 08:13:29 2009 +0000 add queries aligned to overall stats commit c31a7a9b809ec598dc5f48561a04e1329f8aa7de Author: rhead Date: Sat May 2 01:09:47 2009 +0000 Added panTro2 chain and net blocks. commit f231381845b2ec590e6b563ca5c0c004db998159 Author: rhead Date: Sat May 2 01:08:05 2009 +0000 Hide hg19 net by default. commit 439a28d987089d0950f5e23fb89f2326b065c3bc Author: tdreszer Date: Fri May 1 23:43:43 2009 +0000 Hopefully fixed wgEncodeGencode and added wgEncodeNhgriBip commit a0f62bdb49ac482c037967b8b2f3252555f9943c Author: rhead Date: Fri May 1 23:33:24 2009 +0000 Moved hg19 net/chain so that it comes after hg18 net/chain. commit 58c88c97f2830eba9eb63fd107fe68c492414a64 Author: kayla Date: Fri May 1 22:02:00 2009 +0000 commented out some "release alpha" blocks commit 2e2967ae1196dd0700bfc1fbf0f35a5586bf286a Author: hiram Date: Fri May 1 19:01:52 2009 +0000 Updated with strict and warnings and bugs worked out from that conversion commit b1246461a24f8d4f4618905ddfb8a086cd07aebd Author: hiram Date: Fri May 1 17:11:44 2009 +0000 Initial source rescued from /cluster/bin/scripts commit 753595f1894e1a09b67c09ede2a934492112d065 Author: galt Date: Fri May 1 15:00:05 2009 +0000 "Encode release log update" commit 6bee65058d3b13384568fc790d37e3a495a4494f Author: galt Date: Fri May 1 15:00:03 2009 +0000 "Release log update" commit 5735a2f5193b6b5939c2ede399eb9a2a63ac2d79 Author: aamp Date: Fri May 1 06:20:28 2009 +0000 Fixed bug that couldn't find an unzipped file. commit 296bc91b912f5908215f51ec81e0cc10179b7e82 Author: rhead Date: Fri May 1 00:28:11 2009 +0000 Changed IMAGE Consortium link to hudsonAlpha, where it now resides. commit 59c8168b60d555622dc8a1f1ee5ce48f4a5fc212 Author: tdreszer Date: Fri May 1 00:25:57 2009 +0000 Fixed bug where last chr could be truncated if the previous one was smaller commit 9725e44f8f7478cc06f313084b17c2389c06603f Author: rhead Date: Fri May 1 00:00:12 2009 +0000 Fixed link to Affymetrix 10K SNP array. Looks like there is only verson 2 now. commit 20ce12963bd2937e7704403362a0620f060cb7a7 Author: rhead Date: Thu Apr 30 23:19:19 2009 +0000 Fixed broken link to HInv-DB. commit c40dbe5524d2c2153a64502cf805c67cd85776fa Author: rhead Date: Thu Apr 30 23:08:55 2009 +0000 Fixed links to Haussler lab. commit b9201dd6e96701035170b288d49dd1ec4cd71379 Author: kate Date: Thu Apr 30 23:06:34 2009 +0000 Changes from code review commit 116c99bb40d41864104d1867d1004a9b9b7d2b9d Author: kuhn Date: Thu Apr 30 20:43:02 2009 +0000 fixed logic and output to more clearly distinguish betw all gaps and unbridged gaps. it now prints both if there is overlap with both kinds commit 6f66b85c0bf8520c067d2cda1e9dcdb8852f016f Author: mikep Date: Thu Apr 30 19:31:50 2009 +0000 I take the comemnts back. It seems some poeple like to store hash elements as the value of other hash elemnets in hashes. commit 9bb36db32221923ba8c7f3908dcd46febc6a028a Author: pauline Date: Thu Apr 30 18:52:43 2009 +0000 Small edits for clarity. commit 18ae9c01edaa9c957252d26bdb9b69f1dc17d599 Author: ann Date: Thu Apr 30 18:41:58 2009 +0000 fixed links to new CBSE web site commit e7545afddfa6f6182ad9315d7e4e2f378577c447 Author: tdreszer Date: Thu Apr 30 18:28:53 2009 +0000 Added links by trackDb settings to two Gencode tracks commit 1a3ec8c1978ba1e8ed7e675fb384fb6749ddcabd Author: ann Date: Thu Apr 30 18:19:37 2009 +0000 fixed links to new CBSE web site commit 812eb5e7b5ba0f29ef70298f2d926a2efe0f9970 Author: mikep Date: Thu Apr 30 18:12:00 2009 +0000 expanding message which lead to a bug somewhere else commit eef43b3e9b6cc2b18094376f941703ea6e27c881 Author: fanhsu Date: Thu Apr 30 18:02:18 2009 +0000 Added latest h1n1_0429Seq track. commit cdb3e46512605bb0f483ed0ac87e3ca50f44e289 Author: ann Date: Thu Apr 30 17:35:36 2009 +0000 calling checked-in version of updateTimes script (instead of the one in the user's /bin directory) commit 199ef19bd4de246c6b185a3531c69b97c3fbe709 Author: tdreszer Date: Thu Apr 30 15:58:32 2009 +0000 Rewrote getScoreFilterClause to use hui.c::dyAddFilterAsInt() so that all score filtering uses the same rules commit ca1e1888650ca951bbcc58c8690d2c53b208db76 Author: tdreszer Date: Thu Apr 30 15:55:29 2009 +0000 Rewrote score filtering UI and extraWhere to ensure they all play by the same rules. commit ea74270b1228e8dcc4a318027bbe4c709a50e5d8 Author: tdreszer Date: Thu Apr 30 15:48:49 2009 +0000 Just changed function comments commit 8c367ff551ca1d4481182caf95776a68aa6df0b8 Author: galt Date: Thu Apr 30 15:00:15 2009 +0000 "Encode release log update" commit 093945480adcff4985c14ab21c0374256363fa0f Author: galt Date: Thu Apr 30 15:00:07 2009 +0000 "Release log update" commit 7f6c127f181ce1cd560662ddba6ff2f451f11934 Author: mikep Date: Thu Apr 30 08:33:00 2009 +0000 added gaps to legend commit 90a2c1c62bc83c09bb4b9f692ebb2d776433838e Author: mikep Date: Thu Apr 30 06:26:34 2009 +0000 add legend and invert printNOdes optoin commit 8ad3e0162e11770a10afc0bd57f3470a4b6b4611 Author: kate Date: Thu Apr 30 05:30:01 2009 +0000 Fix group assignment for some RNA-seq tracks commit fd40d4574b0c018a1cd33e17508604d166ea0179 Author: kate Date: Thu Apr 30 05:22:30 2009 +0000 Edit GIS RNA-seq labels for consistency and length commit b982d7cfbb8a9353e7c44d8d4d6378dbe1edeb99 Author: kate Date: Thu Apr 30 04:53:56 2009 +0000 Fix labels and colors in Helicos commit 61e44ff60555215f91ab38015e2a6d3cc819c343 Author: tdreszer Date: Thu Apr 30 04:53:15 2009 +0000 Removed some cut and paste errors commit 8c4b6aa9dec000c4259ae8a78397fd69736bd242 Author: kate Date: Thu Apr 30 04:13:23 2009 +0000 Prune Caltech track short labels to size commit 7a08c500e68125e387ed48bc8dd403ce0eb0916a Author: kate Date: Thu Apr 30 03:55:21 2009 +0000 Affy short labels for consistency commit 11d62b7825560f3274ee44f426f2ba1001048cf0 Author: mikep Date: Thu Apr 30 03:32:34 2009 +0000 updated message commit 7308c3bb6665fc7224bd207aecc95c284f28ecf4 Author: mikep Date: Thu Apr 30 03:31:58 2009 +0000 also copy .as files commit 8e23f3eb685aff68385247cc4962cf9629acaed8 Author: mikep Date: Wed Apr 29 23:24:09 2009 +0000 add tagAligns as bigbed becuase they are too big to load to mysql commit 3cf450825e6911f7a9f2bcf099c2e4b8e1fde65d Author: mikep Date: Wed Apr 29 23:22:18 2009 +0000 tagalign files exceed the 4gb mysql data limit commit 755f88e51b357df7d52813a72d9fd78037ca3fac Author: mikep Date: Wed Apr 29 23:21:57 2009 +0000 do make alpha in the encode dirs commit 321045e27816bed0e52feae93c67ffdfc0214db2 Author: tdreszer Date: Wed Apr 29 22:58:55 2009 +0000 No validator for fragLength commit 04f5e9d3e8d5cce0c647f5dd9e21506ea522f467 Author: katrina Date: Wed Apr 29 22:53:27 2009 +0000 fixed redirected link commit f9dbced3cb1d924d31ff29596294f3cd5316f928 Author: markd Date: Wed Apr 29 22:27:07 2009 +0000 fixed bug where wrong profile was used for hgcentral commit 7bfe1a6126549d2e11d33cdf9f6775f6f8c9cf19 Author: tdreszer Date: Wed Apr 29 22:03:10 2009 +0000 Added 8 cell lines for Stam lab commit db87cad3a225ff68d778a38fdcabdceaddafea4c Author: ann Date: Wed Apr 29 21:40:02 2009 +0000 removed ability to filter by score for Alt Events track configuration page (all scores are 1000) commit 8933a5abb22c850249c844d545782a23258f346a Author: mikep Date: Wed Apr 29 19:38:27 2009 +0000 accessor for content_length request header commit 1cc6b58653c29da9a3dd92e8252c808fba3822e8 Author: angie Date: Wed Apr 29 18:47:45 2009 +0000 Fixed another couple off-by-one problems with insertion lines on the right end of thick portion (thanks Brooke!). commit 7c56e09f4fcff7ab76fef25bc68f566b61ee2878 Author: rhead Date: Wed Apr 29 18:22:08 2009 +0000 Turned the link to GEO into an actual link. commit f6963a916f772d4a057c857e2c188775586cbfc6 Author: mikep Date: Wed Apr 29 18:18:44 2009 +0000 more cgi accessors for standard ENV vars commit 7c8fbaa64042b6f2e6c9c17a41bc6b345ea9f304 Author: fanhsu Date: Wed Apr 29 18:14:28 2009 +0000 Added methods for H1N1 (swine flu) sequences. commit 350f798bcf1b113188cb8427de8a25310108aa31 Author: mikep Date: Wed Apr 29 17:59:34 2009 +0000 splitting bigBedFileCreate() logic to load bed records from a file separately from calculating summary and writing files commit 8b3ee4b04c1b9cafa53473b48453e4c2f6b73897 Author: mikep Date: Wed Apr 29 17:50:36 2009 +0000 sorted option is now automatic in the bigBedFileCreate commit 95f7706109061714c568eff3dfe3385c36cf7782 Author: ann Date: Wed Apr 29 17:23:56 2009 +0000 a few tweaks based on Bob's code review feedback (thanks Bob) commit c5d6fd1570c1818ac91cc760eaf597b42741464f Author: fanhsu Date: Wed Apr 29 17:09:49 2009 +0000 Added h1n1_0429Seq track using latest data today (4/29/09). commit 11b9dd76543d6d2ead56b97d046b5b5122285d6f Author: angie Date: Wed Apr 29 16:56:36 2009 +0000 Also need a ctgPosNoVersion search (can't expect everyone to always include the .1). commit 844f3cbd77f184b08eb0f33ad05ee0c05f0952b4 Author: angie Date: Wed Apr 29 16:50:34 2009 +0000 Added ctgPos search with termRegex for new contig names. commit 06441a994fbc7590ee4614338b4f46f6dc9b4cf6 Author: tdreszer Date: Wed Apr 29 16:27:33 2009 +0000 NO_VALUE was moved to cheapcgi.h commit 44d530c76bf3f186baf3f2be44d27030ebc8b3fd Author: galt Date: Wed Apr 29 15:00:06 2009 +0000 "Encode release log update" commit cfe066c76a5c101bb92c9d8267e1e9aa0e92a5a6 Author: galt Date: Wed Apr 29 15:00:03 2009 +0000 "Release log update" commit bdcc43fa1dae3b4eb8c36d39c9b5feea4bb043cf Author: markd Date: Tue Apr 28 23:40:24 2009 +0000 fixed bug where exons within 3 bases of the start of a chromosome are rendered in solid yellow. No idea why this code was this way commit 23d19e84708fd99e01963e8c45296ffc6db37571 Author: tdreszer Date: Tue Apr 28 23:02:15 2009 +0000 Added a few simple defines commit 218eb70956c534189ea132fdf9db963d54b156a6 Author: tdreszer Date: Tue Apr 28 23:00:20 2009 +0000 Unintentionally left some exclamations in validateInt messages commit ea641ee74733fdf1b58d14fbd3bf988e8b0f5763 Author: tdreszer Date: Tue Apr 28 22:58:40 2009 +0000 Added support for a numerical limit having NO_VALUE in the cgiMakeIntWithLimits() and cgiMakeDoubleWithLimits() functions commit 9380d5a6fb62b1c090d692189d4b75d3ffd338b9 Author: genbank Date: Tue Apr 28 22:45:33 2009 +0000 can't use --times commit ef4a7f62242ba51b6132ee1ce6a383c97af0f2a1 Author: fanhsu Date: Tue Apr 28 22:33:38 2009 +0000 updated trackDb.ra commit ba067fb521e250cf14e7e9d363e211c3b77a9d96 Author: fanhsu Date: Tue Apr 28 22:28:08 2009 +0000 Updated trackDb.ra commit 2087e7648f5682cf3a54b84f43cb59bab57d63f4 Author: aamp Date: Tue Apr 28 21:59:19 2009 +0000 Updated description. citation still to come. commit 09359553b9009fa567c7de6a413509f884aac896 Author: kuhn Date: Tue Apr 28 19:50:46 2009 +0000 re-enabled sql version checking commit 3b1216f7d2d1b9ee34781c674f4ae2037aa7cf65 Author: genbank Date: Tue Apr 28 18:28:07 2009 +0000 added locking and time preserve download rsync commit aa999a7bcb15d875beb2f9821253325193a3b4e0 Author: katrina Date: Tue Apr 28 18:00:15 2009 +0000 shortened the shortLabel to fit within the 16 char maximum commit b5dfe96f55adf47181ff4641de9e31bc1cf9b061 Author: ann Date: Tue Apr 28 17:18:00 2009 +0000 changed lower range of score to match reality commit 6e296f6f19853bce43d1421b52b14b5ff7ad0d05 Author: ann Date: Tue Apr 28 17:03:46 2009 +0000 lowered scoreFilter default to catch min values from table in transRegCode track commit 355cb096efb4128668524e56a59b04d55290a7fa Author: fanhsu Date: Tue Apr 28 16:30:25 2009 +0000 Updated idSql for links to Jackson Lab, Gepsis, and Gene Card to bypass non-coding genes. commit bbeb5fb4d5b69392e75a31fa76e87641606bbc0c Author: fanhsu Date: Tue Apr 28 16:29:12 2009 +0000 Updated idSql for links to Stanford Source to bypass non-coding genes. commit b7e599363d80f49c84663e04ffac32c125bb01f9 Author: galt Date: Tue Apr 28 15:00:15 2009 +0000 "Encode release log update" commit 41540e24d1d2bc901fd9a243ade04727e42cf533 Author: galt Date: Tue Apr 28 15:00:13 2009 +0000 "Release log update" commit 0bfa62aaaba3cfdce27023a322b8d5e4e6fb31ec Author: mikep Date: Tue Apr 28 14:28:09 2009 +0000 "New version number v205" commit de0ec3ab29c4a036260f2ca5fa4ceb59d22ff063 Author: mikep Date: Tue Apr 28 14:27:53 2009 +0000 v205 final build commit 7234c155e4e6cc2ba8196e385ec53c9b1bd04b54 Author: sbenz Date: Tue Apr 28 00:35:42 2009 +0000 Added unc miRNA OV data commit 55e9774ab2cb5d6720a1cc20138e5c1025e3b5ec Author: larrym Date: Tue Apr 28 00:09:59 2009 +0000 some HAMethylSeq colors commit d3fcba033da3f82ac7cb21da2f4c91cfd0553798 Author: rhead Date: Mon Apr 27 23:55:56 2009 +0000 Shortened hg19 release name. commit d04938fe680aefb2ea5fbec383701fab220425f1 Author: larrym Date: Mon Apr 27 23:49:51 2009 +0000 aampp => aamp commit 2d1a187c6223d2c8286b21171701b142af2db087 Author: angie Date: Mon Apr 27 23:32:56 2009 +0000 Updated MGI tracks (QTLs, transcripts, phenotype and allele). commit aa19ca569ee22540eb6a92d7ea7f0483fa19d6ee Author: donnak Date: Mon Apr 27 23:26:25 2009 +0000 Edited human item, archived an item. commit a082ab8c729d69f209c6f0d04c07cac0d54f80ea Author: donnak Date: Mon Apr 27 23:26:02 2009 +0000 Archived an item. commit 8015a1cb05e844f9132251f8dd2276392a71ff74 Author: larrym Date: Mon Apr 27 23:02:44 2009 +0000 add some colors commit a576b755641d783ff58a944ff3f2cccc5d0e9828 Author: ann Date: Mon Apr 27 22:41:18 2009 +0000 added info about metadata and schema links commit 2be5c00d86d9b17c694f8a78806fc45fdbd676a5 Author: ann Date: Mon Apr 27 22:09:31 2009 +0000 changed shortLabel for mRNA track (because it was too long before), and added new block for est (from top level) and changed shortLabel commit 56bae4fc93b7b2589ece8a9196659321480d27fe Author: rhead Date: Mon Apr 27 22:00:57 2009 +0000 Added hg19 release announcement to front page and moved ENCODE DCC announcement to archives. commit 2f172fc3a0e2f31bbf78bfb1fc524e661dcd2dcd Author: rhead Date: Mon Apr 27 21:49:36 2009 +0000 Added an explanation of the chromosome names, plus an example search with the new chrUn_contigName chrom name. commit 506b74b1cda6c1cc2fb943b4d88a3b62d1e9a06b Author: pauline Date: Mon Apr 27 21:35:56 2009 +0000 Slight tweaking of wording. commit c560774a13e6cfa356a5b2beb7a6de93a591df00 Author: markd Date: Mon Apr 27 21:34:20 2009 +0000 fixed typo in description commit d6513f0a518ab4ac602aa844cd0aaab79dee6590 Author: pauline Date: Mon Apr 27 21:27:58 2009 +0000 Slight tweaking of punctuation. commit ccebd9817749d3170a8bccbb8e401d6b2ee5b5e9 Author: ann Date: Mon Apr 27 21:15:21 2009 +0000 changed priority of Alt Events track to keep it with other KG tracks commit 171432d3f4634baf0de6613417971ed2e1cf94fd Author: larrym Date: Mon Apr 27 20:25:52 2009 +0000 add colors commit 9f6eba7ca5069a60278d8cd97b3884e77b408588 Author: hiram Date: Mon Apr 27 20:11:50 2009 +0000 done with swap of chain/net to panTro2 commit 2a8add957d8b796461649b7809c57cc6b77360b8 Author: hiram Date: Mon Apr 27 20:11:36 2009 +0000 liftOver to hg19 done commit c80f6a1fb20bca98daaf22a8a21b932390a22de4 Author: hiram Date: Mon Apr 27 20:10:57 2009 +0000 hg19 chain/net swap done commit 3a733ef4f209120d1c3024ba9796101296102d14 Author: rhead Date: Mon Apr 27 20:07:58 2009 +0000 one word edit. commit 6f6a5556dd02e449fd140d4e5eb0198847b019d0 Author: tdreszer Date: Mon Apr 27 19:48:15 2009 +0000 Update Elnitski BiP track and added new UW DNase tracks with Andy commit 026e16a1cdd5ae6e53445f6f68c2c3c3e2c49fdf Author: angie Date: Mon Apr 27 19:31:47 2009 +0000 Corrected hgdpFst and hgdpIhs view limits (thx Pauline). commit 58ce898896b67e74c088e91437827540f50ac02d Author: hiram Date: Mon Apr 27 18:30:08 2009 +0000 Turn off score filter for Eran Segal Regulatory Module esRegGeneToMotif on yeast browsers commit ae3220fd2a6fa6d475358503f1e8513a23071211 Author: hiram Date: Mon Apr 27 18:16:58 2009 +0000 Adding hg19 chain and net to panTro2 commit 136642ade7f32a16dd5e4220c82b6fba253c0e80 Author: hiram Date: Mon Apr 27 18:16:32 2009 +0000 For chains and nets of Hg19 on other organisms commit d2416c7564bfecd66d04e8330d0d17c2041fd699 Author: katrina Date: Mon Apr 27 17:22:08 2009 +0000 Edited link to Eran Segal's website commit bf2dbc2681fa99b1e142aaa58b3df09667e17725 Author: kuhn Date: Mon Apr 27 17:22:00 2009 +0000 typo commit 345209016fac0799dc78d7991eaf132ee6719ff9 Author: ann Date: Mon Apr 27 16:43:59 2009 +0000 if the file is of type wiggle, then call checkWigFiles script commit ac39373ae09cf5c2ebde422787a5fc97c5cfa15d Author: galt Date: Mon Apr 27 15:00:04 2009 +0000 "Encode release log update" commit 2d39a84a39748dc23ee8c4bf6fedbac869fa5332 Author: galt Date: Mon Apr 27 15:00:02 2009 +0000 "Release log update" commit 58cfd3cb0493580f20be3c4a5dffe61447a4dc94 Author: fanhsu Date: Mon Apr 27 03:07:34 2009 +0000 Created trackDb.ra for h1n1. commit 8386b97d829181ca3c62df10a130ccdc95edb4b3 Author: fanhsu Date: Mon Apr 27 03:06:09 2009 +0000 Created h1n1.txt. commit 41a97005ad678727fb2a1f7a668cf7de0492b285 Author: fanhsu Date: Sun Apr 26 19:43:25 2009 +0000 Added h1n1. commit 796f0af706de0876d1d3b9fbc3e9ff099a1b9f0b Author: sbenz Date: Sun Apr 26 16:01:42 2009 +0000 Added TCGA OV gene exon data commit 4d264077d18d96fa541ed5060496406315962d9a Author: sbenz Date: Sun Apr 26 15:52:35 2009 +0000 Added TCGA OV gene exon data commit fe7c82a4fc430acc6e6f052af9ec77ed78d03557 Author: galt Date: Sun Apr 26 15:00:13 2009 +0000 "Encode release log update" commit 9562366b38c2a47efade60cd54245092d6044f43 Author: galt Date: Sun Apr 26 15:00:10 2009 +0000 "Release log update" commit f2208ed00d5bb3ac0de604dad5f1e0f518888a21 Author: mikep Date: Sun Apr 26 07:59:02 2009 +0000 added node names commit b30d31884c463c92fce1f5074ccafde1c8c7fbdc Author: mikep Date: Sun Apr 26 07:58:43 2009 +0000 output structure-coded version of sequence commit 6ec7c53b4c6cb71ca96612910b719498bae53782 Author: genbank Date: Sun Apr 26 07:42:01 2009 +0000 global set of HGDB_CONF for hgsqlbeta commit 3343a4365263bce02ed2ca36a808f2608bc8b119 Author: genbank Date: Sun Apr 26 07:39:42 2009 +0000 handle hgsqlbeta commit 21cac8f82f8e332dcdf85b793a77a09eb91f024d Author: galt Date: Sat Apr 25 15:00:05 2009 +0000 "Encode release log update" commit ba7c1170c04fa461edcf8eb4d7f3d2beb185f1cc Author: galt Date: Sat Apr 25 15:00:03 2009 +0000 "Release log update" commit 52289942bfc0c61fba5f94bd12c8560392cfa9fe Author: sbenz Date: Sat Apr 25 02:13:08 2009 +0000 Added baylor OV mutation data commit 4397adc69b39842f1da8aa2dcc15c8f60a955503 Author: rhead Date: Sat Apr 25 01:46:57 2009 +0000 Format bit about the PARs. commit b5b405e526b2ff02f099aea1e8eeef5dd0bd7290 Author: rhead Date: Sat Apr 25 01:40:29 2009 +0000 Changed PARs to match gold.fragStart and gold.fragEnd fields. commit 9b755f26f699a2788dc055c155f56d7517d3bcc4 Author: markd Date: Sat Apr 25 00:45:14 2009 +0000 positionalTblCheck wasn't being and had code rot commit 1f250191502ec9b3a020f788bc8ab8e34d13eb62 Author: hiram Date: Fri Apr 24 23:42:48 2009 +0000 running swap to panTro2 and make gc5Base download file commit 5b60614502cca1a6eef97eab30d1ffb115f4bac0 Author: rhead Date: Fri Apr 24 23:34:02 2009 +0000 added hg19 commit 7db70f9f0d28d8f1cb3462ccd685d68e89ac9684 Author: rhead Date: Fri Apr 24 23:25:00 2009 +0000 Commented out more missing pieces + minor edits. commit 00d953eddb955eb85d0a7df01bb5b9997d4e456d Author: donnak Date: Fri Apr 24 23:22:32 2009 +0000 Revamped the human credits a bit. commit b183ade7551dd7e01606b12996b19916e4f536da Author: rhead Date: Fri Apr 24 23:11:24 2009 +0000 Reset default position. commit fde4a1fbbce8583ea09e038a36398c7a1cd00bcc Author: kuhn Date: Fri Apr 24 23:06:44 2009 +0000 moved explanation of yeast transReg scoring to Display Conventions section on details page commit bdd87230ee9412e84a4be986344af552fac7126c Author: markd Date: Fri Apr 24 22:52:48 2009 +0000 fix bug with lastDir2, made code more robust commit 4c1d082cf2f76d124d2cd774eb78e48ec7af2ec6 Author: ann Date: Fri Apr 24 22:47:13 2009 +0000 added two new scripts for comparing tables with their associated download files commit c676e32a9ad0fcf38021ec502a352b51fc2da104 Author: ann Date: Fri Apr 24 22:44:57 2009 +0000 This script checks download files against their corresponding table. It accepts a table name that has a file associated with it. It makes sure that the file corresponds correctly with its table by comparing total count as well as size (sum(chromEnd-chromStart)). commit 847f0e869a54ca94b4d9e1c702d7a64059e0f9b1 Author: larrym Date: Fri Apr 24 22:14:48 2009 +0000 fix mysql 'Commands out of sync' problem commit 9eed9b1f0e4407a6150fd2c9937c3123129f8cd7 Author: fanhsu Date: Fri Apr 24 21:20:28 2009 +0000 Updated the processing step to build KEGG pathway tables for UCSC Genes. commit 91cf910f8faaf3d5d061ef76e0f3a0eb73537ddf Author: kuhn Date: Fri Apr 24 19:43:35 2009 +0000 turned on chimp chain by default commit 9344bb1111cc51421a3f9e3a227168989d5d6574 Author: tdreszer Date: Fri Apr 24 19:13:41 2009 +0000 Fix for min score being the same as trackDb default score, and eliminate drag and drop hint when cursor is over longLabel commit b1fdbcaf841db2738e49c7f85ffce06a59216bb4 Author: kuhn Date: Fri Apr 24 18:59:50 2009 +0000 made refGene visible by default commit af0afe5c012637725d551b086cb56ccee0e86e53 Author: kuhn Date: Fri Apr 24 18:49:26 2009 +0000 removed some searches that don't work yet commit 73f01123c94c7e8c0c1f90981efb3ead5e63ff76 Author: rhead Date: Fri Apr 24 18:36:28 2009 +0000 Added hg19. commit 3df5c35d590894142fafdeeed59f06f69c012f1c Author: kuhn Date: Fri Apr 24 18:32:58 2009 +0000 hid venter commit 812cce8e482cb2ac11b02ce1d7fe6b8b23ede8d6 Author: tdreszer Date: Fri Apr 24 18:06:26 2009 +0000 Changed some shortLabels for ENCODE Gencode commit 93e849cd1cdf142fde2c4314a4b730fe2906b508 Author: mikep Date: Fri Apr 24 17:02:37 2009 +0000 updated with RNA extract protocols commit c2ac17094e8d6866c64765bedf372de9242af16b Author: tdreszer Date: Fri Apr 24 16:53:08 2009 +0000 Added wgEncodeGencode tables commit a654428b17016475e680dcd22a41fead1320ec0f Author: mikep Date: Fri Apr 24 16:48:40 2009 +0000 moved protocol dir commit d9835a4dc45590d58fb589c29334e3fcd9e12da9 Author: tdreszer Date: Fri Apr 24 16:47:50 2009 +0000 Explicitly mark Gencode tracks as genePred so that encodeDownloadsPage.pl does the right thing commit b1244cc484525c38b0ad834785d58818c6225bf2 Author: tdreszer Date: Fri Apr 24 16:46:08 2009 +0000 Links, contact and Data release policy added commit 039b3395b5cbc5006b037067e45958a175b09b91 Author: mikep Date: Fri Apr 24 16:25:18 2009 +0000 protocols for rna commit 371d336df3f6678018e6aa2aadeab7316c8fa4dd Author: donnak Date: Fri Apr 24 15:25:52 2009 +0000 Added Melissa's pub. commit 9897d0acfb67a08e86fea65b0c9d89c49f6c5e9d Author: galt Date: Fri Apr 24 15:00:18 2009 +0000 "Encode release log update" commit 80ecf37142f5f5ce59d871efe5028244821cca28 Author: galt Date: Fri Apr 24 15:00:15 2009 +0000 "Release log update" commit 521c000bbc40a3a10ae28c212adffa27b4e0ccf0 Author: mikep Date: Fri Apr 24 08:44:11 2009 +0000 option to hide species where sequence is msising commit beb41c2c4eb163f6d8f1c1beed94737084282e32 Author: mikep Date: Fri Apr 24 08:31:49 2009 +0000 make brief summary output, fix display commit 2508ab86ab641fc5a0b6fba2fe49c056097b0e40 Author: donnak Date: Fri Apr 24 07:21:54 2009 +0000 Added pub by Lathe et al. commit 76cffd05da8e74343efecb85ed2587619b82db96 Author: mikep Date: Fri Apr 24 05:26:33 2009 +0000 after-hours project I am working on to analyze RNA covariation commit 7c95f50a703cc853e489fe4415a68c5036585cf9 Author: jsanborn Date: Fri Apr 24 04:09:30 2009 +0000 added mskcc 1x1M array commit 600295ac334e46c2ee893c8c5a969bb05aa397ce Author: kate Date: Fri Apr 24 02:17:18 2009 +0000 add ENCODE prefix to shortlabel in pushQ entry to alert Q/A commit 4c1f705e0c8d4e088ecae56807bb84570a60a862 Author: pauline Date: Fri Apr 24 00:29:37 2009 +0000 Added uwFootprints tables to tables ignored. commit 6a2ef60b579d781c9e2e9acdb56aec43ddd22ca6 Author: rhead Date: Fri Apr 24 00:21:50 2009 +0000 Clarified the type of BED file for chromTrf.tar.gz. commit 57318de6f91273d954970c1b7a05ddb9e047d28a Author: pauline Date: Fri Apr 24 00:19:07 2009 +0000 Fixed typos and ref format. commit e8fc788ca8de971d6d9890f8ae90c9868e2fe34d Author: larrym Date: Fri Apr 24 00:05:41 2009 +0000 checkpoint commit 8fef913b9d3acd7624085e0947809f1d43310cdd Author: ann Date: Thu Apr 23 23:39:28 2009 +0000 Ensures that a table correlates with its associated wig file commit a014e431a49209d18fdfb894bfc4c2dcabbe9efb Author: rhead Date: Thu Apr 23 23:30:53 2009 +0000 Fixed urchin links to Baylor. commit 9f39a75748cd1d3decb69e6b9b530c1ebf2b0394 Author: rhead Date: Thu Apr 23 23:25:11 2009 +0000 Fixed rhesus links to Baylor. commit 4e496b7a94d7f7474a1c37edceebf9c55a272457 Author: jsanborn Date: Thu Apr 23 23:09:51 2009 +0000 fixed harvard Ovarian array commit 4f3ebcbebae9af298000db548aedc147e7674682 Author: rhead Date: Thu Apr 23 23:05:44 2009 +0000 Fixed rat links to Baylor. commit eac9a1fdf16ddc52e5ce1b06ffe0d1a3f3431de3 Author: kuhn Date: Thu Apr 23 22:50:17 2009 +0000 changed CHIP/CHIP to ChIP-chip to conform to usual commit c9285e09599a2d3b4866888d72310b8faea7b4ce Author: rhead Date: Thu Apr 23 22:46:27 2009 +0000 Got carried away with the http's. Fixed Baylor links again. commit 9d8e4676e45ec39e77feec5d111d6486e78b64a1 Author: galt Date: Thu Apr 23 22:42:28 2009 +0000 fixing cgis so that udcCache dir is set by new hg.conf setting udc.cacheDir= commit 43efc910c76f3d8273bbd5b869da2bbadaa40114 Author: kuhn Date: Thu Apr 23 22:38:16 2009 +0000 changed CHIP/CHIP to ChIP-chip to conform to usual commit d36098ddf7b0514523f0787650205d2100be0471 Author: jsanborn Date: Thu Apr 23 22:26:02 2009 +0000 updated TCGA ovarian datasets commit 02512a51f41fde2e572ff457453b169658d44be4 Author: tdreszer Date: Thu Apr 23 22:09:22 2009 +0000 Okay, when type isn't found in trackDb, then just make it the file type. commit 0be7803c7b96b2c037907515032ec139dd2841b0 Author: katrina Date: Thu Apr 23 22:04:47 2009 +0000 changed CHIP/CHIP to ChIP-chip to conform to the usual commit 469ea0061556d83476ad36165a128c1ad100624f Author: tdreszer Date: Thu Apr 23 22:04:28 2009 +0000 Added lookup of metadata in fileDb.ra (if one exists in downloads directory) commit d95a976f7fc485e25f5a33ec0937ca296187180e Author: larrym Date: Thu Apr 23 21:50:55 2009 +0000 initial commit 3e48301e0c49f6c17962c38be4f68003b285274f Author: tdreszer Date: Thu Apr 23 21:04:10 2009 +0000 Special case coding for Elnitski with her tables scattered across genomes. commit 954f3ceb5c74a1ead8d1158b9bcc5eb0dc9513c7 Author: tdreszer Date: Thu Apr 23 20:52:37 2009 +0000 Added metadata to wgEncodeNhgriBip track commit 9dda127b89cd40a7467a5d50cd30df773e8d4f0f Author: larrym Date: Thu Apr 23 20:47:42 2009 +0000 add BINDIR so we can add this to userApps commit d4ea6ee827d03e9d9bf9430dcfa317456ab2e8da Author: larrym Date: Thu Apr 23 20:46:01 2009 +0000 add DESTDIR so we can add this to userApps commit 74a39f031cceb1d30e8f448b127af5cf8ce79192 Author: rhead Date: Thu Apr 23 20:44:00 2009 +0000 Fixed fly links to Baylor. commit 825745501949bc40a088ed0910c7eb972d1a5fd1 Author: rhead Date: Thu Apr 23 20:25:41 2009 +0000 Fixed cow links to Baylor. commit c8d9b680e731e30beff9234b709579c74a4577b7 Author: tdreszer Date: Thu Apr 23 20:09:41 2009 +0000 Fixed some metadata settings commit 0dc37b9dc5a84b3623dfa8534c56a6a36cda731e Author: kate Date: Thu Apr 23 20:05:59 2009 +0000 Pull out raw signal from Riken (for now) commit 85ff600cbc3090f5aa5623aea45becdde8be8d8e Author: kate Date: Thu Apr 23 20:04:42 2009 +0000 Edit for clarity commit 159e6c40802c6bf0bc9c0604c6fd18b943a84496 Author: kate Date: Thu Apr 23 19:52:17 2009 +0000 Consistency commit f7ae83713a4c1141a3c85dd56be3423777300a85 Author: larrym Date: Thu Apr 23 19:51:20 2009 +0000 fix typo commit ff89f791e1b1fcaa49f973b517e0ab746cd530e2 Author: larrym Date: Thu Apr 23 19:48:50 2009 +0000 use hgsql --host option instead of doing a ssh commit 5e7ad5fd1833e3193f40f1b6677e40a962a0d414 Author: rhead Date: Thu Apr 23 19:10:10 2009 +0000 Fixed honeybee links to Baylor. commit d57c6e0f29bc69b259f99d67edbcbe6ce74848cf Author: rhead Date: Thu Apr 23 18:49:58 2009 +0000 Fixed link to Baylor conditions for use. commit a03ceeb8686fb3e228e0e087bc7696e823306efe Author: tdreszer Date: Thu Apr 23 17:08:51 2009 +0000 dateSubmitted was not getting picked up as it should have been commit 640606f9f0e4cfb39b62f94a0ebe4ba0bf82c24c Author: kuhn Date: Thu Apr 23 16:22:19 2009 +0000 moved explanation of yeast transReg scoring to Display Conventions section on details page commit c94c50b95372ed6ca17a83acb3a48222495086e8 Author: galt Date: Thu Apr 23 15:00:10 2009 +0000 "Encode release log update" commit f430c31a3754a42c4cebca6c4003c0734e57ff42 Author: galt Date: Thu Apr 23 15:00:07 2009 +0000 "Release log update" commit 3236c5e8fb0f7f2f6d54504653bdb17b4caffa11 Author: kate Date: Thu Apr 23 14:55:16 2009 +0000 Label tweak for PhyloP track, by request of Adam commit cbd1bea3a96680ca059c05c6e2281bc83a634900 Author: kate Date: Thu Apr 23 04:27:14 2009 +0000 Fix label for Riken commit 248f37eb1929d314835653c501d235093425a176 Author: kate Date: Thu Apr 23 04:20:19 2009 +0000 Tweak defaults on Riken CAGE commit 1085d9fea4aec96ee4d219b6a8c41bd0bffa4e40 Author: kate Date: Thu Apr 23 03:39:35 2009 +0000 short labels and subtrack ordering adjustments to Riken CAGE commit f070ecd7dc524b4df6e4e921d47deb4b0a8a9461 Author: markd Date: Thu Apr 23 00:35:41 2009 +0000 fixed bogus errors reported for NR refseqs commit 356b22de35be088910de532a089c9895ca6b5410 Author: larrym Date: Thu Apr 23 00:31:12 2009 +0000 modify code to support the normal two column chromSize file format commit fe35aaeac1aea76ada8d6183e7089da8bbc8e376 Author: tdreszer Date: Wed Apr 22 23:57:17 2009 +0000 Support for metadata setting from trackDb commit a714ddb8201c07d77b3612017dae80050907fc15 Author: kate Date: Wed Apr 22 23:51:24 2009 +0000 Change UW labels by request of John Stam commit daec7bae295f614be3e50d8586db301baba44202 Author: kate Date: Wed Apr 22 23:47:26 2009 +0000 Restore mistakenly commented out UW Dnase K562 signal tracks commit 3356eeaf93965f7ad60cf14e84327b4b3ea8e05e Author: markd Date: Wed Apr 22 23:46:25 2009 +0000 *** empty log message *** commit a59ff80724e6ff5345c854ce7446dc6e33b276b2 Author: tdreszer Date: Wed Apr 22 23:21:50 2009 +0000 Support for showing metadata in hgTrackUi commit b40ac380b7585ba7dbb284f85dc8145a6da168a3 Author: kuhn Date: Wed Apr 22 23:11:26 2009 +0000 dropped an errant hyphen commit 9478d6d7d27901472431b8a18c5ebf1a36c420c7 Author: tdreszer Date: Wed Apr 22 22:56:22 2009 +0000 Add support for parsing out metadata settings. commit 92683351b7315a8e838692cbff4c6a79505cbdd3 Author: hiram Date: Wed Apr 22 22:47:14 2009 +0000 GeneLynx.com is no longer available commit 8429aca884f9dee4c0d3aab93d2b0345c1336ca1 Author: mikep Date: Wed Apr 22 22:44:53 2009 +0000 minor text tweak commit f9db0db7896c1dbaefe29ca3d4522942bcf1f0e1 Author: mikep Date: Wed Apr 22 22:44:02 2009 +0000 dont need to free hti because it comes from a cache commit 42ecbb2dbe482cd480833b73f32d177715dbbc06 Author: tdreszer Date: Wed Apr 22 21:02:26 2009 +0000 Kate objects to exclamation marks. commit 2b3244ae281611933de0855c18af91d93294654d Author: katrina Date: Wed Apr 22 20:50:48 2009 +0000 Made formatting edits commit ce7e3748cfe0cdc162687e3dd2e68d314bf94317 Author: tdreszer Date: Wed Apr 22 20:36:48 2009 +0000 Added some missing color to newly added Open Chromatin tracks commit 1b5311ff9b781b18caa640d5b02ed913dd63aff6 Author: kate Date: Wed Apr 22 20:26:15 2009 +0000 Coloring and labels work for Riken CAGE commit 3ed2cbab5212f2ed78507890b98db4a60154d4c5 Author: hiram Date: Wed Apr 22 18:42:29 2009 +0000 Fixup chainSelf business commit 27840723c1c47acd0d0059ba9c87ac9cb41f03b3 Author: kuhn Date: Wed Apr 22 18:41:57 2009 +0000 consistency tweak commit 3fcc3e9acc2cd276d8c84b0a6aa1e6667a2027c8 Author: katrina Date: Wed Apr 22 18:28:12 2009 +0000 Made formatting edits commit 33a5e75eaf4763f3a4ade0ecef8c4201d06c96e2 Author: markd Date: Wed Apr 22 16:56:49 2009 +0000 added initial implementation of gff3 parser. Still has some rough edges and problems due to ambiguities in the GFF3 specification commit 7ead37b2fc2c9d6797a0396d1d9461a4e8fce8ab Author: galt Date: Wed Apr 22 15:00:09 2009 +0000 "Encode release log update" commit fd2b6457db07816258d9d27e34b1782a70c88e29 Author: galt Date: Wed Apr 22 15:00:06 2009 +0000 "Release log update" commit 96713be72aa74eea837680d23744aec2a7017e63 Author: mikep Date: Wed Apr 22 14:52:14 2009 +0000 long rna not small commit c3c4a35c7790e40e35b865d6699564a7250a5a51 Author: rhead Date: Wed Apr 22 03:30:47 2009 +0000 Changed hard-coded tracknames to real ones from trackDb, added checks for mgcFullMrna and orfeomeMrna, changed echoes so that they reflect same command as is run, general cleanup. commit 162d84f735a806ffb119477b4b9d207549a461b7 Author: galt Date: Wed Apr 22 01:57:00 2009 +0000 fix tiny buffer overflow bug discovered by user with ubuntu 8.10 and FORTIFY -- use strncpy instead of strcpy commit bf0fa2202ed0b890cd0de1d2aac59e3c24d7f676 Author: rhead Date: Wed Apr 22 01:00:30 2009 +0000 Changed back to sourcing the qaConfig file using which, after specifying PATH in the crontab that was having problems running this script. commit b2e4a656ec5597bdc80545a11d85c8017b3de2e7 Author: larrym Date: Tue Apr 21 23:02:25 2009 +0000 support -chromSize option commit ccbfb0f8267b2a8a8bccd5d3598468ddd66dc952 Author: tdreszer Date: Tue Apr 21 22:23:34 2009 +0000 Added UNC HepG2/FAIRE commit e7d05e8559fa81aad502496b1fb55ae9d6f33c54 Author: ann Date: Tue Apr 21 21:18:07 2009 +0000 there is no netSelf table for hg19 - and Hiram does not intend to create one. commit 64ccee6c0a0372ba6ae3ef33c6489a5946405e07 Author: ann Date: Tue Apr 21 21:05:12 2009 +0000 there is no netSelf table for hg19 commit 8f168e186d41bc1342ce398739a18f1a5e5d5206 Author: mikep Date: Tue Apr 21 20:55:11 2009 +0000 notes on manual build of helicos data commit bad0f835bc994fa41ac3f14740c5559434a383fb Author: kuhn Date: Tue Apr 21 20:37:00 2009 +0000 changed usage statement commit 41f93d69580b252f7a4f2f4e0a56fa229b572c40 Author: hiram Date: Tue Apr 21 19:53:57 2009 +0000 Fixup rules for hg19 non-split tables and ignore gold commit 37b6a53955f90a9b334c77ccc7a3009001ce3f75 Author: rhead Date: Tue Apr 21 19:00:46 2009 +0000 Changed default position. commit be322a6acf6942b58ff7aecdf2438b4b55e5374d Author: kate Date: Tue Apr 21 18:08:29 2009 +0000 Add track description for Adam Siepel's lineage=specific phyloP commit b0fe5f91755e27ab75199e72a28021ffe1cba13e Author: kate Date: Tue Apr 21 18:07:51 2009 +0000 1. Update phyloP LS track settings based on input from Adam 2. Add GERP cons for Javier at EBI (ENCODE-related) commit 3de3e3a44c4e4c9f3a3ee8c6a0defbd35aa62411 Author: tdreszer Date: Tue Apr 21 16:31:02 2009 +0000 Andy is taking over Stam and Weng labs. commit 2f6e83e28b0164a5f4822a37e9a6792050aa7901 Author: mikep Date: Tue Apr 21 16:23:17 2009 +0000 strand is not sure in helicos data commit ff949b841e1f5b6631f481ffd33230595556fd91 Author: kate Date: Tue Apr 21 16:09:58 2009 +0000 *** empty log message *** commit 5314268ff764053bffbc27bce1eca009b95648d6 Author: mikep Date: Tue Apr 21 15:13:08 2009 +0000 move cvs stuff, dont copy it commit 3bcee4f533552a3797b650d004ab7a8f5c1b67a7 Author: galt Date: Tue Apr 21 15:00:06 2009 +0000 "Encode release log update" commit 64de8c13249808bef020d552fdbb9e18619ece8b Author: galt Date: Tue Apr 21 15:00:03 2009 +0000 "Release log update" commit fb99129f2c84cbce4917d205e54b597803625875 Author: mikep Date: Tue Apr 21 14:40:01 2009 +0000 v205 preview commit ac570bd1e25de266601f066f5e7701e3a4a88363 Author: mikep Date: Tue Apr 21 14:38:29 2009 +0000 no js on hgwdownload commit a17516bd49d1fa795ee61568e97f7082a38ca8fc Author: markd Date: Tue Apr 21 04:24:31 2009 +0000 fixed change on type of accession in refLink commit 8f5a43b0e99f77d11d0c230a7b30df5ad122a318 Author: markd Date: Tue Apr 21 00:14:50 2009 +0000 fix bug where mgc/orfeone psl tables were not updated when clones were deleted from MGC commit f5d28576bef3eecdf1efa962f785109e455f9085 Author: mikep Date: Mon Apr 20 23:21:04 2009 +0000 removed timing messages. added 'sorted' option to speed up creation of gigabyte sized beds. commit 2c30f824c6084d5c01b5720a1323fe7fe9eaa680 Author: mikep Date: Mon Apr 20 23:17:26 2009 +0000 added sort option, also made changes to bigBed.h + bigBed.c commit 4203ffec569c6c143e3be54c8748607806c99431 Author: mikep Date: Mon Apr 20 23:16:18 2009 +0000 *** empty log message *** commit 881f8a480af61814d5473c22efba2789b1ea80a7 Author: katrina Date: Mon Apr 20 22:17:41 2009 +0000 Mailing lists and archives chagned locations. This fixes the links. commit da6b9b33622c4ca3a070d125e375cc60e8814d0f Author: katrina Date: Mon Apr 20 21:22:37 2009 +0000 Made formatting changes to list of publications and removed references to Epub where no longer applicable commit d981cedbc85db0980da0567a083a31be29ef6cad Author: angie Date: Mon Apr 20 19:32:02 2009 +0000 Removing some 5-year-old code that became buggy when we started resolving position to chr:start-end before drawing tracks. A user managed to trigger this by using chr:start-end item names, and viewing the item positions, wrongly turning blue items red. commit 10f9cc03b4fc1eab6dabc9fd48efc4e6ba8f896d Author: tdreszer Date: Mon Apr 20 19:03:49 2009 +0000 Updated to of UNC FAIRE peak tracks commit fe2a1d4fe65c9814e639c2f7ccdef4e6be7d394b Author: rhead Date: Mon Apr 20 18:54:54 2009 +0000 Added xenoEst to featureBits and pslCheck lists, removed unused trackList variable, reordered checks so they match priority in hgTracks. commit d32518129bc401228f3da82ad1fbdf75f9302369 Author: mikep Date: Mon Apr 20 18:45:20 2009 +0000 wiggle data for +/- strands commit 4e7b932f98b93eba5e0d01a11a647261c9093703 Author: tdreszer Date: Mon Apr 20 17:33:16 2009 +0000 If dateSubmitted is ddf ctime, then dateRestricted should use the same. commit 78293e71c7c7d2f8b923c0a0c285a54723403607 Author: mikep Date: Mon Apr 20 16:28:53 2009 +0000 fixups commit e8e9edb007be2bef9a59cce2523385de81dc72fe Author: mikep Date: Mon Apr 20 16:17:32 2009 +0000 fixups commit dd51bca3e4ca77e277cb337eea6184805308fb56 Author: mikep Date: Mon Apr 20 16:15:25 2009 +0000 Helicos description commit 30ef256ab269bc426c718f0b8a7e234836eda569 Author: galt Date: Mon Apr 20 15:00:04 2009 +0000 "Encode release log update" commit 6f55b9db7b9c2346a3df815ebb5f0cdff27aed40 Author: galt Date: Mon Apr 20 15:00:02 2009 +0000 "Release log update" commit 9af0fddd117c3a7c0941738055f78b9b4f40d011 Author: galt Date: Sun Apr 19 15:00:03 2009 +0000 "Encode release log update" commit 9e9ffa9d77e797a1a2b2a0e40923de687ebc30e7 Author: galt Date: Sun Apr 19 15:00:01 2009 +0000 "Release log update" commit 676a191d081b27722a5ad70804cf4316ff238d78 Author: markd Date: Sun Apr 19 05:44:11 2009 +0000 fix bug with name when lastz input is a 2bit commit 0ca172d8250fc62182913b9852c31fd109df9377 Author: markd Date: Sun Apr 19 01:36:14 2009 +0000 refactored alignment code to allow use of genome partitioning in other code. removed outdated iserver code commit dfc7f43f59ee7fbb40286bf8c743f4017addcc9e Author: markd Date: Sat Apr 18 19:40:38 2009 +0000 fixed test problem due to timing of processes commit b5c2d146dd19dc7a6e730b3885ce68da0f9b40fa Author: galt Date: Sat Apr 18 15:00:05 2009 +0000 "Encode release log update" commit 7affa4a49930716a6a0df958b85c5a1001034725 Author: galt Date: Sat Apr 18 15:00:03 2009 +0000 "Release log update" commit f96d9004eb5c3331c92d9ea4860f522a095a10b5 Author: markd Date: Sat Apr 18 05:13:38 2009 +0000 added taeGut1 N-SCAN commit 4fc4ac315e3e74d174b6a4daf79122612ab66f57 Author: tdreszer Date: Sat Apr 18 00:31:55 2009 +0000 A small number of new metadata tags and a very large number of changed ones. Turns out that the metadata generation code did not calc the dataUnrestricted properly commit 53c07ecb793705225449e9b42c94d694d2d6a765 Author: kent Date: Fri Apr 17 23:23:23 2009 +0000 Improving error detection of bedToBigBed. commit 27a3d22313bea1893bb84f9b0cc914d7dc97c81f Author: kent Date: Fri Apr 17 23:22:37 2009 +0000 Adding asTypesIsInt and asTypesIsFloating commit 263d460115c461966e0d8a3b1ed5ffa434cc5be7 Author: kent Date: Fri Apr 17 23:21:56 2009 +0000 Improving error message in lineFileNeedFullNum commit 97fb2938374b6d254e3d7d887a6a36046c681eb9 Author: kent Date: Fri Apr 17 22:02:51 2009 +0000 Separating out basicBed module from bed module, so that basicBed can live in src/lib and be clear that it has no database dependence. commit 61bc4e0e4e261bc0289ec2572e362d2f52670885 Author: kent Date: Fri Apr 17 21:38:49 2009 +0000 Removing bedLoadNBin, which duplicated lots of code in bedLoadN for no good reason. commit cb55c55da447f7b75de5ed1b135e099e7301376e Author: ann Date: Fri Apr 17 21:26:39 2009 +0000 added Credits section. commit ffdafd788fe5c9b32ec7fed2cfe92ff4687f7eb8 Author: angie Date: Fri Apr 17 21:23:55 2009 +0000 One more tweak to hgdpXpehh view limits (thx Brooke!). commit c8a66a6e006e16d0bd4c2aa7a6c269082373e87f Author: ann Date: Fri Apr 17 21:18:38 2009 +0000 removing old junk. commit 33b77c2fe5f90751813ddc4201f46d0f1eee8fda Author: ann Date: Fri Apr 17 21:07:44 2009 +0000 Major edits to get rid of the MS Word stuff. And add the correct tables. And add the fully-edited Methods, etc. commit 88afd93fb679530ee7b6357f5988b4ffa813406b Author: ann Date: Fri Apr 17 20:57:26 2009 +0000 reordered tracks to mimic table on description page commit a93863c828ffa84ee5c76b8c7b130ed353abb6f3 Author: kent Date: Fri Apr 17 20:54:35 2009 +0000 Fixed Wig that should be a Bed in usage message. commit e8a8ef77855a7756e7e23a59888af4aa3e288299 Author: mikep Date: Fri Apr 17 20:17:25 2009 +0000 need to use hgconf for beta because SQL server is on different host now commit 0caee18950d202954b22169216250dfb7aed3d03 Author: angie Date: Fri Apr 17 20:01:41 2009 +0000 Adjusted hgdpXpehh view limits (thx Brooke). commit c07c7f9d9a7d4d1a9125cfcfed3cb1b16e3614bf Author: galt Date: Fri Apr 17 19:41:26 2009 +0000 removing user:pwd@ from head of afterProtocol so that the sensitive login info is not replicated into the udcCache path commit a80f2d5632c7e2338041f103d3a577d23c00c0d4 Author: kuhn Date: Fri Apr 17 19:32:42 2009 +0000 slightly edited text commit 980c31eb9abe3b4503979b221e2d068d7644f583 Author: mikep Date: Fri Apr 17 19:25:26 2009 +0000 tagAlign tables have 'sequence' column instead of 'name' column, but otherwise are BED 6 and should be interpretable like that commit ee1124e5f463067235ca0c518dba6eba3624d570 Author: tdreszer Date: Fri Apr 17 19:24:43 2009 +0000 HTC-116 was removed as this should be the already existing HCT-116 commit f3ae003c05b625819862e54ebc72753bd380a134 Author: kuhn Date: Fri Apr 17 19:22:43 2009 +0000 slightly edited text commit 78f8769d88f73afc7c8203089e0ab2d8f78f3944 Author: kate Date: Fri Apr 17 19:16:48 2009 +0000 Consistency on Affy and Riken track labeling commit e78a869acd5253b1b77059d22f3b806b60065a06 Author: kuhn Date: Fri Apr 17 18:48:20 2009 +0000 dropped comma from usage statement commit 6668e77ef4b084327f27a8dae908b32ea71592e2 Author: kuhn Date: Fri Apr 17 18:28:51 2009 +0000 clarified usage statement a little commit d7ab6645df3151ad8eb8fbefb7bb9e5930c89fef Author: kuhn Date: Fri Apr 17 16:31:59 2009 +0000 clarified usage statement commit bea56033a70cbe0b7f519dc142f0d63fc3f0835c Author: galt Date: Fri Apr 17 15:00:05 2009 +0000 "Encode release log update" commit d529f70cfdf1ecf5c42aa00fb155201500547663 Author: galt Date: Fri Apr 17 15:00:03 2009 +0000 "Release log update" commit 5b1fc31aaae344d78b377fd818a51774f0378bbe Author: galt Date: Fri Apr 17 08:09:24 2009 +0000 added SSL_library_init() which is apparently necessary with newer versions of SSL commit 7b70ca11329668af77228cacccd99a7a006cf8d4 Author: rhead Date: Fri Apr 17 02:02:20 2009 +0000 Added logic to check the database argument. commit 2d4f8e9def024d179e5791d35d362e8f7d7f2e5f Author: ann Date: Fri Apr 17 00:52:25 2009 +0000 removed junk commit 22663b69c313fa3be17bf93b5c510dac29431428 Author: aamp Date: Fri Apr 17 00:28:48 2009 +0000 Removed line about vegaPep.name needing full and unique whatevers. The vegaPep table only exists in danRer5. commit cc76eb2a3cc655e599cbef3efa9ad3ab9e1f0a1e Author: ann Date: Thu Apr 16 23:02:32 2009 +0000 edited types based on Deanna Church's input commit 15f9e33b0f56a58aa009201022d6ec40c5d06e5e Author: tdreszer Date: Thu Apr 16 22:56:55 2009 +0000 validateInt had a bad error message when alpha was entered commit 83cc0c0b935e7cb2143af66baff8988124f1f3b1 Author: fanhsu Date: Thu Apr 16 21:38:52 2009 +0000 Copied over from gsidSubj and updated for the coming wave of new data entries. commit f95523eed553751d4921c371a6aaa9ca216d0e0c Author: tdreszer Date: Thu Apr 16 20:54:19 2009 +0000 Added a lot more metadata settings for Most of Mike's tracks commit 9e7c7dd022051e8b56b3e917c6e73b64fb1c84ed Author: larrym Date: Thu Apr 16 20:38:04 2009 +0000 fix a bug I introduced in the last checkin(s/d use sqlConnect not hAllocConn commit 0308974b84c760ce33085df177de953be29bbe6a Author: kate Date: Thu Apr 16 20:17:46 2009 +0000 format cleanup -- need to make sure this is in validator commit b9f413277fbd9443aae8a12f9bce5b8f1a9e5cb5 Author: kate Date: Thu Apr 16 20:16:29 2009 +0000 Big cleanup of RNA track labels commit f645e43eea939930a295cea917ea84c7dc595261 Author: tdreszer Date: Thu Apr 16 19:03:30 2009 +0000 Support for DDF level fragLength for Alignments to RawSignal. Now creating metadata setting for trackDb and new fileDb.ra commit 8f89bda2372ad051b955fee352c1fc77adb4c1c5 Author: kate Date: Thu Apr 16 18:59:52 2009 +0000 Shrink short labels on Riken Cage track commit 1ccf51ee0691df8654a3f0bf4c938614ce574b10 Author: tdreszer Date: Thu Apr 16 18:55:42 2009 +0000 I misunderstood what Jim Wanted. 'Limit data output to' some number of rows should work with bigWig commit af64dc57b96710bb323414417edd6ec02a5ca94c Author: tdreszer Date: Thu Apr 16 18:52:17 2009 +0000 Added a lot of metadata settings for Broad, Duke/UNC/UT-A, Elnitski, HudsunAlpha, Yale commit efa129f47e1463cbc8afb113ae298bd12b9e5476 Author: angie Date: Thu Apr 16 18:34:06 2009 +0000 64 bytes is no longer big enough to accomodate _sel with the giant wgEncode table names. commit 2b4341ca2b19cdb81069205c19e0c863d8a04d0f Author: fanhsu Date: Thu Apr 16 18:23:34 2009 +0000 Moved comment field to the end. commit d06ce639d91aaeae693697d0c507c00d617832e0 Author: angie Date: Thu Apr 16 18:22:01 2009 +0000 Use new constant for 'No results' message. commit 5b271d028853df2d831d451762bf9b3cf83e3cec Author: angie Date: Thu Apr 16 18:21:44 2009 +0000 Cleaned up another hPrintf vs. fprintf unnecessary duplication and used new constant for 'No results' message. commit 6c04dfb31eb4095226448a316da892c084f5daab Author: angie Date: Thu Apr 16 18:20:40 2009 +0000 Print our usual 'No results' method instead of blank screen when no results (thx Katrina). commit e16dc80c46a6b68a6e289760b2a2d0eacfe9f2ab Author: angie Date: Thu Apr 16 18:18:36 2009 +0000 Added a constant for our 'No results' message. commit 61064d1996049a9673682fe99fcb97d14e52789a Author: fanhsu Date: Thu Apr 16 17:36:38 2009 +0000 Getting ready for the next wave of new data items. commit 1ab61d9f80a1136a6bccff0769efb480f7437d37 Author: kate Date: Thu Apr 16 17:24:06 2009 +0000 Fix syntax err commit c0f27f1666aa3c049baad32a0d6308525a91736f Author: kate Date: Thu Apr 16 16:33:30 2009 +0000 Additional coloring by cell type commit 1593d9f9bf0d006dd4f2b5e348727063f2781a9b Author: kate Date: Thu Apr 16 15:21:51 2009 +0000 Add cell colors, loosely based on GNF conventions commit 238eb83161bc139ef980d0c9186ba64ddc897e2e Author: galt Date: Thu Apr 16 15:00:08 2009 +0000 "Encode release log update" commit 24f7f6d13e9edab0eb24075a03bd0026b277dd70 Author: galt Date: Thu Apr 16 15:00:07 2009 +0000 "Release log update" commit 24fde6aa7882576a1d52f350f3a57daa2a0405fb Author: mikep Date: Thu Apr 16 09:54:28 2009 +0000 updated from Piero commit 3c0c35300d1f2a85179006edda3a69ae5f98ef58 Author: hiram Date: Thu Apr 16 04:11:35 2009 +0000 This source found in /cluster/bin/scripts appears to not be in the source tree yet and it is used by the blastz pipeline commit 7af905dee6a98d0d6b4d6f8da1bb331321ad4be6 Author: rhead Date: Thu Apr 16 03:51:13 2009 +0000 Changed machine to hgsqlbeta, the new sql server that hgwbeta is using. commit a9946e896d6e60f8f1b592ed41705c7fbe485bf3 Author: rhead Date: Wed Apr 15 22:16:45 2009 +0000 Changed hard-coded hgwbeta to target.machine so that mysql machine is found in props file. commit 33d202c2fce07ba5ac58d15adb9fb66299d3a8c8 Author: kuhn Date: Wed Apr 15 22:07:34 2009 +0000 added a 2007 current protocols chapter that donna forgot she did. commit 19f63a5140f540d500bce5557a3d5e47ab62b046 Author: rhead Date: Wed Apr 15 21:49:55 2009 +0000 Honor HGDB_CONF environment variable. commit ff0294d437080ab3e016c3859b2cf75957d0d7d2 Author: angie Date: Wed Apr 15 19:40:43 2009 +0000 Use the more efficient hDbExists in hTableOrSplitExists, and move the sqlDatabaseExists into hDbExists. commit fd40cf88d205571c6d1c1e69e1e2c127641c5ad3 Author: galt Date: Wed Apr 15 19:37:37 2009 +0000 using cmpStringsWithEmbeddedNumbers() which is a bit more general commit 5f8ad7a9acccc9955dce5de40f3c46e2bffd8719 Author: kate Date: Wed Apr 15 18:17:31 2009 +0000 Changing downloads path for easier FTP access commit ed2cb269a41b5dd3362202955a9b7566c7f6bb8d Author: kent Date: Wed Apr 15 17:40:39 2009 +0000 Adding numerically away string compares. commit 44b980985a72453071cd4fe3fdfa60d98c45ec41 Author: galt Date: Wed Apr 15 15:00:06 2009 +0000 "Encode release log update" commit 41b91af9a9dfcb264ac4aa2a2d9896a12d2c38a6 Author: galt Date: Wed Apr 15 15:00:03 2009 +0000 "Release log update" commit facb507f696a7c0e816fe01c7a7fba2076aa8f59 Author: tdreszer Date: Wed Apr 15 00:40:01 2009 +0000 Added link to hgTrackUi into the preamble text. commit a5342fcf91b902141f969643bbe9544f831ace11 Author: tdreszer Date: Wed Apr 15 00:10:53 2009 +0000 Added fileDb.ra definition commit 4ee87f727cc9cd6fefce1388ca07cd157947c9a8 Author: ann Date: Tue Apr 14 23:02:33 2009 +0000 collapsed two sections into one (they were redundant) commit 84a585428cd9538616211f80af076d498a9ca3df Author: mikep Date: Tue Apr 14 20:18:54 2009 +0000 fix up contact commit 6cdf71eeb13f9ebbc2dfb8eefea33d249fbcd6aa Author: mikep Date: Tue Apr 14 20:05:07 2009 +0000 updated message about technologies commit a89bdc89beb4e6fce1f9b70e8f88e408dda4ecf4 Author: giardine Date: Tue Apr 14 19:21:42 2009 +0000 MMR link changed commit 9edae0beb77580c585a376d9003fa069764fc3c0 Author: kuhn Date: Tue Apr 14 18:18:23 2009 +0000 added darwin's foto commit 5c0ff445fd5997210b3051f2960bf26c07b86828 Author: galt Date: Tue Apr 14 18:14:44 2009 +0000 oops cannot mix malloc and freez commit bff4748e33a50dbeb5ed16e86d392bf69f201968 Author: tdreszer Date: Tue Apr 14 18:05:55 2009 +0000 Exclude bigWig from option to limit data output to some number of rows commit eeb45be0f5c2507715c38f3530e88bcccb114320 Author: rhead Date: Tue Apr 14 17:30:27 2009 +0000 Fixed links to Baylor. commit 30d55231f03e29b5530a2de42c276020d500bcb3 Author: tdreszer Date: Tue Apr 14 17:28:31 2009 +0000 Add fragLength so to be specified by replicate commit ba6a3f002dc22a91ff073992da07a4609bf36c78 Author: galt Date: Tue Apr 14 15:00:05 2009 +0000 "Encode release log update" commit cf31da5e29ea01c8070220ccedc60738fd3e5c97 Author: galt Date: Tue Apr 14 15:00:03 2009 +0000 "Release log update" commit 8a0495762db81197d4f525b49f6eae2e6d157005 Author: mikep Date: Tue Apr 14 14:45:54 2009 +0000 "New version number v204" commit 90718acb47cf4b5fb4e3cc4e1768cc0f1ddffc9c Author: mikep Date: Tue Apr 14 14:45:24 2009 +0000 v204 final build commit f90cb49d1e24d8290028cc6b04f926c8f4c6ed1d Author: angie Date: Tue Apr 14 14:22:26 2009 +0000 In tdbFindOrCreate, call hMaybeTrackInfo instead of hTrackDbForTrack so if db is non-genome, we don't get an errAbort due to the lack of trackDb table. NULL was already an OK return value from this. commit 79861d38b08525b6a1d3d5e206ade507b9be05c3 Author: angie Date: Tue Apr 14 14:19:53 2009 +0000 Added check for NULL tdb from findTdbForTable. commit 35d7274a482a1eb5cc96de3a9a1b363bbb7bd99f Author: angie Date: Tue Apr 14 14:16:35 2009 +0000 anyIntersection() was forgetting to check whether the primary table is positional. commit cd4eee5dee1dedd6e59cfbf0378d187b1e9f2fd2 Author: kent Date: Tue Apr 14 08:43:02 2009 +0000 Adding cmpStringsWithEmbeddedNumbers. commit a0bb6e765dc721bbccb23938d24e2181ec2702b3 Author: kent Date: Tue Apr 14 08:43:01 2009 +0000 Adding cmpStringsWithEmbeddedNumbers. commit 8c9a42198cc6831cb1320a3c54341d20492a7a63 Author: galt Date: Tue Apr 14 07:20:02 2009 +0000 rearranging to get openssl to compile with gcc4, mainly by eliminating use of common.h and openssl together wherever possible commit 91d91044e8a15fa704e5ad03d5f557eebbc8722d Author: mikep Date: Tue Apr 14 04:03:29 2009 +0000 fix problem where fillInScore field might contain only -1 values which is the equivalent of a NULL in the not-null field commit ee098ac50d9cbf29b65efe1741c8196367bd7e3a Author: mikep Date: Tue Apr 14 04:00:10 2009 +0000 fixes suggested by Rachel commit 85297c994c988ac25004f65f62d9bc38f8b38dfb Author: mikep Date: Tue Apr 14 03:57:49 2009 +0000 fixes per suggestions from Rachel commit 01d763f71672d899dce3bb30d7cbbd08041206f8 Author: rhead Date: Tue Apr 14 02:00:58 2009 +0000 Changing from which to dirname to find path of qaConfig.csh file. commit 4a114231b9dc2403432a43b97f0867b5b53df990 Author: kate Date: Mon Apr 13 23:36:12 2009 +0000 Correct path for ENCODE downloads commit bff555650eb38af5bee687e1ba2f53eabb12e43d Author: genbank Date: Mon Apr 13 23:14:31 2009 +0000 use new hgsql programs instead of mysql directly commit 5cbd72478479532dd382a8e1bdac5941de97f8e9 Author: mikep Date: Mon Apr 13 22:57:14 2009 +0000 first version of Helicos commit 6121dcf754e45cefe2c531f56b2f246d6f8a9bff Author: markd Date: Mon Apr 13 22:34:11 2009 +0000 added function to determine if a mysql server appears to be remote; ignore SQL_TAB_FILE_ON_SERVER if server is remote commit 1c9de3572e562d24d150b56b1d24c8d72fdbf4c3 Author: mikep Date: Mon Apr 13 21:19:05 2009 +0000 add chromInfo to makefile commit eb9c1fe83340caf641d62c26d0f05abec195e078 Author: markd Date: Mon Apr 13 21:17:35 2009 +0000 added to-do item commit 267ec0387dd09c0489387cf7646e312f59006448 Author: mikep Date: Mon Apr 13 21:17:31 2009 +0000 need chromInfo for bigbed commit a252644df63b180e286eb9f41425de12c670d799 Author: rhead Date: Mon Apr 13 19:38:19 2009 +0000 Removed a redundant set host command that was causing the script to choke when hgwbeta was explicitly specified as an argument. commit b9939c581947994e76e78e5d26f3a246014e2fe9 Author: genbank Date: Mon Apr 13 19:10:57 2009 +0000 set env var for hgsqlbeta commit 8b3563b76d9a8db8bba954cc61f018292b273b09 Author: galt Date: Mon Apr 13 17:59:44 2009 +0000 fixing chrom name compare function, it was not handling pattern chr99_something commit e71cf8610ca7869bf341f8495d76ef9e18cb4c18 Author: kuhn Date: Mon Apr 13 16:13:28 2009 +0000 fixed bug where genomeClade comparison breaks because original tables not sorted commit 4dd25fa026de15c1e48e79c03197630135a531da Author: kate Date: Mon Apr 13 15:59:59 2009 +0000 Update test file to include Tier1 cell line commit 59d7da65b77051c5778492f4126dbdb76a131335 Author: kate Date: Mon Apr 13 15:58:37 2009 +0000 Moving ENCODE downloads down a level commit f01a43c87235f45faa4b365e76835136f813d6b7 Author: galt Date: Mon Apr 13 15:00:06 2009 +0000 "Encode release log update" commit 63ab3dd97b54130de7c185d27c417ab906b68591 Author: galt Date: Mon Apr 13 15:00:03 2009 +0000 "Release log update" commit 3dd12103fe8a3607a69542fdd60e7a9472738973 Author: markd Date: Sun Apr 12 19:00:55 2009 +0000 don't pslCheck empty file, writes warning to stderr commit cac02e4573ccbf9c325ed2e36fbaa8f4d1b80bc4 Author: markd Date: Sun Apr 12 18:45:54 2009 +0000 skip bogus blocks in PSI BLAST output commit b2b60c5141c80846a6e0047b03bbf3e28f4848a2 Author: galt Date: Sun Apr 12 15:00:04 2009 +0000 "Encode release log update" commit 6580fa3c7210ec81df5dd9652bd8e3e01ae38f1f Author: galt Date: Sun Apr 12 15:00:02 2009 +0000 "Release log update" commit f93b28c6d94af9080d5d5ea57e41d4ba3fec28b7 Author: markd Date: Sun Apr 12 05:48:42 2009 +0000 fixed bug parsing PSI BLAST output with no hits commit 5b0b5b128d887a9a0480dbc09e509cdf59c3d99a Author: markd Date: Sun Apr 12 03:47:20 2009 +0000 added support for PSI BLAST madness commit ecfde6ed97eb0930df776b7bd75792fd5fb444a5 Author: tdreszer Date: Sat Apr 11 16:45:18 2009 +0000 Added Mary Yang to the credits commit 9023c2f4b65b530b2fe84df0382f0b9eaa346085 Author: galt Date: Sat Apr 11 15:00:05 2009 +0000 "Encode release log update" commit 1eec7499345b4ad70e348234eb5ac79047127b77 Author: galt Date: Sat Apr 11 15:00:03 2009 +0000 "Release log update" commit b9708742619d0cc229a8701d46b26b3ed54da333 Author: rhead Date: Sat Apr 11 00:56:13 2009 +0000 Forgot to specify entire path to a file. commit 369e511aa566e83f2e54663cc5710b39371792e8 Author: rhead Date: Sat Apr 11 00:43:16 2009 +0000 Changed -h hgwbeta to variable host specified in qaConfig.csh. commit d0d61c158d04063f73d90cc6ee564aa03defc976 Author: rhead Date: Sat Apr 11 00:37:05 2009 +0000 Sourced new qaConfig file at the top. Changed -h hgwbeta lines to look for sql host stored in a variable, specified in the new qaConfig file. commit 2d9f4b3d572d4cf88fdc1bb48f2cf58a8155827d Author: rhead Date: Sat Apr 11 00:32:30 2009 +0000 Initial checkin. qaConfig.csh and qaConfig.bash are configuration files for the remaining scripts. commit c83bdd822c923e5767ff0bd3633c28fb0957c423 Author: tdreszer Date: Sat Apr 11 00:05:19 2009 +0000 Added numeric filed validation by javascript commit 688c0f93ce8718183b5f830fbd3ae0d4508327aa Author: tdreszer Date: Sat Apr 11 00:05:02 2009 +0000 Added numeric filed validation by javascript commit a2f433193ade1dc83a0f0988fa8b61ac771abf43 Author: donnak Date: Sat Apr 11 00:04:41 2009 +0000 Added a few new pubs to 2008. commit 6322f67d08c925535c5413ac6a73e4ee9efc06df Author: tdreszer Date: Sat Apr 11 00:02:13 2009 +0000 Added isSqlIntType so that integer fileds can be validated as such commit ef41c1ae0793e2587ad01bdc5c01e9b2f9787a18 Author: tdreszer Date: Fri Apr 10 23:59:39 2009 +0000 Added new flavor of Text input box using standard class and declarable width commit 997da8a051d1fa5e0b877f963712929de1c8ef57 Author: aamp Date: Fri Apr 10 23:52:18 2009 +0000 Added error Ann suggested when intersection is turned on. commit 814d9031a298a315ff131f57bf0a1c6c723e6379 Author: ann Date: Fri Apr 10 23:12:26 2009 +0000 added description for new chain coloring options commit 4612d357e5655dd13a3ed45e6455854b8afb2e7b Author: ann Date: Fri Apr 10 22:57:36 2009 +0000 moved this down from the /human level, as hg16 is the only human assembly that will not use the new coloring feature for Self Chains. commit cba03a993e33c5be94f1536a641c54650190efc7 Author: ann Date: Fri Apr 10 22:21:54 2009 +0000 added Hg19 to chain list commit 809698567b2b384fb174c50083746c9fefbbc388 Author: rhead Date: Fri Apr 10 21:56:18 2009 +0000 Added doGenbankTests. commit cdd875ff8398bc20ccb5a5362caaac0c72c78050 Author: rhead Date: Fri Apr 10 21:53:45 2009 +0000 Added a date stamp at the end. Put cd in a subshell. commit 15f140fe838349ef7d7841510d9c168a54b0b92a Author: ann Date: Fri Apr 10 21:40:14 2009 +0000 yet more work on this page... commit 7ebf3902547b9def523e49fb0499609d69557e43 Author: tdreszer Date: Fri Apr 10 21:33:30 2009 +0000 Clumsy check in commit d9166efca8f9fd7e64c3095b8a06d0f05a092ef5 Author: ann Date: Fri Apr 10 21:32:46 2009 +0000 mostly edited subtype and A/E commit 19e50058b382d83781d4567e0b8c3ad0f04706dc Author: tdreszer Date: Fri Apr 10 21:30:23 2009 +0000 Fix bug where db was not selected commit 32c41ba3ef4810f62c5261543d339dc0aed24f92 Author: fanhsu Date: Fri Apr 10 21:14:24 2009 +0000 Added "Each positive selection site is labeled by the corresponding amino acid of the consensus sequence." in the Description section. commit 32af72786525999893c69dd17fa07ba964cea45d Author: kuhn Date: Fri Apr 10 20:42:57 2009 +0000 changed -blank to _blank commit d7a41c5e678f344a3c89329b5a90142bb2de2da6 Author: rhead Date: Fri Apr 10 20:37:55 2009 +0000 Initial file. Script to run genePredCheck/pslCheck, joinerCheck, gbSanity, and featureBits on GenBank tables. commit ee42434c54b2aa6e77c790abc35f783d72515d09 Author: kuhn Date: Fri Apr 10 20:30:13 2009 +0000 changed -blank to _blank commit 81295a0c636508e0bbd5ad9a916c6d09dce31c3c Author: tdreszer Date: Fri Apr 10 20:04:30 2009 +0000 Fix many instances of using composite tdb when subtrack tdb is needed commit 32e6e7a63964d89a2dce151f6ed048d5d08e56ad Author: tdreszer Date: Fri Apr 10 20:02:13 2009 +0000 Replaced lookupCt with macro to ctFind() common subroutine commit 638ce55798dcf447931f83436528da67b66aed4c Author: tdreszer Date: Fri Apr 10 19:56:35 2009 +0000 Added subTdbFind() and tdbFindOrCreate() support routines commit 3bd026c7c650efd086755d9b767dae699e194552 Author: tdreszer Date: Fri Apr 10 19:54:41 2009 +0000 Added ctFind support routine commit f0722d6ac21a3c1a625f262e2b9e0682cc5daba6 Author: tdreszer Date: Fri Apr 10 19:52:43 2009 +0000 Added consWiggleFind support routine commit 1d7a46d1497d722ed4597fdba4d393c6abe13c90 Author: larrym Date: Fri Apr 10 17:57:02 2009 +0000 modify qapushq host yet again commit 783b8800c126b71ef526dda1231888b0ed3c5a11 Author: kuhn Date: Fri Apr 10 17:28:16 2009 +0000 added a phrase to communication outage message commit 099bcac61fbcf66abf60aea812039196c3bdd9c8 Author: ann Date: Fri Apr 10 17:01:28 2009 +0000 added news item about outage, bumped two old items to archive page commit be893349e8879b0401188cf3ba2954825b07253a Author: tdreszer Date: Fri Apr 10 16:47:40 2009 +0000 Closest to home commit 886bd362d39f27a1137a8aa38ab19295c97b3099 Author: ann Date: Fri Apr 10 16:45:02 2009 +0000 changed end date for application acceptance commit 78aefaeacd0383612d1e3488d8d9bdddb36e1272 Author: galt Date: Fri Apr 10 15:00:05 2009 +0000 "Encode release log update" commit 4487783980d1fbc2b694eda110cc881885feceb7 Author: galt Date: Fri Apr 10 15:00:03 2009 +0000 "Release log update" commit b7c7b5472806c38fb0bfebdd714191592df77dbf Author: markd Date: Thu Apr 9 23:39:43 2009 +0000 added tests for hgwbeta using hgsqlbeta commit 8625b28bc3889defa3c3792d36e47af957a4b0be Author: ann Date: Thu Apr 9 22:36:50 2009 +0000 Katrina and I removed the 'Fragment' type from the list of types commit 53df8c892f7b45759e966ed3e816a1bfa068097a Author: galt Date: Thu Apr 9 15:00:07 2009 +0000 "Encode release log update" commit b7268d42744670884e135eca4bae9e0e55fb691a Author: galt Date: Thu Apr 9 15:00:04 2009 +0000 "Release log update" commit faecc6937abf1d958c4e7b2af76d86c1e5dc10cb Author: rhead Date: Thu Apr 9 08:29:43 2009 +0000 Added hg19 to hg set. commit fa4eb3523b863ed8f3d0b859df194c8ffa70b271 Author: aamp Date: Thu Apr 9 00:27:05 2009 +0000 Changed a shortLabel. commit d168138816b29e3f6f1a3762874fca92b565e32f Author: aamp Date: Thu Apr 9 00:20:14 2009 +0000 Added FOX2 cluster subtrack to composite track. commit 664de218719f5b5a9fd1cfd63d162f35533f51b0 Author: aamp Date: Thu Apr 9 00:19:37 2009 +0000 Added to the FOX2 track's description. commit 73ee4a884222e3c8e5a835cd85809e164c4a3795 Author: rhead Date: Wed Apr 8 22:17:19 2009 +0000 Adding hg19. commit 53f51e53a3abc11cf29aa6e6dfc267c6d976c044 Author: rhead Date: Wed Apr 8 19:32:13 2009 +0000 Small edits to disclaimer section. commit 5cf89913b41a0b40c2f498c1ead7579ee026413b Author: mikep Date: Wed Apr 8 19:26:58 2009 +0000 first version of gDNA data commit f7697936acdf556b7a155ed867c6dba4588e3ef0 Author: galt Date: Wed Apr 8 15:00:14 2009 +0000 "Encode release log update" commit 16689530fa0a0e5d2b1ff665959444e65935f55e Author: galt Date: Wed Apr 8 15:00:06 2009 +0000 "Release log update" commit 45cb93d6154bb2dcecacf26d829c8b7ece14c2e9 Author: mikep Date: Wed Apr 8 01:39:53 2009 +0000 add a generic options field so we can easily add options to views commit f9806a2de2959b16771f9dcc28f8d2365aee58a7 Author: mikep Date: Wed Apr 8 01:34:58 2009 +0000 allow mirror sites to add their own RNA secondary structure tracks by adding rnaSecStr to the table name commit 05c44f504db09590f004140af009e9d6baee4f3a Author: mikep Date: Wed Apr 8 01:21:48 2009 +0000 chrom info file to send with validateFiles prog commit 9cb87557faadc6a39dc7e986e5f2251568da44d3 Author: rhead Date: Wed Apr 8 00:12:50 2009 +0000 Rearranged PAR section so it's easier to see. Thanks, b0b. commit 0648e2b8f161df03a01bfe9a3b27e169b554a3ca Author: rhead Date: Tue Apr 7 23:43:36 2009 +0000 Adjusted chromStart for the second chrX PAR region by one. The off-by-one was found by a user. commit 7c040e670161530d311f99506b342566301b710f Author: tdreszer Date: Tue Apr 7 23:33:27 2009 +0000 Added tRNAs and polyAs to ENCODE GENCODE track commit 6d63851d49192dcf6d85aecfe317681b7b1e328c Author: larrym Date: Tue Apr 7 23:23:47 2009 +0000 lots of improvements commit 1c8ccbdbf80c5d15cd679253992bb425147a0bf3 Author: larrym Date: Tue Apr 7 21:13:24 2009 +0000 initial checkin commit f4f8eaa2476203c2e081ae05f7b0154e7bd572f5 Author: kuhn Date: Tue Apr 7 20:57:44 2009 +0000 added border around disclaimer commit 3b8392e4d305149c42efba2e0ba83792405d1587 Author: kuhn Date: Tue Apr 7 20:49:24 2009 +0000 added more warnings. Thanks, Katrina commit 6a7a1c7bac554570318281bff3244fe4ba8d536e Author: tdreszer Date: Tue Apr 7 20:17:02 2009 +0000 And if the link has no form to submit, better just follow it commit cdf8f834dfe6cf9c745e2ccab4046c90facb922a Author: tdreszer Date: Tue Apr 7 19:58:54 2009 +0000 More tightening of the postTheForm screws commit 2fb36f2414336be0a1581cf6bb87fbb23a4277ce Author: mikep Date: Tue Apr 7 19:44:43 2009 +0000 v204 preview commit c55e5836d0b03cd428bee89906d6d3228e0d9056 Author: mikep Date: Tue Apr 7 19:33:08 2009 +0000 adding comments about symlinks in htdocs commit 782ab611a7bcbd9ed758b5665499fd4c3dcd36a1 Author: kate Date: Tue Apr 7 18:49:39 2009 +0000 Removing inacurrate replicate info after all commit 153455b2efa0c6683d6e2a7385e25461bbf2bde3 Author: angie Date: Tue Apr 7 18:39:53 2009 +0000 Added "Smoothed" to hgdpFst labels. commit b58190f42a1e68f194675b251eeb9789c052b343 Author: ann Date: Tue Apr 7 18:37:00 2009 +0000 swapped order of sections commit 14da3cf195e8a85e2e7403c6d06fecc388efbd6c Author: mikep Date: Tue Apr 7 18:35:33 2009 +0000 useing ssl stuff commit 6f0dfb2ded1edcd61a3a902f56fe6a795da353ab Author: kate Date: Tue Apr 7 18:23:11 2009 +0000 Update freeze date commit 15cd4d8a3db2d676ab3589bf205fc4a7a6f2448c Author: kate Date: Tue Apr 7 18:21:32 2009 +0000 Subtracks are no longer by default set to be configurable, due to performance issues. Change at wrangler's discretion commit d40df84b98918401a18e1ad8c3256778d163a654 Author: kate Date: Tue Apr 7 18:16:04 2009 +0000 Set subtrack defaults based on cell type (only Tier1 default on). Change at wrangler's discretion commit 7f9d32edc65cbb8009b07d96701948fdfc4f62c3 Author: kate Date: Tue Apr 7 17:53:39 2009 +0000 Add info about replicates commit dba3848f6f05f69bdc21aa8ac8f5a810c6f19f40 Author: angie Date: Tue Apr 7 17:31:01 2009 +0000 Don't call drawCdsDiffCodonsOnly if lf->codons is NULL. (not sure how this was prevented before my recent mods to pslTrack.c, simpleTracks.c and cds.c) commit 5c1a123fe0faef3f5dab5b36e0c02e9dd3f0fcf3 Author: angie Date: Tue Apr 7 16:55:49 2009 +0000 Swapped chains/nets from dm3 to get liftOver chains to dm3 -- user request. commit 8f008e9f40fc01c53b5f2751c9c034f0e7eb7424 Author: tdreszer Date: Tue Apr 7 16:47:58 2009 +0000 Tighten the restrictions on converting links to posts commit 20caf567132b69e4c87f1f5e8025debaf74161aa Author: tdreszer Date: Tue Apr 7 16:46:25 2009 +0000 postTheForm must explicitly set action to POST commit 4db202ed85d97ffb94cd6dc5e199fe764ec2028f Author: braney Date: Tue Apr 7 15:06:31 2009 +0000 add human proteins to mm9 commit c6ca23ddb2eab04c3e68a7b9beb73356cdfd6d72 Author: galt Date: Tue Apr 7 15:00:07 2009 +0000 "Encode release log update" commit b83bc72ca2f58532d2b9c533e8d1f40a7ceb5138 Author: galt Date: Tue Apr 7 15:00:04 2009 +0000 "Release log update" commit 3c5c170bcf6bf5f549ee4b7fb34c877b73a11742 Author: braney Date: Tue Apr 7 14:37:10 2009 +0000 added Human Proteins track commit 7df68551b5a90403d2d88d245f0066934fe0f68d Author: rhead Date: Tue Apr 7 03:22:09 2009 +0000 fixed some punctuation commit 773b06fc52597d6b441f6c011668b02ccc6c51d0 Author: tdreszer Date: Tue Apr 7 00:56:50 2009 +0000 Reworked some CalTech settings to get rid of confusing dimensionZ commit abe3c29bdfc48f4c13f93743350edd9f55bb323a Author: kate Date: Tue Apr 7 00:15:53 2009 +0000 Cosmetics (whitespace in trackDb) commit 33d5736efe29c9748f5855b5e79e9874f9bb1170 Author: kuhn Date: Tue Apr 7 00:07:43 2009 +0000 changed text slightly on search terms commit 53ca2eb1c348d7d9326244163d58bf985fdf0956 Author: galt Date: Mon Apr 6 22:19:09 2009 +0000 reversing ourselves to have USE_SSL=0 be the default since some mirror sites have difficulty commit 5e42f98a6537794197781518f2433f8e2ecbfc4d Author: tdreszer Date: Mon Apr 6 20:54:47 2009 +0000 Fix problem where multi-view without cfgType was causing warn() commit 09ddaa36b7e0a5e637f7eec8b18c9cc9babd4947 Author: tdreszer Date: Mon Apr 6 20:51:50 2009 +0000 Made hgTracks expand/colapse groups work identiacally between config and image version commit 9d91d81da55b39f93ca51cf1bc12dbcec4181e5a Author: larrym Date: Mon Apr 6 20:49:35 2009 +0000 table name changed commit 85b685f539989fb1cfda954f31f3fef389a3c292 Author: kate Date: Mon Apr 6 20:41:16 2009 +0000 Adjust name of HCT cell line to match cv.ra commit 29e9c514f42d1e8253822a7ec3848112c23f6649 Author: larrym Date: Mon Apr 6 20:38:38 2009 +0000 add dcc to downloadDir commit 2adb6872387bf761551b0b83a38c18b9de94e0ec Author: rhead Date: Mon Apr 6 20:31:46 2009 +0000 Removed some parens. commit 7ef6ec65934b891ddd2329937dbc5c15548488ab Author: larrym Date: Mon Apr 6 18:55:36 2009 +0000 add bedItemOverlapCount and bedExtendRanges to userApps list commit 1633131f7e1a98fa611f0aec482a526adbbc51de Author: larrym Date: Mon Apr 6 18:40:21 2009 +0000 support host, user and password args commit c5b4b26e2e65cde5462abe3cde2cdae3793aa4c1 Author: larrym Date: Mon Apr 6 18:36:36 2009 +0000 fix typo in usage commit 7a5f2eee110a3320060eddada48d0eb73c0a0dfd Author: ann Date: Mon Apr 6 18:24:55 2009 +0000 changed priorities so they would order correclty commit 2bd4cfc7053051b232def631c5b32a6347b1c26a Author: ann Date: Mon Apr 6 18:20:22 2009 +0000 removed duplicate entry commit 19830701b13250635f94034bc834d68390916c99 Author: larrym Date: Mon Apr 6 18:13:51 2009 +0000 allow user to use remote db (e.g. mysql.cse.ucsc.edu) commit 5bd49ce92b3ff71d0478ea66674a7439fbcf1d36 Author: angie Date: Mon Apr 6 17:59:09 2009 +0000 HGDP Heterozygosity label and description tweaks after more info from Joe. commit 998da5b9fb22c85cd8c65414569297f61b8781eb Author: hiram Date: Mon Apr 6 17:54:40 2009 +0000 Make it work from parameters commit 00cc2df18033f8b675cda13ddb8e4a9137933625 Author: jsanborn Date: Mon Apr 6 17:52:51 2009 +0000 fixed ordering of lin cnv set commit 82ef5004592050b7a41ee62be751427083243bfc Author: angie Date: Mon Apr 6 17:07:51 2009 +0000 Added comment that 12fly dpse_caf1 is the same assembly as FlyBase dpse_r2.1_FB2008_02. commit e8dc654bee07572c2ee4fd8430fb59eddc8f7fff Author: tdreszer Date: Mon Apr 6 17:00:57 2009 +0000 Added UNC FAIRE HeLa commit c14058af1877f9f93eff34cecf4134bc9c1e3131 Author: galt Date: Mon Apr 6 15:00:07 2009 +0000 "Encode release log update" commit 808c34a784d2878fc82cdee6ac574d2a4ce743f5 Author: galt Date: Mon Apr 6 15:00:04 2009 +0000 "Release log update" commit 1c8cf1cf01f737f03c12508eadd6018932778c72 Author: markd Date: Mon Apr 6 05:42:22 2009 +0000 loaded UW yeast footprint tracks commit a012d508af5e9d737907a9e21c8d19664f207ed0 Author: galt Date: Mon Apr 6 05:41:20 2009 +0000 add genoLayDbChromsExt to handle case of not abort on error commit fd1ce61bc6d4dc85c0fbac5be78f9d43e877326d Author: galt Date: Mon Apr 6 05:40:29 2009 +0000 removing some unneeded bits commit fefc8eb47d4ea9874264d494a0f053bb34be6532 Author: galt Date: Mon Apr 6 05:34:52 2009 +0000 add genoLayDbChromsExt to handle case of not abort on error, also change filtering to only include chr chroms other than chrUn and chrM commit ef9ca86b0fad2dd1a6194502ab504369bf24f0f7 Author: galt Date: Mon Apr 6 05:33:50 2009 +0000 deal with javascript and cases where only cga (clade,genome,assembly) will appear since there are no usable chroms commit b2e4ab7b932504ef0eca324f43d7ae9ecb6b8083 Author: galt Date: Mon Apr 6 05:32:09 2009 +0000 add function checkAndClear so that do commands are not stuck in cart after an errAbort commit aad695caca939d56d0001558291596293606e2ff Author: galt Date: Mon Apr 6 05:31:18 2009 +0000 use genoLayDbChromsExt for chromList commit 0986d186ce5d49860943f4e510533bc39436e65c Author: mikep Date: Mon Apr 6 05:09:44 2009 +0000 some RNA files are > 4gb commit 8ed1a56f80151cf059b83d1de1d1d0d927b89102 Author: mikep Date: Mon Apr 6 05:08:40 2009 +0000 validate csfasta and csqual files with validateFiles prog commit ba48ec63099529b6ce5326b712a43b18540361b8 Author: mikep Date: Mon Apr 6 05:07:22 2009 +0000 try and avoid mysql timeout errors for stuff that takes 14,000 seconds or more commit a7b4856fae19aad7ac01993cc7e47a763b704a4a Author: mikep Date: Mon Apr 6 05:02:47 2009 +0000 first 3 projects of GIS DNA PET commit 277ea199b2ce9617dd19c57ee2650f23b7f19ce1 Author: markd Date: Sun Apr 5 18:10:00 2009 +0000 ignore SIGPIPE in child to avoid timing issue on process completion commit 29360a9d7a1f4d23165c18a1749ff9e4c5c985fa Author: galt Date: Sun Apr 5 15:00:09 2009 +0000 "Encode release log update" commit 49766d62e8509e9ef8fd28095d93c47566fc7468 Author: galt Date: Sun Apr 5 15:00:05 2009 +0000 "Release log update" commit fed1767f723a7e8c4952775fba87ba7e0b42d20d Author: mikep Date: Sun Apr 5 04:56:46 2009 +0000 GIS gDNA PET alignments overflow the 4GB table commit be9e828a474873c649b144991c48f0ed1e2d6cdb Author: markd Date: Sat Apr 4 23:52:49 2009 +0000 added UW footprint tracks to sacCer1 commit cf6805568cbdabdf8ef93e40ed1cccd0882654d3 Author: mikep Date: Sat Apr 4 22:21:17 2009 +0000 GIS RNAseq extra views commit 1df2d0ac9ceb618330ec3aa60bee68a4b9c007f8 Author: mikep Date: Sat Apr 4 22:19:34 2009 +0000 GIS RNAseq initial load commit 740d3281d4f6b85b6e4a51d5b6d29df324d76d25 Author: galt Date: Sat Apr 4 15:00:09 2009 +0000 "Encode release log update" commit c7b1dd3bb74a3fe9b2802b2af2772c770ef86143 Author: galt Date: Sat Apr 4 15:00:06 2009 +0000 "Release log update" commit a8590bc9bfff4fa51bafdf891ee93841ae78f460 Author: hiram Date: Fri Apr 3 23:26:04 2009 +0000 add the mkdir business commit f4c3eae779167d02d2febabca64c849847d89e10 Author: angie Date: Fri Apr 3 23:25:30 2009 +0000 Fix for printf format in cgiMakeDoubleVarInRange so value doesn't get truncated to int. commit 0ab954116654bb5a00a77f65083415a3b96030ea Author: tdreszer Date: Fri Apr 3 23:18:34 2009 +0000 Oops. Reversing accidental check in of experimental code commit a1c6bbbe953d00ef5e4e84710303563ffee46900 Author: tdreszer Date: Fri Apr 3 23:17:11 2009 +0000 Convert all href links to posts in order to save the users settings to the cart commit ebe2eb83616733d1eab1cb181564b78809526d12 Author: ann Date: Fri Apr 3 23:09:17 2009 +0000 added last section commit 67a84a0a5b745f60315daba4b8981ddcc92598a5 Author: tdreszer Date: Fri Apr 3 22:42:51 2009 +0000 Convert all href links to posts in order to save the users settings to the cart commit ef9ee89797f73a34c74f7ea18ed985dcc0b50ec6 Author: pauline Date: Fri Apr 3 22:42:41 2009 +0000 Added SUNY RBP to downloads page. commit 44ed0ca122a6735da0e9b1f81e9a23860db6a713 Author: rhead Date: Fri Apr 3 22:41:39 2009 +0000 Changed wording in methods section. commit 4fd199779d78048740bc70f8eabc4916bf2b1396 Author: tdreszer Date: Fri Apr 3 22:40:36 2009 +0000 No longer need to convert href vars to hidden inputs when converting a link to a posted url commit 7cf96bf0ede5390fa90a8551f3b6b6b86fdb9859 Author: ann Date: Fri Apr 3 22:35:00 2009 +0000 cleaned up table commit e47faafcf4f4b6c7be32b8aaebec4cef01202a4a Author: angie Date: Fri Apr 3 21:11:37 2009 +0000 Shortened HGDP analysis track labels to fit in 80 chars for longLabel, 16 for shortLabel. commit e8be669076a91e2842eea57f7db6e2ea89ff69e8 Author: ann Date: Fri Apr 3 20:34:50 2009 +0000 mostly html tags commit 7b513c981d713545fd9556f3cba2fe2a5f6e3360 Author: kate Date: Fri Apr 3 19:47:14 2009 +0000 Add material about signal and pvalue commit 5b83f321bd9d5b8b10bf37823763fdfc116d1225 Author: larrym Date: Fri Apr 3 19:27:30 2009 +0000 fix Methyl27K56 long labels commit 0bf264b01541c1b9e6fb8dac787b441de535b91e Author: larrym Date: Fri Apr 3 19:24:09 2009 +0000 cleanup commit b07162eda4e070c85fdb1a8030e0c09dd2548429 Author: angie Date: Fri Apr 3 19:08:34 2009 +0000 curTrack is NULL when group is All Tables -- in that case, call hAllocConn instead of hAllocConnTrack in showSchemaDb. commit 8131791229f8f7f3ae2c8a0693b054de520c789f Author: larrym Date: Fri Apr 3 18:26:53 2009 +0000 use pushq B (i.e. to force human review before QA sees the entry) commit 594af8a08e7298d0c53a5287757048b12bbdc703 Author: ann Date: Fri Apr 3 17:31:28 2009 +0000 substituting some html characters. commit f3b403ba6fd49edc3dde19c13691b09e577d89f1 Author: kuhn Date: Fri Apr 3 17:27:21 2009 +0000 removed some commas from usage statement commit a165ac960d19680bab0aeb453cb8b76a0d2b4356 Author: mikep Date: Fri Apr 3 17:16:41 2009 +0000 add quick option to validateFiles commit 76caf02f03a1c8ed067e8fb7341890e21541ecea Author: mikep Date: Fri Apr 3 17:11:08 2009 +0000 option for quick checking of files (1000 lines of each) commit 537f81f922449dea88fe3b7ce895e641339811d5 Author: galt Date: Fri Apr 3 15:00:09 2009 +0000 "Encode release log update" commit 5ec75c50c07781a69f42ad76c7f6a3e12ed57694 Author: galt Date: Fri Apr 3 15:00:06 2009 +0000 "Release log update" commit 15d54eb6c5df67e05e83600fd5b9c99f635296de Author: rhead Date: Fri Apr 3 01:34:30 2009 +0000 Changed note about all Africa and Bantu only populations. commit 78548b313ef08a23e52526837010ebb7f0c6123c Author: ann Date: Thu Apr 2 23:44:58 2009 +0000 continuing major cleanup of MS Word cruft commit b0633611a07e9193d4c98a6c5f4e4f6a22a6cfed Author: hiram Date: Thu Apr 2 23:38:25 2009 +0000 Updated with an introduction commit 3616bbabe51ea00868f1add07eb2748360235b5a Author: ann Date: Thu Apr 2 23:29:48 2009 +0000 continuing major cleanup of MS Word cruft commit 9ad053c1c6bc1da42cfa86cf03d93658dcde1c5e Author: kuhn Date: Thu Apr 2 23:16:57 2009 +0000 made the disclaimer NOTE red commit 8b3ea306c92e7563cef64b0079e1013528f2e4e4 Author: ann Date: Thu Apr 2 23:04:30 2009 +0000 starting major cleanup of MS Word cruft commit b477eaa64773fea1260e39b875b78fcd779937f1 Author: mikep Date: Thu Apr 2 22:50:33 2009 +0000 fix warning on comparison with undefined; add fasta file validation by validateFiles program commit b24f0f33e2b4090e5d7d32a4f0364e53ef9d1de2 Author: mikep Date: Thu Apr 2 22:49:46 2009 +0000 validation of fasta files (single-line of sequence, no quality) commit 2248c815f8d600a864908970cc49c83949f70d74 Author: kate Date: Thu Apr 2 22:48:42 2009 +0000 Fleshing out Methods a bit to summarize analysis and meaning of scoring; expanding acronyms; removing repetitious parts commit f14f5392bef5b737e53fbb2a0b1dc34615d6d714 Author: tdreszer Date: Thu Apr 2 22:31:32 2009 +0000 Added resubmitted Yale inputs as bedGrahps (InputBg) restricting to alpha while wigs restricted to beta. Also some Duke label formatting. commit 2c3e331d6ed1795f887ed7643557c0f2fadcb1af Author: markd Date: Thu Apr 2 22:18:25 2009 +0000 reenabled ccds, but was false alarm commit d244baf1949af80224259621c1e409f43ae05ed0 Author: angie Date: Thu Apr 2 21:49:36 2009 +0000 Added minLimit and maxLimit settings to HGDP bedGraph tracks. commit 3322126987a44fde42aadc40d45c884425e0eaa1 Author: hiram Date: Thu Apr 2 20:58:37 2009 +0000 venter1 chain and net, self lastz chain, chimp lastz chain and net, pushQ entry, PAR region, Gorilla lastz chain and net, lineage specific repeats commit 162ef2ae243f6500562c45262394722475979ef2 Author: tdreszer Date: Thu Apr 2 19:32:26 2009 +0000 Added Duke Hela-S3, UT HeLa-S2 and UT HepG2 commit 9c4e17234e7df477d877ceb233868b94be3e6cbf Author: ann Date: Thu Apr 2 19:18:29 2009 +0000 fixed a bad tag and added Broad Histone to download list commit 5221e8275c1de1ebf3621d7d038c55b8601061dc Author: kuhn Date: Thu Apr 2 18:00:44 2009 +0000 added tags and commas to et al commit af73bb6b3c41f869684428439854ef689b8b7cb9 Author: kuhn Date: Thu Apr 2 17:46:03 2009 +0000 added a space betw refs commit 94d6135b1b127a2572884f74993904e5fe240d28 Author: ann Date: Thu Apr 2 17:07:46 2009 +0000 corrected Reference section commit 50ec2d0ac14e3785acb5488566dbed41f8fe8dc9 Author: galt Date: Thu Apr 2 15:00:11 2009 +0000 "Encode release log update" commit 799a74da688653806b8ec7450fd7803fca578abc Author: galt Date: Thu Apr 2 15:00:05 2009 +0000 "Release log update" commit 4a5c1f30f7f7e077762fb3506bb085683801dae9 Author: mikep Date: Thu Apr 2 04:27:21 2009 +0000 making code easier to read commit 1009aa7fc34fb0227d5f610cfd9caea42aae635a Author: markd Date: Thu Apr 2 03:52:08 2009 +0000 fixed error in style commit dd4dc2d5b8d16951b9d326aaf0cce5da5360fb9f Author: markd Date: Thu Apr 2 01:06:13 2009 +0000 disable CCDS update until a bug is fixed commit d4a845a8d04267fcc66849b5348cf009348194c4 Author: rhead Date: Thu Apr 2 00:15:41 2009 +0000 Refined references. commit 6d125b459eb12be5e8d50c2c0cf08b37fba1cb1c Author: angie Date: Wed Apr 1 23:59:44 2009 +0000 In showSchemaDb's call to hAllocConnTrack, use passed-in db instead of database (genome db) in case db is hgFixed etc. Should still be reachable by selected track's profile. commit 96a2138a48734279a7d8706add75a24a24b63c36 Author: angie Date: Wed Apr 1 23:45:00 2009 +0000 In lfFromEncodePeak, pass scoreMin and scoreMax to grayInRange too, not just to adjustBedScoreGrayLevel. commit 1d7c18b8d060ce05eac03db02ffd22f1054adb64 Author: tdreszer Date: Wed Apr 1 23:08:30 2009 +0000 Partially enable desirable multi-select changes commit 1002320b21fabbd38a89fbb834c0b34bb4360d88 Author: ann Date: Wed Apr 1 22:49:22 2009 +0000 removing release alpha from Raw Signals for Gm12878 cell line commit 818cc1c9f3c694a2575f72e0157127969b58d3f0 Author: mikep Date: Wed Apr 1 22:42:41 2009 +0000 recovered two wiggle tracks for Affy commit 456d8d42633a2feda53d0e77402d7a9ff8e4678f Author: tdreszer Date: Wed Apr 1 21:51:32 2009 +0000 Enable javascript validation of selected integer and double input controls. commit 957b4150100f6055aafc8d0f13dc803a4d6c4225 Author: larrym Date: Wed Apr 1 21:22:25 2009 +0000 cleanup and fix typos commit 50812ef620591e65851c4788f1cf99fd0db5adea Author: angie Date: Wed Apr 1 21:16:56 2009 +0000 Changed 8-spaces to tab to avoid make error. commit 3beb020fd655dd1038fde39870bface683e9338e Author: rhead Date: Wed Apr 1 21:01:59 2009 +0000 Removed a "the". commit f3b5d2a0f37f6e6fe36c9a5233b726fadec3b1d9 Author: tdreszer Date: Wed Apr 1 20:12:50 2009 +0000 Necessary checkin of registerOnChange to bind with jQuery.change(). Also checking in incomplete, but not yet used code. commit fda1c096632ba494a7e4e85345ec1171d87f972b Author: mikep Date: Wed Apr 1 20:07:01 2009 +0000 temporary fix to avoid bug with scoreMax being set to anything but 1000 commit cd99e83d1f9233fb677822203a76d05ba7c9a2f4 Author: tdreszer Date: Wed Apr 1 20:02:59 2009 +0000 Added validation routines for integers and floats commit d8ae71334d1d4e8e9eca72f74dda8a5e1c15c7b1 Author: tdreszer Date: Wed Apr 1 19:59:39 2009 +0000 Moved call to commonCssStyles to here. Now we should expand CSS styles in one place. commit 4d4cb67d78e3982162862c3d57db4854a8f909ca Author: tdreszer Date: Wed Apr 1 19:57:06 2009 +0000 Added controls for int and double which valdate using javascript. Requires utils.js and jQuery.js commit 63a2bddc9b5cd3c89c30371db51038d2c44bba5e Author: angie Date: Wed Apr 1 19:31:59 2009 +0000 Added missing to wigFilterStatRow. commit 14d45d0abe3a35aaae4d1fdf4c2bd065841c217d Author: angie Date: Wed Apr 1 18:39:11 2009 +0000 Must not pass null tdb to hAllocConnTrack, so if selected table does not have its own tdb, use current track's tdb. commit aed71afb2a039fdeae91fc536bab1f75c1e8ffa1 Author: ann Date: Wed Apr 1 18:36:51 2009 +0000 Changed host hgofbeta back to host hgwbeta. commit 98509eb7a7861dc0cb981c9580784f98151dede8 Author: galt Date: Wed Apr 1 15:00:07 2009 +0000 "Encode release log update" commit 92d4302e246d5f0d1496c23c17a2adea2f18bd38 Author: galt Date: Wed Apr 1 15:00:04 2009 +0000 "Release log update" commit 751e38291649591cf774369c8c22a9a6dfca9360 Author: galt Date: Wed Apr 1 06:56:42 2009 +0000 making post action URI query params available to cgi hash, and they take precedence over form vars commit 835c7764eeda77cb82b973e6fe79a77dbb161a8d Author: angie Date: Wed Apr 1 01:33:18 2009 +0000 Calls to hDnaFromSeq are rather expensive for 2bit, so cache genomic sequence from a single hDnaFromSeq call covering all of a track's items (even the ones that are only partly in the window). Replaced several strncpy/snprintf calls with memcpy because strncpy/snprintf can include strlen(source) which can be large (cached seq), bad news when called in codon inner loop. Also fixed off-by-one error that caused blue insert line to be drawn 1 base to the left of the end of + strand items (thx Brooke). commit 95cdf309a44279db0663605929b1ed15a2bff3f4 Author: rhead Date: Wed Apr 1 01:26:20 2009 +0000 Edits to references. commit a257301c4000fe9b1d903320c484471a3bb598cd Author: krish Date: Tue Mar 31 23:55:29 2009 +0000 added L flag to linker commit 37aabc8b3102718461082c2f285bfdb31ec751cb Author: galt Date: Tue Mar 31 22:38:57 2009 +0000 use standard function in hui to get central.cookie - note RR does not set central.cookie, so it has to provide the default "hguid" commit 4502bbe08c0d9de18600e37de501e553bc2c2975 Author: kate Date: Tue Mar 31 21:29:48 2009 +0000 Install cv.ra as part of 'make alpha' commit 0586b98988ca6b52823b8eecf663d5092d899b8d Author: kate Date: Tue Mar 31 21:14:49 2009 +0000 Change vis defaults on Yale for consistency commit 8cc5dd82e67da304389fc37cc4e8971a509933fd Author: ann Date: Tue Mar 31 20:35:05 2009 +0000 fixing cell-line antibody mixup commit e9d951dedcd34301d38e93e6a1ee3be75072f72e Author: tdreszer Date: Tue Mar 31 20:29:52 2009 +0000 Fixed sloppy sortOrder settings for Broad and Yale commit 6ec645156283e10cb61e843ce1a90510ee573f74 Author: ann Date: Tue Mar 31 20:14:03 2009 +0000 decided (for the final time) to not release with the Raw Signals -- as there is currently no access to the gbdb supporting files commit e05fe55b0474d8176971452181db011bbe8f5b31 Author: donnak Date: Tue Mar 31 17:56:10 2009 +0000 Fixed typo in CGB URL. commit 79fdbcd7db400c478ff55c37f5817a39fd99b793 Author: mikep Date: Tue Mar 31 15:22:43 2009 +0000 "New version number v203" commit 62b056a5dd8777f451490a292ebca00e158ecf63 Author: mikep Date: Tue Mar 31 15:22:16 2009 +0000 v203 final build commit fa41297c4638275566031f76ab84110151adb940 Author: galt Date: Tue Mar 31 15:00:13 2009 +0000 "Encode release log update" commit 99d9b389d033f4da67ff605ddd3d504ca2c8c60a Author: galt Date: Tue Mar 31 15:00:06 2009 +0000 "Release log update" commit 7836c6d0ac4dfee71f22edc02bbe0c19d72258cb Author: donnak Date: Tue Mar 31 06:12:16 2009 +0000 added CGB citations info. commit a1b4f71ccc90d01bc170d2c266c3fbf6394dad1c Author: angie Date: Mon Mar 30 23:25:21 2009 +0000 Check -minSize{Q,T} only for fills, not for gaps -- discarding gaps makes the parent fill incorrectly appear gapless. I think it's odd that we discard all of a fill's gap's children when the fill is disqualified because it's possible for some lower-level nets to pass a filter that excludes a higher-level net, but will leave that as-is for now. commit 378408b03853c3c70b7ac7c68420108784740cb1 Author: rhead Date: Mon Mar 30 22:52:17 2009 +0000 Changed some wording; added note about knownIsoforms. commit 5316e136c178544e01c240e3add62d873275384c Author: fanhsu Date: Mon Mar 30 22:15:49 2009 +0000 Moved a "
" printf statement. commit 4d697d32fde85a9a08cd26b57e1bc9b1d738c02d Author: angie Date: Mon Mar 30 22:15:32 2009 +0000 Made a population key image (thanks b0b for suggestion). commit 4f2c6f0163a7413bd74f286a3718107205c82db3 Author: angie Date: Mon Mar 30 22:14:25 2009 +0000 customFactoryTestExistence requires new arg (db). commit b9883afed095a960a83b877272c57f0fefe01639 Author: angie Date: Mon Mar 30 22:13:38 2009 +0000 Use HGDB_CONF environment variable if defined. commit 54dd60160e1f0fa1a45cd343e6b4aae4d0caf294 Author: fanhsu Date: Mon Mar 30 22:06:21 2009 +0000 Updated details page logic for omimGene. commit 393d240ba4d829f792e1035ddf84816349e861e8 Author: tdreszer Date: Mon Mar 30 21:13:57 2009 +0000 Support for setting variable then posting (allows reset to default without ajax and potential reace condition) commit 8ab1c756b91e6f4d7cb7d6341a0a4d19688cca47 Author: tdreszer Date: Mon Mar 30 21:12:19 2009 +0000 Support for setting a variable then posting (allows reset to default) commit 7ebc4392e2650f4cc53065eba646cd91e54b6efa Author: hiram Date: Mon Mar 30 18:58:30 2009 +0000 Adding liftOver to the userApps build list commit ffdf5669771d6eb091bdd2ba73ae1b5f7001268c Author: hiram Date: Mon Mar 30 18:56:52 2009 +0000 Improved for userApps use commit 9cfcd09c7e6d53e9bf8572740d24050e3fe9fbf7 Author: hiram Date: Mon Mar 30 17:55:21 2009 +0000 Initial contents commit 9c3629850c046c92647d9c5a568741825f14d390 Author: hiram Date: Mon Mar 30 17:37:01 2009 +0000 Add note about removing track and browser lines commit 801a7fd78fcb5b0a8d1da405fa98b3709679c249 Author: hiram Date: Mon Mar 30 17:33:17 2009 +0000 Add faCount to the userApps list commit 089b7cb7127047d21882a13d2f57187b1e689a93 Author: hiram Date: Mon Mar 30 17:31:39 2009 +0000 forgot dependency on the $O for the compile target commit 2cea49ac2e50c164f94aa00c502a48f357ce7e3e Author: hiram Date: Mon Mar 30 17:30:25 2009 +0000 prepare the makefile for userApps make target, now with DESTDIR commit 1cbb70e403bc49b2b7db0aabe7885c9469218b6f Author: hiram Date: Mon Mar 30 17:21:33 2009 +0000 Improve the makefile created, add compile target, shorten compile command commit 104f347e08ceafaafa1d4dd523e2a6395a45274c Author: galt Date: Mon Mar 30 15:00:10 2009 +0000 "Encode release log update" commit d52ece41f5de80fddfa4af2ce3314d8144ac49d2 Author: galt Date: Mon Mar 30 15:00:04 2009 +0000 "Release log update" commit d1c9730a414432c0749fd9e37814a4503492d92d Author: galt Date: Sun Mar 29 15:00:05 2009 +0000 "Encode release log update" commit 27867aa36325e6aca29eb36460ee6a06b5aac2bd Author: galt Date: Sun Mar 29 15:00:02 2009 +0000 "Release log update" commit 2ddd0b8b434548f9337e5cb59501cefd5984304b Author: mikep Date: Sun Mar 29 05:19:05 2009 +0000 convert maf to clustalw-like format commit 9fc5fe3bffa040bd445a0c5bfa47b708c3bcd28e Author: mikep Date: Sun Mar 29 05:16:57 2009 +0000 option to strip dots and dashes commit 6b38d2aee482b618628a2ba49b36c5a2b03b4790 Author: kate Date: Sun Mar 29 04:28:27 2009 +0000 change sort order to interleave view commit ba77c4a13c75f4544d35cea39813b9b902ca7a93 Author: mikep Date: Sat Mar 28 20:48:10 2009 +0000 utility to convert maf to fasta commit 1085d7781a4f59bf03319123f7718fc005a8a474 Author: galt Date: Sat Mar 28 15:00:06 2009 +0000 "Encode release log update" commit 539a742eb0bd8b295dbe7266a60c4692836e5c9b Author: galt Date: Sat Mar 28 15:00:04 2009 +0000 "Release log update" commit f7596a51e0586d8b0b4db105be8c0120f288f326 Author: galt Date: Fri Mar 27 15:00:07 2009 +0000 "Encode release log update" commit 16ec24a628329238e37d7fa6058bf138abd4ddac Author: galt Date: Fri Mar 27 15:00:04 2009 +0000 "Release log update" commit 1559464fb75d318a4efb55ad8ad8b571afe4f522 Author: hiram Date: Fri Mar 27 06:25:30 2009 +0000 fixup use of -lm on lib dependency commit d1a9e4fbf0c4489679945c2c2beddc61b1d6d1b8 Author: hiram Date: Thu Mar 26 23:20:38 2009 +0000 Separate lists for executables and documentation commit 1068496d7fb8ede3783e16cdd6cdc4d5fcdf210b Author: hiram Date: Thu Mar 26 23:15:45 2009 +0000 Initial contents commit e00bc31162c55514009ecd06e28e03f7ff8b23f5 Author: hiram Date: Thu Mar 26 20:19:29 2009 +0000 Adding userApps directory to the UTILS_APPLIST directory list commit 996016490a896caed729286e32f10e7d560acefd Author: hiram Date: Thu Mar 26 20:18:41 2009 +0000 updated to use DESTDIR and BINDIR commit 71379ac9ef2a2086b00dc0b2136c2e9ece6bdf2e Author: hiram Date: Thu Mar 26 19:04:17 2009 +0000 Initial contents, honoring DESTDIR and BINDIR arguments commit 84f965aba027633c816707306c94ba852a93ac80 Author: hiram Date: Thu Mar 26 18:40:09 2009 +0000 Properly sort by size DESC, and eliminate useless stdout messages from ftp commit 34bb17714e2b5f926f3ff9d8995589c102677e56 Author: hiram Date: Thu Mar 26 18:29:49 2009 +0000 Initial contents for a script to fetch chrom.sizes from UCSC commit 40559aba2ac84ed3d03e61ff2f494295025b1fca Author: fanhsu Date: Thu Mar 26 18:20:41 2009 +0000 Created omimToKnownCanonical.as. commit 46cc652df883bbf8f9465e70a6193f1a7a50e01d Author: fanhsu Date: Thu Mar 26 17:33:59 2009 +0000 Updated omimGene section, to go after knownCanonical KG and get description from gbCdnaInfo instead of refLink for RefSeq entries. commit 4e6ea64f89f0fe39f387c786f61d50ba5a34ae82 Author: galt Date: Thu Mar 26 15:00:14 2009 +0000 "Encode release log update" commit d282fccbda5a9f088103cadc3792a5880238ade4 Author: galt Date: Thu Mar 26 15:00:11 2009 +0000 "Release log update" commit bcb8dd1ca1ce150348c8a025ad2218d215db9d82 Author: mikep Date: Thu Mar 26 07:01:20 2009 +0000 adding chrom/size checking against hg18 commit aac618da99e431c43b14a5936590e19ebfb780ea Author: mikep Date: Thu Mar 26 06:55:39 2009 +0000 adding better error reporting on signed/unsigned ints and allow dots in sequence in tagAlign/pairedTagAlign commit 9a533e9306fbb10f154f0e53c120ffd38d205d56 Author: rhead Date: Wed Mar 25 23:22:16 2009 +0000 single word change. commit 67d0f6903ecc1d2d6b3bf77dfe50ff493fd9675c Author: rhead Date: Wed Mar 25 23:16:16 2009 +0000 Added a display conventions and configuration section. commit d3d49527b17753d78590b4a69eafc923f5d6d654 Author: ann Date: Wed Mar 25 23:10:08 2009 +0000 removed release alpha for select Raw Signal tracks for Broad Histone commit a0ef274ae03049da7435d944c2d90e4b7db04551 Author: pauline Date: Wed Mar 25 23:04:04 2009 +0000 Shortened methods and moved details to protocols doc. commit 0c5ffad1a7552d76c40896f5f3cac9ae36e49da9 Author: galt Date: Wed Mar 25 22:52:25 2009 +0000 make 64-bit and 32-bit liftOver WITHOUT SSL dependency and then scp to hgdownload commit eabc4488996d57918c3e6f9a6c0449e8a9ca9738 Author: rhead Date: Wed Mar 25 18:29:29 2009 +0000 changed target machine back to hgwbeta (from hgofbeta). commit 5156d016efe63cc2fe850445d09104303db0743d Author: galt Date: Wed Mar 25 15:00:06 2009 +0000 "Encode release log update" commit 81167b7b059394c9ef387cf98961ce3b244b1557 Author: galt Date: Wed Mar 25 15:00:04 2009 +0000 "Release log update" commit 64bcae8669a9b032293c0bfba2b6305d4d7791b5 Author: rhead Date: Wed Mar 25 02:27:41 2009 +0000 Changed OMIM-Related to OMIM-Associated commit e1440be1d9e5e7e545b536b66e53af4670cc9c03 Author: rhead Date: Wed Mar 25 01:19:48 2009 +0000 Reworded first paragraph, fixed reference. commit 1998e16f285c602ae27168b43ca063f8c8a79477 Author: ann Date: Tue Mar 24 23:35:02 2009 +0000 shortened Methods section (thanks Pauline!) and put the details in a new txt doc: /browser/ENCODE/protocols/general/wgEncodeBroadChipSeq.txt commit e1adc899029a3b1f7f4b90c911fb36979c350516 Author: hiram Date: Tue Mar 24 23:01:41 2009 +0000 Proper depend target for userApps build commit c5cf2d4094f53aba830dd6aca7dbdb108287bd56 Author: hiram Date: Tue Mar 24 23:00:04 2009 +0000 creating userApps target to deliver user programs commit edbb1e89da76765aa20d25657308fa29ab7d51c7 Author: larrym Date: Tue Mar 24 22:14:33 2009 +0000 add more details about RawSignal commit c0e414d769b032cb3bd5fcf33888c03d454d2223 Author: mikep Date: Tue Mar 24 20:48:34 2009 +0000 made this a library function, but need to make sure it is semantically identical and tested before removing from featureBits commit a678ec9ddb1084f47922b91e902274a3b4f26af8 Author: rhead Date: Tue Mar 24 19:10:45 2009 +0000 Reverting to -h hgwbeta. commit 5b8bc42521839965d151220c71eeaed81e646d0e Author: rhead Date: Tue Mar 24 18:56:48 2009 +0000 reworded galt's notes about repMatch a bit commit aceda91c68aa3b0561bee692f3aedd8777ebbe87 Author: mikep Date: Tue Mar 24 15:51:04 2009 +0000 make library function to read all chromInfo, and add chromDb option to validateFiles to get chromInfo from DB commit 01e3bcbe548efda15b8fecdee8b2abff9aa1b620 Author: angie Date: Mon Mar 23 18:24:47 2009 +0000 Tweaking name of output file to avoid clobbering the main one if there's a problem upstream or downstream. commit b7a6c4d22932f3c0eb123cb793ebea40a14f7217 Author: galt Date: Sun Mar 22 15:00:03 2009 +0000 "Encode release log update" commit b6e5e57c6a902644ab5eb90f001998e16b76293b Author: galt Date: Sun Mar 22 15:00:01 2009 +0000 "Release log update" commit 473247de58e7206e7357d2516b16ba93a25463d1 Author: larrym Date: Sun Mar 22 02:38:12 2009 +0000 refactor openUtil from doEncodeValidate.pl commit 752afde6e1fd2e3ff8ae828d6116642f5692acfa Author: larrym Date: Sun Mar 22 02:37:47 2009 +0000 refactor openUtil into Encode.pm commit 2592e40ba5353429a3c46bdf6f49e363b5027b81 Author: hiram Date: Sat Mar 21 22:41:56 2009 +0000 Turn on iRows for multizMHC commit ff7cee83a3fd24f83aa42f299813f2a2f2f17705 Author: galt Date: Sat Mar 21 15:00:07 2009 +0000 "Encode release log update" commit 4e42688fd0b9543736d44b94abffa05f542a9d5b Author: galt Date: Sat Mar 21 15:00:04 2009 +0000 "Release log update" commit 3b9fd0ef8451af7e4d128e47d7fed7f1a6b0e220 Author: galt Date: Sat Mar 21 00:47:06 2009 +0000 adding repMatch default note commit 7d8b7c3a4eddc52268c97a3d0b11dd03e906d693 Author: rhead Date: Sat Mar 21 00:29:25 2009 +0000 Changed host hgwbeta to host hgofbeta. commit 1d7fb330b6cc19ea1ac847e316317f9182e95651 Author: ann Date: Fri Mar 20 23:49:01 2009 +0000 adding announcement about two open positions commit 3819ed110f99245c67b197c7c85fab67ff25d158 Author: rhead Date: Fri Mar 20 23:46:19 2009 +0000 Changed host hgwbeta to host hgofbeta. commit 61379889ec367c31ac8967e589ac2b9fdad1d508 Author: rhead Date: Fri Mar 20 23:39:52 2009 +0000 Changed host hgwbeta to host hgofbeta. commit 560aa2758b893c5095a87452fcab10e97d8eeec3 Author: hiram Date: Fri Mar 20 23:38:37 2009 +0000 Adding multizMHC track and fixing up sortOrder error commit f45c9dd0122b0226df1dbe748283e02077bc7321 Author: rhead Date: Fri Mar 20 23:33:29 2009 +0000 Changed host hgwbeta to host hgofbeta. commit 7281f8efd864dbcda7026ddabbfc01f2b138fc38 Author: hiram Date: Fri Mar 20 23:25:26 2009 +0000 Initial image for hg19 MHC multiple alignment commit 7201b7d06ff85015ed6c4fb52bb8246cbbb4f7b2 Author: larrym Date: Fri Mar 20 23:24:56 2009 +0000 hgwbeta => hgobeta commit 6e520aaf6df81a9ebf827125fbf0628a0bd873eb Author: ann Date: Fri Mar 20 23:22:49 2009 +0000 adding back in 'release alpha' to Raw Signal subtracks of Broad Histone (not releasing now -- not enough room!) commit 009a4499d576f0f3c8ad04cc1505b205d5a85bbd Author: ann Date: Fri Mar 20 23:05:19 2009 +0000 fixing citations commit d3bf7c0e48e0fb7855f14bb949eeb5b9a1d355a5 Author: angie Date: Fri Mar 20 23:01:23 2009 +0000 Use hgofbeta instead of hgwbeta as the mysql server for qapushq. commit f79d71da4126a2f1c30afbe8dca5b168de4b1a39 Author: ann Date: Fri Mar 20 22:54:06 2009 +0000 removed release alpha from SUNY and Broad tracks commit 6c8295e472a26abad4087bc688980fea54324e72 Author: tdreszer Date: Fri Mar 20 22:42:12 2009 +0000 Changed sort order on Broad commit 36eb527867b23fbc3f5d404f22af9e3e474903c7 Author: ann Date: Fri Mar 20 22:42:09 2009 +0000 alpha order for citations commit 1f4003986e81e3832125f55bd803bd9fa2f61095 Author: tdreszer Date: Fri Mar 20 22:23:12 2009 +0000 Added data release policy to the end commit ffe8d391784f4c72410bbe59b181bb4cb487a60c Author: ann Date: Fri Mar 20 22:14:35 2009 +0000 cutting lines to 80 chars where possible commit deab5233ac69bda4ec38760724f7008d576e3651 Author: larrym Date: Fri Mar 20 21:46:03 2009 +0000 pull metadata out of README.txt (if any is available) commit ef39ef805effb236e03901c9d018b6904cb6b5ed Author: giardine Date: Fri Mar 20 19:57:18 2009 +0000 Update population variants and MKAR tracks commit ba4eb22df3e34485981e31d749d1143ab923d0b4 Author: angie Date: Fri Mar 20 18:43:25 2009 +0000 Added support for db.host in hgConf, and properly set HGDB_CONF when -hgConf is given so hgsql uses it too. commit 3fcbc5a82986c5fbc2c24869b78553678dd46a32 Author: angie Date: Fri Mar 20 18:42:23 2009 +0000 Added proper HgConf usage including db.host, since we can no longer assume localhost etc. commit d0846ac935482c13de265a2e5642a0cadadd99e3 Author: hiram Date: Fri Mar 20 18:19:50 2009 +0000 Have determined the location of the PAR regions on X and Y commit 611a422bd6c5f7a85aece109e97cebf7bc719945 Author: kate Date: Fri Mar 20 18:18:40 2009 +0000 Add longer ID string commit b3d2dcb44f7600a1a859b4243fe8e4710dbc02ec Author: kate Date: Fri Mar 20 18:18:19 2009 +0000 Add source control identifier string commit abf9d1514c59034231130e17dafce0656610662a Author: angie Date: Fri Mar 20 17:19:13 2009 +0000 Added another duplicate .as to %autoSqlIgnore. commit ed1e1ad1573f6787869e80efa65c1c257de93140 Author: angie Date: Fri Mar 20 17:14:34 2009 +0000 Added date and time to output of error-500 details query. commit 4927a39a0e1c305606e9fec9913bcd6fb7275018 Author: galt Date: Fri Mar 20 15:00:07 2009 +0000 "Encode release log update" commit 205a90386ae99d92d15051d141813f47fcfb866e Author: galt Date: Fri Mar 20 15:00:04 2009 +0000 "Release log update" commit 8b98d800721dc20b114faeec41e83c1dee75e6b2 Author: hiram Date: Fri Mar 20 06:52:14 2009 +0000 Add synNets for chr6 haps commit f6a79b66b48e34523821e9fddcfc66ba3e595c0c Author: galt Date: Fri Mar 20 01:50:47 2009 +0000 dealing with move to hgofbeta commit e238918dae6fb468d6906a7bb185abd158d092e1 Author: tdreszer Date: Fri Mar 20 01:15:56 2009 +0000 Added a contact. commit 483b47da6bd8ba718cedb87b4f618ddf8e665265 Author: kate Date: Fri Mar 20 01:10:57 2009 +0000 Add some explanation of histone code commit 64b6a258d15c42fc1e908b13f7383627f3f232ae Author: kate Date: Fri Mar 20 00:36:50 2009 +0000 Minor changes for consistency commit c13bc1067a53010ebb441abaa5b3ec28b9fc420b Author: kate Date: Fri Mar 20 00:36:33 2009 +0000 Polish Broad Histone settings: add colors, tweak labels & defaults for consistency commit 6ffc0722fea6b910f7825c569db079cbe61acf4d Author: kate Date: Thu Mar 19 23:21:44 2009 +0000 Remove obsolete version commit e37162fdcc295881a33c2900b94bc5fb6e37945b Author: angie Date: Thu Mar 19 22:21:06 2009 +0000 Refactoring for performance issue raised by David: moved all baseColor work that was done at load-time to draw-time, and removed the freeing-by-default of original genePred and psl structs converted to lf. Now, when there are so many items in the window that limitVisibility kicks it down to dense mode, we don't waste time on baseColor stuff that won't be used. Also some refactoring for tidiness in cds.c: got rid of a couple unused function args. commit 525f0815affb1076d54288ad7a647dcb70eb05f3 Author: jzhu Date: Thu Mar 19 22:17:15 2009 +0000 add ispyAgiExpNov08_median_T1 info commit d31a8d0fc2acf7fe6ce5a94545021f1b653ae3e6 Author: tdreszer Date: Thu Mar 19 21:48:50 2009 +0000 No longer need to call jquery from here. Calling in hgTrackUi commit 67d5e245e980c37eda1c996437051f3cd11bb15c Author: tdreszer Date: Thu Mar 19 21:41:00 2009 +0000 For consistency, multi-shad should be defaultingh to '0' not '1' commit a583ca5da89837f9918760db0649a2f8bc4a909a Author: tdreszer Date: Thu Mar 19 21:38:36 2009 +0000 boolshad hidden vars should default to '0' not '1'. commit 24871cd1a0cb10949469bd4767697d77e0b8fb30 Author: tdreszer Date: Thu Mar 19 21:13:00 2009 +0000 Add 'Reset to defaults' to hgTrackUi. Currently only applied to multi-view, because it relies on cart var naming convention {tableName}.{varName}... commit aeb451bcef9ab4dc07e0a8eb665082b9aabf42bd Author: tdreszer Date: Thu Mar 19 21:02:59 2009 +0000 New routines to help reset cart for single table or composite. commit 0d8d2eeb27817da662dc689f4f3c56e7b87d5058 Author: tdreszer Date: Thu Mar 19 20:54:53 2009 +0000 Support for setting reset to defaults variable and submitting self. commit 37713fa9a7f3d091b8da5a3e2e47b568598ef4d4 Author: ann Date: Thu Mar 19 20:54:33 2009 +0000 switched to new hgofbeta MySQL server commit 18b37babf8cb5d5f3cd74469371866ef3a6190c6 Author: fanhsu Date: Thu Mar 19 19:59:14 2009 +0000 Manually updated 1 record in omimToKnownCanonical table. commit 9b616eb25fc08ef1ee27b25dd0ecf3f9803e4da5 Author: tdreszer Date: Thu Mar 19 18:29:52 2009 +0000 Fix to another make Checkbox routing for the hidden var being 0 commit a5365cadcefecd462f8cc48f9335d06a8923d079 Author: hiram Date: Thu Mar 19 16:15:29 2009 +0000 Allow non-split tables, and inclHap option to the blastz pipeline to include haplotypes in the chains commit 1725f1f6470eaa2d9534eb274440a0761eeeb2e4 Author: hiram Date: Thu Mar 19 16:14:35 2009 +0000 Allow some missing TRF files, option to avoid RepeatMasker, and special business to find haplotypes when they are in separate directories commit 833a3daf82f92f6e9a9f3e0cd12c06bc7ee716b9 Author: galt Date: Thu Mar 19 15:00:06 2009 +0000 "Encode release log update" commit adad311ec800be9ada754ed2e64087368df91c44 Author: galt Date: Thu Mar 19 15:00:03 2009 +0000 "Release log update" commit 219cd9a86acf07690d30fa33435d93a818f9aabd Author: kent Date: Thu Mar 19 00:42:38 2009 +0000 Making a lot more of the bigBed stuff work by implementing bigBedGetFilteredBedsOnRegions. commit 12594b4b50fec10079fe0522ca4821cb39900ee2 Author: rhead Date: Thu Mar 19 00:29:19 2009 +0000 Added information about sparse data problems. commit 9a570098a063bccc4b1ded7e81d1da6b90874c73 Author: hiram Date: Wed Mar 18 23:40:53 2009 +0000 Do not show the level limit option yet on netAlign tracks commit 76122677a5321adffa47ff03719dff5658072fae Author: kate Date: Wed Mar 18 23:02:12 2009 +0000 First cut at track description for GERP conservation commit 0a194d309c73dc14659a49aaf5f0fb72b3a57d04 Author: hiram Date: Wed Mar 18 22:45:43 2009 +0000 Fixup known issues as this went into the archae browser commit b55c83276c09d702d39ca14e71d2e8109be28501 Author: rhead Date: Wed Mar 18 22:04:41 2009 +0000 Added more of a description of MGC, lifted from the MGC site. commit 3256c2a2e7c04349f1dd879357c5c55fa9e6c8c7 Author: hiram Date: Wed Mar 18 21:38:33 2009 +0000 Add information about the configuration IP/extensions/ files commit 5cdc7da9590b411073eac4d51ca14d04e496f81b Author: hiram Date: Wed Mar 18 21:36:33 2009 +0000 files to place in IP/extensions/ to turn this on commit b4976384749d58e612d057b8f91406eb2b2121eb Author: rhead Date: Wed Mar 18 21:22:17 2009 +0000 Added more of a description of MGC, lifted from the MGC site. commit f2b45527eae91f11c6660f275767328aa61d6249 Author: tdreszer Date: Wed Mar 18 21:16:57 2009 +0000 Pre-pushQ cleanup commit 2d59515450224a12e2de96a2b218552c5960423f Author: hiram Date: Wed Mar 18 21:16:31 2009 +0000 It is not necessary to have specialized value constants for trackDb entries, they can have spaces commit 7e11550cf87113f71b5b6e9e9a33d584f0a7d4f3 Author: hiram Date: Wed Mar 18 21:13:28 2009 +0000 More constants brought in here from the code commit 2558f85b70b7d6f73f4a280085101183cc42ac99 Author: hiram Date: Wed Mar 18 21:10:26 2009 +0000 Now using the chainCfg business over in ../lib/hui.c commit 017629351e3ccbac3bcb681f9199f45a0254884b Author: hiram Date: Wed Mar 18 21:06:31 2009 +0000 Fixup the broken chain options commit 556c7aa0df58375516811d86d678561a893a3f1e Author: rhead Date: Wed Mar 18 21:05:53 2009 +0000 Added more of a description of MGC, lifted from the MGC site. commit 9fd02a35deb3e5ebde7ea8951008f6589f505d08 Author: tdreszer Date: Wed Mar 18 20:18:03 2009 +0000 Altered Z-dimension to use table columns commit 10d897dba1a73efb8b1b232e2474b79d18137512 Author: kate Date: Wed Mar 18 18:39:36 2009 +0000 Tweak short label (no sites here) commit b2a0ce386d55eff97693ce2a7fc96d8d75542ae4 Author: hiram Date: Wed Mar 18 18:33:41 2009 +0000 Adding netCart to the build commit b9e67c3c42d9cbd579e831400d49db22eefb4af8 Author: hiram Date: Wed Mar 18 18:30:42 2009 +0000 updated usage of chainFetchColorOption call commit d5e173e359fdf90b696054fd32cb90a9c79e11cb Author: hiram Date: Wed Mar 18 18:27:00 2009 +0000 adding netCart settings and cleaning up chainCart settings commit 71f51b9c905e270259973339b8fb265e5c5d6138 Author: markd Date: Wed Mar 18 18:20:43 2009 +0000 removed unused variable commit 77551a8dc528329ae17fe94f1c6a6fddd5cd935c Author: kate Date: Wed Mar 18 18:05:25 2009 +0000 Usability improvements, based on input from SUNY. Ready for QA. commit 33fa79df9e5ad33b303d98f4ea8d777b5479a127 Author: tdreszer Date: Wed Mar 18 17:51:53 2009 +0000 New boolShad logic requires shadow to be '0' even when checked. commit e0ff41607e3d6fb651627bfd5ac852433597be81 Author: mikep Date: Wed Mar 18 16:33:19 2009 +0000 removing a broken track while it is regnerated commit 67801220781e7ea538929fffa3c822b449e93099 Author: mikep Date: Wed Mar 18 15:59:47 2009 +0000 removing a broken track while it is regnerated commit 5b5072995dc3a019c85e339b8d183d736b7e3db4 Author: markd Date: Wed Mar 18 15:41:20 2009 +0000 removed usless yank-n-put declaration commit 99b7bce4c3c982c0d7285ec5f0da03a3500fba63 Author: galt Date: Wed Mar 18 15:00:16 2009 +0000 "Encode release log update" commit 1dc513c70d7b697461fe0e42ffb2dc081edd49dd Author: galt Date: Wed Mar 18 15:00:13 2009 +0000 "Release log update" commit 99bc632678f23b1a39950b8ec6d63e26a6bbaaf5 Author: mikep Date: Wed Mar 18 14:44:12 2009 +0000 fixing conflicts commit 4ac1d5f2ddec6580b1c21ee546b932fc592b7def Author: kent Date: Wed Mar 18 01:34:53 2009 +0000 Getting filters to work on bigBed. Next up - intersections! commit 2347af4ae1cb89d7bdcbca3e7b97b7a241e8c55d Author: kent Date: Wed Mar 18 01:34:07 2009 +0000 Adding bedFilter family of functions. commit 1c84fd43f4f5025aab54b12a396d580d13f7f4c5 Author: rhead Date: Wed Mar 18 01:09:19 2009 +0000 Combined some sections, added a span example for fixedStep. commit 89d4acef6729b137ae52ee9de4c28da22c7e3f91 Author: kent Date: Tue Mar 17 23:31:45 2009 +0000 Refactoring to move asColumnToSqlType to library. commit 787df2b8b34b88c708a3c494347db1ce5da626b4 Author: kent Date: Tue Mar 17 20:48:36 2009 +0000 Starting to add filtering. Collects input now, but doesn't actually run filter. commit 820a9b6538f77680b546b82b7a7069c42138f361 Author: kent Date: Tue Mar 17 20:46:33 2009 +0000 Updating comment. commit 44953b272f718a1252882c477aea73cfcd5159e1 Author: markd Date: Tue Mar 17 19:54:57 2009 +0000 minor speed up of rendering of mRNA/ESTs by checking gbSeq table before seq table, avoiding two sql requests. Also simplified code. commit f101918d722e1bb5572ccc2c2dcb205ff9c9bfcb Author: tdreszer Date: Tue Mar 17 19:49:12 2009 +0000 Multi-view composites toggle dense/full commit dcee5971f9366e5a6b65d62dc87e187fe16362cc Author: tdreszer Date: Tue Mar 17 19:27:20 2009 +0000 Added Yale RNAseq PolyA (temporarily?) to their TFBS composite. First bedGrah. commit 566ab45f87cc30986fd25f87c312b64bc4b4fa12 Author: angie Date: Tue Mar 17 19:05:58 2009 +0000 Added links to population key images. commit e86750d05500ccb57c3e5c4fd55c442458d55618 Author: giardine Date: Tue Mar 17 18:57:07 2009 +0000 Added some padding to table on pgSnp page commit 7fe6f44b5ba75d49318b59f3c9fd80bf2df3a026 Author: angie Date: Tue Mar 17 18:53:37 2009 +0000 Added title for attribution to HGDP. commit 87a707ad0989d304e9f96a75a2e3f0c5114aa74e Author: giardine Date: Tue Mar 17 18:29:43 2009 +0000 Added border to table commit 2475a5cae0bd8ad41aca8bd778c04e0b130a2650 Author: kent Date: Tue Mar 17 18:26:50 2009 +0000 Updating test set to accommodate a harmless change in white space processing due to refactoring. commit f742ab884c398c7f836f8a434e11607fb2fdb6bd Author: kent Date: Tue Mar 17 18:25:47 2009 +0000 Adding asColumnToSqlType commit c42d7aff3b59bfd072d8d54f29f8b8bbe1164e27 Author: fanhsu Date: Tue Mar 17 18:10:47 2009 +0000 Added GSID servers to exclude for general Table Browser functions. commit 4d8b327567c5c9d6541300ee0fcdc60054a5d69e Author: angie Date: Tue Mar 17 18:05:24 2009 +0000 Human Genome Diversity Project population locations. commit ab832fa7eaf75bed16c951794c748e23d8697123 Author: fanhsu Date: Tue Mar 17 18:01:51 2009 +0000 Updated to support logicalDb. commit e6b4aab7dd7b39ba13f13e46ee2860c7d47142cc Author: rhead Date: Tue Mar 17 17:57:45 2009 +0000 Moved note about compression to top. commit 00cb1ec74f9b36a52667a1aeb00a8be5bfafd2f5 Author: hiram Date: Tue Mar 17 17:46:23 2009 +0000 Add in the all_mrna and all_est entries since the tables are unsplit commit 84c508cf5fea53a095d8c8441b24fa53565ae033 Author: kent Date: Tue Mar 17 17:24:51 2009 +0000 Simplifying some logic where code was unnecessarily distinguishing between hPrintf and fprintf(stdout - which is an issue in the Genome Browser, but not here in the Table Browser. Also enabling select fields user interface. commit 968d2f95fe3d22cc2605a8f59e87256946b3d1c6 Author: rhead Date: Tue Mar 17 17:02:59 2009 +0000 Fixed typos, removed update line. commit 47f91cbc8594b0b0a9a2ef2efd810e8dafadd2e4 Author: kent Date: Tue Mar 17 16:28:02 2009 +0000 Adding parameter to bigBedIntervalQuery. commit e1a76eeac64482fe6b41f24d92c398aae9b39a99 Author: mikep Date: Tue Mar 17 16:06:35 2009 +0000 adding link to reports commit 91a65c3a0011dda70ef45ddfe07ae90a609698c8 Author: galt Date: Tue Mar 17 15:00:07 2009 +0000 "Encode release log update" commit bfa8ff5dd154751762e35d25876fcc65378daacc Author: galt Date: Tue Mar 17 15:00:04 2009 +0000 "Release log update" commit b4b5d58221b52af822358fd0fdef252bf3c5685a Author: mikep Date: Tue Mar 17 14:42:44 2009 +0000 v203 preview commit e6d53c69800f82632e8a24f5902e9f8d6ef7ca3d Author: mikep Date: Tue Mar 17 12:03:29 2009 +0000 adding standard blurbs commit f426535412ab63b10f61bdea3c9d1359ec5b0825 Author: mikep Date: Tue Mar 17 11:25:26 2009 +0000 fixing tpyo commit 4cf0824491502ad0902aa6c1052d2d90e19ef249 Author: mikep Date: Tue Mar 17 11:20:15 2009 +0000 making it easier to find .ra bugs commit 6a15dc08b21df9418b269b9caa844a0e5cae4b0e Author: aamp Date: Tue Mar 17 10:13:27 2009 +0000 Adding microarray stuff to output microarray names in the microarrayGroupings.ra file. Also put in some bits to output the microarray groupings themselves but that's incomplete currently. commit 33f8d161b48b43ab15ffd791d0cfa8d3b2be0608 Author: hiram Date: Tue Mar 17 05:56:38 2009 +0000 Remember answers to hDbIsActive and hgDbExists, was being called thousands of times during a simple refresh commit 631ceaed607e70a2e8693e93a3de9861c05acf5e Author: mikep Date: Tue Mar 17 04:48:32 2009 +0000 removing GIS RNA PET Project while I reload it commit 52c553d0dc82b7839c4f49e6086c5bb0fef3d1c8 Author: hiram Date: Tue Mar 17 04:35:44 2009 +0000 allow net tracks to color by gray scale, and fixing chain tracks Ui options commit d15f0ed10ebdfd3245f221b8e9f184b75c6dcb9d Author: kent Date: Tue Mar 17 04:28:39 2009 +0000 Adding parameter to getHti, and creating a hti object for bigBed tables out of the associated .as information. commit 998f6d7db61c04d2aa091c3133b7f23bf86c4a87 Author: kent Date: Tue Mar 17 04:24:28 2009 +0000 Making hFindBed12FieldsAndBinWithConn static. Initializing empty strings a place where it might have been missed, and would certainly do no harm to add. commit 306a6a2ab3988659ea8afd779909f9e5477af41c Author: kent Date: Tue Mar 17 04:23:40 2009 +0000 Removing function prototype for a nonexistant function. commit 134ab85955bca3eb296729869f7ea3317af614a5 Author: kate Date: Tue Mar 17 04:06:03 2009 +0000 Keep configuration panel on by default for SUNY track commit fe4769f70ae25cbb94e7160ff445190b7b978e8e Author: kate Date: Tue Mar 17 03:59:39 2009 +0000 Add settings config for SUNY track commit a878ef2eb088f213b3a050b10587edf7bdf2194c Author: rhead Date: Tue Mar 17 00:58:53 2009 +0000 Major changes to text. Removed description of bed format. commit 3ff334436a54a8fb412d87227929dc850a1eb6e6 Author: tdreszer Date: Tue Mar 17 00:21:46 2009 +0000 HeLa-S3/Input for Duke UTA commit 082b92557d8e05630eb5af3f9fdb410c1d39e1d6 Author: kate Date: Mon Mar 16 23:36:25 2009 +0000 Adjust SUNY track labels and subtrack config for usability commit 71b24844a131e670f73470875a1a68b9bf2da1d6 Author: mikep Date: Mon Mar 16 23:33:58 2009 +0000 fixing problem with CSHL where this track should be short rna not shortDeplRrna commit f6890c23a3cc1dd15e2999ddcb866e6758627fd0 Author: kate Date: Mon Mar 16 23:33:43 2009 +0000 Edited for clarity commit 5a5d4a585f8606b623e29867ee86129890f8908b Author: rhead Date: Mon Mar 16 22:42:10 2009 +0000 Fixed broken link to lior pachter group. commit 8f91f6ebe3d66e6bf26bf020caf84e87517bf951 Author: mikep Date: Mon Mar 16 22:28:00 2009 +0000 added an option to not do downloads (and implicitly not do table load) so that I could regenerate pushq and whatever else gets done, because I loaded 16 GB of data and got a mysql error on the trackDb step immediaetly after the load was complete. commit c7a2500312c1d47402ca761279a6bdc396e40e66 Author: tdreszer Date: Mon Mar 16 22:23:11 2009 +0000 Presort to set priorites in trackDb now defaults to 10000 and above, allowing new subtracks to appear after subtracks known to cart. commit 0f6561d942d3da7a1636f769b9dbaf7e05f8a82b Author: angie Date: Mon Mar 16 21:40:39 2009 +0000 Always show up to 20 most recent error 500's. commit 59802ad57f5a4ee8275b09a25acc0f0d0f4e41b4 Author: angie Date: Mon Mar 16 21:29:34 2009 +0000 Added missing

. commit f51e54d81846fe19809bcab8984d1b84b9d8a838 Author: angie Date: Mon Mar 16 21:26:44 2009 +0000 Fixed formatting error (too many tabs) that was tolerated when hgLoadPsl wrote its own .tab file for loading but caused trouble when hgLoadPsl (with -nobin and -noSort) sent this file directly to mysql. commit cb4d4d355d96318abbe404215a7dd1fca3d9a422 Author: angie Date: Mon Mar 16 21:20:35 2009 +0000 LiftOver to dm3 for genome list q. commit fd0e3c6a51c65760a95bfffd92f683dbda77b5e5 Author: rhead Date: Mon Mar 16 21:17:16 2009 +0000 Whitespace changes. commit 7212301d4d1c1b1b4bd2349a8deaf65af4b50a91 Author: kate Date: Mon Mar 16 19:47:22 2009 +0000 Expand cell type in label, at request of Peggy Farnham commit 0c60e60ad9f5772cbbc388635fb882b2a5e680be Author: kuhn Date: Mon Mar 16 19:32:36 2009 +0000 lower-cased mt-tRNA for mitochondrial commit cdfd7de35e24063fca1e8e8be2b118ff15f246d8 Author: tdreszer Date: Mon Mar 16 19:06:11 2009 +0000 No longer default subtrack list when all are unselected. commit 56c5dd685b0c1169bbddf73536401f79b58fc8e8 Author: kent Date: Mon Mar 16 18:35:13 2009 +0000 Polishing bigBed status page a little. commit be351d0a3512cd58968ddca28b2ddfa167c8522e Author: kent Date: Mon Mar 16 18:34:46 2009 +0000 Adding bigBedItemCount commit 3138de74801072e1dba543fd9f866b9caba4f527 Author: kent Date: Mon Mar 16 18:23:06 2009 +0000 Adding parameter to bedAsDef. commit 6d58994275c75d1ac7e36c074498fc25fb9090ce Author: fanhsu Date: Mon Mar 16 17:44:24 2009 +0000 Added logic to disable other functions of TB (besides view table schema) for CGB servers. commit 6646478dfb299053e9c67d4b5ef3ca1b4fa4fbcd Author: mikep Date: Mon Mar 16 17:31:51 2009 +0000 tracks finally loaded commit 552be11c585a9c79956181768491e02c078c662f Author: mikep Date: Mon Mar 16 17:31:40 2009 +0000 adding standard blurbs to CSHL commit e3cedcd1aad1b113df38e924453198ef56b05381 Author: mikep Date: Mon Mar 16 16:22:20 2009 +0000 add validateFiles to makefile directory list commit fd3fd20b655dcfcbe4cbcc78283541597e813f46 Author: galt Date: Mon Mar 16 15:00:07 2009 +0000 "Encode release log update" commit f671d77af8a4781f27abd5d7759b7b72fbde2c41 Author: galt Date: Mon Mar 16 15:00:04 2009 +0000 "Release log update" commit 3cde2ec522b38a94bb42c8862904288e8470bdd4 Author: kent Date: Mon Mar 16 05:08:48 2009 +0000 Starting to add bigBed support. So far the schema button works at least. commit 1350ba6ff9a883e8f3b59728d9e41bcfe3050e3e Author: kent Date: Mon Mar 16 05:07:54 2009 +0000 Adding maxItems parameter to bigBedIntervalQuery. Checking that asFile field count matches tab-file field count. commit bcc53a737922d2d465986c16edeb1099716a349a Author: hiram Date: Mon Mar 16 04:12:59 2009 +0000 *** empty log message *** commit e5c54ae24ec090fb51e1852586fb2c9fcd4b6901 Author: kent Date: Mon Mar 16 01:01:20 2009 +0000 Testing bedAsDef. commit 4768d3ca1af52cc3157b96dc2f311d952975efa7 Author: kent Date: Mon Mar 16 01:01:12 2009 +0000 Adding bedAsDef. commit b3676bb515a5249edecf78d21a77af268c0db3bc Author: kuhn Date: Sun Mar 15 20:13:45 2009 +0000 added obvious links for download and web config, so users don't have to wade through text to find the right pages commit e790737e635c0a8724e79e60746d08ef18265ac5 Author: kuhn Date: Sun Mar 15 20:07:18 2009 +0000 removed tabs to make indenting only two spaces. cleans up html so it doesn't wrap so badly commit f11c6f640c0a8806cfb697fa1ebe06b60ecadd37 Author: kent Date: Sun Mar 15 18:03:03 2009 +0000 Adding -as option. commit c33b0e3c8dba600e9c324a0b35bbfd4453a2b8d2 Author: galt Date: Sun Mar 15 15:00:07 2009 +0000 "Encode release log update" commit ac1c8441938d23901b2c8e1c004fc1cbae75b7ee Author: galt Date: Sun Mar 15 15:00:04 2009 +0000 "Release log update" commit 20acc5d707225c349d0e250058be04859576e10a Author: larrym Date: Sun Mar 15 02:00:04 2009 +0000 validate all of wiggle files commit 536b9ca7b3f3a70441a8805e90dfeb95f8cfe48e Author: kent Date: Sun Mar 15 00:18:23 2009 +0000 Adding fields flag. commit ad1a80b02b9dc8ff8d920452a4b1a164cf7add00 Author: kent Date: Sun Mar 15 00:17:52 2009 +0000 Adding asFile to bigBed. commit 4206336cacb8e8cc99bac919a3e09ce9199f79e4 Author: kent Date: Sun Mar 15 00:17:14 2009 +0000 Adding udcReadStringAndZero commit 053aa6a838d379e36e287ebbae35e28a87972cfd Author: tdreszer Date: Sun Mar 15 00:16:45 2009 +0000 Checked in cfgNetAlign to get passed compiler error commit 1917981a178d48c74e604b63dc9f7e12bda85dc0 Author: kent Date: Sun Mar 15 00:16:41 2009 +0000 Adding BIGDOUBLE constant. commit c30a27ba486cf6a124688a4db478478affc65ab3 Author: galt Date: Sat Mar 14 15:00:07 2009 +0000 "Encode release log update" commit 47e59f11ec0cdd95a9ce4be406b12dd2e5343b86 Author: galt Date: Sat Mar 14 15:00:03 2009 +0000 "Release log update" commit 8e05a12f7d968c499d771711a36f36871763bc93 Author: mikep Date: Sat Mar 14 07:28:09 2009 +0000 noAutoCreate setting at top-level of daf to control generation of autoRawSignal files, and downloadOnly setting in DAF views to control whether files are loaded or not commit 81fb3eeb23166df510c87d15b86f2fd19f9f0e94 Author: mikep Date: Sat Mar 14 07:26:56 2009 +0000 adding downloadOnly property to Views in DAF, adding validateFiles support in broadPeak, fastq, tagAlign so can validate CSHL data in reasonable time commit bba9c965ed420a2632004c6f2d21eff1c80c9e71 Author: donnak Date: Sat Mar 14 00:21:31 2009 +0000 Added

commit 32fbb7995ba7e8ba42515f7ac02a4ced8f26fe9d Author: donnak Date: Sat Mar 14 00:20:40 2009 +0000 Archived several items. commit 81ec473168c332288be18c1673423eb53c21fc49 Author: donnak Date: Sat Mar 14 00:20:27 2009 +0000 Added blurb abt ENCODE data. commit 0d3f8ebc88f8343cbab99d9a1e600d8516820056 Author: mikep Date: Sat Mar 14 00:12:54 2009 +0000 mods to keep massive sorts under control; sort files independently with mem limit, then do merge sort of all commit a73cdab64f878674fbc79a575db7417f3fa28319 Author: markd Date: Fri Mar 13 23:55:41 2009 +0000 added galGal3 N-SCAN commit 301172917fed9bc14819ba3047e34b7b7a7108a9 Author: tdreszer Date: Fri Mar 13 23:35:43 2009 +0000 Add support for enable/disabling checkboxes by having 4 state boolShad hidden inputs commit 12c2b84d003d35a62b21555702f56fad97411414 Author: mikep Date: Fri Mar 13 23:23:51 2009 +0000 mods to usage message commit ddea4033b5ef1b57a12da00ca09469d78ece571b Author: kent Date: Fri Mar 13 23:04:52 2009 +0000 Putting up message about limits of subtrack merge in summary status page. Getting more extended intersection options back. commit 17e3aa397999434735142eb7a6233c72822b66c1 Author: hiram Date: Fri Mar 13 23:02:08 2009 +0000 Fixup the naming of the chain track variables in the multi-view composite commit 0bc27386239b5f4ed7cfe144d45bd097689ec5a4 Author: tdreszer Date: Fri Mar 13 23:01:27 2009 +0000 Add support for enable/disabling checkboxes by having 4 state boolShad hidden inputs commit 2a9dbc07a664fbf28769683b4f325303fa8e4d3b Author: mikep Date: Fri Mar 13 23:00:02 2009 +0000 added bedGraph as bedType variant and modified usage text commit 38d75edbfadbfef7a2fea98717a8bff262ef9bd2 Author: kent Date: Fri Mar 13 22:51:55 2009 +0000 Fixing problem in bigWig custom track output. Testing (seems to work) with subtrack merge. commit 864dda45b5052a3477b9bfb253f3534eeaeabd07 Author: ann Date: Fri Mar 13 22:36:25 2009 +0000 hard coded link commit 091b42daaaaf5d393bbf73a6367efc881aa5461c Author: hiram Date: Fri Mar 13 22:33:13 2009 +0000 New option -inclHap to pass along to the net stage, and properly find at least some kind of db name from the path commit 92058cdda4ef4ad2050fff4c5d4d8bd40c97bf13 Author: hiram Date: Fri Mar 13 22:27:12 2009 +0000 eliminate the duplicate hiveDataGenomes specification, been fixed elsewhere commit 57adc2d0b864192c3b747323d979eda19c405905 Author: kate Date: Fri Mar 13 22:23:09 2009 +0000 Tweaks to News item for Yale track release commit d109f974aaf842c2bc7d189b3f0ff93a39e5b628 Author: hiram Date: Fri Mar 13 22:14:49 2009 +0000 Updated descriptions to be close to final versions commit b7e66ac59291dab07deb5e64414be7f2560d96bf Author: kate Date: Fri Mar 13 22:10:37 2009 +0000 Turn on K562 experiments by default, to beef up track commit e65e5e8976a32d628171370fdbb2d70faf94484a Author: hiram Date: Fri Mar 13 22:07:58 2009 +0000 Much more closer to a final description commit cc45b0b57cbba4fd4661eeae2ec6be6a2584a9dc Author: kuhn Date: Fri Mar 13 21:44:23 2009 +0000 fixed typo commit c220323a879d2781ef455093a1f42bf0a1b7d650 Author: kuhn Date: Fri Mar 13 21:42:44 2009 +0000 added title of project higher up in text so the acronym in the track name, HGSV, is more clear commit f61fc6489f116b567a382ec966d14e7d90215b6e Author: kent Date: Fri Mar 13 21:40:33 2009 +0000 Making a sweep to make sure that bigWig is addressed everywhere bedGraph is addressed. commit 3c06609514c2ff96f7ad8555501b60ba12e62884 Author: mikep Date: Fri Mar 13 21:36:00 2009 +0000 adding narrow and gapped peaks commit 9fc6155ae4beccd63a5dfcd485e9953fea9453ef Author: angie Date: Fri Mar 13 21:29:22 2009 +0000 Extra vertical whitespace between alt. pcr matches as suggested by Brooke. For HapMap SNPs (Phase III), show average of populations' allele frequencies instead of sum of all individual alleles. commit ac34780b1c904e287e54f6544f9a9c7549ba3d2f Author: angie Date: Fri Mar 13 21:07:50 2009 +0000 Added Browser and Email links after session-update message - thanks b0b for the suggestion! commit 34a1fb36facb294e4a6a18c8a863cc1656741ad9 Author: mikep Date: Fri Mar 13 20:52:41 2009 +0000 support for broadPeak commit ca3c0ca712be230eb5cc7d759a7f51c672487d91 Author: mikep Date: Fri Mar 13 20:15:25 2009 +0000 improved usage message, continue after error in # columns, add csqual, put colorSpace as option commit 74adfeaef8a0bc7fc476a0d981d62fdd7274993a Author: kate Date: Fri Mar 13 20:13:43 2009 +0000 Add news item for first track release, and also Downloads link on left blue bar commit c7c73365840e3a1029406d781949f2c0550e955e Author: hiram Date: Fri Mar 13 19:15:11 2009 +0000 liftOver to hg19 done commit fcd917dd9e2d7574fb449fa1b7e3c995b3a9dab7 Author: hiram Date: Fri Mar 13 19:14:27 2009 +0000 cpgIslands done, genbank run done, blatServers assigned commit 7aeca1325df0a059d289a953c48c995c49a437d9 Author: hiram Date: Fri Mar 13 19:13:34 2009 +0000 Added hg19 - Human - GRCh37 commit 3f1aa02d686086aa663a4f298d7b69b07d2c8e71 Author: hiram Date: Fri Mar 13 19:11:07 2009 +0000 No need for chainColor setting commit 22a4dbc1ac996c7f48eae52c8459041adf7d56bc Author: tdreszer Date: Fri Mar 13 19:04:15 2009 +0000 Change link to static terms doc to absolute path, avoiding problems with releasing index.html to RR commit 260b60a46ba9b58e19543731c7c2316cd92b6ea1 Author: kuhn Date: Fri Mar 13 18:05:26 2009 +0000 changed description of output slightly commit 735c5e3aa79f1ef6072c7b7a760f24d25c3d8eaa Author: kate Date: Fri Mar 13 17:22:43 2009 +0000 Darken color for Hek cell line a bit, at Q/A request commit 9703b519eeb36cfe3a6ec7a2b47f959ea41f1270 Author: tdreszer Date: Fri Mar 13 17:15:07 2009 +0000 Added HepG2 Input for Duke/Terry Furey commit 93e131b98ec7f815251a50b092d199e257d20578 Author: mikep Date: Fri Mar 13 16:45:26 2009 +0000 provide colorspace as option to include chars 0-3 in DNA commit 619c82a559fae150a878fada59c1ef32919372a7 Author: mikep Date: Fri Mar 13 16:39:21 2009 +0000 making everythign use linefile so .gz/.bzip2 files handled automatically commit 136e1ecec96769c17dc57383a2f142f89cbecec4 Author: fanhsu Date: Fri Mar 13 16:31:57 2009 +0000 Disabled Convert on top bar for CGB servers for the time being. commit bd3059b915e5831931ae7d00a0ff93a3c6de38e7 Author: fanhsu Date: Fri Mar 13 15:33:17 2009 +0000 Created hgNotAvail.c. commit eb859e8cdd0abc36090428ea0ec6ca33622227be Author: fanhsu Date: Fri Mar 13 15:32:48 2009 +0000 Created makefile. commit 5c1d0d2d6254903e9f99ed033557b745bd76a191 Author: galt Date: Fri Mar 13 15:00:06 2009 +0000 "Encode release log update" commit 4641235f282cafc569234b2292c57c93d59b58ee Author: galt Date: Fri Mar 13 15:00:03 2009 +0000 "Release log update" commit 43e07386e5c0101ed8b8d75c978a645fca961083 Author: mikep Date: Fri Mar 13 08:22:13 2009 +0000 fix so comment lines only appear at top of fastq, and added csfasta format commit 8e9ecd1f4a9da133b0650cd763e85b728260fe08 Author: mikep Date: Fri Mar 13 05:22:46 2009 +0000 plug the memory leak, > 100bytes per input line, fatal for ENCODE commit f936eb8e34809ea7977d3678890ae8f60b4ba128 Author: mikep Date: Fri Mar 13 04:52:28 2009 +0000 support for fastq commit 6d957d3fd6ccebe2b4960c1d8f37e50b99951fbc Author: hiram Date: Thu Mar 12 23:59:18 2009 +0000 The haplotype mapping to reference is now bed 12 commit ff8a27671eecdf51e8d929c445560861e8435168 Author: mikep Date: Thu Mar 12 22:41:01 2009 +0000 add -type= to main usage line commit 6c145dfbf0af88d588c14688cb23a1e9658b33d0 Author: aamp Date: Thu Mar 12 22:35:13 2009 +0000 Vega genes update. commit 6aee607da39fd4e506bae6a9eab0330e03960bbd Author: mikep Date: Thu Mar 12 22:24:18 2009 +0000 first version of a validator for encode, currently supports tagAlign and pairedTagAlign, much faster than Perl adn does extra checking on start Date: Thu Mar 12 21:51:26 2009 +0000 Disabled the otherOrg section for CGB server for the time being. commit 13a698444226d6ae89ad398bd0cf909e652ce2e3 Author: angie Date: Thu Mar 12 21:08:21 2009 +0000 Added more descriptive info from ref's and added links to source code tars from Joe Pickrell. commit 7404761f12bcae841a0b51481091a92cf8e24182 Author: kent Date: Thu Mar 12 20:56:40 2009 +0000 Adding wigCompareFromString and wigCompareValFilter. commit 982fc35485a75fdf989643fb8da74901f0200f8f Author: kent Date: Thu Mar 12 19:44:21 2009 +0000 Making correlations, and bed output work with bigWig. Possibly subtrack merge works too, but need to make a test case for it. Custom track bigWig output is still broken. commit 7629c550e1402b501ebe403ff9e5fa1ae0951711 Author: fanhsu Date: Thu Mar 12 19:22:32 2009 +0000 Changed hAllocate() to hAllocConnTrack() to fix a bug on CGB servers due to the logicalDb. commit 5367e0af43727a3d3fa8174f7a97db7a682f0789 Author: tdreszer Date: Thu Mar 12 18:34:34 2009 +0000 hgEncodeVocab needed to be built with the BROWSER_BINS commit ef53e386b296279cb11dc4f0d8aa4a7b385d680c Author: angie Date: Thu Mar 12 18:24:04 2009 +0000 Fixed coords of hgdpHzyBantu and reloaded. commit 8b6a85e13214a69d3f4711dcd525cc2b87b5e00c Author: angie Date: Thu Mar 12 18:22:54 2009 +0000 Removed the alpha from hgdpHzyBantu -- coords adjusted, looks good now. commit b059db996f8724ba89255c563ef79a9e6b7e42f3 Author: hiram Date: Thu Mar 12 17:53:09 2009 +0000 Going to try non-split tables for hg19 commit 430fae8859948694efc0994292b8bd030c0e25cf Author: angie Date: Thu Mar 12 17:40:33 2009 +0000 Sort output by target coords unless -noSort is specified. Thanks MarkD for the idea to pipe output to sort! commit c88660adfb4291ec23967d3bcbc3ee4727d75261 Author: fanhsu Date: Thu Mar 12 17:38:30 2009 +0000 Disable TB for CGB servers. commit f882c33b5b1e71b897cf44c1dc537eda620b648d Author: kent Date: Thu Mar 12 16:45:16 2009 +0000 Making filter and non-base-pair intersections work with bigWig. (Base-by-base intersections work 80%, but going to have to change design to get last 20% working.) Fixed bug I introduced in correlation of regular wig that Kayla spotted. Moving bigWig stuff to it's own module. commit a3f90a20d5eb59d3f7516e054cdce8c6b9032c0d Author: fanhsu Date: Thu Mar 12 15:49:04 2009 +0000 Disable TB on CGB servers. commit 437b48894d4b3c6b52f52e65633d6c7a20da2989 Author: fanhsu Date: Thu Mar 12 15:44:31 2009 +0000 Disable CT for CGB servers for the time being. commit 44beb5dbe546bd9a69a7d1c59dcaab78a7e816f7 Author: galt Date: Thu Mar 12 15:00:07 2009 +0000 "Encode release log update" commit 74d6c2bd5fd10d02c0076a2e779358137bea2eca Author: galt Date: Thu Mar 12 15:00:03 2009 +0000 "Release log update" commit 9ea316d142a6770635f798a1b6931ea807bf4858 Author: hiram Date: Thu Mar 12 03:51:44 2009 +0000 Fixup the haplotype multi-view commit 48e6aae604843c0082bc88b3bff6ce9da2e3ac65 Author: hiram Date: Thu Mar 12 00:05:48 2009 +0000 Fixup chain and net trackUi so they will work in multi-views commit f3c6eb42f6f3f821fc8fa0eced6d9a019f7594c7 Author: kate Date: Wed Mar 11 23:58:12 2009 +0000 Expand a bit commit a9773eca0bce5764a43b00ec1e52e13c36c4613a Author: hiram Date: Wed Mar 11 23:57:39 2009 +0000 Move notes about data values to immediately follow the type definitions, indicate default span is 1 commit a3ec58e49d863b934ecf6796fe07a04fa2840579 Author: hiram Date: Wed Mar 11 23:17:59 2009 +0000 Add a date/time stamp at the bottom of the page commit 54ddfed24720c15cf9940cf45eec4c68319125b4 Author: hiram Date: Wed Mar 11 23:15:35 2009 +0000 Clarify the span windowSize settings commit e2cc6966ab2a64b96c5252c17f73e2bcdcda5845 Author: kate Date: Wed Mar 11 23:08:28 2009 +0000 Revert last change -- we need to wait till the RNA data submissions quiet down first commit 7e38b36c7209f567f6315398cd5589f6ad2e70a4 Author: kuhn Date: Wed Mar 11 22:36:20 2009 +0000 added favicons for the three levels of publicness commit 7ec1089f93d322cd15aea3c4ebbc1c1441575130 Author: tdreszer Date: Wed Mar 11 22:32:49 2009 +0000 Change Type to Class in the table of colors commit cdfe45498e0ce78d12a28439b0888d7f7196d542 Author: angie Date: Wed Mar 11 22:30:11 2009 +0000 Restoring option -allowStartEqualEnd which I shouldn't have removed in 1.52 (thanks Kate). SNPs and other tracks with valid 0-length items like insertion points will have to use -allowStartEqualEnd, but most tracks will get the appropriate level of checking b y default. commit 849efa1e774004eeab5bf785f88f660cc05b9ec6 Author: kate Date: Wed Mar 11 22:19:27 2009 +0000 Move ENCODE downloads down a directory level commit ca1f896d9f7b79eb56292d4c5d527854dde31f56 Author: tdreszer Date: Wed Mar 11 20:03:47 2009 +0000 Added HepG2 DNase for Duke/Terry Furey commit 93d9633af609714d5c93b808cb2cfad15f22ac01 Author: galt Date: Wed Mar 11 19:24:31 2009 +0000 fix - erase cart do-commands just in case of errAbort commit aaea8e898419a1e5b7738755e1a53f4865a24460 Author: kate Date: Wed Mar 11 18:34:59 2009 +0000 The Q-value is log after all commit 66bf6a28df2f7678d09408474362e12263958f4e Author: angie Date: Wed Mar 11 18:31:44 2009 +0000 Updated DGV (v7). commit e9dfd129f04fa5c3d993e144483e4820c2ec4090 Author: angie Date: Wed Mar 11 18:30:25 2009 +0000 Added release alpha setting to subtrack hgdpHzyBantu because it seems to be in a different format than the others. Updated DGV's dataVersion to v7. commit b05c73478a0a7b827d7f815f1fca08f44ba5637f Author: angie Date: Wed Mar 11 17:59:09 2009 +0000 Adding sections for Genome Variants subtracks loaded by Belinda. commit 63da2956e711cdf18c9b8a629b7e9ac4c49c18e7 Author: angie Date: Wed Mar 11 17:55:56 2009 +0000 Added Genome Variants tables to tablesIgnored. commit ad102781dfde9d92af55467d8f22f677fd423a9f Author: kuhn Date: Wed Mar 11 17:19:52 2009 +0000 put hgw7 back in commit bbcebeabf24436619ff886cb9ac53a4999b1f9ef Author: angie Date: Wed Mar 11 16:57:06 2009 +0000 hapmapSnpsUi: incomplete html found by Jim in code review. commit e505f8d2223944ddecfc34f7f38bc3ba76059bbf Author: galt Date: Wed Mar 11 15:00:08 2009 +0000 "Encode release log update" commit 72056f7867547884ab277488e61fe4bbfeffb7d0 Author: galt Date: Wed Mar 11 15:00:06 2009 +0000 "Release log update" commit 0ef8e01f1cb907035c6ee18bee50f880c58d9197 Author: mikep Date: Wed Mar 11 08:12:07 2009 +0000 adding a link to the history commit db1cee3f56202d6598eaf9af0bef4223682d5990 Author: hiram Date: Wed Mar 11 03:26:58 2009 +0000 incorrect path for hg19 unbridged lift file commit e05228f16c4ab4e38081c7e854327d3d0b82f7c7 Author: rhead Date: Wed Mar 11 02:15:49 2009 +0000 Moved more periods outside of links. commit e9c3c613958bde4af83f83766b175829888e8613 Author: ann Date: Wed Mar 11 01:06:22 2009 +0000 moved period outside of link (thanks Brooke) commit e0a77451d4b22c7f962d9616580d3ddd7cd8974b Author: hiram Date: Wed Mar 11 00:00:57 2009 +0000 added hg19.lift and hg19.hapRegions commit ef7fcb0e730b57213031a84921aeadc0393b54cc Author: hiram Date: Tue Mar 10 23:39:58 2009 +0000 An attempt at a multi-view chain and net situation commit 94f2c000528bd58a65a6481f0313797788a96a25 Author: rhead Date: Tue Mar 10 23:22:25 2009 +0000 Removed a comma in refs. commit df97227f70d1f1734c47519f66986fd1277cf5e3 Author: rhead Date: Tue Mar 10 23:10:31 2009 +0000 Capitalization. commit ac20a45f357e7de67b8d42a752e5795ab9eda0bb Author: fanhsu Date: Tue Mar 10 22:19:31 2009 +0000 Updated to reflect the KG related tables update. The working directory is at /hive/data/genomes/gs.19/build36/bed/ucsc.11/update2. commit 3aa6af067ff8fb90fe22a8330d07b3b529606315 Author: hiram Date: Tue Mar 10 21:52:36 2009 +0000 Haplotype chains and nets added commit b27299bcc25414247b7b9928f0236ff17c09c5b6 Author: angie Date: Tue Mar 10 21:05:12 2009 +0000 Split off the unreleaseable subtracks of pgSnp (Genome Variants) into a new composite track, pgSnpHgwdev. More polishing of pgSnp.html in preparation for release. commit 1157d86ec1374b0a9a1f4728ab8180e270d6c655 Author: ann Date: Tue Mar 10 20:58:25 2009 +0000 fixing citation commit ebc627dc05b25d37e1d16ece60ff96fec17e6675 Author: angie Date: Tue Mar 10 20:47:20 2009 +0000 Registered pgSnpHgwdev (Belinda's Genome Variants subtracks that should remain on hgwdev for now. commit 70ccd04dcab0018e0885816774374ad5af889eb7 Author: galt Date: Tue Mar 10 20:39:34 2009 +0000 oops do not want debug symbols on by default commit e0cca97f249984d48600d7fa089833383c70a610 Author: galt Date: Tue Mar 10 20:38:38 2009 +0000 remove one stray space commit e66733d0996dc7d6a7cdab250159d5d9954f4285 Author: markd Date: Tue Mar 10 20:30:14 2009 +0000 fixed typo in comment commit 71df635eac133d68bfb29d0476ba902f859729ca Author: tdreszer Date: Tue Mar 10 20:11:40 2009 +0000 Updated labels for Encode Gencode February Freeze commit e5fdbe27e137f643f4f1b7ab65f2894bcc5ca883 Author: kate Date: Tue Mar 10 19:55:22 2009 +0000 comment out downloads link for now commit d92b6ff6f2f55d90e7ed18b2a34fc3e35788001c Author: larrym Date: Tue Mar 10 19:27:47 2009 +0000 change exec to handle cases where /data/tmp doesn't exist commit e2bf7e48595c7a17209c501fa214c0b0352deec0 Author: hiram Date: Tue Mar 10 19:05:42 2009 +0000 Larger entry field for filter by chromosome on a chain track commit f429b6708a7e78e2412863b9e64fed8d92cc0471 Author: mikep Date: Tue Mar 10 18:35:37 2009 +0000 these error files get too large for /tmp so put them in /data/tmp where the rest of the tmp files go commit ce0f08171b740154186ff23721aaa87ab1088960 Author: mikep Date: Tue Mar 10 18:21:16 2009 +0000 last of the affy freeze commit 1262ae743b71b64500a4f2a5512d0d843e99ad00 Author: galt Date: Tue Mar 10 15:00:07 2009 +0000 "Encode release log update" commit 139ed4b9f68b81d8e54fbe8183be0905c3d76975 Author: galt Date: Tue Mar 10 15:00:04 2009 +0000 "Release log update" commit 6fafdd418d82d19e894a1da0f6bad3684fc431d0 Author: mikep Date: Tue Mar 10 14:37:23 2009 +0000 "New version number v202" commit dbe77d4cbbcf6692a6e6b2d7c5cce027f722eafb Author: mikep Date: Tue Mar 10 14:36:23 2009 +0000 v202 final build commit 13a1cad27f64daef5ab5e645b7e8bbdc2d1318f7 Author: cszeto Date: Tue Mar 10 06:26:54 2009 +0000 New datasets commit cc683477d3c3ab84acbc25ad21009202dea54e65 Author: mikep Date: Tue Mar 10 06:04:48 2009 +0000 removing CSHL stuff while it is reprocessed commit fb1353d4cfe9553aacad855823a69037d8d91e8a Author: kent Date: Tue Mar 10 01:25:24 2009 +0000 First cut of bigWig integration. Handles data point and stats output in cases where there are no filters or intersections going. commit e417ee6675110aa55944d859df0d0ac3a913e2c7 Author: kent Date: Tue Mar 10 01:14:53 2009 +0000 Adding bigWigIntervalDump. commit 566ea232e6d018968ac7b117d514569ce3adbd8f Author: galt Date: Tue Mar 10 00:34:51 2009 +0000 Modifications to make system to support optional external libraries, motivated by need for SSL commit 683e7f6f45e777a8c2c031217ca64c7b4ce65eb7 Author: galt Date: Tue Mar 10 00:31:23 2009 +0000 adding https support commit 009c3b7bcdb91b5b677bde346a8ae8b1a9909ffc Author: kate Date: Tue Mar 10 00:18:14 2009 +0000 Switch ENCODE downloads link to appropriate downloads server. Also, Add link to multi-view help. commit 67b80f385252c9b494ed0b6267fa7b0c5c6a9774 Author: angie Date: Mon Mar 9 22:41:17 2009 +0000 Added Human Genome Diversity Project tracks. commit 3ec76ee442b345d08b0832c550520f38c5836997 Author: angie Date: Mon Mar 9 22:23:52 2009 +0000 Resurrecting old human/hapmapSnps.html as the renamed hapmapSnpsPhaseII. Added note about heterozygosity calculation and latest HapMap pub ref. commit 8bced7f78284e65e14deeec5ef75608a18606996 Author: angie Date: Mon Mar 9 22:07:11 2009 +0000 Added hapmapSnpsPhaseII track (replaced by the new PhaseIII track in hg18, but kept around in case folks relied on its het. calcs). Added hapmapPhase setting to snp129. Just for kicks, checking in hapmapRecombRateBW, a BigWig. commit 23599c17510c96632b236fe05a5384c913788ca8 Author: angie Date: Mon Mar 9 21:43:44 2009 +0000 Added support for hapmapSnpsPhaseII track (replaced by the new PhaseIII track in 18, but kept around in case folks relied on its het. calcs). commit 3665369c2f82d82720cd0dc828b694f919644351 Author: angie Date: Mon Mar 9 21:17:52 2009 +0000 Added support for hapmapSnpsPhaseII track (replaced by the new PhaseIII track in 18, but kept around in case folks relied on its het. calcs). commit 08704c95f0406b2ac0acf290d89ab8f0fe6c50da Author: hiram Date: Mon Mar 9 20:53:40 2009 +0000 Add haplotypeChain track commit 1f4dc9c40ceb719a376be77ad60e0917c87b299f Author: galt Date: Mon Mar 9 20:53:19 2009 +0000 ENCODE is really making huge lists commit da213aad032c0e45ca5128e05c6ec809d893ebbe Author: angie Date: Mon Mar 9 19:10:16 2009 +0000 For filter 'matches minor human allele', make sure the minor allele has been observed in at least one sample. commit c104875f2e5b845e75d9e14756eca49cfa81655e Author: mikep Date: Mon Mar 9 19:01:55 2009 +0000 adding standard text like Yale commit fd7dc4f5028d47650006805cc8dd158cff3ecb32 Author: angie Date: Mon Mar 9 18:59:59 2009 +0000 HapMap SNPs heterozygosity label: tweaked to match hgTrackUi. commit 299a9cde47197d3f5cff274db73cb8285731aff3 Author: tdreszer Date: Mon Mar 9 18:37:42 2009 +0000 Stdize view vis select name. Support for disabling view cfgs on hide NOT TURNED ON. Converted more code to jQuery. commit 57b188be7862a98cef33f98199e3684c8750c654 Author: tdreszer Date: Mon Mar 9 18:35:29 2009 +0000 Removed obsolete function commit 575e0405443996deb2a4520a49c6caa38d7b664f Author: tdreszer Date: Mon Mar 9 18:34:55 2009 +0000 Fix for defaulting composite tracks. Requires Stdized view vis select name. commit 769724bfa8a67f6a71305606a930af498d6d95d2 Author: tdreszer Date: Mon Mar 9 18:33:28 2009 +0000 Shift view cfgs to unique positions. Stdize view vis select name. commit 4cdd3b12d32e29650b5fa8268361b687152e4dad Author: mikep Date: Mon Mar 9 18:26:08 2009 +0000 last tracks for RIKEN commit edb32c1757e8c6234ef854d52a32b2bc6c90f3cf Author: mikep Date: Mon Mar 9 18:25:44 2009 +0000 fixing tpyo commit 0e1ab6c35dbaec2e946c380cea2a3917519df9b9 Author: pauline Date: Mon Mar 9 16:47:08 2009 +0000 Turned on genbank updates for new yeast. commit 5621049f9e04b13310242085015d3be43bf85fed Author: hiram Date: Mon Mar 9 16:43:40 2009 +0000 Fixup counting of parts to be more accurate and a uniform %02d output commit d3c65ded38f1f7f7cbf29c2f4bd26b2a4a912a17 Author: mikep Date: Mon Mar 9 15:15:23 2009 +0000 first draft of RIKEN doco commit 1ed23a8323bdc801f23454c79ce1dfd4f4e85492 Author: galt Date: Mon Mar 9 15:00:06 2009 +0000 "Encode release log update" commit e55874bc73decdc1ced4c2bff173a8ac31e4d717 Author: galt Date: Mon Mar 9 15:00:03 2009 +0000 "Release log update" commit 171f4907e6fe3698107b0f87455c585bfbb46878 Author: mikep Date: Mon Mar 9 07:05:19 2009 +0000 Transfrags not required at this stage commit c6fac50607162aef501c4d33fc3644183d6023e1 Author: hiram Date: Mon Mar 9 06:05:37 2009 +0000 fixup ssto_hap6 name to ssto_hap7 commit 080ceb2958468d9839df22e7c0602067821db493 Author: markd Date: Mon Mar 9 05:26:31 2009 +0000 added to-do commit b0e88c4ce43b9cd0c0be2001f1695b44dcc1a76a Author: galt Date: Sun Mar 8 15:00:05 2009 +0000 "Encode release log update" commit e43c6d0337b5d09f9662284e32a1969d049c5204 Author: galt Date: Sun Mar 8 15:00:04 2009 +0000 "Release log update" commit 9a35d2e786e5805830790b87309a303692143b11 Author: mikep Date: Sat Mar 7 23:24:29 2009 +0000 CS fasta can have G sequences evidnetly commit 4aee3541cbefe6db921bf7d32f8e6c909c4d0b13 Author: mikep Date: Sat Mar 7 23:04:19 2009 +0000 open tars commit 320ffc5795293c9cc304b5ee7f4f6491d599c517 Author: mikep Date: Sat Mar 7 22:59:58 2009 +0000 check if a file is a tar commit 96500b663905fba1c25396ab58e296bf352611f8 Author: hiram Date: Sat Mar 7 20:32:16 2009 +0000 Added hg19. commit 3c9887fcc6a326a5e31f12e2b8936274106f9527 Author: galt Date: Sat Mar 7 16:00:07 2009 +0000 "Encode release log update" commit 3f2e88a70dbd9914e3e188dd1abfc88c1ed8d331 Author: galt Date: Sat Mar 7 16:00:04 2009 +0000 "Release log update" commit c7fba6f91ac25a3e608d19111167a372f36acc65 Author: mikep Date: Sat Mar 7 07:22:06 2009 +0000 dont add name indexes onto this highthroughput data commit 16e9e6739fb238572391931172f5daab37462cac Author: hiram Date: Sat Mar 7 05:11:26 2009 +0000 Adding hg19Haps commit 4e289a23e36cce3f1a0a1c101353ffca86e537e3 Author: hiram Date: Sat Mar 7 05:10:58 2009 +0000 Initial set of files describing these haplotypes commit bcd2e0102006d623401b836ae4a20f97dab460e7 Author: mikep Date: Sat Mar 7 04:31:02 2009 +0000 added original Caltech data commit 57b81ed96c83b29dc4f8e3ab630822120fcf5e5d Author: angie Date: Sat Mar 7 01:13:23 2009 +0000 Added HapMap Recomb Rate (rel22) and updated HapMap SNPs (rel27). Moved a shared inline script out (to hg/snp/snpLoad/getOrthoSeq.pl). commit 374f91b6245312c91d2564b7a6a53162fb8bb6dc Author: angie Date: Sat Mar 7 01:03:54 2009 +0000 Moved human/hapmapSnps.html down to human/hg18/hapmapSnps.html. Added clarification of what is meant by heterozygosity in old and new HapMap SNPs. commit 314f2686582c8277e00f5d712295044e2d69b9ab Author: aamp Date: Sat Mar 7 00:06:33 2009 +0000 Forgot to commit some stuff. commit a37f3a38b20a8fe01f93ec977895565111ef4065 Author: angie Date: Fri Mar 6 23:53:51 2009 +0000 More specific longLabel for hapmapSnps. commit 9f6b8545281f6bb263ea926430307a7fa0119cba Author: angie Date: Fri Mar 6 23:37:57 2009 +0000 Adding hapmapPhaseIIISummary, which distills hapmapSnps* and hapmapAlleles* columns into a loading file for the hapmapPhaseIIISummary table, which is used to filter hapmapSnps subtracks in hgTracks. commit 5388687197e32d4a99ee50fc017e2b3a8cdce2a2 Author: angie Date: Fri Mar 6 23:36:37 2009 +0000 Adding script used by both snp129 and hapmapSnps orthologous allele tracks, to get the base value at the liftOver'd position in the other org. commit 4d8aed09eb508f7e7ce65e8f6a2ed06fa3eed38d Author: angie Date: Fri Mar 6 23:34:42 2009 +0000 Adding hapmapPhaseIIISummary: properties used to filter hapmapSnps in hgTracks. commit f871b40f61a3e77fc376e7941bd14012caa16de9 Author: hiram Date: Fri Mar 6 23:33:26 2009 +0000 add -noGoldGapSplit option commit 879baec321c32beda638e2611ef121f91a874ebe Author: hiram Date: Fri Mar 6 23:32:44 2009 +0000 Fixup specification of filesystem locations, and add -noGoldGapSplit option to makeGenomeDb commit 0ed047acb9a160aea7f3a0dc6f9892943166af20 Author: hiram Date: Fri Mar 6 23:27:05 2009 +0000 Done with masking, ready to start genbank when that gets out there commit 25095eed605c590d88d82ed54f09b68d7d9476bc Author: angie Date: Fri Mar 6 23:19:40 2009 +0000 HapMap SNPs: Added distinction between expected and observed heterozygosity for filtering. Finally checking in Phase III filtering code in hgTracks/hapmapTrack.c. commit 9c82eff2228ed17194a8840fcf34c17338179e68 Author: angie Date: Fri Mar 6 23:00:43 2009 +0000 Adding hapmapPhase setting to hapmapSnps. Adding hapmapRecombRate track. commit 22c1ef91eb706579eaef98f2b8c21d2939174092 Author: angie Date: Fri Mar 6 22:59:30 2009 +0000 HapMap SNPs: Added a trackDb setting to determine whether this particular track is Phase II or Phase III. Made the Heterozygosity labels more clear: the older versions of the track have expected het, but as of Phase III we're doing observed het. Fixed avg. obs. het calc ( oops, item- > score is minor allele freq not het! ) . commit 3add8505faebf9b6c232636ff551e0ff8af8b442 Author: tdreszer Date: Fri Mar 6 22:33:44 2009 +0000 Remove extra slash in link commit aaa4f98583478a15dccb68be7645f5b7e264451f Author: fanhsu Date: Fri Mar 6 22:06:58 2009 +0000 Relaxed the abort to warning to accomodate raw data file imperfection. commit f72d47b2d5c61967aaf8d7b9fec3c91db8599d60 Author: ann Date: Fri Mar 6 21:55:06 2009 +0000 removed 'release beta' for Yale TFBS tracks commit 306704b94f32feebf69c5fc638d9ee7bc3fc2e71 Author: tdreszer Date: Fri Mar 6 21:44:09 2009 +0000 Changed Yale tracks from alpha to beta release commit 90e66b8c943d70c07d84d38c93a99b5bf1e3230d Author: fanhsu Date: Fri Mar 6 21:11:51 2009 +0000 Removed an unused sr variable. commit d4d6adaa9a1d197d79043e6c3dbea425b5859964 Author: tdreszer Date: Fri Mar 6 21:10:05 2009 +0000 Protocols are now pdfs not docs commit f149a0f4091464e68abf2708f722d163c84a1c29 Author: mikep Date: Fri Mar 6 20:47:31 2009 +0000 diff header coming from GIS commit dea25289b684f57e2db47f4313836901824aba6d Author: mikep Date: Fri Mar 6 20:36:18 2009 +0000 maybe there are more rawdatas in future... commit 9340bb28ecf3558c6ba53683d43b3712ad9620dd Author: rhead Date: Fri Mar 6 20:18:13 2009 +0000 typo commit 938d0b92985d154e977f689fa9771a0151b49491 Author: tdreszer Date: Fri Mar 6 19:39:13 2009 +0000 Updated ENCODE Gencode to the latest release. Also rearranged some deck chairs in Duke commit 41207a21d9c7c40b7838d7cd22082f94e6d8997b Author: mikep Date: Fri Mar 6 19:37:43 2009 +0000 fixing view names commit fb3f6a3b412c1d6e59ec727b901ec4e87a02fddf Author: mikep Date: Fri Mar 6 19:37:18 2009 +0000 adding second set of data, new cv.ra type commit 38a57945abbfcf3514fb6e58b661355f43e258d1 Author: mikep Date: Fri Mar 6 19:23:02 2009 +0000 added link to downloads commit 62504cc9e7f49238f907ce70b10565713081419f Author: galt Date: Fri Mar 6 19:22:47 2009 +0000 tweak commit b4bab6c907840c33ec05a38d89cc6cfc2e2a9762 Author: mikep Date: Fri Mar 6 19:15:35 2009 +0000 shortend name for table name commit 5ce2241ba951884043af0fb2fa7f7e15397c7e71 Author: mikep Date: Fri Mar 6 19:14:16 2009 +0000 added text for download file method commit 83af3798abe18b97e2355f427f69e2c5e06cd658 Author: mikep Date: Fri Mar 6 18:38:05 2009 +0000 wrapping at 80 chars commit 62daf3b019d3d65ec1fdd09d0458043e721d9eda Author: kate Date: Fri Mar 6 17:40:30 2009 +0000 Correct comments for encode Peaks schemas commit 35186a8db5f3ecf8ed4eececd8e242b2c4ea4059 Author: mikep Date: Fri Mar 6 16:56:20 2009 +0000 cant put pipeline data in daf as it doesnt have variables associated commit f1121bb15fcff427304f206d6f84fb16737a6660 Author: mikep Date: Fri Mar 6 16:53:30 2009 +0000 adding rawdata files for Wold pipeline input data commit 148b64ccb0d9d3cf08eaac93586fa186e7d9f713 Author: galt Date: Fri Mar 6 16:00:09 2009 +0000 "Encode release log update" commit 79cf522b8d80cf8e86f39357eed62583b22523af Author: galt Date: Fri Mar 6 16:00:05 2009 +0000 "Release log update" commit 356db3a70ace8d05882e26be80b367ebc6dce993 Author: kate Date: Fri Mar 6 05:22:14 2009 +0000 Add link to downloads commit cd78ac134c9d46f33636dee4d9a0b063c0596c75 Author: kate Date: Fri Mar 6 05:18:49 2009 +0000 Downloads page for production phase commit ddf97cf1b0174055c88905b985a4e80f78e4c4c1 Author: kate Date: Fri Mar 6 05:00:50 2009 +0000 Uncomment release log commit ae26f970eab45a9a49faf727973d22d7a3eb4dd5 Author: kate Date: Fri Mar 6 04:54:21 2009 +0000 Add ENCODE data restriction timestamp commit f06e59784363d1570040e552f5cc7fde9267cc17 Author: kate Date: Fri Mar 6 04:37:49 2009 +0000 Change downloads section commit f4661416ce32c31aa0f5082bd0c1b364d2b5d0c6 Author: kate Date: Fri Mar 6 04:19:33 2009 +0000 Update comments commit 81bf1e3b4b815fb0f098da39c3157612c0a4d669 Author: mikep Date: Fri Mar 6 00:52:10 2009 +0000 updated DAF to handle more raw data files commit ba99b1e81d4da923ab60717a6b7357de49c210d4 Author: pauline Date: Fri Mar 6 00:37:34 2009 +0000 Edited to short form of PNAS. commit 137bbc4daed63233c2ce106b382c6d17882facde Author: kayla Date: Fri Mar 6 00:36:54 2009 +0000 added TARGET=_BLANK commit 12751690beb6b64a92cfee32b5a0c282eca241c5 Author: mikep Date: Fri Mar 6 00:14:06 2009 +0000 shorter codes commit 751bd944bca8b784873fdfc1e8aa72d2ed3e5603 Author: pauline Date: Fri Mar 6 00:01:17 2009 +0000 Added carriage returns to conform to 80 char/line limit. commit 85530501c4f9617a9211bcc71e0a6a5e76f25658 Author: pauline Date: Thu Mar 5 23:51:23 2009 +0000 Added reference and changed format slightly. commit 80114d9144156f46c3ba4163174b7c53062c2ad2 Author: tdreszer Date: Thu Mar 5 22:23:02 2009 +0000 Added rediculous variable freezeDate, rather than rewrite pipeline commit 3a83b455da02680222a7fb3c4d7b8f28d83021b3 Author: tdreszer Date: Thu Mar 5 22:10:49 2009 +0000 Tim is the Wrangler for Sanger's Encode Gencode commit 58d437aefcfd6c2fbe3e9e0ea85e698e8006b76c Author: pauline Date: Thu Mar 5 21:39:30 2009 +0000 Minor edits to make section references more explicit. commit e31c47754c7b1b089785be0b406006efca880839 Author: mikep Date: Thu Mar 5 21:33:21 2009 +0000 readType validator for Wold/Caltech commit b21b2d912db985b68e5010dd82aa009891d4b6ad Author: mikep Date: Thu Mar 5 21:30:39 2009 +0000 get rid of @_ deprecated warning commit 66c7a5cbfe45661228b243a27fd971b118136fbc Author: ann Date: Thu Mar 5 20:42:14 2009 +0000 fixing citation errors commit 41cc352aa03543d82bd7d320a7b7a75b8d87ba8b Author: mikep Date: Thu Mar 5 20:37:33 2009 +0000 fixing up cell types by removing (+) chars commit 8ca5f96caf6e274cad53bb0e3bdbd22ad5a0c987 Author: mikep Date: Thu Mar 5 20:37:02 2009 +0000 adding links to publication (not in PubMed yet tho) and new cv.ra entry for reads commit 9b9a177bc4811ff8d7c0f783ff9ad61bd1882349 Author: mikep Date: Thu Mar 5 20:33:25 2009 +0000 fixed typo commit a11cd8d49125fba54e8ccc68f77e6d34e19614a4 Author: ann Date: Thu Mar 5 20:28:49 2009 +0000 fixing citation errors commit a640fc0f876fef2eed696d51a86fec619e1a9cf4 Author: mikep Date: Thu Mar 5 20:18:21 2009 +0000 new variable readType for Caltech commit 7ebb2aa9256caad1be1fdf4b76cbcd3f4621f100 Author: mikep Date: Thu Mar 5 20:14:04 2009 +0000 removed some gnarly chars for javascript commit 34bdee4e94b9ee06b90fd5413f2b5cac73192ba7 Author: hiram Date: Thu Mar 5 19:52:55 2009 +0000 Initial database established commit c7d9b161b73d318a76617cda0803a9d0a07892fe Author: ann Date: Thu Mar 5 19:48:32 2009 +0000 alphabetized references commit dd9e022f55b92e6d4117f76d337d640486192531 Author: ann Date: Thu Mar 5 19:45:03 2009 +0000 clarified data release policy commit 6edc0335c6ce13f867716188e154e64f8c12c0a1 Author: hiram Date: Thu Mar 5 18:37:03 2009 +0000 change blastPath commit a1377f096658f663939cc196ff945ca700450d02 Author: kuhn Date: Thu Mar 5 18:11:55 2009 +0000 tweaked usage statement commit 14dd5914916f88c1ad29f388bbff36e4cd7d87f2 Author: mikep Date: Thu Mar 5 17:00:13 2009 +0000 Reformatting Caltech tracks and description commit 79d49a0723ca34e02d237bbcd5bc2db69533dda1 Author: galt Date: Thu Mar 5 16:00:07 2009 +0000 "Encode release log update" commit dfb33ae719772b1a5b10bc8ce5200cee02f32ef1 Author: galt Date: Thu Mar 5 16:00:04 2009 +0000 "Release log update" commit 23e27fbbf7fd73ca6bd1ac152de655ab6a628159 Author: aamp Date: Thu Mar 5 10:09:22 2009 +0000 Added outside link to microarray custom tracks. commit 4e7f3b836c62bf20f40b88010f3e0b6af07cb189 Author: kate Date: Thu Mar 5 06:13:57 2009 +0000 Fix up many long labels commit 0b3e17231c1330af6a6d50cfb98a4b8fb624915f Author: kate Date: Thu Mar 5 04:56:08 2009 +0000 All tracks now have short labels pruned to 16 commit 4c3916d2729ed20d067897fef3cfee9e5675e219 Author: mikep Date: Thu Mar 5 02:57:16 2009 +0000 3 different flavors of rpkm; just check the cols are there commit c9d0ad13528163f319819fb7814635345b08fd71 Author: markd Date: Thu Mar 5 00:41:20 2009 +0000 added functions to get block ends commit 73938d0c1d167294958082ad13d16b4abccbf5ee Author: tdreszer Date: Wed Mar 4 21:17:21 2009 +0000 Anti-spamasized the email commit d58c54c22ab0a3cacba9543f62c1e83cb7381d98 Author: rhead Date: Wed Mar 4 19:55:05 2009 +0000 Wording tweak. commit 3f10aa53165514fe1d67085adc14118bbf4e1257 Author: kuhn Date: Wed Mar 4 19:53:39 2009 +0000 added a comma, added spaces betw numbers and units and lower-cased Kb to kb commit 2c85d3eef08ffb74b29e07cecb543400de1beeb5 Author: mikep Date: Wed Mar 4 19:52:00 2009 +0000 adding TARGET to HREF commit bdde61330c9df65ecf350174b6a4d8081892cf5d Author: tdreszer Date: Wed Mar 4 19:49:00 2009 +0000 Fixed a spanList problem in Duke's K562 Input track commit 457220127c882a7e934bc25a7bd9d04903832ea1 Author: mikep Date: Wed Mar 4 19:48:50 2009 +0000 add contact commit 24882ad34374e8300e1fb380e0e62ad9f35001e5 Author: kuhn Date: Wed Mar 4 19:48:00 2009 +0000 fixed name in reference - converted to initial commit 0f5e11ccea4a2618ceec974bb16970fd5f892a17 Author: kate Date: Wed Mar 4 19:43:25 2009 +0000 For ENCODE Peaks format commit fa9ec45453d804e536e296cca107fb07ab1e3eff Author: mikep Date: Wed Mar 4 19:43:13 2009 +0000 standardising text commit c1d09ae15dee42337c3cd61e61b4ecb3cd78565a Author: kate Date: Wed Mar 4 19:37:51 2009 +0000 Add section header for consistency commit b9698c5129d4bbccf55f57d7b4d35d088c569c95 Author: mikep Date: Wed Mar 4 19:26:05 2009 +0000 adding boilerplate commit f2a0ac4fe382b188205dc8517c8219a3c389b28b Author: kate Date: Wed Mar 4 19:22:35 2009 +0000 Correct misleading label commit a41aa7fa207f0ee9f2ce507f61a7a275c53a2e12 Author: kate Date: Wed Mar 4 19:01:44 2009 +0000 1. Add link for qValue explanation. 2. Condense redundant info commit 7dff965d9a883dbd6d51f997d22b51e0c6f65b1c Author: markd Date: Wed Mar 4 18:59:15 2009 +0000 added new credita to N-SCAN tracks commit b4ee1e222bf22223b453e84d21f411e234570188 Author: galt Date: Wed Mar 4 18:58:35 2009 +0000 runforever for production instance commit cd2915fbb6874c1816d7e7b3669420147017afd9 Author: mikep Date: Wed Mar 4 18:55:45 2009 +0000 adding data release policy, cell culture specs, and changing bold to italics commit 047d09e59c438425925b136d2783e3e2d993606d Author: mikep Date: Wed Mar 4 17:55:10 2009 +0000 validator for frag size for GIS gDNA PET commit f017bec18addf22e03c6b75e372abeac22367cfa Author: kate Date: Wed Mar 4 17:49:02 2009 +0000 Add reference to cell culture protocols. Expand and clean up methods commit 0fa5186c3414d96a15066f9c4489a43365918ae4 Author: ann Date: Wed Mar 4 17:16:11 2009 +0000 open terms page in new window commit 24152b2f08710b7dfe9ff30461852d4e4451f1ce Author: galt Date: Wed Mar 4 16:00:07 2009 +0000 "Encode release log update" commit 5aa99f33305b9794d06a8460cdc1dac42535ec79 Author: galt Date: Wed Mar 4 16:00:04 2009 +0000 "Release log update" commit 639edca9687d8de6180a43280d6b41682b6cb899 Author: mikep Date: Wed Mar 4 15:35:28 2009 +0000 explain why a single view commit 31e5baedb890706ba1654ed2949e6ebfd9516542 Author: mikep Date: Wed Mar 4 07:24:49 2009 +0000 tidying up description page commit ef11499dcb3be6beb7aff09263d7d26a9fb45dcf Author: mikep Date: Wed Mar 4 06:57:34 2009 +0000 put the url around the term id commit 7031b1dbf3f9ce6042ea13c79009da830bb7f1c7 Author: kate Date: Wed Mar 4 06:29:05 2009 +0000 Missed setting color this one commit 0b05f3b40af9b73c916ab5c8326893dfbf49431a Author: kate Date: Wed Mar 4 06:19:41 2009 +0000 Fix syntax error in colors commit e641fb1226cbb15175c6b06d08c7348c49e56f9c Author: kate Date: Wed Mar 4 06:16:09 2009 +0000 Color cells for all tracks by tissue type (Novartis conventions) commit ca7bf3f624258fdbfdc1b71e43bf6f9d682a0d8d Author: kate Date: Wed Mar 4 05:52:59 2009 +0000 Color cell types following Novartis GNF tissue coloring conventions commit 2dfcf0b1280d9c38ea5963d0ecc880868d527ca1 Author: pauline Date: Wed Mar 4 02:36:40 2009 +0000 Removed extraction protocol section and replaced with refs. commit 0bf74fcbf9f318c5a5ce8726fc3ef8d132f56f52 Author: tdreszer Date: Wed Mar 4 01:59:01 2009 +0000 Minor longLabel changes commit 02e34e3d499f64fe46ef725410bb1e7471386f16 Author: tdreszer Date: Wed Mar 4 01:52:28 2009 +0000 Six of one... commit c6c25c9ef87a114edea34fea9741ef2ede874369 Author: kate Date: Wed Mar 4 01:29:46 2009 +0000 Label was confusing in this context commit 6ff07875e33c23347ac363c26400fb36f752e240 Author: kate Date: Wed Mar 4 00:41:21 2009 +0000 Tweak on sort order commit 853f27bd6e79c36bddac9de72ad7e5ebb0555929 Author: aamp Date: Wed Mar 4 00:37:11 2009 +0000 Added monDom5 commit 3ec9fdaf62dfc49bd85f95114c382f7471daee90 Author: aamp Date: Wed Mar 4 00:35:40 2009 +0000 Adding trackDb entry for the multiz9way. commit ec646057f839a92e2b21fa6ebec17274b0b51e03 Author: rhead Date: Wed Mar 4 00:33:09 2009 +0000 Track vs. subtrack wording change. commit 77d00b89d5b2872ab821c199e111404943cc6140 Author: hiram Date: Wed Mar 4 00:29:14 2009 +0000 Adding hg19 commit 30cee7b2cd6acf695448f3a5f2bd5f75e3e48b8d Author: hiram Date: Wed Mar 4 00:26:55 2009 +0000 Initial set of files from makeGenomeDb.pl commit c582b04c9c162df230a3ab03245d98ecb73a7d10 Author: kate Date: Tue Mar 3 23:54:00 2009 +0000 Expand based on feedback commit dd21084bdb25188bd72bf580173d93796afbbf1d Author: mikep Date: Tue Mar 3 23:52:36 2009 +0000 tidy up commit 41a0b06049b199820ba33d9e8ddc6aa93bba2033 Author: aamp Date: Tue Mar 3 23:50:15 2009 +0000 Removed knownToKnown dummy table from affy all exon column. commit 7721f2523532b85fbf54147b466b65a9f2e4b7d6 Author: aamp Date: Tue Mar 3 23:49:42 2009 +0000 Descriptions for the affy all exon columns. commit a927c1c0d3cb396d9d8808c35b6d2841e6660395 Author: mikep Date: Tue Mar 3 23:48:39 2009 +0000 adding links to pubmed and tidying up generally commit 8aa4ff4ded79cb6d09cc5ced435897661f5ef7b2 Author: pauline Date: Tue Mar 3 23:30:04 2009 +0000 Corrected references and updated one in press. commit 6ec56356bbc5f17d45fefabbdfa15e88d7b9a061 Author: aamp Date: Tue Mar 3 23:29:06 2009 +0000 Changed the expRatio column type so that it doesn't need to have a knownTo* table, rather a "null" indicates that the microarray table uses knownGene identifiers. commit cb7495f74951169ec48252ce9a737a55f9365822 Author: rhead Date: Tue Mar 3 23:23:05 2009 +0000 slight wording change commit 7caf42df6f70f515ddc864eaf8485a3aa6d00478 Author: kate Date: Tue Mar 3 23:22:05 2009 +0000 Added ENCODE views verbiage, and specifics for Yale commit dfebcb222b9511b8424d0bfb1e371b7c652f1427 Author: rhead Date: Tue Mar 3 23:15:17 2009 +0000 typo commit ac57faf7d117621d35bf90c00b15771946919a2c Author: kate Date: Tue Mar 3 22:30:47 2009 +0000 Minor changes for usability. Fix errant minScore commit f8934f6dd7d262c60b1bc358f279aaf0a68b88ec Author: tdreszer Date: Tue Mar 3 22:02:34 2009 +0000 Fixed HTML error and ifdef'd out useless code. commit d5a1848b9a4c150617e9f2f0155b00eda149e451 Author: kate Date: Tue Mar 3 22:00:18 2009 +0000 Remove Tiers from cell types. Turn off more tracks by default on Yale commit 421bf81283b797d4edc66bf76932aacf3c0689a9 Author: hiram Date: Tue Mar 3 21:46:55 2009 +0000 Add -ignoreRepeatMasker flag to avoid looking for the *.out files commit fb75a0fd6f3778517815edcde5eda23e09574942 Author: hiram Date: Tue Mar 3 21:46:23 2009 +0000 Special case the 2micron chrom name on sacCer2 commit d1e10ea0543ffe167c14a235edeebbab055ad3a3 Author: kate Date: Tue Mar 3 21:23:29 2009 +0000 Changes for consistency commit ca12a92f511a79f265ba7a198e1c87ecdb141bb0 Author: tdreszer Date: Tue Mar 3 21:17:17 2009 +0000 Change grayLevel even when cart variable has not been set. commit 57259e9dd2e6ccdd5a37bb4a5df3b1ab7d6d3087 Author: mikep Date: Tue Mar 3 21:13:17 2009 +0000 final adjustments to text commit 558caf9facd8d09cb603c3f91e42581a3508e299 Author: mikep Date: Tue Mar 3 21:12:56 2009 +0000 friendlier labels commit 8d17540a71452549a700f94c97f912636014bb48 Author: tdreszer Date: Tue Mar 3 21:11:25 2009 +0000 There isn't actaully a cart var for these commit 277b50b97746ddeae8f0175b93501b32f76ea828 Author: tdreszer Date: Tue Mar 3 20:49:49 2009 +0000 Ouch! Accidental check in of experimental code. commit 0533c5b2c3f22ea1f71016b1beb7a15c25a83d14 Author: tdreszer Date: Tue Mar 3 20:28:52 2009 +0000 Fixed gray level code to use ClosestToHome and cart values commit 1e04fa4a13db6ed70f0d61d1503cc23fe6b7af55 Author: ann Date: Tue Mar 3 19:59:11 2009 +0000 added Data Release Policy commit 3d3defa2c00f5aaf2b7bcc596c64c4ec47b62746 Author: mikep Date: Tue Mar 3 19:55:20 2009 +0000 added contact email commit ad17c071965ea5a91f9e6e5e9a696edc2b56f881 Author: rhead Date: Tue Mar 3 19:54:09 2009 +0000 Added Display Conventions and Configuration section commit ef2d249ebcaf527019ed47fc7d0109fdfbeb8d8d Author: rhead Date: Tue Mar 3 19:53:24 2009 +0000 Changed some quotes to italics. commit a9a0292f6be6dedc9b1aa7c95c5ec9c3f374ceb9 Author: tdreszer Date: Tue Mar 3 19:38:52 2009 +0000 Fixed gray level code to use ClosestToHome and cart values commit af3fa4496645202877d7bf9225bb94c151727098 Author: tdreszer Date: Tue Mar 3 19:36:33 2009 +0000 Cleaning up gray level code lead me to remove these unused calls commit 97c9b8ea8b85f6dd95cff4f4b5c4d99189e15e11 Author: tdreszer Date: Tue Mar 3 18:41:15 2009 +0000 Clarified Large_Fragment description commit abf84f5467e70ff973edb5a4e37bf9b93c2f178c Author: tdreszer Date: Tue Mar 3 18:36:09 2009 +0000 Allow filtering by score on Yale. This is required for min gray shade. commit d3121ca184ca65743f21101b6890b17cdacd2827 Author: tdreszer Date: Tue Mar 3 18:32:33 2009 +0000 Fix filterByScore assumptions commit 980081c56473a47c5670b8e2e5dcea1afb72535d Author: mikep Date: Tue Mar 3 18:19:13 2009 +0000 forgot A targets commit 03bc93687ecfa08b1d8afc2440ac804aa2958391 Author: mikep Date: Tue Mar 3 18:08:54 2009 +0000 fixing to copy the kent src over to each new release because cvs-reports-d does a cvs update, not cvs checkout commit f9d100a874e59adb41ada308b1293f5939b26428 Author: kate Date: Tue Mar 3 17:53:37 2009 +0000 Edit long labels for consistency. Prune Yale long labels for length commit 5686caa3e75a5ec4e9092e4752466f0bbb2d10a5 Author: ann Date: Tue Mar 3 17:04:28 2009 +0000 added Genomics paper to training section commit ab9ce0a26534018a955861489a3aa92aaf7cc496 Author: kate Date: Tue Mar 3 17:04:27 2009 +0000 Prune Yale shortlabels for length and consistency commit b8733d8c2af5a5ee566aa655fd3b5faf7746b4f3 Author: galt Date: Tue Mar 3 16:00:06 2009 +0000 "Encode release log update" commit 312c11c81ba38f56bb9a133f8b466ae6998031d7 Author: galt Date: Tue Mar 3 16:00:03 2009 +0000 "Release log update" commit b7018ac341e1aa162005a5e00ed44e159215d85c Author: mikep Date: Tue Mar 3 15:51:37 2009 +0000 v202 preview commit 3e78cc95c4c72c680ac36ffda3ba32031439b467 Author: galt Date: Tue Mar 3 08:09:46 2009 +0000 fixing need for cgiDecode of user and password in url commit 196f64211a95e05a377644ae2ec991b189a0a632 Author: mikep Date: Tue Mar 3 03:24:09 2009 +0000 fixes to html description and to make long labels nad tags consistent and readable commit e9131c605bcb34657212557a6c9eacd61d94da7f Author: rhead Date: Tue Mar 3 01:46:15 2009 +0000 First try at multi-view instructions. commit cb946c99b44d7aff322b2348698c2e4c8fd5f26c Author: angie Date: Tue Mar 3 01:07:24 2009 +0000 Added some new #defines for the HapMap Phase III updates to hgc, hgTrackUi and hgTracks. commit a1a9fc37cc664f6b5c14801fb492e8bb895d14a4 Author: angie Date: Tue Mar 3 01:03:40 2009 +0000 Added global vars: lists of population codes and ortho-species for HapMap Phase II and III. commit d371cc9e56d5b7e785c19898d4dede199dc39df1 Author: angie Date: Tue Mar 3 01:02:46 2009 +0000 Updated hapmapSnpsUi to handle HapMap phase III (11 populations). commit 27d87b65a216334e9163545543c52fd70512f6e1 Author: angie Date: Tue Mar 3 01:01:04 2009 +0000 Refactored hapmapSnps code to support both phase II (4 populations) and phase III (11 populations) SNPs. commit ca0c48660a1d684149316748c2db0ab97a67140d Author: fanhsu Date: Tue Mar 3 00:07:49 2009 +0000 Added posSelection for vax004 section. commit 9478d73d68d2303e73845bdb999288a00a2f655c Author: tdreszer Date: Mon Mar 2 23:58:03 2009 +0000 Support for Min Gray level in multi-view and for min but not max score filter. commit b03b128140540e3bfd2804aa5e6a00c3ffdc55c0 Author: fanhsu Date: Mon Mar 2 21:41:47 2009 +0000 Checked in the section of the posSelection tracks build for vax004. commit 702088f43d98adcdd5e78f955e2a5725495a3958 Author: angie Date: Mon Mar 2 21:34:19 2009 +0000 Fixed hgdpHzy subtrack priorities (forgot they're int not float). commit f413386bf5793b337e84d3e49393c910e57bc759 Author: angie Date: Mon Mar 2 21:01:53 2009 +0000 Correction: only Bantu populations (not all African pops) were used to calculate iHS and XP-EHH. commit d590bba52d224657d43c74c68796157b533196a1 Author: rhead Date: Mon Mar 2 19:53:51 2009 +0000 Changed 1st to 3rd person in methods section. commit 45ee26c63f5b7b050143352364d1fc791e8f3f36 Author: angie Date: Mon Mar 2 19:04:31 2009 +0000 Added hgdpHzyBantu and changed 'Africa' to 'Bantu' in hgdpIhs and hgdpXpehh. Added hapmapSnps* for 7 new populations in HapMap Phase III. commit 7bbe64c5e47c51c157251f32f9c36aa947c90039 Author: tdreszer Date: Mon Mar 2 19:01:50 2009 +0000 Added Feb freeze tracks for Duke and Yale commit 9dfb0447982331926cc31b99b06cabdcb419f6d3 Author: angie Date: Mon Mar 2 17:53:06 2009 +0000 Some fields can be null -- added checks. commit 04030315a59ff8b72ac9c6c729141973eb11c94d Author: galt Date: Sun Mar 1 16:00:07 2009 +0000 "Encode release log update" commit ae4595d46ca38ea214ae46c8e45144bb54ec0ee4 Author: galt Date: Sun Mar 1 16:00:04 2009 +0000 "Release log update" commit 503866c0fae085c3bc93e0caefce3c4c943ddd15 Author: galt Date: Sat Feb 28 16:00:05 2009 +0000 "Encode release log update" commit 0da267e2b69076f165b4ba61902e62afa8bc7a93 Author: galt Date: Sat Feb 28 16:00:03 2009 +0000 "Release log update" commit 956b825b8a5ca3c3ea124bb2bbc9bfa172273f39 Author: kate Date: Sat Feb 28 00:45:36 2009 +0000 Cosmetic change to views section (no italics, and lowercase wording) for consistency commit 0ccfcf4cd464c17e4f9503392590395724a0edae Author: angie Date: Sat Feb 28 00:38:09 2009 +0000 Use the new sqlSetParanoid to enable extra stderr message if we fail to connect to the central database. commit f0c929045210a24ca79dce75c2eef9d6019c002f Author: angie Date: Sat Feb 28 00:36:42 2009 +0000 Made hgSeqChromSize more concise, and took out a redundant call to it (chromSize is passed down instead). commit 7bcdb268b3f1b4d98655aff9c3ca8b070647f1e2 Author: angie Date: Sat Feb 28 00:34:00 2009 +0000 Added sqlSetParanoid; complain about failed MayConnect only if paranoidness is on (the only time we really should complain is when trying to get to the central database. commit d2104874e2d6dda327fd33e94bed78dedcc85fa8 Author: kate Date: Sat Feb 28 00:16:57 2009 +0000 Whitespace tweak commit 450e140a35a26bc7fec9362fa22222e56f85d6fd Author: angie Date: Sat Feb 28 00:06:51 2009 +0000 Made dbIsFound a global so there's no need to set it again after doMiddle sets it. commit e73c80d7caa9605d3c72f717363d32dfd1716124 Author: aamp Date: Fri Feb 27 23:02:48 2009 +0000 Added multiz9way description. commit a3545a4cae13d057982e00289c0a0813d07cbbbf Author: tdreszer Date: Fri Feb 27 22:42:46 2009 +0000 Changed SREBP1 to SREBP1A as per Mike Willson's request commit 71a7a39a1909223b0422abc3c802f44a1a39305d Author: galt Date: Fri Feb 27 20:29:34 2009 +0000 fixing perm problems commit f13fa4f51daac08b0da8e85a6cb4d6e28894ca98 Author: tdreszer Date: Fri Feb 27 19:36:54 2009 +0000 Added GATA-1, JunD, SREBP1 and SREBP2 antibodies commit a4aca55eb77dc9767283954f4a3c0b91960f5539 Author: hiram Date: Fri Feb 27 19:24:53 2009 +0000 Finished with sacCer2 commit 9a5c24d4cbbcb32104963fb79189d29accf80514 Author: tdreszer Date: Fri Feb 27 19:15:09 2009 +0000 Replaced filterPvalQval with pValueFilter=0.0,qValueFilter=0.0 making filters individually supportable commit a4f36eb4796564e2d28e41b70c3cad833d0da1ab Author: tdreszer Date: Fri Feb 27 19:08:45 2009 +0000 Changed encodePeak support for individual filters: qValue, pValue, signalValue and score commit b96235b611ef2e8fa80e6da5a27aeff51e478b26 Author: tdreszer Date: Fri Feb 27 19:06:22 2009 +0000 Added dyAddFilterAsInt and dyAddFilterAsDouble for encodePeak support commit 495d33d2d476211870f3de63be8eb3da3fefcdbf Author: fanhsu Date: Fri Feb 27 19:05:15 2009 +0000 changed strstr() to startsWtih() per Hiram's suggestion. commit bd4b4405b280d5eb1ee30373133f56cd88a35339 Author: hiram Date: Fri Feb 27 18:47:52 2009 +0000 Fixup Ensembl link for 2-micron genome referenc commit d324def19a4b23c0f0aed3aa8445a609a38b668d Author: galt Date: Fri Feb 27 16:00:08 2009 +0000 "Encode release log update" commit 49d449550a524668e1ce119e720d14fbcaaf093c Author: galt Date: Fri Feb 27 16:00:05 2009 +0000 "Release log update" commit c87eda79eae49597a4dd963e76197c25e1880649 Author: kate Date: Fri Feb 27 05:16:00 2009 +0000 Prune short labels commit 440713c1ecf063f27739fe5ccd02e8896f3fd463 Author: kate Date: Fri Feb 27 04:58:08 2009 +0000 Shorten short labels to approved length commit 47fd709d7652174d9d410adc44ac796c5e86dc11 Author: rhead Date: Fri Feb 27 04:44:42 2009 +0000 More edits to conform to our usual style. commit ae56b41f1233a1cbf745c423760c7b86f8d5b99d Author: kate Date: Fri Feb 27 04:32:51 2009 +0000 Remove individual configurability of subtracks until performance improves commit db68e98e1cd9c2c2e3920ee25fd6a028b1c78a26 Author: kate Date: Fri Feb 27 03:54:52 2009 +0000 Adjust whitespace to conventional commit 2d065544dbb78d370efb97e4c997c3eaebbf3429 Author: ann Date: Fri Feb 27 00:46:20 2009 +0000 corrected downloads link commit 961f0559ca57603645586381a28521882fe102ac Author: ann Date: Fri Feb 27 00:45:17 2009 +0000 corrected credits link commit 6a548e91a61f2fa9cdf24b524bc082aa81fa05fb Author: pauline Date: Thu Feb 26 22:50:10 2009 +0000 Removed release beta in preparation for release of komp track commit 4825594a0cb7057b2c76349f75bcb39577241de8 Author: tdreszer Date: Thu Feb 26 18:24:33 2009 +0000 More regeneration of Duke/UNC/UTA peaks and signals commit a3e72d9fcd0da4ab7329540cd08c7d49e3b9e989 Author: angie Date: Thu Feb 26 17:45:48 2009 +0000 Use sqlConnectRemote instead of hAllocConn (host was being ignored). Reuse one conn instead of realloc'ing in every function. Bump up the verbosity level of most messages, to make the error counts stand out. commit 81c069ea67babed8efe4544fa9f0886dfa389f5b Author: mikep Date: Thu Feb 26 16:52:43 2009 +0000 Helicos platform doesnt make quality scores commit 2d0903c6c3e21d34f0857bfdef39e73ebcd9cd9c Author: galt Date: Thu Feb 26 16:00:07 2009 +0000 "Encode release log update" commit ef670b3b3d330f9c03d2370294f882cf29edc986 Author: galt Date: Thu Feb 26 16:00:04 2009 +0000 "Release log update" commit 201946cf7071c9ae8995ab14c949daeb6d81396d Author: tdreszer Date: Thu Feb 26 04:07:21 2009 +0000 Too many soring messages. commit 25b5217d04c7192e28ed607db4fb55401d7ecc41 Author: tdreszer Date: Thu Feb 26 04:01:13 2009 +0000 class needed quotations. commit 1084fff3c1087eac219ce04039cdcbbf3aa9c51a Author: tdreszer Date: Thu Feb 26 03:56:15 2009 +0000 Fixed some less efficient jQuery calls. commit 3ef1b995a1db3e8e702dab8a5dfe5a6bdb1e3edc Author: tdreszer Date: Thu Feb 26 03:52:15 2009 +0000 Added for Yale, updated Chromatin, change to controlledVocab setting commit 41e7cfc70a24a93ebe17d1b83a9ab7f35f072faf Author: tdreszer Date: Thu Feb 26 03:50:06 2009 +0000 Change contolled vocab link to use trackDb setting, Also change to support javascript multi-view droip downs commit 03e8e045e5392c58dd89c33401b944928ca9942b Author: markd Date: Thu Feb 26 00:05:49 2009 +0000 don't go past end of string if code checked out with -kk commit 0dd91ae02b2f925c63f5918703302e029f659c1a Author: fanhsu Date: Wed Feb 25 23:27:22 2009 +0000 Rebuilt omimGene. commit dca71693236db56a677e115ea1d8a063f4e71642 Author: kate Date: Wed Feb 25 20:04:38 2009 +0000 Sanitize out slash from cell type name (w/ agreement of Peggy Farnham) commit cbaf5dfde51b5c0beeeb5f16892e118e665791e1 Author: hiram Date: Wed Feb 25 19:50:40 2009 +0000 fixup treeImage name commit 23e1929a9c46d2682fef5b35bbdcf106c37e4759 Author: rhead Date: Wed Feb 25 19:48:15 2009 +0000 Took out some titles, tweaked links, added credits. commit ba7d5507509b3cdb842fe51bf8d6315fc8c33d3d Author: kate Date: Wed Feb 25 18:36:21 2009 +0000 More frame size adjustments commit 3db9a8d017ec34dbd4d296526fa5185f39206324 Author: kate Date: Wed Feb 25 18:32:50 2009 +0000 Tell user how to get cell protocol docs. Grow frames for Tier1 & Tier2 to avoid scrollbars commit 880837f1c7d1fde15f55c6d44dfa19fdf4dac106 Author: kate Date: Wed Feb 25 18:26:03 2009 +0000 1. Add links to cell protocol files 2. Add option to set background color commit d8f40b57e0adaae6b93bd96bc450c8c154b21239 Author: kate Date: Wed Feb 25 17:08:38 2009 +0000 Tweak wording commit 39b53a49db324fd17e186450008dda48134837a3 Author: galt Date: Wed Feb 25 16:00:07 2009 +0000 "Encode release log update" commit cd01396a4e4b2d1fe552ab5cb3e2a4acc5f0419e Author: galt Date: Wed Feb 25 16:00:04 2009 +0000 "Release log update" commit 0c89e4a20fd5c371504f1465b50a4be653edba63 Author: kent Date: Wed Feb 25 09:25:55 2009 +0000 Removing some debug statements. commit 804ad42bfcf7d536fce8c6866fbc13ecc0986387 Author: kate Date: Wed Feb 25 01:51:50 2009 +0000 Tell user about new links commit dad35a7079d8211e2c7551642b2230b52a0f6894 Author: rhead Date: Wed Feb 25 01:24:07 2009 +0000 Whitespace changes. commit d3ae91f01fc74363e1c3083bb3cceab3be961fd4 Author: rhead Date: Tue Feb 24 23:56:59 2009 +0000 Twaked the words In-silico per bob commit cf1892229fe75bc6c09d55164c3953224d026b4a Author: kuhn Date: Tue Feb 24 23:55:13 2009 +0000 starting to remove a lot of the detail in Methods. will link to protocol when available commit a00048759c47a68b61088f38223b1196f91d7a51 Author: hiram Date: Tue Feb 24 23:44:33 2009 +0000 proper naming for this Yeast 7-way phylo tree commit 259bc3bfd135dbac3cfc06e4dd2715b709d02b19 Author: rhead Date: Tue Feb 24 23:23:09 2009 +0000 Updated to reflect Angie's change to hgPCR result (primers are visible now). commit 327b613d4279b1583601e955e428848fa681ea4a Author: kuhn Date: Tue Feb 24 23:11:22 2009 +0000 cleaned up links and added TARGET for the contributing labs' info commit d0f5e08039c93946e35fbe8784b721697e1c087b Author: kuhn Date: Tue Feb 24 22:58:24 2009 +0000 changed refs to include 10 names before the et al. commit c1f359a5009be7120c74be99450ffe8248708f83 Author: kuhn Date: Tue Feb 24 22:53:10 2009 +0000 cleaned up html, mostly. made outlinks use TARGET _BLANK and shortened lines to conform to 80-limit where possible. cosmetic. real changes follow, but did want them to get lost in the noise commit e4fb438e7a29afb742cd51899944858e83980bee Author: hiram Date: Tue Feb 24 22:50:16 2009 +0000 two more tables to ignore in sacCer2 commit aa0ac047eec167c74b3844b2832e37ed9051145f Author: larrym Date: Tue Feb 24 22:47:21 2009 +0000 fix bug in updatePosition that caused negative chrom positions when user was at/near beginning of the the chrom commit 15ab016ed05958d8ca5003cddf7f270d36fd8b6d Author: angie Date: Tue Feb 24 22:34:08 2009 +0000 Make canonicalRangeExp accept negative start coord -- hgTracks will clip to 0. commit 6035f4b706be7e3b402dcf8736de84b71ef766b3 Author: hiram Date: Tue Feb 24 22:20:18 2009 +0000 sacCer2 looking pretty good, some tables out in the cold for sacCer1 commit c75e9e9df897f4616a1621bec7c0529dcacb0bdf Author: angie Date: Tue Feb 24 22:12:41 2009 +0000 Correction from Joe Pickrell. commit 0f2f5f939ba7937bb1042f4cc6678db9ddf4e490 Author: kuhn Date: Tue Feb 24 22:09:55 2009 +0000 rest counter to reflect the fact that ting had been dropped from list commit f335ba71ba7a2c74f23da3d87aa42a79e9cea6ee Author: angie Date: Tue Feb 24 20:52:52 2009 +0000 User+local request: show the primer boundaries in hgPcr results. commit a98ea50036f2c090b46140a64a84d2270aee9bdb Author: kuhn Date: Tue Feb 24 20:16:26 2009 +0000 restored the 15-pixel spacing around the image commit c764850e87387ae1860ee05aba660ce69a1b4fbc Author: hiram Date: Tue Feb 24 20:08:20 2009 +0000 Added sacCer2 - S. cerevisiae commit ddfdc55424d477338d9fa0b68e609193ecd7aa06 Author: galt Date: Tue Feb 24 19:41:51 2009 +0000 adding snpArrayIllumina1M table commit ac5034682b607ca65b74b7cfd206092dd289abf3 Author: ann Date: Tue Feb 24 18:30:42 2009 +0000 removed beta block for snpArray track commit 7505756cf5e3b9ed8719d080c622c73d004837ca Author: ann Date: Tue Feb 24 17:51:42 2009 +0000 one stragler! commit 29423c917f0c62b70c9f1257eb896d7668b79bcd Author: ann Date: Tue Feb 24 17:39:49 2009 +0000 Replacing Darwin's picture with the CBSE human picture. commit dd41afb20504839cc0db38fd7416313cd1d28302 Author: tdreszer Date: Tue Feb 24 17:19:42 2009 +0000 Added TCF4 for Snyder's lab commit 849d435c454b382eaa619c2cde298323584079d5 Author: kuhn Date: Tue Feb 24 17:16:00 2009 +0000 added a bit more shitespace around images commit e299e22cbf79cac61dcb898aae7e58d020ecf6f9 Author: ann Date: Tue Feb 24 16:19:35 2009 +0000 a tweak to the subgroup to which the multiz44way belongs -- untying it from the vert clade commit 453b8bdb6c7fcebfd60ee9fc1ca95423d65dac3a Author: mikep Date: Tue Feb 24 16:09:43 2009 +0000 "New version number v201" commit dbaa72573b98dd9bcd240727949958b7b16b9f19 Author: mikep Date: Tue Feb 24 16:04:05 2009 +0000 v201 final build commit de1bbd073f5023435275f546009bfe38a95c4863 Author: galt Date: Tue Feb 24 16:00:06 2009 +0000 "Encode release log update" commit dcd35c3008f122f55df5c5b667606230b877b718 Author: galt Date: Tue Feb 24 16:00:03 2009 +0000 "Release log update" commit 38791bc81b9755ec2ff4a82220121afa68b4ba6b Author: kent Date: Tue Feb 24 03:29:11 2009 +0000 Adding byte-swapping routines for floating point items. Using them in the bigWig read routines. commit 4350b08443edf04533fa199928134dbbe3e39a1b Author: kent Date: Tue Feb 24 03:09:04 2009 +0000 Testing floating point binary representation. commit 9a9e14e73b46e1a17045977bf2baabc59b26205b Author: kent Date: Tue Feb 24 01:50:38 2009 +0000 Fixing bug where isSwapped flag got overwritten false. commit 0160f120cc75ff326c1fa5c9a6d2bf7ff68442b7 Author: markd Date: Tue Feb 24 01:30:34 2009 +0000 remove comments out databases commit a243f3dede2fba5d00c16539ca85afa197716a03 Author: markd Date: Tue Feb 24 01:30:24 2009 +0000 use /data/tmp for tmp files during loads commit 2974eb967afa878a57d6cb5bfc9e8dd627c60e43 Author: markd Date: Tue Feb 24 01:30:11 2009 +0000 added genbank updates for hgofbeta commit ddc66e41796b2d37ca51d74736c15f0a1147e334 Author: fanhsu Date: Tue Feb 24 00:14:48 2009 +0000 Fixed the 2nd part of a typo in omimGene build. commit 75c5a200ccd97827eab283f2100aba9c36dc80e4 Author: angie Date: Mon Feb 23 23:43:20 2009 +0000 Remove thin tails from DGV (SAB feedback). Added 5 tracks from Human Genome Diversity Project. commit c1b8033e5d0ed0330bc0e04e9fb82d77caa29b0c Author: angie Date: Mon Feb 23 23:41:35 2009 +0000 Remove thin tails from DGV (SAB feedback). commit b79bd9dc01bafbb1387d6c1f6e5b7471edf77e0c Author: angie Date: Mon Feb 23 23:41:00 2009 +0000 Added bdtnpChipper (liftOver from dm2). commit e5e2fd62f3e33a9df537d5133a37ad0a0d9bc214 Author: angie Date: Mon Feb 23 23:40:23 2009 +0000 bdtnpChipper (old change): corrected regex, found another subtrack. commit 89c4f13f0d8434043ab5d723c2da645a0cf22112 Author: angie Date: Mon Feb 23 23:38:08 2009 +0000 sc->conn->db can be NULL -- when printing out monitor messages, use 'db=?' instead of NULL. commit a8e4e53a9a00aa78bf2c9f6fd3003e42dc3e4481 Author: angie Date: Mon Feb 23 22:57:30 2009 +0000 Added dgvMethods: filter items by publication reference. commit c116b02a9f6bab8e6d46872b5826466dd1ffc7ec Author: angie Date: Mon Feb 23 22:55:04 2009 +0000 Added dgvUi: filter items by publication reference. commit b821604e810d4b6cec5fb8cf1ecbd5fd36e3300a Author: fanhsu Date: Mon Feb 23 22:50:04 2009 +0000 Corrected a typo. commit 109443545603835c5b6ffe7c20ffd6921e5bb3e3 Author: fanhsu Date: Mon Feb 23 22:31:52 2009 +0000 Added processing for Illumina 1M array. commit d29bfe054a8ef18eac302c7d5e651ca61cde3de4 Author: ann Date: Mon Feb 23 22:27:14 2009 +0000 adding another ID type to snpArray search commit b98f0c71a337076ab59dc1f149e543ee22796dff Author: fanhsu Date: Mon Feb 23 22:09:55 2009 +0000 Added search term for Illumina 1M array. commit 70fc75a2c67202cc319b2813f644e51e1b2a62fb Author: ann Date: Mon Feb 23 22:08:16 2009 +0000 cleaned up an ouput comment to make it specific to a certain type of run (thanks Brooke!) commit 241da8df09bd1cfdd10bc89dc08dc2c32b418268 Author: angie Date: Mon Feb 23 19:36:14 2009 +0000 Corrected description of thickStart and thickEnd. commit e6463dacdb67221b7443a74982bfe7a6762edcfa Author: ann Date: Mon Feb 23 19:24:48 2009 +0000 point Illumina 1M Duo to actual product sheet commit e78cf79ef65d0873dfb622f1dc523f1b3f80bb5b Author: fanhsu Date: Mon Feb 23 18:42:27 2009 +0000 Updated omimGene build process to include "NR_..." related omim entries to omimToKnownCanonical. commit a83c1b518fa483985ea7a8e11d74f3bd4aa16267 Author: mikep Date: Mon Feb 23 18:10:04 2009 +0000 transfrags not avaialble for feb freeze commit b67097f8a9fe79d462d38a7cc0596d794fda171a Author: ann Date: Mon Feb 23 18:07:20 2009 +0000 tightened up the minCheck for this rule commit 0f5df696a5f961eb2d0accf1590ff0f517ff8360 Author: galt Date: Mon Feb 23 16:00:04 2009 +0000 "Encode release log update" commit c9fe52a19b038a75557006b44d54459b81b405ba Author: galt Date: Mon Feb 23 16:00:01 2009 +0000 "Release log update" commit 90fe8e6a3bbd9676f65ca4781ae4e7209125e239 Author: galt Date: Sun Feb 22 16:00:06 2009 +0000 "Encode release log update" commit be97f58d8c53ebd8a91bcd45de6c7bbf790f8a96 Author: galt Date: Sun Feb 22 16:00:03 2009 +0000 "Release log update" commit ec8326c9c1143e89e768334ee52d2b60b65a8a42 Author: galt Date: Sat Feb 21 16:00:07 2009 +0000 "Encode release log update" commit 0168eb5c6dbf33362f600f507c8926d6172e34d7 Author: galt Date: Sat Feb 21 16:00:04 2009 +0000 "Release log update" commit 425a5ce4701b2bbbc74a1ddb6a0fd2c07dd4f7f0 Author: aamp Date: Sat Feb 21 03:22:20 2009 +0000 Turned on p-value filtering (peaks) on each of the big wgEncode supertracks. commit 93bd46e8fcc1fc424348b7edaf8963ce8fcc3602 Author: aamp Date: Sat Feb 21 02:49:33 2009 +0000 Added filters to encodePeak tracks that work in the composite multi-view. commit e40920ac4d4e860f0a0b8b9125cebd301704682c Author: kent Date: Sat Feb 21 02:15:47 2009 +0000 Seems to work. commit f3f84c030539304086fbcfe502daa716dcb32cf0 Author: kent Date: Sat Feb 21 02:14:15 2009 +0000 expected.wig commit 620ca8ace79b08534488c54b67605babe85365d0 Author: markd Date: Sat Feb 21 02:09:23 2009 +0000 fixed search for mgc and orfeome commit dc86c033b4757bb1a0b6ef8610b46997ea84a44c Author: fanhsu Date: Sat Feb 21 00:55:16 2009 +0000 Updated omimGene build process to correct a typo. commit 1bb4ec89f4ae113bbc6aff7392c6659086099838 Author: angie Date: Fri Feb 20 23:49:03 2009 +0000 When testing xrefTable existence, use sqlTableExists instead of hTableOrSplitExists in order to support an xrefTable in some other db. hTableOrSplitExists actually uses a cached 'show tables' from the current db. commit a0ca7caed679160601a5a9c5cbfc23dbbe88728b Author: fanhsu Date: Fri Feb 20 23:38:02 2009 +0000 Created hgGetNrOmimGene.c. This program is needed during omimGene build. The old version MySQL on hgwdev does not support the "NOT IN (....)" syntax, hence a C program is needed to provide the needed function. commit 97f3cd307e087ab35c02df04bc0a01c62dc0b94f Author: fanhsu Date: Fri Feb 20 23:36:35 2009 +0000 Created makefile. commit 7eeaa81bcfe6adbd52050c8c597e120377a2f3f3 Author: pauline Date: Fri Feb 20 23:27:35 2009 +0000 Added restriction enzyme track tables to tables ignored. commit 71df2a10ecce0208930f0e93f0df3d2eef8a8192 Author: ann Date: Fri Feb 20 23:22:38 2009 +0000 chopping lines up commit 3de24f4526009f6ebb70338445cd9163f98ec278 Author: fanhsu Date: Fri Feb 20 23:22:04 2009 +0000 Revised and added more omimGene entries that are related to "NR_..." RefSeqs. commit 040695ca62569d4d311859334f1f23fa52204271 Author: hiram Date: Fri Feb 20 23:21:26 2009 +0000 public functions should conform to naming conventions commit 66bc47e1d3d53f177bce1f5a81628a96d9cfba76 Author: angie Date: Fri Feb 20 23:05:52 2009 +0000 Bugfix: addPslResultToHgp: strip initial all_ from tableName (we used to use the lowercased GenBank type!). commit f91cd00ff853ea4049d597367b70ba9c79a147ec Author: markd Date: Fri Feb 20 22:49:31 2009 +0000 remove duplicated rows caused by using a subset of the data in the LSSNP database commit fee5a46258f5f8bc1ef3f5a7164795c54465aa96 Author: hiram Date: Fri Feb 20 22:45:10 2009 +0000 Adding sacCer2 rules commit f2d050fcda62ce6e838269aa935dc8bb2ad3b4ef Author: angie Date: Fri Feb 20 22:40:47 2009 +0000 Refactored findMrnaPos and its callees, and added support for intronEst. commit e15ae56317238279866caf7491a43f3acdadabd0 Author: hiram Date: Fri Feb 20 22:22:04 2009 +0000 Do not use sqlAllFields() in jksql.c since it doesn't know about databasesIgnored commit 0f676a494aec1fbf6861427d79449c37dcc1eae0 Author: hiram Date: Fri Feb 20 22:19:45 2009 +0000 allow addDatabaseFields() function to be seen external for use in joinerCheck commit a95f12e50ad357408f34d1630904c9660ade607d Author: ann Date: Fri Feb 20 20:56:34 2009 +0000 Changing up the lsSnpPdb rules with the consulting input from Markd commit ed31fa7a65954f7675d7078ac64ddab5e985571d Author: mikep Date: Fri Feb 20 20:44:22 2009 +0000 added comment about quality scores commit 27f13a88b36972e2920280daf6a65292651878e0 Author: angie Date: Fri Feb 20 19:57:50 2009 +0000 New ref for NA18507, new links, reformatting and a couple wording tweaks. commit d5bd6ef698f0ff73e6dd148e76fd975ea167098b Author: angie Date: Fri Feb 20 19:56:17 2009 +0000 Oops, PSU didn't do the sequencing of NA18507; dropping the SOLiD NA18507 subtrack, at least until I can get more info about it. Thanks Belinda! commit 34f362c055adde60903617f4ae728edd21706886 Author: galt Date: Fri Feb 20 16:00:07 2009 +0000 "Encode release log update" commit 2069eabde31f4f70a9ec773855b2b9e28f42fb1e Author: galt Date: Fri Feb 20 16:00:03 2009 +0000 "Release log update" commit 1093b4760191b7686d71342b77398ae5d3180297 Author: mikep Date: Fri Feb 20 06:47:07 2009 +0000 re-doing Riken Cage commit 19c7492c247a061939f1d9be97b8d899e2223b6c Author: aamp Date: Fri Feb 20 02:55:38 2009 +0000 Put this back in for missing RR track. commit eea09259869cbd84d1e6b294a6c1897bc4483d09 Author: aamp Date: Fri Feb 20 02:52:38 2009 +0000 Need to add this back too commit 7e8f6573b4fe845c8962411bfd09178d1aaaefde Author: mikep Date: Fri Feb 20 00:25:02 2009 +0000 first version of caltech doco commit 12ab936ce3f1fc117f3e2e19aaa769534e99f946 Author: larrym Date: Thu Feb 19 22:33:28 2009 +0000 fix typo commit ccfc8e49309144287fdef5d788f0d49c3d2ce048 Author: larrym Date: Thu Feb 19 21:54:29 2009 +0000 fix H9ES-AFP+/H9ES-AFP- tracks commit 0fe0bc8a3b938cf3028ed229bdf4cd83579be87e Author: larrym Date: Thu Feb 19 21:44:31 2009 +0000 deal with +/- in cell type commit 57a67967bb9194594feb38075173d11bca77e31d Author: ann Date: Thu Feb 19 18:33:00 2009 +0000 changed again per Rachel's request commit e605bc98c0d1ffb4f0afe769acf773574870cedb Author: galt Date: Thu Feb 19 16:00:06 2009 +0000 "Encode release log update" commit 85c40888ef1d24fc86b72fc5ff5bca818a292ca0 Author: galt Date: Thu Feb 19 16:00:03 2009 +0000 "Release log update" commit 1c5d8fc35e220f4538d9da7dd3cd3a0c151a6c4a Author: larrym Date: Thu Feb 19 01:22:13 2009 +0000 minor tweaks commit 62a78d8b0b7d1875dac38f379b8f3cd3fe185fa0 Author: larrym Date: Thu Feb 19 01:19:26 2009 +0000 color some HA MethylSeq sub-tracks commit 57798a1db12035ab548775c7c23c65f659c17621 Author: pauline Date: Thu Feb 19 00:52:17 2009 +0000 Fixed refs to conform to standard format. commit 4cd649a1e7946ab7178f7b99efa988deb7980b09 Author: mikep Date: Thu Feb 19 00:25:06 2009 +0000 added wiggle ranges after load commit 1c6f4d7638245f1732a9a75d09638552a91c2614 Author: mikep Date: Wed Feb 18 23:58:35 2009 +0000 inadvertently commited timing on commit 6f7e1f7128e54520515c7506009cae3058911869 Author: ann Date: Wed Feb 18 23:30:43 2009 +0000 changed to the correct name (we had been using the wrong name!) commit 3bd05e9f9ca0e56e6c5a512493311950fe6642a4 Author: mikep Date: Wed Feb 18 23:13:54 2009 +0000 new tracks from RIKEN commit 020fc794525c16c92bf606f84e51bd812669f259 Author: galt Date: Wed Feb 18 22:45:09 2009 +0000 prevent apache cgi timeout by outputting something, also fixed reversed closing tags commit 584e111024d4f1a56f599ee87946f7ef7e49b2ad Author: rhead Date: Wed Feb 18 22:42:55 2009 +0000 Added oryLat2 to human proteins checks. commit 0e456cfa1e2c9bab6961618c4a297ec11a1b6d4c Author: markd Date: Wed Feb 18 22:11:45 2009 +0000 added dbProfile as the prefered name for a trackDb database profile setting commit 952930cfbc1f0293314515a8354c3e8a520f8dce Author: hiram Date: Wed Feb 18 19:54:18 2009 +0000 Set of organisms for sacCer2 orthologs commit 8be0762bf36b856c7202256bb58ec5f8d85ddd99 Author: mikep Date: Wed Feb 18 19:18:38 2009 +0000 SOLiD colorspace fasta format, not fastq commit 8cdfc11493cef0f1b680ac49115c3c9268367124 Author: hiram Date: Wed Feb 18 18:20:00 2009 +0000 Restore memk to the list of clusters to use commit f744096b03b730b2e411e48b8ba3d7230503eab0 Author: mikep Date: Wed Feb 18 16:48:17 2009 +0000 New datatype for Gingeras GIS project commit 40a4689e0c9cb2e0d5895f66117c2ecf389d4a2d Author: galt Date: Wed Feb 18 16:00:07 2009 +0000 "Encode release log update" commit 2fe2bd14ddc3ebade3e1494348e3604ff0babfb6 Author: galt Date: Wed Feb 18 16:00:04 2009 +0000 "Release log update" commit f8d8ddf944eef04e4b96563a7163fa131fce6332 Author: larrym Date: Wed Feb 18 07:51:33 2009 +0000 fix description for HAL commit 46e6e0b3f117a9cb4cc4e67c03cf24ce9a0ad9f9 Author: angie Date: Wed Feb 18 03:07:03 2009 +0000 Updated komp (now called IKMC) w/new data from Carol Bult. commit 2cf879a908ecc2e8307a851f7b46f543c856c6ba Author: galt Date: Wed Feb 18 00:33:25 2009 +0000 Adding FTP support for udc cache lib commit 1bf86290782a78e77c7a3c3b25ab6314ccc02592 Author: mikep Date: Tue Feb 17 23:25:41 2009 +0000 need to create sub-dirs as well commit d027b33c4a27d2f62bd79f0e663c39f56cc10a0f Author: larrym Date: Tue Feb 17 23:15:19 2009 +0000 add descriptions for terms recently added by HA commit b80c4a82b939067ceb8e2e0dadcde9d861053d20 Author: mikep Date: Tue Feb 17 22:08:56 2009 +0000 new system to remember the history of review reports commit d359404569e2f908e300e86c1a9e5a0c264c3c6d Author: markd Date: Tue Feb 17 20:10:28 2009 +0000 fixed bug were previous build partial matches were being excluded from current build commit bb4ea966a930588b231c61f447c374ca25c88be6 Author: kuhn Date: Tue Feb 17 19:30:04 2009 +0000 capitalized a word commit 5e2e712d19a484be1f15f31d53619ad2d89b9d8e Author: ann Date: Tue Feb 17 19:15:42 2009 +0000 un-hiding drag-and-drop announcement commit 29cbb37b3c893c0eb16c5d1404e5f52f0751f567 Author: angie Date: Tue Feb 17 18:08:26 2009 +0000 komp (IKMC): updates from Carol Bult. commit 9769e75c610aa20b37bfe68704aefc272cd5bbdc Author: mikep Date: Tue Feb 17 17:55:08 2009 +0000 pairedTagAlign not implemented yet commit 9161a110993363da4bf86cd157817bad5d5c3750 Author: mikep Date: Tue Feb 17 17:51:13 2009 +0000 Hopefully this is a better error message - I ran into this a few times with new encode track types commit 90a62379e3d80ccdfff4edc95510a8b965b2b294 Author: angie Date: Tue Feb 17 17:07:00 2009 +0000 pgSnp: if I were not making slides for the SAB meeting I would not be spending so much time on capitalization and punctuation, but here we are. commit 12c03d0e8a8544f547be14dbc4245311a12cebfa Author: mikep Date: Tue Feb 17 16:55:48 2009 +0000 new data for GIS PET GM12878 commit 3cc7501e2e9c7505970c2b98314d20ced88debe9 Author: angie Date: Tue Feb 17 16:54:46 2009 +0000 pgSnp: New info from Belinda (thanks!) and a couple more label tweaks. commit 14fb5485b75a736d2eda3e9852a4d532b2a8d47c Author: mikep Date: Tue Feb 17 16:49:45 2009 +0000 new data for GIS PET GM12878 commit 5ed63ea060030971482f166c98c72375fb90682e Author: galt Date: Tue Feb 17 16:00:05 2009 +0000 "Encode release log update" commit 736867489b68336323b01340d97662e585592753 Author: galt Date: Tue Feb 17 16:00:03 2009 +0000 "Release log update" commit 29e827ec6ab902c0b66bf0d0e0347a91426834fa Author: mikep Date: Tue Feb 17 15:41:22 2009 +0000 v201 preview commit 11ede97432176817fa7b531795ecd81f77b8ce6b Author: angie Date: Tue Feb 17 03:46:16 2009 +0000 pgSnp: a few more label tweaks for consistency. commit f41a6935de5ab35014c8edbefd681b4ed85b7794 Author: angie Date: Tue Feb 17 03:35:43 2009 +0000 pgSnp: label tweaks at David's request. commit 1cbc28016d2cc6dfd2575653d7309381f1f4c8e7 Author: kent Date: Tue Feb 17 02:19:55 2009 +0000 Improving comment. commit 1d8b9e7650e4e81d8bd9e742546d45f7c1d40ea8 Author: galt Date: Mon Feb 16 16:00:08 2009 +0000 "Encode release log update" commit 394e567b465a4beee93f19219e1137dfc634abec Author: galt Date: Mon Feb 16 16:00:06 2009 +0000 "Release log update" commit 72bd246fedd5158cfd190b309142ed50d2f6d3d8 Author: kate Date: Mon Feb 16 03:50:33 2009 +0000 Move RNA seq to Expression track group commit 3a7f1984f9507e16c004f429e0e0bd1c2083f93a Author: kuhn Date: Sun Feb 15 21:10:33 2009 +0000 grammar tweak commit ca499f35db7c9e497dd59fbb7d1e8717733bd880 Author: galt Date: Sun Feb 15 16:00:11 2009 +0000 "Encode release log update" commit 4ac7c786bbd9599586501eb8d57026035aea4823 Author: galt Date: Sun Feb 15 16:00:08 2009 +0000 "Release log update" commit 0bc762ef4d6784d47163b7d4f745d6576586172d Author: tdreszer Date: Sat Feb 14 18:47:50 2009 +0000 Fix for Pol2(b) tag and for compareGenomeLinks setting commit cc7bbfadeebdfbb7779c787d30f64295446602a2 Author: galt Date: Sat Feb 14 16:00:07 2009 +0000 "Encode release log update" commit 00c26ae5d74102cf8fc2776f032c2111eaf1d7d4 Author: galt Date: Sat Feb 14 16:00:04 2009 +0000 "Release log update" commit b23f2eae22cdefcc6857eac742e8db695b53f698 Author: mikep Date: Sat Feb 14 08:31:36 2009 +0000 First version of Wold tracks commit 026e5883c01ac85094cc44fc9038d4584414d6b4 Author: mikep Date: Sat Feb 14 08:11:52 2009 +0000 version of D?F that was successfully loaded commit 5ddeab667356d0cdf77ced3d14b34636c21fb01a Author: mikep Date: Sat Feb 14 00:35:21 2009 +0000 shortening names for sake of 64 char table name limit in mysql commit 3e33e096b95e55d4f44f82ec180bc719f5e92dc3 Author: rhead Date: Sat Feb 14 00:18:47 2009 +0000 Fixed links to tree models commit 5c5d312f00af1dde8f110a176d9cd39ba4bc6fad Author: mikep Date: Fri Feb 13 23:46:02 2009 +0000 test for table name too long commit 672ea5d12ca6df068c8da3f0dec846fffb49b704 Author: mikep Date: Fri Feb 13 23:36:19 2009 +0000 allow 12-column beds for Wold commit 55b44201a051140bdce65535d1b970cbd9bb246e Author: mikep Date: Fri Feb 13 23:35:05 2009 +0000 shortening for table name limit of 64 chars for Wold commit 97df718d744fb24850482556b2c567e5e50a7832 Author: mikep Date: Fri Feb 13 22:12:01 2009 +0000 first version of helicos rna seq daf commit 8511db0e9ca38af24f99d83a3f06a4d483387aaf Author: mikep Date: Fri Feb 13 21:59:49 2009 +0000 fixed mismatched duplicates of downloadOnly logic by moving to a function commit e4778f2955f3e4aa0f45be9a5f849169e1e1134d Author: tdreszer Date: Fri Feb 13 20:04:50 2009 +0000 Change in compareGenomeLinks setting commit 37a2ec758a3aed042f2efe76da14bc3c5abbab09 Author: tdreszer Date: Fri Feb 13 20:01:49 2009 +0000 Added support for db.table.column=title setting in compareGenomeLinks commit cf3d03a6a1fb6fe8926b1411afef889fe65cb1f9 Author: mikep Date: Fri Feb 13 19:16:08 2009 +0000 forgot a commit e427fdd47662adca25a52f365871c968d870ec99 Author: mikep Date: Fri Feb 13 19:00:42 2009 +0000 forgot a commit 6f7c89e918bfaa409906cd0343b5c74c7ea921b9 Author: angie Date: Fri Feb 13 18:52:46 2009 +0000 Added continent colors to hgdpHzy, hgdpIhs and hgdpXpehh to match HGDP Selection Browser coloring. commit c262d16ac917e4b2b4523f7a2d42b75a93a65e05 Author: mikep Date: Fri Feb 13 18:52:09 2009 +0000 fixes to first 21 ccolumns of psl format (commas at end of last 3) commit 92e1b7af8a757136e8206a5157c159aecaee262f Author: angie Date: Fri Feb 13 18:33:54 2009 +0000 Added 4 new tracks from the HGDP Selection Browser: FST and Per-continent heterozygosity, iHS and XP-EHH. commit 1f4c4f029073fd24f626e99014a7d4658021b084 Author: mikep Date: Fri Feb 13 18:28:08 2009 +0000 assuming last column is optional as missing from some data commit 65a4e68ef3e78958cb5ff13b994caf1040a04f51 Author: mikep Date: Fri Feb 13 18:21:58 2009 +0000 allow commas commit 2c1fec0796453b794de01c2605d62b091c526129 Author: mikep Date: Fri Feb 13 17:35:43 2009 +0000 allow dots in there commit 27257cc3d5c7fcb43fa5f027b6daed7c4b1e8f06 Author: mikep Date: Fri Feb 13 17:28:58 2009 +0000 no algorithm applicable for some data like download only sequences commit 455e350ec5b673db84d56f620151dc712f9a5a8a Author: mikep Date: Fri Feb 13 16:17:39 2009 +0000 allow pipes in the name in bowtie commit c32ebafc72d9f83e051a80656aa4cc604b864c28 Author: galt Date: Fri Feb 13 16:00:06 2009 +0000 "Encode release log update" commit 3f5cea4153b67d3bea3b7bc591f3529cda4a2986 Author: galt Date: Fri Feb 13 16:00:04 2009 +0000 "Release log update" commit 3644d70c630852a4b7522ac31467ea7725db7a48 Author: mikep Date: Fri Feb 13 11:57:04 2009 +0000 allowing gene name to comprise any char but commit c59f91ecb93f3c08976fe8125a26679b272480f1 Author: mikep Date: Fri Feb 13 11:13:23 2009 +0000 RawData3 and RawData4 types are for Wold lab commit 8b5ee9ff8d2d03e12af2fb5f7c4c8db225f8b513 Author: mikep Date: Fri Feb 13 11:08:33 2009 +0000 validation rules for new Wold download types commit a183d89785da3a2b84eb8c07d884a4774a6f31bd Author: mikep Date: Fri Feb 13 04:19:13 2009 +0000 added null validators for rpkm, fasta, bowtie, psl formats commit 969346018bd24a0504d1bea2c751a647637bb3cd Author: kent Date: Fri Feb 13 02:39:05 2009 +0000 Removed flocks which seem to be unneeded. Adding qEncoding to make directory names easier to pursue under Unix. commit 37f0351b7849ee3e14621e8b61895f5f8974d4c4 Author: markd Date: Fri Feb 13 02:38:28 2009 +0000 fixed some invalid html commit 792570d0a4d5077710b92ec5a18285be2d3d4686 Author: tdreszer Date: Fri Feb 13 01:40:47 2009 +0000 Remove '_' in title commit 829d6ef75858701a622f14d5271deadb7801b502 Author: galt Date: Fri Feb 13 01:34:07 2009 +0000 fix for customTrack when numbers appear in the middle of the track name commit dfd9d3562933c034c2cc410b69abb07da8bdf2b4 Author: tdreszer Date: Fri Feb 13 01:31:43 2009 +0000 added printCompareGenomeLinks for Elnitski's BiP tracks commit eb9dbc5f290575b8f7bbb20416c24c08b10d9b09 Author: tdreszer Date: Fri Feb 13 01:26:57 2009 +0000 Added compareGenomeLinks links to wgEncodeNhgriBip track commit 895d82a5246e0fbe887e70606dac85166d901d04 Author: tdreszer Date: Fri Feb 13 01:24:46 2009 +0000 Added wgEncodeNhgriBip track for Elnitski compareGenomeLinks links commit ac31e8b6a0ce27aa18c5fa558682221dfe658ce2 Author: markd Date: Fri Feb 13 01:02:16 2009 +0000 ignore non-GTF features, as specified by the spec commit ad9f1c6363bf8c132725fd85411dc30fcebc6b6b Author: rhead Date: Fri Feb 13 00:44:03 2009 +0000 typos commit 0c92f40dc3956612abce2139c45d1e4db8c82aa7 Author: markd Date: Fri Feb 13 00:01:04 2009 +0000 fixed typos commit 54a856a04e7a3105120f76d7efdb390a26fa9b7b Author: markd Date: Thu Feb 12 23:56:57 2009 +0000 fixed link to LS-SNP/PDB commit aab6856fbee4b75f3088ed2bd429476045a50829 Author: jsanborn Date: Thu Feb 12 22:56:02 2009 +0000 added two ispy datasets commit abc2ef55cf5facef9de2ce42f0151fe32f64cd18 Author: kate Date: Thu Feb 12 22:42:29 2009 +0000 Add primate and glire lineage specific phyloP commit 73c1785c426d6a43c0a8be8816ce047dbc349d7a Author: angie Date: Thu Feb 12 22:36:03 2009 +0000 Expanded to describe the International Knockout Mouse Consortium of which KOMP is part. commit 8e0d3bf3b9a1ea830049afaa01b292efc6af9171 Author: ann Date: Thu Feb 12 22:30:23 2009 +0000 temporarily commenting out drag-and-zoom announcement commit bfdd55918e035d7d8f4578172af6dc720abeda3e Author: mikep Date: Thu Feb 12 22:22:21 2009 +0000 new tag map algorithms for Wold commit 58a3810ffd00fc043063c59d1ed1e672f3662fa1 Author: ann Date: Thu Feb 12 22:13:35 2009 +0000 indexNews.html commit 8a95c23ae9bc2cc7787774f458fdf3214943e535 Author: mikep Date: Thu Feb 12 21:38:14 2009 +0000 get stdin from dev/null commit 99b278db38ae1de974a75f6b8c22400ffc2f5744 Author: hiram Date: Thu Feb 12 21:38:10 2009 +0000 gap off, and most conserved on pack commit f22e723e392e9f835aece413da526f92efc7a055 Author: angie Date: Thu Feb 12 21:36:12 2009 +0000 Added alpha and beta release settings for komp, which is having its labels changed from KOMP to IKMC (Int'l Knockout Mouse Consortium). commit 1ddab1c3727a67717a6ee82055830f157baff7a3 Author: hiram Date: Thu Feb 12 21:27:10 2009 +0000 Adding 7-way multiple conservation track commit 7bcb62cb77e97cf683a6ed4ca36c5abc543899dd Author: hiram Date: Thu Feb 12 19:50:19 2009 +0000 Finished 7-way conservation business commit a1742fd4a3fb5db4096660a1b5e172ba06116911 Author: tdreszer Date: Thu Feb 12 19:02:20 2009 +0000 Added K562/ZNF263 for Yale commit 8a3366bda8ccc24d78082d1b948e370faf368263 Author: galt Date: Thu Feb 12 16:00:07 2009 +0000 "Encode release log update" commit e0e1ac4f86bb2e44749fda4dc991f08b0f42a271 Author: galt Date: Thu Feb 12 16:00:04 2009 +0000 "Release log update" commit f62ca162712567c46cabaa6acfaec9c4624f56f2 Author: giardine Date: Thu Feb 12 14:42:53 2009 +0000 Added some data for the Asian SNPs. commit fc285fbf2dafa62f8c388f768b6f60e89744b69f Author: aamp Date: Thu Feb 12 08:42:17 2009 +0000 Put missing ordering back in. commit 2fef49842aab40b0d81f648d4ae205fefc0570cd Author: aamp Date: Thu Feb 12 08:41:39 2009 +0000 Put missing columns back in. commit 3631790133935350bf54940a05b73e2e51406564 Author: galt Date: Thu Feb 12 01:18:00 2009 +0000 adding FTP support for byterange url commit c82df974047074a90265ccd8841850c145f6122a Author: galt Date: Thu Feb 12 01:13:52 2009 +0000 fixing options to ignore equals in ftp and https (and not just http) commit 4e3fb2abac87b532f6cb188b8dba76b28f271c4f Author: markd Date: Thu Feb 12 00:59:24 2009 +0000 correctly handle $$ escape in variable subtituion commit c02ac127b51a4c9564062051d769a2259b750705 Author: kent Date: Thu Feb 12 00:20:38 2009 +0000 Testing simultanious writes. commit 409235d8525740df895a66265161833e64998f40 Author: galt Date: Wed Feb 11 23:44:11 2009 +0000 moving some udc http declarations to .h file so I can call them for testing commit 872cc50dacf472f5b617705ac08d534650e546bb Author: galt Date: Wed Feb 11 23:43:09 2009 +0000 moving some udc http declarations to .h file so I can call them for testing commit 1ee5d14fb4275438d307079b2caec29eb00ed029 Author: galt Date: Wed Feb 11 21:57:21 2009 +0000 moving some udc http declarations to .h file so I can call them for testing commit 36dbe81c9a346ef1170ef61a0ea6a67918f45953 Author: aamp Date: Wed Feb 11 21:47:51 2009 +0000 Putting back in an old one. commit 0094a46d324c2ba5496fd73dd329360c74391783 Author: angie Date: Wed Feb 11 18:49:44 2009 +0000 Performance fix for tableExists: use sqlTableWildExists only when table name has a wildcard, because in large dbs like hg18, sqlTableWildExists is ~100x slower than sqlTableExists (0.090s --> 0.000s). When joining through gbCdnaInfo, we may call tableExists 255 times to find a path to tissue.name. commit 0b7adf4fd46af4dc298a39ba8b9f4c453e7aa5ad Author: kuhn Date: Wed Feb 11 18:09:54 2009 +0000 dropped trailing slash on cgis commit e746ad9d9b21fc13116578f8c23bbaa0538f7c1b Author: tdreszer Date: Wed Feb 11 16:38:51 2009 +0000 Added ZNF263 antibody for Yale. commit 7444cc13a2f7561e8302c94d828dedddb20bc96e Author: galt Date: Wed Feb 11 16:00:06 2009 +0000 "Encode release log update" commit 51676b0c74965c76a9f4739ba3d981b61aabe2de Author: galt Date: Wed Feb 11 16:00:04 2009 +0000 "Release log update" commit e676fedb66177f2d1db4ab10bffa29753b6aba0d Author: mikep Date: Wed Feb 11 04:38:11 2009 +0000 dont hang on input commit c65e8ecda6eff80ce912528fca2b9a92028f7fa8 Author: kent Date: Wed Feb 11 01:36:51 2009 +0000 Cgi-encoding file names in cache dir. commit cd6f8ee8bc1a1748af02d62694c06943fddbc5d9 Author: larrym Date: Wed Feb 11 01:33:38 2009 +0000 add some itemRgb's commit 6d86ea87b90f6021f67d4d83e42b537a8784e543 Author: hiram Date: Wed Feb 11 00:49:43 2009 +0000 Straighten out business with fr2ScaffoldEnsemblLink() commit 487c8f8cad752983db71dc906d12594f851582d8 Author: larrym Date: Wed Feb 11 00:02:03 2009 +0000 tweaks to wgEncodeHudsonalphaMethylSeq commit 46b89d9c0ed869113846654856ad10cb97defb25 Author: hiram Date: Tue Feb 10 23:56:21 2009 +0000 Human proteins done by Brian, and multiple alignment in progress, genbank done commit 8307a5695509fd394aabe6c71bab9a1d29b51c2e Author: donnak Date: Tue Feb 10 23:36:42 2009 +0000 Added Cancer Browser pub. commit 18d5175758f16f743d80ec0f5209b5bf33c023f0 Author: larrym Date: Tue Feb 10 23:01:58 2009 +0000 new cell lines from Rami (they are not yet approved and we still need more details) commit f3e81e91b69ed12c2bca8054ed4169fe31606f88 Author: larrym Date: Tue Feb 10 22:59:56 2009 +0000 tracks for data from uploaded by rami commit 7c2bcc4220aa604688ac10d28cdfcac7765d5b7d Author: kent Date: Tue Feb 10 22:27:09 2009 +0000 Adding crTree utilities. commit de911ee2dd13b5393f8f16a9e25a42c7b0875c72 Author: kent Date: Tue Feb 10 22:26:34 2009 +0000 Adding a comment. commit ce19d14877fff0eb4dde2a33bc048e0eda5342cb Author: kent Date: Tue Feb 10 22:25:52 2009 +0000 Adding hgBbiDbLink. commit ce2912b35ba98ac37295f354edf1eb3d42ffdb9b Author: kent Date: Tue Feb 10 22:24:24 2009 +0000 Wrapping a read in netReadAll instead because it's so big it sometimes seems to come back in parts. commit ec408e16b6a79a6ca75d2291e22d28754e0c5325 Author: kent Date: Tue Feb 10 22:22:59 2009 +0000 Removing stray (big!) test file that somehow got committed. commit 37996992805bb7238588fef7704e3b8bab63b763 Author: kent Date: Tue Feb 10 22:22:08 2009 +0000 Freen makes a 2 column file for testing. commit cfbc923f2e976b98ab85e64d1be10ff7ab02504a Author: kent Date: Tue Feb 10 22:21:09 2009 +0000 Allowing remote databases. commit 40affb5b411dfee4f8de58c759702871923c2a7e Author: kent Date: Tue Feb 10 22:19:24 2009 +0000 Updating worm link commit 8a1bec03a4f0c36af8a859a3b2b90d585644f78b Author: braney Date: Tue Feb 10 22:19:18 2009 +0000 added Human Proteins commit d055cf69f24bed217b0d3fe1e1f4f487b395f9e9 Author: kuhn Date: Tue Feb 10 22:17:41 2009 +0000 small diffs commit a48b05a2537f4f2b9ee01c04801546d0039647ec Author: kent Date: Tue Feb 10 22:17:39 2009 +0000 Creating bigBed type custom tracks. commit d469bc9062aaba9e201bb4aed383b5d2f4c6a70e Author: kuhn Date: Tue Feb 10 22:16:34 2009 +0000 small diffs commit 223c46198d6521c985c52518a53dd1d589897d0e Author: kent Date: Tue Feb 10 22:11:00 2009 +0000 Adding fieldCount and definedFieldCount to bbiFile header for bigBeds. commit d009d866e2ae02bba7fdab923f84a8019241dfc0 Author: kent Date: Tue Feb 10 22:10:19 2009 +0000 Testing some fool thing. commit 5b142b13bd261ca9cc3839aa097757481dea128d Author: kent Date: Tue Feb 10 22:09:37 2009 +0000 Removing unused code. commit 7c4fad33f451867faaabe3d04b6dc20778c56ec9 Author: kent Date: Tue Feb 10 22:08:57 2009 +0000 Bumping bigBedSig due to slight change in format. commit 9a1e05d8df506872022b5cccbf940b85e4109106 Author: kent Date: Tue Feb 10 21:59:11 2009 +0000 Makin blat work with U's instead of T's if q=rna is set. commit b765527260651ff117f8042d75f8c3d9447d980e Author: galt Date: Tue Feb 10 21:43:14 2009 +0000 fixing FTP so it does not waste 1 second waiting to see if there is going to be an error, this should make it faster to retrieve multiple FTP requests commit 9aa0492f8e673b6ce2a3b7de697279c3a13d2f59 Author: cszeto Date: Tue Feb 10 21:32:34 2009 +0000 Merged maser sets and added mouse set commit b63264def99be57d15583c280ef5e2bdb49845c4 Author: galt Date: Tue Feb 10 21:00:42 2009 +0000 cleaning up, udc stuff already moved by jim to udc.c commit 47c2414b1787eafbcc87c6a301e49e551a46d301 Author: hiram Date: Tue Feb 10 20:27:54 2009 +0000 Ran liftOver to rn5 back in December commit eb5e99d98f8aa1f889e20d4dc5fbe186770226cc Author: hiram Date: Tue Feb 10 20:27:13 2009 +0000 Initial work has genome up and running, sgdGene tracks functioning, running genbank commit a1bcefd14e092a99fe5e213ff5c6a59ad563b134 Author: hiram Date: Tue Feb 10 20:26:33 2009 +0000 Ran the liftOver to sacCer2 commit 064da60c21860b49879d232b9fecc85cfdde1343 Author: hiram Date: Tue Feb 10 20:26:08 2009 +0000 If we translate the type five_prime_UTR_intron to 5utr and use the -gtf option to ldHgGene then it seems to work OK. commit 70cf6bdb276afc4dcc84ea0450d9bc3da6f2c303 Author: hiram Date: Tue Feb 10 19:26:59 2009 +0000 Added sacCer2. commit 19d113dffe34fac49a82f9bd8937042f7f50efc5 Author: ann Date: Tue Feb 10 19:05:20 2009 +0000 removed stranded found by test robots commit 12e504ceb87a446e52b9cfd6b9d66b39196e226a Author: angie Date: Tue Feb 10 17:59:18 2009 +0000 Per-SNP geographic map data and scripts from Human Genome Diversity Project. commit db3db2b53216fd05803892930cffb851ea31a765 Author: mikep Date: Tue Feb 10 17:18:38 2009 +0000 draft including discordant tag alignments commit ee98bff9983f8e9aea7c731dc896a109be0277c7 Author: fanhsu Date: Tue Feb 10 16:22:19 2009 +0000 Got rid of lots of gobbledy-gook. commit b54e7777b1399ce7e54e29400c19c9a669ef7def Author: fanhsu Date: Tue Feb 10 16:20:22 2009 +0000 Get rid of lots of ... commit 9775472c61e1baa9f69bc70b0511870d11b0ace9 Author: galt Date: Tue Feb 10 16:00:07 2009 +0000 "Encode release log update" commit dcc0117ac80b71c667a7a36602609feca24a254b Author: galt Date: Tue Feb 10 16:00:04 2009 +0000 "Release log update" commit 35aa8ed700a40439e758fa84bcea21688af04975 Author: giardine Date: Tue Feb 10 14:29:58 2009 +0000 Updated UniProtSearch link to use new URL, UniProtVar link still uses the old links internally at UniProtKB, so left that one as is. commit 000e7b8c115ada780be5fc20fd4fdc8308b038a6 Author: kent Date: Tue Feb 10 08:18:18 2009 +0000 Shortened 'clipDontDie' option to just 'clip' commit e08aeb388b156daee08b3b3d8db39e000167cce8 Author: kent Date: Tue Feb 10 05:13:19 2009 +0000 Making this handle clicks from bigWig custom tracks. commit 9c8e8d9481166ff4f7e14a84bbbf9fb0aba76a1d Author: kent Date: Tue Feb 10 02:39:23 2009 +0000 Adding -test flag commit 4b63da5e0e86afc7467299941561c3be3f5176c4 Author: aamp Date: Tue Feb 10 01:22:53 2009 +0000 Error fixed for trackDbSetting thinking trackDb is NULL in the peaks tracks. commit 3d0f8e08f7a43d789765fba8f25fba2ceb76441b Author: fanhsu Date: Tue Feb 10 01:19:16 2009 +0000 Got rid of lots of gobbledy-gook. commit ffeb8ba54c02ab87a8587a5474856e06153413e5 Author: tdreszer Date: Tue Feb 10 01:13:04 2009 +0000 Obscur change to allow filterBy Dropdowns to load properly in ms ie commit 7d885d98232c6722b0e3d7cc27a15fc8edc740f3 Author: aamp Date: Tue Feb 10 01:09:30 2009 +0000 Compile-error fix. Library code changed years ago and this one didn't get updated then for some reason. commit f415652ba814d1e9fcc24466cf61534860402b93 Author: aamp Date: Tue Feb 10 00:57:58 2009 +0000 REBASE update. commit 2427a27562b1bdbc578051d4d05d49820bf5ca70 Author: galt Date: Tue Feb 10 00:47:47 2009 +0000 fixed memory allocation error commit be60c0e7cdcfef42f3943a6e4f6e8724e576d7ed Author: aamp Date: Tue Feb 10 00:17:47 2009 +0000 Removed affyHuEx1 commit ef9a44d706112f4b6677cda7abdc9164cc91a567 Author: angie Date: Mon Feb 9 23:51:13 2009 +0000 Made bdtnpChipper full by Mark Biggin's request. commit 994efb2520f248f3ea976719e60fa9a2048357bf Author: angie Date: Mon Feb 9 23:35:10 2009 +0000 Another addition from Graham Coop in Methods, and another reference from John Novembre. commit 8733b8d661bf58b41308a023ccf1345a610629c2 Author: tdreszer Date: Mon Feb 9 23:14:11 2009 +0000 Added gappedPeak as an approved multi-view type because Mike asked really nice. commit f3372f36f74762ff7355af6681b5cf4b7ac90d03 Author: angie Date: Mon Feb 9 22:30:25 2009 +0000 Use hg.conf settings to determine GMT executable paths and enable/disable images, instead of hIsPrivateHost. commit 6b537d8d636e10ad42d350dd71c3facbc9c49469 Author: kuhn Date: Mon Feb 9 22:28:30 2009 +0000 adding darwin image for his 200th birthday commit b6ccc8c28d4978d0497589610ee1f76dbe7f4057 Author: larrym Date: Mon Feb 9 22:24:08 2009 +0000 turn on dragZooming by default commit 9383ca76979a1cb8e7e073bf21dce4c27c0f27a1 Author: larrym Date: Mon Feb 9 22:07:04 2009 +0000 turn on drag-and-zoom by default; "Drag selection/zooming" => "Enable drag-and-zoom" commit 8c3c888780dce16fa36706497e5c94e691b974b6 Author: mikep Date: Mon Feb 9 22:05:10 2009 +0000 "New version number v200" commit 767173f00e4fe5353c828fdf52dd4673dbb882f1 Author: angie Date: Mon Feb 9 22:05:05 2009 +0000 Oops, the Bounding Box was the only beneficial change there -- the other two messed up the EPS and PDF orientation. commit b2f96f4fdeffe3073afce5c4838884e450429b68 Author: mikep Date: Mon Feb 9 21:39:00 2009 +0000 v200 final build commit dc382397f193b315753ad58059f5eef4e9ebb3c7 Author: larrym Date: Mon Feb 9 21:30:50 2009 +0000 Drag Selection/Zooming => Drag selection/zooming commit 0a753147adb99863d366e81f080bebc4ed918256 Author: tdreszer Date: Mon Feb 9 21:26:02 2009 +0000 Lightened Dark purple and grey commit 8b2b7b5c70e1fac52bb12734db20dcd15f53d61c Author: tdreszer Date: Mon Feb 9 19:52:22 2009 +0000 Changes to Encode Gencode including the new filterBy support commit b84ac934170ac2122980d4a88ac4287efc893691 Author: tdreszer Date: Mon Feb 9 19:49:28 2009 +0000 Add table of classes with current colors. commit fdd4029bd6f452533916a5242e045f92c3571e3c Author: rhead Date: Mon Feb 9 19:46:43 2009 +0000 Fixed broken links to downloads (thanks, Jen). commit 2e0c86cf5b8742b752f8319a6e1ef0b8c6a4d048 Author: tdreszer Date: Mon Feb 9 19:46:15 2009 +0000 More conversion to jQuery. Support for persistent cfg open. commit 6b52dfaa63384335dcaed59b639d4341c8cf45b8 Author: tdreszer Date: Mon Feb 9 19:44:15 2009 +0000 Added filterBy support for genePred. Fixed cart propagation to subtracks to handle multi-selects commit ed8e0f6be03001716766556e09e7eddab6c1ed30 Author: tdreszer Date: Mon Feb 9 19:42:22 2009 +0000 Moved genePred Cfg UI to hui.c allowing support in multi-view commit 4bfb209e7cf056239b95b9e282c2dc836404a799 Author: angie Date: Mon Feb 9 19:41:53 2009 +0000 Use the ps2raster -Te diffs to make the output EPS a bit more standard/portable. commit effbe59ad37651808471dfa6d440cbd69f974287 Author: tdreszer Date: Mon Feb 9 19:40:43 2009 +0000 Added filterBy API supporting multi-select. Extended multi-view support to genePred. commit c591096612be6c32aae3f25f496215bc32fbe23d Author: tdreszer Date: Mon Feb 9 19:37:31 2009 +0000 Added genePred to approced CghTypes and made warning optional.. Also extended trackSettingOn to accept '1' in addition to 'on', etc commit 20fdd894e3b2a61adb64db743ae570c27184016f Author: angie Date: Mon Feb 9 19:14:56 2009 +0000 Improvements suggested by Graham Coop. commit 215bf05d408f0830af802a520491d39aa78d2a9a Author: kent Date: Mon Feb 9 19:12:35 2009 +0000 Putting in bigWig custom tracks. commit fb2360ae8da68f0bb9c4a52185de2128f0514521 Author: angie Date: Mon Feb 9 18:52:35 2009 +0000 Print frequencies with %.4f because that's what we store. commit 91dba6ceddf5d367f293170a930afbdc1c94ad22 Author: fanhsu Date: Mon Feb 9 18:22:41 2009 +0000 Change error message workding according to Ann's suggestion. commit 7e681a0709aa3cc76c3a9fe284107870179a16cd Author: fanhsu Date: Mon Feb 9 18:19:25 2009 +0000 Changed Swiss-Prot to UniProtKB. commit ceaf40be865a100d5c2026eb422dae7aaf483b2d Author: larrym Date: Mon Feb 9 18:16:37 2009 +0000 make missing javascript files a fatal error commit b927b8410d51018cb0334c61570a6bbc18e26489 Author: hiram Date: Mon Feb 9 17:57:22 2009 +0000 Now using a hash for field9 instead of looping through that array commit 3371e90df76ea68150cd451e20469847d6c6384d Author: tdreszer Date: Mon Feb 9 17:39:13 2009 +0000 Special case for ENCODE Gencode link to Vega or Ensembl commit 7e597a16ee2e8d2904054808c29a9aaa7962a085 Author: tdreszer Date: Mon Feb 9 17:01:06 2009 +0000 Made cartLookUpVariableClosestToHome public, fixed cartUsualBoolean to handle 'on', added one more ClosestToHome flavor commit 0ac0515ede9d52b7eafbbd6b60df6bb8ec2b8421 Author: hiram Date: Mon Feb 9 16:59:18 2009 +0000 Now making otherFeatures.bed and descriptions.txt files commit 3640e84cf6bf910ba117543c04ea8b26d4db09bd Author: galt Date: Mon Feb 9 16:00:07 2009 +0000 "Encode release log update" commit 68081c7974287425823e6c7c74f7d96d0ec5e304 Author: galt Date: Mon Feb 9 16:00:04 2009 +0000 "Release log update" commit a5c05bde1d8d3c2c2b98e52a4376eb397dbac843 Author: kent Date: Mon Feb 9 04:33:23 2009 +0000 Adding -test flag and -cacheDir flags. commit 1b2893d5b6b3fb68e4939bc81bf1e6938fd3c946 Author: kent Date: Mon Feb 9 02:53:36 2009 +0000 Improved default blockSize and itemsPerSlot. commit 9fab54ec8d5407c9cc5344b8890e376724346a8c Author: kent Date: Mon Feb 9 02:51:42 2009 +0000 Converting the b+ tree, r tree, and bbiFiles to use udcFile instead of FILE handles for i/o. Refactoring logic in bwgQuery to gather data in one big block rather than relying on file buffering, which caused a http request to be sent every 8k. commit 7ccdade4d19658abcb1e0373e34c9bdac4f8799c Author: kent Date: Mon Feb 9 02:43:23 2009 +0000 Converting the b+ tree, r tree, and bbiFiles to use udcFile instead of FILE handles for i/o. Refactoring logic in bwgQuery to gather data in one big block rather than relying on file buffering, which caused a http request to be sent every 8k. commit 0248cdb036e1280f50971a92d48f53a7cbcf36d1 Author: kent Date: Mon Feb 9 02:39:31 2009 +0000 Added a family of memRead functions and macros that parallel readBits32 etc. commit d395a03b582a6fdf28376a04021a7bd2126eed51 Author: kent Date: Mon Feb 9 02:38:08 2009 +0000 Adding some convenience routines to udcFile handling. Adding logic to treat files without a protocol prefix with a minimum of processing. commit 0a198b83a666d746ea54ff913966a691ddafbb0f Author: markd Date: Mon Feb 9 00:02:02 2009 +0000 added length of sequences to stats output commit 7e0dda3aed0618aeb6b95899e9def009625a5d2c Author: galt Date: Sun Feb 8 16:00:06 2009 +0000 "Encode release log update" commit 8c091f632bdb51c1ce38177fc5c4b718dd04ce00 Author: galt Date: Sun Feb 8 16:00:04 2009 +0000 "Release log update" commit ea201ea277f724fe540bc3b5cdcc4090ee258317 Author: angie Date: Sat Feb 7 23:14:14 2009 +0000 Added links to PDF and EPS. Instead of generating the files every time, save trash files with stable names and use those if they exist. commit 63e97b5960f2ebd765e78787c010d7415ecf5d65 Author: larrym Date: Sat Feb 7 22:26:16 2009 +0000 update based on new doc from Rami (mostly ES related) commit 475d41517b908a731566f8c95de403ae7846cff4 Author: kent Date: Sat Feb 7 19:36:27 2009 +0000 Improving error messages. Fixing a bug that manifested when file names were long. commit 1ffed6a4cf88454fe79a439158ae2314bf663652 Author: kent Date: Sat Feb 7 18:53:31 2009 +0000 Modifications to allow byterange queries. Also some example stuff meant for udc.c commit a50d2d7cf5493d1bc38341c74ca86a62b13cd689 Author: kent Date: Sat Feb 7 18:17:24 2009 +0000 Adding http protocol stuff from Galt. commit f128393dae7ae6c6417b6be84195074f283c1314 Author: kent Date: Sat Feb 7 18:12:56 2009 +0000 Fixing prototype for udcSetDefaultDir. commit dbdafc00a5bdf8b720cdac0e74c0c08669785b98 Author: kent Date: Sat Feb 7 18:12:20 2009 +0000 Adding lastAccess to fileInfo structure. commit 9763aa89fa35e77602b0fb10e92c22fccc4cae7c Author: kent Date: Sat Feb 7 18:11:41 2009 +0000 Adding bitToByteSize() commit a07639bd2f0de1ffe45a03c6f2bfc6e99101de42 Author: kent Date: Sat Feb 7 18:08:05 2009 +0000 Addng udcBitmapSig commit f3f6d99ab7d47940f27d5c4b698d719aa83bfb31 Author: kent Date: Sat Feb 7 18:06:50 2009 +0000 Adding udc module. commit 89827561a3c3fbce4b1536ec8b163f060993c42f Author: kent Date: Sat Feb 7 17:47:28 2009 +0000 Adding udcCleanup to makefile. commit 88747ff2be02ee67714688376dbc184ff8c872b5 Author: kent Date: Sat Feb 7 17:46:40 2009 +0000 Adding udcDefaultDir and udcSetDefaultDir. commit 4b8720f507fa1c19e6e7e635f2cae12fd7eccdfd Author: kent Date: Sat Feb 7 17:42:08 2009 +0000 Seems to work. commit b976625172e3580b40d70dc78aeb56089363ce16 Author: kent Date: Sat Feb 7 17:23:22 2009 +0000 Moving udc stuff to library and adding slow: protocal for testing race conditions and udcCleanup. commit e7bd13e9e5bfbc03a3cb709901ae8f253b688e0a Author: galt Date: Sat Feb 7 16:00:05 2009 +0000 "Encode release log update" commit fa72196f3a881b95a9de8ca9a618d153095fd119 Author: galt Date: Sat Feb 7 16:00:03 2009 +0000 "Release log update" commit e2f814dad3c09e6a347f2fa7cc38c8b171d31377 Author: angie Date: Sat Feb 7 06:27:56 2009 +0000 Added printCustomUrl (surprised it wasn't there already!). commit 00815418c0f1fdf23b61d304845307ff1c1abc32 Author: angie Date: Sat Feb 7 06:23:06 2009 +0000 Added printCustomUrl to hgdpGeo, for linking back to contributors. commit 8a542786f81f4dffb76c7608501b49abd31d45f5 Author: angie Date: Sat Feb 7 06:22:31 2009 +0000 Added printCustomUrl to doHgdpGeo, for linking back to contributors. commit 74847490ac9eba47c07b760c6d7708d06c8417bb Author: larrym Date: Sat Feb 7 04:18:35 2009 +0000 add methylseq commit 118c57c40e1f92ba043c33ca4e887fcea93508fd Author: larrym Date: Sat Feb 7 03:40:51 2009 +0000 initial checkin commit 107b2c6cbbb24cac47a7f5c0523f9d930177fd34 Author: larrym Date: Sat Feb 7 03:39:00 2009 +0000 add wgEncodeHudsonalphaMethylSeq commit 31828a04f4e4112aa18fd3526f4f33d815aa8771 Author: larrym Date: Sat Feb 7 03:33:18 2009 +0000 first pass from Rami commit 3ebff30ca41767fa5f0d2081600b3795f7d3096e Author: larrym Date: Sat Feb 7 03:11:56 2009 +0000 remove invalid chrX_random commit daef2c3310cce6f4daefa4453341c5fa8856eca9 Author: larrym Date: Sat Feb 7 03:11:32 2009 +0000 fix cell type commit a7e20bd8403a3be7069f3b85b4689fae493b709e Author: larrym Date: Sat Feb 7 03:09:59 2009 +0000 make not enough/too many fields error better; don't generate RawSignal for MethylSeq commit 73a87a72dd1fc85069c3cd93842a47ea4b5e28b4 Author: larrym Date: Sat Feb 7 03:01:09 2009 +0000 fix hard-link problem (change link => ln -s ...); support bed 9 commit 5bd46d782e6e3e192e3bb38b63c41fd706513e28 Author: larrym Date: Sat Feb 7 02:12:30 2009 +0000 initial checkin commit 9bb78f4edd2de0b06c1567c13127e8829ec4e9e2 Author: kent Date: Sat Feb 7 01:52:05 2009 +0000 Removing a bunch of debugging uglyfs. Changing a few to verbose(2) statements. commit 361f8015762df7ecc84e6451f02942af3c32af26 Author: kent Date: Sat Feb 7 01:25:28 2009 +0000 Rearranging locking and stuff to hopefully make it play better with multiple cache users and stale data. commit 68e9125781cbd3f5e71b02ab9e877a5a3ec1b641 Author: angie Date: Sat Feb 7 01:13:05 2009 +0000 Added a general reference for HGDP. commit 935615ab4e8543dd14d625f669b279520e0605f2 Author: cszeto Date: Sat Feb 7 01:12:48 2009 +0000 Merged two datasets commit de115bd9b96e18fe4d525b1490cc6e2fe1da5ac1 Author: cszeto Date: Sat Feb 7 01:12:05 2009 +0000 Merged two datasets. commit 912b9c7de3b77ffb1fc10ee24df60455df6f2341 Author: angie Date: Sat Feb 7 01:02:40 2009 +0000 A few more details. commit 87d390155b8b00ae0f433e6a9096a32e868ce3cf Author: angie Date: Sat Feb 7 00:52:05 2009 +0000 Skeletal description. commit 89a04f44217b9bfefc1903d0e082e7d71088dfe4 Author: braney Date: Sat Feb 7 00:33:51 2009 +0000 Human Proteins commit 2f06279fcd0e16bce34246b3f54021f2263d49fc Author: angie Date: Sat Feb 7 00:25:30 2009 +0000 Adding hgdpGeo. commit 46bec511601937f91bd27a6c84c8558fa4a896ec Author: angie Date: Sat Feb 7 00:14:20 2009 +0000 Added pipelineAppend option for pipelineWrite mode. commit 4da74160f69c50e8741787946621bf581ac5b43a Author: angie Date: Sat Feb 7 00:11:10 2009 +0000 Added hgdpGeo, Human Genome Diversity Project alleles and frequencies for 53 populations worldwide. This includes generating a world map image with allele frequency pie charts, using the Generic Mapping Tools (psxy and ps2raster) to recreate John Novembre's rendering flow in the HGDP browser. Until the GMT tools are installed in a more appropriate place (using /hive paths), this only works on hgwdev. commit b574a3f5caf8e0ace9a92b90955e3f4b136dcbfa Author: kuhn Date: Sat Feb 7 00:10:17 2009 +0000 flipped NHGRI announcement above PCR commit 83c29629c9c6c5cc0c72797915ba7ecaa7639eb0 Author: angie Date: Sat Feb 7 00:02:59 2009 +0000 Adding hgdpGeo, Human Genome Diversity Project alleles and frequencies for 53 populations worldwide. commit 8dc6624990c0d4efeb9a6200716a0922833a2c20 Author: pauline Date: Fri Feb 6 23:39:07 2009 +0000 Added hyperlink to 2bit sequence download for assemblies without browsers. commit 15ffdf07d990263c00d3203a9db98cf229e14b8b Author: kent Date: Fri Feb 6 22:58:29 2009 +0000 Breaking remote reads into sections if they are over 256k. Cleaning up handling of partial data in final block of cache. commit 6f47275b9914f6d2e0042e5e0bb7ab309e1db079 Author: hiram Date: Fri Feb 6 21:43:15 2009 +0000 Initial source commit a5f40c32b498a7aac90b7dd41b74db52748631ed Author: kuhn Date: Fri Feb 6 21:32:52 2009 +0000 made in silcio in italics commit 249ffe5f4e9bc804634df8fafdca0a3347da4486 Author: kent Date: Fri Feb 6 18:51:47 2009 +0000 Reducing remote accesses. Removing some debugging. commit 9fc77f5921abbde9c40226ba3a97957ea2c6690f Author: fanhsu Date: Fri Feb 6 17:44:04 2009 +0000 Added rule for Illumina 1M SNP array. commit 5c8e3202f476c5bfc7a98faa9b571875c588a9b5 Author: fanhsu Date: Fri Feb 6 17:22:43 2009 +0000 Putting back description for Illumina Human1M-Duo. commit 0cb59758f41887aff4c8bfb019b67d3f8f2e0168 Author: kuhn Date: Fri Feb 6 17:12:49 2009 +0000 dropped hgw7 temporarily so hgw6 can be diffed (against hgw5) commit a1c1411f6f9d8f20431e147b01b00ab72a219c25 Author: kuhn Date: Fri Feb 6 17:05:11 2009 +0000 made usage statement more clear commit e009db7c7155d9c2023a25188b3c09bb63bb8b70 Author: galt Date: Fri Feb 6 16:00:06 2009 +0000 "Encode release log update" commit 2f014e9110961c2a6ddf238a381ee5bd1aab28dd Author: galt Date: Fri Feb 6 16:00:04 2009 +0000 "Release log update" commit b92a3cedc148dfb9517be058e5e72846159382b7 Author: kent Date: Fri Feb 6 08:26:52 2009 +0000 Still a lot of work to do including the locking. Starting to pass some run time tests though. commit f4b8e95444ea1b265eaf8b1b271134e5fca84993 Author: kent Date: Fri Feb 6 04:55:39 2009 +0000 More work on cacher. Running (and failing) the first run time tests now. commit f8378d4c5ad71b4adc6588c15f4961b69c9c46ba Author: donnak Date: Fri Feb 6 04:50:28 2009 +0000 Archived an item. commit 4f833f856593552d0d39324284e3ede2958bfb2d Author: donnak Date: Fri Feb 6 04:50:13 2009 +0000 Added 2 new items, archived an item. commit 355075310208e9d835f3001c1f463e32415dc0fd Author: kent Date: Fri Feb 6 02:16:58 2009 +0000 Some more work on cache which is still not complete enough to test. commit 77778eace5711656cd66fa327445112d873ea1c9 Author: kent Date: Fri Feb 6 00:35:52 2009 +0000 More work on data cacher. Still not even first draft complete, though what's there does compile at least. commit f1767a3ceff02b0f35d8fbb8545e89a7a2d6462f Author: ann Date: Thu Feb 5 22:45:34 2009 +0000 setting rmskRM327 to hide (per Angie) commit adec2a6f7b6304c2d456211554b4c4db6e3baa89 Author: markd Date: Thu Feb 5 22:31:13 2009 +0000 log creation of mafs commit 56d751fdd801cb0ee6fe0a171c689350397c3d39 Author: donnak Date: Thu Feb 5 22:01:08 2009 +0000 Removed CBSE phone number to prevent the CBSE admins from getting tech support calls. commit 5728b9ad8384f8f52e5ceba67b48ebd79a43cfdb Author: kuhn Date: Thu Feb 5 21:59:27 2009 +0000 made rt-handed helix image only 250x250 commit d12b20b32607a2674301e2c8563c7ac725463423 Author: hiram Date: Thu Feb 5 20:53:24 2009 +0000 More information on error output so it can be determined what is wrong with the file conversion commit 60b204e0a8d0d359b704d7a9ab7b1032ca92cd15 Author: kent Date: Thu Feb 5 20:49:48 2009 +0000 Improving nan usage. commit 883f6ea78e8258582f2a7a5aef5afca827f4d12f Author: kent Date: Thu Feb 5 20:45:05 2009 +0000 Fixing a few things found in code review with Hiram. commit c153fa8736446e927e320f6bb05df0917c059c17 Author: kent Date: Thu Feb 5 20:44:37 2009 +0000 Renaming bbf to bbi. commit 8aa48b7fd96d8a87bf927720d7fcdf1518de9c7b Author: kuhn Date: Thu Feb 5 20:39:52 2009 +0000 reversed helix to make it right-handed commit 9525283ba0a3195d95c51a227ed866bf31ed274e Author: kent Date: Thu Feb 5 20:34:45 2009 +0000 Adding maybeSetCurrentDir and makeDirsOnPath to our portable os library. commit 986d27ef6079e5e1e92762703cc7eb1910edecef Author: mikep Date: Thu Feb 5 20:15:40 2009 +0000 brief description of gPET Encode data from Atif at GIS commit 93b376399151924cff027b911b128788cd1d634d Author: kent Date: Thu Feb 5 20:02:41 2009 +0000 Starting work on local file cacher. commit db68c08a31b46e6ce88555549ea30389580d2f4b Author: mikep Date: Thu Feb 5 18:18:01 2009 +0000 new frag size for gPET (see GisDnaPet.daf) commit cfa26a2d8626e44796742c7b402764b6a41c1396 Author: mikep Date: Thu Feb 5 18:17:23 2009 +0000 need comma in vars field commit 785d139a24dd2b62bfbf81c74d96f62d482e8d90 Author: kuhn Date: Thu Feb 5 16:56:40 2009 +0000 added hyphen commit ef0285d11e7dc01a098e3a15d859fd1d5b022edf Author: angie Date: Thu Feb 5 16:29:36 2009 +0000 On new machines, tail +N must now be tail -n +N. commit 6e82a8ca55b05cdd553481b586990f9ad3505492 Author: galt Date: Thu Feb 5 16:00:05 2009 +0000 "Encode release log update" commit 6b18f3b5485930526c1da6a4df14f50ae3be15f3 Author: galt Date: Thu Feb 5 16:00:04 2009 +0000 "Release log update" commit 96b2bf0c06092d84e8567cd82d12d8f0c8497e1b Author: markd Date: Thu Feb 5 08:06:26 2009 +0000 open chimer help page in a new window/tab commit cb3fe9ad118c06cde2890bc315a77bd6b4d663e0 Author: markd Date: Thu Feb 5 08:05:17 2009 +0000 link hgGene to LS-SNP/PDB commit 30ec0a19f4612a50aac221c017260ca763a2040d Author: markd Date: Thu Feb 5 08:04:11 2009 +0000 start file with comment that hints to need to configure as a helper app commit 90e50b46536aac88e9877e690e86a18cbbb30586 Author: kuhn Date: Thu Feb 5 04:24:35 2009 +0000 made image a bit smaller to avoid overwriting (shoulda been able to do it witgh HTML, but couldn't) and added a little padding to position query examples commit 1925e496776ad010d87f6921b4c0692245cdc92d Author: braney Date: Thu Feb 5 01:17:56 2009 +0000 re-did RM again to fix something (what? I don't know) commit 031331c4e8b65848a41104872ac62526c5a404a1 Author: angie Date: Thu Feb 5 00:54:24 2009 +0000 bdtnpChipper: More flexible default visibilities. commit dfdad6b96e39ef48791b215c4d941db565ad5efb Author: markd Date: Thu Feb 5 00:52:02 2009 +0000 added rules for lsSnpPdb commit 3f395769e997ce622253543a6f60c43e054c656c Author: angie Date: Thu Feb 5 00:21:55 2009 +0000 typo fix in warning message. commit e5545f14eba1ec093144a4d1a8bfeedb089dad23 Author: angie Date: Thu Feb 5 00:19:13 2009 +0000 Bugfix in subtrackInherit: subtrackTdb->type can be "", not just NULL, so test for both. commit 392c6d03d021740bb10d304186d645a0db9a7040 Author: kuhn Date: Thu Feb 5 00:16:58 2009 +0000 added a little padding around search terms commit cda42f5d99c27c79d363e6b907250955ea01bb3e Author: kent Date: Wed Feb 4 23:57:03 2009 +0000 Restoring no data label when appropriate. commit 25e3222ca7d5bffdb475bd4354a1f53844ba5e6f Author: angie Date: Wed Feb 4 23:48:01 2009 +0000 bdtnpChipper: punctuation/capitalization tweaks to be consistent with description updates. commit 0ce35897f9c929d7143162fe9769289121eaeb1b Author: angie Date: Wed Feb 4 23:39:20 2009 +0000 Updates from Mark Biggin. commit bb853fac833f40f19a69365e5e9c90a097176622 Author: kent Date: Wed Feb 4 22:27:20 2009 +0000 Adding clipDontDie flag commit 8ae36978b14126e986dbc54b409962c559d42693 Author: angie Date: Wed Feb 4 21:30:02 2009 +0000 bdtnpChipper: added views and regulatory class. Re-ordered and re-colored subtracks per Mark Biggin's request. commit ee76ddb59b4270117f3d3d902e6ffe24056f43df Author: mikep Date: Wed Feb 4 20:20:15 2009 +0000 new RikenCage data commit c309c9829fa335bcde4697e57a98fe3b9c2ec022 Author: kent Date: Wed Feb 4 20:12:15 2009 +0000 Making composites know how to configure bigWigs (and bigBeds) commit db3b2a0d4fe65e8c3b9f8a3cd5fab48d8d6fba6d Author: kent Date: Wed Feb 4 19:57:58 2009 +0000 Putting in more checks on input file - avoiding things not in chrom.sizes or outside of chromosome coordinates. commit 54a37f4165726518ab3d670a17f357b259fb28dd Author: kent Date: Wed Feb 4 19:53:34 2009 +0000 Updating expected results for fixes. commit 8a4ffda10a0fc614bb83d543449ae1fc549ebe16 Author: mikep Date: Wed Feb 4 19:38:46 2009 +0000 added new AffyRnaChip stuff; added CshlRnaSeq stuff; fixed conflicts in UwDnaseSeq additional track settings such as span commit 12b4c1557e36a530558c97f0f2e9ed629f7ed239 Author: galt Date: Wed Feb 4 19:21:52 2009 +0000 need to flush before fork commit 2f2b44ec97b99a8009a055656fb70b0d16fbf992 Author: hiram Date: Wed Feb 4 18:38:25 2009 +0000 Remove memk from the kluster pool until it becomes more reliable commit c1af1a763f16bbf30f8c843290f3c2309f6d2ff1 Author: kent Date: Wed Feb 4 18:38:03 2009 +0000 Making left labels work for bigWigs. Streamlining code that figures out graph upper and lower limits. commit 1b61aacdd474f0985762d9be11ed7e5380285dc7 Author: kent Date: Wed Feb 4 18:35:55 2009 +0000 Making summary routines work better at extreme close up views (multiple pixels per sample point.) commit 03febbaff904b6397d3f1f308d7e216b2a10fd62 Author: hiram Date: Wed Feb 4 18:34:49 2009 +0000 Update v52 business to sacCer2 commit 606ea5792dd98f018e4843bcfb91f7e4bfba6fed Author: hiram Date: Wed Feb 4 18:34:25 2009 +0000 Correct comment to indicate hive data genomes location commit 797fe936e586c3f9b44bfde31aa97df27f910534 Author: galt Date: Wed Feb 4 16:00:05 2009 +0000 "Encode release log update" commit 7f585ba6736517e43635de71526464ce83ea71f0 Author: galt Date: Wed Feb 4 16:00:03 2009 +0000 "Release log update" commit f5c9d147310c3746dc9836d39026529289bd7ddb Author: galt Date: Wed Feb 4 06:59:57 2009 +0000 trying to handle some FTP servers needing the control conn kept open for the entire data conn transfer commit e61b5dcefdaa93a9dc97b4ee7d1c84a1ce8e688c Author: kate Date: Wed Feb 4 06:13:56 2009 +0000 Tweak defaults. Try using max of stdevs across all tracks (chr1 only) for max viewlimit commit ea39d4cf668d049a460f73b601e9b5a8807be82e Author: markd Date: Wed Feb 4 05:17:05 2009 +0000 added support for create upstream mafs for more than one alignment commit cb86c70aae086436afad5102226644d5098d6db7 Author: kate Date: Wed Feb 4 01:46:37 2009 +0000 Shorten shortlabels to <=16 and standardize (cell type first) commit a11ab1c39beb6e29a0c35904825573b354aa83f3 Author: kate Date: Wed Feb 4 00:14:33 2009 +0000 Labels for control experiments, edits for consistency commit 946133dca3c9255aa72c773419756cda993ac8c0 Author: kate Date: Tue Feb 3 23:56:38 2009 +0000 Ordering cell type first in HudsonAlpha TFBS short labels, for consistency with Yale. Leaving others for now, in case we reverse course before release commit 43c247894de17c40a985e9266343cc32466b28cc Author: markd Date: Tue Feb 3 23:42:57 2009 +0000 fixed really bogus html commit 45d1fd2881fb6db653c28956c582b9884ad1e2ba Author: hiram Date: Tue Feb 3 23:32:15 2009 +0000 Added yeast image, and better description pages for sacCer2 commit af86ee16bc1ad2c11fd104d1bd30ef8452c8f7f6 Author: kate Date: Tue Feb 3 23:16:10 2009 +0000 Tweak long labels for consistency and to fit 80char length limit commit 9f9c5ae0a62ac593b35ec217914108b3dac38f8f Author: hiram Date: Tue Feb 3 23:07:35 2009 +0000 Photo courtesy Maxim Zakhartsev via SGD public pages with permissions there commit f6956369e49f83689b814dfe856e93dae893aee5 Author: tdreszer Date: Tue Feb 3 23:02:29 2009 +0000 cartUsualBoolean as macro was faulty commit 79798e632668bec45ebedf0468ccf37e6e48e508 Author: hiram Date: Tue Feb 3 22:49:17 2009 +0000 Initial files from makeGenomeDb.pl commit dc9beceb0171a7e7ab90584ef9877c91d0e19246 Author: kuhn Date: Tue Feb 3 22:42:08 2009 +0000 added trademark R in circle commit 0ffe74760eddb591ae19942a003b0ff6ca183d25 Author: hiram Date: Tue Feb 3 22:40:37 2009 +0000 uiState might be empty, print it at the end of the URL commit 0999751add85ad6ed59360c512b38c2a7a7f4b49 Author: kuhn Date: Tue Feb 3 21:58:23 2009 +0000 put in correct reference now that it is in print commit 8818179e9507b74f717cf83805a46812444069a5 Author: kent Date: Tue Feb 3 21:37:40 2009 +0000 Adding genericBigBedClick handler. commit 1cb6562544bc4cb042c4f4c8b22ae2cd93ee6cc2 Author: kuhn Date: Tue Feb 3 21:29:41 2009 +0000 dropped extra tag commit 04bedafc2ea1b8fb1123c36fd4971deda410cec4 Author: kent Date: Tue Feb 3 21:04:04 2009 +0000 Making a generic bigWig click handler. commit 0002d1129093a1c0d222bd451aa4b93a323452ac Author: galt Date: Tue Feb 3 20:59:05 2009 +0000 adding a trivial url fetcher to make testing URL fetching easier commit 11536e4c6b0b0a5c982d6daa219e604e4808ccce Author: kent Date: Tue Feb 3 20:50:29 2009 +0000 Adding calcStdFromSums and calcVarianceFromSums. commit f0b1f58b79efc9368610dfa0a6d255bdc04696c3 Author: donnak Date: Tue Feb 3 20:27:50 2009 +0000 Removed clickable link from GDB entry on STS Markers details page (GDB website is currently defunct). commit f35e9f793ee696e08fbea3f515b317640b65a867 Author: hiram Date: Tue Feb 3 20:11:47 2009 +0000 Allow override of mitochondrial sequence max size check, yeast has a big one commit 69a9225ea41999e018edd041b33c8c8adf0d689a Author: kuhn Date: Tue Feb 3 20:06:58 2009 +0000 adding image to hg18 gateway page commit 16d7e8ae890abf2a9013c7645ab5c78d72a8bc19 Author: kuhn Date: Tue Feb 3 20:04:24 2009 +0000 adding graphic for human pages commit 2d98521f3db67b9130523916cce7a67ee9c2c90d Author: kuhn Date: Tue Feb 3 18:25:13 2009 +0000 fixed the wording and added a link to morbidmap commit 90c26526b0ddd70ddec2ba008ccd48ec2db8009a Author: hiram Date: Tue Feb 3 18:11:32 2009 +0000 Ensembl blue bar link now works for ci2, gasAcu1, and fr2 commit d3f9665ff8e461abd1695f1969770a7a69e53e18 Author: fanhsu Date: Tue Feb 3 17:57:28 2009 +0000 Added checking for ccds. commit 237b13fb7bba98567d8b453440dda2520d8244f6 Author: tdreszer Date: Tue Feb 3 17:49:12 2009 +0000 Fix script error (not always silent on IE) commit 7b0e0996b1acac94c824b3cc6266b87d3ddddd4b Author: mikep Date: Tue Feb 3 16:39:47 2009 +0000 v200 preview commit 7e374647d7bfafc1f9c6456c192a3045438e24f0 Author: galt Date: Tue Feb 3 16:00:07 2009 +0000 "Encode release log update" commit a57284ac1692d43b33b233edc35f26025368af76 Author: galt Date: Tue Feb 3 16:00:04 2009 +0000 "Release log update" commit 571a02f0d1e91c687a9c9318a3c5048b4d5ddffd Author: aamp Date: Tue Feb 3 09:19:37 2009 +0000 Genscan and N-SCAN. commit e5bcfafa30e5fef58f0488092dd53e59b09acd9c Author: aamp Date: Tue Feb 3 09:06:45 2009 +0000 Added N-SCAN bit that it's a lifted track. commit c823f83474cab83f38975950d5603f9a512af89e Author: kent Date: Tue Feb 3 08:20:04 2009 +0000 Making bigBed packable. commit 0ce8b314f692bdf9203f481a68a87b2b94d80bc5 Author: kent Date: Tue Feb 3 08:19:05 2009 +0000 Making new module bedTrack, with most bed things, and making it so that bigBed works there. commit adcb838d22d001cce68900b9fc397acb7ae070b3 Author: kent Date: Tue Feb 3 08:18:53 2009 +0000 Adding retCHromId paramter. commit eb56156d2fba66808d1dfa5eec7473910ab9f7fc Author: kent Date: Tue Feb 3 08:18:24 2009 +0000 Adding bigBedIntervalToRow. commit e5bb0bb544826545310c3253eb80651335d65f18 Author: markd Date: Tue Feb 3 07:11:41 2009 +0000 enabled LS-SNP/PDB integration commit 01381af4a4eb9007f6c6fc232425bfe96c5822e9 Author: kent Date: Tue Feb 3 05:04:07 2009 +0000 Refactoring so that wigTrack also shares wigDrawPreDraw along with bedGraph and bigWig. commit 4611efb13500586bea3d6b7e523ac0978ddd2d40 Author: kent Date: Tue Feb 3 04:47:05 2009 +0000 Making bigBedIntervalQuery keep to just the chromosome being queried. commit d02bce8dac6f63bd74a473a75f72736dc31705f3 Author: kent Date: Tue Feb 3 04:31:06 2009 +0000 Fixing Bed/Wig mixup. commit ff15fd2c4011d2e92472e86c2d3c1005cd0fc379 Author: kent Date: Tue Feb 3 03:33:35 2009 +0000 Adding bigWig support. commit 0efeee0e37c672dc5f9db19094c2e9bee2f763c8 Author: kent Date: Tue Feb 3 03:31:47 2009 +0000 Shockingly, bigWig seems to work as a built-in track type. commit 82c381507f45b9eb70361ce78fb1d71996f7643e Author: kent Date: Tue Feb 3 02:50:39 2009 +0000 Adding SummaryArrayExtended function to bigWig and bigBed (and bbiFile) commit b625a4c6603cede728f6f770cfa45eb4d77b3d54 Author: kent Date: Tue Feb 3 02:14:58 2009 +0000 A little refactoring of wig stuff to make more reusable. A first crude cut of a bigWig track - doesn't use the summary info yet. commit 49982aca4f497ca85ffbcd841a0fc1abaaeef843 Author: kent Date: Tue Feb 3 02:03:23 2009 +0000 Seems to work. commit ad1bbbae46fc92f3789e4e94326335d619c92392 Author: tdreszer Date: Tue Feb 3 01:27:57 2009 +0000 Elnitski BiPs are separate track, EncodeGencode changes commit 4b48bbddddec7bba612fd095e1b276f763f8ee23 Author: angie Date: Tue Feb 3 01:03:06 2009 +0000 And a subGroup Factor definition for that one last antibody. commit 12352ae1c6e4a849873549ac1e913870fc53b1dd Author: angie Date: Tue Feb 3 01:00:28 2009 +0000 Oops, one more antibody! for bdtnpChipper. commit a17cd09cbea63288841c51c267d5d0d850e72241 Author: kent Date: Tue Feb 3 00:58:58 2009 +0000 Updating test set in light of some fixes. commit 6eec7ed96807c2402d08a2d72ed558a9c18c25c0 Author: kent Date: Tue Feb 3 00:43:28 2009 +0000 Limiting initialReduction to something reasonable. commit 18e51ee984b8cf00e6c508e1d42dead17ff1524c Author: kent Date: Tue Feb 3 00:39:44 2009 +0000 Refining library interface. Reducing memory use of bigWig encoder in fixedStep and varStep cases by close to 2x. Adding version number to file. commit 9e4efeb09360ecb0787063255da0981e876423c4 Author: angie Date: Tue Feb 3 00:06:40 2009 +0000 Added new subtracks for 15 new antibodies (23 experiments) to bdtnpChipper. commit b1dc76d4af6037adb86b18ba426e61c1a0245786 Author: tdreszer Date: Tue Feb 3 00:04:48 2009 +0000 Error message more trouble than it is worth. Beds that are configured by score are fine in multi-view commit f24fb9d8ee11d48548705f629194fe2d47e22331 Author: kate Date: Tue Feb 3 00:01:21 2009 +0000 Ignore non-track stanzas (e.g. searchTable) commit 95bf48afa8e45ea6aa0f1d3b540ea349e803ec4c Author: kate Date: Mon Feb 2 23:52:07 2009 +0000 Allow comment lines as in trackDb.ra files commit 7e68f64037bb4c464c5b47f90313e959cb5767e3 Author: angie Date: Mon Feb 2 23:50:11 2009 +0000 Added new subtracks for 15 new antibodies (23 experiments) to bdtnpChipper. commit c484af5b50968f894d264bb4e63f8f6b608e4d65 Author: markd Date: Mon Feb 2 22:45:52 2009 +0000 made explict nscan track entries so there is no BUG setting after make scrict commit b4e13039a6859d4238d69819275b01440701d915 Author: markd Date: Mon Feb 2 22:30:05 2009 +0000 removed obsolete MGC stuff commit 6770210c7b399aba1684c41c1837a3d18fe46db5 Author: fanhsu Date: Mon Feb 2 22:28:07 2009 +0000 Updated using doc from Marcos/Keith. commit e8ab618ecd17918d2e73938a91206959380d889e Author: fanhsu Date: Mon Feb 2 22:23:20 2009 +0000 Updated by doc from Marcos/Keith. commit ecee5046ed8c8e3e5652806a420aceef2c55ac40 Author: fanhsu Date: Mon Feb 2 22:21:26 2009 +0000 Updated with doc from Marcos/Keith. commit 715d217aad6aa6173e1c3c093be3a406ff3f6d0d Author: pauline Date: Mon Feb 2 22:11:44 2009 +0000 goldenPath/help/pbTracksHelpFiles/pbpepRes.txt commit 3a4bbfc64189e07fa40b0215060cb334346dfabf Author: tdreszer Date: Mon Feb 2 22:10:50 2009 +0000 Support for scoreFilterByRange commit 00ef3e7feaa01d0c4b3f67d7feced7c44a90b830 Author: tdreszer Date: Mon Feb 2 22:10:49 2009 +0000 Move Downloads and Schema links and support for EncodeGencode commit 2638196db9ec8ce3caa3f51e776efebf098fc661 Author: tdreszer Date: Mon Feb 2 22:10:33 2009 +0000 Support for ScoreFilterByRange, move Downloads and Schema links and support for EncodeGencode commit 9e9ccd25f5f374efcfb1b9722a5361596b87c3ed Author: tdreszer Date: Mon Feb 2 22:06:39 2009 +0000 Renamed sortContainers to prioritizeContainerItems and moved it's call to just prior to sorting by priority. commit 271fb9e77c540fc678fdca6fbd953a4c4921fa6a Author: braney Date: Mon Feb 2 21:32:31 2009 +0000 Human Proteins commit 88ebdb4c7baa098a14d3ce765a46145e98bdd584 Author: larrym Date: Mon Feb 2 21:30:36 2009 +0000 add pseudo-versions to js script tags commit 0d7eb3b98483ca30c65aa9ec35cad25b004b2a76 Author: hiram Date: Mon Feb 2 19:41:44 2009 +0000 Updated to work with Yeast files 2009 commit 901b652afde133472c86a9f15794ed3e982dc52f Author: ann Date: Mon Feb 2 19:35:38 2009 +0000 updated list of ensGene upstream MAFs commit 5dd108335202f4edd57041ada478c8c4b8a558b4 Author: hiram Date: Mon Feb 2 19:18:17 2009 +0000 Moved bedCmpExtendedChr() function out of bed.c to here to avoid SQL linking commit c7c8edabe85183d37cedf42d4a7918770ef90e22 Author: fanhsu Date: Mon Feb 2 19:04:58 2009 +0000 Created vax004PosSelVac.html commit 1c570ac95913fdd5688e5d15cdcd2a5e8212e6dc Author: fanhsu Date: Mon Feb 2 19:04:29 2009 +0000 Created vax004PosSelRace.html commit 6fdcd7eec89650a8a6eab5e07a52fc4d89f4dd44 Author: fanhsu Date: Mon Feb 2 19:04:04 2009 +0000 Created vax004PosSelLoc.html. commit 80ee7f016d6ffc0a79095747cf53a1aa2f424d56 Author: fanhsu Date: Mon Feb 2 19:03:38 2009 +0000 Created vax003PosSel.html. commit 62125c20a40f80bd7071671145e1678e1d6253f5 Author: fanhsu Date: Mon Feb 2 19:03:10 2009 +0000 Added entries for Positive Selection tracks. commit c1e9815dcffe0dfedb9bb6c5324a5fd31bacd09a Author: pauline Date: Mon Feb 2 18:08:22 2009 +0000 Updated UniProtKB links commit a737ac14ea062568e43392518bd752449179e5c3 Author: kent Date: Mon Feb 2 16:28:44 2009 +0000 Fixed integer overflow problem. commit 527c8f69073157d32ea8b189b8906d92024f143a Author: galt Date: Mon Feb 2 16:00:06 2009 +0000 "Encode release log update" commit 78ad2f3e87d189ae8415986423dd41bac89e97af Author: galt Date: Mon Feb 2 16:00:04 2009 +0000 "Release log update" commit 80ad2e61c65774ab19c88fab689652ed92688097 Author: kent Date: Mon Feb 2 06:05:52 2009 +0000 Refactoring to put shared bigWig/bigBed stuff in bbi module. commit 0fbb258b91cb1067be9850d6e8b1f9bb88de6679 Author: kent Date: Mon Feb 2 04:19:38 2009 +0000 Refactoring to put shared bigWig/bigBed stuff in bbi module. commit 13c377f85523636d9224599e76062b09fa1b8e56 Author: galt Date: Sun Feb 1 16:00:07 2009 +0000 "Encode release log update" commit 5e4a3aeed69fcf7a76a5e44223a7169518b00667 Author: galt Date: Sun Feb 1 16:00:03 2009 +0000 "Release log update" commit 7823f7f7a68006fdf9a38b3f0bbbf42f8064dff4 Author: kent Date: Sun Feb 1 04:06:19 2009 +0000 Tweaking debugging statements. commit e48a3132dde260b476abdf4a61f6b5781b8d03a5 Author: kent Date: Sun Feb 1 04:05:37 2009 +0000 Adding include. commit d7a92f7a53e43f80c90fa45003317e46849046f0 Author: kent Date: Sun Feb 1 04:04:47 2009 +0000 Adding bigWig and bigBed to makefile. commit aab6b4021c95d94b1278a6418643cbd9a98780ff Author: kent Date: Sun Feb 1 04:04:07 2009 +0000 Fixing missing include. commit 8aeed6b617c92919ee315eef591d60907a92629c Author: kent Date: Sun Feb 1 04:03:24 2009 +0000 Making a int into a long for really big files. commit 44a29aaa99b059eea96a190f04ceb404ebeb410c Author: kent Date: Sun Feb 1 04:02:25 2009 +0000 Making nan() call conform to spec better. commit 7bb778d6318157a1e56803883f9f5a23227ca9ef Author: kent Date: Sun Feb 1 04:01:19 2009 +0000 Seems to work. Worth testing. commit 4f023197ec254229bcf5a7de553231fbd26b731c Author: kent Date: Sun Feb 1 03:55:44 2009 +0000 Seems to work. Worth testing. commit 5d0e2adfc215f690742cd185ac2f6e4963a58d90 Author: kent Date: Sun Feb 1 02:37:29 2009 +0000 Seems to work. Worth testing. commit 23c8982742f1517e0947b8914f58bf022b81d708 Author: kent Date: Sun Feb 1 02:28:46 2009 +0000 Might work. Worth testing. commit 13d0074760fce9314e88fcadf08474ae4cf04fb4 Author: kent Date: Sun Feb 1 01:59:13 2009 +0000 Adding bigBed creation routines in new library module. commit 5eaa22b0caa9444e571aaee1c00884f4297b4814 Author: kent Date: Sun Feb 1 01:45:51 2009 +0000 Working on query side - most of which is already in libary actually. commit 2c4ff7a079746ff1048a40f56e0ec1c2dc7dcf59 Author: kent Date: Sun Feb 1 01:34:21 2009 +0000 Shortened awkwardly long function name. commit 001d2b4d5b34b6de29813229bf747c662d4dc411 Author: kent Date: Sun Feb 1 01:30:39 2009 +0000 Minor changes to get it to compile on hgwdev. commit 79c3a441baac31bf87267b52a62af08ef8220ebb Author: kent Date: Sun Feb 1 01:29:51 2009 +0000 Adding rangeTreeAddRangeToCoverageDepth commit bcc3ef81b1a247159071b11d375d14bc38662cf5 Author: kent Date: Sun Feb 1 01:27:38 2009 +0000 Adding bigBedSig commit 6dde9c902dad323bdd495e8a4fbfdbfd6ad2b702 Author: kent Date: Sun Feb 1 01:26:44 2009 +0000 Adding bigBed. commit 5198cc437e78dbaf2f204f713d8dbccbc1e28cd3 Author: kent Date: Sun Feb 1 01:20:35 2009 +0000 Adding bigBed. commit 3ba559bf28b46cfcbf95b6754b0222f82d31bb3a Author: galt Date: Sat Jan 31 16:00:06 2009 +0000 "Encode release log update" commit add3f21bdd85afa7e05cf17892a24cdc1d358620 Author: galt Date: Sat Jan 31 16:00:04 2009 +0000 "Release log update" commit 725536dd08ed6697c3edbbdb37cb53a1436c1d7f Author: aamp Date: Sat Jan 31 07:45:33 2009 +0000 Just a little comment about using a fixed value. commit 55e3791f8b9933512a2851294a83e6ef148e3276 Author: aamp Date: Sat Jan 31 07:28:55 2009 +0000 Fixed "max" error, and another error having to do with "hgFixed" being hardwired into the code. commit 2e7229bf61e56a07fe14fa613ac584b2603218f1 Author: aamp Date: Sat Jan 31 06:05:28 2009 +0000 broken build fix? I think so. hgExpLabelPrint needed another arg. commit 9e950a2e181b7c0a8ad254b65742440b6de59452 Author: angie Date: Sat Jan 31 01:04:29 2009 +0000 Adding rmskRM327 and nestedRepeatsRM327 so we can provide more current RepeatMasker annotations without disrupting original RepeatMasker results which affect many analyses. commit 708efc1a512ef0f7cf7149897d4e5ac92e8a55e5 Author: angie Date: Sat Jan 31 00:39:21 2009 +0000 Added chr%_rmskRM327 and nestedRepeatsRM327 to tablesIgnored. Tried to use RM% but it didn't work. :( commit af5a290af420c27380482a116f4e3475b2e6d2c0 Author: angie Date: Sat Jan 31 00:26:56 2009 +0000 Instead of overloading the original chr*_rmsk tables, make new chr*_rmskRM327. commit 88dbc2a3469a35d836aa4822160702dc0084bae8 Author: ann Date: Sat Jan 31 00:15:26 2009 +0000 added announcement about equCab2 (removed from home page). added (commented out) sections for 2009 stuff. commit 2c5323b2cc57d076e4f90d31aaa60202351890b1 Author: ann Date: Sat Jan 31 00:14:49 2009 +0000 added announcement about 44way Conservation track. shrunk announcement about equCab2. commit 6f0c31631e96b4d7eab13bd7d42ed8455a010d3f Author: fanhsu Date: Fri Jan 30 23:51:14 2009 +0000 Changed UniProt to UniProtKB. commit 2a4041c94f9a20d6fa3727da309eeb942edef257 Author: kate Date: Fri Jan 30 23:50:30 2009 +0000 Another common cell type was added commit d28538b1a8a08fe8400ef0bc29e5048daf1f4ad5 Author: kate Date: Fri Jan 30 23:49:29 2009 +0000 Use relative path for CGI commit f7e4298f461e33303e2e0451ab6321e97c32e71d Author: fanhsu Date: Fri Jan 30 23:46:53 2009 +0000 Changed UniProt UniProtKB. commit 3f0e02f577cee359f294633ab6c5b41dd6e3b477 Author: rhead Date: Fri Jan 30 23:44:27 2009 +0000 Added dupeOK to kgXref.geneSymbol, per Fan. commit 37fa3914eef7956c908b63a02d85c523b0b0d4e6 Author: fanhsu Date: Fri Jan 30 23:40:18 2009 +0000 Changed UniProt ot UniProtKB. commit b8372964832fbb94e1109138ec2de44c707ae4e2 Author: fanhsu Date: Fri Jan 30 23:38:27 2009 +0000 Changed "SWISS-PROT/TREMBL" to UniProtKB. commit 9be49e2f0eb3d42185568b8f4b9c497b6549e60b Author: fanhsu Date: Fri Jan 30 23:36:21 2009 +0000 Changed UniProt to UniProtKB. commit bf6647d5f3b92098edc0bdb7c8e143f9c5b7af48 Author: fanhsu Date: Fri Jan 30 23:20:14 2009 +0000 Changed UniProt to UniProtKB. commit 91fa35ae71b8deb4f2ff3a483c17dc5b22d73c69 Author: angie Date: Fri Jan 30 21:38:30 2009 +0000 Loaded up Robert Hubley's results from running RepeatMasker 3.2.7. Original chr*_rmsk tables are now chr*_rmskOrig on hgwdev. commit 2e9ada3b17cfe67b2e3d76784f6c53bbd7992a6e Author: kate Date: Fri Jan 30 20:05:12 2009 +0000 Correct spelling commit e85de235abf9a36a402211a8e1e028abbcdc7251 Author: kate Date: Fri Jan 30 20:01:10 2009 +0000 Remove obsolete ref to stylesheet commit a64132c9a64f6ee9f933efcb7f7ddef200e77df4 Author: ann Date: Fri Jan 30 18:13:32 2009 +0000 changed reference to UniProtKB as requested by UniProt commit 05adfea27d2c1488328605a2a181f292ded4afce Author: pauline Date: Fri Jan 30 18:13:22 2009 +0000 Added line to connect hgnc to kgXref by UniProt accession. commit 0df64d38777799a37badd0bcb58d11dff24906de Author: galt Date: Fri Jan 30 16:00:06 2009 +0000 "Encode release log update" commit 2062924bcf6d95af892e7da82ed716ea05c8f490 Author: galt Date: Fri Jan 30 16:00:03 2009 +0000 "Release log update" commit ac78d3f26c6f3da23768d3a0a16cdd52e735eecd Author: braney Date: Fri Jan 30 15:48:31 2009 +0000 add RM track (thanks RMH !!) commit 2e3c21e39e257813427996a075ac9dbcd1a5711c Author: tdreszer Date: Fri Jan 30 07:59:32 2009 +0000 Bad news. Left out this define in the last check in and irritated everyone. commit 45ce45cff28d04216211149f13aa7b8701b17e0b Author: markd Date: Fri Jan 30 01:00:33 2009 +0000 removd unneeded code (thanks Tim) commit 7e97cb881d70dfcc38a46649bc4c3b2585f89d0a Author: kent Date: Fri Jan 30 00:52:40 2009 +0000 Adding test chromosome size file. commit 0cb121ac3291d9781591e43e48123c4b1cd1cdc9 Author: kent Date: Fri Jan 30 00:28:01 2009 +0000 Updating tests. commit d07d8666f5df233e6d890c264b50e3aa7463e384 Author: kent Date: Fri Jan 30 00:26:59 2009 +0000 Generating bigTest results. commit 8421f5bff1495884a31579a32d26bd8d703a0a42 Author: aamp Date: Fri Jan 30 00:09:27 2009 +0000 Instructions for Affy All Exon probesets tracks. commit 6b43e63f8e4e71f3b97671786becf5d2075ae637 Author: aamp Date: Fri Jan 30 00:02:57 2009 +0000 Instructions for Affy All Exon columns. commit 78029701f37059ea6e78c99a408746b8fc603e43 Author: aamp Date: Thu Jan 29 23:51:17 2009 +0000 Top-level affy all-exon supertrack. Removed HTML and entries in human/mouse/rat subdirs. commit 0dd6419a7c7cfc7c57f154700663b6a1d1a90abf Author: angie Date: Thu Jan 29 23:46:43 2009 +0000 Moved bdtnpChipper composite track description up from drosophila/dm2/ to drosophila/ -- shared by dm2 and dm3. commit 00883c2072af69b5e7102d9afbea2dfa245c38d8 Author: tdreszer Date: Thu Jan 29 22:55:38 2009 +0000 Too many inappropriate warning messages. Also add gencode to multi-viewable list. commit 74631b814e8747f98ce8c773f1fb9d0c87bf1b34 Author: kent Date: Thu Jan 29 22:11:15 2009 +0000 Fixing a bug in clipping of fixedStep bedGraph output. commit 1028b4c7400e6da26204f5c4f6d4e0947ef14216 Author: ann Date: Thu Jan 29 22:04:08 2009 +0000 correcting viewLimits! commit 002e275dbc45bf701a8459a0922ad1342e9f3abf Author: ann Date: Thu Jan 29 22:00:48 2009 +0000 undoing change 1.365 as this is not yet supported on the RR (it's in the v199 CGIs that go out tomorrow) commit 87bc35324969676c11afc0f821f4f4cee63fcdc0 Author: aamp Date: Thu Jan 29 21:57:44 2009 +0000 Forgot to commit some stuff for my change to hgNear. commit 28a663ee5d0880e87968952ff4e30ad87dc4fb45 Author: kent Date: Thu Jan 29 21:51:39 2009 +0000 Fixed bug caused by a stray mustReadOne. commit 151d144a5770fca903d413f2a42da209f088b264 Author: ann Date: Thu Jan 29 21:11:04 2009 +0000 remove 'release beta' blocks from 28- and 44-ways (also remove word 'release alpha) from the final blocks. commit bec40d1fbe2723b8abec9ad510a0288c0c8e29f2 Author: ann Date: Thu Jan 29 20:56:25 2009 +0000 Kate says if its in the settingsByView, then it doesn't need to be in the individual tracks below. commit f306524d4ff44c7f4282e0e6b45f70ad158f1516 Author: ann Date: Thu Jan 29 20:42:33 2009 +0000 duplicating Kate's changes in the alpha/beta blocks. Adding the viewLimits change to the settingByView. commit e9aa9b0923ed5d85e6611f45ac6db6e001d80557 Author: mikep Date: Thu Jan 29 19:53:33 2009 +0000 added missing newline to usage msg commit 895d9b096edcb8eb3e3cb5484ec62db047270507 Author: kate Date: Thu Jan 29 19:52:19 2009 +0000 Additional tweaks to configuration, based on input from Jim commit 259c5a1bb36c6068707110fac95ba9b66a0bb160 Author: kent Date: Thu Jan 29 19:39:51 2009 +0000 Catching desiredReduction of 0 commit 5efd47ae4f18eb3f11c0bc4f2c2ea1c80a74ab98 Author: angie Date: Thu Jan 29 19:39:03 2009 +0000 Instead of skipping checks on fuzzy rules, report how many hits there are, for a reality check on the rule. commit 6f56d78015951bd45f2a79d9d7c9178d78424947 Author: kent Date: Thu Jan 29 19:32:53 2009 +0000 Adding expected output of test script. commit 2532ead60b5fa0c87a995276ea9d856d6bb43c6a Author: rhead Date: Thu Jan 29 19:13:47 2009 +0000 Changed the tail one more time, so it gives results starting at row 3 of the mysql output. Apparently the old syntax, with a space, wouldn't work on hgwdevnew. commit 00ef24eebe9281157ef5113747a488b40b3bae4e Author: kent Date: Thu Jan 29 19:11:10 2009 +0000 Starting to work on a test script. commit 11017f6fc8d9dcfa3e2b736007cd4b67ee44d9a4 Author: kent Date: Thu Jan 29 18:45:40 2009 +0000 Misc fixes to test generator. commit 5ead5b41ed7c2933be346f81576acd3aff54e02c Author: kent Date: Thu Jan 29 18:17:53 2009 +0000 Adding test case generator for bigWig. commit 310c575ce1c2a923fe796650c6616164b9f31ca9 Author: kent Date: Thu Jan 29 18:15:09 2009 +0000 Removing some debugging code and catching case of empty wig file. commit b1f706dae1ccf8f71d54a5ffe81c10153603a856 Author: kent Date: Thu Jan 29 18:00:38 2009 +0000 Making program to make wig test sets (since don't want to commit millions of lines of static test sets to the source tree! commit 1ff0a978a2428da4ba4636e856c1cd87d7bd830c Author: galt Date: Thu Jan 29 16:00:06 2009 +0000 "Encode release log update" commit fe327d0d40907c12e7f22eb17e2542c73ea4dd98 Author: galt Date: Thu Jan 29 16:00:03 2009 +0000 "Release log update" commit 3b673127d9e0bd7d0126ece0c404f1b967d18259 Author: aamp Date: Thu Jan 29 09:06:56 2009 +0000 Added Affy All Exon columns for human, mouse, rat and changed expRatio column handling a bit. Got rid of some hgFixed hard-coding. commit e47703b7cc4a2798533a102178ece29ac35b0611 Author: kent Date: Thu Jan 29 05:35:39 2009 +0000 Removing no longer needed .h files. commit 8ddcff7f6acd467949bdd37453dadd7ad45df156 Author: kent Date: Thu Jan 29 05:34:36 2009 +0000 Fixing memory leak commit 38c8e8e42c96af9c374dab9370e3986063a294f3 Author: kent Date: Thu Jan 29 05:32:33 2009 +0000 Moving zoom queries to library. commit a7587e57c0d3d9d762109bffddb670017d449749 Author: kent Date: Thu Jan 29 05:31:16 2009 +0000 Adding functions to convert between bigWigSummaryType and strings. Updating comments. commit 40d101e83094eac0b5d3ff261cf757bbead15d8b Author: kent Date: Thu Jan 29 05:30:29 2009 +0000 Exposing bwgAttachUnzoomedCir commit c9593f07f8d83940664b08764a815cfb42e51b32 Author: kent Date: Thu Jan 29 05:24:39 2009 +0000 Updating comment. commit 457fe17a98e91543e4932d6827e991ea17921bd4 Author: kent Date: Thu Jan 29 04:10:23 2009 +0000 Exposing bwgAttachUnzoomedCir. commit 09ab0e467b5658458ca0920bd9f890276f6b7ef3 Author: kent Date: Thu Jan 29 04:01:12 2009 +0000 Implementing other summary types. commit e9b4ae9c1ef78ec753037e2272a51df509c0e3af Author: kent Date: Thu Jan 29 03:32:44 2009 +0000 Removing debugging statements. Clarifying code in one loop. commit 55ff22acca7e21e3c0e7762df898fbf841b9a32a Author: kent Date: Thu Jan 29 03:17:40 2009 +0000 Making it work on lower zoom levels. commit bdb71cc886ae1673f36c6337567692ecc392e26e Author: rhead Date: Thu Jan 29 02:36:43 2009 +0000 Fixed broken link to conditions for use. commit eaa606cbf987ff5dcb351ea89fed7e929c9e765c Author: markd Date: Thu Jan 29 02:01:41 2009 +0000 change URL to new IMAGE site commit f09067cdf1afeaca9b5d227b5b587b505937fb8e Author: markd Date: Thu Jan 29 01:49:17 2009 +0000 removed unused variable commit 8ce60c245eb03576fcb774238352d963ac219f62 Author: kent Date: Thu Jan 29 01:27:33 2009 +0000 Summary of zoom-level seems to work. commit 251fb851d5eaffd9151223e5b4f465d68e20da39 Author: rhead Date: Thu Jan 29 01:24:02 2009 +0000 Added grayscale/score table. Thanks, Angie\! commit e2200f1030cbcc2ac4ac0e049a274e073ad4cf26 Author: kent Date: Wed Jan 28 23:30:13 2009 +0000 Removing debugging statements. commit da7bf76eb0715cb64b019c59f63b76005795dbcc Author: kent Date: Wed Jan 28 23:27:26 2009 +0000 Checking in very preliminary version that has enough working parts amidst the debugging statements I don't want to lose it. commit 1af15b535e6fea2fec4352a4748e3e23b3b0c149 Author: kent Date: Wed Jan 28 23:15:27 2009 +0000 Adding start/end parameters. commit 0690848f8ad0e95651f9f35105c674d1a863bf00 Author: kent Date: Wed Jan 28 23:11:33 2009 +0000 Debugging zoom levels in bigWig files. Still including a bunch of uglyfs, but wanting to save while it seems to work. commit 16ade07e9bdd31dba1da1bd437836d9737402961 Author: kent Date: Wed Jan 28 23:09:19 2009 +0000 Making idSize array a structure. Making bwgSectionOnDisk and bwgSummaryOnDisk structures. Bringing bigWigFile and bwgZoomLevel to .h file. commit 8ec304980c768c2458d980ff8ea72f918ccf1a0a Author: kent Date: Wed Jan 28 23:06:26 2009 +0000 Changing start/end parameters from int to bits32 in bigWigSummaryArray. commit 3afdf60ed319e89a8b20bd76f8a2e4d680939427 Author: kent Date: Wed Jan 28 23:05:23 2009 +0000 Changing sig with change in file format. commit 64be8bb7c397277a35c816d7d667620af8eff124 Author: aamp Date: Wed Jan 28 23:02:43 2009 +0000 Fixed bug that prevented next-item buttons showing up. Turns out this bug was introduced when fixing another bug that the next-item buttons were showing up on the top label of composite tracks (e.g. hg18 Agilent Arrays). commit 99b0e3d3647ef79ef701ae6ab3bde5f71d95a5e7 Author: angie Date: Wed Jan 28 22:53:52 2009 +0000 Added shades-of-gray vs. score key to BED score description. commit ba7921377beecbe8951d39f2010de9efdbc9ede9 Author: galt Date: Wed Jan 28 21:44:44 2009 +0000 using errno is more informative than just boolean error stat commit 1fc3c06474098d01f68b22379d802a1b63a280df Author: galt Date: Wed Jan 28 21:40:17 2009 +0000 using errno is more informative than just boolean error stat commit 1a3d47d240c281eaa6a320d577da5a545ec07bf5 Author: galt Date: Wed Jan 28 21:34:24 2009 +0000 using errno is more informative than just boolean error stat commit c93c161efcb5879c036579facc39be6d7d35b94c Author: galt Date: Wed Jan 28 20:28:37 2009 +0000 logo change for DCC commit fa82ca8d1bea963965521c55f2c3e6282203cf9c Author: fanhsu Date: Wed Jan 28 19:59:18 2009 +0000 Added rules for omimGene. commit b0907347ff331a42f49d760e12dd673149bbef8c Author: kate Date: Wed Jan 28 19:41:32 2009 +0000 Add prefix for ENCODE production tables commit 505ffd7a3eb53372112aaa0de96376d956d11c18 Author: tdreszer Date: Wed Jan 28 19:00:24 2009 +0000 Added H1_ES human embryonic stem cells commit 240efc708f5fb71eab25de84cbab2b45c9dfe36f Author: kent Date: Wed Jan 28 17:46:54 2009 +0000 Adding start and end options. commit ff763eeffe7aadc7328e37cfcb9dc061c42453dd Author: hiram Date: Wed Jan 28 17:34:39 2009 +0000 Better checking of the chrom name and coordinates given in the annotation position box commit cc281a96f24beeeff50574f466fc1d7ac081c287 Author: galt Date: Wed Jan 28 16:00:06 2009 +0000 "Encode release log update" commit 83faab1bfa2550505921a512027dec78e6c45221 Author: galt Date: Wed Jan 28 16:00:04 2009 +0000 "Release log update" commit 21a1b7106ffe0262245653f121c02307150501f8 Author: kent Date: Wed Jan 28 14:42:08 2009 +0000 Convert bigWig to bedGraph seems to work. commit 5f712e1a48fd2230f0949cf0fea2036c0cbac243 Author: rhead Date: Wed Jan 28 04:22:05 2009 +0000 Removed closing html anchor tag that was left behind in last diff. commit 0325655e29078b004dc1e412a043956dea70d410 Author: kent Date: Wed Jan 28 03:12:05 2009 +0000 Fixing compile on hgwdev. commit 5bda16bd82c9ce1c7d1c65fbd0696be6f40a2957 Author: kent Date: Wed Jan 28 02:44:43 2009 +0000 Exposing bigWigChromInfo. commit f5a4b2ca56c58bd31233c8f1c8e2859154769b28 Author: kent Date: Wed Jan 28 02:44:04 2009 +0000 Putting start of query side into library. commit ddcc46d4bdcff63b3a778be94e7cbdfc66082513 Author: tdreszer Date: Wed Jan 28 01:15:51 2009 +0000 fixed one more major bugs due to misplaced semicolons commit 0c7153945c9da8ba52e898e5a8686230e10b7954 Author: angie Date: Wed Jan 28 01:03:52 2009 +0000 Removed stray semicolon that caused cart settings to be ignored. commit 1d34d735941eb04fdc6a60d2b14b443e7e315f64 Author: tdreszer Date: Tue Jan 27 23:58:50 2009 +0000 Sorts containg tdb's (initially just composites) and sets contained tdb->priority accordingly commit 12489096b3f789336a2ae178f3accf951f21d39f Author: tdreszer Date: Tue Jan 27 23:56:40 2009 +0000 No longer need to tell javascript to presort commit e1ee086fb039f3b19f070686b70a63de9cb2ea14 Author: jsanborn Date: Tue Jan 27 23:34:42 2009 +0000 moved Ovarian datasets to controlled access for now commit 13016eef96ea1e413ddc55ad66424f91c48ff0c7 Author: tdreszer Date: Tue Jan 27 23:34:41 2009 +0000 Change to support Elnitski BiPs commit 37f1add71f6aecdbfd7a19d4f55a3104d0c12a86 Author: kent Date: Tue Jan 27 23:02:40 2009 +0000 Adding command line program to create bigWig files, and some test sets. commit b6f452bf3899ca1a3d18cf634f380fd798c96884 Author: kent Date: Tue Jan 27 22:58:47 2009 +0000 Adding bwgCreate module to library. Creates bigWig files. commit cb96f118ea9c4a50a957800c9d1dc642a4b90614 Author: kent Date: Tue Jan 27 22:58:03 2009 +0000 Renaming totalFileSize to endFileOffset for clarity, since sometimes the cirTree is just indexing part of a file these days. commit aa60567b7a9cd31ccbbbf7c4d6e91cd647ced8bf Author: tdreszer Date: Tue Jan 27 22:55:25 2009 +0000 Code added to allow BiP/cBiP validation for Elnitski commit e06a926e40d0ebcb5d6b05d26e3f31c3dea1c1eb Author: kent Date: Tue Jan 27 22:15:36 2009 +0000 Rationalizing names a bit. commit 70a5982d7794c4f3ce1abb0cf75fed2a9081ee5d Author: kent Date: Tue Jan 27 22:01:06 2009 +0000 Expanding bigWig interface and separating out internal parts. commit 6b306a77506e2583b8fc923c99e014755531954e Author: kate Date: Tue Jan 27 21:32:00 2009 +0000 *** empty log message *** commit 19ad2143e2526bd2b80d281da1a75675c50db230 Author: kate Date: Tue Jan 27 21:30:25 2009 +0000 Add field to pushQ entry commit 7f979b1b40118da2c8c34c8d5717b96837096bae Author: angie Date: Tue Jan 27 21:29:32 2009 +0000 Added Galt's new pushQ column, releaseLogUrl, to create and insert statements. commit 802078e463764c8b23bb83d0b677e86d1a659786 Author: tdreszer Date: Tue Jan 27 21:16:47 2009 +0000 Added species dog commit 6653893bd8deef660038e68b67c7b771a738548f Author: tdreszer Date: Tue Jan 27 21:03:07 2009 +0000 Tighten the screws one more time on the sortableTdbItems API commit a670af96e74610dd2959e6038a831c58360f9779 Author: tdreszer Date: Tue Jan 27 20:36:59 2009 +0000 Handle inconsistent sortOrder setting in sortableTdbItems API commit 1de81929968f06aa79b0d05d3539059394529e39 Author: mikep Date: Tue Jan 27 20:24:21 2009 +0000 add CLASSPATH into build environment to save confusion commit 41ef26d9021ae9dbaf73ce87a49d03d8bf4163e3 Author: mikep Date: Tue Jan 27 20:23:17 2009 +0000 refresh button on hgTracks changed its 'name' from submit to hgt.refresh commit 440222478358d78558e4375a138df0a11d711afa Author: tdreszer Date: Tue Jan 27 19:46:41 2009 +0000 How could I be so sloppy on the last checkin? commit 296179e31ac5ad89a547082959fca01d30c71d5f Author: tdreszer Date: Tue Jan 27 19:43:48 2009 +0000 Added sort API for tdb sortOrder setting support commit 60a0f7bbc250ef30f9f3b1ac984de71adf8761af Author: ann Date: Tue Jan 27 19:38:52 2009 +0000 edited phyloP list to include new 44way tables: phyloP44wayAll, phyloP44wayPlacMammal, phyloP44wayPrimate commit f770651dd0e540acc402ef86d4f54ed9fa579ddd Author: kate Date: Tue Jan 27 19:12:41 2009 +0000 Update tests to confirm with validator changes commit d3a74eef64cdd851cb1c4396f9587b3f4507a5ac Author: kate Date: Tue Jan 27 19:04:45 2009 +0000 1. Finish/redo downloads for phyloP 44way 2. Start lineage specific phyloP runs commit 7f6c84fc716bdda9dac5c9b5503ca29e3608b585 Author: ann Date: Tue Jan 27 19:02:08 2009 +0000 changed dasNov from 1 to 2 (because that is the actual assembly used). commit 353d55a08fc273a3c340ec949ae6d6c96514e77c Author: hiram Date: Tue Jan 27 18:53:29 2009 +0000 Update customTrash settings to now be mandatory commit e9ea2903c20af707b593080c6b391e3aa722cd3c Author: hiram Date: Tue Jan 27 18:32:53 2009 +0000 SiepelLabCorrectedMafs now in place for the 44-way commit 85b5697eac23fea86c16e21551dd9a5d06833fc9 Author: kate Date: Tue Jan 27 18:01:22 2009 +0000 Minor output formatting changes (for consistency) commit ef417f880600baffdc0d20364e321ab747f52581 Author: kate Date: Tue Jan 27 17:43:58 2009 +0000 Refix previous fix commit c002c982b033386e6461726584756838f1ae8a6b Author: kate Date: Tue Jan 27 17:34:44 2009 +0000 Fix syntax err commit 73170a8ab4aaaa440134ffd38f426ab7461be224 Author: mikep Date: Tue Jan 27 16:42:23 2009 +0000 "New version number v199" commit 398311118545fd70314e95b80dc0bc77bc6bc9d1 Author: mikep Date: Tue Jan 27 16:41:15 2009 +0000 v199 final build commit 8473ca7d92f9a6f99faa7a7fa2056141965cd56b Author: mikep Date: Tue Jan 27 16:39:10 2009 +0000 fixes for new java environment on new dev machine commit 5a9a35b6d9a657493cc604eaa22f66d313c25835 Author: galt Date: Tue Jan 27 16:00:16 2009 +0000 "Encode release log update" commit c5d98c4a33ccbadf2de496073c9829beb6ee5f2e Author: galt Date: Tue Jan 27 16:00:13 2009 +0000 "Release log update" commit 4f3c5a8959f5f49e328cf0d2ecc329dcbbbbdad1 Author: mikep Date: Tue Jan 27 15:47:37 2009 +0000 more accurate description commit fceda253d7c2a7b9f55adade4acc67ff3209a460 Author: galt Date: Tue Jan 27 10:36:28 2009 +0000 adding new field to store an optional URL link for the release log entry commit 73033c1d37b3ebd2f459f853d84e47baa253d289 Author: kent Date: Tue Jan 27 07:14:24 2009 +0000 Improving comment that describes binary file format. commit 61845454c0f8f39b8e78821694df85701da118ec Author: kent Date: Tue Jan 27 03:54:02 2009 +0000 Reading in zoom headers. commit 5749fe9e1cf20986c442995f79afb56f13747c4a Author: kent Date: Tue Jan 27 03:05:47 2009 +0000 Polishing zooming. Saving it to file. Indexing it. commit e3d9b515eca01c882718d0c85b60ecd6a5ef14bb Author: kate Date: Mon Jan 26 23:29:52 2009 +0000 Add/adjust some settings and format in anticipation of first track release commit 061d2b77f10d34d5add5419c3f20c2ada0812444 Author: kate Date: Mon Jan 26 23:24:58 2009 +0000 Add checks for label lengths commit ecbcca16c83a6fef33c6d78bd7ad288a8d54e87b Author: kent Date: Mon Jan 26 22:57:42 2009 +0000 Implementing first pass of zoom/reduction. commit 20981df2297842a0cf735c0e21d89351d7fa6863 Author: angie Date: Mon Jan 26 22:43:09 2009 +0000 Corrected case sensitivity of the p in flyBaseToUniProt. commit 7cb2cbba9aa5a564f4fbd9e9a8adde456b268e57 Author: larrym Date: Mon Jan 26 21:48:39 2009 +0000 change name of some submit buttons (from 'submit' to something else) to fix problem with drag/zoom not working when showTrackControls is false commit b15f2db214e97506ab9ba2bc15c707dafbe2fcb9 Author: angie Date: Mon Jan 26 20:27:39 2009 +0000 Experimentation with phastCons params, just for the record (results unused). commit 8b54c964502c6e65998ccf42294494925a15b70e Author: angie Date: Mon Jan 26 20:26:03 2009 +0000 Fixed copy-paste ce6->ce5, 5-way -> 6-way. commit 91edb2c0232ee1c16b61584261bd84f18cc4e6c4 Author: kate Date: Mon Jan 26 19:54:35 2009 +0000 Tweaks resulting from NHGRI feedback commit dc0a8997f2f077d9b5a4f22172ce0850611c5e9a Author: kate Date: Mon Jan 26 19:44:52 2009 +0000 Add release alpha to new ENCODE subtracks commit 52e9e0cfffe3524381a6e1c19a38293f5f86a2d6 Author: kate Date: Mon Jan 26 19:38:28 2009 +0000 Fill in cell type setting for all cells in a track -- this is required when using _(Tier ?), so that only the specified parts of the label is used to lookup in the controlled vocabulary commit 4af2343c9e6ad8baa3b70d5fe666bf4303f82cc8 Author: fanhsu Date: Mon Jan 26 19:01:17 2009 +0000 Updated UniProt URL. commit ff8c46dd769100410e0b0aaeff60064f1a293d84 Author: fanhsu Date: Mon Jan 26 18:50:22 2009 +0000 Updated UniProt URL. commit 73734ec39e9d8c12056f8a4d546888b502f51c3a Author: fanhsu Date: Mon Jan 26 18:35:49 2009 +0000 Updated dm1 UniProt URL. commit 5f4a7edded0cb8c099775587f9b68a9131a8daf7 Author: fanhsu Date: Mon Jan 26 18:34:47 2009 +0000 Updated UniProt URL. commit 3089bf6c500ffe194e11f606afde2ef36833ee13 Author: hiram Date: Mon Jan 26 18:31:39 2009 +0000 Remove debug statement commit 23619a0b21170c2a1e0b212d392ebd1c4fd6b30c Author: hiram Date: Mon Jan 26 18:31:22 2009 +0000 Fixup Ensembl Blue Bar behavior, now works correctly on chrM and chr*_random when within a contig commit feea9671e08f7cad46ed3ad6ac10ba6bc83d0bc7 Author: kate Date: Mon Jan 26 18:24:33 2009 +0000 Rename setting added for ENCODE data policy; it indicates when data can be freely used, not when the data was released by UCSC commit b82756753fbbd4ac9595e2aa467566e492a4a81c Author: kate Date: Mon Jan 26 16:42:53 2009 +0000 Restore whacked setting commit c63f54db2e1687efa7c676c1250e8b3072463823 Author: galt Date: Mon Jan 26 16:00:03 2009 +0000 "Encode release log update" commit 2b4c6daa17adf4c9b9173d52d5a929e92ff743c0 Author: galt Date: Mon Jan 26 16:00:01 2009 +0000 "Release log update" commit 9e7b50ff888af57e0be2181370f7d7c084981995 Author: kate Date: Mon Jan 26 05:56:07 2009 +0000 1. Add dataVersion entries that are missing 2. Remove timestamp from submission dates commit f389a7c41769d518373347038b8f03a242b5e7aa Author: galt Date: Sun Jan 25 16:00:03 2009 +0000 "Encode release log update" commit 2620d14bf292df55f3fb4a0cfec658272171361f Author: galt Date: Sun Jan 25 16:00:01 2009 +0000 "Release log update" commit bf298388b415b5467e64a42d740c2724e24e2ca5 Author: markd Date: Sun Jan 25 04:08:19 2009 +0000 remove runtime subsitution of variables in trackDb commit f100033d6d812d603a154bd8b40515fa7dbb3ede Author: markd Date: Sat Jan 24 22:13:37 2009 +0000 fixed bug in previous commit commit 9177fdef72edd65db4707334714839e7b5e6e709 Author: markd Date: Sat Jan 24 22:00:16 2009 +0000 fixed missing change of track override syntax commit 31661a75c0c73d76ac5a20a442b8d5f444b124ea Author: kent Date: Sat Jan 24 21:06:12 2009 +0000 Starting to work on zooming. commit 323097e5735cf2fa4307039942308b86874b0f7e Author: galt Date: Sat Jan 24 16:00:07 2009 +0000 "Encode release log update" commit 1576c0271e16fa44353f476d7634484310078d98 Author: galt Date: Sat Jan 24 16:00:05 2009 +0000 "Release log update" commit 8024406048af8a65cdbfba5fa83b56e58263cf3d Author: kent Date: Sat Jan 24 06:38:43 2009 +0000 Changed from double to float. commit 3e368ec834baea4be2d1088561e41ce98b5ad30a Author: markd Date: Sat Jan 24 02:58:12 2009 +0000 changed trackOverride to track name override at kates request commit c340d2bae0ae847f1b9323de0a0cf10d61da7b30 Author: tdreszer Date: Sat Jan 24 02:35:21 2009 +0000 Have been sitting on insignificant diffs in this file since Dec 4th commit 1adbc77ecd154c95b8ff28f353f7660ae86e7444 Author: kent Date: Sat Jan 24 02:05:53 2009 +0000 Moving bigWigSectType to inc/bigWig.h and renaming things in it a bit. commit d817a28f63d3d90c1d27e1e3dc5b838af85cc8bf Author: tdreszer Date: Sat Jan 24 01:43:36 2009 +0000 Removed subtrack priorities because empty cart sort will override. Moved a lot of settings to settingsByView commit 5edad3b75949dd870a55769bccb24eb55e222c62 Author: kent Date: Sat Jan 24 01:33:38 2009 +0000 Removing a special case, renaming a variable. commit f2710cbabcf87fe2b4977543ecaa308015a71dbc Author: kent Date: Sat Jan 24 01:32:58 2009 +0000 Updating call to reflect polished interface to bptFileFind. commit 1d0cbb5388f30c2dec739cdfb4967de3dacad1d5 Author: kent Date: Sat Jan 24 01:32:27 2009 +0000 Added bptFileTraverse. commit 02eab2d84c8561ec5d40e92027d87842cfb43fb6 Author: kent Date: Sat Jan 24 01:31:09 2009 +0000 Starting bigWig interface file. commit 031defe00f43ea7b90241dfe649b629aa11c5c2c Author: kent Date: Sat Jan 24 01:22:50 2009 +0000 Adding bigWigSig. commit eb9aa9837ce30ab46e4e22e1076a4bd70a1a9c4e Author: kent Date: Sat Jan 24 01:20:57 2009 +0000 Improving commenting and adding bptFileTraverse commit cedec5d420df8b7b28fd0b8092332295f551a309 Author: ann Date: Sat Jan 24 00:43:14 2009 +0000 the script was bombing on the +3 tail. I edited so that it will now give correct output. commit eeea53ca0c8fc96912f367673c1736d003724514 Author: tdreszer Date: Sat Jan 24 00:26:11 2009 +0000 Changes to support new view->hide->subCB->disable paradigm. Also support for inital sort of table when no cart priorities are found. commit 643c826044516a9eba25629de61b4bcc5e338d09 Author: tdreszer Date: Sat Jan 24 00:21:43 2009 +0000 Changes to support the new view->hide->subtackDB->disabled paradigm. And some other stuff. commit e6f4138e293dca54052d5619b425d6990bb0d146 Author: tdreszer Date: Sat Jan 24 00:16:06 2009 +0000 tdbSortPrioritiesFromCart now returns TRUE if any priorities were found in the cart commit 19c7098a45a4bab267deb95125caa829b20f1eba Author: tdreszer Date: Sat Jan 24 00:13:51 2009 +0000 Moved cfgTypeFromTdb() to trackDbCustom per Kate's request commit 40937f44158dcafaa28f08ce8f29ba108486bdf0 Author: tdreszer Date: Sat Jan 24 00:03:04 2009 +0000 Moved cfgTypeFromTdb() to trackDbCustom per Kate's request commit 7daa5eb9c17ab650e48724ecc41c9a98129650e3 Author: tdreszer Date: Sat Jan 24 00:01:17 2009 +0000 Allow hideOrShowSubtrack to hide disabled as well as unchecked. commit 48628163a8fbc143cd923d53fc46cddc42d5995e Author: kate Date: Fri Jan 23 23:42:39 2009 +0000 Use more informative CVS keyword commit 3b0d692378917c503ebd519cb61f3e96d45dd8d5 Author: tdreszer Date: Fri Jan 23 23:38:10 2009 +0000 Allow noInherit to be set in settingsByView commit 9e27d9e0ab864fdd17b2eb7052637a50c49e9560 Author: kate Date: Fri Jan 23 23:34:11 2009 +0000 Add utils to help batch-edit trackDb.ra files commit cdfb280e2bad54cd1777dca1a791844ced9f2f67 Author: kate Date: Fri Jan 23 23:33:37 2009 +0000 Fix paths after directory move commit 1c20b57e842cba147f358325786f4aed6fe800dd Author: kate Date: Fri Jan 23 23:29:55 2009 +0000 utils/raToLines commit fd0182f2e3123d19dfad11f7ec552358b17f968a Author: tdreszer Date: Fri Jan 23 23:28:43 2009 +0000 Added strLower/strUpper which are like tolowers/touppers but return the string commit e0f4307194969a3e253c95974c010808738360e6 Author: tdreszer Date: Fri Jan 23 23:27:50 2009 +0000 Added strLower/strUpper which are like tolower/toupper but return the string commit feafe09e121bdcb87768e6b2a3b7bf116366a68b Author: kate Date: Fri Jan 23 23:26:32 2009 +0000 All whitespace changes. Reformatted with standard indents and whitespace usage, to ease batch editing commit 231ec7fdae6a064fbd6f8ab7f146d9ad0d9b09b2 Author: kate Date: Fri Jan 23 23:24:53 2009 +0000 Put back newline lost in batch edit commit 3082bb267e5cc7374951edf52180d4c7e5b65865 Author: tdreszer Date: Fri Jan 23 23:16:35 2009 +0000 Added a couple of dystring macros to make reusing dystrings easier commit 68696936c8729a4173619f473d35d046c120cf6f Author: tdreszer Date: Fri Jan 23 23:11:28 2009 +0000 Allow noInherit to be declared in settingsPerView commit 4fcc24c6ed336e72f7f7bebe300f29a88d2521b1 Author: kate Date: Fri Jan 23 23:10:44 2009 +0000 Remove errant blank line added during mass edit commit e1faf2a6f856fcea0537e86c2d30790645fdc4b6 Author: tdreszer Date: Fri Jan 23 23:10:09 2009 +0000 Composite/multi-view wiggles had lost the way to the cart. Fixed. commit 672914f23b0b6cb46db3db685a30f9a3c490be15 Author: hiram Date: Fri Jan 23 23:07:25 2009 +0000 Adding LOGIN_EXPIRED business commit 3ac539619916d9f7c9f301b06b85d9c7733b9936 Author: hiram Date: Fri Jan 23 23:04:54 2009 +0000 Fixup ciona Ensembl blue bar links. commit cfbe2d00f2ec4904ee1f837c87cd4372880281f2 Author: tdreszer Date: Fri Jan 23 22:55:13 2009 +0000 Added species for Elnitski's Bi-direction promoter submissions commit 7f3c2f4ebb7fc6492878a433740ec38ecda29199 Author: markd Date: Fri Jan 23 22:46:56 2009 +0000 fixed bug in html commit a2a0aa080f641ce5f6499539fb79b93691ebb54f Author: hiram Date: Fri Jan 23 22:39:53 2009 +0000 I think this will solve the wiki login timeout situation, will have to wait to see ... commit 4ce3eec466d64105d5ed601dea1b63e5c2c3e05d Author: hiram Date: Fri Jan 23 22:24:06 2009 +0000 Add -quiet option for better automatic monitoring commit 60c4f7b2239082e74cc70a723c2e74c39e73fd31 Author: markd Date: Fri Jan 23 22:19:52 2009 +0000 added trackOverride functionality and demoed it on nscan tracks commit 722488c7859b0ffc409908461529c061c51abf26 Author: angie Date: Fri Jan 23 22:07:32 2009 +0000 Corrected the default behavior for -{t,q}Repeats -- netClass assumes rmsk. commit 4b6870370c7f18daa50907ecf52e11ef5ddf237b Author: kent Date: Fri Jan 23 21:16:24 2009 +0000 First cut of bigWig reader. Just handles unzoomed. commit a9bb61c34be4fe919bf1eca9b57079f733b75991 Author: galt Date: Fri Jan 23 16:00:06 2009 +0000 "Encode release log update" commit e92d40187d1a9c1d773e8cb2ea183f0951b8b3f8 Author: galt Date: Fri Jan 23 16:00:03 2009 +0000 "Release log update" commit 1bf0db7cb5e49412562d1d8eedb0f47f3ff90360 Author: markd Date: Fri Jan 23 08:38:28 2009 +0000 added check for non-ascii characters commit 85e260185c1324ca8a35b060956b5b2b99fa078a Author: larrym Date: Fri Jan 23 06:38:42 2009 +0000 fix invalid HTML 3.2 (add name attributes to some new inputs and move some new inputs inside of forms) commit 6893786ffad8d9ee18cd90dff0ba7f647faffbf4 Author: kent Date: Fri Jan 23 00:50:03 2009 +0000 In theory it's writing a bigWig file, but so far just the main data and index, no zoom levels. commit f7b9ccb5b3b55823ba5a77eac2198f2f27b1dc36 Author: pauline Date: Thu Jan 22 23:13:52 2009 +0000 Removed oryLat1. commit 7ba3ec07fc9190680adb9938da18b8519ba4cba2 Author: hiram Date: Thu Jan 22 23:10:37 2009 +0000 rangeTreeNew() function has no arguments, do not send it any commit 65fb6c8b6baf0237043fa4ba626191e273ee374e Author: markd Date: Thu Jan 22 22:45:46 2009 +0000 opps, broke makerule commit cbb8c895f86f154654bea60713d9fde6172e19ce Author: kent Date: Thu Jan 22 21:48:08 2009 +0000 Implementing bedGraph parser. commit 95ba62049cd76ba8c370bb304d9d4370f65ad9a9 Author: aamp Date: Thu Jan 22 21:44:40 2009 +0000 Added Wallaby net description. commit 765cec1015521ff688b15fc695a6fc2de5d52965 Author: hiram Date: Thu Jan 22 21:30:53 2009 +0000 v52 update completed commit d9dfba43f39ba587bad150d269265ca20de48f17 Author: markd Date: Thu Jan 22 21:25:58 2009 +0000 changed cluser due to problems with old OS ok pk commit 4cbeaab08884c1d05dfd3f116a1356aa75e7c067 Author: mikep Date: Thu Jan 22 21:22:39 2009 +0000 trying to fix the TrackCheck error: Can\'t get mysql jdbc driver build.xml QADBLibrary line 299 commit fbcf9e92b2438b286edd7bfa5f28fb37c785ffc5 Author: kent Date: Thu Jan 22 21:15:01 2009 +0000 First pass of wig file parser. Doesn't handle bedGraph yet, though do have test case for it. commit a998b078bbe71546e70d66476eaca4af9ba5e1ba Author: markd Date: Thu Jan 22 19:57:12 2009 +0000 bogus make rule that used gcc explictly rather than via variable commit 177c51f3b5e0a5b7c0fbfba2c00c04410e69b073 Author: aamp Date: Thu Jan 22 19:54:51 2009 +0000 Added some trackDbs for opossum. commit 7733cd72b1b96d9e70bdadc21e0b89e9e890bd4a Author: aamp Date: Thu Jan 22 19:31:00 2009 +0000 Added some more tracks. commit fb8a4441cfaf1f0db1a4c622476854708764c477 Author: ann Date: Thu Jan 22 19:27:33 2009 +0000 added release alpha/beta for 44-way and for the three 28-way tracks. changed visibility accordingly (44-way now on by default) commit ecdf864459317e0155696be85923429cbc48eab3 Author: galt Date: Thu Jan 22 19:00:01 2009 +0000 getting rid of bad or corrupt 2bit test file commit 99ad6e44fad155d9819f87e29a44c9030704d7ab Author: markd Date: Thu Jan 22 18:59:53 2009 +0000 restored file that should not have been deleted in MGC cleanup commit 467b31d39cab8aa21697c4cd14906558ccc665ee Author: galt Date: Thu Jan 22 18:59:04 2009 +0000 getting rid of bad or corrupt 2bit test file commit 147285f5a835bb9fa0b9a9ac04da552dcbcb7394 Author: galt Date: Thu Jan 22 16:00:06 2009 +0000 "Encode release log update" commit a2e2518dfed933e157279d96f2a8bd3ee61dcc80 Author: galt Date: Thu Jan 22 16:00:03 2009 +0000 "Release log update" commit b3dc80f968e13d558b29a6aa955322ea501ccc4b Author: ann Date: Thu Jan 22 01:31:36 2009 +0000 sent links to hgdownload server commit 3a929049f118e8dd25e19804f469d2c505b7af9d Author: kent Date: Thu Jan 22 00:43:58 2009 +0000 Improving a comment. commit aef55334002ddd311acc1d33d243e3aeea19dd41 Author: kent Date: Thu Jan 22 00:43:30 2009 +0000 Adding parameter type checking to verboseTime. commit d4b6ae34d81799ed5d5c7c0d9b9e75b66f770da6 Author: ann Date: Wed Jan 21 22:17:03 2009 +0000 removed in press reference from Zweig paper commit a99fca7012ed19193bed79bfe17982e9c2726c75 Author: ann Date: Wed Jan 21 21:46:02 2009 +0000 added HRs before years (to match the rest of the page). also added ascii code for a-with-acute commit 899da50388282491855bf94a61ebc3af84c85bf9 Author: kent Date: Wed Jan 21 20:35:11 2009 +0000 Creating little programs that use crTree stuff to index and search bed files. commit 4c82e71df4ea15d80f49e1d36b3024bca17b702a Author: kent Date: Wed Jan 21 20:16:28 2009 +0000 Moving crTree and cirTree modules to library. commit aafe41af7547416631483a4ce4a7cdf08e0889c6 Author: hiram Date: Wed Jan 21 19:55:32 2009 +0000 Eliminate a stray line at the top commit a43632ad103fe8fe9b49129a3e93c9f40b4b424b Author: kent Date: Wed Jan 21 19:53:36 2009 +0000 Fixed extra level of indirection. commit 78b3ffdf02cfcdeaa0ca1a1e8ba7782b91d24724 Author: kent Date: Wed Jan 21 19:43:15 2009 +0000 Adding crTreeFileCreateInputCheck to help detect input errors. commit 6e8cace23a6dd90b84864a009c3307ba009c5390 Author: hiram Date: Wed Jan 21 19:19:53 2009 +0000 Adding v52 definitions commit d767bf1f95029f2006d3f400f310bfa0e3f4797f Author: kuhn Date: Wed Jan 21 19:19:12 2009 +0000 moved NAR paper to new 2009 section commit a3b7ce1ee1e047dec30b0bc80f1b1dad3726c44d Author: fanhsu Date: Wed Jan 21 19:09:29 2009 +0000 Added position info section for omimGene. commit b81fdd91a3938eeaeebbd16f5beeb257b8ef5506 Author: kent Date: Wed Jan 21 18:27:28 2009 +0000 Adding signatures for chromosome r-tree index files. commit 482696363b29ae53007af0b2d8ec44ce893c1635 Author: mikep Date: Wed Jan 21 18:27:07 2009 +0000 new release commit a45418b4dcc4f4866c004d13b056738931d8db5e Author: fanhsu Date: Wed Jan 21 18:26:11 2009 +0000 Relaxed the omimGene query a little by not requiring the entry be part of omimToCanonical table, to cover the NR_... entries. commit e89e1a1bf3b61e499339c840abe5b41d9fb07246 Author: kent Date: Wed Jan 21 18:23:25 2009 +0000 Refactoring to simplify interfact to crTreeFileCreate. commit 0f4001884b07c1cc799ea2591b85587db95c0d44 Author: fanhsu Date: Wed Jan 21 18:00:07 2009 +0000 Updated logic of omimGene section to deal with situations where one omim ID has multiple KGs at different locations. commit 16118b212e33df6d6d75dab31dacbd43e6f54b25 Author: kent Date: Wed Jan 21 17:19:13 2009 +0000 Improving commenting. commit fd6aa2750b3d7d066697a182bcbb7fa61a240db4 Author: kent Date: Wed Jan 21 17:18:26 2009 +0000 Adding some more bPlusTree stuff - stuff to make btrees inside of other files. commit 4673a7d7b32d7f8be4bfbe8579020e17dab94c8a Author: kent Date: Wed Jan 21 17:17:22 2009 +0000 Adding some more bPlusTree stuff. commit dbf081e3968b259d327621a676e8bd7cc08cbdf1 Author: galt Date: Wed Jan 21 16:00:11 2009 +0000 "Encode release log update" commit 276dbc99cb1bde81f19ede117a8569116a0d4c46 Author: galt Date: Wed Jan 21 16:00:04 2009 +0000 "Release log update" commit d5fadaf76571f13d8b0d8712b98c7b12a94169e4 Author: kent Date: Wed Jan 21 02:18:16 2009 +0000 Adding fileOffsetSize structure - which is shared by several of the indexing modules. commit 624b2b954641c1f52a5cf920135167de3cabe13b Author: kent Date: Wed Jan 21 00:44:41 2009 +0000 Seems to work. commit 49eab46a7ebc54404c1dc8567b5d0a5deb7eaa31 Author: tdreszer Date: Wed Jan 21 00:40:15 2009 +0000 Use new 'ClosestToHome' API commit 23982fa3e39f60342a04c78a1695fdf1aafbf005 Author: tdreszer Date: Wed Jan 21 00:37:43 2009 +0000 Alter adjustBedScoreGrayLevel() to pass tdb instead of tableName commit 081c340c47996467c6353009b61960eff501e3e0 Author: tdreszer Date: Wed Jan 21 00:29:55 2009 +0000 Use new 'ClosestToHome' API commit b56001f2e4026730b65a840e1c494a6481dbc83f Author: tdreszer Date: Wed Jan 21 00:28:48 2009 +0000 Moved second submit button into hui.c commit b7688471f9615c504ff10081106eddd6284a5537 Author: markd Date: Wed Jan 21 00:27:55 2009 +0000 enable load-time variable subsitution commit 4587a3f62a1c8c9c05acd8bb34d5fdb39ab2b43b Author: markd Date: Wed Jan 21 00:26:39 2009 +0000 fixed invalid variable substitutions that are now detected commit a5188e647baf39bc798dc35074f5a2ca8ad3db5b Author: tdreszer Date: Wed Jan 21 00:22:27 2009 +0000 Use new 'ClosestToHome' API commit 0a5af1045177a8cb4b2526eaefb6aefc56c9460a Author: kate Date: Wed Jan 21 00:16:39 2009 +0000 Add option to set background color to yellow to match table color commit 9f74b2377c5ab6517c673872c889a591ca6bcbfc Author: tdreszer Date: Wed Jan 21 00:15:34 2009 +0000 Added : Exp$ and comment last checkin was to further jQuery paradigm and fully marry view dropdowns with matrix checkboxes commit 8aba306e577eacb8354b18467a2e2a06b79f9fec Author: tdreszer Date: Wed Jan 21 00:12:40 2009 +0000 Revoke last accidental checkin commit f7170fef847b495155d69d2a23d09a83f0bdca58 Author: tdreszer Date: Tue Jan 20 23:58:55 2009 +0000 Recheckin 1.9, which alters setCheckBoxesThatContain to use beg.end.middle args commit 4d5c5432c79b5d065a17af3c5516263125b0b4c5 Author: tdreszer Date: Tue Jan 20 23:56:41 2009 +0000 Use 'ClosestToHome' APIs, implement isNameAtCompositeLevel and begin coding for encodePeaksCgi commit 14478fe723ec6169ecd34a8de29ebc9d16bd03f2 Author: tdreszer Date: Tue Jan 20 23:30:20 2009 +0000 Added cartStringClosestToHome for subtrack/view/composite resolution of cart variables commit 760fbd73aca4a7a0ccc5b8f92a39db0656d08682 Author: tdreszer Date: Tue Jan 20 23:28:37 2009 +0000 Added isNameAtCompositeLevel for subtrack/view/composite resolution of cart variables commit 66a4bcdadde22494b24eb236018cbb9f7af5888a Author: tdreszer Date: Tue Jan 20 23:23:45 2009 +0000 Added trackDbSettingClosestToHome for subtrack/view/composite resolution commit ace5b21fda1fc80a961b0de69b676de3bb4c7701 Author: ann Date: Tue Jan 20 22:30:39 2009 +0000 removed this file. replaced by cons44way.html commit a0498de2afdbbe20b1acf03e3603381b54d9bb4b Author: hiram Date: Tue Jan 20 22:29:59 2009 +0000 Indicate gorGor1 using ensGene track to run annotations commit c6da961bf3c2bac14bd097e8d6a4bbfa8d73b150 Author: kent Date: Tue Jan 20 22:01:23 2009 +0000 Seems to be working, but there's a bug that is causing it to lose efficiency still. commit 4fa2d3f1c83eafb26ee533e43d6795fa670ba86e Author: ann Date: Tue Jan 20 21:51:52 2009 +0000 added links to downloads commit f4735c60b08969d4c9e1b22d983168c74892267e Author: ann Date: Tue Jan 20 21:41:50 2009 +0000 spelled out alignment type in Table 1 commit 82a15ff2361017836e666a0436164addeb64f1c7 Author: ann Date: Tue Jan 20 21:36:50 2009 +0000 alphabetized list of orgs in gene table commit 2b224b1c11ffc5374e9ab4fd473e2de9f8c31499 Author: kent Date: Tue Jan 20 21:16:53 2009 +0000 Implementing open/search/close side of crTree. Still needs debugging. commit a5fd2d3eb15ba5d631dba015b2fb475fc2de0243 Author: ann Date: Tue Jan 20 20:38:53 2009 +0000 alphabetized list of orgs commit 32f679d04f40898accf15f47e2519f9d2235580c Author: tdreszer Date: Tue Jan 20 20:21:26 2009 +0000 Fixed osteoblast order info and comment on no order info for Th1 commit 2775cc468e00107917ab148062f78132ffea88b1 Author: ann Date: Tue Jan 20 20:15:11 2009 +0000 removed hyper-links for assemblies for which we do not have browsers commit 08cb95cff50c687a3bdb7c39b98fa027d175248d Author: kent Date: Tue Jan 20 20:02:40 2009 +0000 Starting to build cr-tree - a combined b+ tree to look up chromosome index, and r-tree to find ranges in chromIx:start-end format. This involves a couple of new modules. Checking in this draft even though not fully debugged just to have backup and record since a lot of changes have been made. The straight r-tree stuff had some refactoring, and still works using createOld and findOld options. commit 79fab5c7e116a8d1f7bd62a96516f622578bcff4 Author: tdreszer Date: Tue Jan 20 19:59:56 2009 +0000 Fixed HeLa-S3_IFNg termUrl commit 40ea778112828729dbf6b894d1c57ecead79609b Author: tdreszer Date: Tue Jan 20 19:53:19 2009 +0000 Fix K562 orderUrl commit 10f5ea13a450148eec55da3d48d737e5dd5b3e29 Author: kate Date: Tue Jan 20 19:26:05 2009 +0000 Fix outdated links for pilot contributors commit 1573cee4381b0d76c106c32c58a4769e2ab8a544 Author: hiram Date: Tue Jan 20 19:24:47 2009 +0000 Had the fixup for sparc incorrect commit 3da56d6f2361a9fc2d236a859ed9280bd0d63d84 Author: giardine Date: Tue Jan 20 19:05:14 2009 +0000 Do pgSnp displays for all subtracks commit 730ae8d2d47f016368962147df227bdf19d96598 Author: mikep Date: Tue Jan 20 18:46:14 2009 +0000 added new categories of short RNA commit 0c0c077893fdab66c0693a014ac1b7b9f5b83064 Author: giardine Date: Tue Jan 20 18:14:35 2009 +0000 Updated listing of genomes commit 8d77137f3d12a9bc3366c74e114286308f3ef926 Author: galt Date: Tue Jan 20 16:00:06 2009 +0000 "Encode release log update" commit 8c27502832c09d9dad2eb72972b186e3c7b1e18f Author: galt Date: Tue Jan 20 16:00:03 2009 +0000 "Release log update" commit fa91d750120cc4384bdf4bc0c82a4496230d3dcc Author: jsanborn Date: Mon Jan 19 18:52:15 2009 +0000 added joe gray user datasets commit eb4caa1f1503d7c1e05942044c95fdc01d753abd Author: galt Date: Mon Jan 19 16:00:04 2009 +0000 "Encode release log update" commit 25cad0c8836114de24b0b8ab108a106230533d44 Author: galt Date: Mon Jan 19 16:00:02 2009 +0000 "Release log update" commit 8420fb463b494b8f0fdb216a1216ff7965296eb9 Author: kate Date: Mon Jan 19 03:55:28 2009 +0000 1. Add ENCODE freeze (dataVersion) 2. Fix date format inconsistency 3. Add comments 4. Add HudsonAlpha CNV track commit 3096b6bd632ea268d9c41ee84d02401e0cb4ca9f Author: galt Date: Sun Jan 18 16:00:07 2009 +0000 "Encode release log update" commit 59b5e225cccd23a48bd0ffb8fcf1b9f03d916f41 Author: galt Date: Sun Jan 18 16:00:04 2009 +0000 "Release log update" commit 9e01e792849381307eb527ad463fb2d37f206563 Author: galt Date: Sat Jan 17 16:00:08 2009 +0000 "Encode release log update" commit 93a0dc2c04639e4741d39eba6e288cdbf875cc32 Author: galt Date: Sat Jan 17 16:00:05 2009 +0000 "Release log update" commit c4a1d3d60745c436fc8fefb48666e7af2ddfeec9 Author: aamp Date: Sat Jan 17 14:51:31 2009 +0000 Needs a zero. commit 128fe272f43cedd4d166de68e42a33584964047b Author: aamp Date: Sat Jan 17 14:44:44 2009 +0000 Changed 43,000 to 42,000 because that's more accurate. commit 2983c43ec2d5af1c78be0b6c97183d737fd174d6 Author: galt Date: Sat Jan 17 02:23:09 2009 +0000 fix cart variable .vis name for GS cust marker col commit 36e31c7303bcaa4bbe2006851d22e7a1335599b0 Author: galt Date: Sat Jan 17 02:07:18 2009 +0000 fix cart variable .vis name for GS cust marker col commit 848905986e8178e456a7d104947dd9e74545ded5 Author: galt Date: Sat Jan 17 01:54:54 2009 +0000 cgi-encoding the column name in the URL commit 04f4cb909564af6abc46b46e2ba2c8b03573685f Author: tdreszer Date: Sat Jan 17 00:41:06 2009 +0000 Added new Yale control tracks: Hela-s3: Large_Fragment, MNase, Mouse_IgG and Naked_DNA commit db6abe4b84b35c8e4f7cf91ae233eab1f4e80927 Author: ann Date: Sat Jan 17 00:40:57 2009 +0000 removed links from orgs that have no browser commit efc824538d11dd087d136be6586b5be4363ce655 Author: angie Date: Sat Jan 17 00:28:40 2009 +0000 Sanger Genes liftOver'd from ce6; Conservation & Most Conserved. commit 9e923d9e8bf5851420a4adb8a0cc2b8bdef25fb2 Author: angie Date: Sat Jan 17 00:25:38 2009 +0000 Added compGeno tracks for modENCODE. commit 0395903d2960c2bed6540de83bf637bf036f53ca Author: markd Date: Sat Jan 17 00:06:37 2009 +0000 removed old MGC track stuff that is no longer needed commit 2320514071f5b0667b4c406d6c9f915acca7558d Author: kent Date: Fri Jan 16 23:58:04 2009 +0000 Moving the r-tree stuff to a separate module. commit 4db1412b6135875a8fe2e8e9663714b23b9c1dcb Author: pauline Date: Fri Jan 16 23:32:44 2009 +0000 Fixed broken link. commit 544a6539960cda8d58b93700cfd917b1b44b4f16 Author: kate Date: Fri Jan 16 23:05:40 2009 +0000 Restore Tim's setting name changes (stepped on by me in 1.354 checkin commit d2cfa07325c0a4c681b643af663d73f4e5524fde Author: kent Date: Fri Jan 16 22:44:50 2009 +0000 Made itemsPerSlot a command line parameter. commit 1d191a7a3c4c40e03253737875918b5b3bfa813c Author: ann Date: Fri Jan 16 22:38:18 2009 +0000 added hyphen to shortLabel and longLabel of FOX2 track to match documentation commit 43714aacfb49a2fae3ae125619390962132200b3 Author: kent Date: Fri Jan 16 22:37:47 2009 +0000 Made it so that number of items per slot at the leaf-level index is part of the API, separate from the index block size. If this is set to 1, I think it becomes the more usual r-tree. commit eacc709c80f03d552b3806c99ae1896867f0c51c Author: kent Date: Fri Jan 16 22:19:46 2009 +0000 Putting in filter to only output the part of the block that is actually in range. commit b8beb4a77ae7223be60bab36723e6c8f0d1e95b0 Author: angie Date: Fri Jan 16 21:11:10 2009 +0000 Updated use of hg16 to hg18 in doTest (Fan's code review suggestion). commit 2cedb70d7399173eee047145387efff545104409 Author: giardine Date: Fri Jan 16 20:36:31 2009 +0000 Adding back in missing personal genomes commit 05c422fb0ac50c41bb497d1cc089ed05a919ed43 Author: kent Date: Fri Jan 16 20:36:15 2009 +0000 Working in moderate sized test. Still lots of debugging output. commit 9f6d1378c6140e66a83baebdcf7921844fb48c43 Author: tdreszer Date: Fri Jan 16 20:21:06 2009 +0000 Added HEK293(b) for Yale (different protocol from Stam's HEK293 commit a7df4fae2a34e44f8b22889269d12fad9c153e70 Author: tdreszer Date: Fri Jan 16 16:34:56 2009 +0000 Backing out change that affected conservation plus/minus buttons. commit 33aa08a2403d953174e38a2b0293015a1410beb8 Author: galt Date: Fri Jan 16 16:00:09 2009 +0000 "Encode release log update" commit 5a18a3f1ca661d4f83ff3ade289b8fe1309d5115 Author: galt Date: Fri Jan 16 16:00:03 2009 +0000 "Release log update" commit 67f732b6aaf5dc90e8a8e4921691553a0900283a Author: hiram Date: Fri Jan 16 05:47:21 2009 +0000 Remove unused variable and broken compile commit 4378d2d3db7520e1b8271a8cafb6b2ee95dfc203 Author: hiram Date: Fri Jan 16 05:44:14 2009 +0000 It is OK to strip the binary created commit a7d6b61942e7bc9946fc642f775ae06dfdb85b0e Author: hiram Date: Fri Jan 16 05:42:15 2009 +0000 translate Ensembl Gorilla gorilla gorilla to UCSC Gorilla gorilla commit 392d52712cf68f5b0a2a016a07e0c2c5080f2f98 Author: hiram Date: Fri Jan 16 05:40:49 2009 +0000 proper %02d for the numbered parts so they will sort easily commit b6bb3f5fb78174331f7c27596c4bb451f1174f45 Author: hiram Date: Fri Jan 16 05:23:04 2009 +0000 fascinating slip of a finger moved a bracket up a notch, no compile errors, but completely non-functional commit 9d68be6b6c67e2c3ed900ed99f39a2e6641e2f6c Author: aamp Date: Fri Jan 16 02:10:36 2009 +0000 Removed next-item button for Agilent tracks until the next-item composite track bug makes its way into the browser release. commit c884ca84abf8bef35d1b1fb1a5f64c73895c4b26 Author: aamp Date: Fri Jan 16 01:54:33 2009 +0000 Bugfix: composite tracks have next-item button on main longLabel. Clicking them prompts an error. This turns those off. commit cfabb10e258859d0e2ed54ea61867f1f241bdc6e Author: aamp Date: Fri Jan 16 01:53:00 2009 +0000 Turned on exonArrows in mouse and rat Agilent arrays and turned off score filter. commit 54319b53843e4734bfd6d54dffdd42b4ffc1c1de Author: pauline Date: Fri Jan 16 01:10:00 2009 +0000 Turned off genbank updates for oryLat1. commit 7f9d588c9bef35289361645c67589189e2160a17 Author: kate Date: Fri Jan 16 00:46:37 2009 +0000 Downloads for phyloP commit e2c1dc54b736a827fc55b76e6c1d941ad10a91be Author: donnak Date: Fri Jan 16 00:20:38 2009 +0000 Clarified news item abt oryLat1 update. commit 6a99d4d4772d63d45967a671add34fdc6b1a85b1 Author: donnak Date: Fri Jan 16 00:18:43 2009 +0000 Changed oryLat1 -> oryLat2. commit 9ad380589dea828984e9defd859193b9f25fc924 Author: hiram Date: Fri Jan 16 00:04:39 2009 +0000 Do not mess with HGDB_CONF in the pipelines, and fixup limits returned for wiggle encoding commit 5a45b361d669f46205a15c2564e0882aad11f4b3 Author: kent Date: Thu Jan 15 23:22:35 2009 +0000 First draaft of r tree index writer and querier compiles. Fails run time tests still. commit 50361d04a195cba1148dc3dfe13f89bf77ca51b8 Author: kuhn Date: Thu Jan 15 23:11:32 2009 +0000 dropped malfunctioning substitution for ting commit 32837ebe007fdb963cc19d7929191b2691881440 Author: fanhsu Date: Thu Jan 15 22:58:33 2009 +0000 Updated URL to UniProt. commit 7f5aa410f775085ceef077742846b6f83d100542 Author: hiram Date: Thu Jan 15 20:29:01 2009 +0000 Ignore missing extFile table when asked to clean. commit 708415d91a717a1362bd7ab80f987d6bf5bde633 Author: kate Date: Thu Jan 15 19:56:02 2009 +0000 Edits from Adam. Other cleanup. commit 216ed9cd3996fa04e0a1a37d066e4dfa9d99372d Author: galt Date: Thu Jan 15 16:00:06 2009 +0000 "Encode release log update" commit 9c7e494b4391693d9f01a95c81ba9f44401e77a6 Author: galt Date: Thu Jan 15 16:00:03 2009 +0000 "Release log update" commit 31e498d484aaf97dfab067fcce2ac887c68b6e15 Author: markd Date: Thu Jan 15 07:12:51 2009 +0000 implemented substituting arbitray setting from trackDb, support substitutions at load time, however this is temporarly disabled commit 7086dc8fd997154732ae5fe80a3fcee5d76e5e1d Author: mikep Date: Thu Jan 15 06:41:58 2009 +0000 dont override it, but set if not already set. Test this by removing hg.conf from the /cgi-bin/ directory, setting HGDB_CONF to point to a different location, and trying to load a custom track commit e689b6fbeab8800d43eff25fcbf4a81f0b6518b6 Author: markd Date: Thu Jan 15 06:37:16 2009 +0000 fixed typo in help message commit ce901db96d12a8692ed3c72457342bf1dc556d2c Author: markd Date: Thu Jan 15 06:35:27 2009 +0000 add header to per-net type info files commit 6e74f847e9be257c92c135bf4c7e985f5d75cd09 Author: jzhu Date: Thu Jan 15 01:13:26 2009 +0000 *** empty log message *** commit bd21e8054fb1e98f75f3783f3e32dc70955c0f39 Author: galt Date: Thu Jan 15 00:33:58 2009 +0000 adding totals for categories of tables (mysql disk), gbdb (hgnfs1), and goldenPath (hgdownload) commit 5e717c42b2bbb89f73baf2e4fe95fb4b46fd7766 Author: hiram Date: Thu Jan 15 00:05:41 2009 +0000 Add phyloP to the ignored list commit 1166e825ab750c38a7c833be3a82c4e4cf7b5d49 Author: hiram Date: Wed Jan 14 23:56:13 2009 +0000 Updated with Primates annotation instead of Euarchontogliers commit ba4cf4f64d82e5e43fe2b1fcbf70049b1f065404 Author: ann Date: Wed Jan 14 23:54:12 2009 +0000 updated with snp129 data (the previous data was from snp126) commit aac78b39715378a76047ac847231e33c2de39064 Author: galt Date: Wed Jan 14 23:50:58 2009 +0000 red is for errors commit 760ce55d675676c271f26a8141710193143a3158 Author: galt Date: Wed Jan 14 23:34:26 2009 +0000 extending listDirX to tolerate stat failures commit 55148713cf609a64b40b12ecd3158c34fab96121 Author: hiram Date: Wed Jan 14 23:30:02 2009 +0000 Finishing up the 44-way phastCons business, downloads, and pushQ entry commit e3534ed8cb0c3c4542f61fd65d92c778d46dfd55 Author: galt Date: Wed Jan 14 23:06:29 2009 +0000 extending listDirX to tolerate stat failures commit 4e9b925d7be68ccf2f5111e609da2ca7cd7db4b9 Author: tdreszer Date: Wed Jan 14 22:49:28 2009 +0000 jQuery lib is now required regardless of dragAndDrop commit fd271afce3abb9efd019c99232a338063cb6c9f4 Author: fanhsu Date: Wed Jan 14 22:12:56 2009 +0000 Updated UniProt URL. commit 679539c00163280ab0c6e167d1aaba37483fb9da Author: fanhsu Date: Wed Jan 14 22:07:03 2009 +0000 Updated UniProt URL. commit a2414c46483eca9c05ab2e03310f3db78ef6c5e2 Author: mikep Date: Wed Jan 14 19:29:01 2009 +0000 dont interpret the jQuery javascript commit 82b9761438df2277854e564d942479e6427d3373 Author: hiram Date: Wed Jan 14 18:59:18 2009 +0000 Fixup upper and lower limits for data range when processing wigEncode and error out on an empty file processed commit 76acf1597b2c7d15b7327d581652f270826d0442 Author: angie Date: Wed Jan 14 18:54:54 2009 +0000 When comparing trackDb types, ignore the min and max following "wig ". commit 71321b618a04354e60598e17dcd4e76a250a96c9 Author: markd Date: Wed Jan 14 18:43:35 2009 +0000 coded simplification commit cc2d78213c484e77dfee592fdafd90036449d2d0 Author: fanhsu Date: Wed Jan 14 18:29:20 2009 +0000 Added positive selectioin tracks for subtype B. commit 048a5341d6cd230efb4fb81ea6417b18ed7b7456 Author: fanhsu Date: Wed Jan 14 18:24:49 2009 +0000 Added positive selection tracks for VAX003 subtype B and AE. commit de4714824a1ba6ecefd945c13cf9d5c6ac7b0fad Author: hiram Date: Wed Jan 14 18:13:40 2009 +0000 Add note about building on sundance commit 5483b7a0322fea025b090e3cde868891b96f5aa4 Author: fanhsu Date: Wed Jan 14 18:10:52 2009 +0000 Added VAX003 subtype AE positive selection tracks. commit 92d48fc1fdd69d427394c4626b7efeff1f19bdc8 Author: fanhsu Date: Wed Jan 14 18:02:50 2009 +0000 Added VAX003 subtype AE positive slection tracks. commit 7fc20e5691801c6661f53ddab00642eb993f444c Author: fanhsu Date: Wed Jan 14 17:56:00 2009 +0000 Added VAX003 subtype AE positive selection tracks. commit ab07a9d0cf4742aa85c02c34e392753d93fa1a52 Author: fanhsu Date: Wed Jan 14 17:31:53 2009 +0000 Added positive selection tracks for VAX003 subtype B. commit 1e165688818965ca3dcbe4c0760758c228963cf9 Author: fanhsu Date: Wed Jan 14 16:51:43 2009 +0000 Corrected a typo. commit 94322dd1c26f7fa29bcb6398c587570495ebfe43 Author: galt Date: Wed Jan 14 16:00:14 2009 +0000 "Encode release log update" commit 3074ff2c9ba5ccddc55448bfb0e1b8157b0c6587 Author: galt Date: Wed Jan 14 16:00:05 2009 +0000 "Release log update" commit 707f1f07c101dc36a45f415af48a3f02e902b77e Author: kate Date: Wed Jan 14 00:43:56 2009 +0000 Switch to production phase logo commit c4f61fd87772040759ad352f94fc83cf9bbe46f2 Author: kate Date: Wed Jan 14 00:30:23 2009 +0000 Fix for Safari commit 33bfd495d948af160e461e11247274f3429a8a71 Author: markd Date: Wed Jan 14 00:21:21 2009 +0000 fixed bug with -overlapThresholdCeil criteria commit 590674992cbcff98e56a23c18320548c6ea3a59d Author: kate Date: Tue Jan 13 22:39:19 2009 +0000 Change News item title for consistency commit e62ebb1c8366f9d0d7c820fd415ed301ac9a32f4 Author: kate Date: Tue Jan 13 22:33:37 2009 +0000 Changes to intro suggested by Jim. Some expansion of News commit 6a1ad3147f9cdf2da41b7df55a666aa1e023a010 Author: tdreszer Date: Tue Jan 13 22:33:24 2009 +0000 Fixed bug that crashed on bad index when trackDb.ra entry was inconsistent commit 318d6c4da0d90995a114418dab726692eb96d638 Author: mikep Date: Tue Jan 13 21:43:23 2009 +0000 first version of a daf for solexa commit 41207edd070e3413b7383bacd277309d6dab6c17 Author: pauline Date: Tue Jan 13 20:49:58 2009 +0000 Removed links to old medaka assembly. commit bb07384b603e25b4e3b77eb4aede870f06aa1c40 Author: angie Date: Tue Jan 13 20:44:51 2009 +0000 Added ce5 to DBS. commit 2038b9df70fc944fc98a6aa699cc0e494d50f254 Author: angie Date: Tue Jan 13 20:42:35 2009 +0000 Initial trackDb.ra for ce5 commit a048e6b1ded4ad0c928eb2619cbf776fa50cc03f Author: angie Date: Tue Jan 13 20:40:57 2009 +0000 Initial descriptions for ce5, copied and modified from ce6. commit 112e6979a7317bb0579c10bb10675290659597d3 Author: larrym Date: Tue Jan 13 20:17:37 2009 +0000 collapse/expand groups => collapse/expand all commit 8ac03535ba07d8090888ddc72e7993d0730e1610 Author: galt Date: Tue Jan 13 18:57:51 2009 +0000 increasing size limit test by factor of 10, Hiram hit limit with 44way track commit af1b84852350ebd21bf409f9dc705e5e7e39a0f2 Author: mikep Date: Tue Jan 13 16:56:39 2009 +0000 "New version number v198" commit e6988728449f55af03926d1ad90dcc3112d06fe9 Author: mikep Date: Tue Jan 13 16:55:59 2009 +0000 v198 final commit de5a679bce89b6bd784e5e1dd29e41dbf8179bdd Author: galt Date: Tue Jan 13 16:00:06 2009 +0000 "Encode release log update" commit 0eab48137999cad0854bccac69bacc7a816c9f41 Author: galt Date: Tue Jan 13 16:00:03 2009 +0000 "Release log update" commit 0a11cf63eb56895c716b234b0f94112a8ba11d7d Author: kate Date: Tue Jan 13 01:05:54 2009 +0000 Add information for phyloP commit 7b36559304efac0a09ede8952eab08cf770441be Author: kate Date: Tue Jan 13 00:20:34 2009 +0000 Add another submit bottom to long composite pages commit d84feb7523d008c9b7e6c532d20698fd49bfc718 Author: kate Date: Tue Jan 13 00:10:21 2009 +0000 Remove euarch, adjust config after feedback from Jim commit 872e1ea0f023806642500d185e1ed1ddd5c8ea77 Author: galt Date: Mon Jan 12 22:36:21 2009 +0000 adding more snpTables commit c9477caa2633e55b952812426588881da9c595d1 Author: fanhsu Date: Mon Jan 12 22:12:46 2009 +0000 Added a complex query to get the gene symbol of the exact KG that matches not only ID but also genomic position. commit 08aaad6cc93de105c04162601abfd74b005bd6dd Author: larrym Date: Mon Jan 12 21:46:19 2009 +0000 move collapse/expand group buttons down commit 060d32b4a06832d8b630a4a9f3ead622112d5e5b Author: kate Date: Mon Jan 12 21:42:34 2009 +0000 Another track name for 44way (multi-view composite version) commit b0b8bbd02f76df7bd10a4faee4d29f7d4dd8dc96 Author: fanhsu Date: Mon Jan 12 21:15:17 2009 +0000 Changed to "OMIM gene or symdrome" per Bob and Brooke's suggestion. commit b3b562227e743773bdff53d0841b53832f29ce60 Author: larrym Date: Mon Jan 12 20:40:44 2009 +0000 add IE specific mapHtml code commit 86c5b4403638208cfa9dec0d03d4fb4cc343a3b4 Author: fanhsu Date: Mon Jan 12 20:00:27 2009 +0000 Updated to "OMIM gene or symdrome" per suggestion from Bob and Brooke. commit bec53bb7c265f624161c890e262f91bd2558b80a Author: kate Date: Mon Jan 12 19:59:37 2009 +0000 Propagate default view limits to subtrack until setVisibilityDefaults works fully commit 8e6d870ce493a234b3e1d57c19974002b69d2dcc Author: kate Date: Mon Jan 12 19:14:47 2009 +0000 More adjustments to wiggle settings commit a7f2716af406a2d2891519f83ea5b2d8493ea74d Author: fanhsu Date: Mon Jan 12 19:13:31 2009 +0000 Removed a redudant declaration. Broaden the bed entry to 3 bases instead of 1. commit ab291f07acaf0a546040721bd333fb11f6d7b269 Author: fanhsu Date: Mon Jan 12 19:06:05 2009 +0000 Updated omimName logic to be more fool proof. commit 295c7215ec6261f53b519808e961cec6b05d6d69 Author: hiram Date: Mon Jan 12 18:52:06 2009 +0000 The settingsByView for the fox2 density tracks needed limits commit 7f2b18b3356241f27eda5ff129bf2d1b5d9a5512 Author: ann Date: Mon Jan 12 18:42:47 2009 +0000 tweaked for consistency with help page commit d4e3a23ebbca9d892057c5b03114df8768de2958 Author: ann Date: Mon Jan 12 18:35:03 2009 +0000 small tweak to gene sorter column commit 8c9757437f9898dac4bce8faf2edba8da5ff5821 Author: fanhsu Date: Mon Jan 12 18:12:38 2009 +0000 Updated logic of omimMorbiMap to list all disorders. commit 9c6e43ec23570542749601d96885c534cf7a3ddc Author: kate Date: Mon Jan 12 18:07:32 2009 +0000 Merge phyloP and conserved elements into 44way track commit 440ba507dd2ac2277d7c418df76f2f181bd4d49e Author: tdreszer Date: Mon Jan 12 17:48:38 2009 +0000 Expand 'inputArrayThatMatches()' to handle selects as well. Also 'setCheckBoxesThatContain()' should look for beg/end. commit ecb1cdfd73b0ecb470f003a6446355ff3ff985dd Author: ann Date: Mon Jan 12 17:46:09 2009 +0000 made a note that the correct name of the rock hyrax is actually proCap1 commit 1a8cc8d28e86a2be0555b678ce08561f61118f7d Author: tdreszer Date: Mon Jan 12 17:42:44 2009 +0000 ENCODE GENCODE genes track should use display name2 which is trascript name commit 1fec8ad534de027dd8cc0ad6729aefd56539cb56 Author: galt Date: Mon Jan 12 16:00:08 2009 +0000 "Encode release log update" commit 814e23aaf04fe118d1e83b92aaafcd090eb43dc5 Author: galt Date: Mon Jan 12 16:00:05 2009 +0000 "Release log update" commit 0e60cff54e531ab21cfc5ad9a8b8400ef1036116 Author: galt Date: Sun Jan 11 16:00:08 2009 +0000 "Encode release log update" commit 3e5be77d98fbca1c59b6a64fc4adb83adb6fede2 Author: galt Date: Sun Jan 11 16:00:05 2009 +0000 "Release log update" commit 180720d1fe15b50eec4b879af79cfdc6119fb4bf Author: galt Date: Sat Jan 10 16:00:09 2009 +0000 "Encode release log update" commit 749055a7828900134bcc32e07884cd556940afab Author: galt Date: Sat Jan 10 16:00:06 2009 +0000 "Release log update" commit dd5f54a680b24802f62cfea119704c8029886002 Author: tdreszer Date: Sat Jan 10 01:30:59 2009 +0000 Two more datasets for Yale commit b76161edfcd1b7874a5a252af2fb1957f99547ec Author: tdreszer Date: Sat Jan 10 01:07:02 2009 +0000 Added settingsByView to mult-view description commit f7a8e1aad4c9ca68cb401047900525bdb5fd87fc Author: tdreszer Date: Sat Jan 10 00:46:58 2009 +0000 Altered settingByView parameter names to avoid future confusion commit 4fca533bc8763726f9fc6dc64841d3f0b5664488 Author: tdreszer Date: Sat Jan 10 00:43:25 2009 +0000 Changed settingsByView to interpret 'viewLimits' the same way asfor subtracks commit 0cf481f208f28fdaa6a397ed6ede42e8ce868596 Author: tdreszer Date: Sat Jan 10 00:39:32 2009 +0000 Added define for wiggle settingByView 'viewLimitsMax' commit bb2956e94084268de2d35e109de263438656917c Author: kate Date: Sat Jan 10 00:05:36 2009 +0000 Add phyloP conservation wiggles for 44-way alignments commit f7911a94baae05e98504ab71f591b115ade87785 Author: tdreszer Date: Fri Jan 9 23:53:24 2009 +0000 Fixed typo commit 8a999a97db10f7bf6146715fe4012c20a6e0c436 Author: tdreszer Date: Fri Jan 9 23:37:58 2009 +0000 Allow control terms in Cell Line commit 054fab6c601b690c7a3671c5e7afbdeb676549aa Author: tdreszer Date: Fri Jan 9 23:31:47 2009 +0000 Added Reference_Genome for support tracks built on hg18 commit a70fab56ed1dba63d2b6f8b60be789ef121d1185 Author: ann Date: Fri Jan 9 23:19:07 2009 +0000 added extra paragraph marker to cause full iframe to display commit 1fa81a5dd754e37121a0da754edfb1a94748d28d Author: ann Date: Fri Jan 9 22:28:59 2009 +0000 explanation of the new drag-n-zoom feature (thanks to Kayla!) commit 8cb049a5ec2c4cd717221d2f67eb3bec7ca8dbe3 Author: kate Date: Fri Jan 9 21:16:54 2009 +0000 More phyloP work -- primate run, stats, and beginning of lineage-specific runs commit d519f392756747e76e8c2b3256d1bb4fbb34ddc9 Author: tdreszer Date: Fri Jan 9 21:11:16 2009 +0000 Added NF-E2 for Yale commit ce67686bd4966df045678ae59c127d0447741aa5 Author: tdreszer Date: Fri Jan 9 20:03:55 2009 +0000 Control terms are now in cv.ra commit 01f39e01b732cea42be7e53166329038cf152c67 Author: hiram Date: Fri Jan 9 19:46:16 2009 +0000 Adding search terms for fox2ClipSeq track commit 169c4269cd0794c75e51eb9ba8722b5f46a26e0c Author: hiram Date: Fri Jan 9 19:28:58 2009 +0000 Add the noScoreFilter option description commit ad6d97306ea136b1d170b1d0a9898baf3b5d08f5 Author: hiram Date: Fri Jan 9 19:24:09 2009 +0000 It is now January, no November, what were you thinking ? commit d51e3c02a4d68c87b91c160367b4c0d4e25d3474 Author: tdreszer Date: Fri Jan 9 18:54:01 2009 +0000 Added type control to handle growing number of control terms commit 786b2b4ce4f7cbae45a0c0616efe76af8f678202 Author: hiram Date: Fri Jan 9 18:49:59 2009 +0000 Add dataVersion and noScoreFilter for the fox2ClipSeq track commit ea308a179fb5eaef129b98b1fba7b12b71dd9223 Author: tdreszer Date: Fri Jan 9 18:49:55 2009 +0000 Added actual control cv type, so removing impolicit control type code. commit 71f9fcd0b668669498bb4e2f5ce54a35b6aadd2d Author: kate Date: Fri Jan 9 18:42:08 2009 +0000 Adjust height on iframes to suppress scrollbars commit c76089ce1ad2e0969790a6f06af8399b3b425a24 Author: hiram Date: Fri Jan 9 18:41:46 2009 +0000 Add install targets to get the rsync done commit d5e748c1b081064cb4ed3484b98a1597841de67c Author: hiram Date: Fri Jan 9 18:24:19 2009 +0000 better consistent names on the Fox2ClipSeq track commit 5ffe82f5db88c59b9e066fb7ef78b54132ef1fb2 Author: ann Date: Fri Jan 9 18:12:59 2009 +0000 added fox2 human tables to tablesIgnored (they have no relationship to other tables) commit 69c7e87ead1bdcddc00521c6b8b140949afcd874 Author: ann Date: Fri Jan 9 17:35:57 2009 +0000 Hiram changed the names of the tables, I changed these entries to match commit e1ad272b8522a0ea46eac184061995d57dfcd354 Author: ann Date: Fri Jan 9 17:29:09 2009 +0000 removed a paragraph marker commit 2101381710da865811b25a3dcaac161535c2f1dc Author: tdreszer Date: Fri Jan 9 17:09:19 2009 +0000 Added Max antibody for Snyder commit 57033dfeb9b3b7e64483e444e100892408202ab7 Author: giardine Date: Fri Jan 9 16:49:27 2009 +0000 Adding more Personal Genomes commit 525167dc1f2e835eabb86391898913bc741a802f Author: galt Date: Fri Jan 9 16:00:07 2009 +0000 "Encode release log update" commit bb0160c6a7b825ca352b59dff9bbedf0da92fc6b Author: galt Date: Fri Jan 9 16:00:04 2009 +0000 "Release log update" commit 0b0711735f50d44906e08047169feefa03db4b0b Author: kent Date: Fri Jan 9 10:17:40 2009 +0000 Adding bpt* to makefile. commit 0319f9cd70aa5e6d0db34fe585d7cebc083b1b79 Author: kent Date: Fri Jan 9 10:15:39 2009 +0000 Removing unused variables. commit 65f8d1e74a345d4506f3446f73d9727a9f0d3c87 Author: kent Date: Fri Jan 9 10:14:33 2009 +0000 Adding twoBitOpenExternalBptIndex function, which adds bPlusTree external index support to twoBit. commit e80d85d506a4712ac2734118eb8d705f21e679af Author: kent Date: Fri Jan 9 09:28:36 2009 +0000 Fixing bug when value not 64 bit. commit 25d03fbc609823faabb50cd7a11b68b9cae119b4 Author: kent Date: Fri Jan 9 08:39:08 2009 +0000 Seems to work. commit ce743e4968e96f57af8ba8f6481d49dde844d580 Author: kent Date: Fri Jan 9 08:29:07 2009 +0000 Adding signature for b+ tree files. commit b58da8943abb0e95ee6e867c575502076786ac25 Author: kent Date: Fri Jan 9 08:27:16 2009 +0000 Adding bPlusTree. commit f7edaca322d1f8607ea41a576c6957ca1a37a17f Author: kent Date: Fri Jan 9 08:09:37 2009 +0000 Moving B+ routines to library. commit b8657c8daf8c5823291758d787217017377deb3c Author: tdreszer Date: Fri Jan 9 04:15:47 2009 +0000 To speed up code, I switched to filtering CBs by class. Very important changes for Broad's 184+ track composite. commit 971098e8f4d877ecb9948fdc5a2b70b0ae4c09ae Author: kent Date: Fri Jan 9 02:59:37 2009 +0000 Fairly generic b+ tree for data warehousing (no incremental additions and no deletions implemented, just bulk load, and query). Right now in same module as programs to create and use a specific b+ tree type. Will move most of code to library module shortly. commit d1545aee8b9b7f97bb753c682a71067b5da30c7d Author: donnak Date: Fri Jan 9 01:30:45 2009 +0000 Minor formatting edits. commit 55333bde8c2f07274291cddef5820e53ec6d72f4 Author: donnak Date: Fri Jan 9 01:20:41 2009 +0000 Added list of DCC staff, per kate. commit 153fbca58e37ecba69e4f92c2d90d2bd4b68e46c Author: galt Date: Fri Jan 9 01:05:48 2009 +0000 adding documentation for custom GS columns from GG markers commit f7bbea8ffecbd209658d100a48d27fb9a4ace078 Author: kate Date: Fri Jan 9 01:04:32 2009 +0000 Stats for phyloP commit 3a728f65df1ab59d60361f924a164c318ffacebd Author: angie Date: Fri Jan 9 00:58:27 2009 +0000 Speed up pasted/uploaded identifier processing when #IDs is at most 10000, both when checking submitted IDs and when using IDs as a filter while getting output. When #IDs > 10000, we still use the old method: querying all rows in table and then looking up IDs in the hash. For tables with millions of rows, that takes so long that it can time out. But when #IDs <= 1000, add a big 'field IN ('id1', 'id2', ...)' SQL expression so that the server returns rows only for those IDs (fortunately IN is case insensitive). filterClause() is used to fold the new expression into the query. commit 40a6a35c46223792ca71f1f4e2a9c7d7fb4377b8 Author: galt Date: Fri Jan 9 00:53:36 2009 +0000 adding documentation for custom GS columns from GG markers commit b246783375f570584f015b408f3e6402c0f5d81d Author: galt Date: Fri Jan 9 00:14:35 2009 +0000 adding custom GS markers column from GG commit 8e7e6610809014a44548dea87f2cfcb9b4b4eec5 Author: donnak Date: Fri Jan 9 00:14:19 2009 +0000 Added Kate to news item acknowledgement list. commit 78a7c8375d12a0aefc5b11fb8017da5278135cb0 Author: donnak Date: Fri Jan 9 00:01:58 2009 +0000 Added some more pubs, per Kate. commit d4abb2c86ef686995b708528e523ba38128a920b Author: ann Date: Thu Jan 8 23:33:15 2009 +0000 a few additions commit 448f69cd95bfe5659ed04429d773fda90541ec64 Author: donnak Date: Thu Jan 8 23:26:59 2009 +0000 Added news item, removed commented-out section. commit 9bfaf95b1b664a2fd48c71bcd3a1482d9587feb6 Author: hiram Date: Thu Jan 8 23:02:39 2009 +0000 Add fox2ClipSeq track, and phastCons primates for 44-way on hg18 commit f8ee58024a05b3bd404f927d0f17ac76d52eda51 Author: kent Date: Thu Jan 8 22:48:18 2009 +0000 renaming readBits64 and writeBits64 to msbFirstReadBits64 and msbFirstWriteBits64 to avoid name conflict with pattern established by byteSwap32/readBit32 function pairs. Adding some other minor utility functions. commit dea13b69a85c0441517e9b0e6488168bb89efbb4 Author: larrym Date: Thu Jan 8 22:16:48 2009 +0000 refactor duplicate code into setSelection function; use getElementsByName instead of getElementsByTagName commit e1c6f354d627b3fbe90c5d7bb0092e7e41e07795 Author: hiram Date: Thu Jan 8 22:06:52 2009 +0000 With Donna's edits and mailto link securified commit 9e706a20a34279d6fc27933e1bc6374155a86389 Author: hiram Date: Thu Jan 8 22:01:39 2009 +0000 Moved the fox2ClipSeq track to a higher level so it will apply to both hg17 and hg18 commit b885ffcb94d9ba7910a2d39f57e23a6eb3b3f402 Author: kate Date: Thu Jan 8 21:04:45 2009 +0000 More phyloP for the 44way commit 00502551e7227eb9abd12556a0cf370379ac5e5b Author: donnak Date: Thu Jan 8 20:10:03 2009 +0000 Added hyphen to CLIP-seq. commit d8c0ef3cadfecac94879b2b808b4202cd9d25c05 Author: markd Date: Thu Jan 8 19:35:24 2009 +0000 added ignore entries commit 4a4f874768529f51d3b63bcdfd46cdaa63c16c1b Author: kuhn Date: Thu Jan 8 18:49:07 2009 +0000 massaged text a little commit 3afd643c0ec2e60103bc41cada7dd5a8f319ec18 Author: fanhsu Date: Thu Jan 8 18:04:07 2009 +0000 Updated URL to UniProt per UniProt's request. commit da3ce785a674bcfd023e6276e6618471bc11eb6e Author: fanhsu Date: Thu Jan 8 18:02:01 2009 +0000 Updated URL to UniProt per UinProt's request. commit b1ce62ced4df8fd64394088e641b500b0c0876be Author: fanhsu Date: Thu Jan 8 17:57:06 2009 +0000 Updated UniProt URL per UniProt's request. commit a39b7f5611e476835dd8e9afde32a933bee728e9 Author: galt Date: Thu Jan 8 16:00:07 2009 +0000 "Encode release log update" commit 4eecc0ed2ac663ff722a0c5d227055f7458ed184 Author: galt Date: Thu Jan 8 16:00:04 2009 +0000 "Release log update" commit 0c2f5c2597c73d08bef903cadcc6478845bad52d Author: kayla Date: Thu Jan 8 02:09:50 2009 +0000 fixed a priority to bring netTetNig1 back to chainTetNig1 commit f209942faeeb29083594504f486063e5c300b4c6 Author: kate Date: Thu Jan 8 01:29:43 2009 +0000 Tweak for clarity commit 3ff3ca252811f63ba3fa336b60b4c165c714870b Author: hiram Date: Thu Jan 8 00:56:16 2009 +0000 Turn the FOX2 CLIPseq track into a composite with two density wiggle graphs commit ff9aa47064b590782f93508fe3894a41e6cb5c37 Author: larrym Date: Thu Jan 8 00:49:22 2009 +0000 ignore single-clicks that are down inside of tracks (i.e. areas where there are no map items) commit d781743a2d2e1ac704989895fc3ab651f8623e1d Author: hiram Date: Thu Jan 8 00:43:42 2009 +0000 Instructions to use this business in Mediawiki source version 1.13.0 commit 1813f7105cb432fc065c9c5ce1dbfd58b666f6ec Author: hiram Date: Thu Jan 8 00:38:37 2009 +0000 Files to add to mediawiki source to turn on the ucsc login system commit 82cd786d7421e749ba6450abf9a2d751728cf576 Author: kent Date: Thu Jan 8 00:30:28 2009 +0000 Adding byteSwap16 and readBits16, which are very similar to byteSwap32 and readBits32 but work on smaller sized integers. commit 86d67e4c1353a16682657cbb76d7b7d4a73f0d14 Author: kent Date: Thu Jan 8 00:28:53 2009 +0000 Implemented a 32-bit-integer-keyed b+ tree for a chromToPos/chromPosLookup pair of programs that we probably won't ever really use (so this is all in oneShot at the moment). commit 72c20e1aee465e68cdc4c394bfe3bdb16443386d Author: ann Date: Wed Jan 7 23:44:28 2009 +0000 added missing paren commit ec3063a58a4769b75d6ea6d2854539bbd0073baa Author: hiram Date: Wed Jan 7 21:42:21 2009 +0000 Adding FOX2 CLIPseq track commit 75219ab8521c7e96d2aeadec2633ae2bbe179347 Author: tdreszer Date: Wed Jan 7 18:54:08 2009 +0000 Fixed some screwed up settings for K562/H4K20me1 commit 848bb6ca4cada8ba5203827b318fc0e76b1a4f7f Author: kate Date: Wed Jan 7 18:36:49 2009 +0000 More work on 44way phyloP commit 76c5a799e24a92809aa10bb444a2a6fd47c23bbb Author: tdreszer Date: Wed Jan 7 18:13:32 2009 +0000 Rearranging deck chairs commit ee1bdfdf249dec03d1763a8630fc2c322abc5211 Author: tdreszer Date: Wed Jan 7 17:55:28 2009 +0000 Tarjei updated alignment methods from ARACHNE to MAQ commit 00ef461bccd47918ef75b6baec8b6e94b52010bf Author: tdreszer Date: Wed Jan 7 17:53:41 2009 +0000 Added lots of Broad tracks commit 5ead50fe1c6bf8bc8fb205b6e35b35ca09a00a96 Author: donnak Date: Wed Jan 7 16:20:33 2009 +0000 Edited Jakob's name. commit 0b454fea8d06ec0fa379654988311bf03abd59cb Author: galt Date: Wed Jan 7 16:00:10 2009 +0000 "Encode release log update" commit 0dae2ff85524ee845fd91b6b45899d0a0313520c Author: galt Date: Wed Jan 7 16:00:07 2009 +0000 "Release log update" commit 45c74b2c9a630681db8c93c6329e18ea6fa6a24d Author: angie Date: Wed Jan 7 05:56:00 2009 +0000 Added more .as files to ignore. commit 2914630e090e584dbf898b1e51811e1312c67523 Author: larrym Date: Wed Jan 7 02:33:09 2009 +0000 Remove code which clipped selection area to remove left track list, because it caused the selection area to be lost (apparently due to a bug in jquery.imgareaselect.js). Fixed off-by-one errors which are apparent when viewing very small regions commit 5fdee02ecd2d52c21cba72d89c6b83fdc2afd35f Author: markd Date: Wed Jan 7 01:12:46 2009 +0000 added NCBI taxId as a required parameter commit 124f0900c1497680e7c7adf62f98768303c80ea6 Author: markd Date: Wed Jan 7 00:45:15 2009 +0000 fixed scientific name commit 3f835a6e0b77f77d97532b466d6a32d92a98bf76 Author: mikep Date: Tue Jan 6 23:41:32 2009 +0000 added a function like hGetBedRange() but which returns only the count of matching rows commit da50e6da45cdd4397eb57fb541e7c071ccadb06a Author: hiram Date: Tue Jan 6 21:49:07 2009 +0000 Properly label the different phastCons results commit d1a2537da3f7c3ad70d0da73edc62f6267e0ee0e Author: hiram Date: Tue Jan 6 21:44:34 2009 +0000 Rework the phastCons runs for the 44-way commit 14d9f8a49e1da95361f0dcba4a461de436ec85de Author: larrym Date: Tue Jan 6 21:16:52 2009 +0000 change singleClick logic to allow user to select regions smaller than 10 pixels commit 8ac3c9db3c3187f051fcfc6db06616b1b3366484 Author: kate Date: Tue Jan 6 20:05:05 2009 +0000 Tweak left menu bar item commit 782c9a196677fdf30ecd8e3cbbb006fa9ef19a30 Author: mikep Date: Tue Jan 6 20:04:54 2009 +0000 v198 preview commit 7ca6eb1377104c516cceb300c3d95834d3ed4a80 Author: kate Date: Tue Jan 6 19:55:58 2009 +0000 Add link to actual document commit 2c60417879a26d591c327424b361cf54ab21521d Author: angie Date: Tue Jan 6 19:51:44 2009 +0000 Fixed itemRgbHeader and itemRgbDataOut to print to the alternate file handle if present, like the resot of doTabOutDb(File) output. Merged the nearly-identical doTabOutDb and doTabOutDbFile so there's only one function to maintain. commit c44d4d09b0a6794db05333503766bfe4416d6bb6 Author: mikep Date: Tue Jan 6 19:13:23 2009 +0000 making two identical error messages unique to help debugging commit 4c51b8f9e9f75f203daf736c902c5b4b091cbb3e Author: kate Date: Tue Jan 6 19:13:04 2009 +0000 Cosmetics commit fd59dd06e9d7e406dbea497bb8d2edc65dbab005 Author: mikep Date: Tue Jan 6 19:12:17 2009 +0000 removing inadvertent commit of commented-out debug code commit a355c25222c367fa5adeb305336feb654ea0b111 Author: fanhsu Date: Tue Jan 6 19:05:44 2009 +0000 Created gsidPosSelect.c to generate GSID positive selection track. commit c8dbfa92ca3ce001f6e7e2335d492cd03f3f9a37 Author: fanhsu Date: Tue Jan 6 19:02:35 2009 +0000 Created makefile. commit 820bec52edc4b9042ccdcd01a4beb520cb88331f Author: tdreszer Date: Tue Jan 6 18:56:55 2009 +0000 Kate called me out on this quick little work around. Removing the temporary NHEK commit 24a2b0ad8dfe051634b3aaff857a74be3c120457 Author: kent Date: Tue Jan 6 18:25:21 2009 +0000 Committing so as to switch development to hgwdev from my laptop. commit 6453ff203bdc1b434c59e5ddb12d381cf0314ae8 Author: kent Date: Tue Jan 6 18:13:48 2009 +0000 Updating design based on input from programmer's lunch meeting. commit 5942e0b7e20f404d20cf1a274853e2afbe21b5ce Author: kate Date: Tue Jan 6 17:42:39 2009 +0000 NHGRI logo for pilot phase commit 3b111d157483e733630b4c83af9a62d0335f0b05 Author: ann Date: Tue Jan 6 17:26:22 2009 +0000 fixed typo commit 5c356c08adac39e66c4de5d284b355f401ed6e31 Author: kate Date: Tue Jan 6 17:16:23 2009 +0000 NHGRI program staff commit 67fe7a37eee4bbdf31195ab85ad6bbfe7c678239 Author: galt Date: Tue Jan 6 16:00:08 2009 +0000 "Encode release log update" commit c48c4cb0fea64d1b6f8b5ebe060aedad876ccca9 Author: galt Date: Tue Jan 6 16:00:05 2009 +0000 "Release log update" commit a93a045094028b6ff4dd829f9653e7521617393f Author: tdreszer Date: Tue Jan 6 01:14:56 2009 +0000 Temporarily add NHEK to allow Tarjei's submission of Keratinocytes to work commit 1c377c08fcc2064ef2d66cdda29093c581a58792 Author: ann Date: Tue Jan 6 00:54:01 2009 +0000 fixed two broken links found by linkChecker. commit eff25efbaa1a0e51d70ff0e59975f0e2a39274d5 Author: kate Date: Tue Jan 6 00:22:10 2009 +0000 Suppress alignment display when conservation tracks are in dense or squish mode (alignments would be misleading when only the conservationis displayed) commit 4d8aba4798452c743af2b92877b7dd07d2380d97 Author: angie Date: Mon Jan 5 20:49:55 2009 +0000 Don't show xrefTable examples (by doing a join of xrefTable and curTable) if xrefTable has been selected as the curTable. commit 70dbdf19661fc3dfc7bbb490f0441ac13be86ff4 Author: larrym Date: Mon Jan 5 20:41:09 2009 +0000 change alignment details commit d25b7cbdf1189602cecc278526fb3b0d993991db Author: rhead Date: Mon Jan 5 20:18:35 2009 +0000 Fixed broken link to affymetrix transcriptome site. commit 7e63925047f343483e7fa3daf23cfd3699f6e4ee Author: aamp Date: Mon Jan 5 19:31:09 2009 +0000 Added a little bit about the next-item button setting nextItemButton off. commit cf6a754a276addb4abc533edd4306ff6928b886a Author: hiram Date: Mon Jan 5 18:59:21 2009 +0000 Updated with most conserved for 44 way and indicate gene annotation sources commit 81ed173f62f46e662764d831a9524930c88d8ee1 Author: galt Date: Mon Jan 5 16:00:07 2009 +0000 "Encode release log update" commit 4187c37977fef734ae4eb9698c1294d69d3ab739 Author: galt Date: Mon Jan 5 16:00:04 2009 +0000 "Release log update" commit 10f8a07a00bff0bf07669c661dfd0f90f3efbc3f Author: galt Date: Sun Jan 4 16:00:14 2009 +0000 "Encode release log update" commit 81d14e94a1620a49028610b805fc088cf7a7d92f Author: galt Date: Sun Jan 4 16:00:10 2009 +0000 "Release log update" commit 1f877e1faa3d4df99b74cdf023b1437f69270172 Author: kent Date: Sat Jan 3 21:14:58 2009 +0000 Starting to write up design. commit 368f01c2eed9f52589ee40751d60814c7a24524f Author: galt Date: Sat Jan 3 16:00:04 2009 +0000 "Encode release log update" commit a8cc5c05f3dee019a99feee959de3623429b8596 Author: galt Date: Sat Jan 3 16:00:02 2009 +0000 "Release log update" commit 391ca1b21ee403895f9c219b0fa4be502a2dcd7d Author: hiram Date: Sat Jan 3 00:21:16 2009 +0000 Finished with first pass on phastCons runs for 44-way conservation commit 2b24c839d0b6daf03ae7fe1c497250a681ebdb89 Author: hiram Date: Sat Jan 3 00:15:50 2009 +0000 turning on the phastCons tracks commit e0374a5bd92e595b2272617eef96701026ce9028 Author: tdreszer Date: Sat Jan 3 00:09:54 2009 +0000 Download directories are symlinked to /cluster/data/encode/pipeline/downloads commit bd771c7520e6ab1612aaa41e8c326de37f5452ca Author: tdreszer Date: Fri Jan 2 23:44:05 2009 +0000 Fixed minor bug with controlled vocabulary and allow view without dimensions commit d9428c28836d527e39da8acad48e9e7a78e4f16e Author: larrym Date: Fri Jan 2 19:56:51 2009 +0000 add a tooltip title to trackMap if dragZooming is on commit b443fb3aba4aa4a05e2efb87966f878ae6a0a455 Author: tdreszer Date: Fri Jan 2 18:01:30 2009 +0000 Turned nextItemButtonable off for composite but not subtracks. commit cc83a99fa102157023bea9d33ae5457be3dabd5c Author: galt Date: Fri Jan 2 16:00:06 2009 +0000 "Encode release log update" commit c14e0b67b09ff33211584f2afdc0b6d5eb869ca6 Author: galt Date: Fri Jan 2 16:00:03 2009 +0000 "Release log update" commit 77a06ab6b0978c13ffbf04998ce2f4c7f921db25 Author: galt Date: Thu Jan 1 16:00:07 2009 +0000 "Encode release log update" commit 4dab2ea1c48244cb3bdd3ae3250a78ecb4297528 Author: galt Date: Thu Jan 1 16:00:05 2009 +0000 "Release log update" commit e568ac0678cca7ba1954f6106c6c8fa0f5f9fdf6 Author: galt Date: Wed Dec 31 16:00:03 2008 +0000 "Encode release log update" commit 3172bc7f1f1069ae4d5a6a7348316b57521c638d Author: galt Date: Wed Dec 31 16:00:01 2008 +0000 "Release log update" commit a7fe37471092723f89ae88e573396d04080665e0 Author: larrym Date: Wed Dec 31 05:29:46 2008 +0000 yet more fixes for reverse display commit c1b860a99fc150cfce9af0edabfaa57904fdc6c6 Author: larrym Date: Wed Dec 31 04:12:36 2008 +0000 add back in local changes to version 0.6.2 commit 72448962b8ebadd847519d286a6fa8611fe39aaf Author: larrym Date: Wed Dec 31 04:11:27 2008 +0000 upgrade to version 0.6.2, which fixes problem where selection area was off if the user had scrolled down in the window commit dcd95055a7278ef89ced26062814d3e8e81c7345 Author: larrym Date: Tue Dec 30 20:22:24 2008 +0000 fix bug in drag selection when display is reversed commit 683e2d91fad733acd85100441845faaf03f6ec87 Author: larrym Date: Tue Dec 30 19:58:28 2008 +0000 use explicit dragSelectionEle.value test to correctly turn off dragZooming code commit bd1acfb85553cf314a38fa1edaae7a6ce97732e2 Author: galt Date: Tue Dec 30 16:00:08 2008 +0000 "Encode release log update" commit 5fc56a606cdd99bfb1d696e4aa1ecc5bfd35c3c0 Author: galt Date: Tue Dec 30 16:00:04 2008 +0000 "Release log update" commit 62fc14a0e57fd2decf6cabf53fd19949ecd51d0e Author: galt Date: Fri Dec 26 16:00:07 2008 +0000 "Encode release log update" commit 4b29b0ee88d42f08aef7ee4e8b133cd3213ba5be Author: galt Date: Fri Dec 26 16:00:04 2008 +0000 "Release log update" commit c7d617a88c0933fb09420524f96681db37f7580f Author: galt Date: Thu Dec 25 16:00:11 2008 +0000 "Encode release log update" commit 57bbe6870b31415938407bc1bab740f730e32c9f Author: galt Date: Thu Dec 25 16:00:08 2008 +0000 "Release log update" commit 04f7ae5bac01f539f6d2418714bbc3ac7e6077b1 Author: larrym Date: Wed Dec 24 18:27:09 2008 +0000 revert back to 1.344 to fix problems with tracks trying to use localDb profile commit 73fc4ca33a732f49c0d36a67aadab6a1bd4957da Author: galt Date: Wed Dec 24 16:00:03 2008 +0000 "Encode release log update" commit a9c7e13cdf7d6a3c5b9e5f047bce71e55d87cbbc Author: galt Date: Wed Dec 24 16:00:02 2008 +0000 "Release log update" commit 39b550622775582ecfc7521036fc8f50fec43983 Author: lslater Date: Wed Dec 24 15:15:45 2008 +0000 used in json test commit c0c0a484614552c957e1660f51e73cbe13576cbe Author: lslater Date: Wed Dec 24 15:13:55 2008 +0000 output from json test commit 387799bf5c1d2aebcfe1972198d7a4d13cfe052a Author: lslater Date: Wed Dec 24 15:12:49 2008 +0000 generated in json test commit 2ff0f939520d3fcd33e8404f06148b015288d544 Author: lslater Date: Wed Dec 24 15:10:27 2008 +0000 JSON output test code commit 2791cd3b903e9f00712cd1c8604b449e14fc5385 Author: lslater Date: Wed Dec 24 15:01:21 2008 +0000 Add JSON output tests to makefile. commit 8c08911514c7696719ac9f7e89fb5cd834d46072 Author: lslater Date: Wed Dec 24 14:59:43 2008 +0000 Add JSON output of object to autoSql. commit c34e4645920eeb630a63fbb915e0e9369069ba4f Author: jsanborn Date: Wed Dec 24 03:05:47 2008 +0000 cleaned up tcga trackdb files commit 03958d4b90b52fb5321d9ddc465cae072474ea59 Author: jsanborn Date: Wed Dec 24 02:25:56 2008 +0000 added maxItems 2000 to all entries to avoid compressing datasets and not allowing access to hgc page commit be7fd12cfd7d072347044852cfb8b906a0ccf200 Author: jsanborn Date: Wed Dec 24 02:21:22 2008 +0000 fixed bug with COSMICsummary commit a31de41c8cbab145384f0ddb2265362e878b4be5 Author: jsanborn Date: Wed Dec 24 02:05:41 2008 +0000 backing out change i committed accidentally commit 5b8b855f72a180dc6327db3bee9aa1582007f3cb Author: jsanborn Date: Wed Dec 24 02:04:29 2008 +0000 updated track db for genome-cancer server commit 6cb7b6fe8787bc6596aaffa983ea01121b399984 Author: fanhsu Date: Tue Dec 23 20:18:38 2008 +0000 Added logic to put in URL link to Subject View for cancerGenomics tracks. commit 5cef687daffd88e2b3d39862e15cbc0c90cbaa76 Author: galt Date: Tue Dec 23 16:00:06 2008 +0000 "Encode release log update" commit 4893d84c90e7976b6a1165be4e11547e580828a1 Author: galt Date: Tue Dec 23 16:00:03 2008 +0000 "Release log update" commit aa030be8fec18f86cc31fffdec27b444e04560aa Author: kate Date: Tue Dec 23 00:33:20 2008 +0000 Neutral tree models for 44-way multiple alignment commit daa7e5114914d72d682337b9dedc0f8c2a0f5d9a Author: fanhsu Date: Mon Dec 22 23:36:45 2008 +0000 Changed back the MAX_CONTROL_COLUMNS-1 to fixed number of columns (4) for GSID. commit 17ce14ef11739368a810fc08a652c74d2bd57b63 Author: rhead Date: Mon Dec 22 22:36:53 2008 +0000 Changed pust request slightly per Erich. commit 8c80ac42e837b6149d254fa0ad95094ce5b109f1 Author: angie Date: Mon Dec 22 22:23:22 2008 +0000 For pcrResults, lf->extra is non-null even when there is no symbolic name, because of the new coords. Watch out for non-null lf->extra with coords only. commit 71227ba486dd8670f4fdf8b6435b4e60c12671f8 Author: angie Date: Mon Dec 22 21:06:01 2008 +0000 Use the passed-in coords to test target-alignments, not just genomic. commit 9eee150a05a496c269b27b95a7e7a4607a8a2cbc Author: angie Date: Mon Dec 22 21:05:28 2008 +0000 For pcrResults on target sequences, the item name passed in from hgTracks now includes the start and end of amplicon within target sequence (|-separated). Pass those coords to pcrResultGetPsl to make sure we select the correct amplicon-PSL from the results file. commit 16024b0f753e3dd099eba7ab86c1b1e79d1f0325 Author: angie Date: Mon Dec 22 21:03:54 2008 +0000 For pcrResults on target sequences, add the start and end of amplicon within target sequence to lf->extra. The coords are used in cds.c and hgc.c to make sure we select the correct amplicon-PSL from the results file. commit 78b89a1f696c87c0335f06d743f2056acb32627f Author: larrym Date: Mon Dec 22 20:38:32 2008 +0000 alwasy include jquery.js commit 0195ba2796e8e001f584a350ddcc364d82d4d3a2 Author: aamp Date: Mon Dec 22 20:20:41 2008 +0000 Fixed up entry for Agilent probes... again. Made the identifiers fuzzy because no array is the full set of probe names, but they do share probes. commit a1af09271339b8455c915ee465da00e08d16feec Author: hiram Date: Mon Dec 22 19:13:23 2008 +0000 Avoid NULL reference to row[updateTimeIx] commit 3048c72d8760ea248c6064c9d087a8d71784c0df Author: galt Date: Mon Dec 22 16:00:03 2008 +0000 "Encode release log update" commit 582fb9d31c44d5fd8cdcd2a4c6d1468487a71615 Author: galt Date: Mon Dec 22 16:00:01 2008 +0000 "Release log update" commit 27b3b3d8919b75b8c1ba5c897b44e57bd8267a48 Author: jsanborn Date: Sun Dec 21 23:02:17 2008 +0000 updated genome-cancer track db commit 68825f2ac5bdd981d741a9ee9ea86ac4c77d37e5 Author: jsanborn Date: Sun Dec 21 22:59:57 2008 +0000 updated genome-cancer track db commit 4926ec4859dbccd7f2b6913e788bfa86e12b4c57 Author: jsanborn Date: Sun Dec 21 22:56:33 2008 +0000 updated genome-cancer track db commit 7367040b262e542e5460c0307cc243b8ee1a2511 Author: jsanborn Date: Sun Dec 21 22:31:41 2008 +0000 change from group x to group cancerGenomics commit f7de87c327b0fbc1787d0b7b01d700da783a46fe Author: galt Date: Sun Dec 21 16:00:04 2008 +0000 "Encode release log update" commit 92c762c2689a849a5bc9e3f96fb89935ba40f8ed Author: galt Date: Sun Dec 21 16:00:02 2008 +0000 "Release log update" commit fcc62ce732a8c927c2af90ebf2c36acb53dca04d Author: galt Date: Sat Dec 20 16:00:07 2008 +0000 "Encode release log update" commit e8f32b114bc902af7885548a113c2cf0b98bae51 Author: galt Date: Sat Dec 20 16:00:05 2008 +0000 "Release log update" commit b89bb16899f0e58346b0b737386eaf75b48800b8 Author: tdreszer Date: Sat Dec 20 01:08:06 2008 +0000 Minor edits recommended by Larry commit 800c5a6f55ece6ac65ca9e2b70c8440e7139ce8a Author: fanhsu Date: Fri Dec 19 23:55:15 2008 +0000 Added db info to link to PB. commit e948334e8f0f0bee6af1c0c85b48141660b4772f Author: larrym Date: Fri Dec 19 23:32:01 2008 +0000 use dragZooming config commit 14ce1fae0afbf0585d5192f669fb43ac3190f67c Author: larrym Date: Fri Dec 19 23:31:16 2008 +0000 add dragZooming config commit ca821d706bbaad02afdb220f5be3d7165b6fa491 Author: larrym Date: Fri Dec 19 22:58:39 2008 +0000 turn off DRAGSELECTION commit 9bafcbcaa8f4621d742b9a13db9c7210871e0d5d Author: hiram Date: Fri Dec 19 22:37:10 2008 +0000 Adding ctgPos2 track to indicate Ensembl scaffold names commit f9a1dc18036b68812f640ece58861249b3e732fa Author: rico Date: Fri Dec 19 21:25:40 2008 +0000 There was a bug when Scott Schwartz's blastz-run shell script was translated to perl. A copy of the original script can be found in /cluster/bin/scripts/blastz-run. Specifically, line 68: BLASTZ_M=${BLASTZ_M:+"m=$BLASTZ_M"} BLASTZ_M was used in blastz-run to set blastz's "m" parameter. The blastz-run-ucsc perl script uses BLASTZ_M to set blastz'z "M" parameter. This bug was uncovered while using the new "lastz" program to do genome-wide alignments. Essentially, the bug had us dynamically masking when the count reached 40,000,000 and using the default traceback of 80,000,000. My fix removes the default BLASTZ_M parameter from this script. We should be using (b)lastz's default of M=0. commit f2aec105b165686c8e0c4486102734948137846a Author: larrym Date: Fri Dec 19 21:18:26 2008 +0000 cleanup commit 8f82263f0c20b45d7e70dcc71bb191dd8e8e0e52 Author: larrym Date: Fri Dec 19 20:58:31 2008 +0000 use revCmplDisp to fix zooming when in reverse mode (still not quite accurate) commit 387407e9df8603e76d9c0fe89beab8be974c72bd Author: larrym Date: Fri Dec 19 20:14:18 2008 +0000 add hgt.revCmplDisp hidden variable commit 17c05ed4c9405d03d46147bef3ee5f226a68e653 Author: larrym Date: Fri Dec 19 19:43:50 2008 +0000 fix typos, minor word-smithing commit 6b740c6b13842fd71a95a02bd03e59f0855f454f Author: donnak Date: Fri Dec 19 19:25:47 2008 +0000 *** empty log message *** commit efdfd4d267bdda53250049935e2797ddf2e53082 Author: galt Date: Fri Dec 19 16:00:05 2008 +0000 "Encode release log update" commit d9ab7c10985724eaf949f0b2c3a9eb944dcc3da9 Author: galt Date: Fri Dec 19 16:00:03 2008 +0000 "Release log update" commit 024854504cd6c81b71d75679c8b02360fd194308 Author: markd Date: Fri Dec 19 09:11:46 2008 +0000 fixed score on bedGraph; did some refactoring commit 7682efd48a737133f047ade5b4679d27ba351fbe Author: larrym Date: Fri Dec 19 08:54:39 2008 +0000 revert to version 1.2 (imgareaselect version 0.5) because newer version broke single-click functionality commit cc525a024851900a5fc1ad4c953d04115fe493a2 Author: larrym Date: Fri Dec 19 08:39:54 2008 +0000 restor initial position and size if user cancels commit 0f41d683d9eb5151d93c47e049a7da9681b47496 Author: larrym Date: Fri Dec 19 08:37:16 2008 +0000 another mistake commit 558fa947ad53f215eacbe19d098a8f335beb232a Author: larrym Date: Fri Dec 19 08:34:54 2008 +0000 add my local changes to version 0.6.1 commit 8b121188796ca6978bf56405776d1a2f467bec78 Author: larrym Date: Fri Dec 19 08:32:35 2008 +0000 upgrade to version 0.6.1 commit b048eef703ac0ad672116e573dd69e96751145a0 Author: hiram Date: Fri Dec 19 07:14:07 2008 +0000 Setting default display width of 800 and 6 columns of control buttons commit cdb936506fae6d4c1f0ba9ba909fa2f7506601b1 Author: larrym Date: Fri Dec 19 06:02:02 2008 +0000 fix typo commit c9d10d86f025da5f0a2d3103e9c17cc34008fc1e Author: larrym Date: Fri Dec 19 05:51:16 2008 +0000 add drag-selection code and setAllTrackGroupVisibility commit b37fa7d8eb980ad6ad882d4755bc3c8835e2c530 Author: larrym Date: Fri Dec 19 05:50:37 2008 +0000 add drag selection code; can be turned off via DRAGSELECTION commit d30b482a0d5bd0b8d72d749f5d3aba58c8020c50 Author: larrym Date: Fri Dec 19 05:44:53 2008 +0000 show the default "Your browser does not support JavaScript..." message only once commit cf5e502f060a482a36dd645cbb499c2c4fd94304 Author: galt Date: Fri Dec 19 01:54:04 2008 +0000 fixing path so it can be used by both releaseLog.html and the encode releaseLog.html commit 70ab44ed01ef67d5141c90c9fce1f083d74fcb92 Author: markd Date: Thu Dec 18 23:48:36 2008 +0000 added ignore entry commit 5b4ab135fb6ae56f9f40e097ab71add7747f2b24 Author: larrym Date: Thu Dec 18 22:23:25 2008 +0000 add jquery.imgareaselect.js commit 75d0458fad9fb93f77af9ab1858565636151d055 Author: larrym Date: Thu Dec 18 22:22:59 2008 +0000 my diffs to version 0.5 commit c0f85ee4d499298467b754f5778f39e1ec8c0782 Author: larrym Date: Thu Dec 18 22:22:23 2008 +0000 original version 0.5 from http://odyniec.net/projects/imgareaselect commit ed29072c918bb3532477304485dbd3a1c600e886 Author: larrym Date: Thu Dec 18 22:13:22 2008 +0000 version 0.5 from http://odyniec.net/projects/imgareaselect commit 475074d25a79f2b228268696caf7c2be965d2d9a Author: larrym Date: Thu Dec 18 22:12:37 2008 +0000 inadverdantly checked in file with version number commit 60d18ba69f46e05c33dcdc15765b17454f0686a2 Author: larrym Date: Thu Dec 18 22:10:11 2008 +0000 original from http://odyniec.net/projects/imgareaselect commit 2d2d9f1d17a242ee3f5c6727026059a67c94e629 Author: fanhsu Date: Thu Dec 18 20:23:08 2008 +0000 Updated one record in omimGene table to reflect correction UniProt is going to make. commit 562a54e7d1b200b1e4f95f857d7efdff3260309a Author: galt Date: Thu Dec 18 16:00:06 2008 +0000 "Encode release log update" commit 58db65bd0e4575be66af0f721b4e38e7a0544983 Author: galt Date: Thu Dec 18 16:00:03 2008 +0000 "Release log update" commit da7a2bc246a3940a216d4ec2cdacb7c9ce545cc7 Author: larrym Date: Thu Dec 18 05:54:58 2008 +0000 add hButtonWithOnClick commit 36dab41df681b059933a50d238df1571dbb7dc68 Author: larrym Date: Thu Dec 18 05:53:24 2008 +0000 add cgiMakeButtonWithOnClick commit a6296813ceecaed8c8e9716e8c96bc235c1a46ad Author: aamp Date: Wed Dec 17 22:59:17 2008 +0000 Lifting Affy Mouse Exon probeset to mm9. commit 7c298a657130c602b168e7cf3e3eea5adceed771 Author: angie Date: Wed Dec 17 21:45:42 2008 +0000 Added set and clear buttons in snp125OfferGeneTracksForFunction. commit 4a15bf26558873cfac2f0263544ee49846ae0e63 Author: angie Date: Wed Dec 17 21:44:33 2008 +0000 Added jsMakeCheckboxGroupSetClearButton. Also, in jsMakeSetClearButton, use precomputed vertPosJs instead of always using jsSetVerticalPosition() so that the currentPos input is used correctly. commit e4eb5108f60e3f6a2cfad79623f80635c650015c Author: markd Date: Wed Dec 17 21:36:31 2008 +0000 output more information and make output easier to parse commit c5851673be0a541e06fb457b8a57bc47309b9ae7 Author: giardine Date: Wed Dec 17 20:01:17 2008 +0000 fixed order of lines commit 30303a0bf863e0100dd8420b73dc22b595c03112 Author: angie Date: Wed Dec 17 18:02:24 2008 +0000 Fixed off-by-one error in printSnp125NearGenes (thanks Brooke). commit c52a84e24805e98966e7b829aaf52ceb7f569a38 Author: braney Date: Wed Dec 17 17:34:27 2008 +0000 added chains and nets to Wallaby commit cb4b28e48fb484826e450be91293a1ece75350d8 Author: galt Date: Wed Dec 17 16:00:06 2008 +0000 "Encode release log update" commit 5ce9fe604161e9f5bdca52abb0e382712a5daa1e Author: galt Date: Wed Dec 17 16:00:03 2008 +0000 "Release log update" commit 4e765c2619836bb0c0a50adf7abd7a4af4960174 Author: mikep Date: Wed Dec 17 15:49:03 2008 +0000 new localizations for Encode commit d27163c20589a2a63848d0cb3edb87aa6e74afd2 Author: fanhsu Date: Wed Dec 17 14:46:39 2008 +0000 Changed omimGene search to bed. commit 02959ddaea383995cff96973e5edc308ac002874 Author: mikep Date: Wed Dec 17 10:40:04 2008 +0000 dont limit tagAlign records for Cshl project for now commit 01889d955cb30e0cc3907cc23192d2d4714463c1 Author: mikep Date: Wed Dec 17 10:24:40 2008 +0000 missing closing bracket commit 8843c77ea8a4938a8d0de67ef68937b15937d8bc Author: mikep Date: Wed Dec 17 10:16:39 2008 +0000 dont load CSHL alignments yet - too large commit 5a24124f0ab944e3876c6fce7407654ebcf20761 Author: mikep Date: Wed Dec 17 08:17:54 2008 +0000 adding the number of lines to timing commit 60a0425d5275b45c448ab8c0de7864f3a1e41ab4 Author: mikep Date: Wed Dec 17 08:10:16 2008 +0000 setting a maximum number of rows allowed ; CSHL RNA Seq had 464M in one file due to repeat expansion problem commit 8fee97ebb08a685dffde2f74ce057e7c8825b313 Author: mikep Date: Wed Dec 17 07:56:28 2008 +0000 adding some more timing and tracing output commit cb2eb45021ec34f9241617a66c62b46f9a231220 Author: larrym Date: Wed Dec 17 00:28:44 2008 +0000 refactor a bunch of code into validateWithList; speedup validateGappedPeak and validatePairedTagAlign commit 279c03606442ae5bf65d59e9eba3e43e6fff613b Author: larrym Date: Tue Dec 16 23:35:04 2008 +0000 add listToRegExp to speedup file validation commit c411824f2ceee9d7c536fb09a9e7adbfc0f0f716 Author: fanhsu Date: Tue Dec 16 22:21:32 2008 +0000 Added buttons for users to select omimGene gene label. commit ef90876fcc056fee11c3b5d6b88bcf515a4cec52 Author: fanhsu Date: Tue Dec 16 22:18:37 2008 +0000 Updated default color and gene label logic for omimGene track. commit 8553b987d93973c81b01677161b4e062880ebfd5 Author: fanhsu Date: Tue Dec 16 22:14:37 2008 +0000 Changed default color of omimGene to darker blue. commit 2df81da8d0eebb1819c8bf6222b994733d02283f Author: rhead Date: Tue Dec 16 21:17:06 2008 +0000 Consolidated the omimGene blocks to the human level. Kept the bed 4 type instead of genePred type. Kept Bob's new url. commit 69dd660e4d8e96eeb07551deadb60969bfdc2110 Author: donnak Date: Tue Dec 16 21:03:25 2008 +0000 Added Jakob's mirror to list. commit 5556eb42bd319ee251c991d147452ac00b1aa36b Author: ann Date: Tue Dec 16 17:55:17 2008 +0000 further removal of superfamily tables from rules and dependencies commit a868052c97db4e6dcad4bb38313f0ee41b49c516 Author: ann Date: Tue Dec 16 17:51:50 2008 +0000 removed instances of checks for superfamily-like tables. these tables are no longer maintained. commit 1f4ad68e6a7645bd5888efdbfd2c74a4d140002c Author: mikep Date: Tue Dec 16 16:30:36 2008 +0000 v197 commit d13e4acaed6108556896d0d180a7bfe12eb5d7c7 Author: kuhn Date: Tue Dec 16 16:20:24 2008 +0000 backed out change. something broke commit cc58cfc77536d72a09c10e15411e0edbd85844ff Author: galt Date: Tue Dec 16 16:00:13 2008 +0000 "Encode release log update" commit bf6a476c14e8cbf96e2470e0a6dee0f46c68d27e Author: galt Date: Tue Dec 16 16:00:11 2008 +0000 "Release log update" commit 0452f20ddf401ea189b503db0fe28f08c94d472e Author: kuhn Date: Tue Dec 16 15:49:26 2008 +0000 tweaked human omimGene url commit 0aef35fe7cdc47709c70fc539e46dd686ffd9f3e Author: kuhn Date: Tue Dec 16 15:45:20 2008 +0000 dropped hg18-level block for omimGene commit 91fe3604e36aefaeef4f5aeb572bdf830250080f Author: mikep Date: Tue Dec 16 15:20:45 2008 +0000 "New version number v197" commit c76534b0af20bdd5aa2ba49fe64581f4c57a69c5 Author: kuhn Date: Tue Dec 16 09:00:08 2008 +0000 added chrom limitation to omicia track commit 4bd73b6feb9f44f87f03189a7693d25f79077bff Author: larrym Date: Tue Dec 16 01:33:50 2008 +0000 optimization: move @list out of while loops commit a1ca9526dcf8529749be27d6032b545c1b5728db Author: ann Date: Mon Dec 15 23:45:30 2008 +0000 loosened up refSeqId rule check for older human assemblies as they are drifting a bit commit 456c66f6f08d9145a715c4484c10f4a36c5982ac Author: tdreszer Date: Mon Dec 15 23:17:45 2008 +0000 wigMaf visibility problem addressed in -r1.136/1.137 left bug for multi-wiggle wigMafs commit 3df664729ff6009db46a71f541b863e53f384d55 Author: aamp Date: Mon Dec 15 22:45:51 2008 +0000 Added monDom5 commit f9a3ef43c1145bd35bbc04c046271f19208e8dff Author: fanhsu Date: Mon Dec 15 22:15:56 2008 +0000 Added morbidmap info. commit 5c9c69d505bb777bc28c230d43a342116a3bb768 Author: fanhsu Date: Mon Dec 15 22:10:38 2008 +0000 Updated details page for omimGene to include info from oimiMorbidMap table. commit 515653596496d762c3af6b2fc14221aecd0ad671 Author: ann Date: Mon Dec 15 21:05:45 2008 +0000 corrected, based on MPO website commit 20e676d417894b2251ae17f21d1519576a46223a Author: fanhsu Date: Mon Dec 15 20:16:01 2008 +0000 Added omimMorbidMap table for omimGene. commit d66e176e6f0b78dd59075baf99cde42fe75c17b9 Author: fanhsu Date: Mon Dec 15 20:09:53 2008 +0000 Added omimGene methods for color and display name. commit 2d3c3f55566839793ba2a21616a5502f8cddb71e Author: markd Date: Mon Dec 15 19:45:49 2008 +0000 fixed memory corruption problems with var args commit 6d8224300117dffee105dc1016e2e0388abfeea7 Author: donnak Date: Mon Dec 15 19:06:49 2008 +0000 Added phrase abt healthy individuals, per Jim. commit 11a0cb6afd172168b088cddd03382b07e9981b90 Author: fanhsu Date: Mon Dec 15 19:00:55 2008 +0000 Created omimMorbidMap.as. commit 6926854ad3fc92af5dd3e582a64c9e0dff03ca8b Author: markd Date: Mon Dec 15 17:43:01 2008 +0000 added program to compute distribution of query to target mappings in chains commit 996d4ccf6b3e37e59eab77608c5508e2ce010c9f Author: galt Date: Mon Dec 15 16:00:04 2008 +0000 "Encode release log update" commit 797e2bf697bdb7b1ca3c4a83bc79f341edca32ab Author: galt Date: Mon Dec 15 16:00:02 2008 +0000 "Release log update" commit 5809967e693212b4168267b797cb4bd0c59d0edf Author: galt Date: Sun Dec 14 16:00:07 2008 +0000 "Encode release log update" commit 634c8af1932b0e816ffe976987d6d07c9b7eee1b Author: galt Date: Sun Dec 14 16:00:04 2008 +0000 "Release log update" commit 01ad6cc3f14669de747dc00d074f8de65f212268 Author: cszeto Date: Sun Dec 14 04:48:53 2008 +0000 Added a summary COSMIC dataset commit 50877d07984dd82cd21c229b0545cceb284ac831 Author: fanhsu Date: Sat Dec 13 19:28:06 2008 +0000 Updated the URL link to "HIV sequence database" in the Credit section. commit 6fbd2c1bb5f6e9b02745fe8f4482340a8aaf109c Author: fanhsu Date: Sat Dec 13 19:09:26 2008 +0000 Use gcc34 instead of gcc to avoid openssl compatibility issue. commit bf874da04de4d4127b264e0aa4ccb19f55847758 Author: galt Date: Sat Dec 13 16:00:08 2008 +0000 "Encode release log update" commit b874f4df5b0733e77ca3082dedcd05a6894b2b7f Author: galt Date: Sat Dec 13 16:00:05 2008 +0000 "Release log update" commit 46f9fab08d3e0b1105598af61dff98767fd4c423 Author: larrym Date: Sat Dec 13 02:17:15 2008 +0000 add info about number of CpG sites assayed (from Illumina product literatur) commit 8429e13f9d3d9e08211e4a3cb030b792b364713c Author: mikep Date: Sat Dec 13 01:03:06 2008 +0000 make error message more accurate commit 8904d97b86876c3bb63e6081ba890aee019f9e72 Author: mikep Date: Sat Dec 13 00:41:03 2008 +0000 use validateWithList for validateGappedPeak, and added filter for track lines in bedGraph uploads commit de4db8dcd1efa22d06c6f31d976a51c99dbe32af Author: ann Date: Sat Dec 13 00:16:44 2008 +0000 leading users to the contacts page (instead of the direct ML address) so they will have a greater chance of seeing the disclaimers and other ways to search commit 3fd9e36826904ceaa994a890d426883d63b30836 Author: ann Date: Fri Dec 12 22:41:29 2008 +0000 needed to ssh to hgwdev when the script is being run from hgwbeta (which it is when it is called from joinerBatchKeys) commit 2f54072e58bb48dc144b872c0ef5781619b496c1 Author: aamp Date: Fri Dec 12 20:12:48 2008 +0000 Added tables into tablesIgnored that were previously IDs commit 2c5f7f942c7685733dd196759f8b021e40e13d4e Author: pauline Date: Fri Dec 12 19:24:08 2008 +0000 Replaced '+' with 'over' to make entries consistent. commit e0c646256b7b5a45e4e5a2fa93319ca0efb9063c Author: donnak Date: Fri Dec 12 19:14:20 2008 +0000 Edited description to make it less market-speakish. commit 0a7611388c6a48fe044803c16a6c5d3783e84a34 Author: ann Date: Fri Dec 12 18:50:13 2008 +0000 added mm6 and hg17 chain/net to this level (because this assembly still uses them) commit df553596db20fe4b0b856215c5d8a58340846de0 Author: ann Date: Fri Dec 12 18:39:57 2008 +0000 fixed old error of o_db vs database name in mm6 and hg17 chains/nets commit ed08533a5bcd706b3976748cd26b5baec3f5de4f Author: galt Date: Fri Dec 12 16:00:08 2008 +0000 "Encode release log update" commit ec680f50cbdc659cfc1db6473ed47873b2df1162 Author: galt Date: Fri Dec 12 16:00:05 2008 +0000 "Release log update" commit 4fbeebb47fde79a067378181dae746b41246fb19 Author: cszeto Date: Fri Dec 12 08:31:08 2008 +0000 Added COSMIC datasets commit 5a541c595caef009955c357ac9ab0236027373d4 Author: mikep Date: Fri Dec 12 06:06:55 2008 +0000 adding 'spanList first' trackDb option which will query the first span value from the wiggle track commit bd3466dddd1270d510cd0a249b699390aa8ca620 Author: mikep Date: Fri Dec 12 05:24:55 2008 +0000 committed this in error commit 18ed50960d9ce984fde3e81102b3c1d19c4018d2 Author: aamp Date: Fri Dec 12 00:49:52 2008 +0000 Removed score filter on Agilent tracks (they're all 1000 anyways). commit 2c2831f7847c00edc4cfba97b8f494de559fc6b4 Author: aamp Date: Fri Dec 12 00:13:44 2008 +0000 Fixed some stuff for the Agilent probes track. commit 1963ea0af5a7b9fd699d5ada509abe54e9ad3268 Author: hiram Date: Thu Dec 11 23:50:05 2008 +0000 removed make of fixcr, better version is in ../utils/fixCr commit 2b312ef741591b72ac3b1a820ac4d0513a9fba43 Author: hiram Date: Thu Dec 11 23:47:35 2008 +0000 better more up to date version is in ../../utils/fixCr commit f86ffd5c810ad8a45fe41c97b8fb762d709968cd Author: hiram Date: Thu Dec 11 23:32:26 2008 +0000 fixup for compile on sparc solaris commit 97ead0c0f56f456abc10f5860373670901ab459c Author: hiram Date: Thu Dec 11 23:27:11 2008 +0000 fixup for compile on sparc commit 17f7e37c125e95e67f33f0cff6dd6305db742b33 Author: hiram Date: Thu Dec 11 23:24:07 2008 +0000 fixup for compile on Mac OS commit 959c994f36c3e61a69e8a3c82599c898bd839747 Author: hiram Date: Thu Dec 11 23:14:50 2008 +0000 Fixup for compile on sparc commit 1f4e79a539f9fa83aad968a4d9e3b3d026ad2b0c Author: kuhn Date: Thu Dec 11 23:09:48 2008 +0000 made full version - other one was just a corner commit c77670963ad60c2f5eac9bad2fa3e22361f20441 Author: kuhn Date: Thu Dec 11 23:06:52 2008 +0000 schema for knownGene commit 7aee8d8901f394422461bd3d207e6b4e01987f9f Author: hiram Date: Thu Dec 11 23:02:10 2008 +0000 fixup for compile on sparc commit d74c96a3ee4ed047ede0d2c8473e22ca4362949c Author: fanhsu Date: Thu Dec 11 23:01:45 2008 +0000 Changed grp x into grp cancerGenomics. commit 8a9bb2f4719bd838f8d7503999da63fe6dd4ee4c Author: ann Date: Thu Dec 11 22:54:00 2008 +0000 new script added: copyExtSeqRows.csh commit ed14ffcbb16606d8ab32a9afdb71a1b17d404afd Author: ann Date: Thu Dec 11 22:52:59 2008 +0000 this script copies rows from seq and extFile tables on hgwdev to hgwbeta commit 471cd1f9e2283106db3337bcdbf51346a6e764ad Author: hiram Date: Thu Dec 11 22:48:19 2008 +0000 fixup compile on sparc commit 25e9122e1345e82c061007bb301650eb519ca061 Author: hiram Date: Thu Dec 11 22:41:56 2008 +0000 Fixup for compile on the Mac commit 6fe7654bbf6107b549c1b55e255c5828f0aabf27 Author: aamp Date: Thu Dec 11 22:39:28 2008 +0000 Added latest opossum. commit ce3303e164a40fa23dda3ca85ff52bdb78dc9523 Author: hiram Date: Thu Dec 11 22:35:12 2008 +0000 Get the mmap business to compile OK on sparc commit 04e3be52a84f6e15e80e152f279868fd937dad31 Author: larrym Date: Thu Dec 11 20:22:03 2008 +0000 spanList first => spanList 1 commit 4b505987f8f7f3a5d6fc6ef649bb6436076307fe Author: larrym Date: Thu Dec 11 20:01:59 2008 +0000 TAF-II in GM12878 and K562 commit 334cb7104543f0d332720af9ac69ee7e75feddfe Author: larrym Date: Thu Dec 11 19:42:05 2008 +0000 cleanup (delete span's, fix links) commit 16016f0ab417e4b4d7e1ae4935d8fa9365aa0bc0 Author: fanhsu Date: Thu Dec 11 17:53:02 2008 +0000 Updated omimGene section to accomodate change from genePred to bed 4. commit c55f7056148a44b60309e6b367c71bb85e2cfe73 Author: fanhsu Date: Thu Dec 11 17:49:50 2008 +0000 Updated processing of omimGene because we changed from genePred to bed 4. commit e065e10e0bc289c0e528c4f19e3eb37817ee96ff Author: fanhsu Date: Thu Dec 11 17:48:42 2008 +0000 Added omimGene. commit 86d8b90ea54b6d8963b8d4a0cfde233a23081c7c Author: fanhsu Date: Thu Dec 11 17:09:27 2008 +0000 Created omimToKnownCanonical.sql. commit 6e9614303c1ffe75a3229a561ba84bd392cc8720 Author: ann Date: Thu Dec 11 16:58:16 2008 +0000 added information about using the new copyExtSeqRows.csh script commit b157c758c84afea4527b28f9ceffe41c3f03a915 Author: galt Date: Thu Dec 11 16:00:17 2008 +0000 "Encode release log update" commit 38eeb750e5b0cb8d0610d0303d4813c226e8830c Author: galt Date: Thu Dec 11 16:00:15 2008 +0000 "Release log update" commit 42ffe3ba7f020b1df59a9ca135ca4c3b21b3bc5e Author: aamp Date: Thu Dec 11 00:07:21 2008 +0000 Fixed custom-track error message bug. commit 2742045268c50e621a6cb18fbe4cf268cb1d2c4b Author: larrym Date: Wed Dec 10 22:06:07 2008 +0000 add %chromInfo and use it to validate chrom's based on assembly's chromInfo table commit 53e35f2646116e0a8a72c72cdcfd0fae52a7aaae Author: larrym Date: Wed Dec 10 21:58:35 2008 +0000 add getChromInfo commit 5714f2fc6c57056c67a2c655493ab68c0b836cbb Author: ann Date: Wed Dec 10 21:01:13 2008 +0000 new rule for transMap UcscGenes to the other org commit 55f269ad94ff34ccf00312684d561e3eb45bfd15 Author: mikep Date: Wed Dec 10 19:48:16 2008 +0000 encode wiggle tracks allow only 1 span commit c9cbadf348d7037cac50d114c7fe2b40f66de0f8 Author: hiram Date: Wed Dec 10 19:07:23 2008 +0000 HOST env variable not always present commit a8711db9db783cf852a4f4bfc56042973939b8c9 Author: angie Date: Wed Dec 10 19:05:16 2008 +0000 In cgiMakeCheckboxGroupWithVals, added quotes around the checkbox values in case they're needed in the future. commit e1f3c7d68bb524d3de2e48baa5e5eb558f2aa2cc Author: angie Date: Wed Dec 10 19:02:53 2008 +0000 Fix for empty multlists: don't put a NULL entry in the cart because it will be saved as "" and then the next CGI will see a list length 1, value "". commit 30b83e41ce42d1b1f3eff052df8c8dd10bbef6ce Author: giardine Date: Wed Dec 10 18:34:08 2008 +0000 added link from UniProt variants back to the UniProt database commit b48664746e545486ce8f81ad2e2453c5feb75158 Author: ann Date: Wed Dec 10 18:00:58 2008 +0000 added rules to connect more transMap tables commit 01fe490cf45f35f2c99d7a31b96f3580a1b5be91 Author: angie Date: Wed Dec 10 17:51:39 2008 +0000 Added cgiMakeCheckboxGroupWithVals. commit 30d2ddf8ded3fe2bd7bc629f67f46603ec6594a6 Author: angie Date: Wed Dec 10 17:46:33 2008 +0000 Added snp125OfferGeneTracksForFunction. commit 3d52b2c99f33e3e83e338a0225752ed1177a4016 Author: angie Date: Wed Dec 10 17:46:00 2008 +0000 In getGPsWithFrames, load genePred (no Ext) tables correctly. commit 237fa2e8bdd9901a2e1bb27c4a9bb2b70ad0d373 Author: galt Date: Wed Dec 10 16:00:09 2008 +0000 "Encode release log update" commit 37dbea3e8b56f8c1804ea9c763e3351634b1d12a Author: galt Date: Wed Dec 10 16:00:06 2008 +0000 "Release log update" commit 9e03956b338ec0bf0c4d0702a7a00e07bb708de7 Author: kuhn Date: Wed Dec 10 02:31:09 2008 +0000 removed block that's breaking dev and added a huphen to longLable for omimGene track commit 84ecceebaa2c93becbb823fb69c433c734f1ec6b Author: aamp Date: Wed Dec 10 02:08:01 2008 +0000 Colors for Agilent probesets changed to alternate. commit 58cf526a1ae3b39955a26cf95e220590dda310f0 Author: aamp Date: Wed Dec 10 01:43:53 2008 +0000 Added Agilent CGH Probe IDs and updated entries. commit 7eb38fffdd73f0257b2bfec3b9d89839e278a7a4 Author: rhead Date: Wed Dec 10 01:02:48 2008 +0000 Changed wording in methods section, fixed broken link, tweaked references. commit 9c4768f4bb8f4158333cecf852672da1e6844056 Author: hiram Date: Wed Dec 10 00:51:44 2008 +0000 44-way Frames annotation done commit 564eb7b252455b0623337b1cb9d06b80999e27d9 Author: aamp Date: Wed Dec 10 00:39:29 2008 +0000 captialized a word. commit 5d219b6b1c19ac5054c70a5f9c0c0f5382cdbe1c Author: aamp Date: Wed Dec 10 00:23:28 2008 +0000 Added more Agilent CGH arrays (SurePrint G3). commit e001e040c1610763298a84547c6b1c3918860e4d Author: fanhsu Date: Tue Dec 9 23:23:25 2008 +0000 Added subject link per Ann's suggestion. commit 8f190348584c6dab5d8e4786187c032fe0caa886 Author: hiram Date: Tue Dec 9 22:45:05 2008 +0000 Turn on Frames for 44-way commit fe26a1759f7f61ee0396574eed86500980d7ee96 Author: rhead Date: Tue Dec 9 22:18:54 2008 +0000 Fleshed out description with text from most recent NAR Genome Browser update paper. commit 365d3cbdbdc73fbab9376bc5e4652a66b9fc0895 Author: ann Date: Tue Dec 9 21:44:00 2008 +0000 added checks for hg16 and hg18 for existing cgapAlias rule commit e3076180f84f22ae856e45be0424de2bd2928572 Author: ann Date: Tue Dec 9 18:13:28 2008 +0000 removed all instances of oryLat1 except for chainDest (still chained to danrer4) commit 065a2c8160accf9687eec06b8db4e74f13174893 Author: donnak Date: Tue Dec 9 18:07:25 2008 +0000 Added a credits section. commit 1f02121058c86eeddd74eb11bafea49ae7abd8d0 Author: ann Date: Tue Dec 9 18:04:00 2008 +0000 alphabetized list of orgs commit 7adba87717251ae3c05412390d8ce35579a93919 Author: ann Date: Tue Dec 9 17:36:20 2008 +0000 removed all instances of mm6 except for chainDest (still chained to canFam1, hg16, monDom1) commit 50c2d7d989651323a4fbf6049dbfc0e0916454e2 Author: ann Date: Tue Dec 9 17:11:25 2008 +0000 removed all instances of mm5 (it is archived and not involved in any rules) commit c1ffa037367239cabb2bdd66d12fad85bf2dee5f Author: mikep Date: Tue Dec 9 17:11:20 2008 +0000 Wold lab commit 91a01dbefe04b2470a5b88ce3037ae0f8a0be62e Author: ann Date: Tue Dec 9 17:00:06 2008 +0000 removed all instances of danRer2 except for chainDest (still chained to galGal2, monDom1) commit 1a9fadf0b297c856261ea6c04ee27c866432579a Author: ann Date: Tue Dec 9 16:56:19 2008 +0000 removed all instances of rheMac1 except for chainDest (still chained to mm7) commit 1f90dc57da6cf0c5ace2d69f1b215187573b7387 Author: mikep Date: Tue Dec 9 16:47:53 2008 +0000 map algorihtm used by Wold, in addition to other RNA project stuff commit 0685aec0fd39bb6b761cc875174dd9937e6bda16 Author: mikep Date: Tue Dec 9 16:23:33 2008 +0000 additional vocab for Wold lab commit 2815af0b5c6f3186d9716cb13382d7bec442a7b2 Author: mikep Date: Tue Dec 9 16:20:06 2008 +0000 wrong version of blat for Wold lab commit f44b9a50556dec5c166f296ecc77a5cf0aa9b6d2 Author: mikep Date: Tue Dec 9 16:15:29 2008 +0000 first version of wold lab data commit dd923a316065a30b13fec263586c91115278b4ab Author: galt Date: Tue Dec 9 16:00:07 2008 +0000 "Encode release log update" commit 09f7ee53451b1e77818ec40fbcb2b6f46f5974a5 Author: galt Date: Tue Dec 9 16:00:05 2008 +0000 "Release log update" commit 9f320eac48e489eeab9883f8f8aa3b84c9788007 Author: mikep Date: Tue Dec 9 14:54:14 2008 +0000 I think the default is mean commit 8de7a3a0dc49988d879876f386f55d14fb39abc9 Author: mikep Date: Tue Dec 9 14:42:32 2008 +0000 fixups for UwDnaseSeq commit 3077b17cf56bb10ce11295948bca419c54f6007e Author: mikep Date: Tue Dec 9 12:39:06 2008 +0000 defaulting configurable=on for RawSignal commit 039d526b79ba2ee58f25351abf78e63e5e76b35e Author: galt Date: Tue Dec 9 08:11:46 2008 +0000 fixing minScore commit b88f9208a2fedc8021cbd0b6f12bcfa236619cc3 Author: angie Date: Tue Dec 9 07:28:24 2008 +0000 Added scoreMin and a couple other tweaks to wgEncodeUwDnaseSeq for the new track_minGrayLevel cart setting in hgTrackUi. commit daa0b630fe46ea16b3206c3303af215ff3bbb39f Author: angie Date: Tue Dec 9 07:18:28 2008 +0000 Tweaks to scoreGrayLevelCfgUi, scoreCfgUi and the bed clause of specificUi to support track_minGrayLevel settings for composite tracks and ENCODE peak tracks. -- about the bed clause of specificUi, why does it apply only if wordCount is 3 (not 2 or 3)? We ignore the 3rd word and don't always include it in .ra. commit 842a8a09e11184304b994fe5a553a57d806b561b Author: angie Date: Tue Dec 9 07:13:42 2008 +0000 Added adjustBedScoreGrayLevel, for use with the new track_minGrayLevel tdb setting. Apply it to bed tracks and ENCODE peak tracks. commit e6a70be24aacc86ee099b6712f3f437ede9cec61 Author: mikep Date: Tue Dec 9 02:05:01 2008 +0000 give the configure power to the people commit 374bffcfb528caa14f7aa00fb1e3cb06941f46d1 Author: mikep Date: Tue Dec 9 02:01:31 2008 +0000 fixed up spanList=20 again commit 54ec3e32f66148a5b05b8b30963d30e39800693b Author: tdreszer Date: Tue Dec 9 01:49:19 2008 +0000 Changed some naming for Yale and Broad commit 7271a3ff89d00f452158039e92d164306c1819d8 Author: mikep Date: Tue Dec 9 00:55:43 2008 +0000 reloading peaks and hotspots for replicates commit e1d23f31d772e0597544d9ae8ed6d4a08c682862 Author: ann Date: Tue Dec 9 00:45:00 2008 +0000 removed all instances of danRer1 except for chainDest (still chained to xenTro1) commit 19b842c967a327200d97477585522efb5d2c5944 Author: angie Date: Tue Dec 9 00:41:20 2008 +0000 Trim leading and trailing whitespace from varName -- tired of being foiled by extra whitespace from FireFox copy. commit f19cc6aeef69f993ef9f6f6927d7176f681d3625 Author: ann Date: Tue Dec 9 00:36:39 2008 +0000 removed all instances of ce1 (it is archived and not involved in any rules) commit 84e47a9b810be23225e42e360770b59b0ae96df0 Author: ann Date: Tue Dec 9 00:27:15 2008 +0000 removed all instances of mm3 (it is archived and not involved in any rules) commit 6341d51ce517467af85fd2f79e9664ed3afcdcff Author: ann Date: Tue Dec 9 00:15:36 2008 +0000 removed all instances of hg15 (it is archived and not involved in any rules) commit 27af854fe0be7b004ef7760de72345d851f155c9 Author: ann Date: Tue Dec 9 00:10:46 2008 +0000 removed all instances of mm4 (it is archived and not involved in any rules) commit 85ed7e229a92eacbab025e183e1415f42b5c0e15 Author: ann Date: Tue Dec 9 00:08:24 2008 +0000 removed all instances of rn2 (it is archived and not involved in any rules) commit 8f046f8a6a105b52bd4400e160c9c2b7f0eb168e Author: ann Date: Tue Dec 9 00:04:35 2008 +0000 removed all instances of bosTau1 (it is archived and not involved in any rules) commit 13020c12d3580729648c77992aee3cbd3077a5e3 Author: ann Date: Mon Dec 8 23:59:07 2008 +0000 removed these archived assemblies from the chainDest group (as they no longer have chains or nets from other assemblies to them): Hg15,Pt0,Mm2,Mm3,Mm4,Rn2,Ce1 commit 71f8a84fac3e2bd6e31e070557dfce61f7f0148e Author: angie Date: Mon Dec 8 23:54:31 2008 +0000 In doTrackMap, if we skip making mapboxes for a non-full subtrack of a full composite track, add subtrack's height to y. commit 6750ca29c431bcca97e3da6dd34543690eb12c07 Author: donnak Date: Mon Dec 8 23:19:43 2008 +0000 Changed fonts used for omimGene details page. commit 178482c7608ddbb5f197b21fe3b15933da039830 Author: mikep Date: Mon Dec 8 22:38:41 2008 +0000 option to skip validating humoungous fasa files once they have already been validated commit 986efc00f8d9061d24bcc3e650a2b224e296997a Author: donnak Date: Mon Dec 8 22:28:36 2008 +0000 Edited this page. commit 8e737f584ed94d664e21c37bc990eaf8e48e2890 Author: mikep Date: Mon Dec 8 21:05:11 2008 +0000 fragSize for GIS DNA PET commit 1b9dd66b727176be324f57e04d21b9afc99cf37b Author: mikep Date: Mon Dec 8 20:54:16 2008 +0000 first version of new project for GIS commit 26dfeffeec9f2b1e8dc1c6376d31ce0fd4c80a9d Author: mikep Date: Mon Dec 8 20:20:52 2008 +0000 Peaks have no replicates, Hotspots for replicates commit 84ff43eee1fe0fadceafc40292f650fca40034bc Author: mikep Date: Mon Dec 8 20:05:35 2008 +0000 span must match Wiggle file or you wont see any data commit ad67a172f8cd230a10fb4e2e8ce8b36ad330d1e4 Author: ann Date: Mon Dec 8 20:04:30 2008 +0000 edited citation commit c47b0830913b5fe98c90947906a0f397f4ccea01 Author: fanhsu Date: Mon Dec 8 19:28:17 2008 +0000 Changed "New Query" link to gsidPbGateway instead of pbGateway. commit 47207b75f2181753a41feae6fa9bc548fb291ec5 Author: fanhsu Date: Mon Dec 8 19:24:40 2008 +0000 Added GSID specific error message. commit b62d33955c13821dbc412c10c56c533086488853 Author: angie Date: Mon Dec 8 19:07:06 2008 +0000 Added scoreGrayLevelCfgUi: lets user select the lightest shade of gray used for bed* tracks with scoreMin setting. commit b12d374702ff15b47f70ddad1de1eac51139e02c Author: mikep Date: Mon Dec 8 17:37:54 2008 +0000 fixing up lost stuff commit c2d67a12f8c03ebc34883a92c844258859180b09 Author: mikep Date: Mon Dec 8 17:24:04 2008 +0000 have to put GTF files on download site also commit c1a398adb6bae6ab9c7f91fa9215ba726064baa0 Author: hiram Date: Mon Dec 8 17:22:03 2008 +0000 Ensembl v51 update done commit 31ab5aae702ffd43ad93930f3cef578193d4e42c Author: tdreszer Date: Mon Dec 8 17:17:24 2008 +0000 Fix bug in IE where view level cfg didn't update subtrack values commit afd76d2cf9701c4d4f9e1cf269aca7aaf627f244 Author: hiram Date: Mon Dec 8 17:12:10 2008 +0000 Add note about the broken lift of the quality scores commit 9ee71c5ca776e4bcc42ae5e3a819f0de11410f39 Author: hiram Date: Mon Dec 8 17:11:33 2008 +0000 Ensembl v51 update done commit 79126cae8815daf4ed8d85a2aeda0e942995cf5b Author: hiram Date: Mon Dec 8 17:10:06 2008 +0000 44-way mafs done, with I-rows and quality annotations commit 058b2112436cecc3785619548897a067916ca98b Author: tdreszer Date: Mon Dec 8 16:43:06 2008 +0000 Make UW raw signals configurable commit 4d48627f16d37a7844ef62e7ff5950d62a4cda0f Author: tdreszer Date: Mon Dec 8 16:20:08 2008 +0000 Added Duke/UNC K652. commit 870609f76b67fb969e3b9645913e1c2730a736fc Author: mikep Date: Mon Dec 8 16:17:57 2008 +0000 K562 data for UW commit 493bb0039393903ee6ed379fef8c914660e3872b Author: galt Date: Mon Dec 8 16:00:07 2008 +0000 "Encode release log update" commit b6c392e44f955b6cf7b7d6879649798a5338b630 Author: galt Date: Mon Dec 8 16:00:04 2008 +0000 "Release log update" commit 273f89e741222ba89bc2b473c27a50e98f05ddcc Author: aamp Date: Mon Dec 8 08:18:00 2008 +0000 Basic 2X Wallaby setup. commit 35c57f2cab014a9d5229349c15184b0070c7a488 Author: braney Date: Mon Dec 8 02:15:46 2008 +0000 hgPal for 44way commit 7f2f2bf6389228e0ba86a9133baf3e40315d37f4 Author: galt Date: Sun Dec 7 16:00:07 2008 +0000 "Encode release log update" commit a90db59e8d3ff037c1e9256e95b5e2194187b8d2 Author: galt Date: Sun Dec 7 16:00:04 2008 +0000 "Release log update" commit 1aa0fbe05fc12238ff504b4da404d4267daa8610 Author: galt Date: Sat Dec 6 16:00:06 2008 +0000 "Encode release log update" commit d3bd91ebda73248011b9477254b4910a26be2c96 Author: galt Date: Sat Dec 6 16:00:03 2008 +0000 "Release log update" commit 6d824be953ee0b68cf101e382e96e517e1adbe14 Author: angie Date: Sat Dec 6 06:56:29 2008 +0000 Bugfix: when forming a position URL in printPcrSequence, extract accession from glommed target sequence name if necessary. (thanks Brooke!) commit 57d476591aeae2383bd8ffab24d35e11b14964ed Author: angie Date: Sat Dec 6 05:44:17 2008 +0000 More work on printSnp125Function and components: Simplified the way we call getSnpTxBase hgc.c; changed terms to be more consistent with NCBI's function annotations; factored out printSnp125FunctionInCDS from printSnp125FunctionInGene, so longest function is 64 lines. commit 45df7511ed76ca2437e4457532689442de52f062 Author: tdreszer Date: Sat Dec 6 05:20:08 2008 +0000 Adjusted a bunch of wig settings commit f6f90a4bbd7036c01186f93df6dd9971d05a4917 Author: kuhn Date: Sat Dec 6 00:44:25 2008 +0000 fleshed out descrption with text frm OMIM site commit b84a1575fb31976edbf6d6e3035b4c50d66bf2c0 Author: kuhn Date: Sat Dec 6 00:36:27 2008 +0000 changed omim search term to require exactly numbers commit 7cf88d45b330c8da2711c7ad7dd7d6c3947a5731 Author: tdreszer Date: Sat Dec 6 00:29:48 2008 +0000 Wig defaultViewLimits for composite needed to handle double, not unsigned int commit 04509d34512a57f77eb2e668baaef77d558298e1 Author: kuhn Date: Sat Dec 6 00:24:21 2008 +0000 moved omimGene track up to human level and moved a track block up with the others, so search bloicks remain together in trackDb.ra commit f275241927bd18a7a235a8276aeddd46270b0c8a Author: kuhn Date: Sat Dec 6 00:23:36 2008 +0000 moved omimGene track up to human level and moved a track block up with the others, so search blcok remain together in trackDb.ra commit 4d7ca32ae3ea02d31900d2a70f2a191689b80602 Author: kate Date: Sat Dec 6 00:18:19 2008 +0000 First pass review of track labels and defaults for consistency commit 086e54223dcdcc9c887dbf464d1b1d5d5a872379 Author: kate Date: Fri Dec 5 23:53:56 2008 +0000 First pass review of track labels and defaults for consistency commit 65753e1f535161d413ea6def3419dba0bebf6ed9 Author: tdreszer Date: Fri Dec 5 23:40:36 2008 +0000 Fixed bug in sohwConfigControls() where two views' boxes were opening at once. commit 6fdd1e483e16bc477d145758676e1d5b4d16662f Author: tingwang Date: Fri Dec 5 23:19:00 2008 +0000 update Hudsonalpha Methyl27 html commit 8d9a2b1e9acf005d9c49d66eafba2c6b26b33c00 Author: mikep Date: Fri Dec 5 22:08:13 2008 +0000 style consistency with ripAntibody commit 820d53089e51cc32603d7f89286d25a2e3841507 Author: mikep Date: Fri Dec 5 22:05:03 2008 +0000 putting linebreaks in for convenience commit 55dce3a655f7c6dd487330df33de3bbcd156308e Author: tdreszer Date: Fri Dec 5 19:38:19 2008 +0000 Extended some antibody target descriptions commit 6ca3e67d3b14bb728baa03454f7205ffabebe238 Author: kate Date: Fri Dec 5 17:46:04 2008 +0000 Presumed error commit 3da0f8d7472f150fabe7e55eee63c9775e50aec4 Author: ann Date: Fri Dec 5 17:25:55 2008 +0000 uncomment equCab2 refGene line - it is needed for the upstream gene files commit c13279f3efbb3397fa19711ab1db047c38e37d45 Author: tdreszer Date: Fri Dec 5 16:27:30 2008 +0000 RawSignal should display as 'Raw Signal' commit 3ad1370ab55dc2329363b20018c23f6f78f0b191 Author: tdreszer Date: Fri Dec 5 16:22:42 2008 +0000 Added K562 Input to Duke/ChromatinMap commit fc4334ecdd7c8552b3a1b640361e018444e2d72d Author: galt Date: Fri Dec 5 16:00:07 2008 +0000 "Encode release log update" commit c98cc460de7d042b72d757adb228d18bae20a637 Author: galt Date: Fri Dec 5 16:00:04 2008 +0000 "Release log update" commit a2b7e625774c7d55091f22d2f63077140f3e141f Author: mikep Date: Fri Dec 5 08:28:33 2008 +0000 for now use bed 6 instead of pairedTagAlign as it is not implemented and will cause a segfault in the browser commit d0f5ea0a804b676e82bda76248db2b1264bfe860 Author: mikep Date: Fri Dec 5 08:17:11 2008 +0000 avoid segfault here if track 'type' is not known commit dabb422ab4851b1e6770de7fceac64e3b66bd418 Author: kuhn Date: Fri Dec 5 06:01:04 2008 +0000 dropped LI tagsw on refs and reformatted to 80-char per line commit 7114a6c1c5a0811f98915b4dd80b5c3fa24bb1d1 Author: fanhsu Date: Fri Dec 5 00:43:02 2008 +0000 Created omimGene.html. commit e536ffd97b7bd4333a2f45b6d8a431937ffdb1b3 Author: tdreszer Date: Thu Dec 4 23:41:36 2008 +0000 Readded Duke Extra stepped on by a checkin and set updated wig ranges commit cdf8e6135c320801c4de51ef4910d3284446653f Author: fanhsu Date: Thu Dec 4 23:21:29 2008 +0000 Added omimGene. commit 2346c92ec5c9b0c192dfa4ec47166ba5ff5d9169 Author: ann Date: Thu Dec 4 23:10:26 2008 +0000 commenting out the lines that cause the equCab2 upstream MAF files to be made (as the multiz6way is not correct) commit c97a5e6b865a8ff6b9c8feec8692bc8d428cb593 Author: fanhsu Date: Thu Dec 4 23:06:37 2008 +0000 Created omimGeneMap.as, which describe all the cols of the downloaded OMIM genemap file. commit 1ac716faa82c0879fa8cba2e88a117834ba698fb Author: mikep Date: Thu Dec 4 23:02:15 2008 +0000 added plus and minus rawsignals commit e67e96db346eb29e63a7e096ded68c9e3b7453e9 Author: mikep Date: Thu Dec 4 22:49:51 2008 +0000 GisPet data loaded #105 commit 35f3e36779c0f3dcfc57949b94fc9df456721c2c Author: hiram Date: Thu Dec 4 22:26:31 2008 +0000 Avoid trying to process the 'e' lines commit 3ea07ed2b6ba255dc01703f4ef0afbe1b2aae822 Author: hiram Date: Thu Dec 4 21:45:52 2008 +0000 Fix bug in counting, add compile target commit bd43d8b708ae51d3810fb57303b0138227e994bd Author: galt Date: Thu Dec 4 21:00:46 2008 +0000 unable to use bcc with mailing lists like encode-staff since the list software treats it like radioactive spam commit 82dfd67ccadd5e60210efaf8653610a09d05d18e Author: tdreszer Date: Thu Dec 4 20:31:24 2008 +0000 Fixed bug that failed sending bed 6 to downloads dir commit 9b6c7c071d42f0907eb5ce3bb266b5c074900eaf Author: tingwang Date: Thu Dec 4 20:09:26 2008 +0000 add wgEncodeHudsonalphaMethyl27 data commit 72ff4598ec66f4eb8956e59bb454ffd824841af7 Author: tingwang Date: Thu Dec 4 20:09:03 2008 +0000 add wgEncodeHudsonalphaMethyl27 html commit e03200b2b6dc3f2d95479165be2797d10fc44edf Author: hiram Date: Thu Dec 4 20:08:46 2008 +0000 Update to be correct commit cd7dc97cf31bdd665dd25ae0017effb1ec1ce404 Author: fanhsu Date: Thu Dec 4 19:42:13 2008 +0000 updated omimGene logic to defend against an OMIM entry that does not show up in omimGeneMap table. commit a30da52ae94d4dfb697b09b1f293630055f37b26 Author: tdreszer Date: Thu Dec 4 19:23:00 2008 +0000 Added Duke's extra tracks commit 4b995e7512f83988ba20f25f48132df4264f389d Author: hiram Date: Thu Dec 4 19:17:53 2008 +0000 MAXALIGN is now 50, and fixup hFreeConn() references commit 992d99a8be6666ca28922c45e87d8e3c330d295d Author: donnak Date: Thu Dec 4 18:59:30 2008 +0000 Fixed some html errors related to display problem reported by user. commit 1dabf6b11754f4d610b7b8d2f47dc6f720e2c37b Author: mikep Date: Thu Dec 4 18:46:26 2008 +0000 no PK on chrom commit e05f25bf5f4009de1e632d1f00367c4ef58acf25 Author: fanhsu Date: Thu Dec 4 18:40:22 2008 +0000 Added omimGene. commit 1f6f9da38012c1d945e471c22f7fb1c8193f89fc Author: tdreszer Date: Thu Dec 4 18:39:50 2008 +0000 Added Peggy Farnham to credits and altered references at Yale's request. commit cb90fa3f7687c66e357c83d4512650e1e2e6fb26 Author: mikep Date: Thu Dec 4 17:21:13 2008 +0000 catch error in score calculation commit 5f25465aea716ddfb0a9ef6e02665b9e27c2300a Author: galt Date: Thu Dec 4 16:00:06 2008 +0000 "Encode release log update" commit b787bf837a47d292b3a4b76b4c9c3cc2f4391dba Author: galt Date: Thu Dec 4 16:00:03 2008 +0000 "Release log update" commit 304a19671bcde1678ea5bdb0dba91b3802a9d9cd Author: aamp Date: Thu Dec 4 06:38:42 2008 +0000 First version of a CpG islands auto-script. Works but no clustering. Still finishes in a couple hours on a mammal-sized genome. commit 3efa56d0c73550301c55c257765e9e10201badba Author: kate Date: Thu Dec 4 02:15:51 2008 +0000 Fix spelling commit 6f5540ca80bb7b94dbf85ba8d9c601065ec46371 Author: hiram Date: Thu Dec 4 01:00:28 2008 +0000 ensGene v51 update completed commit 10e0dcf16cbc5f23286c2a416fecf3e24708e0e7 Author: hiram Date: Thu Dec 4 00:59:07 2008 +0000 ensGene update v51 completed commit e8b2b4f57eb129dbcc14fa23cc591f35f43ab6ff Author: donnak Date: Thu Dec 4 00:29:03 2008 +0000 Updated equCab2 news announcement date. commit 035b5cf3fb95f7aa5e9e9f2848735c14f98f10ab Author: fanhsu Date: Wed Dec 3 21:47:39 2008 +0000 Updated to process omimGene. commit 7e9551684424eb65e25100c11832a0b6c51d0f37 Author: mikep Date: Wed Dec 3 21:35:35 2008 +0000 make rawdata tracks configurable and put composit track for GIS commit 3bd9f4051f2214b8a2a4e09a26c747362af189a2 Author: tdreszer Date: Wed Dec 3 21:19:07 2008 +0000 Fixed composite-full/subtrack-dense bug that made subtracks clickable. commit 9a895182d0c2124c58701bc8036814c0f74c952c Author: hiram Date: Wed Dec 3 20:04:39 2008 +0000 extractGtf.pl needs to be on the scripts commit 118af1d118a6305f2221053aaeef74feb63323ed Author: hiram Date: Wed Dec 3 19:56:05 2008 +0000 Remove kk from cluster list, update for hive location, and add swarm and hgwdev to workhorse list since hive is being used now commit 51099ab2587fcd47e752c62980bd1b2303fdab4a Author: hiram Date: Wed Dec 3 19:54:08 2008 +0000 Updated for v51 update, and fixups for hive locations commit 9341ff682602cc75bd5255bf9ac494382288bd41 Author: kuhn Date: Wed Dec 3 18:57:11 2008 +0000 added newline per ann commit 0e8600cefc29f70bf373da2a436b761a8f8bc053 Author: kuhn Date: Wed Dec 3 18:54:41 2008 +0000 fixed declaration of variables per ann commit 9d372be1c09df85b2c1928a5002bf82c97325fe4 Author: braney Date: Wed Dec 3 18:32:33 2008 +0000 template for steve commit 14fd1a1ecaa89d02d45e663aa9bb87f4f69a6c97 Author: ann Date: Wed Dec 3 18:21:51 2008 +0000 added comma - thanks Bob commit a399f75fcce76972a562e97e1118c707594198ac Author: ann Date: Wed Dec 3 18:18:34 2008 +0000 added y - thanks Bob commit c7e46f1eafcb67642187d78ff08cd5f01784906c Author: braney Date: Wed Dec 3 16:27:42 2008 +0000 use POST instead of GET. Thanks Tim ! commit 80c41defaa8924edc02cfa54531b1b54cd4325f8 Author: galt Date: Wed Dec 3 16:00:06 2008 +0000 "Encode release log update" commit 4e9697ceda364a4aa498e4ec4ba805529b49325e Author: galt Date: Wed Dec 3 16:00:03 2008 +0000 "Release log update" commit 4d890f8125edac8e6b943e75fa0a134f594e47f5 Author: mikep Date: Wed Dec 3 12:37:13 2008 +0000 moved function up, and use validateWithList for pairedTagAlign, and fix so name is string, not sequence commit 6b81ebc30069aa9d452fc70fdf854230e4c49020 Author: mikep Date: Wed Dec 3 11:30:26 2008 +0000 make very dark for UwDnaseSeq project until they work out what scoring they like commit 95801b873a14ace92878dc2d5275213b12d15312 Author: mikep Date: Wed Dec 3 08:24:19 2008 +0000 stam lab wants darker features so increasing the min score from 100 to 200 commit 4e487c3695229ede33e06408c155b042313c1675 Author: mikep Date: Wed Dec 3 08:03:56 2008 +0000 making minScore an option and default back to 100 commit fc52cba6cd196526188078d115a9b6c8d0065daf Author: markd Date: Wed Dec 3 01:05:20 2008 +0000 Fixed tSizes in transMap tracks commit 6fc989f424b26fd92ba6c6581bd23449beb75533 Author: ann Date: Tue Dec 2 23:58:18 2008 +0000 adding a rule to capture relationship between hgFixed.transMap table and knownGenes commit 3b26e2dc64dfc972f470695c07430d959dc5c05c Author: pauline Date: Tue Dec 2 23:55:45 2008 +0000 Added equCab2 to genbank updates. commit 14724711cbce3f5e2c4cd2d11834bdfceb5a866e Author: angie Date: Tue Dec 2 23:34:34 2008 +0000 When printing out predictions of a snp125 item relative to selected gene tracks, use formatting, use shortLabel instead of table name, and show gene symbol if available. Also refactored out some code from printSnp125Function to printSnp125NearGenes. commit 0e02ecef656299a3f945318c92b0beda9be48ddf Author: hiram Date: Tue Dec 2 23:06:17 2008 +0000 Update to Ensembl v51 commit 51cad7aa5bbb025e1e52d0e25cfb7bc767f0d67e Author: markd Date: Tue Dec 2 23:02:45 2008 +0000 remove old lsSnpPdbChimera.py before installing to fix permission problems commit 423c26a392daf5f28bb72ef7459cefce3e70800f Author: aamp Date: Tue Dec 2 22:48:00 2008 +0000 RepeatMasker, TRF, WindowMasker. commit 36f03033e676db16a0ec9866b8adc486cb76e051 Author: larrym Date: Tue Dec 2 22:22:18 2008 +0000 support -skipLoad option commit a6c04c30ec5f9cf109f196a62f76eba68a2dd1ea Author: tdreszer Date: Tue Dec 2 22:09:12 2008 +0000 Oops. Two of these month 0-11 ranges. Fixed the other one commit b7d960efe93e5f1fcb3ce2bebc2526f4752791a0 Author: aamp Date: Tue Dec 2 22:02:33 2008 +0000 Slight update to fix on prev-item button. It looks like a lot, but actually only one line was added and an existing for loop has been indented. commit 70c67bff674c84b36a2c1fe2f65320c8324356f8 Author: angie Date: Tue Dec 2 21:51:09 2008 +0000 Don't offer all fields & selected fields as output type choices when an intersection or subtrack merge has been specified. commit b94b405ca7f3163fd9cb78dc1028c0253a5f4e7b Author: mikep Date: Tue Dec 2 21:28:10 2008 +0000 100 is too light for min score, using 300 by popular demand commit d300048f1c575c0b9b72c5a7dbb3f8c2cb9ee42b Author: mikep Date: Tue Dec 2 21:25:11 2008 +0000 fixed up labels on Suny data commit f1327a20cf81d7aebb9a13f11ecb4a26bb6e91b1 Author: mikep Date: Tue Dec 2 21:10:34 2008 +0000 fixed to do labels for RIP SunyAlbany project commit 87e798e5bd1f08a3080f96ff9184b7af55c8a67e Author: mikep Date: Tue Dec 2 20:52:27 2008 +0000 renaming for better clarity commit af2ab00b58b4f1f85be434362fe7dd5d3b9bac68 Author: hiram Date: Tue Dec 2 20:43:23 2008 +0000 Done with Ensembl v50 gene update commit e6df2adec678e5f7211f8c9b9718a45b5211941b Author: tdreszer Date: Tue Dec 2 20:12:42 2008 +0000 Fixed default to Defaults for MAF commit c626c9742ce167094c730c55e8614c3e8aad61db Author: pauline Date: Tue Dec 2 18:37:40 2008 +0000 Removed gap type that wasn't applicable to this assembly. commit 98e852b8687a8b84ebc37ebb79feda6cfdc9742a Author: hiram Date: Tue Dec 2 18:17:04 2008 +0000 Trying to get gnfMouseAtlas3 done, still trouble, and experiments with rn4/rn5 blastz to evaluate rn5 assembly commit 3e8a1f32c4b0c898e947daed70f3d9e1b78e3450 Author: hiram Date: Tue Dec 2 18:15:18 2008 +0000 Rerunning the equCab2 blastz, and continuing annotations on 44way commit e98e3d6e351005bcf85a54f60884b19eeb4ecee9 Author: hiram Date: Tue Dec 2 18:07:23 2008 +0000 Run a test lastz to mm9 to evaluate rn5 assembly commit 2b735209ca60c9c563a6725096a512082d70b239 Author: hiram Date: Tue Dec 2 18:05:38 2008 +0000 initial assembly complete, lastz to Mm9 complete, genbank done, evaluating assembly now commit 3958988a48389c1a244fc10410890dfdeaa047b7 Author: hiram Date: Tue Dec 2 18:02:13 2008 +0000 Add NCBI identifiers to description in dbDb commit 1dac3cb9a707083526d45847e7aad77defd86a04 Author: hiram Date: Tue Dec 2 18:01:45 2008 +0000 Remake the UnScaffolds 2bit and sizes commit 493031f440e18971b2f87f247b4289e393fdb347 Author: hiram Date: Tue Dec 2 17:55:39 2008 +0000 Proper ordering of species for checkboxes, no matches tree diagram commit 96a98df6bf5168174a019a22e7fcf828456018b5 Author: angie Date: Tue Dec 2 17:36:44 2008 +0000 Updated liftOver.gz link in liftOver/README.txt file (thanks Ann). commit 7f2af044d22c3852460f3fb64a17f8795e82b3c9 Author: mikep Date: Tue Dec 2 17:21:43 2008 +0000 first version of affy doc commit 29d71416bb2b28bf3e064c8d2c6017cf1b21d46c Author: tdreszer Date: Tue Dec 2 16:55:43 2008 +0000 Send peaks files to the downloads directory commit 067bdb2d0eef856277a70fc62ec928b69cdca67f Author: galt Date: Tue Dec 2 16:00:07 2008 +0000 "Encode release log update" commit 5a2929c1cdac0c60e2a9282a3ff5bfeff25bc371 Author: galt Date: Tue Dec 2 16:00:04 2008 +0000 "Release log update" commit 628f576252fdc971c6d0e1de4ccf19bbc4696abf Author: mikep Date: Tue Dec 2 15:07:39 2008 +0000 v196 final commit 1bf07fa545518c8cb1c58409a96994f74213c6d6 Author: aamp Date: Tue Dec 2 14:13:48 2008 +0000 Fix for previous-item button wrapping around to the end of a chrom. commit 803b27fce78993d9912295c3f3b52299fe397658 Author: aamp Date: Tue Dec 2 13:48:57 2008 +0000 Turning on next-exon buttons by default. (forgot the config screen defaults to unchecked... now it's checked). commit 7cddf9532867a0df1bbaf888efeade3e675932d4 Author: aamp Date: Tue Dec 2 13:47:14 2008 +0000 Turning on next-exon by default. commit 308167d6bfb3ff007783c97578c51811fcb110a0 Author: aamp Date: Tue Dec 2 13:29:18 2008 +0000 Added filters for score, p-value, and q-value for encode peak tracks. commit 357d11d0005265b4e28c6630e8fff19a259ace31 Author: aamp Date: Tue Dec 2 13:23:30 2008 +0000 Had double-output of "View table schema" and all that stuff. commit b3903fea94ca96dd54b49b945cd57d1f2e4e8723 Author: cszeto Date: Tue Dec 2 11:21:20 2008 +0000 New TCGA data commit 0dcd23f6a02ed8ec5248be22a6238d325a245c34 Author: angie Date: Tue Dec 2 07:35:26 2008 +0000 For snp125 tracks, added code that displays the effect of each observed allele on genes in selected tracks. For example, UTR, intron, coding (show codon change if simple SNP), or up/downstream of a gene. The new stuff will not be displayed unless you manually add cart variables like snp129_geneTrack=knownGene. commit 238f5133ac31ebadc63dd3b1661444dd286245c7 Author: markd Date: Tue Dec 2 07:29:34 2008 +0000 fixed english commit b8134165efeedf9724a912f8eacaeacfe75d5cb6 Author: mikep Date: Tue Dec 2 07:05:25 2008 +0000 "New version number v196" commit f7d68888ada09d562dc63cbcee97dfaad698bade Author: markd Date: Tue Dec 2 04:40:09 2008 +0000 added version requirment commit 68b590f79a82965c889ea99efe5c32238585225d Author: markd Date: Tue Dec 2 03:19:59 2008 +0000 fixed section and title commit 7c94f36f05a6f397cb479c11cd4007a245aee9c9 Author: markd Date: Tue Dec 2 03:15:23 2008 +0000 use syntax that works with python 2.4 for older chimera versions commit dce7ceb756459475fda690569e3f85c43b9afa30 Author: markd Date: Tue Dec 2 01:37:02 2008 +0000 prototype of Browser/Chimera/LS-SNP integration, only enabled on hgwdev commit 7f84103191dde0e18beb1e8cabaf5963790d07a5 Author: markd Date: Tue Dec 2 01:35:54 2008 +0000 fixed failure to check for required profile commit 3a870119a6407789efe00fd4f306e36d2bb7cc46 Author: markd Date: Tue Dec 2 01:34:56 2008 +0000 fixed invalid HTML commit be5aeb93ccb04dda30f8b56774067bb6dc34159d Author: markd Date: Tue Dec 2 01:08:49 2008 +0000 added help file for chimera integration commit 91377e09e0118e9daea3ef50ff2aa80bdbbd59c6 Author: tdreszer Date: Tue Dec 2 00:52:46 2008 +0000 Oh and forgot to change the ter ChipSeq to ChIP-Seq commit efe07a0e909362ecafa627ff61328680d91a05f5 Author: tdreszer Date: Tue Dec 2 00:48:33 2008 +0000 Removed an exact duplicate prototype for wigMafCgiUi() commit 0efcd490403c9cfb9231c60f8dce00657a7cfb30 Author: rico Date: Tue Dec 2 00:47:12 2008 +0000 Added error checking to report on a problem reported by Hiram. commit be0570a77fda3d4faccca5a657db43284c74455e Author: tdreszer Date: Tue Dec 2 00:45:42 2008 +0000 Pushed Broad's control to the bottom in the sort and forced autoScale off for them commit e9a0e3bb660d7bfbd9ccc251b9c470209cccf8c9 Author: larrym Date: Tue Dec 2 00:27:15 2008 +0000 fix priorities for HudsonAlpha commit 58f5da312814555b60143fff76d81ac1fccd830d Author: larrym Date: Tue Dec 2 00:24:09 2008 +0000 add dateReleased to the egrep commit dec1e66ff647aca61afce69e79ddd7209e76b110 Author: tdreszer Date: Tue Dec 2 00:17:48 2008 +0000 Correct 0-11 month. Add promoter to metadata types commit b2f930741e328955f51cfe14d8f35a2f38675799 Author: mikep Date: Mon Dec 1 23:57:50 2008 +0000 fixed accent characters commit bcc10fe336475925aac646753c829237984e7942 Author: mikep Date: Mon Dec 1 23:52:48 2008 +0000 HubbardGencode should be SangerGencode commit 18d278a34cb7b75f467143e317d0406afba64f9a Author: mikep Date: Mon Dec 1 23:44:16 2008 +0000 first version of Gencode doco commit d0d7c87ef16087dd72437f3b6e0bb182c71ce3bf Author: mikep Date: Mon Dec 1 23:34:46 2008 +0000 first version of CSHL doco commit 6fc82383a2be4ee979ce93b4a8a397f68724af7b Author: tdreszer Date: Mon Dec 1 23:26:18 2008 +0000 Use JS for default button in wigMaf species table commit df16b8a197678c739f5683ce401b884aea47ebc4 Author: mikep Date: Mon Dec 1 23:22:04 2008 +0000 minor formatting of references commit 62c95a0b059b2abb56d5716253d08657f7da2d73 Author: mikep Date: Mon Dec 1 23:13:00 2008 +0000 added references commit c10f1672d4de400f4716efd64890c8f31e650cd2 Author: mikep Date: Mon Dec 1 22:56:02 2008 +0000 fixed up html entity codes, and split the preformated code over 3 lines commit 576e86df7a0590961e082820d9d198059c3ae4c8 Author: tdreszer Date: Mon Dec 1 22:48:35 2008 +0000 Lineage text should cite source commit 6c03c88ec61ba23703bc5e7dd1327fdafa656afb Author: mikep Date: Mon Dec 1 22:48:10 2008 +0000 first version of Tenenbaum doco commit 0fa9a8007544016c3af5f6e0f5092273448ca6aa Author: donnak Date: Mon Dec 1 22:30:43 2008 +0000 Activated "make user" now that we have individual doc trees. commit 46899235b1dcc3fb59268dcd22e286f93a9625d4 Author: donnak Date: Mon Dec 1 22:16:24 2008 +0000 Edited these files & did a bit of reformatting. commit 3d2d88aea799852c65e3085bcd034bc3be9762a5 Author: mikep Date: Mon Dec 1 21:15:11 2008 +0000 first version of Stam lab encode doco commit f960c857a2c38c16d9431847ddfe1dd6cbe02ab1 Author: tdreszer Date: Mon Dec 1 21:12:44 2008 +0000 Added Broad K562 control commit 03d7cff4d0a51086253b08fab203e2fc14e22825 Author: kate Date: Mon Dec 1 21:11:27 2008 +0000 Fix maf count in output commit fed6659e764fa9558a002316efbf44c30afea16c Author: mikep Date: Mon Dec 1 20:13:17 2008 +0000 first version of GIS doc for Encode project commit cd1596fc17f9dc160aed773a2fa6760017496357 Author: mikep Date: Mon Dec 1 20:12:19 2008 +0000 backing out bad commit commit 1e10aa49e4dd3d5b69f476e964f8c34e1e5b800a Author: mikep Date: Mon Dec 1 19:57:50 2008 +0000 first version of GIS encode doco commit d26977bc53548546c31221d148fd1e164181902c Author: galt Date: Mon Dec 1 16:00:07 2008 +0000 "Encode release log update" commit 96323bbbf00fe1446a8c2244b81c55b04b9991e3 Author: galt Date: Mon Dec 1 16:00:04 2008 +0000 "Release log update" commit a8e3fc14bd784c66c3934676766f80067c6cf43d Author: tdreszer Date: Mon Dec 1 05:39:29 2008 +0000 Required files do not apply to control or input commit 05487cf9f3b1f7fd760f4a61801bae0673c915d8 Author: tdreszer Date: Sun Nov 30 19:32:28 2008 +0000 Autogenerated name is different from orihinal ChIPseq name commit 6a6912bfa06ff65b478738dc59612d345a926101 Author: galt Date: Sun Nov 30 16:00:08 2008 +0000 "Encode release log update" commit 1e9e31c052495c0d45d3d713b6375da35ecea62c Author: galt Date: Sun Nov 30 16:00:05 2008 +0000 "Release log update" commit c6b66d6dac0cbf52bc948dcc319c6ac15151a001 Author: markd Date: Sun Nov 30 06:13:03 2008 +0000 added style for LS-SNP PDB hgc commit 641e22461598aef062a8e5fa10ff249d3ad542da Author: tdreszer Date: Sun Nov 30 00:34:40 2008 +0000 Added Broad K562 commit cf3c60866c36737f27ca14c3648e7b7a9dc19539 Author: markd Date: Sat Nov 29 21:44:18 2008 +0000 fixed CCDS/transmap table CSS problems commit 8f5871150f250d9a09634d8c00b51fb4162d92a8 Author: markd Date: Sat Nov 29 20:00:33 2008 +0000 fixed invalid html commit 61e7565354820cadfa3533d680cccfd5fd8a5b4d Author: galt Date: Sat Nov 29 16:00:09 2008 +0000 "Encode release log update" commit be561a2f02e8568d9179af5b314f20ea9116b0f6 Author: galt Date: Sat Nov 29 16:00:06 2008 +0000 "Release log update" commit d968984332e331ddbedef71b012260a69a78feab Author: rhead Date: Sat Nov 29 10:08:01 2008 +0000 Changed broken link to broad for genetic map to the link you get when clicking on Mouse genetic and physical maps from broad site. commit 33ae38ec18d2106e13a9367387bd74fc77d3a636 Author: rhead Date: Sat Nov 29 10:01:13 2008 +0000 Whitespace changes. commit 55b9197593ec1167c6eb5899621411128f09eed4 Author: galt Date: Fri Nov 28 16:00:05 2008 +0000 "Encode release log update" commit 6a2167093d1c305ad6078851a8924eae494922d1 Author: galt Date: Fri Nov 28 16:00:03 2008 +0000 "Release log update" commit 08cc8195d99459ce2eef12f416c1f6d5b9da2c23 Author: galt Date: Thu Nov 27 16:00:08 2008 +0000 "Encode release log update" commit a256b2658dc4a879abb888341f89138d7eb2afa0 Author: galt Date: Thu Nov 27 16:00:05 2008 +0000 "Release log update" commit 68bb63a582025b0a42226e80e9fe78b9e9868a85 Author: markd Date: Thu Nov 27 05:05:06 2008 +0000 added ignore entry commit 7e7b0511ffa28c37584aa0de434416749c853777 Author: tdreszer Date: Thu Nov 27 02:39:12 2008 +0000 Minor rearrangement of the deck chairs commit 6fa027fc2b3f958a1b8904e794955c9cf97dfab2 Author: tdreszer Date: Thu Nov 27 02:19:25 2008 +0000 Added Yale GM12878/Pol2 commit edc2e275e9cf7cc0f372315c5b2a0e5f4bcb9f6b Author: angie Date: Wed Nov 26 21:59:32 2008 +0000 In baseColorOverdrawQInsert, make sure we pass a start coord, not an end coord, to drawVertLine. I.e. if we obtain a coord by adding blockSize to a start, or subtracting a start from tSize, subtract 1 to turn that open end coord into a closed start coord. commit ece71bd6d8d82ce6fca0c0d47c90a46e49428eea Author: kuhn Date: Wed Nov 26 21:57:32 2008 +0000 added targetDb commit df3d64e6d9cfeb3b7b6a6e83186792094369397f Author: kuhn Date: Wed Nov 26 21:50:43 2008 +0000 added targetDb to list of tables to backup commit c5648d77cfd0d05dc5ce78a7574186972d55c4eb Author: galt Date: Wed Nov 26 21:44:18 2008 +0000 fixing url download resume commit 9affe892aee09ba2fd4acf31029498ddb368a06d Author: kate Date: Wed Nov 26 21:21:31 2008 +0000 Add item names to Chai elements commit 4ba480e62398c261cecb59ef471b2f59677bdb50 Author: kuhn Date: Wed Nov 26 21:19:33 2008 +0000 a coule of format changes commit 2d29b272f2be77dd022f2568b3a1178607f7ad5f Author: kuhn Date: Wed Nov 26 21:08:39 2008 +0000 added comment in Config explanation section about new Target funtionality commit 287923c84824e0c9bd2e4c3cd4ddd8219940ae64 Author: galt Date: Wed Nov 26 21:05:18 2008 +0000 oops, need this change commit 161e954d567ca9cd23b2590a4dcef1bbe0f21937 Author: kate Date: Wed Nov 26 20:59:24 2008 +0000 Additional methods for binCons and Chai commit 22146ad9a5f045cb67e018e8387b33a25209959d Author: mikep Date: Wed Nov 26 20:47:50 2008 +0000 loaded UwDnaseSeq data #50 commit d41fc766d9d34fe0eae3ee209f60ad9e6a72cdca Author: mikep Date: Wed Nov 26 20:24:18 2008 +0000 loaded UwDnaseSeq data #49 commit a35e7ebcb63cb4b4b5d33695c27df94ca0b711cc Author: mikep Date: Wed Nov 26 20:03:48 2008 +0000 loaded UwDnaseSeq data #48 commit a5e38daa02bbd9345c2059aa1dd88fe393c6e278 Author: galt Date: Wed Nov 26 20:01:36 2008 +0000 making friendlier failure message commit 5cd167a7bb7abbe51518bb089010ff69e4a903fa Author: kate Date: Wed Nov 26 19:58:14 2008 +0000 Remove ENCODE setting. This removes the ENCODE-specific logo and downloads link. This data isn't really pre- the ENCODE production phase. commit f1d8ae8ac67278213015cc3df5806a453c00c05d Author: hiram Date: Wed Nov 26 19:58:06 2008 +0000 44way default vis should be hide commit 7aea4d6c9aa761eefd34334882f314221665a833 Author: galt Date: Wed Nov 26 19:45:35 2008 +0000 minor niceness for ease of using ps aux with grep commit 18f319fbe5941ca86cc0803375a07b572f488d9b Author: rhead Date: Wed Nov 26 19:32:14 2008 +0000 Changed RR to hgnfs1 in the push-request text, as that is where the RR's hgcentral db actuallyr esides. commit 79625fcec476a394ac664e29769d22b788a601e9 Author: mikep Date: Wed Nov 26 19:22:50 2008 +0000 loaded UwDnaseSeq data #47 commit 65d8870f9218f8556535883a9bcb9dad72ef60c3 Author: ann Date: Wed Nov 26 19:12:17 2008 +0000 removed scoreFilterMax as this composite track no longer has scores commit 1080e7c268c2fb134c9c2c6b57f8412bca273e9f Author: tdreszer Date: Wed Nov 26 19:07:07 2008 +0000 Minor formatting issues commit be04c199996488b0769956d9f506db29de567fe3 Author: mikep Date: Wed Nov 26 18:56:59 2008 +0000 loaded AffyRnaChip data #74 commit 538a18abdc880e39074a5971568e95ce8b361bdd Author: mikep Date: Wed Nov 26 18:53:41 2008 +0000 loaded UwDnaseSeq data #46 commit bac72fb9812de03d8f710ee37ccb82cbc0eb7b1d Author: mikep Date: Wed Nov 26 18:39:49 2008 +0000 need to check all files in list if they are .gz and work out what cat command to use commit 7325d5ede59e9a166230d8250d5b76dcedb1c757 Author: ann Date: Wed Nov 26 18:28:51 2008 +0000 added back edits I made to original sangamoDnaseHs html file commit 54d6e942f57ac3daf1ce2dcfc64bc43aa8cde102 Author: hiram Date: Wed Nov 26 18:21:25 2008 +0000 Added rn5 commit f7b89189ea86446cd3beec26bf3f259dee925db8 Author: ann Date: Wed Nov 26 17:03:10 2008 +0000 shortened longLabel commit c024307a46248fb3bd71b4c7a9a84ed853d90f37 Author: galt Date: Wed Nov 26 16:00:10 2008 +0000 "Encode release log update" commit 7c9eb31a8699c07f9722b957284c4478b19541cc Author: galt Date: Wed Nov 26 16:00:06 2008 +0000 "Release log update" commit 6594839b06d39514aaf52eddefb8b675ef3bb500 Author: larrym Date: Wed Nov 26 08:47:29 2008 +0000 HudsonAlpha Pol2 and NRSF (pids 52 & 70) commit d95c31095d00217dde909436195e1e3ac15698b9 Author: markd Date: Wed Nov 26 06:08:03 2008 +0000 added function to programaticly set database profile host/user/pass commit d09ab7a5af92fedcb47c58b4d067d4c178893643 Author: tdreszer Date: Wed Nov 26 04:48:18 2008 +0000 Missing quotation marks commit 36585798d85e091f8355d3c5a98e0f818968dabe Author: tdreszer Date: Wed Nov 26 04:47:32 2008 +0000 Updated methods from Terry Furey commit 7d6dc50488ad1fcf11ef81d3c9777a9c3dc28200 Author: donnak Date: Wed Nov 26 02:27:03 2008 +0000 Archived an item. commit b3d583b53e15ac87fe11965184fef9b61d0ee92b Author: donnak Date: Wed Nov 26 02:26:49 2008 +0000 Uncommented equCab2 news item. commit ab0e8020a51a664eef5db612f96466a0ecb98408 Author: donnak Date: Wed Nov 26 01:53:19 2008 +0000 Uncommented equCab2. commit 9221d7559ad109d97e727391cfd1e3e177312709 Author: galt Date: Wed Nov 26 00:54:39 2008 +0000 adding email notifications to user for all failures and for load success commit 9094dd26e9847793df1d2b785ee2104d84eb559e Author: fanhsu Date: Wed Nov 26 00:53:05 2008 +0000 Changed sangamoDnaseHs track to eioJcviNAS per data provider's request. commit ded425383698e2b6d3cb7805c14b82eef660654c Author: fanhsu Date: Wed Nov 26 00:41:21 2008 +0000 Created eioJcviNAS.html to replace sangamoDnaseHs.html as requested by data provider. commit 6d08d86a98f9d45b80d36e36647140cbc3a24c45 Author: mikep Date: Wed Nov 26 00:40:19 2008 +0000 shorter names because we hit 64 char table name limit commit 703cbf8fc641d6df079e634a858d3d3349d96766 Author: fanhsu Date: Wed Nov 26 00:38:19 2008 +0000 Changed sangamoDnaseHs track into eioCjviNAS track per data provider's request. commit 2793f427f5d86becee95c5f9f092bd4af7661b95 Author: ann Date: Wed Nov 26 00:02:29 2008 +0000 fixed formatting and citations commit 9f921f8baf188e926b5c084a09fdb4a1f2aa0ce2 Author: hiram Date: Tue Nov 25 23:34:56 2008 +0000 Browser up and running with quality and gc5Base tracks commit b3d2dd5c702d2ca6b057d231444dd343f860dc66 Author: hiram Date: Tue Nov 25 23:30:42 2008 +0000 Add monDom5 to the build commit 2c8057e4374192f99044425ae71122d3371250c4 Author: hiram Date: Tue Nov 25 23:29:42 2008 +0000 Initial contents from makeGenomeDb.pl commit 31c017837dc2fcac85e974c56c584aa7c1aeb4fd Author: ann Date: Tue Nov 25 23:18:27 2008 +0000 removing release alpha from phyloP Conserv 28way commit 07822066ea5030755add00a76d88a96848aefb7e Author: larrym Date: Tue Nov 25 23:14:02 2008 +0000 add -metaDataOnly and -skipAll; use Encode::isControlInput and lc "CONTROL"/"INPUT" commit a75a46f6bc6ef5e0f04afd454fd406e11bb30260 Author: larrym Date: Tue Nov 25 23:11:13 2008 +0000 add isControlInput commit 4a73709d9a86c2571fa5c2d801da4087a013b65b Author: angie Date: Tue Nov 25 22:48:07 2008 +0000 In doTrackMap, account for center label height of composite tracks (they used to have no track-level center labels in non-dense modes, but now they do). commit 48ba5b5ac750ef1f569bae6d20575f21351ad4ea Author: mikep Date: Tue Nov 25 22:44:01 2008 +0000 tracks for SUNY commit c5ac755330e8097eaa13e43a818dad0356506aed Author: hiram Date: Tue Nov 25 22:40:50 2008 +0000 Need to get db=0 on the hgg_chrom=none org URL line to get the reference to ignore cart contents commit 6c75f9a6f2fc20bbb3338aa1a236e733cc4a6597 Author: mikep Date: Tue Nov 25 22:23:18 2008 +0000 need to shorten table names commit b831f317ba80de772e1e399efc0f2a313695871c Author: tdreszer Date: Tue Nov 25 22:03:23 2008 +0000 Added 4 tracks for Elnitski commit 47ad7684be8ea7eee3a75e9bcff489a5b8cfccf0 Author: ann Date: Tue Nov 25 20:45:20 2008 +0000 more tweaks to citations commit 6682d1eab909d9266cb0718a0a8e6f02c99bdb38 Author: hiram Date: Tue Nov 25 20:25:31 2008 +0000 Add quality track during 44-way annotations commit bb002b594a9058ebd475db7a992a472410ee10bf Author: hiram Date: Tue Nov 25 20:22:45 2008 +0000 Add quality tracks during 44-way annotations commit a1cd370958f824f5f3167bb3363582c099718a8a Author: tdreszer Date: Tue Nov 25 20:18:33 2008 +0000 Added some Yale tracks commit 93e89ebd1998cafa3d5551a8d8df35d7948fe8c0 Author: mikep Date: Tue Nov 25 19:43:19 2008 +0000 added submission 73 commit b61142ebf65c8904119af5f15a8f76d369ef0748 Author: mikep Date: Tue Nov 25 19:41:31 2008 +0000 added submission 75 commit a37585efbec6f96db7aab5f5c258d4f6bb794646 Author: mikep Date: Tue Nov 25 19:32:12 2008 +0000 standardized ripAntibody names commit 0badd9e765c95d483f1676f0d28d6fdb85e44297 Author: mikep Date: Tue Nov 25 19:20:48 2008 +0000 new format for ripTgtProtein commit c07db277d991f2696bf3c9d1a7e32d06dba6fa9b Author: mikep Date: Tue Nov 25 19:11:30 2008 +0000 standardized ripTgtProtein names commit 44d1815605bee05b472de001ef32892cf1a9d130 Author: rhead Date: Tue Nov 25 18:52:49 2008 +0000 Fixed broken link to LS-SNP at UCSF. commit b1bc968e3c6823ac0fc544de6f699b797c3925c3 Author: ann Date: Tue Nov 25 18:47:26 2008 +0000 added two tables to ignore list commit 11b64583c0018e652fb026a72f93a2dadfd2eb9f Author: ann Date: Tue Nov 25 18:46:04 2008 +0000 fixed citations commit a97619585b500a12b0633da1349d1edadd6a6b11 Author: rhead Date: Tue Nov 25 18:43:24 2008 +0000 Fixed broken link to Perlegen chr21 haplotype browser. commit 3e51079f903403f0d412f73c7f323791b0cfa415 Author: fanhsu Date: Tue Nov 25 17:59:26 2008 +0000 Changed scoreMax to scoreFilterMax. commit 59fb014c934e4f9cc56dfa2f38c707deb0fae564 Author: fanhsu Date: Tue Nov 25 17:57:43 2008 +0000 added scoreMax lines for sangamoDnaHs tracks. commit 20fe36ad5b3acbbfa06b18b0b700332a260999d1 Author: mikep Date: Tue Nov 25 17:37:57 2008 +0000 fixed submission 82 commit d191f28d6eb198df3e0eaa5e397c4d305f24fbc5 Author: fanhsu Date: Tue Nov 25 17:11:26 2008 +0000 Shorten the long label of sangamoDnaseHsNeg track to 64 chars. commit 101d79ae82137f5d45662586cd63e7d69cba7924 Author: mikep Date: Tue Nov 25 16:02:01 2008 +0000 added submissions #77,78 commit 25d534b28181e0af1a1517a66ad5263bf4ed578d Author: galt Date: Tue Nov 25 16:00:07 2008 +0000 "Encode release log update" commit 0ac9b422206bfef0e8ebc5a1b6e2f300a9d351e1 Author: galt Date: Tue Nov 25 16:00:05 2008 +0000 "Release log update" commit 6122c440b5b0bfb16f19e5ec62cbbed157855067 Author: mikep Date: Tue Nov 25 09:03:47 2008 +0000 added submission #82 commit e89ce684dee312d837dfd5d485b0323601d8f098 Author: mikep Date: Tue Nov 25 08:49:51 2008 +0000 new rnaExtracts, cell, and localizaton commit 50c4f2be81690a145c3be0f6bba9b876c5d1d4e9 Author: mikep Date: Tue Nov 25 08:43:42 2008 +0000 Affy Submissions 81,90 commit 924dda7fe9951efec53c86054d17653f5dfb1a19 Author: mikep Date: Tue Nov 25 08:02:01 2008 +0000 need to specify full path, eg, when using command line commit a0f7ba51c5171480cda5d286b15a4f8cf26beb58 Author: mikep Date: Tue Nov 25 07:20:54 2008 +0000 -pg flag for gprof profiling commit 9a1b57f7068a92de3c61fce1ad10906fc1a61671 Author: mikep Date: Tue Nov 25 07:17:45 2008 +0000 one of these caused a buffer overflow with size 64, wgEncodeAffyRnaChip tracks, which have 60-char-long table names commit 5bfb6d40171ba4ffdac2e2b58927bedabeb4e0d0 Author: mikep Date: Tue Nov 25 06:47:06 2008 +0000 added submission 89 from Affy commit 7a1bb45ba04dcc18eff8710d9a194267dc598471 Author: mikep Date: Tue Nov 25 06:01:01 2008 +0000 Affy RNAchip tracks commit 756399d3abf8f3b0661e617e159abae63ab3efca Author: mikep Date: Tue Nov 25 03:52:31 2008 +0000 Unfortunately does not look like you can have 2 terms of the same name even if their types are different commit 6ccb20c71a44a9fe432bdd7d2a34618e1f2777f2 Author: mikep Date: Tue Nov 25 03:35:17 2008 +0000 ripAntibody and ripTgtProtein for Tenenbaum labs commit 1f5897adea47151abc9e8d9306b8e8748e447739 Author: mikep Date: Tue Nov 25 03:32:49 2008 +0000 Tpyo in PA Binding Protein commit d0712286188f6dc681355a8f6891d3e115ea84cd Author: mikep Date: Tue Nov 25 01:28:23 2008 +0000 support for Tenenbaum lab ripTgtProtein, ripAntibody commit 5beddeda5181777aefb6fba4f2e86f5242fe4352 Author: mikep Date: Tue Nov 25 01:21:59 2008 +0000 target proteins for RIP-chip Tenenbaum project commit aae95a14e05ac2140b123d61b19c7546385b3bec Author: galt Date: Tue Nov 25 01:04:08 2008 +0000 turn off autorefresh for big submission-projects list commit 7d4f8d092b660ec9b1f63187191c161aed63ba1c Author: ann Date: Tue Nov 25 00:45:04 2008 +0000 alphabetizing references. commit a5468b6d9aaa4b8c740f251be0fbb86a29c167bf Author: tdreszer Date: Tue Nov 25 00:42:36 2008 +0000 Additional information for several new cell lines commit 478e95c6b237c86855460ba3e36ad9026637338f Author: fanhsu Date: Tue Nov 25 00:26:51 2008 +0000 Refined sangamo track labels per data source request. commit aaa946b2c9b3df0ee0ba84f70b6136b9bbed38bd Author: ann Date: Tue Nov 25 00:23:16 2008 +0000 just chopped lines to 80 character length commit d37e72f2fd8ac3bec9e06257f401203db4276c92 Author: rhead Date: Mon Nov 24 22:43:19 2008 +0000 Changed petMar1 download links to braFlo1 links. commit 9a25e1da33e5233fef17991fa3dc90429c481cfb Author: fanhsu Date: Mon Nov 24 22:15:52 2008 +0000 Added sangamoDnaseHs composite tracks. commit 3cbcade049ac4ea6cab622b872ca625af810a469 Author: fanhsu Date: Mon Nov 24 22:01:27 2008 +0000 Removed 1 extra line not needed. commit 2597fb43a7540f63e56b78fada5c5e0467fe5db7 Author: fanhsu Date: Mon Nov 24 21:27:20 2008 +0000 Added two sub-tracks for sangamoDnaseHs. commit ece5a8f23c9869f36b8d581118368547e6bcc365 Author: tdreszer Date: Mon Nov 24 20:00:57 2008 +0000 Added a bunch of tier 3 cell lines, but the protocols have yet to be approved. commit dfa9cd68771b6372979a0747c985e60d13d640f8 Author: fanhsu Date: Mon Nov 24 19:28:33 2008 +0000 Created sangamoDnaseHs.html. commit bd65533367e98d06876dbdf1154da678ff7168b3 Author: galt Date: Mon Nov 24 16:00:20 2008 +0000 "Encode release log update" commit e3055cb6a1cb91329966738fdf7159bd6e6e09f5 Author: galt Date: Mon Nov 24 16:00:14 2008 +0000 "Release log update" commit b580f6237759a137373be0b30e5dd93fa7e668d1 Author: jsanborn Date: Sun Nov 23 22:29:43 2008 +0000 added some private datasets to test authetication commit 3c126a31fa13ad07500ccef8de2a4925e23175db Author: galt Date: Sun Nov 23 16:00:06 2008 +0000 "Encode release log update" commit 91d1e691e48e8c21b5d4cfe1b73f702de99ea102 Author: galt Date: Sun Nov 23 16:00:04 2008 +0000 "Release log update" commit b5753f4d9cd52c40403e180ed306fb58bb633bb3 Author: larrym Date: Sun Nov 23 09:46:04 2008 +0000 add HudsonAlpha GABP data commit 448ceb68c72502378d5dd313f4f23101a5c034bd Author: larrym Date: Sun Nov 23 08:08:26 2008 +0000 set $ENV{TMPDIR} commit 2819da15f09fc6d33fca3bc98a796dffb24dcf3f Author: larrym Date: Sun Nov 23 08:03:18 2008 +0000 add $tempDir commit f159f78c39ab91b63ca7d244457977d55ad92d10 Author: tdreszer Date: Sun Nov 23 06:41:13 2008 +0000 Added Duke DNase Base Overlap Signal commit 6ed46eff0559e52d80cc0ca4a2da6df3873ce43e Author: larrym Date: Sun Nov 23 01:51:43 2008 +0000 GM12878 and K562 control data commit ffad10150acf4f977d7d1ea49dd6396bccc8bc66 Author: larrym Date: Sun Nov 23 00:43:00 2008 +0000 add SRF data commit be133a49035b5904ba5f7cac22cbf4e5041b940c Author: larrym Date: Sat Nov 22 23:48:39 2008 +0000 tell sort to use /data/tmp as temp directory (was running out of room on /tmp) commit b6465cb1d28e100bddb6a26c76cb26f2043f9d8e Author: galt Date: Sat Nov 22 16:00:07 2008 +0000 "Encode release log update" commit b743a5a76ae8992c6dfe95502d0b52c441f7e333 Author: galt Date: Sat Nov 22 16:00:04 2008 +0000 "Release log update" commit 6430d5b9476b4a18443d5472445fe1decad0542e Author: mikep Date: Sat Nov 22 02:22:00 2008 +0000 view for functional stuff commit d40958b42db9159b8211c976f5068f59760fabdb Author: jsanborn Date: Sat Nov 22 01:51:48 2008 +0000 updated TCGA cancer tracks for GB commit f49a9473e7ea5e69e665429bd16abca6dfbef136 Author: tdreszer Date: Sat Nov 22 01:31:49 2008 +0000 Added FAIRE Base Overlap view commit d56bcee7403ea375282bab8e3f02338b0d44f9b8 Author: mikep Date: Sat Nov 22 00:54:13 2008 +0000 field-by-field validation of gappedPeak, validation of pairedTagAlign commit 335088fd36da06e5445b6c5848d3f123e6836330 Author: tdreszer Date: Fri Nov 21 23:37:48 2008 +0000 Added Yale K562/c-Fos,c-Jun and c-Myc tracks commit 0763afc10b6aab0c6299310d198d06d5dd4b70f2 Author: mikep Date: Fri Nov 21 22:32:52 2008 +0000 added flag to ensure wiggles do not have overlapping spans commit f29e4df940db9840c5ef2186bf0136bbf1139196 Author: hiram Date: Fri Nov 21 22:17:35 2008 +0000 Add noOverlapSpanData option to wigData to catch overlapping data points when span is being used commit 5a5178fffe138863d4ed6bb6cff8421bf9dabedf Author: mikep Date: Fri Nov 21 22:02:46 2008 +0000 added suggested changes from Scott commit 21ceaf1d63095c9fc85df47e04c9a2610b719948 Author: tdreszer Date: Fri Nov 21 19:59:24 2008 +0000 Error message was referencing the wrong line commit 9154f7d08fc0aae99e65b6d6cdb0e5cc484fd729 Author: tdreszer Date: Fri Nov 21 19:19:17 2008 +0000 Registered some antibodies commit baa280e9905be0d31eac105aacd0e8a9471dbd1e Author: markd Date: Fri Nov 21 16:02:09 2008 +0000 added mount point to nfs keep open hack commit 3909874242e8a91c2ad2756b9a7a2ae50a3fe0ea Author: galt Date: Fri Nov 21 16:00:07 2008 +0000 "Encode release log update" commit 65499a604193edec2f3ae8f082ed03725ef982a3 Author: galt Date: Fri Nov 21 16:00:04 2008 +0000 "Release log update" commit c39aff611aec47bc01d417da660682987732a966 Author: aamp Date: Thu Nov 20 22:17:26 2008 +0000 changed makefile so it wouldn't break cron scripts. commit 1d915e0662fff66047fcbdf718fc2dff671dd6e6 Author: larrym Date: Thu Nov 20 21:49:24 2008 +0000 add validateWithList and use in narrow and BroadPeak validation to improve error messages commit 38ecdd546728c9d95350f078427375cb17d25728 Author: larrym Date: Thu Nov 20 21:44:43 2008 +0000 add qValue fields commit 94b7306fbc6d0a9762f10ef6f832335c0afb67ac Author: rhead Date: Thu Nov 20 21:19:23 2008 +0000 Commented out links section until data is deposited with NCBI GEO and humanbrainatlas.org site is working, per Matt Johnson's suggestion on 6-25-08. commit 138e76d3331846341e75474fc40a4ae08c6738a0 Author: kate Date: Thu Nov 20 21:07:09 2008 +0000 Make link to NHGRI doc more visible commit a5841c031a8bf9ac6536eefe1fbb47ee8e121df6 Author: kate Date: Thu Nov 20 21:02:15 2008 +0000 Update section on data release policy. Other mods for readability, ease of use. commit 9c89386156978a29895d594419c0e32cc3efab01 Author: donnak Date: Thu Nov 20 20:05:35 2008 +0000 Added Contributors link. commit a4fa8a9d205fab558c8ab3d30b4a5865b8f8d949 Author: donnak Date: Thu Nov 20 20:04:08 2008 +0000 Updated this page to contain some info from the NHGRI ENCODE page & links to several of their pages, per Kate. commit 178905acb482707d4bf249b82e64e4354efb0119 Author: fanhsu Date: Thu Nov 20 19:40:31 2008 +0000 Updated hFindBed12FieldsAndBinWithConn() per Mark's code review input. commit 1b936666b1f26ab073f14229322b8e402c6f6b68 Author: fanhsu Date: Thu Nov 20 19:39:41 2008 +0000 Updated hFindBed12FieldsAndBinWithConn() and hFindTableInfoWithConn() per Mark's code review input. commit 0bd573635d5685503e4b2c55e916b0b8fc403f7f Author: hiram Date: Thu Nov 20 18:52:49 2008 +0000 Adding hedgehog commit 58f8408657f102f15ff0191566b3409745b91b62 Author: hiram Date: Thu Nov 20 18:52:24 2008 +0000 Initial set of files from makeGenomeDb.pl commit a69716cc37d9cd929eb3df0d2ac0e117a1d8f850 Author: hiram Date: Thu Nov 20 18:47:47 2008 +0000 Add sorAra1 to the build commit 6a6745c96fef2c151898673f12e931be61a1aed4 Author: hiram Date: Thu Nov 20 18:46:30 2008 +0000 Initial set of files from makeGenomeDb.pl commit 5c7f8fefaa319583a3c4d987d1b4ce4a3f61b6cc Author: galt Date: Thu Nov 20 16:00:07 2008 +0000 "Encode release log update" commit 502418dd8786c9baf2c2d17773753d34f2b8b0eb Author: galt Date: Thu Nov 20 16:00:03 2008 +0000 "Release log update" commit ad604847d62b4788d89012f56441816cb0a42249 Author: markd Date: Thu Nov 20 01:42:09 2008 +0000 fixed bug that causes table browser to crash when there were multiple trackDbs in hg.conf, but not all of the tables existed commit d2ec4e6d6a6421531b9d42422147407cc0109e86 Author: donnak Date: Thu Nov 20 00:46:15 2008 +0000 Removed Tools link -- not needed in production phase menubar. commit b699eee6284e6831e1e12302d745df81d64aaf83 Author: donnak Date: Thu Nov 20 00:44:29 2008 +0000 Added GEO & Pubs links, removed Submissions link. commit 8fa9fc8057c6900dd4efbea3f4e1660a47ba0133 Author: donnak Date: Thu Nov 20 00:40:59 2008 +0000 Added page showing ENCODE-related pubs. commit 85d288f1eb659c7e5d21718806d53af4e15b8c39 Author: pauline Date: Thu Nov 20 00:24:50 2008 +0000 Removed release beta - old version of dgv in prep for release of track update. commit 2291d9d92f1f50ebb195e9ddba71fd4b6341e2c4 Author: tdreszer Date: Wed Nov 19 21:41:13 2008 +0000 Removed bothersome 'NULL's commit 9858ebad7a6c39888c2dfef20f294745abc70a8f Author: kate Date: Wed Nov 19 21:36:08 2008 +0000 Add ID to help wranglers commit 42278f1bfaccc20c10aece7cc95dafcb5cdfea74 Author: donnak Date: Wed Nov 19 20:26:53 2008 +0000 Changed contact information for Vanessa. commit 81048004cf8ef199734c95d26ac7230f9995663e Author: donnak Date: Wed Nov 19 20:15:12 2008 +0000 Fixed typo. commit 0a7c0b9db7373c9879980a7d95dcd81d1dac6540 Author: cszeto Date: Wed Nov 19 19:13:29 2008 +0000 Added TSP and Vogelstein datasets commit 4ae1eff58fc110b5314604947577f42499b60895 Author: fanhsu Date: Wed Nov 19 18:57:43 2008 +0000 Updated doStamps.c to deliver a scaled back version PB for GSID. commit 828a7813d1014c04238bddf544e853618cdc8d8b Author: galt Date: Wed Nov 19 16:00:15 2008 +0000 "Encode release log update" commit 9f85f856652916d1386d18de0a14566354869103 Author: galt Date: Wed Nov 19 16:00:07 2008 +0000 "Release log update" commit a1ed9355c30c92af5e83245ba26f6c24aea7f939 Author: jsanborn Date: Wed Nov 19 06:18:03 2008 +0000 updated ABI datasets commit d4d22a2e8b55f76a68e357d7756346f1e5f368ec Author: donnak Date: Wed Nov 19 05:56:40 2008 +0000 Edited. commit 9337e3259425af1f549039f11d4059e9fa27838d Author: donnak Date: Wed Nov 19 03:30:02 2008 +0000 Fixed typo. commit 423950faae81aff5e02833b087bbd523d3e613d3 Author: donnak Date: Wed Nov 19 03:29:21 2008 +0000 Replaced nhgri.ico with nhgri.gif to fix Win IE display bug. Minor editing & formating. commit b940f26bf4fc1b1ed7bc557a3f927d7928bdd504 Author: donnak Date: Wed Nov 19 03:27:55 2008 +0000 Added new images for ENCODE webpage titles & embedded gif. commit c6d6176e78ef3cfa239b6e6248d606c0a31ecb98 Author: pauline Date: Wed Nov 19 00:25:49 2008 +0000 Added equCab2 to list to stage on beta. commit c45bd65812fa3ac5815a51e92742bf6e70d7f0c3 Author: kate Date: Wed Nov 19 00:01:09 2008 +0000 Remove default species commit 0e7dd7403b851961e8751df50079d1dbc73bd359 Author: pauline Date: Wed Nov 19 00:01:04 2008 +0000 Corrected shortLabels to reflect absence of equCab2 nets and chains. commit 2cb7e0d0c1264188b5c1f3dcaa8c3e6df771be1f Author: fanhsu Date: Tue Nov 18 23:51:12 2008 +0000 Adjust background box width for GSID Protein View. commit 0c90179ee1a8bfd9a5cd40b9be284272c27599cc Author: mikep Date: Tue Nov 18 23:31:28 2008 +0000 added new RBP's commit 16bee232f25fd0ee023681a8aca38978fc41a1e9 Author: donnak Date: Tue Nov 18 22:59:07 2008 +0000 Added topbar specific to terms page. commit 17934a8dacee1e6596dfa579f8f46d713f303a72 Author: donnak Date: Tue Nov 18 22:58:03 2008 +0000 Added title images. commit 76279bab8304c4c34eae29bcabc1f43b55779084 Author: hiram Date: Tue Nov 18 22:08:14 2008 +0000 Added rn5 commit 9c04b3874a200e90e8584abf778cd8b471f97a24 Author: mikep Date: Tue Nov 18 22:04:08 2008 +0000 new class of antibodies for RIP project commit 7a4c591b3c860085abefba1bba16f11cb9ac3827 Author: galt Date: Tue Nov 18 21:26:18 2008 +0000 try to detect if BINDIR exists commit 001ee17622d86f9e8fc26a80a4febe5b1ae89767 Author: donnak Date: Tue Nov 18 21:23:37 2008 +0000 Added title .jpgs. commit d5fc907bce137b6d61474fda6e742e1a8c717a30 Author: mikep Date: Tue Nov 18 21:22:42 2008 +0000 First version of Tenenbaum DAF commit 64956b1d681f9ef6cf05ff5aca6144d0a7439d8e Author: mikep Date: Tue Nov 18 20:29:14 2008 +0000 v196 preview, day 2 commit 164bb33af8d0dc3e1627f84da57bde39dd1a53b5 Author: angie Date: Tue Nov 18 20:18:35 2008 +0000 Bugfix: escape quote character when building javascript to check for overwrite of existing session. commit addf6d547d9db485d617c2148ee2141a0c2a6ea6 Author: mikep Date: Tue Nov 18 20:10:17 2008 +0000 v195 commit dd3113df23d486c47c43e0739b8b891082142a0d Author: aamp Date: Tue Nov 18 18:17:19 2008 +0000 Added .sql copying to makefile. commit e64a111358dc9f8ba877dec5322f37f39694d49f Author: galt Date: Tue Nov 18 16:00:06 2008 +0000 "Encode release log update" commit 54cbc714042e442782d10439b99356b8c811cc45 Author: galt Date: Tue Nov 18 16:00:03 2008 +0000 "Release log update" commit 822bedd1595f10d4385ac16631fe6a82f20b1206 Author: kate Date: Tue Nov 18 04:45:19 2008 +0000 Add phyloP conservation track commit 2e76d548e423cfd6bd3951a36cb4b0062c74135e Author: kate Date: Tue Nov 18 04:29:24 2008 +0000 Additional description from Adam. And fix citation format commit f0fb768515054975e488b6c441e8451aa7707dd6 Author: kate Date: Tue Nov 18 01:06:09 2008 +0000 Convert references to pubMed format commit 9b942604532857d3191ac4521dcb5a53c39261f4 Author: angie Date: Tue Nov 18 00:58:47 2008 +0000 Added link to Session Details section of user guide (thx Pauline). commit d33372dd0babb33604c00d817d303620cf253584 Author: pauline Date: Tue Nov 18 00:01:35 2008 +0000 Added new section about session details feature and minor edits to reflect angie's code changes. commit 4e76f4bfd21bb6d0a01f819ea7a4524d867710d1 Author: mikep Date: Mon Nov 17 23:55:29 2008 +0000 until PATH in beta site is fixed not to point to ~galt/bin, put full path to binaries to make sure correct version is picked up commit df714a5fde8c82c5afd41d1d6f06e739513e04e9 Author: aamp Date: Mon Nov 17 23:54:39 2008 +0000 semicolon in comment messes up the command when run by hgCustom running hgLoadBed. commit 25132fdf15f09498a3ee58c754becfbe5406bef5 Author: braney Date: Mon Nov 17 23:37:35 2008 +0000 use sqlDatabaseExists since it's there already commit 98fda2b0d36fe3a90be3a3476ab1494bbeaad883 Author: braney Date: Mon Nov 17 23:36:53 2008 +0000 take out function that replicates sqlDatabaseExists() commit 0fa59811975ba66be6d0e6f4d26d85f223e1aa10 Author: braney Date: Mon Nov 17 23:36:32 2008 +0000 use the correct function commit 4adbfd91d6d1cc573c85df91ee12acdec9f2f3ed Author: braney Date: Mon Nov 17 23:36:17 2008 +0000 this function was the same as sqlDatabaseExists(). D'oh! commit 432b0ba3f13cb29772a6459d61b5ab78ad28bac3 Author: markd Date: Mon Nov 17 22:35:20 2008 +0000 added fixme note commit e0d2c0cb58fb4fb44395dbc0eac250776bd9fe97 Author: hiram Date: Mon Nov 17 21:59:04 2008 +0000 Done with repeat and TRF masking, ready to start alignments commit 61bfbbfc2d4a696c3e01e66f82fdfe51cb3a824a Author: hiram Date: Mon Nov 17 21:58:20 2008 +0000 Fixup the location of finding /hive/data/genomes/ vs /cluster/store* and fix the bug in the determination of .gz present files in the config.ra file commit 101c385aa0ec011c6d300a5566aa617dceef4343 Author: braney Date: Mon Nov 17 21:30:23 2008 +0000 clear up confusion between a database being active and it's actually exisiting. commit 4188b14c616793b4b5518e489bbc18319f86a32c Author: braney Date: Mon Nov 17 21:26:58 2008 +0000 use dbIsFound() to see if we have a database before putting out hotlinks commit 4a531894d962cda6a6ffcfa3267730e58d7d88a6 Author: braney Date: Mon Nov 17 21:25:59 2008 +0000 added function to see if we can actually connect to a database commit a684a8f83531e18b7c6c0f113072f680d8ef861e Author: braney Date: Mon Nov 17 21:20:55 2008 +0000 add new function to check if one can connect to a database commit e1f1201fdc5778854f9e1242b1095775a44f79a1 Author: hiram Date: Mon Nov 17 19:48:05 2008 +0000 Beginning to add the 44way description page commit c5eea40bb69257ce1e7967d5b00a96de1da339ee Author: mikep Date: Mon Nov 17 19:41:20 2008 +0000 skip comments for all bed types; broadPeak, narrowPeak, gappedPeak commit 1aa352a6683b85fd3f26abbd3d1c05266ef53f8c Author: fanhsu Date: Mon Nov 17 19:13:59 2008 +0000 Added link to Protein View. commit bd9d53666dd9f2c8c46d6efce1c486c7184f6f94 Author: fanhsu Date: Mon Nov 17 18:59:13 2008 +0000 Added an example protein ID. commit f10f50857b3a0bc055361d5cd9e4644b26bb6daf Author: mikep Date: Mon Nov 17 18:40:42 2008 +0000 Whole cell short+long+polyA+/- for Affy RNA tiling array experiment commit 0eccee01a0a7bc4c1253439dc20b414c3d7806aa Author: hiram Date: Mon Nov 17 18:32:12 2008 +0000 Updated with three categories identified commit fc5e328b0867917a7e987572a7d7155e91caf6c2 Author: galt Date: Mon Nov 17 16:00:07 2008 +0000 "Encode release log update" commit 3ca13c8bc85da4d260151dbee7690d03253190de Author: galt Date: Mon Nov 17 16:00:04 2008 +0000 "Release log update" commit 8178e5ab3f6768e20b64c394ee04516b83a6841f Author: jsanborn Date: Mon Nov 17 05:32:33 2008 +0000 updated wustl ABI commit 5fcace7f73334608f2d1aff9bc78f28b7ccfe3ca Author: jsanborn Date: Mon Nov 17 03:58:56 2008 +0000 updated/added datasets commit cee01cedd52d9ca43261f15db577dc28c060a325 Author: braney Date: Mon Nov 17 00:27:20 2008 +0000 back to using only upper case in hgTracks maf display commit c82b24c068a8585628908174056a8263e6c53be0 Author: hiram Date: Sun Nov 16 22:19:29 2008 +0000 Adding gorilla chain and net commit 8b02524795393c88dd72996522d231d32bbd8f76 Author: hiram Date: Sun Nov 16 22:13:59 2008 +0000 Correct order for gorilla, chimp commit 83dd7ddc8ad38b668c71f0bed8f9339b8b8ddcd8 Author: galt Date: Sun Nov 16 16:00:07 2008 +0000 "Encode release log update" commit 13300fee5cb9091e72ecffa25e799aaf73c8af53 Author: galt Date: Sun Nov 16 16:00:05 2008 +0000 "Release log update" commit 94fd0f9d113adcd24be4b5de5cc5fb70aaf65dbb Author: hiram Date: Sun Nov 16 05:21:22 2008 +0000 the 44-way track is up and running, needs gene annotation and phylop scores commit a54ad535a019f98bd8eb9e522fd7de5ebab133bf Author: hiram Date: Sun Nov 16 05:11:38 2008 +0000 Turning on 44way multiz track commit 37b768f82091966c1a8fdc436c0ca03bff84cb7c Author: markd Date: Sat Nov 15 16:43:12 2008 +0000 tmp disable of equCab2 commit 41d2719a6b30cddc95a8d4b5a4e8093d2433ab9a Author: galt Date: Sat Nov 15 16:00:06 2008 +0000 "Encode release log update" commit 7cdc354546d1270f9b0836dd37da337a166fa776 Author: galt Date: Sat Nov 15 16:00:03 2008 +0000 "Release log update" commit 7afdd04561c42edc5c87abade3323bd04fba08f4 Author: markd Date: Sat Nov 15 07:07:30 2008 +0000 make safe to include in C++ code commit 9d3abb13403abe3d81673aec4454c0b99e2ac819 Author: kate Date: Sat Nov 15 01:14:01 2008 +0000 Add entry to the project status history table commit 527fad0c60b01cf92da477bee5012f9fe7e81f55 Author: kate Date: Sat Nov 15 00:50:41 2008 +0000 Back out last change for now -- it broke default off button commit 01b50a8bf35d065c157d4afc1509cc9305b2ae4b Author: hiram Date: Sat Nov 15 00:43:47 2008 +0000 The beginnings of Rnor4.0 commit 9acd833742ee8539a58c3244f385ae5637b476eb Author: hiram Date: Sat Nov 15 00:36:17 2008 +0000 Adding gorGor1 and rn5 commit 281f464e3177898bc1a78afb4914186c4fba7a95 Author: hiram Date: Sat Nov 15 00:35:38 2008 +0000 Initial files from makeGenomeDb.pl commit 5fea57de5006fd94273e7c2fac0459ff1c87aaef Author: mikep Date: Fri Nov 14 23:52:38 2008 +0000 new cell lines from Stam lab, pending approval commit 41b144b09d8d001f7b7b55a261d608bd93e201f3 Author: mikep Date: Fri Nov 14 22:15:27 2008 +0000 put version info in, like doEncodeValidate.pl commit 5475f1585d615199edb94fb9f8850ab30fd8d449 Author: kent Date: Fri Nov 14 21:57:40 2008 +0000 Adding Burrows-Wheeler Transform stuff to makefile. commit 094df8cc8e34d3f381ae9e438ca46ebc5f3a3cfc Author: kent Date: Fri Nov 14 21:56:41 2008 +0000 Fixing linux-specific warning. commit 7fd9f858f3a3a00d392af19908d695317ae3d7d0 Author: aamp Date: Fri Nov 14 16:07:54 2008 +0000 Forgot this one. commit 4d1e9938246027d43cb6419425bd104cc28c6411 Author: aamp Date: Fri Nov 14 16:00:12 2008 +0000 Big changes to encodePeak tracks. Added custom track type and changed core encodePeak data structure to bed 6+. commit e7cc6045ed7df0dff66e73e13478784634c9306d Author: galt Date: Fri Nov 14 16:00:06 2008 +0000 "Encode release log update" commit 7d21adbc789f12a01ea5e2aaea0f296d1f978389 Author: galt Date: Fri Nov 14 16:00:04 2008 +0000 "Release log update" commit 0b4bd62a4ff9a7c7a7a1d3b5c64059b3dd1b9b88 Author: mikep Date: Fri Nov 14 01:10:30 2008 +0000 track def in expectation of Uw DNaseSeq data commit 6d8030332ef27f962ee29dd929ed864da239c56e Author: larrym Date: Fri Nov 14 01:00:07 2008 +0000 add encodeThumbnail.jpg next to ENCODE tracks commit 2c14587c3fba362903336a56eb60d6a53729c55c Author: mikep Date: Thu Nov 13 23:51:25 2008 +0000 handle .tar.gz download files, for example, containing multiple fastq files for one experiment commit 2d190aaf85813a5829d4db94cdab0adddcadfa76 Author: hiram Date: Thu Nov 13 22:40:51 2008 +0000 No message in wikiTrackUi() - currently empty commit f3629fd352af5a520bdbfcf2b411421a996304ea Author: hiram Date: Thu Nov 13 22:39:09 2008 +0000 Track Ui is OK, just fix it so it is OK with an empty Ui commit 992dfd1d1470966d82cce5638dc1355e6af0056b Author: hiram Date: Thu Nov 13 22:04:07 2008 +0000 No trackUi at this point, maybe later commit 01419d1f2988c1f407c7643fb451aa2e68f29f6d Author: hiram Date: Thu Nov 13 20:10:25 2008 +0000 Done with Gorilla lastz, now working on the 44-way alignment commit 2da27d0ce2544a0aa30148ffc205ea262da9a97a Author: galt Date: Thu Nov 13 19:41:30 2008 +0000 distinguishing users from robots by presence of hguid cookie commit ff607f6e80d4a9e335dc384995eefe108ccd20ad Author: mikep Date: Thu Nov 13 19:07:47 2008 +0000 forgot that + line name is optional commit d335df5ffc2bee1299eb92a9237cc3699eb3dfe6 Author: mikep Date: Thu Nov 13 19:04:03 2008 +0000 plus line should have same regex as @ line commit 7e035a6879c64213dde5efe8829598fc47aefaba Author: mikep Date: Thu Nov 13 18:27:31 2008 +0000 allow / in fastq seq name (GisPet project), and allow comment lines in bed files commit 002029b92ca923ebcfc8f8bfe35d6e710aab0e21 Author: galt Date: Thu Nov 13 16:00:07 2008 +0000 "Encode release log update" commit 3757d7cea647e50c0cb5a82c629784775891f227 Author: galt Date: Thu Nov 13 16:00:04 2008 +0000 "Release log update" commit b48743f235ec1579fbb3fdaab83d5310aa267832 Author: rhead Date: Thu Nov 13 02:11:16 2008 +0000 Fixed broken links to GRIB/IMIM/geneid. commit 5bf1c0dfb9cd9bc543c8a110f8c5e843dae6101a Author: rhead Date: Thu Nov 13 01:39:03 2008 +0000 Fixed broken links to GRIB/IMIM/geneid. commit f5ebd616b51955a6245368ed1ca80adc4d55830b Author: angie Date: Wed Nov 12 22:45:42 2008 +0000 Updated DGV to v6. commit a8c4aec1f4f36ff69c5e4ec9895b159336e636c1 Author: angie Date: Wed Nov 12 22:40:45 2008 +0000 Added alpha entry for dgv v6. commit 0b50a2b9393e6af5cc72b106200111ab6d595d39 Author: mikep Date: Wed Nov 12 21:58:09 2008 +0000 typo on attatched commit e59a9ca61d630097b7cddc029b3b5f9bbe781072 Author: kate Date: Wed Nov 12 21:27:02 2008 +0000 Change to format name commit 67d0f2049ad1d89b5171f03d6de4cdc4d91bfc15 Author: kate Date: Wed Nov 12 21:03:05 2008 +0000 Add DDF and update DAF for Chromatin Conformation experiments commit c74307c88d4aaaf386ed5f8e6befa082b373e9c3 Author: mikep Date: Wed Nov 12 19:55:07 2008 +0000 matching gzipped tarballs commit 4673f5a5551924951a1371e8f8ffd5a26a1b4815 Author: hiram Date: Wed Nov 12 17:28:41 2008 +0000 The 44-way alignment tree diagram commit 58f79274e545442f863e272d36a374c70d5e2b9d Author: galt Date: Wed Nov 12 16:00:07 2008 +0000 "Encode release log update" commit 959e59ff42f7e2dfa84c555d248a17cde2bcf3b0 Author: galt Date: Wed Nov 12 16:00:04 2008 +0000 "Release log update" commit d0d3a7ca9234828d8b2b56cbf0e47a32875baff7 Author: mikep Date: Wed Nov 12 04:25:09 2008 +0000 "New version number v195" commit f0dcc3f92c5c96cc6d813b9167d706fd7c13a38a Author: larrym Date: Tue Nov 11 20:58:22 2008 +0000 use encodeThumbnail.jpg instead of encode.ico and add a link to ../ENCODE for the encode thumbnail commit 0a63ec22ded42c0aafbd885f5f8f8527667cfb68 Author: larrym Date: Tue Nov 11 20:53:19 2008 +0000 image for display next to hgTracks groups commit 47bcf457cf9f3ce2570c2b951931ca8ae5fe65a5 Author: braney Date: Tue Nov 11 18:02:07 2008 +0000 added a tiny snippet about 'T's in 'i' lines commit 2f04abb8fc1132572760b8f3203d388f6dc9530d Author: braney Date: Tue Nov 11 17:54:36 2008 +0000 added TANDEM annotation commit 277e2f8cc12d568c606dec8bc5b5c150da539915 Author: galt Date: Tue Nov 11 17:43:32 2008 +0000 getting rid of DOS CRLF commit 8e99a3afe0ab726cbaf5d2a0653ba8085d7a354b Author: galt Date: Tue Nov 11 16:00:06 2008 +0000 "Encode release log update" commit 9e5bb24d1206c9cccd0ef606e700d1b7d63e5eb9 Author: galt Date: Tue Nov 11 16:00:03 2008 +0000 "Release log update" commit a2b68dcce5e79079d1f7f95fbb68d9ef31cf4b7f Author: kent Date: Tue Nov 11 15:06:10 2008 +0000 Fixing bug in maf.doc. commit 0367342fad47d89f0c8b2f982f709bf66d2af9d7 Author: kate Date: Tue Nov 11 01:35:31 2008 +0000 Fix species default off feature commit 9fb972244d5fbab9c15e3683df360181f8c13a06 Author: galt Date: Tue Nov 11 01:11:13 2008 +0000 miniBlat improvements commit 8080f11813748e606745617a5718180d41890b45 Author: markd Date: Mon Nov 10 23:45:40 2008 +0000 remove rsync of gbdb symlinks to genbank server commit 032b04684a615144078967cb94d45e363b1a2a7d Author: angie Date: Mon Nov 10 22:45:41 2008 +0000 Added confirmation dialog box to warn when we're about to overwrite an existing session. commit ceb0e5d88ad42e7f379d884cfaa7fcc476f964a5 Author: hiram Date: Mon Nov 10 21:32:17 2008 +0000 Blat server assigned, quality track added following successful fastq processing commit bc8db68651a2409d219923fd0eb5a943ddd08ea9 Author: angie Date: Mon Nov 10 21:00:52 2008 +0000 Added settings field to targetDb (like trackDb.settings). commit 3dfb8201c5d33d3793ebd11271f4ea9d8ee9b0a8 Author: angie Date: Mon Nov 10 20:28:18 2008 +0000 Added PCR target on Ucsc Genes. commit 673f6050cbb6c033fc23e1efe772e4e58567b226 Author: angie Date: Mon Nov 10 20:27:14 2008 +0000 Updated PCR target for Ucsc Genes; got official blat server for it from cluster-admin. commit be7282a0edb179837b2b6b803a5c7ce69168ef28 Author: kate Date: Mon Nov 10 19:40:31 2008 +0000 Add ENCODE restriction date display to table browser commit 33cea0c92ac540eeda2881382b07d3ee53176c0d Author: angie Date: Mon Nov 10 19:15:09 2008 +0000 Tolerate non-existence of toDb; we can show coords even when we can't make an hgTracks link. commit 70b235ff4e961d07a23cf3b277023936da13c9fe Author: angie Date: Mon Nov 10 19:14:15 2008 +0000 Make hDbDbListMaybeCheck public for use by hgConvert. commit 4581234536a623d0d0e2e26e9790f3d0411fc00e Author: angie Date: Mon Nov 10 19:04:09 2008 +0000 When we know fromDb, use liftOverChainListForDbFiltered instead of liftOverChainListFiltered to greatly reduce the number of file stat calls. commit 9c9bcb45d761add332761ace87a2b08b78e18f10 Author: angie Date: Mon Nov 10 19:02:03 2008 +0000 Added liftOverChainListForDbFiltered and make liftOverChainForDb handle NULL fromDb. commit 319a68fdfaf668689f7459d0eedb03ddd115fd4d Author: hiram Date: Mon Nov 10 18:15:56 2008 +0000 This appears to work OK, for both single line sequences and multi-line. The Solexa scoring system has not been tested commit d689bda1b265ff16876da61740cf2c26009d410d Author: angie Date: Mon Nov 10 18:01:01 2008 +0000 When performing the conversion, don't repeat the complex logic used to choose the most fitting chain for the given from and to genome+db, just use the passed-in fromDb and toDb. In the complex logic, don't exclude inactive dbs since we do offer liftOver chains for some of those (we simply don't make links to the resulting db coords). commit bcc9eb49ff99e44bdac8f4f98efa34b051b5361d Author: kate Date: Mon Nov 10 17:40:02 2008 +0000 One more quick pass of rodent multiz for U. Munster group commit ccc70135d998a494ba86e0454634112a10ed06c9 Author: donnak Date: Mon Nov 10 17:18:30 2008 +0000 Added Bob's NAR pub. commit 41df6d86515a80d89e614465550483585f653568 Author: galt Date: Mon Nov 10 16:00:06 2008 +0000 "Encode release log update" commit e5ff145c94f1fe04e8156fc0583ee51963bb2358 Author: galt Date: Mon Nov 10 16:00:03 2008 +0000 "Release log update" commit 90267b8eb6f330173aaba5b96d90e4f26ebe3469 Author: tdreszer Date: Mon Nov 10 02:35:51 2008 +0000 Backing out Crawford hack until I get back and can deal with complications commit 5e100df1cb1da0b6d269b57d8407149f1faee036 Author: tdreszer Date: Mon Nov 10 02:28:54 2008 +0000 Setting these actually used DAF and DDFs in for posterity commit a722968caac951368221c20e8ba18ab2939b932a Author: galt Date: Sun Nov 9 16:00:06 2008 +0000 "Encode release log update" commit c2abf8325496be951eebd3459a4e0f0b20507f5e Author: galt Date: Sun Nov 9 16:00:04 2008 +0000 "Release log update" commit 5d98e9396c3d534faec45a4ad2e27cd32c1fc1af Author: tdreszer Date: Sat Nov 8 19:25:07 2008 +0000 Just about as trivial a checkin as can be imagined commit 786510ae356fe8540be1da79f7e4036605004bfb Author: galt Date: Sat Nov 8 16:00:07 2008 +0000 "Encode release log update" commit 7603b380d914158d857ecadf9a6dde45ceab46df Author: galt Date: Sat Nov 8 16:00:05 2008 +0000 "Release log update" commit 57c3e9398b5c1494ef9f91fb4512f25fc9472772 Author: kent Date: Sat Nov 8 10:46:05 2008 +0000 Code to count occurrences of a string using the BWT transform seems to work. commit 97356699a70bc561f69b164837019505ec5a580b Author: galt Date: Sat Nov 8 05:37:40 2008 +0000 fix archive.status commit 69ee6869387ec759eb518af48fd69f7d973303c9 Author: kate Date: Sat Nov 8 03:18:42 2008 +0000 Add phyloP conservation track commit f7a62d59011aaffe1ecd883e64805a5936ff88a6 Author: galt Date: Sat Nov 8 02:59:24 2008 +0000 bugfix commit ca29728ffd746327ba8456bda29fc80a4f8ce01b Author: galt Date: Sat Nov 8 01:40:58 2008 +0000 better-looking links hopefully commit 5dbd6eb67732c92092c5bab9f87ba49ce3b5052f Author: jzhu Date: Sat Nov 8 01:21:47 2008 +0000 change cancer genomics track setting commit 418695d67979adc274ccdd416ede4de447922422 Author: galt Date: Sat Nov 8 01:17:44 2008 +0000 re-working the links commit 7dbe7a9ca6b470d30c8232fa1ee8b5a4782aea66 Author: angie Date: Sat Nov 8 00:31:38 2008 +0000 Changed pcrResultItemAccName and pcrResultItemName to not collapse XyX__XyX to XyX -- sometimes those are what we get as input, and we need to build them back up to XyX__XyX. So in hgTracks, lf->extra can be NULL -- if so, don't use it. commit 172d40e8de8ad3f0c1d3f8af132cf702a6318f8a Author: galt Date: Sat Nov 8 00:17:50 2008 +0000 adding unload as an admin command available to help when the project has already proceede through to loaded, and re-loading validation would cause already exists error commit 87b3cb86cb9a935e581cf033bb5177efb39f2193 Author: kent Date: Fri Nov 7 23:56:44 2008 +0000 Taking out a lot of debugging. commit 855b26a146a4c1e3072f59a86d444d14f3342194 Author: kent Date: Fri Nov 7 23:55:21 2008 +0000 Polishing diagnotic output. commit 2ef512cb763d790efbbadf5bd9ef3916deb93594 Author: kent Date: Fri Nov 7 23:54:52 2008 +0000 Making suffix output a little nicer. commit eb27cbf6e2d860d6114c8b7dd0425553cf80d47b Author: jzhu Date: Fri Nov 7 23:39:09 2008 +0000 remove outdated -updateLocal and -alphaLocal option commit be1b400068e5d7540fd8530eacccbe2c751637df Author: ann Date: Fri Nov 7 23:14:45 2008 +0000 Added explanation of new chain coloring and chain filtering features. commit 23c078b8b48c891aa3f7e5471dc5c10d90bd0a8a Author: tdreszer Date: Fri Nov 7 22:40:52 2008 +0000 Checked in the wrong version last time. Jeez. commit 1c753967f5168464b7e1b9a78a871e6c21f54924 Author: galt Date: Fri Nov 7 21:38:34 2008 +0000 creating user.role and allowing admin users to login as others to help the wranglers out commit 625f68016c98e6099491d1b575d2f06096136c91 Author: tdreszer Date: Fri Nov 7 21:20:14 2008 +0000 Special case Crawford to put all tracks into a common composite commit c146ea9ddbe6f1d5ad8e3a0c3651a6183635efbd Author: tdreszer Date: Fri Nov 7 20:47:10 2008 +0000 Fixed Restricted until link for ENCODE commit a67c42fd2637dc76e2ba2682f341accd5989c09d Author: tdreszer Date: Fri Nov 7 20:46:10 2008 +0000 Fixed link to Restricted Until document commit 08bbbb8f754e759b3a807d66d0de634b135dfcb0 Author: tdreszer Date: Fri Nov 7 20:44:56 2008 +0000 Additional download only file types for RIKEN/mikep commit 1c5d64a1e1b482ec942966f2a46dbc5e16308753 Author: kent Date: Fri Nov 7 20:38:19 2008 +0000 Niave reverse bwt seems to work. commit e510cbd9c19ebd83e226808b993903350d65fb94 Author: kent Date: Fri Nov 7 20:37:23 2008 +0000 Adding option to output suffix tree. Debugging an end condition. commit e553d6098e388c2d7cbaa11de75f42380be65ca5 Author: donnak Date: Fri Nov 7 20:28:35 2008 +0000 Added a bit more clarification abt oryLat2. commit 528c24f2d0f47efc1850888b575882060aaa7d0c Author: tdreszer Date: Fri Nov 7 19:48:40 2008 +0000 Okay, giving up on decoy composites as a bad idea. Reordered Duke tracks. commit 6b98b39e97e2bde1086382550d2d1b991d3de57a Author: mikep Date: Fri Nov 7 18:26:20 2008 +0000 singular form commit 7a2edfa41974eb1f1d62f9a08509a5f39b850162 Author: kent Date: Fri Nov 7 18:16:31 2008 +0000 Very simple implementation of Burrows Wheeler transform. commit d5225cfb0e1e1ad34d25f10114a165b72a386438 Author: ann Date: Fri Nov 7 17:48:57 2008 +0000 fixed typo commit 4acdb0f0a7293e729fbe5b2d373baccab7a00d2c Author: kate Date: Fri Nov 7 16:56:16 2008 +0000 Leave off submission date that triggers UI for data release restrictions until the explanatory web pages are finalized (with agreement of submitter) commit 811a1bfcb86ffb534fe0ab3c6034e8510ba5bbb4 Author: galt Date: Fri Nov 7 16:00:07 2008 +0000 "Encode release log update" commit 17ae399a672c96d23ffadae22d53da0938eab59f Author: galt Date: Fri Nov 7 16:00:04 2008 +0000 "Release log update" commit aef8779f9afd5ce49aabf3a43e7c0502ac84d96d Author: kent Date: Fri Nov 7 07:06:40 2008 +0000 Fixing a bug in the maxGap=0 case on the reverse strand that was making it so that matches were lost. There remains a bug that makes the matches one base smaller than they should be. commit f8a462713f1c7bcccd46f0d89f6bf440e4a69fa9 Author: tdreszer Date: Fri Nov 7 05:45:48 2008 +0000 This should allow loading submission dirs even when there is no composite track yet commit 9960cba5295d7279756dbea8e7c8032049e6c699 Author: tdreszer Date: Fri Nov 7 05:32:39 2008 +0000 Additional settings needed for decoys commit 3ce74387a146403be7a8544c2403e45826c8fd54 Author: kate Date: Fri Nov 7 02:54:39 2008 +0000 Reannote mafs to include Brians improvements ('T' lines for tandem dups) commit d647e663062e993db737187c4beea291640b3c8b Author: kate Date: Fri Nov 7 02:46:17 2008 +0000 Switch ordering of subtracks and fix default off list commit 6fc92121c9ba9309fbd827af4395398e4e4406e9 Author: kate Date: Fri Nov 7 02:26:42 2008 +0000 1. Change species defaults after input from Elliott Margules -- limit to NISC assemblies with highest coverage 2. Add summary table commit 16d904de196837285326d1e195cda0e0cbe89412 Author: tdreszer Date: Fri Nov 7 02:06:48 2008 +0000 Added DECOY composite tracks for ENCODE pipeline commit 6beb420264148cb6304c4fc5a2e099d419f1f961 Author: tdreszer Date: Fri Nov 7 01:11:36 2008 +0000 Forgot dimensions setting in trackDb composite track settings commit 1fa1be03f82ed4338dd3c495a65538fd0c4fccff Author: galt Date: Thu Nov 6 23:42:07 2008 +0000 getting rid of chmod we do not have permissions to perform anyway commit 9c2810ef8cee78ca5f90a7b9f945b77b11f9cd87 Author: tdreszer Date: Thu Nov 6 23:36:41 2008 +0000 encodeftp is no longer mounted. Use /cluster/data/encode/pipeline/bin commit 4e50377127e368270b25abb3af88af2272846988 Author: markd Date: Thu Nov 6 23:12:51 2008 +0000 reenabled hack to keep NFS directories open commit df6fb67bb7efb5c40cfbcec8616a3ccda4fa3ea7 Author: tdreszer Date: Thu Nov 6 21:55:51 2008 +0000 Minor formatting issue commit 76dee17b0593c420150b4627d9d0f49b3da32aa9 Author: tdreszer Date: Thu Nov 6 21:54:55 2008 +0000 Minor formating fixes commit eb527ffd93fb4939ff71e52deefe5f76c070544d Author: tdreszer Date: Thu Nov 6 21:54:06 2008 +0000 Cut an pasted makefile referred to schemas commit c9d4e33f4ede3103af921bbb2674ab9f015f1432 Author: fanhsu Date: Thu Nov 6 21:41:09 2008 +0000 Changed genome-cancer to cancerGenomics for group. commit 563fc3d4686e6985fa7056371e40ab3dfa620bea Author: kuhn Date: Thu Nov 6 19:58:58 2008 +0000 moved ucscGenes up in priority so Gencode track is not in front of it commit 4cadebac9c3e74ba0d696f8020c4aa6fa5f89cc1 Author: kent Date: Thu Nov 6 19:25:04 2008 +0000 Making it work on genomes larger than 2 Gig. Suppressing reads with N's. commit 43259ebe0df27e76b68c93b5ffa2e3a17b730141 Author: pauline Date: Thu Nov 6 19:23:34 2008 +0000 Added new medaka to genbank update list for RR. commit 285c6f65dc89fca293b8fc2f7d5b2175f4782d4f Author: kate Date: Thu Nov 6 19:03:23 2008 +0000 Change sorting slightly commit 779aaa304d926aae94ce3d9c8db65b9ced665d88 Author: kate Date: Thu Nov 6 18:57:49 2008 +0000 Remove debugging bit commit 583c00497a04e382a89843fa738d6839b3e6f6c5 Author: fanhsu Date: Thu Nov 6 18:53:57 2008 +0000 Changed "group x" into "group genome-cancer". commit c9ee0436d32892d6f82a54a84839860b00334387 Author: kate Date: Thu Nov 6 18:32:59 2008 +0000 Cosmetics commit ee48f8dc7188333315a22fd2fb412d07877a0c73 Author: kuhn Date: Thu Nov 6 18:23:25 2008 +0000 tweak commit 598602b678b441a304cf51948795ae8d407e2422 Author: fanhsu Date: Thu Nov 6 18:09:41 2008 +0000 Changed hAllocConn() to hAllocConnProfile(). commit fe5f31c952a5141b6aa9dca7279bf463def8893d Author: kate Date: Thu Nov 6 17:58:57 2008 +0000 Checkin Tim's changes: add update time and link to track in browser commit 8665be3dc5190017dfde62da568b21d1d7cf19a3 Author: kent Date: Thu Nov 6 17:33:18 2008 +0000 Adding randomPos option. commit ee0e52f919a8d5bd72ba1ff5411a76f2fded6492 Author: fanhsu Date: Thu Nov 6 17:14:03 2008 +0000 Added hFindTableInfoWithConn() to support that tracks data may be from different hosts. commit e8b6e3352a8e68cf499a264c8a52ab81124578a3 Author: fanhsu Date: Thu Nov 6 17:11:38 2008 +0000 Added getTrackProfileName() and hFindTableInfoWithConn(). commit 7427e31c4ca21924d73ec709c8fb735a4a29266e Author: galt Date: Thu Nov 6 16:00:10 2008 +0000 "Encode release log update" commit 8ba3b68d0ed55e82a6f529b8893d4b01872244a5 Author: galt Date: Thu Nov 6 16:00:07 2008 +0000 "Release log update" commit 1d456fde8c3f3ff94ddba5ea17a2443869bb95e9 Author: kent Date: Thu Nov 6 07:03:00 2008 +0000 Putting in copyright notices. commit 3d9116477ae837a9c6d016d899340c55621f2591 Author: kent Date: Thu Nov 6 06:59:01 2008 +0000 Commenting out unused variable. commit b8064097bdaa6ec9a766e1b44f9d1f83b630f3d9 Author: kent Date: Thu Nov 6 06:58:26 2008 +0000 Fixed comment. commit f175cb37641e83a2ae8262fbf504e13117e9bd21 Author: kent Date: Thu Nov 6 06:58:00 2008 +0000 Got rid of a debugging statement. commit efdb10e809a4ba8585481d59d9a93bff79c44300 Author: kent Date: Thu Nov 6 06:57:11 2008 +0000 Adding splat output optoin. commit 00a3eba9e03b0faa07612919df11698396ff5834 Author: kent Date: Thu Nov 6 06:56:37 2008 +0000 Adding new shortRead programs to higher level makefile. commit ba266208bb1ea35adec5a5c337dd10f13b080ded Author: kent Date: Thu Nov 6 06:55:57 2008 +0000 Moving some routines to library. commit fbbc41c22d8d871c639432f946b786b135df313d Author: markd Date: Thu Nov 6 06:46:36 2008 +0000 fixed missing org name when transMap labels defaulted commit 638a1db725536bd9002dce97ba7cb280f75324d4 Author: kent Date: Thu Nov 6 06:45:01 2008 +0000 Implemented -multi option commit 4f55a10ee09c25bc4db9ac2bc532ac278973e8e6 Author: kent Date: Thu Nov 6 06:41:14 2008 +0000 Adding test case commit 86d9148bc64eb9250dc1834e4b8eb847dd4ce5c6 Author: markd Date: Thu Nov 6 06:05:17 2008 +0000 don't wipe out LD_LIBRARY_PATH commit c93cd178d69f700c6b984343beac8fce980cc494 Author: markd Date: Thu Nov 6 05:08:06 2008 +0000 add another subspecies commit ab1c7a3e2981153bac5a24ae8984a74fc3620923 Author: kent Date: Thu Nov 6 05:07:06 2008 +0000 Moving several routines from splatMerge to library. commit 0513af87aa2381218db1b6b5ea1173c9852b3880 Author: kent Date: Thu Nov 6 03:54:09 2008 +0000 splat to eland format converter seems to work in the non-multiple case. commit 67d34042edd28da1d9b6c7843999b105d58bd4c9 Author: tdreszer Date: Thu Nov 6 00:32:14 2008 +0000 Extended the controlled vocabulary lookup nomenclature commit 67ad254f809224bccfbbd3890735ebdb8cf6ff56 Author: pauline Date: Thu Nov 6 00:31:12 2008 +0000 Changed default position to one with more features. commit 8666cb93470864dd73ce5a2d2240bc3b4f9a4f16 Author: tdreszer Date: Thu Nov 6 00:30:19 2008 +0000 Extended options for controlled vocabulary lookup commit f4eabb3f5c027b1d180db08d28af974d67f8d43b Author: tdreszer Date: Wed Nov 5 20:16:32 2008 +0000 Almost done scrubbing. commit f785193ea07a4cae7424d0fbe21ce075f7e7780b Author: tdreszer Date: Wed Nov 5 19:33:10 2008 +0000 Renaming DukeDNase to this Chromatin Map page to hold Duke/UNC/UT-Austin data commit b6cb8dc19baad7f3038c84b57f069571dfc5a046 Author: tdreszer Date: Wed Nov 5 19:28:39 2008 +0000 A bit more cleanup before contacting Terry commit c289213df171adab9e73ea50ee509a7cc7a70eff Author: tdreszer Date: Wed Nov 5 19:19:34 2008 +0000 Adding ENCODE Chromatin Map from Duke/UNC/UT-Austin commit c9338f8fef7f1ba1e16132ab85743ff8032b8688 Author: kent Date: Wed Nov 5 18:37:56 2008 +0000 Looks like it works, at least on the eland outputs I've got handy. commit a6b8fdf51cbbda41df586aaa17985715d7fcfeb4 Author: galt Date: Wed Nov 5 16:00:06 2008 +0000 "Encode release log update" commit 53400a319f3c9af3f7b28a1b50c39fd3d59bdbc9 Author: galt Date: Wed Nov 5 16:00:04 2008 +0000 "Release log update" commit 7ad44677a714c97d6ff315eb887911fb7180b5c7 Author: braney Date: Wed Nov 5 14:10:27 2008 +0000 add ability to *not* color chains and to filter on a particular chrom commit 4347e8272da9b43b46688175448af63eb1a3fa55 Author: kent Date: Wed Nov 5 08:01:27 2008 +0000 Adding worseToo, maxRepeat, repeatOutput, minScore options. commit 35cfec77337d5c7752cc03ed805cca80fa4c0aa1 Author: kent Date: Wed Nov 5 05:51:02 2008 +0000 Removed some unused variables. commit 24978087a288e51133121c74e0bba1871dcea07a Author: kent Date: Wed Nov 5 05:50:05 2008 +0000 Conversion program from eland to splat format seems to work. commit 943c016f4424a152ddf32c637613a1b69d5031ea Author: kent Date: Wed Nov 5 03:55:35 2008 +0000 Just checking in to take it home. commit cda355c17ab80945743e94fdc57ad8b270495d1f Author: kent Date: Wed Nov 5 00:02:09 2008 +0000 Checker for short read aligners (including splat) on MAQ-derived test sets seems to work. commit e31bb8e94045e2028d96dddb3587a36ce0b060a5 Author: hiram Date: Tue Nov 4 23:26:31 2008 +0000 done with repeat masking commit f687d8148c6878d9c39b9f6a12f276f28a0c1a97 Author: hiram Date: Tue Nov 4 23:16:07 2008 +0000 Please, no mention of Adrian commit 809d05c54efbe8c9bce117179652339408d99755 Author: fanhsu Date: Tue Nov 4 22:40:51 2008 +0000 Created trackDb.genome-cancer.ra for the public cancer genomics browser. commit ef4446bad8b17fbe8524d4ebbade7dbcdaac6f75 Author: donnak Date: Tue Nov 4 22:12:18 2008 +0000 Minor edits. commit bead5bdcb626ce1eaa1f93676003f94ae606cf85 Author: kent Date: Tue Nov 4 20:28:26 2008 +0000 Got rid of unused variable. Tested. commit b361de32dca75e59068a4fae8bb1715937382ccd Author: kent Date: Tue Nov 4 20:21:37 2008 +0000 Utility to convert bfast mafs to something that actually is a maf might possibly work. Needs testing. (FOrgot I was working on laptop and needs testing at UCSC, hence the commit..) commit 101400d4178d4ab093803b904d32e8ed8aa7bbe5 Author: hiram Date: Tue Nov 4 19:45:02 2008 +0000 updated with appropriate photograph commit eb2aae7f7a96fc5958b74be4d9116ea98b27390d Author: hiram Date: Tue Nov 4 18:58:16 2008 +0000 Gorilla image from Adrian Pingstone, Wikimedia Commons commit 3e084ba4fd617f6ba46a6625fb98aebc029ec979 Author: kayla Date: Tue Nov 4 18:35:28 2008 +0000 typo: editting --> editing commit 44841d94bf3b41212547f771e15014bcac049f0d Author: galt Date: Tue Nov 4 16:00:06 2008 +0000 "Encode release log update" commit 1f91379f0573d196f5802d05af4810c9e3de8670 Author: galt Date: Tue Nov 4 16:00:03 2008 +0000 "Release log update" commit 1a3b8500428801933e24f8a2b024c4cced14614b Author: mikep Date: Tue Nov 4 15:03:11 2008 +0000 added FilteredRawSignal and fixed up ddf commit 813e5abc176a9b77200092eb6e2e20b9009472fe Author: galt Date: Tue Nov 4 09:50:33 2008 +0000 workaround for minor rails problem, can not use the word load in a controller action commit d0484d39833b7c57e77206fd5bf3f82cb8966ca0 Author: galt Date: Tue Nov 4 08:39:45 2008 +0000 fix security so admin user is reserved from normal users, but if login admin is set externally, then user admin can is authorized to change other users projects commit 789da6f8b03e8747c80601338fa3336ed852883a Author: mikep Date: Tue Nov 4 07:22:27 2008 +0000 195 preview settings commit ba6ab0333b86b3ec445633d4ad87e06a14b6934f Author: angie Date: Tue Nov 4 07:19:34 2008 +0000 More accurate description of upstream*.fa.gz in bigZips/README.txt (Thanks Ann and Mark). commit 1c99711c9828cb25cf95557ae9fe40eb3bfba956 Author: galt Date: Tue Nov 4 06:55:36 2008 +0000 use rename instead of copy and del, set perms to 664 on expanded files commit 9da642308ebc7cfb17ab33a7b3021002867b8071 Author: tdreszer Date: Tue Nov 4 05:47:49 2008 +0000 No validation needed for softwareVersion commit 28b0032f3c6fc10411c3db870085993223152f9d Author: galt Date: Tue Nov 4 05:33:15 2008 +0000 fixing security bug to restrict unauthorized users from more than just looking - we meant to do this and then forgot commit e4fa203838e9313d45ecc2ffb1c72abce4425f8f Author: galt Date: Tue Nov 4 05:12:06 2008 +0000 delete_archive should never have been in the exception list commit 48e200cc62087ff9cf0f2ac48d47f36f39af66a0 Author: fanhsu Date: Tue Nov 4 01:01:52 2008 +0000 Re-built the gsidClinicRecWithSeq table. commit 519817c097ff97d4f81b4b0183fce8ae38ef43e6 Author: fanhsu Date: Tue Nov 4 00:59:52 2008 +0000 Re-Built the gsidClinicRecWithSeq table. commit e068f3a2a9f39ca0eac18ff5718b2234166d978b Author: fanhsu Date: Tue Nov 4 00:57:49 2008 +0000 Re-built the gsidClinicRecWithSeq table for all 4 genomes. commit 4823fbd8a8262c67a7daf3150a51c9f8afd793b7 Author: donnak Date: Mon Nov 3 19:29:06 2008 +0000 Edited this page. commit b612e1f2ec2282af0df5267b98009587da5eae2b Author: kent Date: Mon Nov 3 19:07:33 2008 +0000 Making a routine that just reads a single twoBit structure from an open file. commit c4644ca0ff1a63e470fdfbd739b6528035d770d0 Author: kent Date: Mon Nov 3 19:06:30 2008 +0000 Just doing some preliminary timing tests. commit d9d7000ba5014f04a0d3efce4ae03ddaec8ca317 Author: mikep Date: Mon Nov 3 18:28:58 2008 +0000 added an optional FilteredTransfrags view for stuff which affy have filtered to remove known annotations commit 9b3c57f4ad41279f7f0ade00104f27658ab23080 Author: hiram Date: Mon Nov 3 18:16:18 2008 +0000 May have an assembly now, running RM and TRF commit 478c825b565ee8f58c646ae8f7ca674be4f4b259 Author: tdreszer Date: Mon Nov 3 17:31:40 2008 +0000 Check in support for building index.html in downloads directory commit 193d8d3d3e229a33a8a802ebbbcfc53b36a71194 Author: tdreszer Date: Mon Nov 3 17:28:47 2008 +0000 Make sure to default sendMail as false commit eb224770564268badcc60df7d5104711127eb182 Author: mikep Date: Mon Nov 3 17:00:49 2008 +0000 adding script and time for debugging commit 91164335784447ce920a0e79ea1dd85065284806 Author: galt Date: Mon Nov 3 16:00:04 2008 +0000 "Encode release log update" commit 7c982f330d2b1be17e36687b9734aa0f78646e3d Author: galt Date: Mon Nov 3 16:00:02 2008 +0000 "Release log update" commit 4ff856368b177127d9e4ec305c1f669812fac6eb Author: kent Date: Sun Nov 2 20:18:05 2008 +0000 Fixing bugs in mismatch case. commit 472ca8fb5c03dd021c1daa8eec6a234f82193a3f Author: galt Date: Sun Nov 2 16:00:03 2008 +0000 "Encode release log update" commit a607e7e29e931976e802991ad9e23c0c9e78155c Author: galt Date: Sun Nov 2 16:00:02 2008 +0000 "Release log update" commit 71f61594d75e1e67cb5b1b0c367231eb1113ecc3 Author: markd Date: Sat Nov 1 22:04:50 2008 +0000 implemented building blat target db files for mRNAs commit 13e9712d508a44c7f5375227f8306554b1e4aa1c Author: galt Date: Sat Nov 1 15:00:05 2008 +0000 "Encode release log update" commit 7f8f8692e111e9f001f9434e66132f30effcd0e6 Author: galt Date: Sat Nov 1 15:00:04 2008 +0000 "Release log update" commit fbb05294db819492c03c9810f0f17bbdcfecbaa7 Author: angie Date: Fri Oct 31 23:55:42 2008 +0000 When invoking customFactoryTestExistence, I used to pass in NULL, and cFTE would get the db from the custom track, in order to avoid an hSetDb when cFTE calls hGetMinIndexLength. Unfortunately the Genome Graphs CTs don't have db in either of the places I found them in custom tracks. Fortunately, Mark has fixed up hdb so that there is no hSetDb and I can pass in the appropriate database to use. commit 0fae1f1332370d862d2f1b18ec87f7c30b13eec2 Author: fanhsu Date: Fri Oct 31 22:34:29 2008 +0000 Added hIsCgbServer(). commit d1baa7e9a7b9af55a6c1ec5fef1578d92d9fe06d Author: donnak Date: Fri Oct 31 20:54:04 2008 +0000 Added pub by Baertsch. commit d4b9ba3d4104550b684da8f81f127a8bb5625c5a Author: hiram Date: Fri Oct 31 20:42:19 2008 +0000 Rebuild linSpecRep to continue running syntenicNet alignments commit e8023606b9b81a431cd4ec232d54ae1fa3e040b1 Author: hiram Date: Fri Oct 31 20:41:48 2008 +0000 Run a syntenicNet on galGal3, RecipBest for Lizard and Platypus for 44-way multiz commit ee3e2a6d885446ac6cf81088a5c99da73b12be6d Author: galt Date: Fri Oct 31 19:52:28 2008 +0000 adding checks to make sure that the project is not already doing background work commit f536b603368571cdb2a394243fc75bba3d5bd958 Author: galt Date: Fri Oct 31 18:32:53 2008 +0000 fixing another wording change - back to the future! commit ad4b45e6ee91b4910761db3053883e30bdb8b480 Author: fanhsu Date: Fri Oct 31 16:54:03 2008 +0000 Added ";". commit 30bbca8e9c83464191ce4c40f0657c1a2b30b782 Author: fanhsu Date: Fri Oct 31 16:22:53 2008 +0000 added sqlGetHost(). commit f41222f907e6ed70383e15afe5f53546bfe41a25 Author: galt Date: Fri Oct 31 15:00:06 2008 +0000 "Encode release log update" commit 40375d011592537de600aa68a361da4ff9c4ee3c Author: galt Date: Fri Oct 31 15:00:03 2008 +0000 "Release log update" commit e82b01f27aaf51c478d85ca9c8e4d20f99dd80b0 Author: kent Date: Fri Oct 31 05:51:59 2008 +0000 Making exact searches a bit faster. commit f0482b8b21a3992e5d2bd3f234bf42fd11238a33 Author: kent Date: Fri Oct 31 05:45:05 2008 +0000 Adding -maxCount parameter to help tame itsaDump large files. commit 0e79408054152597f1eadfa7b2ab9c1f17cced72 Author: kent Date: Fri Oct 31 05:44:21 2008 +0000 Tinkering on allowing substitutions in itsaFind, but still not working. commit 89b02aaeaae1a3ac22c6920e7877747e000eb705 Author: kent Date: Fri Oct 31 02:54:36 2008 +0000 Doing a simple 16-base index for speed comparison. It ends up actually not being as fast as the suffix array stuff, which makes me happy. commit 5837d4bfb024c2eea558e8f58211c72dd8fbd1f7 Author: markd Date: Fri Oct 31 00:38:35 2008 +0000 fixed bug combining -meFirst and -txStarts options commit 3fb744410aa3a7f5614d53a1aeefb8fbd5712571 Author: angie Date: Thu Oct 30 18:00:12 2008 +0000 In printPcrSequence, correct the link text to use tStart+1 -- don't know why I thought in 1.1465 that gfPcrLib's outputFa didn't. commit dc25a37a0182fa1270c18017e22430d9a891d93d Author: tdreszer Date: Thu Oct 30 16:49:17 2008 +0000 Initial checkin for utility to make the ENCODE downloads (index.html) using preamble.html and trackDb entries. commit 4bea9b17f3567f6680c9a9e93df233ad9afae4f4 Author: kent Date: Thu Oct 30 16:11:41 2008 +0000 Some work towards supporting mismatches, but it's not far advanced. commit 5f59d0c36bc10ebc5eb211a43f1fbd5a3379a1fb Author: galt Date: Thu Oct 30 15:00:06 2008 +0000 "Encode release log update" commit 7cbd830f910982792a78aee14cb4e60c92fb3dea Author: galt Date: Thu Oct 30 15:00:03 2008 +0000 "Release log update" commit 395977fa488650be6569e701fbbbed4f40a0c45f Author: kent Date: Thu Oct 30 09:27:59 2008 +0000 Adding dnaSeqCmpName. commit df2a96623879a53c59350aa0a9ccb09e2e310f93 Author: kent Date: Thu Oct 30 09:27:23 2008 +0000 Adding verboseTime - like uglyTime but not just for debugging. commit d04fcefce18298ffd9159223ce1ca7429b5e20a6 Author: kent Date: Thu Oct 30 06:59:34 2008 +0000 Moving some little shared base-converting utility stuff from itsa apps to itsa libary. commit ee6730593c58250afc8a893f2a6468bc93204c4b Author: kent Date: Thu Oct 30 06:54:15 2008 +0000 Making it a little more friendly about reporting status during this long build process. commit afd72a383f8621b809f44b61b83a996b811d5f8d Author: donnak Date: Thu Oct 30 05:51:14 2008 +0000 Archived an item. commit 6d058622baf8577e35ff0f8faf0a34eb27e141e6 Author: donnak Date: Thu Oct 30 05:51:03 2008 +0000 Added announcement abt oryLat2. commit c111a677a35198b30dd4148152251a1f1229623a Author: kent Date: Thu Oct 30 05:16:32 2008 +0000 Replaced the big read with netReadAll. commit e8997017c2884d745b304e2e8fb72e0778b7536d Author: kent Date: Thu Oct 30 05:07:10 2008 +0000 A little cleanup. commit 378b21acc1e6b5289c69d5d47ef0b39031de0623 Author: kent Date: Thu Oct 30 04:54:22 2008 +0000 Removing stray newline. commit c01137d6fc50ca93e01d57a138faac9e2c7c701e Author: kent Date: Thu Oct 30 04:54:07 2008 +0000 Adding itsa utilities to makefile. commit 038abf350859dfc416d8c2dc69a6c29626a4a121 Author: kent Date: Thu Oct 30 04:39:24 2008 +0000 Changing read to netReadAll, since on /hive the read stops after 2 gig. commit 1430f0b87efa24cfdfd785b469e96ed60044ae56 Author: kent Date: Thu Oct 30 04:38:29 2008 +0000 Removed some unused code commit 614e424a5a37e8c1fb74ab88e39357d443e77691 Author: kent Date: Thu Oct 30 04:37:06 2008 +0000 Adding itsa module. commit 755eba5ac4caff92ee2474f4a70c21a9c1ede8bf Author: kent Date: Thu Oct 30 04:34:09 2008 +0000 Indexed Traversable Suffix Array (itsa) check in, basically seeming to work. commit af348b4c556e20c7cde8c09a3af376a1b0facc23 Author: kent Date: Thu Oct 30 04:29:26 2008 +0000 Fixing some ints that should have been bits32 that caused problems on full genome tests. commit 040d229388c1ecbdf577282915fa2ca60e3217ad Author: kent Date: Thu Oct 30 03:13:08 2008 +0000 Changing netReadAll to return size_t instead of int, which works better on files bigger than 2 gig. commit 03bc38fcee7f1406e44d0939df753ecc1c094980 Author: donnak Date: Thu Oct 30 00:35:51 2008 +0000 Added a note abt oryLat2. commit 0b25585c135bd89b9f373b91e714e3cb5e913a96 Author: donnak Date: Thu Oct 30 00:31:12 2008 +0000 Replaced oryLat1 with oryLat2. commit 39ff6c3f42261d68cd82a4490f57ff2d41043940 Author: markd Date: Wed Oct 29 23:38:54 2008 +0000 fixed incorrect check for refseq NM; beer for mikep commit 7cd0937ca4b3a43c74308aae6204a3eb2b57a7bc Author: donnak Date: Wed Oct 29 23:30:41 2008 +0000 Added oryLat2. commit 3de88dbfbabff8ced6d9228233b7e36e26aeaa10 Author: hiram Date: Wed Oct 29 23:27:06 2008 +0000 vicPac1 done with recipBest commit 15636374401d14451ce843624e6f3f66c01b3913 Author: jzhu Date: Wed Oct 29 18:34:55 2008 +0000 change makefile to add option to build public cancer browser html pages commit 093df99c73e397f9388635b2ed799ff90fef9c85 Author: mikep Date: Wed Oct 29 18:14:48 2008 +0000 added optional Signal for when replicates are sent commit d73aab0f803af5abc0cd4fd00036967f1840fde4 Author: mikep Date: Wed Oct 29 18:10:17 2008 +0000 added replicates to UwDnase for Richard commit 7d5c2a3af26fba1384b823fae5cf1196f12ca10e Author: hiram Date: Wed Oct 29 17:38:20 2008 +0000 Set some long-ago done items to status DONE, finished with alighments for pteVam1, tarSyr1, proCap1, choHof1, dasNov2, loxAfr2, almost done with vicPac1 commit ccf1c529285cd89a4824e215a222913ac9cebbed Author: galt Date: Wed Oct 29 15:00:05 2008 +0000 "Encode release log update" commit f38d28574fad6bf9d1863be143098e60ae2404cd Author: galt Date: Wed Oct 29 15:00:04 2008 +0000 "Release log update" commit 508867d6fa5283278c1f1daff03e5024998f9bd2 Author: braney Date: Wed Oct 29 14:05:22 2008 +0000 oops... take out spurious printf commit 266c5ac4acf405a3697b626d45af8d8da485ad3d Author: kent Date: Wed Oct 29 02:01:00 2008 +0000 Changing an int to 64 bit in hopes of preventing overflow on 3 gigs... commit 0364023ba82d21ac609851b5315fc0435396435b Author: kent Date: Wed Oct 29 01:59:02 2008 +0000 Adding timing info. commit 84bf4acf68940caea79bce45da6c042c62449024 Author: kent Date: Wed Oct 29 01:54:41 2008 +0000 Describing the data structures and algorithm for the traversable suffix array. commit 4bbd1aa627287f3fb0edcb15a636f7b654d57a94 Author: kent Date: Wed Oct 29 01:30:55 2008 +0000 Improving comment. commit 050091d0fc49b0d2c60efdc5c6d0d5643b5345fb Author: kent Date: Wed Oct 29 01:27:13 2008 +0000 Fixed typo in comment and improved layout of comment a little. commit 734d4d979681b4dbd1130d03746c8bacec4f6aeb Author: kent Date: Wed Oct 29 01:23:11 2008 +0000 Fixed typo in comment commit 33208b2738e4654eb40d7f7b8669a8f70f6465c7 Author: kent Date: Tue Oct 28 23:38:22 2008 +0000 Putting copyright on all files. Some of them are licensed on the spot, but the less obvious ones I'm reserving all rights for now. commit 2986c06ab859eb606de329a7594cbd634c58467a Author: kent Date: Tue Oct 28 23:24:39 2008 +0000 Seems to work with mismatches. commit 6be8941092a106cc32e1693d2ef3ce9b4ea87d9f Author: angie Date: Tue Oct 28 22:45:37 2008 +0000 Replace other uses of "Load" with "Use" or "Restore". commit 28eb35de57402ce5b8095cdc862523a43cd4f8c8 Author: ann Date: Tue Oct 28 22:39:55 2008 +0000 Removed incorrect statement. commit 76db14a09320b9843743fc7fdeea593ff10b9a2f Author: angie Date: Tue Oct 28 21:48:42 2008 +0000 Changed label of loading buttons to "use" -- Pauline felt this would be less ambiguous. Added confirmation dialog to delete buttons. Several updates to details page: 1) when changes are made page, "accept changes" button background changes color; 2) "use" button also accepts changes before loading; 3) added cancel button. commit 60b6b3b272e469f796f2fddb66f56f9434685d1e Author: hiram Date: Tue Oct 28 21:37:56 2008 +0000 Update sourceName description with NCBI project number and LOCUS accession commit c51f657c1940926bd09d218f932207f9cecc449f Author: tdreszer Date: Tue Oct 28 19:49:15 2008 +0000 Added -sendEmail option commit 05fd9130fea496e87ca7f09da835abf988e9a157 Author: kent Date: Tue Oct 28 19:09:19 2008 +0000 Added end condition that handles matches to short queries. commit 74e6c716da15df054599338eae3972d77aaf7204 Author: kent Date: Tue Oct 28 19:07:40 2008 +0000 Some tests for various end conditions. commit 8032de63836b3b5226dcecf6f78b32fbf8051a9d Author: kent Date: Tue Oct 28 19:04:23 2008 +0000 A diabolically simple test set. commit 4b2789c0bcdda7c8336b91adfe190d555a3c9cf7 Author: mikep Date: Tue Oct 28 17:35:40 2008 +0000 day 9 commit 98120a5a953cadf2ac940bce91b60bf8bd252c65 Author: mikep Date: Tue Oct 28 17:35:26 2008 +0000 added host to debug output commit f54ecaf003193c10e736494584e90c48e0ff0086 Author: tdreszer Date: Tue Oct 28 17:24:48 2008 +0000 restricted to RESTRICTED trivial change commit 41028aedcde2818cdd08ff84955404f4379ca400 Author: tdreszer Date: Tue Oct 28 17:20:54 2008 +0000 Minor formatting improvements and dateReleased put in place commit 019b5ee9080f1ad0568428bc50dedede66fbf689 Author: tdreszer Date: Tue Oct 28 17:19:34 2008 +0000 Keeping up with expections isn't easy commit 2bb5790ead12844c470c56d2718303cfeda2bad8 Author: tdreszer Date: Tue Oct 28 17:18:27 2008 +0000 Highlight RESTRICTED in readme commit e6ec4cbec61cfc905b5f9adbad79dfd4d85bbc1c Author: tdreszer Date: Tue Oct 28 17:11:05 2008 +0000 DAF v1.0 commit b647993150cf6832cfb601b8dccd661e0d420c14 Author: mikep Date: Tue Oct 28 16:48:27 2008 +0000 download changes to view=RawData type=fastq commit 0a1ed49ead25e9fe53d337ee149eeb7e1cacba5a Author: mikep Date: Tue Oct 28 16:45:14 2008 +0000 update from richard sandstrom commit f744cf752b84e98f415d9efd8ff0991ab051d2b3 Author: tdreszer Date: Tue Oct 28 16:43:46 2008 +0000 Allow verion 1.0 DAFs commit 3e85f7d0761acc668e5735e2217be5e5ca3499b9 Author: mikep Date: Tue Oct 28 16:36:23 2008 +0000 "New version number v194" commit 9027cf9bf5bc0034fafc63b7add48e7701540100 Author: galt Date: Tue Oct 28 15:00:06 2008 +0000 "Encode release log update" commit a2f142de2fb301b6b7e8c4ba8f742e4e1b57e6ef Author: galt Date: Tue Oct 28 15:00:04 2008 +0000 "Release log update" commit cad982857473dc57c146b60ef567a67d37bcfade Author: braney Date: Tue Oct 28 13:48:15 2008 +0000 deal with TANDEM dups commit a438c054ee479062c23eb6574be1a321078ffbf8 Author: braney Date: Tue Oct 28 13:46:14 2008 +0000 deal with TANDEM blocks ---------------------------------------------------------------------- commit c3c402e156bc0ebf74ec77413b1a5633cea96f44 Author: braney Date: Tue Oct 28 13:44:38 2008 +0000 deal with TANDEM blocks commit 7234f8e348ff1ac4237ad228241b95f8fc843b23 Author: galt Date: Tue Oct 28 08:19:58 2008 +0000 adding better support for local uploads and bigger tmpdir space commit 9bd15bd7cbec3f84ec9e9496f0bdafdb7070dba2 Author: kent Date: Tue Oct 28 07:39:05 2008 +0000 Got rid of unneeded mysql.h include commit c4c0e63e5a64007c5b2a7d45aec901c761e929dc Author: kent Date: Tue Oct 28 06:39:30 2008 +0000 Removed some debugging. Added some comments. commit f38e3347b18af11a93d0e5aaa627b8309039e7a3 Author: kent Date: Tue Oct 28 06:14:38 2008 +0000 Taking out last memcmp from the main loop. You still need a few memcmps after the array traversal has narrowed things down a lot. commit 7243be497d34b322f217b775e64b09f1b0cadfbd Author: kent Date: Tue Oct 28 03:49:57 2008 +0000 Removing debugging messages and improving commenting a hair. commit 727aae07eb0be2ef3c49aaa6386c75628ff7f02e Author: kent Date: Tue Oct 28 03:45:00 2008 +0000 Slight reformulation of traverse list seems to do wonders for some bothersome end conditions. Eliminates a memcmp from the loop. commit d1dbaa39455a9d97df6c0d60795b07673be97ff7 Author: kent Date: Tue Oct 28 00:59:13 2008 +0000 Optimizing use of a memcmp to short circuit searching sometimes. commit 3c4aa306e4dc77f03409dae52d5548a222b5389b Author: markd Date: Mon Oct 27 23:39:07 2008 +0000 enable NR refseqs on RR commit fdcb53ed316cff0bfb3f53100b41ffbecb2a0e1d Author: larrym Date: Mon Oct 27 23:27:58 2008 +0000 modify the install target to also make bad tars commit c4568253ffcc9f5b95528668a81046e1bac39024 Author: tdreszer Date: Mon Oct 27 22:00:33 2008 +0000 Fixed problem with semicolon in comment commit b25de30d56c7c2fd6e266efd988f495bc1e10ee8 Author: tdreszer Date: Mon Oct 27 21:59:37 2008 +0000 Found missing Yale K652 Pol2 replicate. Added accessions commit eede8e17ae89a9ffe5ff665568d36a7c3b6f4b21 Author: hiram Date: Mon Oct 27 20:55:11 2008 +0000 With some assembly statistics commit 12becb549626af7c0ea32de8cd263c7e366b2ef6 Author: hiram Date: Mon Oct 27 20:29:51 2008 +0000 Initial raw source from the makeGenomeDb.pl script commit 8a9dbbbce35cdd3f6cb8f6f896d8941d1b2374b5 Author: angie Date: Mon Oct 27 20:10:07 2008 +0000 Added n/a entries to flyBaseToUniProt for genes with no mappings, because hgNear's dm3 oneGeneQuery can't find a gene unless the xref table has a row for it. Regenerated tables that depend on flyBaseToUniProt. Regenerated upstream*.maf with new FlyBase Genes and with Mark's new mafFrags -txStarts flag. Added note that Mark removed the automated refGene upstream*.fa generation -- using flyBaseGene for upstream*. commit a6db7c7a64d02dbb3ff8049b9edff9d8746429a2 Author: galt Date: Mon Oct 27 18:53:26 2008 +0000 adding run_stat flag to eliminate possible race condition; cleaned up show.rhtml, and use the new run_stat commit ace2e0469198f29011584e594cec8ce7e9d9c408 Author: galt Date: Mon Oct 27 18:50:56 2008 +0000 need to capture output for debugging commit 8e82bd71df8bb3e2511671a817cfae46e4ade55b Author: ann Date: Mon Oct 27 18:12:36 2008 +0000 final edits to bring xenoRefGene track into line with new changes. commit c7c0265a9608dc863f28f7f2a9cc8603a8077900 Author: braney Date: Mon Oct 27 17:54:53 2008 +0000 treat tandem dups like insertions (single line) commit e15f1ec400d7d09c5335ac3759360cf28d909e0c Author: ann Date: Mon Oct 27 17:53:30 2008 +0000 final edits to bring all refGene pages in to line with new changes. commit 869224f110d5dd29b6338a9564554110496bdff0 Author: braney Date: Mon Oct 27 17:52:19 2008 +0000 add a function to check for CONTIG or TANDEM commit f251bf3fb2c2a8fa865f6619b891d4c52d5ac492 Author: braney Date: Mon Oct 27 17:51:58 2008 +0000 add a function to check for TANDEM or CONTIG commit 98492e3bf9bb0a8930ff5f2326cb6f7e8c8f69e3 Author: markd Date: Mon Oct 27 17:14:39 2008 +0000 don't auto-create dm3 upstream downloads commit a69ed08484024725394b864358c0aec3b43044af Author: kent Date: Mon Oct 27 15:59:57 2008 +0000 Adding sufxDump and sufxFind. commit 5986df92047488b7cc1c514482590b1eb52cadac Author: kent Date: Mon Oct 27 15:58:40 2008 +0000 sufxDump debugging tool seems to work. commit 8ea8a806825b658d78f86f366bfc2862e2fa504d Author: galt Date: Mon Oct 27 15:00:06 2008 +0000 "Encode release log update" commit d6fd4d46381a48bb1ded29814ecd2df1aa2118ea Author: galt Date: Mon Oct 27 15:00:04 2008 +0000 "Release log update" commit 3fd2880cd2c028fe628c65508d0d2f84886d8563 Author: kent Date: Mon Oct 27 07:47:55 2008 +0000 Removing a few unused vars. commit a0ac1cdd7f05c4f6640f55cfbc16355b61cbea6d Author: kent Date: Mon Oct 27 07:46:31 2008 +0000 Removing unused variable. commit d27179e5f9e160d2747a1e339bb1a938a3c76740 Author: kent Date: Mon Oct 27 07:45:25 2008 +0000 Adding several new short-read oriented programs to makefile. commit 6a0e160f05ea13ba9af11c23b6ebdb23eff5c30c Author: kent Date: Mon Oct 27 07:43:15 2008 +0000 Correcting some unsigned/signed mismatches that led to crashes when working on more then 2 gig of DNA. Adding some more optional verbose output. commit 9783735d6550e1b12a444157dc9ddb014590531a Author: kent Date: Mon Oct 27 06:26:24 2008 +0000 Removing stray line that is no longer needed commit e1297b5ceed90621601a2ce7fd43e195f7630721 Author: kent Date: Mon Oct 27 06:10:16 2008 +0000 Fixed off by one bug. commit f61eeada2914781b022e9112930a1385294ca6c4 Author: kent Date: Mon Oct 27 05:55:53 2008 +0000 Added another end condition that's needed alas. commit 4c63a3064403d8beebd13c1f0fd1e553ea4e1a00 Author: kent Date: Mon Oct 27 01:54:47 2008 +0000 Traversable suffix array query seems to work for exact matches, at least some of the time. commit 1f9c990ef5d174fc4af8bca25a9e37b48a9f5359 Author: kent Date: Mon Oct 27 00:44:45 2008 +0000 Oops, using wrong array! commit c050d5153846b93f0ea26e0443f445ea4bbaa1f3 Author: kent Date: Mon Oct 27 00:04:21 2008 +0000 Oops, forgot to delete a line during last change. commit 87337194b31f04045f55fe72bc2a2c371c8d7aa8 Author: kent Date: Sun Oct 26 23:52:16 2008 +0000 Making it use huge memory rather than large for the arrays so that it works genome-wide. Fixing bug where memory not cleared in traverse array on start. commit af24c2697cf374a48ff3966762ffd7bf43d0f0de Author: kent Date: Sun Oct 26 23:36:55 2008 +0000 Addinga little more information to stack overflow message. commit f1cffc03add0300189d86240a0b96b54c1292e61 Author: kent Date: Sun Oct 26 23:28:11 2008 +0000 Bumping up stack size on traversal array generator - 256 not enough for chr18. commit bc82cba64ca7fa35ec703fd42fd78c6ea4673a15 Author: kent Date: Sun Oct 26 23:16:35 2008 +0000 Taking splatAli from library. commit 16a8f1d61c0e5de4eabb4ca0eebab3cb2a2341bd Author: kent Date: Sun Oct 26 23:12:14 2008 +0000 I _think_ it's creating a proper traversable suffix tree, but need to write the other end of it for real testing. commit 5e8cf44b7a04dc126f72a42499368e0f240e78bf Author: kent Date: Sun Oct 26 20:10:56 2008 +0000 First cut of library code for traversable suffix arrays. commit 0b0a08a411c888456af46bbf94898d00fda59dcd Author: kent Date: Sun Oct 26 20:10:18 2008 +0000 Changing 'basesIndexed' field name to 'arraySize' for better readability. commit 6a585f8e6c09eda5e5b696cfde68ee289e3a64d9 Author: kent Date: Sun Oct 26 20:09:03 2008 +0000 Refactoring so does what sufaMake used to do in half the memory. commit f8dc49165d418d09670000fb80e7c8ac6a978aaf Author: galt Date: Sun Oct 26 15:00:12 2008 +0000 "Encode release log update" commit 84795a2e7f983dfd405b3495dd7f5c30ec469e41 Author: galt Date: Sun Oct 26 15:00:10 2008 +0000 "Release log update" commit 5d9a399a8d39b6e58dfc316581a9ae921cc43452 Author: kent Date: Sun Oct 26 10:01:26 2008 +0000 Making rather generic sounding 'pointerOffset' function static to avoid name conflicts. commit ab44fb16fcdd93ed41212f78b6731fcbd7112aba Author: kent Date: Sun Oct 26 10:00:47 2008 +0000 Adding routines to interface with suffix array. commit 3937344224a2ad4c973b4394a33cf5b4f92316ee Author: kent Date: Sun Oct 26 09:56:20 2008 +0000 Improving comments. commit aec6609500291d2a71a82780625c237813c94eb7 Author: kent Date: Sun Oct 26 09:42:56 2008 +0000 Writing simple binary file for extension. Just a temp thing. commit 417986b129ce45cf39cdb2107c4f06c0f567618e Author: kent Date: Sun Oct 26 09:38:30 2008 +0000 Adding maxMismatch option. commit 4dc98008b76243a0b059ea7cca6dd4ad88686546 Author: kent Date: Sun Oct 26 09:34:37 2008 +0000 Experiments with an extended suffix tree. Not extended the usual way that I've read about at least, but seems to be just the thing for fast substring searches. commit b8b291ea838477b5440592f0ba0a1899a328d63c Author: kent Date: Sun Oct 26 08:08:58 2008 +0000 Improving commenting. commit e54fd448c09cbab2ba78782f669536b7887094e7 Author: kent Date: Sun Oct 26 05:50:55 2008 +0000 Starting to work with 2 mismatches. Not as fast as splat though. commit 11685a70f84adb1322ef2e038d66ea2a6918da3b Author: kent Date: Sun Oct 26 03:27:10 2008 +0000 Experiment searching suffix arrays starting to work. commit 037cfc0595db544e0cba52cac5625cdb17a2864c Author: kent Date: Sun Oct 26 02:02:21 2008 +0000 Short repeat finder based on suffix array seems to work. commit ef192fd2f0d636098b4ad8fdc35c6d334548c002 Author: kent Date: Sun Oct 26 00:15:43 2008 +0000 Fixed some bit shifting errors. Renamed some constants. commit 8265eb66dd3848474c14c7c2705d8989414bd3e6 Author: kent Date: Sat Oct 25 20:45:48 2008 +0000 Some tweaks to get it to compile here. Removing unused items. commit a4d79df289abb1be688a8998c10a647c244f2fe4 Author: kent Date: Sat Oct 25 20:45:00 2008 +0000 Adding sufaMake to makefile. commit 3c133f30e6340bd4a80076c38909730ca46d51ec Author: kent Date: Sat Oct 25 20:43:31 2008 +0000 Suffix array maker seems to work. commit 40b77ba7bc03b4be3ee34f25bddfa77723da5217 Author: kent Date: Sat Oct 25 17:08:51 2008 +0000 Making splixMake able to take multiple input files on command line. commit aa436febd432b766dd626b3fd58627d5e2f4e1a0 Author: galt Date: Sat Oct 25 15:00:07 2008 +0000 "Encode release log update" commit 227c2f354357aeb78b2749b368490c1078a98184 Author: galt Date: Sat Oct 25 15:00:04 2008 +0000 "Release log update" commit 951f91a3fb72e4e3ddd17c89cbde07479a9b22d8 Author: kent Date: Sat Oct 25 05:36:32 2008 +0000 Optimizing for speed. commit 12143dd0a6f07bce83bac5a81128795f75d2df22 Author: kent Date: Sat Oct 25 04:44:06 2008 +0000 Decent speed tweak (running in 80% of former time) from making tags allocated out of same local memory pool as hits, and using same pool for both strands. Optimizing pool block size - best between 4k and 8k. commit 9f110c36da4fb78ad1c489b334191a36875b559d Author: kent Date: Sat Oct 25 03:49:26 2008 +0000 Making command line a little safer. commit 9fe93d00bc5f2048a8fb4724e561942966c3ab94 Author: kent Date: Sat Oct 25 03:48:18 2008 +0000 Fixed bug in extension phase that caused crash on splix files with multiple sequences. commit 2f01cb89085d984db8d8b15e1fc03f289d5eb237 Author: markd Date: Sat Oct 25 00:28:49 2008 +0000 also load non-protein-coding on refseqs commit 12b27d3494f23d3f3d914a7e8efde473280ea5b2 Author: rhead Date: Sat Oct 25 00:05:11 2008 +0000 Turning the big broadChromatinChIPSeq track to hide by default. commit 89199961755a5d17ca261942b6f9a7164da5b6ec Author: tdreszer Date: Fri Oct 24 23:13:41 2008 +0000 Fix bug in displaying composite: conflicting vis and always show composite center label commit 625a6604a9ece60067c7f72b9f4b1fd26c7aedac Author: tdreszer Date: Fri Oct 24 23:13:11 2008 +0000 Fix bug in displaying composite: conflicting vis and fix css style declaration commit 37073a0964a8c36db9f0b9bfb1d06f314ff6965c Author: kent Date: Fri Oct 24 22:42:37 2008 +0000 Utility to check alignments made with test sets generated with splatTestSet seems to work. commit e300722b074486f8d6ce15076e0879ec7b1fdcf0 Author: kent Date: Fri Oct 24 22:42:00 2008 +0000 Splat output file merger seems to work for small files. The -big option still has to be implemented. commit 89ae9e7e3d30239875fc37e8c63d1666af63e34f Author: kent Date: Fri Oct 24 22:40:20 2008 +0000 Adding autoSql generated splat alignment parser. commit 77c74fd6f3183ef64dc11091c37306500e4b9cdd Author: markd Date: Fri Oct 24 22:32:40 2008 +0000 fixed english commit 722bc1bdf32fe880e9e195b01cb8e3649188483f Author: kent Date: Fri Oct 24 22:31:20 2008 +0000 Pretty major speed tweak (running in ~2/3 of time it used to) by replacing rbTree with a simple list for hits. commit 3fc047a7f894feda5aba1365d09edc40ee898d7b Author: hiram Date: Fri Oct 24 20:38:41 2008 +0000 Initial source, doesn't work because agp and fasta do not match commit 13b039c28e297c8c360c41721d04d9ae1767509e Author: angie Date: Fri Oct 24 19:48:26 2008 +0000 Updated ce2 -> ce6. commit 4716bfaa3dbfbb24463486d42729fa22511a669b Author: tdreszer Date: Fri Oct 24 19:18:10 2008 +0000 Added qValue commit f2881cc2be72964695567af10efafcbc77cfbf2c Author: tdreszer Date: Fri Oct 24 18:42:23 2008 +0000 Avoid error due to adding qValue to peak tracks commit 610af7cbefa929d49508fbde4785abc792fd3775 Author: kent Date: Fri Oct 24 18:39:59 2008 +0000 Adding "over" file which contains overused 25-mers, which can speed up search. Making hexamer subindex search binary rather than linear. Should speed up some aspects on larger target sets. commit daa5c3a9406e6acba04e36121631436d1e17d128 Author: ann Date: Fri Oct 24 18:32:05 2008 +0000 updated to new FB release commit eab6e1af24a705059c85f994a4aa07fc0a3fe2d6 Author: tdreszer Date: Fri Oct 24 18:31:16 2008 +0000 Added accession to the trackDb.ra settings commit 964fadce76095be0f2045b3b7467ba220cb29c5c Author: kent Date: Fri Oct 24 18:20:17 2008 +0000 Adding basesToBits64 commit 323e6317d60bc6cf042ac69bab8cd89c15978b0b Author: angie Date: Fri Oct 24 18:08:07 2008 +0000 Updated FlyBase Genes version from 5.3 to 5.12. commit b53ea25a05bf56e6edc85107561310eaa1706ab9 Author: angie Date: Fri Oct 24 17:53:54 2008 +0000 Bugfix for LD: when drawing a subtrack, use composite track name when looking up cart variables that are set at the composite track level in hgTrackUi. Replaced some throwaway dyStrings with char[]'s, and moved ldInv lookup out of the inner drawing loop. When linking to hgTrackUi, use composite track name if this is a subtrack. commit 9d944772951dd1216cfeaeb424178fd313699c03 Author: angie Date: Fri Oct 24 17:47:11 2008 +0000 Added comment about mapDiamondUi's current redundancy with mapTrackBackground. commit c970b10605ddd4b3ea18158a96331ae4e0405332 Author: galt Date: Fri Oct 24 15:00:08 2008 +0000 "Encode release log update" commit 29a64bd744e97ec21d3941110be937fe2ea9e69d Author: galt Date: Fri Oct 24 15:00:05 2008 +0000 "Release log update" commit b808d3eccf39cc6c585f96fbaa33d88c5999e19c Author: kent Date: Fri Oct 24 01:09:24 2008 +0000 Actually implementing seed parameter. commit b432900227b846e50e1098ba73e9ddc05e6d3326 Author: aamp Date: Fri Oct 24 00:17:40 2008 +0000 Removed eight microarrays from Sestan Brain dataset. commit 44075bda0448f38fb40173de36b7f3788c7d0eef Author: angie Date: Thu Oct 23 23:47:58 2008 +0000 Added search on KOMP names (gene symbols). (thanks Brooke) commit 5d52d425cddac7da018096c4ef9be6392ecf9120 Author: angie Date: Thu Oct 23 23:34:30 2008 +0000 In showTableField, when searching for a table in an slName list of all tables, use case-sensitive search. This fixes a bug found by Kayla: when viewing All Tables, and then switching to another db, if that db has a case-insensitive match for the selected table but not a case-sensitive match, we mistakenly thought we had the same table. commit 2598d750df9ccbed017aed0491b678a7d4073666 Author: tdreszer Date: Thu Oct 23 23:33:10 2008 +0000 Eliminated some specialized code and made term= case insensitive commit 50ae50833257ce1d42f034661555864293af842d Author: angie Date: Thu Oct 23 23:31:39 2008 +0000 Added slNameInListUseCase -- case sensitive version of slNameInList. commit df6e18fe9b1f9bd55028a7a28995496b34b39b56 Author: tdreszer Date: Thu Oct 23 23:11:02 2008 +0000 Added qValue to narrowPeak and added broadPeak and gappedPeak validator routines commit 889657276f0290f3e944b7ee337be7722901c44d Author: tdreszer Date: Thu Oct 23 22:59:50 2008 +0000 Make sure RESTRICTED UNTIL is visible commit 4985c194aeebca596258c58c2724e6b60fae84c8 Author: hiram Date: Thu Oct 23 22:58:42 2008 +0000 There isn't any ENV MACHTYPE in perl scripts when running on kluster nodes commit 655aa1418637462f39d8a1dc31a5ff305864d6a8 Author: tdreszer Date: Thu Oct 23 22:47:04 2008 +0000 Make sure releaseDate is put into trackDB and add default composite entry. commit 81255a273898fc2b00ff040386b82bc93d2b66fa Author: tdreszer Date: Thu Oct 23 22:43:15 2008 +0000 Fixed restricted date calculation commit 52ec7386e9acf0d675f07324ce7b843dee895005 Author: hiram Date: Thu Oct 23 22:29:52 2008 +0000 eliminate obscure references to "sh" make the system call safer and more efficient by eliminating ambiguity about what to operate on commit eba20838d0c96fa83d7a41f366bafe2e6472fa47 Author: rhead Date: Thu Oct 23 21:46:09 2008 +0000 Tweaked the reference format. commit 5e87f2b1a0f5cf4a1ca4fc4fb7f885bbbf65d51a Author: kent Date: Thu Oct 23 20:21:58 2008 +0000 Adding shortReadFind and shortReadMerge to shortRead higher level makefile. commit 1751e23bb912fae89933c8e36fe93b18835e6281 Author: kent Date: Thu Oct 23 20:04:20 2008 +0000 Utility to create short repeat count files seems to work. commit 74bb2fa01cfa3194d7034c0abb788bc7b754e078 Author: kent Date: Thu Oct 23 20:03:59 2008 +0000 Utility to merge together two short repeat count files seems to work. commit 2d37fe4d99ab794086e56cdde0a7a4f180828b0d Author: kent Date: Thu Oct 23 19:59:47 2008 +0000 Adding cmpDnaStrings commit 8b415726bbbabb9614737589cc6e975915e17101 Author: kent Date: Thu Oct 23 19:59:17 2008 +0000 Starting to add overused 25-mer screening. Not done yet. commit fd6386cb5c3dcd40659a504f4a38d9acedbfae05 Author: ann Date: Thu Oct 23 17:02:35 2008 +0000 Removed sentence that is no longer true. commit e26a7b1604f070316442cc4f91300d5b4a1655da Author: ann Date: Thu Oct 23 16:55:09 2008 +0000 fixed citation. also fixed some other parts to make all similar with top-level xenoRefGene description page. commit 0db1902e2e2300b96ba275148de7bed30d6b0210 Author: ann Date: Thu Oct 23 16:36:37 2008 +0000 no longer a true statement commit ef551a9a1dbe3626e9e5838d6301be7eee460a85 Author: ann Date: Thu Oct 23 16:26:02 2008 +0000 removing diffs between various refGene description pages commit e992fa089d457ba5ed3be46e42af88fcd88291aa Author: galt Date: Thu Oct 23 15:00:22 2008 +0000 "Encode release log update" commit ef70114c9300bb3d1d23acc91b4d2d0131a77255 Author: galt Date: Thu Oct 23 15:00:19 2008 +0000 "Release log update" commit e7dc90ea0da505e0c3e8dd20171b27d21d913b1e Author: kent Date: Thu Oct 23 02:31:23 2008 +0000 Chromosome/contig packer seems to work. commit 1afcb735e63d7732a4f601c11b47cd0c981875be Author: kate Date: Wed Oct 22 23:35:18 2008 +0000 Polishing up 36-way TBA: turn off some species (those already in 28way), remove extraneous species from gif commit 51441d559f24b187c677b4e50890b41799c0e31f Author: kate Date: Wed Oct 22 23:32:28 2008 +0000 Prune the NHGRI tree to just the 36 in the alignments commit ec8be032c9830a4557e2e71e549d635adaf0b25b Author: hiram Date: Wed Oct 22 23:05:00 2008 +0000 Completed repeatMasking and TRF simpleRepeats, prepared kluster scratch files and fixed scientificName in dbDb commit 45d8e6a6af0e46a2c2551274522b9a1d6964398f Author: hiram Date: Wed Oct 22 23:03:51 2008 +0000 done with lastz run for turTru1 and dipOrd1, running proCap1, choHof1, dasNov2, loxAfr2 commit 216d639b1f19900e489ce25b706dfbc5e68cb0ba Author: kate Date: Wed Oct 22 22:42:34 2008 +0000 Fix page layout of wigMaf controls and tree image commit ba4c797b7a2da327dc8adb6affba7b5127a7361b Author: mikep Date: Wed Oct 22 20:40:29 2008 +0000 removed most hardcoding of variables for subGroup and addidional fields commit 0e0aa99a9e9dc904d5d035664bd03a04a907b700 Author: mikep Date: Wed Oct 22 20:29:28 2008 +0000 put the variable in the subgroup to get the checkbox to appear commit 1f7ee912083f9ad92d2c3562512bbe904a678fb6 Author: markd Date: Wed Oct 22 19:23:55 2008 +0000 don't output CDS related links for non-protein coding RefSeqs commit f30795922882620b1a98ea5ffec755f26337e756 Author: hiram Date: Wed Oct 22 18:28:48 2008 +0000 Prepare for kluster runs, and update sourceName in dbDb to include NCBI project id and LOCUS accession number commit d23fbc2e979b151f64719f4b639aa77d01603d7a Author: hiram Date: Wed Oct 22 18:27:35 2008 +0000 Prepare for kluster runs, and reset sourceName in dbDb to include NCBI project number and LOCUS accession commit 0e377e5f0f4e7cf2a6c6582c10ed8a7565e6160f Author: markd Date: Wed Oct 22 18:20:42 2008 +0000 updated refGene and ucsc genes search regexp to include NRs, although this doesn't actually appear to be used commit fcfec8c21e5702974dbbd530ee2f6953e26f3159 Author: markd Date: Wed Oct 22 18:19:15 2008 +0000 include NR_ in refGene search commit 224a46cd2846a424fb0a2dd12d6892a98a275e70 Author: hiram Date: Wed Oct 22 17:00:25 2008 +0000 Need to make sure previous liftOver is out of the way as new one is copied -p commit e73685eee3b864c14bcdbd282f82282e8def0587 Author: galt Date: Wed Oct 22 15:00:06 2008 +0000 "Encode release log update" commit c1d271766e11725ca3b6a776e8fecb0874411688 Author: galt Date: Wed Oct 22 15:00:03 2008 +0000 "Release log update" commit 88d04ad68d910b2b54f2c3ea139d49cf76cf3be0 Author: kent Date: Wed Oct 22 07:11:17 2008 +0000 Turning dnaSeq.h to dnaseq.h. (Mac file names case insensitive for me.) commit b302257cd9ecd76b586e199ced2ba7d2e757eebd Author: kent Date: Wed Oct 22 07:09:41 2008 +0000 Making banded extension proceed out from the midpoint of the best block found during the tag-mapping phase. commit 71bcea25d071bb3537cb44629f33ead676b341e4 Author: angie Date: Wed Oct 22 06:02:18 2008 +0000 Updated FlyBase Genes, FB Noncoding and hgGene/hgNear tables to FlyBase version 5.12. commit a27bba65c53115a346cca17655da9fc85cd9ea95 Author: kent Date: Wed Oct 22 06:00:27 2008 +0000 Put in banded extensions. Still some refinements to go to allow Smith-Waterman to improve existing alignment, but basics are working. commit 673b07de3fffba6846d92ee184f5dc294165f860 Author: kent Date: Wed Oct 22 05:17:13 2008 +0000 Making bandExt include localmem.h, which it needs. commit ab955d107b6c39cb2dba98603495ca1d0fcfe6b2 Author: kent Date: Wed Oct 22 05:06:41 2008 +0000 More refactoring to make alignment just have a chain. commit e1c024018459820c6280c922b3e47a622f3d163e Author: kent Date: Wed Oct 22 04:17:49 2008 +0000 Some more refactoring in preparation for putting in banded extensions. commit b721dfad0b45f88bcbad327cf8f4e7f12329660c Author: kent Date: Wed Oct 22 03:44:58 2008 +0000 Moving splixOffsetToChromIx to library. commit 4a46444af1116552d7deaba0de66bd9bf6bbfb94 Author: kent Date: Wed Oct 22 02:38:36 2008 +0000 Refactoring to make output modules take an alignment list instead of a tag list. As part of this output routines work on chains instead of splatTags. commit 3e7f0b1ec25d62c943a3dabee9037bc3779bd5ea Author: mikep Date: Wed Oct 22 02:18:50 2008 +0000 turn pipe into safepipe, and add the genePredExt flag to load the name2 field commit f51bc1b49e63bcd73f6c1e125a2babc62cd208c2 Author: mikep Date: Wed Oct 22 02:17:17 2008 +0000 validate freezeDate from Sanger, and remove the temp output file from gtf->bed validation commit 757703989a9dcdf33f40d1127a0b3b5e0ffd36c1 Author: kent Date: Wed Oct 22 01:17:55 2008 +0000 Separating out module that handles output from main module. commit 194267529ccc7797f6182eed4639dd4d7d252e9b Author: kent Date: Wed Oct 22 01:16:03 2008 +0000 Moving cBlocksFromAliSym routine to library. commit 60bcd3bb24ee364a564f9639f5023bbc5e697adc Author: kate Date: Tue Oct 21 23:50:41 2008 +0000 Remove sort order as it doesn't add any value. Conserved elements can be dense to start commit 27537eed08f81d3e80a3aaeaeb6f1fcf0d3da035 Author: hiram Date: Tue Oct 21 23:22:23 2008 +0000 Started last runs for Kangaroo rat, Megabat, Dolphin commit 9c1205bfba93be775e0f5eb7dbd89e9a7f218f40 Author: hiram Date: Tue Oct 21 23:10:15 2008 +0000 Add NCBI project ID and LOCUS accession number to dbDb sourceName commit 9007d9ee195bd3a5612e96aeb6d38977fe7dd3ce Author: hiram Date: Tue Oct 21 23:03:37 2008 +0000 Finish RepeatMasker, TRF SimpleRepeats, reset description name in dbDb to have NCBI project number and LOCUS id, create scratch kluster data files for lastz runs commit cad0b25378f39c5a7f84ffc6967b9eece9d397b9 Author: hiram Date: Tue Oct 21 22:59:52 2008 +0000 Finish ooc file and prepare scratch for kluster lastz runs commit d332cd4918d94e74c6ce08fae5815a4255cf3265 Author: hiram Date: Tue Oct 21 22:59:19 2008 +0000 Starting blastz tarSyr1 commit b51d6b232f5e55a06cc338cc2b26219d0f8d7327 Author: hiram Date: Tue Oct 21 22:58:48 2008 +0000 Finish RepeatMasking and TRF simpleRepeats, prepare kluster data scratch, fix description name with NCBI project and LOCUS accession number commit 380923d83ff60b7d2d5ed51a08447da9938a154e Author: hiram Date: Tue Oct 21 22:49:57 2008 +0000 Run the faSize on the resulting rmsk masked 2bit file commit 055fab0bd719c5625f51990b596ec25f06216d96 Author: hiram Date: Tue Oct 21 22:33:17 2008 +0000 Load the windowMasker table into the db so it can be monitored there commit 7672d194567bdc81e5e14f6b3957969ae32bebd1 Author: hiram Date: Tue Oct 21 22:27:24 2008 +0000 Load the windowMasker table into the db so it can be monitored there commit 6023624b2232c59d28ee76fe6dafff8279f91eae Author: angie Date: Tue Oct 21 22:21:56 2008 +0000 Added kiddEichlerValid* to tablesIgnored $hg. commit 45690aa946421cc7a3dbce5f15c4da2dca9f7f2c Author: hiram Date: Tue Oct 21 22:16:31 2008 +0000 Create a database instance to make this easier to work with, repeat masked and simple repeats done, blastz kluster ready commit f718492ea785c42397f3616f4125f219dbbc6537 Author: kuhn Date: Tue Oct 21 21:46:18 2008 +0000 fixed filename for knownGeneLists.html commit 4c76528dc43395cd7c3053ce1ea9583917881683 Author: kuhn Date: Tue Oct 21 21:43:31 2008 +0000 added exit in error if-statement commit 188fda64a0140d982110f6c885be6f015c1ef56e Author: kent Date: Tue Oct 21 21:20:57 2008 +0000 Bumping version. Putting in a debugging routine or two. commit 05af299882cbd6ec646a791284d1d0e9bec4ef65 Author: hiram Date: Tue Oct 21 21:04:21 2008 +0000 add this assembly to the database to make it easier to work with, run repeat masker and simple repeats, create blastz kluster directories and fix description with correct NCBI project and LOCUS identifier commit 5229175c909883cd28e17c91161670bde04e9eeb Author: mikep Date: Tue Oct 21 20:55:36 2008 +0000 updated with new view commit 47470b7736c84d3a9979874761d8684e13d307fd Author: hiram Date: Tue Oct 21 20:50:21 2008 +0000 Repeatmasker and simpleRepeats TRF done and ready for blastz kluster runs commit caf87ee1583a8b9f3db73c777e276cec60e4a17d Author: hiram Date: Tue Oct 21 20:47:17 2008 +0000 RepeatMasker and SimpleRepeats TRF done, prepared for kluster blastz runs commit e7784d929d8645366cf03508ffc70438728b60b0 Author: hiram Date: Tue Oct 21 20:37:24 2008 +0000 Set a better default position, same as it was for oryLat1 commit 7f4430b1fbdfceeabcddf316bfb48b095973e341 Author: hiram Date: Tue Oct 21 20:36:26 2008 +0000 Running repeatMasker and simpleRepeats, and creating a database for ease of query commit d0d3b1a472dae6b9d482d673c38ccd2ae1229c10 Author: hiram Date: Tue Oct 21 20:35:48 2008 +0000 RepeatMasker and TRF simpleRepeats done, prepared for blastz kluster runs commit 3876a52387de77c95bceb1ce640da0c96cf44445 Author: mikep Date: Tue Oct 21 20:35:35 2008 +0000 added freezeDate and split levels into two views commit 90fb66115eb4cbd297e6f6a5e99e0623c53caf16 Author: hiram Date: Tue Oct 21 20:35:06 2008 +0000 Add project and LOCUS accession numbers to description commit 2a83fdfcd4abf1f27033c3c49a4847d19d731612 Author: kent Date: Tue Oct 21 20:16:36 2008 +0000 Removed unnecessary prototype line. commit 46d0e3a939d6bd725d27c815bb2cadbe766e6053 Author: mikep Date: Tue Oct 21 18:23:40 2008 +0000 sanger variable is freeze date commit 3b96bf6da721badb1fe7a98491605a225c53d84c Author: mikep Date: Tue Oct 21 17:30:55 2008 +0000 Plus/Minus raw signal added commit e1b4d34ee9ad06e0a3ff3be16cbae5ee39bab98a Author: mikep Date: Tue Oct 21 17:21:23 2008 +0000 tagAlign type is trackDb type bed 6 commit ae48ea7de837bbb336978e0b1ee036b9b8507241 Author: mikep Date: Tue Oct 21 17:20:12 2008 +0000 working version of RIKEN with Alignmnets and Plus/Minus RawSignal commit 56269bcc7bce896c87790f1c68c15863f8efe3b4 Author: markd Date: Tue Oct 21 17:11:04 2008 +0000 don't pass outdated flag to cvs-reports-d commit 04edc62da7cd6b854a7e2c9520526a5ad97a03ad Author: mikep Date: Tue Oct 21 17:02:05 2008 +0000 fixed up dates for env variables commit a407b6a0c6a00162fa2acd8f91ee9ab70c7cf0cf Author: ann Date: Tue Oct 21 17:01:27 2008 +0000 added optional active paramater which returns only those databases on the RR that have active=1 in hgcentral.dbDb commit 7482bfd689377e682bc11d91198527591d26eb0d Author: angie Date: Tue Oct 21 16:51:00 2008 +0000 Tweak to KOMP: forgot to subtract 1 from start coord; fixed. commit a0666de334c1696abff3e849199e5d25075a6665 Author: tdreszer Date: Tue Oct 21 16:20:18 2008 +0000 Added wgEncode accession. Added green line to separate Z dimension. commit a84b5192ad5a662a3ffa3f157557666e93cd4ee8 Author: braney Date: Tue Oct 21 15:55:05 2008 +0000 add TAnDEM dup type to irows commit 93a0b3e70375f03ff27e57741f6b9445b13c0744 Author: mikep Date: Tue Oct 21 15:28:03 2008 +0000 latest day 2 commit b110ca084a35e8be233a9359b76d2834c5984620 Author: braney Date: Tue Oct 21 15:17:19 2008 +0000 add another relation type for 'i' rows commit a7e0b287e452d92b9586328e29591da83fc6a392 Author: galt Date: Tue Oct 21 15:00:07 2008 +0000 "Encode release log update" commit 013cb15067e67b319223c167e4567ae4ed57f993 Author: galt Date: Tue Oct 21 15:00:04 2008 +0000 "Release log update" commit 9f155c405b2c5cd65fecb67d11774dd6b530f9f8 Author: kent Date: Tue Oct 21 06:05:58 2008 +0000 Fixed reporting bug in number of reads multiply aligned. Made 25th base always count. commit 49da158aefaa429cdad4e690976bdff5ae7fbaf3 Author: kent Date: Tue Oct 21 02:54:46 2008 +0000 Fixing a bug where it would sometimes output a spurious ^. Making it open read file (which is quick) before loading index (which is slow) to catch typoes in command line faster. commit 7d0d99a031a5e7cc70537b1e753626f7061c36de Author: kent Date: Tue Oct 21 02:51:42 2008 +0000 Adding a new test case. commit f90a1fee0ec62969bfa0be5a972dc98e212d5cd0 Author: kent Date: Tue Oct 21 02:21:44 2008 +0000 explaining difference in version commit 636b71d922ead68fd8d0363c4464d8c4083a70b2 Author: kent Date: Tue Oct 21 02:10:17 2008 +0000 Fixed bug where when there was more than a single 18-base hit to the index, only the first hit was being extended. Fixed another very subtle bug that was discriminating a little too much against insertions vs. substitutions. Changed minScore option to maxDivergence. commit ffd3d233f7ecd467b7876965f0c58f3902d9b7dc Author: kent Date: Tue Oct 21 02:06:13 2008 +0000 Adding a bunch of test cases for bugs that have existed and been fixed - to help make sure they don't come back commit 12a94b349a72bc91640b3bfa973df82004abd1dc Author: kent Date: Tue Oct 21 00:28:35 2008 +0000 Fixed a bug where it was not finding _all_ of the places a multiply-mapping read mapped. I hope this doesn't slow things down too much! commit 047e281f693ded1f115b3ab4dcdf96db1395c4e6 Author: tdreszer Date: Mon Oct 20 22:22:52 2008 +0000 I left off 'noInherit' from Zhao nucleosome composite. commit 8ad2d5a844d05a6df5e0fd6aef3e9408c74010f4 Author: angie Date: Mon Oct 20 21:32:48 2008 +0000 Added komp (KnockOut Mouse Project). commit edf3185b23e9d4a407b78076963a553c4eda66d4 Author: markd Date: Mon Oct 20 21:14:43 2008 +0000 fixed bug in mgc/orfeome details sequence links commit 99618bdddadea22da1d422a88a5532b624f6a6e0 Author: angie Date: Mon Oct 20 19:11:15 2008 +0000 Adding dupeOk for kompName because sometimes both production centers target the same gene. commit b615e0b4e308f76819f6ff8c4354dbad991b8609 Author: tdreszer Date: Mon Oct 20 17:42:03 2008 +0000 Added Barski 2007 ChIP-seq datasets commit 7c35989d252ca5dae866055cd09d5835015e5f5f Author: angie Date: Mon Oct 20 17:27:29 2008 +0000 In hgSeqConcatRegionsDb, handle the interaction of repMasking and casing options when first fetching the sequence instead of after cds/exon-casing. commit eba154ada7780da4689e01a63b047eda8da22197 Author: galt Date: Mon Oct 20 15:00:06 2008 +0000 "Encode release log update" commit ae01ac1926a9d1ab3a118dca1d1322587554b985 Author: galt Date: Mon Oct 20 15:00:03 2008 +0000 "Release log update" commit ca3d104ce2711ee71ab4d7c3023873a91709b625 Author: kent Date: Mon Oct 20 08:13:52 2008 +0000 Tinkering on status messages. commit 1a11fc6ea1a053b35d05d40b6a08734e65a528f3 Author: kent Date: Mon Oct 20 05:49:53 2008 +0000 Fixed delete+sub bug. Fixed duplicate reporting of matches. Also made it only report best matchings by defaultand only up to a fixed number (default 10) of matches per read. commit 409464385b5cc149b77b3134796e17b79070443a Author: kent Date: Mon Oct 20 03:17:38 2008 +0000 Changed algorithm so it will work with larger numbers of lines to pick decently. commit e5ffe1f8f15a736fc6a1d1e1fbdda39c62da7665 Author: kent Date: Mon Oct 20 02:45:35 2008 +0000 Adding -maxN option. commit 9651f6cd47c1b8353ac2e7280d0e8339fddcff37 Author: kent Date: Sun Oct 19 20:57:26 2008 +0000 Fixing a couple of bugs that reduced coverage in insert+sub and especially delete+sub cases. Still a small bug (affecting ~2% of cases) in the delete+sub case. commit 6f62017e0f79348706f6049b952653620fae0e3b Author: galt Date: Sun Oct 19 15:00:09 2008 +0000 "Encode release log update" commit 9a12a0b8cdc1af1818044ed2b50ef4ef214a5649 Author: galt Date: Sun Oct 19 15:00:06 2008 +0000 "Release log update" commit 6e8ebaa099a5d4aaa0bb3da17207f14ddb930fac Author: kent Date: Sun Oct 19 06:05:09 2008 +0000 Making it fill in score field in tagAlign format properly. Reports mapping totals at end of run. commit 4ab9e069c2893241c76bc36f1926ccd29dc50510 Author: kent Date: Sun Oct 19 05:20:22 2008 +0000 Making it have tagAlign, maf, and psl output. (Old style output is gone). commit 2735a89e3cf9bdac03250712789c3fe33e2b3cdd Author: kent Date: Sun Oct 19 02:57:21 2008 +0000 Adding some test cases. commit 1d5819c68d48b3fc277bad01a657da043c0a45e0 Author: kent Date: Sun Oct 19 02:53:18 2008 +0000 Refactoring so that get a list of matches in memory as an intermediate stage before writing out to a file. This will make it easier to further extend tag matches, and to have various output options. commit 3287c28615ab66203fc87688dd3314dc51e44a83 Author: kent Date: Sun Oct 19 00:59:08 2008 +0000 Adding splix.c to makefile. commit 4cb18a72070c368cb76744f6043022ed92cad0ad Author: kent Date: Sat Oct 18 23:55:34 2008 +0000 Adding splat version note doc. commit aca1bdfe914092af2c6319056c83a47aebb6ee5a Author: kent Date: Sat Oct 18 23:54:46 2008 +0000 Adding mid-level makefile. commit 25efe28ca4a552860ca9fe8e1250e7f25d7fe3e5 Author: kent Date: Sat Oct 18 23:48:44 2008 +0000 Adding separateMutations and spaceForDel options, and making numbering a little more robust. commit beb6d96baeb14b708110fa6093c59e0ede375207 Author: kent Date: Sat Oct 18 23:48:15 2008 +0000 Preventing gappy extensions at ends when maxGap=0 commit 57c34dab6837184a66f019565bad2e28227ffc3e Author: galt Date: Sat Oct 18 15:00:07 2008 +0000 "Encode release log update" commit 62ab4e87dad1714e8754f2e2edc67c6a458a8c8f Author: galt Date: Sat Oct 18 15:00:05 2008 +0000 "Release log update" commit 3c6324a7daeaa726bde56ffdf8098d611da1a488 Author: kent Date: Sat Oct 18 09:29:18 2008 +0000 First check in of splat - a short read aligner. commit aa1fde4c45b1909c4cdec00b13ad96a7303a4318 Author: markd Date: Sat Oct 18 03:53:28 2008 +0000 added ignore entry commit 2793bac210fc8b9566fecf48d1041cca988b2b2b Author: aamp Date: Sat Oct 18 02:26:57 2008 +0000 Added column-sorting in "All Submissions" and "My Submissions" pages. commit 6e925a52c931ed4222d513cf2cfb106386bef412 Author: tdreszer Date: Fri Oct 17 23:19:06 2008 +0000 Add support for exponents in floatRegEx. Used Hiram's recommendation. commit 1fcb3670231e6305e0f24f92828b16d59d88b77a Author: tdreszer Date: Fri Oct 17 23:14:32 2008 +0000 Eliminate +/- buttons on Z dimension and use css for table boxes commit e2b748c7546f23020a5f81a1cf3edc2db5ff7744 Author: markd Date: Fri Oct 17 23:00:08 2008 +0000 removed mistakenly configured oryLat2 upstream commit f01c6c8cfaa357a6c3e671caebf26e12fb020ecf Author: donnak Date: Fri Oct 17 22:44:57 2008 +0000 Added news item abt QA job opening, per Bob. commit d380538f2fccd219493b01d620da0c9b69fdead7 Author: rhead Date: Fri Oct 17 19:22:56 2008 +0000 Added search for bacEndPairsBad (cloned bacEndPairs search). commit 9577a4dc7dccbe09c8f8dfde6041e29b84e0ae56 Author: pauline Date: Fri Oct 17 19:20:52 2008 +0000 Fixed typo, column in trackVersion is called db, not dbs. commit 1f252396a2970cb227cb55bf3c391c5cd34eaf86 Author: hiram Date: Fri Oct 17 18:29:12 2008 +0000 Fixed up to work properly on the hive filesystem commit 461f911f9a4a6fefef2544d8dee5a562d5bc7383 Author: galt Date: Fri Oct 17 17:35:48 2008 +0000 new pipeline background job running method commit 7d78b45700467d56619c6e1c4b00e7ef1ccccc60 Author: galt Date: Fri Oct 17 17:01:52 2008 +0000 new logo for encode commit 321aa2cbde045f2da3b23be8c6d0ea8a1d91446b Author: hiram Date: Fri Oct 17 16:43:48 2008 +0000 Finished with masking commit 350cc6e05a7caa4b934ca9d64f8ad1f88b6e76a7 Author: hiram Date: Fri Oct 17 16:07:19 2008 +0000 Add an install target for that type of build and install commit 803432b0ac12698114ec32a6e7587b5abffd5bd3 Author: galt Date: Fri Oct 17 15:00:07 2008 +0000 "Encode release log update" commit cb9f471284362ce49e9a1a71fd98f49b7679088b Author: galt Date: Fri Oct 17 15:00:04 2008 +0000 "Release log update" commit 902c85e13a21f36584d38e16c3dae7c2b8fee3c5 Author: hiram Date: Fri Oct 17 03:37:59 2008 +0000 A copy of the oryLat1 version commit b05416b07ca3f91169d28d7584a38f85f901a6ac Author: hiram Date: Fri Oct 17 03:37:03 2008 +0000 Fixup oryLat1 references, and proper xenoMrna note for tetNig1 annotations commit d4a3ffc6120a50288cd1de317170448871e00946 Author: kuhn Date: Fri Oct 17 01:09:33 2008 +0000 tweak commit 09c8a59cd3b6f9c32cc838dcd7726a89fc10b61f Author: markd Date: Fri Oct 17 01:06:36 2008 +0000 automated upstream file creation as part of genbank pipeline commit 30835715c13899a1dcfbb2d49300d6d44ee24a07 Author: rhead Date: Fri Oct 17 01:04:40 2008 +0000 Italicized journal name. commit d088d49dea5a47a2a1ceb34edff53a1e34a57316 Author: aamp Date: Fri Oct 17 00:44:41 2008 +0000 Committed too much by accident. Backed out everything except the one line recognizing MIME types. commit 8af3d2dab1b8a80c2b1c1e147a907238ca05f788 Author: rhead Date: Fri Oct 17 00:30:23 2008 +0000 Took out typo sentence from methods section. commit c1e4485dce3384040567eb200111393ce592fcec Author: kuhn Date: Fri Oct 17 00:04:33 2008 +0000 added some more files not to check with linkChecker commit d9c0dc7478d803d525d60b5cc85ab1ec691c5adb Author: tdreszer Date: Fri Oct 17 00:03:52 2008 +0000 Oops. Change 'Antibody' to 'Target' on Barski commit 3b60959d14ad78735f99accca3ecef2c165195f6 Author: tdreszer Date: Thu Oct 16 23:59:36 2008 +0000 Converted for Zhao composites to one and added barskiChIPseq commit 7f04a45e377e9bf9f813b1b91b4d03dd88ec94bf Author: pauline Date: Thu Oct 16 23:48:47 2008 +0000 Fixed species order. commit e3095fcac041086f49ba91e8f7b30ab5291e6ecd Author: rhead Date: Thu Oct 16 23:19:41 2008 +0000 Added a reminder to ask for the mysql tables to be pushed, since these are automatically updated only once a week now. commit 81ae11db5ab0b44ebd08fbea7e7cd53d80bcde33 Author: mikep Date: Thu Oct 16 21:33:55 2008 +0000 loading alignments for Gingeras project commit 77f166ed1156327bd669bbc630d77044d97621a0 Author: mikep Date: Thu Oct 16 21:19:23 2008 +0000 chrom cannot be primary key; and chrom,chromStart should be an index commit c3b1d3caaea120fae4ea3bd52b2d9b7b2b9953be Author: hiram Date: Thu Oct 16 21:17:36 2008 +0000 Add new reference to newer paper on this business commit 503cf7696f61be34c51870a52adcd496dae33afb Author: larrym Date: Thu Oct 16 21:07:24 2008 +0000 autoCreated1.bed => autoCreatedRawSignal1.bed commit 19ea053d6db40dad78f69281712844a6f525a2ff Author: hiram Date: Thu Oct 16 21:07:05 2008 +0000 Initial source, now with reference to a new paper from the old Atlas 2 one. commit 29aa51bcf7e892eb261f0edac1a9eb277f719926 Author: hiram Date: Thu Oct 16 21:06:33 2008 +0000 Slight reordering of tissues in the selected group for GNF Atlas 3 commit f7e2ed7a6cecb649738efaf7c015fdb24f9eec57 Author: larrym Date: Thu Oct 16 21:05:59 2008 +0000 support -skipOutput commit 46e0b1ed0afe656cd8fd64beb63ce023fbc9692a Author: pauline Date: Thu Oct 16 20:58:23 2008 +0000 Added description of new creation date column. commit 9af596a2de037774c409d581c2bdf8e320e8d1e9 Author: hiram Date: Thu Oct 16 20:25:43 2008 +0000 Make the group order of Atlas3 the same as Atlas2 commit b3e5a66bcddd0dd8c315cf5cdd904ff572344815 Author: larrym Date: Thu Oct 16 20:08:44 2008 +0000 support projects.lab, data_type and track commit b18dccc3d45df920ed580c191dca8b9c1b4a3784 Author: markd Date: Thu Oct 16 18:58:10 2008 +0000 change update frequency and filters for hgdownload rsync commit 24c895c84fec57ef7e1b1c3878adf68edb4863c2 Author: hiram Date: Thu Oct 16 18:08:30 2008 +0000 Make the width of the label columns the same as the color boxes below them commit 6fda2dad3891424d527c3d668733246e45d5c306 Author: hiram Date: Thu Oct 16 17:48:36 2008 +0000 Proper short and long labels on GNF Atlas 3 track commit b75e61d6a7f183135ea476621e999905772a8618 Author: mikep Date: Thu Oct 16 16:26:55 2008 +0000 shortened this prefix as it now will also include the View name commit 89ca20be9f96c4bed0532dd62b46f29a8422fe6b Author: mikep Date: Thu Oct 16 16:25:48 2008 +0000 added autocreation of PlusRawSignal/MinusRawSignal optional tracks commit ec3866360d77c9db5382d9d6b778f2bdb47becb8 Author: ann Date: Thu Oct 16 15:58:12 2008 +0000 cleaned up the link to the User's Guide commit 1a282d054990f33a02db7b30a0cf4a5c7877f614 Author: galt Date: Thu Oct 16 15:00:06 2008 +0000 "Encode release log update" commit fa161d859cbf0d63287513feaa36a7e00cefc1bf Author: galt Date: Thu Oct 16 15:00:03 2008 +0000 "Release log update" commit 0ece0ec513301d6e16b37e79a596ef93d726a99c Author: cszeto Date: Thu Oct 16 06:28:30 2008 +0000 Added one new set (Kaiser) and changed some nomenclature on others commit 75b31e14732b1499315126c067f72771c106db66 Author: cszeto Date: Thu Oct 16 06:27:38 2008 +0000 Added new set (kaiser) and changed nomenclature on others commit cfe42f277831bf8b891764e8fc34182cb9e3f827 Author: kent Date: Thu Oct 16 02:39:51 2008 +0000 Making a way to pass data to a rbTree traversal call-back function without using global/statics so can be multithreaded & recursive safely. Using this in intValTreeKeys() function that returns all keys in an integer-keyed tree. commit b81b00779b915be006575be5bfe373c705ef0304 Author: kent Date: Thu Oct 16 00:10:56 2008 +0000 Utility to convert fastq to fa by stripping quality scores seems to work. commit 13c1868a031829122b8ebaf8e7aea4b2a0bfcc3d Author: kent Date: Wed Oct 15 23:52:15 2008 +0000 Utility to convert fasta file to fastq file with dummy quality values seems to work. commit d1f5bba4d476400b45b8fd161ee2b8d78440669e Author: hiram Date: Wed Oct 15 19:39:02 2008 +0000 repeatMasker and simpleRepeats done, sequence masked with both commit 09fd614b9a10208a2c3054c49a467aed57b2b2cc Author: kuhn Date: Wed Oct 15 19:14:04 2008 +0000 added ORDER by qadate to query commit 75254274f8c27495118907983ddfe1acce2f32e1 Author: kuhn Date: Wed Oct 15 18:54:17 2008 +0000 fixed so all recipients see the cc: list commit 11569e55358bc5f9aeecaef61741d18e4cff5ad4 Author: tdreszer Date: Wed Oct 15 17:54:44 2008 +0000 Riken needs to be marked as ENCODE commit 1aaf6e74849fb0a1a9888c6119f61fb45c4f3918 Author: galt Date: Wed Oct 15 15:00:05 2008 +0000 "Encode release log update" commit 30e8ba89068d9d8f73ae917ea1dea1e8ba1c1437 Author: galt Date: Wed Oct 15 15:00:03 2008 +0000 "Release log update" commit 45dac85bb848cdb9b9a2982320a835c753db63ae Author: aamp Date: Wed Oct 15 08:37:10 2008 +0000 Put in -trimSqlTable description and removed the stupid -bedPlus option which didn't do anything useful (-notItemRgb does the trick). commit b17289b073d6ff676cb15734fff75edb3ef8cdeb Author: markd Date: Wed Oct 15 05:30:59 2008 +0000 added ignore entries commit c50396066fd61f93e0c31305b326a66b0029d224 Author: ann Date: Tue Oct 14 23:47:32 2008 +0000 moved Chester M to the bottom section commit 105c703b66dcbd035f051de2fe5eb230c709a805 Author: aamp Date: Tue Oct 14 23:43:15 2008 +0000 Next-item button custom track cleanup. Braney suggestions in review. commit 11ce46f1413ec07594aafef1c80cb0fdc4f85010 Author: ann Date: Tue Oct 14 23:23:09 2008 +0000 added block to remind folks to check for udpated upstream MAF files commit ea24b53ded42c61360440c2b688514e71d668430 Author: markd Date: Tue Oct 14 22:51:10 2008 +0000 changed format of upstreamMaf variable; enabled maf building commit d563a58be8a6f5685d92ca499fc5e2c35f2538cb Author: tdreszer Date: Tue Oct 14 21:29:08 2008 +0000 Change priorities on Yale commit c558ba1400cb459f908d6cd922415e13e39575aa Author: tdreszer Date: Tue Oct 14 21:25:21 2008 +0000 Added Yale K562 Po2/Input commit 9e459ee93d79540b912606a07199acf859bc9b2d Author: cline Date: Tue Oct 14 20:58:59 2008 +0000 Added the steps to build the affyExonTissues track commit 26f973c1aa29470b7f22d24d0629e3d7adbf63c2 Author: cline Date: Tue Oct 14 20:54:38 2008 +0000 Added build instructions for the affyExonTissues track commit db162df074c1dc0333c2bac0d2163db06e3f6a6a Author: markd Date: Tue Oct 14 19:38:37 2008 +0000 don't generate error if cvs outputs lock warnings to stderr commit 984c35bc6e818e70b9823973fbcbfc5f40f94e69 Author: aamp Date: Tue Oct 14 19:20:37 2008 +0000 Fixed score filter for illumina track and removed parameter for freeing struct. commit f0073b045b9cfa529b519fa2ed05941814f3b004 Author: mikep Date: Tue Oct 14 18:50:52 2008 +0000 adding time and script to debug messages commit 0e5a595395123d66e23a58999759189c58194498 Author: hiram Date: Tue Oct 14 18:26:51 2008 +0000 Added MOE430V2 chipset with GNF Atlas V3 data commit 40b133d91880a91a85b5838e31373866ed46ef71 Author: hiram Date: Tue Oct 14 18:25:38 2008 +0000 Added quality download files commit 22c2c76c468f643078c83c610da7a3f758bb83b4 Author: aamp Date: Tue Oct 14 18:06:25 2008 +0000 Lowered minCheck for Sestan Brain to accurate threshold. commit caf87b8c9dfcbe8f288bcbcbecce6d923261667f Author: aamp Date: Tue Oct 14 17:58:24 2008 +0000 Added another possible MIME type for the pipeline to recognize. commit 222738f937801c0de7a6c579da15000e85eda307 Author: markd Date: Tue Oct 14 17:35:16 2008 +0000 get geneName from GENE features for non-coding RNAs commit 1f357519fbad17ccd31fd3811aa85c233b608110 Author: markd Date: Tue Oct 14 17:34:44 2008 +0000 sort BED for upstream, rsync gbdb to genbank server commit b5bf9f1628214db591d1712db5b4b46cf351d7b1 Author: mikep Date: Tue Oct 14 17:08:14 2008 +0000 "New version number v193" commit 0e41cbb37cefacc70119bd55bf979ffe6a6c18cd Author: mikep Date: Tue Oct 14 17:07:51 2008 +0000 added script and time to echo messages for simplifying tracing and debugging commit e40df2de9c9795708410228d74a2a13565c1bff3 Author: hiram Date: Tue Oct 14 16:38:47 2008 +0000 Eliminate references to the FTP server locations, instead always use rsync commit 5c4cf6b8fa74dbb175ba86eddfcdcd1d0bb0ae30 Author: braney Date: Tue Oct 14 16:15:33 2008 +0000 check for NULL nibPath commit 056aeecf5ebaa3ab6e432d9c381058c5015302fc Author: galt Date: Tue Oct 14 15:00:06 2008 +0000 "Encode release log update" commit 88a5a0422e87125426cb2a6b9992ccd63fa841c4 Author: galt Date: Tue Oct 14 15:00:04 2008 +0000 "Release log update" commit ad48860dfbe9218ba528829eb420c41eee76b5d9 Author: markd Date: Tue Oct 14 02:02:15 2008 +0000 removed inactive databases from initial upstream specs commit 2a5f5df62bc3aa695e16e233c497168a1e60c53d Author: markd Date: Tue Oct 14 01:52:18 2008 +0000 more upstream additions commit 381c2c0eaee2181561740ff9060e18eb52301c09 Author: pauline Date: Mon Oct 13 23:52:37 2008 +0000 Added microsat to tables ignored. commit 2af3f0caa89610682c3dd27a6b63d82f63fdd3cb Author: tdreszer Date: Mon Oct 13 23:22:00 2008 +0000 Introduced 4th dimension (Z) to Riken commit 2b505136496becce15a34f47a29f8e70eb82bd0e Author: tdreszer Date: Mon Oct 13 23:09:27 2008 +0000 Added dimension Z to the composite by matrix UI. commit 79e6214153f1aae12492e1219d42642d49f456c5 Author: kuhn Date: Mon Oct 13 23:08:07 2008 +0000 added some error checking for missing exclude file commit f540a777654e872c84eca025ac2c289e1af0cd0f Author: tdreszer Date: Mon Oct 13 23:07:22 2008 +0000 Garf am I ever sloppy. commit 244b823ccd9c26f812cd3c8228b3a62a04e2b862 Author: tdreszer Date: Mon Oct 13 22:59:28 2008 +0000 Cleaned up memory allocations on advice from Jim commit 9796ca08f00cda9757dc22fa985c455fca7fa6f5 Author: tdreszer Date: Mon Oct 13 22:56:03 2008 +0000 Added cloneFirstWordByDelimiter and a couple other simple routines. subChar() is now macro of memSwapChar(). commit a578fc834606a96754f3ff6b1dd6f88f72e73e7e Author: aamp Date: Mon Oct 13 22:40:25 2008 +0000 Next-item capability for custom tracks. commit 33831705282254c7687864e136cfe3b2bba28533 Author: tdreszer Date: Mon Oct 13 22:14:37 2008 +0000 Support for dimension Z commit f58c227e015cd1161b8b8c0cbfde21fcc45d369d Author: tdreszer Date: Mon Oct 13 22:13:16 2008 +0000 Labs added FAIRE and ChIP-seq methods on wiki commit c9b8985bd55d637384c88d7b30dbc9a1a7af8da8 Author: hiram Date: Mon Oct 13 20:48:29 2008 +0000 Adding Zhao lab graph tracks commit ece7a40f6d300bc96648571c544538ab7e70d66e Author: markd Date: Mon Oct 13 19:46:05 2008 +0000 yet another try to get hg16 right commit d3217493bcc2b6ed92884f1538622916c05f96c3 Author: markd Date: Mon Oct 13 19:33:19 2008 +0000 fixed hg15 multiz table name commit c1245c64b674eea3607f0942d2af17e025ca6f53 Author: markd Date: Mon Oct 13 19:13:14 2008 +0000 fixes to upstream maf definition commit c8536eb9fae027f259d3175f9503c84f360e5424 Author: hiram Date: Mon Oct 13 17:58:53 2008 +0000 Raise the 1 million window size limit to 100 million to do histograms on wiggle data commit 9982b65cf843a298e8b7fa7f53ee063d06d19bf5 Author: markd Date: Mon Oct 13 17:32:24 2008 +0000 don't require ccds profile when loading hgwdev commit f1cc9736024c8101d01009545f113a4c643a045c Author: larrym Date: Mon Oct 13 16:11:39 2008 +0000 add All tests passed msg commit 05b870adb4b71ec7664054c15aa0519b6c01dd9e Author: larrym Date: Mon Oct 13 16:08:26 2008 +0000 support narrowPeak, broadPeak and gappedPeak commit 09d6a5b84f43d48126a44f7c1d4cdcbe73c66fcf Author: galt Date: Mon Oct 13 15:00:09 2008 +0000 "Encode release log update" commit 4ed63fa98dc813bc1278c77714c0ad98325986c3 Author: galt Date: Mon Oct 13 15:00:06 2008 +0000 "Release log update" commit 9ebe2f5f4d20b7f20a78d738ff3bf0c41dc22617 Author: markd Date: Mon Oct 13 06:21:18 2008 +0000 add description to RefSeq page commit 7327cc801d0d498c839c91357d809177b048705e Author: markd Date: Mon Oct 13 04:52:00 2008 +0000 enable rsync of /gbdb links to genbank server commit adfa31194a7caa043a67a88cf9d69459344ae8a8 Author: markd Date: Mon Oct 13 04:48:19 2008 +0000 enable refseq non-coding on all hgwdev databases commit 3db4970420ecf2d76b9eeb2ff7fb384b313af7cf Author: galt Date: Sun Oct 12 15:00:08 2008 +0000 "Encode release log update" commit f2c01d936d4d19df2e9f2314f92fb866e23e6023 Author: galt Date: Sun Oct 12 15:00:05 2008 +0000 "Release log update" commit 4833fda0b135cb075688f93bc99672edcdf0cd8c Author: markd Date: Sun Oct 12 07:33:02 2008 +0000 hopfully fixed problem with MGC alignments not being deleted when clone is removed from mgc commit a3a20a2104d6d195bd7848853d98e6a6034874b3 Author: markd Date: Sat Oct 11 20:17:35 2008 +0000 fixed prototype problems that lead to undetected parameter mising parameters commit 59c0cbd2e9ce08f5289f7501bdab5de359c94f4a Author: larrym Date: Sat Oct 11 19:56:04 2008 +0000 fix typo commit c9ade29206ab3a968118bd2a60972606b9160324 Author: markd Date: Sat Oct 11 19:54:42 2008 +0000 to avoid extFile table clashes at mirror sites, suport MAF tables with a single MAF file in track settings commit 131316890c2b17a59d4d0f505b18e6f8252d9c5e Author: galt Date: Sat Oct 11 15:00:11 2008 +0000 "Encode release log update" commit cf61ed84072fd2bd0491040f1bd15dd1d429aeb7 Author: galt Date: Sat Oct 11 15:00:09 2008 +0000 "Release log update" commit 5a03abf354914040968f9c9c380469dfa8eb1920 Author: tdreszer Date: Fri Oct 10 20:22:40 2008 +0000 Was expecting Kate to check this in, but I better do it before I forget. Composite multi-view alignment cfg open by default. commit 1237520480d01f36ef6cd5e982924152c11ddb5d Author: pauline Date: Fri Oct 10 19:01:22 2008 +0000 Fixed white space missing carriage return. commit daf11ecc6df995beaef332ffe0f414ebdf5ba873 Author: pauline Date: Fri Oct 10 18:58:02 2008 +0000 Adding kgTables so that it is under CVS control. commit 53ca21594f68ed680207bcc220ca5bc88ad6bbaa Author: pauline Date: Fri Oct 10 18:51:02 2008 +0000 Changed temp local file name to prevent deleting original file. commit dafae6cfd912d2ddc785d75a208ef441f5f8f421 Author: braney Date: Fri Oct 10 17:39:12 2008 +0000 add definition of 'e' lines commit 4e0dbdc60e56d9da2f7d7e054af2092f38b5cbaa Author: kuhn Date: Fri Oct 10 17:27:43 2008 +0000 added linkCheckExclude commit 5280a352936f90ffe44b820711f210456f5c5e5a Author: markd Date: Fri Oct 10 16:56:06 2008 +0000 improved wording commit 7689a5f72ce29ed20faa941253f452c4e20d7c52 Author: kent Date: Fri Oct 10 16:38:44 2008 +0000 Handy little utility to hard mask a soft masked file. commit 36bdc24b27dd52620364c553c85a7b9ee22aa8d9 Author: mikep Date: Fri Oct 10 16:38:26 2008 +0000 tags (or sites) are not required initially commit d2c79b4f4dba0f96e5380f0597ec7ca4fb263dd8 Author: ann Date: Fri Oct 10 16:07:56 2008 +0000 added explanation for new hgPal configuration commit 9d95b2d159615af52bd09a4414d5adba4f33f296 Author: galt Date: Fri Oct 10 15:00:08 2008 +0000 "Encode release log update" commit ed46f9485ac7839dc66d55747f4d35d7dc25b060 Author: galt Date: Fri Oct 10 15:00:05 2008 +0000 "Release log update" commit d296c95e99115480e3b3e232c7295349d76d2c99 Author: markd Date: Fri Oct 10 06:06:58 2008 +0000 added support for updating upstream FASTA and MAF files, howver not yet enabled commit b9db08d3c0cdb6bfe8f1e5ed18761276db7b25ae Author: markd Date: Fri Oct 10 06:02:24 2008 +0000 added maf r lines, to indicate how maf regions were defined commit 66f61503d8874a3dc3fd9f2300a54f7a43696e2b Author: pauline Date: Fri Oct 10 01:40:02 2008 +0000 Updated reference. commit 83138595f0be258a7c1e15af9f64f02d8be6a4dc Author: rhead Date: Fri Oct 10 00:38:49 2008 +0000 Adding origAssembly to nuclesome tracks, as they were lifted from ce4. Note that last commit was accidental (-r1.10), and the message is incorrect. commit d7023fb32f0bb462468386274449c1422d5d95d7 Author: rhead Date: Fri Oct 10 00:12:58 2008 +0000 Changed ftp path from ce4 to ''. commit 61178eeaa4dadf05f0ab6734666dd7affd580c91 Author: hiram Date: Thu Oct 9 23:11:45 2008 +0000 Add Zhao lab nucleosome test data set for chr1 commit 3be8d635d006aa5ca1e984eff0c7a5bbf1ce170f Author: pauline Date: Thu Oct 9 23:03:03 2008 +0000 Updated reference. commit 56f9e2e5b56e42dbe3189106e0ba81e352874440 Author: aamp Date: Thu Oct 9 21:45:53 2008 +0000 Removed references section until that's complete. commit dc94f0fa11812e0f3577a5f919291e756a2b9f9d Author: hiram Date: Thu Oct 9 20:32:27 2008 +0000 Adding gnfMOE430v2 for this Atlas 3 GNF business commit 6a892ae67016b890636c864f5e8c6a561abaf098 Author: kuhn Date: Thu Oct 9 19:24:24 2008 +0000 added emphasis to et al. commit abf1eb964e68fe18d3f1fb038ee05dcf729d6229 Author: rhead Date: Thu Oct 9 18:56:09 2008 +0000 Added 25mersRepeats to tablesIgnored in c. elegans browsers per Hiram. commit cfc9bdfbe154ff40f4063942e4ab5bc7f6273c8a Author: hiram Date: Thu Oct 9 18:32:05 2008 +0000 Implement the red/blue on white option for expression tracks commit cba433a14473edf6506267222874980dd3e4499b Author: hiram Date: Thu Oct 9 17:28:46 2008 +0000 Better error message for out of order coordinates commit 56a91731d400ed793f1a2b5c00aee79314319ffe Author: braney Date: Thu Oct 9 01:49:44 2008 +0000 try to make error message more clear. commit 272e2fb0c4660dd1c8ecf5383184cc1ed7f57ee4 Author: markd Date: Thu Oct 9 01:10:48 2008 +0000 remove old NFS hack commit 221a66873236e6e51b6c5e9af495f7f368c46fc9 Author: aamp Date: Thu Oct 9 00:04:32 2008 +0000 Added Microarray custom track schema page. commit 3a41284a83e363749b5f6346e6095f89a44a2c4b Author: hiram Date: Wed Oct 8 23:32:10 2008 +0000 Added selected gnfMOE430v2MedianExps gnfMOE430v2MedianRatio gnfMOE430v2Median commit 7a449488c4cfcc948eaa638f5f8449e92bf1f024 Author: mikep Date: Wed Oct 8 20:40:11 2008 +0000 affy does not have repicates either commit affd47e1dbfef4d64b2fe25976962ee23c5a7512 Author: ann Date: Wed Oct 8 20:36:42 2008 +0000 added the other three types commit 6853592e3950c52b7b81b5d50c6dcb2dfbcb83d5 Author: hiram Date: Wed Oct 8 20:14:18 2008 +0000 Adding expGnfAtlas3 commit ac45187d15ff35bb44d424beb8c0060503d62149 Author: hiram Date: Wed Oct 8 19:08:42 2008 +0000 This appears to be working better for the MOE430 V2 GNF Atlas 3 data commit 16ec7ff894cbac9fec33cc74f72c1339966319a1 Author: larrym Date: Wed Oct 8 18:38:00 2008 +0000 add fragmentLengthRange commit 7e157a967699e042f14493b695b9077a901da2a5 Author: larrym Date: Wed Oct 8 18:37:46 2008 +0000 change medianFragmentLength logic so it only is required for dataType eq ChipSeq commit 063e3ca3cef2e55943e8701d9b0163edd6b42186 Author: larrym Date: Wed Oct 8 18:31:44 2008 +0000 add medianFragmentLength commit 9e93ab74411fcea377b0e295c4ee733aa0b8dd58 Author: larrym Date: Wed Oct 8 18:30:41 2008 +0000 stopy using diff --ignore-matching-lines (it wasn't working) and go back to using tmp files for filtering out stuff that is variable commit 6574e9fcf359996836c54678233a3f77ea784b1d Author: larrym Date: Wed Oct 8 18:28:06 2008 +0000 update to reflect changes to validator commit 477890a1a8e96c9134d2cfa658acf631f84c2e90 Author: braney Date: Wed Oct 8 18:19:15 2008 +0000 add hgPal alignments, update status on 44 lastz's commit 24ef4fe044e2bdf221a7dd7123d27d2c67db5517 Author: braney Date: Wed Oct 8 18:14:04 2008 +0000 add hgPal downloads commit d96c11362b2dcbe593f3ac27c18c675169886b17 Author: braney Date: Wed Oct 8 18:13:19 2008 +0000 add md5sums commit 0ff9a311c93136d0ca25b465259f37d33aa7ed55 Author: ann Date: Wed Oct 8 17:59:30 2008 +0000 added discussion of two new config features commit d22c6447f0834ab4bb5f45134d184548c7e63f00 Author: larrym Date: Wed Oct 8 17:55:22 2008 +0000 change Weng and Hubbard wranglers commit da1fe1b6804197b3de3f1d1814a29da7ff7ad069 Author: markd Date: Wed Oct 8 17:48:53 2008 +0000 explictly specify hive locations of files commit a8d292701373b034001fbba56772a0b555692f3d Author: markd Date: Wed Oct 8 16:56:11 2008 +0000 exclude CCDSs marked as replaced commit 09f90150d737bbf1f69ef1692510290800baac03 Author: ann Date: Wed Oct 8 16:23:34 2008 +0000 hiding netXenTro1 track by default commit 1da2043ca04588ecd8031810c79076bf8d02543f Author: galt Date: Wed Oct 8 15:00:06 2008 +0000 "Encode release log update" commit 802f71398f2abc24b24af19ad3b130c6ef4a94f5 Author: galt Date: Wed Oct 8 15:00:03 2008 +0000 "Release log update" commit d3b73395d34122f652e49bf77a1af915f3529df9 Author: giardine Date: Wed Oct 8 13:54:13 2008 +0000 added Oreganno update commit 99d044c257c677853acb95eb8feee0fbddba5279 Author: mikep Date: Wed Oct 8 05:26:19 2008 +0000 updated version from lessions learnt after CSHL call commit 7e21d2ae844a88fc3f59c0d1de38cc5cc7364903 Author: mikep Date: Wed Oct 8 05:16:13 2008 +0000 temp file for validation only, not loaded commit d3440edba424b2800fb54354b12191ebeab2446a Author: mikep Date: Wed Oct 8 05:14:06 2008 +0000 First version of daf for Sanger commit 3290ee235e6ed7479d2cfd3bed617395d4cfe9ce Author: mikep Date: Wed Oct 8 05:04:21 2008 +0000 handle GFF as well as GTF formats commit 5f1816bd69cb73b695e38e3b14cd44e312373ab3 Author: larrym Date: Wed Oct 8 01:09:41 2008 +0000 medianReadLength => medianFragmentLength commit 8a01a8fa88b0abcde7afd6597f290b44a2ee3892 Author: braney Date: Wed Oct 8 00:28:46 2008 +0000 re-re-download. Build database. commit 68a35bf8d2fc03d900f9729eea94197cc687e188 Author: braney Date: Wed Oct 8 00:21:50 2008 +0000 re-re-download sequence. Make database. commit 3e497f975e6addc55a3641c3d50a82c4a05cd267 Author: mikep Date: Wed Oct 8 00:06:46 2008 +0000 load and unload gtf (genePred) files for Sanger Gencode commit 107f61ea9a357868abcf250abc1ede4f2d3e90b8 Author: mikep Date: Wed Oct 8 00:05:07 2008 +0000 fixing output from validator commit ed4f8f439880597ea0cae6a860a6397855563547 Author: mikep Date: Tue Oct 7 23:59:57 2008 +0000 convert the gtf to bed and keep it, also, change the trackDb type to genePred commit c55e724066cb1c8c81cfd90289100c01ae606bf2 Author: cline Date: Tue Oct 7 23:54:07 2008 +0000 Added entries for affyExonTissues in mouse and rat commit 82a20857e1d43cf9bee8c22abd62cfe6ccfd8e49 Author: rhead Date: Tue Oct 7 23:35:14 2008 +0000 Standardized reference. commit 7b7e427ecf6f55f4ab2cd7131ae7432bea9ace54 Author: angie Date: Tue Oct 7 22:39:58 2008 +0000 Oops, one more tweak to make it still work with single matches. commit 7e8524a999026c603d10eb20f2f4293ae8e0cef4 Author: braney Date: Tue Oct 7 22:39:43 2008 +0000 finish up masking commit 49bc174620486be192f5dafda90d5604f9bc3e2f Author: mikep Date: Tue Oct 7 22:30:52 2008 +0000 allow empty variable in daf for Sanger Gencode commit c7a464e022a4028a76a6f6481519ccfbdae7d343 Author: mikep Date: Tue Oct 7 22:18:07 2008 +0000 Encode track for Sanger Gencode commit bb6f477527fb53dd72898606ae0527e568bf0d13 Author: angie Date: Tue Oct 7 22:17:57 2008 +0000 Fixed bug that lurked for years: doesn't match w/multiple terms was a no-op because the not was misplaced. Caught by Ann testing new multi-select for enums and sets. commit 2539620ad8df0383f9a8ab65afe426c4c0daf48b Author: hiram Date: Tue Oct 7 21:26:14 2008 +0000 initial contents properly made the groups for GNF MOE430v2 Atlas V3 commit a41c622f309762c2f9655f4ff5069bf1e1503562 Author: ann Date: Tue Oct 7 21:15:34 2008 +0000 relaxed allenBrainGene rule to account for UCSC Gene update commit 9e5b6e2eb78738d9e80afbfc3da927ca10917a9e Author: braney Date: Tue Oct 7 21:14:43 2008 +0000 re-re-download . Build DB. commit 1858780fa07be1fdaa484462cd5aae13a9c6999c Author: braney Date: Tue Oct 7 21:06:27 2008 +0000 re-re-download. Make db. commit a1f3f4c4c52fa8c443e4c972e53d4368bc812ca8 Author: mikep Date: Tue Oct 7 20:51:39 2008 +0000 adding the host name to messages commit 7fc097d35b9c1824874fcc426ff0462a8ae56c85 Author: hiram Date: Tue Oct 7 20:49:28 2008 +0000 readjust affyMOE430v2 track settings, adding URL to affy commit d892666fa58569a2b6a1548679cbfee53f9398cd Author: hiram Date: Tue Oct 7 20:39:34 2008 +0000 adding affyMOE430v2 to the list for doAffy() items commit a3e6214f94286e005180af92d3ee9b98101d0110 Author: braney Date: Tue Oct 7 20:34:22 2008 +0000 verify same as Broad, re-do masking commit 1edab6afa7c63d259e6189fb7f9119f1999c0a57 Author: mikep Date: Tue Oct 7 20:22:14 2008 +0000 day 2 commit 61274efebda122cda905659378b2b4a7e2bb492f Author: hiram Date: Tue Oct 7 19:58:03 2008 +0000 Better to use %g instead of %f in the bedOutputN_Opt() function for micro array data values commit 37d41b28c63f91d8de4b6147126028162023338c Author: braney Date: Tue Oct 7 19:40:06 2008 +0000 re-re-download and build database commit ec8a71cfdec0ec753a3bee5396b6d857fb6fd6ea Author: kayla Date: Tue Oct 7 19:38:11 2008 +0000 changed priorities on taeGut1 net/chain commit 02b984c83aac219020eeafddddc802e02a533576 Author: braney Date: Tue Oct 7 19:25:19 2008 +0000 add option to not truncate headers in table format commit f4ca3721f47d48fe6dd2d54e1d50134aa51f8435 Author: braney Date: Tue Oct 7 19:19:25 2008 +0000 add option not to truncate the headers in table mode commit 1b9cdd92c0105be816bf5c7aa98b10f4282cd6ce Author: braney Date: Tue Oct 7 18:44:26 2008 +0000 fix up connection stuff resulting from Mark's db changes commit bf2b195d19f91930502df3e827f395610315ec9c Author: mikep Date: Tue Oct 7 18:17:53 2008 +0000 has replicates is no everywhre commit ab551cd850f70a2169718b009d3d4c637697732e Author: braney Date: Tue Oct 7 17:54:51 2008 +0000 alpaca re-re-downloaded commit 0a045f490480daa9a07be735e69a851205bb806f Author: mikep Date: Tue Oct 7 17:50:49 2008 +0000 no replicates, so no signal commit 8039bcb980d667f9d9343cc7bec2dde39a207818 Author: braney Date: Tue Oct 7 17:42:40 2008 +0000 re-re-download again commit 0046871664c2003d70e91dd6fb7cab5232714866 Author: hiram Date: Tue Oct 7 17:40:06 2008 +0000 Updated to represent the proper chipset and gene atlas v3 data commit 8c40cecf369129b9ee79de599f06416436333bd4 Author: ann Date: Tue Oct 7 17:02:13 2008 +0000 small edit to docs link commit 70c17de33dab1e88e19417e38e61f907f42c8eea Author: mikep Date: Tue Oct 7 16:17:45 2008 +0000 adding date and script to output commit c1f6321a0ce432d1fb7595c3e0dc05ccb04e1088 Author: mikep Date: Tue Oct 7 16:01:38 2008 +0000 adding times in output commit 0dc10d73b0fe13c3a8098ce27feb3b05ebf4d695 Author: braney Date: Tue Oct 7 15:04:06 2008 +0000 add mafGene commit eb19f60d97b9504057552e21ed337de51cb246f2 Author: braney Date: Tue Oct 7 15:03:19 2008 +0000 add argument (unused in mafGene) commit 7dea512f2dc57597393ca8fc58adeb86f514428f Author: galt Date: Tue Oct 7 15:00:07 2008 +0000 "Encode release log update" commit 47169006ef3cd6c88c511ad90c19ab76c918897f Author: galt Date: Tue Oct 7 15:00:04 2008 +0000 "Release log update" commit b766d9b393f22500bcf0ceb3b554a78785afda70 Author: mikep Date: Tue Oct 7 14:46:22 2008 +0000 changed cell line which changed table names commit 71dd3daa7c9817fd6284d7bb41707518be74c29f Author: mikep Date: Tue Oct 7 14:44:43 2008 +0000 added option to skip validation of files, added localization and rnaExtract variables from cv.ra commit 99e509aca3052b4be99c7988abdda9f38d4b26a5 Author: mikep Date: Tue Oct 7 14:43:47 2008 +0000 change debug into option which loads only 1000 rows, turned debug messages into verbose commit 3a20384b5e4f18b1db54bf180a51490ef214f60c Author: mikep Date: Tue Oct 7 14:41:35 2008 +0000 adding prostate cell line temporarily while we figure out what it should be for gingeras commit 14c3421bd4e3f15839254bd0aec5ce701936d802 Author: larrym Date: Tue Oct 7 00:50:12 2008 +0000 use daf->{medianReadLength} and bedExtendRanges (most of this delta is just existing code shifted over in a new if/else block) commit ee4b3a5ba2c4ac4fc96177a032276f381328c6a8 Author: larrym Date: Tue Oct 7 00:45:46 2008 +0000 add medianReadLength commit 1bffb159ecd6656f71967de232c8b488398a1f2c Author: angie Date: Tue Oct 7 00:26:03 2008 +0000 Added settings field, so we can add arbitrary attributes (like trackDb's settings). commit dec6ed248410bf1c64ff9b748cc87ee6ff398f1c Author: angie Date: Tue Oct 7 00:22:03 2008 +0000 Changed table of existing sessions to include creation date; added table headers and shortened load button label to make room for date. Added description page w/editable session name and description field when namedSessionDb has a settings column. commit 24831e5926b35b797cc10d2905ee35c068d25c67 Author: larrym Date: Tue Oct 7 00:04:41 2008 +0000 improve usage commit c9c802d9315fa3aa37efc7c66070f3dc1b1d1dff Author: larrym Date: Tue Oct 7 00:04:16 2008 +0000 add chromBoundaries.txt commit 9ac4a14710b50ceb0fce9c2dcf9db80f93f85f7b Author: larrym Date: Tue Oct 7 00:03:58 2008 +0000 initial checkin commit b89c23ba87f28f867c7bb4636e1a033fbb933d30 Author: larrym Date: Mon Oct 6 23:49:26 2008 +0000 initial checkin commit 9ad41bbc5ff62c62f921e17d123de41a34a0a7d5 Author: angie Date: Mon Oct 6 23:33:47 2008 +0000 On the filter page, for enum and set fields, offer a table of checkboxes instead of a dropdown so multiple values can be selected. Multiple values are OR'd. commit cc726913c6d1d3ad5e9a04c0613c15f80eb5d231 Author: angie Date: Mon Oct 6 23:27:15 2008 +0000 Added cgiMakeCheckboxGroup (same CGI behavior as a multi-select input, but all choices are displayed). commit 04e42662a8ecf145ba5c6f895149e0b277794346 Author: ann Date: Mon Oct 6 22:38:52 2008 +0000 fixed typo commit 83de5e3760c8ab557e72bbd0f7f7359654cd3330 Author: mikep Date: Mon Oct 6 21:33:41 2008 +0000 working version of daf commit 0d96ab8ef0bae03d52adda70f2705c41a1cd1af5 Author: braney Date: Mon Oct 6 21:21:12 2008 +0000 add table output format commit 32aba663764ed4dfc00701e693259bca0854cd43 Author: braney Date: Mon Oct 6 21:19:27 2008 +0000 add table format commit 7c359ee1edffab5e0766191b1c3b6c7213889f7d Author: braney Date: Mon Oct 6 21:12:21 2008 +0000 add option to print out alignments in table format commit 42672cc9d5b21434f501c957d8130c79197afec6 Author: ann Date: Mon Oct 6 20:31:18 2008 +0000 removed beta release from xenTro2 c/n block of top-level trackDb.ra file. and removed entire c/n xenTro1 blocks from hg18-level file. commit 8fe82ef1cb38dd0f0cdc77a0c23a16ac8dde6c8d Author: rico Date: Mon Oct 6 19:20:13 2008 +0000 removed unneded link to jkhgap.a, added clean target commit 99954b7671b5adc9dbb1c2b432ee903d6e5e606e Author: rico Date: Mon Oct 6 19:18:56 2008 +0000 removed unneded link to jkhgap.a commit 6935f535ec8b10dc362e4e17b653d78f02eb4160 Author: hiram Date: Mon Oct 6 18:35:05 2008 +0000 Now displaying the gnfMOE430v2 business correctly commit 01a9165a94c0f0a53a3cca8672762bcd6597eec9 Author: hiram Date: Mon Oct 6 18:34:09 2008 +0000 Have the gnfMOE403v2 business now correct commit ffcfea51f6036dd8cd9b99acc03bf9f97d6d5407 Author: mikep Date: Mon Oct 6 17:39:53 2008 +0000 updated with wig parameters from doEncodeLoad.pl run commit 980a0e3f9411d21d0a28131a9b4f6f14f860b3b3 Author: angie Date: Mon Oct 6 17:32:56 2008 +0000 In adjustSqlTableColumns, check for -noBin before adjusting numFields. commit 76f08f26f5652bfbf65066069b2ab87840619e44 Author: angie Date: Mon Oct 6 17:18:27 2008 +0000 Added hgSessionName. commit 8df2f371e67c5afd9bfb8faa6edac45fed285253 Author: hiram Date: Mon Oct 6 17:04:17 2008 +0000 A bit more informative on errAbort messages about "not found" commit df9537b8b1ba840dee1c75bf8ca2de44a9bc495b Author: galt Date: Mon Oct 6 15:00:06 2008 +0000 "Encode release log update" commit 983006dede93b477638c03186b27bc8824399005 Author: galt Date: Mon Oct 6 15:00:03 2008 +0000 "Release log update" commit fd3ff64438be3f6e69cd18aaca1351cddc69fe5c Author: cszeto Date: Mon Oct 6 00:35:50 2008 +0000 Added information for 7 new datasets. commit f963137caf3aa0cff5f39c62e72b93854bca6f52 Author: galt Date: Sun Oct 5 15:00:07 2008 +0000 "Encode release log update" commit 901e0fa2d8e27cd9851790cbeb634ce4b2d08b36 Author: galt Date: Sun Oct 5 15:00:04 2008 +0000 "Release log update" commit ac1563377a39a3d8597990840e4897f5ebcac33f Author: larrym Date: Sun Oct 5 04:03:36 2008 +0000 fix bug in code which auto-fills in score column (fixed code to be case-insensitive) commit b3ad2415f37a478a6860b9ff58afcdacc2233b3a Author: kate Date: Sat Oct 4 18:58:47 2008 +0000 5C project metadata file commit 74b79032bd5d81547af5726dcab52a24e9a2a1c4 Author: galt Date: Sat Oct 4 15:00:11 2008 +0000 "Encode release log update" commit 3b819417418975c8237bd8f2639801f7de83dc4e Author: galt Date: Sat Oct 4 15:00:08 2008 +0000 "Release log update" commit fba31f0ec3f283eb80c0d132584e85def38d8395 Author: mikep Date: Sat Oct 4 09:59:00 2008 +0000 adding 'bedGraph 4' as a format commit 44f1aeef3fb091225ccf1747d2e0927a1befe706 Author: tdreszer Date: Sat Oct 4 01:22:18 2008 +0000 Now that I recognize the second bug that was really at fault, I can fix it properly. commit 6aae4e552fc67518264b074cf968689788007410 Author: mikep Date: Sat Oct 4 00:02:35 2008 +0000 changed unloader to ignore 'downloadOnly' types, rather than hardcoding 'fastq', since I also have csfasta and csqual types, and chagned error message to report program, to distinguish between do*Load.pl and do*Unload.pl scripts commit 37f47cfa50f0d5a79de0938f7e8f51e73b80afec Author: rhead Date: Sat Oct 4 00:01:59 2008 +0000 Changed PicTar link to mdc-berlin, Rajewsky's current location. Not sure how much they maintain this site, but the nyu pictar site is gone. commit 26706db310fa4a98a909bbfc74544092285c0042 Author: mikep Date: Sat Oct 4 00:01:16 2008 +0000 added (type bedGraph 4) with loader and fixed error message to report program, to distinguish between do*Load.pl and do*Unload.pl scripts commit cf793ab5a1e650838dcc6b9224b9a11c1bf9f680 Author: kuhn Date: Fri Oct 3 23:43:59 2008 +0000 new script for letting people know about B-queue content commit 85f7fd9a1b307c12dfb0891a5887bc3d69b5dffb Author: kuhn Date: Fri Oct 3 23:43:26 2008 +0000 tweak commit f696fed9e703c33e1a2ad897755f0713cb7bbc62 Author: kent Date: Fri Oct 3 23:02:11 2008 +0000 Making it so that refGene has a hide-noncoding option. commit 8ee71eb9122f357cd2a70203693d18943532a289 Author: hartera Date: Fri Oct 3 22:45:58 2008 +0000 Updated the regular expression for the genscan search so that it works for the Tetraodon Genscan IDs. commit 0e3799975df0314ced8b4bdcb7b2be0d31991926 Author: kent Date: Fri Oct 3 22:34:55 2008 +0000 Removing geneIdConfig2 routine by absorbing it into it's only user - refGeneUI commit ed15fff2b432dbe8d181aabac94ca76a6d42ba06 Author: kent Date: Fri Oct 3 22:33:07 2008 +0000 Simplifying logic in geneIdConfig that no longer is used for RefGene tables. (geneIdConfig2 is used for these tables now. commit c930ee412495aab08d7211a6e441d2da50a06b70 Author: angie Date: Fri Oct 3 21:17:02 2008 +0000 Added KnockOut Mouse Project (KOMP). commit 4cc46cc9a5ba84644ae0f5fdeaab30b53480fa9a Author: tdreszer Date: Fri Oct 3 19:19:13 2008 +0000 Fixed bug of trying to free the return from firstWordInLine() (Thanks Angie) commit 915d818c6b41ba0dc5286c7f51514c349a14ad27 Author: angie Date: Fri Oct 3 17:38:23 2008 +0000 Added KnockOut Mouse Project (KOMP) details. commit d690f11e98ab7bff02e0b6a1fe3b191abb627b8a Author: tdreszer Date: Fri Oct 3 17:26:26 2008 +0000 Added a comment describing a function: I had forgot what it does (gasp) commit 10c4c6f671e952f64c4ba4b75c718e2eda91649f Author: tdreszer Date: Fri Oct 3 17:19:27 2008 +0000 Added support for composite level view-specific default settings in trackDb.ra 'settingsByView'. Also added support for composite level view cfg expanded by default. commit 1dab18a9edbea2965f24d4815abb317433395e76 Author: tdreszer Date: Fri Oct 3 17:11:53 2008 +0000 Added support for composite level view-specific default settings in trackDb.ra 'settingsByView' commit 24c895a26ea186c663e6c3e73a8aaa95ddc58041 Author: fanhsu Date: Fri Oct 3 16:10:56 2008 +0000 Simplified a sentence. commit 271380d5998f9bdb860883bd7ec0042497fa78bf Author: galt Date: Fri Oct 3 15:00:08 2008 +0000 "Encode release log update" commit e585158f5dd6830cfc35d908fd4441f1bd8ce2aa Author: galt Date: Fri Oct 3 15:00:05 2008 +0000 "Release log update" commit 53861fd3dc4b5c2372ab5dc94e2f3d73de13ad48 Author: braney Date: Fri Oct 3 01:14:36 2008 +0000 trust the case from the nib or 2bit commit 50d478a53c27611f76b0da68bc2f95214f6f8761 Author: braney Date: Fri Oct 3 00:06:07 2008 +0000 fix spelling error. Who's replaced with w-hose commit ecdbb21ffae61ad8cccd67a8dad46f1527127c5f Author: braney Date: Fri Oct 3 00:00:46 2008 +0000 change interface to accept beds instead of just names commit 7727b04a32147a684f14662b1151a19965de3741 Author: braney Date: Thu Oct 2 23:59:40 2008 +0000 changed library interface commit 06fc62665973d8d5e585d24bca16e5db9aa4704f Author: braney Date: Thu Oct 2 23:59:05 2008 +0000 fix "small problem". commit eba9b7e30a233d8e4ddacd60b3aa9db06342bbac Author: braney Date: Thu Oct 2 23:54:02 2008 +0000 make gene definition more exact. Need name *and* position commit 5eea7611c97aa0796f76587c49b2e70035ec1bcd Author: aamp Date: Thu Oct 2 23:50:08 2008 +0000 Added a few more fields to project. commit 7254271b37a95179e8a97b416fb0bfcfbec65382 Author: hiram Date: Thu Oct 2 23:39:41 2008 +0000 added Affy MOE430 version 2 with GNF expression data commit 02881c2d6008b090a79b228d01cff2daf7c2e929 Author: angie Date: Thu Oct 2 23:15:47 2008 +0000 Added support for variables with multiple values, e.g. from multi-select form inputs. cartAddString can be used to add multiple values for the same var to the cart hash. cartOptionalSlNameList returns a list of all values for the given var. cartRemove removes all values associated with the given var, not only the first value found. loadCgiOverHash is more complex: it builds a separate has of cgi var-val pairs, removing all values found for those variables in the cart hash, and then puts all cgi var-val pairs into the cart hash. This is so it can distinguish old values of list variables from new values. commit 37333cba2690883f57172535ae0a6a753e59c6dd Author: hiram Date: Thu Oct 2 23:09:18 2008 +0000 Initial track instances for the affyMOE430v2 chipset and GNF expression data commit 3db04e6e3dc92c2dbe16c19562549ea6a09ea2e0 Author: hiram Date: Thu Oct 2 23:07:51 2008 +0000 A copy of gnfAtlas2.html for this new chipset with GNF expression data commit b445cb7b10c9821e677a40daa9af48442d999bf8 Author: hiram Date: Thu Oct 2 23:06:09 2008 +0000 A first attempt at gnfMOE430v2 entries commit 527223281bbf7e994206dce6efc98f0b6a54111d Author: angie Date: Thu Oct 2 23:00:05 2008 +0000 Added cgiMultListShadowPrefix() and hidden shadow variable for multi-select inputs, so we can detect the case when all inputs have been deselected. Updated cgiMakeMultList to take a list of checked items, instead of just one. commit c29e8a198aab25c5ffdf3dbd6c0b2b580183d56e Author: rhead Date: Thu Oct 2 22:24:02 2008 +0000 Fixed broken link to Len Pennacchio. commit 37fc9c82ead1a839559d75ec64b5e42d956556b9 Author: angie Date: Thu Oct 2 21:25:03 2008 +0000 In printPcrSequence, fixed the position link to use start+1, but not the link text (to remain consistent with hgPcr's output format). commit 3d1373e151a741d80d9bcd31f6601be86b0a69c5 Author: angie Date: Thu Oct 2 21:10:43 2008 +0000 When intersecting items (not bp-wise), pad each zero-length item with 1 base on each side so that overlap with adjacent bases is counted. commit 8ddbf34d08f4f7319f355fdfb08549858e6cefa6 Author: braney Date: Thu Oct 2 21:01:58 2008 +0000 fix stupid mistake letting all tables get CDS commit 497a3a322664af095a35d84049fd6c3e864421a6 Author: markd Date: Thu Oct 2 20:34:24 2008 +0000 handle new column in CCDS dump files commit fb34f684d44c58673d4790c81975f42dfaaef259 Author: markd Date: Thu Oct 2 20:34:04 2008 +0000 changed location of cluster master commit 11ba6fa4a374875e906c43d18f76189f24fa3aa8 Author: kuhn Date: Thu Oct 2 18:23:30 2008 +0000 added logic to pass error msg from getAssemblies to stdout and quit instead of making a bunch of files from the error string commit 3055e9d719b717e637e2e1ccbf52cb2da8bfe6a2 Author: hiram Date: Thu Oct 2 18:01:36 2008 +0000 Classifications for GNF expression data on Affy MOE430 version 2 chipset commit efedc10ece86d132c3da2ff96f3d769c47a81347 Author: angie Date: Thu Oct 2 16:09:24 2008 +0000 Remove duplicate definition of dyStringQuoteString (was libified from hgTrackDb -> lib/dyString.c). commit 48b2e55e63fda1d5461f39d3e09a90fbee0b8baf Author: donnak Date: Thu Oct 2 15:27:23 2008 +0000 Added link for email address. commit 3597ce14a8e791500b881395d5779ba6b096e587 Author: donnak Date: Thu Oct 2 15:23:29 2008 +0000 minor formatting, added email link. commit 8ef5cf57d6c33817a6c95772d93b2acf4e4c7304 Author: donnak Date: Thu Oct 2 15:12:44 2008 +0000 Added a comma. commit afa2cb6092854d0237e7aaa53baee7293b893e38 Author: ann Date: Thu Oct 2 15:11:39 2008 +0000 a few changes suggested by Pauline during code review commit ab1baf20a1da71d07aa1b9520e47ebb94c5542a8 Author: galt Date: Thu Oct 2 15:00:07 2008 +0000 "Encode release log update" commit d93159c697bb45e002b1988b17bc224960286e9c Author: galt Date: Thu Oct 2 15:00:05 2008 +0000 "Release log update" commit 935e02659a9d23b8e0fff146cd444875639a29d9 Author: kate Date: Thu Oct 2 14:50:03 2008 +0000 Add secondary sort on name commit 7558d475a459e535aeeb44eff3f9c87a39904c21 Author: larrym Date: Thu Oct 2 01:22:52 2008 +0000 wordsmithing commit 2d809783319d010295bce3ade3377eafeada226d Author: larrym Date: Thu Oct 2 01:20:30 2008 +0000 add description of the views commit af2b32e17ced6f4e7f2923f52beab43fe710e5bd Author: kuhn Date: Thu Oct 2 00:10:07 2008 +0000 tweak commit 94d73aaa30c91e3ba79a3d78e5899570c1e3b805 Author: pauline Date: Wed Oct 1 23:59:00 2008 +0000 Fixed typo. commit 4117c9585559c8614f4ee9e3c8924c5b795336c2 Author: larrym Date: Wed Oct 1 23:16:38 2008 +0000 add wig entries to README.txt; move isZipped to Encode.pm commit 5c96c26c6afefbe0f65b60dc7224331d15a3c014 Author: kate Date: Wed Oct 1 23:08:04 2008 +0000 Correct regions link commit caddab57223a36feca9265a3d3f3c1aae6ee4dfc Author: larrym Date: Wed Oct 1 23:05:27 2008 +0000 gzip files which we put in the downloads directory; add missing CR when appending to an existing README.txt commit ddcb75d28ec582333b04e18d1b253d923993691a Author: kate Date: Wed Oct 1 22:58:10 2008 +0000 Portal update for production phase commit 42bb6eb679ceb627b409fed993799c9c9b423dfa Author: larrym Date: Wed Oct 1 22:57:33 2008 +0000 add isZipped commit d9910ee958a6ccf941ac8c83a1ce51d9c09a8daf Author: kate Date: Wed Oct 1 22:56:54 2008 +0000 ENCODE portal update for production phase commit 46a462a12bc0239fe13e2e626fdb16416d65cfbf Author: kate Date: Wed Oct 1 22:55:10 2008 +0000 Images for ENCODE portal update for production phase commit 94cf4dbc68a9b7ba0c8d48bbd2d75069c8520c56 Author: braney Date: Wed Oct 1 22:14:01 2008 +0000 add method to get genes for a bed file (useful for canonical sets) commit 8e7acae5fc8d5a732ada2498e53a08bbbfa4aeaa Author: kate Date: Wed Oct 1 19:54:47 2008 +0000 Add termUrl fields commit 823bea9c2aedbd2541262363e59b11dfd991d18f Author: tdreszer Date: Wed Oct 1 19:32:48 2008 +0000 Added the ability to have composite view configurable seetings shown by default commit ed9d335e9bdbd253cf32f42467af90f8b38eba64 Author: tdreszer Date: Wed Oct 1 19:06:54 2008 +0000 Fixed the dataVersion tag for NHGRI and Yale commit 12b688a3fb306ae4d041de10100d99f0a84b1e0a Author: tdreszer Date: Wed Oct 1 18:54:48 2008 +0000 Removed the cell type and antibody table since this is done via controlled vocabulary links now commit 03687c794a05aa8ddced6be4d69cce2346023840 Author: tdreszer Date: Wed Oct 1 18:53:20 2008 +0000 Added Yale Hela/Pol2 and Hela-IFNg/STAT1 commit 70fad8786037b4950f76727ad3d578c067c3abbd Author: ann Date: Wed Oct 1 18:10:55 2008 +0000 noted mytouch of the pscreen table commit 45a30aad4d490efab5c2e7994dc3af028575c463 Author: angie Date: Wed Oct 1 17:55:02 2008 +0000 Added minCheck to dm1.pscreen.geneIds -- outdated w.r.t. dm1.bdgpGene.name. commit 42048f20bea7a29e051a2e011ff033fc9525fdb4 Author: angie Date: Wed Oct 1 17:21:01 2008 +0000 Moved dyStringQuoteString from hgTrackDb.c into lib/dystring (for use in hgSession). commit 61d2a67de52a41fb0e838a972585f6a46e330afb Author: ann Date: Wed Oct 1 17:19:00 2008 +0000 fixed search to fall within gehome commit 324ef886acf97e84e5f56cccefc7d7428445210e Author: aamp Date: Wed Oct 1 17:15:39 2008 +0000 Swapped PI and Submitter columns ordering. commit 13774918a0f9d50f59cfc18c6a92b3ca51c74aac Author: galt Date: Wed Oct 1 15:00:07 2008 +0000 "Encode release log update" commit bbcd686b0833497bdf2d48cb2d836971f3d34da7 Author: galt Date: Wed Oct 1 15:00:04 2008 +0000 "Release log update" commit aae3daa15f755ee3570762ff94d4431481336171 Author: fanhsu Date: Tue Sep 30 23:53:00 2008 +0000 Added makeRedBlueShadesOnWhiteBackground() to support new color scheme for expression track. commit 65c9b173f10c2188f44aefae4a8b03e9abcd2457 Author: fanhsu Date: Tue Sep 30 23:47:02 2008 +0000 Updated expressionScoreColor to support new expression color scheme, red/blue on white background. commit 08a76c9bc300300788bdb04a1fdf2dec1e6dae52 Author: fanhsu Date: Tue Sep 30 23:41:34 2008 +0000 Added makeRedBlueShadesOnWhiteBackground() to support a new color scheme for expression track. commit 8e60b32a17a617e844a5f9e6fd3066bf59eb02cd Author: cline Date: Tue Sep 30 23:39:37 2008 +0000 Added the Affy Exon Tissues track commit 612bf76b3d9f319b9186053229ae423b838f7f22 Author: fanhsu Date: Tue Sep 30 23:38:36 2008 +0000 Added "red/blue on white background" check box for expression track. commit 9d46629e7720646072aa219958a1ae0ae499a4d9 Author: braney Date: Tue Sep 30 23:17:24 2008 +0000 had to re-do these alignments commit 36034027d62aaa19929d31d63e5385c296e84a8f Author: braney Date: Tue Sep 30 22:21:24 2008 +0000 had to re-do the pal alignments commit 1f96b97d4a0145231a56dbe8ef96c419ae669c0b Author: hiram Date: Tue Sep 30 21:43:46 2008 +0000 Lifted Nucleosome tracks from ce4 to ce6 commit 6cd8824f38625b900ff0b04e66cc2cf28241a31b Author: ann Date: Tue Sep 30 21:40:18 2008 +0000 relaxed refSeqId rule to account for drift in ccdsInfo table commit 5c0c2e09d30a30bc6396085aa82ad519b9547f22 Author: kuhn Date: Tue Sep 30 21:33:30 2008 +0000 added comment about niming of transchrm annotation commit 970ace7a2c31c0d39616b9782471752133799f85 Author: ann Date: Tue Sep 30 21:26:32 2008 +0000 removed rn3 from wormBaseId rule as it no longer has a ceBlastTab table commit 555716eb11c499acd5a8e71071e9513fc9ddc5eb Author: braney Date: Tue Sep 30 20:37:12 2008 +0000 don't output zero length AA exons commit 1de0a4fe215535e9b112a1a5f02a67437d743f1e Author: tdreszer Date: Tue Sep 30 20:06:39 2008 +0000 Making view dropdown non-hide should flip main display dropdown non-hide commit 1ae069f7f528f74111194e8e9b253f3972a66491 Author: ann Date: Tue Sep 30 19:15:50 2008 +0000 relaxed ensembl rule for felCat commit fa811fa66a2f4d9b2c85ab8b742c5ba09603127e Author: mikep Date: Tue Sep 30 18:59:11 2008 +0000 adding host/date to echo output for easier timing and problem solving commit a475b54639b62643169f94ef46158d33236ea4fb Author: mikep Date: Tue Sep 30 18:57:47 2008 +0000 adding name and date to echo messgaes and cleaning up commented duplicaetd code commit 7c54f44d653436cf5b07d8835393817fac039716 Author: tdreszer Date: Tue Sep 30 18:39:39 2008 +0000 Commented out table of Cells and Antibodies since these are viewable as controlled vocabulary commit ee1950da1053ddef4f247de4a328bf501651584f Author: hiram Date: Tue Sep 30 18:38:45 2008 +0000 document pages moved up one level so they can apply to ce6 also commit f07ce85136b974b75113d1e738e791cf62e4e7e3 Author: hiram Date: Tue Sep 30 18:37:51 2008 +0000 Lifted the nucleosome tracks from ce4 to ce6 commit ba830a8221495ce8271f842454412c294c99029e Author: hiram Date: Tue Sep 30 18:37:24 2008 +0000 These tracks now appear in ce4 and ce6 commit 758d66a30e04bd4479a6f8dfb98329c2eb4b1246 Author: hiram Date: Tue Sep 30 18:03:48 2008 +0000 Need to use hFreeConn with hAllocConn commit acb4512b2cd04d72878dd6c30ef7915b233fe752 Author: tdreszer Date: Tue Sep 30 17:55:22 2008 +0000 Support for circular chrM should still reject bed items completely beyond chromSize commit 97893e527f71fe0f648da9b287d88737985ca6b5 Author: tdreszer Date: Tue Sep 30 17:53:47 2008 +0000 Both 'input' and 'control' are special terms commit dbcb4c4fc586ea70e8f61f5901c461b90f349d48 Author: pauline Date: Tue Sep 30 17:42:51 2008 +0000 Updated 2 references. commit 3be0170f2e9e5b3efc4f52791e75c690fb091506 Author: angie Date: Tue Sep 30 17:27:30 2008 +0000 Added search on NCBI clone accessions with kiddEichlerDisc mappings as b0b suggested. commit a9985be9cd5ffe779ef6fc6f17da6ddffaa9f1ba Author: mikep Date: Tue Sep 30 16:29:07 2008 +0000 v192 branch commit e5f505792604fe8974e62f407f08bb4dda3a633e Author: mikep Date: Tue Sep 30 16:28:41 2008 +0000 added user id to lock output so we can ignore our own locks commit 628624ced2025a5c0ee65b964a0ac86f432101d8 Author: mikep Date: Tue Sep 30 16:25:01 2008 +0000 "New version number v192" commit c4e30eac14c3012010ef0404d4390da41be1fcc4 Author: galt Date: Tue Sep 30 15:00:07 2008 +0000 "Encode release log update" commit a8f7e460639c620eb74e18b8d5716cc711f5e1f6 Author: galt Date: Tue Sep 30 15:00:04 2008 +0000 "Release log update" commit 8684f4c9c0a49f4189241d3f132f28c308907689 Author: braney Date: Tue Sep 30 14:42:38 2008 +0000 oops... add DONE commit 5fa9e7474f037f669fc31482ef92b9761929cdeb Author: braney Date: Tue Sep 30 14:42:37 2008 +0000 add hgPal downloads commit f9643c2378b1cef2582d80634d6ef046e5b7893c Author: aamp Date: Tue Sep 30 06:57:44 2008 +0000 Bugfix for next-item: composite tracks in dense with next-item ON would have a button that doesn't work. This turns it off. commit 27728545d0ac07bacf5fa166deb488e724261507 Author: kuhn Date: Tue Sep 30 05:53:24 2008 +0000 added coverage stat commit fa81827cf1ebba1a070911cde9c15e53347ad61e Author: kate Date: Tue Sep 30 00:08:56 2008 +0000 Trivial script to display data submissions in the ENCODE production pipeline (used on ENCODE wiki) commit 2c2ffd660fdf0791b2b872f49ba050e560d52fee Author: tdreszer Date: Tue Sep 30 00:03:53 2008 +0000 Controlled vocab terms cannot include blanks commit 6c7bf8fd84a2fe8476c10def57b64032f4e4225c Author: tdreszer Date: Tue Sep 30 00:01:01 2008 +0000 Fix bug I just added, sorry and thanks Fan commit 3aa2a4915298397c1e49453a2d3734e8541e45da Author: tdreszer Date: Mon Sep 29 23:47:17 2008 +0000 Initial submission of input tracks for Yale commit 2cc4b9b23651e3f3b0e06d0d1a3d4c21e1942810 Author: tdreszer Date: Mon Sep 29 23:09:02 2008 +0000 wigMAF in dense mode had wrong height. commit f05c0e9c37f5bcd4f0ebf3152305059c7c0c23a2 Author: tdreszer Date: Mon Sep 29 22:55:02 2008 +0000 Moved restricted link to header, added download link; adjusted formatting and sqashed one DOM error commit 5faba73a8a7c69a2e3bfffce490d283a3512fa6e Author: angie Date: Mon Sep 29 22:44:59 2008 +0000 Changed kludgy table to
as suggested by b0b. commit a67ba56cc4e1ec854ec6b62c0c27ee68d7a9cf4b Author: larrym Date: Mon Sep 29 22:33:56 2008 +0000 put link to draft release policy into README.txt commit 2c3c6c8a76d6b89c3d9c5c176ecd195db2244b9d Author: tdreszer Date: Mon Sep 29 22:33:42 2008 +0000 MAF subtracks of composite track were not being recognized by isMafTable() commit c68b417bf3f9d125ae58449d1b6de1179ba007d7 Author: kuhn Date: Mon Sep 29 22:24:19 2008 +0000 tweaked reference commit 5a081c5e43fa58512b89540008c2aae261b7e113 Author: tdreszer Date: Mon Sep 29 22:16:40 2008 +0000 Initial Submission tested version of Elnitski's NRE DAF and DDFs commit e1d88d0e5ea8fa7886603a1e6b42c2ec7d3da65a Author: mikep Date: Mon Sep 29 22:03:47 2008 +0000 updated Riken CAGE with latest track defs from validator commit 2c830f3b5dadc543509a36d8fc954a54a919a297 Author: tdreszer Date: Mon Sep 29 21:58:03 2008 +0000 Initial Submission tested version of Yale's DAF and DDFs commit 8848ea9164f6e03de6df193aebfba4d9694f80be Author: fanhsu Date: Mon Sep 29 21:44:26 2008 +0000 Changed hivmn1 to hivgne8v2. commit d44131b115fbc132dab22a3fce78c9ff5e6d6441 Author: fanhsu Date: Mon Sep 29 21:43:43 2008 +0000 Changed hivmn1 to hivmn2. commit ba592e5ec5633fe89f4261d28b9bdc257e16e28b Author: fanhsu Date: Mon Sep 29 21:38:30 2008 +0000 Removed the paragraph about the variable regions, since none could be found to align well enough. commit 7902d3513f37aa84a4a502a7418556daa255e05d Author: mikep Date: Mon Sep 29 21:31:55 2008 +0000 added RawData2 as non-table datatye, unzipped replicates data when autogenerating wiggles, added timing function commit aab5cc2702168fdde58e95ded22f01c774d7aee2 Author: fanhsu Date: Mon Sep 29 21:31:44 2008 +0000 Updated external links to maps of HIV regions. commit 81f14e8396698da3d8ef5e4ea4e92aa2ce8b31e0 Author: fanhsu Date: Mon Sep 29 21:28:18 2008 +0000 Updated "V2 and V5" to "V2, V3, V4, and V5". commit afa4219bc8f2f2977aff71da8fb5dfb5ba07769c Author: fanhsu Date: Mon Sep 29 21:22:09 2008 +0000 Updated external links to maps of HIV regions. commit e7cef25cf421579c8f68ca57f5e543090c99e722 Author: fanhsu Date: Mon Sep 29 21:16:18 2008 +0000 Updated external links to maps of HIV regions. commit 117232c7f8499399a4c2988c0623d7626bb30d39 Author: braney Date: Mon Sep 29 19:32:18 2008 +0000 add a option to suppress blank lines, remove some crufty code commit b8bab5f714ce6c5c55a72c4668d55fab18311b4a Author: aamp Date: Mon Sep 29 18:47:14 2008 +0000 Preventing p-value from displaying -1. commit a0274cb5aa93455c30139db0ec371c22a3612baf Author: ann Date: Mon Sep 29 17:25:46 2008 +0000 added lots of missing stuff commit 305d349561543710109b65579ffac7b0a5261877 Author: tdreszer Date: Mon Sep 29 16:19:25 2008 +0000 Added support of 'promoter' controlled term type commit e5c8af01c5356a310d52070c52e28336059f0c14 Author: galt Date: Mon Sep 29 15:00:07 2008 +0000 "Encode release log update" commit a3765df9e1f2d5e7ab53e257b48c156ca1c91f26 Author: galt Date: Mon Sep 29 15:00:04 2008 +0000 "Release log update" commit 253c016ea621cc86894bc67f26e11125792e52c3 Author: galt Date: Sun Sep 28 15:00:07 2008 +0000 "Encode release log update" commit 2121a592a0945277fc8adf34adb517b2fbe2122b Author: galt Date: Sun Sep 28 15:00:05 2008 +0000 "Release log update" commit 1d015febb5d6b7f3886a093b954e0ffbc6dfdd53 Author: galt Date: Sat Sep 27 15:00:12 2008 +0000 "Encode release log update" commit 311a58ace572034f2b591dab3c80ddbca178ea77 Author: galt Date: Sat Sep 27 15:00:09 2008 +0000 "Release log update" commit d892d7cd113074bc609bcbed03d347ec73eed629 Author: mikep Date: Sat Sep 27 00:04:32 2008 +0000 FastaQuality and ColorSpaceFasta should never have been generated as tables commit a91ad3f7d317bac919b094a20c9c0f5ed2796897 Author: ann Date: Sat Sep 27 00:03:31 2008 +0000 Brooke's final suggestions commit ed9e7947b03c68c60d5597d6df0ce57b51837fa4 Author: tdreszer Date: Sat Sep 27 00:00:13 2008 +0000 Restoring c-Myc, which I somehow shot myself in the foot with KDevelop and lost. commit 9e579e909c4e415286bafa154ba53a16715b1ca7 Author: tdreszer Date: Fri Sep 26 23:54:33 2008 +0000 Need to handle chrM as circular chrom (bed items can cross chromEnd) commit d28e24aebe58f8580420080d83d850a1212a466d Author: ann Date: Fri Sep 26 23:43:06 2008 +0000 separated the Methods section commit 6d10d736b435aeba313bf3a2a09c3b4f156c776a Author: ann Date: Fri Sep 26 23:39:03 2008 +0000 changed species list to table format commit f7396e54f32232ceb8e3dec2f1c7b3bc36f8c9de Author: larrym Date: Fri Sep 26 20:51:35 2008 +0000 tolerate negative values in narrowPeak peak call column commit d15c67d76c6cc0ab77636d618b674957ec099347 Author: aamp Date: Fri Sep 26 20:46:25 2008 +0000 Added column to list page to show submitter in addition to the PI. commit da293b2feb3de679ec75f6c1ffc6db9e899d8c9c Author: braney Date: Fri Sep 26 18:48:34 2008 +0000 output a message if we're not outputing anything else commit 35efaadd720110ab8a0ccdd2a2a5f30a12aefc6c Author: braney Date: Fri Sep 26 18:48:09 2008 +0000 don't count genes that don't have a coding region commit 8390b5f4d5fd53cfde779cf2fd93958ba8a3a05e Author: ann Date: Fri Sep 26 17:42:26 2008 +0000 added more explanation of CDS FASTA sequence format commit c9ed6526b8b631a780045f897d599c37e490c01f Author: mikep Date: Fri Sep 26 17:27:10 2008 +0000 test version of the riken cage tracks commit dacad86b773db136bfe7973c19ab84bef990562b Author: galt Date: Fri Sep 26 15:00:06 2008 +0000 "Encode release log update" commit a1e96180206ff15a43ec0056d388afa813106778 Author: galt Date: Fri Sep 26 15:00:03 2008 +0000 "Release log update" commit 2786889c4ff1f13f6374ac724202e997ba6afcbc Author: kate Date: Fri Sep 26 03:59:56 2008 +0000 Shrink short labels. Add colors to distinguish experimental from controls (following convention for by-tissue coloring of cell types for ENCODE) commit 8c4c31825a95c360f2d28866ef7038cc3a189405 Author: kate Date: Fri Sep 26 03:59:05 2008 +0000 Include mapping strategy (from Rami Rauch at Stanford) commit 57481c267d3ea20851ee889c01d1492ed6d64e77 Author: braney Date: Fri Sep 26 02:48:18 2008 +0000 added flyBase hgPal alignments commit 4ef1af7c0b039febfc769b51704bc662bae0fa7e Author: braney Date: Fri Sep 26 02:47:48 2008 +0000 add hgPal output to wormBase track commit 4f5e8ce0a0cf862028a83d87b6e7037ff5986789 Author: braney Date: Fri Sep 26 02:45:55 2008 +0000 be more careful about selecting a conservation track commit dc5c2edc3433aef189bb018a425f85c2ab2dc8fb Author: larrym Date: Fri Sep 26 00:56:17 2008 +0000 add -quick option; enable update of count/metadata fields commit 631ff98a370a49167b5d31a41fd9ef2261cd85a2 Author: ann Date: Fri Sep 26 00:12:50 2008 +0000 one tweak for Brooke commit 56e1c6031903a42b54a4a420791ff09542ffccb9 Author: ann Date: Fri Sep 26 00:03:37 2008 +0000 first stab at an example for CDS FASTA commit 3ecacf0a48cb73d28c8b39fc97a803def325bf41 Author: ann Date: Thu Sep 25 23:27:33 2008 +0000 fixing typos commit 187febd1450dbcd3d4a83b340a4a7af750aa21f2 Author: ann Date: Thu Sep 25 23:25:48 2008 +0000 fixing typos commit 08cf216b0a5f4fcbcdf0a78cc4407a23a112ea1c Author: ann Date: Thu Sep 25 23:23:15 2008 +0000 first pass at an example for CDS FASTA commit 8208b31f5e9aef26e5678dc89fbe441e3429a6d7 Author: fanhsu Date: Thu Sep 25 23:19:04 2008 +0000 Added int cols to faciliate indexing. commit d9386a0acbfaebfcd47c853b58a58170a6c872f8 Author: angie Date: Thu Sep 25 23:11:00 2008 +0000 Re-indented line to clarify how nonsynon codons are drawn in drawCdsDiffCodonsOnly. commit 2c0d0c90eab5ebf0acdbcf5515b56f7a4d7fb09e Author: larrym Date: Thu Sep 25 22:48:17 2008 +0000 tranfer from encodewikie commit 145bfba854263a96700b3b944f753f8b7e525575 Author: braney Date: Thu Sep 25 22:23:55 2008 +0000 make sure there is a maf table before offering pal link commit 84539dbf62015b80ca93c8bfd2fb25124d4f76ec Author: braney Date: Thu Sep 25 22:22:19 2008 +0000 only add pal link if there's a suitable maf present commit 1a1ae53d7d72c11c06073dc9086a87f0d3c280a1 Author: braney Date: Thu Sep 25 22:20:11 2008 +0000 put checking for table type in hdb.c commit 3737e14620e4ac3d97da714a0a132e01ae569ccc Author: braney Date: Thu Sep 25 22:19:10 2008 +0000 oops, check for the buffer size ignoring dashes commit 2bbffaed0f6671d0317ebf2c2c1ff7ff87b6ea8e Author: braney Date: Thu Sep 25 22:18:21 2008 +0000 add routine to check for tables of a certain type commit 261d74396d6d6c8b48abe29a44a3861e4bf34a4e Author: braney Date: Thu Sep 25 22:16:01 2008 +0000 add new routine to check for tables of a certain type commit 67e38478068583524fe599dac3a32be2d2e7ecdd Author: angie Date: Thu Sep 25 22:07:34 2008 +0000 In addFeature, don't reject 0-length features; they might be insertion SNPs. If padding is specified, then the retrieved region will be >0 bases; if not, there will be a '# Null range' comment in the output, better than no output for those features. commit 287a2df98c5d05773c4c70aca0786c00542f09ac Author: mikep Date: Thu Sep 25 21:38:53 2008 +0000 full line-by-line validation (ignoring header comment lines) of colorspace .csfasta and .qual files commit 6de43fe67000275e72818b682f700ed0452247fb Author: mikep Date: Thu Sep 25 21:27:02 2008 +0000 suggested second version after first upload commit b4574e86e00bd0d232ea2e2cb714eb3ef966367b Author: ann Date: Thu Sep 25 21:16:19 2008 +0000 standardized paragraph. added transltation statement commit e9fe14f878b493b151cf347fd753b5d5863f10b0 Author: larrym Date: Thu Sep 25 21:09:32 2008 +0000 wgEncodeHudsonAlphaChipSeq => wgEncodeHudsonalphaChipSeq; round 2 of importing initial HudsonAlpha data commit 6de913c316cc17cedde549ebe2bee6d700bbf121 Author: ann Date: Thu Sep 25 21:04:43 2008 +0000 adding headers commit f5316026534d27310957f3dcb02386ccb71aa117 Author: larrym Date: Thu Sep 25 20:50:33 2008 +0000 add wigMinMaxPlaceHolder logic; tell hgLoadBed to use /data/tmp for temporary beds commit cb95179341a3faf32e66187b0d7698d863317661 Author: galt Date: Thu Sep 25 20:47:42 2008 +0000 removing link to obsolete page; fixing webStart to work with MarkDs new system commit 4b2de5fddfae586296d1da63b5a4e470a5f19e9e Author: larrym Date: Thu Sep 25 20:43:55 2008 +0000 add wigMinMaxPlaceHolder commit 81f9c31b9cddff2894e889bab0ea8112d92c63ca Author: larrym Date: Thu Sep 25 20:42:56 2008 +0000 add -skipAutoCreation; add wig min/max placeholders to trackDb.ra; add (currently dead) count and metadata code commit cbaca27c59229e11532384bc55a45ef1e432dcd2 Author: tdreszer Date: Thu Sep 25 20:26:02 2008 +0000 tagAligns may have Ns in sequence because of 1 or 2 base mismatches commit 4b95320fa6a978ca39041d7e37883d064e57d132 Author: braney Date: Thu Sep 25 19:49:54 2008 +0000 take out comments, check for bad maf commit 7ebcdc8c8f1f60a2038a8a3715cff7342ab85c81 Author: ann Date: Thu Sep 25 19:46:27 2008 +0000 added explanation of nucleotide to aa translation commit 0cb66aff2c13c6cd3c9e7641badb600e4a63d779 Author: angie Date: Thu Sep 25 18:21:40 2008 +0000 Expanded remapRange and bedOverSmall to map bed8's thickStart and thickEnd fields. commit da8cb04e3adba6048553bcbee34b3e38f3dd0819 Author: angie Date: Thu Sep 25 18:20:23 2008 +0000 Added test for bed8. commit d3cf350a9a2d5bcd2078ca11c01bb7c3c2aa1950 Author: angie Date: Thu Sep 25 18:12:36 2008 +0000 Clarified usage comments. commit fee3db38086a59ae0966bc0a4b624ce602526f7e Author: braney Date: Thu Sep 25 18:12:13 2008 +0000 if no mafTable defined yet, look for Conservation track commit 3b5746baf4617829f826f1affd308f2fd5d7aca8 Author: ann Date: Thu Sep 25 18:06:56 2008 +0000 reordered. added warning about genome-wide queries commit 02e6c5f3af91f252cf84683c998e82ffcef6602a Author: braney Date: Thu Sep 25 16:40:25 2008 +0000 add link and change button text commit 2bf1a5cd06bae22a2e75b606b9837d0996f431a3 Author: galt Date: Thu Sep 25 15:00:07 2008 +0000 "Encode release log update" commit 5991c0ccdc7e82909be220eca8687899ce0964a7 Author: galt Date: Thu Sep 25 15:00:04 2008 +0000 "Release log update" commit 6f5a05e92f1fc84336015e7c8ef5470f2516c391 Author: kate Date: Thu Sep 25 03:44:23 2008 +0000 Suppress D links unless database exists commit 4d0fdba77fe46b71cd6bce80ad2a24356d75fdb7 Author: mikep Date: Thu Sep 25 00:39:57 2008 +0000 modifications to get RikenCage.daf submission working commit e797ce9847a96fc3d56d0cc2444bac11fbb5ae0a Author: mikep Date: Thu Sep 25 00:38:10 2008 +0000 added term for whole-cell commit 56bb81aca562ee78cea7576cec9e3c9955e30498 Author: tdreszer Date: Thu Sep 25 00:16:13 2008 +0000 Added validateNoValidation routine for accession to call commit 02ef378599ce199afc10ecb100f2d23640eb9c76 Author: aamp Date: Wed Sep 24 22:53:55 2008 +0000 Added two columns to project commit f4da1f99e4a229063de222d95645190c2b4bb405 Author: larrym Date: Wed Sep 24 22:32:33 2008 +0000 ucfirst variable values in tablename computation; tweak shortLabel logic commit 8f662e6385863b1fc9dd398c4f9421a2ea9c5827 Author: kate Date: Wed Sep 24 22:16:29 2008 +0000 Add setting for default vis of views commit 80facd388ffc4bdf1a8c070de0184e64fa347254 Author: larrym Date: Wed Sep 24 22:03:04 2008 +0000 ucfirst lab name in compositeTrackName; fix 2/31 problem in restrictionDate commit aa6fe8d0e51724d45a79e3166b54c6484083f6bf Author: kate Date: Wed Sep 24 19:28:54 2008 +0000 Minor correction to entry for TBA 36-way commit 0869500e5d937482f41115ad9991fcaa3754c3a4 Author: kate Date: Wed Sep 24 19:26:59 2008 +0000 Minor correction to entry for TBA 36-way commit ec7455a5ea1f5522c7629f18c7a8e6ec98954b33 Author: kate Date: Wed Sep 24 19:12:24 2008 +0000 Rename ENCODE MSA track commit d0bf34d75fd2741e3e0b86033254a9022646db90 Author: tdreszer Date: Wed Sep 24 18:52:04 2008 +0000 Fixed HeLa-S2 name and added IFNg treatment for HeLa-S3 commit a7abb5181075648c5786ccb9efc0bcf75728255f Author: ann Date: Wed Sep 24 17:47:25 2008 +0000 details about finding the table name commit 3244ef92333a55317191d5a13ddca864ef067b0b Author: angie Date: Wed Sep 24 17:43:44 2008 +0000 Update MGI tracks (jax*) with new data. commit a3b376c3b7954e0ea9f0d94eb76045d102893e85 Author: tdreszer Date: Wed Sep 24 17:33:35 2008 +0000 Elnitski to NHGRI commit 8f736249f0008d26c39b9e08d939cd977ab58a48 Author: tdreszer Date: Wed Sep 24 17:29:06 2008 +0000 Surviving the rename storm commit 0a287803be797e772c2d410e5418aa73cd78b91d Author: ann Date: Wed Sep 24 17:13:12 2008 +0000 referring to new FAQ commit d78dc375b9e0d3a98a89dd84d22358b186b7c503 Author: ann Date: Wed Sep 24 17:12:25 2008 +0000 placeholder for exaplantion about finding the tablename for your track commit 86024721c1a69ed8623d443963bf295c81a3ecfb Author: tdreszer Date: Wed Sep 24 16:51:33 2008 +0000 Registered c-Myc from Vishy Iyer commit b69aeffa1c9c4638e369d1a41c8011113ece1a39 Author: ann Date: Wed Sep 24 16:37:57 2008 +0000 added info about positional searches and how to find MAF table names commit d6e32f0de4d7ed119e9e513937b49b2e5ff420b2 Author: galt Date: Wed Sep 24 15:00:08 2008 +0000 "Encode release log update" commit a611135b39519bcb91bcc721781c8fa5559c8952 Author: galt Date: Wed Sep 24 15:00:05 2008 +0000 "Release log update" commit e47d8629a76b34f01839507fa186f4194f2a812c Author: donnak Date: Wed Sep 24 06:08:56 2008 +0000 added 2 pubs by J. Ma. commit d4b212b64a6fce2426ef6bff4a1ed68514706a49 Author: tdreszer Date: Wed Sep 24 01:18:04 2008 +0000 Added Treatment to ddf commit 9a009f4916d8455daf9088c58810c073f27a36f8 Author: pauline Date: Wed Sep 24 00:25:21 2008 +0000 Fixed matrix. commit bbcf029737b1399131918dcfaf36bfbe3af7f670 Author: larrym Date: Wed Sep 24 00:25:14 2008 +0000 handle validating gzipped files (i.e. gunzip on the fly); add ddfReplicateSets to fix bug introduced by previous version commit 53b1cb7e18cd0bf1259f8f3140f5fbc1261ebd06 Author: pauline Date: Wed Sep 24 00:25:05 2008 +0000 Fixed priorities. commit ca3f1cb7d63ea98e3cdea764ee93e13ccf226683 Author: pauline Date: Tue Sep 23 21:41:32 2008 +0000 Added oryLat2 to chain section. commit 1d7727d92fe59f52104013fcdbef68d429755197 Author: tdreszer Date: Tue Sep 23 21:18:18 2008 +0000 Added HCT-116 tier 3 cell line commit 37fc07fe3eca5c18cd3fa482c418191a3f2bb891 Author: tdreszer Date: Tue Sep 23 20:59:56 2008 +0000 Added Yale ChIPseq and 2 placeholders for Duke commit 9c23cc429484d2ecd37ba8b4ef60b3ec2eff0ca8 Author: ann Date: Tue Sep 23 20:26:32 2008 +0000 small edits to CDS FASTA aglinment explanation commit 32e2cf4a28da0283a64737d2f20e8d58860cf444 Author: larrym Date: Tue Sep 23 19:47:53 2008 +0000 add replicate to ddfKey commit f689dc89fb30ebfe5aab90d9bd0af974b0c8772d Author: larrym Date: Tue Sep 23 19:43:11 2008 +0000 HudsonAlpha FOXP2 data commit 3c3114a85ce08d6260cc24de744ad5c746fccc9f Author: kuhn Date: Tue Sep 23 19:07:28 2008 +0000 made some MySQL commands use CAPS commit e24615213d42b64f0eb79ea142736e4054d2fb9e Author: ann Date: Tue Sep 23 18:49:54 2008 +0000 some formatting. and another pass at the wording. commit 59c203afeb67a4c96d5cbacd19c5218344f9bbe8 Author: kuhn Date: Tue Sep 23 18:46:12 2008 +0000 fixed grep filter to properly remove comments lines when parsing getLiftOver.csh output commit 3e95539cb82a52e18edf3136736c0ed4578af9ab Author: mikep Date: Tue Sep 23 18:12:59 2008 +0000 Cshl RNA-seq first version commit 53c0aea5347d56286622a9f92af516e252ed6ca2 Author: hiram Date: Tue Sep 23 17:33:07 2008 +0000 freez needs a pointer to a pointer commit 518c9761fe2346c8ac57c7fbc2220e78ddffefc1 Author: mikep Date: Tue Sep 23 17:31:11 2008 +0000 v192 preview commit 756f010833dbb2d3bf76022a9bfd2b9801d7f4a1 Author: mikep Date: Tue Sep 23 17:30:47 2008 +0000 adding timestamp to track what takes a long time commit 8d3510e64a696f4de3542c47f2d1b5672d8f27a4 Author: mikep Date: Tue Sep 23 17:30:18 2008 +0000 moving the style to a stylesheet commit 46ce1316fd219150381a14cca017396f27023061 Author: galt Date: Tue Sep 23 15:00:06 2008 +0000 "Encode release log update" commit 3687ac8f478f1beab24675da702afd35915a1a63 Author: galt Date: Tue Sep 23 15:00:03 2008 +0000 "Release log update" commit 6748c72186dd8e1a561e6fae39e5e046c210b91d Author: markd Date: Tue Sep 23 10:45:27 2008 +0000 backed out accidental commit of test of /hive files; leason: no commits before coffee commit 7744f976df90c7803bdc15a0585fd2cf85cfa4ad Author: markd Date: Tue Sep 23 10:20:52 2008 +0000 changed referencet to /cluster/store FS commit e7fbeefa18ef200c20d36a1554e6633ab240b0e8 Author: kuhn Date: Tue Sep 23 05:48:28 2008 +0000 added detection of {Human,Fly,Worm} Proteins associations commit 97cc2ef71f0eef0beaadadb9c02a3849a78c4d33 Author: kent Date: Tue Sep 23 04:34:54 2008 +0000 Fixing glitch where can get RefSeq protein assigned to noncoding mapping of RefSeq. commit 87a42057f380c0e7d6690fda1159abc3a32d1061 Author: ann Date: Tue Sep 23 00:06:10 2008 +0000 first pass at edits to new CDS FASTA section commit 168c3f332ebceb33f3fa68647fc49858d33a3101 Author: mikep Date: Mon Sep 22 23:52:40 2008 +0000 v191 commit 0bccacd880fd8720e14422710a5139075c8b5eb9 Author: larrym Date: Mon Sep 22 23:36:12 2008 +0000 use hgLoadBed ... -fillInScore and mkdir downloaddir when applicable commit 6f48cb2058baffbedd243fffe9c6b44ff5049e98 Author: mikep Date: Mon Sep 22 23:34:27 2008 +0000 try -n flag so any input required is taken from /dev/null instead of the script hanging for input commit 247ade940a4347d5d2a851002c7b95a0bee3db81 Author: mikep Date: Mon Sep 22 23:32:25 2008 +0000 hgWarn.o triggered warning commit 9431c0ca8dcb970f2277f348839ad9913bd1afa9 Author: larrym Date: Mon Sep 22 23:31:11 2008 +0000 support validateFile option commit 78d72a9fb9e02c4bd0d2b3548cfa2173773e7599 Author: mikep Date: Mon Sep 22 23:24:52 2008 +0000 Checking in Wold Lab stuff I did at end of July commit fa231e6dcd9d861d774c0cadf5014f011f90aac4 Author: kuhn Date: Mon Sep 22 23:17:18 2008 +0000 removed temp files created during run commit 10b8db916e1170b38e3ddcffe5bb7cc8fb4ab100 Author: kuhn Date: Mon Sep 22 22:52:54 2008 +0000 renamed findArchPartners.csh to findDbPartners.csh commit 1e6f1f5aeb98357b0d7b1f91f83200a0538a7e24 Author: kuhn Date: Mon Sep 22 22:13:47 2008 +0000 added support for knownGenes commit 314503a24446729a9a9af4d69592aa1856655daa Author: fanhsu Date: Mon Sep 22 21:43:11 2008 +0000 Created 3 cols arrayVal.sql. commit 2157ea407a35c01910f6e3ec47aa93f6903440d3 Author: kuhn Date: Mon Sep 22 21:33:41 2008 +0000 utility finds any assemblies with links/connections to an assembly becking nets, conservation, liftOver commit 89690fef0ac1f70ec68ed47ac5253a8c14588852 Author: giardine Date: Mon Sep 22 18:53:00 2008 +0000 added rcsid line commit 93aa7741f49e27b42d94a186cce758fc01383cab Author: kuhn Date: Mon Sep 22 18:03:51 2008 +0000 restored references to original settings for archived ce1, mm5 and mm6 commit 34510160d4c4312d1e297ab310ce77072966549a Author: ann Date: Mon Sep 22 18:02:53 2008 +0000 removed release beta block from MGC Genes. commit 32e598ae864d5dca248212cc2e6942682dc461dd Author: angie Date: Mon Sep 22 17:56:17 2008 +0000 1.35 left measureTiming on -- turning it back off. commit 1aaccf42280d39ee226bf3b1a074943fc77078f3 Author: kuhn Date: Mon Sep 22 17:55:35 2008 +0000 minor rewording commit 1e3244a2a23f09842641c2847fa5c7a55747bb59 Author: kuhn Date: Mon Sep 22 17:55:03 2008 +0000 minor rewording commit 55b70304914e4d8842b1e365acd5d7d47e6f89be Author: galt Date: Mon Sep 22 15:00:06 2008 +0000 "Encode release log update" commit d7c20ea3aae89972678d2fede5e12f669ddb3932 Author: galt Date: Mon Sep 22 15:00:04 2008 +0000 "Release log update" commit 0c63898067e5cfbceba3ec6875c4e78166b0e88e Author: larrym Date: Mon Sep 22 05:18:59 2008 +0000 remove a debug printf commit 9a9e69783a8b48923f762397cc91dd2fe5a9ced9 Author: galt Date: Sun Sep 21 15:00:07 2008 +0000 "Encode release log update" commit 8836eda0cdcfd3fddf0826317417fb234b4c67bf Author: galt Date: Sun Sep 21 15:00:05 2008 +0000 "Release log update" commit 8daec23cc8c161d8004058579ac20ec9ebe1b76f Author: braney Date: Sat Sep 20 20:10:20 2008 +0000 allow hgPal choice commit 6f3a1a01006e9c6be57d571c80fbb7edb8084685 Author: braney Date: Sat Sep 20 20:08:45 2008 +0000 add link to CDS FASTA alignments commit cf2a4118bb12e26187824e15fb515831a89fe5ec Author: braney Date: Sat Sep 20 20:07:36 2008 +0000 add hgPal commit 93212786ec32b2d057b5b0e036f860763f96cd5e Author: braney Date: Sat Sep 20 20:06:47 2008 +0000 add pal link to refGene page commit f414d4c4be5ac76049efd057c220e89e5848b6db Author: galt Date: Sat Sep 20 15:00:08 2008 +0000 "Encode release log update" commit 43ccbf3c61dbcbdb15402c3af189ab025ce0a24c Author: galt Date: Sat Sep 20 15:00:05 2008 +0000 "Release log update" commit 1f6db3c9a63dd426ecae7aade22d3b1aa18a227e Author: baertsch Date: Sat Sep 20 09:35:15 2008 +0000 change blending color from orange to brown and move color blending code to void drawScaledBoxBlend(struct hvGfx *hvg, int chromStart, int chromEnd, double scale, int xOff, int y, int height, Color color) /* Draw a box scaled from chromosome to window coordinates. * Get scale first with scaleForPixels. * use colorBin to collect multiple colors for the same pixel, choose * majority color, break ties by blending the colors. * Yellow and red are blended as brown, other colors not implemented.*/ commit 99c159b7ce6e6030d2b729e40ad0175d4eae6f7b Author: hiram Date: Sat Sep 20 00:01:33 2008 +0000 Fixup the bare URL reference so it will work despite cart contents commit 5f7632fb07ef0f7a98f3956185673238a976d357 Author: kuhn Date: Fri Sep 19 22:42:06 2008 +0000 restored references to newly archived ce1, mm5 and mm6, but changed to ce2 and mm7 for now commit ad6629ce462e7ac8adc146f04ad1faf97f129185 Author: kuhn Date: Fri Sep 19 21:54:59 2008 +0000 removed references to newly archived ce1, mm5 and mm6 commit 54c9a69b04c4507b014508534fb8d8edff441e52 Author: aamp Date: Fri Sep 19 20:38:48 2008 +0000 Added the beta database.yml to CVS to make updating beta easy. commit fe0a813a2d7efb1c53a5ed87a3488b7cc3bf725d Author: kuhn Date: Fri Sep 19 20:21:31 2008 +0000 typo commit 34e89b2f6e30f9895474fb8d1b2c4baa2c02502b Author: markd Date: Fri Sep 19 20:10:56 2008 +0000 fixed use disconnect when should return conn to cache commit 397a6c9a30935986ab2ab1036162b2607dde45d5 Author: braney Date: Fri Sep 19 19:17:09 2008 +0000 add info about CDS FASTA alignments commit 79db2652d19541af76a4131d234da888969e9b8a Author: markd Date: Fri Sep 19 16:14:16 2008 +0000 changed wording on PS/PDF page to use consistent terminology commit d700276af422bb7708b0fcc4b03f63a9d21af5f9 Author: markd Date: Fri Sep 19 16:10:41 2008 +0000 fixed tiny memory leak commit 242b076a3fc80d9e7c34603724124ce963d1a5e6 Author: galt Date: Fri Sep 19 15:00:13 2008 +0000 "Encode release log update" commit 2ed0b4a794cb88f1bb8906698f7b6b1a422c6db4 Author: galt Date: Fri Sep 19 15:00:06 2008 +0000 "Release log update" commit d727852e65e536b42f642e8c63b461aa023c9393 Author: angie Date: Fri Sep 19 06:24:58 2008 +0000 Added liftOver to droMoj2 (user request). commit 056b080a603dec6d7a1989b8300719a47693d884 Author: angie Date: Fri Sep 19 06:24:30 2008 +0000 Added liftOver to dp3 (user request). commit 906a71191203e03a282f64722cbe80c1248e4173 Author: angie Date: Fri Sep 19 04:38:08 2008 +0000 bluearc is gone; use /hive/data/genomes as default path for 11.ooc now. commit 0d4db1f101b5ffca1ba6cc76a2a9c6569ba36ea2 Author: angie Date: Fri Sep 19 04:36:22 2008 +0000 Added swarm, removed iscratch and bluearc, added /hive/data/genomes to cluster storage. There is probably plenty more to do to get this completely up to date -- these changes are just what was required to get doSameSpeciesLiftOver.pl to run. commit 977fb497bbc46e0b1af8ce3c100645bad6833d2e Author: tdreszer Date: Fri Sep 19 00:37:14 2008 +0000 Elnitski's first track pushed through the pipeline. commit c7a9d6922dd2663e78296bfe85a6ee2aec2da403 Author: tdreszer Date: Thu Sep 18 23:54:20 2008 +0000 Oops, get the right name. commit a2ff6338cc02453156439df560c99d2e096d7be7 Author: tdreszer Date: Thu Sep 18 23:51:03 2008 +0000 Addign Elnitski composite so I can get the pipeline to work commit 9e03358fb99e68bbb6400a8d5851ac5b218be69c Author: tdreszer Date: Thu Sep 18 23:42:14 2008 +0000 Added cv type 'promoter' commit 3d98d893d555b522be987cb876a16acae59d94f1 Author: ann Date: Thu Sep 18 23:31:17 2008 +0000 noted pdf file commit 92823fc62e51e2821db34f7394da20e28a49c6ee Author: markd Date: Thu Sep 18 23:21:30 2008 +0000 add gene fishing tutorial training.html commit ad036cd40f0e9d1fe6540e24d883086ee5197776 Author: tdreszer Date: Thu Sep 18 22:29:46 2008 +0000 Added two promoters commit f714c769a396608026c5675b972ab7bf65875fa4 Author: angie Date: Thu Sep 18 22:09:18 2008 +0000 Tweaked wording at top of page: 'Description' --> 'Format description' because Description was sometimes misinterpreted as track description. commit 0ae2a0b23f8fafed5d7b33eb5592e1b3c7b84854 Author: angie Date: Thu Sep 18 22:02:01 2008 +0000 Ignore some duplicate .as files with confusing (db-specific) descriptions. commit 7f2574667a319b4b5a187476f02c44a43e1c0dcf Author: angie Date: Thu Sep 18 22:00:50 2008 +0000 Added a reference to multiple alignment display since this format so far has been used as MAF only. commit bd745b44b45c364331485a5b7c7b4136f1692339 Author: braney Date: Thu Sep 18 21:57:35 2008 +0000 add a link to get info about CDS FASTA alignments commit d657f46c2c97c6460ba06f338ee62801450b5b51 Author: hiram Date: Thu Sep 18 21:47:05 2008 +0000 Newer versions require a more strict URL for the action=raw edit function commit 3951a091fea45bc9918ad5febacbf48cd061951d Author: hiram Date: Thu Sep 18 21:46:22 2008 +0000 use parseQuotedStringNoEscapes() function instead of parseQuotedString() for HTML text to allow backslash in token string values commit a9e4c2e849f35b7f4da64ce9ae1929eedbf4b211 Author: braney Date: Thu Sep 18 21:36:15 2008 +0000 add some text describing CDS FASTA alignments. commit d18972fef81953945f43ed96d36b7118a155fb9a Author: braney Date: Thu Sep 18 21:35:45 2008 +0000 take out spurious capitalization commit beaed3cb3073b639a9ce27e278af4eb8161b5db2 Author: hiram Date: Thu Sep 18 20:02:45 2008 +0000 Adding function parseQuotedStringNoEscapes() to avoid MediaWiki HTML parsing problems commit cac66aebd5f173a1500f21a44edc8f3c68f08260 Author: hiram Date: Thu Sep 18 20:00:32 2008 +0000 Add a parseQuotedStringNoEscapes() to avoid MediaWiki html parsing problems commit 1400b53a8394ea39d118854669846f3c171d8e41 Author: hiram Date: Thu Sep 18 19:59:11 2008 +0000 Add a simple test to check parseQuotedString and parseQuotedStringNoEscapes commit b7ebb33cfaa4be4ae373670e43866c0d31feea0d Author: kuhn Date: Thu Sep 18 18:55:15 2008 +0000 backed out the previous changes for now commit 7a42f028d38a3fd5c9ebf1022142b9c6b6e2c548 Author: ann Date: Thu Sep 18 17:02:38 2008 +0000 added new getLiftOver script commit 1bd4a6680ff8db3fc35bb92369ddb3c527de9b62 Author: ann Date: Thu Sep 18 17:01:36 2008 +0000 this script returns the list of liftOver files to/from an assembly. commit ad9b96c6b61efd461f0274bf82dc0cfeb2850aec Author: galt Date: Thu Sep 18 15:00:07 2008 +0000 "Encode release log update" commit 3a9428f84c2895ca0ba8d1a4f806dfca1d6930c0 Author: galt Date: Thu Sep 18 15:00:04 2008 +0000 "Release log update" commit 561d04cc99d73d4f776b34153999afcb559668c9 Author: kuhn Date: Thu Sep 18 06:06:06 2008 +0000 removed arhived assemblies, including several that were archived long ago commit 05796c2978c66e8cac95ce5d6fd46ae49093555b Author: mikep Date: Thu Sep 18 03:51:57 2008 +0000 fixing to name conventions commit 254f694c3cc03d637c2cc599b47c75dc72645f39 Author: larrym Date: Thu Sep 18 00:52:03 2008 +0000 add fillInScore option (for use by ENCODE loader) commit 52533c71bb0e499c0e9e416cd249107b9dc7d776 Author: kuhn Date: Thu Sep 18 00:49:21 2008 +0000 dropped archived assemblies commit da5e091465f3c46b91488b611649552c7d2d00df Author: kuhn Date: Thu Sep 18 00:44:39 2008 +0000 added mm5 mm6 and danRer2 to ARCHIVED_DBS commit beeff32818149f9b15465aac7b443249b0d71bcb Author: kuhn Date: Thu Sep 18 00:43:45 2008 +0000 added mm5 mm6 and danRer2 to ARCHIVED_DBS commit d71042302726e92bc5373f64e257f756683d7d31 Author: galt Date: Thu Sep 18 00:38:20 2008 +0000 use gifread to compare existing to current to check for update needed - faster, avoids using NFS commit 1c4e2ff3eda31d57f2b0fe287e0ba3315fe8d169 Author: galt Date: Wed Sep 17 20:10:43 2008 +0000 adding rcsid commit dd9cb638e15b04c9e9bb6c0ae79ba0dfec74ec4d Author: mikep Date: Wed Sep 17 19:45:00 2008 +0000 added rcsid tag commit 08aa029ea30ed0b90965b907ea9b9856b96bd56e Author: galt Date: Wed Sep 17 18:36:35 2008 +0000 adding rcsid commit f4134452bca9d06e4f19f9e10c7811f2eaaff046 Author: kent Date: Wed Sep 17 18:10:14 2008 +0000 Adding rcsid's to a bunch of things. commit 78e7d137c323b67b49823eccc8ab65cef84a58b0 Author: galt Date: Wed Sep 17 18:00:47 2008 +0000 adding rcsid commit d3d84909336bb6f517ca3609cf662816ea0dd082 Author: kent Date: Wed Sep 17 17:56:38 2008 +0000 Adding rsid to a bunch. commit 588b34059770ac41cb2971782c3ba0f8b9d638d7 Author: braney Date: Wed Sep 17 17:54:03 2008 +0000 added rcsid commit ce74b5e42f4d51810f18a9efb74f19e87af332bd Author: mikep Date: Wed Sep 17 17:51:32 2008 +0000 adding rcsid line commit 76acb1bd8070f3698ff6a968b64946239bcac316 Author: tdreszer Date: Wed Sep 17 17:44:52 2008 +0000 Moved broadChromatinChIPseq composite to trackDb.ra as per QA request commit 738dcc1efe0f0501ad40ed37f6648c36d5308560 Author: mikep Date: Wed Sep 17 17:40:40 2008 +0000 rcsid was missing from this file, so /usr/local/apache/cgi-bin/dependeicies script could not see what was dependent on this commit 9212191ceb3bab003980d6930e643caf66735005 Author: markd Date: Wed Sep 17 17:27:39 2008 +0000 some ORFeome clones don't have IMAGE ids, so don't insist commit 8d6874dc93923d99e1b2e6a101c22cb3aba6344e Author: braney Date: Wed Sep 17 17:15:59 2008 +0000 re-do some of the downloads that had the wrong stuff in them commit ee69d8e1c149fe5b9133d6a0ca5bf13d78ab0927 Author: donnak Date: Wed Sep 17 16:21:40 2008 +0000 Archived a news item. commit 40f042da51ab4011cabe1f690acf76614ec2c1dc Author: donnak Date: Wed Sep 17 16:21:24 2008 +0000 Edited news item, archived some news items. commit 008a45790908361f8932a6dbbd709f18ddf1e888 Author: fanhsu Date: Wed Sep 17 16:13:22 2008 +0000 Changed to count quoted words in a file for items in a filter. commit b5db8fc5c04fe6a15388587c85a339f82b9cebea Author: galt Date: Wed Sep 17 15:43:57 2008 +0000 adding missing chips commit 5dd5cff6aef5204a3d5527257e553339b79b67db Author: galt Date: Wed Sep 17 15:00:09 2008 +0000 "Encode release log update" commit dbc03582546fdf123d43a355f5d6f6a39377c902 Author: galt Date: Wed Sep 17 15:00:07 2008 +0000 "Release log update" commit 5b91494c29bc34c4742ad9be723c8998fd732547 Author: donnak Date: Wed Sep 17 08:49:43 2008 +0000 Updated date. commit 2d47c57ee9476618037cafa5d4a23c000c604534 Author: fanhsu Date: Wed Sep 17 03:15:01 2008 +0000 Created for HIV A244 genome. commit b1d6a563afa7dfd8b703c2d853a4f7dd6aaf8bb9 Author: kuhn Date: Wed Sep 17 02:49:20 2008 +0000 logged and announced archiving of seven assemblies commit ed87ae65422036221419565cc1cd75057e59b543 Author: kuhn Date: Wed Sep 17 02:23:53 2008 +0000 logged and announced archiving of seven assemblies commit 55af7f9bde511e08f8a90118bb00fb79aeacf520 Author: markd Date: Wed Sep 17 01:01:51 2008 +0000 fixed and worked around bugs retrieving sequence that were cause by switch to psl track commit a5ed15721b017e8a0d3546cc5b774979a75cfc98 Author: markd Date: Wed Sep 17 00:17:35 2008 +0000 don't run genbank rr updates on sunday to stay out of rsync's way commit 1e6933223ba814588f59da06899d6ee5fc6bb74a Author: aamp Date: Wed Sep 17 00:02:27 2008 +0000 A few more places where "Project" was changed to "Submission" commit f249c14c5d5e7d7dbd19001bc2ce6d398c12f037 Author: aamp Date: Tue Sep 16 23:55:17 2008 +0000 Changes discussed in encoder meeting Mon. 9/15/208 e.g. "Project" -> "Submission" terminology change. commit fc934ef4680b317bcc71370ddc96ef38e6e172ab Author: kate Date: Tue Sep 16 23:18:56 2008 +0000 Alpha sort on label if priorities are the same. Already in hgTrack. commit 0d50ceb99f54f40bf74002826eb0ca114e553a91 Author: ann Date: Tue Sep 16 22:26:35 2008 +0000 added tableDumpDates.csh commit e930814cfb32771d0d44e22d006787a14bf178a2 Author: ann Date: Tue Sep 16 22:25:44 2008 +0000 Checks to see if the genbank table statuses are being dumped from the RR machines in a timely manner. commit 2e678637bf11c016e8f7681d3100298200fd778c Author: ann Date: Tue Sep 16 21:47:29 2008 +0000 Removed stray tag that was found by hgTables. commit c640d4df082ba5070d7b5adae5ef126006e38f44 Author: braney Date: Tue Sep 16 21:29:05 2008 +0000 add galaxy output commit ba3b5ecf874a66ce68b4278cc7ef43a7270b273e Author: braney Date: Tue Sep 16 21:16:54 2008 +0000 change type of pal output to fasta commit a7308a41a96dd77f04fd062262614bbdc6d79713 Author: larrym Date: Tue Sep 16 20:09:17 2008 +0000 fix type commit e07531eb31b07033847c13aa29cf9069e21ca5c6 Author: larrym Date: Tue Sep 16 20:07:46 2008 +0000 add $autoCreatedPrefix commit 716e58f33ab855afc14268fc3d640939e7a6b3e3 Author: larrym Date: Tue Sep 16 20:06:28 2008 +0000 minor edits commit 6afe808a6f3e9b72a3990fa423e8a123d8442f8d Author: larrym Date: Tue Sep 16 20:06:04 2008 +0000 copy non-autogenerated signal data to hgdownload commit 0bdc89ebe676fd59f8115b63cef0a198bed78cc2 Author: larrym Date: Tue Sep 16 19:41:05 2008 +0000 more fixing steps commit e21137da72991033ca3495c4ee43b17eb18b3323 Author: pauline Date: Tue Sep 16 18:58:43 2008 +0000 Fixed typo. commit e641eaf24fe84b65b4263a3506803d625885db8e Author: angie Date: Tue Sep 16 17:59:15 2008 +0000 kiddEichlerDisc: endFudge is needed for hg17 but not hg18, so move it down into hg17/trackDb.ra. commit 15be9e570d185f0ef2302aa679e733914acab6fd Author: angie Date: Tue Sep 16 17:57:43 2008 +0000 Updated kiddEichlerId expectations for hg18: more mappings to hg18, same number of NCBI IDs, so lower expected percentage for G248. commit eecf8a6d559ca5a1a082db3a450529275658ef2c Author: angie Date: Tue Sep 16 17:56:32 2008 +0000 Added discordant clone mappings from Kidd/Eichler '08 (Human Genome Structural Variation project). commit 819378072c30545a98e15ff2246af6855d8dc5ab Author: braney Date: Tue Sep 16 17:31:00 2008 +0000 add hgPal to list of CGI's with "Genome Browser" link commit c6735b15e9086ec99c420a5a93fb2758766bf5fb Author: braney Date: Tue Sep 16 17:30:39 2008 +0000 save mafTable in cart if it isn't there already commit 1d05aa166d659d97420b3bd2ad25a06940773013 Author: ann Date: Tue Sep 16 16:36:57 2008 +0000 removed beta block for orfeomeGenes (replaced by orfeomeMrna) commit cf3655c0b96fc4e37d21f0341e105610427b7186 Author: mikep Date: Tue Sep 16 15:49:29 2008 +0000 "New version number v191" commit 9e41d28bac0eb9323ae535b3a5e37d5b25c44bf0 Author: galt Date: Tue Sep 16 15:00:11 2008 +0000 "Encode release log update" commit 726629058e256480232c904dcc4fabb3bdb39114 Author: galt Date: Tue Sep 16 15:00:05 2008 +0000 "Release log update" commit 99e8f4e1a2d78e5895a0c682b337eb2c4a3b55ec Author: braney Date: Tue Sep 16 00:43:51 2008 +0000 use routines from ../lib/pal.c commit b2b257fc2d77bc4883756990869d5baa672efdd2 Author: braney Date: Tue Sep 16 00:41:18 2008 +0000 put most of stuff in ../lib/pal.c. This module hgTables specific. commit 4318c4430c7f5f197556a1f4a31e5bda220d22d6 Author: braney Date: Tue Sep 16 00:40:26 2008 +0000 add pal dialog module commit 02c11e02a6afeaec4285ce70e1e92cf9e2ebc42b Author: braney Date: Tue Sep 16 00:39:31 2008 +0000 re-introduce some changes someone stepped on commit b815ac33db5f3530e4d4beaadec5342b04b8b4a5 Author: braney Date: Tue Sep 16 00:38:45 2008 +0000 the pal dialog (maf selection and option setting for CDS FASTA alignments) commit 74b98237f020e92888999a34cb0de0177de38ae5 Author: galt Date: Mon Sep 15 23:55:50 2008 +0000 better handling of race-condition and atomicity commit c1dab781648b2767a09b8018ab3d82929d661ae0 Author: galt Date: Mon Sep 15 23:42:00 2008 +0000 fix freez missing commit 05165e9f48263fbbbe31aa97e5a9ceb93dfee45f Author: galt Date: Mon Sep 15 22:51:48 2008 +0000 test for psOutput commit 226dedcac34c24ee33130a537fda145be1bfd91c Author: braney Date: Mon Sep 15 22:47:28 2008 +0000 protein fasta alignments from genePreds and MAF files commit 71b47ba52dc601ac651ae0f5879c9f7dd565c1c8 Author: donnak Date: Mon Sep 15 22:26:07 2008 +0000 Added news announcement abt ENCODE data release plan. commit 2b6d451e8765a6b8d9202147189bca611b6a7a8a Author: ann Date: Mon Sep 15 22:08:16 2008 +0000 removed hg18 from cgapAlias rule. We connect to CGAP using the kgAlias. commit 9b3cdda708ad92a5f0cccfd555e8b1ff8188cc48 Author: braney Date: Mon Sep 15 22:05:28 2008 +0000 change string commit 821330f1dbae19a5a539b64f9caedeee1456a333 Author: rhead Date: Mon Sep 15 21:56:59 2008 +0000 Added links to references section. commit 3a7f1dbe88e6c4d21715ac686535788575cddfba Author: ann Date: Mon Sep 15 21:29:53 2008 +0000 Removed. Now using identical file at top level. commit c45fffdf0318fcbc942bcf28d09d3c6ecfde5d22 Author: ann Date: Mon Sep 15 21:23:44 2008 +0000 Making Description more generic. commit dc909605ca15146f30a439d70ec38d608b744e0b Author: ann Date: Mon Sep 15 21:19:46 2008 +0000 correcting Description section and making it more generic. commit 7efba550f6596934356b3cf7b828026366679275 Author: galt Date: Mon Sep 15 20:59:55 2008 +0000 adding agilent cgh 244a; also changed upload form to allow pasted text commit 740016c0626aa6a380c5d08c07db5497ff833b50 Author: galt Date: Mon Sep 15 20:59:19 2008 +0000 adding agilent cgh 244a commit bf45de9a54e2008f70ad3cb0167d4055cc0b2260 Author: markd Date: Mon Sep 15 20:57:26 2008 +0000 fixed nemVec1 reference to san commit 434c5084c6efaca3ee8fdec5250f203167b89aad Author: fanhsu Date: Mon Sep 15 20:46:13 2008 +0000 Added "hFreeConn(&conn);". commit 5280364efd6dd547628d522d67c36a391d89d1b8 Author: fanhsu Date: Mon Sep 15 20:41:48 2008 +0000 Removed "FreeConn(&conn);". commit a3df846d2cda7b341905232e2826e9bd2c9a1420 Author: larrym Date: Mon Sep 15 19:13:42 2008 +0000 support MS-DOS EOLs in readFile (I've gotten those from an ENCODE lab) commit df6c153d0ab895a82f4a87e12a037c8990bd5ad0 Author: larrym Date: Mon Sep 15 18:53:24 2008 +0000 create/append to README.txt (text still needs to be fleshed out) commit 180ccb623af91155336b567454fe08c1ffa84383 Author: fanhsu Date: Mon Sep 15 18:36:36 2008 +0000 False alarm. Revert to the original. commit 2cdd67d2e8c65fa4ef18ee693e161e81c5c46531 Author: ann Date: Mon Sep 15 18:03:03 2008 +0000 added taeGut1 to Human Proteins rules commit ef036e8e9921a9ebf13d691a303e753167cec513 Author: tdreszer Date: Mon Sep 15 17:21:16 2008 +0000 Changed pipeline path to use hive version. commit f7933ebbd686532f8bea68a8f299c8aa0eb303d8 Author: tdreszer Date: Mon Sep 15 17:20:18 2008 +0000 Added LNCaP newly approved teir 3 cell line commit 15f4c4eedf8f23a254cdb7973334fc62a67b6932 Author: fanhsu Date: Mon Sep 15 17:15:50 2008 +0000 Updated hgExpLabelPrint() so that the temp file is created under trash/nea instead of trash. commit 6c5714a89b38e8addd0c50b51e9c6b72c32be3de Author: fanhsu Date: Mon Sep 15 16:13:42 2008 +0000 Updated hgExpLabelPrint() to create and use temp file name to avoid conflict with other users' files. commit 345c96faf9c748cc39ccdd644fe62a47b8833364 Author: galt Date: Mon Sep 15 15:00:34 2008 +0000 "Encode release log update" commit 8e230d6095677dec35d8312456a03ccdca3136c6 Author: galt Date: Mon Sep 15 15:00:32 2008 +0000 "Release log update" commit 20700b23efcb12155b0350a14e44dc4104f7ae73 Author: fanhsu Date: Mon Sep 15 01:42:17 2008 +0000 Created hivA244.txt. commit 3c17e43e58eda5c380b3137b2f65e355fd2f407f Author: baertsch Date: Sun Sep 14 23:44:23 2008 +0000 fix dislay bug with blending commit 273a1680f25d1f0ac6269773d45884c4a9eef586 Author: baertsch Date: Sun Sep 14 23:22:37 2008 +0000 add blending of pixel colors when zooming out. Only red and yellow blending supported currently. commit 650fd04d5c3ab902847b87647592262c8d42b50f Author: markd Date: Sun Sep 14 16:49:56 2008 +0000 fixed uninitialized var warning commit 5e424bc7c69c862363ea5313504817e6c92b8e9a Author: galt Date: Sun Sep 14 15:00:08 2008 +0000 "Encode release log update" commit f406d04cd088785d541a1d941c2a9e9823ca1fcc Author: galt Date: Sun Sep 14 15:00:05 2008 +0000 "Release log update" commit 2c9e6e4c6d00f5baa555be7f9438d90cf44558ce Author: markd Date: Sun Sep 14 08:08:28 2008 +0000 added missing parameter not detected by compiler commit e4e7c4edc7eba31650996f6b17c979223d4496e7 Author: markd Date: Sun Sep 14 03:43:31 2008 +0000 removed stray conn free commit bc052cc2342310d3e3fbf09cc4be5805dc79561f Author: markd Date: Sat Sep 13 20:43:35 2008 +0000 include ideogram files as part of ps/pdf commit aa3ba2a023b3ff2703178e8b0c2ac00ce16ed14c Author: markd Date: Sat Sep 13 00:58:02 2008 +0000 put code back the way it was, hiram was wrong commit d77db22deafe98b78131772e26467c44a35b7e90 Author: markd Date: Sat Sep 13 00:47:09 2008 +0000 fixed bug with spliced stop codons commit 7e94287f74b7c1047784fb259e75a55f4043abb7 Author: markd Date: Sat Sep 13 00:46:54 2008 +0000 added assert commit 37b50ca324f49f8e65bfbf1165329eb62482088d Author: tdreszer Date: Sat Sep 13 00:01:23 2008 +0000 Latest visibility and configurable settings commit 950fdc437ecc2430d4b103deef26cce0bef23d77 Author: braney Date: Fri Sep 12 22:37:21 2008 +0000 deal with the filters and interesections like seqOut does (rather than how the wiki routines do) commit c8e2f6050d9683104fd1a55480d34efff28616d3 Author: larrym Date: Fri Sep 12 21:49:50 2008 +0000 add DAF view list (dafList) fields commit 7af5b059151a6443f1cfda23a6f89439b123b1a9 Author: larrym Date: Fri Sep 12 21:38:21 2008 +0000 DAF with lots of errors commit 2d779dbc21cb2258d94bd1fe4aed6911869bc6cf Author: larrym Date: Fri Sep 12 21:37:48 2008 +0000 add badDaf commit 299c884165129b12fd48af5e83aa2b1e4f471acb Author: larrym Date: Fri Sep 12 21:37:16 2008 +0000 validate fields used in DAF view list; remove obsolete & function call prefixes commit 0a13dc9bb3b8a572b74bb6509310ce0415dce572 Author: pauline Date: Fri Sep 12 21:26:21 2008 +0000 Edited custom MAF text for clarity. commit fbef30766f068bee81a3bd643420c1fd8f7f2c4b Author: larrym Date: Fri Sep 12 20:22:00 2008 +0000 shorten file commit d4715845be2cdcdd58ff122ecc398e8e53c4b61a Author: rhead Date: Fri Sep 12 20:14:14 2008 +0000 Moved eponine track back to regulation group. commit 4e6f6a715025feb2b1f55691cda1c56b9c424517 Author: larrym Date: Fri Sep 12 20:10:31 2008 +0000 add pushError; fix test for suspicious chars in filenames; special case control/input metadata commit 75426d33eca119736fedbe4ec699dfc6733ed240 Author: larrym Date: Fri Sep 12 20:08:57 2008 +0000 add bad rule commit b0e4a923350f62d9be78ab6df7f9608d864e6217 Author: larrym Date: Fri Sep 12 19:56:27 2008 +0000 nonreadable.txt => unreadable.txt commit 60bf11c43bb689657777185fa77ad5b2fcd914a1 Author: larrym Date: Fri Sep 12 19:53:51 2008 +0000 test of bad DDF entries commit ce59cfeb8567794627aaffed04ed2accd0f9ec59 Author: tdreszer Date: Fri Sep 12 18:47:12 2008 +0000 Added support for requesting the implied term 'control'. commit 117d6942872c4fd4de467024518c6c90c8f9937f Author: kayla Date: Fri Sep 12 17:51:16 2008 +0000 took out danRer2 per bob. commit f9778606dc8dcd248dcb8e733c59f5122455a420 Author: tdreszer Date: Fri Sep 12 17:13:31 2008 +0000 Added visibilityViewDefaults and configurable to composite multi-view tracks commit 873f65f75b83ae5195477d4589cae77ebc94573c Author: tdreszer Date: Fri Sep 12 16:57:24 2008 +0000 Oops, forgot configurable 'on' for Hudson commit d28f7af78123d4e6cefb6eb951f720d5d5e3957f Author: tdreszer Date: Fri Sep 12 16:42:38 2008 +0000 Added visibilityViewDefaults and configurable to composite multi-view tracks commit 30ef640435c1e95cba72aa5e85ec447a81a0793d Author: galt Date: Fri Sep 12 15:00:06 2008 +0000 "Encode release log update" commit e83221f3b7ae656a06706b64702bfac39f9abc98 Author: galt Date: Fri Sep 12 15:00:03 2008 +0000 "Release log update" commit 9b3a22b02d9a400a944d7d89d62cfb68c946274d Author: larrym Date: Fri Sep 12 08:22:12 2008 +0000 fix shortLabels commit 0056eb242bc53cdd15299da5d8a98915efc43a56 Author: larrym Date: Fri Sep 12 07:59:58 2008 +0000 fix HudsonAlphaChipSeq subGroup1 commit c47217479e6a4c1d4a0c0debda3c22a6a13251c2 Author: larrym Date: Fri Sep 12 07:52:39 2008 +0000 add control tracks for wgEncodeHudsonAlpha commit 407713516707ebdb5ae1a1fab8ddfd506e7ae3cb Author: larrym Date: Fri Sep 12 03:22:48 2008 +0000 extensive changes to modify code to report multiple errors commit f756453159a8c55d4f66d80e08c36006f8f83228 Author: larrym Date: Fri Sep 12 02:48:21 2008 +0000 modified code to report multiple errors commit 5b50d1ed64d81b05b537f1c620d15eb2f88966b8 Author: kate Date: Fri Sep 12 01:36:06 2008 +0000 Draft doc from NHGRI posting for community input commit 5a117a1f8d886a17f35f41a6c4f931ba42af736c Author: kate Date: Fri Sep 12 01:25:45 2008 +0000 Improve code style, based on review commit 32cd0009d93469953765e431e83ab4dfae14519e Author: tdreszer Date: Thu Sep 11 23:41:19 2008 +0000 Support for individual subtrack configuration in composite commit 1a55fc9aa2ab3d5a947b443bd995fb6489fc7126 Author: tdreszer Date: Thu Sep 11 23:23:12 2008 +0000 Fixed minor bugs to broaden applicability of common functions commit e3b8ae544a5b602a788df08d5083b469503e49fd Author: hiram Date: Thu Sep 11 23:22:44 2008 +0000 Was missing sending the cookies to the wiki on the submit of the edit commit 9cf2fa853a39c2a0be635b7003d8f3cae1315b78 Author: galt Date: Thu Sep 11 23:19:30 2008 +0000 improving free/busy cpu counts commit a259906dcc183179cd02fb509d4e7778976b7535 Author: galt Date: Thu Sep 11 23:18:46 2008 +0000 new version commit 5d65171b8f11ad6fba3106b047bfae8017689e07 Author: galt Date: Thu Sep 11 23:17:51 2008 +0000 Fixed minor param-checking bug in parasol check dead commit 6924408487597cc5c5097dfcecdcdec89c383ffd Author: tdreszer Date: Thu Sep 11 23:15:41 2008 +0000 Added trackDbSettingOn for boolean settings commit e2fff83488d9eae46374533b6ed61a851cfad435 Author: pauline Date: Thu Sep 11 23:11:10 2008 +0000 Added new medaka assembly. commit 16f2376ea714fe729ab5f0a03944617e27d338c4 Author: rhead Date: Thu Sep 11 22:33:42 2008 +0000 Fixed broken link stickleback page at Broad. commit 1e968d1be4cef8a01779aeab2fafa9d414e03db4 Author: larrym Date: Thu Sep 11 22:11:11 2008 +0000 create README.txt fragment commit dfa507e657f3e13ec8dc78b6a18a4e244aea585c Author: larrym Date: Thu Sep 11 22:09:48 2008 +0000 add restrictionDate commit a37282c7a3785334d0c9cd5d616e876e3844b607 Author: braney Date: Thu Sep 11 21:41:43 2008 +0000 better flow control commit 5895543efb102cdecd699aed457ca98642272e1a Author: braney Date: Thu Sep 11 21:40:50 2008 +0000 string change commit c09e3b2933f517dbad38c8ce66e6493aea089adf Author: braney Date: Thu Sep 11 21:40:38 2008 +0000 make strings easier to understand commit c4edf13bcbad2d51c8f0c052b1c4e89e2511ffd3 Author: braney Date: Thu Sep 11 21:39:30 2008 +0000 a bug fix, and change string in dialog commit 72093b9b301d521a34b5ed5bac10ed5f4a3eccdc Author: hiram Date: Thu Sep 11 20:33:52 2008 +0000 Correct date for assembly Oct 2005 commit 81d13f560cb322791008548ee03af3c39e4eed90 Author: larrym Date: Thu Sep 11 19:47:58 2008 +0000 redo-genbank auto update commit 51e432d41dc2d0e4b50e5e41c3e5df01c98dbfb0 Author: braney Date: Thu Sep 11 18:37:53 2008 +0000 change to follow model set up by intersect.c (still have problem with Set and Clear buttons) commit f739ea7c6708740d3334ae4798819dff05e6db05 Author: larrym Date: Thu Sep 11 18:14:38 2008 +0000 initial checkin commit 64e7cbd37441b6eb604b0749488f70f4c04e25b1 Author: larrym Date: Thu Sep 11 18:14:11 2008 +0000 add update-expected rule commit 711f9684289316d74796b35f3908c3cbd38fbac4 Author: hartera Date: Thu Sep 11 17:38:53 2008 +0000 Changed GIS to correct expansion of acronym in this context. commit b4e6f7a953fef68cb8263caa6d6a3d9814d3c647 Author: hiram Date: Thu Sep 11 17:35:35 2008 +0000 stray white space eliminated commit 6c0c8cb579c92a7124d184826c8b24f50772cbab Author: hiram Date: Thu Sep 11 17:34:23 2008 +0000 InnoDB tables have Update_time == NULL, avoid compare problems with that commit 7ef0305d368efdeab2a042b6e4f783ab2ef5fc55 Author: galt Date: Thu Sep 11 15:00:06 2008 +0000 "Encode release log update" commit 4570e34b96f727345304305724841b9650e6b205 Author: galt Date: Thu Sep 11 15:00:03 2008 +0000 "Release log update" commit 0e5a900aa2578372672b2beb86016e7b13ec30a7 Author: braney Date: Thu Sep 11 01:38:45 2008 +0000 some improvements, only available for genePreds, some changes to support re-entry commit e3940ec8090c19fb0076499e7d3f94d5c61137b7 Author: kate Date: Thu Sep 11 00:13:36 2008 +0000 Add Vendor ID column (as for Antibody) and add links to BTO terms commit 0ad35b3a31dbbcab975c3417a3c53059b63a77a0 Author: kate Date: Wed Sep 10 23:39:40 2008 +0000 Assign supertrack members pri 300 to assure reasonable display on configure page with track reordering. These will be restored to 0, along with supertracks, when new hgTracks is released. commit 15aa026dece95366738805537ddb5e9b65732aa7 Author: mikep Date: Wed Sep 10 23:23:03 2008 +0000 function to convert an array of range (start/size) from disk into a range tree commit f629f9369616ac6cb78050c5c1d582f1ef93c210 Author: kate Date: Wed Sep 10 23:20:41 2008 +0000 Split Expression & Regulation into two track groups commit d15dd5fc8005ff827c0290cead7be06b348270b5 Author: mikep Date: Wed Sep 10 23:20:29 2008 +0000 fix up parameter name to be more readable (oBama = output Bama file) commit 6d4eee985fd4c8409e02c3cf869260323c95cabe Author: kate Date: Wed Sep 10 23:19:39 2008 +0000 Split Expression & Regulation into two track groups. Assign all tracks priority 0 so that they will be alpha sorted by short label commit c4ebcd720f291e8689f52c6fcf13daf5029df30d Author: markd Date: Wed Sep 10 23:12:26 2008 +0000 fix some silly code I wrote and hiram found commit 6708a53062e7361c9c06c415f2de859b3a720588 Author: angie Date: Wed Sep 10 23:10:24 2008 +0000 In hgSeqBed, when handling bed 8, if thickStart == thickEnd == 0 then set them to chromStart so the address arithmetic isn't broken. Ultimately there should be a trackDb way to specify that thickStart and thickEnd don't mean anything for a table (hti->hasCDS=FALSE) and it's also clunky to always say CDS when a table has thick* fields. commit 7225622a11d6a1360e7b07b3b1968612cede6cb3 Author: larrym Date: Wed Sep 10 22:59:14 2008 +0000 break out of loop after wibSizeLimit msg to avoid printing stuff from other commands in the pipe commit e28cb635aad047f8f99d89700b29a2402e2c166c Author: larrym Date: Wed Sep 10 22:57:05 2008 +0000 make exceeding wigSizeLimit an error rather than just silently skipping the rest of the data commit da0fe6ba885512eeceb36dcfc6f0543a6532a02c Author: fanhsu Date: Wed Sep 10 22:24:55 2008 +0000 Updated the entry for H-Inv to accomodate new web site URL. commit 7d484e464fccfd872f0bf3468356f1eb1e55c299 Author: donnak Date: Wed Sep 10 22:16:23 2008 +0000 Archived an item. commit f125d7608d8d1206feba19b1e5b593ff4fcfb4f8 Author: donnak Date: Wed Sep 10 22:16:09 2008 +0000 Added UCSC Genes announcement. commit eae4c272651e4dfdacf396e710a7065506e2687f Author: kate Date: Wed Sep 10 21:30:14 2008 +0000 Copy cv.ra to DOCUMENT_ROOT for access by cgi's commit 92ad7636cc40e64d31265a497023298a02b2f5d9 Author: kate Date: Wed Sep 10 20:31:50 2008 +0000 Downloads for ENCODE TBA track commit 6e1f84320fdd40a74fa6a023ecfca4334bd9d583 Author: braney Date: Wed Sep 10 20:17:22 2008 +0000 add chain to zebra finch commit 0bf6d9ae1303fa9bdf4df47b516019e3e1f6c2e6 Author: braney Date: Wed Sep 10 20:17:02 2008 +0000 need for chain to chicken which uses default matrix commit 6202a14955995fafcfd9738e59853e51d23fd4aa Author: larrym Date: Wed Sep 10 19:52:27 2008 +0000 get rid of remaining obsolete & prefixes in function calls commit 8659964195bf5a8e28ced40f7e6b0837564834dc Author: mikep Date: Wed Sep 10 19:50:46 2008 +0000 adding rnaExtract,localization variables to DDF validator in anticipation commit 0ce5f89ad27a72316336e2e495d589113854120b Author: braney Date: Wed Sep 10 19:27:39 2008 +0000 re-do zebra finch changes commit 46b0017e0e32d70f1d3da5784995081b16db155a Author: braney Date: Wed Sep 10 19:26:20 2008 +0000 re-do hg18 chains commit a5e92b27d53b2fdc30de6944b975dd822f9011c8 Author: mikep Date: Wed Sep 10 19:11:55 2008 +0000 this weeks day 2 commit 4c0b8591eeaeb3c7e68e59d45f3c57b349e823c9 Author: mikep Date: Wed Sep 10 19:11:26 2008 +0000 added a date/time after the lock file name so you can see if it is old or new, and removed the error message which comes up on transient locks which have gone after find found them commit 15c0c80a56ee49ee489474a02c091047640eff1d Author: mikep Date: Wed Sep 10 19:09:06 2008 +0000 first version of DAF sent to GIS commit 84659ee6d5529f22290433814f3a72f7702e0159 Author: larrym Date: Wed Sep 10 19:01:36 2008 +0000 allow just filename when -validateDaf option is present commit 4e7528c325db67c15caa5171c4d0089f56d9bdce Author: larrym Date: Wed Sep 10 18:53:38 2008 +0000 make sure daf filename is fully qualified commit 72a2f0d8e2eb9eab764b308b2a03b11d1f32993d Author: braney Date: Wed Sep 10 18:41:25 2008 +0000 take out some old stuff, javascript submit on MAF file commit bb3c421e822cfa89e0f281ca711caa891ae5e6dc Author: larrym Date: Wed Sep 10 18:37:07 2008 +0000 refactor some of getDaf into parseDaf commit 9ef73cc345a8b4efe7b83bb1cddc37ed22195855 Author: kate Date: Wed Sep 10 18:36:55 2008 +0000 ENCODE alignments commit 172e2bea2886cf54d3d27872b9106e2a50e81f84 Author: braney Date: Wed Sep 10 18:29:45 2008 +0000 allow there to be another (fourth) parameter to URL commit 04e3f49df1e66c265fdec9b76c38b1bb0a1e1682 Author: hiram Date: Wed Sep 10 18:02:08 2008 +0000 No need to worry about the NullOK now ... commit 3d4be3f1a68552d7c53f267def4da5c104c7c5c9 Author: hiram Date: Wed Sep 10 17:55:09 2008 +0000 Safer string check on cart variable to enable running without a cart commit 2f28864e2225d1648593f79d3d95abee109d9e75 Author: mikep Date: Wed Sep 10 17:49:56 2008 +0000 checking the status outside the if (mode=review) block did not detect the error condition so I moved the check up to directly after each command commit 883fd55beca6c26ca1a5e6a30c71a9320e2b5747 Author: mikep Date: Wed Sep 10 17:49:06 2008 +0000 add ssh n flag to redirect stdin from /dev/null commit c1ffbec2ba2db25bbd6aaba2bb12ba669b45cc65 Author: hiram Date: Wed Sep 10 17:19:27 2008 +0000 Adding oryLat2 to the listings commit 2dd177bbcc2a22d05f761c2285902cb93bffbb4e Author: hiram Date: Wed Sep 10 16:17:49 2008 +0000 Handle both oryLat1 and oryLat2 on the outlink to UTGB commit 57619aa45897bee22b1f4111337655372971d136 Author: braney Date: Wed Sep 10 16:01:38 2008 +0000 remove pre-existing goldenPath directory for chains commit f77708bbe52192e9de5cb7860106f238f3379dfc Author: galt Date: Wed Sep 10 15:00:07 2008 +0000 "Encode release log update" commit be6f618652f9a4e092c2d17907de8dfd7e3d540c Author: galt Date: Wed Sep 10 15:00:04 2008 +0000 "Release log update" commit 7c25a8d8317ad8dd7ea4c9db4308726c2422a70b Author: aamp Date: Wed Sep 10 08:59:21 2008 +0000 Added Sestan Brain Atlas instructions commit f399bf57037594e827e9a460591264c322bfc5e1 Author: aamp Date: Wed Sep 10 08:58:50 2008 +0000 Added Sestan Brain Atlas stuff. commit 848d211a9166f7292e5b005c64afd2f670f171bc Author: markd Date: Wed Sep 10 05:29:06 2008 +0000 restore wrapper script commit 33dc7eedf9d8e0a9d46cc5bf699674ecf0ac561c Author: kate Date: Wed Sep 10 04:42:21 2008 +0000 Enable automatic alpha ordering of same priority tracks when they appear in the priority.ra file commit 1faa9dc0fcc035a1f7b202e3e34b68d129150ed4 Author: kate Date: Wed Sep 10 04:40:49 2008 +0000 Fix alpha ordering of same priority supertracks by consolidating some code commit 6b5df2880b0ec399705530c60b327ad04539a1de Author: markd Date: Wed Sep 10 01:44:54 2008 +0000 fixed incorrect abort when cleaning up all connections commit 21eccc2189120e958ba1707e7f497cefb8ca01c3 Author: braney Date: Tue Sep 9 23:36:36 2008 +0000 HTML files for chains and nets to zebra finch commit f1b71afdb271e20c0615fc28ee3291dc6073cf38 Author: markd Date: Tue Sep 9 23:13:18 2008 +0000 added more checking for using deallocated connections commit 599959719af3a64bfee4176da1211a243f17a507 Author: markd Date: Tue Sep 9 23:12:42 2008 +0000 removed debug printf commit f10d275b2ca4e48972e58862745b55f26adb9a00 Author: markd Date: Tue Sep 9 23:11:56 2008 +0000 remoted free of connection that wasn't owned; fixed connection leak, tiny refactor commit 3e113ad3d14f0c8391ccc6571d628b9dd72a1e50 Author: braney Date: Tue Sep 9 23:11:44 2008 +0000 fix up to Mark db standards, use genePredReader, commit b3063144fc08aa3502c951d71a654c3e46dd8e26 Author: kuhn Date: Tue Sep 9 22:47:58 2008 +0000 commented out dbs on way to archive commit 693165abfbbeab90a915f73f3ed6df6692c52a6c Author: kuhn Date: Tue Sep 9 22:44:08 2008 +0000 removed errant space in oldKG longLabel commit 5b1fbd993ac8a8346cd0c056eb3734c0aae7917e Author: larrym Date: Tue Sep 9 22:01:05 2008 +0000 add more notes about removing scaffold copy commit 7ce71d907295038c5382779f8a49fdfceb490259 Author: galt Date: Tue Sep 9 21:59:09 2008 +0000 adding visiGene downloads-howto commit 35d56dfc6ad56eb1a4a2571ce9bb56265ffc1f81 Author: donnak Date: Tue Sep 9 21:26:01 2008 +0000 Changed Gerald -> Vanessa. commit f9af3652d191f529ef2f78c230e55d2815de0bb4 Author: braney Date: Tue Sep 9 21:22:45 2008 +0000 use genePredReader commit 08aa79674bd5b24459cf6d981b9a293e75f4d98b Author: braney Date: Tue Sep 9 21:21:26 2008 +0000 add exon frames if they aren't present commit 638716267024fdfe164c3a360a65540705422dbb Author: larrym Date: Tue Sep 9 21:07:00 2008 +0000 notes about removing duplicate scaffold_34 commit 93596999ae1f1c80fd5bea9db40687aba7d18fd4 Author: markd Date: Tue Sep 9 21:02:55 2008 +0000 fixed bug getting seq/extFile file from another table commit 1701cf3f9b0bdbafaa97b6e94022808242659bab Author: mikep Date: Tue Sep 9 20:54:58 2008 +0000 change function name from rangeTreeFile[Union|Intersection] to rangeArray[Union|Intersection] commit e5c2c518ecf839c608afc2b6690fa0db6da27da1 Author: mikep Date: Tue Sep 9 20:27:42 2008 +0000 library function moved from lib/genomeRangeTree to hg/lib/genomeRangeTreeFile commit 8a77204b68ebbc0ae7ab2681ce1b2c0f4e42b222 Author: mikep Date: Tue Sep 9 20:25:12 2008 +0000 baseMaskToBed function moved to library function genomeRangeTreeFileWriteToBed() commit 91808e2cf6ec2462b31e2da9010d00966831f335 Author: mikep Date: Tue Sep 9 20:24:21 2008 +0000 stats function moved to library commit 94078241485cdad84044106faffd0513413d7dbf Author: mikep Date: Tue Sep 9 20:23:49 2008 +0000 fix MYLIBS priority commit 368f54c40e8f66b59a7cfde908230dbee55bf727 Author: mikep Date: Tue Sep 9 20:22:53 2008 +0000 fix makefile to use MYLIBS variable commit 392715bb34e8f4ba31cc8e64549166dd54a22857 Author: mikep Date: Tue Sep 9 20:21:43 2008 +0000 add bed as an output format for rangeTreeFileUnion() and method to convert rangeTreeFile directly to bed file commit add194c4c1f8e4735c261262de3b9c2c00c8612d Author: larrym Date: Tue Sep 9 19:24:43 2008 +0000 redo equcab1->equcab2 liftover commit 379a77816f9b9ee341fd49b1801a2c7674712b0f Author: hiram Date: Tue Sep 9 18:34:06 2008 +0000 Create download files for the 5-way alignment commit 87d8f20076b1c7af93c3bb71cc6c8820f4a184c5 Author: fanhsu Date: Tue Sep 9 18:30:53 2008 +0000 updated vax003.sql. commit 03a08ef0a2dad712630d61eb7f4d5520dba54a6f Author: braney Date: Tue Sep 9 18:25:29 2008 +0000 some small changes commit 86cefe37c5e0118d180a2e0605d1b6d2275856ed Author: fanhsu Date: Tue Sep 9 18:15:22 2008 +0000 Added vax003.sql. commit fd63ef50f6964022573f31835b82aae49c5fcfc4 Author: kate Date: Tue Sep 9 17:49:32 2008 +0000 Fix DNA extended case/color configuration page to suppress hidden tracks lacking cart variables commit b24343c226d8ca8acc0b7ee3af31e0ca1657478b Author: fanhsu Date: Tue Sep 9 16:50:33 2008 +0000 Added trackDb.ra for hiva244. commit dd86028a434109f2875db59b4f6932f3f11733cc Author: aamp Date: Tue Sep 9 16:41:36 2008 +0000 Strand showing up as '.' commit 9343e21445f09514f97bda4eefb25e454ee8167c Author: mikep Date: Tue Sep 9 16:35:08 2008 +0000 using new caching connect commands commit 112341f123122d53255eab63aea61880432daa24 Author: markd Date: Tue Sep 9 15:26:39 2008 +0000 fixed null ptr deref when there is no RefSeq track commit c432058114797b7bb3b8924b3bae4a5b18e8a757 Author: markd Date: Tue Sep 9 15:00:46 2008 +0000 removed forgotten debug statement commit 8a8e9277633eb98a59082482e9671cb438e2bbbb Author: galt Date: Tue Sep 9 15:00:08 2008 +0000 "Encode release log update" commit 18e12abcddf0c35304fe99e489535066ab57458e Author: galt Date: Tue Sep 9 15:00:04 2008 +0000 "Release log update" commit 404920b1a1b6d423c9fb70b45f5213e88394daa0 Author: markd Date: Tue Sep 9 04:17:39 2008 +0000 fixed incorrect include (what was I thinking) commit 398b88ced322b5cec125036da44f816da9e825b8 Author: markd Date: Tue Sep 9 04:13:04 2008 +0000 fixed bug building list of databases when remote profiles are configured commit ce18f82592a2698ceb9e81135f2ae618dc5ae249 Author: tdreszer Date: Tue Sep 9 00:17:44 2008 +0000 I believe all is recovered and now I am adding sortOrder,dragAndDrop and controlledVocabulary commit b7307d55f38e7143084bc87141f16803a41dfa7f Author: braney Date: Mon Sep 8 23:36:03 2008 +0000 hgPal routines commit a18a69bf3213f8f4664bc5539f834566ee2090c9 Author: braney Date: Mon Sep 8 23:35:41 2008 +0000 add a parameter commit fdfbe28df84f2160997ac536d3972c0a7e69983a Author: braney Date: Mon Sep 8 23:35:11 2008 +0000 add another parameter commit 30dc40bb1bd0c9c354d5a260b529228a983341ea Author: braney Date: Mon Sep 8 23:34:54 2008 +0000 divide up some of the tasks of the wigMafUi so species selections is separate commit 3ad495938e7e2eea1baaaf0d5a2bed80ba73fb2a Author: braney Date: Mon Sep 8 22:28:38 2008 +0000 add hgPal technology commit e5bae913d94d2f78eb72830a2cb492346d54b7cc Author: braney Date: Mon Sep 8 22:27:06 2008 +0000 hgPal routines commit e8aa6b743c39f2dc899847c99e8cda5af02bdd5a Author: braney Date: Mon Sep 8 22:26:45 2008 +0000 work with Mark's new database setup commit 85653b62e17078a136a661b49f4f609533405aa0 Author: braney Date: Mon Sep 8 22:26:07 2008 +0000 add some functions for getting species list from maf trackd commit d2152bea234f620ceee94bfa842fd89a4d1b08e0 Author: kate Date: Mon Sep 8 22:01:15 2008 +0000 Suppress more hidden tracks (those without cart variables) from extended case/color options configuration commit f5c410f1945777dd00c724f2f043966941599af2 Author: braney Date: Mon Sep 8 21:59:00 2008 +0000 add some hgPal stuff commit a3f8edb8e36bdbb523de156e52bc92ca8f45788b Author: fanhsu Date: Mon Sep 8 21:39:24 2008 +0000 Fixed a typo. commit 793918e7b0025c99198004e4a98b56490ed612ca Author: larrym Date: Mon Sep 8 21:29:23 2008 +0000 add cv.ra to pushQ commit ccc2a43827c0301dd0340bd1d943fcc49072a21e Author: hiram Date: Mon Sep 8 21:14:34 2008 +0000 5-way track completely done commit 27c8d00ab1b4b9d05bccc86431647caec78b9967 Author: hiram Date: Mon Sep 8 21:11:20 2008 +0000 Have created the pushQ entry commit 78dd0670ecdd6ad44d155b6ddd5942ff2c49e00b Author: larrym Date: Mon Sep 8 21:08:49 2008 +0000 strip all non-alphanumerics out of track names commit abdf68b9258df16629961eed0b84983c6ed2e075 Author: hiram Date: Mon Sep 8 21:00:06 2008 +0000 Forgot this was a comma separated list commit 6a7bd665fdbd3b0cd6be88e752892840714bab58 Author: hiram Date: Mon Sep 8 20:57:01 2008 +0000 Adding oryLat2 to the mix commit a5f610536162dfea9aa3b830383173490783228e Author: mikep Date: Mon Sep 8 20:09:28 2008 +0000 moved rangeTreeFile and genomeRangeTreeFile to hg level because it will interact with bed stuff and tracks, etc commit bb0bfb449cb05bc102599bf5be899686e27b8994 Author: tdreszer Date: Mon Sep 8 19:54:40 2008 +0000 Added sortOrder, dragAndDrop and controlledVocabulary settings commit bd0ba5b428c95e806a7c7d7de17d4fa7ed991546 Author: tdreszer Date: Mon Sep 8 19:51:36 2008 +0000 Oops, select by term had a bug. commit 96ea94f864d9d286ae0081c4e72459139b0ff339 Author: galt Date: Mon Sep 8 19:49:50 2008 +0000 move visiGene data to hive commit 073da8a9c3cb92ff6932a8e35ccf0a481c966922 Author: galt Date: Mon Sep 8 19:49:09 2008 +0000 move visiGene data to hive commit 39ee58dce1d53bfdfcb9eeaa8c6ec7a060464665 Author: mikep Date: Mon Sep 8 19:36:50 2008 +0000 fixing up compile-time include errors after rangeTree was split into rangeTreeFile commit e04a015143c08be16cf3905b1fefa19a0a4e825c Author: mikep Date: Mon Sep 8 19:29:09 2008 +0000 split file IO operations into rangeTree and rangeTreeFile commit 17199cb888f1c486ed84ac6f0163d36a1e34eafe Author: mikep Date: Mon Sep 8 19:02:17 2008 +0000 split the genomeRangeTree and genomeRangeTreeFile stuff commit 25e193d905d19629f0c78186e21a050b079267da Author: larrym Date: Mon Sep 8 18:36:46 2008 +0000 tagAlign for ENCODE commit 28807708f8475b575fd6b6c9e1cbd19fb178b604 Author: mikep Date: Mon Sep 8 18:30:21 2008 +0000 split the File IO from genomeRangeTree to genomeRangeTreeFile commit fd0c89b9829faeec57921be2658079d933edcec8 Author: tdreszer Date: Mon Sep 8 18:22:04 2008 +0000 Fixed wigMaf visibility conundrum which prevented multi-view composite from supporting wigMaf commit 7ebfe73b8ed9534dd21e7d4b9d1994b47660f55e Author: markd Date: Mon Sep 8 18:20:38 2008 +0000 added option to disable All Tables in table browser to support collaborator commit 41c326e3979d70b3ef7853d67f5359ef7ac82228 Author: tdreszer Date: Mon Sep 8 18:08:37 2008 +0000 Added limitedVisFromComposite for wigMaf visibility conundrum commit 1522dc61a6bdc33ff85fc734dc3b6d50b1174f9d Author: tdreszer Date: Mon Sep 8 18:02:47 2008 +0000 Added limitedVisFromComposite for wigMaf visibility conundrum commit 1a034e5f8144536734fabeff588c60217219f528 Author: hiram Date: Mon Sep 8 18:02:23 2008 +0000 Properly null terminate the string copied into a linkedFeatures name field commit f9a12d55289b3a5ce7559848954712ecf7dba3e2 Author: tdreszer Date: Mon Sep 8 17:59:12 2008 +0000 More work on wigMafCfgUi and fix for subtrack cb state persistence. commit 07ad572b5b4d81f0b441dcd82ab7883b71b6dc23 Author: tdreszer Date: Mon Sep 8 17:56:51 2008 +0000 Streamlined some code on way to fixing subtrack persistence bug commit 42e6e28823118f103c45f59b55d6ef7fccb08c2a Author: fanhsu Date: Mon Sep 8 17:52:37 2008 +0000 Added pwdtest. commit aee979479d8b955712cc3e035ae7e1dbe425c077 Author: tdreszer Date: Mon Sep 8 17:51:21 2008 +0000 Added tier column to cells, ability to select single term, and multiple tiers commit 8fc4c475e6680f8edc5c8446eb708617f8a43c6b Author: kuhn Date: Mon Sep 8 17:49:00 2008 +0000 dropped s from end of Jackson Lab commit c911a0f109373aac76d83d3437b67d25d093bf9f Author: fanhsu Date: Mon Sep 8 17:42:26 2008 +0000 Updated again. commit c55655baadd35100d49e2231aa6ca2774ad181db Author: tdreszer Date: Mon Sep 8 17:36:55 2008 +0000 ra lib trips on commented-out cell line. Remove for now. commit a6f6e999e3211dceae5071514eded1d7881a7ff8 Author: fanhsu Date: Mon Sep 8 17:33:09 2008 +0000 Added more subdirectories. commit fc7794ec08864cba82ea917b4314641227044d7b Author: tdreszer Date: Mon Sep 8 17:26:09 2008 +0000 Four more cell lines approved by Resources working group commit fe837961803e4283e195138f2026c305648694ed Author: markd Date: Mon Sep 8 17:20:03 2008 +0000 change to pass database in changed function signatures commit 3bbe044ab35baf147b007111fd80007def410369 Author: fanhsu Date: Mon Sep 8 16:41:39 2008 +0000 Temporarily removed to avoid a conflict due to tableDescription script. commit d6326135c593833154944786d24eec133d0e42be Author: hiram Date: Mon Sep 8 16:39:32 2008 +0000 Done with phastCons5way and multiz5way business commit 5ff996fdeb2807645e74730fadab02f69520f0f1 Author: fanhsu Date: Mon Sep 8 16:36:53 2008 +0000 Moved from kent/src/hg/lib for the time being to avoid a conflict problem due to tableDescription. commit 69e130cdc7a5c05e3293147a9604c6f6c20eac43 Author: fanhsu Date: Mon Sep 8 16:05:04 2008 +0000 Updated to accomodate Mark's new remotDb change. commit 53061ddff53c472937e58b024f963f02c6b51034 Author: fanhsu Date: Mon Sep 8 16:00:55 2008 +0000 Updated to be compatible with Mark's new remotDb change. commit f6048d1b282d9dcc89c1647205bd676c99843772 Author: galt Date: Mon Sep 8 15:00:10 2008 +0000 "Encode release log update" commit 099adb20432004f36315918b8cf47e27c2fa11e2 Author: galt Date: Mon Sep 8 15:00:04 2008 +0000 "Release log update" commit 487d9a65c5efea5188e894deee5f7e2a31adf875 Author: markd Date: Mon Sep 8 07:45:14 2008 +0000 fixed missing parameter not detect by compile commit 501460019654560ee52b17f560aebe06cd380545 Author: markd Date: Mon Sep 8 03:55:58 2008 +0000 fixed outdate, fs specific path commit 967348ee9485fcb61de03f34355ab853b1b9bd26 Author: braney Date: Sun Sep 7 18:16:26 2008 +0000 re-do blastz to finch commit 2e035ecdd8d9f49679e3e00d4089d1762447199f Author: braney Date: Sun Sep 7 18:15:49 2008 +0000 re-did swaps of blastz to chicken and human, also human proteins track commit c47d8f7c843d7ef4c24203be48fcadee48767ac8 Author: braney Date: Sun Sep 7 18:12:46 2008 +0000 add support for lifting protein psl's when liftSpec is on negative strand commit 9a9e7c177ad5acb60811193f1c17634d625372ac Author: galt Date: Sun Sep 7 15:00:08 2008 +0000 "Encode release log update" commit ccb24c80aec3d118d83b91451a573fbc6ebb1177 Author: galt Date: Sun Sep 7 15:00:05 2008 +0000 "Release log update" commit cb76e0e0bd68d224e53f96a2f5419e7c384fb5da Author: markd Date: Sun Sep 7 04:39:10 2008 +0000 fixed typo in last ingore entries commit 5fb044ccce11fa44411ffacf786601f461a690fc Author: markd Date: Sun Sep 7 04:35:26 2008 +0000 added ignore entries commit 3685f680793179d3d62c19b15222190c9a8e460c Author: markd Date: Sun Sep 7 02:30:19 2008 +0000 copied mgc genes HTML so psl tracks will pick it up commit 0cecc96fb846c845939e96fac30b672f54e4f7dc Author: markd Date: Sun Sep 7 02:24:23 2008 +0000 fixed table name for alpha version of mgc genes as psl commit 14cec8e91e6ed18f4f3853cf4e674388f58bb7b4 Author: braney Date: Sat Sep 6 19:28:00 2008 +0000 some code to build hgPal links, remove archaic code now causing problems with protein alignments commit e69d865ff7e8fcf5bf23e507632cd185b7774e20 Author: galt Date: Sat Sep 6 15:00:06 2008 +0000 "Encode release log update" commit e2cc71572695cfda520ce86666233eaad975013b Author: galt Date: Sat Sep 6 15:00:04 2008 +0000 "Release log update" commit 8cda43a5c0e4e381aa502fbbd1193408599abfa7 Author: markd Date: Sat Sep 6 04:06:52 2008 +0000 Fixed bug getting list of all databases that crashed the table browser. commit ca0d6936456e2de7d06a8ccdfb410674464fb135 Author: galt Date: Fri Sep 5 22:52:53 2008 +0000 some more comments added commit f4badaa6216954b87de2990a9c48c054acb5ca79 Author: galt Date: Fri Sep 5 22:36:14 2008 +0000 making ftp info on upload form more friendly commit 54b00ef976f8c5993e1adb19d8fd28578f6688dd Author: galt Date: Fri Sep 5 22:35:06 2008 +0000 proper handling of to-be-customized sample stop script commit 886a6f970138d9c363c613de4615c1e15f0887c7 Author: markd Date: Fri Sep 5 22:21:03 2008 +0000 moved cvs-reports-d to weeklybld/cvs-reports-delta and removed obsolete scripts commit d66644bf98716a6aee25d4dc9d4353b5454404dd Author: mikep Date: Fri Sep 5 22:06:01 2008 +0000 cvs-reports-delta has been moved to this directory commit efde101188c30d9ebeb333eb102f9c44e1b78eac Author: hiram Date: Fri Sep 5 20:26:24 2008 +0000 Thoroughly turn off this makefile, the code is no longer valid commit 9f78e4ba1a82f6fdb1ab2b6a7b685e19418ba070 Author: giardine Date: Fri Sep 5 20:22:35 2008 +0000 Fixed bug that hide ORegAnno track items on initial display commit d999ceae754b6bdb5c070d86bcf4bd084f7e7797 Author: aamp Date: Fri Sep 5 06:14:43 2008 +0000 Mentioned by Larry to fix. '.' names suppressed and "P-value" changed. commit 32587ea93467462b199c907fcb9e4b26680e03d6 Author: braney Date: Fri Sep 5 00:23:14 2008 +0000 chains and nets to zebra finch commit e7d02ab2a049dcce9ea57f093b9b6d0dd08169eb Author: braney Date: Fri Sep 5 00:20:35 2008 +0000 chicken and human alignments commit 44913ddcc01e5d1f9ce52387624eda06af71107f Author: galt Date: Fri Sep 5 00:07:43 2008 +0000 clean up old unneeded comment commit 405cd3dc7b85755ff93748b1c675c471c2ea584b Author: braney Date: Thu Sep 4 23:02:15 2008 +0000 add zebra finch chain and net tracks commit d4c35aeb53c5895025cdfb9579ed5eeac1282026 Author: braney Date: Thu Sep 4 21:31:04 2008 +0000 swapped chain with chicken commit 0bda7630384f852f34bb42eca71ab6817789349c Author: galt Date: Thu Sep 4 20:05:43 2008 +0000 making the new optimized threaded version the default target commit dd2be8398a8bfa40f442eca79132d3df0f977b6d Author: galt Date: Thu Sep 4 19:31:23 2008 +0000 optimizing the qsort compare commit 5500ff308f6a01203666a38d7c9d42b0e5c22b28 Author: larrym Date: Thu Sep 4 18:54:55 2008 +0000 remove extra newline after comment (which screws up our ra parser) commit 6310332ea714a78c9c3410bca472660f34cc9441 Author: larrym Date: Thu Sep 4 18:51:26 2008 +0000 CV_FILE => cv_file(), which looks for file in cgi-bin/encode commit 2d8d587935e21cd6dc349212d1b15679699247fc Author: larrym Date: Thu Sep 4 18:21:57 2008 +0000 add encode/encodeValidate to cgi rule commit aec11f68fe9d6e056588a7eae7b0a0ffd95735aa Author: larrym Date: Thu Sep 4 18:17:34 2008 +0000 copy cv.ra to the cgi-bin/encode commit dcef55933a6ba60d138e15ebd39cdeafca196a08 Author: ann Date: Thu Sep 4 17:40:28 2008 +0000 moved a couple of commands into their proper place commit 282b15fc537bf241c4d0a011729073a40edf2fa2 Author: mikep Date: Thu Sep 4 16:24:29 2008 +0000 use the new hdb and jksql routines commit a50d3a18f9e4dcd0d02c6155effe0d5e1bf617ff Author: braney Date: Thu Sep 4 15:07:54 2008 +0000 prepare for blastz runs commit 5fe34a4917c6e150257199b6e9917a3cd4e88c9d Author: braney Date: Thu Sep 4 15:07:35 2008 +0000 add blastz to zebra finch commit 325bca934d627c312186a2a46ac689aed1592054 Author: galt Date: Thu Sep 4 15:00:10 2008 +0000 "Encode release log update" commit d99dcb8047a416149e337a9f81e4d1d9ed39758a Author: galt Date: Thu Sep 4 15:00:04 2008 +0000 "Release log update" commit 802d35f583910cb840ca08f2d4332c879f0b76cc Author: tdreszer Date: Thu Sep 4 00:16:04 2008 +0000 Fixed a bug in composite subtrack display. commit 966318d9a7f06ca9609fdbf89785fb2048e706d7 Author: kuhn Date: Wed Sep 3 23:38:37 2008 +0000 added mrk's name to Transmap credits commit dd819d724d7a5ea0a340de12b0b7290d133deedf Author: larrym Date: Wed Sep 3 23:14:06 2008 +0000 fix typo (pid => qid) commit 87de5e7100ccbc86936c65b26c78d1c0a5c16260 Author: mikep Date: Wed Sep 3 21:53:48 2008 +0000 libified commonBaseMask.c into hg/lib/baseMaskCommon commit 677d7b620ffb8321b299a8cdf8b870662db1a9f1 Author: markd Date: Wed Sep 3 21:13:03 2008 +0000 comment on obsolete option commit 2361fa6e1e4e03ea905d503e18a52244fc7f3385 Author: jsanborn Date: Wed Sep 3 21:04:42 2008 +0000 added van de Vijver 2002 dataset commit 9fee84491682d8ceb777e7fa7f3cd1c93708411d Author: markd Date: Wed Sep 3 20:33:49 2008 +0000 fixed warning commit b7cca1d9fe8364959e4d10af7591ad3be7cbf321 Author: markd Date: Wed Sep 3 19:21:53 2008 +0000 removed global databases from CGI library; implemented abilility to have remote genome databases commit 90e15db05032ec7c7091d9feda365d03ad7317e0 Author: aamp Date: Wed Sep 3 17:32:27 2008 +0000 Recent updates to description. commit 948a497218af2da9211a0de5f417e3a4e37217cf Author: donnak Date: Wed Sep 3 17:22:58 2008 +0000 Hyphenated GIS-PET, per Rachel. commit f7a2cee2069d9919293fd7cfca1f4b468ec19efd Author: mikep Date: Wed Sep 3 15:45:44 2008 +0000 donnak and kate are in browser-qa list commit a5664104f3931c6bb46c008e5b18539a13d71066 Author: galt Date: Wed Sep 3 15:00:06 2008 +0000 "Encode release log update" commit 11aeab50eff5ec374edf5d0699c0aa69ad7d8681 Author: galt Date: Wed Sep 3 15:00:03 2008 +0000 "Release log update" commit c01bd1fe77e7deb12e5b45004e2abd3b32cb1b47 Author: mikep Date: Wed Sep 3 09:42:47 2008 +0000 added donnak and kate to notification commit cfb5acd1c4102a0fc83765a5ac6d6e58a1224698 Author: mikep Date: Wed Sep 3 09:42:26 2008 +0000 fixed split line commit 739961593851b7596959f72398bd615a3f3c123b Author: mikep Date: Wed Sep 3 09:28:19 2008 +0000 fixed to not remove the gbWarn text for log readability commit 354ed8b6d0a5b12f6678d9ce46bcc3106938d135 Author: donnak Date: Tue Sep 2 23:13:57 2008 +0000 Adding a reference correction I forgot to commit eons ago. commit 334446dadf0158d5e118ac84412dbbbb2ed3a28f Author: donnak Date: Tue Sep 2 21:58:03 2008 +0000 Corrected some GIS acronym expansions, removed others, per Rachel. commit de4cec39cb1530ffdda3aba336367487ff02def2 Author: tdreszer Date: Tue Sep 2 19:06:27 2008 +0000 Fixed Sort comlumn TODO and subtrack show/hide by js when id was not unique. commit f4e2a028302f441f027748993906b167da687fbf Author: mikep Date: Tue Sep 2 18:52:47 2008 +0000 latest build commit 43d1d5777ef938735db736b2a8e0cd51b32a8598 Author: mikep Date: Tue Sep 2 18:52:21 2008 +0000 program gbWarn.c trips the error check commit 926afb178844928321ef0a2f1a93a4552fe9af12 Author: larrym Date: Tue Sep 2 18:25:38 2008 +0000 add PSFK-1 and SK-N-MC (which are submitted and pending approval) commit a674c9a7f106f5a67a82ce3961fab5ecdeacb1c1 Author: larrym Date: Tue Sep 2 18:09:30 2008 +0000 convert mac => unix EOLs commit 3b5b44b2303ec8eecded938b3ca7a36a0f0f4477 Author: tdreszer Date: Tue Sep 2 17:47:45 2008 +0000 Remove single 'view table 'schema link on composites, since each subtrack gets its own link. commit 8454f534c3408b5fbd4d094581e640ec0f6a5b3e Author: tdreszer Date: Tue Sep 2 17:46:17 2008 +0000 Divorce sort,dragAndDrop and matrix dependencies. commit 3580fb14fb82e34706f02f24a63665f1c7b74026 Author: tdreszer Date: Tue Sep 2 17:45:11 2008 +0000 Suport work for divorcing sort, dragAndDrop and matrix composite track dependencies commit 6063edadd8102af0d53f402bc81a7eb761e9ec26 Author: tdreszer Date: Tue Sep 2 17:43:08 2008 +0000 Support for divorcing sort, dragAndDrop and matrix commit 242fe4a7b5bad5ff90cbe1a4e10da403e60edaa6 Author: rhead Date: Tue Sep 2 16:41:11 2008 +0000 Fixed broken link to Broad. commit 2a75fc89731472aea7e1e5254dfa035ea5f81359 Author: mikep Date: Tue Sep 2 16:29:10 2008 +0000 "New version number v190" commit 69e4f364738ae74e62abc5071506e05fb16dff49 Author: galt Date: Tue Sep 2 15:00:03 2008 +0000 "Encode release log update" commit abbb1ff5bc5c84e77643142ce74ac52a3e6ae5c7 Author: galt Date: Tue Sep 2 15:00:02 2008 +0000 "Release log update" commit 3fcc5718f0d71ddf5577f47b962a75dce118e0a7 Author: galt Date: Mon Sep 1 15:00:04 2008 +0000 "Encode release log update" commit 08bb9d60ffeaba11836a513aa4c961099b8b9e91 Author: galt Date: Mon Sep 1 15:00:02 2008 +0000 "Release log update" commit 0531370bea456ef78bb59871599e1c0bf1023c8b Author: galt Date: Sun Aug 31 15:00:03 2008 +0000 "Encode release log update" commit 614803fc1a390bf4dfb1ec68b2593862c0bb7e91 Author: galt Date: Sun Aug 31 15:00:01 2008 +0000 "Release log update" commit 5f35febab7ee1fe197132e79d35e3be5cc710a76 Author: tdreszer Date: Sat Aug 30 16:28:49 2008 +0000 Fixed missing param from call to hCompositeUi() commit 54c13ea59c6936bd2a70fc1a1a37abc7dfb82931 Author: galt Date: Sat Aug 30 15:00:07 2008 +0000 "Encode release log update" commit 93b7fb546d18473307d73c432ffd682e25c0de49 Author: galt Date: Sat Aug 30 15:00:04 2008 +0000 "Release log update" commit ef32b118fe09ea60053f6cc97a116c3a86c9448d Author: markd Date: Sat Aug 30 04:04:52 2008 +0000 major cleanup; fixed problem with branches being included on trunk report; add support for branch reports commit 41bc938e76359019e83a62ccd1543893578deaa3 Author: kent Date: Fri Aug 29 23:08:45 2008 +0000 Updated C. elegans link to point to ce6 commit b6042a00004bd0188b36c623c6d547124b3c23e8 Author: donnak Date: Fri Aug 29 22:44:03 2008 +0000 Fixed incorrect acronym expansion for GIS, as reported by Rachel. commit 07773fc22e52f8ff689b83b14ca12f7f1a1f5a4d Author: pauline Date: Fri Aug 29 22:36:25 2008 +0000 Re-fixed broken link. commit 8cb910c587886cf6cc9e0a1e1181674b176b4541 Author: kate Date: Fri Aug 29 22:25:20 2008 +0000 Reverting -- 'easy' fix to problem with multi-view causes other problems commit fa2141b1809d567e0ea071f2d031559037010774 Author: larrym Date: Fri Aug 29 22:17:24 2008 +0000 improve priority logic by using existing subTracks of compositeTrack and the order of views in the DAF commit 7adab1463a63fbb3eabfffd99ee51d346e92ace4 Author: larrym Date: Fri Aug 29 22:16:10 2008 +0000 add quickQuery commit d15bf09aed9c0fa79827e60cac256cffdb706ec2 Author: larrym Date: Fri Aug 29 22:00:27 2008 +0000 remember track of order commit 100d4899195710c8df307f3a65565ec2e4ddfbb3 Author: kate Date: Fri Aug 29 21:28:19 2008 +0000 Support for wigMaf in multi-view composites commit 057395b8c293cf793fbd4809844add3a1d51e8b6 Author: kate Date: Fri Aug 29 20:56:40 2008 +0000 Fix to problem during multi-view commposite use commit daca765dd9746c97207336f6bf30a600b3680864 Author: kate Date: Fri Aug 29 20:56:11 2008 +0000 Move wigMafUi to lib to enable support in multi-view composites commit ec5e7d432542d8faac2b36a512d78335b600623e Author: kate Date: Fri Aug 29 20:55:04 2008 +0000 Support for wigMaf tracks in multi-view composites. First cut commit 131806b1402b4d4bcb15d666cf690d4b45baa9e3 Author: kuhn Date: Fri Aug 29 20:25:30 2008 +0000 data were commit a30d2ec8f36b9907b8cb32100fc88ba9718cb31b Author: larrym Date: Fri Aug 29 20:25:01 2008 +0000 copy over .sql files commit 1fabaac96172e72f58f9b6f148ab42ccf97b8d11 Author: larrym Date: Fri Aug 29 20:24:47 2008 +0000 copy of .sql files commit 3fb55b5db47f056f82e2dbc93c1ad522d98f534d Author: lslater Date: Fri Aug 29 20:01:40 2008 +0000 Timing versions of original and multi-threaded hgExpDistance. commit 777048ef12f57b833f6ca4ee93cbc6998f750d0c Author: lslater Date: Fri Aug 29 19:59:30 2008 +0000 Checks for existance of two DB tables and examines differences. commit 3a127456297fb4e9256387fb8065edb34bffa611 Author: lslater Date: Fri Aug 29 19:55:56 2008 +0000 No pthread_exit() to prevent DB write. Timings/tests in makefile. commit 79d6c821b037e80fd8fccb26f741642beb82d568 Author: larrym Date: Fri Aug 29 19:36:24 2008 +0000 pairedTagAlign for ENCODE commit cd5d9161c67d8bea77dcfc2f84e88c07f8278252 Author: kent Date: Fri Aug 29 19:19:09 2008 +0000 Making it so that hgGene can search an alias table (by default kgAlias) if it doesn't find hgg_gene in the main gene table. commit cac95b9a8fa89f42a8c8cf3f2a0a50ccaf122321 Author: kent Date: Fri Aug 29 17:44:19 2008 +0000 Relaxing minimum overlap size with best pick from 90% to 50%. This allows in particular swissProt annotations of genes that are defined by RefSeq to be larger to still be attached to the UCSC genes. commit 6781528be716ad5477fe20906beda5a628abebe4 Author: ann Date: Fri Aug 29 17:31:46 2008 +0000 rule to capture relationship between the previous version of UCSC Genes and the cross-reference table. commit e0f7d7eb018d1d74041fb77f4a5729e496eaaa3d Author: braney Date: Fri Aug 29 17:27:59 2008 +0000 added genscan track commit ba02a43fc98824e952651eca7e22bb543662138e Author: ann Date: Fri Aug 29 17:23:36 2008 +0000 fixing previous attempt. it worked on dev but not on beta. using a more sure-fire method of connecting to the description page. commit c40ef412d39fa984d6008190268c5a41b6eaf996 Author: larrym Date: Fri Aug 29 17:14:18 2008 +0000 allow antibody to be eq 'input' or 'control' commit dfd26a0e07d0540d847784003bc9617640bbdf37 Author: ann Date: Fri Aug 29 17:12:40 2008 +0000 added link to current UCSC Gene description page commit ec9ac9dba704f28d101f1d7d3e821499dd04d4ad Author: kent Date: Fri Aug 29 16:52:54 2008 +0000 Adding script from treefam folks to assist in mapping known genes to treefam (via ensembl). commit ee96fc206ab3a07501c1def03763b929801f0964 Author: galt Date: Fri Aug 29 15:00:06 2008 +0000 "Encode release log update" commit 0fc9345b4732e8fcf115fa5cc962605ddba7f092 Author: galt Date: Fri Aug 29 15:00:04 2008 +0000 "Release log update" commit 7ab0b40ae62e2b1f5e47b150c268df4b76a1acfc Author: kent Date: Fri Aug 29 01:37:00 2008 +0000 Adding old ids to alias tables. commit eefa5c2b0d5ab86acaa0a7437a354fd057f71c25 Author: kent Date: Fri Aug 29 01:36:48 2008 +0000 Adding old IDs to alias tables. commit 1c23b5579262fc6b3a97bfdd8945b471918b0399 Author: tdreszer Date: Thu Aug 28 23:31:58 2008 +0000 Initial checkin commit 7f29879021dada0f3053560bb6815f47084ab5f6 Author: tdreszer Date: Thu Aug 28 23:30:39 2008 +0000 Minor changes commit b8edab57d6d3de2690bd3ce2fa17c713dd8e6f74 Author: mikep Date: Thu Aug 28 23:11:15 2008 +0000 refactored code into library; handled different chromInfo db and table dbs correctly commit 57c31271a6553287c9930e3eb146e64130a7353f Author: mikep Date: Thu Aug 28 22:49:27 2008 +0000 function to scan genomeRangeTree file and output num chroms, nodes, and total range size commit ab536dd2686763c7de64b81e47d1181cf8b8098b Author: fanhsu Date: Thu Aug 28 22:11:42 2008 +0000 Updated URL for H-Inv. commit 4ab4d02450a036b42619cafc05d88f22e1340879 Author: mikep Date: Thu Aug 28 22:01:09 2008 +0000 report the difference between ERROR and EOF commit b5b2d937de0953e932b6d5e427909fd9ae50d7f2 Author: hiram Date: Thu Aug 28 21:18:59 2008 +0000 Done with oryLat2 blastz runs commit 2f433e9ea75ae299915251ffdcbd2566e3183cd1 Author: pauline Date: Thu Aug 28 20:36:20 2008 +0000 Fixed broken links. commit f8980a91258377f59ad9d29a7215d6b6d84a20fd Author: tdreszer Date: Thu Aug 28 20:27:30 2008 +0000 Since negative signal densities been removed as no data, 'non-negative' verbage is confusing. commit 940babd47f8a82ab04ec6485d066b92cabd16bce Author: hiram Date: Thu Aug 28 19:12:29 2008 +0000 Setting order for oryLat2 chains and nets commit 98322bcd63a2f0749c08222c81a175f4b9c50676 Author: hiram Date: Thu Aug 28 19:07:59 2008 +0000 Setting the order for oryLat2 chains and nets commit 861f1eb6bc993c37fff4c326734a98cb3d820a73 Author: hiram Date: Thu Aug 28 19:04:18 2008 +0000 Setting the order for the oryLat2 chains and nets commit cbbd54eaf276bef30c0ba8d93a1760a8df8dfc72 Author: hiram Date: Thu Aug 28 18:56:16 2008 +0000 Adjust priority for oryLat2 commit e85381500739392fb3c415a3ea3e5ede207162d1 Author: kuhn Date: Thu Aug 28 18:53:10 2008 +0000 made new line for caeJap1 in nativeEstAccession to allow for non-split tables commit 8a272fb3c2634261c3f053d8a0b964382328a05a Author: hiram Date: Thu Aug 28 18:46:48 2008 +0000 Setting order for oryLat2 commit 7416e7a7783dba883423341b9cf92af06a4f6d92 Author: hiram Date: Thu Aug 28 18:30:42 2008 +0000 Setting priority on oryLat2 commit ba34fc65e688263064721f6bda6c72a71be2760a Author: pauline Date: Thu Aug 28 18:17:54 2008 +0000 Fixed broken links. commit fce747b6e89e8c491ab0d8f41917618a7077b435 Author: hiram Date: Thu Aug 28 18:02:01 2008 +0000 Turning on oryLat2 chains and nets for the other orgs commit bc40586a71edea37601092b740e03c335c4651e0 Author: kayla Date: Thu Aug 28 17:51:00 2008 +0000 added taeGut1 commit 4402a1ecf5328e55936e89ffb553c155008bfdf9 Author: galt Date: Thu Aug 28 15:00:06 2008 +0000 "Encode release log update" commit 45f29488adeb8e48935ac504e7ad170a10dfc502 Author: galt Date: Thu Aug 28 15:00:03 2008 +0000 "Release log update" commit e54b7809218504a7b6f412751355f51935b90c03 Author: mikep Date: Thu Aug 28 12:22:19 2008 +0000 fixed to update cache file rather than keep old cachefiles, and work from cache file time stamp rather than time in the file name. Also made default usage message nicer commit 7e822ece933fefd24b2251cda3b630dbbe0fcc2d Author: tdreszer Date: Thu Aug 28 06:20:52 2008 +0000 Turning on subtrack sort and dragAndDrop for the first time. commit 3140c07b5d9915d4693563618297cb3ffddd0ca6 Author: rhead Date: Thu Aug 28 01:20:21 2008 +0000 Fixed broken link to build statistics page. Couldn't find replacement for 'finished' link commit 1418a8b256aa0dbd048fb949316c78381106c538 Author: rhead Date: Thu Aug 28 01:19:51 2008 +0000 Fixed broken link to build statistics page. commit f7f1fab678a417faf0ae5aecca094b17e6fdb313 Author: galt Date: Thu Aug 28 00:19:24 2008 +0000 updating new location on hive commit 2b2305d7a3d4900e7544436a41df3aba736bdf64 Author: rhead Date: Wed Aug 27 23:20:16 2008 +0000 Changed link to Ariel Schwartz to current location at UCSD. commit 88e943816985785d6b1c79c5320d26e3dd11106f Author: kate Date: Wed Aug 27 23:06:37 2008 +0000 Remove obsolete line commit fffec7dc909146dfe97f6084c04a3d71f18207d2 Author: rhead Date: Wed Aug 27 23:05:06 2008 +0000 Fixed link to Adam's recomb2004 paper. commit f86a65471ad10ac225e74dd349237a74d50ae52f Author: ann Date: Wed Aug 27 23:04:53 2008 +0000 removed dependence on store9 -- switched to hive commit 8da36b7a9412b264b991ab7ea25c3f877335fa04 Author: kent Date: Wed Aug 27 23:02:15 2008 +0000 making it compile under new gcc, fixing a nominal bug in process. commit c3e7422e51093bca9e562a059759a979472ae97a Author: kent Date: Wed Aug 27 23:00:40 2008 +0000 Adding some verbosity for debugging purposes. commit 9e1bab3cc0ece87d8b235e6ff189577c38689985 Author: kent Date: Wed Aug 27 22:38:24 2008 +0000 Adding probesDb option. commit 71f7251ae8fb4328dac9feeb673d146cea105529 Author: kent Date: Wed Aug 27 22:35:33 2008 +0000 Moving fopen/fclose to mustOpen/carefulClose for better error handling. commit ad467b6d6f9a96c4b9c98173374032551dc05d6c Author: kent Date: Wed Aug 27 22:35:00 2008 +0000 Putting in check on buffer overflow commit b7b89786f6de3097961aba75ba1e36dddeed7c5b Author: kent Date: Wed Aug 27 22:34:32 2008 +0000 Fixing error message. commit 7b774f1ded1e1329b5dff4ba9e010efb0fd62103 Author: kent Date: Wed Aug 27 22:34:06 2008 +0000 Testing chromBins. commit a3630b4d22bf604a0cc46f800ce4b55494f2a3f4 Author: kent Date: Wed Aug 27 22:28:14 2008 +0000 Adding table descriptions commit cafa0adcd30c0b53c514316ca889498c3fa76a61 Author: kent Date: Wed Aug 27 22:27:41 2008 +0000 Adding a few more changes done for the known genes rebuild. commit 9e3b2fd1bda3f15ce5254374db807f76fe1ef6dd Author: kent Date: Wed Aug 27 22:27:13 2008 +0000 Adding knownToHprd commit c02d190d036c71eb97df22c6321e855be7a9c184 Author: braney Date: Wed Aug 27 20:57:35 2008 +0000 pad out alignments commit f5f0835b1061372883643d409c1961f7bf713ce9 Author: kent Date: Wed Aug 27 20:56:00 2008 +0000 Adding comments to point Mike to where to start. commit 894a1bf82ec1d9d55d046eab7667e6870c7fae39 Author: donnak Date: Wed Aug 27 20:13:52 2008 +0000 Updated citations, added ENCODE. commit 135f58ffb26b4da1fd612510e09ba99f6fd3dd04 Author: mikep Date: Wed Aug 27 19:44:51 2008 +0000 added bob to the list of emails commit cec3a1f170c4232587298669c672b752fa907249 Author: mikep Date: Wed Aug 27 19:25:30 2008 +0000 send an email to notify this step is complete commit 515c71a51fe0f0120dbd62c083108fcedf041370 Author: tdreszer Date: Wed Aug 27 19:19:38 2008 +0000 Support for users changing subtrack priorities by sort/dragAndDrop commit be205ff4ff6554281b6a67c396465d025ac75ced Author: tdreszer Date: Wed Aug 27 19:13:35 2008 +0000 Added a function to sort composite subtracks by priorities saved in cart commit a2946365f02e06b845e78c3068af35a2f1ca5587 Author: tdreszer Date: Wed Aug 27 19:12:24 2008 +0000 Adding support for subTrack sort and dragAndDrop commit 88c2cd511cc77961ecc67522a9aa51a96aebc26b Author: tdreszer Date: Wed Aug 27 19:11:31 2008 +0000 Adding js for subTrack sort and dragAndDrop commit b96cd0f61a8b47fa4f0ff174a3c037c96e4ae3ae Author: larrym Date: Wed Aug 27 19:08:46 2008 +0000 scp js files commit 03ccc7d6b8150448c4d8100b2d1c88ea00e27b2e Author: kent Date: Wed Aug 27 19:06:12 2008 +0000 Making it catch all fields with an identifier, not just first. Adding some examples to doc. commit 46a92846e026b9520b67b3558111e0acc5bf9dfb Author: kent Date: Wed Aug 27 18:45:33 2008 +0000 Adding dbFindFieldsWith to makefile. commit 0ab97da41ccd1c3e11aa764e82990388ccadec53 Author: kent Date: Wed Aug 27 18:20:53 2008 +0000 Updating handling of kg3ToKg4 and kg2ToKg3 tables in light of new build of known genes. Also making minCheck of cgapAlias match expectations. commit 60158d0c9106276cd2ec5874d7b7340a0a8bf547 Author: kent Date: Wed Aug 27 18:00:21 2008 +0000 Removing humanNormalDistance table. commit acd023899d95b5445cad9103af147c76c3b28877 Author: kent Date: Wed Aug 27 17:55:30 2008 +0000 Commenting out info on non-longer-updated pseudoGeneLink which never made it to round robin. commit 57180166306441e9d1b677eba1f0f307a89769e0 Author: kent Date: Wed Aug 27 17:49:26 2008 +0000 Putting up 'no protein' instead of a blank in the sequence and links table for noncoding genes. commit 550c9f149a953168ef06ce19bc9851b7f24ade5b Author: mikep Date: Wed Aug 27 16:25:57 2008 +0000 fixed up to use code from hgTables.c to determine chr*_table commit 04838fa933f600c7e24247145bc9ee7ec931c44f Author: galt Date: Wed Aug 27 15:00:06 2008 +0000 "Encode release log update" commit c64579dee475f0d19ee877dd14ad4e2cf8dac77e Author: galt Date: Wed Aug 27 15:00:03 2008 +0000 "Release log update" commit 9eff95b0f8d02ab0513b16ecce1feff8f20a7903 Author: mikep Date: Wed Aug 27 08:28:06 2008 +0000 new program like baseMask which will cache tracks as bama files and process them. commit 9d58b1a04144164847ecef321cee31bcd787f3f9 Author: markd Date: Wed Aug 27 03:40:13 2008 +0000 - support mgc tracks to be either PSL or genePred (temporary) - remove unused mgc code and track config - use PSL tracks for MGC only on hgwdev commit 737d37113395696ad4649a84856167841ceaa545 Author: larrym Date: Wed Aug 27 00:06:19 2008 +0000 add pipelineDb and projectDir commit 908502ae0dde4b9d4775dbd1e5eb13b64eb4e926 Author: galt Date: Tue Aug 26 23:35:38 2008 +0000 added automatic retry for pmSendString and sickBatch; also added extra info to Strange time in ... message; fixed typo in usage message commit 6a3f941498a5aeaf7e29db11e62c56da519dea16 Author: larrym Date: Tue Aug 26 23:32:53 2008 +0000 put line feeds in pushQ files and tracks entry; replace temp file code in loadBedFromSchema with hgLoadBed ... -renameSqlTable commit 9df3d4a498855f34b33c97d2e098b5321597c3e7 Author: donnak Date: Tue Aug 26 23:25:15 2008 +0000 Fixed up some links. commit 03e86e5d7554cd7fd7de79decad06798147236c5 Author: larrym Date: Tue Aug 26 22:57:20 2008 +0000 add pushQDescription to load.ra commit f5f2c99d0172b26eda90c878f451bd394cd6f11d Author: braney Date: Tue Aug 26 22:56:45 2008 +0000 add current database to orgs commit 6c71ca8bb089f06abd5ba5040c3f8f50c0f23b7b Author: larrym Date: Tue Aug 26 22:56:01 2008 +0000 encodePeak => narrowPeak commit f1262ef960b29e33644aafb000122f406d7986b7 Author: braney Date: Tue Aug 26 22:55:35 2008 +0000 some fixes... still need to get rid of warn commit 37ba3624236bed247cd0692f711b7d93be18fef4 Author: braney Date: Tue Aug 26 22:54:30 2008 +0000 add mafGene commit c8ea9c10e7e9a4b97b897a41254f1c5fc54f674d Author: braney Date: Tue Aug 26 22:47:52 2008 +0000 add some option bitmasks and change routine to handle them commit 4d1b4f8484f15b3eac5d428dc4a1045db01b32fd Author: larrym Date: Tue Aug 26 22:47:51 2008 +0000 remove lots of incorrect stuff; support install target commit eb560e808fc60bb05316f7db2aa7fdbcf6163b0a Author: larrym Date: Tue Aug 26 22:47:12 2008 +0000 add encodeStatus to PIPELINE_DIRS commit d902eeb8f05132419561df7ae05f331b1c3d4cd6 Author: larrym Date: Tue Aug 26 22:36:17 2008 +0000 print out pushQ command when status is changed to approved; simplify code commit b8ebe1d807b09af4e57e20c75884becf0fbc36b8 Author: braney Date: Tue Aug 26 22:25:12 2008 +0000 adding hgPal commit 79c51bea2e43543cf06fe51014a99d2c4c71dfcb Author: braney Date: Tue Aug 26 22:17:38 2008 +0000 a first cut.. sort of works as link out of refGene commit c25983aa82510ea9388616be5d4b905a1bd67ea7 Author: tdreszer Date: Tue Aug 26 21:48:02 2008 +0000 Removed reference to signal values of -1. These values represent no data and were removed. commit 895de278eae5e827e1b006fc3ac60901885e7bda Author: donnak Date: Tue Aug 26 21:34:28 2008 +0000 Added Pauline to zebra finch credits. commit c0744e9cb5109bbceaf38eb4f5a0bfabeb8f7ee2 Author: donnak Date: Tue Aug 26 21:33:39 2008 +0000 Edited taeGut1 credits. commit 22e263b0e3f6f0dd15c29164175117f76a64b4b8 Author: larrym Date: Tue Aug 26 21:28:34 2008 +0000 fix rank computation in pushQ creation commit c5ace234e6877b55a523ef8a124d07baf4ecc9d0 Author: donnak Date: Tue Aug 26 21:26:53 2008 +0000 Added news item about zebra finch. commit d5fc467cf9f68211cbccb74b6f0e30cf20b13328 Author: larrym Date: Tue Aug 26 21:12:49 2008 +0000 lots of changes to wgEncodeHudsonAlphaChipSeq commit 00bb630f9c81a791838cb2cba9409631f839504e Author: donnak Date: Tue Aug 26 20:52:23 2008 +0000 Updated zebra finch entry. commit fe7871ab9e761ce41dd374fb2c85d9372a5468db Author: tdreszer Date: Tue Aug 26 19:26:43 2008 +0000 Wigs in Dense mode were not recognizing limitedVis commit c9f7b4d6e0af7197a5ade0fc94b674c9c4e23f05 Author: tdreszer Date: Tue Aug 26 19:23:34 2008 +0000 Insignificant wrapFont change commit db522ed82c9f73188b6e9f8cddfa8002e6d278c4 Author: tdreszer Date: Tue Aug 26 19:21:00 2008 +0000 shortLabel Name changes to fit leftLabels commit 8439c8725d3e0641e414eef10f48e91620781749 Author: tdreszer Date: Tue Aug 26 19:15:54 2008 +0000 Defaulting to the production ra files commit 0f85861171a0a1f974f7571805f1c189a941b4b4 Author: tdreszer Date: Tue Aug 26 17:52:36 2008 +0000 Added newly approved teir 3 cell line GM18507 commit b96c825854e18c846f88c446a1702b3e46db7610 Author: hiram Date: Tue Aug 26 16:20:01 2008 +0000 Indicate how to build utilities as well as CGI binaries commit 6fc11c71e1605ce4cdd3708edaac71cbf75a8ae7 Author: hiram Date: Tue Aug 26 16:19:31 2008 +0000 Indicate how to build utilities as well as the CGI binaries commit 4dab9697deb4ca64f6667cd8e630ee52156fa9fb Author: galt Date: Tue Aug 26 15:00:06 2008 +0000 "Encode release log update" commit 8cf50952e7659a9812168a8ac90399f18dee017d Author: galt Date: Tue Aug 26 15:00:03 2008 +0000 "Release log update" commit f6ee20f170a48c78ed4dcb7b892581fc5c9a901a Author: aamp Date: Tue Aug 26 11:28:55 2008 +0000 Oops, copy/paste error. commit d34e002b45974650c4ffc62d13d5303c4de4c583 Author: aamp Date: Tue Aug 26 11:22:40 2008 +0000 Added details to encodePeak tracks. commit f160054f44349b9dd88aeaf85683a8c3aeb5c047 Author: kent Date: Tue Aug 26 01:46:40 2008 +0000 Updating knownGeneId commit ae9f97c36ec21d435c83b619ef42cb5a6f5d9678 Author: kent Date: Tue Aug 26 01:42:25 2008 +0000 Utility to find tables with fields that contain a regular expression. Seems to work. commit 752b43006f2b9f5c7f0075d540991e056e5574fb Author: larrym Date: Tue Aug 26 00:17:59 2008 +0000 suppress table suffixes for production tables commit 0c182732a7fe38781599ba6ce2411026ff1267cc Author: larrym Date: Tue Aug 26 00:17:48 2008 +0000 suppress table suffixes for production tables; create pushQ entry commit 2ccad8920a59108801f3f797b4586759a755ae1d Author: mikep Date: Mon Aug 25 23:23:11 2008 +0000 added ability to specify only one input file, and print out statistics, plus test commit cc0e23262b5ad055fee592ad802061fd6f71b722 Author: donnak Date: Mon Aug 25 22:52:28 2008 +0000 Added zebra finch. commit e11d835a7c19810c3db5e5b18133157f3e25ef0c Author: larrym Date: Mon Aug 25 22:38:34 2008 +0000 use more sophisticated diff to get rid of tmp file code commit 5b5667362f693dbc6f649f952eaf7beac960cb76 Author: larrym Date: Mon Aug 25 22:30:27 2008 +0000 add allowReloads option; add validateNarrowPeak commit cc9dc33c360a6fa2e8072d1861038dad17086071 Author: larrym Date: Mon Aug 25 22:26:38 2008 +0000 add narrowPeak etc. to extendedTypes commit 803920f1a64ab3da337704ef7f50ec854f9964ab Author: donnak Date: Mon Aug 25 22:09:52 2008 +0000 Added taeGut1. commit b351d28296800f9b84a016df8813a982a5d99d25 Author: aamp Date: Mon Aug 25 21:54:40 2008 +0000 Added a little function to spit back the names of fields in a table. commit beab72a7dbcad204ceb4497d53d6afddb5a37f97 Author: fanhsu Date: Mon Aug 25 21:49:10 2008 +0000 Created genFedTableDef.c. commit 62c09b93c2254c3b05e44fc6e8272f8722fc804d Author: fanhsu Date: Mon Aug 25 21:48:35 2008 +0000 Created makefile. commit 381b0752c873231fef04b88bf498411b6b5cf394 Author: aamp Date: Mon Aug 25 21:46:51 2008 +0000 accidentily broke the build. forgot a couple things. commit 3e6c6cff97a335c6853278ea0805603583025fd0 Author: kuhn Date: Mon Aug 25 21:37:25 2008 +0000 added spacing around image commit 33539c078d262d196dcb01616743023017c1f20b Author: aamp Date: Mon Aug 25 21:36:48 2008 +0000 Added code for encode peak track types. commit 121bf7b32a8a031c41423dd509ef4d2716314de3 Author: aamp Date: Mon Aug 25 21:35:48 2008 +0000 Changes to encodePeak module include blocks. commit d016afde131d696af5e7cec36e210dbfb153ba2b Author: aamp Date: Mon Aug 25 21:00:07 2008 +0000 Added some functionality regarding the -sqlTable option. Now it doesn't matter if the bin field is in the .sql or not. Also the -bedPlus option to be used if loading custom bed formats is failing e.g. bed > 8 assumes itemRgb in that field. -trimSqlTable option allows optional fields in the custom bed... it fits however many fields are in the file being loaded. commit a30cefd69464e1f649a09459b0f09fb3a80d7f15 Author: kate Date: Mon Aug 25 20:55:38 2008 +0000 Add support for bedgraph views to muti-view composites commit 9188db6dbd29a2c79470151e7bfc67fb5ed7dab2 Author: aamp Date: Mon Aug 25 20:50:36 2008 +0000 Added .as and .sql files for encode peak types. .c and .h unnecessary in the current implementation. commit 4319094af8ea8ca50ebf1171e9caa5d1b9c7e829 Author: donnak Date: Mon Aug 25 19:56:11 2008 +0000 Added Zia. commit 4f15d5049b1c2ecd70a598c4509c8a8510759f3d Author: donnak Date: Mon Aug 25 19:52:02 2008 +0000 Fixed broken links caused by photos being removed. commit 1701e68cc94e1d6a8f84f97779d7e3273260cbe4 Author: kent Date: Mon Aug 25 19:04:44 2008 +0000 Updating known genes description per Ann's suggestions. commit 45e43c609aa8ac15312c001aea99e67ada648d75 Author: kent Date: Mon Aug 25 18:18:39 2008 +0000 Using new program to explain differences. commit 9f977f513bacba87a3d7ae1fdf27e7f13e04346b Author: kent Date: Mon Aug 25 18:18:22 2008 +0000 New program to explain version differences between UCSC genes. Seems to work. commit 06c5461e75774dbe99f17a95cb00aaeaf62989e5 Author: mikep Date: Mon Aug 25 18:02:34 2008 +0000 first draft of UW DAFs commit 21fa8e754f2af48fde0b818253a31374929a291c Author: kent Date: Mon Aug 25 16:54:48 2008 +0000 UPdating known genes. commit f28374b7282e59f45645b8968715704e2bde7cc8 Author: kent Date: Mon Aug 25 16:04:16 2008 +0000 Updating comment and fixing a missing equals. commit 6eb786eeef6c10535a09899cc730135863695b75 Author: galt Date: Mon Aug 25 15:00:04 2008 +0000 "Encode release log update" commit 58bff0d9e144a34c6111a7728817fb2e86d13b42 Author: galt Date: Mon Aug 25 15:00:02 2008 +0000 "Release log update" commit 25e8ecfa441286cd2895d6028b3def375da7520a Author: fanhsu Date: Sun Aug 24 19:14:53 2008 +0000 Replaced '|' with ':' to avoid a minor bug in BLAT. commit 4dc5753460508af5477b03e4bfd1461b9c897a75 Author: galt Date: Sun Aug 24 15:00:03 2008 +0000 "Encode release log update" commit b7eba226a3f8a5018321c793e46256783937a533 Author: galt Date: Sun Aug 24 15:00:01 2008 +0000 "Release log update" commit c4138279fc01dced03a7b386aff02fdaf9ccb27b Author: braney Date: Sat Aug 23 23:31:53 2008 +0000 a utility to output fasta alignments given a maf table and genePreds commit 2acf7dc8cdbf0505f52dd143e6306e8274bdc32a Author: braney Date: Sat Aug 23 23:24:57 2008 +0000 a library routine to output a fasta alignment given a maf table and a gene pred commit 3fefe3575a73d399d82165f7193e066ce932a4d6 Author: braney Date: Sat Aug 23 23:24:12 2008 +0000 a library module to output fasta alignments given a maf table and a gene pred commit baa318848094755a996214e86473cfc20f883bad Author: galt Date: Sat Aug 23 15:00:06 2008 +0000 "Encode release log update" commit 5ffcd45375dc10b2eadfb28cbb69aa30a32b9f71 Author: galt Date: Sat Aug 23 15:00:03 2008 +0000 "Release log update" commit ce2fe4eec7228437fe527abfe3915a197ab2d5d6 Author: larrym Date: Fri Aug 22 20:43:25 2008 +0000 soft-link download files into the appropriate directory commit 90c8e90c39abe4afdaff864dcdce81bd2e05b598 Author: larrym Date: Fri Aug 22 20:27:10 2008 +0000 add view and downloadOnly info to load.ra commit 86d883ae26daee5205e3c968ae88083db66ae3af Author: larrym Date: Fri Aug 22 20:17:06 2008 +0000 add compositeTrackName and downloadDir commit 7b68515e9c93e7d7a2ba0470d66433ea0e0c4c75 Author: mikep Date: Fri Aug 22 19:49:09 2008 +0000 added tests commit ec5a30f057bfb11bb9ff905e1e0d6d2c7d21e950 Author: mikep Date: Fri Aug 22 19:41:09 2008 +0000 tidy code, fix a bug where I didnt move the file handle on (fseek) commit 7cdf22e97a6489a1f0ecb6db8561a6c6ed5a62ab Author: angie Date: Fri Aug 22 16:59:55 2008 +0000 Merged snp12*{Short,Long} searches -- both were using semiShortCircuit so it was no longer necessary to separate them. (Thanks Jim) commit 3c7d6bf2df0467ecc95b246294568bc6d3f97eb1 Author: galt Date: Fri Aug 22 15:00:07 2008 +0000 "Encode release log update" commit deeca1e1210ac7d99d63337e5f1490a638502366 Author: galt Date: Fri Aug 22 15:00:04 2008 +0000 "Release log update" commit 51653a07a19dccc8fe6fcc694959caa327d821bf Author: kayla Date: Thu Aug 21 23:22:05 2008 +0000 added taeGut1 commit 94cb4ab68b3b17b0e82c81bc825145066edfd113 Author: aamp Date: Thu Aug 21 22:07:38 2008 +0000 Possible fix of chromGraph visibility bug after second screen after hgGenome. commit c43deae8bad9a16e45cde2df32b60f2ec0a7cff8 Author: pauline Date: Thu Aug 21 22:01:46 2008 +0000 Removed release beta to update track for hg17 hg18, dgv. commit 59f25fcfe1a38bb86ddf574f2ccddc3d60c5e229 Author: mikep Date: Thu Aug 21 19:48:05 2008 +0000 first draft for RIKEN - incomplete right now commit defcd6b46dff543ad2955567b2171a2fdcd3d335 Author: larrym Date: Thu Aug 21 19:40:44 2008 +0000 fix problem with duplicate scaffold in equCab2 commit f9dadc8e0be57078a2d810e18b2fc2c87a2712a9 Author: braney Date: Thu Aug 21 18:59:51 2008 +0000 fix up to reality. commit f8ce82032b35be37b9a507a632909f3504b03475 Author: kate Date: Thu Aug 21 18:56:14 2008 +0000 Update downloads paths for ENCODE TBA alignments commit b5690e00ad73090fad074b991a042328d43e0794 Author: kate Date: Thu Aug 21 18:53:47 2008 +0000 Add conserved elements and downloads to ENCODE TBA track commit 66efa80443830a157e75adb31c5bd690201d2de0 Author: kate Date: Thu Aug 21 18:52:32 2008 +0000 Add tree image to ENCODE TBA track commit 33c12500c423d2b4d09dccc04233973656d13ed4 Author: mikep Date: Thu Aug 21 18:42:51 2008 +0000 first version of AffyRnaChip project commit a4905defcfe1c4bd625abd5426c6cab985fd0226 Author: braney Date: Thu Aug 21 18:03:52 2008 +0000 zebra finch BAC's are like dog BAC's commit cb33871d5822e3bb53a87c9d02347460ab26fc5b Author: ann Date: Thu Aug 21 16:19:44 2008 +0000 fixed usage statement based on feedback from Pauline. commit 6dabb780951ee2b34613fb551213109050ac595e Author: galt Date: Thu Aug 21 15:00:06 2008 +0000 "Encode release log update" commit d55ec0528122e622bf381765080e3548eef81ad7 Author: galt Date: Thu Aug 21 15:00:03 2008 +0000 "Release log update" commit ad4435214c4170b5397b10265a383944b4957c0f Author: ann Date: Wed Aug 20 23:05:41 2008 +0000 turning off genbank updates for equCab2 on rr (while we sort out the horse chr27 issues) commit 51181981d8333913d855e772f2c7f276b2a5d3fb Author: hartera Date: Wed Aug 20 23:05:30 2008 +0000 Removed acedb directory. commit 29622d6e022fbd1b7a4f79ca3ad57fcbc475f291 Author: larrym Date: Wed Aug 20 18:52:33 2008 +0000 add buildUtils.csh commit 317efe9d820113cf818b9ba1b1dc5732cd604594 Author: braney Date: Wed Aug 20 17:46:56 2008 +0000 fix up maf example commit 22e41b4ef7b4d2f29554dc0ed387d8d7695c4a3c Author: ann Date: Wed Aug 20 15:54:52 2008 +0000 turning back on hg17 updates -- sync is finished commit b97f04e9c9d290e70562888e7798486a8c56ed73 Author: giardine Date: Wed Aug 20 15:35:40 2008 +0000 Took out highlights until know range should be highlighted for hydropathy commit 0bc88b517659388e2b86edcb053139090f399beb Author: galt Date: Wed Aug 20 15:00:07 2008 +0000 "Encode release log update" commit 53901659e8c3d239faf7202386a67b756c4117c8 Author: galt Date: Wed Aug 20 15:00:04 2008 +0000 "Release log update" commit 045910c3fb407b48ebf3ee46bc120544628a6210 Author: mikep Date: Wed Aug 20 10:42:24 2008 +0000 fixing tests - function name was changed commit 9606ccac8159a028c45ddc245c19aae0a6b2f837 Author: mikep Date: Wed Aug 20 10:12:54 2008 +0000 refactor code; added 'intersection' option commit 8a129f28c41fa7c9acf9132c7ec1f3e428bc991a Author: mikep Date: Wed Aug 20 10:11:29 2008 +0000 added 'and' option to baseMask, 'id' and 'merge' to baseMaskToBed commit fc89d25ed8fb1ea770193b3a242841f8d2880e13 Author: markd Date: Wed Aug 20 04:15:48 2008 +0000 fix reference to non-existant database on partial mirrors commit 5ce030a1220b724e24d1fc2c9ac64a015fc0dd67 Author: larrym Date: Wed Aug 20 00:23:13 2008 +0000 re-calculate stats to reflect deletion of scaffold_34 from chrom27 commit fd234baa9577a2b72c4592161acde476df18d2f6 Author: markd Date: Tue Aug 19 23:49:46 2008 +0000 added RefSeq CDS similarity table for MGC/ORFeome commit 8f50e09aaa094813dd853ea96f517ef2c8f49088 Author: hiram Date: Tue Aug 19 23:42:29 2008 +0000 Running oryLat2 lastz commit e955a09eef233181b72e75b20b62a886e7152ac9 Author: braney Date: Tue Aug 19 22:49:16 2008 +0000 some text about custom tracks commit 6b0153d6eda62886a8225850e6838d3ff6817cf9 Author: larrym Date: Tue Aug 19 22:48:54 2008 +0000 notes about deleting extra copy of scaffold_34 (on chr27) commit f54dbf930a02f35350736fb42e3e2a636a80d1af Author: hiram Date: Tue Aug 19 22:41:01 2008 +0000 Now have gold, gap, and ctgPos2 tables correctly loaded with these descriptions to go with them. commit 21f9c6dfea7f6182bcd041f5bc7660b2065f607f Author: braney Date: Tue Aug 19 22:30:45 2008 +0000 add MAF custom track type commit 78f01c84af9d3d1d2b28587e42d7114c6c0b8425 Author: braney Date: Tue Aug 19 22:22:18 2008 +0000 add MAF as a custom track type commit d88f0e63160e61133d5c34bb31de299210c6644a Author: braney Date: Tue Aug 19 20:29:34 2008 +0000 push q, bac-ends, blat-servers commit 9498c2dcec4f06e1f4b7e2e2bf6c98a762594e78 Author: larrym Date: Tue Aug 19 18:57:54 2008 +0000 "New version number v189" commit 82d2ec0d01f4c732dc73d46b28f4e6984325aa3f Author: braney Date: Tue Aug 19 16:03:24 2008 +0000 change to use lastz by default instead of blastz commit faec6e5d17b5095dc560f0f6f7943e09149b0379 Author: galt Date: Tue Aug 19 15:00:10 2008 +0000 "Encode release log update" commit ab490a32fd392c8596965b960cee220f51a012c0 Author: galt Date: Tue Aug 19 15:00:04 2008 +0000 "Release log update" commit 0e41f673e03fa166f36fdaf0fc4a3f5cd6b90815 Author: kuhn Date: Tue Aug 19 13:38:15 2008 +0000 turned off hg17 for sync and also dbs being archived commit 502b59987802d91b4adda9175354baad49520e6f Author: donnak Date: Tue Aug 19 06:17:03 2008 +0000 Removed link to gbDescriptions.html. commit 46a634921799061f22bfbec8596ba3ce5e9f75c8 Author: donnak Date: Tue Aug 19 06:14:45 2008 +0000 Commented out news item about equCab2 until data problems are resolved. commit 038989d1de234ac99b6c5184e99ceb3426ff428a Author: pauline Date: Tue Aug 19 01:49:46 2008 +0000 Added explicit instructions for missing steps. commit 64309e66c4dbe3ceb32992ebdd76284744351d65 Author: pauline Date: Tue Aug 19 01:39:12 2008 +0000 Fixed pseudo-sql statement - no 'name' field in that table commit 7360a90711b5739a6d14fe465c0574f1991d3280 Author: kayla Date: Tue Aug 19 00:04:38 2008 +0000 fixed 2 typos commit bee6835c712de921ff0aebe51b7ecd34e9033f14 Author: kuhn Date: Mon Aug 18 23:48:55 2008 +0000 removed last updated line commit d82d47864c1bbf82d37d838071f17c25d4480346 Author: mikep Date: Mon Aug 18 23:45:10 2008 +0000 added a method to count range size over whole tree commit 85baf6f7f211ccd0e2ceb81edeb4c6da0271eeb1 Author: mikep Date: Mon Aug 18 23:43:33 2008 +0000 added count output similar to 'featureBits -countGaps' and made output of bama file an option commit e0c378fe541784a24d2964a21aec3ca964433486 Author: ann Date: Mon Aug 18 21:59:40 2008 +0000 Added check to make sure tables are sorted by chrom. Added section to show other related tables that need QAing. commit dc86815af6de789a1a7c3b5ec0b163f4085339f5 Author: ann Date: Mon Aug 18 21:06:36 2008 +0000 Changed ensemblTranscriptIdFelCat rule (didn't need the chopAfter), and the minCheck causes it to miss a couple of problems that Ensembl needs to fix. commit 6a5acc49033f81649eab32e93d2c2f7a21249ad4 Author: donnak Date: Mon Aug 18 21:02:31 2008 +0000 Archived an item. commit 6b7427e48d2245718b18287e932537c9e4dacc83 Author: donnak Date: Mon Aug 18 21:02:14 2008 +0000 Commented out equCab2 lines until data are fixed. commit 496e06e08dae94a371b35da7aa4e72b93d2e1f16 Author: donnak Date: Mon Aug 18 21:01:03 2008 +0000 Commented out equCab2 until data are fixed. commit 0fccf38f9ce0da0d27f528b6185442330b6a06dc Author: markd Date: Mon Aug 18 20:51:54 2008 +0000 changed generation of 3UTR features to match what is now defined in GTF document commit c0b117627393e9a6522d8fd1c15d5e5a83d5eb18 Author: kuhn Date: Mon Aug 18 18:02:20 2008 +0000 resized image to use full size and added whitespace around it commit 36f749a6e299ef5d6006ba27c9a74d38a7250644 Author: markd Date: Mon Aug 18 16:20:26 2008 +0000 fixed expected output order due to rangeTree change commit cc0c1c28f1c84cae592bd52dae971533eeadde7e Author: galt Date: Mon Aug 18 15:00:03 2008 +0000 "Encode release log update" commit 724644fdba59375d500c69d9734b4261d6e14ca5 Author: galt Date: Mon Aug 18 15:00:02 2008 +0000 "Release log update" commit 5161e9f02e849d3dfb51194f1ec1452864ac821d Author: mikep Date: Mon Aug 18 09:19:13 2008 +0000 added baseMask programs which read, write, and overlap genomeRangeTrees commit b636a3c739255dbd620e914307e745be35764397 Author: mikep Date: Mon Aug 18 09:18:32 2008 +0000 fixed logic error for ranges which end on same base commit 668ceb074d9596d6cb0fe0f94250b28e197521f4 Author: mikep Date: Mon Aug 18 09:17:32 2008 +0000 fixed comment and mem leak commit 2f5b40c276e8dfd078695c6afa248fe37e5be172 Author: baertsch Date: Mon Aug 18 07:46:02 2008 +0000 register ucscRetroAli commit 59ed98e67985cddb9f17f26a3897f2803fc3f3d3 Author: baertsch Date: Mon Aug 18 01:59:09 2008 +0000 change table name from retroMrnaInfo to ucscRetroInfo commit 7a9ed3840fcaf395904bf063eebd92778d61f2e4 Author: baertsch Date: Sun Aug 17 16:35:39 2008 +0000 from retroMrnaInfo.as commit 4cf4ecdd5481095a196e282d5e00eb2b5dd18049 Author: galt Date: Sun Aug 17 15:00:07 2008 +0000 "Encode release log update" commit 2f608dbac34d293d611fc4a0e81afa58b558edda Author: galt Date: Sun Aug 17 15:00:04 2008 +0000 "Release log update" commit eb663bdf850a5df95234402b4b477a57e4c2b213 Author: baertsch Date: Sat Aug 16 21:03:26 2008 +0000 add yellow to mismatch codon coloring for transmap and retrogene tracks. yellow = positive blosum score, red = zero or negative score commit 316a4e3d9d704702e9b437db73f9fd4b1732767b Author: galt Date: Sat Aug 16 15:00:07 2008 +0000 "Encode release log update" commit ccc292463377ae39bcecf050065c773ba0ab4208 Author: galt Date: Sat Aug 16 15:00:04 2008 +0000 "Release log update" commit d68f6bcb6c71ad0a34608dd784895c56472f2d4b Author: hiram Date: Fri Aug 15 22:28:06 2008 +0000 More fuzzy searches for Sanger and Ensembl gene tracks commit 745b2bb81bae6cf31ad2994ffbb3ffacd466c36f Author: markd Date: Fri Aug 15 22:26:12 2008 +0000 to-do item on tandem genes commit 901faa6957f25319398fc68880a0df31e3c49e92 Author: tdreszer Date: Fri Aug 15 22:10:25 2008 +0000 Added only the currently needed jquery files to this make commit 12a6709a6b2f7ed8fc041ae77a59f8e237120fa4 Author: tdreszer Date: Fri Aug 15 22:08:51 2008 +0000 Inital checkin of jquery library commit 359df41837b5280ccecaf10fba7dac2d6402e1c8 Author: kayla Date: Fri Aug 15 21:53:40 2008 +0000 put in vertical viewing range values for the uwNucOcc subtracks. commit 60b648f336583f19d0c22bf6c0c2092264105001 Author: hiram Date: Fri Aug 15 21:53:32 2008 +0000 Fixup load of blastCe6SG tables to get them properly loaded sorted commit a2827f05d0b94259ac016c83cb32f0798e075b68 Author: tdreszer Date: Fri Aug 15 21:49:10 2008 +0000 Added NT2/D12 (Ntera2) cell line since Farnham's protocol was approved commit e0c22b2e1608e1136cd6a21b3c6d9e2273d102e3 Author: hiram Date: Fri Aug 15 21:28:00 2008 +0000 Dog is merely Canis familiaris at Ensembl, not our Canis lupus familiaris commit 042c05320d250310526085e16633bda76f0eefa4 Author: hiram Date: Fri Aug 15 21:20:48 2008 +0000 Fixup ce6 rules to get ensGene checks to be OK commit e04fcbd7a171ccc47ae257aaa6a3123132f0367a Author: mikep Date: Fri Aug 15 21:02:49 2008 +0000 added ability (and tests) to save genomeRangeTree to binary file, and to merge to files into a new genomeRangeTree file commit fe613bfb2b964b9134deb46880706977a52b6751 Author: hiram Date: Fri Aug 15 21:00:06 2008 +0000 Special ensemblTranscripId check for C. elegans - different Ensembl gene naming scheme for ce6 commit a04ed161d80cffb9a3a9492a6dc23a4eac86fc44 Author: hiram Date: Fri Aug 15 20:51:22 2008 +0000 Adding an ensemblWormGenes search definition commit 8f99cd9d3217503eef2bca55af077e95e6c4c5e5 Author: hiram Date: Fri Aug 15 20:20:36 2008 +0000 Different Ensembl naming scheme for names on ce6 ... commit 9d2039813de4682c987cf4f153b6e5f19779ff14 Author: markd Date: Fri Aug 15 19:47:39 2008 +0000 made short labels in Nucleosome Occupancy subtracks more meaninful for table browser commit 49fa1e88d044d0a8d47ba4b7a427232a6702f657 Author: donnak Date: Fri Aug 15 18:52:23 2008 +0000 Fixed sample searches. Still need to edit assembly text -- waiting til we resolve discussion re: Broad assembly errors. commit 727fd3e4333b3419995f3cd9a40c4cec392316d3 Author: hiram Date: Fri Aug 15 18:35:05 2008 +0000 oryLat2 needs no==perChromTables commit 8478aeb7e1ad8b02ea65475382472c34f87b4f79 Author: angie Date: Fri Aug 15 17:54:31 2008 +0000 kiddEichlerDisc: found the Abc8 clone -> NCBI xref files and updated kiddEichlerToNcbi. commit 9ade50ba863de4f47920c7de9ee8742644401f3e Author: angie Date: Fri Aug 15 17:48:07 2008 +0000 Fixed kiddEichlerDiscId rule for Abc8. commit 038bd0ddb3b6ed4fb814fd6957aa6469e72d4f6e Author: angie Date: Fri Aug 15 17:46:49 2008 +0000 For fields with enum and set SQL types, include only those values that appear in the data, so we won't show TB filter choices that will never match. commit 40a00fb464a305caa93f97ee648ed10411c90968 Author: hiram Date: Fri Aug 15 17:42:05 2008 +0000 Copy from oryLat1 fixed up to eliminate the chrUn references commit f31dc862eb521cd330aa8c43e1f7dc4f90ff021c Author: hiram Date: Fri Aug 15 17:37:07 2008 +0000 Finished genbank, but have a null result ? commit a7159b7c6057f661ca37b49de788a0f433802338 Author: hiram Date: Fri Aug 15 17:30:02 2008 +0000 Adding oryLat2 commit 2f90383d2311fffdc7813dcf979b7958742c48bf Author: hiram Date: Fri Aug 15 17:26:55 2008 +0000 Added oryLat2. commit 28547ce25ed3d51dea182972c36f6ea4900b0924 Author: galt Date: Fri Aug 15 15:00:06 2008 +0000 "Encode release log update" commit a99011c7d96013735c0da848a9453c73d5f14bc5 Author: galt Date: Fri Aug 15 15:00:03 2008 +0000 "Release log update" commit e530bab8dc11298ce82dd1f6b72ac31af23ef47b Author: kayla Date: Fri Aug 15 00:42:41 2008 +0000 edited references commit 93d943c7cff1ba86d719d2c12d844d8e9c5638a4 Author: hiram Date: Thu Aug 14 23:40:37 2008 +0000 Beginning the genbank run commit ce1cd317329cc50e783c1dafc35faf30805d2ec8 Author: hiram Date: Thu Aug 14 23:38:41 2008 +0000 need to specify a lift file for oryLat2 commit 5193ddbb3118bb724e2c37332883ff4d6a48376a Author: donnak Date: Thu Aug 14 23:19:03 2008 +0000 Added equCab2. commit fd0b13438df9a2a42ce26785589c1b6a53f6f50b Author: hiram Date: Thu Aug 14 23:07:35 2008 +0000 Adding oryLat2 commit e896c24e367b4556a2ff84f9700f9535d6fb45af Author: hiram Date: Thu Aug 14 22:48:16 2008 +0000 Initial procedures through masking commit 4eb36f5ba2ef9f680962d7c1de0c6e74944e18a6 Author: galt Date: Thu Aug 14 22:34:37 2008 +0000 a little cleanup and added one test target commit 2bf570c730398b8ddc48d758346578045331c069 Author: pauline Date: Thu Aug 14 22:21:54 2008 +0000 Added new horse. commit 8f9c920accb253c09689b361c8ea8806fd5f8554 Author: angie Date: Thu Aug 14 21:41:41 2008 +0000 Added utils-alpha target so that util scripts are installed by top-level alpha target. commit 8df4a6e42e868a5450a9304f86b4d2d35dfd1757 Author: ann Date: Thu Aug 14 21:14:04 2008 +0000 hiding this track by default commit f4f597b8ba0dce8ea538fe8d5ffcd81a3e687589 Author: galt Date: Thu Aug 14 20:59:52 2008 +0000 cleaning up accidental duplication from Andys branch-merge for prev/next item, caused duplicate click-map in the Toggle section - been around since 2006 version 1100 commit 2aec83f2b6ca2952f644a0d04999f72f647502e1 Author: ann Date: Thu Aug 14 20:55:12 2008 +0000 a better way to delete lines starting with # commit 2da71d819d2cfb3291bb166d3ad68242f78ee6a1 Author: larrym Date: Thu Aug 14 20:53:27 2008 +0000 rearrange so more processed tracks are up top commit 2d999199095f3e9a4985384b11def9391cdf76f8 Author: galt Date: Thu Aug 14 18:00:20 2008 +0000 fix paste/upload so terms are quotable as they should have been commit c0f4b87d62d5f9ef80da53bfc6217d6ec26bb610 Author: markd Date: Thu Aug 14 17:23:31 2008 +0000 fixed typo commit eebc2b1973849459c86f138aa6584cea6d197bc5 Author: ann Date: Thu Aug 14 17:05:16 2008 +0000 cutting short label back to less than 16 chars commit 70f38594eb05e3e7075ef9c25dadf8c4cb709f5c Author: ann Date: Thu Aug 14 17:04:47 2008 +0000 italics for species names commit 93ee3010f10db979cf682862dc999227ffadb5cb Author: ann Date: Thu Aug 14 16:21:29 2008 +0000 using CVS file location, becuase the other file doesn't get updated very often commit 11e1a44021dc3394e1424e953c0524f5960cfb18 Author: galt Date: Thu Aug 14 15:00:07 2008 +0000 "Encode release log update" commit 5e779a4fca541c00841520f042d0450071f5cb59 Author: galt Date: Thu Aug 14 15:00:04 2008 +0000 "Release log update" commit b4b7d35be2b1d8f967453ad630d38c4b0c9fa27e Author: markd Date: Thu Aug 14 07:20:00 2008 +0000 UW nucleosome occupancy predictions commit 1078dcd75bd6d67d14930881a90ea467c60155bc Author: markd Date: Thu Aug 14 04:17:31 2008 +0000 changed long label commit 41918474b2f65bcb16ca2161aea4a1b06770fe4f Author: markd Date: Thu Aug 14 03:14:35 2008 +0000 fixed typo commit 90853f5406aa1e1dd8ebedf68436790e2c437132 Author: markd Date: Thu Aug 14 02:45:12 2008 +0000 added Nucleosome Occupancy tracks commit 4e14be831ef8041414f77536c2a58df8193567c9 Author: kate Date: Thu Aug 14 00:59:51 2008 +0000 Remove unregistered Tier 3 cell line commit 01d85c4abfd35f0182c61d4d53a8573397363532 Author: kate Date: Thu Aug 14 00:16:12 2008 +0000 *** empty log message *** commit c41a148b1a00075b03a2a9b9cb609f729332ea74 Author: kate Date: Thu Aug 14 00:10:40 2008 +0000 Prune track labels commit 8f9853a3fd4d5c1e2574bfb6b69dd5f26cda2f9d Author: kate Date: Thu Aug 14 00:02:28 2008 +0000 Add conservation track to ENCODE Dec07 freeze TBA alignments, and package as super-track (till multi-view works) commit bd239adc62662dc219147c4f3e7ae0f73edc279a Author: lslater Date: Wed Aug 13 22:03:28 2008 +0000 Multi-threaded hgExpDistance file Mutex version commit 57f7f6c4c9daeeef000e635ad89e9ffea21fe82f Author: angie Date: Wed Aug 13 21:50:08 2008 +0000 Added explanatory comments for kiddEichler name parsing (as Jim suggested in code review). commit 8e4f0635a879965b779e9421300f307c6a3b14d1 Author: ann Date: Wed Aug 13 21:49:11 2008 +0000 added activeGenbank.csh script commit 532956922a427269f6c43f55840f6e3f40a979a4 Author: ann Date: Wed Aug 13 21:48:43 2008 +0000 added two mice to list to ignore (they are being archived) commit 4e4fe3390a6288ff513fda0448118a3b3ff2b9f0 Author: angie Date: Wed Aug 13 21:42:39 2008 +0000 Added explanatory comments for kiddEichler name parsing (as Jim suggested in code review). commit f85e63e5db85b9188667791c2866e5acb39bbfd4 Author: ann Date: Wed Aug 13 21:34:15 2008 +0000 this script compares the list of active databases on the RR with the list of databases getting genBank updates. Reports diffs. commit ace3e5f02388dea84a981a28b4902b924ed1f79d Author: fanhsu Date: Wed Aug 13 20:30:35 2008 +0000 Use nextQuotedWord() instead of nextWord() to support filtering on multi-word term. commit 3f46b1d0073fe9dc41306b6e2f6d4b6d1103aa9d Author: kent Date: Wed Aug 13 18:57:35 2008 +0000 Making full text index work again. Making foldUtr table generation work. Putting in docs for building knownGeneLists. commit 94240d22b42c9a5e32875f39aa6352db08da9b99 Author: pauline Date: Wed Aug 13 17:47:48 2008 +0000 Added text to clarify exon feature assignments by table browser commit 0eafd831a883ea917e3164e8c99d943a39cf8645 Author: lslater Date: Wed Aug 13 16:22:09 2008 +0000 New file queue version that feeds synQueue with ptr to sorted arrays instead of individual distances. This version is faster than the file mutex version for N=4 threads. commit 9df8d889ddc9ffffe6b1a2fa9266e2d0eb349df5 Author: braney Date: Wed Aug 13 16:03:51 2008 +0000 looking for DNA when there's no active database commit d0ddf5b8f95d89fbbc093ea0d592ec8ce4a4a7ba Author: galt Date: Wed Aug 13 15:00:11 2008 +0000 "Encode release log update" commit 73ab72bbf6e3c35361ecc3f143d3ea76cf084592 Author: galt Date: Wed Aug 13 15:00:05 2008 +0000 "Release log update" commit 526b68f70863e3975e143b06036aa9a7c17eb8f1 Author: genbank Date: Wed Aug 13 02:37:50 2008 +0000 added -byPassGbLoaded option to force updates commit 72b893dd62f9fbf351637ae36a97a0e7a7e3cc69 Author: galt Date: Wed Aug 13 01:40:20 2008 +0000 bugfix in which part of the code thought the default visibility for blat was pack (correct) and the other half thought it was hide (wrong) - reported by a user when they clicked PS/PDF link and their hidden blat track was being drawn on the postscript output commit 888350bc78e971ceabf42d2651fa64fef81c5080 Author: kate Date: Wed Aug 13 00:43:39 2008 +0000 Fix problem with supertracks commit 1e06b9f10295b0b169142037908b14350fe51c23 Author: kent Date: Wed Aug 13 00:31:20 2008 +0000 Updating UCSC genes description to include CCDS. commit 606d39289a1114bbbb0ad22470dd8cc2beeb7f97 Author: genbank Date: Wed Aug 13 00:04:43 2008 +0000 enabled ponAbe2 commit 538c5d5feb063d3fa3644467ecb499d619e29d30 Author: larrym Date: Tue Aug 12 23:29:12 2008 +0000 allow lower-case .ddf extension commit 70d928faf47fc6f6bcf4a2061f7b52caa3bebaea Author: larrym Date: Tue Aug 12 23:28:56 2008 +0000 allow lower-case .daf extension commit 174e4e77bf441be7b5c876843f388f8995e6f40d Author: genbank Date: Tue Aug 12 23:14:58 2008 +0000 added ability to handle only one database commit 3eba7c331c668e42be30c0af4b49a34e98b9f3e3 Author: larrym Date: Tue Aug 12 23:10:41 2008 +0000 add validateValueList commit 83fe53dbcc1cc03feca1971511c65603a61d711f Author: larrym Date: Tue Aug 12 23:09:54 2008 +0000 add type fields commit 4d93bea9bcac19daedb7d340dd6ff3ce4624248e Author: larrym Date: Tue Aug 12 23:09:19 2008 +0000 use validateValueList to improve error checking; change ddfLines to contain a list of hashes commit f612fc94aba48224fd3623641ef39ab2eb414819 Author: larrym Date: Tue Aug 12 23:07:45 2008 +0000 fix test rule so we bail out on error commit a0532df1c5d30c5ab4b9ea4b6bf65327d336feca Author: hiram Date: Tue Aug 12 22:53:22 2008 +0000 Initial files from makeGenomeDb.pl commit f28302ececde601bd1e7660d3a0cf8edffe0e13e Author: kent Date: Tue Aug 12 22:29:52 2008 +0000 Doing KEGG and CGAP updates commit 03a4b690034b3db6ccc9298c5961c8d74051ddf7 Author: kent Date: Tue Aug 12 22:29:08 2008 +0000 A little cleanup of a temp table. commit 55c43d92fb25167806c33173923241ca7fce6e0c Author: baertsch Date: Tue Aug 12 22:22:08 2008 +0000 intial version commit a228f098f74765b1f72d100c7a4cfa5fabd94bce Author: baertsch Date: Tue Aug 12 22:21:10 2008 +0000 rename retro tables to ucscRetroInfo3 and ucscRetroAli3 commit 7741e53dd633156410afa12635fcc456abce9f02 Author: baertsch Date: Tue Aug 12 22:19:48 2008 +0000 sql for retroGene table (from retroMrnaInfo.sql) commit 65850a7a3c592f505ae4c28e6d7e7b9ae0e550f2 Author: baertsch Date: Tue Aug 12 22:18:41 2008 +0000 rename retro tracks from retroMrnaXXX to ucscRetroXXXX commit 2ee549095a283370a4620c833a68695621e0536d Author: baertsch Date: Tue Aug 12 22:18:10 2008 +0000 change retro table tables from retroMrnaXXXXX to ucscRetroXXXX commit db40b171ac7cf9593bd83a896b54ea5c368cfda8 Author: kent Date: Tue Aug 12 22:10:27 2008 +0000 Seems to work. commit ef36997c84d266fce884258cfec2a1f77c6484dc Author: angie Date: Tue Aug 12 21:53:01 2008 +0000 Added clarification of terms (<= 127 vs. >= 128) to Function section. commit 4ce9c8edc96067a30c37bf98a8fb751c1059d785 Author: larrym Date: Tue Aug 12 21:35:09 2008 +0000 tweak how we find unloader; add grant/lab to wrangerl email commit 89a04f1822d8adcec22425757958633c4c5cc44e Author: larrym Date: Tue Aug 12 20:56:13 2008 +0000 pif => daf commit 3d8861831d70690c5a4506e933c9c89356756111 Author: larrym Date: Tue Aug 12 20:50:27 2008 +0000 pif => daf; lab => grant; switch to using hash refs rather than hashes for daf etc. commit b24dfdf0bda38f3fd518ff3d14cb30e7a0693946 Author: larrym Date: Tue Aug 12 20:38:04 2008 +0000 pifVersion => dafVersion commit 39921bb66c948d2b73f1e4eb9c249d3d68566768 Author: larrym Date: Tue Aug 12 20:35:24 2008 +0000 StanfordChip.PIF => StanfordChip.DAF commit 4f93131d70e71f479b4715110366bde34678a83a Author: lslater Date: Tue Aug 12 20:22:03 2008 +0000 corrected make for multi-threaded versions commit 5a341b0732853024b505eb8d6452c1c704b6fb6f Author: angie Date: Tue Aug 12 19:30:18 2008 +0000 Added settings to kiddEichlerDisc for linking to NCBI. commit 2fd240fc91ae2b5967b9afba47cf2c2bc2193cdb Author: lslater Date: Tue Aug 12 19:27:35 2008 +0000 *** empty log message *** commit baa7efffd592a155c8a9f5bd1a400c389c62bf88 Author: angie Date: Tue Aug 12 18:43:04 2008 +0000 Added links to NCBI when mappings are available for Kidd/Eichler IDs. commit 2257422ea2669b17533ac5a6293154ac23af7adb Author: larrym Date: Tue Aug 12 18:38:57 2008 +0000 fix install rule commit df600e66b3fac7c75ce45bab49698be45c9f6d7c Author: larrym Date: Tue Aug 12 18:18:40 2008 +0000 add install target commit dc7b651573fd2d463de813c3090a18917573e629 Author: larrym Date: Tue Aug 12 18:17:59 2008 +0000 add ENCODE_PIPELINE_BIN commit 3e1d28878dbc8b6ea7e90186a5b71e22a5c9e46d Author: larrym Date: Tue Aug 12 18:16:42 2008 +0000 moved doEncodeUnload.pl here from encodeUnload dir commit 5b54ea37b3458ab0b82d9530a093325c0c279610 Author: larrym Date: Tue Aug 12 18:16:01 2008 +0000 moving doEncodeUnload.pl to the encodeLoad directory commit dd14e128799b62108b2285ebcdcc1ecc66b03a0a Author: larrym Date: Tue Aug 12 18:14:12 2008 +0000 change install target to support production pipeline commit 19f7405871d40bcd8930d76e387d88d7df816e4b Author: galt Date: Tue Aug 12 15:00:06 2008 +0000 "Encode release log update" commit baaeaca6771bc86fbff528e6512ad62b13224b45 Author: galt Date: Tue Aug 12 15:00:04 2008 +0000 "Release log update" commit d03a3c1be4a4a077e3ffcfd480b36c0e0809865d Author: mikep Date: Tue Aug 12 07:04:36 2008 +0000 added read/write to genomeRangeTree + rangeTree, plus tests commit 1961bdeaafc446427ed221aa946850be38700f5b Author: lslater Date: Tue Aug 12 03:05:38 2008 +0000 *** empty log message *** commit 2c308abed36f7ac7d3fc7185afc5b6ae8f9bd87b Author: markd Date: Tue Aug 12 01:04:36 2008 +0000 converted to using genomeRangeTree commit d3514195d768bcc1733283d23db70645e35b3926 Author: tdreszer Date: Tue Aug 12 00:53:07 2008 +0000 Commented out alignments because they represent too much data to be pushed to the RR commit 816f4e6684d1376735586ac6fa6e613c3deb1ec3 Author: angie Date: Mon Aug 11 23:52:28 2008 +0000 Added kiddEichlerId identifier. commit cf718c9c9b5419d3e69e219afa7cd8fc4ff55dcb Author: angie Date: Mon Aug 11 23:51:47 2008 +0000 Added alpha/beta dataVersion to DGV (v4 is on RR, v5 on hgwdev). commit fdc443385237040686724ce623d14711da06f13c Author: kord Date: Mon Aug 11 23:51:00 2008 +0000 added description image commit e24c8db8ae1008f1134a029905262ca5f9291f11 Author: angie Date: Mon Aug 11 23:46:17 2008 +0000 Map clone IDs from Kidd..Eichler '08 to NCBI clone accessions and/or end read trace names. commit c2fcc1869da2b90efac5deff8e77c6d98e771ab9 Author: kord Date: Mon Aug 11 23:45:27 2008 +0000 Updated link to image ref commit 9d7fb017f110934e07cea47f8c9bcb559aaf86a1 Author: kord Date: Mon Aug 11 23:41:43 2008 +0000 Initial image for N. vectensis commit 380bbc58e86d2450b18c93aa7a63fadb3e470ebd Author: angie Date: Mon Aug 11 23:39:33 2008 +0000 Updated DGV to v5. Added kiddEichlerToNcbi ID xref table for HGSV. commit fd28aba73a5bc3ccca78862583bda9e73d02e422 Author: fanhsu Date: Mon Aug 11 23:24:12 2008 +0000 Change '|' to ':' for protein squences. commit 3f67966b9f334506005f6e92849152b5a9de68cc Author: kord Date: Mon Aug 11 23:11:59 2008 +0000 GENSCAN predictions and makeDowloads done commit f864b325f00b0cae0254f557329ae216a08ddfe0 Author: kord Date: Mon Aug 11 21:09:27 2008 +0000 Completed GenBank Alignment commit f5d16be9e1f18cced5adb939b8dbe0d75a6af904 Author: kord Date: Mon Aug 11 21:07:54 2008 +0000 Added N. vectensis commit cf4176d4971aa563a524997e334efe931f891a4a Author: hiram Date: Mon Aug 11 21:00:37 2008 +0000 Running self Blastz runs for the request from João Fadista Joao.Fadista at agrsci.dk commit 03b11cd3ad1c6284e67d0a216ac49165921314ff Author: hiram Date: Mon Aug 11 20:57:46 2008 +0000 Adding the bit about updating hgFixed trackVersion table commit a5cccffecd622ddaeb5d3346c89121ca09b3ff1f Author: hiram Date: Mon Aug 11 20:30:30 2008 +0000 Done with ensembl v50 update except for the cleanup of the trackVersions table in hgFixed to up date the "current" indicators commit 6a5b3df5e47f4b2af60f9cf6537a475bde472dd9 Author: ann Date: Mon Aug 11 17:26:25 2008 +0000 removed hard tab commit 92afdd00e42d33de95bb74b83df363a8871d65ff Author: ann Date: Mon Aug 11 17:14:54 2008 +0000 added uniGene_3 table to uniGene rule commit 180e07379236923f6fa902ad39aca42a4b0136a0 Author: kord Date: Mon Aug 11 17:13:30 2008 +0000 updated nemVec1 clusterGenome and ooc path commit 76a1cdeba2f1872ef05b84a53cfa96ece5f24002 Author: lslater Date: Mon Aug 11 16:29:22 2008 +0000 *** empty log message *** commit ed699a4a0b9623ae175dc07648afeaa3588e8f2d Author: hiram Date: Mon Aug 11 16:24:22 2008 +0000 Now running the full Db loop to get them all to v50 commit fb7edd98dd872754b1eaa01a8d225981a7da1215 Author: kord Date: Mon Aug 11 15:59:27 2008 +0000 updated nemVec1 2bit and ooc path commit 082425ac7f3f697d02b1d9d666d279f7b848b3bc Author: galt Date: Mon Aug 11 15:00:07 2008 +0000 "Encode release log update" commit 8a839ad6600ba2f3ce36a6d75630ae0bf421b839 Author: galt Date: Mon Aug 11 15:00:04 2008 +0000 "Release log update" commit 20d7e17faf8ec95a8ec9d62d7d910c394ec42abc Author: giardine Date: Mon Aug 11 14:24:13 2008 +0000 added highlights to amino acid property changes commit be4769d85676ca909bb7595eab8dfb5cd8e8c1e6 Author: baertsch Date: Sun Aug 10 19:46:02 2008 +0000 text changes commit 3e331f27e03645e273c626b7832388fbc4df28dd Author: baertsch Date: Sun Aug 10 19:17:06 2008 +0000 text change commit d245b71d04257f654cefad2fac05687156f67761 Author: baertsch Date: Sun Aug 10 19:15:30 2008 +0000 fix intron count ; remove intronbases display commit c53aa725ee5fd27a348842f967718d3423ca72a1 Author: baertsch Date: Sun Aug 10 17:24:23 2008 +0000 remove debugging message from details page. Remove bad link commit b7115668b15de4d90d356223dc7dfbeaff2bdda0 Author: baertsch Date: Sun Aug 10 17:01:22 2008 +0000 initial versions commit baea62244b7a598dff047afa2dfe99129ad15298 Author: galt Date: Sun Aug 10 15:00:07 2008 +0000 "Encode release log update" commit add01b1b797636b87c127a445b1f84ae4ac67747 Author: galt Date: Sun Aug 10 15:00:04 2008 +0000 "Release log update" commit c1e78741b8d2a51a5d13393e8f57fffba2c315c1 Author: markd Date: Sun Aug 10 06:28:10 2008 +0000 added to-do item commit b0fff18adb49620730e7ed17f3225eb61282cb01 Author: baertsch Date: Sun Aug 10 01:30:22 2008 +0000 retroCdsAli3 retro track with colon coloring added commit bcf9c3d71df40abae6fdfc62b879e4424bf22d13 Author: baertsch Date: Sun Aug 10 01:17:53 2008 +0000 add psl tracks support for retroCdsAli commit 6febf556b198d9bcef3633df5593284898a20040 Author: baertsch Date: Sun Aug 10 01:11:06 2008 +0000 add support for psl tracks and codon coloring for retrogenes commit 00f901aac0e4b0700c3e40e59e7a7c567441b9e9 Author: larrym Date: Sun Aug 10 00:45:36 2008 +0000 don't allow hg17; code cleanup and commenting commit 361e27d8b081c7098af49e9d847c0f10babaaa9e Author: baertsch Date: Sun Aug 10 00:07:17 2008 +0000 add struct retroMrnaInfo *retroMrnaInfoQuery(struct sqlConnection *conn, char *table, char *mappedId); /* load a single transMapInfo object for an mapped id from a table, * or error if not found */ commit a5b270f34045f73b26064c3f9f562ad815bfeb10 Author: baertsch Date: Sun Aug 10 00:06:48 2008 +0000 add struct retroMrnaInfo *retroMrnaInfoQuery(struct sqlConnection *conn, char *table, char *mappedId) /* load a single transMapInfo object for an mapped id from a table, * or error if not found */ commit b868ebcf6863315e97cae5b9c426f7306379a947 Author: braney Date: Sat Aug 9 23:36:17 2008 +0000 add minimal zebra finch entries commit d5c1669cfe49490df45c621292d6528f62b60d9d Author: braney Date: Sat Aug 9 23:22:00 2008 +0000 don't output message about extended color options if there aren't any. commit c77ff8549c9c0ec16d00e59b0fb6bf119826e3b3 Author: fanhsu Date: Sat Aug 9 20:41:34 2008 +0000 Add the hgLoadSeq step for UniGene. commit 02fb94c5a3563324a7552c4095525db5bed7eadf Author: galt Date: Sat Aug 9 15:00:07 2008 +0000 "Encode release log update" commit 1767c64cecc47a30b19b32f441482012406a6cf1 Author: galt Date: Sat Aug 9 15:00:05 2008 +0000 "Release log update" commit 77d47dcfccefb73cc974f75e3541495ed3b90b81 Author: baertsch Date: Sat Aug 9 00:31:52 2008 +0000 add version to alignment details commit bcbfd8c7bc52dfa9fb406493b250a24888b175f6 Author: baertsch Date: Sat Aug 9 00:04:57 2008 +0000 update retro version number commit 78e7b0d708e90eda92c6d4a47e78860a1b3dffc3 Author: baertsch Date: Fri Aug 8 23:59:56 2008 +0000 remove stale code and update for retroGene alignment details commit f9a0df7cc3734379c5fd54cb8a036c0b8d9531e3 Author: larrym Date: Fri Aug 8 23:21:09 2008 +0000 add DIRS and parameterize test and install rules; chipseq is currently the only working dir commit ff1e9ae158e6857fefb7a59378a64bd650460744 Author: tdreszer Date: Fri Aug 8 23:15:37 2008 +0000 Changes in subgroups to support sorting and drag and drop commit 72bb9f8015d4f2813af1664911ab5bf89985065d Author: baertsch Date: Fri Aug 8 22:47:34 2008 +0000 add version handling for tablename commit d784d4e8227812eabeb744668105754406b1642a Author: giardine Date: Fri Aug 8 22:20:26 2008 +0000 added amino acid properties to display commit 7d86fc22905c07c2b95c4ca998a65e433357165a Author: larrym Date: Fri Aug 8 22:10:40 2008 +0000 add protein/lib to the hgLib rule commit 2d760cf43e8f06730a6dac30659fe3bdc8f58b35 Author: larrym Date: Fri Aug 8 21:38:43 2008 +0000 fix bug in RawSignal generating code; don't generate a trackDb entry for RawData commit eebbcd797edea6a0d5703ffc173906da7aa1d005 Author: larrym Date: Fri Aug 8 21:36:59 2008 +0000 fix bug in wrangler email code commit b93f166df62f05b0a971db81d5b57fbf311a0574 Author: baertsch Date: Fri Aug 8 21:31:00 2008 +0000 add support for suffix to table for data versioning commit 991e5e2a48537ff6659d65cea9079db5206ea039 Author: kord Date: Fri Aug 8 21:24:30 2008 +0000 added nemVec to dbToSpeciesMap[] commit f8e7d550837a27a1ad5fc089dd0f3dfdc3a22545 Author: hiram Date: Fri Aug 8 20:58:55 2008 +0000 Fixup version on ochPri and do not check for previous versions when they do not exist commit d81a953a3ad1ea4f32f338139aab3fd7c65a4c5c Author: larrym Date: Fri Aug 8 20:49:56 2008 +0000 turn required yes/no into a real boolean; add $sqlCreate and @extendedTypes globals commit 21227bc11b4ad61f7a91a8326bf45cb2cd244a48 Author: larrym Date: Fri Aug 8 20:48:37 2008 +0000 improve usage; move variables into Encode.pm; make unloader location more fault tolerant commit 2dfd8b96ba707ec3f6deab40c18f65439d31313f Author: larrym Date: Fri Aug 8 20:48:22 2008 +0000 code cleanup; use %extendedTypes commit fb729a2d8241c5e54da35ebd6e6faa0bda65cf05 Author: larrym Date: Fri Aug 8 20:43:19 2008 +0000 fix wig settings; fix problem with $outPath commit a2faf06839c8f37a41c0cb92906d693b3f365f60 Author: larrym Date: Fri Aug 8 20:40:59 2008 +0000 chrX ChIP-seq data from Stanford commit 3dab27030f051ec035c258ee1089a2cadcfb4013 Author: larrym Date: Fri Aug 8 19:48:55 2008 +0000 dink with table suffix logic; fix bugs in loadBedFromSchema; support fastq files commit a114c6ca4917df5f60b29cc297f6f9cbbdfb04bf Author: baertsch Date: Fri Aug 8 19:30:18 2008 +0000 add retroMrnaInfo* to ui commit 446ea140d321a5dde7bf7af789568f05124ddb30 Author: rhead Date: Fri Aug 8 19:23:11 2008 +0000 Added QA notes about sudo mytouch on snp128 and snp129 tables. commit ca0d4a06505e4af2bf3ddf31a4cfd6ddf67ed8df Author: braney Date: Fri Aug 8 19:22:49 2008 +0000 stick in release notes commit 17234ba14450dddf6404c188a23b17b7140b1fad Author: baertsch Date: Fri Aug 8 18:50:17 2008 +0000 add retroMrnaInfo3 commit 0ff63bfd0168d46788eed069401129d9f60a6564 Author: ann Date: Fri Aug 8 17:48:34 2008 +0000 Fixed link that was being redirected at NCBI. commit 422099206a3a8a1bf726bc4f14c0d871457963cf Author: ann Date: Fri Aug 8 17:27:17 2008 +0000 corrected link commit 2e5c948a09e8ad16afdeaf3d97be95e7467c458e Author: fanhsu Date: Fri Aug 8 15:25:13 2008 +0000 Updated to remove unused variables. commit 943b6716985303732b0cd1640241d28015ca71fa Author: galt Date: Fri Aug 8 15:00:06 2008 +0000 "Encode release log update" commit b0f9c5ba6a391b0cb887dc797a7a5101ce0cf23f Author: galt Date: Fri Aug 8 15:00:04 2008 +0000 "Release log update" commit e61053b23d209145d9917f8862378c580d91359e Author: markd Date: Fri Aug 8 05:29:19 2008 +0000 use name2 as gene_id if available commit b1048e45fa5ffa92ff3d8c571a473212d145ba48 Author: larrym Date: Fri Aug 8 01:58:36 2008 +0000 add validateFastQ; fix some problems with other validators; fix RawSignal creation pipe commit 11911af241a1ae3b2e4ff2dfbd4baac8329504ea Author: kate Date: Fri Aug 8 00:29:55 2008 +0000 Fix problem with supertracks commit 9d6d974d90a9eaa2ca5e195159f9c936dba3fe45 Author: fanhsu Date: Fri Aug 8 00:17:47 2008 +0000 Removed Illumina 1M info. commit 89264ee67d5dd6b724221a62a8e5a465a5806de5 Author: kord Date: Thu Aug 7 23:50:24 2008 +0000 added nemVec1 refseq lines - yes for xeno, no for native commit bdaec0d951c35870ed70f34e99fa5839bec0b7d4 Author: fanhsu Date: Thu Aug 7 23:50:11 2008 +0000 Shorten the short label of Illumina 1M track. commit 8713994a84428b1b8c171bbebb290523816b18a9 Author: hiram Date: Thu Aug 7 23:49:36 2008 +0000 Starting Ens 50 update. Have done Mm9 and BosTau4 commit d09942a6ac6aa61107d057c7300f9f7dc239be6a Author: angie Date: Thu Aug 7 23:45:23 2008 +0000 Added note about the molType fasta header value swaperoo that we fixed locally (see hg18.txt). commit 25d497df5e06b0e6eaca77c6da6e66e63fc84539 Author: fanhsu Date: Thu Aug 7 23:40:39 2008 +0000 Created snpArrayWith1M.html. commit 3659c17314501860d2548126ecf5cdc4ac406398 Author: fanhsu Date: Thu Aug 7 23:40:07 2008 +0000 Added release alpha and release beta per README for snpArray track. commit da1ae0f9fea8d0b58492631ab46eae34c7be7dd6 Author: angie Date: Thu Aug 7 23:36:24 2008 +0000 Reloaded snp128 and snp129 with new auto-generated .sql that includes enum and set values only if they appear in the data, so TB filter doesn't show misleading choices. For snp129 only, dbSNP's fasta headers have genomic <--> cDNA swapped, so I swapped them back. Also changed several hgwdev commands to use /data/tmp instead of /scratch/tmp (small & full on hgwdev). commit aeb13c107ba07143269a9ccf11c63948c6775230 Author: fanhsu Date: Thu Aug 7 21:53:59 2008 +0000 With Illumina 1M added. Waiting to be tested. commit 70db6f10c92b87305f71aeb634d6444f4540fd16 Author: hiram Date: Thu Aug 7 21:50:42 2008 +0000 Specifications for Ensembl 50 release are in commit c15ac53eaee1c72db991a83d5d871831450eafd4 Author: galt Date: Thu Aug 7 21:22:20 2008 +0000 more debug info in para "strange time" message commit 3a22e5ebe58d2a5f161434358f6b3ab21805e73b Author: galt Date: Thu Aug 7 21:21:00 2008 +0000 adding more debug info to warning commit e87e41b59f3fdf1e17998dfd07f19aaf51a7965f Author: galt Date: Thu Aug 7 20:59:16 2008 +0000 typo fix commit 06b27d722bb825a557ad89b7a239ab5e66e1d5c7 Author: larrym Date: Thu Aug 7 20:46:11 2008 +0000 use up-to-date chipseq commit f21ae1ba3f844548a91c26419c7beb58df529b76 Author: ann Date: Thu Aug 7 19:06:31 2008 +0000 fixed typo commit 3d3a8c913a42ac6d7e73e0fe57a6143beaa8b56a Author: fanhsu Date: Thu Aug 7 17:25:56 2008 +0000 Updated to call getPfamDomainList() instead getDomainList() for Pfam domains. It is necessary to get around the problem of different pfamDesc definitions. commit 33906227f3f1a7d13c303c04fe8a567395a3b342 Author: fanhsu Date: Thu Aug 7 17:15:29 2008 +0000 Call getPfamDomainList() instead of getDomainList for Pfam to get around the unique definition of pfamDesc table. commit 3a4067da7b534f778b49beaaa083b741739db267 Author: fanhsu Date: Thu Aug 7 17:13:33 2008 +0000 Added getPfamDomainList(). commit fdc313c134d606a621e107d0d7d5ecff58c86750 Author: hiram Date: Thu Aug 7 16:53:41 2008 +0000 Allow creation of the table upon first use when it doesn't exist commit 7602319367be8f99c77b1cf01de7ad31de62a302 Author: galt Date: Thu Aug 7 15:00:07 2008 +0000 "Encode release log update" commit a6ca2ce77b1593ba3417a5afd6a378e8bd1cd98c Author: galt Date: Thu Aug 7 15:00:04 2008 +0000 "Release log update" commit a5f9c04d9bead30f0f7f2bb3e3e3cf6876c3e2e2 Author: giardine Date: Thu Aug 7 13:13:38 2008 +0000 Fixed some errors. commit 1b13da10a10cc1bf89522790fa43a4a13ba22397 Author: baertsch Date: Thu Aug 7 05:17:04 2008 +0000 add version number to mrna sequence. access new tables retroSeq and retroExtFile commit aa4a296f09a3c4a61297452b5ed5a92365c99f7c Author: rhead Date: Wed Aug 6 23:31:23 2008 +0000 Removed lonely end anchor html tag. commit 2fcfed521dcfe0c5872c73723e535616ef199888 Author: braney Date: Wed Aug 6 23:29:55 2008 +0000 re-do with chr in front of LG chroms commit e626fd543c58ad49ddbbd856d1fffd4ce0467c0b Author: larrym Date: Wed Aug 6 21:50:21 2008 +0000 use replicate to number tracks; remove unused track setting from load.ra; add -validatePif option commit aed56e87bf96acc372536e301c5d1a25d412eb64 Author: larrym Date: Wed Aug 6 21:43:07 2008 +0000 Stanford => HudsonAlpha commit 683e4ec479f17a02137401c2d0082bc0afd4ddf9 Author: fanhsu Date: Wed Aug 6 20:05:34 2008 +0000 Fixed a subtle bug. commit 0a853dbee3194e2c0ab487b3615a36d86d3453da Author: fanhsu Date: Wed Aug 6 19:52:02 2008 +0000 Fixed a subtle error. commit 0756733220db33cf6a4e7e9431fd3382afa6fe9b Author: larrym Date: Wed Aug 6 19:47:46 2008 +0000 implement hasReplicates commit 8838f31a4311d024abd24292588883ad41130017 Author: larrym Date: Wed Aug 6 19:46:41 2008 +0000 add replicate and softwareVersion commit a7a60554d55f183e14bb2d89612b16bb10e6aca2 Author: larrym Date: Wed Aug 6 19:44:30 2008 +0000 bump up $pifVersion; add hasReplicates logic commit fb858d979cf0827b0dccb10fcaf5f750078c0982 Author: tdreszer Date: Wed Aug 6 18:02:16 2008 +0000 Fix for supertrackUi which failed to show subtracks that are composites commit dbb22f935064e3ada6842f5781125c1f8d1bc3d9 Author: aamp Date: Wed Aug 6 15:26:06 2008 +0000 .sql files don't often work right after autoSql. This one's no exception. added bin, and changed up the indexing. commit b6f9590ae023f16af385d5b8e140eef3135efd63 Author: galt Date: Wed Aug 6 15:00:07 2008 +0000 "Encode release log update" commit 42e40ba00424f34b0829557699411791468f1f4d Author: galt Date: Wed Aug 6 15:00:04 2008 +0000 "Release log update" commit c94c876fb19d481ff5f455f39477dcaa86957b15 Author: kent Date: Wed Aug 6 01:24:25 2008 +0000 Updating bioCyc pathways. commit 69ad7f3b44750df927d66c2ebcd3522da46072e8 Author: kent Date: Wed Aug 6 01:16:16 2008 +0000 Reworking this program so that it doesn't require a bunch of preprocessing of the bioCyc data before running, and so that it uses tables we actually have in the database. commit a2ca42f0115f43a1150cb373eee35c37b82c03b1 Author: rhead Date: Wed Aug 6 00:49:02 2008 +0000 Fixed link to Bryappa Venkatesh. commit 5b2bde7e318132af1a213e3ac8184fbb89976382 Author: larrym Date: Tue Aug 5 22:20:58 2008 +0000 add a bedGraph test to an existing wig test commit 9193a8e2cebf680056375eb375c1f9c07dc7315f Author: larrym Date: Tue Aug 5 22:20:18 2008 +0000 remove bedGraphTotalHeight and use wigTotalHeight instead; this fixes a problem with disappearing zero values in bedGraphs and removes duplicate code commit 2f503652b723a41dbf46715c9cdfd23d1c887c29 Author: braney Date: Tue Aug 5 21:56:22 2008 +0000 finished sloth alignments commit 8c16d8f88faea80c333f999b5dcdd8ea6f653a97 Author: larrym Date: Tue Aug 5 18:28:50 2008 +0000 leave copy of wigLoad stderr on disk (so wranglers can get wig upper/lower limits) commit e6ebe6da453dd65e5e27bb959015e1c7c5728dea Author: larrym Date: Tue Aug 5 18:09:10 2008 +0000 allow user specified STDERR file commit 50112d663901833cb98ef97c825d860501b05013 Author: larrym Date: Tue Aug 5 18:07:55 2008 +0000 use explicit glob for file list; use space as separator so we can use list in shell commands commit 7cfcdac15ff8eebd138f39ce2276abd91497c5a5 Author: kuhn Date: Tue Aug 5 17:54:00 2008 +0000 added line to usage commit 151d56e1df769bd07a6a022d0fb419b1791361ca Author: braney Date: Tue Aug 5 17:48:11 2008 +0000 finished squirrel blastz commit 82bb3804634424c7e09692407d813acf17f8d4a5 Author: kuhn Date: Tue Aug 5 17:32:11 2008 +0000 shortened some of the cell-type names to better fit teh space commit d1f6598843e1fcd0d239666a88b0e2a7649ef9c3 Author: kuhn Date: Tue Aug 5 17:20:06 2008 +0000 typo commit 64da7836b4ab19e8a01dcfea5651e2b3917388d0 Author: larrym Date: Tue Aug 5 17:13:43 2008 +0000 "New version number v188" commit 395e8473a4ae56205983b4f1cd1c8f8809debf43 Author: galt Date: Tue Aug 5 15:00:06 2008 +0000 "Encode release log update" commit 31ce85f81565ca3ce29f9fce3f2e7fd3e607da46 Author: galt Date: Tue Aug 5 15:00:03 2008 +0000 "Release log update" commit f4c5ad0ea1b3f80ba394bb7f852d7e008c186005 Author: braney Date: Tue Aug 5 14:36:41 2008 +0000 be careful about calling hChromSize since there may not be an active db commit 8a477596333b41af2c0b52bb1491bf5a833600dc Author: aamp Date: Tue Aug 5 12:33:55 2008 +0000 Added encodePeak track type. commit c65d1544d0edecf27332fd7f5526bc896394d22f Author: larrym Date: Tue Aug 5 00:09:12 2008 +0000 lab => grant commit 06b1537e40b0137891b561c545471c51a6303736 Author: larrym Date: Tue Aug 5 00:08:36 2008 +0000 remove project field commit 02de87ff5a86d0860fd98ec70f057f712eeacd5f Author: larrym Date: Tue Aug 5 00:08:24 2008 +0000 validate bed5Float; support group and dataType; die if composite track doesn't exist commit 4d1f3d69cb731f2ba03880cc3385c4e83bc0c6de Author: larrym Date: Tue Aug 5 00:04:23 2008 +0000 wgEncodeStanfordChip => wgEncodeStanfordChipSeq commit 3b2f0e3c44172195563a332ba755ff9ef56462e4 Author: larrym Date: Mon Aug 4 23:48:57 2008 +0000 add grant and dataType fields commit 4fa92fe3b3b35ecf5724f8b4137234f780ecc36d Author: larrym Date: Mon Aug 4 23:41:28 2008 +0000 add @extendedTypes commit 2b9c1a6dd54883b3d55ac09fed5a8a75de542b3a Author: kuhn Date: Mon Aug 4 23:27:07 2008 +0000 fixing up multizMm3Hg15 so archiving works commit d0e51db3f3b7af795e77d1da7dbb6149909605b6 Author: fanhsu Date: Mon Aug 4 22:32:33 2008 +0000 Updated Illumina 1M to reflect the fact it was now built based on snp129 instead of snp128. commit 6755efb3a7c8492cb95f09d7fdf4455c6f9f70b5 Author: fanhsu Date: Mon Aug 4 22:25:44 2008 +0000 Updated Illumina 1M sub-track short and long labels. commit abed573295bdce7149bea88ac4bfa82755518fec Author: fanhsu Date: Mon Aug 4 22:22:50 2008 +0000 Added Illumina Human1M-Duo. commit e3100a3e02f0711497ddfd3579447adfcd86d5df Author: pauline Date: Mon Aug 4 22:11:51 2008 +0000 Fixed species order. commit ac7f29ef0c253c2cb7959f19e60fe3111d55cff5 Author: braney Date: Mon Aug 4 21:06:52 2008 +0000 armadillo and mouse lemur finished, starting squirrel commit 477aed5f9e021fbbff9a4aa5a77a15b9ed03fe9f Author: larrym Date: Mon Aug 4 18:27:32 2008 +0000 add $unloadFile and pushQFile commit 87c4ae8cac6f6180c03f50e495defcc5caef8721 Author: larrym Date: Mon Aug 4 18:19:13 2008 +0000 start code which creates pushQ file commit d66aeb2013e1794948d9684ed8eb1d7f2068e719 Author: larrym Date: Mon Aug 4 17:34:52 2008 +0000 use SafePiple commit 57c095fb0ef623415b228e036238ae3f2ce9263a Author: braney Date: Mon Aug 4 17:21:50 2008 +0000 sloth commit f89294102a66060e9fec28a67ecb9c006e930f1a Author: angie Date: Mon Aug 4 17:11:49 2008 +0000 Orthologous alleles (liftOver'd human SNPs) in chimp, orangutan and macaque. commit 0d516b684cfa2f52283ac8954aa5ca0413bc37bc Author: mikep Date: Mon Aug 4 17:06:06 2008 +0000 Renamed argument for clarity commit b9ed3546a2a780250b9ad09a36bac416157bce68 Author: braney Date: Mon Aug 4 16:48:24 2008 +0000 zebra finch commit 547bc4cb78bc042830b80397b5ff9776b9c2b3c7 Author: braney Date: Mon Aug 4 15:23:38 2008 +0000 squirrel commit 2bf230316b646e9f38ec4a40235baf96e3b3afaa Author: galt Date: Mon Aug 4 15:00:06 2008 +0000 "Encode release log update" commit be6690d22f35ff174f29ceaded69dfcc2299f506 Author: galt Date: Mon Aug 4 15:00:03 2008 +0000 "Release log update" commit 3f502b0b41078c317d047e805a8b34d72a352b11 Author: mikep Date: Mon Aug 4 13:50:04 2008 +0000 added method to add range.val default for Count and List commit 809b86dd5de582efa1a4e48a336d4f3889396017 Author: kord Date: Mon Aug 4 02:56:50 2008 +0000 Added nemVecNames for Nematostella vectensis commit 925f5c67157b990526828f01dbe13baa01c140aa Author: braney Date: Sun Aug 3 20:15:09 2008 +0000 finish blastz elephant, add mouse lemur, start multiz commit a53a99e387ccfad8eb1f89e04e59d4c3e25d566f Author: braney Date: Sun Aug 3 19:42:49 2008 +0000 add featurebits commit 27e3a0bf653ead732e48181f619061732a35a41c Author: braney Date: Sun Aug 3 19:24:19 2008 +0000 genbank and downloads commit e0948f281529d7d2a7c70c8941328bb3b63d764d Author: braney Date: Sun Aug 3 18:51:29 2008 +0000 mouse lemur commit 8fc2c325e00d72855649b957809ab9e9e3a02653 Author: galt Date: Sun Aug 3 15:00:07 2008 +0000 "Encode release log update" commit a30d47b8d8152b34d2bd367f7e398d0e3738a0cd Author: galt Date: Sun Aug 3 15:00:05 2008 +0000 "Release log update" commit 3e6e27beae443873082012b30fa6285a7c3d083f Author: braney Date: Sun Aug 3 01:28:06 2008 +0000 new armadillo commit b81c1aa4e52dab08ab7bea496afc6bf4bfc90f3c Author: jsanborn Date: Sat Aug 2 22:14:00 2008 +0000 added separate RA files for TCGA open and controlled access data commit ca9ce38f729677889594ce1b6852a1aa4dba6249 Author: kent Date: Sat Aug 2 21:40:51 2008 +0000 Removing unused rangeTree.h commit 27f3425ac3a0e9102e45bde4ffba5e3c349acad8 Author: braney Date: Sat Aug 2 21:05:53 2008 +0000 Added taeGut1 - zebra finch commit 51e7de23d946e97327e8fbcb54b313bf2edb9679 Author: braney Date: Sat Aug 2 20:22:07 2008 +0000 finished microbat blastz commit b17a78948841b1104955cbd620b77b16b7ea40aa Author: braney Date: Sat Aug 2 17:56:29 2008 +0000 rock hyrax commit aec118d78c622b08a0db535ca87a743bd9cd8a07 Author: galt Date: Sat Aug 2 15:00:09 2008 +0000 "Encode release log update" commit 13e3d5a57602375c48713c9c92d1cb939160b1ad Author: galt Date: Sat Aug 2 15:00:06 2008 +0000 "Release log update" commit 204b2dccf3c6215938ad284f2b390fb20e16dcc8 Author: braney Date: Sat Aug 2 14:37:15 2008 +0000 fix up ooc location for taeGut1 commit 9a1dfcd7d31bd72b43107ceb3198002963884319 Author: rhead Date: Sat Aug 2 06:49:08 2008 +0000 Changed snp128 visibility to hide. commit f48c8169e0a8b17a3a51b18c90e89bdd81331588 Author: kord Date: Sat Aug 2 00:27:36 2008 +0000 updated 11.OOC, started GenBank, added more notes on simpleRepeat cluster run redo commit 929950ce6b31c31478e6ae12059b782d9f75cf4a Author: rhead Date: Fri Aug 1 23:54:14 2008 +0000 Clarified 'human only' phrase and added a sentence about orang ortho alleles. commit dd579bd737d04b7742fe46558bd45d9722a9b4f2 Author: tdreszer Date: Fri Aug 1 23:43:48 2008 +0000 Replacing woldRnaSeqSignal and woldRnaSeqSplices with matrix composite woldRnaSeq commit aee54099315026385aaf13865f94eadbfdbe1f76 Author: tdreszer Date: Fri Aug 1 23:39:07 2008 +0000 Fix mistaken short labels commit 618d6598d2dc48b18c402de4f31ec6c59b36bbe7 Author: tdreszer Date: Fri Aug 1 23:36:21 2008 +0000 Replace wigUi and scoreUi with lib routines: wigCfgUi and scoreCfgUi commit dbd9a41cc097e5e69ef0435893e23dd198cddf97 Author: fanhsu Date: Fri Aug 1 23:31:33 2008 +0000 Added snpArrayIllumina1M. commit dbd3bf7e9b62bbd70a2bbd033358945a0399b879 Author: tdreszer Date: Fri Aug 1 23:31:24 2008 +0000 Made wigCfgUi and scoreCfgUi common to replace wigUi and scoreUi commit 033f669e2e71496d6c275629d18194bc23400ba8 Author: fanhsu Date: Fri Aug 1 23:16:37 2008 +0000 Added snpArrayIllumina1MRaw.sql. commit 81942712dbeb42171fbbbb357a1db138ff2c2e4f Author: fanhsu Date: Fri Aug 1 23:14:23 2008 +0000 Created illuminaLookup1M.c. commit 4367da72e24fc17a3a5914a85ad0061b6988f610 Author: fanhsu Date: Fri Aug 1 23:13:31 2008 +0000 Updated makefile to include illuminaLookup1M. commit 0889148de70f7a01f8ed7414d01a96b29f40c799 Author: rhead Date: Fri Aug 1 21:56:56 2008 +0000 Also nudged snp129Long priority so that snp129 search results will appear ahead of results from earlier builds. commit ed2ed932d9f548da8efbd2f0e805e6541b4778cd Author: rhead Date: Fri Aug 1 21:44:26 2008 +0000 Nudged snp129Short priority so that snp129 search results will appear ahead of results from earlier builds. commit a3c3903be412fd103471b2c4eb04fc6e4a59633f Author: braney Date: Fri Aug 1 19:47:03 2008 +0000 initial description commit 252e830242dce6bf396beabbfc2a58867940f64e Author: braney Date: Fri Aug 1 19:45:13 2008 +0000 change name of assembly commit e7cae50ee8a692f14f52c9c6d3284202194a2628 Author: aamp Date: Fri Aug 1 18:42:34 2008 +0000 Moved peak module to lib/encode. commit 76443175ce7f56690b2733a32f8e3c8832383f31 Author: aamp Date: Fri Aug 1 18:03:49 2008 +0000 Moved more encode stuff into lib/encode... this time some table-only modules. commit 31813d9bb10bbf07776032f298b301fe4abce4a8 Author: aamp Date: Fri Aug 1 17:59:44 2008 +0000 Moved the "custom" portion of the encodeRegionInfo module into lib/encode. commit 3664450a0ab615841abbf11fb827770e3cf68c0f Author: braney Date: Fri Aug 1 17:56:27 2008 +0000 more mammal blastz's commit 649fa7b9c40dbf6b94b5e87913c86bb7e74a283e Author: aamp Date: Fri Aug 1 17:55:36 2008 +0000 Forgot to remove duplicate module files. commit 39c590eefd260b5b841b8be9b751d27ab1e5cf62 Author: aamp Date: Fri Aug 1 17:49:15 2008 +0000 Stashed encode modules in lib/encode. commit 3d73fcc85b16fdf6f130d6f99e12d326f4e6cc59 Author: braney Date: Fri Aug 1 17:47:58 2008 +0000 elephant commit 78b497e038182a171df6b1669a3ca64413d2ed0c Author: rhead Date: Fri Aug 1 17:44:02 2008 +0000 Typo. commit aec96151b11629ec690e23e22110f4f820c2eea7 Author: braney Date: Fri Aug 1 17:31:13 2008 +0000 Added taeGut commit bc1f08b696e43c56d107c3480a00a1127b82004d Author: braney Date: Fri Aug 1 17:25:24 2008 +0000 Added taeGut1. commit 75d5b707fb6406dc9c9ae55196a465c80e29f761 Author: hiram Date: Fri Aug 1 17:21:41 2008 +0000 Adding reference to recently published paper commit 3afef64610293a73a206e4f7f45f46c598f628f5 Author: galt Date: Fri Aug 1 15:00:11 2008 +0000 "Encode release log update" commit f985df5c7bbf3fd3b06746d1383a498b963e4b0a Author: galt Date: Fri Aug 1 15:00:08 2008 +0000 "Release log update" commit c4d649a9c4f2979e2b2b0f2a724b51c38ab0a108 Author: braney Date: Fri Aug 1 03:27:28 2008 +0000 Initial descriptions for speTri1. commit 36ce6ac02e208a3f68205610bc751860c793d455 Author: braney Date: Fri Aug 1 03:27:24 2008 +0000 Added speTri1 to DBS. commit 9a04646064de6f6ed60521d54025bdc1508c83ec Author: rhead Date: Fri Aug 1 00:33:04 2008 +0000 Chanaged analysed to analyzed. commit 2314e66c7fd5add2936c86bf7c82a7d553ee8e93 Author: fanhsu Date: Thu Jul 31 21:59:22 2008 +0000 Replaced '|' with ':' to avoid a BLAT bug. commit 49f73c66cb9f195c92add42407a596afd0d5f2c9 Author: pauline Date: Thu Jul 31 21:32:58 2008 +0000 Added priorities for new horse. commit d63bd00757c060ad27be96c8c590f3b24ab4e3b0 Author: pauline Date: Thu Jul 31 21:12:56 2008 +0000 Adjusted priorities to accomodate new horse. commit 6fd8a1d047cbc4648990fcd55af322447cde718b Author: mikep Date: Thu Jul 31 18:11:47 2008 +0000 Library routine for genomeRangeTree, extending rangeTree, fixes for rangeTree, and test program for genomeRangeTree library routines commit b3bb965f948c0420092151a0667af85212b9f1e3 Author: donnak Date: Thu Jul 31 18:02:49 2008 +0000 Added link to "Session". commit 73da83c543f86a2fb39f784d72f3e2da1994d749 Author: kuhn Date: Thu Jul 31 17:50:38 2008 +0000 fixed to work with explicit RR machine names. thanks, brooke. commit aaf32c238b5f819b10217395aa9dcd8ad6f21d99 Author: braney Date: Thu Jul 31 16:47:59 2008 +0000 take out check that depends on hgcentral. Moving this to hgSeq commit 619cebdffa9fad130945608b968da71ad3004485 Author: tdreszer Date: Thu Jul 31 16:39:45 2008 +0000 Revert to Mike's tracks so Wold can view both commit bd0f9fd91baf7f218cec4e5aa1b0e95bcc52f457 Author: galt Date: Thu Jul 31 15:00:07 2008 +0000 "Encode release log update" commit 552b757188fdabc00e776c53dca5617e13e1fbd2 Author: galt Date: Thu Jul 31 15:00:05 2008 +0000 "Release log update" commit d910bc69c23a8701a511ccfa5917cae0dbd54a7b Author: braney Date: Thu Jul 31 14:13:33 2008 +0000 Initial descriptions for dasNov2. commit c9983c32e53850d4c0bb14c5bd4bcecdeca8943e Author: braney Date: Thu Jul 31 14:13:29 2008 +0000 Added dasNov2 to DBS. commit 36e5c7235a93e83768644e3cb248caf3f1d63935 Author: aamp Date: Thu Jul 31 01:19:07 2008 +0000 Added peak module. commit 8251b3414049f24faf1d6c79ea6c36e622fe006a Author: kate Date: Thu Jul 31 01:00:33 2008 +0000 Smarten up super track handling -- add to sstrict list only if a component track (or composite) has a table loaded commit 95a3d4cbc2321e898cad177ce68107b341cafd57 Author: braney Date: Thu Jul 31 00:59:44 2008 +0000 pika alignments done commit 1f1a77777143c332956432445495562b39926c6a Author: tdreszer Date: Thu Jul 31 00:46:52 2008 +0000 Changes short name for woldRnaSeq commit bffa60e056ede8038a924245f1d5c8e2e253fd03 Author: tdreszer Date: Thu Jul 31 00:43:41 2008 +0000 Master composite of Wold's RNA-seq tracks is renamed commit 58d0f60398ebbff2c705fd3715b40b6f0629a340 Author: tdreszer Date: Thu Jul 31 00:42:31 2008 +0000 Wolds Tracks by matrix UI commit ccc982b00ca7ec508e7230b61049d761629d7756 Author: tdreszer Date: Thu Jul 31 00:41:33 2008 +0000 Matrix composites have 'maximum' display mode drop down commit 0485115151ae466f68d8bb221cae5c2493c627a8 Author: tdreszer Date: Thu Jul 31 00:40:10 2008 +0000 Added js for matrix initialization commit 30762adb1923a1438bbecaa5b0b353084ccd935d Author: mikep Date: Thu Jul 31 00:12:32 2008 +0000 Sample RNA-seq bed 12 data from Wold commit a3dc9b20549941defd755adb976cfc14e50b7269 Author: braney Date: Wed Jul 30 23:16:35 2008 +0000 started over, using windowMasker masking, next up : genbank commit bf0a5ebda31d08a8ae210e5f4b3cd9272c96cace Author: kate Date: Wed Jul 30 23:09:04 2008 +0000 Need autoscaling with this initial load, as the 2nd replicate isn't normalized commit 50de35196d22155b2495a400ae7721ed0516dfc8 Author: kate Date: Wed Jul 30 21:50:19 2008 +0000 Correct view limits for Wold RNA-seq track commit 9d6cb39f897294588012bbd5ffe6ad023a8bc49d Author: kate Date: Wed Jul 30 21:39:35 2008 +0000 Stub for RNA-seq data from CalTech commit c7b36ba1fe051c6de7fc4a4810a334b90197176f Author: kate Date: Wed Jul 30 20:51:51 2008 +0000 Add CalTech (Wold Lab) RNA-seq commit 6d8479f161a5296e9fa8c1572df7728467ccb869 Author: larrym Date: Wed Jul 30 20:50:02 2008 +0000 .rb => .pl commit e4f9d79c996bf4e46bdc0bbd6f2ffb893e20ce22 Author: larrym Date: Wed Jul 30 20:45:13 2008 +0000 support new file types; remove use of tableType (replaced by use of type); fix wib ln bug (wasn't including path); code cleanup commit ac6b65f111c2cf5bcabec16e05a51350b3d006f6 Author: giardine Date: Wed Jul 30 20:10:22 2008 +0000 Added new links for locus variants track commit 58e46d71eef7dc7477bf8183292b7dcfd4214dea Author: giardine Date: Wed Jul 30 20:09:30 2008 +0000 Added new LSDBs, left logos at PSU, so don't have to add logos to code tree that may never get to genome. commit 5319a9376dc8c7770063124b8a498415284b795e Author: braney Date: Wed Jul 30 20:02:39 2008 +0000 Initial descriptions for loxAfr2. commit f5aa23c172fb192a95c98512881adcf40e175aa7 Author: braney Date: Wed Jul 30 20:02:35 2008 +0000 Added loxAfr2 to DBS. commit 09e2b15c6ed67a8cdef6769c83fb88b991c16bcf Author: larrym Date: Wed Jul 30 19:49:52 2008 +0000 remove obsolete PIF field tableType; add missing newlines from die's to suppress line numbers commit a0e5e8376c76f49eea287aa3647008ed2ff694d0 Author: galt Date: Wed Jul 30 15:00:06 2008 +0000 "Encode release log update" commit 7708500484cd776ff9f93193181c52e294e0c9fd Author: galt Date: Wed Jul 30 15:00:03 2008 +0000 "Release log update" commit 5564a330459c4da094a8f1d168f5fb335db83fdc Author: markd Date: Wed Jul 30 01:33:57 2008 +0000 put ccds tab file on local disk commit 35b67969940609627fafdb95ce20cb8076069045 Author: braney Date: Wed Jul 30 00:47:59 2008 +0000 change vicPac1 to vicVic1 commit 3a41a5a051dee984e17ed80e2c4edb0a26a450f5 Author: braney Date: Wed Jul 30 00:32:38 2008 +0000 tarsier commit c7103df2d44c238e3effeb986cdf016c182de33c Author: braney Date: Wed Jul 30 00:12:44 2008 +0000 alpaca commit 261cce779a619144b38fccc18d7e2382509dfe2a Author: braney Date: Wed Jul 30 00:06:55 2008 +0000 change vicPac1 to vicVic1 (stupid brian) commit 4728fdeebdb0dd01bb12d80550c968967eb544e4 Author: braney Date: Wed Jul 30 00:00:33 2008 +0000 copying from vicPac1 commit 5ba69a6ef6c17ab87f04acaa65b309b857a44b56 Author: larrym Date: Tue Jul 29 23:21:23 2008 +0000 use pl unloader; use HgAutomate::verbose commit 7bfbeda6e0bd9d7587483252a0abffea074661b5 Author: fanhsu Date: Tue Jul 29 23:11:46 2008 +0000 Created spToSpXref2.c. commit 84482a35d5fe0a0488b27988d252106e3da14ef3 Author: fanhsu Date: Tue Jul 29 23:10:49 2008 +0000 Created makefile. commit be05e04f995a2f62e11fcfaa7685f41826ea9174 Author: fanhsu Date: Tue Jul 29 23:09:39 2008 +0000 Added spXref2 table. commit 399d89c71616fa8fb9798810c442bd7da869ab61 Author: larrym Date: Tue Jul 29 23:08:14 2008 +0000 support encodePeaks and tagAlignment types commit 61ade85141e14ca1af9c6e330418f27713b020af Author: fanhsu Date: Tue Jul 29 22:58:09 2008 +0000 Added spToSpXref2. commit d35ce4d34b74182f157aaeedc0cacddbb832d888 Author: larrym Date: Tue Jul 29 22:57:08 2008 +0000 add tableExists, dropTable and dropTableIfExist commit 17de01c09fe9b05d490b05ccc40baad868bab2b7 Author: larrym Date: Tue Jul 29 22:56:08 2008 +0000 move some code to HgDb.pm commit 1a98dfe6ed288352729e8bfe8c3d838e2fd2c6ec Author: larrym Date: Tue Jul 29 22:47:00 2008 +0000 doEncodeUnload.rb => doEncodeUnload.pl commit 4999a10fd1790a474f89603d2accfd7c5b7d3cb3 Author: larrym Date: Tue Jul 29 22:45:09 2008 +0000 converted from doEncodeLoad.rb commit e9cf854b58c80dee7beebd452f5fb388a9d7dced Author: braney Date: Tue Jul 29 22:31:15 2008 +0000 microbat commit 4483795bf38dbd0191cd55312f2c443d366a8bf6 Author: braney Date: Tue Jul 29 22:14:09 2008 +0000 rock hyrax commit 5d898cbff0dfe2959d8c6439090ba2a8243d37bc Author: braney Date: Tue Jul 29 22:11:53 2008 +0000 starting up a couple more blastz commit 89e4af3ebd189d5fca4ffd9769fd333d9f410da8 Author: kuhn Date: Tue Jul 29 21:57:26 2008 +0000 changed format a tweak commit e56f7f6d51813945c1d5bac45fba7aaf405bc45e Author: braney Date: Tue Jul 29 21:51:00 2008 +0000 pika commit 18612a8c3600f3033d742e60201795edaf11c34a Author: larrym Date: Tue Jul 29 21:50:27 2008 +0000 add validateTagAlignment and validateEncodePeaks commit 00525b2632736bd5ca692c4c188bb7485385ffbb Author: angie Date: Tue Jul 29 20:28:58 2008 +0000 Added link to help page; more changes to make sure jsInit is always called after cartWebStart (not before). commit 9cc1b5733c331f460194b464e3bb489a5d8a7aa0 Author: larrym Date: Tue Jul 29 20:08:22 2008 +0000 move lots of code here from doEncodeValidate.pl commit a7551752040a4b9bf7ec8c6ef3259fcda5932a60 Author: larrym Date: Tue Jul 29 20:03:48 2008 +0000 move lots of code to Encode.pm; move email notification to doEncodeLoad.pl commit 9a9337f6fed666ac39492761bc68be6a64489e17 Author: larrym Date: Tue Jul 29 19:56:39 2008 +0000 move email notification here from doEncodeValidate.pl commit 5c8d06a20365a70432b0086b5101685b135a59ed Author: kent Date: Tue Jul 29 19:15:56 2008 +0000 Reverting to older column names for pfamDesc table, which seem to be what everybody but this routine expects (and database are built that way). commit da1c6787bcc11e0868c789b2cc543776e69b6476 Author: larrym Date: Tue Jul 29 19:13:09 2008 +0000 add Encode.pm and SafePipe.pm commit dbccb1113fdf8e0d2d54d95e9ab5829bfd844fb5 Author: larrym Date: Tue Jul 29 19:12:55 2008 +0000 utility stuff for Encode scripts commit 9d625270018b4f53e594497b400069df56d39390 Author: kent Date: Tue Jul 29 19:11:44 2008 +0000 Restoring pfamDesc fields to older names that are used by Gene Sorter and hgGene, and existing proteome databases on round robin. commit 90514f8c2d021d0fd9ddc4bef2486778da51cf3b Author: larrym Date: Tue Jul 29 18:52:08 2008 +0000 move readRAfile to RAFile module commit a17b3f87b5668489bad5b758d3b48f4964b0c1fa Author: larrym Date: Tue Jul 29 18:48:53 2008 +0000 change return value from readRaFile to conform to format used in doEncodeValidate.pl commit e4a09cdef93d173048a99c6d3cb9c2aa4d8bf2d3 Author: hiram Date: Tue Jul 29 18:26:21 2008 +0000 Trying out the knownGeneLists.html link again, fixup galaxy reference, remove absolute references, remove MGC comment commit e69d6ab939fd60d5b5cc67c4a89a0cb96effc766 Author: angie Date: Tue Jul 29 18:02:09 2008 +0000 Added noScoreFilter to MGI (jax%) BED tracks, where score is only a placeholder. commit f19530dc0c8794ce42ba3a390e2a006848046394 Author: rhead Date: Tue Jul 29 17:53:42 2008 +0000 Fixed broken link to credits page. commit eff973fc3c912e898690943138d19d60ccaa5f47 Author: pauline Date: Tue Jul 29 17:31:21 2008 +0000 Fixed short labels for equCab2 nets and chains on other orgs commit b7d7f0c864835f0cd88aae59617497b947130352 Author: galt Date: Tue Jul 29 15:00:20 2008 +0000 "Encode release log update" commit 19691c325e1d087ffec2c2e7fe106cccbd579a95 Author: galt Date: Tue Jul 29 15:00:17 2008 +0000 "Release log update" commit fc28b547d776c656b86489091b92762bf7b2fa1b Author: braney Date: Tue Jul 29 03:02:14 2008 +0000 Initial descriptions for micMur1. commit f600d10f46c3943e5efb10404682cacba0914549 Author: braney Date: Tue Jul 29 03:02:12 2008 +0000 Added micMur1 to DBS. commit 60c095c5caa287ad37305b79c848c8fc0f23ae30 Author: pauline Date: Tue Jul 29 01:01:09 2008 +0000 Fixed matrix lines for new equCab2 assembly. commit 0cd4f63cb76c0c82ee78afa33ff73dd1f12f49f3 Author: larrym Date: Tue Jul 29 00:38:36 2008 +0000 remove obsolete stuff; add DOWNLOAD_DIR logic commit 4c706bc910ece8564a8b14dec52dccc6d1e854c9 Author: larrym Date: Tue Jul 29 00:38:06 2008 +0000 add -noEmail option commit 8d317405092a741797a053de6f6d9058d8528c5b Author: fanhsu Date: Mon Jul 28 23:29:22 2008 +0000 Created snpArrayIllumina1M.sql. commit 9be7046af942ab625a3d96b7a7ad92c422d0ea63 Author: braney Date: Mon Jul 28 21:41:48 2008 +0000 fix human proteins track to be completely sorted commit 0da5c6d3bb4b62459419c99dd7f232177c607609 Author: ann Date: Mon Jul 28 21:24:47 2008 +0000 reworded data message commit 899cf63072446b161d6be84a0e57c319fc2558d1 Author: ann Date: Mon Jul 28 21:21:58 2008 +0000 made room for new Human Proteins track (based on hg18). commit 86d04c58537c003f2086280ab59b36eaf4a490dc Author: ann Date: Mon Jul 28 21:06:15 2008 +0000 added tetNig1 to blastHg18KG rules commit 7abf6262a5ccf991c35619f5f953ebc07336dd1f Author: giardine Date: Mon Jul 28 20:48:20 2008 +0000 changing filters on ORegAnno track from exclude to include when checked commit 1cd0bb7681534908138fbf4c37f51ec6054e5167 Author: giardine Date: Mon Jul 28 20:44:25 2008 +0000 switch ORegAnno type filters from exclude to include when checked commit becfbde72c2c9ed4f1b23e2bd219d1d7d8a98863 Author: braney Date: Mon Jul 28 19:14:29 2008 +0000 copy files to the san commit 472791f41c043e5247ae45aa32f042d4c7dc2cef Author: braney Date: Mon Jul 28 18:35:40 2008 +0000 vampire bat (megabat) commit 9ee5878d06ded69615593d0456f9a66a3fb1eb8f Author: donnak Date: Mon Jul 28 18:34:11 2008 +0000 Commented out Rachel's pub until it hits the streets (ETA 2009!). commit 3f296b199155c758b634b8c39e5bae80677956c5 Author: braney Date: Mon Jul 28 18:14:28 2008 +0000 finish up blastz of vampire bat commit afa611f19727712d9f9b93c4c03b4a859e043225 Author: markd Date: Mon Jul 28 17:28:48 2008 +0000 allow empty fa files, needed for peptide file when a refseq update contains only non-coding commit 7e42567b3d7b24a26ca77a9b3c7e0022b44cfa5c Author: galt Date: Mon Jul 28 15:00:03 2008 +0000 "Encode release log update" commit 2c8087876bd198de4238f0777f741dc407847ea8 Author: galt Date: Mon Jul 28 15:00:02 2008 +0000 "Release log update" commit 073aa65ca5604650ce56dfbbbb9e1da4245d15a6 Author: braney Date: Mon Jul 28 14:15:29 2008 +0000 add blastz tracks to 2X species commit 224943462a4dfbec43c479b637d1fa71b030c643 Author: braney Date: Mon Jul 28 04:21:11 2008 +0000 Initial descriptions for myoLuc1. commit 0e2ce688ee157166aa9e1921010589e32b0bd806 Author: braney Date: Mon Jul 28 04:21:02 2008 +0000 Added myoLuc1 to DBS. commit 8c104ab5eb4f11fdbabf832aa5957699fa3553a4 Author: kate Date: Mon Jul 28 04:15:09 2008 +0000 Fix to scaffold-based syntenic net routine commit 1d8c026b2d1c57dbf8160680a5abdbb51233d650 Author: braney Date: Sun Jul 27 21:01:00 2008 +0000 this is kangaroo rat commit 5891b57996250927cd0e88e0838718cc462871e7 Author: braney Date: Sun Jul 27 20:38:32 2008 +0000 Initial descriptions for ochPri2. commit c65c640f60885898b948e8fb0236f119d0b9e7e1 Author: braney Date: Sun Jul 27 20:38:28 2008 +0000 Added ochPri2 to DBS. commit 61f7df4334374df25a0b475ae2a92fad9753c1a4 Author: galt Date: Sun Jul 27 15:00:07 2008 +0000 "Encode release log update" commit 560f0128ff1ed3d9bff718cdb2d15249457beeba Author: galt Date: Sun Jul 27 15:00:05 2008 +0000 "Release log update" commit 18a008bbe6f0b7ba0768bbb4636bcdcc53b753bc Author: larrym Date: Sat Jul 26 23:47:15 2008 +0000 code cleanup commit b352273e76745409b5cc76b3eb4ac168e2eaf5de Author: galt Date: Sat Jul 26 15:00:07 2008 +0000 "Encode release log update" commit 4f33af9d5571e424e7d95539e97841d778316b54 Author: galt Date: Sat Jul 26 15:00:04 2008 +0000 "Release log update" commit 50f4cc06a53869e44be03f366447c0f5b4b4b007 Author: larrym Date: Sat Jul 26 02:11:55 2008 +0000 create missing optional views; use SafePipe commit 948c59c47ac6fc20bcec0cef8bd6f6e55a43d276 Author: larrym Date: Sat Jul 26 02:10:00 2008 +0000 module to get status codes from all commands in a pipe commit ec5179917698b7953a0ac1f30f431db5bbb8f134 Author: larrym Date: Fri Jul 25 19:05:10 2008 +0000 replace cvsFiles with a list of files (JS_FILES) so mirrors dont have to install utils commit c73d1f0af4954835d418198db4dd29138be9132a Author: kuhn Date: Fri Jul 25 18:58:58 2008 +0000 a few formatting tweaks commit 6e8a9a68aff100aea1a33bbb0cdc0c795a2ea0f3 Author: kuhn Date: Fri Jul 25 16:56:49 2008 +0000 turning off mm5,6 updates commit cf722bdbd50e2474cdd467b3192493c894491e09 Author: galt Date: Fri Jul 25 15:00:08 2008 +0000 "Encode release log update" commit 594dc9d62754629abe9c2ad9e46b3edb3d4d80bf Author: galt Date: Fri Jul 25 15:00:06 2008 +0000 "Release log update" commit 11d066c9ff73401c52f7d5b38d140ca9734f3cd9 Author: markd Date: Fri Jul 25 06:01:47 2008 +0000 restrict transMap spliced ESTs to hgwdev commit 8a1a2d1f5664fb9bc66bc82827f9e58daaec984a Author: markd Date: Thu Jul 24 23:44:59 2008 +0000 fixed typo in conf file commit 9895b398d6017b762310c018d1342e3af9829c21 Author: mikep Date: Thu Jul 24 23:41:15 2008 +0000 fixed header to be TH not TD commit 8a102c2e034242c4f17882f8566fd8a619c5d5e1 Author: mikep Date: Thu Jul 24 23:25:26 2008 +0000 added new controlled vocabulary types plus the cgi ra file viewer commit 4bc0dfc1be173c2f3f2a3b5565e5e5bef7918d9a Author: kuhn Date: Thu Jul 24 22:09:52 2008 +0000 mod to spacing of choices in arguments -- usage statement commit 4e06a9f30865080eb09944841dd38c2b0509bfed Author: larrym Date: Thu Jul 24 21:50:54 2008 +0000 remove some redundant lines commit 6eb137f01624fc6d4fb886c3f8c45f9084bd65b0 Author: kuhn Date: Thu Jul 24 21:07:39 2008 +0000 added some whitespace for readablility commit bb46835137368748f6f4ce783ce4b4a412f9e2e2 Author: kuhn Date: Thu Jul 24 21:04:23 2008 +0000 added some end-paragraph tags commit d74ffe46c4ece96c19f620e953d4767193b9d130 Author: pauline Date: Thu Jul 24 17:43:39 2008 +0000 Fixed broken link. Thanks Hiram commit e7fd55dde48e2f715e3d7e0363c912c330373fd5 Author: kord Date: Thu Jul 24 15:29:41 2008 +0000 Added nemVec1 commit d7e87efe24ea12d94dfd0356ec4826244ef17d0b Author: galt Date: Thu Jul 24 15:00:09 2008 +0000 "Encode release log update" commit 204c1a22b51f61d1e222744b16d7a1fa2b2f1c21 Author: galt Date: Thu Jul 24 15:00:04 2008 +0000 "Release log update" commit 622a5728311f914f2b5823aded4d2ecc4c59c245 Author: larrym Date: Wed Jul 23 21:46:52 2008 +0000 add pifVesion commit 140b38caf542e54c4f1914bc473164a3aa13ab9e Author: larrym Date: Wed Jul 23 21:46:28 2008 +0000 add duke test; mark older tests as obsolete commit d795cd86477de550c14cc1b7e327d97ea81ea7e2 Author: ann Date: Wed Jul 23 21:38:23 2008 +0000 switched hard-coded link to genome -- made it relative commit f90a746f932376696219730e1188e71a12b77533 Author: fanhsu Date: Wed Jul 23 20:55:15 2008 +0000 Added logic to check the max number of proteins does not exceed the declared max. commit 33ed195235d426fdbe7bab807dff8f8e29ffc3b4 Author: kate Date: Wed Jul 23 18:51:12 2008 +0000 Use GB colors commit d93a35ff4fe9e4da5b049f1278cf03b6ba7dba0c Author: kate Date: Wed Jul 23 18:15:01 2008 +0000 Add CGI for displaying controlled vocabulary commit 9cb06ed32856106321d309a6d166ce99e3eddf02 Author: kate Date: Wed Jul 23 18:12:01 2008 +0000 Program for displaying ENCODE controlled vocabulary commit 8b62b657407055cfa73c57796995fc655dc9b0d5 Author: ann Date: Wed Jul 23 18:11:42 2008 +0000 added FAQ for finding centromeres commit 800c5eebbcd46c69947b76facaeb27f5fe054aee Author: kate Date: Wed Jul 23 18:10:30 2008 +0000 Another typo in field name commit b5a0434ee930a27f2f9714fb3a42ad1193b1680e Author: kate Date: Wed Jul 23 18:10:08 2008 +0000 Another typo in field name commit b887ac48153ff7899e84cde78f086aa256b778fa Author: kate Date: Wed Jul 23 18:07:03 2008 +0000 Correct bad field type commit bcfac7647e5a1426efc5bc691377eb873e3198c5 Author: ann Date: Wed Jul 23 17:32:29 2008 +0000 fixed link. commit 3c65e7f20cfa8f01468d7620b870be0fb2e75a05 Author: kord Date: Wed Jul 23 17:04:26 2008 +0000 added missing

tag for formatting commit b71f714ba799a0a8bde3704b181b916ad10be6ac Author: kuhn Date: Wed Jul 23 17:02:56 2008 +0000 formatting, mostly commit cc9c7f0939d7370c5396e2d3afdfccdd66c28158 Author: fanhsu Date: Wed Jul 23 16:59:36 2008 +0000 Corrected the date for UniGene update. commit 9bdf8982549041b444c89117047ac1e8c3327c97 Author: kord Date: Wed Jul 23 16:57:56 2008 +0000 Marked the N50 description with (N50). Linked to JGI download page for JGI text and conditions of use. Udated the chr -> scaffold. Once the Genbank alignments are ready, I'll update the author, mRNA, etc. examples. Added the citation. commit db8bbeb3ddd96905687f9172455bc1098fc7b704 Author: fanhsu Date: Wed Jul 23 16:56:08 2008 +0000 Updated UniGene track. commit b61e69e4b18ba7665d98b3bb48d97c7a31a4f6e8 Author: kuhn Date: Wed Jul 23 16:53:59 2008 +0000 added slash to end en EM tag and added TARGET = _BLANK for offsite link commit 4052bfe8c090c0267519c28f8e8287fabde33c6b Author: kuhn Date: Wed Jul 23 16:50:33 2008 +0000 added italics on et al. commit 304fcdab2432d9b65e3200deed9bd30a6011c2e0 Author: galt Date: Wed Jul 23 15:00:13 2008 +0000 "Encode release log update" commit 9a133eee6ecbd1b472b59192c73c2ee8de972bdf Author: galt Date: Wed Jul 23 15:00:09 2008 +0000 "Release log update" commit 5851291a717ba2c1ad05ba1867ea47cfac9f37d4 Author: hiram Date: Wed Jul 23 12:43:35 2008 +0000 The reference to google/index.html is no longer useful. What ever became of the knownGeneLists ? commit 02f82c5ed054ca0ce17299969fa5300c1331d08d Author: ann Date: Tue Jul 22 23:56:41 2008 +0000 fixed link and citation. commit 857f9b17a919e89453bc84a3eda357540921d234 Author: ann Date: Tue Jul 22 23:46:23 2008 +0000 fixed citation. commit ce9b44492058bb26b62cf0c150d100de103babef Author: markd Date: Tue Jul 22 23:44:01 2008 +0000 added missing html file commit f00696c68c943eeacbde42e9566be6ad4e138355 Author: larrym Date: Tue Jul 22 23:38:50 2008 +0000 comment validator section; remove some dead code commit 70f17d5603794ca717faefb1a4dca6a489385390 Author: ann Date: Tue Jul 22 23:33:17 2008 +0000 fixed link and citation. commit eaae3d420623a445c8e42a818f6d24060162a219 Author: ann Date: Tue Jul 22 23:28:05 2008 +0000 fixed citation. commit b6914f7680951f1eda0d8859bfe4603e83c4f73f Author: donnak Date: Tue Jul 22 23:19:10 2008 +0000 Minor edits. commit eb8d0f2310031de8f74286f372610f3d5644f41f Author: ann Date: Tue Jul 22 23:06:40 2008 +0000 fixing citation commit aec94716898b6a51a8812b65b8a4c8943492c3b3 Author: ann Date: Tue Jul 22 22:56:57 2008 +0000 updated link to point to their new website. commit 7ba23de573ea8250594c5b8a884a7f3f34a4469d Author: larrym Date: Tue Jul 22 22:34:25 2008 +0000 remove a lot of globals; die if a track has already been loaded commit be13cb0bc2b9f62ecdda638e19b056b1f5717f36 Author: kayla Date: Tue Jul 22 22:25:21 2008 +0000 added ce6 commit 6b8910d7c231dee9d5e46219084101dbefb010b6 Author: donnak Date: Tue Jul 22 21:50:49 2008 +0000 Archived 2 items. commit e81229b32dde8204c534eae551f210d5416c3dd4 Author: donnak Date: Tue Jul 22 21:50:36 2008 +0000 Added news item for ce6. commit 7ffcdb766f93e9867ae43ebf6fbc2b6346a34c93 Author: markd Date: Tue Jul 22 20:35:20 2008 +0000 added HTML for experimental tracks to eliminate warnings commit 39491bcb3645e622e7f796847c9d4fd92282d393 Author: larrym Date: Tue Jul 22 19:40:23 2008 +0000 "New version number v187" commit 34a3b8f5a727f4dc5d1be77306f17a273dd25706 Author: larrym Date: Tue Jul 22 19:37:32 2008 +0000 add hButtonWithMsg commit 5b38ff6493d271e5217f95d9e158b86837a30f98 Author: kuhn Date: Tue Jul 22 18:24:38 2008 +0000 added a close-paragraph tag to give some whitespace below text commit c9bb0283baab0b563c94fbeeeafa76871ad88acd Author: markd Date: Tue Jul 22 18:14:31 2008 +0000 don't include optional count in types response, resulting in 37x speedup on chr22 commit 5a39252b79b49e3a480203f952c4a0056a4f4294 Author: markd Date: Tue Jul 22 17:53:35 2008 +0000 added validating parser to tests; fixed DTD conformance errors commit 1465779928deb8702024829c51775f605cb21ed9 Author: markd Date: Tue Jul 22 17:18:18 2008 +0000 treat specifiying both type and category filters as an AND commit 1e3680ba4abff771d089992e2de09d3bf18edc6b Author: galt Date: Tue Jul 22 15:00:13 2008 +0000 "Encode release log update" commit a6c22d6b594b0a6a8e40a523e3699a88901d7766 Author: galt Date: Tue Jul 22 15:00:07 2008 +0000 "Release log update" commit d47d67e8200116ff51bc815845030f60576f4e5d Author: jsanborn Date: Mon Jul 21 23:13:59 2008 +0000 added combined ABI tracks commit f51d181103837fa40e841873c74e10e88c57ff7a Author: larrym Date: Mon Jul 21 20:50:31 2008 +0000 add labs.ra commit 4e07800951307ea7328a570a5d8c774354af5a13 Author: larrym Date: Mon Jul 21 20:50:09 2008 +0000 add pifHeader fields; tag all fields with file attribute commit d4f8e9092f782829f489f86011140b5e6fc579ab Author: braney Date: Mon Jul 21 18:07:16 2008 +0000 take out exit if the number of blocks isn't exactly right commit d487637f358102a2b388296f7167e54d0d669b38 Author: angie Date: Mon Jul 21 16:54:42 2008 +0000 Added a note about cart.c cartCopyCustomTracks(): needs to be updated when *File members of customTrack are added/removed. commit ddc7c15ba3c4700d7f2577b8c3ecbef892b27151 Author: angie Date: Mon Jul 21 16:51:31 2008 +0000 Updated DGV to v5. commit 8d11281491cfab3823e852e88aaddd6c68f7d585 Author: galt Date: Mon Jul 21 15:00:09 2008 +0000 "Encode release log update" commit 5e38d5dece9eb1945dc7427abf554f2436510711 Author: galt Date: Mon Jul 21 15:00:04 2008 +0000 "Release log update" commit 462f7a0ba4bf8368860dc0da36346a3797e8a236 Author: jsanborn Date: Mon Jul 21 01:18:50 2008 +0000 added new tracks commit 606fb849b1819e7bc6d8472f5349d8788d7c34c4 Author: braney Date: Mon Jul 21 00:49:18 2008 +0000 Initial descriptions for proCav1. commit ec2b2643ac290618f913cc2048b42c0f706da55d Author: braney Date: Mon Jul 21 00:49:15 2008 +0000 Added proCav1 to DBS. commit c640496e17bbb8d516dfaed31525c4b778655d39 Author: jsanborn Date: Mon Jul 21 00:10:47 2008 +0000 added new datasets, fixed a bug commit a9ff65aa4aa5d2f6e5dfbf796afce42a011ec9d5 Author: galt Date: Sun Jul 20 15:00:07 2008 +0000 "Encode release log update" commit e30c5775015a0b85e0c950c528887169a7a4cd2f Author: galt Date: Sun Jul 20 15:00:04 2008 +0000 "Release log update" commit 400bab8badfa302dab793966814a375c8f8f0926 Author: galt Date: Sat Jul 19 15:00:06 2008 +0000 "Encode release log update" commit 9257fb096729f18dab24c03c8b9b4cf1eb53abb3 Author: galt Date: Sat Jul 19 15:00:04 2008 +0000 "Release log update" commit 86364a87e5291d0fbab48825ce9aa59738aa7bb3 Author: markd Date: Sat Jul 19 05:55:40 2008 +0000 fixed bug with spliced stop codons commit e89400699762cde64d5e9e668f4b5e9e0563ee44 Author: tdreszer Date: Sat Jul 19 04:03:29 2008 +0000 Added Broad ChIP-seq tracks for me1,me2 and whole brain commit 2d5fc243e4d1c364361e9d12c3e1ee46de3e0d25 Author: tdreszer Date: Sat Jul 19 03:54:33 2008 +0000 Added in Tarjei's new tracks commit 9f62425322e2831b8135148e0b53e8bf2b7cb0d5 Author: jsanborn Date: Sat Jul 19 03:06:58 2008 +0000 updated harvard and mskcc groups commit 2a27cc3dfc594c7f028e2cef5d8b777c0433f786 Author: markd Date: Sat Jul 19 00:40:43 2008 +0000 fixed bugs in handling start/stop codons; some restructuring, removed option I should have never put in commit be746588277021d91d765236e002d864cfad8496 Author: tdreszer Date: Sat Jul 19 00:08:47 2008 +0000 Removed nonsensical inlines commit 8c3f312970aa7090a7021b96e147d982539bb944 Author: tdreszer Date: Sat Jul 19 00:07:57 2008 +0000 inline made right commit 3fb28140d571fb961783b4b2a2e30cf95c68e93e Author: genbank Date: Fri Jul 18 23:34:07 2008 +0000 fixed commited mistake commit 4d04b2c36cffe6ffc75835c9a1e576c5de96d6c5 Author: kate Date: Fri Jul 18 23:08:06 2008 +0000 Add new antibodies from Wiki commit 3169e9bc46792aad11f8d84fa3666489853c35db Author: braney Date: Fri Jul 18 23:07:14 2008 +0000 a mapping to homPan20 and homIni20 commit 9b295ba18bb277c977c2ca5c1f03c135844f0531 Author: kord Date: Fri Jul 18 21:42:32 2008 +0000 # REPEATMASKER (DONE - 2008-Jul-16 - Kord) # MASK SEQUENCE WITH RM+TRF (DONE - 2008-Jul-16 - Kord) # MAKE 11.OOC FILE FOR BLAT (DONE - 2008-Jul-16 - Kord) commit f9aaea0a6220a4cd09ecdcd237f7a6095dd594c3 Author: tdreszer Date: Fri Jul 18 21:34:42 2008 +0000 Fix map-box bug: subtracks pointed to parent tdb rather than subtrack tdb commit 728a16030bffdc5126418124cb8fe9079cf9fb90 Author: braney Date: Fri Jul 18 18:19:59 2008 +0000 add human proteins (hg18) track commit 9f808e0a158fae267c4eea7ddbf72d9feb7b0e8f Author: markd Date: Fri Jul 18 18:07:58 2008 +0000 removed old mgc files commit 178a2d8bc83031e45f4effacfe57d1f07a4fa82a Author: genbank Date: Fri Jul 18 18:06:17 2008 +0000 rsync download files via 10-net commit 3a52597dc12005fab77473f4a9a9c4ab6b401826 Author: markd Date: Fri Jul 18 18:03:40 2008 +0000 copy from genbank via the 10-net commit a29a81392b6aeffb2cda0fcbb8e128b6c5d7e105 Author: markd Date: Fri Jul 18 18:02:02 2008 +0000 removed log format that generates junk with older rsync commit 6a008fa280191a1252fc3f0a9f0997fb459d1419 Author: ann Date: Fri Jul 18 16:18:17 2008 +0000 corrected count commit 85620f5b4eb448a1d28f150f528887a93f4372a3 Author: ann Date: Fri Jul 18 15:47:59 2008 +0000 added Pos Sel Gene track table commit dab241372f0b64a12029bb4d36af3c83c16bed4b Author: galt Date: Fri Jul 18 15:00:10 2008 +0000 "Encode release log update" commit 45d026aa01add4af4666eccaedf96bcbca15b3a1 Author: galt Date: Fri Jul 18 15:00:05 2008 +0000 "Release log update" commit b5e96004c01befc05b7b77a2e70a1d3d2d3395dd Author: jsanborn Date: Fri Jul 18 06:13:09 2008 +0000 updated for Broad SNP 6.0 commit e1051379ca026d4f54490019d0df002187a28e92 Author: markd Date: Fri Jul 18 04:44:43 2008 +0000 enable autoupdate of CCDS on any server commit 87fa00cc419f5ab1cf780d5586c4d68646e0045a Author: markd Date: Fri Jul 18 04:37:03 2008 +0000 added program to check order of positional tables commit 5dcd9e23cf31378909dd0b8e13832760457d3c53 Author: pauline Date: Fri Jul 18 01:26:05 2008 +0000 Added new assembly to update list. commit 73271eeaec232cf3e372554ecf22a858972a9350 Author: tingwang Date: Fri Jul 18 00:06:44 2008 +0000 added stanford snp data commit 38a48fdb0492418d2d9d688ff903e8b3cb1c7dde Author: markd Date: Thu Jul 17 23:28:51 2008 +0000 fixed display of source org when db is inactive commit 16dfbd6df5d12ef87411503e4b835bb4e4cb1a17 Author: markd Date: Thu Jul 17 23:12:42 2008 +0000 fixed typo commit f3ea8ce964b512f5c0b8b95f66127d93f34772d9 Author: galt Date: Thu Jul 17 23:07:48 2008 +0000 fixed warning commit 055a909a435fb5f27be6c15c30dee366ffaf7635 Author: markd Date: Thu Jul 17 22:57:35 2008 +0000 control level of zoom for added CDS annotation to speed up transMap tracks commit ea5ee15f92c43950bc33031a2d940f6271647021 Author: markd Date: Thu Jul 17 22:56:46 2008 +0000 added more control over zoom level where code attempts to render CDS for PSL tracks commit da3d3bd16ccb768d02af65d8f7add2fe7f0a7320 Author: markd Date: Thu Jul 17 22:54:45 2008 +0000 added function to get float setting commit 5acfaea817c173f27ecf970e14ba6ca821cc7f16 Author: donnak Date: Thu Jul 17 21:58:03 2008 +0000 Edited this description. commit 291b090e6cbca85e2d2e693fcbb0100e8850c3b1 Author: galt Date: Thu Jul 17 21:53:23 2008 +0000 fixed typo in usage message commit 6bd4f4c96dddb808d373da9fcee2aca3e9fc2f02 Author: galt Date: Thu Jul 17 21:39:46 2008 +0000 typo fix, thanks TimD commit dbd1feb58600efcfdc9ee7c6d64b97ddcb8371af Author: donnak Date: Thu Jul 17 21:21:41 2008 +0000 Added ce6. commit 66032d4efb28d837dfd04fb17583ff7049785632 Author: markd Date: Thu Jul 17 21:13:43 2008 +0000 added description of multiple trackDbs/grp tables commit fdf76bec5d3760152e539f116ac07ff73e26781c Author: rhead Date: Thu Jul 17 21:13:21 2008 +0000 Fixed typo and reworded pslMap section. commit 7b0daec66e4322f3f0f4088a510a23fa66653a53 Author: donnak Date: Thu Jul 17 20:38:18 2008 +0000 Updated grad/post-doc section. commit 720cb235a9ba261fc78bcce58a18f3782a5a8e89 Author: ann Date: Thu Jul 17 20:30:23 2008 +0000 a little more organizing commit 68006ccd58ccefd58b0b81dfce10a226e63c9e90 Author: donnak Date: Thu Jul 17 19:56:22 2008 +0000 Added Ann's tutorial. commit 891b874140e906f4f449a1bc3fba10b20aa11298 Author: ann Date: Thu Jul 17 19:15:03 2008 +0000 general clean-up commit 83703c12eb31d06eebf1db1fb1ac4c4f0659c51d Author: jsanborn Date: Thu Jul 17 19:10:12 2008 +0000 fixed bug in broadABI track commit 5b4471c9ad25d89ae5644af7b8d9d3efe727844e Author: larrym Date: Thu Jul 17 18:48:16 2008 +0000 add validateFieldList to improve validation of fields in PIF and DDF commit 2b77358513068935770b502516cd28df4cd99cbb Author: tdreszer Date: Thu Jul 17 18:37:46 2008 +0000 Fix bug due to composite tracks not always pointing to children. commit e4bc66a758785e0f4d2d5ee5b8fa455c43e6ce00 Author: larrym Date: Thu Jul 17 18:36:56 2008 +0000 fix typo commit cd457f3261e6277764808f645a73724c84c73053 Author: tdreszer Date: Thu Jul 17 18:35:38 2008 +0000 Temporary finction until all composite tracks point to their children commit f181dccd538eb0bf3d7075d4514777c7847464c9 Author: larrym Date: Thu Jul 17 18:30:53 2008 +0000 refactor HgDb::new to fix some bugs and improve readability commit e98268cb61a4aceb29eaac63540fbdd438f0163b Author: markd Date: Thu Jul 17 17:47:40 2008 +0000 move non-coding logic to common function commit be24edb29b8b7f6a9c5ea3b32c7b4e4350e57db4 Author: markd Date: Thu Jul 17 17:47:24 2008 +0000 use /data/tmp for scratch area commit 9db9f429e018cbb7e1cf4184fb4c39d3ec811c67 Author: ann Date: Thu Jul 17 17:12:07 2008 +0000 fixed a double-backslash. these were causing problems when they were contained in frames. commit 4409f36bd2bff6320f8533c850e79a229d379883 Author: galt Date: Thu Jul 17 15:00:06 2008 +0000 "Encode release log update" commit de211af142c0df0c319c406c548421c7b0db3384 Author: galt Date: Thu Jul 17 15:00:04 2008 +0000 "Release log update" commit 64e26a9851b4a27e11ea8e182aa1a2b336c7da22 Author: tingwang Date: Thu Jul 17 06:41:36 2008 +0000 stanford data added commit 52ce578a8372e2f735f02074e286af9ffcad8c80 Author: jsanborn Date: Thu Jul 17 06:16:13 2008 +0000 updated to move datasets to group tcga commit 73a198e83cb75630b6ae14886ac7d76f36d4f7ca Author: mikep Date: Thu Jul 17 04:58:26 2008 +0000 fixed reference format and made sure link opens track commit ca0a0ce856a7d718a7ba676bcc8f01d397030a87 Author: galt Date: Wed Jul 16 23:40:23 2008 +0000 data in uniProt changed slightly, updating test expected commit 6aa7446ce192f4fa440418e783a05877e00bbe26 Author: markd Date: Wed Jul 16 23:30:33 2008 +0000 fixed bug were labels were set even when forced into dense mode commit 7db520fe4da77ec99161beb578403c654ccc7f13 Author: hiram Date: Wed Jul 16 23:24:47 2008 +0000 Indicate where the source data can be downloaded from commit 24cfce210f49391cfdcdedfcbf6648a71db9637d Author: markd Date: Wed Jul 16 23:24:00 2008 +0000 don't try to get CDS for ESTs; remove conflicting zoom option commit a53d95a735c47af193d18de3fa646eb730fd1936 Author: markd Date: Wed Jul 16 22:46:32 2008 +0000 don't print live link if database not active commit 70d099609a3eba425464a692bdb1965f638c0038 Author: angie Date: Wed Jul 16 20:42:41 2008 +0000 Added MGI (jax*) tracks. commit 9027286319eabe96a907e0e46d2677cf48968e6f Author: larrym Date: Wed Jul 16 19:42:56 2008 +0000 dink Stanf ChIP commit d001b3b422eebdfe5cb35c6eb2e5daf7a761fcd7 Author: markd Date: Wed Jul 16 19:33:05 2008 +0000 change short labels on transmap tracks to make them not truncate in dense mode commit 1fc3e7c13548c052a46b6d42f1bb6a9c407e4a8d Author: braney Date: Wed Jul 16 19:12:22 2008 +0000 change an atom handler to use a new track commit 1f08c5e48ffeaa34389084f7b39cfb14b96dcf94 Author: tingwang Date: Wed Jul 16 17:24:52 2008 +0000 stanford hap550 tracks added commit cb27babe28dd23f391dcb6b1bdb88fc39c3c82c0 Author: braney Date: Wed Jul 16 15:27:36 2008 +0000 Initial descriptions for dipOrd1. commit 2914b50073a2c1cd7cbc325e0001c3bc2df86bc7 Author: braney Date: Wed Jul 16 15:27:31 2008 +0000 Added dipOrd1 to DBS. commit 658dfbf0edeacb814f7c874f970a8fd87bf31c49 Author: galt Date: Wed Jul 16 15:00:11 2008 +0000 "Encode release log update" commit 772e6100bc583e50a784772a077cccbcdaaac925 Author: galt Date: Wed Jul 16 15:00:04 2008 +0000 "Release log update" commit 7b1303d32453f320c00ea96d6397bd357900e16b Author: pchan Date: Wed Jul 16 07:26:52 2008 +0000 fix blastp track table when genome doesn't have subclade commit f9f09427eb4a5c9179b42e40a344c29da3c0d3d6 Author: kate Date: Wed Jul 16 06:08:28 2008 +0000 Need to remove empty lines for ra lib commit 4b3b097e755f9efb19ea61b487abd0f0b431668d Author: jsanborn Date: Wed Jul 16 05:28:27 2008 +0000 added new datasets for TCGA commit 84969c359efa403339741653fc351b15a0997a78 Author: markd Date: Wed Jul 16 03:49:22 2008 +0000 work around long stating bug that cases errAbort when doing codon coloring with a single base block surounded by small indels commit 7887ce7670a6c2f841752f70f73dc8c079c49f56 Author: tdreszer Date: Wed Jul 16 01:02:19 2008 +0000 Credits and References from Tarjei commit 15a94534efc0db2baebb39d815a4979a6ce628d1 Author: kate Date: Wed Jul 16 00:05:04 2008 +0000 Add antibody section from wiki, expanded to include 'Target Description' commit 0d3ad3c5ef0454561b8bae2892da612ea5e5b90c Author: ann Date: Tue Jul 15 22:40:05 2008 +0000 edited chain matrix to panTro2 to go with new chain/nets commit 754e97eaa93f6203cd19a980bc0d8ff6487b4c8d Author: larrym Date: Tue Jul 15 22:28:30 2008 +0000 die if there are missing required views; change a bunch of code and variables to try to make code more readable commit 250c7f7abc942fad65e91f4aba58c9238a9742de Author: braney Date: Tue Jul 15 22:21:05 2008 +0000 a chain to the chimp/human ancestor commit e7f91574a04c6837579dd3d1b3489bf223b89617 Author: braney Date: Tue Jul 15 22:08:37 2008 +0000 atoms for homIni20 commit 041747a9a21f47a08179a663ae84a5ae992d68a8 Author: donnak Date: Tue Jul 15 21:41:57 2008 +0000 Removed references to SARS. commit 2b87d57d464bb6cb94de51235554ea0a89b17e32 Author: rhead Date: Tue Jul 15 21:12:54 2008 +0000 Fixed transMap longLabel. commit 4784e3b79eed8c02be6387860164f07f665a892e Author: markd Date: Tue Jul 15 20:52:40 2008 +0000 added note on problem dm3 alignments commit 282286b3ac958b024eb01690d69a9525fd80c5fd Author: markd Date: Tue Jul 15 20:45:46 2008 +0000 fix problem with transMap searchs due to hgFindSpec not working with entries starting with space commit 75bdfa830c52254174bf1e4301bfce36433b72a5 Author: aamp Date: Tue Jul 15 18:53:34 2008 +0000 Some contributed documentation. Still a work in progress. commit d41a854501228ac21719dd11395dd28709a0062d Author: hiram Date: Tue Jul 15 18:37:45 2008 +0000 Done with blastTab tables commit f02ec9337ec8484d4cd31dea4e7dfb6a09901b5b Author: braney Date: Tue Jul 15 17:57:19 2008 +0000 Initial descriptions for tarSyr1. commit 084ded06228679533f7bfa7dc756ef12c71436b6 Author: braney Date: Tue Jul 15 17:57:15 2008 +0000 Added tarSyr1 to DBS. commit 678ba6a8fcffdd10fa91a3702c13002c2a482631 Author: galt Date: Tue Jul 15 15:00:12 2008 +0000 "Encode release log update" commit b0698195faa99369d91dcfa635548ca788bfc720 Author: galt Date: Tue Jul 15 15:00:07 2008 +0000 "Release log update" commit cfce1c8954d04ea8e822f071124d3cad4cd7c271 Author: rhead Date: Tue Jul 15 01:02:25 2008 +0000 Two more tiny tweaks. commit 2263dc7812ffc70fa20b9750ea3112e1bde3bad1 Author: rhead Date: Tue Jul 15 00:44:15 2008 +0000 QA edits. Mostly fixed typos. commit d72d4fdbdafff7204d35bef59aad50998b7a198e Author: donnak Date: Mon Jul 14 23:52:10 2008 +0000 Added error msg. commit ad36bff093e016255affabffe309f5a045aa00b7 Author: tdreszer Date: Mon Jul 14 22:34:44 2008 +0000 Minor changes requested by Tarjei commit e3a8e29b4320ac00ada25011740a54aedfa3cd2b Author: kord Date: Mon Jul 14 21:58:15 2008 +0000 makeGenomeDb done commit 8b412100a34cc57097adbd16cfd83dbc77f4268c Author: kord Date: Mon Jul 14 21:47:57 2008 +0000 Initial descriptions for nemVec1. commit ad874af781b556a5958f6674432a246d88ca2fc6 Author: kord Date: Mon Jul 14 21:47:46 2008 +0000 Added nemVec1 to DBS. commit 4a1f29af7ab06c59cff10a7637f2b8b5f3f3361c Author: angie Date: Mon Jul 14 21:24:16 2008 +0000 Apply jax* track rules to $mm not just individual databases. commit 80f88801c989cde719e14ac21e29d7527ec1ec5f Author: angie Date: Mon Jul 14 21:22:28 2008 +0000 Now adding jaxQtl instead of jaxQTL. commit e6a2ea25237ceaf0ee89d18029a5cf1fe1b621e2 Author: angie Date: Mon Jul 14 21:21:23 2008 +0000 Split jax/MGI track def's into alpha and beta instances for shortLabel highlights on the old liftOver versions. commit 118018c8ac97a2fd2645bbad7c4906ada56d0470 Author: kate Date: Mon Jul 14 19:29:04 2008 +0000 Provide link to conservation stats when cart is clean (use default). Bug found by Hiram commit 2e3136f9753bb05a30d4c901d635467dc9495fe2 Author: kate Date: Mon Jul 14 19:27:59 2008 +0000 Cleanup for easier maintenance -- use lib routine to generate cart variable names commit 3e39763239c0eae727e972a4f7a086878ece1f36 Author: fanhsu Date: Mon Jul 14 19:01:52 2008 +0000 Re-built VAX003 conservation and MSA tracks for hivgne8v2, using shortened MSA sequences. commit 498e5ecac03171259c2a50c194beb59041326897 Author: fanhsu Date: Mon Jul 14 18:56:42 2008 +0000 Updated VAX003 AE and B subtypes conservation and MSA tracks. commit ca71aae79f34be1c212a585f12cfa1ac890b60bd Author: larrym Date: Mon Jul 14 18:51:55 2008 +0000 replace dummy placeholders with tabs (the word "warning" was screwing up the buildZip.csh script) commit 0bc901dbb834efb3d107f73dbaef47ddcc6b5700 Author: kent Date: Mon Jul 14 16:49:39 2008 +0000 Adding bits about freshening proteome and uniProt database symbolic links. commit 59415ef425dc66aebee133c822e55064e0b3dbc6 Author: galt Date: Mon Jul 14 15:00:09 2008 +0000 "Encode release log update" commit b2e52198afc566c475bfe9eb96e99534e30da58f Author: galt Date: Mon Jul 14 15:00:03 2008 +0000 "Release log update" commit f637b1c1bfc97dc376417380fed8504762787607 Author: kent Date: Mon Jul 14 13:15:03 2008 +0000 Adding full path for swapInMysqlTempDb command commit ecbec71fba8e1c0496155aa4e984e8ceed618af0 Author: kent Date: Mon Jul 14 13:14:28 2008 +0000 Adding steps for affyAllExon array column. Adding in final table swap-in. commit 916b72ee599ae0df4bfcac9dfa7f20ec71f5a42e Author: kent Date: Mon Jul 14 13:07:19 2008 +0000 Adding a few things that were missing that I noticed while rebuilding UCSC genes. commit 91e92e388e15f13438a38bd66b58c7de8a97b67e Author: galt Date: Sun Jul 13 23:19:54 2008 +0000 1st cut at new docs for parasol v12 commit 0f586f28c9e008609374dce95177f5a110189a2d Author: galt Date: Sun Jul 13 15:00:07 2008 +0000 "Encode release log update" commit 52730e05aa26ef0130bf7cd9c7b2c7c8d7f27788 Author: galt Date: Sun Jul 13 15:00:04 2008 +0000 "Release log update" commit 10c208474f435dfa45f390eac4697521f62592ae Author: galt Date: Sat Jul 12 15:00:08 2008 +0000 "Encode release log update" commit 935cbaa131e3740337d458c517dfa8301ad8f6d9 Author: galt Date: Sat Jul 12 15:00:05 2008 +0000 "Release log update" commit 946b5bebd9834257527138c021563f542ec422df Author: markd Date: Sat Jul 12 06:34:48 2008 +0000 added handling for reconstruction transMap tracks commit 3301fed3c84063e80bb0850151c703e833e2fdce Author: markd Date: Sat Jul 12 05:52:54 2008 +0000 added human/orang ancestor commit 5e651935aee01d9c9532aeac86bb49d8a2315589 Author: markd Date: Sat Jul 12 05:44:44 2008 +0000 add support for reconstruct transmap tracks commit af0e80d01a262776acd6c874c142a9f5100c127f Author: markd Date: Sat Jul 12 04:40:58 2008 +0000 fixed build in reconTransMap track def commit a45f354ce0582130b622b9e2c88d1c0b26a4ee34 Author: markd Date: Sat Jul 12 04:22:58 2008 +0000 added reconstruction transmap tracks commit 6640d1aba4e0385b1b9a9dcf122c981d608ba7c5 Author: donnak Date: Sat Jul 12 00:06:56 2008 +0000 Added 3 new pubs for 2008. commit d84c89ea783020e141668f99caae509f7e4aaf88 Author: tdreszer Date: Fri Jul 11 23:44:20 2008 +0000 Finally finished multz8way commit dcd2c698b9bc9ef429fd2b40fc72cfe7f89be523 Author: hiram Date: Fri Jul 11 23:12:12 2008 +0000 Updated 2008 group photo CBSE commit caab892ceb9c485cce102a02a658d787ae35e826 Author: hiram Date: Fri Jul 11 23:10:58 2008 +0000 First edition of the CBSE group photograph commit 920fab3f2109b6697cd1b5104314334ed3041040 Author: hiram Date: Fri Jul 11 22:50:44 2008 +0000 Better error message on missing external file commit a39cc2370bd6eb7eb7b1ee41516dbb8ebd4a2ee6 Author: fanhsu Date: Fri Jul 11 22:39:20 2008 +0000 Added checking on overflowing MAXN, max number of proteins. commit c23ef45aa2b81c3558d82398617673f294e62b2f Author: fanhsu Date: Fri Jul 11 22:31:19 2008 +0000 Added checking against overflowing MAXN, max number of proteins. commit 8c386c419379f4c0ad2ad99383b90b3267d400c6 Author: hiram Date: Fri Jul 11 22:01:21 2008 +0000 Adding ce6 to the gene details display to enable other organisms blastTabs commit eda9edf20f5efe685d5fb3860e1e5e3170ceae17 Author: hiram Date: Fri Jul 11 22:00:58 2008 +0000 Correct WormBase ID name where it usually says UCSC ID for C. elegans genes commit da8f4210500bbe17fef5a1efc5c13694a21b89e8 Author: hiram Date: Fri Jul 11 21:59:02 2008 +0000 Turning on ce6 properly in the gene sorter commit 8345f3213604d78c2772e8c764bba4bbd4cab056 Author: galt Date: Fri Jul 11 21:58:15 2008 +0000 added note about new actual ram/cpu cost charging commit 3bafb539fc5feeadf2de02e000f2bb924ec45dc2 Author: braney Date: Fri Jul 11 21:54:35 2008 +0000 download and repeat-mask dolphin commit caa2f7cd253f09c5fb96540168dd46077ee151f2 Author: galt Date: Fri Jul 11 21:54:15 2008 +0000 added actual cost for using more ram and/or cpu; increased ramUnit to long long; suppressed debugging messages in parasol plan commit dd3c6e3945f078fdc88001790a9ce5211c496d82 Author: fanhsu Date: Fri Jul 11 20:51:03 2008 +0000 Added VAX003 conservation and maf tracks rebuild for hivVax003Vax004. commit 19075dc890c7ddea2819e73a52cf64c1c09c8dea Author: kent Date: Fri Jul 11 20:33:01 2008 +0000 Removing build instructions for dropped version of uniProt. commit 81097e1c3ec7e3c4971100bc3aab30e42330d4a5 Author: kent Date: Fri Jul 11 20:31:59 2008 +0000 Adding instructions for new build of uniProt. commit e92c959a2fe55bcf66eeebada0b78d723dd8f2fc Author: kent Date: Fri Jul 11 20:08:03 2008 +0000 Building an updated protein database. commit 660875a2de85cbcf8e7a084fdddf806d528764a4 Author: kent Date: Fri Jul 11 19:30:42 2008 +0000 Looks like have worked through this file for the update of the hg18 UCSC genes at last! Still will be adding in a few new knownTo tables that didn't exist last time..... commit b2dae47413e1a4061c9a77709ff908cb986fcd61 Author: kent Date: Fri Jul 11 19:27:21 2008 +0000 Reducing an error to a warning until we figure out what to do with the amino acid 'u' commit d01000d40ec87ffc429ad317b6d6364fb65782f9 Author: kent Date: Fri Jul 11 18:11:03 2008 +0000 Speed tweaking, upping max limit, and putting in a warning when you go over max limit. commit 718a176df55258a5bd3f1e98e5fc5e1305e6229d Author: angie Date: Fri Jul 11 18:10:02 2008 +0000 Loosened database name format to allow hiv.*. Since the Lowe Lab databases are almost all gone from hgwdev, perhaps we don't need to check db name format anymore. commit 14312e23f88db117ff7774b62cd3b9bc033230d3 Author: braney Date: Fri Jul 11 18:00:55 2008 +0000 Initial descriptions for pteVam1. commit 3224acb8c63cac2d0f047ea80b0893cca5d8cf84 Author: braney Date: Fri Jul 11 18:00:47 2008 +0000 Added pteVam1 to DBS. commit 79e618f55cf21afd606f1e21a18a55650b160173 Author: fanhsu Date: Fri Jul 11 17:52:04 2008 +0000 Changed MAXN from 100000 to 100000. commit cf451f1946832b0bb5df1b3ee5c4b44adf420e4a Author: fanhsu Date: Fri Jul 11 17:48:18 2008 +0000 Updated max protein count from 4M to 10M. commit 4f8baaa0c93ed5cea91f1ffd419b5d3a18b6ac80 Author: fanhsu Date: Fri Jul 11 17:44:16 2008 +0000 Increase maximum protein count from 4M to 10M. commit ad529d0334e652d7de55a94f85f52debdaae7f92 Author: larrym Date: Fri Jul 11 17:16:03 2008 +0000 add pifVersion and a bunch of validation commit 424c772e2cabefe9a806cb6a865c1be1f8f8cd8f Author: rhead Date: Fri Jul 11 17:09:09 2008 +0000 Another tweak to BGI links. commit 84b6b1902746deef333c5d568b7a5536619e4f50 Author: braney Date: Fri Jul 11 16:46:45 2008 +0000 Initial descriptions for vicPac1. commit 6aeac30ada2a3ef679ca87357290c916aeb82a1a Author: braney Date: Fri Jul 11 16:46:40 2008 +0000 Added vicPac1 to DBS. commit a4be431a12c505eebb3c807bd6e9faa2fb661a3a Author: kent Date: Fri Jul 11 15:58:12 2008 +0000 Adding pbCalDistGlobal to makefile since it is used. commit 808e8cc266d642c2c889ac607a037314681b210f Author: kent Date: Fri Jul 11 15:57:51 2008 +0000 Removing unused variables. commit c01a414a46965b535e308efc3207158c502aceea Author: kent Date: Fri Jul 11 15:18:24 2008 +0000 Replacing some strdup with cloneString to ensure everything really does go through the memory managment routines. commit 28a1e029e4e491a97fdb3c30a68593651b27b7cb Author: galt Date: Fri Jul 11 15:00:09 2008 +0000 "Encode release log update" commit c68387eb4ce6d70b9d590912d656e1e8087a875f Author: galt Date: Fri Jul 11 15:00:04 2008 +0000 "Release log update" commit a940083bfcc58f1f29cc22957e19355f0c94534a Author: kent Date: Fri Jul 11 14:17:29 2008 +0000 Removing some extranious stuff that is causing problems from table create statment. commit 07508766f569d0b1dee717e6ed0fe2d5abc4d22c Author: kent Date: Fri Jul 11 12:56:40 2008 +0000 Changing description field from varchar(255) to a text object since it is in 8000 or so cases now loger than 255 chars. commit 06c4409e1fc603bc1e1459b36a0fbd7901519512 Author: kent Date: Fri Jul 11 12:55:07 2008 +0000 MOdernizing and debugging some. Finding it so slow it's not worth saving, since there's another method to make these tables. commit 3307bc9d6df3c92a3f7f33ee1a96b4bff2e09d65 Author: kent Date: Fri Jul 11 06:57:53 2008 +0000 Going through known genes build and updating this doc at the same time. Mostly fixing a few places where output going to main rather than temp database. Also fixing a few paths. commit 35e4d2ca731ca226fbe86ea9042f4709694fb4a6 Author: kate Date: Fri Jul 11 05:12:39 2008 +0000 Make casification of species name match hgTracks commit 19b759ce0501a572997a461b79ceb00bcb07f18d Author: braney Date: Fri Jul 11 01:41:04 2008 +0000 Added turTru1 to DBS. commit 7304d9605a09bb89fc6d5df1b9201bcdc1c5428b Author: braney Date: Fri Jul 11 01:39:23 2008 +0000 Initial descriptions for turTru1. commit 3fa534c78805f3bfba85dfb8b26b0a1a8df51fa6 Author: larrym Date: Thu Jul 10 23:53:17 2008 +0000 convert encodeStatus.csh to perl; support many new parameters/flags commit 478de0b3e1add2a9f1132dce2972b96386c65f34 Author: larrym Date: Thu Jul 10 23:51:18 2008 +0000 use correct conf file commit ac1af799ce2c7c268fb79b80467b886f499f4465 Author: markd Date: Thu Jul 10 23:51:13 2008 +0000 improved wording of doc commit bdc03b36b09f0d6d0be2fca5707a89442930afea Author: markd Date: Thu Jul 10 23:51:02 2008 +0000 improved wording of doc commit 9d674851cd17e722557e9b1e4edffc99f3755b1f Author: fanhsu Date: Thu Jul 10 23:44:27 2008 +0000 Created for VAX003. commit 08be93508e776abc9035e6e2115b03635c358710 Author: kuhn Date: Thu Jul 10 23:42:08 2008 +0000 refactored to give 'no locks' return even if running in 'go' mode commit 56d7a844d87f2f29e060f9781f9f5505690ada6e Author: kuhn Date: Thu Jul 10 22:06:37 2008 +0000 added logic to protect against running ti with some random parameter, as all params != 'go' would remove locks commit 020216696e4ff3272b0cf42949ba99cf1bb0f87b Author: larrym Date: Thu Jul 10 21:08:52 2008 +0000 add HgDb.pm and RAFile.pm commit 71c71f32bdb0842c12fdc7d02df686188d3c160a Author: larrym Date: Thu Jul 10 21:08:18 2008 +0000 Class interface to the mysql databases commit 65e8252755d959fc927b40af9905bc9cbd0fd045 Author: kuhn Date: Thu Jul 10 18:50:30 2008 +0000 changed usage a bit commit ab709ebf8918a15f7e32d240aa43dc9b60d2e449 Author: larrym Date: Thu Jul 10 17:57:32 2008 +0000 all.joiner, make downloads and pushQ entry commit 38fb86014e8fd14ab67b419a8b382960225c1a5a Author: larrym Date: Thu Jul 10 17:56:44 2008 +0000 equcab1->equcab2 liftover commit 21e4165fbfd5fa05c075cfde33a3ce1f3fb86b79 Author: tdreszer Date: Thu Jul 10 17:44:22 2008 +0000 Added methods commit aaffa0bd6b7c9913c6073872540a7b69f4308216 Author: tdreszer Date: Thu Jul 10 17:42:44 2008 +0000 Fixed a few typos and shortened text. commit ad082b5f500bcb2d314992d43b5c0676d624745c Author: tdreszer Date: Thu Jul 10 17:39:00 2008 +0000 Remove obsolete function commit b62f14e495efbadd5cc786da9f53425c61133fc5 Author: tdreszer Date: Thu Jul 10 17:37:17 2008 +0000 Remove obsolete function calls commit d34f0f8787309d416bd2f34d5a041d147cf693ac Author: tdreszer Date: Thu Jul 10 17:33:41 2008 +0000 Remove obsolete function call commit d10f8c0813794711a3b254a5983b29549beeb717 Author: tdreszer Date: Thu Jul 10 17:30:23 2008 +0000 Remove obsolete function call and other cleanup commit 3a4b83854fc27e9508e638282652b39eec887a17 Author: tdreszer Date: Thu Jul 10 17:29:08 2008 +0000 Supertracks children must point to parent, supertrack sometimes points to children commit 130db68f75371c180df8773bb5b2971bf49c533c Author: fanhsu Date: Thu Jul 10 17:08:31 2008 +0000 Created vax003BMsa.sql. commit 94d18ed367480698eb17ea7da155d9dbd02365a1 Author: fanhsu Date: Thu Jul 10 17:07:12 2008 +0000 Created vax003AEMsa.sql. commit 2b70a229a9e6561e74060d9ddc0d3f849f2f6414 Author: kord Date: Thu Jul 10 15:32:14 2008 +0000 initial start commit 4a08f4848c44ad989b39385a93b33e589f5b7110 Author: kord Date: Thu Jul 10 15:25:17 2008 +0000 CREATE LIFTOVER FROM strPur1 TO strPur2 commit 607a7603d6d1b78052c6f619bc5493870634b79a Author: galt Date: Thu Jul 10 15:00:08 2008 +0000 "Encode release log update" commit 8f2e88d0e6074c6a3d3b551a30d164739f8a1572 Author: galt Date: Thu Jul 10 15:00:05 2008 +0000 "Release log update" commit 6e9e6a0a4ddb9a54780467b787c43d2e0eb98888 Author: markd Date: Thu Jul 10 07:45:37 2008 +0000 removed unnecessary code that caused verticle, one pixel bars to be omitted in reverse mode ps/pdf files commit f13693b7b01c97721b2d35e5871fff1a91f5abf9 Author: braney Date: Wed Jul 9 23:19:31 2008 +0000 update to handle more than one sequence in a block from the same species commit 6ed08fc87123ffb1518542045aa73bd45d727ac5 Author: angie Date: Wed Jul 9 22:56:36 2008 +0000 When making a new copy of saved-session custom tracks, make new copies of any auxiliary files referenced in the main custom track file. commit 0c53cefc5a3dcce8b0e6aed7b26fecbff87268fe Author: angie Date: Wed Jul 9 22:55:35 2008 +0000 Added copyFileToTrash. commit 0cdab8930c6abbb43f9805f3c86d52d9a6d9a011 Author: sbenz Date: Wed Jul 9 22:25:35 2008 +0000 Added ABI sequencing datasets commit 523bb6e16a5f4d2a2776ea515cc9d9e43ab09d81 Author: sbenz Date: Wed Jul 9 22:25:18 2008 +0000 Added ABI datasets commit 02b3ff11039ee6c0de793955ce6dce34fc5990e4 Author: markd Date: Wed Jul 9 22:10:40 2008 +0000 duplicated methods decription in all transMap subtracks commit 88641e6a52adb79188cb195d6f205a4bf07eef52 Author: markd Date: Wed Jul 9 22:00:03 2008 +0000 changed transMap priorities due to conflict when in table browser menu commit 5aee4eb91b8a5df61c123220cba7c7d88dfc26d4 Author: markd Date: Wed Jul 9 21:51:33 2008 +0000 removed transMap mm8,hg17 that were dropped commit 94c8df57a55d279365dd1b9e163a2c2c40e2f453 Author: giardine Date: Wed Jul 9 21:00:56 2008 +0000 added new species for oreganno tracks commit 645a8e22eb10e6c001eb31d392e3c58c1b4f90f2 Author: markd Date: Wed Jul 9 20:36:51 2008 +0000 fixed invalid html commit 5788fd29b16cf26b47db688392c458bca4fbc5e3 Author: galt Date: Wed Jul 9 19:43:17 2008 +0000 simple hash resize optimization suggested by jim runs 10% quicker commit 1e856adae0a663bc7c382c757f6e0f122d5f2900 Author: kuhn Date: Wed Jul 9 19:00:09 2008 +0000 removed limit variable because using DISTINCT to remove second record (allows wildcard search, e.g., hg). fixed 'all' functionality commit 2fcb806fe4b0b85e136319891ff46fc7456d7635 Author: braney Date: Wed Jul 9 18:56:43 2008 +0000 add custom option to forego using extFile or history tables commit d2e75d0a343551cfd3569a6a114b3d0016e78efb Author: braney Date: Wed Jul 9 18:44:15 2008 +0000 get custom track filename out of track settings commit a29e9ccd19cc2a4a7be2f1e4145a9797fcae3fb6 Author: braney Date: Wed Jul 9 18:42:57 2008 +0000 get custom track maf filename out of track settings commit f6a899bb6d1a036f64d826f2dd25ab15a3111233 Author: braney Date: Wed Jul 9 18:41:57 2008 +0000 remove code not supposedly executed and replace with error message commit af7c2d211cfc416a12b44b95ceeccc4e667db062 Author: braney Date: Wed Jul 9 18:41:07 2008 +0000 remove routine, no longer used commit 37ddd48c7d20adf308a6959c0c6bd43513168243 Author: braney Date: Wed Jul 9 18:40:39 2008 +0000 change the way we find a custom maf track file commit 8b7dd8c56d48c7b6a862583d75b3632f16c225bc Author: braney Date: Wed Jul 9 18:35:19 2008 +0000 pass in possible custom file name commit f694fe2001afa32ea7666cab03bae5b73686c052 Author: sbenz Date: Wed Jul 9 18:30:57 2008 +0000 Added UNC miRNA dataset commit a76ba835bc0fb4b9f866e76912b00a883b2a7aa8 Author: braney Date: Wed Jul 9 18:18:53 2008 +0000 take out CVS string from acs checkin commit 90c62d92e61b9b32f71ce0067f036d26c8b2020d Author: larrym Date: Wed Jul 9 18:07:27 2008 +0000 add EquCab2 to chainDest commit 801d5f1ffc54e78c28e7e757088e9d2a9975b496 Author: fanhsu Date: Wed Jul 9 17:18:23 2008 +0000 Disable hgCustom button on GSID server. commit b5200f17ebf5e7732d25b9333acd5eb6aa778109 Author: sbenz Date: Wed Jul 9 16:33:26 2008 +0000 Fixed longLabel for unc commit 995ae6925544b843ce99c0e13370915756912cdb Author: sbenz Date: Wed Jul 9 16:32:52 2008 +0000 Added new sample names for TCGA data commit 487c3cd4f792f970ff2e4945c9f79464bdc74421 Author: galt Date: Wed Jul 9 15:00:07 2008 +0000 "Encode release log update" commit 7da3b828e17df51ffcc0f7353bbdcc9a8284184d Author: galt Date: Wed Jul 9 15:00:04 2008 +0000 "Release log update" commit b8068f6b7bcc57f2612faebcdb0db637b7a13f83 Author: tdreszer Date: Wed Jul 9 14:43:37 2008 +0000 Convert macros to inlines commit fce8070dc88e558572ed3f25bfb715a8c4bb9509 Author: tdreszer Date: Wed Jul 9 14:37:46 2008 +0000 Convert macros to inlines commit 0c9858f0681732924af1e4832d32eaf93554996a Author: tdreszer Date: Wed Jul 9 14:37:16 2008 +0000 Use the right function call commit e61ff51efb1ea60a69387a1d8c50df1c9a052dc9 Author: kent Date: Wed Jul 9 08:48:27 2008 +0000 Fixing typo in comment and rearranging comment a little to put more frequently used hashFree closer to top. commit 7482372c66e176377063fe6d9d132273581ea561 Author: kuhn Date: Tue Jul 8 23:55:00 2008 +0000 fixed a bug commit cf7429fd6524f017328fc69556fba4f56298b886 Author: kuhn Date: Tue Jul 8 23:21:42 2008 +0000 added support for getting all the dbs from blat host and also for getting info from hgwdev or hgwbeta commit a87da58839e131135ff25fe0a51288aedb8a70f1 Author: kuhn Date: Tue Jul 8 22:15:01 2008 +0000 removed script that is never used commit 4748b8bc27a35f48fe62c32d3707dd3af5c8f1de Author: larrym Date: Tue Jul 8 22:10:58 2008 +0000 add equCab2 commit 88fce1481d43dd4342a3d78e95420ca4bdb45e02 Author: braney Date: Tue Jul 8 22:08:35 2008 +0000 a utility faster and smarter than mafsInRegion (but has additional burdens) commit b3bec1da2c5d0e227c9beb621f772bc69900b5e8 Author: hiram Date: Tue Jul 8 21:23:25 2008 +0000 even more clarification on the MACHTYPE setting commit 92ba6e4e72a66a8a0602595b67d68ce6ab0e98a6 Author: braney Date: Tue Jul 8 21:01:54 2008 +0000 fixed bogus non-linked B when database isn't active for un-aligning sequence commit 13d978bb6b64f01b2b054469774af7864315f9b7 Author: sbenz Date: Tue Jul 8 20:26:34 2008 +0000 Updated Broad Affy Exp sample names commit 2a1acbb1dff7305f83888573548a86a0319e61fc Author: ann Date: Tue Jul 8 20:25:14 2008 +0000 removing hide visibility from transMap superTrack line (when it was there, the track wasn't showing up as a superTrack on beta commit 3877bb15339c3c4f4bfe236ae310e13130f601a0 Author: angie Date: Tue Jul 8 18:31:26 2008 +0000 Another stderr logging message: show mysql_error when connection attempt fails, even when we don't abort. commit 57e85b45a3d60c2040b9b5bb08f416a331df26bd Author: fanhsu Date: Tue Jul 8 16:47:30 2008 +0000 Added logic to display a row of "N/A"s if the subject has demographic data but no clinical data. commit b5ab8d91fc66abc4fb0bd8c107067f8efc60ce96 Author: larrym Date: Tue Jul 8 16:44:45 2008 +0000 "New version number v186" commit b67a45913305de31a2100a32bc35f70e9769fe11 Author: hiram Date: Tue Jul 8 16:24:04 2008 +0000 Adding the noComment option to the hgLoadBed and hgLoadWiggle loaders commit 84a0c648511016a702303848b5ca3745eb387e6e Author: hiram Date: Tue Jul 8 16:08:58 2008 +0000 Add a noHistory option for custom tracks commit 1d55356882f9fe6dbf9548a93caf36f44ce14ef1 Author: hiram Date: Tue Jul 8 16:05:26 2008 +0000 Adding noHistory option commit cafd1a3ce2e2bbd23fb2728e239a5d0a3f1ad7fc Author: hiram Date: Tue Jul 8 15:56:36 2008 +0000 Explicitly note README.building.source and the uname commands to determine MACHTYPE commit 72b83a66fae8d6c9f2dbd1d5f6ccc4a19049be2b Author: hiram Date: Tue Jul 8 15:47:27 2008 +0000 indicate the uname commands to determine the value commit 0072df2c422f6435d927acc92b200cdf4b7fd39d Author: galt Date: Tue Jul 8 15:00:10 2008 +0000 "Encode release log update" commit 4e0b7a2d671546c3f6b0b12dfa35391a2dc81034 Author: galt Date: Tue Jul 8 15:00:04 2008 +0000 "Release log update" commit 9bd7fdc35aa1aad26e380367b6e60029c7c29b90 Author: braney Date: Tue Jul 8 14:59:27 2008 +0000 Initial descriptions for taeGut1. commit 01f98bf99ef37326c3787a3106d933be9bbd4fd8 Author: braney Date: Tue Jul 8 14:57:02 2008 +0000 add zebra finch commit 7961289e2fa51d184782814b02ade41d146ad5ba Author: braney Date: Tue Jul 8 13:50:34 2008 +0000 initial doc, copied from cavPor3.txt commit f94a76387b5bdb36e1aed3b8f3e7ffab66662d24 Author: giardine Date: Tue Jul 8 13:35:05 2008 +0000 updated ORegAnno tracks commit eb35cde7dc9f3f20ff660d2df445d325c0925a9d Author: giardine Date: Tue Jul 8 13:31:00 2008 +0000 added reference commit 22c7eac97488f36bae24fd19c59267c1e794b5ad Author: angie Date: Tue Jul 8 07:54:21 2008 +0000 Added diagnostic stderr messages to sqlTableOk. commit b13212fc4f27a5083e63605aec0e7f276a104a0f Author: angie Date: Tue Jul 8 07:52:34 2008 +0000 Added pid to cartTrace messages, so we can match up with pre-cart messages (e.g. hgConnectCentral). commit aeb19b0f908dfa4583e2dbe56352af149342c6ea Author: angie Date: Tue Jul 8 07:51:40 2008 +0000 Added stderr log statement when hConnectCentral fails over (scary that this has been totally silent). commit 4fb258071ccd48d5bcf19fca02bde8002a3f949d Author: markd Date: Tue Jul 8 05:38:50 2008 +0000 added check for -raName being a simple file name commit 497b3fc3f136d381debc0c2ec5d2ffdcde2152b8 Author: markd Date: Tue Jul 8 05:28:55 2008 +0000 added missing terminator to list of options commit 2fafa73acf275142f82129e8867db24bdc3c89d8 Author: hiram Date: Tue Jul 8 04:44:41 2008 +0000 Do not add another / if pathPrefix ends with / Can still get a double // if the path name starts with a / commit 8670805469823550fe9b56412288ab985f8d47db Author: braney Date: Tue Jul 8 00:25:31 2008 +0000 move positively selected genes to genes section commit ef394f1f24e4fcd0edaa8f532393c3a78cdb5e10 Author: larrym Date: Tue Jul 8 00:23:25 2008 +0000 add/improve error messages; add some more trackDb entries commit 7b6c74ba2381777ed38fbb4756ee6ef9a0bff524 Author: larrym Date: Tue Jul 8 00:03:12 2008 +0000 lab metadata commit f1a9de0323151f7929a7e8b79c3f80d999d75ee6 Author: larrym Date: Mon Jul 7 23:58:24 2008 +0000 convert tests to new format commit c226fa878850cb7d862e13473ae6b52465a1543a Author: donnak Date: Mon Jul 7 23:52:57 2008 +0000 Added Schattner book. commit 292c032de98fb63266c490c236f2067cc54b196f Author: braney Date: Mon Jul 7 23:22:11 2008 +0000 add index on chrom for table mammalPsg commit 493c11a0bfe7e0dee1e3d09d3b61716e4ad3e578 Author: hiram Date: Mon Jul 7 23:10:23 2008 +0000 Fixup absolute references to /trash/ commit 80164d0a245821351e66d5eaa4ca69bf60275c98 Author: tdreszer Date: Mon Jul 7 23:06:26 2008 +0000 Supertracks do not (yet) contain their 'subtracks' commit 20247f4915a3972e53d600118bd351ff82cd761d Author: donnak Date: Mon Jul 7 22:41:33 2008 +0000 Minor edits. commit 743706aa3630a65e35f7244ffe9f11a68c23044e Author: donnak Date: Mon Jul 7 22:41:25 2008 +0000 Fixed incorrect link & typo. commit bf977b08ab9a195af4b64508fc3f84f8fc0680bb Author: hiram Date: Mon Jul 7 21:39:02 2008 +0000 Proper SQL query for bed-items with the same names commit fa896c85c5f1f0f9414f17b408817131107c9fa9 Author: braney Date: Mon Jul 7 20:55:43 2008 +0000 added positively selected genes track from Adam Siepel at Cornell commit e6f925338a990e09733a1d40845a2498664cbb9b Author: braney Date: Mon Jul 7 19:31:11 2008 +0000 get mammalPsg images out of local directory rather than from Cornell commit 8b41fd767399819af768a743e33008c724b6b485 Author: larrym Date: Mon Jul 7 19:02:23 2008 +0000 icon to identify wgEncode tracks commit 14d12235b0b3e5480064c7abbe67efab92645d6c Author: larrym Date: Mon Jul 7 18:55:05 2008 +0000 use defaultIsClosed in isCollapsedGroup commit cb35cbd0dbb165ce3619bbc2af8aeb7f01addb15 Author: rhead Date: Mon Jul 7 18:51:00 2008 +0000 Removed cbseweb address entirely. Too many emails going to the wrong place\! commit ba786ffcd712bac0352a489cbe76a4c01a7b58ca Author: larrym Date: Mon Jul 7 18:44:55 2008 +0000 support defaultIsClosed; show encode.ico if wgEncode track setting is set commit b6777666112fd9de19177b81efd1e8c21a725b28 Author: larrym Date: Mon Jul 7 18:12:38 2008 +0000 add support for (optional) grp.defaultIsClosed column commit 19a1a7335b931c5109710d22abcc50976f177c3a Author: braney Date: Mon Jul 7 18:04:10 2008 +0000 check to see if custom maf files are still available commit 7a73d4768e580fd8c6a3a9827f601031ce75b688 Author: kent Date: Mon Jul 7 18:01:02 2008 +0000 Another stab at making transferExceptions work with CCDS. commit 4b6738ebdf975e4a2505535d358b4221a16e3be3 Author: angie Date: Mon Jul 7 17:17:04 2008 +0000 Added snp129. commit 2d9d7c149eb5c958cfc58e77f28f0b4aa0f925a6 Author: angie Date: Mon Jul 7 17:16:33 2008 +0000 Swapped dm3 chain/net. commit 22ed39fd031576c0da9fb512ad0e0680403a1df3 Author: tdreszer Date: Mon Jul 7 16:15:49 2008 +0000 More clearly mark and distinguish between parent/child and super/composite tracks commit 390abb4a877268e217276eb85572f4d8df62b813 Author: hiram Date: Mon Jul 7 16:04:07 2008 +0000 Add note about uname to determine machine type commit f914c3faddebab0e66ca170e03c530510ac7442a Author: galt Date: Mon Jul 7 15:00:04 2008 +0000 "Encode release log update" commit 6e5e51ee4c8c5425df47c93f5dc1ea8c15fe7a7d Author: galt Date: Mon Jul 7 15:00:02 2008 +0000 "Release log update" commit ad643211104cefdde7f6ddcefb20a9a4c2bd9223 Author: kent Date: Mon Jul 7 13:47:11 2008 +0000 Making transferException survive CCDS. commit a1903c096f815130939579004cad96d303a6f297 Author: galt Date: Mon Jul 7 07:32:47 2008 +0000 not using zcat on gzipped files because it is not POSIX compliant commit 4923a7cc39b5eda43aef27646bdd583d4c3d15d6 Author: galt Date: Sun Jul 6 15:00:07 2008 +0000 "Encode release log update" commit fbe520223577a2f4f353368b7710590f89b5ae7b Author: galt Date: Sun Jul 6 15:00:05 2008 +0000 "Release log update" commit 413b22e857735d1d52430d435dab67ea5bf2860f Author: kent Date: Sun Jul 6 09:07:19 2008 +0000 Added usage comments. commit b5cf3046d4ffc936329feb5155c33953b51946b4 Author: markd Date: Sat Jul 5 20:20:49 2008 +0000 updated doc to describe LIFO behavior on multiple keys commit 135dcafff56467123f38971621d36c73119059d1 Author: galt Date: Sat Jul 5 15:00:03 2008 +0000 "Encode release log update" commit 460412b88b05e656b077d09e17e1c318bf9276e1 Author: galt Date: Sat Jul 5 15:00:02 2008 +0000 "Release log update" commit 11c68ecde485663bf055e726914e08cb1aeb39eb Author: galt Date: Sat Jul 5 06:33:38 2008 +0000 removing dependency on jkhgap.a which never was needed or wanted for kent/src/lib stuff commit daec6cc357d5b628e6e1c9fe6181e9d63aa11d85 Author: fanhsu Date: Fri Jul 4 16:55:04 2008 +0000 Added gsidClinicRecWithSeq.sql. commit 8d4939ef7fa09971cbbe35960655a22220a3912a Author: fanhsu Date: Fri Jul 4 16:53:08 2008 +0000 Update gsidClinicRec.sql to allow NULLs. commit 4b187df55883dd2160f810e1366aab363ab46d7d Author: galt Date: Fri Jul 4 15:00:07 2008 +0000 "Encode release log update" commit 5fe443e5e8c11666a346665e300922e3cf4a8db3 Author: galt Date: Fri Jul 4 15:00:04 2008 +0000 "Release log update" commit ee438fed0e61d5cb2344c96e503db7894f1966d2 Author: hiram Date: Fri Jul 4 08:08:08 2008 +0000 Take care of the behavior where wigTotalHeight is called multiple times and yet limitVisibility is actually setting track height properly once the first time and we don't want wigTotalHeight resetting it again commit 04683e760bba5c86120a380e5df6201fffffd91f Author: angie Date: Thu Jul 3 22:57:07 2008 +0000 hChromSize now gatest with hDbIsActive, so make our own testChromSize so we can use the test database. commit 46bac8a8cc13ab8927960085d0cbad8f02e2affb Author: fanhsu Date: Thu Jul 3 22:54:25 2008 +0000 Changed doVax004() to doVax003Vax004(). commit e0377ddce2edd3a5c868a07aec48cb977243a966 Author: ann Date: Thu Jul 3 22:23:45 2008 +0000 Corrected typo (VAX004 -> VAX003). commit cdbd95de7c611b22e480488d9860e8986fff264c Author: angie Date: Thu Jul 3 22:06:17 2008 +0000 In isSubtrackVisible, if subtrack's limitedVis has been set, gate with it. commit 384e52f8fb9607722c62e50f2108111b3f30578b Author: acs Date: Thu Jul 3 21:54:15 2008 +0000 support for new pos sel genes track commit ea5f0f9f0f2a83daaf538404b9e7e3eeaa22f8bf Author: acs Date: Thu Jul 3 21:52:24 2008 +0000 autosql files for new pos sel genes track commit 1f9a1089e8e6ae090eb66fb99eed28c3f90f6cd0 Author: tdreszer Date: Thu Jul 3 20:34:18 2008 +0000 Matrix cfg had one too many 'Show table schema' links commit 87deea509f968f04441e646d259b9a915408c428 Author: tdreszer Date: Thu Jul 3 20:31:57 2008 +0000 Added a couple minor features and reorganized code to use structs commit 4ed1b81496aae99ead9d45de0a1c32636c49e3c6 Author: markd Date: Thu Jul 3 20:17:05 2008 +0000 added notes on tandem dups to look at commit 27964f29e51c33f30d210cd48b7fa08fe7d56312 Author: tdreszer Date: Thu Jul 3 20:11:51 2008 +0000 Function to determine if a composite track uses matrix style cfg commit ffa87b1e146bd474f8c2bf45d8ecc146de465630 Author: galt Date: Thu Jul 3 18:14:55 2008 +0000 reducing for machines with smaller ram commit 8e9f213aab89725e8ad1ab6f213d750b50ad7b3d Author: fanhsu Date: Thu Jul 3 17:51:43 2008 +0000 Updated wigMafUi() for GSID maf with logic to display entries that are on the specific maf track only. commit 65626695b2cf33394160562e085fa65f95c5e97b Author: mikep Date: Thu Jul 3 17:24:24 2008 +0000 added tables to joiner and copy wig ascii files to goldenPath commit 1929b10bbbb19dd5b83fa5828f49cc46fe9a50c3 Author: mikep Date: Thu Jul 3 16:29:50 2008 +0000 added Tig3 to track labels per author request, and commented out my home dir paths in .txt commit ae283c9c1f2579d2a39ec144df5b7bae4e73d11b Author: galt Date: Thu Jul 3 15:00:06 2008 +0000 "Encode release log update" commit a379a7a9a310bbb5977d3da57e2d9cf00123d057 Author: galt Date: Thu Jul 3 15:00:04 2008 +0000 "Release log update" commit 7a67e4c1ea1485485a5b273a0b4bf04ac980c36e Author: lowe Date: Thu Jul 3 08:36:40 2008 +0000 Fixed outdated Pfam links on Pfam detail page. commit 5eee2dfd047f76faada5f4e3eb9ccb689956e924 Author: markd Date: Thu Jul 3 06:59:51 2008 +0000 removed deprectate regexp filtering, which was preventing modern clients from correctly filtering by type commit c5f55ed1b00858eda416e3b951d286158553de73 Author: markd Date: Thu Jul 3 05:33:23 2008 +0000 added doc commit a058f482f23df2871d7e0a4ac096022faf5b8977 Author: markd Date: Thu Jul 3 04:52:47 2008 +0000 fixed typo in date commit 8b7a006178599984c4008ae38db8cce8bdad1aa9 Author: markd Date: Thu Jul 3 01:31:55 2008 +0000 update ccds every night for hgwdev testing commit 631de8237281178e3ba68fe4c783f10e0bd908a9 Author: braney Date: Thu Jul 3 00:49:25 2008 +0000 add something for filtering maf custom tracks commit e4b15cd538430b1e696dd17ca63b79d6c0724ead Author: braney Date: Thu Jul 3 00:09:02 2008 +0000 add the ability to get DNA even if there isn't a browser commit b11b34e632259ec4d8aeddd0a3c2a4d13cf16c1d Author: tdreszer Date: Thu Jul 3 00:02:35 2008 +0000 Matrix tracks need visibility commit a8233ec9e4306343cf382eaa888a88c7f2d7b65c Author: tdreszer Date: Thu Jul 3 00:01:33 2008 +0000 For Larry's too. commit 592272d822948d18b795b7ce9b3c961db2848a0c Author: tdreszer Date: Thu Jul 3 00:00:24 2008 +0000 Matrix subtracks need visibility commit b4842831d346f41e2f77d8827b4d37021f12a7b2 Author: braney Date: Wed Jul 2 23:33:58 2008 +0000 handle getting DNA from a species without an active DB commit d8651c05acdb22fe238b88664cc3833401e62d68 Author: braney Date: Wed Jul 2 23:31:29 2008 +0000 handle case when we don't know the chrom size, the 2bit routines will complain if we ask for too much commit ef09e0655098dae1b5946891543ec7bf7ecf4ec0 Author: braney Date: Wed Jul 2 23:30:39 2008 +0000 return 0 for chromSize if database not active, get nib file location from dbDb if database is not active commit 1f9da111dd982bec715eb7b7a8477479b57b8864 Author: braney Date: Wed Jul 2 23:29:11 2008 +0000 don't output hotlinks bar if database isn't active commit a4253a6d205e75c2397b3f195a85a581cf8d8df4 Author: hiram Date: Wed Jul 2 23:14:23 2008 +0000 Fix broken intersection when given bed file. It wasn't making it to the end of the most extreme chromEnd bed element commit 18a2911aefa6d887a634af9793b63786e04ea482 Author: braney Date: Wed Jul 2 23:09:23 2008 +0000 put out schema for custom maf track commit 5d3081df302c0faef7cae30088d042e6a11cef82 Author: angie Date: Wed Jul 2 20:59:40 2008 +0000 Added support for a new orthologous-allele-table setting for snp12* (orangutan in addition to chimp and macaque). commit f5c9a634ac659d3bd38bcef65abcbe13c88cfc91 Author: galt Date: Wed Jul 2 20:57:16 2008 +0000 expanding max hash size limits commit 1e34e094ba6c447f459f2e9d479c15c3ecf817a6 Author: sbenz Date: Wed Jul 2 20:49:29 2008 +0000 Added base level broad mutation data commit c7155768238bf5f8325b86dd37571f5244ca1ca7 Author: sbenz Date: Wed Jul 2 20:48:45 2008 +0000 Added base level mutation data and increased coloring on summary broad data commit bebc035937ce00ec666786800fba452e84abf776 Author: angie Date: Wed Jul 2 20:46:43 2008 +0000 Added snp129. commit 42378941101c23b794ca015304c37dbeb3f624a5 Author: tdreszer Date: Wed Jul 2 20:44:50 2008 +0000 In for a penny: height for dense was wrong too commit 5b9165603f77a2cc79dedd19b716731fd9b0a7cf Author: angie Date: Wed Jul 2 20:44:48 2008 +0000 Sequence masking & orthologous allele predictions for snp129. commit 3094995caf49e286cc8fb92d104b1df43d5ef1cc Author: tdreszer Date: Wed Jul 2 20:33:56 2008 +0000 Hiram called me out on the hardcoded wiggle heights commit d4c562d8ad49ebde080397fa2fc84f13850d5e50 Author: braney Date: Wed Jul 2 20:32:42 2008 +0000 let hgLoadMaf tell us the default position commit 03ab4c9537b9767c3d45cb33de291d4873c2cc12 Author: braney Date: Wed Jul 2 20:29:13 2008 +0000 add argument to let hgLoadMaf decide what the default position should be commit 374789ff0997b445337204d6db94571cb524242e Author: angie Date: Wed Jul 2 19:21:42 2008 +0000 When writing the tab file, if there is a write failure, exit immediately instead of sailing along and loading part of the table. commit ee577438f33c58284e45b347178fce8e7a8a7b19 Author: fanhsu Date: Wed Jul 2 18:56:06 2008 +0000 Cleaned up some errors exposed by new hPrintf() and added special logic to handle doGetText() for dnaSeqs and aaSeqs. commit 3abfd01c90206a32a57f0bdef6e3cffbf8364e63 Author: angie Date: Wed Jul 2 16:23:39 2008 +0000 Oops, accidentally deleted a subGroups line in previous rev. commit 019c33b1b68a767fd0efaf963e837244a8349c98 Author: galt Date: Wed Jul 2 15:00:30 2008 +0000 "Encode release log update" commit 16edb7e210c5e17bc6ab9dcc784b01ee7eb82252 Author: galt Date: Wed Jul 2 15:00:22 2008 +0000 "Release log update" commit d18f122c0981af181f88cc656d4e7ea261bac7b7 Author: mikep Date: Wed Jul 2 00:41:30 2008 +0000 laminB1Super track documentation and .ra (NKI Nuc Lamina, Guelen et al 2008) commit f243d4f815e3eed733b304ff3e2b058dde003cd7 Author: mikep Date: Wed Jul 2 00:28:11 2008 +0000 Figure supporting documentation for laminB1Super track (NKI Nuc Lamina, Guelen et al 2008) commit 4fef33804937ed174d6e631d514b78ea9dd34a8f Author: braney Date: Wed Jul 2 00:11:18 2008 +0000 add link to native database for xenoRefGene item commit fb79d10d484bfb9d070856c13cb4a1bb5820f283 Author: braney Date: Wed Jul 2 00:09:35 2008 +0000 a couple of routines to get db from scientific name, and to get nib path from dbDb table commit 8c26d4c9b58bc01f941d1c26612090e34987cbf3 Author: braney Date: Wed Jul 2 00:08:07 2008 +0000 add a couple of routines to get database from scientific name, and to get nibpath from the dbDb table commit 8078ed11ecc44b76d7f4e5ccfde4a438e095726c Author: angie Date: Wed Jul 2 00:03:42 2008 +0000 Call jsInit *after* the routines that call cartWebStart, so the script stuff doesn't appear before the HTTP headers. commit a22156b61b8b00b94a91acd454b2b2c244aeef9b Author: jsanborn Date: Wed Jul 2 00:00:39 2008 +0000 fixed a bug with broadABI commit 73d7fac5cd7021cd3a03a613ab034fd8cbd9896b Author: galt Date: Tue Jul 1 23:42:36 2008 +0000 remove duplicate paragraph from MarkD. slight edit. commit 16eeb4acecfa20d25567ea7e5310a43c67f55b98 Author: fanhsu Date: Tue Jul 1 23:39:56 2008 +0000 Updated gsidSubjSeq table (for Table View) commit 0f4c527c3faeacf38cfda1d44bbf12221e5f44ce Author: fanhsu Date: Tue Jul 1 23:35:08 2008 +0000 Updated gsidSubjSeq table. commit 94f8afc8ff0eb032dc649650529990a00739cc73 Author: sbenz Date: Tue Jul 1 23:13:48 2008 +0000 Added jhu-usc methyl data commit 62285671ee7b7d74f98af1abd511a93fa3761c0c Author: sbenz Date: Tue Jul 1 22:48:21 2008 +0000 Adding broad ABI data commit 242eb31616b042950a6c63186da428bf8816566f Author: markd Date: Tue Jul 1 22:41:42 2008 +0000 error on missing hg.conf entries rather than generate bogus command line commit 4cb6752e571095aafcef4e02ff88496a3088adc7 Author: donnak Date: Tue Jul 1 21:31:38 2008 +0000 Added several new folks. Still need to update the grads/postdocs. commit 37746c3a191bb383dd358355a45f0f2a8c3912d4 Author: ann Date: Tue Jul 1 19:08:44 2008 +0000 turning off VAX003AEMaf and on VAX003BMaf by default. commit f38a56bfb99622dbc5f52899b6a8fb2f17b8a534 Author: angie Date: Tue Jul 1 18:05:35 2008 +0000 Removed noInherit and redundant settings from 'subTrack bdtnpChipper off' entries, because noInherit is no longer required in order for 'subTrack ... off' to work. commit 93fc63212aef51296ac4285ed29819b3c38c6478 Author: angie Date: Tue Jul 1 17:17:58 2008 +0000 Added marker variables textSize and trackControlsOnMain to cartTrace. commit 8c29f81bc1897f8b47fc973bd32170d6b193cd11 Author: markd Date: Tue Jul 1 17:12:27 2008 +0000 don't autoupdate mm8 ccds commit b855df3a24845f90abb0ef34c502955d79f04a07 Author: markd Date: Tue Jul 1 16:53:03 2008 +0000 transMap rebuild commit 584bdbe1ef92f428befb6a95e8f7cf122396dd3d Author: angie Date: Tue Jul 1 16:51:06 2008 +0000 Made cartTrace message more concise. commit 0eb936893789ecde613e9ff80e7842b5868d8158 Author: markd Date: Tue Jul 1 16:50:14 2008 +0000 fixed doc for new arg commit d12df51002e25c7ee39af2dd36f187eb3ebaba32 Author: markd Date: Tue Jul 1 16:49:41 2008 +0000 added xeno refseqs commit 829fd0ba5db607e248210565f6e9413ac7e29210 Author: ann Date: Tue Jul 1 16:22:49 2008 +0000 Added VAX003. commit 99039080efc483fef7b4bc44073f39e4597d8c2e Author: angie Date: Tue Jul 1 16:22:34 2008 +0000 In cartCheckout, call cartTrace after saveState (not before). commit ac93ee6fee6f7b4481af63e13f207545af70278e Author: galt Date: Tue Jul 1 15:00:21 2008 +0000 "Encode release log update" commit ccc7f944305d5f5a1792e4ac9d4c58e848bbe503 Author: galt Date: Tue Jul 1 15:00:18 2008 +0000 "Release log update" commit 599059215d62a6a8b8296e33ec60e585dfeac5be Author: markd Date: Tue Jul 1 07:57:54 2008 +0000 added auto load of ccds tables, initially only on hgwdev commit 7dc3eee3cfec906b31f9401ad79126e92b31c524 Author: angie Date: Tue Jul 1 07:19:53 2008 +0000 In saveState, when incrementing cookie use count due to cart-stuffing bot check, leave session alone (don't erase it!). In cartTrace, query to get actual length of contents because content string has been chopped up if used. commit 135038136296eae52bb7b86e1b4c97de8b757297 Author: markd Date: Tue Jul 1 07:09:37 2008 +0000 changed build times to try to get hgwbeta loaded before QA wakes up commit 90c5c584027c93f36bf4a2e277731400398c6c18 Author: markd Date: Tue Jul 1 06:42:37 2008 +0000 added function to configure databases via profile specified in hg.conf (generalized sqlConnectReadOnly) commit 2b037e9a28c9e6fe7812d968f21dc2af634361fb Author: markd Date: Tue Jul 1 06:40:46 2008 +0000 added support from download and import of ccds data commit 235360655c9ff4f2c232b77301793db95ff25d09 Author: ann Date: Mon Jun 30 23:44:19 2008 +0000 switching the order of the tracks so that the maf track appears directly below the corresponding conservation track. commit 66e8825fa7ae1c172f75650114cf363de88bb11c Author: ann Date: Mon Jun 30 23:35:44 2008 +0000 moved the order of the tracks so that the maf would appear directly below the associated conservation track in the display commit 3e714bced8bf1a3faf03c7c36ba4f8db8deba3fd Author: angie Date: Mon Jun 30 22:29:46 2008 +0000 Added snp129 core tables. commit dfd0ae4565a450421ea92b30641f26c0508eecbf Author: angie Date: Mon Jun 30 22:03:48 2008 +0000 In saveState, even when we don't write out suspiciously long contents, do increment the useCount. Apparently a user may follow an hgsid link for a bloated cart, get a cookie, and keep clicking around with the bloated cart. Previously, useCount was stuck at 0; neither userDb nor sessionDb was ever updated. The empty-contents cart entry is already there in userDb, so this doesn't require any extra db space. commit 6965c70c4246a94243db9ef66fd647bf5aea9333 Author: angie Date: Mon Jun 30 20:56:30 2008 +0000 Removed duplicated bit of perl (thx Belinda). Added kiddEichlerValid. commit 428ab316d0fd4e8dc0277f1d39492929b74775a6 Author: angie Date: Mon Jun 30 20:52:53 2008 +0000 Some more format-broadening for human 129. commit 48a12a56cbcde65a12b1dbc9e72cdcc749a7a4f4 Author: angie Date: Mon Jun 30 20:51:19 2008 +0000 In printSnpAlignment, watch out for fasta entries with unambiguous SNP char -- we can't reliably figure out which base is the SNP. dbSNP human 129 has 5 of these; they'll be fixed in the next release. commit b9d0d9c4b0e76abc242077b87829e9327316b5fb Author: ann Date: Mon Jun 30 20:51:18 2008 +0000 changed wording of message about retreiving wiggle data commit 1075819e8c89281d6dc45d95d3918ca544e69713 Author: angie Date: Mon Jun 30 20:14:29 2008 +0000 If hg.conf has cart.trace, print out some cart properties when opening, overloading (hgSession) or closing the cart, to see if we can catch the getting-somebody-else's-cart bug. commit 1b91b580dd0e2d8307882edbcb301fcf7ea5847c Author: hiram Date: Mon Jun 30 18:28:44 2008 +0000 Do not copy a lift over when isSelf, it does not exist commit 3bc68f771284f1e24920a0a81b054477742ee691 Author: markd Date: Mon Jun 30 16:56:02 2008 +0000 added chainType to transMapInfo commit 9f53c64d42d1a8db2d85bcff6289d58ca7d984fd Author: ann Date: Mon Jun 30 16:35:48 2008 +0000 rearranged and added detail. commit 7baddd91b474a13cc74df4c8b48c934d8667a96a Author: ann Date: Mon Jun 30 16:25:56 2008 +0000 fixed typo. integrated links into text. commit b1ee4a9832845bf10e10ee1ac1f64e76d8a8bd01 Author: galt Date: Mon Jun 30 15:00:11 2008 +0000 "Encode release log update" commit 46de9d1998f5aa1b630953b5c51f849cca22ebc2 Author: galt Date: Mon Jun 30 15:00:08 2008 +0000 "Release log update" commit b582ada466020ceaf592dd1eb78bccf57893523e Author: markd Date: Mon Jun 30 00:37:48 2008 +0000 updated transMap description commit c0645cb798181497335207c76c393dd94f69f961 Author: kent Date: Sun Jun 29 16:26:16 2008 +0000 Fixing broken EST link to NCBI Entrez. commit d76b6538a4a8075e4410f52c62699a90030c0c28 Author: markd Date: Sun Jun 29 16:02:24 2008 +0000 recognize compessed files with .Z or .bz2 extensions commit 7a43b6c347c4ddf66a1773966c6a63df90b62470 Author: galt Date: Sun Jun 29 15:00:10 2008 +0000 "Encode release log update" commit 7567a94709006ac5510c4aa189777b267c933760 Author: galt Date: Sun Jun 29 15:00:07 2008 +0000 "Release log update" commit f5ed7c32b5c51886bfaacbc29809e4aabad26a8b Author: markd Date: Sun Jun 29 06:36:41 2008 +0000 doced changes commit 8a25632bf04fa8ed5a641bd159f4003268c5f12a Author: galt Date: Sat Jun 28 17:21:00 2008 +0000 another bug found by GNU printf checking commit db383e10612be26067cb37a8d4a8da5739ea2c5f Author: galt Date: Sat Jun 28 16:56:04 2008 +0000 another bug found by GNU printf checking commit 29033a396be84859ba2f36de96e5ed9448e20eac Author: galt Date: Sat Jun 28 16:45:17 2008 +0000 another bug found by GNU printf checking commit 8b010dc5923929a3acbaa98aa0ef773efd979b44 Author: galt Date: Sat Jun 28 16:40:37 2008 +0000 proper printf escaping commit 4f83ec78e6df4bdd22654320d80c13700cd5e04c Author: galt Date: Sat Jun 28 16:37:57 2008 +0000 adding needed cast commit 79954188bb4d7be3bd04760b8d385faa5bd5a4ad Author: galt Date: Sat Jun 28 15:00:08 2008 +0000 "Encode release log update" commit 3c8cbe2b12a3d034d15c9a8831cbb0f5385339a2 Author: galt Date: Sat Jun 28 15:00:05 2008 +0000 "Release log update" commit b8aa5642e4ef85f2a63ea52c5870781efc1de20d Author: markd Date: Sat Jun 28 05:10:35 2008 +0000 added support for control over batch and job working directories commit 593ea1d34f4e80442e7d33cfd977102383f2b98e Author: galt Date: Sat Jun 28 01:56:14 2008 +0000 adding hash test suite commit df2cd37a50e32ab26e017167cfa1fb6861d0cdcc Author: galt Date: Fri Jun 27 23:49:00 2008 +0000 fixing list reordering commit 9e82963ac5e3eea4f1a4eea1d7fa4f05f216f0b0 Author: ann Date: Fri Jun 27 23:01:08 2008 +0000 made a rule for Illumina tables, removed them from tablesIgnored commit 0d2f79017df917fbdc0d72b41c7c0bbe9b129b7d Author: rhead Date: Fri Jun 27 21:58:45 2008 +0000 Changed link to KRIBB Genome Research Center to a page in English. commit cb63c29f1f7bb54e88290a40846168529454ed83 Author: braney Date: Fri Jun 27 21:55:37 2008 +0000 fix bug when 'track' line has no options (seg viol) commit 7ca2c8014c1dc2b6b00b9239bd213374270f0242 Author: galt Date: Fri Jun 27 19:51:52 2008 +0000 fixing some printf bugs in my code and two others from somebody else commit b44d5297b99bae62d35eb6be9aecd25964b1d957 Author: galt Date: Fri Jun 27 19:49:20 2008 +0000 adding better printf parameter checking commit 54c28dd10ff2cea5831906b8a7c1e764dc5aa251 Author: larrym Date: Fri Jun 27 19:33:36 2008 +0000 modify wgEncodeStanfordChip entries commit 6e77f7846c4d1656f1ca1a3872779203473a54cd Author: galt Date: Fri Jun 27 19:33:07 2008 +0000 making Home and Genomes links more consistent by including org,db,hgsid commit 2d482843829b153f9670dd06ad00e09ab1480899 Author: larrym Date: Fri Jun 27 19:30:48 2008 +0000 modify short label and subTrack code commit 9647e57daf1ab0a0a37ef2f526398bfb5fcc7b52 Author: galt Date: Fri Jun 27 19:15:55 2008 +0000 trivial commit 372f04ba9bd67d7ae24fd6333fa37156bfd51261 Author: markd Date: Fri Jun 27 18:46:54 2008 +0000 Changed setCurrentDir/getCurrentDir to abort on errors rather than return a status. This fixed many cases were status was not checked. commit 2c683d8edec74e9f3dff30047d7fffa903b43950 Author: donnak Date: Fri Jun 27 17:46:18 2008 +0000 Added note that SARS assembly has been dropped. commit 5229222eb9b2dfe7fe2b5c05ac8c405ef8ae47ef Author: donnak Date: Fri Jun 27 17:41:44 2008 +0000 Removed SARS. commit b97a6e04d12b45dba11c530d121e9a916010f408 Author: donnak Date: Fri Jun 27 17:36:24 2008 +0000 Removed reference to SARS downloads. commit 2317588b1482cf62898c01d07ce021c325e23379 Author: donnak Date: Fri Jun 27 17:32:51 2008 +0000 Removed SARS from release table. commit 9f9887b440626634ce94fa500bb616c8dd8477ec Author: kuhn Date: Fri Jun 27 16:30:12 2008 +0000 removed hard-coded refs to help docs in separate pbGlobal tree, which is not is cvs commit 414b9c9f260fb020a1c0b050ac3dcb6b3ba2ae7e Author: galt Date: Fri Jun 27 15:00:12 2008 +0000 "Encode release log update" commit acca8533a764901420f3536ccb490aee9acffdf6 Author: galt Date: Fri Jun 27 15:00:09 2008 +0000 "Release log update" commit 3a8fa937e531e7346694a4ad6e2754dd479386b2 Author: donnak Date: Thu Jun 26 23:23:23 2008 +0000 Added C. japonica. commit 199eecaa5b7b94f145d17a0fc7bb76af3aefe9dc Author: hiram Date: Thu Jun 26 21:16:49 2008 +0000 Always show the "hide all" button even if track controls are off commit cb74cf41222f596155155381be9dcbbf3468a240 Author: larrym Date: Thu Jun 26 21:09:24 2008 +0000 add FOXP2 and SK-N-MC commit 9652efb535a19067d52707d5b7abe8892aaf9e20 Author: larrym Date: Thu Jun 26 21:08:45 2008 +0000 switch to simpler field names commit 54ba782a673d4062d6586287c47ef754875ceb6a Author: larrym Date: Thu Jun 26 20:50:34 2008 +0000 lots of trackDb changes commit 568970e0dbc57ee0e60cfe749bf3d51e0572d7a4 Author: markd Date: Thu Jun 26 20:44:06 2008 +0000 removed bogus table reference for transMapped ESTs commit a4aa0dad444aa9893ce71adedf8c03e5bd6c8271 Author: angie Date: Thu Jun 26 18:35:09 2008 +0000 Pass stdin to stdout for further processing (at this point, tracking what files have expired). commit 47dcc40fcae16ce293870655d7edfae77599fd40 Author: galt Date: Thu Jun 26 18:17:59 2008 +0000 Proper session separation commit 3aadc6ccf6466b3abb0ce455b373a3e3aa340373 Author: larrym Date: Thu Jun 26 17:54:54 2008 +0000 massive number of changes to support new PIF and DDF design commit f4d13fcb5784ad88d8847cd2cf1c0bff2c66a991 Author: braney Date: Thu Jun 26 17:39:40 2008 +0000 check for nBed file with no contents commit 449264659e0b010d9a31f19a983be8436da56fcf Author: tdreszer Date: Thu Jun 26 17:29:13 2008 +0000 Duke DNase by matrix, even though there are only two subtracks commit e3d3d25a4b10b647c236f873306fed1f56acd42d Author: braney Date: Thu Jun 26 17:03:55 2008 +0000 add buildMaf track commit 540f20ad11387ec43884881aa2a8da9abbf4f336 Author: kayla Date: Thu Jun 26 16:44:21 2008 +0000 added caeJap1 commit 051aef139d652ea2660f10b037d67aa475165ad9 Author: kayla Date: Thu Jun 26 16:43:35 2008 +0000 added ce6 commit b4e68f15df03a450fbfcbe63270040c6d5c3354b Author: tdreszer Date: Thu Jun 26 15:01:45 2008 +0000 Dangers of cutting and pasting - fixed uninitl'd var bug commit 8829502e1136588332b53140606026e2fec4a468 Author: galt Date: Thu Jun 26 15:00:07 2008 +0000 "Encode release log update" commit fd7e2834ec0c641e84cc5355ca5285d07a7a8925 Author: galt Date: Thu Jun 26 15:00:04 2008 +0000 "Release log update" commit 25e4b90505240d5affe99fc801b99d54e2803ed6 Author: aamp Date: Thu Jun 26 08:25:28 2008 +0000 Fixing bug that would bring up configure screen instead of the tracks display in hgTracks if the "Genome Browser" link is clicked in the blue bar navigation. An example of this is from hgCustom if hgCustom was accessed through the configure page. commit 06d25cf5661f6d9bc7b70c9d1acd7999596484a3 Author: markd Date: Thu Jun 26 04:23:37 2008 +0000 removed redundant comments commit 1607cd354242d1d3e635c35a2608b1b6fbec1604 Author: galt Date: Thu Jun 26 00:45:10 2008 +0000 updated script commit fe832bec6f9d9670bf349d7198e1a1bb3e970aa8 Author: braney Date: Wed Jun 25 23:02:48 2008 +0000 add some chain tracke commit 907e38cab02bad608f2e49ad1ce05f5444b77021 Author: braney Date: Wed Jun 25 23:02:34 2008 +0000 add chain tracks to hg18 panTro2 and homINi20 commit de717b26831feb7e4a05554073adf2eecb6804ac Author: braney Date: Wed Jun 25 22:40:44 2008 +0000 Initial versions commit f8685dc7f341014a5698534a99503469369edcf9 Author: aamp Date: Wed Jun 25 21:31:18 2008 +0000 Little fix for position links in hgCustom caused by the fast-configure-as-default business. commit 0725b72769bcc09a44e895b5f56c079189150e8d Author: angie Date: Wed Jun 25 21:04:18 2008 +0000 Check custom track existence when saving a session (not just loading). commit 863b28af4947822662d8eee38c26b9d4a18ce22b Author: braney Date: Wed Jun 25 20:53:55 2008 +0000 Initial descriptions for homPan20. commit 29ae01cad4cb0b9432c47faf8565fb8676cb9cde Author: kuhn Date: Wed Jun 25 20:47:39 2008 +0000 added whitespace after periods on text below image commit 4c7b79c6cc9bdd4bf487fcb3c2baa6f874f141fc Author: tdreszer Date: Wed Jun 25 19:58:02 2008 +0000 Allow wig to display as squish or packed. commit fa737b6750877ca9e01eed2dc821364477ff9e70 Author: tdreszer Date: Wed Jun 25 19:57:26 2008 +0000 Allow wig controls to be accessed by composite. commit 86f2d5a1f0fb737476b73df5115e469df3d10ca7 Author: tdreszer Date: Wed Jun 25 19:57:00 2008 +0000 Allow simple bed controls to be accessed by composite. commit 5a114c49fef35efad8b0fc2133de5dc6bd44cfac Author: tdreszer Date: Wed Jun 25 19:55:47 2008 +0000 Big Changes to support composite cfg by matrix commit 0e2532b0494fa2a5cbbda2947e03a225aeba0a6e Author: tdreszer Date: Wed Jun 25 19:55:03 2008 +0000 Big changes to support composite cfg by matrix commit 4f5dec060644c8e563a758e0bfd74a3b1674c8a9 Author: hiram Date: Wed Jun 25 19:22:57 2008 +0000 Add a dummy compile target to avoid make warnings during 'make compile' commit 60f90209bc922a71b9d24d981cfda2b0a4f62f73 Author: giardine Date: Wed Jun 25 18:25:46 2008 +0000 adjusted control of label to a global commit 5ea65f4bc21e8b944b1347f67895d6b4a2d7d440 Author: donnak Date: Wed Jun 25 18:21:10 2008 +0000 Archived 1 item. commit c0e010904c603f67ae30cbf7656ddb73449f0836 Author: donnak Date: Wed Jun 25 18:20:59 2008 +0000 First pass at news item for caeJap1. commit 9cf7619edc0f25da5aed40f637cea46a98b91095 Author: donnak Date: Wed Jun 25 18:15:56 2008 +0000 Initial pass at editing this file -- have one more pass to go. commit 1d373d206f2b4c519510001318b7b3bdae50da25 Author: jsanborn Date: Wed Jun 25 18:01:34 2008 +0000 adding naderi 2007 dataset commit c353e9733d3a75fce2a39a6eacf162575145efc1 Author: jsanborn Date: Wed Jun 25 18:00:57 2008 +0000 Added naderi 2007 dataset commit e281df3188390a06c05498f5682e7a36dc09a3c7 Author: tdreszer Date: Wed Jun 25 17:11:43 2008 +0000 incremental changes trying to get squirrel chains commit 15ab5a8aa44143ba79f3e710ebad23af74c1dc4c Author: tdreszer Date: Wed Jun 25 16:15:57 2008 +0000 subtracks of composite tracks need their parent pointer set commit c439920d05c26a028c59c2ab3bd042078faad18c Author: hiram Date: Wed Jun 25 16:14:47 2008 +0000 Place release log comment in those chains and nets when on the other Db commit b2665bf5c64a461677b74f70eded95ae50c8f6e6 Author: tdreszer Date: Wed Jun 25 16:13:14 2008 +0000 Needed to divorce some wiggle settings from tdb->name commit 94abdeb64872a80a396fe5788dfe9da8cc3a2e7d Author: hiram Date: Wed Jun 25 16:08:23 2008 +0000 Removing kki from the list of cluster machines. That one is history. commit a653b7c20d647d1c3282830bf6b7c1e9ca1c208c Author: larrym Date: Wed Jun 25 15:56:00 2008 +0000 assume unload program is in the same location as loader (fixes problem with misconfigured qateam environment) commit 0ace2c964fe7b23d3f9ea08baaa9a596bd0f0e23 Author: galt Date: Wed Jun 25 15:00:14 2008 +0000 "Encode release log update" commit 4fa12a378e4c7cca75f55e52351526239f5349ba Author: galt Date: Wed Jun 25 15:00:11 2008 +0000 "Release log update" commit 3a42101563be1220f2488842649a94a26e3f1c30 Author: markd Date: Wed Jun 25 01:51:08 2008 +0000 added warnings about problematic cDNA sequences to mRNA/EST details page commit 57b1f60cbd379959a6856e3523de3f54d9a8219d Author: donnak Date: Wed Jun 25 00:59:00 2008 +0000 Added caeJap1 to release list. commit 1c60f42b6f178a72c3e18eb25e374eae86c14a91 Author: donnak Date: Wed Jun 25 00:28:28 2008 +0000 Made a few minor mods to worm news item. commit d6c04c434bb395bcfd45b3b1c18272b0138fd559 Author: aamp Date: Tue Jun 24 23:48:03 2008 +0000 Added next-item to bed tracks where it's a simpler BED (< 9 columns). commit 808a32b675a8d8dcba3d4212c578c2ce69e838af Author: tdreszer Date: Tue Jun 24 23:41:50 2008 +0000 using clickIt(force) commit 5cdfbb9e244e1314cb2317bbe09192dc49568091 Author: tdreszer Date: Tue Jun 24 23:37:34 2008 +0000 Added a clickIt(forcr) function commit 498358adee55780fa5a2c374b10040fe40867738 Author: ann Date: Tue Jun 24 23:17:46 2008 +0000 fixed searches commit 39cb8100fe3a6ae074651aa57916af088f767810 Author: hiram Date: Tue Jun 24 23:13:16 2008 +0000 Finished with the pushQ for caeJap1 commit 067ec9bf3a77adf2b79c89cfee8652cb9f27e8ed Author: hiram Date: Tue Jun 24 23:00:53 2008 +0000 Run the liftover from ce4 to ce6 commit b1a175666998c0f4b6344132d0cfa9f8745fc663 Author: fanhsu Date: Tue Jun 24 22:48:41 2008 +0000 Deleted to avoid conflit with hprdToUniProt.sql. commit e0c2fa378b62e8d7ed87232863e71c368270f8b4 Author: pauline Date: Tue Jun 24 21:29:15 2008 +0000 Fixed short label to accomodate addition of ce6. commit 6fef3ab90fbb82006cbb7bf43e3cfb213a24d9d1 Author: pauline Date: Tue Jun 24 21:09:24 2008 +0000 Fixed broken links. commit a40c1aa5f08ca07f2df5eae36a13343a70688d99 Author: rhead Date: Tue Jun 24 21:03:43 2008 +0000 Removed explanation of fast configure mode, as its functinality has been replaced by new default behavior in v185 cgis. commit 4399310971cf81ad6f7677990c7a924973bce486 Author: galt Date: Tue Jun 24 20:32:54 2008 +0000 catching up docs on rudp checking and new parasol commands commit 181546608370d785b477b0cef2816cb828e96662 Author: tdreszer Date: Tue Jun 24 20:28:22 2008 +0000 Latest settings to use 2 dimensional configuration commit 3e1470161ab0635746df5fe50c23e38b5b24b1e7 Author: tdreszer Date: Tue Jun 24 20:22:36 2008 +0000 Added desciption of Composite track ADDIONAL OPTIONS commit bb3d36d2dd602c3cf9beb29998c9a85102d3b805 Author: galt Date: Tue Jun 24 20:20:57 2008 +0000 adding command requested by admins commit 0baff79d7f298d2a2fae94938f5f00d644fb0c1b Author: galt Date: Tue Jun 24 20:12:35 2008 +0000 adding command requested by admins commit 4d5af8713006f7b00f60a92f7468c1bdda88aecf Author: galt Date: Tue Jun 24 20:03:39 2008 +0000 remove unneeded commented out lines commit 423ce617e80e0f099a481aac6bea16d8a755a1dd Author: galt Date: Tue Jun 24 20:00:53 2008 +0000 adding parasol command to clear sick stats on a batch, for the benefit of users not using a para client; also fixed little bug in addjob commit b4a8d2fb0a0e918b70af1db6c0df4b93bd179491 Author: ann Date: Tue Jun 24 19:59:46 2008 +0000 fixed up references commit 41a690368c60580e0f32f6ab4716a761179929f1 Author: galt Date: Tue Jun 24 19:09:43 2008 +0000 changing hashes used only during startup to non-local mem commit ad00e57ebb923041b0699ae5b2902290670d6f65 Author: braney Date: Tue Jun 24 19:05:01 2008 +0000 always dink at least 1 base, zero width ranges go to 2 base window rather than 2000bp window commit 8bb6b05575012027b754fc6518db9f9721c9eb17 Author: hiram Date: Tue Jun 24 19:04:26 2008 +0000 Updated long label on 6-way alignment. commit dd82dea6057eeba8ab78b2ab61bfd0750b401a9a Author: hiram Date: Tue Jun 24 19:00:28 2008 +0000 Corrected 6-way tree diagram for Ce6 commit de03c16a412902a101e29319554b6f49b201b3ea Author: galt Date: Tue Jun 24 18:59:02 2008 +0000 just adding a comment commit 037d1c0c8f30a558b99ba1e45d65b8dec93bba34 Author: hiram Date: Tue Jun 24 18:58:45 2008 +0000 Correct the re-arranged tree diagram for the 6-way commit a5f182146b001eb17bf751ec7d00c4752edce4c5 Author: hiram Date: Tue Jun 24 18:49:17 2008 +0000 Set a topDir default and properly output option values with verbose 2 commit 68aaea6b27e8b71bb543eecc2b5814ed5f1a1180 Author: galt Date: Tue Jun 24 18:47:15 2008 +0000 making freeBatch more effective by having sickNodes hash info not in local mem commit e93050042f6ed5f2364a15e62155e8a7e146f433 Author: ann Date: Tue Jun 24 18:28:57 2008 +0000 clean-up commit c4e7b989264a737a97868e54abe945ab81606dc1 Author: ann Date: Tue Jun 24 17:55:30 2008 +0000 removed space for photo commit c7b6612d7f0177c76795f54b27ce8d2bb393464c Author: aamp Date: Tue Jun 24 16:52:04 2008 +0000 "New version number v185" commit 20e55232ae4b9342e3f93ae45b2ee9af88bf13e7 Author: galt Date: Tue Jun 24 15:00:07 2008 +0000 "Encode release log update" commit 11f3618bd9c24d9ec567da46f4238eee03421a22 Author: galt Date: Tue Jun 24 15:00:05 2008 +0000 "Release log update" commit a9f7aa9727c851066e8b1473f5013859aa6ad6b0 Author: markd Date: Tue Jun 24 14:40:04 2008 +0000 added function to find chains in hash without aborting if missing commit 8d8046ef488ef0531f9911de8a1beb42121b5845 Author: fanhsu Date: Tue Jun 24 14:16:23 2008 +0000 Removed extra DOS format CRs. commit 7f3f76a8e0e90a8683fb6d1f9c5be21e37b39fdf Author: aamp Date: Tue Jun 24 08:26:47 2008 +0000 Removed fast-configure mode and strange behavior of enabling fast-configure mode, going to the browser display, going to the UI page for a track, hitting submit, then being taken back to the configure page and not the main display page. commit a7254bb1f70f373c880694abae17c705c50a719f Author: markd Date: Tue Jun 24 05:10:50 2008 +0000 added option to skip chains that have been filtered commit da8aef4c1fb4a9d246895ca76dd5ea4df9a6e9d0 Author: galt Date: Tue Jun 24 01:12:58 2008 +0000 bug fix - duh need to save the full hashval before masking, also fix new size param on expansion triggering commit 005365eceef81c04e1e89b21cae2f58f696f99f0 Author: markd Date: Mon Jun 23 22:36:22 2008 +0000 added some verbose output commit 0abe27f713dc0f8cb49cbe90d03d4971bf7d8b21 Author: markd Date: Mon Jun 23 22:36:09 2008 +0000 fixed more locations commit 96bd7bed02bd276ccf127795d1b84d01ca8a3533 Author: hiram Date: Mon Jun 23 22:31:01 2008 +0000 There are two tree models for this phastCons run commit 6a5568848a8a437dac77e8ed82dc8c205a52687c Author: kayla Date: Mon Jun 23 22:29:40 2008 +0000 added caeJap1 commit 4a02259013367fb23e19a1a19a13bcbfc3602c25 Author: hiram Date: Mon Jun 23 22:27:13 2008 +0000 Creating the 6-way download files commit cc7887198457951b01c76ae102343c25b1b20dc9 Author: hiram Date: Mon Jun 23 22:18:07 2008 +0000 Updated text to modern version commit 94046e17c7cf001350b6bc1220bdd8cd809855f5 Author: galt Date: Mon Jun 23 22:07:54 2008 +0000 oops semicolon not wanted commit d286ab4c878f0d66473caef8338a085fc12df39d Author: markd Date: Mon Jun 23 22:07:14 2008 +0000 fixed bogus ooc spec commit 8d88b6ae55d02aaf614706646ff059458d9ce7fe Author: galt Date: Mon Jun 23 21:51:05 2008 +0000 suggested alias supporting newer naming conventions commit bff19153da1f16126bd38167df5660e849f3fcf8 Author: hiram Date: Mon Jun 23 21:49:16 2008 +0000 Incorrect reference to human and lineage specific repeats commit f5c0829600983ef08a0851d22b80f3badc5a24ce Author: galt Date: Mon Jun 23 21:47:55 2008 +0000 Add capability to remove duplicate packets received, this helps make rudp more reliable so the receiver is not confused by duplicated messages commit 32a0f2fd4c757b8f645d6692347b5bf8ecd395a7 Author: galt Date: Mon Jun 23 21:21:53 2008 +0000 Adding ability to resize hash quickly, and turning on auto-expansion by default commit 2c1758b96b1aa9a553f7f7da4dd3d1770275a239 Author: markd Date: Mon Jun 23 21:12:08 2008 +0000 fixed previous fix to file location commit d89a3227163e9a96ee687657194a343bbc0b342e Author: markd Date: Mon Jun 23 21:10:48 2008 +0000 fixed file location commit 105054f634d97109047b210f2f13bf0c5a40df1a Author: markd Date: Mon Jun 23 21:10:04 2008 +0000 fixed check for optional files commit bf20a275f5cada38a998d327e95441249ba125fa Author: angie Date: Mon Jun 23 18:15:15 2008 +0000 Removed stray * from regex singleBaseExp. commit edd4430265d5c9753e3897c225c9ae1ddf373527 Author: sbenz Date: Mon Jun 23 17:59:10 2008 +0000 Adding ucsfNeveCGH and chinSFGenomeBio2007 data commit f7f5210994f2e1faa17d22dc47ec208e6814046e Author: sbenz Date: Mon Jun 23 17:56:25 2008 +0000 Adding ucsfNeveCGH data and chinSF 2007 data commit f85d4fd93a9bb8a13008a9f94d6d9dab450c9266 Author: angie Date: Mon Jun 23 17:34:30 2008 +0000 Write pathnames for hgnfs1. commit 82004f69d7797f470d9719b9d268b56df13b337a Author: markd Date: Mon Jun 23 17:06:04 2008 +0000 added xenTro alias commit 0fe93c31205d3dba10c7d874caffb03b023d1140 Author: markd Date: Mon Jun 23 17:04:19 2008 +0000 moved build to pk commit cd4e26175d374b4adea9503f319d834ab80a26d1 Author: markd Date: Mon Jun 23 17:04:07 2008 +0000 added ignore entries commit c35d9275b732f5555996c20f1fa7097df2739775 Author: fanhsu Date: Mon Jun 23 16:33:07 2008 +0000 Created makefile. commit 963ec4e41e3c2ec8d054d6956b0fd59ce1306f2c Author: fanhsu Date: Mon Jun 23 16:32:53 2008 +0000 Created gsIdXref.c. commit 89a61bcc499677107dbce05d55150647c270d8a9 Author: giardine Date: Mon Jun 23 15:07:46 2008 +0000 switch to composite tracks, color boxes on more than base view, bug fix for pack displays commit 6855fb85205583a8dd43c406885f382ff3954f6c Author: galt Date: Mon Jun 23 15:00:19 2008 +0000 "Encode release log update" commit 77d86cf44f55ff7f45e2aab872c5646d039328e5 Author: galt Date: Mon Jun 23 15:00:13 2008 +0000 "Release log update" commit b2cd81e56a1ebe41e60ee324be1915d87a606a7b Author: giardine Date: Mon Jun 23 14:50:26 2008 +0000 Updated html pages commit ba4dd77df68ac0aec27c4db25ee77255f49e0a7d Author: giardine Date: Mon Jun 23 14:47:00 2008 +0000 Changed tracks to composite tracks commit c01fe9e6f49627286ba5a5dcd747712061fcb46b Author: markd Date: Sun Jun 22 19:22:01 2008 +0000 added options to check for existance of files specified in conf files commit 93796443fe85964eae4bb63ab3847f8216fea524 Author: galt Date: Sun Jun 22 15:00:03 2008 +0000 "Encode release log update" commit 5bf8055c7ea4fd659ba5535bfa8aa69dbeefaadb Author: galt Date: Sun Jun 22 15:00:02 2008 +0000 "Release log update" commit 900b9aaa1fe21ae512d83d258822657615449885 Author: braney Date: Sat Jun 21 17:54:38 2008 +0000 allow specifying only one coordinate in position string (eg: chr3:33) commit 0ae70b51a64114f178d3fc24840827dad41a0197 Author: galt Date: Sat Jun 21 15:00:06 2008 +0000 "Encode release log update" commit 44500b46ddfc3b583f6791114667473d3fe5bf34 Author: galt Date: Sat Jun 21 15:00:03 2008 +0000 "Release log update" commit 8cc359ffb287a64d59074526ae927339895266c8 Author: jsanborn Date: Fri Jun 20 23:33:07 2008 +0000 Adding chin2006 Expression dataset commit 484049ce26e926e19cc608e0da1584b633fb6c95 Author: braney Date: Fri Jun 20 23:18:40 2008 +0000 support "all fields" for custom maf track type commit 7469239179a602c915efa8e26f39005fc5e305c5 Author: braney Date: Fri Jun 20 22:57:37 2008 +0000 go into dense mode if we're in summary view rendering a custom track commit d4dff20cda4e4d987ded2024c9fbe0e3daaf59a0 Author: kayla Date: Fri Jun 20 22:40:09 2008 +0000 typo commit 4655ed3d8cfdd67f2d5431eb4edf26bacdba0083 Author: fanhsu Date: Fri Jun 20 22:34:02 2008 +0000 Documented the VAX003 clinical data processing and tables creation. commit dac55b73046111596997a4eb594d7308aef53cb1 Author: hiram Date: Fri Jun 20 21:57:58 2008 +0000 ce6 is in the pushQ commit 00a6708b932880c6ec749723818f57625fcc9bea Author: braney Date: Fri Jun 20 21:21:08 2008 +0000 move call to get index length to after we set the database, thanks Hiram commit 83c09077a1e04c53d98147cea951351b9988eb52 Author: angie Date: Fri Jun 20 20:53:45 2008 +0000 makefile commit cf9a29bf6e09b7642c8e7c5207f828fd404e2053 Author: angie Date: Fri Jun 20 20:50:40 2008 +0000 Read -verbose=4 output of refreshNamedSessionCustomTracks and write a file (trash/ctDoNotRm.txt) of full pathnames for the cleaner script to ignore. commit b676f2c71cf917e39ed75f4a0c06a78fc4297429 Author: angie Date: Fri Jun 20 20:49:34 2008 +0000 Added support for reading a file of full pathnames. Compacted a bit. commit f81ecd33109e207cd828b35344883156abe546fd Author: hiram Date: Fri Jun 20 19:28:50 2008 +0000 Fixups to get all checks for ce6 to be correct commit f415b79950cb33587dd54402f02e38f4c3675081 Author: donnak Date: Fri Jun 20 19:26:07 2008 +0000 Added Pauline to worm credits. commit b1b5b3a6d54ea35fdcaf4866cb1f1ae963ea19cf Author: donnak Date: Fri Jun 20 19:24:00 2008 +0000 Fixed up sample queries. commit f3078bc515aa4034132c079955792622ad89de3b Author: donnak Date: Fri Jun 20 19:23:52 2008 +0000 Fixed up sample queries & made a few edits. commit 8146e9d0cc9ea8ff7c5df3d31cae1f3af7a8115c Author: donnak Date: Fri Jun 20 18:58:31 2008 +0000 Made a few minor edits. commit 6f39ebb09ea26154ee61cca21f76f142711368f2 Author: donnak Date: Fri Jun 20 18:58:04 2008 +0000 Fixed up sample queries & made some other edits. commit ca187367d2a108d3f62266f4333d1361c554e905 Author: hiram Date: Fri Jun 20 18:52:20 2008 +0000 Completed annotations for the 6-way alignment commit 7df47574f28d835f599c29a07834df4393b5608f Author: hiram Date: Fri Jun 20 18:51:01 2008 +0000 Complete html pages for ce6 release commit f85a1e361fe0b9deb85532d50d2125d57d85cd4f Author: donnak Date: Fri Jun 20 18:37:39 2008 +0000 Fixed up the sample search section. commit d45da59bd53ded9ffc3845dd834556e84c640c8e Author: galt Date: Fri Jun 20 15:00:07 2008 +0000 "Encode release log update" commit 6e0f82171c5d306d62cb4311d8dfaa232bcce593 Author: galt Date: Fri Jun 20 15:00:04 2008 +0000 "Release log update" commit 32a06bb454ee5c2b87e0770688ad984fc82f67ca Author: angie Date: Fri Jun 20 06:40:00 2008 +0000 Instead of stuffing all subtrack visibilities into the cart whether they have changed from the default or not, prune redundant cart settings to avoid cart bloat. 'subTrack ... off' now works without noInherit. commit 428ffe26caa6e4acd2078e4146f90ce2bd36c4be Author: aamp Date: Fri Jun 20 06:33:03 2008 +0000 Fixed bug that allowed bed links to appear in restriction enzyme track when click wasn't from hgTracks. commit 1f8903d8235c7df2105f55a99f811a5c89b9dd91 Author: donnak Date: Fri Jun 20 00:23:55 2008 +0000 Edited this draft. commit bdc2148edb9e07ebac5004e20a5640754b6fa181 Author: kayla Date: Fri Jun 20 00:20:35 2008 +0000 added caeRem3 and caePb2 commit f34f34bd0547ab1b59e420d2ad8b3e19238450ef Author: angie Date: Fri Jun 20 00:04:29 2008 +0000 Removing the 'off' from hapmapLd subtracks. It has been ignored -- up to this point, hgTracks didn't see the subTrack setting unless noInherit was used. I am about to check in a fix for that. commit fa1ebcc3d4ae3fbf0c3b4732aabd742b52885b48 Author: angie Date: Thu Jun 19 23:47:15 2008 +0000 Always prune redundant (with trackDb) track vis settings to avoid bloating the cart. Takes <1ms. commit c3666cc190284d28dbb679048d949e8f4f43e88d Author: donnak Date: Thu Jun 19 22:57:55 2008 +0000 Archived 2 items. commit 92ad6b83279ebd750e3cd1eb35b6a72085c61081 Author: donnak Date: Thu Jun 19 22:57:38 2008 +0000 Added news item for caeRem3 and caePb2 release. commit 006aa4a9b257a7c7fcca5a03460920343336019d Author: aamp Date: Thu Jun 19 22:24:44 2008 +0000 Just ignoring the Illumina tables for now. commit d2cf6957412f1d19cb7f274602399e3e39b90abb Author: donnak Date: Thu Jun 19 22:19:04 2008 +0000 Added caePb2 and caeRem3. commit a44b5e7db01c500205e10cc9f192dd3d76d618b0 Author: hiram Date: Thu Jun 19 19:47:08 2008 +0000 Finished with the Ce6 tblastn proteins track commit 3e4cbf46a6b70ad2879b6af1914a65cc9e992aa7 Author: hiram Date: Thu Jun 19 17:30:22 2008 +0000 Indicate type F for chrM commit 2d94ba0350f20317f24277822477d3ff11bd1db3 Author: braney Date: Thu Jun 19 17:22:34 2008 +0000 don't try to get maf's when they haven't been loaded commit 5abbfe04c3ab198b06377ca5913a1f255170b365 Author: galt Date: Thu Jun 19 15:00:06 2008 +0000 "Encode release log update" commit 531d705ecfeb3070840a64a97ca8aa6cf4a72918 Author: galt Date: Thu Jun 19 15:00:04 2008 +0000 "Release log update" commit 2261410e01a0817aa9104477e81340ac9acbf515 Author: aamp Date: Thu Jun 19 09:14:16 2008 +0000 Added Sestan Brain Atlas groupings. commit ae795bc5bec5f7408145df9be0cb13efaa7fb254 Author: aamp Date: Thu Jun 19 09:13:34 2008 +0000 Added trackDb stuff for Sestan Brain Atlas track commit 8d8135d1036d88731d099b89c475d1a29c448f81 Author: rhead Date: Thu Jun 19 00:30:48 2008 +0000 Sprucing up the sparse default tracks by turning on GC Percent and WindoMasker. commit 6606741089e628ecc2d047be09a069e3a43183be Author: rhead Date: Thu Jun 19 00:09:07 2008 +0000 Livening up the rather sparse set of default tracks. Turned on GC Percent by default. commit e101119281061bd81f4ad793df2e05bca1c61337 Author: angie Date: Wed Jun 18 23:49:32 2008 +0000 Registered track handler for snp129. commit 9e74a1df89431c72ba85443daf4b419448af2481 Author: angie Date: Wed Jun 18 23:44:59 2008 +0000 Adding snp129. commit 2bcaa7dd796a5fd7a952e98376a7560cac164e5c Author: hiram Date: Wed Jun 18 23:44:01 2008 +0000 Reworked the tblastn ce6 sanger genes to avoid non-bridged gaps commit 9b754ba5574cbeeb65e76813ded9622eeef6ff58 Author: hiram Date: Wed Jun 18 23:43:20 2008 +0000 completed phastCons6way wiggle table for multiz6way track commit 086c039b42a373658d2cda017bb56fe48d56f91c Author: hiram Date: Wed Jun 18 23:42:24 2008 +0000 re-ran genbank to clear up ests, and finished tblastn of ce6 sanger genes commit 67ccb0de223da48a6d973e0f61642df2175e2b13 Author: hiram Date: Wed Jun 18 23:40:49 2008 +0000 completed tblastn of ce6 sanger genes commit 79e0733ea1ad4b787dea7a1cffd4432e29a82a06 Author: hiram Date: Wed Jun 18 23:23:45 2008 +0000 There is no ctgPos2 table in bosTau1 commit 5fa7b44bccffcd45e7630a40b9bcdd422e0b08b7 Author: hiram Date: Wed Jun 18 23:20:42 2008 +0000 Add searche for blastCe* tables, and fixup wormbase URL references commit 3c6dd7040032b18e2071e877bb9306fc4d4dde69 Author: hiram Date: Wed Jun 18 23:17:34 2008 +0000 Adding caeJap1, and the blastCe* tables for ce4 and ce6 proteins and some chains that were not mentioned before commit 2d6b9785d94a715c89c02c06552e24014d0f8f1b Author: hiram Date: Wed Jun 18 21:33:21 2008 +0000 Fixup for ce6 blastSG references commit 132a95fc7dfdbbfe2162b9d0818fc5c98aef46b2 Author: hiram Date: Wed Jun 18 19:24:48 2008 +0000 Adding in chain and net for Ce6 commit 39cde49715fc6088b0185dab58a1bdd28de93bab Author: hiram Date: Wed Jun 18 19:14:00 2008 +0000 Turn on the phastCons5way wiggle track in the multiz6way track commit 632f1e4a83cdde816cd8a2926c56da898a0c3ab8 Author: hiram Date: Wed Jun 18 17:27:41 2008 +0000 Adding a type cgtPos to ctgPos2 commit 99edb5db7e84a222c6f86edd385c387cf7a70c1c Author: galt Date: Wed Jun 18 15:00:06 2008 +0000 "Encode release log update" commit a4cede82921bdb0fb9e9026bc4d4cd305fe61ecc Author: galt Date: Wed Jun 18 15:00:03 2008 +0000 "Release log update" commit 1e263ca6858ef1fff33069fb505ff84e73101899 Author: giardine Date: Wed Jun 18 13:46:35 2008 +0000 switched default to hide for pgSnp type tracks commit 1f8505e3a30d0bb5b51d9adf50b3c7a27b4b1062 Author: angie Date: Tue Jun 17 23:51:49 2008 +0000 Oops -- use parent tdb isShow, not visibility. commit 691eb896b2a1daa0d2c782fc2403998a0fb4e1a5 Author: hiram Date: Tue Jun 17 23:50:49 2008 +0000 The assembly date is May 2007, not Jul. 2007 commit 0d24680c66b365c30579a9d5570244f1cfdd2e04 Author: hiram Date: Tue Jun 17 23:48:48 2008 +0000 The date is Feb 2008 not Apr 2008 commit 1e78b0aa3f019457935cddc4f2b5715896d69327 Author: rhead Date: Tue Jun 17 22:57:33 2008 +0000 Changed sample mRNA to one that works on caeRem3. commit fc91fb5905d40f20666c029aa4a31bf141b36a2a Author: angie Date: Tue Jun 17 22:46:44 2008 +0000 Call compositeTrackVis only if the composite track is visible. commit 466c477658db76de90bdc2f7c72fc8b9412499eb Author: hiram Date: Tue Jun 17 22:01:00 2008 +0000 No 10 second delay to display the wiki page commit f8a1fa16a4258019772effd9492237da73ae38f6 Author: giardine Date: Tue Jun 17 21:52:22 2008 +0000 forgot this file commit 95916dda7f350f1759b40000626959e9e4ae334c Author: rhead Date: Tue Jun 17 21:51:24 2008 +0000 Two small punctuation changes. commit 14751667674f413a9b8a640d6c850475705a0f8a Author: hiram Date: Tue Jun 17 21:51:22 2008 +0000 fixup emailVerified to really check that edits are possible commit 991c9972ae9b22e664fd113ddaf582f879910bcd Author: giardine Date: Tue Jun 17 21:49:53 2008 +0000 added quality scores, switch to subtracks commit 8b4ec8d8522672de32f5b58a2170cafac96b1dcb Author: galt Date: Tue Jun 17 15:00:09 2008 +0000 "Encode release log update" commit 0dbc75a98cc8a443e6813e9f587d59863b08de5f Author: galt Date: Tue Jun 17 15:00:03 2008 +0000 "Release log update" commit bc9c5ef2b327974f0ea798e1dbf362246f6be3b4 Author: aamp Date: Tue Jun 17 09:45:57 2008 +0000 Instructions for Illumina probes track. commit b253fcff77e6c16e1614fc177a1254cb6f92a238 Author: rhead Date: Mon Jun 16 23:16:15 2008 +0000 Removed the -h option from rsync directions. On some systems it means human-readable, but other systems it means help! commit ceb40985b6ffd9a83c896a540b44b46f2a2d1545 Author: ann Date: Mon Jun 16 22:51:06 2008 +0000 removed debugging statement commit 972aa8438f7e3a52ef4d18a995866643ef1a24f0 Author: ann Date: Mon Jun 16 22:48:50 2008 +0000 added findBlatServer.csh commit 7f2a5bdc837c8333265a165c46064626d5d400a3 Author: ann Date: Mon Jun 16 22:47:31 2008 +0000 script to find out which blatServer hosts which database commit 9b68bb1a867432f79d1eedd23da241280a3aa9f2 Author: hiram Date: Mon Jun 16 22:23:49 2008 +0000 Identify the C. elegans protein version, WS170 or WS190 commit f11e6bec1f1162189d8a52575b34a2ebc1841bbc Author: hiram Date: Mon Jun 16 22:17:24 2008 +0000 Update the google verification key commit 245e522a20825d6ef99d66456c70afc892b6a8d9 Author: hiram Date: Mon Jun 16 20:23:24 2008 +0000 turn on caeRem3 and caePb2 with lift file in correct location commit 6d0c27163743a665d8748a9ed5a9362c9fe459fe Author: galt Date: Mon Jun 16 19:29:05 2008 +0000 oops undo commit c04eca7cf5553d01b2cc1a7f80d2f956a321655e Author: galt Date: Mon Jun 16 19:28:28 2008 +0000 I forgot to update the blat version here commit 743279873a245866266c44b04f21d57decb0a4fd Author: hiram Date: Mon Jun 16 16:59:48 2008 +0000 Get some of the worm lift files back to /cluster/data/ where they can safely be found from the genbank machine commit 2ad44be3f4edabdeeb1f8f125c83bc83e350e6b3 Author: angie Date: Mon Jun 16 16:21:59 2008 +0000 Abbreviations requested by b0b for Kidd/Eichler tracks' item names. commit a72a914080a05100d108d6780c27b847083e20ac Author: giardine Date: Mon Jun 16 15:09:58 2008 +0000 adding some new displays for personal genomes (pgSnp) using Venter, Watson, and HapMap data commit fd2e003a5f3eb473a75fe8d5f9be9bd53a136a18 Author: galt Date: Mon Jun 16 15:00:03 2008 +0000 "Encode release log update" commit 0a78d8c00487ad3ed6836132b266382669ba8147 Author: galt Date: Mon Jun 16 15:00:02 2008 +0000 "Release log update" commit eec04f6de06e04605971a0a0c74cad3fdf03d23c Author: braney Date: Sun Jun 15 16:17:07 2008 +0000 add extFile definition commit ee562e11bf99c83909b5e267e0307f45c59f7331 Author: braney Date: Sun Jun 15 15:40:22 2008 +0000 add code to clean up extFile table (and to not delete it even if it's old) commit ced3862f67f6341e030da8ac4654979257125597 Author: galt Date: Sun Jun 15 15:00:03 2008 +0000 "Encode release log update" commit 65c82f53961e8912885a2fe61685876dee20c706 Author: galt Date: Sun Jun 15 15:00:01 2008 +0000 "Release log update" commit 267e68958c2c5009ce8e76f23c2237e9b66730dc Author: markd Date: Sat Jun 14 22:48:08 2008 +0000 disable caeRem3 due to incorrect configuration commit ebfae839597b1d7ddb818899aca18a2b1bd36014 Author: braney Date: Sat Jun 14 19:51:53 2008 +0000 restore check for custom maf table now with checks for NULL pointers commit 5b919ddb057bd306371f0c7d55f6e87368587e11 Author: markd Date: Sat Jun 14 19:13:22 2008 +0000 disabled caePb2 due to missing data files commit 17ef0bb99b59d5bb2b32b18fcdc44c4e88e83810 Author: galt Date: Sat Jun 14 15:00:05 2008 +0000 "Encode release log update" commit 627b803945ae0a8f48225147bd16cd4048e9a373 Author: galt Date: Sat Jun 14 15:00:03 2008 +0000 "Release log update" commit 8c8d1b8b5129914a07490c132d22af404207eded Author: braney Date: Sat Jun 14 14:17:56 2008 +0000 catch errors in maf processing so we can remove the extFile id that we need to allocate before parsing since the id is in every scoredRef record commit 1d1fb4fdfb98cde405cbb365bac5fcada194bea3 Author: braney Date: Sat Jun 14 14:15:41 2008 +0000 add a routine to purge an extFile row commit 912b6b1dce4b2d85f896dd43c53b30dd97c1435c Author: galt Date: Sat Jun 14 02:25:27 2008 +0000 more ntohl help commit 2d76399626b9efa41b7beb40a8f1bc0ae2b01cce Author: galt Date: Sat Jun 14 01:58:21 2008 +0000 little bit of host vs network cleanup commit d9b4d02c01c4c0cf3a54fed3f85da2c06603144f Author: galt Date: Sat Jun 14 01:22:26 2008 +0000 added network-to-host-long convert call ntohl commit 63e912939dc7e5bacc8fb7e4d4d3f7edaf4468a1 Author: pauline Date: Sat Jun 14 00:17:21 2008 +0000 Moved reference and added citation. commit 516d329014b92c676b4035b2fee924cb1f9f907d Author: kayla Date: Fri Jun 13 23:59:44 2008 +0000 added caeRem3 and caePb2 commit 6fa27bb57654203c159867f5fa3f46665095b7f7 Author: galt Date: Fri Jun 13 23:08:55 2008 +0000 better ip formatting for warning commit 34db13da89e98c1890b802928bb668774120e5df Author: galt Date: Fri Jun 13 22:50:48 2008 +0000 tidbits commit a544430c2e3300e682cc2a150feeeb58ffa46e86 Author: galt Date: Fri Jun 13 21:21:19 2008 +0000 fixing resend because sometimes a packet gets sent even when os returns err commit 3a66ebcd6299e68e7b320e03f2e70de5ff36d168 Author: galt Date: Fri Jun 13 20:13:53 2008 +0000 oops, only need one version of the socket close commit bcba46ede346d5951b3b71c13b44a89a592d45ff Author: hiram Date: Fri Jun 13 19:22:22 2008 +0000 Set up the tblastn sanger gene source files commit f062318ff614c38f988fa70c985aab305d75192e Author: hiram Date: Fri Jun 13 19:21:02 2008 +0000 Running the ce6 sanger proteins tblastn mapping procedure commit e5ddb194de71e4c2ffb1f407175dc2e493f3b6ce Author: hiram Date: Fri Jun 13 19:06:02 2008 +0000 Set est.native.load for caePb2 and reset some iscratch references to scratch/data commit e47ee831ad2027029c5418b43dcd072fd4e5bc24 Author: hiram Date: Fri Jun 13 17:17:18 2008 +0000 Add a verifyWibExists() function to verify a wiggle custom track is still good to go commit 603688b298171dfaccb890fee31f0884ad7a9228 Author: kuhn Date: Fri Jun 13 16:02:52 2008 +0000 dropped some eperiods from a shortLabel commit 09db3ffcf0baae5f30b00203c050ba9cf162a996 Author: kuhn Date: Fri Jun 13 16:02:04 2008 +0000 moved some tracks commit 92fcb807a4f29132006c5c7cedafbe65a1c5b03d Author: ann Date: Fri Jun 13 15:42:36 2008 +0000 fixed broken link to David H's page commit 177dfbdd6bff2f58b1aeaddf846c141868236644 Author: galt Date: Fri Jun 13 15:00:07 2008 +0000 "Encode release log update" commit f7e13b8b85451d2af9aead48666ccac7acfc5499 Author: galt Date: Fri Jun 13 15:00:04 2008 +0000 "Release log update" commit 58b29a5a6177e2f28407712c3816c00da8037ccb Author: galt Date: Fri Jun 13 08:52:47 2008 +0000 readyMachines is better than busyMachines for hub restart add job commit c75c6f7c6dd232931de77d719e26ac730bbbb3b8 Author: galt Date: Fri Jun 13 08:42:32 2008 +0000 fixing hangman - do not need the dlRemove always commit 4e56ef3d8338c9b26d2d7bc49ced557e6fa93eb9 Author: galt Date: Fri Jun 13 08:11:09 2008 +0000 fixing hangman - revised, reworked hangman properly using new hang list to check for hanging, and new job.lastChecked commit 1ef41bbb0b72172d34d61cd8d8d2f5bd73851ec2 Author: galt Date: Fri Jun 13 08:02:54 2008 +0000 fixing hangman - revised, reworked hangman properly using new hang list to check for hanging, and new job.lastChecked commit cee31b4482112e9e979cd46db8af6ae720fae964 Author: galt Date: Fri Jun 13 05:31:48 2008 +0000 fixing hangman - using existing runningJobs and lastClockIn works great instead of old busyMachines list commit d897c24340775a6ceff2b6c1d4c79c48bd216697 Author: larrym Date: Fri Jun 13 01:16:52 2008 +0000 send data is ready email to wrangler; improve short/long labels; improve/fix validation code commit 23dcbd4de2af568416efe932234f87615db637d9 Author: aamp Date: Fri Jun 13 00:28:41 2008 +0000 Added Illumina Probes track description plus a few changes to the trackDb. commit e6be0ba617826b58e5384a9823351b960da97651 Author: kent Date: Fri Jun 13 00:11:21 2008 +0000 Fixed inverted logic bug in coding/noncoding case that Fan caught. commit d4de87421117c055f2f1d96234e634062b94b590 Author: braney Date: Thu Jun 12 23:12:39 2008 +0000 fix check from maf custom track commit d670405abf99a9c798b4061cbe2b3aaec7668a3c Author: larrym Date: Thu Jun 12 21:14:32 2008 +0000 tweak Stanford tracks commit 06ffe91bd3169aa5a33201d8e2412a4ce411bb8a Author: hiram Date: Thu Jun 12 18:44:49 2008 +0000 Adding blastCe6SG and fixup http URL references for blastCe4SG commit a74df0373f12ca75d4f1f0bec2d018c8c7b463f4 Author: hiram Date: Thu Jun 12 18:41:14 2008 +0000 Finished Ce6 sanger gene tblastn alignments commit 48f840b2c4fa4d91738066c5daebe1b225fbb411 Author: kuhn Date: Thu Jun 12 17:44:18 2008 +0000 added some empty lines to delineate the different goupds of orgs and moved the deuterostomes above the flies commit aa4437c93a43abd7ed2d4c41183f85487dce1e16 Author: larrym Date: Thu Jun 12 16:39:02 2008 +0000 add Stanford stuff backin; add wgEncode settings commit 39b91edf14ae34fa0c15e8e68b870040978447a7 Author: galt Date: Thu Jun 12 15:00:08 2008 +0000 "Encode release log update" commit f78ae64dc4c4950ee105ed0719336108e89f5d80 Author: galt Date: Thu Jun 12 15:00:05 2008 +0000 "Release log update" commit 3210d26ed113b847806731af1753206ea631c251 Author: galt Date: Thu Jun 12 09:46:17 2008 +0000 showing unitsizes, jobdefaultunits, and clustermaxunits commit a4e8d4c0b440773d0a19610ca8b4746d93f0d77d Author: galt Date: Thu Jun 12 09:33:55 2008 +0000 trying to keep the nodes busy commit 20ccbbac9e728822f925909c8ed4d32f3c1eb0eb Author: markd Date: Thu Jun 12 07:06:17 2008 +0000 added support for chains; refactored commit 9e97c4dfef1058672b9baad2961a2948a4275ad8 Author: markd Date: Thu Jun 12 05:35:36 2008 +0000 actually check options commit 87235dc5a9931437e6f9c1e6f1801822a0c656df Author: pauline Date: Thu Jun 12 00:20:41 2008 +0000 Moved Reference to bottom and added hyperlink. commit 69bb383d3c1ebb5ea11e6e784e94e47e1e4b4733 Author: tdreszer Date: Thu Jun 12 00:19:31 2008 +0000 Fixed composite track to bed 5 + commit ab3947b03c22f1f39587bd43cdf57d4425278157 Author: kuhn Date: Wed Jun 11 23:55:36 2008 +0000 added checking on gateway page for broken links commit 19ec81a65a3c5826552e384910fd1f7ddbe45b8c Author: larrym Date: Wed Jun 11 23:39:13 2008 +0000 change validateBed so it actually validates the bed data commit a546502999d4072b742a26a80a103eda71145113 Author: galt Date: Wed Jun 11 23:38:08 2008 +0000 adding more detail to rudp warning commit b0f8d4f7649a44dc76913d18a6a22daba82e1f40 Author: ann Date: Wed Jun 11 23:31:18 2008 +0000 moved Archana to the bottom. Fixed some links to open in new window. commit 2810a43da0cb6cee52c1e508369721a2886355cc Author: angie Date: Wed Jun 11 23:12:20 2008 +0000 Added noScoreFilter to kiddEichlerValid. commit 5f7a5064ac258d546bc638c83597067166723aeb Author: angie Date: Wed Jun 11 23:06:28 2008 +0000 Pass tdb to bedPrintPos so it can check for trackDb setting noScoreFilter (and others if they're ever applicable). commit f2719ee58682c83d3b8e7bf812cfddea1a899378 Author: angie Date: Wed Jun 11 22:27:47 2008 +0000 Added kiddEichlerValid: validated sites of structural variation/rearrangements from Kidd/Eichler 2008. commit 2e43868e49c16b5d975d71ab32593713696b818d Author: larrym Date: Wed Jun 11 20:34:04 2008 +0000 add first Stanford ENCODE ChiP-Seq data commit 4e152d5a6aeabdec3a6a0df522364ec7b1220d53 Author: markd Date: Wed Jun 11 20:30:24 2008 +0000 added valgrind suppressions commit 35c5fa35141c14d3f7ab2b58a89356b2fe79f7ef Author: larrym Date: Wed Jun 11 20:29:46 2008 +0000 initial checkin commit 080538ff78c97be27f0ac4be712a07c24b98ea1d Author: tdreszer Date: Wed Jun 11 20:21:44 2008 +0000 Minor long name correction commit 42cca584be4fada682ebac5cea190e12bc995290 Author: tdreszer Date: Wed Jun 11 20:21:04 2008 +0000 Fixed some broken links and added the first cell type commit b81bfe97d954fe368141df7652c8eeae875e519b Author: tdreszer Date: Wed Jun 11 19:46:34 2008 +0000 Greg Crawford's description and methods for WG Encode Duke DNase tracks commit f04089788b5e93a94212183fa3654a8b184161b7 Author: galt Date: Wed Jun 11 19:02:00 2008 +0000 need to use the vars before the pmClear runs commit bf19605de694e2e6305f309c4d565431bdad79d8 Author: hartera Date: Wed Jun 11 18:56:22 2008 +0000 Fixed broken link for GM06990 cells. commit 73aba61ed2744354aa2c124a817f73c90da38075 Author: angie Date: Wed Jun 11 18:35:25 2008 +0000 Added itemRgb and more coordinate fixes to kiddEichlerDisc. commit 12162a385805c3064d5db69d53dbade23335f72b Author: angie Date: Wed Jun 11 18:34:53 2008 +0000 Added composite track kiddEichlerDisc: discordant clones from the structural variation study Kidd..Eichler 2008. commit d4a103929d0df6300c84fc401ba21be3fc3af529 Author: larrym Date: Wed Jun 11 18:00:37 2008 +0000 add validateMappedReads; improve trackDb.ra code commit b21559c6250789d661980cb8b9b1511125a1bb6d Author: galt Date: Wed Jun 11 15:00:09 2008 +0000 "Encode release log update" commit 3751cd30e7e2d70d3cfe9c60fbedb6e529392e7c Author: galt Date: Wed Jun 11 15:00:08 2008 +0000 "Release log update" commit 07c09fed6d1092e458843d601645a7dbb7b44de6 Author: galt Date: Wed Jun 11 09:04:02 2008 +0000 trivial commit c95301d627f5a4adc602c32fc01b66537e0dd72f Author: galt Date: Wed Jun 11 08:28:47 2008 +0000 fixes, primarily for negative user runningCount commit 915a0b0512a5fef9fa5140f6b3fbea365f07072a Author: galt Date: Wed Jun 11 08:22:57 2008 +0000 fixes, primarily for negative user runningCount commit fbcfc02b126eb32e213d5ff2d04758a316bca3ae Author: tdreszer Date: Tue Jun 10 22:11:58 2008 +0000 Added Duke DNAse first WG Encode dataset commit de9788d6177d9019bc011f3db594dd34062f6ea5 Author: pauline Date: Tue Jun 10 21:49:25 2008 +0000 Changed hypertext to refer to local pdf file. commit ddfb006b5d596beea5b0558a1327bbf9b4801720 Author: galt Date: Tue Jun 10 19:53:42 2008 +0000 fix signedness complaint from gcc4 commit 12acd524819668e444f06e033ca0cc621ce1e4ee Author: larrym Date: Tue Jun 10 17:19:16 2008 +0000 "New version number v184" commit c48f7f0f5973b985a8ba29507d85e8488863a797 Author: larrym Date: Tue Jun 10 17:16:48 2008 +0000 do more error checking/reporting for misconfiguration and missing js files commit 03907ba71a7883aa50fdab796dfbfb28b21f5078 Author: kuhn Date: Tue Jun 10 16:32:02 2008 +0000 local copy of this doc. it keeps disapearing or moving on Wellcome Trust site commit fb2bee5fe3899f71b1fac8f0adfd3528b5c9cc97 Author: ann Date: Tue Jun 10 16:30:49 2008 +0000 adding chain/net prio for lamprey commit a7554970456e069d9e5b77a365d972ea29932cca Author: ann Date: Tue Jun 10 15:10:43 2008 +0000 added Pauline to credits. fixed link to Credits. commit a9fb23369cea889638c350a0cbfcda07d8146b6b Author: galt Date: Tue Jun 10 15:00:15 2008 +0000 "Encode release log update" commit 69449ce7c80a258dde4b354f2a8d4f90278f0598 Author: galt Date: Tue Jun 10 15:00:12 2008 +0000 "Release log update" commit 2f49a6543a3cf514ccf106a4f9337fc71c673f5b Author: galt Date: Tue Jun 10 05:27:12 2008 +0000 multi-messaging protocol commit dce738f0dd4ba5e197f81214dadc40a3e2312092 Author: hiram Date: Mon Jun 9 23:51:09 2008 +0000 Mask with window masker and make up masked contigs 2bit file for better blastz results commit d1c1050b69429a6528b07eb3532c570e01deb91d Author: hiram Date: Mon Jun 9 23:50:38 2008 +0000 First pass on 6-way alignment done. All pair-wise alignments done commit 8e391e1eeac177baef09376a8a02f76373d59453 Author: hiram Date: Mon Jun 9 23:50:14 2008 +0000 Change the ooc size, and add in maskedContigs 2bit construction for better blastz results commit c4d8334ab64e5366a8e77b15771ecbfa1c37774e Author: hiram Date: Mon Jun 9 23:44:28 2008 +0000 This is WS190, not WS170 commit b29a44fadb38a677f7ec81eee3bba5272ba817c3 Author: hiram Date: Mon Jun 9 23:42:15 2008 +0000 Add in the 6-way trackDb entry, and html pages. Rearrange the chain/net order to be more correct commit 8a2c0d177c4016a9b8e23f9fa6fe914f8ba49e12 Author: donnak Date: Mon Jun 9 23:27:21 2008 +0000 Added news items for petMar1 & braFlo1. commit cc43d9c76cc9c12c5a0090de9efa28e1b02a9daf Author: hiram Date: Mon Jun 9 23:24:35 2008 +0000 6-way tree image for Ce6 commit 9cd88a1ff93501f76a3618ee1191498cf9b011e8 Author: pauline Date: Mon Jun 9 23:20:41 2008 +0000 Fixed typo in usage statement. commit ba929c91554931c0901ed2fbd26c2e278549fb1a Author: ann Date: Mon Jun 9 22:38:25 2008 +0000 added lamprey chains/nets to place in correct order commit 8b2d69b675e734226a776b2ee513389385f34917 Author: hiram Date: Mon Jun 9 22:29:39 2008 +0000 Rearrange the chains and nets to be in order by priority commit 18032d699556a13e8d7e7605c107eb1660af67b4 Author: hiram Date: Mon Jun 9 22:23:01 2008 +0000 Pb2 and Rem3 are defined in the top level commit 83011dda472a0b0c333f231ab8a81a9859e01d8e Author: hiram Date: Mon Jun 9 22:20:48 2008 +0000 Adding in CaeJap1, CaeRem3 and CaePb2 tracks and html pages commit 50ee7f86ce74e6a8bff95a25c2e1656c48ad0231 Author: ann Date: Mon Jun 9 21:44:08 2008 +0000 added Pauline to credits of lamprey and lancelet commit 4c5dc4f4c0189df8d723a82019e29922f0bb0177 Author: kayla Date: Mon Jun 9 21:23:17 2008 +0000 added braFlo1 and petMar1 commit fb76972b6e20c3c199036a6448b9b8fc20517167 Author: larrym Date: Mon Jun 9 21:15:37 2008 +0000 change jsIncludeFile to use a new hg.conf setting (browser.javaScriptDir) to support developer specific javascript directory commit f47397d534003f5269977ee46c384eac7ba515dc Author: kuhn Date: Mon Jun 9 18:26:46 2008 +0000 removed hiram's util for encoding mailto:s it was already in /cluster/bin/scripts commit 2521f3643dd108cb3810270c368920b98efa9f82 Author: kuhn Date: Mon Jun 9 18:24:40 2008 +0000 added hiram's util for encoding mailto:s commit 8fe967acb0a21858acc7c7fe02d9806c1342f8ef Author: angie Date: Mon Jun 9 18:04:27 2008 +0000 Discordant Clone Ends from Jeff Kidd, Eichler Lab. commit 5307404465b4543f18337574ee36d9273d32ff55 Author: angie Date: Mon Jun 9 18:03:38 2008 +0000 When including strand in BED output, include a stub score so we print legal BED6. commit ea1f60e67c80ac9c2bae8bc11b0bf805d195e2eb Author: galt Date: Mon Jun 9 17:56:27 2008 +0000 fix para make and para check to errAbort on sickBatch commit 38f915df720c01ccbbe0b2e4d1131bb364d3f942 Author: kate Date: Mon Jun 9 17:10:00 2008 +0000 makefile commit 0168d72652302d2373d2f47730cbc6841a6858ff Author: kate Date: Mon Jun 9 17:09:42 2008 +0000 Files from duke for validator testing commit 2367840c6b651e30a142c2b48a1f96206857c44a Author: hiram Date: Mon Jun 9 16:34:45 2008 +0000 Adding Pb2, Rem3 and Self chains and nets commit faeb087bbb484d4824b20e25f9bf9f32557490c8 Author: galt Date: Mon Jun 9 15:00:06 2008 +0000 "Encode release log update" commit 1b669f4387e2a0e0dcb53828393266735c602175 Author: galt Date: Mon Jun 9 15:00:05 2008 +0000 "Release log update" commit b5d4e66bf9033b240bd6499ff8b13947a2fda339 Author: tdreszer Date: Mon Jun 9 05:16:03 2008 +0000 Still trying to make progress on speTri0 blastz. commit a0fffa1c8fea90a7585d41d82e4bda55e2420fb4 Author: markd Date: Sun Jun 8 19:26:43 2008 +0000 added option to use 2bit file directly instead of going through chromInfo commit f4af7c08c32655ced90f67b433ad3f37f30bbf42 Author: braney Date: Sun Jun 8 19:12:00 2008 +0000 output postion strings from native species (rather than just reference species) commit 7798a01f7151889a7e87d844ef0e92b7f3f10fe1 Author: kate Date: Sun Jun 8 16:38:52 2008 +0000 3way rodent multiz commit bdae6c2c0f6f5ab8faeb1d8c4d0c84b097da6265 Author: galt Date: Sun Jun 8 15:00:10 2008 +0000 "Encode release log update" commit cb717f19ef2b597428baba836a2f59432ee0c84e Author: galt Date: Sun Jun 8 15:00:07 2008 +0000 "Release log update" commit 67484d66e2654c3fa7ccfd29bd291e9eac621058 Author: kate Date: Sun Jun 8 05:28:43 2008 +0000 Ground squirrel alignments commit e8a6807fede414f1308828326834fb88cb7313d4 Author: galt Date: Sat Jun 7 15:00:06 2008 +0000 "Encode release log update" commit 65e04d72f8d416d21ac19fc16378e90fd8f0e25d Author: galt Date: Sat Jun 7 15:00:05 2008 +0000 "Release log update" commit 61d908fde5395ebc0d044eb74974f780b6c0a5cd Author: donnak Date: Sat Jun 7 14:52:39 2008 +0000 Archived an item. commit 064cbb2e18a1d22761ca218535da4213e0659ddf Author: galt Date: Sat Jun 7 10:13:08 2008 +0000 changed maxNode to maxJob (a much more accurate name) commit 9e05a11e2df7952b6a71c00f5366914b177994ff Author: galt Date: Sat Jun 7 09:59:56 2008 +0000 adding new version of system with new resource allocation based on requested usage of ram and cpu commit 6e18ce5169c333d68733366c0fde5eee1bb73694 Author: kate Date: Sat Jun 7 04:22:56 2008 +0000 Stanford NRSF chip-seq commit 29c1bfc79aa60016ad89ba1bdf75edf8aa0a32cc Author: kate Date: Sat Jun 7 04:22:35 2008 +0000 Add hg18 version of Stanford NRSF chip-seq commit 382556c707410d053d6315b1526d52f8c50ca91d Author: kent Date: Sat Jun 7 00:41:09 2008 +0000 Changing logic to be more robust to number of antibody fragments. commit 133ec89fcd217af7e3dab3d75c60ff463a25bfc5 Author: kent Date: Sat Jun 7 00:22:43 2008 +0000 Main gene build done. Starting to work on tables that link it to everything else, currently in tmpFoo2. commit 30ab23c038bc6ffcb34d4bffd8b99920f2424350 Author: rhead Date: Sat Jun 7 00:02:48 2008 +0000 Added quotes around table var so that wildcards will work commit 7dd9f438c2cbc88555d68c2ec47ffc106c0667d0 Author: larrym Date: Fri Jun 6 22:18:11 2008 +0000 make DDF/PIF file parsing more fault tolerant; remove hyphens from sql table name; start adding code to create a trackDb.ra file commit 7d029500f37694207c02b01dff3ad925b63e2832 Author: aamp Date: Fri Jun 6 21:56:58 2008 +0000 Brooke suggestion to fix. commit b2f9201acd81b56b2f76ba79a9c310095b35647d Author: kent Date: Fri Jun 6 21:48:32 2008 +0000 Making it so that truncation only in UTR areas of terminal exons just causes a version bump rather than a new accession for noncoding as well as coding genes. commit 099047fdbd3df3421171cfd88be50e10aa9f1fd9 Author: donnak Date: Fri Jun 6 21:35:53 2008 +0000 Added lamprey & lancelet credits. commit ff266692a8b63def2450cbc9cfae9acf1c97909f Author: donnak Date: Fri Jun 6 21:12:05 2008 +0000 Added lancelet & lamprey to release list. commit 6e51683381dceff3e6453f4fb21fc6fcaf58c4c6 Author: hartera Date: Fri Jun 6 17:53:29 2008 +0000 Fixed broken link for GM06990 cells. commit e4aebd3f61095a0e24e001d6e49415d6acb27475 Author: rhead Date: Fri Jun 6 17:45:28 2008 +0000 Fixed broken links to BGI. commit 3f5b1c72ef62b392b620a641a8442fd8aa82e9d8 Author: fanhsu Date: Fri Jun 6 17:43:25 2008 +0000 Updated the default subject list logic for GSID. commit 44e87d833a7301e23af44dd97d2aae8878528a07 Author: hartera Date: Fri Jun 6 17:35:00 2008 +0000 Fixed broken link for GM06990 cells. commit c72bec518f403e949dac96916173ed218b57062c Author: ann Date: Fri Jun 6 16:29:48 2008 +0000 reordered list of orgs to match everywhere else commit 0a00db3e604083e6a67e0b03a06f53d40764758f Author: galt Date: Fri Jun 6 15:00:09 2008 +0000 "Encode release log update" commit 6b0b858ada6467c9c0abd541e71fadf6e8f34287 Author: galt Date: Fri Jun 6 15:00:04 2008 +0000 "Release log update" commit 7720a688046386f3731066303f6faa6e27191d57 Author: larrym Date: Fri Jun 6 07:47:09 2008 +0000 support Mac EOLs in PIF and DDF files; support Antibody_REF commit 28db33cb2e666a20bbdd53fadd99c51ab061bc06 Author: rhead Date: Fri Jun 6 02:58:54 2008 +0000 Two was/were grammar tweaks. commit 1e41d84eee5d5b465ad67eff7bb71d8b4c6bddf2 Author: ann Date: Thu Jun 5 21:50:01 2008 +0000 bringing these two html pages in-line with one another. They have similar methods, but are both different in the same way from the other mouse miRNA tracks. commit 0aa199de2e2e3877daba18241152b4e3bff0adc8 Author: ann Date: Thu Jun 5 20:56:09 2008 +0000 bringing down to this level. It is different from the other miRNA tracks in that it no longer has thin blocks for the stem-loop portion. commit 8c803b8c4678e279bd2edbb847611485e0aa9dc5 Author: ann Date: Thu Jun 5 20:23:43 2008 +0000 adding better links commit 2dd26546db6f1431a8d7fac12986617a3851dd51 Author: larrym Date: Thu Jun 5 20:13:44 2008 +0000 refactor code into setCartVar; move getURLParam to utils.js commit bbdd0e4f8640bde2258204d77961e0fe65999992 Author: donnak Date: Thu Jun 5 19:29:04 2008 +0000 Fixed typo in guinea pig credits. commit 012dd5df640bb80137a3d6cd652f770300bc1dfc Author: ann Date: Thu Jun 5 17:33:35 2008 +0000 adding better links to articles commit e2ae797a8bf2bc4854426b2d47eebb460f544a40 Author: ann Date: Thu Jun 5 17:00:28 2008 +0000 re-adding tableDescriptions table to list of tables to ignore. Bob agress that it should be out. commit c1f569a6275e048b23a00d57b626b718fb6c2fff Author: ann Date: Thu Jun 5 16:48:39 2008 +0000 backing out previous change. Bob wants this table left in the output. commit 8ba0e1acea66b9ddaf97dd16b0b62a70defef8b2 Author: jzhu Date: Thu Jun 5 16:41:38 2008 +0000 microarrayGroups.ra commit b6145c61e30c787012ce0c0304ad5b8c4bc713d5 Author: ann Date: Thu Jun 5 16:39:51 2008 +0000 adding tableDescriptions table to list of tables to ignore commit 86e8ab57fa9646b36067703afa6f1e140af4c306 Author: galt Date: Thu Jun 5 15:00:06 2008 +0000 "Encode release log update" commit 382f5fc108df3232c71c8049f6be21a8e8f0eb30 Author: galt Date: Thu Jun 5 15:00:04 2008 +0000 "Release log update" commit c2840651fdf6e63ac67c489b38856874f6c7cb15 Author: larrym Date: Thu Jun 5 01:52:28 2008 +0000 add getURLParam commit 5ac9c2725397aeacc1d6bbb21f7624c13cecfa86 Author: larrym Date: Thu Jun 5 01:51:47 2008 +0000 support noDisplay option to suppress output commit b40278e124a5662b19ae31876e63beb444408e2d Author: larrym Date: Thu Jun 5 01:51:03 2008 +0000 add setCartVar commit 453927354c899ef6107eba71a306506ef1f9fb2a Author: larrym Date: Thu Jun 5 00:33:09 2008 +0000 change some comments; head->cat commit 7132e4c4fa7e9995a8755af4c84db96d4a0d0f27 Author: angie Date: Wed Jun 4 23:55:55 2008 +0000 Added bin column and indexes in case the contents are actually used. commit 39f13649f0c17f335016b37721b87113598123b1 Author: donnak Date: Wed Jun 4 22:18:42 2008 +0000 Uncommented cavPor3 info. commit b991eafa61ac5daa56ca067824e05772c8e100fa Author: donnak Date: Wed Jun 4 22:17:48 2008 +0000 Uncommented guinea pig news item. commit fd8ab5511c4efda0b4c2b0dea44ae1359974d6c0 Author: larrym Date: Wed Jun 4 20:35:08 2008 +0000 add some (currently dead) code to send message to hgTracks when user changes open/close state commit 8bae479264548e65cedc2403fc1a689269626cdc Author: larrym Date: Wed Jun 4 20:33:24 2008 +0000 add overloaded loadXMLDoc commit 7b22ed40978774162e08f9b0d112517131aa41f7 Author: larrym Date: Wed Jun 4 20:25:48 2008 +0000 ajax utility code commit 60b645f5250a842604ebdcd4e2d046cef30d69f8 Author: markd Date: Wed Jun 4 19:30:44 2008 +0000 added option for output conf with defaults added for each genone commit 392aa0915886993a936665aa9f7321af234d7b64 Author: kayla Date: Wed Jun 4 19:23:00 2008 +0000 added cavPor3 commit a4f3f18964c22a957402f817c4d894beeb05c731 Author: hiram Date: Wed Jun 4 19:10:40 2008 +0000 Looks like the sanger gene track is all done, complete with gene sorter function and everything. Now have a blat server and have set the default position. commit 02524994ff5f240487bc66d5e3cefa5f963a3f7e Author: hiram Date: Wed Jun 4 19:10:00 2008 +0000 Make better 11.ooc files commit 674dcf1b66282e9c0e9f2f21386c846592a05b08 Author: larrym Date: Wed Jun 4 18:25:15 2008 +0000 include - when looking using prefix to fix bug caused by tracks with same initial substring commit 3e8118532d7d5c15e6efebf9d6fc88ba90db191e Author: hiram Date: Wed Jun 4 16:39:48 2008 +0000 Adding ce6 to the elegans list commit 2c28d8f570d3469f89e684552058ce5fc2e6d6d7 Author: hiram Date: Wed Jun 4 16:31:08 2008 +0000 There is no need to put   in the warning messages. Those characters become encoded HTML upon output and appear as that string instead of a space. A simple space is good enough. commit 72b60539ab569c5363a8922c76f3b98643a8d753 Author: braney Date: Wed Jun 4 15:33:29 2008 +0000 add multizPrimate commit 501ce2f0646c593dac1c15fc14ce6962d7b0f061 Author: braney Date: Wed Jun 4 15:30:27 2008 +0000 doc this alignment commit 7cd57a833ad5c11c8956d7a69676626011219588 Author: galt Date: Wed Jun 4 15:00:11 2008 +0000 "Encode release log update" commit e2744217f2150f359737267f721100d279993b51 Author: galt Date: Wed Jun 4 15:00:04 2008 +0000 "Release log update" commit 1608891a38b4b36ee8682baaf3ec0b3c60108aa4 Author: markd Date: Wed Jun 4 06:42:09 2008 +0000 added Platypus xeno refseq commit ffa4fd124796996400b54a71d00b27bd7fea2d33 Author: pauline Date: Wed Jun 4 00:46:51 2008 +0000 Fixed typos. commit 754fc4ab17682c6a7f226d376d2d98a6a32ea5aa Author: ann Date: Tue Jun 3 23:58:26 2008 +0000 fixed typo commit 56663c8df1eb3c9b4862b1f1a658e545d798963a Author: larrym Date: Tue Jun 3 23:38:51 2008 +0000 change errAbort to warn in jsIncludeFile (so we don't fail on misconfigured servers) commit ee47557bc967c04295ccb0b2c256dbf1f9650303 Author: larrym Date: Tue Jun 3 23:37:52 2008 +0000 support dynamic open/close of track groups (i.e. w/o a round-trip) commit 7aa87ed6ac767cf1584d1f18893c4c0a672967a9 Author: ann Date: Tue Jun 3 23:24:33 2008 +0000 remove marketing commit 14ca66a950297776f2fddbdc48ddbc055eea96f4 Author: ann Date: Tue Jun 3 23:21:43 2008 +0000 one more change commit b161f6828ca38938d77839077f4c2c2750190d5c Author: ann Date: Tue Jun 3 23:18:22 2008 +0000 removing a table from agilentCghRn4Id (rat does not have this table) commit ee9a68612cd14e90929647334c38736c5af1a4b1 Author: markd Date: Tue Jun 3 23:17:56 2008 +0000 fixed just introduced bug that caused CGIs not to work under the debugger commit 9d4b13062038b27f7fb00f67c42eb07eb38fe6d0 Author: ann Date: Tue Jun 3 23:14:37 2008 +0000 general clean-up commit 1b0855cb56dbaaf6e205d9ef7e6fb634da40f5bb Author: kuhn Date: Tue Jun 3 22:32:01 2008 +0000 fixed header to display the machine you are on instead of the same thing everywhere. also removed link in list for the machine you are on commit 1edcc619756b66f6cf4744cb9ec027ec80e6989d Author: kuhn Date: Tue Jun 3 22:28:08 2008 +0000 changed an is to an are and N's to Ns commit 58d9e4f50f48559ff586fcfd0f6acd0abf75525e Author: ann Date: Tue Jun 3 22:06:12 2008 +0000 citation changes commit 781c1e630caf8ec4404e0d2f7d9b1e547f80da58 Author: kayla Date: Tue Jun 3 22:06:08 2008 +0000 fixed error in a sample search. commit 01ca2bef2da34d3069d238dbd88750a9762c372a Author: hiram Date: Tue Jun 3 21:44:15 2008 +0000 sanger genes mostly done, a bit of tweaking required to eliminate bogus sanger links commit 2e8ad88f0ca68820a1c78bb006699150049a7c90 Author: ann Date: Tue Jun 3 21:41:00 2008 +0000 more small changes commit bbea2b7d65aa503431bc1b3090f48fead134f115 Author: ann Date: Tue Jun 3 21:40:39 2008 +0000 general cleanup commit 038a724ad284e6a6f23f36e75735a1f4aae424c4 Author: ann Date: Tue Jun 3 21:09:26 2008 +0000 fixing up formatting, citation, references, etc. commit d8f3f2b550ef8022fe512cfe637c8e6ecf4ec165 Author: fanhsu Date: Tue Jun 3 20:11:06 2008 +0000 Created for hivgne8v2. commit 0bfc8236527cb64c37d32e57c84ae959a6c94a56 Author: larrym Date: Tue Jun 3 19:53:52 2008 +0000 code converted from doEncodeLoad.pl commit 56f54be3d5aa8d4bcb97e1dbfd17717f60a2afad Author: larrym Date: Tue Jun 3 19:31:24 2008 +0000 add noScriptMsg parameters to jsIncludeFile commit d307d5d45f82a478911aac61b080e10d81db6cc0 Author: fanhsu Date: Tue Jun 3 18:02:37 2008 +0000 Added hivmn2 and hivgne8v2 commit 3e51f4ec2a0f5da1a0cdb921741859e0429283ab Author: angie Date: Tue Jun 3 17:43:48 2008 +0000 Missed a spot that needed ->totalHeight() instead of height earlier when adding support for different limited visibilities in different subtracks of a composite track. commit 1a6ee4f2aeb15407d6fac703f356b331e87ed89d Author: kuhn Date: Tue Jun 3 16:53:28 2008 +0000 added hgwdev commit ab403177bc7ee6891e87c1e075f0552b63fad0b7 Author: kuhn Date: Tue Jun 3 16:53:03 2008 +0000 removed trackDbs and hgFindSpecs from list commit 262af0f83e5c3f1c09ec8c205069eff9baef1c7d Author: galt Date: Tue Jun 3 15:00:07 2008 +0000 "Encode release log update" commit d482dc377e724a529975a3207e9257bd78c2b68e Author: galt Date: Tue Jun 3 15:00:04 2008 +0000 "Release log update" commit fef09cfc6dca50611c1def6ae6692e01f146ec9f Author: markd Date: Tue Jun 3 01:03:34 2008 +0000 added support for include in hg.conf files commit 38769f78c2683d567c2a2c1918892356bbd1b932 Author: hiram Date: Mon Jun 2 18:04:07 2008 +0000 Added ce6 - C. elegans WS190 commit 98900b552ec328c592f89b831c03bbe20d92759b Author: fanhsu Date: Mon Jun 2 17:21:59 2008 +0000 Added VAX003 tracks. commit 0028f55fdc80a59c51eebbfd6bf9b9df28e2e872 Author: markd Date: Mon Jun 2 16:01:31 2008 +0000 Moved nowrap style to DIV, as some pages generated by hgTracks, like search selecting from multiple alignments, break. commit f2f84fd38b45fcfb206480771d62d2cb7a0acdd3 Author: galt Date: Mon Jun 2 15:00:06 2008 +0000 "Encode release log update" commit 11be5fca0b25b00bf374376a460ebecdc4ed144c Author: galt Date: Mon Jun 2 15:00:04 2008 +0000 "Release log update" commit 5bb6696e463a37cf5dd367bee44d5a2738a98b88 Author: kuhn Date: Sun Jun 1 19:59:55 2008 +0000 checked in images already in ues commit 518e323a2e9a99ac979e864c68f4fb24428bf534 Author: tdreszer Date: Sun Jun 1 15:14:30 2008 +0000 A couple steps forward on speTri0 maf, then a couple steps back... commit 9b88317e6f6250e97be636cd9b6c4ff4335b1185 Author: tdreszer Date: Sun Jun 1 15:07:47 2008 +0000 Naming convention, arguments[] and 'force' option changes. Double click() may be slower but is more universally effective. commit 826639dad7a6c18f2caf4ede19f9c270e5952dcc Author: tdreszer Date: Sun Jun 1 15:04:55 2008 +0000 Used arguments array to handle vargs and added 'force' option to setCheckBoxesThatContain() commit b77fbd551e8346c43359851feaf55936673593c1 Author: galt Date: Sun Jun 1 15:00:11 2008 +0000 "Encode release log update" commit bb9b8e4f6fe7a49c2f2d73181fb67d7547568887 Author: galt Date: Sun Jun 1 15:00:08 2008 +0000 "Release log update" commit 27bb0368e6717f42bf6a1d9563350492fee79dcb Author: tdreszer Date: Sun Jun 1 14:58:25 2008 +0000 changed a chk box function to static and common so that fundementals are abstracted from uses commit 6567f4f1e4967c0454afab10b464998cd1b57818 Author: markd Date: Sat May 31 21:14:19 2008 +0000 added ability to set html backgroud color in hg.conf commit 4bd69b228351b1d64592bdd9d55f6674b69a7995 Author: braney Date: Sat May 31 15:59:25 2008 +0000 add hgLoadMaf to browser loaders commit b093847850907184987e6cc500d456ebdd6d19cc Author: braney Date: Sat May 31 15:42:37 2008 +0000 add support for loading custom maf tracks from loader directory commit d3952b4fb2a317c782215370e83ca4e2d5e6cee4 Author: braney Date: Sat May 31 15:39:32 2008 +0000 upgrade form to support copying to loader/ directory commit b5cfe7c12e50784c243cf82bf17b7ceceebaf660 Author: braney Date: Sat May 31 15:32:15 2008 +0000 add support for custom maf tracks commit 8c288cb241c6b83d02e332acb800277cf9a6c648 Author: braney Date: Sat May 31 15:31:13 2008 +0000 add support for clicking on custom maf tracks, some atom track changes (track type not destined for RR) commit 8d5e1972ef8f629277aada9779a3df14e9c7da4d Author: braney Date: Sat May 31 15:28:55 2008 +0000 add declaration of routine to handle custom maf clicks commit f8ed050c37875d887d51803db5a64016cf4d8cc9 Author: braney Date: Sat May 31 15:25:51 2008 +0000 add support for custom maf tracks, make irows the default commit f678460a3a4a9d9bb0c7fb06f2f7ec6cd6674d25 Author: galt Date: Sat May 31 15:00:07 2008 +0000 "Encode release log update" commit a623c0dbd1670deb512339127a6881f7b06b533c Author: galt Date: Sat May 31 15:00:04 2008 +0000 "Release log update" commit d557eab719c6783d1bf3e8d99a3816e1d509763e Author: braney Date: Sat May 31 14:19:58 2008 +0000 add support for custom maf tracks, make "irows" trackDb pointer unnecessary unless you want to turn irows *off*, draw custom track maf's with scoredRef table rather than summary table, add mafDots to trackDb settings to allow default display to be "show dots when base is same" commit 45806ce8f4c6c06db4ef55d28bfc3c4445e8d076 Author: braney Date: Sat May 31 14:16:49 2008 +0000 create a structure that is referenced through the customPt pointer of the track structure commit 38d3a1b02f92b02c34d2ba3fc2a74ff684a4b0a5 Author: braney Date: Sat May 31 14:16:15 2008 +0000 add support for maf custom tracks, fix bug causing blank rows when alignments are clipped by the edge of the screen, change way list of maf's is accessed through track customPt pointer commit 935e05722564ecd5ba44c47b4f4cf8e7ce7c8720 Author: braney Date: Sat May 31 14:13:51 2008 +0000 add support for maf custom tracks commit 556e84416bd343eb0d2ed259eaa90c41548b3a87 Author: braney Date: Sat May 31 13:54:29 2008 +0000 add support for custom maf tracks commit a5a15910ae69e1285c3c2bc8d157b67f9e6e33ba Author: braney Date: Sat May 31 13:44:52 2008 +0000 add a function to unlink a tab file (used by hgLoadMaf) commit eb5ab93debe51f720c405e3f92f50bcb6557b242 Author: braney Date: Sat May 31 13:44:21 2008 +0000 add new function mafLoadInRegion2 that takes two connections so we don't have to open a connection to the extFile database every time the extFile table changes, this since custom tracks are getting the extFile table from customTrash, rather than the current database. commit 41f5ddb8366c952ff0b933a9c467cd8bbe6494e9 Author: braney Date: Sat May 31 13:42:37 2008 +0000 add support for maf tracks commit c46ac9cfe57cf18a833d88cc6d5ef8c0dfd64355 Author: braney Date: Sat May 31 13:41:07 2008 +0000 make hExtFileNameC() a global function, now called from hgTracks commit 624376098678a6bb2e7281debc643995897030a7 Author: braney Date: Sat May 31 13:40:13 2008 +0000 add routine hgRelate.h to unlink tab file (called from hgLoadMaf) commit d6510ea899acdeb14fcf6a0d12a0c0a736088567 Author: braney Date: Sat May 31 13:39:21 2008 +0000 add routine mafLoadInRegion2 that takes two connections instead of one. mafLoadInRegion opens a new connection each time it accesses the extFile table commit 34a8e555ed15367dc33c1ff6ba2d4488ade85129 Author: braney Date: Sat May 31 13:38:21 2008 +0000 make hExtFileNameC global so hgTracks can access it commit be69e471376fe39853e6281c967fb048940bdbd3 Author: galt Date: Sat May 31 07:56:06 2008 +0000 12.06 minor bugfixes and code-review changes commit 8cb575dbbd7a08cab47d4d1e82a28c10f942980a Author: galt Date: Sat May 31 07:39:20 2008 +0000 adding new slIntFind function to search an int list commit 226c39f2497f211325f8732a0e1d9e03b2c87de2 Author: larrym Date: Fri May 30 23:49:25 2008 +0000 specificy DOCUMENTROOT so make alpha can copy the js files somewhere; fixes build problem on titan commit a7c05eaef2450fdec339201e2d7f63024e6d20e3 Author: hiram Date: Fri May 30 22:25:55 2008 +0000 Enable intersect with wikiTrack when it is second table commit e896f3288c8c107b5aace5e9408e303045229df1 Author: hiram Date: Fri May 30 22:05:46 2008 +0000 Started WS190 C. elegans build. Now running genbank commit f77f63c8296eb40c5d144531460e007d8f40f438 Author: hiram Date: Fri May 30 21:59:33 2008 +0000 ce5 was supposed to be ce6 commit b950ef174434857496c55d11b5818bb503fe6f32 Author: hiram Date: Fri May 30 21:54:45 2008 +0000 Adding ce5 to the alignments commit 3ef1067bfc2792bb08dd623cd9a83d89284dee6f Author: markd Date: Fri May 30 21:17:08 2008 +0000 imported N-SCAN cavPor3 commit bacc0ddb65e273dd2d8de12ae1b48aa6d6799a81 Author: hiram Date: Fri May 30 21:09:32 2008 +0000 Updated the comments to be more informative to tableDescriptions on hgcentral commit f5885fb090d09caf3f163762519833a9f4ee5d32 Author: hiram Date: Fri May 30 21:06:57 2008 +0000 Properly cgiEncode the track name for the configure page links commit 2e9d8d6d230ac7c171ae6dc6e3960a9f7e3eb1e2 Author: hiram Date: Fri May 30 20:59:34 2008 +0000 Allow chrUn when it is the only chrom commit 7a2b52355ca0432dee4828e382de7fd0d0b85f6a Author: hiram Date: Fri May 30 20:45:36 2008 +0000 Properly htmlEncode the item names on the hyperlink display commit 7724e5622eb1d506f960cf74dff0ac71d5cf3a85 Author: hiram Date: Fri May 30 20:44:53 2008 +0000 Had lost the ability to specify item color commit f74befd86420cfca5e6c36e22ef85700fa98036b Author: larrym Date: Fri May 30 18:48:16 2008 +0000 add MAKEPARAMS hack to force use of gcc34 on titan commit 69358fcbd6003bab505d9f94ecf1db4d77905f34 Author: hiram Date: Fri May 30 18:38:45 2008 +0000 make a local function private, and need to encode the displayed names for the sample list of identifiers commit 3d16a46ca3431ef23293d53c00246a22c6b12c34 Author: hiram Date: Fri May 30 17:49:55 2008 +0000 Adding ce6 to the list commit 0b86108393fb2320d4938ac3536e9564df8088b6 Author: hiram Date: Fri May 30 17:49:21 2008 +0000 Fixed up to represent WS190 release commit 4e9f3550c98ee6da455d238648ad750555e933ea Author: hiram Date: Fri May 30 17:41:46 2008 +0000 Original files from the makeGenomeDb operation commit 6103f98f0c490e9844729e77273a7998f25c574d Author: fanhsu Date: Fri May 30 15:26:25 2008 +0000 Added wgRna section. commit 7e821b68d7e45c6ad58cdd01cfdc2424708ef112 Author: fanhsu Date: Fri May 30 15:23:01 2008 +0000 Created wgRna.html with updates from Michel Weber. commit da526cc0b571c90bbf74eb39960ec7dcd5bec6fd Author: galt Date: Fri May 30 15:00:09 2008 +0000 "Encode release log update" commit f5587a98e6bd3fc59bd8e36d42755d0f96fa2104 Author: galt Date: Fri May 30 15:00:03 2008 +0000 "Release log update" commit c3215ce1d84a9c164f0c2f7b4e79c99c28da71af Author: markd Date: Fri May 30 03:09:47 2008 +0000 set wrap style to prevent buttons from wrapping commit e1d7b7ac430957cac92c48cadc7c3154012ccd98 Author: rhead Date: Fri May 30 00:46:07 2008 +0000 Typo. commit 79d989b80eda7470c39c846fe2d35b05c93177d2 Author: hiram Date: Thu May 29 23:39:02 2008 +0000 Properly manage the deletion of multiple loci gene annotations commit 75c34c14f0d0a1145df47955a0ca728a3d5afacc Author: larrym Date: Thu May 29 23:28:50 2008 +0000 startsWith -> startsWithWord commit 1b71cabdc5277b40b9e1fce5b6b7feabb7f42a2b Author: larrym Date: Thu May 29 21:21:14 2008 +0000 break out of zoom loop in exerciseTracks when we encounter >= 10000 links to solve a performance problem/running out of memory failure commit f6c31a99d8a7a297858f1c26c2b797f030f7d41f Author: galt Date: Thu May 29 21:20:22 2008 +0000 fix warning commit cf8178e3f4d74c5d9945caa29fc5b8d8435f41d6 Author: galt Date: Thu May 29 20:32:56 2008 +0000 fixing 32-bit compiler warnings about signedness commit 583d63db823afeb8b37ce178ad7736dd0c9c5dda Author: markd Date: Thu May 29 20:25:28 2008 +0000 added check for sequence not matching psl when coloring; added info about things that make the code hard to understand commit c32a2743f88a7d81993daf5fa56c9814a3d74b9f Author: galt Date: Thu May 29 20:18:42 2008 +0000 fix bookmark-related problems commit c1af7e3368a7cccdf7810d96ec36dd4f8627cf0e Author: larrym Date: Thu May 29 19:35:25 2008 +0000 set canPack to FALSE for custom bedGraphs commit 17efc891a0c4dad2385050ca9e61df1a4df12d66 Author: fanhsu Date: Thu May 29 19:00:30 2008 +0000 Updated miRNA track. commit faacba1b5de217df5a2db57af3c1d8e7285bd6af Author: fanhsu Date: Thu May 29 18:28:55 2008 +0000 Updated wgRna track. commit c860b7ba18c96814bad9d4320df7ca25289034fd Author: hiram Date: Thu May 29 17:49:24 2008 +0000 Properly close wiki db connections commit 2f219cd7e819aabf29ed50a96a53a167eded9bf4 Author: hiram Date: Thu May 29 17:32:18 2008 +0000 Identifiers now works for the Wiki track on the name column, and properly encode an item name for output in the range histogram in case they have unusual characters for display in html output commit 931d01bbc33824e7cd4c9f9165ff4c26de9febf4 Author: galt Date: Thu May 29 15:00:07 2008 +0000 "Encode release log update" commit e23d36ca2b69c1655fa2879b0ee2db7b17ec69dc Author: galt Date: Thu May 29 15:00:04 2008 +0000 "Release log update" commit 7384fe51ac59e097973e65fe8e7b3a460b4506d5 Author: markd Date: Thu May 29 07:26:36 2008 +0000 cache two bit for other seq access functions (suggested by hiram) commit 363a4723034caafe5db1b9ce4ad89b4488efa46e Author: markd Date: Thu May 29 07:12:37 2008 +0000 use function suggest by hiram commit ca95e12c1e3105b0a28a7fa14430426785260883 Author: hiram Date: Wed May 28 23:05:15 2008 +0000 Clean up the window masker track and get rid of the masked gaps commit e782c32a436a1b504c2f38a7052e5121de5e25b6 Author: aamp Date: Wed May 28 22:12:49 2008 +0000 Added description for affyHumanExonDistance column. commit f010c1a05c998550d7c38121f43aa1b43806c010 Author: larrym Date: Wed May 28 21:36:00 2008 +0000 fix a bug where shortLabel and longLabel were copies of hash values rather than being cloned strings commit 8c60873fbc7aa53b79840d9abae971814307adb5 Author: galt Date: Wed May 28 15:00:06 2008 +0000 "Encode release log update" commit 894d97761446313bea311eec071066f25f9eae3a Author: galt Date: Wed May 28 15:00:04 2008 +0000 "Release log update" commit c5e7ffd2d6a9b1750b688f31e19159f659a24e3e Author: galt Date: Wed May 28 08:09:30 2008 +0000 remove moot para time option -eta commit 423bb8a5170a52345911f1d857f0bcd58f6dccca Author: galt Date: Wed May 28 05:17:05 2008 +0000 removing final period for consistency and better readability commit dc335e56c3af82598b642e3363c5b9d735403eca Author: galt Date: Wed May 28 05:06:39 2008 +0000 moot fix commit 7c137de5441d6ff86068eee1b01abd721d442503 Author: galt Date: Wed May 28 04:55:31 2008 +0000 moot, cleaning up commit e7a01438c5870da1d0d15eb3ec91ddfd3b4b5c65 Author: pauline Date: Wed May 28 00:03:00 2008 +0000 Fixed typo. commit 75d6e581ff4b917ea25799aa51dd317094a91600 Author: hiram Date: Tue May 27 23:54:10 2008 +0000 Fixup references to the wikiTrack connection to be generic functions commit 93d0a55893d92813915ff901f962780b9c526bfa Author: hiram Date: Tue May 27 23:48:28 2008 +0000 The initial steps to support the wiki track. describe schema works, filters work, and some of the get output functions commit db00a876fbb3f1233725844ed067634a2a95e333 Author: pauline Date: Tue May 27 23:14:52 2008 +0000 Fixed typo. commit 6c4926f89e4a078d9bd07cca496f8f868fac07e9 Author: pauline Date: Tue May 27 23:09:56 2008 +0000 Clarified text about wig vs bedGraph files. commit c93e55e3fe259627aee99f9b628e3e3ecda0ceb0 Author: markd Date: Tue May 27 22:56:15 2008 +0000 used real engrish instead of abbreviations commit 151ed42637e1b1cdb9d1354549721e25942d03cf Author: markd Date: Tue May 27 22:54:37 2008 +0000 fixed typos and made informat displayed clearer commit 53a1547934ad43cdd9444f57b46640f7e1a05327 Author: angie Date: Tue May 27 22:44:27 2008 +0000 Adding back my changes from r1.100. commit 7f4a602a5916105db891a286be8461f7aee545bc Author: markd Date: Tue May 27 22:09:15 2008 +0000 use mRNA definition of frame when display codon annotation commit 5acff2cab3a8b6e13964cc9d9280d397f1bea75f Author: fanhsu Date: Tue May 27 21:50:01 2008 +0000 Added cartGetOrderFromFileAndMsaTable(). commit 67db03a5c603c484180fe1232c3255327decaf1e Author: fanhsu Date: Tue May 27 21:00:37 2008 +0000 Added cartGetOrderFromFileAndMsaTable(). commit 26dc6c345a991f2d49ac5d6045ce06a2f05759ba Author: fanhsu Date: Tue May 27 20:55:33 2008 +0000 Added logic to restrict displaying data for selected subjects that have entries in the track being displayed. commit c6ed89420a674d6d73d90124089f0b8dfe70118a Author: larrym Date: Tue May 27 19:54:05 2008 +0000 remove misleading (b/c unsupported) backslashes in the track line example commit 3cfe1d424a8abadc72dc1868b05425cbbd89f795 Author: larrym Date: Tue May 27 19:27:52 2008 +0000 add comment about wiggle compression algorithm causing loss of precision when exporting commit a04e3a61ccf6e125175d3269addcde791f40dcb7 Author: ann Date: Tue May 27 19:25:16 2008 +0000 needed to quote variable in case there was more than one lock found commit 6da681755cabd84910acc7ecb5c4994c2b086206 Author: kuhn Date: Tue May 27 19:23:16 2008 +0000 removed kuhn link commit dbb70d453c83bec5d2875960b209978068ac8f4d Author: kuhn Date: Tue May 27 19:16:53 2008 +0000 removed heather's link commit b809f9824db4cc28f3dad954e9ceb38c06864630 Author: larrym Date: Tue May 27 19:16:34 2008 +0000 add bedgraph link commit fd6b0b08c6f49491d17e38a7057b544260b11a4f Author: larrym Date: Tue May 27 18:49:43 2008 +0000 minor edits commit 0bc0e8d418910ebfa8894aee364154f5aed10361 Author: kuhn Date: Tue May 27 18:01:35 2008 +0000 util to monitor new tables as they appear commit edf4c12dc74f59c29c53706071ab0e3f89aeacfc Author: markd Date: Tue May 27 17:30:59 2008 +0000 transmaps mRNAs to use non-syn coloring by default commit 5103ef85a77425181f11cbfddbf979d12488024e Author: angie Date: Tue May 27 17:23:29 2008 +0000 Yet more #ifndef GBROWSE around code not needed/supported for standalone track drawing lib. commit 029d7df37424a85fc5e2c052780fdeb6a4bd57a3 Author: hiram Date: Tue May 27 17:01:55 2008 +0000 Fixup the dates of assembly release after clarification by John Spieth commit dfbb5ab3241815837aecb44adffccac191101eb0 Author: larrym Date: Tue May 27 16:06:51 2008 +0000 "New version number v183" commit ec9567f299b152059ed5ce1c2dee8ed5079f6f9d Author: galt Date: Tue May 27 15:00:06 2008 +0000 "Encode release log update" commit 59c8e77ff467a86548cfbde8d15cdafa1241dc96 Author: galt Date: Tue May 27 15:00:04 2008 +0000 "Release log update" commit 5664cba458c1e9db33fda3b3cc23521796dceca0 Author: aamp Date: Tue May 27 09:22:01 2008 +0000 Added Illumina probes stuff (trackDb, hgTracks code, hgc code). commit e155dc3d3bbd3370e2609d4df96e696930bda199 Author: markd Date: Tue May 27 02:48:22 2008 +0000 make codon coloring code a bit easier to understand commit 07a5d700b423705551ba7d30018051c594391bb9 Author: markd Date: Tue May 27 00:58:16 2008 +0000 use prefix search for transMap commit 4f87b0425c568c98e7b325e62131bb9ae0bfc8dd Author: markd Date: Tue May 27 00:27:59 2008 +0000 fixed typo commit 952396754c4a14a1030251d91483c845b64b8f7d Author: galt Date: Mon May 26 15:00:07 2008 +0000 "Encode release log update" commit fffaa874ec3d4b0280e5d1354885bf9e0d193d26 Author: galt Date: Mon May 26 15:00:04 2008 +0000 "Release log update" commit 440d3155787ef654e9f3e634f16069bd34fcb65e Author: markd Date: Mon May 26 01:53:58 2008 +0000 fixed invalid value in transMap tracks commit abf235b923e76880e3203b46e658c55b9ff1e512 Author: markd Date: Sun May 25 20:11:55 2008 +0000 added transmap tracks commit 0cf6693844196298d32561e35a86e94d1c51ab38 Author: galt Date: Sun May 25 15:00:08 2008 +0000 "Encode release log update" commit 524931d54d86e460de11241b77e259bda1b8d9b0 Author: galt Date: Sun May 25 15:00:06 2008 +0000 "Release log update" commit f7f0314be47c0a5a16b3a708001bb82561cb6d2b Author: markd Date: Sun May 25 06:28:48 2008 +0000 if show codons in PSLs, draw entrie sequence narrow if no cds is available. Don't get CDS unless is going to actually be used commit 31edd8f8f3f03f95db6fdee86a704efe084f1af0 Author: markd Date: Sun May 25 04:09:19 2008 +0000 changed colors on transMap tracks commit 44ce0233b2607122e96571ada636d846ec54057a Author: markd Date: Sun May 25 03:31:24 2008 +0000 add indel display options to transMap controls commit ac6bf80eb9aed858e3c43c11b75e71251367a760 Author: markd Date: Sun May 25 03:00:40 2008 +0000 added transmap tables commit 8b7b1249e7b9a97482befe234c06c54123d213ae Author: markd Date: Sun May 25 02:44:17 2008 +0000 cache twobit open commit db603b70fee1888211570d8b576d1fe36627db8b Author: markd Date: Sat May 24 20:55:41 2008 +0000 added index commit 327c6aaabbf1c15b01ace9b6deafe9dc78fab2fb Author: donnak Date: Sat May 24 19:28:37 2008 +0000 First editing pass at this file -- should probably do another pass to add more info before releasing. commit 44fc20770e00bf5bbd71d10c7078ebbd0f55969d Author: donnak Date: Sat May 24 18:36:25 2008 +0000 Archived an item. commit 31f602fb5756ddc29afd6e601efe4bca8890908f Author: donnak Date: Sat May 24 18:35:57 2008 +0000 Added cavPor3 announcement (commented out) & archived GSID announcement. commit 826ed1b3fceaf48f218d1319d9bc7d1c942af39b Author: donnak Date: Sat May 24 18:15:45 2008 +0000 Added cavPor3 credits. commit 54aaf7ed90f275c5f5315a82121f69fbf945a251 Author: donnak Date: Sat May 24 17:47:06 2008 +0000 Added cavPor3 (commented out). commit 09a0a3d0400edb3a482763576378792ab6f50b9d Author: galt Date: Sat May 24 15:00:32 2008 +0000 "Encode release log update" commit c0170f7a6a8da478713976907525f1e5a90a8dea Author: galt Date: Sat May 24 15:00:29 2008 +0000 "Release log update" commit 3566e2ee26faaf28371373b96a13fe5fae189488 Author: tdreszer Date: Sat May 24 00:26:37 2008 +0000 Initial checkin of javascripts that support subtrack conjfiguration by matrix commit 0c37b6768c016fccb8951df603881b5f5106d95d Author: tdreszer Date: Sat May 24 00:20:11 2008 +0000 Added functions to support finding and checking cb's by name and showing and hiding tablerows containing other objects commit 6d4a192822e140027306ca55d0fe083b771676f7 Author: kuhn Date: Sat May 24 00:08:41 2008 +0000 refactored so it will print links to show overlaps with gaps even if not checking against unbridged gaps commit 5e970f06b2452ee61282ace7951bddd333c0523d Author: markd Date: Fri May 23 23:59:33 2008 +0000 clarified transMap text commit 6fb89d16027ff56e65dd970bd51692e8ff52a9f1 Author: tdreszer Date: Fri May 23 23:48:51 2008 +0000 Redesigned subtracks for 'dimensionX' and 'dimensionY' which will have special meaning in 'matrix' style subtrack configuration pages. commit cfab04610f4972ac4b929d69d4cd9ab7bd20d4ce Author: tdreszer Date: Fri May 23 23:44:57 2008 +0000 Reran genbank because of missing params and refinished genscan. commit 89096b446d951804b2972a9ee053de7f0d7b07c2 Author: tdreszer Date: Fri May 23 23:43:41 2008 +0000 Added javascript option for checkbox and dropdown commit ba1eeea9632d83e56017a3720833c6d72a7102a6 Author: hiram Date: Fri May 23 23:39:40 2008 +0000 Update to wiki help files commit 08656adb86894366bdf79157b8c96bbd605ca912 Author: hiram Date: Fri May 23 23:34:31 2008 +0000 Fixup incorrect order of db and name in the delete comment commit ceb0ee3d9c99ddf2e450a269ea7e4ad6c3e2b67a Author: tdreszer Date: Fri May 23 23:26:42 2008 +0000 Added memSwapChar which I find very useful commit 38ed8cb3bbe2d51353c26207d03d2ccb1f573e93 Author: tdreszer Date: Fri May 23 23:26:12 2008 +0000 Added memSwapChar which I find very useful. commit 00741a256dfd67be5e65a5b3e4c171323589f56b Author: hiram Date: Fri May 23 23:19:41 2008 +0000 Fixed md5sum path name when it was a whole path name commit fe020f9874a890de9fec8ff16c0e782f6255470e Author: hiram Date: Fri May 23 23:07:19 2008 +0000 created liftover for caeRem2 to caeRem3 commit 197266124cd1aafacba07b85ce9fb9259be44bbf Author: hiram Date: Fri May 23 23:06:39 2008 +0000 Assembly done, in pushQ commit 48aaab6ca75b2fc259f46df12076663d07f07cfe Author: rhead Date: Fri May 23 23:02:56 2008 +0000 Small tweak (sequences --> sequence). commit e97e9937fb4990c1108a3836df4c017ec9aa869b Author: hiram Date: Fri May 23 23:02:18 2008 +0000 Fixup the bogus reference to mm8 commit 368196832b537f6c242e1d2b6414a3716e84a74f Author: rhead Date: Fri May 23 22:46:58 2008 +0000 Changed wording slightly to match trackDb/mrna.html. commit f4014c3992c6b13323aa46fffa3aaa678f49ddff Author: hiram Date: Fri May 23 22:37:37 2008 +0000 Adding caeRem3 commit 171f85106ec96f6e42fee4d4fdbdde7bd897f1c7 Author: hiram Date: Fri May 23 22:17:39 2008 +0000 Added caeRem3 - C. remanei commit ffda401af1437f8bd89e87d3b6fee43fa414baa4 Author: angie Date: Fri May 23 22:14:58 2008 +0000 Added #ifndef GBROWSE's around code not yet supported for standalone track-drawing lib. commit 098398b8bd7e6d12884932068b4a3fb7a7eb6b78 Author: angie Date: Fri May 23 22:10:26 2008 +0000 Added cgiResetState for standalone track-drawing lib. Added #ifndef's around code not yet supported for standalone. commit 7af2ce51e6b8fcc932276ef35976890a92cf26b7 Author: angie Date: Fri May 23 22:09:56 2008 +0000 Added cartNewEmpty for standalone track-drawing lib. Added #ifndef's around code not yet supported for standalone. commit 9adfaf154bdb8b2f880f0c09344dd474ca483db1 Author: angie Date: Fri May 23 22:09:05 2008 +0000 Moved a couple more global vars for standalone use. commit 93bd6412c7175c38aa35d57687f7747ef883eb1d Author: angie Date: Fri May 23 22:08:33 2008 +0000 Moved the standalone initialization and drawing code from gbrowseTest harness into its own file, oneTrack. commit 1d5db538e191d668b793ceddfe87d5ca445fdfb1 Author: markd Date: Fri May 23 21:49:01 2008 +0000 compute frame for gtf if its not in genePred commit 11d5cd7bc7879d657b2eb8955be0ccae588a0ab7 Author: angie Date: Fri May 23 21:48:29 2008 +0000 Cron path is now tiny -- use full path for hgsql. commit d2d4b6a7d159ba164a596adc96febd6cc98a3e42 Author: markd Date: Fri May 23 21:17:00 2008 +0000 removed keep option that was added for testing commit e52bcd491eff45bf0080c1056cef4fa1fb231ce6 Author: kuhn Date: Fri May 23 18:44:34 2008 +0000 fixed usage statement, added an all-important dollarsign to a variable in two places, added headers in final output file. thanks brooke! commit ece48cbffb5e23396be99fddde596b6f0bc8cad0 Author: hiram Date: Fri May 23 18:43:26 2008 +0000 Add the ctgPos2 definition, and the all_mrna and all_est definitions commit d89f3a4641ccd3d9c7f3fa0ec14e58b4a26bfbf4 Author: hiram Date: Fri May 23 18:40:00 2008 +0000 A copy from caeRem2 updated for caeRem3 commit 076bf2c15f2548c658fdda8e78145960b691f887 Author: hiram Date: Fri May 23 18:26:58 2008 +0000 some line spacing to look better commit 0cddff00cdfe306242b1b48c838da99cb2b9c224 Author: hiram Date: Fri May 23 18:19:32 2008 +0000 adding caeRem3 commit c965ed359cd362265ea7e7f2f9ddb92c4b97e9d8 Author: hiram Date: Fri May 23 18:19:17 2008 +0000 Updated to represent this assembly commit eedcaeca490b463ee298a2a17f8a8df87b88a337 Author: hiram Date: Fri May 23 18:01:54 2008 +0000 Initial files from makeGenomeDb.pl commit 2614927e4776d705777ace97dede1bcf83a93983 Author: hiram Date: Fri May 23 17:32:30 2008 +0000 Added caeRem3. commit b76d24e402066fd7261ca6aab5fd706381af74a0 Author: markd Date: Fri May 23 16:45:28 2008 +0000 fixed NULL dereference commit 66ba293a3fced9708f490850acfc4de83bf0cfce Author: galt Date: Fri May 23 15:00:08 2008 +0000 "Encode release log update" commit a675fb658a00673cff4216ce76d8e48d7d23a9d0 Author: galt Date: Fri May 23 15:00:04 2008 +0000 "Release log update" commit 975180f26590e7bc08f0416453f2e1dc17a158b5 Author: markd Date: Fri May 23 04:46:33 2008 +0000 fixed bad engrish commit d49a245afbcceb816e3f7cb9d898da15a8e20044 Author: hiram Date: Thu May 22 23:32:58 2008 +0000 Assembly loaded, RM and windowMasker done, waiting for simpleRepeats, elapsed time so far, 1 hour commit 1912a95042176879c172eb35232638dc4fee9a77 Author: larrym Date: Thu May 22 23:20:41 2008 +0000 return a value from toggleTrackGroupVisibility which can be used as return from onclick handler commit 5f32a32debec094ebdb01a03159601724d783f0c Author: rhead Date: Thu May 22 22:56:15 2008 +0000 Fixed broken link to UCSF Cancer Center. commit 15863cae1cdbb514043113d38774a37eb68708be Author: kuhn Date: Thu May 22 22:49:03 2008 +0000 oops. had to remove accidental copy commit 1bbcc1c008b945e72127a907e098fd84aef739c6 Author: kuhn Date: Thu May 22 22:47:55 2008 +0000 just moved two lines to alphabetize commit 7b5fc6feb8015f2501e4d25312aceff28c1ecc43 Author: hiram Date: Thu May 22 21:57:51 2008 +0000 should be close to complete commit d2fd0611c2712ce9a10215ed5eb71f7e8a3170a1 Author: larrym Date: Thu May 22 20:49:57 2008 +0000 fprint -> errAbort; improve jsStripJavascript commit 94a89f6807f5416dfd10abd7086aae68f8f69761 Author: tdreszer Date: Thu May 22 20:44:53 2008 +0000 Typo fixed commit dbb4f2c19c6d5c194191f95338d825528628c2ec Author: tdreszer Date: Thu May 22 20:39:45 2008 +0000 Turned off native and on xeno. commit 9edc53f8da42c2b3a3187743d546d64c7b8f555f Author: larrym Date: Thu May 22 19:12:44 2008 +0000 fix typo commit 65b2ea243689a450284c24ac98e7b1bbe78590b1 Author: markd Date: Thu May 22 16:18:10 2008 +0000 added transMap tracks commit 7ba6ccca4c1916b43b277be5de51350ef38fa590 Author: galt Date: Thu May 22 15:00:07 2008 +0000 "Encode release log update" commit 8da1ea00929ccfa1d45211f92547f7dffa993e18 Author: galt Date: Thu May 22 15:00:04 2008 +0000 "Release log update" commit 9b17f6587ef54c4e2e5c347dd80950fd9703c324 Author: markd Date: Thu May 22 07:34:29 2008 +0000 added org change ignore commit 83dd722722dc11877a115af2b4345d92322193fb Author: rhead Date: Thu May 22 00:12:59 2008 +0000 Changed links to www.ncbi.nih.gov to www.ncbi.nlm.nih.gov (which is where they have been getting redirected to, anyway.) commit 1387c5b081edb5c67890c356bd68b0de6b7f0d6c Author: rhead Date: Wed May 21 23:52:00 2008 +0000 Changed links to www.ncbi.nih.gov to www.ncbi.nlm.nih.gov (which is where they have been getting redirected to, anyway.) commit 944600dbb5af897c6c0c17a6753a336fdd33d73f Author: markd Date: Wed May 21 23:41:02 2008 +0000 don't generate bogus value on invalid track visibility string commit 5460dfd3a0e58b52318271e797730df35c242bec Author: pauline Date: Wed May 21 23:15:24 2008 +0000 Fixed scaling on tree. commit fd5e1b592fc624aae2a04f72191626199dce1fc9 Author: fanhsu Date: Wed May 21 23:11:11 2008 +0000 Created for VAX003. commit 8b255ea79451da45331633917185eaa1d3f4f9a9 Author: fanhsu Date: Wed May 21 22:55:45 2008 +0000 Created for VAX003. commit 67bc09712b393ab661297e26b9124586e8afb429 Author: fanhsu Date: Wed May 21 22:50:12 2008 +0000 Created for VAX003. commit 5d9eb6bdb76dba76ba4f4a5cd46fcf4500ad28f3 Author: galt Date: Wed May 21 21:59:38 2008 +0000 Added the ability to specify cpu and ram usage of jobs commit 9c9dd72e491683802da468135ecd3d89590f9fe5 Author: markd Date: Wed May 21 20:32:19 2008 +0000 added todo- commit 124b8f4e5edac5570f1fa8f81386cfbc19381629 Author: fanhsu Date: Wed May 21 20:25:58 2008 +0000 Created hivVax003Vax004.txt. commit 07be07184210f06edf834f517be7a26a17069e82 Author: larrym Date: Wed May 21 19:52:48 2008 +0000 downloads creation steps commit 62ac407c46ce33afb84a40cace958ad2a8145e93 Author: larrym Date: Wed May 21 19:29:44 2008 +0000 add use warnings and use File::Basename for file parsing commit 0745691a44ad3a45039683f1fe0bd04e9686055d Author: pauline Date: Wed May 21 19:19:15 2008 +0000 Fixed typos. commit 169095a1337b7629933c08c87f652990dfe29f20 Author: larrym Date: Wed May 21 18:53:45 2008 +0000 handle custom bedGraphs in bedGraphLoadItems commit 744d8750cae2f7142fdeeea0d292cc8228908baf Author: larrym Date: Wed May 21 18:48:44 2008 +0000 print out same info for custom bedGraphs as normal bedGraphs commit 2e26a6e16e4db17fa317d18ad5f42dc768a1b1cb Author: hiram Date: Wed May 21 18:29:04 2008 +0000 Only check for NULL pointer. empty string is OK. commit 456ac41724cc90dd56bcd930bb5ace67751845d0 Author: hiram Date: Wed May 21 17:49:39 2008 +0000 Properly encode all printouts of short and longLabel commit 11bf7f7708d197974d2cd5299449ed730a5b9da2 Author: hiram Date: Wed May 21 17:46:40 2008 +0000 watch out for empty strings in htmlEncode() commit 20cc858c224cfd7b04baff0e487c922b7fa8bbfa Author: markd Date: Wed May 21 17:18:07 2008 +0000 removed old trackDb entries commit b281f0f30a74e73a2f742add510beae68b031d4f Author: angie Date: Wed May 21 16:58:39 2008 +0000 More rearrangement of code to make a lib subset for GBrowse plugins. commit 743f03ef68bdaf8c384d5c383d82fceede993514 Author: angie Date: Wed May 21 16:55:33 2008 +0000 Test harness for the subset of code that is libified for use in GBrowse plugins. commit 0b15d129137f9505e3a3ba999108652cb4895b4b Author: angie Date: Wed May 21 16:43:47 2008 +0000 Added another duplicated .as to %autoSqlIgnore. commit 28e65a317dde663d99f05ae3c9ba661825cbec1d Author: galt Date: Wed May 21 15:00:06 2008 +0000 "Encode release log update" commit 06ec0b5d09903dc22fe2a9d4f7c02481993dbc0b Author: galt Date: Wed May 21 15:00:04 2008 +0000 "Release log update" commit ce2dbf4edcb95adbcd0a372c7f613afd01af75e4 Author: galt Date: Wed May 21 09:30:28 2008 +0000 removing debug, restoring regular settings commit 43830116918f98036dfddc0848c445d01e8a3906 Author: markd Date: Wed May 21 06:22:16 2008 +0000 added update target commit 9cf23e4e0655656995cd41ff542941520062e953 Author: markd Date: Wed May 21 06:10:54 2008 +0000 use super tracks for transMap commit f9e49348b0bb3fcd6fad99ddda703fc9c2d1e801 Author: galt Date: Wed May 21 03:17:04 2008 +0000 added warning that the .as output file jobResult.c had been modified after generation by autoSql commit 8d5a74583268a1a15ef0b03cc15bc7c77cbaa39a Author: markd Date: Wed May 21 00:02:06 2008 +0000 remove use of guessed read for ESTs that can't be oriented by splice sites commit 2ae4c436c60296ef2754be9229e212f1439bf3c1 Author: markd Date: Tue May 20 23:49:23 2008 +0000 removed desciption of using guested read direction for orienting EST commit dec78a159615ed3869c705670d5e9edd9e2d7ba9 Author: larrym Date: Tue May 20 22:22:00 2008 +0000 support custom bedGraphs commit 88a08e481f68926eba52a701e7027129e425cbb8 Author: larrym Date: Tue May 20 21:11:15 2008 +0000 free => freeMem commit b7f439dba2c869a4822889b8cc1db285d201b16f Author: larrym Date: Tue May 20 20:42:18 2008 +0000 add entry for bedGraph in newCustomTrack commit a2c9d1470f3247b320127dfe9fd39a01ce41c7ac Author: larrym Date: Tue May 20 20:22:48 2008 +0000 add links to bedgraph.html commit d5d51b940a764173478acf9cf45eec48a69a7769 Author: larrym Date: Tue May 20 20:20:59 2008 +0000 remove javascript from user html commit 58063e74639be714784f59d9544c598dd0309144 Author: larrym Date: Tue May 20 20:20:33 2008 +0000 support custom bedGraphs; remove javascript from user supplied tableName, shortLabel and longLabel commit 97ffa1250b3b731f0f567000480c9e1d542822dc Author: larrym Date: Tue May 20 19:41:02 2008 +0000 remove a fprintf commit 15a23e12447cb5ed19b40891353210fe3f9ce00d Author: rhead Date: Tue May 20 19:22:36 2008 +0000 Changed link to NCBI from www.ncbi.nih.gov to www.ncbi.nlm.nih.gov (the first link gets redirected). commit 4b309e5783b62eb14ca7d350ec4d3d0fa9ac5b55 Author: angie Date: Tue May 20 18:34:05 2008 +0000 Adding support for different subtracks having different limited visibilities. For example, a composite track and most of its subtracks could be pack, with some subtracks limited to dense because of pileups. Also removing unnecessary estimateVisibility. commit 9196144f4e2968174d70e2c465e4db49ad02e694 Author: angie Date: Tue May 20 18:34:03 2008 +0000 Adding support for different subtracks having different limited visibilities. For example, a composite track and most of its subtracks could be pack, with some subtracks limited to dense because of pileups. commit 7c70d3cb017e3d197ab2058d158870787ca95c2c Author: angie Date: Tue May 20 18:23:07 2008 +0000 Removing unnecessary estimateVisibility so we don't have to maintain it in parallel with limitVisibility. commit 9d2ece42b4ff27a59a3b2509215f92231785ee9f Author: fanhsu Date: Tue May 20 16:49:24 2008 +0000 Changed effective MAX_CONTROL_COLUMNS from 5 to 4 for GSID Browser. commit 2bcce850cf0b80d12277b0853c9bf0fd588a4b94 Author: larrym Date: Tue May 20 16:43:36 2008 +0000 add jsStripJavascript commit b70d4ef5b426dd2f5d531c9fe7c6b16f58fe7547 Author: larrym Date: Tue May 20 16:42:22 2008 +0000 Parse builds/versions-list.html etc. and automatically create versions.xml RSS feed commit 1649f53baa9ec96126491a05a171cefac81f0558 Author: fanhsu Date: Tue May 20 16:39:32 2008 +0000 Changed html heading for GSID. commit 438654c11b968b0190d06c0e9ea35faf0ad3cacf Author: galt Date: Tue May 20 15:00:11 2008 +0000 "Encode release log update" commit 3be680a63f8adcde3a9676e296173a8dc2a7ac0e Author: galt Date: Tue May 20 15:00:05 2008 +0000 "Release log update" commit 9323f2f40abae2b94e9976b98579aaa6f3f05511 Author: markd Date: Tue May 20 04:33:02 2008 +0000 fixed invalid call to slReverse; don't know how this ever worked commit 380801a9d3bbf76828e67011847bea6417d736f5 Author: galt Date: Mon May 19 23:14:50 2008 +0000 Remove machine sends feedback; fixed parasol add machine bug commit 18dd6f822041c25b0103fb1f515eee8c3eae0ca6 Author: pauline Date: Mon May 19 22:25:20 2008 +0000 Fixed typo in species name. commit 892e0ef7811913f4903b6a81b49b7740f415e934 Author: markd Date: Mon May 19 22:04:13 2008 +0000 ensure js parent dir exists before rsync commit 883612eec397d4866d679a0e12e92075c6b855cf Author: braney Date: Mon May 19 22:03:00 2008 +0000 fix up the routine that outputs untranslated exons commit 16969e5d1585519829fa24761e100d7b543bccfd Author: braney Date: Mon May 19 21:56:23 2008 +0000 add textBox and a tweak to fill ellipse commit acaed194c7bee65f5a85f92bf88a0d021e3d9813 Author: galt Date: Mon May 19 21:56:03 2008 +0000 direct users towards .2bit instead of .nib commit 51952fded3943833c48bf6708f1968fec6025702 Author: braney Date: Mon May 19 21:55:46 2008 +0000 add textBox and a few comments commit e3aada05af212c7000225861bd172e318c3fef4f Author: pauline Date: Mon May 19 21:49:01 2008 +0000 Fixed species order, removed irrelevant comment about 'none' line, and removed medaka as it is not in the multiz alignment. commit 4c9458d49b42e2ffb7cd0e087aef0e35cab959bd Author: larrym Date: Mon May 19 21:40:47 2008 +0000 remove cvsup from user target rules commit 4ce5becfe5f509547a5decdd982363a1aafd9ad7 Author: angie Date: Mon May 19 19:08:18 2008 +0000 Regenerated multiz15way/up*.maf.gz download files after user found that NM_[0-9]{9} IDs were truncated. commit 044287d4ec8f420dec119e9395fac5ba0427c808 Author: braney Date: Mon May 19 19:05:38 2008 +0000 add textBox (why are there two checked-in files ??) commit 0c38dd358b7450574583bd3e9b6014e0b9c878b6 Author: larrym Date: Mon May 19 18:34:17 2008 +0000 htmlEncode user input to in genomePos to fix XSS attack reported by David Hoover commit 6ad6ae7c66b9117324eef82f772223c7bb71554e Author: markd Date: Mon May 19 18:16:12 2008 +0000 added code support for transMap tracks commit 63da86dc8e4c05551dd895ad2bfd3a7529db1132 Author: markd Date: Mon May 19 18:14:36 2008 +0000 removed unneeded cast commit 87114b10bc92d3a1ebe7d101a67dd020738bd618 Author: angie Date: Mon May 19 16:35:38 2008 +0000 Libification support for sharing code with GBrowse plugins: moved all track method code (except for dynamic tracks) from hgTracks.c to the new simpleTracks.c. Added some #ifndef GBROWSE around spots of code that can't/won't be ported. commit 46917b6683d60ebf22ffdbd7d8b533f5cba3c196 Author: galt Date: Mon May 19 15:00:10 2008 +0000 "Encode release log update" commit e18f8d4c0726cc407c953f810ac52cb573370e8c Author: galt Date: Mon May 19 15:00:05 2008 +0000 "Release log update" commit df841cecf99fad894acc6872c2bab50144eaee8f Author: galt Date: Sun May 18 15:00:06 2008 +0000 "Encode release log update" commit 4bbb74bb570f0ed4e5029100eeb2cc8ac1da0c78 Author: galt Date: Sun May 18 15:00:04 2008 +0000 "Release log update" commit 2007151aa399cac26a30fbdaaee03477e7483e56 Author: markd Date: Sun May 18 04:11:54 2008 +0000 added identity and aligned functions commit b35824659cecc2e473ebbc27a8638b8acfce25f6 Author: hiram Date: Sun May 18 00:43:34 2008 +0000 Fixup compile error for Mac uninitalized variable. commit 5917921d765652f38a0b6e29c7753a00366b8f34 Author: hiram Date: Sun May 18 00:38:06 2008 +0000 Eliminate a Warning as Error on the Mac for uninitialized variables commit 00df53076df6f78ab05a0a18005cb2785530a07d Author: galt Date: Sat May 17 15:00:06 2008 +0000 "Encode release log update" commit 584e4eda42b5101ab0f19b2a5162c4cf58168281 Author: galt Date: Sat May 17 15:00:04 2008 +0000 "Release log update" commit 1753489f9007b25785ed882443613db57a9ac36d Author: galt Date: Sat May 17 05:54:36 2008 +0000 checking in 12.02 with proper nodes and resources commit 6cae03cc37361ab1fa7fb733364e25272844fa93 Author: hartera Date: Sat May 17 01:12:55 2008 +0000 Descripiton for the mouse Vega genes composite track consisting of a protein-coding genes subtrack and a pseudogenes and immunoglobulin segments subtrack. commit 0fbc0c76775244962469e3d5aeccddf11a5109eb Author: hartera Date: Sat May 17 01:09:20 2008 +0000 Corrected URL for human genome annotation page at Vega. commit 767c87095b8716d38adef1cce69eb2d2e6fdc1d7 Author: hartera Date: Sat May 17 01:02:49 2008 +0000 Changed the url for the vegaGeneComposite track to point to Vega transcript reports. Added a url label. commit 981ad410d4c2293b0678338069b68085fcd67c66 Author: hartera Date: Sat May 17 01:01:03 2008 +0000 Added links to the human genoma annotatin project summary on the Vega website and added a link to Vega acknowledgements including publications. Other minor edits. commit d1f241ae0bffe7757620eb95b574698a135792e6 Author: hartera Date: Sat May 17 00:38:52 2008 +0000 Description for Vega gene set composite track consisting of a protein-coding genes subtrack and a pseudogenes and immunoglobulin segments subtrack. commit 6b60c91a508e96752672353dd78817ee81b4ef8e Author: larrym Date: Fri May 16 23:32:55 2008 +0000 add info about DOCUMENTROOT variable commit a76bd9f1ec2f2f6d6b5ae6c0039d70ed61b5f104 Author: pauline Date: Fri May 16 22:35:36 2008 +0000 Fixed type-o. commit 4194146d6a141a1d4bbde7dee004648c4b5fa1a0 Author: kuhn Date: Fri May 16 22:00:55 2008 +0000 allowTraffic.csh commit 02b1edc5f15a66c1aa128a1cce24354e11367bd3 Author: kuhn Date: Fri May 16 21:16:38 2008 +0000 tweaks commit 2cc2d486daa6550b9e369d4bddfcae1a07d1f10a Author: hiram Date: Fri May 16 20:26:05 2008 +0000 Now clicking straight through to the wiki page from the hgTracks display commit 6bd52430e6b86210c89ebc4ddb619b98d024b49d Author: angie Date: Fri May 16 19:57:39 2008 +0000 Added perf so hgTracksRandom will be included in top-level make (thx Larry). commit d3a216ad178803f017e8f4e6e2dac09c93c64f33 Author: rhead Date: Fri May 16 19:42:44 2008 +0000 Fixed broken link to Nature paper. commit 0c2c219519667f6c1b82851b9e464ff28ec43cd3 Author: hiram Date: Fri May 16 19:04:40 2008 +0000 More simple configuration check commit 638523507004dbf8234a1e0a73e641b41a3957d0 Author: angie Date: Fri May 16 17:38:36 2008 +0000 dgv: name and coord tweak. commit a467094868a4ddb9ef63c86fc95def31968cba36 Author: angie Date: Fri May 16 17:37:17 2008 +0000 Added dgv to tablesIgnored $hg. commit 1bb8702226e525411843b1a543799aedc67075fa Author: larrym Date: Fri May 16 17:15:36 2008 +0000 fix typo commit 46c35665a5764bb7b2265ac8a66119676deffeed Author: galt Date: Fri May 16 15:00:05 2008 +0000 "Encode release log update" commit 03cae060ba397405aa5189c4f1e66c851bda918e Author: galt Date: Fri May 16 15:00:03 2008 +0000 "Release log update" commit 61721f9b638d775dfa5abfb9b6ecc45fa60565ea Author: larrym Date: Fri May 16 01:34:20 2008 +0000 Get rid of trailing slash in hCgiRoot to be consistent with hDocumentRoot commit 8a5814c1761158075a2e223045a91047d60f2da3 Author: rhead Date: Fri May 16 00:58:00 2008 +0000 Changed description of dense display for native ESTs. In dense display mode, darker shading indicates a larger number of aligned ESTs. commit b113e1581d19de9a7c42699987fb2668e5bfb106 Author: larrym Date: Fri May 16 00:31:56 2008 +0000 remove hartera and use browser-qa for mails commit 1cd839a8561dcfb3b35ca990bef07d2729254344 Author: pauline Date: Fri May 16 00:31:05 2008 +0000 Fixed type-os commit 8d2a8c546192b5a1dad8448cb529ebc1035a21cb Author: hiram Date: Fri May 16 00:11:20 2008 +0000 Adding vega genes latest version commit eae40b507bb468a7575f473e8add664b5675a9b0 Author: larrym Date: Fri May 16 00:09:13 2008 +0000 change emails to remove hartera and use browser-qa alias; remove doRobots.csh step (now done manually) commit ff56d687b80b2faf4df977b8901354aa3d25ff32 Author: hiram Date: Fri May 16 00:06:57 2008 +0000 Also bed 8 and 9 custom tracks scoreFilter honoring commit 10275ff9ffcfd913fc53de95514cba9d787f482b Author: hiram Date: Fri May 16 00:04:02 2008 +0000 Properly filter bed 12 custom tracks commit b8feaed4c0a54f9f0bf1dcf8905c53dde187663e Author: rhead Date: Thu May 15 23:56:36 2008 +0000 Fixed broken link to assembly release notes. commit fa1870aaed7fe20ed872e039d2c53f134cbdec85 Author: hiram Date: Thu May 15 23:42:44 2008 +0000 Proper list of chroms for these vegaGenes commit c6bd0e579701394c749179133d1945ec3a6d250c Author: hiram Date: Thu May 15 23:39:18 2008 +0000 Adding vega gene composite track to Mm9 commit f7afcaad9bcd3fa06ebaa937cafc2895895c5947 Author: galt Date: Thu May 15 23:31:44 2008 +0000 fix typo in comment commit 07b8fd3b7c14c8bf29f1faf7444c1c1d79cf3b8a Author: hiram Date: Thu May 15 23:11:56 2008 +0000 Vega genes are now a composite track commit c9ee1e2bcd395a0045bed3a0386df2a1636ecc18 Author: hiram Date: Thu May 15 23:07:16 2008 +0000 cgiEncode the URL link for the track name commit dc1460fd65e0b5470caf5757a9b230ff4482d744 Author: larrym Date: Thu May 15 23:02:52 2008 +0000 initial checkin (using code moved from utils.js) commit b183cc05eb09fc7943b3ce993fbd2603d355a8e5 Author: larrym Date: Thu May 15 21:23:30 2008 +0000 add DOCUMENTROOT variable to support js rsync commit f5a6e7dbd9876649e64d83b6e58dbbd2ccf695f0 Author: larrym Date: Thu May 15 21:22:26 2008 +0000 modify to rsync files to DOCUMENTROOT; support install target commit 105b8ef977b909680966fc82a7d82d0c4a33a182 Author: larrym Date: Thu May 15 21:20:06 2008 +0000 modify jsIncludeFile to use yet another location for the js files (in htdocs/js) commit 077aa6a5b3f916823c9c7c1b33fd526cd14e2d56 Author: hiram Date: Thu May 15 20:03:56 2008 +0000 do not allow bare make entries commit d98d385b4ac071e8bcc7325dae0881eab1292b22 Author: larrym Date: Thu May 15 19:13:00 2008 +0000 remove comments after dummy targets to avoid confusing people commit c8cfcfc0c65aeded4c3e4bd192981c40548a671f Author: hiram Date: Thu May 15 18:18:50 2008 +0000 ran liftOver to caePb2 commit 7e05d82dbe04e0febdbeed0ecf9a8277cd74c34b Author: hiram Date: Thu May 15 18:15:53 2008 +0000 Added new vega genes commit 9cfea1a51925fd71e70fb88be5bab66e2873c840 Author: tdreszer Date: Thu May 15 17:38:18 2008 +0000 Working through multiz commit b92a22f0974c70580bb869892cd7229e0dc32f5f Author: larrym Date: Thu May 15 16:53:32 2008 +0000 add dummy clean, compile and install rules commit a07c935ca12902ca4ae2b732d8e10c07735ad734 Author: hiram Date: Thu May 15 16:32:29 2008 +0000 Was making an error marking the ends of chromosomes as gaps. Don't do that. commit ce9fd3412a81c3815c2a120c7a643cacc58c1b1e Author: galt Date: Thu May 15 15:00:12 2008 +0000 "Encode release log update" commit 1e7be6c02eb476b048215cd1a32e4b2f39d21409 Author: galt Date: Thu May 15 15:00:05 2008 +0000 "Release log update" commit a433dc16b8b2d38aeac2051390d71c702fd666b2 Author: fanhsu Date: Thu May 15 05:49:44 2008 +0000 Added a sentence called for by Melissa. commit d396cf73ce78e6a48b6e1fcfc89c40b416a51f24 Author: fanhsu Date: Thu May 15 05:48:12 2008 +0000 Added a sentence by Melissa. commit 6e37ace4630ea3ad6475aa744726d60ec1d35080 Author: fanhsu Date: Thu May 15 05:43:55 2008 +0000 Added a sentence called for my Melissa. commit bea5fa399792089e94bceb880ef5b6215b02a432 Author: galt Date: Thu May 15 00:42:27 2008 +0000 adding parasol version to all of parasol as requested by Jorge commit 66a193765ec6febaf4d56466c096898e59c82cef Author: larrym Date: Thu May 15 00:22:16 2008 +0000 add js BROWSER_BINS commit 17c04ed5ed10646e036cac28ded40703b17555a2 Author: hiram Date: Thu May 15 00:03:13 2008 +0000 Fixup display of vega genes when there is no info table commit 749ac6aa7946a7622ac0b939c388b732ee03103f Author: larrym Date: Wed May 14 23:57:18 2008 +0000 initial checkin commit e1e8e2b3ddbdeec75bb99b93a1896eb611db79ef Author: galt Date: Wed May 14 23:38:17 2008 +0000 optimize flushResults, just flush for the batch we are interested in commit 453337c4965b3ccddfad60ab778aa43846a99843 Author: hiram Date: Wed May 14 23:29:09 2008 +0000 fragments are draft sequence type D commit b3b1c47e8d1282b9e4ccf9ec26efe68b797740de Author: galt Date: Wed May 14 23:22:47 2008 +0000 adding batch->queuedCount so that dlCount() on big batch->jobQueue is avoided commit d956b2d4847c5e25b497f3aab512181ce38f3638 Author: galt Date: Wed May 14 22:55:10 2008 +0000 starting totalQueuedJobs global var, also cleaned up the findLucky a little commit cc3a7f2d4b82db260bafe44d630b071adf8ce5f1 Author: aamp Date: Wed May 14 22:42:49 2008 +0000 Haha a third demo. commit 8c5a5adfac3a2879ca71e451b797786955503f08 Author: aamp Date: Wed May 14 22:42:02 2008 +0000 Another demo. commit 31de5bce31b833351ab5e4d61836a40abf644214 Author: aamp Date: Wed May 14 22:41:28 2008 +0000 Branch tag move demo commit b69e2702fe063dc2bb295869ca2b6a96bfae0c46 Author: galt Date: Wed May 14 22:41:00 2008 +0000 actually done by Jim commit e351f4e50e21bc3d4e9191c2f3db5d1413840303 Author: galt Date: Wed May 14 21:03:24 2008 +0000 better name commit 2de6c0e779f34aec1c8bc23e1364bf17c71efc76 Author: larrym Date: Wed May 14 18:51:07 2008 +0000 send mail browser-qa to report non-fatal html missing errors commit bef38d888bb03b26ac8c00af1ac77f8265903b66 Author: galt Date: Wed May 14 17:56:32 2008 +0000 more code-review tidbits commit 1869999b84a073b97e2f3a1e216428c3401414fa Author: aamp Date: Wed May 14 17:40:20 2008 +0000 Lowered the ratioMax on the affy exon column to make it brighter overall. commit 387df570ff9090ae0fbaa03310ec94364e67e31a Author: galt Date: Wed May 14 15:00:09 2008 +0000 "Encode release log update" commit 69c9f3c06fe3009a8074e242ff9eda6e0a20192d Author: galt Date: Wed May 14 15:00:04 2008 +0000 "Release log update" commit 3ef59458e39c2a4747f8838173e53d76a5af4946 Author: galt Date: Wed May 14 11:05:01 2008 +0000 changes after code-review commit 7dabe14805009460f491120f9e82a4d9917eeb88 Author: galt Date: Wed May 14 08:31:54 2008 +0000 code-review improvement commit c60b83ef34cf3da321a2d964c20ce942ea55fafe Author: galt Date: Wed May 14 07:29:50 2008 +0000 fix old minor bug in balancer commit 00f35b42ea1476a18b27b7a3d84c22c69f933b5d Author: markd Date: Wed May 14 07:19:22 2008 +0000 add -uniq flag to drop dups commit 28b0048dc6a976bf464e0f4c4dbf5fcd18ee29ba Author: aamp Date: Wed May 14 05:08:28 2008 +0000 Added Agilent CGH probe build instructions. commit b86100433757aaea0aaab0c580866c827af6a7a1 Author: pauline Date: Wed May 14 01:04:41 2008 +0000 Fixed type-o. commit cf25b645204ad7b9f14956470a252a743f39178c Author: markd Date: Wed May 14 01:02:18 2008 +0000 fixed reverse display of dense ESTs commit 1f190fc3176b2e17407ffdbe05f1e6745a7e6538 Author: galt Date: Wed May 14 00:46:50 2008 +0000 little bit better commit dc10c0815e1be582dc4c8dafdc61e0d32b9691db Author: kuhn Date: Wed May 14 00:15:52 2008 +0000 added some checking and warning if files are missing commit ac42cad67f2088a93eda2dd20d6b415f6b94b650 Author: hiram Date: Tue May 13 23:59:40 2008 +0000 Adding caePb2 to the caePb list commit d6206e253fb584e7c588ddccb0de8e9fbf442b85 Author: galt Date: Tue May 13 23:58:30 2008 +0000 making hash large enough is important for speed - for million-job queues, this speedup is a factor of 20 for processing the pstat list against the sub hash lookups commit 08d17c255457a1f800fe6cdf98a87d1a4c12cc76 Author: hiram Date: Tue May 13 23:52:27 2008 +0000 add missing html page commit 18cc5b85f101a7f63203b0ae0627fdccc9a846f0 Author: hiram Date: Tue May 13 23:50:12 2008 +0000 C. brenneri built in one day commit 378a5d3615b8295db5023caf362a065445133ebd Author: hiram Date: Tue May 13 23:39:48 2008 +0000 Added caePb2 - C. brenneri commit 45dabadde8dd3929a08df992c49dde6cbe0ee8ca Author: rhead Date: Tue May 13 23:16:36 2008 +0000 Tweaked link to LBME again. commit 4f71a99c674fbc70a1378908cd407979af29e818 Author: aamp Date: Tue May 13 23:14:18 2008 +0000 Added Agilent CGH probes track. commit 83cb970207922e76c4038dade5e6cef3370e772e Author: kuhn Date: Tue May 13 22:02:09 2008 +0000 added to usage statement commit 93fe8cb536ad2fc64277173f7f5e36447b67ae7b Author: kuhn Date: Tue May 13 21:55:24 2008 +0000 utility for finding contigs lacking alignment in all of the nets commit b11e2f2ac2fe987ad6fe693d0a78398489278ae3 Author: galt Date: Tue May 13 21:41:42 2008 +0000 making faster pstat with multiple lines per packet and sending only needed info for queued jobs commit d92a74dc2247a3457b330e2629fc2e8cddd48312 Author: hiram Date: Tue May 13 21:03:34 2008 +0000 Proper name on the gold track "scaffolds" commit ba4a0456af6153cdda86d86c45a2d8c7c69ca9f1 Author: hiram Date: Tue May 13 20:41:18 2008 +0000 Adding caePb2 commit cc6d0acb9db85fd5bd6118e673fe486a48536044 Author: donnak Date: Tue May 13 20:40:53 2008 +0000 Fixed typo. commit cfb7520a249b9eebe642dac09557c69fb10171d4 Author: fanhsu Date: Tue May 13 18:43:33 2008 +0000 Added vax003 track. commit 34dac673ceba2dc6a89e9bc51f16edf3ab1c69da Author: hiram Date: Tue May 13 18:06:06 2008 +0000 fix a broken sentence commit f281486223d8c451cb194674e25f3a0c6e98a231 Author: hiram Date: Tue May 13 17:28:14 2008 +0000 Adding ctgPos2 and updated description page commit 060f6beddcde5f9db47c50605dd0ff35d3e94688 Author: hiram Date: Tue May 13 17:20:58 2008 +0000 Updated to represent current assembly commit 3e63b3341f8ebcec283e39e8239cac9d85d91dba Author: fanhsu Date: Tue May 13 17:08:00 2008 +0000 Added vax003 track. commit 807e7b82fd437f242c6903d42768c945b0ed2621 Author: hiram Date: Tue May 13 16:45:30 2008 +0000 Adding caePb2 commit 5fadf0953d9a1db967f39bb239ef462596d6427a Author: hiram Date: Tue May 13 16:44:58 2008 +0000 Initial files directly from makeGenomeDb.pl commit 382f2bfb6224210aad25446489ca10d3c6118f82 Author: larrym Date: Tue May 13 16:30:30 2008 +0000 "New version number v182" commit ff27d6123c5f4a7108b8d05219d786fa952a905c Author: fanhsu Date: Tue May 13 16:26:09 2008 +0000 Initial check in for hivmn2. commit 7aa2dcaae833ca7d7c3717a939130bcd980d2626 Author: galt Date: Tue May 13 15:00:23 2008 +0000 "Encode release log update" commit ab6e935b8dd6205c0e91dfaa64a1e7389fd184db Author: galt Date: Tue May 13 15:00:16 2008 +0000 "Release log update" commit 1f5a1a06473aedbdb7defce9bf0c78d69c9eaa73 Author: galt Date: Tue May 13 07:41:00 2008 +0000 adding timing info to para via -verbose=2 commit 68fc7b4ff98a24cfd77178e9b6fb1d6fd0eddf28 Author: jsanborn Date: Tue May 13 01:49:04 2008 +0000 Adding Johnson & Johnson data commit 581d48ea332e2bcb5ccd476c45cde81517f571f6 Author: fanhsu Date: Mon May 12 22:33:05 2008 +0000 Added "indelQueryInsert on". commit bc0537b235aaccddf247a72c90969948e8b4505a Author: fanhsu Date: Mon May 12 22:31:10 2008 +0000 Added "indelQueryInsert on" commit c2aa7f62c50c8a92239ef198b82bc4cfd5ba90e4 Author: angie Date: Mon May 12 22:27:25 2008 +0000 Updated dgv url format -- I truncated the prefix from the names at David's request, so add it back here. commit 80d3c044411042de1a3dfa43c3f1ce495a641e27 Author: larrym Date: Mon May 12 22:11:39 2008 +0000 fix typo commit c72c937db37eddc2137df097c695ec3899f55b62 Author: larrym Date: Mon May 12 22:09:15 2008 +0000 equCab2 blastz commit 286040ca37d3e053642860a609d04a642bda23d6 Author: larrym Date: Mon May 12 21:33:17 2008 +0000 move hgTracks specific code to hgTracks.js commit 9c6ddc59b366670cc59d86f1ba6c0477ae7ef799 Author: larrym Date: Mon May 12 20:59:27 2008 +0000 finish phastCons commit 058c0cdc1711a4fec79e18d1b75a84d6b65d107f Author: hiram Date: Mon May 12 20:54:37 2008 +0000 Do not include the protein link from the wiki text back to the protein browser commit 6f4d098bc4b3707742ef080ad151c73c4fc60af6 Author: hiram Date: Mon May 12 20:53:00 2008 +0000 Displaying the wiki text in an iframe commit acba468d7a32fc00d9b67995556e32153d12bae4 Author: hiram Date: Mon May 12 20:52:35 2008 +0000 Tweak the comments output for an hgc click on a wiki track item and properly URL link to ucsc gene id commit 3d550f7d5a2db8a44436e2ba77bb67211d866bef Author: hiram Date: Mon May 12 20:34:16 2008 +0000 Fixup description of types of components commit fcc548e45e2c2e820c308c462ba2ff1f48eda3e4 Author: pauline Date: Mon May 12 18:36:17 2008 +0000 Fixed grammar. commit 11cff7afbbb5148216a383b99b1e7dd0d4c1534b Author: rhead Date: Mon May 12 18:18:08 2008 +0000 Added a note about overlap-by-one error in phastConsElements7way data. commit 01b2d3e47491717c26f4bcdac98c0d98e7b280a7 Author: galt Date: Mon May 12 15:00:05 2008 +0000 "Encode release log update" commit 5dd3cd94c3cd27e7192dd528927334096f0fbf47 Author: galt Date: Mon May 12 15:00:04 2008 +0000 "Release log update" commit 4fc0a336023d2e10d56e627b70d9c1727b703321 Author: fanhsu Date: Mon May 12 01:08:01 2008 +0000 Turned on dnaSeqs and aaSeqs cols. commit 6f0442a35c82f46fa07202e7c8b84e3aeb95b2c5 Author: markd Date: Sun May 11 20:31:14 2008 +0000 added option to drop unique-ifying suffix commit 837bcd8e91fd06678c018c728553f98c5fc5cc98 Author: galt Date: Sun May 11 15:00:06 2008 +0000 "Encode release log update" commit 6422689edba1b868e0f66d29b3e35323fec28bf1 Author: galt Date: Sun May 11 15:00:05 2008 +0000 "Release log update" commit e638888426a4f8b866c1226a2427d351b196eb5b Author: galt Date: Sat May 10 15:00:15 2008 +0000 "Encode release log update" commit 70362267b7da7f9a949f1341a24d50a7315173c9 Author: galt Date: Sat May 10 15:00:13 2008 +0000 "Release log update" commit 4c511c981132c2aa2095e82f6104be7d76abef8d Author: galt Date: Sat May 10 00:12:40 2008 +0000 have to read the bookmark at startup commit 33c62591695b3d3e96bb6427c048deff20fe3d18 Author: hiram Date: Sat May 10 00:12:35 2008 +0000 Add business about the gap construction commit 2aca0f01debce06bb6d861f93e603e8f7662b2a5 Author: markd Date: Sat May 10 00:07:44 2008 +0000 reloaded genbank commit 1cc5c20f36baf0206b3843b058cf5bbaf1e65242 Author: hiram Date: Sat May 10 00:06:46 2008 +0000 Add the fragment description commit f687a29b9233facc75d31600a1936098994f75ef Author: pauline Date: Fri May 9 23:37:59 2008 +0000 Edited text for brevity. -thanks Brooke commit 71c6378758e9501153ddd3fb9a7cf2663f761a66 Author: markd Date: Fri May 9 23:36:11 2008 +0000 only load non-coding for hg18 for now commit 8eb7bc2a8c7b0b2e4c0801f158ba24e6c3577a9e Author: angie Date: Fri May 9 23:34:37 2008 +0000 README.txt reference-formatting corrections from Brooke. commit 031db9df7049567b0b7bae30ef8ed3877b15fc60 Author: angie Date: Fri May 9 23:25:52 2008 +0000 Bugfix: forgot to add hgsid in link to hgTrackUi. commit 620e1b49e0368e1998b16a7971b57eb09ff92ffb Author: pauline Date: Fri May 9 23:01:57 2008 +0000 Added trackDb.ra entry to correct chain matrix. commit e79b236a5b8a4ba9d010845e905554ff95257145 Author: galt Date: Fri May 9 22:52:54 2008 +0000 Adjustments to handle http code 300 thru 304 and 307 redirects commit f87c7e2a2d93b2aebcd55b27c87e435a6a3bb43d Author: pauline Date: Fri May 9 22:31:33 2008 +0000 Added cavPor3 gold to tables ignored. commit a4341b7ccfe8960d3d4492d205e1644bbb04c202 Author: tdreszer Date: Fri May 9 21:38:13 2008 +0000 Added Broad Chromatin Mapping using ChIP-Seq: singals and alignments commit 8007bd621b601b32e141772924d89e62a42e01e8 Author: kayla Date: Fri May 9 21:33:54 2008 +0000 added cavPor3 commit b29edccbca8de13187fbcebc6e41608f331650f6 Author: galt Date: Fri May 9 21:26:30 2008 +0000 Adjustments to handle http code 300 thru 304 and 307 redirects commit 4a2497877b4940c368cbf8a5e0f2792f6a321133 Author: tdreszer Date: Fri May 9 21:15:32 2008 +0000 A little reorganizing of all the subtracks commit 25dcf832eb3cb215f6b69ab0f689e5207c358dbb Author: tdreszer Date: Fri May 9 21:14:51 2008 +0000 Adding descriptions from Broad commit 8c2e11bd4bc8ec07626750d559d83f2984e4daac Author: larrym Date: Fri May 9 21:03:59 2008 +0000 initial checkin (after copying and modifying from ponAbe2) commit 81a41e99ebc0b1faf3e9594c44bbcd735f864add Author: angie Date: Fri May 9 20:41:19 2008 +0000 Added Database of Genomic Variants. commit 4466a4c13d92cd1bcc6f910f744a6c03292fc202 Author: angie Date: Fri May 9 20:39:50 2008 +0000 Tweaked sequence names for PCR on UCSC Genes to include both uc accession and display name. Added Database of Genomic Variants. commit c962b9aa98a73f5a162cb3d2383e5061038c73b4 Author: angie Date: Fri May 9 20:37:48 2008 +0000 Added itemRgb colors. commit 85faaf1b755b4576b6588f24190220d26e30e625 Author: rhead Date: Fri May 9 20:36:36 2008 +0000 Fixed notes regarding types being on the correct levels. commit 378dece4a52c53247e69575a55037a1771559ed0 Author: ann Date: Fri May 9 20:21:01 2008 +0000 fixed searches commit 5bb6e85e77e2009ec1873aef6026a9d1531f00b8 Author: ann Date: Fri May 9 20:11:02 2008 +0000 fixed searches commit 52f42aad2b6302d00fe82102d15c15dbd9836bc0 Author: tdreszer Date: Fri May 9 19:29:37 2008 +0000 Adding Broad Stem Cell ChIP-Seq Data commit 537674e095bbf19f6526a8fe4814299cd636f52c Author: ann Date: Fri May 9 19:19:36 2008 +0000 adding to include all_mrna track commit d4fab0704141101c4b22f1a3761b1110ffa4d0bd Author: ann Date: Fri May 9 19:17:00 2008 +0000 adding file to including all_mrna track commit c9c55231a63c2aa2f691b923a261ac845e5ac2b8 Author: galt Date: Fri May 9 15:00:07 2008 +0000 "Encode release log update" commit 2cb75e28df0092c817a6b3a7f03f27aa70661d54 Author: galt Date: Fri May 9 15:00:04 2008 +0000 "Release log update" commit aeecd63c9305a0bd10dc4d9738afb91cfd57bf92 Author: galt Date: Fri May 9 08:42:14 2008 +0000 added para.bookmark to mark how far results have already been processed, thus only new results need processing commit f2369f9e9e311f17886db6efd67fb93548a80d22 Author: galt Date: Fri May 9 03:53:20 2008 +0000 code cleanup remove forward references, replace para.results with resultsName commit 328fd45eea76fae7c0c3b038fc16c89499dde399 Author: galt Date: Fri May 9 01:26:03 2008 +0000 fixing bugs and improving messages in new freeBatch command commit b774847bed7289bfbd389174c7cd920a8a53252f Author: galt Date: Fri May 9 00:44:31 2008 +0000 fix bug, we were freeing the name twice because it was in hash and in batch commit 1e11771101ef937cd75f0ec3ce5581b2848a0c59 Author: galt Date: Fri May 9 00:19:45 2008 +0000 adding para freeBatch command commit 431d0a09cf1cd7905a2992b14644c32f13670ecd Author: angie Date: Thu May 8 23:51:09 2008 +0000 Added Database of Genomic Variants. commit e2eeae85b3c9e8ee1d4a18197920e642cb599795 Author: ann Date: Thu May 8 23:22:15 2008 +0000 removing felCat3 from generic ensemblTranscriptId rule (as it has many dupes due to the scaffolds). Also adding a few tablesIgnored for lamprey and lancelet. commit c4ff3826445d923d80484c2c6275c1bf397a296e Author: galt Date: Thu May 8 23:11:12 2008 +0000 adding para resetCounts command commit e93c9d44bf9e6046ce7ac7f99e20421002827197 Author: larrym Date: Thu May 8 22:00:10 2008 +0000 add refresh a button to every track group title bar; remove obsolete hNbSpaces function (b/c now using a table to center group title) commit dae9c0971fc25cf0adac0125bad5bccc30e0dac6 Author: hiram Date: Thu May 8 21:44:04 2008 +0000 This should have a comment line after the function declaration commit 0df0cce4ddbd056ca576e14bb52b0e137c4f6e26 Author: hiram Date: Thu May 8 21:42:07 2008 +0000 Prevent re-entry and duplication, and properly check for the actual host name commit ca7986770a9764298e63a23a7a8acf22792fa459 Author: hiram Date: Thu May 8 21:19:30 2008 +0000 Fixup usage of htmlEnd cartEnd to lessen their proliferation and add googleAnalytics commit e2b984a5180c1f380414aea952731118ac132ba9 Author: kuhn Date: Thu May 8 20:57:03 2008 +0000 typo commit 184ade9e7947962334f3712b68bde2905908b130 Author: hiram Date: Thu May 8 19:14:14 2008 +0000 Use hPrintStatus() instead of the private variable reference commit fa4477d4c39ed95aafb04e0d14ab9267f29af36d Author: hiram Date: Thu May 8 19:11:49 2008 +0000 Add hPrintStatus() query function to query the 'private' variable commit bb858ae8c91bc29e9fe3b346764cdfa2ba19d644 Author: hiram Date: Thu May 8 19:09:52 2008 +0000 Now I find that the 'private' variable is used all over the place .... So, add a status query function to query the 'private' variable commit 32264e2dad7ace259762f1a277dd3265a1abd066 Author: galt Date: Thu May 8 18:59:17 2008 +0000 dont lose cflags from above commit 7529d8d29080742032ae016e543b46dfcf93008c Author: galt Date: Thu May 8 18:49:17 2008 +0000 dont lose cflags from above commit 1ed9a0f26419aff92c223acd2a27f9a4acc5fb99 Author: hiram Date: Thu May 8 18:44:31 2008 +0000 No longer need the hPrint functions here, they are in the library now. commit 2343d568ceca1f4cde7f68f9aa8d80248590baa9 Author: hiram Date: Thu May 8 18:43:21 2008 +0000 Private variables should be private, not public. commit 7b52ed295971a397059dbdc99c87f74d39f1a7b4 Author: hiram Date: Thu May 8 18:41:37 2008 +0000 Do not ever declare variables in include files. This is not good. commit 570d7e42c34d3b52c74289d731cdccb853166f18 Author: galt Date: Thu May 8 18:41:32 2008 +0000 dont lose cflags from above commit 82c1fe2d1c95536e8ffa149a424c893539ff3cc9 Author: hiram Date: Thu May 8 17:37:46 2008 +0000 the track sibTxGraph is unique to mm8 and mm9 due to URL setting, moved to each of those commit 306d4d22f1b1fbfa9cc8f8ee9c22ab24f1c4d3b6 Author: pauline Date: Thu May 8 16:59:27 2008 +0000 Changed text to include explanation of sequential lifts. commit ef09aaba87492d949218e0d8a7ffb4867c756a45 Author: galt Date: Thu May 8 15:00:07 2008 +0000 "Encode release log update" commit f7fbab658c7a1b5defe872983f93682a059c2218 Author: galt Date: Thu May 8 15:00:05 2008 +0000 "Release log update" commit f267fe1e69131c90ba083f4439002aedf2a0c88b Author: galt Date: Thu May 8 00:33:46 2008 +0000 better handling of sick batch in hub and para - need to get para to stop shoving commit cacbae961cce87a284494203c3a93b3796b628ee Author: galt Date: Wed May 7 19:03:37 2008 +0000 minor fix to help commit 2e6f9664b2c44971d9ab94cc08780037f8ab29d0 Author: rhead Date: Wed May 7 18:06:38 2008 +0000 Added note about overlapping datapoints bug in phastCons15way data. commit 9a154a4e64f38e6eac91a95fa5b0b08ff9ae2f9e Author: ann Date: Wed May 7 16:53:02 2008 +0000 collapsed rm lines. also made the file names nearly unique by adding the 22606, which is the process id of the runnign process (thanks Hiram). commit ecd27f72cf67e747ba650a59c6cbc44d8ea3c240 Author: galt Date: Wed May 7 15:00:12 2008 +0000 "Encode release log update" commit a9c2ffe3337beac9ef50f13598f65767538cb89b Author: galt Date: Wed May 7 15:00:06 2008 +0000 "Release log update" commit afcfbca93352d2675ad4caad12414d7e035c5106 Author: galt Date: Wed May 7 05:33:57 2008 +0000 changing para check to also show sick node summary commit b19c431f2a5cede0061e4a074a80aab69b7647e6 Author: galt Date: Wed May 7 05:31:10 2008 +0000 making the report only show machines fully at the threshold as failures commit e76fd122cfbdbcae03a60b0db2418bb32266507b Author: angie Date: Tue May 6 23:38:23 2008 +0000 Added $images constant (htdocs/images). commit 9152ad3394b5b10786283e2e3c8254f750e6272b Author: angie Date: Tue May 6 23:37:34 2008 +0000 Ann's suggestions: add gateway page photo and (if there's a multizNway) phyloGif image. Also added new genbank table gbWarn. commit 9fd713a027af1be6ffb8b3d25b0d74b5f8646d33 Author: hiram Date: Tue May 6 22:59:56 2008 +0000 The sibTxGraph URL needs an explicit db=mm8 argument commit b5766438fdc4f02020757adda922ad30b5cda71a Author: hiram Date: Tue May 6 22:55:32 2008 +0000 The sibTxGraph URL needs an explicit db=mm9 commit 2520dfe005aa57b2692200c2932b92f0e509a56b Author: hiram Date: Tue May 6 22:54:58 2008 +0000 The URL for sibTxGraph needs explicit db=mm9 commit 57ea15338bf185d611c08cce878c10de945b175d Author: hiram Date: Tue May 6 22:30:07 2008 +0000 Adding Transcriptome and alt splicing graphs from SIB commit 86be95609d0fd8a4056b2f7f0390cf9e37f2de6f Author: hiram Date: Tue May 6 22:21:14 2008 +0000 Add definition with specific URL for sibTxGraph track commit 4dcb7dbce9090769f0fdd2c4e4ce8ffdf9b84c53 Author: pauline Date: Tue May 6 22:10:13 2008 +0000 Fixed text to remove plural. commit c787d80f554bf2081e34d067ef24be104b2975f8 Author: ann Date: Tue May 6 21:42:13 2008 +0000 fixed it to be in-range of this Contig commit 9150d80ac68446de5d7f0111a98edb5e62f07a68 Author: ann Date: Tue May 6 18:59:08 2008 +0000 added missing matrix line commit cf1f907ba3b4627c41ba6e3d00a4a1d613ddc5aa Author: galt Date: Tue May 6 18:18:09 2008 +0000 making hung and slow mutually exclusive commit abef392f0213101928dbff457ee54759fbc678a5 Author: hiram Date: Tue May 6 18:18:07 2008 +0000 Adding transcriptome track from Christian Iseli at licr.org commit bd20390f876acf3661d8063d850a8f6855675aae Author: hiram Date: Tue May 6 18:07:53 2008 +0000 Text from Christian Iseli for transcriptome track commit f289ac3830808193339544f8e73f558dd8cd3a7e Author: kayla Date: Tue May 6 17:29:28 2008 +0000 added braFlo1 and petMar1 commit 5a6a04f9290cc2acf293388da202b164268bee28 Author: hiram Date: Tue May 6 17:25:45 2008 +0000 25mers repeat track from Anton Valouev commit e8b8c1bb4feb657b629d267cd049f8e343a40565 Author: hiram Date: Tue May 6 17:10:00 2008 +0000 Add gc5Base.wib to the expected list of gbdb files commit 531357ba26ac12d7c4de0963eb5a7ffbea223ea5 Author: hiram Date: Tue May 6 17:05:18 2008 +0000 Add ensGene files to the scripts delivery commit 823f56956445306e1e84f741c9d2ae800a0aea93 Author: hiram Date: Tue May 6 17:02:27 2008 +0000 Fixup missing -minScore=0 for one of the chainNet commands commit 3bf5f5f091eda5fc6e7d2de6beb5c63704f5bd82 Author: hiram Date: Tue May 6 16:58:49 2008 +0000 Text for 6-way phast cons most conserved track commit 45e4b1e0ec93bb943ec868ac1905a748cd3cea18 Author: hiram Date: Tue May 6 16:57:13 2008 +0000 Text for 5-way phastCons track commit f0bc41bf8a307f11ce058b9f9ae5eb549861e8a3 Author: hiram Date: Tue May 6 16:46:49 2008 +0000 Pages for chain and net PetMar1 commit 0c5e5f6f70cd2bd41f69c032925f102be7bc90be Author: galt Date: Tue May 6 15:00:09 2008 +0000 "Encode release log update" commit 291a08227fcd1a5e067aa8aca645343ea1a51102 Author: galt Date: Tue May 6 15:00:05 2008 +0000 "Release log update" commit 9646ed1c1a65a4f4666517b6bff661849e8f4993 Author: markd Date: Tue May 6 01:29:52 2008 +0000 install NR refgene only on hgwdev commit 95dd0b00a1eea93748830b92652cea735a5e4cbd Author: angie Date: Mon May 5 23:31:08 2008 +0000 Added support for non-genomic PCR target items with accession plus display name encoded into the targetDb 2bit names. Target PSL qNames are just the accessions. Works the same for targets with just accessions. commit 60fa2184d7823ab3d07147bc6ba0ebac71bc9b38 Author: donnak Date: Mon May 5 23:04:27 2008 +0000 Archived a news item. commit 44ce50c8761eef09b82ee0fa5c036fd07611258d Author: donnak Date: Mon May 5 23:04:17 2008 +0000 Added GSID HIV browser announcement. commit a588fc081b117b27a1c80a4affbc8fdf1375c843 Author: galt Date: Mon May 5 22:40:57 2008 +0000 trying to make cookie work on both hgwdev and hgwbeta to reduce login hassles commit 0e9c51057d32151136e3d2e022deda7078d22bc7 Author: galt Date: Mon May 5 22:29:58 2008 +0000 trying to make cookie work on both hgwdev and hgwbeta to reduce login hassles commit e3701e2e3e72eee36246b47306396cf2b875cdf4 Author: kuhn Date: Mon May 5 22:15:23 2008 +0000 added namedSessionDb to hgcentral backup script, but set chmod to make it off limits to the world commit b88adebbaa5270d01b2ec9c7a9c18eed5a637c36 Author: galt Date: Mon May 5 20:55:46 2008 +0000 fixing bug - when user would click on the mrna or protein link on the hgGene details page, before the page had finished drawing, the cart would not have been updated yet, and the user sees whatever was the last gene looked instead of the gene they were on now commit b72db8a0244b5f7ac13ebfab65b1bb01b64db850 Author: angie Date: Mon May 5 18:27:31 2008 +0000 Added UI setting to PCR Results track: non-genomic target results can be drawn either with the matching part tall and the non-matching parts short, or just trimmed to the matching part. commit 018d8cce018bed2455a17dd3fa52b54b0380db2b Author: kent Date: Mon May 5 18:10:01 2008 +0000 Committing latest version of ucsc genes build. Still a work in progress. commit f0a0fc1dfbba00160bce11429b4a6d39034b076d Author: kent Date: Mon May 5 18:08:37 2008 +0000 Got rid of abortive attempt at UniProt update. commit 121df716b28b211aad8564b260b046786cf8b506 Author: kent Date: Mon May 5 18:05:52 2008 +0000 Saving procedure for creating new uniProt database. commit 5ea3dc3feebff4500d13659f7987b14166af8502 Author: kent Date: Mon May 5 18:04:15 2008 +0000 A new test case for blat. commit f7a174f67e9c11fc12b8ea81043b41cec120be80 Author: ann Date: Mon May 5 17:55:01 2008 +0000 added new assemblies: petMar1 and braFlo1 commit 5493559c099f587668fa2075ecfc3e3030d8f5e6 Author: rhead Date: Mon May 5 17:42:14 2008 +0000 Removed link to the genomewiki version of the mirror instructions. commit a626a78a31e7440d7c368d8329e273893e824931 Author: angie Date: Mon May 5 16:34:39 2008 +0000 Added pscreen. commit b38be22f2aa0d1764bd5da9fc173bc639db020c7 Author: galt Date: Mon May 5 15:00:07 2008 +0000 "Encode release log update" commit 222b4df3872942c1523aeea6eec2c577a37d9c7f Author: galt Date: Mon May 5 15:00:04 2008 +0000 "Release log update" commit 554ec45b7a5ba961a814ff3aec5da1c287f5676b Author: galt Date: Sun May 4 15:00:06 2008 +0000 "Encode release log update" commit ba34e921114585b38789b88a8167a8284758cf93 Author: galt Date: Sun May 4 15:00:04 2008 +0000 "Release log update" commit 52b46eeeca7c24f579624e03d3e3c1e1e274327c Author: kent Date: Sun May 4 14:15:35 2008 +0000 adding bedBlockSizeInRange and related functions. commit e76a74db510b5d51caa939bfc664fd2f88a664f6 Author: markd Date: Sun May 4 05:44:48 2008 +0000 fixed bug in -ignoreQUniq commit 2be30b85d3b822ee2e5f4cf79065ff2096f930d3 Author: markd Date: Sat May 3 21:23:45 2008 +0000 CCDS update commit 45d708a0b11cf486f27073bbf0e3895d680061de Author: galt Date: Sat May 3 15:00:10 2008 +0000 "Encode release log update" commit 4f8681786c45c439df9a543076482e5ceaca406e Author: galt Date: Sat May 3 15:00:08 2008 +0000 "Release log update" commit 4928208f77a42395d640396f4e54ef7cd6ed7e1f Author: rhead Date: Sat May 3 00:09:47 2008 +0000 Removed sizes from the rsync connection test instructions -- Erich removed the numbers from the config file. commit 02c56519cefdadba3ad47397e7bf7a00695fe7df Author: markd Date: Fri May 2 22:57:05 2008 +0000 added -ignoreQUniq commit 1e89546aea9d60a7a5639895f80931188736635d Author: rhead Date: Fri May 2 22:56:10 2008 +0000 Replaced static data sizes with instructions on how to figure out sizes. Collapsed detailed instructions on getting data for each database to a single example, with instructions on how to find a list of available databases. commit a92183015acca737245f0f1723fc4c294c21704e Author: donnak Date: Fri May 2 22:26:21 2008 +0000 Fixed broken link. commit 80d72fcb3d46620266a363b9cddd9d71245a7706 Author: larrym Date: Fri May 2 21:55:50 2008 +0000 add multiz6way and phastConsElements6way commit 46ceb52f996547aca9db7d321a5a02c6acc1c7e1 Author: larrym Date: Fri May 2 21:49:41 2008 +0000 6-way phylogenetic image for equCab2 commit 908dacd6d61f8515e3271d495f2019355236efcd Author: lowe Date: Fri May 2 21:27:41 2008 +0000 For LOWELAB, changed min match length and max seqs values, more appropriate for small genomes. Default browser code not affected. commit 52e20b568ac92399574ac6d986bee51d2be48230 Author: angie Date: Fri May 2 21:23:08 2008 +0000 Changed the load step to install, and moved up a couple earlier operations that could overwrite top-level files into the install step. Thanks Robert H. for pointing out that -stop mask test runs had side-effects. commit a9cb6874f5bc8128a3b4c934f57782aa90fba3b6 Author: angie Date: Fri May 2 20:23:30 2008 +0000 Two changes to help InnoDB performance, where count(*) causes a very slow full table scan: 1. In sqlTableExists, use describe instead of select count(*). 2. In sqlTableOk, try the select query first and count rows only if it fails. commit 1139927e16225f42d74cc2091a96260148abae5c Author: angie Date: Fri May 2 19:32:49 2008 +0000 Use the new hFileContentsOrWarning. commit 3e518915a24a79627b8d2d6934a3ed6eca5e0f52 Author: larrym Date: Fri May 2 18:21:59 2008 +0000 working on Annotate 6-way multiple alignment with gene annotations commit 23992e19cbb721e6268cb05b6db965ebf3c0e9b1 Author: angie Date: Fri May 2 18:13:54 2008 +0000 Moved most of web.c:webIncludeFile out to hui.c:hFileContentsOrWarning so the error-checking can be shared with code that stores the content (e.g. in tdb->html) instead of immediately printing it. Also changed the return type of webInclude{,Help}File to void because all callers ignore it, and it simplified the code move. commit 937d356bc3946eadf0c6130509e5f5df83461816 Author: rico Date: Fri May 2 17:43:20 2008 +0000 Added description of options to usage(). commit df90340efc974d7960904421d311930d5c4d073a Author: hiram Date: Fri May 2 16:08:01 2008 +0000 Complete downloads for 6-way multiz and phastCons commit bdace148b8e84957db2b292387c20562a3239765 Author: hiram Date: Fri May 2 16:07:30 2008 +0000 5-way multiz and phastCons done. downloads made, pushQ done. All done. commit 2ac78ea0818396088c8fd8abd568b346e1dd6e1b Author: galt Date: Fri May 2 15:00:10 2008 +0000 "Encode release log update" commit 0c6b58181442c41b2f6f23357b7c520a12e8440d Author: galt Date: Fri May 2 15:00:08 2008 +0000 "Release log update" commit 43dd70dfd96863bd7dbdf4535fbc073b6b7ccc2a Author: ann Date: Fri May 2 00:40:07 2008 +0000 some small tweaks commit fc8fdec215f35c54938a9efa48e3fd5d9b6b72a4 Author: angie Date: Thu May 1 23:45:19 2008 +0000 Replaced createPageHelp with webIncludeHelpFile. commit 491aad88e706fc2241a137bcab0f646f33731922 Author: angie Date: Thu May 1 23:42:46 2008 +0000 Use the new webIncludeHelpFile (replaces duplicated code). commit 32cff50dd674712ec6a4956988cf47efcf73f910 Author: pauline Date: Thu May 1 23:36:31 2008 +0000 Added cavPor to whole genome shotgun orgs list. commit 00b47f3005a4f9875375a1bab2fd9f01ce26e490 Author: galt Date: Thu May 1 23:26:48 2008 +0000 little improvements made after code-review suggestions commit 7fb51666ba954b50e0f425275fc3a0ac1974882e Author: angie Date: Thu May 1 23:19:10 2008 +0000 Added webIncludeHelpFile to replace a bunch of similar safef+readInGulp's. webIncludeFile now accepts either absolute or relative path. commit dae12065b0908e36ab410751358125b370f9bb0a Author: angie Date: Thu May 1 23:14:52 2008 +0000 Added hHelpFile to replace a bunch of similar safefs. commit 8ecbe58a5e21afc01dbb521b944a8d118c1ad2fe Author: angie Date: Thu May 1 23:01:00 2008 +0000 Use constant instead of hardcoded name. commit 0a62835d53c01b6fdac39f8490e08cd4181d7abb Author: angie Date: Thu May 1 22:57:44 2008 +0000 Removed unnecessary index. commit d780c1ca4ae16ae0139f658e8081287d83cd6678 Author: markd Date: Thu May 1 22:43:12 2008 +0000 fixed typo commit bb6cdf2ca39c853b50d02b7fe42e4f476976cc59 Author: markd Date: Thu May 1 22:35:14 2008 +0000 added warning about invitorgen clones being included onces more commit 666b6a8055a4659927a68efaa1bac4e81898fbb4 Author: hiram Date: Thu May 1 22:20:43 2008 +0000 Take out developer comments commit c94f2bc5ce26262989c5da85f33ce01c5b48da43 Author: galt Date: Thu May 1 21:42:10 2008 +0000 adding some more instructions for updating users table on dev from beta commit 76d18092d5787ddb14700b9b722d841ba450e21d Author: angie Date: Thu May 1 21:36:58 2008 +0000 Updated doPscreen's obsolete external links, and added support for FBgn IDs in pscreen.geneIds. commit c53431d3581aaa9efe0df9b14fabd87fb5ef4c1e Author: angie Date: Thu May 1 21:28:23 2008 +0000 Added pscreen. commit 4459bd0a8a652dc78ae3ffa6763da2d1215d2453 Author: angie Date: Thu May 1 21:28:03 2008 +0000 Tweaked pscreen: added link back to contributor, inhibit hgTrackUi score filter. commit c37a90e76eeb78416d8ccac878113ec051fc140c Author: angie Date: Thu May 1 21:26:10 2008 +0000 Added minor correction from contributor and updated References format. commit a2e2ed857d1aee986f11e0440c41d9902d0d1743 Author: larrym Date: Thu May 1 21:20:13 2008 +0000 in the middle of 6-way multiz commit 72c0ace371d5351e6d1604faa8de353d8d667f51 Author: kuhn Date: Thu May 1 20:58:26 2008 +0000 changed some priorities commit 14e3fc0f3c0a01cf2cb09206098196a120855466 Author: hiram Date: Thu May 1 20:57:18 2008 +0000 Initial contents for 5-way description page commit 49350f46e39e2e628d0eca72b3ee176a965adf29 Author: galt Date: Thu May 1 20:54:45 2008 +0000 adding increment int function to hash commit db70c16a4d5dc38087e6550b61f5c4a737b473da Author: galt Date: Thu May 1 20:52:52 2008 +0000 adding increment int function to hash commit 874e627af4697a20e45506470e8c002c2fef1749 Author: hiram Date: Thu May 1 20:52:05 2008 +0000 5-way conservation track is complete commit f20fa04a3472b2565109941e0f424ab4fc38be99 Author: galt Date: Thu May 1 20:43:43 2008 +0000 more verbose showing start, end, elapsed commit 49e93f2a3818b4e17edd78b0f3fabce9e0132b55 Author: donnak Date: Thu May 1 20:39:06 2008 +0000 Added several new pubs from our grant progress report. commit 723f3e0131366204011a8e2a954bcc9c729a8cc6 Author: rhead Date: Thu May 1 17:57:56 2008 +0000 Fixed broken link to Ohio State. commit c4fa7b7dd612cc79932b11fb03160bfa48bb4552 Author: kuhn Date: Thu May 1 17:50:32 2008 +0000 added -w flag to grep to avoid picking up more than intended IPs commit cec798d40db43aec66e5d55ac33fe8f96ee95a81 Author: hiram Date: Thu May 1 17:44:07 2008 +0000 Image for Lanclet 5-way alignment commit 599c4d19e14b3089fc775208f8e883850f815251 Author: rhead Date: Thu May 1 17:42:24 2008 +0000 Fixed broken link to marshfield clinic. commit 4c757292bf17639b0a6223178020a9c433070c76 Author: angie Date: Thu May 1 17:33:48 2008 +0000 Added pscreen.geneIds. commit f3d11f001979f6345940aa86e7dc348886c94dc9 Author: larrym Date: Thu May 1 16:48:31 2008 +0000 temporarily backout javascript changes back to 1.52 (will restore after v181) commit b014a57dc76ab083359e04d1e45b560e47aa2b5b Author: kuhn Date: Thu May 1 16:41:25 2008 +0000 small changes commit ca28a8da42ae242327030ed79e8ac72c6f47f782 Author: kuhn Date: Thu May 1 16:29:39 2008 +0000 allow use with dev and beta commit 25804e247388e3c042e63b3d5e5d269f7d0711e4 Author: galt Date: Thu May 1 15:00:07 2008 +0000 "Encode release log update" commit eb1c4c3de0fbbb2fe713997d2e933e94f2c98633 Author: galt Date: Thu May 1 15:00:04 2008 +0000 "Release log update" commit 34c420ece54052cb4bba71c04381836168afc8bd Author: rhead Date: Thu May 1 07:18:17 2008 +0000 Also made the dless link open in a new page. commit a4348285fab0bfa9d4eed2e3e4d0c30c303cdd70 Author: rhead Date: Thu May 1 07:13:02 2008 +0000 Fixed broken link to the dless paper. commit a7301cd41765863b9e942933dd52815fea8a6756 Author: rhead Date: Thu May 1 06:54:20 2008 +0000 Fixed broken link to IGBMC for Drs. Thisse, who appear to have moved to a place called Morphogenesis. commit 44861faac6bcbe2a88cd974d05bcbe8bdbe98209 Author: markd Date: Wed Apr 30 23:18:13 2008 +0000 added option to output stats in a parseable format commit 942f8a3b08bcf5b69eee0e5c11eb149dd35cfa4f Author: ann Date: Wed Apr 30 19:30:11 2008 +0000 added check for dateReference column commit 4ae49260124b4677a838771680a78315801d5b94 Author: ann Date: Wed Apr 30 18:29:20 2008 +0000 added new gbWarn table to gbCdnas rule commit 280bf01c91d54df06be975b80198acf56521bfd3 Author: galt Date: Wed Apr 30 16:09:54 2008 +0000 adding note about fix to lib/blastOut.c commit b39e166e01358ee30bf732bf04f233e7cce98a1c Author: galt Date: Wed Apr 30 15:00:10 2008 +0000 "Encode release log update" commit 48251c2061c56e29fe1f4b3de2287256f53594a1 Author: galt Date: Wed Apr 30 15:00:05 2008 +0000 "Release log update" commit 7a9ffa961ba2fa839c441a8caab4781d6b50e2fe Author: larrym Date: Wed Apr 30 00:26:06 2008 +0000 change errAbort to fprintf(stderr,...) (will revert once apache configuration is in place for all developers) commit 7f5fd198d2ea1dc6d61bbc89398bdce03fa7a5c9 Author: galt Date: Wed Apr 30 00:18:14 2008 +0000 based on suggestion by MarkD, we are turning killTime off by default, since it has not been working for years. commit 28ee254fd7971788017fde1d32b43ebd33a417c3 Author: kuhn Date: Tue Apr 29 23:46:18 2008 +0000 parameterized sleep time between BOT resets commit da797a9d07b7c6f7bc2badbb8aa797e9113976c0 Author: larrym Date: Tue Apr 29 23:41:48 2008 +0000 add a missing arg to cgiMakeCheckAllSubmitButton commit 66aad9096a50a627dc4fbbe84d2828e9f2952f13 Author: larrym Date: Tue Apr 29 22:29:57 2008 +0000 move javascript specific code into cgiMakeCheckAllSubmitButton commit ed8f8ac9f9f173c7037939a737455c8e05e0dc3a Author: larrym Date: Tue Apr 29 22:27:12 2008 +0000 change jsIncludeFile to locate files in cgi-bin/js; add jsCheckAllOnClickHandler and cgiMakeCheckAllSubmitButton commit e3dd2d617eb5aa854a8214f2d0e04082f480cf18 Author: tdreszer Date: Tue Apr 29 22:13:11 2008 +0000 Comment lines beginning with '#' and empty lines are now ignored. commit 6bf14e60e2ee4c099c178147791652856e035738 Author: hiram Date: Tue Apr 29 21:50:00 2008 +0000 Downloads and pushQ done. Fini. commit e615d26f1fbec8ca04d8a03c7bba9f62f2275f9a Author: larrym Date: Tue Apr 29 21:40:47 2008 +0000 utility javascript moved from old location in the browser cvs repository commit 85ea6b5bd2dca7eedae028c759ad5e7ae1d2799d Author: larrym Date: Tue Apr 29 21:06:42 2008 +0000 add hCgiRoot commit a2e9e5fe9d36f499002eb2ab45264ee2c391345e Author: markd Date: Tue Apr 29 20:58:32 2008 +0000 fixed typo in nscan commit 8858734668b783a25f569b7d1b7686417d242a50 Author: hiram Date: Tue Apr 29 20:53:07 2008 +0000 Adding html for 6-way track, and turn on phastCons graph commit 08fbde639ddafac92c9165e704ea5015d441b665 Author: hiram Date: Tue Apr 29 20:48:48 2008 +0000 6-way image for Lamprey commit 133987d0efb81e4f6cf79e9743590b1398525f8f Author: markd Date: Tue Apr 29 20:45:54 2008 +0000 added nscan gene predictions commit f5c42c3e483cd8b8ee953ba9df209eddb07dc7f0 Author: hiram Date: Tue Apr 29 20:45:10 2008 +0000 The gene annotations for Orangutan, Marmoset and Dog is Xeno mRNAs, not "none" commit 2b792ba59feb3ef4e9e1511a9cf01384b0beeb47 Author: angie Date: Tue Apr 29 20:08:59 2008 +0000 Suggestion from Tim: just show strand, instead of the confusing pair of revComp (whether we rc'd genomic sequence) plus strand (item strand, or '?' when there is no item. strand is now like the old meaning of revComp, but reflects the item strand when there is an item because we don't offer the revComp checkbox in that case. commit e29cd2c02ed89078fdf7f4fd3f6f4905a55f1e2a Author: larrym Date: Tue Apr 29 19:19:56 2008 +0000 equCab2 swap commit 43616f61b9152f0f46ecda7fd9b2f9bf45dff8c5 Author: hiram Date: Tue Apr 29 19:19:51 2008 +0000 Completed phastCons6way business commit c7bf8a3555f25ad56841ddb76e3be99bdc3bc562 Author: hiram Date: Tue Apr 29 18:27:07 2008 +0000 Up to date with v49 entries commit f9a5e90062dba347542bbaae6b44d99080a73872 Author: hiram Date: Tue Apr 29 17:34:48 2008 +0000 Fixup tromer URL link to include mm9 commit 33d498426ce196bd7b38110a357b7990f96ed5d1 Author: hiram Date: Tue Apr 29 17:16:39 2008 +0000 Make the -noOverlap be the default, can now specify -allowOverlap commit 06dca8e4c812c7050780cf2e72b26aad57b3b4bd Author: aamp Date: Tue Apr 29 16:55:28 2008 +0000 "New version number v181" commit 0103b7f99a3576a056e36dbaba4ed61fa88e6613 Author: aamp Date: Tue Apr 29 16:51:46 2008 +0000 Added "Show ruler" option to base position track plus a warning that ruler cannot be turned off if everything else is turned off. commit 7976172989ea44f71d7e1111efe120cc6a63b240 Author: galt Date: Tue Apr 29 15:00:08 2008 +0000 "Encode release log update" commit 4184fc016b0cc565880a437fc34eb7c919a95b70 Author: galt Date: Tue Apr 29 15:00:04 2008 +0000 "Release log update" commit 6b8c8afedb91607950166998b355fd66e71cddbc Author: galt Date: Tue Apr 29 10:14:11 2008 +0000 added the para slow command based on -warnTime, it calls paraRunning like para hippos does, and also extended para running to display slow status commit 20b9fa72b1eb34677c145adca7329c5d853eb0d3 Author: galt Date: Tue Apr 29 09:36:48 2008 +0000 bugfix on para check report relating to hung jobs commit 9a68db25246cf8b2320126ac08b3a2f510c2618b Author: markd Date: Tue Apr 29 07:47:37 2008 +0000 removed hTrackDbName, which will cause grief if used with muiltiple trackDb tables commit 202c45e3cf07d165e8823b4569328f5813eb9fad Author: markd Date: Tue Apr 29 06:19:28 2008 +0000 fixed bug crashing on tables without end position; some cone cleanup commit 9b6de5206fba6485f880048fab2267a175910912 Author: markd Date: Tue Apr 29 06:18:12 2008 +0000 added a basic test framework commit ba251326e75c5e28aaf95b17ec7987fbba735906 Author: galt Date: Tue Apr 29 05:18:30 2008 +0000 finished implementation of -killTIme and -warnTime which have been unfinished since at least 2002 commit 8b5c3834050287b8fba269b42cc58c8bc63c8f7b Author: markd Date: Tue Apr 29 04:37:08 2008 +0000 fixed incorrect comments commit 2c4eaabc0a08e3fbbbd2804b5085a58cdbe9c06f Author: angie Date: Tue Apr 29 00:01:23 2008 +0000 Use constant for PCR Results track name instead of hardcoded name. commit 71bf2ed60bedfe9c17ba6650c1346fd94bdf3896 Author: angie Date: Mon Apr 28 23:58:14 2008 +0000 Use constants instead of hardcoded names. commit c88b37a9fbaad42c5770339088ea819f3b74c743 Author: angie Date: Mon Apr 28 23:57:50 2008 +0000 Adding one more constant so that all base coloring option names have constants. commit 5e5d47618def8183ed2a91f072fc217bd45fbbfb Author: pauline Date: Mon Apr 28 23:49:45 2008 +0000 Removed text to make gap types match to those in gap table. commit 4ffe7b10a9ffc29a7773ae0e9e2871d327cec9ce Author: fanhsu Date: Mon Apr 28 23:16:04 2008 +0000 Added hivGne8v2.txt. commit b6f018cca6dff865ed0aec503185700e267a65a3 Author: markd Date: Mon Apr 28 22:36:13 2008 +0000 keep alignment results around for a while commit a7d2bb19bbb187423161e51051e9eb70de08314b Author: larrym Date: Mon Apr 28 21:45:10 2008 +0000 remove wiggle specific stuff commit a6a816ee1211326139c97532d66ae933322f0179 Author: hiram Date: Mon Apr 28 21:40:21 2008 +0000 Gene annotation done for 6-way commit 83881fc1c4d95a687a804e5aa5e88daaf37a9797 Author: larrym Date: Mon Apr 28 21:22:05 2008 +0000 finish platypus -> horse; start 6-Way Multiz commit 6eab44a740fbfb477f7c08be02b466f62a4b5b7f Author: hiram Date: Mon Apr 28 21:12:33 2008 +0000 Got the 6-way to the point of annotation commit a31d82338e45e17beb5760455aac462090728b8e Author: hiram Date: Mon Apr 28 21:12:11 2008 +0000 Finished off some blastz run time stats commit 9593e7d1ae0135f58cf8edb976a553e8f8072d1e Author: larrym Date: Mon Apr 28 19:28:37 2008 +0000 documentation for bedgraphs commit 08e969ca583e1da969c88db6af66134fa22a68a5 Author: ann Date: Mon Apr 28 18:12:20 2008 +0000 changed variable name to make it more intuitive (thanks Brooke). commit bc017096e47a07e6baff5f585dd2e56655c1c038 Author: ann Date: Mon Apr 28 16:54:51 2008 +0000 changed bp to base pair (suggested by Brooke) commit 6df8bb9413958bfec9324f675a90dee8a9e82f6b Author: markd Date: Mon Apr 28 15:32:25 2008 +0000 added ability to no generate errors on particular files not matching ftp site commit 94b0b0a8fce09d0e21864976bd27311369fe1f7b Author: galt Date: Mon Apr 28 15:00:06 2008 +0000 "Encode release log update" commit 2c63d6094da8fb8b7dc1f4329bf2d6c43e8b7742 Author: galt Date: Mon Apr 28 15:00:04 2008 +0000 "Release log update" commit 7d3ea0f38ce6ef4339ee9bfdef5709c672d0611d Author: kent Date: Mon Apr 28 13:08:46 2008 +0000 Testing txGeneAccFromId commit cb50d97f552b31c10d83e5c94a3f30d271babe92 Author: kent Date: Mon Apr 28 12:25:36 2008 +0000 Moving routine to turn numerical IDs into uc123ABC type accessions to library. commit b3e7a2056b2a8da48143ab7ce0c805eb755076ba Author: kent Date: Mon Apr 28 10:16:01 2008 +0000 Seems to work. commit a930b79abc0b879db9332a517b1c2a63e8d50022 Author: markd Date: Mon Apr 28 08:03:31 2008 +0000 added ability to no generate errors on particular files not matching ftp site commit 2ff6cf936e854545896c1bfe28a7b082c3fa35d1 Author: markd Date: Mon Apr 28 07:41:06 2008 +0000 added ability to no generate errors on particular files not matching ftp site commit 48471dd616872862c66edd4f26f05f173f4ea036 Author: galt Date: Mon Apr 28 07:30:38 2008 +0000 fixed minor bug in -out=blast where display should be +- instead of -+ for non-translated dna searches commit 46bc0f61f49d24b207821b5c8268402c4fc4e5b7 Author: galt Date: Sun Apr 27 15:00:06 2008 +0000 "Encode release log update" commit 2f9187a21b272760baa139695196b0615707b930 Author: galt Date: Sun Apr 27 15:00:05 2008 +0000 "Release log update" commit d0bb58e790803dddf32f761f7495b0dc502e7572 Author: fanhsu Date: Sun Apr 27 01:57:03 2008 +0000 Added sequence ID tags. commit 7a8567018b30737a41d8305960d19a37c941a9e1 Author: fanhsu Date: Sun Apr 27 01:52:55 2008 +0000 Updated logic to process dnaSeqs and aaSeqs. commit 6d8d8829815ef25af2e8ba86b3f6fd8676ee5726 Author: fanhsu Date: Sat Apr 26 23:18:58 2008 +0000 Added dnaSeqId and aaSeqId. commit beaf2b1f85719298c804794c094919de02c7603b Author: braney Date: Sat Apr 26 22:38:22 2008 +0000 human proteins commit adf3e2bacaae02f2f03ffadc57b5e538972a5485 Author: galt Date: Sat Apr 26 15:00:05 2008 +0000 "Encode release log update" commit 75c3d78e18836eb5187b3a4391587ae00786263f Author: galt Date: Sat Apr 26 15:00:03 2008 +0000 "Release log update" commit 44f69a4c42da72f822b5d2c39e3b8738799847e2 Author: markd Date: Sat Apr 26 07:45:37 2008 +0000 added gbWarn commit 38023c9e50e172da792662237a3e52b5256a5dd0 Author: markd Date: Sat Apr 26 07:09:22 2008 +0000 added genbank gbWarn table and let back in invitrogen evils commit 7d79e43e2bff0c64660bfa5b1903e4f290268640 Author: rhead Date: Sat Apr 26 00:55:15 2008 +0000 Fixed broken link to GERP program. commit 0b9bc2d1d6a2a757c21745f32b761989bbd56473 Author: galt Date: Fri Apr 25 23:57:12 2008 +0000 added option -extended to hub and parasol listJobs so that the batch working directory is shown as a new last field in the output commit 40a5ad43d4de4bb0ea778da233342b8cf3b7c91b Author: galt Date: Fri Apr 25 23:55:32 2008 +0000 added option -extended to hub and parasol listJobs so that the batch working directory is shown as a new last field in the output commit 8e34845e303a2dc392d7eb2a5313f6d33e8f304d Author: galt Date: Fri Apr 25 23:29:06 2008 +0000 making the pstat command more efficient by restricting the list the hub produces to one batch that is needed from para - parasol pstat still works the old way showing all jobs commit 0fecdc5fd4853f89a22602095386e95d6a43b5ca Author: ann Date: Fri Apr 25 23:21:44 2008 +0000 moved sections so that the ouput would be in a more intuitive order (thanks Brooke) commit 89c9407e9c3bb4c5ee8578569e872041c5eddc2a Author: ann Date: Fri Apr 25 23:18:37 2008 +0000 added another qualifier to trackVersion query (thanks Brooke) commit c2929b112011ba01cf0119cf12922aaf02022b58 Author: galt Date: Fri Apr 25 21:50:49 2008 +0000 added comment that -warnTime and -killTime were never completely implemented commit ce3eac2919e5d751f10f9bddd01a8c71030697e6 Author: galt Date: Fri Apr 25 20:11:52 2008 +0000 minor bug - if clauses switch, compare to line 1060 which has it right commit f1decc8b2c4e6b7cc4a05a00e076b34fb96e33fe Author: rico Date: Fri Apr 25 17:38:39 2008 +0000 added some functions commit 8d873ac2771511b95abc2f11a402933e1f835a53 Author: rico Date: Fri Apr 25 17:38:21 2008 +0000 Added some functions commit 6dc3a8bdc710a7a03edc8a1ed737ce33a63e2de2 Author: rico Date: Fri Apr 25 17:35:58 2008 +0000 code to expand segments out to alignment anchors. commit 492d1c136c5098739bd2b0e3c6218f8085ce2631 Author: fanhsu Date: Fri Apr 25 17:30:53 2008 +0000 Added gsidSubjSeq.sql. commit 70d70d8148e53151acd473c9c8422bf8f6f6f67a Author: rico Date: Fri Apr 25 17:26:31 2008 +0000 fixed commit a265ac466719aada6b97291eb653b2c712db6c6f Author: rico Date: Fri Apr 25 17:25:15 2008 +0000 Added option to limit species under consideration commit 1b8f3f988d4afd43536e883a5f60e0a554b42f4f Author: angie Date: Fri Apr 25 17:04:44 2008 +0000 Added SQL code from Tim to increment the varchar(6) qid at runtime, so the developer doesn't have to make a last-minute edit before running the sql. commit 40e2eb0dc20997706aa938294ccafba154852d96 Author: aamp Date: Fri Apr 25 16:35:13 2008 +0000 Centered the scalebar. commit 0283fd812dff8f2fb3e4ee25cf81b56f94e3c164 Author: galt Date: Fri Apr 25 15:00:10 2008 +0000 "Encode release log update" commit 92541632d26183a13cb3c91988d64573b285dbf4 Author: galt Date: Fri Apr 25 15:00:04 2008 +0000 "Release log update" commit 80c7e17d7af4307fd115999fd22a5d7cf82fed4a Author: kent Date: Fri Apr 25 12:28:29 2008 +0000 When a new transcript can be viewed as an extension of multiple old transcripts, pick the closest old transcript as the extension. Allow the terminal UTR exons to contract as well as expand and still consider it compatible with previous accession - a new version rather than a new accession. commit a002eb3cf86ff65e322d46bd37ab2f7a9ed04e5b Author: rhead Date: Fri Apr 25 00:11:26 2008 +0000 Changed clear out of releaseLog field so that notes for other orgs are kept. We want release log entries for these (for nets and chains, for instance). commit 5e3da432ec727a7caca2869d0ad2b0b69c06e8af Author: tdreszer Date: Thu Apr 24 23:34:39 2008 +0000 Placed cavPor3 in the pushQ commit b403234919ba3f886c6c5809bb50be6f231062b6 Author: aamp Date: Thu Apr 24 23:13:02 2008 +0000 second draft on the scalebar. commit a674eb8871739e46f36303324564c7897cc85f42 Author: angie Date: Thu Apr 24 22:48:38 2008 +0000 One more slight tweak to wording at end. commit cb5f0c5b75f204886f2c3e4f8360ee328bb56d05 Author: angie Date: Thu Apr 24 22:44:13 2008 +0000 Added more detailed suggestions to the advice printed out at the end. commit 5fb819223312d4e0877b7336df7590a82c84fc1b Author: tdreszer Date: Thu Apr 24 19:10:13 2008 +0000 The cavPor3 doc file which does 6 blastz's (hg18, mm9, rn4, oryCun1, monDom4, galGal3). No multiz yet and not quite done with the makePushQ step. commit 7cf944569622648aee9b64b620737b7c0029f2d3 Author: angie Date: Thu Apr 24 17:28:32 2008 +0000 Put isEmpty check before sameString (thx Hiram). Added to warning about non-genomic target match on - strand. commit 285af6813a05acdd4fc12e9ce39633604e2c8f96 Author: kuhn Date: Thu Apr 24 16:21:14 2008 +0000 simply rearranged an labelled existing contents commit 0eaa97a74535b09c97fc3eb7f1d8c1e640ddc77f Author: galt Date: Thu Apr 24 15:00:08 2008 +0000 "Encode release log update" commit f58afccbdfbab968783d59f274943b2224379519 Author: galt Date: Thu Apr 24 15:00:05 2008 +0000 "Release log update" commit e45014e8ee0ea0c1623e71ea38b6e8a3d4fab924 Author: galt Date: Thu Apr 24 00:17:51 2008 +0000 v12 = detect sick nodes and batches commit 43fdfc3a313b658fe3ec434f23f02e352798c395 Author: kuhn Date: Wed Apr 23 23:14:31 2008 +0000 rearranged some chains/net priorities commit a35f2af9c90253b384ddb99bab8c3483843d20b3 Author: tdreszer Date: Wed Apr 23 23:02:11 2008 +0000 Took Angie up on the offer to add the default usage for Broad. commit 0c89856ad1347c9e65b98e1b32fa4b689036a308 Author: ann Date: Wed Apr 23 22:48:02 2008 +0000 bringing this up to the latest version (see marmoset/calJac1) commit affe4e5f37039cdbfe528059aadbfe63b585c192 Author: kuhn Date: Wed Apr 23 22:44:30 2008 +0000 added image for old frog conservation commit d9752e3c0deb2eecffdfb6e127f99143554fcd39 Author: rhead Date: Wed Apr 23 22:33:38 2008 +0000 Moved mouse to match conservation track. commit f4386c98e0f938e07724a93f4be9a737c8d01310 Author: kuhn Date: Wed Apr 23 22:21:01 2008 +0000 removed some kruft from the output so the sort works properly commit 52d83b88bd12291efaa8225234b37a0785a1afdf Author: hiram Date: Wed Apr 23 20:52:55 2008 +0000 Add credit to Hiram for track display advice commit 09f2ecaad640c7b16329f80d5a0ade2572d0dadf Author: hiram Date: Wed Apr 23 20:50:57 2008 +0000 Add Methods description commit b391858eade5b43cfc81ff03f29a083656e4c847 Author: pchan Date: Wed Apr 23 19:11:18 2008 +0000 change wiki server from cali to lowedev commit f23ce5267e807f00f8bbad560411d819af2cb1fb Author: donnak Date: Wed Apr 23 19:06:40 2008 +0000 Fixed a few typos. commit f1e58a4001258dad02bb5f3156ff11aeaa44d0f1 Author: donnak Date: Wed Apr 23 18:52:52 2008 +0000 Added calJac1 news item. commit ce005e08b46ae5acc2b90c1ee9b528d72dfe89a2 Author: donnak Date: Wed Apr 23 18:52:11 2008 +0000 Updated the marmoset credits. commit 81d613aec38bf24639c92b840543f45010d2c416 Author: donnak Date: Wed Apr 23 18:36:59 2008 +0000 Archived 1 item. commit e485e1ce848b97bb406d2a2257619698e07e1ba8 Author: angie Date: Wed Apr 23 18:36:12 2008 +0000 Rolling back previous change -- needs to be fixed in trackDb (pcrResult.c). commit a43e75da8abc9b9889a62f460e1db55054887c46 Author: donnak Date: Wed Apr 23 18:31:46 2008 +0000 Updated Assembly Details section. commit cf96e2b3b3ae56b39cca8190da0fc7479cc4f423 Author: angie Date: Wed Apr 23 18:31:33 2008 +0000 Disable next/previous buttons because that code relies on db queries. commit a83db40bebc39a9607e0aaca4955455431f16d01 Author: angie Date: Wed Apr 23 18:12:43 2008 +0000 Fixed stupid bug: copy/paste from hgc. commit 07b51d4e4e9567d31d0dd2c97e0eaf0f89d9fe59 Author: angie Date: Wed Apr 23 18:12:02 2008 +0000 Disable next item/exon buttons since that code uses database queries to search. commit f19e06f4507b38045e15716839a1a4797b1a0d2c Author: angie Date: Wed Apr 23 17:53:28 2008 +0000 Added hgPcrResult so base diff coloring can be enabled/disabled. commit 4d2cc2c41ae0cc55a3afceae2f6ce0c3cabfbf38 Author: angie Date: Wed Apr 23 17:52:48 2008 +0000 Use the new pcrResultFakeTdb and printTrackHtml instead of manually slurping in help file. commit a3eb7bfd1bc9faf26b743e365a12e657e11576b4 Author: angie Date: Wed Apr 23 17:52:11 2008 +0000 Moved code from hgTracks.c up into hg/lib/pcrResult.c for sharing with hgTrackUi and hgc. Enabled hgTrackUi link for pcrResults in hgTracks. commit 9e246888687c5fd5606491c22b96893c60378be9 Author: angie Date: Wed Apr 23 17:48:28 2008 +0000 Added hgPcrResult to baseColorGotSequence. commit c8813c94bb0591fef9e8dad0fef5b5818d31ae46 Author: donnak Date: Wed Apr 23 16:50:09 2008 +0000 Added calJac1. commit 0f5d6b908678d487c1cafd8bc83d1f3b60730df2 Author: ann Date: Wed Apr 23 16:13:21 2008 +0000 tidying up commit f5a8c9c7b0b93c415e9ac6085611e0f9df96e5bf Author: galt Date: Wed Apr 23 15:00:14 2008 +0000 "Encode release log update" commit e1f5ed9e0d9efc8a3056b3ee22855cd1790ecc7e Author: galt Date: Wed Apr 23 15:00:11 2008 +0000 "Release log update" commit 98cd8b789f25659747177e6e1e6da83d087c2b4f Author: markd Date: Wed Apr 23 06:19:37 2008 +0000 added option to get trackDb.sql out of another directory commit fe2c86e539525ed10988701419acde0dc9decc35 Author: aamp Date: Wed Apr 23 00:57:38 2008 +0000 Added scalebar to Base Position track. commit 03df3694f019455a0289745143f612a341d0e810 Author: hiram Date: Wed Apr 23 00:09:47 2008 +0000 Update ensGene to v49 for bosTau3 commit 2534127791432ebe19741926e2dbe06728a14e5c Author: ann Date: Tue Apr 22 23:48:26 2008 +0000 added optional flags for getting priority and visibility locations commit a23ecfe60d1c77213c6055c8149c0386f8392466 Author: angie Date: Tue Apr 22 23:28:54 2008 +0000 Added a note about the hgc sequence display. commit 2665866fe1c8147d3ba6dfc1bf9433bfb2c4326b Author: angie Date: Tue Apr 22 23:22:53 2008 +0000 Updated again: base differences are highlighted. commit 97856fe86c045cf8d1bbb35b53e82dcc54987c26 Author: angie Date: Tue Apr 22 23:07:06 2008 +0000 Added baseColor/indel support for PCR results. commit 1cc58a1a53e46a85bd0533058a7e50e18b3a559b Author: angie Date: Tue Apr 22 23:04:21 2008 +0000 Moved hgc code for reading PCR Results primers file and psl file up into hg/lib/pcrResult.c for sharing w/hgTracks. commit 7f2e2eb746e1e6da88a5a7731e95988f8cd0a238 Author: kayla Date: Tue Apr 22 22:09:12 2008 +0000 added calJac1 commit c66a5a38bb6218f64a640838dfa92060d533d3a3 Author: tdreszer Date: Tue Apr 22 21:56:55 2008 +0000 Added rabbit blastz nets for guineaPig commit 673d78374da0b51e02678902c8d99e04bb76865b Author: tdreszer Date: Tue Apr 22 21:56:27 2008 +0000 Added Rabbit blast chains for guineaPig commit f11b09f7973685b2f5ef1c9b3f77a03d61c84fda Author: tdreszer Date: Tue Apr 22 21:54:44 2008 +0000 Added rabbit(OryCun1) which will show up on guineaPig browser commit b15ee43f223b3594d428a191ceed2d5115d9d84f Author: ann Date: Tue Apr 22 21:00:43 2008 +0000 moved this section to the training.html page commit e37f8d8ff0b373d5bcebcd79e839a26538c167c4 Author: ann Date: Tue Apr 22 20:56:26 2008 +0000 moved links from FAQ index page here and reorganized them. this page used to redirect to Open Helix. commit 761cffe70c55690ae173e64f9a7ed31abaf607b5 Author: larrym Date: Tue Apr 22 20:06:55 2008 +0000 galGal3 and canFam2 swap commit ec00bfeaab99a2fe4f8a546fca36397e147392aa Author: braney Date: Tue Apr 22 19:40:21 2008 +0000 finished human proteins track commit ce20198d87c00dc99e3beb61af595cda8cf97079 Author: larrym Date: Tue Apr 22 16:13:46 2008 +0000 finish dog vs. horse commit 8d41a1a27cc4102b8af4e118d9a942da90a37984 Author: galt Date: Tue Apr 22 15:00:05 2008 +0000 "Encode release log update" commit 133e8f97f1ff0c4aa3ec6d0f5af40be640a1f362 Author: galt Date: Tue Apr 22 15:00:03 2008 +0000 "Release log update" commit ea9f78c1edc95c638cdfbc332631be01234cdbaa Author: angie Date: Tue Apr 22 05:16:12 2008 +0000 Updated to match display change. commit 44df684c8f8a277d200ed37c95089328d3341a8b Author: angie Date: Tue Apr 22 05:09:20 2008 +0000 Cosmetic: changed variable names bed->psl to reflect changes in track storage. commit a209ea7e60b627498fc1007df8eb07bb3c0a2838 Author: angie Date: Tue Apr 22 05:06:15 2008 +0000 Use psl instead of bed for saved PCR results, because we'll want to hook into the psl base coloring code. Also, draw PCR result as one block (with exon arrows) instead of one block per primer. In pcrResultTg, build tdb first and call trackFromTrackDb on it. commit 7644d8fd54b1d765c107ee70411bc4e5c8dd61a5 Author: angie Date: Tue Apr 22 05:05:52 2008 +0000 Use psl instead of bed for saved PCR results, because we'll want to hook into the psl base coloring code. commit a2d2142b735e0d660a72191bec6f5be358e45702 Author: markd Date: Tue Apr 22 01:13:15 2008 +0000 added N-SCAN gene predictions commit 7e79ba5c78d6ea30684d31e51964084f87308497 Author: angie Date: Mon Apr 21 23:18:10 2008 +0000 Woops, need to revComp PCR result seq when strand is -. commit a0ef9492ba94bab63ea284511ee8b123fbc82ec6 Author: fanhsu Date: Mon Apr 21 23:14:47 2008 +0000 Created hivMn2.txt. commit 8a2fe0f5442a6ac2bf5653fee4a75e954d896875 Author: ann Date: Mon Apr 21 22:52:44 2008 +0000 refactored how the lists are created and displayed (by grouping) commit 2ee9ea5a454925a4a9a7f1875d7b312a832ce649 Author: kuhn Date: Mon Apr 21 22:46:04 2008 +0000 clarified a head commit b74fc7cba02b8b84826598209131edf771077965 Author: kuhn Date: Mon Apr 21 22:19:22 2008 +0000 added mm9 to dbs not using knownGeneLink commit eae3e37401a9eccce7af3cd5d0d31cf277b41ab3 Author: aamp Date: Mon Apr 21 21:02:24 2008 +0000 Added affy human exon distance. commit d07cfef546b553d91e774061801c300ad86d4a46 Author: kuhn Date: Mon Apr 21 18:29:52 2008 +0000 reordered list of orgs to match display and fixed typos. thanks, pauline commit a84218edfc8936225573ca0f2582266ac63583e7 Author: braney Date: Mon Apr 21 17:43:14 2008 +0000 starting human proteins track commit 4f2ff5150eb55339c9d9a86384f1c1e95a3d8c29 Author: angie Date: Mon Apr 21 17:32:00 2008 +0000 Updated the sections on setting up non-genomic PCR targets (for UCSC Genes and a snapshot of native mRNAs). commit a018f157737fac7265e06a12adaa1f02e020a87b Author: braney Date: Mon Apr 21 15:15:51 2008 +0000 finished human proteins track commit b728d3e9243e787ecba9b5e83e96ccb71c3c232f Author: galt Date: Mon Apr 21 15:00:04 2008 +0000 "Encode release log update" commit fc074ac9c9bac3658cf3255561484a1b0d5de38b Author: galt Date: Mon Apr 21 15:00:02 2008 +0000 "Release log update" commit 7eff3d9970659674c4c53d76782b4c285ead0a44 Author: angie Date: Mon Apr 21 05:07:52 2008 +0000 Added PCR Results track. commit cd0a9ecc11fbce3125493573076b11371424c1cd Author: ann Date: Sun Apr 20 23:43:51 2008 +0000 added some clarification around the Gap line display. commit 1d3d3556cc5f71a10e7e3b05f5a40adb241022b2 Author: larrym Date: Sun Apr 20 18:16:59 2008 +0000 Fix decleration for cgiMakeCheckBoxWithMsg commit bd6e06f2223f3c8fcd12f9555640a29364cf8af5 Author: galt Date: Sun Apr 20 15:00:05 2008 +0000 "Encode release log update" commit a7b757880edd3a7eae0c6b121b34f9980a6ee1dd Author: galt Date: Sun Apr 20 15:00:03 2008 +0000 "Release log update" commit a636733f925dfdd77c9840ac8050e4e0cc471024 Author: donnak Date: Sun Apr 20 07:00:08 2008 +0000 More mods to marmoset credits. commit 64ee3e2f4ba3e260da77a01b6b29692f1a57dea8 Author: donnak Date: Sun Apr 20 06:59:01 2008 +0000 Added more people to marmoset credits. commit eb9fad294d2cf48bbaa0cf7db09ec731d62f538a Author: donnak Date: Sun Apr 20 06:56:18 2008 +0000 Initial draft of marmoset credits. commit 5b83914e85a1195929288dfe0f6940b7da9ada90 Author: donnak Date: Sun Apr 20 05:55:11 2008 +0000 Added some new pubs. commit b3b3d4d9356a8a10564e18251ecc57680143e073 Author: braney Date: Sat Apr 19 21:41:28 2008 +0000 started human proteins commit 92500ec207e38392dd9dd8a9bd0f4481b4792846 Author: donnak Date: Sat Apr 19 20:27:22 2008 +0000 Updated several pubs with current links. commit e877ccb9eca87d9afc6a70d75bf987d9dc6ee6f9 Author: braney Date: Sat Apr 19 18:46:06 2008 +0000 finished human proteins track commit e0d271f29a7ab90950d64a68a9e18df0b9a5b10f Author: galt Date: Sat Apr 19 15:00:06 2008 +0000 "Encode release log update" commit 9ece9b2e89932939128444e135361afef592ff34 Author: galt Date: Sat Apr 19 15:00:04 2008 +0000 "Release log update" commit cacec630bfb451433790a7f02a6c014c3c5f7b08 Author: hiram Date: Sat Apr 19 00:17:55 2008 +0000 First look at the 6-way conservation track commit 29b355180d033becfccf2c738995dd7583e461c3 Author: hiram Date: Sat Apr 19 00:15:56 2008 +0000 Adding the 6-way multiz commit 0bf35a92389d841d65069db0a1c73bba44de8d57 Author: larrym Date: Sat Apr 19 00:15:04 2008 +0000 use javascript to support check all and clear all w/o a round-trip commit bd70ed63d9b16242dad12b6a3c0ff9588bc3c875 Author: tdreszer Date: Sat Apr 19 00:11:53 2008 +0000 Overode chain matrix for hg18 and mm9 commit 1baa873c4c5f142e29f6cba6427570996ce6f4ca Author: larrym Date: Sat Apr 19 00:11:06 2008 +0000 add cgiMakeCheckBoxWithId commit eba4d6124638a19c0e6d21c9e7e7814f6ecee1a6 Author: kuhn Date: Fri Apr 18 23:59:16 2008 +0000 fixed a label on chainRn3 track commit cf7fcd5ee951455c769ec1812c85f67529869a54 Author: angie Date: Fri Apr 18 23:55:57 2008 +0000 Added PCR Results track. commit 2a8b934065b53b8c449264deceb17d1b837ce6a7 Author: kuhn Date: Fri Apr 18 23:53:17 2008 +0000 rearranged priorities for nets and chains for canFam1 commit 10487016495695b7d7334c52064b1277b3c46aaf Author: hiram Date: Fri Apr 18 23:50:22 2008 +0000 Added reciprocal best for each blastz, and started the 5-way multiz. Have problem with hg18 recip best did not work commit a73a089d9c311bcb41609259ad13db276943ac5e Author: angie Date: Fri Apr 18 23:49:52 2008 +0000 Use struct targetDb instead of inlining its fields in targetPcrServer. Write out results to trash files and cart variable for use as a track. Also moved out targetDb validity-checking code to targetDb.c. commit 088bab71435c0d52aa208f7631577fe11729aba8 Author: kuhn Date: Fri Apr 18 23:49:22 2008 +0000 rearranged priorities for nets and chains for canFam2 commit 5cc6e94c63e0244a762e5a972c37a9dc85081a4b Author: hiram Date: Fri Apr 18 23:48:51 2008 +0000 Add reciprocal best for braFlo1 Lanclet commit a68e83aec4d29ab0c412f3cd11d717e24fad0e7c Author: hiram Date: Fri Apr 18 23:48:18 2008 +0000 Added all the swaps, and started the 6-way multiz run commit c2d040d8651885a810bd098cb18a540515d8f9f6 Author: ann Date: Fri Apr 18 23:48:13 2008 +0000 logic error commit 041eed99b49ff2616679bbeaf52aa002d3d17b44 Author: tdreszer Date: Fri Apr 18 23:48:06 2008 +0000 Added cavPor3 chain/net and prioritized it with rodents commit 2d3291625701a7cf9fec9ba612ee32c28aaba54b Author: tdreszer Date: Fri Apr 18 23:46:38 2008 +0000 Chain matrix for guineaPig was overridden from root trackDb.ra commit 85dc313e9e3edd826b51631f21f628f0298dbdba Author: tdreszer Date: Fri Apr 18 23:41:35 2008 +0000 Added cavPor3 as a rodent commit f3c01ce2caa9e9c412447082a1f3187fb8837d17 Author: tdreszer Date: Fri Apr 18 23:40:48 2008 +0000 Added cavPor3 near as a rodent commit 177f8e2657ede4b7c77be26309b0c469029631d0 Author: angie Date: Fri Apr 18 23:34:16 2008 +0000 Added targetDb.o and pcrResult.o. commit dd9d72bc2a0929c049126274e6a45452d81cc260 Author: angie Date: Fri Apr 18 23:32:43 2008 +0000 Support for internal data track of hgPcr results. commit c5e79e88c0941e5aa240513254b1105c8d27be39 Author: angie Date: Fri Apr 18 23:31:33 2008 +0000 Describes non-genomic targets, i.e. collections of sequences that have been aligned to a genome assembly as well as tables in that assembly's db that map sequences to the assembly. Added some extra code to query the central database and check validity of results. commit 956bf4d12ab66beff9b6b2938d3f69ddfb8dcb75 Author: angie Date: Fri Apr 18 23:29:28 2008 +0000 Added support for BED 12 output to gfPcrOutputWrite* (one block per primer, spanning the product range). commit 0230b476974e926c74eee57aa395f6bd246d1979 Author: ann Date: Fri Apr 18 23:25:45 2008 +0000 removing felCat3 from generic ensGene rule commit 5942d829f46c90baa70355512265f4a5eedd5c05 Author: kuhn Date: Fri Apr 18 23:23:25 2008 +0000 rearranged priorities for nets and chains for rn3 commit 10bd259706099008d9bdd9e323571569971877c2 Author: tdreszer Date: Fri Apr 18 23:21:11 2008 +0000 Chain matrix for guineaPig was overridden from root trackDb.ra commit 60b5c792215bca778b155f4b1f94ad574476d9b3 Author: tdreszer Date: Fri Apr 18 23:18:07 2008 +0000 Rewrote Assembly Details and reduced the photo size commit 339d4115c953b1376ba986b617ff52d4df59ff38 Author: tdreszer Date: Fri Apr 18 23:16:39 2008 +0000 Adding Net description for Guinea Pig commit d988a51dd954cccca09c37a74325bd18950f20e5 Author: tdreszer Date: Fri Apr 18 23:16:26 2008 +0000 Adding Chain description for Guinea Pig commit a3d9c3b0b524702b623a207847d2aa5d561d9007 Author: kuhn Date: Fri Apr 18 23:15:16 2008 +0000 rearranged priorities for nets and chains for rn4 commit 7b5b48745cebdd9eeded2d9629c3df2e06fc7bb1 Author: kuhn Date: Fri Apr 18 23:01:09 2008 +0000 simply ordered chains by priority number to aid in cleanup commit 35bd5d420e41b66938219bb40a2824ebfeb4d751 Author: ann Date: Fri Apr 18 22:36:33 2008 +0000 fixed broken link to photo credit. commit d432af30a9c09917f422be0320fa522508d878f0 Author: rhead Date: Fri Apr 18 22:30:51 2008 +0000 Changed link to Journal of the American Statistical Association to the site the original link was getting redirected to. commit 05d33c1f2c2ff87b6875780c45616e8cb5db7f84 Author: kuhn Date: Fri Apr 18 22:28:49 2008 +0000 rearranged chain/net priorities commit 2644ef48315ebac57dca26e8aa5b76ce509e7489 Author: ann Date: Fri Apr 18 22:21:53 2008 +0000 fixed capitalization and duplicated items. commit 518f4c7b316f5a11cbddc05abb0aa039f4374e42 Author: ann Date: Fri Apr 18 22:20:59 2008 +0000 fixed link to photo credit commit 9e2af7fbb4409430b519f2f0472aabb88a534fc4 Author: kuhn Date: Fri Apr 18 22:15:08 2008 +0000 renamed chainMon1 to use org name as that is the version on the RR commit 55e3e8117988ca20adee1aed93d710fda185e0f3 Author: kuhn Date: Fri Apr 18 22:11:16 2008 +0000 rearranging hg17 chains and nets. moved elephant block from hg18 to human. renmed some chains to use o_db where older than current on RR commit 2f7af876bf6d5be09e4ec6ad28fc5d1286ba4cb9 Author: rhead Date: Fri Apr 18 22:06:34 2008 +0000 Reworded section on using human EST clusters as evidence. commit a9f342b0884d5078675beee8a616cab5fa2616bc Author: larrym Date: Fri Apr 18 21:51:17 2008 +0000 start dog vs. horse commit a495d8c102d3e4af19b1d3d4f504926a72c1400d Author: angie Date: Fri Apr 18 21:51:00 2008 +0000 Barebones description -- no mention of non-genomic targets for now (hold off on that until we're ready to release those). commit a9f96f1ffb62c0d92e49c05b540e454cabc3982e Author: kuhn Date: Fri Apr 18 21:14:04 2008 +0000 overriding some upper-level priorities commit a5fbfb5a8a569de06770b9c87c7eb0f7ab919a7b Author: hiram Date: Fri Apr 18 19:14:16 2008 +0000 Rearrange ordering of tracks and fix some text in a description commit 86909b8066e3fab461a13e3fd40efb6c93ed3364 Author: ann Date: Fri Apr 18 19:08:24 2008 +0000 added special rule for ensemblTranscript for cat (the way Ensemlb put it together, it ends up on several scaffolds, so dupes are OK) commit 62829467912870fa199239e4d1a0bd0bd9499254 Author: larrym Date: Fri Apr 18 18:53:42 2008 +0000 finish equCab2 blastz commit 8f0fb48ba8436ffc9c45e5c035d82e60eed99ebc Author: larrym Date: Fri Apr 18 18:44:20 2008 +0000 suppress putting Ensembl link in nav bar for unknown chroms (b/c Ensembl doesn't do unknown chroms) and remove hardwired tests for databases, b/c this logic has been superceded by trackVersion table (this also fixes a bug that was causing bad Ensembl link for dm2 in RR) commit c37a94f90d5a677c638b75ff6321c2335efd9679 Author: ann Date: Fri Apr 18 18:42:01 2008 +0000 fixing up commit ff7402fe16c853e1da34ef105384a935a957eff2 Author: larrym Date: Fri Apr 18 18:25:16 2008 +0000 add isUnknownChrom commit cfd101909c3abb663ffb70c3b99a805a4476db08 Author: braney Date: Fri Apr 18 18:04:33 2008 +0000 working on human protiens track commit 203f16e67a3026113d27463bf3b239d65bb57a3e Author: kuhn Date: Fri Apr 18 17:53:57 2008 +0000 rearranged chain and net priorities to reflect phylogenetic tree for hg18 commit f285e9af375da28a31faf4068a6cb08bbe75ebbb Author: angie Date: Fri Apr 18 17:27:13 2008 +0000 Added cart variable hgtaUserRegionsDb so we don't show regions as an option if they were submitted for another database. commit af76a822b6e7389a7c48d5f797cd45bc87f7607b Author: kuhn Date: Fri Apr 18 17:11:45 2008 +0000 removed realease alpha/beta from chain/netXenTro2. no reason not to have it say 'X. trolicalis' everywhere. commit d79de2ca106e6cc10423a6a46c495d4d57bfc1df Author: angie Date: Fri Apr 18 17:01:14 2008 +0000 Bugfix: if regionType is encode but db does not have encodeRegions, force regionType to genome. commit 95c9be3af4f928207170d12a23ad633543183982 Author: kuhn Date: Fri Apr 18 16:44:11 2008 +0000 simply ordered by priority to aid in subsequent rearrangements commit 173b3ce9132c7facdab966dec593a6d3b5ee41c7 Author: galt Date: Fri Apr 18 15:00:05 2008 +0000 "Encode release log update" commit 3f493983e6f7e51d78eff8e28c52d048beccdac8 Author: galt Date: Fri Apr 18 15:00:04 2008 +0000 "Release log update" commit d7800a27a52564f7e73f12caea21016c17358ab0 Author: kuhn Date: Fri Apr 18 08:51:22 2008 +0000 rearranged nets and chains to get assemblies not on RR into phylogenetic order on dev for mm8 and mm7 commit 765873ba0d49cfc2e23f7048589a155201890e59 Author: kuhn Date: Fri Apr 18 08:37:57 2008 +0000 rearranged nets and chains to get assemblies not on RR into phylogenetic order on dev for mm9 commit a0d66e36d5507321f24c02807122ebc7de3ecc29 Author: kuhn Date: Fri Apr 18 08:01:08 2008 +0000 simply ordered chains by priority number to aid in cleanup. made some small changes in the numbers that do not affect the ordering on beta. commit 443fc3463d53a8a60dd4a50c78667f1631de1ae9 Author: rhead Date: Fri Apr 18 00:44:46 2008 +0000 Standardized use of 'n-scan pasa-est'; whitespace changes. commit cd1d57e9cabc1513f006b4776e9677d1baf46fab Author: larrym Date: Fri Apr 18 00:24:36 2008 +0000 swap hg18 and mm9 blastz runs commit dccbea14af70390a2ca8b9fb4377a7e2abbb807d Author: rhead Date: Thu Apr 17 23:53:27 2008 +0000 Turned n-scan genes track on by default. commit 6000a50a0778996a046b8a22aa88e470b3795dc5 Author: rhead Date: Thu Apr 17 23:09:41 2008 +0000 Added gold to marmoset tables ignored, per Hiram. commit 848be5baceb958c005a3cfeb47aade2e6e35738c Author: rhead Date: Thu Apr 17 22:49:14 2008 +0000 Added more rules to the gbCdnas identifier per markd. commit 9e1cbdb4d7ac21a281feacf926f71bbaca5edde4 Author: rhead Date: Thu Apr 17 22:45:49 2008 +0000 Removed gbMiscDiff table from cow tablesIngored. We check it now! commit 03723eed3e5a9abf18d49bf5bb57fc20144b6545 Author: rhead Date: Thu Apr 17 22:39:27 2008 +0000 Added rule for gbMiscDiff table per markd. Also tweaked comment line, per markd. commit d67bc3c26e99fffdc46b053c4689e5ab3d6cc313 Author: angie Date: Thu Apr 17 22:29:41 2008 +0000 Use length constants instead of hardcoded sizes in splitPath. commit cfd77d4bb9bb5ffedaa9dc9d47f4e11b3ce8bd7b Author: angie Date: Thu Apr 17 22:28:32 2008 +0000 Added length constants for file name and file extension, taken from splitPath. Since filePath.h now includes common.h to get these new constants, make the duplicate declaration of splitPath here conditional on not having FILEPATH_H. commit ad7724698bc42ca3ff806391ecb0941778dbbdd2 Author: rhead Date: Thu Apr 17 22:22:49 2008 +0000 Added multiz%way to tablesIgnored for all assemblies per Hiram. commit 57e0c7d83d1b11d95b9b0ea925bfef656f137c10 Author: ann Date: Thu Apr 17 22:20:02 2008 +0000 if there is no ensGene table on beta, do not run the beta tests commit b758a956951c509494c0e9ab197586f758048ce8 Author: angie Date: Thu Apr 17 21:58:02 2008 +0000 Added links from gene names to hgGene (also Jim's request). commit 32cc2f0b1d6b3433f4fba319d533a933ce0d26ff Author: rhead Date: Thu Apr 17 21:50:02 2008 +0000 Added unsplit gap table to $gbd tablesIgnored and removed it from assembly-specific tablesIgnored. commit 716a67494f0183eddc071a8d7d517d3be2221b5c Author: rhead Date: Thu Apr 17 21:40:07 2008 +0000 Added unsplit rmsk table to $gbd tablesIgnored and removed it from assembly-specific tablesIgnored. commit ca1d0371ca152730b52bae929ae99bd3512ac27a Author: angie Date: Thu Apr 17 21:31:30 2008 +0000 Added note about compact default view (changes that Jim requested). commit 1182c5c622ff91e49237caa92c5382631902c46b Author: angie Date: Thu Apr 17 21:02:16 2008 +0000 Added this to hide several tracks that were visible by default to make room for BDTNP ChIP/chip -- Jim's request. commit ed2930bd08b53dc99e18b20f7eab85417094e024 Author: angie Date: Thu Apr 17 21:00:47 2008 +0000 Changed BDTNP ChIP/chip settings per Jim's requests: dense by default, but with FDR 25% and extra antibody subtracks off; PolII moved up to the top because it is more general. commit 7ff309434563b237460d9fa0a7ff994fbb339219 Author: kuhn Date: Thu Apr 17 20:59:43 2008 +0000 replaced archana with pauline in notifications commit 73588e5b3113f7a32e58b90a9f50ad82360bb232 Author: larrym Date: Thu Apr 17 20:53:18 2008 +0000 use shortLabel as secondary sort key in tgCmpPriority commit 5a790ccd9de14bbbf87ea1b8250a81c6c849783c Author: hiram Date: Thu Apr 17 20:38:15 2008 +0000 Special case the Orangutan scientific name difference between UCSC and Ensembl commit 058548fcfef4c06579c2ed8e3cc2514b99e9ab7d Author: donnak Date: Thu Apr 17 19:39:56 2008 +0000 Updated Archaeal Genomes link. commit 1b22bb09a2e7b15e37764bb85feae87d80e760ec Author: donnak Date: Thu Apr 17 19:36:24 2008 +0000 Updated date on archaea news item. commit 4f50e1d5a41037f9661fbcd7b224e36e185d96b0 Author: larrym Date: Thu Apr 17 18:59:57 2008 +0000 equCab2 blastz commit cb971577fbd8ee4ddb7f2950fa147f237d3b44c6 Author: kent Date: Thu Apr 17 17:19:03 2008 +0000 Clarifying a comment. commit 4ff5c89fb7ffd737ce45f25decc2fb2d306d637a Author: hiram Date: Thu Apr 17 17:14:55 2008 +0000 Add the 25mersRepeats track commit 3eef661d9e93bf8584bcbaa29365b869e045b837 Author: galt Date: Thu Apr 17 15:00:10 2008 +0000 "Encode release log update" commit 2668b77655db184a03311ae86f90efdfc57719bf Author: galt Date: Thu Apr 17 15:00:04 2008 +0000 "Release log update" commit d1e4cdeec78028ae4a66f4c000e898050378404a Author: donnak Date: Thu Apr 17 06:34:58 2008 +0000 Commented out Regions link on topbar -- not needed on ENCODE homepage menubar for production phase. commit 71fd26f9fc2283b6ab4761fd4500c1d27b2c4b2d Author: ann Date: Thu Apr 17 00:21:49 2008 +0000 cleaning up these very dense docs. commit 11d6f4e8c8e69b72fc503ebbed45c0e6cbbef85c Author: kuhn Date: Wed Apr 16 23:20:05 2008 +0000 rearranged priorities of chains and nets to accomodate new marmoset. thanks, pauline commit f32dbf65fce966794fb8a96992f8c6ae488b75e4 Author: kuhn Date: Wed Apr 16 23:13:16 2008 +0000 rearranged priorities of chains and nets to accomodate new marmoset. thanks, pauline commit 72285e4e18e15e16023b306679b3b5c9b3f447d3 Author: hiram Date: Wed Apr 16 20:54:55 2008 +0000 Initial comments to go with this track commit 85e4f74147b580ebab0c5eea56b80727ed1babfc Author: fanhsu Date: Wed Apr 16 18:50:39 2008 +0000 Cleaned up some unused variables. commit 2b18495c32b98d3c4e9118618a6cec60c16e884e Author: angie Date: Wed Apr 16 18:14:46 2008 +0000 Make sure to reset wp_target when we are not drawing the wp_target select, so we don't get something old from the cart. commit 5ff5badbd5ed196d4c2de4d43c4720931a994039 Author: ann Date: Wed Apr 16 17:53:55 2008 +0000 corrected spelling of testis. commit 6b4cdacb307cfea32dba319413103d368f36f285 Author: kuhn Date: Wed Apr 16 17:50:18 2008 +0000 added exit after checkUnbridged failure per ann code review commit 78d1b4e3c0c847880a36e9d908a4f4076c762dc1 Author: angie Date: Wed Apr 16 17:22:53 2008 +0000 Watch out for cart variables that exist but are empty. commit 9f90c2a871504434a7ce32067944e5f36fdb80c5 Author: hiram Date: Wed Apr 16 16:50:16 2008 +0000 Show Medaka and chicken blastz swaps commit c9173c743caa189f1d3aec8f72afc77254bb4b4c Author: hiram Date: Wed Apr 16 16:49:43 2008 +0000 Clean up ancient abandonded blastz experiments commit 7561934c6ae3abbcfcb4ce07d1b7a59a50b305e2 Author: hiram Date: Wed Apr 16 16:49:15 2008 +0000 Show Lamprey and Lanclet blastz constructions commit cf2a9ac3f174b4f083192dffe0877373d4650ac4 Author: hiram Date: Wed Apr 16 16:48:50 2008 +0000 Show swap for chicken galGal3 commit 385d0b7526715d4e0bb6a8cd331dc7052810e8b3 Author: hiram Date: Wed Apr 16 16:08:05 2008 +0000 Showing the procedure for ensGene v49 update and subsequent cleaning to satisify joinerCheck commit 845ce3f96db65b5511f86e77f1dd9c7c5c8b69c3 Author: hiram Date: Wed Apr 16 16:07:07 2008 +0000 Describing cleaning operation on oryLat1 v49 loading commit c15805f929665287ca0a68ab01e99b631dfbd370 Author: hiram Date: Wed Apr 16 16:06:11 2008 +0000 finishing up the Nucleosome track loading commit ec1ab00a428c4cd4706e208b4d0885a0fb3b5e1e Author: hiram Date: Wed Apr 16 16:00:40 2008 +0000 Done with Lamprey and Lanclet blastz. And loaded transcriptome data commit fd8e8f570d83aa378dc492ad0c92b3e16f9963dc Author: kent Date: Wed Apr 16 15:46:54 2008 +0000 Adding ccds processing - trumps even refSeq. commit 02cf2190a8b1980a0a1002a45f1760d8537b8249 Author: kent Date: Wed Apr 16 15:38:33 2008 +0000 Adding ccds field to cdsPick structure. commit 5675a7f06d098fcafdf8b20290bbb74ad9420e61 Author: kent Date: Wed Apr 16 15:24:27 2008 +0000 Making this calculate CDS position in RNA coordinates and produce properly formatted output. commit f2025cf839cd8fc2ca3d226c8f63f4d9dc0a3c46 Author: galt Date: Wed Apr 16 15:00:06 2008 +0000 "Encode release log update" commit 958f89b549973cf1db2646c771fe9d6defcb5931 Author: galt Date: Wed Apr 16 15:00:04 2008 +0000 "Release log update" commit ca1b65224db6ad5b22e54db95718282e3db6ed2c Author: donnak Date: Wed Apr 16 07:28:39 2008 +0000 Archived a news item. commit 2190a5d4a8fbd064f1f8d8a1c2aff176c3c810da Author: donnak Date: Wed Apr 16 07:28:25 2008 +0000 Added archaea browsers news item. commit ca5b6a5c211976fa0751ed33cae5b1f6cd1d9365 Author: donnak Date: Wed Apr 16 06:35:25 2008 +0000 Added "Archaeal Genomes" link. commit a00dbb97487fd2b0233ca05fc39a2578678ce07c Author: braney Date: Wed Apr 16 00:19:20 2008 +0000 allow < and > in names, make sure reRooting NULL's the root (courtesy M. Pheasant) commit cbbca225505bd644f8d35c8b199bb7119ae6357e Author: kuhn Date: Wed Apr 16 00:18:20 2008 +0000 clarified that example is from human (hg16? maybe? still works in hg18) commit a887ffe8aefca5be0528593c1defba0192075237 Author: kate Date: Wed Apr 16 00:04:03 2008 +0000 Broad stem cell ChIP data in progress commit 2a7365cf5458a4edb50762c94b7987df42351f45 Author: hiram Date: Tue Apr 15 23:14:56 2008 +0000 The transcriptome data certainly looks like genes commit e9ba6c2dc821f0a84f588417a7f0122b35b15ae5 Author: hiram Date: Tue Apr 15 23:09:55 2008 +0000 Adding Transcriptome database track commit a3cbca8b73cba33f6389947d89fceda12afd1e05 Author: kuhn Date: Tue Apr 15 22:13:06 2008 +0000 oops. cavPor3, not 2 commit fda5913b7ac69453602b024b2a9c2c75f95cd4ca Author: ann Date: Tue Apr 15 21:40:11 2008 +0000 added section for hgFixed.trackVersion commit 0a80115d809fa11e6c4b26bd22f91e6c265237de Author: kate Date: Tue Apr 15 20:29:09 2008 +0000 Add support for syntenic net on scaffold-based targets commit 58a5c7c3429f6d11ba31b7f7a4c72bb3cfa2901b Author: angie Date: Tue Apr 15 20:06:36 2008 +0000 Bugfix to recent fix in compositeTotalHeight: maximumTrackHeight() is per-subtrack, not per-composite. commit 0612a62a90693cb4c905462243ddd2ef5a8d269f Author: ann Date: Tue Apr 15 19:34:51 2008 +0000 making page more readable commit edf430418f26d674462da6e7af96f9893be4ddff Author: ann Date: Tue Apr 15 19:33:25 2008 +0000 Ensembl changed the gene name prefixes. I changed the search spec accordingly. commit 63d03702b28ed99524689ccf6e34bc7aa3243a08 Author: kuhn Date: Tue Apr 15 18:45:31 2008 +0000 added whitespace around image commit 9bc54247e57c657ae248b1688440ad22f1c6e76a Author: hiram Date: Tue Apr 15 18:27:19 2008 +0000 Removed duplicate text that doesn't belong. commit 6b5abac78a49be9a3c6c098d53a80767b4ac0ec1 Author: rhead Date: Tue Apr 15 17:51:24 2008 +0000 Changed unbridged to bridged, added description of white lines representing bridges, fixed spacing. commit 7e60340af05f7a6a4b9288fc65e166344e41d86f Author: ann Date: Tue Apr 15 17:12:18 2008 +0000 adjusting priorities of nucleosome tracks commit e3c0dbe197b8eb52325f841d466a18045f81b9d9 Author: aamp Date: Tue Apr 15 16:50:56 2008 +0000 "New version number v180" commit 0a8c6a9d4eacf9df015611997e67844352d9dc11 Author: aamp Date: Tue Apr 15 16:48:25 2008 +0000 Fixed EC names. commit 37e07ebdeb6cfa1ede2fac670b90232f28a43393 Author: aamp Date: Tue Apr 15 16:47:56 2008 +0000 Fixed names in EC track. Kind of a pain. commit 844d1bd1afe7760e92a79ba48d9b092548e96fe1 Author: ann Date: Tue Apr 15 16:47:30 2008 +0000 added nucleosome tracks to tablesIgnored for ce commit 7414cf874eaddda1d67c30aff85beafc8ca678a6 Author: hiram Date: Tue Apr 15 16:39:03 2008 +0000 Remove superfamily link display for ensGene tracks, no longer works correctly after ensGene updates commit 3f57289c7df0db926bdc239ad468b898f679721b Author: galt Date: Tue Apr 15 15:00:18 2008 +0000 "Encode release log update" commit 84af3573fc6df4f5e3d34026f0aa3491c758ab66 Author: galt Date: Tue Apr 15 15:00:13 2008 +0000 "Release log update" commit 9b454c19ba627a696dc258af360cfaad19421f07 Author: pauline Date: Tue Apr 15 00:01:52 2008 +0000 Fixed type-o in script name. commit a31c4053a701fee5b5c6d84568cd3994ff2deffa Author: angie Date: Mon Apr 14 23:50:08 2008 +0000 Check existence of file/table before checking timestamp. When showing results from a non-genomic target, add a short note at the top of the page. commit 3fdab384127adf702614f7903f1746e743b3a00a Author: pauline Date: Mon Apr 14 22:55:20 2008 +0000 Added trackDb file to add matrix variable for calJac1 chain. commit c99ec6529bfcb68ea7d10787527ee436e0ecb0c5 Author: pauline Date: Mon Apr 14 22:53:27 2008 +0000 Fixed matrix variable for calJac1 chain. commit 845895d837f60f56bf3ce6c89a63c18f44da6a67 Author: pauline Date: Mon Apr 14 22:47:49 2008 +0000 Added trackDb file to add matrix variable for calJac1 chain. commit e54c6379c3e39250d00ffcd87cc1716c884f0c08 Author: kuhn Date: Mon Apr 14 22:47:07 2008 +0000 reordered nets and chains commit adc90fb2673b47816b48b0890ade2fdc475e0c46 Author: kuhn Date: Mon Apr 14 22:41:15 2008 +0000 tweak commit ef513d2f874e0e9406abf38ee9a545df4988e352 Author: pauline Date: Mon Apr 14 22:39:51 2008 +0000 Added trackDb file to add matrix variable for calJac1 chain. commit 9d74eb9ff2a96844382cc2ec390ff840067a7e9d Author: kuhn Date: Mon Apr 14 22:28:01 2008 +0000 reordered nets and chains commit 11e4ee03a09f4a1a7ad755168a7792cba6755156 Author: fanhsu Date: Mon Apr 14 21:55:37 2008 +0000 Created gsidPbGateway.c (a customized version of pbGateway.c) for GSID. commit a38df77e2425cad9cd0e7c1a7678c8f1cc82acc8 Author: fanhsu Date: Mon Apr 14 21:52:00 2008 +0000 Created makefile. commit 66b2189554e6ad631ee715e7c2e5c4257b08392b Author: fanhsu Date: Mon Apr 14 21:30:57 2008 +0000 Updated for GSID needs. commit f801dd00ac185971cac6684731fb511e7168a1f8 Author: pauline Date: Mon Apr 14 21:30:16 2008 +0000 Added matrix variable for calJac1 chain. commit d16d57436f1855aaf3a0e8513e38bae09beee1b7 Author: hiram Date: Mon Apr 14 20:59:50 2008 +0000 Adding Sidow lab reference in the Credits commit 74edabecba51303714418f74e311b347ad948228 Author: pauline Date: Mon Apr 14 19:15:59 2008 +0000 Added matrix variable for calJac1 chain. commit 4e4bcee91aa15e710ffda3e416d1728e7b58df8a Author: pauline Date: Mon Apr 14 19:00:42 2008 +0000 Added matrix variable for calJac1 chain. commit 436ec5218dbd859760bf0479ad22b97621a78976 Author: kuhn Date: Mon Apr 14 18:58:58 2008 +0000 moved horse chain from betw human and rodent commit 10508d19cbd94f20091518585182f3bd727f4d5a Author: larrym Date: Mon Apr 14 18:24:57 2008 +0000 equCab2 chain/net commit 75a5abdc2f3383ec0a572d06a0bd7aecf2fe4295 Author: larrym Date: Mon Apr 14 18:10:59 2008 +0000 initial checkin commit cf03a28a5eab3674038765d08cec6d7ea6b46353 Author: larrym Date: Mon Apr 14 18:09:09 2008 +0000 add ctgPos2 commit eaba7017fbc9c8cb71c1f51c20a6dd894cf2d997 Author: larrym Date: Mon Apr 14 18:07:26 2008 +0000 add equCab2 commit 6055483e1e3b166cf66253506238fa570c348a5a Author: larrym Date: Mon Apr 14 18:05:06 2008 +0000 initial checkin for equCab2 commit fd7aa4e20bd0d96502c63b874dc084129f8a81ec Author: kuhn Date: Mon Apr 14 17:58:54 2008 +0000 removed redundant block of horse chains commit 8664cb215d63c9cffc77d4d648a92f19fe7370d8 Author: hiram Date: Mon Apr 14 17:23:37 2008 +0000 Adding ensGene construction instructions commit ccbf5ba0999c2f571167a2ccf1123cbb0ae8c9c5 Author: kent Date: Mon Apr 14 16:37:13 2008 +0000 Implementing an improved strategy for CCDS/UCSC Gene associations. The previous strategy would associate multiple CCDS with the same UCSC Gene several hundred times. This is reduced to four now by preferentially avoiding transcripts with upstream start codons, and by when multiple mappings are possible and otherwise equivalent just using an unused transcript if available. The four remaining cases are all quite interesting and unusual, and worth fixing in an abstract way, but not worth holding up the release for. commit 22954516e3878e12ca877b86a5b9cc2ab127011f Author: galt Date: Mon Apr 14 15:00:06 2008 +0000 "Encode release log update" commit 47f6a7f63632eb2e293e7a53832ba8aa2d47e2db Author: galt Date: Mon Apr 14 15:00:04 2008 +0000 "Release log update" commit 0aba498a1153a0797fdff6a859e97b63b727bc4b Author: kent Date: Mon Apr 14 11:58:13 2008 +0000 Fixed logic error in properSubsetOf. Added some (ifdefed out) debugging code. Tweaked verbosity level to aid debugging. commit d848e3f7eb2b5b7dc66c9281f117067f3a05eaba Author: fanhsu Date: Sun Apr 13 23:45:29 2008 +0000 Added clinical dates section. commit 8fb308e018d9aedaa86bdeccc589f129c315c025 Author: galt Date: Sun Apr 13 15:00:05 2008 +0000 "Encode release log update" commit bc226e9746ea513ee69ee8559f2d38ebcbba56dd Author: galt Date: Sun Apr 13 15:00:03 2008 +0000 "Release log update" commit 45e3cf39773ec33ff0bc284a2e2c4162c4382667 Author: hiram Date: Sun Apr 13 04:11:08 2008 +0000 Swap blastz from braFlo1 Lanclet commit 639ad1988fcad40baa4d706174710a75a50669c6 Author: hiram Date: Sun Apr 13 04:10:35 2008 +0000 Running petMar1 Lamprey blastz and swap commit 590536b2ae1916e4a86dad6b3b4ce1b48ef02a71 Author: galt Date: Sat Apr 12 15:00:33 2008 +0000 "Encode release log update" commit 0200883580438ea41904e43e3b130e133a170d0e Author: galt Date: Sat Apr 12 15:00:30 2008 +0000 "Release log update" commit 014f6e6d461996e5f53029d2e67da8fd80caad78 Author: galt Date: Sat Apr 12 01:27:07 2008 +0000 fixing ftp text and behavior on upload form commit 9d824bfc16068bd8b95f839c3d920f8e047a7f24 Author: pauline Date: Sat Apr 12 00:16:04 2008 +0000 Copied chainCalJac1 block from top level and added matrix parameter. commit ecdff900a54de403d2df21ec29771199b068e56e Author: rhead Date: Fri Apr 11 23:45:18 2008 +0000 Replaced a multitude of multiz and phastCons tables under gbd tablesIgnored with wildcard entries. commit 0fa0c35281d29100e279ae4d73021f796fee3013 Author: hiram Date: Fri Apr 11 23:39:04 2008 +0000 New maximum limits for nucleosomeControl*Coverage and monoNucleosomes* commit 4c7537af1e93ae52b0aed4d2cb06648bb04240ff Author: ann Date: Fri Apr 11 23:30:24 2008 +0000 indenting correctly commit a32e0d5fe9c3f5f6d4c8b17de13635aefd93a36e Author: kuhn Date: Fri Apr 11 22:15:18 2008 +0000 dropped hg18 from knownGeneLink relationship - the table is gone in KGIII commit cda41841783fc9fd34b19e55da14fd3721a2049a Author: kuhn Date: Fri Apr 11 22:04:22 2008 +0000 added rule for gbCdna relationships as well as guinea pig and horse2. thanks pauline and mark commit 8952d245b8f0a4bbaa03d8ed86c8ac509c5ce27f Author: ann Date: Fri Apr 11 19:14:53 2008 +0000 made one big loop per database, instead of looping through each test commit 6c40fec80807ba2c85cd4a4c8ee691ba98d41edd Author: pauline Date: Fri Apr 11 18:28:59 2008 +0000 Fixed broken links. commit 86e51c8afdfd8d2a3a48b47610e0b5e5679dae37 Author: larrym Date: Fri Apr 11 17:04:34 2008 +0000 add equCab2 specific stats commit b7784bef77b1f025cd69a001c4ac51947e4bdd80 Author: fanhsu Date: Fri Apr 11 17:00:42 2008 +0000 Added conservation tracks for two VAX003 strains. commit c17b0b388410d6d3add20b9c22febe47a3fb4dc4 Author: kuhn Date: Fri Apr 11 16:57:53 2008 +0000 changed Regions link commit a5be5248ff7b0ab5b52acbec88db2afbfa8d6a5f Author: galt Date: Fri Apr 11 15:00:07 2008 +0000 "Encode release log update" commit b4bc71abd3b710773315becde59f16166a8846e9 Author: galt Date: Fri Apr 11 15:00:04 2008 +0000 "Release log update" commit fdd19164dc9da5d9d2e765af9987f21eb53b4858 Author: pauline Date: Fri Apr 11 00:08:24 2008 +0000 Replaced link with updated url. commit 8650dc645253a981db3208042e1587a95eb2e2de Author: hiram Date: Thu Apr 10 23:58:13 2008 +0000 Beginnning template for equCab2 blastz commit 0fc9efc5a5fd8191515f2554ce94369fc7793663 Author: fanhsu Date: Thu Apr 10 23:51:25 2008 +0000 Updated HGNC data. commit e2f9a315c36a175199d63f2b7ef92f2ae85036ea Author: fanhsu Date: Thu Apr 10 23:44:45 2008 +0000 Updated with latest Perl program generated at new HGNC site. commit 70647bb4d9adef91aa85ee2f361bb3db51371cc8 Author: ann Date: Thu Apr 10 23:37:40 2008 +0000 made spelling the same as table commit 101dd77c61ab2c57c066aac12246dd53384333cc Author: hiram Date: Thu Apr 10 23:34:56 2008 +0000 Correct the example search terms commit 677156fed322262ac6052638f239bb223c2b9080 Author: angie Date: Thu Apr 10 23:33:44 2008 +0000 Added some old notes about comparing snp126 to snp128. Added PCR target servers (temporarily manually running on kolossus...) for UCSC Genes and Human mRNAs. commit c094da57a8ca07dc70cd165cdb02cbddb725bd5e Author: angie Date: Thu Apr 10 23:30:31 2008 +0000 Data update from contributor. commit 97215ddef52e5849afd5555148ea9797d6ffb000 Author: galt Date: Thu Apr 10 23:21:08 2008 +0000 improving FTP instructions commit 32eb16185dadf77221b47c902ddac57a212e4f2b Author: hiram Date: Thu Apr 10 23:17:16 2008 +0000 Fixup descriptions to be more correct commit 7affad3748155f4d32fba47fddcf4f6070664002 Author: larrym Date: Thu Apr 10 23:11:40 2008 +0000 Importing steps up through and including GenBank update commit b2ee931345bdb5becc35c1731d6aa5216049d6a9 Author: larrym Date: Thu Apr 10 22:53:51 2008 +0000 Added equCab2 - Equus caballus commit ba64222c401d7cabccc3dc8e1549032ca5882d13 Author: angie Date: Thu Apr 10 22:45:20 2008 +0000 Describes non-genomic targets, i.e. collections of sequences that have been aligned to a genome assembly as well as tables in that assembly's db that map sequences to the assembly. commit d136ea4a0565d21cc61e48710e58836d2cf7df66 Author: angie Date: Thu Apr 10 22:36:26 2008 +0000 Added support for PCR queries against servers running on non-genome targets, i.e. collections of sequences that have been aligned to the genome assembly. If the central db has a table targetDb, then we search that table for targets associated with the current (genome) database. We reject targetDb entries that are not newer than the tables and sequence file that they reference. If there are valid targets, then we draw a new Target select input, with "genome assembly" as the first/default choice, then those targets. If a target is selected, then we send the query to that server, and display matches against target sequences with links to hgTracks with position = sequence name. commit 3c5e64a80ae34e73023fbc3198fb0f372b38a34d Author: pauline Date: Thu Apr 10 22:21:23 2008 +0000 Replaced link with updated url. commit 6d6c6d13b54cf14656f01f9dff53c49ff4cdad1f Author: angie Date: Thu Apr 10 22:07:30 2008 +0000 In sqlDateToUnixTime, set tm_isdst to -1 so that mktime will attempt to determine whether DST is in effect for the given date. This is important for differences <1hour between sql datetimes and file stat times. commit cca97e74d72eac8549ecabb51fa2243d218a755c Author: angie Date: Thu Apr 10 22:05:08 2008 +0000 Added gfPcrOutputWriteOne so caller can add stuff before/after each item. commit 49ce0bddc5f91ba5c500fbc6d46607426ec8f839 Author: ann Date: Thu Apr 10 21:23:00 2008 +0000 a little clean-up commit a0d2bc708d151790c769e36645327cdebc5c9d13 Author: ann Date: Thu Apr 10 21:16:06 2008 +0000 some cleanup commit 000df7e2fee97ad08aa7537e66ab3c981dd8a8bd Author: galt Date: Thu Apr 10 21:03:06 2008 +0000 removing status from default show - as more detail than most people want to see. - may add advanced-view feature in future that would show all commit f43df2c4496f5c15b4fd2c80c1862b0d069b47dc Author: galt Date: Thu Apr 10 20:57:49 2008 +0000 removing upload-only button, adding more explanation about FTP usage commit f59a3cba1f3480a0262e708d5830238190f7307a Author: galt Date: Thu Apr 10 20:56:50 2008 +0000 removing upload-only button commit 213c283c6195c9b01738c4d79155d07432951bec Author: larrym Date: Thu Apr 10 20:08:16 2008 +0000 .ra file access utilities commit 38925c8cffa68ef623455601f182d2b9d957dbb1 Author: larrym Date: Thu Apr 10 19:50:59 2008 +0000 change continue to next to fix a bug when reading comment lines commit db663a6ecca0bcd47863fc23cdd7877e9ab5ed85 Author: larrym Date: Thu Apr 10 19:33:27 2008 +0000 use relative location for src tag and use fileExists to vet the existence of fileName in jsIncludeFile commit 3f59846407a9f0f9e50fbdfc586978d2b599fef6 Author: ann Date: Thu Apr 10 19:25:24 2008 +0000 shortening very long longLabel on Affy EC tracks commit 1b4c565e0f1edfd777d08cb323cd02688cb37cb6 Author: tdreszer Date: Thu Apr 10 18:47:37 2008 +0000 Added cavPor3. commit 90989b51716500ae62333d371406d4e467fc965b Author: galt Date: Thu Apr 10 15:00:11 2008 +0000 "Encode release log update" commit b2afb148df7991e61daf230677d72508106a6dc5 Author: galt Date: Thu Apr 10 15:00:06 2008 +0000 "Release log update" commit 491ed206fcf5d077d21364f7499aeaad8e679820 Author: donnak Date: Thu Apr 10 06:43:44 2008 +0000 Added pub from Jian Ma, updated my NAR DB pub to 2008. commit a559390d5503ede419c7820d803af09e6a73b949 Author: rhead Date: Thu Apr 10 01:46:53 2008 +0000 added italics commit da80ef684d0bf00799772163384bedae33f6edcd Author: galt Date: Thu Apr 10 01:23:29 2008 +0000 removing something Robert accidentally checked-in long ago, with his approval commit 8ee6f95ed5a983fcd0709db74c2fb55b205bb353 Author: kayla Date: Thu Apr 10 00:13:58 2008 +0000 added bosTau4 commit 4982143861a8e3a30771199cac76fe647236b610 Author: hiram Date: Wed Apr 9 23:19:02 2008 +0000 Bogus wikiTrack debug printout left in code commit cba91d669bcc4300aed4ef80e181ab0fa73ae590 Author: hiram Date: Wed Apr 9 23:10:20 2008 +0000 Add hgUi click function, default description page help doc, remove category pull-down menu commit d49689b5664f61bf78f72484c442561521264b14 Author: hiram Date: Wed Apr 9 21:04:03 2008 +0000 Updated notes commit 33b2675f4295dc9e7374dc7b73e644c768da8139 Author: hiram Date: Wed Apr 9 20:49:01 2008 +0000 Initial text for a description page to the Wiki Track commit b3ef64cba264e48dd0ed3ce8a2dac9569f912ff5 Author: angie Date: Wed Apr 9 20:42:59 2008 +0000 Adding BDTNP ChIP/chip composite track. commit 26cd36ed4423663294fb1c07af2724c9f81ccdbb Author: kate Date: Wed Apr 9 18:25:40 2008 +0000 Expand usage message to clarify how to specify machine names commit 92f7ddcfe1430895b2f4b277f7def73f88743730 Author: larrym Date: Wed Apr 9 18:01:56 2008 +0000 add equCab2 commit ae287b0b80c689910f255e83525c1b0c9c67b14a Author: galt Date: Wed Apr 9 15:00:06 2008 +0000 "Encode release log update" commit 43e37e068faae402b17e9783d93751075438b2c0 Author: galt Date: Wed Apr 9 15:00:04 2008 +0000 "Release log update" commit fc22654ed30088ade4ec2630f35cad6c58cabf38 Author: donnak Date: Wed Apr 9 04:29:05 2008 +0000 This is the news archive page for the ENCODE production phase. It's currently empty except for a link to the pilot phase news archive. commit ce3667124a1dd5af168e44ea20692eed44dc872a Author: donnak Date: Wed Apr 9 04:27:59 2008 +0000 Archived a pilot phase news item. commit 3b89ce6708557067326c3197a1ad0b1be4b39daf Author: donnak Date: Wed Apr 9 04:27:26 2008 +0000 This is the new home page for the production phase of the UCSC ENCODE portal. The old index.html page is now called "pilot.html" and is access via the ENCODE Pilot Phase link. commit c358f16fe4ce977da4503eaa129dbf94ac548207 Author: donnak Date: Wed Apr 9 04:26:31 2008 +0000 This is now the contributors page for the ENCODE production phase, accessed via the Contributors link on the ENCODE index.html page. commit 86e1bfdc99d2983e3c36e35e0435d365bca00dcf Author: donnak Date: Wed Apr 9 04:25:44 2008 +0000 This is the old contributors.html page from the ENCODE pilot phase. It is now accessed from the pilot.html page. commit e8dc22e893d937242cfc070b9a053bb7c9d4502b Author: donnak Date: Wed Apr 9 04:24:52 2008 +0000 This is a modified version of the old index.html page for the ENCODE pilot phase. It is now accessed via a link off the new ENCODE index.html page for the production phase, and archives some of the old pilot phase information & links. commit 73bc8a899bfe3343be9bbf6e322b0a8631b469ee Author: donnak Date: Wed Apr 9 04:23:00 2008 +0000 Changed topbar to encode.prod.topbar.html (removed Regions link). commit 0ca6e303094a0e74cae6ac69caa7345c08b64223 Author: kuhn Date: Tue Apr 8 23:55:03 2008 +0000 rearranged the chain/net priorities to match conservation track commit 716ad752b6a08050eec65605c96e544c984595ed Author: hiram Date: Tue Apr 8 23:41:03 2008 +0000 No debug printout please commit 38c6f2ebecf9fe014504817c7c40d8e1fab00151 Author: hiram Date: Tue Apr 8 23:36:44 2008 +0000 Enhance wikiTrackEnabled to check against database list commit e4710cee02d2d184da009580bfe9db1e2d2a183d Author: fanhsu Date: Tue Apr 8 23:29:01 2008 +0000 Updated query to get HGNC id. commit d473799fb738c7fa0bf543587b32aace187d34bd Author: hiram Date: Tue Apr 8 23:04:36 2008 +0000 The names have gotten longer commit c50093ae110c37b1a7a08a4a6536bc0975f00ceb Author: hiram Date: Tue Apr 8 22:34:12 2008 +0000 done with ensGene v49 update commit f1b4538bd319699e083741d531146a5c222256c5 Author: hiram Date: Tue Apr 8 22:33:06 2008 +0000 Loading the Nucleosome tracks from the Fire lab commit 9e4c7f9b72f920db23f41cbc9b0a868eaf2e5fda Author: ann Date: Tue Apr 8 22:13:22 2008 +0000 added info about accessing data on a password-protected server commit c5887144a15c86e5997935c1e504b5aa4218fa7b Author: hiram Date: Tue Apr 8 21:54:06 2008 +0000 Updated descriptions commit b3e9544abad47481463de883913c2ff65848de74 Author: fanhsu Date: Tue Apr 8 21:45:01 2008 +0000 Created trackDb.ra. commit 571b9091de954b3c165fea3e3d9a5681ae13ff3f Author: fanhsu Date: Tue Apr 8 21:38:39 2008 +0000 Created for hivVax003Vax004. commit 0f3ff2e1f03f34e4b63d5be4b700d1f4791a0d60 Author: tdreszer Date: Tue Apr 8 21:30:44 2008 +0000 Added guinea pig commit c50064a36c43143ab5986ffc7e65d4303bc69537 Author: tdreszer Date: Tue Apr 8 21:08:38 2008 +0000 Added cavPor3. commit eea7ab6f0523e35e26adbe75401da5f9d0040fdb Author: kuhn Date: Tue Apr 8 19:11:39 2008 +0000 added logic that allows for checking against unbridged gaps only if specified. commit 60a4d8b78867b0168bcc569fd688d4d0296e35f7 Author: ann Date: Tue Apr 8 18:45:54 2008 +0000 fixing order of chains and nets commit bd21e2bfeb0f7c0de7a18c4651f111260bdeb981 Author: hiram Date: Tue Apr 8 18:05:21 2008 +0000 Add liftOver to bosTau4 commit d95b424db8d0d70970935bac7b0175185de8607a Author: ann Date: Tue Apr 8 17:51:18 2008 +0000 adding chain/net blocks to this level because bosTau3 became o_db at top level commit fc3a072ca87ed05e8eee58ffcfab08ae629850f3 Author: ann Date: Tue Apr 8 17:40:07 2008 +0000 making bosTau4 the default chain/net, and bosTau3 the previous one commit e865d0751f41ac50277ae251563f9bf2338c158c Author: ann Date: Tue Apr 8 17:24:07 2008 +0000 adding priority.ra file to order the nets & chains properly. commit 9730216ffdd4fdefbdb5689bde28deb848367dcc Author: ann Date: Tue Apr 8 17:00:23 2008 +0000 changing priority of human nets/chains commit f95705c9a953b8913167f0de7a802a6d76735deb Author: galt Date: Tue Apr 8 15:00:06 2008 +0000 "Encode release log update" commit fc056191b031bcc46aeaa00ed58224ebe0b487eb Author: galt Date: Tue Apr 8 15:00:03 2008 +0000 "Release log update" commit 2bd7d2e7769d8578e99b5e7b6f4c6e54f6b71425 Author: angie Date: Tue Apr 8 05:14:54 2008 +0000 Changed database README.txt to refer to TB schema page instead of obsolete gbdDescription. Thanks Brooke and b0b. commit 87bd0babce2dd6001d611ebab68478cec23aeede Author: angie Date: Tue Apr 8 05:09:01 2008 +0000 Added bdtnp* (24 TF ChIP/chip wiggle subtracks from Berkeley Dros. Transcription Network Proj.). commit 03a00c598e1aeb341fd5bcadf8e75d17a2a3fa79 Author: angie Date: Tue Apr 8 05:03:29 2008 +0000 Added missing knownToGnfAtlas2.name to knownGeneId. commit d2bc144abb0bad006243989b12d58169b533d5ef Author: angie Date: Tue Apr 8 00:53:11 2008 +0000 In compositeTotalHeight, if one subtrack is over the per-subtrack height limit, pretend that all subtracks were, so that the composite track's height is over the total height limit. This is so that limitVisibility will bump down vis as it should. commit ad5942624e7d13d48d62dcfdc8bd3730f45fb418 Author: fanhsu Date: Tue Apr 8 00:19:29 2008 +0000 Updated Reactome tables. commit 38f088ef2b999924aa9111e80cc1dc6b2bc7f462 Author: kuhn Date: Tue Apr 8 00:00:24 2008 +0000 improved the formatting of the percent values, replacing an awkward sed with an improved awk. thanks angie. commit f4ba0bc678f70b8f1dfd53beeee8c6b7479919be Author: kuhn Date: Mon Apr 7 21:54:48 2008 +0000 cleaned up the logic a little. thanks, pauline commit fe4f00418a663907678f99d69512523faa53ed22 Author: kuhn Date: Mon Apr 7 21:32:38 2008 +0000 added some debugging statements and changed asText to getText. thanks, pauline commit 49eb7a6d07dc28990b6d9c08d5f43e7a71e115b9 Author: ann Date: Mon Apr 7 20:24:43 2008 +0000 adding -N to hgsql command so that the header line is not returned with the SQL results commit 9d5f45e6b282595f7c96a7971178007be6ee5e35 Author: tdreszer Date: Mon Apr 7 19:08:20 2008 +0000 Initial description page of assembly track for Cavia porcellus (guinea pig) commit fbe23d8642c7fb1b62b544c91bba5a748137b0a8 Author: tdreszer Date: Mon Apr 7 19:08:00 2008 +0000 Initial description page of gap location track for Cavia porcellus (guinea pig) commit b2a01815bb26d38a745ce0e0803f7318eee99448 Author: tdreszer Date: Mon Apr 7 19:07:45 2008 +0000 Initial description page for browser gateway of Cavia porcellus (guinea pig) commit ca2645b9f292dd020131022b83fa249000ac3190 Author: larrym Date: Mon Apr 7 18:06:38 2008 +0000 copied from equCab1 (no changes needed) commit 002775c203a1f60d32ef4048426f88eb260f5a53 Author: kuhn Date: Mon Apr 7 18:02:49 2008 +0000 cleaned up navigation to/from/within hg16. thanks, pauline commit b6e2671f95a1e8b662eed5f09f64301af40ebe78 Author: galt Date: Mon Apr 7 15:00:11 2008 +0000 "Encode release log update" commit dfe9591200e920ebc9d22d647c4d16334527b0dc Author: galt Date: Mon Apr 7 15:00:05 2008 +0000 "Release log update" commit 29269264889fbd62d65f0337e7de41bb9d0d1c20 Author: galt Date: Sun Apr 6 15:00:03 2008 +0000 "Encode release log update" commit 643febd343de1ee2d917bc1de85fc7f3d2c4176f Author: galt Date: Sun Apr 6 15:00:01 2008 +0000 "Release log update" commit c44b535053f319c644ac51dd74238c43262dbb56 Author: markd Date: Sun Apr 6 00:40:06 2008 +0000 add some extra indices for use by ccdsMkTables commit 96cffa3472873b0b07c78a3e49b1259675b96651 Author: markd Date: Sun Apr 6 00:39:43 2008 +0000 paramterize with NCBI build; add option to get entries regardless of status commit 1f3d3a1fae149e6ab734f4f582795b4c8a46dbdd Author: galt Date: Sat Apr 5 15:00:05 2008 +0000 "Encode release log update" commit 9ad6fe42765ac45a8b940b101d213c2cba53ce11 Author: galt Date: Sat Apr 5 15:00:03 2008 +0000 "Release log update" commit c6417ec7dabf034617cf50973cbc3dde55e447a3 Author: galt Date: Fri Apr 4 23:11:50 2008 +0000 got rid of word Japanese in NIBB name commit 9ebf3082261c566fad5f30e2efbb3374ece8967a Author: hiram Date: Fri Apr 4 23:01:15 2008 +0000 Added blat server and default position commit cdb20005fe82278d4933179de8ad183974247901 Author: kuhn Date: Fri Apr 4 22:59:25 2008 +0000 typo commit f01ee55f5f4ae7a7e1ac932c5fb33f83d03c6e79 Author: galt Date: Fri Apr 4 22:57:02 2008 +0000 removing Japanese from NIBB submission source name as requested commit 96683bf3af18935652e9b7ebb0cb7b20e6a13f66 Author: kuhn Date: Fri Apr 4 22:56:47 2008 +0000 tool to atch hgSessions commit 4de1dfe41c98c854fa5e866d818d177361e364df Author: hiram Date: Fri Apr 4 22:00:02 2008 +0000 Adding ctgPos2 description and default visibility settings and update gold description commit bee2befedacf8c865dc9f6ae04a3abab4392211a Author: kuhn Date: Fri Apr 4 21:02:18 2008 +0000 typo commit 9a43430e69edecbabbc433df0cabd15bf97d949d Author: tdreszer Date: Fri Apr 4 20:55:48 2008 +0000 *** empty log message *** commit ec1b5964fd19ba0320daf794680ba6d3a651a5a3 Author: donnak Date: Fri Apr 4 19:53:16 2008 +0000 Initial edit of gateway pate -- needs another pass before release. commit d7a387a2749bdbfb4e03cdb3452e3089f0687377 Author: hiram Date: Fri Apr 4 18:47:01 2008 +0000 Finished with genbank run commit f3e728297d5af1ac4537cc05f04fc7a49cbf5cc0 Author: hiram Date: Fri Apr 4 18:46:28 2008 +0000 Added caeJap1 - C. japonica commit 99c1395ed8fce6013414b36bd87d884ceaa07009 Author: donnak Date: Fri Apr 4 18:16:28 2008 +0000 Added some additional text abt the assembly (taken from the indexNews.html page), updated the credits. commit 858e4c26da0ece226ebcd2ba34ad4505e29e027e Author: donnak Date: Fri Apr 4 18:15:40 2008 +0000 Added bosTau4. commit ddb414e5a5117995c838b4a093aec33744bd9210 Author: donnak Date: Fri Apr 4 17:52:33 2008 +0000 Changed bosTau4 conditions for use link. commit abd86e7e8abb2ccb7b8e22e5076e3e863237928b Author: donnak Date: Fri Apr 4 17:46:10 2008 +0000 Changed credits for bosTau4. commit 02578db1fb41bf3669493ba599906b8fe6607e31 Author: donnak Date: Fri Apr 4 17:45:22 2008 +0000 Changed credits for bosTau4 & made a few minor edits. commit 42f6afa97d22af1eb340ac2bf9c5ffdfe6cdc0b8 Author: fanhsu Date: Fri Apr 4 17:24:14 2008 +0000 Added logic to support local expression tracks for cancer genomics browsers. commit b08a149b5138378a0d9cefad83989d29d95b1983 Author: braney Date: Fri Apr 4 17:17:21 2008 +0000 fixed bug when there are multiple frames per exon commit 1ca51504c50f2abb1f0bcd6be81c48f71a6f96a8 Author: galt Date: Fri Apr 4 15:00:06 2008 +0000 "Encode release log update" commit 1b9a2e1ad656a32406cb671a6419f9d0e111fe07 Author: galt Date: Fri Apr 4 15:00:04 2008 +0000 "Release log update" commit f29ec86bad32f281bdf1fe96e77b7384e32259d3 Author: hiram Date: Fri Apr 4 07:02:42 2008 +0000 Started genbank run commit 1d1c0ddfb70dcdc14b0d718039c600be2f47a719 Author: hiram Date: Fri Apr 4 07:00:33 2008 +0000 Adding C. japonica caeJap1 commit c4441bd19ee365b6ecbd427d7b5d97cd7d933a04 Author: hiram Date: Fri Apr 4 06:46:55 2008 +0000 Added C. japonica commit 812a51dabab7887b58fe9635dae23e20325f6dd9 Author: hiram Date: Fri Apr 4 06:37:30 2008 +0000 Add the RepeatMasker trial commit d61f11c3d78569bf73ec89a3dfb6b8fb9e81a00c Author: hiram Date: Fri Apr 4 06:29:59 2008 +0000 Adding a new nematode to the zoo commit b4d3dc177b5d076bd9bb1f6a70b40a8976362435 Author: hiram Date: Fri Apr 4 06:14:07 2008 +0000 Adding caeJap1 commit 2756877051f8e44d7d2e21db6ff678baac92d2da Author: fanhsu Date: Fri Apr 4 00:08:15 2008 +0000 Added more logic to handle non-hg18 scenarios in trackDbConn(). commit 20bdc34a42ce1f066a95f3350181924c29431681 Author: hiram Date: Thu Apr 3 23:56:32 2008 +0000 Fixup some names and comments and timeout on wget to only 2 tries instead of 20. Need to fix chooseFileServer to force it to the fileServer regardless of what it thinks is best. commit e552d9ff37b17bf550b796754e475a03c95b24b5 Author: hiram Date: Thu Apr 3 23:55:20 2008 +0000 Properly display the version list from the library commit 5c4f5898502dd7ed43b4239653111c6005395350 Author: kuhn Date: Thu Apr 3 23:38:34 2008 +0000 removed extra 'goldenPath' from link. thanks, pauline commit e4bac5b7ac15a08fbf1169c9900596548300f8c9 Author: rhead Date: Thu Apr 3 23:01:22 2008 +0000 typo commit 53937029c775fbc195e9a204bd6336bf1631c0bd Author: hiram Date: Thu Apr 3 22:59:08 2008 +0000 Fascinating, autoScaleDefault On is actually autoScale On commit 85e34cf4cf90c5b2d8714125a9a3f390568b9469 Author: kuhn Date: Thu Apr 3 22:52:36 2008 +0000 removed a block of script that was duplicating all.joiner and taking forever commit 1cf97657d8e77f3bd2d5e84b0b542995f1850f76 Author: kate Date: Thu Apr 3 22:14:56 2008 +0000 Initial descriptions for cavPor3 commit 686f2fbc03549c7e0c72393217d6d29e4124d125 Author: kate Date: Thu Apr 3 22:14:34 2008 +0000 Added cavPor3 to DBS commit df12228a8b138fde1eea4834eaec588a1eea1072 Author: angie Date: Thu Apr 3 21:41:44 2008 +0000 Oof... topology does not reflect common ancestry... but this is how we ran multiz and phastCons. commit c84b50266b6cc1f78461a35b829b85ae0c3d3a4f Author: angie Date: Thu Apr 3 21:41:03 2008 +0000 Added treeImage setting to multiz4way. commit ed3fc22cad5ff702bb4b81f72747694a145f9678 Author: hiram Date: Thu Apr 3 21:39:08 2008 +0000 Should be good to go here. Has been edited since makeGenomeDb.pl commit 2313e247e98dba9149d376178f4d4fa295a9d8ab Author: galt Date: Thu Apr 3 21:03:33 2008 +0000 comment-out debugging statements commit a9de517601390332e39547995be21287ad67432d Author: pauline Date: Thu Apr 3 18:52:48 2008 +0000 Fixed broken links. commit 6a4125b69ceb83480024efdf737a4290a45cc9af Author: ann Date: Thu Apr 3 18:49:51 2008 +0000 typo commit 64ed57e0f4dd58141bd6f79e7ab05a5e77887797 Author: ann Date: Thu Apr 3 18:47:33 2008 +0000 added bosTau4 commit fb72997fd7b8114e00e9125a109f7cc1170930df Author: ann Date: Thu Apr 3 18:39:49 2008 +0000 bumped from indexNews page commit e748eb90add80d78cb5cec8b53b0be3f4ed72330 Author: ann Date: Thu Apr 3 18:39:07 2008 +0000 added bosTau4 release, shortened OH announcement, bumped Reverse Functionality commit 0d8ac9f51847f6ecc530c69181835518315b8b9a Author: hiram Date: Thu Apr 3 18:29:35 2008 +0000 Rearrange some nucleosome business commit 24d34e0001ebdccbe1cec039de8ad0f189fc8c17 Author: kayla Date: Thu Apr 3 17:26:33 2008 +0000 Added text for clarification. commit c18c15104f8907db70731fcc91264c9ab5b8297c Author: markd Date: Thu Apr 3 16:16:08 2008 +0000 added marmomset N-SCAN gene predictions commit 2a0c853c4ead078dbef6ad8bff212fc82d43e4ed Author: galt Date: Thu Apr 3 15:00:05 2008 +0000 "Encode release log update" commit 418e88ac26608e31d8c9f2e903d20b8a1c5c14ff Author: galt Date: Thu Apr 3 15:00:04 2008 +0000 "Release log update" commit c2bae20638c132f7f9df7d3f108a14474c9776da Author: larrym Date: Thu Apr 3 00:59:39 2008 +0000 add jsIncludeFile commit 6db23927bd12f9dd06144a727b2622014ee42b78 Author: galt Date: Thu Apr 3 00:52:03 2008 +0000 update ftp_passwd when user signs up commit c2cc72bbf067baccb1177247eac9a0fd18311e3c Author: galt Date: Wed Apr 2 23:40:30 2008 +0000 fixing contact page to be ERB-capable so we can use config settings for encode contact email commit cb05d16dcef420e520f9471f3cbd6f729a527153 Author: galt Date: Wed Apr 2 23:30:08 2008 +0000 fixing contact page to be ERB-capable so we can use config settings for encode contact email commit b8803a72f0e2bee1fd5989b2ebd0f59288324511 Author: aamp Date: Wed Apr 2 23:09:33 2008 +0000 Turned on exon arrows in NCI60 stupid old track. commit bf4297c48530a0ae504bd218673545e33a38cdde Author: ann Date: Wed Apr 2 20:30:02 2008 +0000 made link to bosTau4 for consistency (suggested by Pauline during code review). commit 16a63f38000a389240c3e2f7cfad7fdd8c727488 Author: kuhn Date: Wed Apr 2 19:35:21 2008 +0000 cleaned up the logic that gets left-justified without headers. thanks, brooke. commit 2c6c8eaea05c2e99234cdd990f465f1824ee30eb Author: fanhsu Date: Wed Apr 2 18:59:21 2008 +0000 Added trackDb.cancer2.ra to keep trackDb entries specific to cancer2 server (for cancer genomics). commit 51cd9d0fd62aaaf3d4eeb975ea1932b6f1aa0657 Author: fanhsu Date: Wed Apr 2 18:29:01 2008 +0000 Added trackDb entries specific to tcga1 server (for cancer genomics). commit 59fe9af85867d91125e50800d44bc87a40c592c8 Author: aamp Date: Wed Apr 2 17:38:25 2008 +0000 Changed stuff around for old NCI60 microarray track. commit b0acde1726ff822b15f8656ad5dd1fecba862c12 Author: pauline Date: Wed Apr 2 17:11:44 2008 +0000 Added comma. commit 0f01be304d9eeb64fe35c6821ce2a5319bc3c8ea Author: braney Date: Wed Apr 2 16:38:50 2008 +0000 Ooops, get the right species names commit fc35b431a061973c45f233a1fe86660325f221be Author: braney Date: Wed Apr 2 16:35:34 2008 +0000 change the names of some elephants commit 6c0fa692ba444ecfb7166aa23f9bfadfa624f38f Author: galt Date: Wed Apr 2 15:00:05 2008 +0000 "Encode release log update" commit 01268ecbee974a64bea30da23beab4f8f334b39c Author: galt Date: Wed Apr 2 15:00:04 2008 +0000 "Release log update" commit 98926081160297371485a0610923bdd6fbfb4958 Author: larrym Date: Wed Apr 2 00:08:29 2008 +0000 add equCab2 commit 733f7675a9723d9f6a55b8fbafad11811078915f Author: larrym Date: Wed Apr 2 00:01:18 2008 +0000 initial files from makeGenomeDb.pl commit 386f4ddfaf96462610468cb65629353508e98a36 Author: ann Date: Tue Apr 1 22:16:09 2008 +0000 copied from oryLat1 commit 25af100627fd2f4a0fa9cdece957719952a5fe10 Author: fanhsu Date: Tue Apr 1 21:35:42 2008 +0000 Updated URL to UniProt. commit 7f962ae186fd419369c3caa968b42cf0a7b539a3 Author: fanhsu Date: Tue Apr 1 21:11:30 2008 +0000 Added freeTrackDbConn(). commit e38a607e1772cc844ecfd0aaed6bed15029cb1a7 Author: fanhsu Date: Tue Apr 1 21:07:40 2008 +0000 Added ";" commit 188dfc8c5b3cf139b835db931161e7a0469c9d73 Author: fanhsu Date: Tue Apr 1 21:06:18 2008 +0000 Added trackDbConn() and freeTrackDbConn(). commit 83763df0fd0ff42fec4108539afb1c44c3b2242c Author: galt Date: Tue Apr 1 19:23:22 2008 +0000 removing troubling boolean from migration code commit abbae9797406c709e83cdc340a9b16c0e10fd808 Author: aamp Date: Tue Apr 1 17:54:13 2008 +0000 "New version number v179" commit d9dd652840177ee485c425ae477724e6df57970e Author: aamp Date: Tue Apr 1 17:51:05 2008 +0000 Added yellow/blue color options to hgTrackUi. commit 60ed505e4d9a0d9e65cc7ad07bbb6cd9d416d216 Author: aamp Date: Tue Apr 1 17:50:56 2008 +0000 Added yellow/blue color options to hgTracks. commit b5ea417dd081231564073dc51ab8190c67cd393e Author: aamp Date: Tue Apr 1 17:50:21 2008 +0000 Added yellow/blue color options to hgc and ripped out a ton of obsolete track-specific code. commit 314e38dc811fb02b748466c60feda48e49049046 Author: galt Date: Tue Apr 1 17:30:17 2008 +0000 additional column identifies who changed the state -- requested by Bob Kuhn commit 3c556c0faa7f8c9509e2591aac65ac905c09d6ac Author: kuhn Date: Tue Apr 1 17:18:31 2008 +0000 added option to get assembly date, alphabetized and set format to left justify commit e577e142053d636a0f9e81a89eb7cb82bb854f69 Author: pauline Date: Tue Apr 1 16:25:30 2008 +0000 Added italics on et al. commit 672efdcd7c78970600a127932c873baa2807a14e Author: galt Date: Tue Apr 1 15:00:06 2008 +0000 "Encode release log update" commit e637a90eb5359cd9c3316d198fcfb3ac9e8bd85f Author: galt Date: Tue Apr 1 15:00:04 2008 +0000 "Release log update" commit d57448d660a46660f75b2a2fc177abc41a1849ec Author: fanhsu Date: Tue Apr 1 13:31:27 2008 +0000 Added hConnectLogicalDb() and trackDbConn() to support loading trackDb from different DB than the regular DB. commit 488aaba913d19febbe779a75524496c879914c2a Author: jsanborn Date: Tue Apr 1 01:29:26 2008 +0000 removing vantVeer entry to fix problem with genome-test commit 0444bce11205ced74dcded71c04d8d6b82d349ac Author: pauline Date: Tue Apr 1 00:57:43 2008 +0000 Reverted to original version of table 2. commit 7808fb3a57cacc2614e2c5b163a7a5e82150af09 Author: pauline Date: Tue Apr 1 00:50:29 2008 +0000 Reverted to original version of table 2. commit 5735e9708c6cbf1a41fda53f554fffd8918af991 Author: pauline Date: Tue Apr 1 00:42:55 2008 +0000 Reverted to original version of table 2. commit d7fe99849ead4ba41f5034ea14e3ef9d7ca64a92 Author: kuhn Date: Tue Apr 1 00:34:14 2008 +0000 some formatting of HTML commit ec8e4e082bf4b46e49cbc360d626ec7702e018ab Author: markd Date: Tue Apr 1 00:25:12 2008 +0000 ccds import commit 28dae8279b21583572fe9440eb46a02b468fb214 Author: fanhsu Date: Tue Apr 1 00:08:53 2008 +0000 Removed #include trackDb.instinct.ra line to prevent causing problem on general genome browser. commit 1da7b8919e2d278652f7c7c4cf5c9cbae17d0f87 Author: pauline Date: Tue Apr 1 00:06:50 2008 +0000 Swapped columns in table 2. commit c20e18408778b8b29fcc06a0101f2f65bb061889 Author: pauline Date: Mon Mar 31 23:50:34 2008 +0000 Swapped columns in table 2 and added italics to et al. commit a62449126505102c39c73a5ae6a6c5fc179058e1 Author: larrym Date: Mon Mar 31 23:49:05 2008 +0000 initial commit 77826fa07bc51f4db10014c73b96d51560a2821b Author: fanhsu Date: Mon Mar 31 23:32:04 2008 +0000 Hide all INSTINCT tracks by default. commit 44b0572341301b79fe945fa66e98cf3b4d4ff972 Author: fanhsu Date: Mon Mar 31 23:11:16 2008 +0000 Added logic to connect to a logical db to support VM server systems. commit 5a81b65058612e1ba937186497f2becb10a4d936 Author: fanhsu Date: Mon Mar 31 23:05:15 2008 +0000 Added hConnectLogicalDb(); commit 75bf4ecc1798fe70ee161afceeec0ed62c9496a2 Author: ann Date: Mon Mar 31 23:01:01 2008 +0000 correct assembly! commit 1d045f012d329d6b7cec38b8ca14c111a82d0c72 Author: ann Date: Mon Mar 31 22:56:38 2008 +0000 new file to capture priorities for chain/net tracks commit c1aa49e8652fb02624281581e0af7f372a782ec0 Author: ann Date: Mon Mar 31 22:48:04 2008 +0000 brought bosTau4 chain/net down to this level commit 3e9a93e01977e9685ced8892fa1dec7522df0968 Author: ann Date: Mon Mar 31 22:18:08 2008 +0000 adding chainMm9 block at this level so that I can change the matrix line (from the top level) commit fe4d12704140cf794816c21152698880f5ac5482 Author: pauline Date: Mon Mar 31 22:09:58 2008 +0000 Reversed columns in gene track table commit 3effe1557aaf3bf564ed446bda9c56e2a0985844 Author: pauline Date: Mon Mar 31 22:01:03 2008 +0000 Added italics to et al. commit 1c1be5dc8153e9d42279bb77b13ddb4018ad5e7d Author: kuhn Date: Mon Mar 31 21:07:22 2008 +0000 reversed order of primates commit 82321284daa106656702e61f34dcc0db6586bab7 Author: ann Date: Mon Mar 31 19:56:45 2008 +0000 simple script to return the name of the organism, given an assembly name. commit 4c7e004cce9fcaa7ed9fa7393d30fb60bdb212f0 Author: ann Date: Mon Mar 31 18:23:59 2008 +0000 conforming with citation standards. commit fbba1353f40e333fc7de540cf9f2a2be1c315ec1 Author: ann Date: Mon Mar 31 17:45:54 2008 +0000 adding bosTau4 to this rule -- it has a new human proteins table commit 5b4853cc6671a123eff564af0475ab3061f3e582 Author: jzhu Date: Mon Mar 31 17:27:29 2008 +0000 add van't Veer microarrayGroups.ra file commit 5194a2e5f758128f98a974f897fdb62e7949e2cf Author: kuhn Date: Mon Mar 31 17:26:58 2008 +0000 flipped the primates to put non-ape primates together commit 69deb6cc895655e967e2c3c6cb4fef2b18541df3 Author: ann Date: Mon Mar 31 15:33:33 2008 +0000 fixed typo commit d389e303b06af930448121966eca29a29bb356ac Author: galt Date: Mon Mar 31 15:00:04 2008 +0000 "Encode release log update" commit 3320ffc79dfd19023c22c805b873d8aef6556929 Author: galt Date: Mon Mar 31 15:00:02 2008 +0000 "Release log update" commit 852a1c6e3089d23a071eda09428174c71a3a5f82 Author: galt Date: Sun Mar 30 15:00:06 2008 +0000 "Encode release log update" commit 070e3e050dbc46f6b2c0d62c6f61644eaf1ef0ca Author: galt Date: Sun Mar 30 15:00:04 2008 +0000 "Release log update" commit 4b1b05a723531bdb92267ecb3db3b8d3b5bc6c37 Author: galt Date: Sat Mar 29 15:00:12 2008 +0000 "Encode release log update" commit b1f9a8f3bac78c211653477df01b7560e00b0bb6 Author: galt Date: Sat Mar 29 15:00:09 2008 +0000 "Release log update" commit af2e37b48c003db18b3d2aeb069189851fb11d47 Author: markd Date: Sat Mar 29 04:46:52 2008 +0000 fixed bug were derived not cleared on a forced reload commit d1fb8e7097e044a5d12966c391119a912bd9d0b5 Author: markd Date: Sat Mar 29 02:07:44 2008 +0000 fixed uninitialized variable when forcing a reload commit 243bd5d289ba5ba9b57e42d08ccc10bba3e1b553 Author: jsanborn Date: Sat Mar 29 01:00:06 2008 +0000 adding van 't Veer data commit b25516216c6aa832ac5a7ff9978952e35e919fcc Author: hiram Date: Fri Mar 28 23:40:52 2008 +0000 This may be ready for the update procedure now. Wait to see if the comments are OK with QA. commit b455999fab25bc62ade5af80b748f70c51efc236 Author: hiram Date: Fri Mar 28 22:53:07 2008 +0000 Create the 5-way downloads commit c723311b526d990ddd5352cbace49ce6bdc76656 Author: hiram Date: Fri Mar 28 22:52:26 2008 +0000 Make the 9-way downloads commit 5de99c3eaa80042bad2730d9d9fec65286e60826 Author: hiram Date: Fri Mar 28 22:42:52 2008 +0000 Correcting a period to be a comma in numbers commit 3e7908604c2c3db31cd40b920c5f96010ce196c1 Author: hiram Date: Fri Mar 28 22:41:56 2008 +0000 Fixup references to placental alignments, not in this one. commit e99930adaeb501098280b5908cb8b9059e2ea90f Author: braney Date: Fri Mar 28 20:35:48 2008 +0000 human proteins track commit 77a93c64ac59b165b287cd3b849a027a483ab780 Author: galt Date: Fri Mar 28 15:00:08 2008 +0000 "Encode release log update" commit 95ac551242c5dd0e609532a88ef296936df99873 Author: galt Date: Fri Mar 28 15:00:05 2008 +0000 "Release log update" commit b71e4795d260bede4dc2a59a23661d2c50f47ad4 Author: pauline Date: Fri Mar 28 00:31:44 2008 +0000 Added text to clarify visibility. commit 1a93969cccd1c4e6e66c7d38df1fed4432505fbe Author: ann Date: Thu Mar 27 23:04:44 2008 +0000 made some changes suggested by Brooke during code review (mostly adding more words) commit 5884417177fa8462e45b8de4ed88f321194b7354 Author: ann Date: Thu Mar 27 22:32:48 2008 +0000 bosTau4 passes this rule commit 916439ce0b2a2bea318868160868b61e5fa7c417 Author: ann Date: Thu Mar 27 22:28:28 2008 +0000 added ensGene to priority.ra file. ensGene has a different (higher) priority in Zebrafish assemblies than in most other assemblies. commit 05566517709847c57f9d4be4f612feab27f61b43 Author: ann Date: Thu Mar 27 22:23:52 2008 +0000 apparently you can't place priority.ra files at the org level. Or at least not at both the org and assembly level -- this one was ignored in favor of the ones at a lower level. commit c909029fb3b10d1a0962bff39e3fbd5fd546381a Author: ann Date: Thu Mar 27 22:15:15 2008 +0000 adding priority file to include ensGene track (whose priority for zebrafish is different than for most other assemblies) commit 315ab5eaa67d706e892229eb17c030a7f6fe9684 Author: ann Date: Thu Mar 27 22:07:49 2008 +0000 backing out my last commit, which was committed accidentally (and caught by Brooke during code review!) commit 281005df0945d3b5a017dd7fe15b199d0e0c4822 Author: jzhu Date: Thu Mar 27 19:44:18 2008 +0000 add lajosJCO2006 setting commit af2398101f37b836e9132dddf806622053861aa7 Author: galt Date: Thu Mar 27 18:21:43 2008 +0000 adding FTP upload support commit 6872e1609dbed1e5d02ac6d5628acbe51af34964 Author: kuhn Date: Thu Mar 27 17:43:23 2008 +0000 typo commit 5bb151ae616b941794dec466a1e788f48295e820 Author: jzhu Date: Thu Mar 27 17:01:17 2008 +0000 breast cancer cell line track default to hide mode commit 698941f0c3095b39294b11f3ac54c42b2d13f0f7 Author: hiram Date: Thu Mar 27 16:29:42 2008 +0000 Reload geneid genes on bosTau3 commit cfd0fd68b8feeed89ce3e81fc9d15b7fc18476aa Author: galt Date: Thu Mar 27 15:00:06 2008 +0000 "Encode release log update" commit 9d77c8f06d3c83f47856b51e162accafe144f159 Author: galt Date: Thu Mar 27 15:00:05 2008 +0000 "Release log update" commit ee754ec8e97a5abb38b9d3ef8b057495fa58f2c3 Author: braney Date: Thu Mar 27 01:24:05 2008 +0000 add PSU mammoth maf. This will be a custom maf soon, but now I need it on genome-test so I can trash hgwdev-braney while I work on custom mafs commit c6325020e5d138e50fec0a1c51ff886af3950744 Author: braney Date: Thu Mar 27 00:41:51 2008 +0000 working on human proteins track commit bc7c052a1c89b0db1694262dabe66aaf53cd4070 Author: kate Date: Wed Mar 26 23:51:10 2008 +0000 not a marmoset commit f08be19f2e16f05ac34b92376a8eb08fa340c5bf Author: aamp Date: Wed Mar 26 20:13:54 2008 +0000 Added origAssembly for EC tracks. commit 42f5f76a407946c997988e01bc84203acd32c4f8 Author: aamp Date: Wed Mar 26 19:57:16 2008 +0000 Added tables to be ignored. commit 9edf11953710008f16077e97ddf3ad4ee387c34a Author: aamp Date: Wed Mar 26 19:56:48 2008 +0000 Fixed inconsistency commit 0e0e52d3177e89fcf970b8082c060888aecd1f7a Author: kent Date: Wed Mar 26 19:32:51 2008 +0000 Fixing an edge condition in bedCompatibleExtension. commit 15e53281473dd794a982549a0673ab5f272bd7c1 Author: kent Date: Wed Mar 26 19:32:13 2008 +0000 Making accession checking routine handle CCDS accessions. commit e5d5fa6b284ae679ab084077c4ffa043e3c56acf Author: pauline Date: Wed Mar 26 19:03:19 2008 +0000 Removed 'tab-delimited' from text as per Kate's request. commit 8ed79bd79872efa76f2cf2cc0aef098f0f6bda96 Author: galt Date: Wed Mar 26 15:00:07 2008 +0000 "Encode release log update" commit c5710e4aa5cba9a13505c9e56d7c0ba72275d6a2 Author: galt Date: Wed Mar 26 15:00:05 2008 +0000 "Release log update" commit edc1fc52656b9833d74b8618483ac5f8396489d2 Author: kent Date: Wed Mar 26 13:55:50 2008 +0000 Making it so that vertices from CCDS edges are not snapped in a way that would cause the transcript to be made smaller. commit 4ffcb5258b027a17f2fbbb4e0c855650991889a8 Author: galt Date: Wed Mar 26 00:36:57 2008 +0000 fixing code to match labels commit 43b36d00de4909e2152e50b44fab3ff04b3dc671 Author: ann Date: Tue Mar 25 17:29:44 2008 +0000 fixed copy-n-paste errors commit 87f60eb6d36a2d9a4fe80ff1a7635331b3397d25 Author: ann Date: Tue Mar 25 17:27:23 2008 +0000 removed line about species with no frames commit e02a798a7e7a4ba718e6d07db1e753e126a86265 Author: ann Date: Tue Mar 25 17:12:24 2008 +0000 fixed statement about clone gap size commit fda5f1a8ea8e7408fe463d72dbdf87cae35c2b7d Author: angie Date: Tue Mar 25 16:32:31 2008 +0000 Fix: added tests for 0-length range (bitCount of 0) to bitSetRange, bitCountRange and bitClearRange. Previously, when startIx was a multiple of 8, endByte was 1 less than startByte and 16 bits were set. commit 6593bc15c976b409db51e30d45a38d3d67bfb2db Author: hiram Date: Tue Mar 25 15:51:56 2008 +0000 Initial description of 5-way track commit 465cdadbcf4d6d9063dc58e15943091febde22f2 Author: ann Date: Tue Mar 25 15:10:23 2008 +0000 changing bosTau2 to bosTau1: not sure how that happened commit 5e1d1c8292437d51055d4909937d5f70ec3b08a3 Author: galt Date: Tue Mar 25 15:00:06 2008 +0000 "Encode release log update" commit 338c934281ba6f628281d8f2c847dcfde6dced0c Author: galt Date: Tue Mar 25 15:00:04 2008 +0000 "Release log update" commit 9daed66a5831d7bce4e6472842633f5ff2a03fd6 Author: aamp Date: Tue Mar 25 04:42:14 2008 +0000 changed a dir name... hardly worth the commit. commit 24b81b473a4c89f0b94f7746ab15c02c9d3d7910 Author: aamp Date: Tue Mar 25 04:34:27 2008 +0000 Moved html files from assembly->species level. commit d2210d77c50a0b81121a6bbf8034df9c3e9d5916 Author: aamp Date: Tue Mar 25 04:30:45 2008 +0000 Moved EC supertrack into species level. commit 0ec1ead8fc9438cf1abfc751e565ee34dccd2a30 Author: aamp Date: Tue Mar 25 03:00:45 2008 +0000 Changed up Affy encode extension (EC) tracks a bit to reflect recent changes. commit 4485607e2948fc3a9a53b1dc6359425d62dc113f Author: aamp Date: Tue Mar 25 02:58:19 2008 +0000 Added Affy encode extension (EC) instructions for hg17 commit 747a059735661c808b2651be18e7094cf91b62b3 Author: kuhn Date: Mon Mar 24 23:30:08 2008 +0000 changed link to adam's paper to cornell copy. commit 20085fcc959edeb0db0e783e235c654b18bcc8c3 Author: kayla Date: Mon Mar 24 23:20:38 2008 +0000 added bosTau4 commit 3ee26bce1d8c1da7f0ff1f0e53a06cc4393f32ad Author: ann Date: Mon Mar 24 23:20:01 2008 +0000 moved a sentence. commit 1ef60bc5fdcde38975173ffa817499498bd844b0 Author: fanhsu Date: Mon Mar 24 22:11:37 2008 +0000 Documented the update process to clinical data tables using the latest updated raw data from GSID. commit e70d8b190e6d7ee233bc600926fc89cbbcc359ac Author: ann Date: Mon Mar 24 21:15:15 2008 +0000 added new assembly: bosTau4 commit 2a08508c049f84360a6c6b5cd7bd84ba1dc1be76 Author: fanhsu Date: Mon Mar 24 21:14:45 2008 +0000 Changed GAD into "GAD View" per GAD's request. commit 5b5bbf13ba3fee81585b24fe754ee19333875d2f Author: angie Date: Mon Mar 24 19:49:31 2008 +0000 Add mention of Tajima's D to tajdSnp longLabels. commit 8768fab55ebad5a45a3d7e64b2493ba20d1ada47 Author: donnak Date: Mon Mar 24 17:52:59 2008 +0000 Added announcement abt OH institutional seminars. commit 866552174a39e77d23edc658c4e09f30ec461f22 Author: donnak Date: Mon Mar 24 17:52:38 2008 +0000 Archived 2 items. commit 8c6d4a886ce31ed96c8c13e6757ca010143e4114 Author: galt Date: Mon Mar 24 15:00:04 2008 +0000 "Encode release log update" commit 287c8d545828538fe9039b9b9bec833ee5a4b886 Author: galt Date: Mon Mar 24 15:00:03 2008 +0000 "Release log update" commit 7574ffb990e8036df179e6825be94d60f8b4d41c Author: kent Date: Mon Mar 24 14:25:42 2008 +0000 Finishing implementation of -checkSeq flag. Seems to work, but actually not as useful as I'd hoped. commit 0c5c45af73c325b4fa019a7f8be404e05510f807 Author: kent Date: Mon Mar 24 14:24:27 2008 +0000 Adjusting test case for reordering of evidence. commit b3ad04eb097d52371701fe54360513b3eff78e5b Author: kent Date: Mon Mar 24 11:03:13 2008 +0000 Adding rangeTreeMaxOverlapping commit 9a1123fdb7732e2af6690db6c09b90c49145c2f6 Author: kent Date: Mon Mar 24 10:54:47 2008 +0000 Fixed a bug where evidence was being lost during the merge double-soft stage. Starting to add checkSeq option, but not fully implemented. commit 808861d489c17b548a58e8b86db2b5aa2dccc719 Author: galt Date: Sun Mar 23 15:00:08 2008 +0000 "Encode release log update" commit 100b87a109a4fcadf3f69cf37a655a667b25609e Author: galt Date: Sun Mar 23 15:00:05 2008 +0000 "Release log update" commit e708b53b6ec1ded2cb5898048aa8e2c30f21862f Author: galt Date: Sat Mar 22 15:00:05 2008 +0000 "Encode release log update" commit 9fd536293c5bd5fda255d6f6eaec9984a4cfc9f8 Author: galt Date: Sat Mar 22 15:00:04 2008 +0000 "Release log update" commit 298f8d9c12e71395472854b3aaf4983cb978dce4 Author: kuhn Date: Fri Mar 21 23:31:50 2008 +0000 removed assembly names to conform to standard commit e22a3143135e76e758c38aceff071ebb4fb97bd1 Author: angie Date: Fri Mar 21 23:14:49 2008 +0000 Add tableDescriptions to supporting tables & files entry instead of ignoring it -- Ann's request. commit c155dc1fe6addabf3446fb21858857c6d3d0d9f0 Author: ann Date: Fri Mar 21 23:11:06 2008 +0000 fixed up usage statement commit 6f0683fd104b8f5ccf42f7a80ffd280ad12ff16b Author: ann Date: Fri Mar 21 20:47:53 2008 +0000 one more minor correction commit 6858b0211cce58a1ae5d204cb45ddc67d7b830bc Author: angie Date: Fri Mar 21 20:31:55 2008 +0000 When linking to hgCustom, make per-db links instead of letting it default to the current db, which might have no CTs. commit 7bd6cc9061826c8a09e069be1d90a53124aecc52 Author: ann Date: Fri Mar 21 19:35:13 2008 +0000 added new script to QA Ensembl Genes tracks. commit 1377cadf4edf50c9cef14403228b6a801ab1dda6 Author: hiram Date: Fri Mar 21 16:38:40 2008 +0000 Combine control + and - tracks commit 2e8e22fa303b0dbb7fe506b88d513084832345b4 Author: donnak Date: Fri Mar 21 16:36:56 2008 +0000 Made some minor edits to this page, fixed table display problem w/Win IE6 browsers, etc. commit 489af747d126f15fbc782f7cf166f0ae1d9472d5 Author: galt Date: Fri Mar 21 15:00:07 2008 +0000 "Encode release log update" commit 0016304e60b9f93020e4808840c49067cffe3530 Author: galt Date: Fri Mar 21 15:00:04 2008 +0000 "Release log update" commit 6038c71d92a98d785768384b3b6f120b169c1388 Author: hiram Date: Fri Mar 21 07:33:17 2008 +0000 Adjusting colors commit 4cbbddde8ce8b2287607a211d75b27222c6df4c6 Author: hiram Date: Fri Mar 21 07:16:07 2008 +0000 Update some coloring and so forth commit a310587595f39e89d51b4b2d30f6f248308a5bef Author: hiram Date: Fri Mar 21 05:06:17 2008 +0000 Add nucleosomeStringency wiggle track commit a59494b13b47e635e2753576e0763c0173853d27 Author: angie Date: Fri Mar 21 04:03:58 2008 +0000 snp125Ui: added a Set defaults button to color controls. commit 3f09c67a59deaa6facb3159737ad1b70545aa4b3 Author: angie Date: Fri Mar 21 00:24:05 2008 +0000 Factored out a bunch of safef's to jsHelper:jsPressOnEnter(). commit cf52a100fe6cc81891e9cf6401bf47a768e6e285 Author: angie Date: Fri Mar 21 00:23:16 2008 +0000 Added jsPressOnEnter(button) to get javascript for that button. commit 456f02439a525a2f7eb2a50e44b26d133d329d79 Author: ann Date: Fri Mar 21 00:17:03 2008 +0000 fixed some typos commit 191c123a1fcdf41f6cd1c7737a66dc1232ec2313 Author: hiram Date: Fri Mar 21 00:01:08 2008 +0000 Adding control tracks commit d4f71153fe3a9b6ce0ba1959a90f592103d7c864 Author: hiram Date: Thu Mar 20 23:37:33 2008 +0000 Adding version 49 definitions commit 146d6d4ba9b291ede870967a797573141ec8d4f7 Author: rico Date: Thu Mar 20 23:14:09 2008 +0000 Added slNameListToString commit be3c3084ad4d6640f854141075d22d7d6e87873c Author: rhead Date: Thu Mar 20 19:30:41 2008 +0000 Fixed italics and capitalization. commit f2c1cebdc217aa93ffa2e58cf9204a3dfe62b90c Author: rhead Date: Thu Mar 20 18:47:35 2008 +0000 Fixed typos. commit 0d524c97fa94109f1eda8559873d6944c057f5b8 Author: fanhsu Date: Thu Mar 20 18:06:40 2008 +0000 Changed priority of Human Brain Cortext to 10. commit 9ed929cdda9131a0fbe8ca49feef727c0f827331 Author: kent Date: Thu Mar 20 17:39:43 2008 +0000 Adding ifdef DEBUG around debugging routines. commit 828dbdcd548732965aa1d8c951f6354a8df895d2 Author: kent Date: Thu Mar 20 17:38:35 2008 +0000 Adding a few comments, and a couple of debugging routines. commit e0e94080b2c52437c9f9110867da17f38f0552c2 Author: kent Date: Thu Mar 20 17:38:13 2008 +0000 Removing comment that refers to debugging code that is no longer here. commit a90017ac6147b75be3e70767b8a6c88a51cfd43b Author: fanhsu Date: Thu Mar 20 17:31:01 2008 +0000 Added the table for Allen Brain Cortext genes. commit d54b74f2902000db8bbfb23a5fdb0efd61cff29d Author: ann Date: Thu Mar 20 17:23:57 2008 +0000 rule for new table: allenBrainGene commit 8a2f88cd9ab61db2d9522fe07b35fb85ce1651dc Author: fanhsu Date: Thu Mar 20 17:23:07 2008 +0000 Created allenBrainGene.sql. commit ddf8be99d431cdc5268d411fcc5751868e19ce1e Author: ann Date: Thu Mar 20 16:49:35 2008 +0000 adding findPushQLocks script commit 3417d696573b07c4498378dbbab4a207eb3e019b Author: ann Date: Thu Mar 20 16:48:13 2008 +0000 this script finds (and drops, if asked) all locks in the pushQ on beta commit 723564d89d128ac351d6284a5701c906f5469556 Author: kuhn Date: Thu Mar 20 16:45:52 2008 +0000 removed assembly names from image commit bb242b85ff32813509f7d4a84681a0ca343f9164 Author: hiram Date: Thu Mar 20 15:29:27 2008 +0000 Add links to sequencing center and photo credits commit c2d1eaa3438884817cc18a2fe25d161fa34cdd4d Author: galt Date: Thu Mar 20 15:00:06 2008 +0000 "Encode release log update" commit d761089680d1277caae42584e257cf66ef9bd85b Author: galt Date: Thu Mar 20 15:00:05 2008 +0000 "Release log update" commit dee22ee63e3398050f6c5e349a478406a858e33a Author: kent Date: Thu Mar 20 10:40:15 2008 +0000 Putting back in a sanity check that fell out when introduced CCDS handling. commit f20d835d037c36b2855bcb0bd65b4ef21efbc697 Author: angie Date: Thu Mar 20 04:42:24 2008 +0000 Use cgiMakeOnKeypressTextVar and jsHelper javascript functions so that when the user hits Enter in a text (or file) input, we either ignore it or force a submit with the appropriate button, instead of the default behavior of pressing the first button on the page. commit a917df0e749cd3f156ac422a3177a3e9cfaf05dc Author: angie Date: Thu Mar 20 04:37:17 2008 +0000 Added cgiMakeOnKeypressTextVar -- text Input with onkeypress (java)script. commit 2dee2cfbf3e63192fae70b52b04814ec530b4160 Author: angie Date: Thu Mar 20 04:35:23 2008 +0000 Added javascript function pressOnEnter, which clicks a given button when the Enter key is pressed (usually within a text input). commit 88047e23bd3abd58f2adb8a8690bd1969b9f8eef Author: rhead Date: Thu Mar 20 00:27:57 2008 +0000 Added some breaks to long link names so they won't keep the entire page's text from wrapping. commit 877d304f2cf73d636bb44755f419544f55d87e18 Author: hiram Date: Wed Mar 19 23:51:56 2008 +0000 Made download files and pushQ entry commit 7ab635917a437174ecab86d4ea82f48f66b143a2 Author: ann Date: Wed Mar 19 23:38:56 2008 +0000 fixed typo commit 9571d198697cd45d21452f737aac50e730b3f5cd Author: ann Date: Wed Mar 19 23:37:19 2008 +0000 some small edits commit b53f5f934a863eb6851594d49466dfbd7377b5e7 Author: hiram Date: Wed Mar 19 23:05:27 2008 +0000 Turn on phastCons5way track commit 7a85b85f0995122452b86750b12431db1a4943f3 Author: hiram Date: Wed Mar 19 23:04:56 2008 +0000 Do not use nice in the generated csh scripts, causes problems when controlling shell is bash. commit c0ee7dac43034733976c3c4951e257139fcc1012 Author: hiram Date: Wed Mar 19 20:19:13 2008 +0000 Finished with phastCons5way commit 9d37dd308b7eef2637111113e5de3c1db17abd42 Author: giardine Date: Wed Mar 19 19:25:56 2008 +0000 Added warning when users attempt to send MAF data to Galaxy. commit aebb24e0ef88481fd77d41250758178d804447ac Author: rhead Date: Wed Mar 19 18:38:44 2008 +0000 Changed a lower-case to an upper-case in chain definitions. commit 98e46e642e7f4c5505ce779c71f458fceb448cfd Author: angie Date: Wed Mar 19 18:23:02 2008 +0000 Added Tajima's D and Tajima's D SNPs, liftOver'd from hg17. commit a3a3a8f0c003237852950eed17959d9717369962 Author: angie Date: Wed Mar 19 17:38:09 2008 +0000 Added hgtaIdentifierDb cart variable so that we don't keep the same processed alias-ids when changing database. commit efcadbca88a20921c2118d3bd29f9190a8ebc7ba Author: galt Date: Wed Mar 19 15:00:07 2008 +0000 "Encode release log update" commit 72c877218a02e18e834d33efffcf6eb850e62e44 Author: galt Date: Wed Mar 19 15:00:05 2008 +0000 "Release log update" commit 711208c8eb38bbfda1f45ca22497a6f7573a12d8 Author: angie Date: Wed Mar 19 05:38:58 2008 +0000 Made id-matching case-insensitive to be consistent with our SQL filters and user's expectations (thx Brooke aand MarkD). Also restricted example aliases and hashed aliases to those whose IDs actually appear in curTable. commit 33797815231f40c8539fe92f4f8391f07aad3f81 Author: angie Date: Wed Mar 19 04:39:03 2008 +0000 Added sqlRandomSampleConn -- passing in conn allows us to pass in a temporary table name. commit 2071a14fc420c1ea123f3df9c92f623df9ee76d8 Author: hiram Date: Tue Mar 18 23:46:48 2008 +0000 Have 5-way conservation done. Ready for phastCons or phyloP commit ed5deb5960aac3c409f69365c9f53f08bd7e6b40 Author: angie Date: Tue Mar 18 23:35:49 2008 +0000 Use jsSetVerticalPosition in the check all and clear all buttons on the big select fields page, to keep the same vertical position after refreshing. commit 07816dbbb95f63d8de33ec0900d945ef42df47e3 Author: angie Date: Tue Mar 18 23:34:08 2008 +0000 Added cgiMakeOnClickSubmitButton. commit 0a0a4ca1d8b92a9aac5605d621b2cbf177232b91 Author: hiram Date: Tue Mar 18 23:30:24 2008 +0000 Correct name for 5-way image on Cow bosTau4 commit 664838879c1d5716f26d69e1b1928fbd02afd69b Author: hiram Date: Tue Mar 18 23:26:17 2008 +0000 Adding the 5-way definitions commit 3014e343e2a8cfd9be219b9ff52950a4b180293b Author: hiram Date: Tue Mar 18 22:22:13 2008 +0000 Misspelled word commit 7e4953735ed9c6d16bdebb9cafbdbbe1617a9579 Author: angie Date: Tue Mar 18 22:17:28 2008 +0000 Make use of the new jsSetVerticalPosition to keep the same page position after clicking on a track group hide/show/default button. commit 53d60cfdd9306f9c90d11582b87477adda4a4793 Author: angie Date: Tue Mar 18 22:15:19 2008 +0000 Moved makeSetClearButton up to jsHelper. Make use of the new jsSetVerticalPosition to keep the same page position when updating the snp125 controls. commit 76bb5825dcee5542aef8b2d7eecf58f53f1ce8b2 Author: hiram Date: Tue Mar 18 22:14:49 2008 +0000 Bring up to date with correct information commit 06f7ddd3d3be24747decdb37f491d7249c24806f Author: angie Date: Tue Mar 18 22:12:57 2008 +0000 Added jsInit, jsSetVerticalPosition (for returning to the same place on a page after an update/submit), and jsMakeSetClearButton (for setting/clearing a list of checkboxes). commit 106f69bd5bf00cde1ae22ce40a409c9333cfd967 Author: angie Date: Tue Mar 18 21:59:10 2008 +0000 Further improvements to SNP null alignment message in printOffsetAndBoldAxt. Also sneaking in a convenient link to hgTrackUi, just after the View Table Schema link. commit 2c0c3eb3893358d42dd0a739bbdbc6058b8f9a67 Author: angie Date: Tue Mar 18 21:55:47 2008 +0000 Correcting yet another couple bugs in the includeEdgeGaps addition to axtGetSubsetOnT. commit c0b78b87fa5ba4f10095aff5fada94ff22f9981f Author: kuhn Date: Tue Mar 18 21:51:20 2008 +0000 tweak commit e59b4fe630e34d996a62f62944101abef489f852 Author: kuhn Date: Tue Mar 18 21:49:38 2008 +0000 tweak commit 909b26fc531a2f5cbebdeb7470f51c526a586fe3 Author: kuhn Date: Tue Mar 18 21:48:53 2008 +0000 cap Sumatran commit 86af4a4c8f5cb2db0b3d5356b7334a598ecdef98 Author: kuhn Date: Tue Mar 18 21:45:58 2008 +0000 made species name italic and added a space in 50 kb commit 581e95ec61c4fe06effb72a2d0cbb4eb972fd9b1 Author: angie Date: Tue Mar 18 20:58:51 2008 +0000 In axtGetSubsetOnT, if includeEdgeGaps has expanded the symbol range for a 0-length target range, bump the symbol pointers inwards if one is still sitting on a real base. commit 22a4c7367aac94086ed7cf9f02d05ec6135aae81 Author: ann Date: Tue Mar 18 19:32:26 2008 +0000 removed both ensGene blocks. Rachel had started setting up Ensembl genes to use hgGene but never finished. We'll let it default to the top-level now (like all other assemblies) commit 426f8c94ce69e7fca309f3074d150360f2cdf6f1 Author: ann Date: Tue Mar 18 19:25:45 2008 +0000 added back ensGene block (need it here becuase the ensGene.html page is slightly different for fugu). commit 9b59a85f5ddb054d0bd5b3566cf6e6ae12497e08 Author: ann Date: Tue Mar 18 19:02:58 2008 +0000 removed ensGene block (use top-level). commit d7832df69137b1e1cdf38847dc552e6aed15920e Author: ann Date: Tue Mar 18 19:00:05 2008 +0000 removed ensGene block (use top-level) commit 23c3c90cb30583b3f1368ebef33fa8db1411a3c7 Author: ann Date: Tue Mar 18 18:51:20 2008 +0000 removed block for ensGene (use from top-level) commit 61dc02e6d5a06170d5e1a51253e2e02821988c45 Author: angie Date: Tue Mar 18 18:47:31 2008 +0000 Oops, restoring refGene's idXref to refLink -- too many refGene's do not have name2. commit 2b68b2fb0446cd9246bb14306bea94043bded2bc Author: ann Date: Tue Mar 18 18:45:04 2008 +0000 removed ensGene block (use top-level) commit 64a226ca078635bb3d204db681ec34e5430aa547 Author: angie Date: Tue Mar 18 18:40:58 2008 +0000 Handle missing xrefTable (or field) more gracefully (ignore instead of making a doomed query). commit 765eab4ba12ebb970972a63c049afedad9ff3d67 Author: ann Date: Tue Mar 18 18:40:41 2008 +0000 removed esnGene block (use top-level) commit ae74a63b391206dd1b0f3a1ab0e7895493e8c1b4 Author: ann Date: Tue Mar 18 18:35:29 2008 +0000 removed ensGene block (use top-level block instead) commit 94cd63697d45a8ef405bcd466829267b42d77d32 Author: ann Date: Tue Mar 18 18:29:27 2008 +0000 fixed commit 1cf6c2dc2026a301c631fa71e972340ad6003ae3 Author: ann Date: Tue Mar 18 18:24:04 2008 +0000 removed block for ensGene (it will use top-level block). added visibility to new vi sibility.ra file. commit c1983b8e2e9cc035357d291455c12777323e7f64 Author: ann Date: Tue Mar 18 18:23:31 2008 +0000 removed block for ensGene (it will use top-level block). added visibility to new visibility.ra file. commit aefa0006cb199f21a18dc58af542ff8681c60425 Author: ann Date: Tue Mar 18 18:17:36 2008 +0000 removing ensGene block (can use block at top level) commit d6bb348d9c28eafc018a89fc4477d88681d8d4f4 Author: ann Date: Tue Mar 18 18:15:51 2008 +0000 adding visibility.ra file so I can take away the ensGene block in the trackDb.ra file (to use top-level block). commit e97721a5948c20bfb3413ad550eb1740081e5bc9 Author: ann Date: Tue Mar 18 17:37:07 2008 +0000 Removing: use top-level file instead. commit 3f57458127d134a724130f38cc6fe2a2d5e8109f Author: kent Date: Tue Mar 18 16:43:49 2008 +0000 A bit more progress on this version of the ucsc genes build. Still adding in CCDS to the pipeline here and there. commit f01ef0ba67f0275048b3e88ec5e52cf9fb6b3d69 Author: kent Date: Tue Mar 18 16:42:48 2008 +0000 Starting new program to help connect the CCDS with the txWalk. Still only half implemented. commit 4297b0779152a6cfb47f77a2d93f00e6e762b682 Author: galt Date: Tue Mar 18 15:00:29 2008 +0000 "Encode release log update" commit 2d143fdc4b503b44fea4a9df00493d725ce60c8d Author: galt Date: Tue Mar 18 15:00:26 2008 +0000 "Release log update" commit dd4d2e241b281d91335eabedbcf3e7921aff1b30 Author: aamp Date: Tue Mar 18 14:37:53 2008 +0000 "New version number v178" commit afbbe9f536c75ef3fee054e13e64cac84cbd889c Author: angie Date: Tue Mar 18 08:02:08 2008 +0000 In printOffsetAndBoldAxt, improved message for 0-length bold (SNP) section. commit a811e85263c8c3912cc9b7d31df3c6f94010ec40 Author: baertsch Date: Tue Mar 18 06:17:21 2008 +0000 move retroMrnaInfo to gene group and update priority commit f23dafdb0e9201a8e0ae32474eb90b87093fc628 Author: baertsch Date: Tue Mar 18 05:11:24 2008 +0000 add function sqlSignedForgiving(char *s) /* Convert string to signed integer. Unlike atol assumes * all of string is number. */ commit c682510ff98df7986e6f4fad0c0cba8918f57214 Author: aamp Date: Tue Mar 18 04:59:18 2008 +0000 Added stuff for Affy Human Exon column. commit eeec27f637dac3d93b4c20f3ecfa16a149d32b65 Author: angie Date: Mon Mar 17 23:57:25 2008 +0000 Changed refGene's idXref setting to use its own name2 field (refLink is too broad, has xeno entries too). Thanks Brooke for the suggestion! commit f0986d681582afcd3dee93b847e34053c57f1f18 Author: angie Date: Mon Mar 17 23:40:38 2008 +0000 If alias table is same as main table, mention only the alias field. commit 65685af82c20392957452e9d5858bc145292e756 Author: hiram Date: Mon Mar 17 23:30:33 2008 +0000 before v43 there are no GTF files commit 521e21e98e4de6ab8c60810e4c3047c817882e19 Author: markd Date: Mon Mar 17 23:11:15 2008 +0000 todo item commit 5efe404cda454bb5cb2327cc0399dc82eea6832e Author: kuhn Date: Mon Mar 17 23:01:33 2008 +0000 italicized de novo and dropped space from midle of orang utan commit 9cd83135e44e4b65168755ecc0fe07cbd37064e5 Author: angie Date: Mon Mar 17 22:32:16 2008 +0000 Adding local definition and description of tajD and tajdSnp to emphasize that they were liftOver'd from hg17. commit 918c4f653ded3f64316fe9a25a40ef178ac510f7 Author: angie Date: Mon Mar 17 21:13:26 2008 +0000 One more tweak to axtGetSubsetOnT for includeEdgeGaps. commit a44972b0ab5abf26ac441987b2b5ba131ae4e352 Author: angie Date: Mon Mar 17 19:37:20 2008 +0000 Improved table layout in printSnp125ColorSpec (thx Brooke). Also, use anchors for buttons and color feature select for snp125 filter/color controls so we get zapped to control section instead of top-of-page. commit fdbac9025e3c9bc6e44efb6411a5de7046ca7fe5 Author: angie Date: Mon Mar 17 18:10:12 2008 +0000 Updated comments for snp128 tables (including reloads of snp128ExceptionDesc and snp128OrthoPanTro2RheMac2. commit 436cf0265d639d51906cc644fa1653e4e2afaa80 Author: angie Date: Mon Mar 17 18:05:29 2008 +0000 Added note about reload of snp128ExceptionDesc. commit 6252b063f6032467031eb0a751ad1d5cc7c98d24 Author: angie Date: Mon Mar 17 18:04:37 2008 +0000 Added newline to make HTML output a bit easier to read when debugging. commit 797e535d46b5f6c4e894ee5b1d305019808ab3a6 Author: galt Date: Mon Mar 17 15:00:08 2008 +0000 "Encode release log update" commit ea156f9851ae1872972b9fec9a0f6fefe73ec1f0 Author: galt Date: Mon Mar 17 15:00:05 2008 +0000 "Release log update" commit 35680f6e3b76620ee4ab6f312e44a2a462e56bca Author: galt Date: Sun Mar 16 15:00:06 2008 +0000 "Encode release log update" commit b9e4ac8ef77f379f9617daa1b1151b5e397da8c3 Author: galt Date: Sun Mar 16 15:00:04 2008 +0000 "Release log update" commit 0bf71e4751739ec83f4822ad8673fd2276a93293 Author: galt Date: Sun Mar 16 02:55:52 2008 +0000 fixing refresh problem with more javascript to disable after a link has been already clicked by user commit d9f1caa700e6f0eece959fb2146d465dfbff616b Author: fanhsu Date: Sat Mar 15 19:52:50 2008 +0000 Updated to turn off Beta Test mode and turn on payment processing. commit 53321603c4655bf83f19bb40c3b400f5f4e95672 Author: galt Date: Sat Mar 15 15:00:08 2008 +0000 "Encode release log update" commit 88ad7d6956dc993cd3f52ee96ecd4229d613413e Author: galt Date: Sat Mar 15 15:00:05 2008 +0000 "Release log update" commit 651794f6e295255faa57f5cc845ba2bd9966899d Author: markd Date: Sat Mar 15 00:07:31 2008 +0000 made some functions static to make code easier to understand commit 82cab3e01099fce4bca0cc51ab638bb4e7fb31d7 Author: angie Date: Fri Mar 14 22:03:09 2008 +0000 Simplified the passing of t and q sequences from generateAlignments to printOffsetAndBoldAxt: instead of swapping t and q in generateAlignments, do an axtSwap just before printing. Now that axtGetSubsetOnT is called using genomic coords, dbSNP mappings are highlighted better in the alignment. commit 80e97b682406cb50854dd401d90397d5c84b7522 Author: angie Date: Fri Mar 14 21:05:52 2008 +0000 In printSnpAlignment, make strand more explicit (thx Brooke). commit 0dba106be27b21688b28594af8a162cdd1b0078d Author: hiram Date: Fri Mar 14 21:00:51 2008 +0000 Beginning the 5-way alignment commit b972c57cc4d2b76ca1f473409bf1706a7cb21394 Author: hiram Date: Fri Mar 14 21:00:32 2008 +0000 Place Sloth in correct order in the dbDb orderKey pull-down menu choice, next to Armadillo commit 2bc3d5d910579e835bdb33338d0fbbdce56febc3 Author: markd Date: Fri Mar 14 20:10:06 2008 +0000 removed panTro1 xenoEsts commit b1461471f4e555ad3a4a5d8f7762038fd1876bfa Author: angie Date: Fri Mar 14 18:33:37 2008 +0000 Enhanced printSnpAlignment to show the annotated SNP in bold when printing genomic and flanking seqs, and also to print a separate, bold alignment block for the re-aligned SNP. Also display the correct genomic coords (and flanking even when trimmed) in the alignment. It's a little tricky because generateAlignments swaps t & q so that the genomic sequence appears on top; so down in printOffsetAndBoldAxt, t is the flanking sequence and q is genomic. commit 86ed7c1b377e33c7b2506ba8a191d840617dc9bd Author: ann Date: Fri Mar 14 17:29:03 2008 +0000 fixed math error found by user commit 12c9c3b517321fbd6080e79162d62c9cf1518c1e Author: fanhsu Date: Fri Mar 14 17:03:27 2008 +0000 Updated per GAD John Garner's request. commit fcf6b40d6ef51095419cdaca8bc4d25f902e566c Author: hiram Date: Fri Mar 14 16:09:48 2008 +0000 Platypus ornAna1 blastz done commit 35a81ed98348dcce607902bea9596d56df643cc3 Author: kent Date: Fri Mar 14 15:13:29 2008 +0000 Making txInfoAssemble handle CCDS. commit 4332a8b483d67fa1bb7f0cd3bc003d3543d14646 Author: galt Date: Fri Mar 14 15:00:06 2008 +0000 "Encode release log update" commit f46c8e4e5a7a8ece5ced91f065c793e7bc3503e1 Author: galt Date: Fri Mar 14 15:00:05 2008 +0000 "Release log update" commit 1733c40f10f6d2de77ab81879387f99681dc0b9d Author: angie Date: Fri Mar 14 04:27:53 2008 +0000 Extended axtSubsetOnT to add axtGetSubsetOnT, which is just like axtSubsetOnT except it modifies an axt instead of writing to a file, and has an option to not trim gaps adjacent to the range. Extended axtPrintTraditional to add axtPrintTraditionalExtra, with optional reversing of the printed coordinates (for when the axt alignment was created on sequence that was already reverse-complemented). Both additions were motivated by hgc/snp work. commit 5ceae46bd77ad0996fa5a02cd227a8ab9a51aabf Author: fanhsu Date: Thu Mar 13 23:04:30 2008 +0000 Added index on name. commit aa01f038125154441523688ba4ca7f6b972083f9 Author: fanhsu Date: Thu Mar 13 22:45:11 2008 +0000 Added search index for rnaGene. commit 5daae931dabb0f705fbcc4bbfebc07a9fbd49052 Author: rhead Date: Thu Mar 13 21:44:39 2008 +0000 Added calJac1. commit 6ca3ddb7abf07e6c46c2c48ac265b9f42a32fce8 Author: galt Date: Thu Mar 13 20:11:46 2008 +0000 fixing cancel button on new project form; also add return after similar redirect from another cancel I noticed commit ff8105ac74db07d95117d02f05eafb87121a29a7 Author: galt Date: Thu Mar 13 20:05:23 2008 +0000 bugfixes - minor tweaks needed from testing commit 3c12026733be25d82a69588ed66d890329d0163b Author: galt Date: Thu Mar 13 17:53:02 2008 +0000 restore line to previous more specific value commit d85bf25cb12ad9d3dfbcf54be68b08956e84ffe5 Author: galt Date: Thu Mar 13 15:00:07 2008 +0000 "Encode release log update" commit 7c6bb23de9d32fadaf8b411ffd1549a4920e7800 Author: galt Date: Thu Mar 13 15:00:05 2008 +0000 "Release log update" commit e0360d0062f59787b7334efd650cb5ab4462ac02 Author: markd Date: Thu Mar 13 00:12:34 2008 +0000 to-do item commit be39c44d521b1960b288a799222a7da703b59869 Author: markd Date: Thu Mar 13 00:12:24 2008 +0000 beginnings of a script to make copy download more robust commit 202e966e09b347a90dad39f8c34996ad95fb0c81 Author: markd Date: Thu Mar 13 00:05:03 2008 +0000 fixed bug were some paths to script didn't generate correct gbRoot commit bcb2f4aa417fbf363c379daa6c51e9d8fabd54ec Author: hiram Date: Wed Mar 12 23:36:46 2008 +0000 Running the swap to bosTau4 commit 548e0c2487375d879c730f557bdd18e53a4cdddd Author: galt Date: Wed Mar 12 23:34:51 2008 +0000 fix IE click - workaround uses javascript reload instead of meta refresh commit 4c7f02cf5d609855123dd49d6b405bc1d3a05e76 Author: hiram Date: Wed Mar 12 23:29:12 2008 +0000 Text for nucleosome density graph commit e1b439106020d13d0a2345fc812c959b474612b2 Author: hiram Date: Wed Mar 12 23:28:19 2008 +0000 Added density graphs for the nucleosome maps commit fa2b19338bee4b37794f64522a2a897d026303a8 Author: hiram Date: Wed Mar 12 23:01:30 2008 +0000 Finished blastz to bosTau4 commit f24234971b7b4d0f9ddd31e7a2d25450cb60e4c1 Author: hiram Date: Wed Mar 12 23:00:56 2008 +0000 repeat masker and simple repeats done, blatServer assigned commit 5f44578decb8e965a8c9be523af08c3c1a6f7b18 Author: hiram Date: Wed Mar 12 23:00:26 2008 +0000 Running blastz with bosTau4 commit 5cd799f5e5a40f4a432dcb90b65c20b96d70e89a Author: hiram Date: Wed Mar 12 22:59:52 2008 +0000 genscan done, blastz human and mouse done, blatServer assigned commit 3de96799ff5a98dbd0226c391e6dc121179b0b6a Author: angie Date: Wed Mar 12 22:54:58 2008 +0000 In addMrnaPositionTable, use gbStatus.orgCat to distinguish native from xeno when possible. If gbStatus does not exist, fall back on the hashed organism.id. commit 84b9614fd803c34b2f4843803d52c4c59740fc1d Author: hiram Date: Wed Mar 12 22:11:11 2008 +0000 hack in the auto-increment and datetime business commit ffdb9495ea176091a6a6b42554735ef073b89ee3 Author: kuhn Date: Wed Mar 12 21:59:43 2008 +0000 changed the usage statement commit 0cffd12b514d0f55172d09f986bf01a1b675b587 Author: kuhn Date: Wed Mar 12 21:59:03 2008 +0000 changed the usage statement commit e6dacce755ee73e07261858cb03e1f25f3b0e084 Author: markd Date: Wed Mar 12 21:56:21 2008 +0000 added nscan gene predictions commit 2a3922f8d1c54c3e8ad69d5240f96ee66bb19b0b Author: fanhsu Date: Wed Mar 12 21:53:52 2008 +0000 Added commments on each field. commit b5f67146f5d9d9d41772913872b97797c4cf91bd Author: angie Date: Wed Mar 12 21:47:30 2008 +0000 Corrected a function comment. commit b858d8f87bd6a2303cd231731f3cea439b374df0 Author: angie Date: Wed Mar 12 20:11:02 2008 +0000 Added slNameListFromStringArray. commit 7b09a9a248166f8925943c8ae07a1c480b841036 Author: angie Date: Wed Mar 12 20:10:24 2008 +0000 Modularized out some set/clear button code from wigMafUi into makeSetClearButton. Added set and clear buttons to snp125PrintFilterControls. Removed a few spots of unused code. commit 7f332d54a7847c6702af9fd291e000f919684888 Author: hiram Date: Wed Mar 12 18:52:43 2008 +0000 Add information from the ASSEMBLY file from WUSTL commit 81b0ae6144f3e167d9d37d2ea38078bfc51af4b0 Author: ann Date: Wed Mar 12 18:49:22 2008 +0000 loosened two dm rules to account for drift from FB genes to refSeq commit f40805298765ebb2fa4ae1754100d385c43fce9c Author: ann Date: Wed Mar 12 18:39:11 2008 +0000 Hiram refuses to fix these tables, so I am excluding ce2 from the rule. commit 12542632d9516bae81351b8a1ad9be4fe340e73d Author: kuhn Date: Wed Mar 12 18:29:09 2008 +0000 typo commit ef566501f66c38f9d498e619b731b22e40a31ae0 Author: hiram Date: Wed Mar 12 18:27:02 2008 +0000 Image permission obtained from Dr. Tanya Dewey commit 8cd92abac67b71467494ba9098d2a7f5d60d6630 Author: ann Date: Wed Mar 12 18:09:26 2008 +0000 removed MGC from usage statement commit 24e3e2a6cae0cffb2fa0da7318b28958afed0c03 Author: hiram Date: Wed Mar 12 17:39:30 2008 +0000 Adding bosTau4 chain and net commit c9beead9a097286b8a0fcd659c31d674e04c0140 Author: galt Date: Wed Mar 12 15:00:08 2008 +0000 "Encode release log update" commit ec9c94784960b0ec158f3020356899c2b294ac4e Author: galt Date: Wed Mar 12 15:00:06 2008 +0000 "Release log update" commit b1450c07b0ee4c438bf9f218b507e109348e89a8 Author: hiram Date: Tue Mar 11 23:23:05 2008 +0000 A run time from a January run commit 89a1d452f62167aa3646ceaad38c3fe102ee3299 Author: hiram Date: Tue Mar 11 22:44:32 2008 +0000 Turning on the Nucleosome maps commit fbd16f28073bfda32ad860ef505f9d734240a571 Author: markd Date: Tue Mar 11 21:56:27 2008 +0000 fixed problem with overall count of number of errors commit fc23c72e6fbdacb8cde722233f08934de36de487 Author: ann Date: Tue Mar 11 21:44:40 2008 +0000 dupes are OK in these two tables (says MarkD) commit f97cec6fb1cb24e3ad4866fce4a423357f8a86cf Author: markd Date: Tue Mar 11 21:19:31 2008 +0000 removed too-agressive sanity check commit 5ac74ec49fc998c01b6f6b9096f355387f16688a Author: kuhn Date: Tue Mar 11 20:38:30 2008 +0000 added marmoset and also added snp128 commit 5b6764d476031d740e4342bca3eebf144f20f923 Author: hiram Date: Tue Mar 11 19:02:49 2008 +0000 Ensembl gene update done commit dc0d09043e4d59ca2c1d4d2aea272ae3fea22600 Author: hiram Date: Tue Mar 11 19:02:05 2008 +0000 A stray run-time left over commit 186d9bfbc83c772cec7ef816d1e4ace67d53ec00 Author: hiram Date: Tue Mar 11 19:01:39 2008 +0000 genbank run done, CpG Islands done, genscan running commit 5d5f66149b49ae77f6d630e537c9d347059f2c96 Author: kuhn Date: Tue Mar 11 19:00:49 2008 +0000 changed a Credit and flipped an accent commit 47bbe52f273f794a09658691714f47dd3a3909b3 Author: kuhn Date: Tue Mar 11 18:22:11 2008 +0000 fixed description commit 36f5cb3e143ca83662fe712d4acec8bb16e7ea21 Author: rhead Date: Tue Mar 11 18:15:06 2008 +0000 Set snp127 visibility to hide. commit 49d7bba8d5d8753ed7f4bd95b66dd5e158fabf11 Author: rhead Date: Tue Mar 11 18:13:25 2008 +0000 Set snp126 visibility to hide. commit 5184b46e7995b172dde2d0b9ba9228b1e7e43911 Author: kuhn Date: Tue Mar 11 18:04:56 2008 +0000 fixed description commit 89ae7a85f921d452abeba3808deb71752fb4d68b Author: rico Date: Tue Mar 11 17:03:49 2008 +0000 now using segFirstCompSpecies from seg.c commit a6ef9e9cffa08b84ee505d2b2ae785dd914e455a Author: hiram Date: Tue Mar 11 17:03:24 2008 +0000 Added bosTau4. commit 26663c5fb879a7fddc38813d90f6d06732e4b042 Author: galt Date: Tue Mar 11 15:00:07 2008 +0000 "Encode release log update" commit 069abd6ef057237098c6f1cd31d85a5e3441fe5e Author: galt Date: Tue Mar 11 15:00:04 2008 +0000 "Release log update" commit f8a870bb9725d8d64d8f5b027c2252c64d1e7ed2 Author: galt Date: Tue Mar 11 06:34:54 2008 +0000 fixing upload form cancel button commit 27f6bfe6de4982ee1fcf627e86cec1b9221670d4 Author: galt Date: Tue Mar 11 06:28:59 2008 +0000 add .tgz as allowed archive extension commit 785775297ec9b48d3455c765fe9c20765b2569c0 Author: galt Date: Tue Mar 11 06:16:28 2008 +0000 fix double email notifications on password change commit e48e6a6f5b5e4404bb3fb7a9f5067537efc262c1 Author: aamp Date: Tue Mar 11 05:42:47 2008 +0000 Moved ultraconserved entries from assembly (hg17) to species level to accommodate lift to hg18. commit c3184735b9754689bec185979404812c01904727 Author: aamp Date: Tue Mar 11 05:31:28 2008 +0000 Lifted ultraconserved tracks to hg18. commit ea8051b98d57895e90fd6f221c85a85a29b3e865 Author: markd Date: Tue Mar 11 05:08:16 2008 +0000 allow large delete flagg to override org category change delete commit 63919d5cdb5587934b8eb95df76f0bc3562f8673 Author: markd Date: Tue Mar 11 05:07:23 2008 +0000 turn down verbosity of acc reload messages commit aacd21d4c400e5f5a434d840643680218c8e3f12 Author: galt Date: Tue Mar 11 04:38:20 2008 +0000 do not fight the framework commit b3ae856544061a6c85ca12becc9f3fc9601e0255 Author: markd Date: Tue Mar 11 04:32:36 2008 +0000 fixed bug setting CDS and frame when gene overlaps start of target with CDS before the start commit 73d7d713b600bda07277ad743d8f3af18531db42 Author: hiram Date: Tue Mar 11 04:27:54 2008 +0000 adding quality track commit a394f5939db9bab480663ab1debf92410220f1fd Author: angie Date: Tue Mar 11 04:13:51 2008 +0000 Added emphasis that the genomic mapping is taken directly from dbSNP, based on Brooke's suggestion/ commit aca1c0a7b3035eacfee8f8308e7da7e0bb3f76c1 Author: hiram Date: Mon Mar 10 23:07:18 2008 +0000 Adding san filesystem OK for memk, and some older Ensembl version definitions commit b3043c18a39a6fc1daf651f5f9f5423af38f4074 Author: rico Date: Mon Mar 10 20:47:06 2008 +0000 -merge is now working correctly commit eba6d91619d6decc96010783a5ca63ea20291219 Author: hiram Date: Mon Mar 10 20:38:15 2008 +0000 Added bosTau4. commit e119ff4636bfe822587a1a95db212e4365a72e13 Author: kuhn Date: Mon Mar 10 20:25:52 2008 +0000 moved text away from image commit 0011f9821832cf3eb46926021a966c06d433ecdf Author: hiram Date: Mon Mar 10 20:19:31 2008 +0000 Add Hoffman's two toed sloth, choHof1 commit 8d5e682dd209aa93795b8002f6a3e3b3e7021268 Author: kuhn Date: Mon Mar 10 20:13:47 2008 +0000 moved text away from image commit 7fd1e6dc3000121f76b3acc0e2a654f1fc505bb3 Author: donnak Date: Mon Mar 10 20:12:49 2008 +0000 A few more orangutan mods. commit 3e631c78b71ae608a4813cea99af8d3019d702d8 Author: donnak Date: Mon Mar 10 20:04:58 2008 +0000 Added a few people to orangutan credits. commit 92b79c682c638e274fc6ee5b5364cfe2471b4ad6 Author: donnak Date: Mon Mar 10 20:03:25 2008 +0000 Fixed a typo & made a few edits. commit 7a8ffb9489c9eaad9ec8700af86e7d7fbac37a3e Author: donnak Date: Mon Mar 10 20:03:12 2008 +0000 Made a few small edits to orangutan section. commit f8b3cc7f00d47e822dfeb2c642787e2af15e6e71 Author: hiram Date: Mon Mar 10 18:43:49 2008 +0000 Initial contents from makeGenomeDb.pl commit 89138b498cd80a4928cd755ffeb1104217d30df5 Author: rhead Date: Mon Mar 10 18:42:25 2008 +0000 Added a note about masked fasta files for human. commit 495fe5f09967a46ce59c5b8eb28a3046a5379e47 Author: hiram Date: Mon Mar 10 18:02:50 2008 +0000 Fixup the multiple names to genbank and add a quality track commit 9668f3808891fc4dbc5a2a5338b8d674077a627f Author: hiram Date: Mon Mar 10 17:49:27 2008 +0000 Now finding a date string from hgFixed.trackVersion for Ensembl archive references commit 248561734a87e4ec8ae0dd199b93a24a3de8f408 Author: hiram Date: Mon Mar 10 17:48:11 2008 +0000 Adding an archive link option to the constructed Ensembl URL commit d0d3ce90d8ecc593bd9e415319a1cf9629224522 Author: hiram Date: Mon Mar 10 17:47:52 2008 +0000 Adding archive link option to the constructed Ensembl URL commit a3e89d9c1c45a5eca4d1eba63ac4961f96dd1c33 Author: rhead Date: Mon Mar 10 17:35:08 2008 +0000 Changed 'Reference' to 'Reference (coding)' to match hgTrackUi. commit a5a7ae8b64abaea87bb212b2f9e4bc69bde9388d Author: galt Date: Mon Mar 10 15:00:06 2008 +0000 "Encode release log update" commit 176e88c1e93f745bdf80c35e74eb245dfb5a1e52 Author: galt Date: Mon Mar 10 15:00:05 2008 +0000 "Release log update" commit 43878bbdab71d00c1e57327c67b5f919903c758c Author: galt Date: Sun Mar 9 15:00:36 2008 +0000 "Encode release log update" commit ebdb29c5fead37efd7a6ade128a0131fc2ffb1eb Author: galt Date: Sun Mar 9 15:00:33 2008 +0000 "Release log update" commit cd0e25dfb295532b707fba32be4f23966bc31251 Author: rico Date: Sun Mar 9 01:13:09 2008 +0000 left an extra } commit 6f58affa267d7e6852aee3445b31baf13a72f359 Author: rico Date: Sun Mar 9 01:09:53 2008 +0000 merge isn't working the way i want it to. i need to rethink. commit 43802159c5c3ba9fd60c889c90005348b367c2df Author: rico Date: Sun Mar 9 01:03:08 2008 +0000 changed to output list of lists. added -merge option commit 8c4f27eddd2e5fcf87724018a6d82d5479cd9451 Author: donnak Date: Sat Mar 8 17:13:50 2008 +0000 Added news announcement for ponAbe2 browser release. commit d2daea149d449e158f023d249494a0e6178c256f Author: donnak Date: Sat Mar 8 17:12:32 2008 +0000 Edited & updated this file. commit 95ca0478cfeb2f5554156346ad8009fd8f0b16c9 Author: donnak Date: Sat Mar 8 16:11:42 2008 +0000 Expanded credits for orangutan. commit 80d5ad4aaed637ce095b0b787ea005c7a5a60d8f Author: galt Date: Sat Mar 8 16:00:06 2008 +0000 "Encode release log update" commit eb72a094505ffb5889f7d30c5a3f6daa9083e430 Author: galt Date: Sat Mar 8 16:00:04 2008 +0000 "Release log update" commit e1d5a1dde4953b42fdd36416902da8bc2f7802b3 Author: markd Date: Sat Mar 8 15:27:56 2008 +0000 removed assert for state that is valid if doing a forced reload of some sequences commit 8275c7a01fe19b36822f9a813ed0a91b7a6921b4 Author: markd Date: Sat Mar 8 15:13:58 2008 +0000 handle EU152113 with delete commit b818f03df26b74cb8a30626bd3c6e3a1e2aa55cc Author: fanhsu Date: Sat Mar 8 15:05:44 2008 +0000 Added target=_blank for GSID tutorial links. commit e71ddbecb1c21e94df8e32118f6565f328450d21 Author: donnak Date: Sat Mar 8 14:44:57 2008 +0000 Added section on orangutan. commit 52f564e7c25b0fbf6661e8cc0c9ceb42aef9c933 Author: donnak Date: Sat Mar 8 14:42:08 2008 +0000 Slight rewording. commit 991fdc47255e59ff9d86f9c490512ea99b12c47b Author: rhead Date: Sat Mar 8 01:47:12 2008 +0000 Added links to Open Helix in strategic locations. commit 408d89a4baaa464c6c2bfc7140ad414aa9c1cbb2 Author: hiram Date: Sat Mar 8 01:23:32 2008 +0000 Beginning Cow 4.0 and Sloth commit 36cd7cc97582b484e446ff9758cacf4ca7b9d5f4 Author: kuhn Date: Sat Mar 8 01:11:31 2008 +0000 added mention of reverse button and archived job announcements commit f93c8f0070cc3724d9f0c54489e825186c997db3 Author: markd Date: Sat Mar 8 00:53:40 2008 +0000 disable transMap details page while new one is being developed commit 10fb4850ba7d2ac7f73e4c6002fbce3c608b4502 Author: markd Date: Sat Mar 8 00:52:52 2008 +0000 removed outdate use of gene-check in ensembl commit d1e5d46704f83563a0fde579032549bb57a24c5e Author: hiram Date: Sat Mar 8 00:52:03 2008 +0000 Fixup a couple of 3.1 references commit dd5748a4acef85040b2898f0366324aa25552191 Author: hiram Date: Sat Mar 8 00:47:37 2008 +0000 Updated to be the same as was in bosTau3 commit 2da1ab0d6c989c27376fe4f0c6cc5cb5ee3e42c3 Author: hiram Date: Sat Mar 8 00:45:30 2008 +0000 Updated to represent bosTau4 information commit 1c8a20ea8b321a167505d0b183bf2f5ec1e5a349 Author: hiram Date: Sat Mar 8 00:36:48 2008 +0000 Initial files from the makeGenomeDb.pl commit 2bf1189b71c88041bc83dea54dfd9b7e0a81212e Author: kuhn Date: Sat Mar 8 00:31:09 2008 +0000 added mention of reverse button and archived job announcements commit 24f06717d7701481f5218a6a49271ea19e512a91 Author: kuhn Date: Sat Mar 8 00:29:37 2008 +0000 added mention of reverse button and archived job announcements commit 373974dcecfdafc7e165aa0b7da08a60d08eeb7f Author: fanhsu Date: Sat Mar 8 00:21:28 2008 +0000 Updated CTD build section. commit a9af42809dfeaf071ef2ec4ecd5ebb869a854e26 Author: fanhsu Date: Sat Mar 8 00:19:36 2008 +0000 Created ctdSorted.sql. commit 0c0aff43ecd7f5d7ccb9bdc3baade47e7b176732 Author: fanhsu Date: Sat Mar 8 00:18:34 2008 +0000 Updated to get CTD data from hgFixed DB instead of ctd DB. commit b28ac14867714053be05aab56b583e49584444a7 Author: kate Date: Sat Mar 8 00:05:05 2008 +0000 Changes for modENCODE configurability: 1. Add subtitle for window title and page header. 2. Reference logo from standard location 3. Add Contacts page. Also, expand Help page. commit ca6d64c961519643144416d0af8820f59032343d Author: kate Date: Fri Mar 7 23:55:48 2008 +0000 Change 'edit' to 'rename' in various places, since that's the only edit we can currently do commit 364f5faaeb5c4b8ae1aa73b9ce49c5ad9f0f4e56 Author: kate Date: Fri Mar 7 23:55:14 2008 +0000 Change 'edit' to 'rename' in various places, since that's the only edit we can currently do. Also, use 'submit' instead of 'upload' when it's clearer to user (requests of modENCODE) commit 4ecc7bbe90f228d8633f843e4e57de20c949efad Author: kate Date: Fri Mar 7 23:53:56 2008 +0000 Add some more explanation to upload page. HTML tidying. commit fa95362000e8a87effb0a2cd6bcbffd57d853404 Author: kate Date: Fri Mar 7 23:51:15 2008 +0000 Remove commented out code. Add timezone, by request of B0b commit 866c993ceeb9bfab8c5814afaaa711f7b6048bde Author: kate Date: Fri Mar 7 23:49:05 2008 +0000 Distinguish form buttons (Save, Cancel), from action links (Change Email & Password), by request of Galt B. commit 207a45e3b481e8c677abc54ebd5641c0e71d82a0 Author: kate Date: Fri Mar 7 23:47:54 2008 +0000 Change 'Back' link to 'Cancel' button for uniformity commit a9c29ca524fd6bc049f5cd3b36ef4e7c05dbc720 Author: kate Date: Fri Mar 7 23:47:11 2008 +0000 Include full user name in sign-up confirmation (by request of Donna K.) commit d66e8fa7aa27aba5e3ed34544bd2cc5652c89957 Author: kate Date: Fri Mar 7 23:41:46 2008 +0000 Change navigation after creating new project so that it goes directly to upload page (request from modENCODE) commit aaa7494aa2073ed5f6e2f457631501250271d134 Author: galt Date: Fri Mar 7 22:41:27 2008 +0000 preserve previous value of status so it can be copied to archive record commit 669e78b96159c04ab6a51c9de94d5431f3636328 Author: galt Date: Fri Mar 7 22:29:23 2008 +0000 now postgres compatible binary value true instead of 1 commit f250f3a702ea974a916cc02267de2963b9f4a182 Author: galt Date: Fri Mar 7 22:16:52 2008 +0000 putting back something needed for local file uploads commit 416ddab139fe1202b50c81c81665768705c4a647 Author: angie Date: Fri Mar 7 21:38:03 2008 +0000 Improvements to exceptionDesc wording. commit af671d459b997241a4a80e40a1cd6412ae685154 Author: kate Date: Fri Mar 7 21:37:15 2008 +0000 Add logo to Rails dir commit e1887bce4cb801f08f8efe6e24cdbe3295ab1198 Author: angie Date: Fri Mar 7 21:33:52 2008 +0000 Added description of UCSC's re-alignment of flanking sequences to genome sequence around the SNP. commit ceb1f6a34cf997bdd2133948563ed823a2032c2d Author: markd Date: Fri Mar 7 18:47:41 2008 +0000 fixed uninitialize variable in hvGfx that crashed hgGenome commit d6aeb890f4fadfacdd35c945c9e0f61a2f167a78 Author: galt Date: Fri Mar 7 16:00:07 2008 +0000 "Encode release log update" commit dbb1baf74e5b4d4c96ae6e4b80ba38a639ad4654 Author: galt Date: Fri Mar 7 16:00:05 2008 +0000 "Release log update" commit 484b609a377c34999d33e2e8642f126b519866fb Author: kate Date: Fri Mar 7 04:45:14 2008 +0000 Have cancel of email change navigate back to profile change commit 8aae8b57e06cbfd18fda6d1f5d3ec1a0b86597e0 Author: kate Date: Fri Mar 7 04:44:58 2008 +0000 Allow navigating back to Change Profile from Change Email via Cancel commit 8dc88c8dfd25fe2f34b67730cb5e1509f801fefd Author: kate Date: Fri Mar 7 04:10:56 2008 +0000 Temp error recovery for failed upload from local file commit 6da849b947d227a104df053b83bf8764b4b9d307 Author: kuhn Date: Thu Mar 6 23:42:41 2008 +0000 added a bit more explanation and a few more checks commit 81ee404976b84d5108cadad37b5645499535743e Author: donnak Date: Thu Mar 6 23:05:55 2008 +0000 Added ponAbe2 to releases list. commit 420f40928dd0be6b90e631c39ffa832e066692c3 Author: angie Date: Thu Mar 6 23:05:50 2008 +0000 Fixed order of snp125ColorEnum to match menu order (which now matches color priority order). commit 7c01fdcc621381672f338c7996dc2175e5079d78 Author: fanhsu Date: Thu Mar 6 22:46:13 2008 +0000 Removed the limit of 50 subjects from default saved subj list. commit ab0ac6624041e5413300af71ab62f90ee176f696 Author: hiram Date: Thu Mar 6 21:34:43 2008 +0000 Top level ensGene definition is good enough commit 1fbac0f5d8daa2d2615fa039e7fa1054ff0cb508 Author: ann Date: Thu Mar 6 20:34:29 2008 +0000 new rule for new HuGE table and its relationship to kgXref table commit a379748a80a20f06d2160837bb4d364aaf33628c Author: hiram Date: Thu Mar 6 20:20:14 2008 +0000 Now constructing Ensembl archive link from trackVersion table when not overridden by trackDb entry commit 818b17fc9338fa435335c1c800fd57070a40b04f Author: hiram Date: Thu Mar 6 20:15:32 2008 +0000 Top level trackDb.ra is good for ensGene and mouse visibility.ra sets it at dense commit c75bf220411518aaf726e859365120815b00b842 Author: fanhsu Date: Thu Mar 6 20:02:21 2008 +0000 Documented huge table build. commit 4e93df369feebe99daa116a492157b27053b376e Author: fanhsu Date: Thu Mar 6 20:00:30 2008 +0000 Added huge table for HuGE link. commit b554b227986218d6cad2197a804799f1590ba1ac Author: hiram Date: Thu Mar 6 19:07:27 2008 +0000 Adding trackVersion table access routines commit 2fb85c153b298cfb2dcddf8698e5b93bd0785a49 Author: hiram Date: Thu Mar 6 19:05:39 2008 +0000 trackVersion table definition for hgFixed commit bf54ff66e85ff189c3832b54fd7430a95270329f Author: angie Date: Thu Mar 6 18:19:26 2008 +0000 Oops, needed to include snp125.h to pick up snpVersion prototype. commit 574878cf7611ffcdcfa189a1e42d0218cba1a1e3 Author: markd Date: Thu Mar 6 17:30:25 2008 +0000 added gffToGenePred was premature commit de71790fa198885d22ae796173c85c3174b0425f Author: markd Date: Thu Mar 6 17:28:02 2008 +0000 added build of gffToGenePred commit eeb8e7bb4a5c6c31d5e3a67e1ced50c3152ebd07 Author: rico Date: Thu Mar 6 17:10:55 2008 +0000 Get info about a segment file. commit 63efc56f8fd5853ea3faec9c83c04fba0310a408 Author: markd Date: Thu Mar 6 17:01:59 2008 +0000 added ignore entry commit 7a89e57ff4d7c3bf8249b77666d1b59dd6b6a46a Author: markd Date: Thu Mar 6 16:58:41 2008 +0000 don't sort xenoEst commit e113444a6158756ed53e65e5c0882d703c92b44e Author: galt Date: Thu Mar 6 16:00:07 2008 +0000 "Encode release log update" commit 09b26a7fa99cb292ac8294345dc45e809764a205 Author: galt Date: Thu Mar 6 16:00:04 2008 +0000 "Release log update" commit 56bd1b63f654031b0ff94a664a522b7c36de7127 Author: angie Date: Thu Mar 6 06:56:49 2008 +0000 In snp125Ui, changed description of filter checkboxes to match the new and improved behavior (see hgTracks/variation.c). Moved snpVersion up to lib/snp125.c, and use it in dispatch chain. commit e85ee2322fd10aa4b859428a2bfde70cdfd70de3 Author: angie Date: Thu Mar 6 06:55:02 2008 +0000 Fixed snp125 filtering: most snp125 filters returned the answer for the first matching term, which may not be corrent when the item has multiple terms. Changed the filtering from exclusion-based (which caught both Brooke and me off guard, especially when items have multiple terms) to inclusion-based. Don't apply locType filter from cart if version >= 128. Apply snp125 filters in a single pass through tg->items, instead of a pass for each filter. commit c4ff97388b8eb1857f6171b8282dc0d157203467 Author: angie Date: Thu Mar 6 06:42:25 2008 +0000 Use the new snpVersion instead of inlining. commit 3bd295e5476fffa6b3fdcf63be9a61fd633f047a Author: angie Date: Thu Mar 6 06:40:29 2008 +0000 Added snpVersion to support the various CGIs that need to know the dbSNP version. commit f97e97c9c6fd718b5603e2ed14255b0e4bde3583 Author: angie Date: Thu Mar 6 04:03:45 2008 +0000 Got rid of bogus 'ignore' mappings in snp125Func filtering; those have been replaced by the cds-reference mappings that should have been there all along. See lib/snp125Ui.c. commit 2b05482642d9df3e8f89d3376c1e4c89da10c498 Author: angie Date: Thu Mar 6 04:02:25 2008 +0000 In snp125Ui, added note about priority order of colors. commit a42e4ede19a11b7493f8971181128e2031cbb63c Author: angie Date: Thu Mar 6 04:01:25 2008 +0000 Bugfix: although snp125FuncLabels included 'Reference (coding)', snp125FuncDataName had 'exception' instead of 'cds-reference', causing that selection to be a no-op because 'exception' does not appear in the func column. Changed it to cds-reference and got rid of the bogus 'ignore' mappings. Also changed order of colors in menu to match priority of colors. commit 237adacc950cb5556c92329a34e73a0ea6ffa161 Author: jzhu Date: Thu Mar 6 01:36:29 2008 +0000 *** empty log message *** commit 746e9f53f6cc0e7c2007083849eaaa1269d9af25 Author: angie Date: Thu Mar 6 00:06:26 2008 +0000 For version 128 and later, omitting locType from ColorSource menu. commit e252e123571b37c82f5368cd7845e6a713100fe1 Author: angie Date: Thu Mar 6 00:02:20 2008 +0000 In snp125Ui: oops, forgot to remove locType from coloring controls for versions 128 and later. Thanks Brooke! commit 92ad1a974cfd621fdadb4038f3a8ecb1edfbb3c4 Author: kate Date: Wed Mar 5 23:45:26 2008 +0000 Stub for help file commit 23edb60ca6f2d8634e602dd1f9c9d37f5b9a6763 Author: kate Date: Wed Mar 5 23:42:56 2008 +0000 Fix path to help page commit f13dba2c5cc794699480263352abc8b3e2c71716 Author: galt Date: Wed Mar 5 23:09:06 2008 +0000 temporarily upload to assembly specified (rather than errorMessage or LiftOver commit 3a229cdb9cae1883ca149f11cdcfcd3e79b692bf Author: angie Date: Wed Mar 5 22:43:50 2008 +0000 In snp125Ui, added html tables around filter and coloring controls. Also fixed bug caused by unnecessarily independent forms, and refactored out a bunch of duplicated code. commit f87cb5d56c8916e0dc2ebdf8e5d77b68d9831065 Author: hiram Date: Wed Mar 5 20:40:19 2008 +0000 Today's version of hgFixed.trackVersion contents commit 69971a151fc39e011db5514616be4f72e0db5ad2 Author: hiram Date: Wed Mar 5 20:11:03 2008 +0000 Remove all the extra nonsense for txStart/txEnd - it is unnecessary commit 7f827c9f5c100853949403f37b2e8c3eb455a6a5 Author: hiram Date: Wed Mar 5 19:18:20 2008 +0000 The new Ensembl Gene Link breaks older assemblies that do not extended gene preds commit 4b7bd269576b60eb14e844edff0e7ef30f070ed9 Author: hartera Date: Wed Mar 5 19:02:57 2008 +0000 Defined chromosomes with data for chainSelf and netSelf. Neither track has data for chrUn or chrNA and this fixes the problem where the Browser was breaking if the chainSelf track was turned on while viewing these chroms. commit 02525257ff7957aa797cf4362eff015767f5a208 Author: kate Date: Wed Mar 5 18:42:01 2008 +0000 Remove extra line commit b6fb228bdf69f60c90e3558ec1b9692406428121 Author: kate Date: Wed Mar 5 18:18:14 2008 +0000 Needed to use the specified step value commit c294197a32a17be92f59ba23f8567473ea03c2cb Author: aamp Date: Wed Mar 5 17:30:26 2008 +0000 Just a little converting-wiggle util. Doesn't do everything. commit 5eb676e1a3c7c0e706845d5ed76cdc7fb4d6f34d Author: galt Date: Wed Mar 5 16:00:06 2008 +0000 "Encode release log update" commit a53c0af0d3da48387d37077dd4cd8a4e942984b4 Author: galt Date: Wed Mar 5 16:00:04 2008 +0000 "Release log update" commit 98f9e85988e4f73d1d5e019f8392dbe3e7f723c5 Author: fanhsu Date: Wed Mar 5 05:39:11 2008 +0000 Updated links to "Method and Convention". commit 50584991a7341fb78eaceedf0297bd8435162eec Author: markd Date: Wed Mar 5 02:12:47 2008 +0000 fixed bug with generating image map for LD tracks commit d1fc7ec462ee55b20960494231b01f453646dd39 Author: fanhsu Date: Wed Mar 5 01:15:39 2008 +0000 Updated gad.c so that when user click on expanding the list, it would present the GAD section directly. commit a28dfbfe8c4abb7fcea241311c280917936409e4 Author: angie Date: Wed Mar 5 01:00:01 2008 +0000 In hConnectCentral, test not only that we have a connection, but also that cart tables are apparently not corrupted, so that hopefully next time userDb or sessionDb gets corrupted, we will fail over gracefully. commit 6f8a8fa9f138e77e836259c0832c346ef1de841d Author: angie Date: Wed Mar 5 00:47:37 2008 +0000 Added cartTablesOk, so we can (hopefully) detect table corruption and failover gracefully. commit 747642f73504288b2374dacd2c965e95a89ae7bf Author: angie Date: Wed Mar 5 00:45:04 2008 +0000 Added sqlTableOk, which is like sqlTableExists except it also ensures that if the table is not empty, we can get data from it. Hopefully this will help us failover more gracefully in case of userDb corruption. commit 673ed39cd710ce3b95746ba3c938bb4e6ee3429e Author: markd Date: Wed Mar 5 00:02:58 2008 +0000 fixed crash cause by guessing wrong track type. Enable printing DOCTYPE commit 22fb58315e2e47b696dfd86c1200da98947642c8 Author: hiram Date: Tue Mar 4 23:53:23 2008 +0000 Initial description commit 3310e1ec13800b3a43108c85cab9a2f16639391d Author: fanhsu Date: Tue Mar 4 23:51:08 2008 +0000 Updated logic to deal with NULLs and links to "Method and Convention" page at GSID corp server. commit 2c19c4d05cf7de720c16f24ceaf154f68becf153 Author: kate Date: Tue Mar 4 22:13:25 2008 +0000 Standardize and expand email greeting to include full name, by request of Donna K. commit da02c9e04116fac4a66b2a4b10a29cf14cb187d5 Author: ann Date: Tue Mar 4 22:11:41 2008 +0000 added link to newly-published paper. cleaned up citations. commit a4b62d7acc6c162de93bded16d4a3b2a6a3e69ad Author: kate Date: Tue Mar 4 22:11:15 2008 +0000 Expand user message commit 0de105f15646d06908fbca17195af02769310baf Author: kate Date: Tue Mar 4 22:10:30 2008 +0000 Left align column headers, by request of Donna K. commit 46ba89d3363b4bf6a07f297d577009b6918c0725 Author: kate Date: Tue Mar 4 22:07:59 2008 +0000 Remove hard-coded DCC address, replacing with a config variable, 'encodeDCC' commit 07f49ee29cd11b822df2ac9b7fab016c5be453b1 Author: ann Date: Tue Mar 4 20:50:20 2008 +0000 added link to newly-published paper, and cleaned up citations commit 1c57b3a440b6d2b2c0e0e09c48a2ea51f89de255 Author: rico Date: Tue Mar 4 20:41:27 2008 +0000 Split a segment file pairwise by block. commit 2e5918b0025cb539237c04f2491e0eb7635772ac Author: rico Date: Tue Mar 4 19:59:42 2008 +0000 added cloneSegComp(); commit ebaea2ecc8c21dee2132c6525d5bf60b5f247ac1 Author: rico Date: Tue Mar 4 19:59:32 2008 +0000 added cloneSegComp() commit a42eb3716693e8971363b7b66ce7401ee55063fa Author: rico Date: Tue Mar 4 19:48:50 2008 +0000 added setWriteEnd (even though it does nothing right now) commit 561d230dc29b38447b703f2bd767ab0dba5c578a Author: rico Date: Tue Mar 4 19:23:38 2008 +0000 added the freeing of the speciesHash commit 850c0b4884f9a6b5110eef3160c2c529b71cbf1e Author: aamp Date: Tue Mar 4 17:56:40 2008 +0000 "New version number v177" commit f80f1af3a57beeb45864fa3a874785acfebee449 Author: galt Date: Tue Mar 4 16:00:07 2008 +0000 "Encode release log update" commit bfb2da1e846082b6076068493a242ea4732f9eb5 Author: galt Date: Tue Mar 4 16:00:04 2008 +0000 "Release log update" commit 4e6a1f45be6d1c781b7e5c186592f139eaa44910 Author: kate Date: Tue Mar 4 00:44:37 2008 +0000 Add renameSqlTable option for use with sqlTable option. This eliminates the need to edit generic .as files when creating new tables using generic table types commit 66cc259ede36e84679b6883f18f41de8d49cd654 Author: hiram Date: Tue Mar 4 00:44:29 2008 +0000 Record of Ensembl updates to Version 48 commit 67e9c8825c9587da9d362f79771b8b1057093bdb Author: kate Date: Tue Mar 4 00:43:29 2008 +0000 Suppress Item label when item name is empty commit 32e16db846a892499912a1c2db52ba5e993f1eab Author: hiram Date: Tue Mar 4 00:39:24 2008 +0000 Usage message should be consistent with the name of the configuration file. commit e6f7253f45df26941675d938ac2b36a2abd23e61 Author: hiram Date: Tue Mar 4 00:33:14 2008 +0000 Ensemble has the next version of anoGam commit 47706b9995453efeae7cca5d2be1a6368097a127 Author: hiram Date: Tue Mar 4 00:28:58 2008 +0000 Add the organism and db to the comment line in the make doc commit e4d7f226f5a9d20a0e7c6873a6d50d45bdbc0d43 Author: hiram Date: Tue Mar 4 00:20:38 2008 +0000 Add a makeDoc step commit 66ab8dfc218d84a55c0b4373fff3517e30881c8c Author: jzhu Date: Mon Mar 3 23:28:13 2008 +0000 modify ucsfNeveExp track commit b95b31b322703a7bfe00f9dcc0fb4a4e25294982 Author: jzhu Date: Mon Mar 3 23:14:36 2008 +0000 add ucsfNeveExp track commit 416344a0a9e21673137ba717c3455dfe8fb0de58 Author: markd Date: Mon Mar 3 21:45:15 2008 +0000 removed xeno ESTs from mouse and rat commit 557fc16960e631480b816b140fc428853ed9547f Author: hiram Date: Mon Mar 3 21:00:53 2008 +0000 Free up the gpList, and found an unused variable that appeared to be used. commit 6349c4c102a9660b8e904c6f913ef9d69a4e0aa3 Author: jzhu Date: Mon Mar 3 20:52:19 2008 +0000 add -local option to connect to host defined as localDb.XXX variables in .hg.conf. commit 1fd5b4cae87e39b73691c0679093b067cf96454f Author: hiram Date: Mon Mar 3 20:00:27 2008 +0000 Add Ensembl geneview link commit 4a9127d713038cb08002316209b114797138c1cb Author: hiram Date: Mon Mar 3 19:49:41 2008 +0000 liftAcross has an off-by-one error fixed, coordinates have shifted commit ab1129fdcfc93049fb458d9e04925bfe999ce0db Author: angie Date: Mon Mar 3 19:14:12 2008 +0000 In snp125Ui, don't display locType filter options if version is 128 or higher. commit e56c5e0ae0fe1460c4f03816dfd9b3b1386611e9 Author: jzhu Date: Mon Mar 3 19:11:05 2008 +0000 modify ucsfNeveExp commit 6ad17eccb3fe50d435d10302f4c7788b74332146 Author: jzhu Date: Mon Mar 3 18:31:43 2008 +0000 add ucsfNeveExp microarry setting commit 4e990140c124ba146b55890753e71e21e47e894f Author: rico Date: Mon Mar 3 18:12:39 2008 +0000 Added a '.' at the end of a sentence. commit 684f3159b9a17f0d36892172b4d9a8041141ca5e Author: rico Date: Mon Mar 3 17:55:08 2008 +0000 added segMayFindCompSpecies, segFindCompSpecies commit 007053d4453a3c5d28e08b3dc9c4e44b06ecc361 Author: hiram Date: Mon Mar 3 17:10:44 2008 +0000 Generic ensGene definition at top of hierarchy is good enough commit 818944cff204ce0a221f75d40ef86d26bf63e160 Author: rico Date: Mon Mar 3 16:48:32 2008 +0000 cleaned up, added chromBreak records to indicate chromosomal breaks commit f5762c4a83cb0d30d0e8733f5640661dee69f2fd Author: galt Date: Mon Mar 3 16:00:05 2008 +0000 "Encode release log update" commit d128e6ba3f6988b46770754ce9ec9f61f6bcfbf4 Author: galt Date: Mon Mar 3 16:00:03 2008 +0000 "Release log update" commit 9cbaf0714eb9e7db2fdb21d69c7d487d03b15d8a Author: giardine Date: Mon Mar 3 14:43:07 2008 +0000 Removed variome track from genome-test commit a5e69f8118a24a887481469ef447b2fe773626ad Author: fanhsu Date: Mon Mar 3 00:19:43 2008 +0000 Changed wording when no sequence data found. commit 45246875ad848b0acce24f2805dc4cb1a7c23e73 Author: kate Date: Sun Mar 2 20:50:12 2008 +0000 Change column headers to left-aligned, as per Donna's UI review. Also add some spacing between columns for readability commit c72c011fbe5cdb1e3632dd3ee510964bf084f4ca Author: kate Date: Sun Mar 2 20:12:12 2008 +0000 Display current email separate from input box for new email, responding to Donna's UI review commit b56db46bde3f965d635140dc614bfe5ea0904ca1 Author: kate Date: Sun Mar 2 20:02:52 2008 +0000 Change display of email to disabled field for consistency with other fields commit b7548d71f417987331109ad547b81105ae9289d4 Author: kate Date: Sun Mar 2 19:52:37 2008 +0000 Fix button layout problem on IE commit 615b9aac0f563d6688404517e4af742d386e6e98 Author: fanhsu Date: Sun Mar 2 17:47:59 2008 +0000 Added logic to indicate so if no sequence data available. commit d6f60ec90d8dc2cf0ab21201f22ee96e00a7901e Author: rico Date: Sun Mar 2 17:01:41 2008 +0000 Added a prev pointer to a segBlock. commit 3c2d38163c2daf31235e6a281fd9ad7c4b9d2a29 Author: rico Date: Sun Mar 2 17:00:54 2008 +0000 Used tail pointers instead of slAddHead, slReverse. Updated to use prev pointers between blocks in segReadAll. commit 440738941677fa906aab127299bc2e6e0e41afb0 Author: galt Date: Sun Mar 2 16:00:13 2008 +0000 "Encode release log update" commit dd9b0cf24b4d62b7651d19a338a8b0a38a2906aa Author: galt Date: Sun Mar 2 16:00:12 2008 +0000 "Release log update" commit bb9a0a44faa5962b3615438a248bdd96ff46b78b Author: rico Date: Sun Mar 2 15:53:09 2008 +0000 wanted to cloneString(val) not cloneString(name)!! commit f79da7bd16e69ebed0289fd49e89f42d97e8067a Author: braney Date: Sat Mar 1 17:26:15 2008 +0000 add dbName to chrom position in header commit 97126b2b479ba4b04f27422b172d1ca1df592f4f Author: braney Date: Sat Mar 1 17:12:02 2008 +0000 use genCode for hg18 gene frames, rebuild frames with exon flags commit 2a6bed09340c10e73ea0f8edc80dbf5898ac2c8a Author: galt Date: Sat Mar 1 16:00:19 2008 +0000 "Encode release log update" commit 1c01f7cd57151329f6a47cb4e830ad0dab34062c Author: galt Date: Sat Mar 1 16:00:16 2008 +0000 "Release log update" commit 82692cd9e384678974003f2c4d5d93a814805407 Author: jzhu Date: Sat Mar 1 08:39:56 2008 +0000 fix a mistake in -local option commit 80359381d08f2ba7903aedd5c0106748bfa60165 Author: jzhu Date: Sat Mar 1 08:21:01 2008 +0000 using hgsql or hgsqlLocal to check if db exists commit a332f0709dffd11b7671f2844870da637749bdda Author: jzhu Date: Sat Mar 1 08:11:10 2008 +0000 *** empty log message *** commit b22db3e0154db6f44e32b16d78fc043433752447 Author: jzhu Date: Sat Mar 1 08:10:31 2008 +0000 hgsqldumpLocal for access local host (defined as in localDb.XXX in .hg.conf) when the default host is set to on a remote server commit 5ddc5195bb42ae8edc0ef3eeb328bd0a984deb01 Author: jzhu Date: Sat Mar 1 08:08:22 2008 +0000 modify usage prompt commit 5a8238effb9665212e946c2809ad779dec17784f Author: jzhu Date: Sat Mar 1 08:03:38 2008 +0000 hgsqlLocal to access local host when default host is set to be on a remote server commit df6b997c66668fa46b5a0e4604a614be25537b88 Author: jzhu Date: Sat Mar 1 07:57:23 2008 +0000 restore hgsqldump commit bd7c15c6ea2ae91e71390f921ac5c5c1463c8401 Author: jzhu Date: Sat Mar 1 07:55:20 2008 +0000 restore hgsql commit 695c4ab7a8f4a434a15bf20530587403162c6cd5 Author: jzhu Date: Sat Mar 1 00:42:23 2008 +0000 remove hgsqlLocal and hgsqldumpLocal from directory for compilation in makefile iii: ---------------------------------------------------------------------- commit 5fc75b74bea1ca108c950ec499d399c43be88260 Author: hiram Date: Sat Mar 1 00:40:50 2008 +0000 Watch out for NULL result from trackVersion SQL query commit b2382fbde909589298ec8338c3fe0186d281da25 Author: braney Date: Sat Mar 1 00:34:51 2008 +0000 add shrew to 36-way commit 4e3096be0a784aed0e27207b9c0a23d060268051 Author: jzhu Date: Sat Mar 1 00:33:29 2008 +0000 replaced with hgsqldump -local option commit 71f712c9614a0407accfeec8c140f9b2bcf4d00a Author: jzhu Date: Sat Mar 1 00:31:24 2008 +0000 replaced with hgsql -local option commit 47038b9c4ccd91ccf752c06ec73ad1795784c6ee Author: jzhu Date: Sat Mar 1 00:23:25 2008 +0000 add -local option to screen prompt; purpose is to access localhost (defined as localDb.XXX=XXX in .hg.conf) if the default host is set to be on a remote server commit 52187dae44e201b9713a6bbb108b9f01aebf1067 Author: jzhu Date: Sat Mar 1 00:23:00 2008 +0000 add -local option to screen prompt access localhost (defined as localDb.XXX=XXX in .hg.conf) if the default host is set to be on a remote server commit 9302955a2867dde069c96b0f04ad63af49cfad17 Author: jzhu Date: Sat Mar 1 00:21:51 2008 +0000 add -local option to access localhost (defined as localDb.XXX=XXX in .hg.conf) if the default host is set to be on a remote server commit 9bc3d487e1f1cd120c6ec6a0bb41f8ab9ec7716c Author: hiram Date: Fri Feb 29 23:44:38 2008 +0000 Default ensGene track is dense for mouse, have that in visibility.ra commit e5113967333941d5b8ba3e0e260fc25d9768c7f3 Author: jzhu Date: Fri Feb 29 23:34:55 2008 +0000 capability to access localDb when the default host is set to be a remote host: 1. loadTracks: -local option is added to the screen usage prompt commit 0dc0f55ffba757e9183afdfaa297945caa04ee7b Author: jzhu Date: Fri Feb 29 23:32:22 2008 +0000 capability to access localDb when the default host is set to be a remote host: 1. add -local option to hgFindSpec; commit 5ccc0a85d413d70e7a1370352b7ab4c4899b8890 Author: jzhu Date: Fri Feb 29 23:32:08 2008 +0000 capability to access localDb when the default host is set to be a remote host: 1. add -local option to hgTrackDb; commit 62a089224655d1df209d334de5c578b220c89abc Author: jzhu Date: Fri Feb 29 23:31:27 2008 +0000 capability to access localDb when the default host is set to be a remote host: 1. add -local option to loadTracks; 2. add make updateLocal; 3. add make alphaLocal commit 3d3616c886fc95a8578d68b923c6b2f19c17f261 Author: hiram Date: Fri Feb 29 23:24:37 2008 +0000 Was missing rn4 definition for MySQL tables at Ensembl 48 commit 8e3349b2a7dc055fadf99f8d5df5a4da007427f0 Author: hiram Date: Fri Feb 29 22:56:39 2008 +0000 Better said ensembl version as "Ensembl 48" since that is how they do it. commit 34dc0d18c2ae13da97ebb02c1d27c2a2e90ed3d4 Author: hiram Date: Fri Feb 29 22:54:51 2008 +0000 The least you could do is write it correctly ... commit 8861fa71a14ec21b8d85f133b6100779e6b139c1 Author: hiram Date: Fri Feb 29 22:53:08 2008 +0000 Need to liftUp the gene scaffold bed file too commit d37c36af0125b4dc5fbd0194ed825ed4a3e42d57 Author: hiram Date: Fri Feb 29 22:41:14 2008 +0000 Add haplotypeLift for Human hg18, and liftUp for Bushbaby otoGar1 commit c451fb2f1f8412fba938e0043edd527ab69dae9b Author: braney Date: Fri Feb 29 21:55:08 2008 +0000 changes from code review with Kate commit c24968f89933ea61d7bbfa0a04aa7344a488e9d3 Author: angie Date: Fri Feb 29 21:13:53 2008 +0000 Made the table comment more generic because this is still used for dbSNP versions beyond 125. commit e695bcd501f4c080e7ea004296769e8c5239b2d8 Author: kuhn Date: Fri Feb 29 20:46:27 2008 +0000 renamed getTablesize.csh getTableSize.csh commit c2d84263cc77758fab5532c9b54fa8c51065b573 Author: kuhn Date: Fri Feb 29 20:44:54 2008 +0000 removing old utility that used now-defunct sudo. use getTableSize.csh instead. commit 90af21531173f434a25d27c18e134fd9dd98a59d Author: hiram Date: Fri Feb 29 20:28:35 2008 +0000 It was not correct to shift negative lifts by 1 base ... commit d1f4908920cccb34489251b4d9d3b511e52bf23c Author: braney Date: Fri Feb 29 20:23:53 2008 +0000 add some comments, take out commented-out lines commit 0730df994030fe85342db754c589f9ae05d55056 Author: braney Date: Fri Feb 29 20:14:47 2008 +0000 a tiny bit of modularization commit ef1304a16ec54ee6a4e85222dcd59ee906ad8cc8 Author: markd Date: Fri Feb 29 18:57:38 2008 +0000 fixed arg parsing bug, improved messages commit c6234f523530ffcaebfc54151cc7fb276de6f641 Author: fanhsu Date: Fri Feb 29 18:15:43 2008 +0000 Added tag at end of URL for "more ...". commit 7e7b8958480a068383aacca6609939a119eda305 Author: markd Date: Fri Feb 29 16:43:30 2008 +0000 added support for multiple iteration commit 225d54f9bcabbce00b694f70107aed09e3b75d12 Author: galt Date: Fri Feb 29 16:00:05 2008 +0000 "Encode release log update" commit 299dd9f40c6729a877d25b45b9695ad9d2fc9e47 Author: galt Date: Fri Feb 29 16:00:04 2008 +0000 "Release log update" commit d7d88f79879a9ad80ed0b00d0c079c6d8e7921fb Author: markd Date: Fri Feb 29 08:19:23 2008 +0000 added program for timing range queries commit 1acd841a303721df27a35e66b6199c302d913dbd Author: angie Date: Fri Feb 29 06:30:45 2008 +0000 Removed note about initial incomplete release. commit a5ea8ddb9681f31388b89df242b217ecf4b22568 Author: fanhsu Date: Fri Feb 29 00:59:29 2008 +0000 Added checking existence of kgXref table. commit 99ca9b7bba56df8089e71163fee1002dbed5243a Author: hiram Date: Fri Feb 29 00:11:09 2008 +0000 Automatically print Ensembl version when it can be found in hgFixed.trackVersion commit 1ba661c1a3dd3dd3de98c626e9fea4eb46a3e35e Author: fanhsu Date: Thu Feb 28 22:59:09 2008 +0000 Slight format change of the message. commit 9afec81a3b2a41df1dfab6722b383c8a476652ad Author: hiram Date: Thu Feb 28 17:22:43 2008 +0000 Missing explination of tDb and qDb in the usage message. External users do not understand what they are. commit 691341816766be062185e4bb9564e9a4907db569 Author: galt Date: Thu Feb 28 16:00:08 2008 +0000 "Encode release log update" commit c35c130963d9560950cd3c36913f17af313f7519 Author: galt Date: Thu Feb 28 16:00:05 2008 +0000 "Release log update" commit 4a8e2a51396afa8f3d446b0fa9be7e7c51015d3f Author: giardine Date: Thu Feb 28 14:27:07 2008 +0000 start of description page for divMKAR track commit 82a7936d0b521df0b25a0da09a3e0746bf1953b4 Author: giardine Date: Thu Feb 28 14:26:27 2008 +0000 updated divMKAR track, removed earlier versions, added y=1 line to FDR commit aeca16da9187882e5293e1b00e87d6e043a75950 Author: markd Date: Thu Feb 28 02:01:21 2008 +0000 add quick and dirty tool to sort positional tables commit 4f6b1ef52320c58075d2eca99907f1e42c560142 Author: kayla Date: Thu Feb 28 00:43:24 2008 +0000 added ponAbe2 commit 64ebd4d35a4c16dca1014601e8287c27cbc55b6f Author: ann Date: Thu Feb 28 00:35:41 2008 +0000 switched from pdf files to real abstracts commit 036118cf11a834656d427414a7a78b782f418c0f Author: fanhsu Date: Wed Feb 27 23:25:32 2008 +0000 Added some defensive code to make sure that spreadAlignStringProt() is used only on GSID server. commit 2b1cb5e89fac894c9487963f6a400fd84f1ee6be Author: ann Date: Wed Feb 27 22:52:29 2008 +0000 added wording to explain that default tracks include custom tracks. commit 2c39be5875ead2ee4a4d1edc02740b8f7431cf05 Author: fanhsu Date: Wed Feb 27 22:32:06 2008 +0000 Updated to disable "reverse" mode on HIV DB server. commit 6f095a1fd8dfbf4fd15f35ab8e49bdfad3375c22 Author: galt Date: Wed Feb 27 16:00:23 2008 +0000 "Encode release log update" commit 89438df85cfbd4493741f92b2d1ac8e2614b310f Author: galt Date: Wed Feb 27 16:00:21 2008 +0000 "Release log update" commit 674a3154cef2c14013ee1c527a83aefac2c7f2fa Author: jzhu Date: Wed Feb 27 06:41:23 2008 +0000 *** empty log message *** commit 1f7e8663f5ddc118c473d9249026084f1acda00c Author: jzhu Date: Wed Feb 27 01:41:17 2008 +0000 add program to connect to database using localDb.XXX variables set in .hg.conf, this program is similar to hgsqldump commit dfa86b81ea95b3e384c30a63a1cf52b0442bc765 Author: jzhu Date: Wed Feb 27 01:40:09 2008 +0000 add program to connect to database using localDb.XXX variables set in .hg.conf, this program is similar to hgsql commit 6c43cf0f8239d9607315c20e731e570f934a1477 Author: jzhu Date: Wed Feb 27 01:37:25 2008 +0000 add sqlExecProglocal function commit 0d503b71dc35b6d4c3f09b854394293b34e952e2 Author: hiram Date: Tue Feb 26 23:11:27 2008 +0000 Make ensVersion be a command line argument, and add -skipInvalid option to the config file commit 71e836a62f49b56e8a94c621a9506b055fe9466a Author: fanhsu Date: Tue Feb 26 19:21:01 2008 +0000 Removed hard wired statement. commit e024ad30d39c3f9ab388cff4d9bfd63530f15a51 Author: aamp Date: Tue Feb 26 19:02:38 2008 +0000 Utility for re-sequencing trace work. commit 62f7b8e9d809daf1420c704e97317116985540f9 Author: aamp Date: Tue Feb 26 19:02:33 2008 +0000 Utility for re-sequencing trace work. commit 766c5c51ed81639b80b69843a561b2aa3a91f683 Author: hiram Date: Tue Feb 26 18:23:38 2008 +0000 parsing the infoOut.txt file from gtfToGenePred to extract ensGtp.tab table data commit c29b7fde2f5bb21664ec03c229016061af6b2bf0 Author: jzhu Date: Tue Feb 26 17:16:21 2008 +0000 add function prototype for struct maGroupoing *maHashToMaGrouping(struct hash *oneGroup) commit 1e01a7ef1d3daeaf4b63b39170c69293dba7988f Author: galt Date: Tue Feb 26 16:00:14 2008 +0000 "Encode release log update" commit 13fff96925c5c7e256dab7a411a0481f4d8d5f0f Author: galt Date: Tue Feb 26 16:00:12 2008 +0000 "Release log update" commit 57af97fbc6ddff125c94ad76753e35d800e0d60a Author: markd Date: Tue Feb 26 05:44:47 2008 +0000 have next/prev item/feature alway have prev as to the left, and next as to the right commit d421ef4e9b4ede9ef7d27c1c6776b2baa6e7725f Author: markd Date: Tue Feb 26 04:56:38 2008 +0000 adjust base display to correct for a off by one pixel problem that is especially obvious in reverse-complement display commit 9c123698a9246072fee6ad91bf27e018d41b6bd0 Author: markd Date: Tue Feb 26 01:32:24 2008 +0000 have genePredCheck and hgLoadGenePred report errors on invalid chroms instead of aborting commit beca6af19a6b071b8067114b50819290521f1570 Author: angie Date: Tue Feb 26 00:09:46 2008 +0000 In hTrackDb, added a couple missing calls to hLookupStringsInTdb. commit 3b987be238fffb085598072e9735c55625727371 Author: hiram Date: Mon Feb 25 23:58:20 2008 +0000 Add the auto_index ix in front of everything commit a21121f0fca84d06936745214dce46b39d849af2 Author: hiram Date: Mon Feb 25 23:36:24 2008 +0000 Recording the contents of the table hgFixed.trackVersion commit c36e7c132dfa69ca546b5d8e5d8cdd5b5b667022 Author: kuhn Date: Mon Feb 25 19:16:13 2008 +0000 shortened list commit ad248c422d76e9e95a51eb66aff47aab355d47d0 Author: kuhn Date: Mon Feb 25 17:16:10 2008 +0000 added findBigFiles.csh to ease cleanup when a disk is full commit f59bd1ce97dfc3996c43942848ae7a64f49653dd Author: galt Date: Mon Feb 25 16:00:07 2008 +0000 "Encode release log update" commit 565a64cc7214b4cbd9d1cb7f26e5348d34a7b691 Author: galt Date: Mon Feb 25 16:00:03 2008 +0000 "Release log update" commit e4e6ef38f045f5b9efe07ba7ceb9f3219c28cda5 Author: kate Date: Mon Feb 25 05:28:53 2008 +0000 Changes from Donna's UI review commit 771dc49f167583d0bf367a6cfcace61f7e8c2b3b Author: kate Date: Mon Feb 25 05:17:58 2008 +0000 Changes from Donna's UI review commit bd5c96d2d3e33df48ae4431a0a5b09572d5785b4 Author: fanhsu Date: Sun Feb 24 23:53:03 2008 +0000 Added clarification text about enclosing multiple words for filtering search. commit 71bed18e2bfa6c370b5883628180497ccff31afa Author: braney Date: Sun Feb 24 19:47:25 2008 +0000 better headers, all modes working commit f94a58ac8ba9fd204d3269640bf16c892bb06436 Author: galt Date: Sun Feb 24 16:00:06 2008 +0000 "Encode release log update" commit 6116b1f4125447fb8447e4a91eb696a8b49ba748 Author: galt Date: Sun Feb 24 16:00:05 2008 +0000 "Release log update" commit 23a97420cd2902c55fd6c22799c09aafa0513bc6 Author: galt Date: Sat Feb 23 16:00:06 2008 +0000 "Encode release log update" commit f4995c070782b96147f4e92b22d7e4742064aa70 Author: galt Date: Sat Feb 23 16:00:04 2008 +0000 "Release log update" commit 610737c28988bc805f5319374dfe17614241a167 Author: braney Date: Sat Feb 23 15:49:55 2008 +0000 fix gcc 4.1 compiler warnings commit 5fc0594f378b13daad1f30e00a00bdf8e46f0122 Author: angie Date: Sat Feb 23 01:24:07 2008 +0000 Added automation subdir to scripts target so make alpha will install. commit ca5c296eb0edb7c9c8cb16b0c1eee5fb83d23b12 Author: hiram Date: Sat Feb 23 01:10:07 2008 +0000 Finished off petMar1 Lamprey chains and nets and swaps commit 1432ddac1238cffb08ce8ad0ab451ad31e4f867b Author: rhead Date: Sat Feb 23 00:36:36 2008 +0000 Removed extra period. commit 414b11176155a140e6743416262f670e97eede02 Author: hiram Date: Sat Feb 23 00:20:10 2008 +0000 Allow knownToEnsembl to be updated if specified in the config.ra file commit 93983ca9cc0b9c75a3990175bd8cde609b1c1674 Author: fanhsu Date: Sat Feb 23 00:09:26 2008 +0000 Changed Help link on top bar to open a separate window. commit 8d08ce8f8a204c18f4411a32d44a200f1b48cb38 Author: hiram Date: Sat Feb 23 00:01:29 2008 +0000 Sample run of the ensGene update script for testing, ensGene v48 now loaded commit ad4cab754d6955c1af75b928f3dc056c904f1e24 Author: hiram Date: Fri Feb 22 23:49:29 2008 +0000 Added ensGene v48 as a test of the automatic update script commit 7eb872497f3302aa10d51032c3f826da5bb7101b Author: hiram Date: Fri Feb 22 23:23:56 2008 +0000 Keep the working files gzipped for space efficiency, and now functioning through cleanup step. commit 8be05d1675fa653228d656c2f855d6363d9d8259 Author: kuhn Date: Fri Feb 22 23:14:53 2008 +0000 added a hyphen on 'drop-down' commit a667914c77dafd73992a8dc95aa7a5c5c9af0a84 Author: hiram Date: Fri Feb 22 22:52:10 2008 +0000 Now successfully building a scaffold assembly gene track, with GeneScaffolds commit 230f400566821bfb027cf3d7af609107f4d8f2a7 Author: hiram Date: Fri Feb 22 22:51:28 2008 +0000 ensGeneScaffolds.pl is the correct script, not ensAssemblyChain.pl commit d42315a5470249d718cf3d77779e0392b277d18d Author: kuhn Date: Fri Feb 22 22:23:37 2008 +0000 made microsatellite track as favor for old friend commit 0be04e834b07539923915a0451440353f6023212 Author: angie Date: Fri Feb 22 21:09:08 2008 +0000 Added support for xrefLookup and xrefOrg settings, to allow translation of names in columnDb.ra lookup queries. Added those settings to flyOrtholog specs for databases whose dmBlastTab table has CG* IDs instead of FlyBase's preferred FBgn* IDs. commit 76fabef9ffe525cfaf46f7afdc31d16931ed91a2 Author: hiram Date: Fri Feb 22 20:37:53 2008 +0000 Fixup comment about the usage of path2 commit ee20c7412ed9b425908e719761bb0ecd5eac5843 Author: hiram Date: Fri Feb 22 20:00:45 2008 +0000 Produce lift file from Ensembl tables seq_region and assembly for GeneScaffold to scaffold coordinate transforms commit 79570b9d38576c575752526853fa73ad824114ac Author: hiram Date: Fri Feb 22 19:53:59 2008 +0000 Adding liftAcross to the build with test commit 44cf2869f635b8a8dc4b71b3c4bc7aa89b712059 Author: hiram Date: Fri Feb 22 19:50:53 2008 +0000 Adding ensemblGeneScaffold track definition, and rearrange petMar1 chain and net priorities commit 5fba96c3f4de0f8bcb0a89051c09b2366aa59913 Author: hiram Date: Fri Feb 22 19:48:14 2008 +0000 Now testing the bedOut option commit 8a86318f579441b1fdab288bab38e855bc33ade9 Author: hiram Date: Fri Feb 22 19:46:09 2008 +0000 Can now transform the lift file into target bed coordinates to produce the ensemblGeneScaffold track, with color shading for out of order segments. commit fbbcd96244fa50aa5831388588ee0547cc4157a2 Author: kent Date: Fri Feb 22 19:29:39 2008 +0000 Clarifiying minimum size of sequences. commit 189e2081e24cecab9cbea56b8a390cb56deddc87 Author: kate Date: Fri Feb 22 19:27:34 2008 +0000 Change overall UI to improve look and feel commit 8ed78839ad11c851b9598ee8732609ba0ef3584d Author: fanhsu Date: Fri Feb 22 19:15:07 2008 +0000 Added CTD data. commit 8b13648628493f47ecc3e7d8e8803d83c35875a1 Author: fanhsu Date: Fri Feb 22 19:04:32 2008 +0000 Created chem_gene_ixns.sql for CTD. commit 071d822180c63969f26895b0118b8384c4489736 Author: hiram Date: Fri Feb 22 18:22:12 2008 +0000 Moved to test directory commit b6d4b15c7c6c4cddff6f138ffa2bb567dfe6add7 Author: hiram Date: Fri Feb 22 18:21:10 2008 +0000 Add the test target commit d17d7618c33042d935254c5bffc4396d26f11cba Author: hiram Date: Fri Feb 22 18:08:17 2008 +0000 Well, it would be nice to check in the correct expected outputs commit f66becbffb6783cdf817669829790a41c32a859b Author: hiram Date: Fri Feb 22 18:02:15 2008 +0000 Don't forget the cleanup commit c17f7775e945d4b824f63697e8d2adf402d9efc5 Author: hiram Date: Fri Feb 22 18:01:40 2008 +0000 Complete set of files to run tests on liftAcross commit 93b5e98831c96448d8fb03b0bdb8ef144f79510a Author: fanhsu Date: Fri Feb 22 17:57:20 2008 +0000 Updated hot link to Help when Select Subject is selected. commit 87ff642744115ba42db3452cea2f7b711630261d Author: hiram Date: Fri Feb 22 17:37:11 2008 +0000 This appears to be working correct for all strand issues and mixed up exons and is fairly clean. commit ba64120b48dde3868246a642b96b88e965186fb3 Author: fanhsu Date: Fri Feb 22 16:58:06 2008 +0000 Updated ctd.c per Angie's code review suggestions. commit 34bb7a2c7f481aaf3f3a1473ebb32bdc62d3341d Author: markd Date: Fri Feb 22 16:40:22 2008 +0000 updated expected results commit 4b2ed9c735d88281c5371a189624d720d5ee58b4 Author: galt Date: Fri Feb 22 16:00:07 2008 +0000 "Encode release log update" commit 81ff9dd786cad82c3dfa3b4ae88a8da4e24f7ce1 Author: galt Date: Fri Feb 22 16:00:04 2008 +0000 "Release log update" commit bdbbb0d54bf2376c297a4553a832f91667dc8300 Author: markd Date: Fri Feb 22 08:11:46 2008 +0000 fix something I just broken with making complement variable local commit 644fc5b322cebe549da8069f3eef9959b482f4b3 Author: markd Date: Fri Feb 22 07:42:35 2008 +0000 removed non-posix option commit b4636dcb86e0008a15eaccca66e1cafc2e19a0fe Author: markd Date: Fri Feb 22 07:33:49 2008 +0000 fixed incorrect argument, not sure why this wasn't detected commit c74356a8dba652aad4ccd51d28b367b5be3e942c Author: markd Date: Fri Feb 22 07:30:46 2008 +0000 fixed GCC 4.2 warning commit 20b86aecdc550b140399eae32a646a4543e18499 Author: kate Date: Fri Feb 22 05:54:10 2008 +0000 Correct the species lists commit 1577495d26bd2bfa3087ceeab6ff8d490725d4d4 Author: kate Date: Fri Feb 22 05:07:31 2008 +0000 Correct species list and adjust frames section commit 34dee760db7be51aced586428cd2a9f42e367d64 Author: rhead Date: Fri Feb 22 00:34:14 2008 +0000 Updated visigene section to match kent/src/hg/visiGene/hgVisiGene/hgVisiGene.c. commit f5c534208d591f27efa2021657db43f3d0996d45 Author: fanhsu Date: Fri Feb 22 00:30:17 2008 +0000 Changed Allen Brain Atlas to Human Cortex Gene Expression. commit 9ed26d453703df8a8ee386650ce4e13e9f356470 Author: rhead Date: Fri Feb 22 00:13:53 2008 +0000 Updated two broken links; one minor wording change. commit 3a1f7f7df8c527abee3cffdd2034c33fadfdf1db Author: braney Date: Thu Feb 21 22:38:25 2008 +0000 fix a bug I introduced last night and made Kate waste her morning (sorry kate) commit 18d0f26e4f2bbc4c7b7bad917d52fcdd7e672b1f Author: kate Date: Thu Feb 21 21:52:21 2008 +0000 Work-around problem caused when viewing base level when frames are missing commit cc38ec873aa81d89d47ee849ffbbccd7bbf0aafe Author: jzhu Date: Thu Feb 21 20:11:47 2008 +0000 cast char * to unsigned char * so that it will compile on tcga1 and cancer2 commit 97c85a54bfe17408650c7047aa3b6565dc6ef319 Author: jzhu Date: Thu Feb 21 18:31:33 2008 +0000 modify hConnectLocalDb so that the function will not abort, instead return NULL when cannot connect commit 14a4dd94b41898930605da7d3adee14c96ea93d1 Author: jzhu Date: Thu Feb 21 18:30:41 2008 +0000 expose sqlConnRemote function in hdb.h commit 3692f610c5842b4b56e815f827eb6bfb2f24bd72 Author: jzhu Date: Thu Feb 21 18:14:50 2008 +0000 change hConnectLocalDb function commit 950b795e12223221420f0939446ecfe6c95e7705 Author: kate Date: Thu Feb 21 18:13:40 2008 +0000 Add Dec07 freeze TBA alignments from Margulies lab commit 00c9392e992a81191d52fafe3104b963b4c39750 Author: galt Date: Thu Feb 21 16:00:08 2008 +0000 "Encode release log update" commit 2199616585c0d64033df2f238b22921fd4f7ee5f Author: galt Date: Thu Feb 21 16:00:04 2008 +0000 "Release log update" commit 3c6f4c2e8fa8968ff92f38c776a31d0d2825207c Author: fanhsu Date: Thu Feb 21 15:21:11 2008 +0000 Changed Sequence View to Sequence View Gateway on the top bar. commit 36975085153e928b919fb7685ce4fae01792422b Author: giardine Date: Thu Feb 21 12:39:18 2008 +0000 switched colors commit b8da69759ffde143ff4e8a7cae02a024bf8815b0 Author: jzhu Date: Thu Feb 21 10:59:48 2008 +0000 add function to connect to local database on local host as defined in hg.conf commit ec22e2b5959e1a882b69221103e5d1f4d22c99d0 Author: braney Date: Thu Feb 21 03:44:54 2008 +0000 another change to support old style mafFrames commit f4d50be46abde10f23de39e8b92ee5a21cdc60e6 Author: braney Date: Thu Feb 21 03:26:48 2008 +0000 routine to load old style mafFrames format commit 6b8ee513eee06775985024ceca6b8ab98b0deba3 Author: braney Date: Thu Feb 21 03:26:21 2008 +0000 allow loading of old style mafFrames format commit 5b4b1f811c70925e4e6f5c1fb46c03a545d2713d Author: braney Date: Thu Feb 21 03:25:48 2008 +0000 support new mafFrames format commit 251ee519a1a99cc5e83fc3783128eba4ccce9b17 Author: markd Date: Thu Feb 21 02:13:26 2008 +0000 remove old JK_WARN hack that was added when warnings were only enabled for some modules commit 18c8a74a370fb797efd4a45100b4eb3816e7f24c Author: braney Date: Thu Feb 21 01:59:39 2008 +0000 add a few more places to fix a bug I fixed elsewhere earlier commit 71c19c6f547783dc55d0c92a138bbc934bf02433 Author: markd Date: Thu Feb 21 01:24:07 2008 +0000 set GFF/GTF cdsStart/cdsEnd to txEnd instead of zero when there is no CDS commit 8f64963e7671b82cffd83bb53cd56ea4a650e8f9 Author: kate Date: Thu Feb 21 01:02:32 2008 +0000 Replace TBA alignments with newer set from Margulies lab, NHGRI (Dec-07 sequence freeze) commit 78b969ffb7d7ae58047bd63bf5f9bd9c06a3fa99 Author: markd Date: Thu Feb 21 00:21:43 2008 +0000 added flag to indicate if frame is on an exon bound; fixed inconsistency in table columan and struct name in a backwards compatible manner commit 90e069fba2d035aa733a104e4bed61caf91b520d Author: markd Date: Thu Feb 21 00:11:45 2008 +0000 make complement and display reverse cart variables local to a database commit 83bdd63caf6224b1fb0037d8b5a5181b73048baa Author: fanhsu Date: Wed Feb 20 23:23:07 2008 +0000 Updated query to CTD table. commit ee764aa91d0412362a28e645b6376f1b86dcae6a Author: fanhsu Date: Wed Feb 20 23:14:15 2008 +0000 Updated HuGE URL. commit b60931d39d3e734ff50dba3d4871ffcd5142ca63 Author: fanhsu Date: Wed Feb 20 23:01:43 2008 +0000 Updated HuGE link and added allenBrain link. commit ae913ddb3dbf1e13b9055818116bb96a71113061 Author: giardine Date: Wed Feb 20 22:21:20 2008 +0000 Added new MKAR tracks commit 8b603e222863001cb568aca83de97fd5f5d230ec Author: fanhsu Date: Wed Feb 20 18:12:34 2008 +0000 Fixed a bug in ctd.c. commit 3ef5bdbaf5d950c407324efa88d720686eee2d5d Author: galt Date: Wed Feb 20 16:00:08 2008 +0000 "Encode release log update" commit 2c5e00fe6fdc11d46dc9c1c75a799b49c7565eaf Author: galt Date: Wed Feb 20 16:00:04 2008 +0000 "Release log update" commit 268a1aec12c45122105bd53a7f0f7c988fe48bae Author: markd Date: Wed Feb 20 06:17:09 2008 +0000 make base complement arrow direction match display direction commit 513ef1c0a2bad6830567d0e2425b2420212de7e0 Author: markd Date: Wed Feb 20 00:42:33 2008 +0000 added reverse complement display mode in main browser window commit ada538633adee49af86ffb5b9c149ffd92b7ba7f Author: fanhsu Date: Tue Feb 19 21:00:51 2008 +0000 Added ctd.o commit 2bfab86a05ba9f1b9c972cc0d48b5ffba1ba2d76 Author: fanhsu Date: Tue Feb 19 19:55:49 2008 +0000 Added CTD section. commit 5c2ef0fde053035cf80d3c18b2b85cf1b73a52d8 Author: kuhn Date: Tue Feb 19 19:27:56 2008 +0000 recording knownGene assignments for new, stable uc IDs commit acf552f722b07f0ffb2d009268cf6799b0c14ec7 Author: aamp Date: Tue Feb 19 19:06:17 2008 +0000 "New version number v176" commit 389181d1a567a8f5dfa18b07314b3bafbcb81c43 Author: braney Date: Tue Feb 19 18:16:54 2008 +0000 clean up, add comments commit 70abc4b53bdf6350ac116f2f17a0929e106de9e8 Author: giardine Date: Tue Feb 19 18:06:20 2008 +0000 Added new link commit 677e2ff51653e845b3059146eac138e6f3852a4f Author: giardine Date: Tue Feb 19 18:00:03 2008 +0000 Added 3 new LSDBs to data and credits. commit 8ba19dc45d09262c99dd295df9a54438979e8eca Author: fanhsu Date: Tue Feb 19 16:52:17 2008 +0000 Added CTD section. commit e56dd90cc07476c695abb12d93b899fa96292b74 Author: fanhsu Date: Tue Feb 19 16:45:15 2008 +0000 Created ctd.c to process CTD data. commit 193b94b109315859c3a5369468e8b47311d9dabc Author: galt Date: Tue Feb 19 16:00:05 2008 +0000 "Encode release log update" commit 35dab561ce5d05306e9998a3800d99a557b0e4b8 Author: galt Date: Tue Feb 19 16:00:02 2008 +0000 "Release log update" commit bd3ad1a03dc352072f0a10f534f3e21b507387e5 Author: rico Date: Mon Feb 18 20:44:02 2008 +0000 Replaced old anchor interface with new segment list interface. updated makefile accordingly. commit 1ffa01c7237f468d0950b0cda65d0d581998c8ab Author: rico Date: Mon Feb 18 20:43:14 2008 +0000 Replaced old anchor interface with new segment list interface. commit b55e14a86f58b4557af885a8d218e9ab99e54951 Author: rico Date: Mon Feb 18 20:42:01 2008 +0000 Switched to my new segment list interface from the old anchor interface. commit 2f6bbbe5c0f964c561b0d45dcb54043309a7b775 Author: kate Date: Mon Feb 18 20:04:39 2008 +0000 New ENCODE project logo from NHGRI commit fd991c10358627d4ce12ab504a990af21cd5cb45 Author: markd Date: Mon Feb 18 19:38:28 2008 +0000 exclude .svn directories from rsync, for benefit of code importers commit 1f09d8e541065b97f53304758e63e983b8e6abc7 Author: galt Date: Mon Feb 18 16:00:07 2008 +0000 "Encode release log update" commit 9319582bf1803e0950dab601202f69084c55c3d6 Author: galt Date: Mon Feb 18 16:00:04 2008 +0000 "Release log update" commit 4d16bd0ad97705aefa3a8023017b492d0ccde748 Author: kate Date: Mon Feb 18 02:12:27 2008 +0000 Update stop/start instructions commit 179916912f77f98cfbc959a17c9c0585a9a2c902 Author: kate Date: Mon Feb 18 02:11:31 2008 +0000 1. Allow non-owner to view errors for a project. 2. Alphabetically order projects for display commit 9da70f97f39a8a16aadfb3fead3a7fd4936938de Author: kate Date: Mon Feb 18 02:10:11 2008 +0000 Allow multiple logins with the same email address commit 7825341098642b020a44fec5b2ebf3f4bab80475 Author: kate Date: Mon Feb 18 02:09:30 2008 +0000 Require project name to be unique commit b69ce076278da05d5edfb5999860750e3b918cf5 Author: kate Date: Mon Feb 18 02:08:50 2008 +0000 1. Remove link for current page. 2. Increase refresh rate commit f667ad4ae075c9ee2184619c4f3250c3217c806d Author: kate Date: Mon Feb 18 02:07:40 2008 +0000 1. Hide obsolete/internal items from display, except for admin. 2. Format date consistently/succinctly. 3. Display archives most recent first. 4. Replace 'see current' with project status commit a63458b353c741f866f68b65364a306046637f2d Author: kate Date: Mon Feb 18 02:05:03 2008 +0000 1. Hide obsolete project Type, except for admin user. 2. Replace deprecated Rails method (start_form_tag) to remove log warning commit 2031898726ed0aa48b0925b7303bca8803506d9b Author: braney Date: Mon Feb 18 02:05:02 2008 +0000 working fairly well, needs to get gene models for exon output commit 995c3fa449faf46633019a4b9c9cfc68ad741998 Author: kate Date: Mon Feb 18 02:03:58 2008 +0000 1. Hide obsolete/internal items from display, except for admin user 2. Format dates consistently/succintly 3. Hide uninformative Investigator column when listing user's own projects 4. Add column headers to list commit babbf854d7e986b4a03a535282b988b0e177d36e Author: kate Date: Mon Feb 18 01:59:13 2008 +0000 1. Hide obsolete project type (except for admin user) 2. Update deprecated Rails method (start_form_tag) commit 83a7b825e52741aa7db41d97c8cce4f5bf65f35c Author: kent Date: Sun Feb 17 18:50:08 2008 +0000 Refining usage of ccds a bit. commit d04d062486c92f5e794c77c008ab9e1ad069e571 Author: galt Date: Sun Feb 17 16:00:06 2008 +0000 "Encode release log update" commit 3e9e00114ec9237f0407388f6ca186a34714c513 Author: galt Date: Sun Feb 17 16:00:04 2008 +0000 "Release log update" commit 60f1aa0fe1ad2378384c2b9030b4e72eb0edf77d Author: braney Date: Sun Feb 17 04:56:03 2008 +0000 working a little now commit a8456a84987d2f1e34cd9144fdb690664cbe1e1b Author: braney Date: Sun Feb 17 03:09:23 2008 +0000 first cut of a program to output protein alignments from maf file commit 0f6ea6ddcecddd019f9b89b09c25425e19da6f68 Author: braney Date: Sat Feb 16 17:17:06 2008 +0000 a fix to check for buffer overflow on maf's with short sequences commit 3538ac05e8eb10ebeae917656071708b04205b24 Author: galt Date: Sat Feb 16 16:00:08 2008 +0000 "Encode release log update" commit 4a935fca9e39503d7a6b0fbc9140a20bb1af155f Author: galt Date: Sat Feb 16 16:00:05 2008 +0000 "Release log update" commit f5c9b040bea1949d7d6aef51787b2d27ca6a47f2 Author: kent Date: Sat Feb 16 04:10:03 2008 +0000 Handling empty lines better commit 1cbe84d7280efcf21b775539331d758d4381cd50 Author: galt Date: Fri Feb 15 16:00:07 2008 +0000 "Encode release log update" commit 418fcbdfb77a1a2605d0be86cd663cd1bc2309de Author: galt Date: Fri Feb 15 16:00:04 2008 +0000 "Release log update" commit e523401490fd39efa97993e82a30f6121406ad6a Author: kent Date: Fri Feb 15 02:13:51 2008 +0000 Working on hg18 UCSC gene update - still a ways to go. commit d268908d401704ded2e98efd568e6a9acf780f04 Author: kent Date: Fri Feb 15 02:06:12 2008 +0000 Adding ccds as type where we keep evidence. commit b2ef6e1720ae085be2688c0fbd4ef9c94c764f53 Author: kent Date: Fri Feb 15 02:00:23 2008 +0000 Centralizing logic to decide what is a trusted source, and adding ccds to refSeq as such. Making it so that enclosed soft exons from trusted sources are not removed. commit 7d5769849c2e0adefaead9a70e6d6a6518c7bd65 Author: rhead Date: Fri Feb 15 00:55:40 2008 +0000 Removed extra dash. commit 4fc85ff08ef169d4a04a5888890aac793b53057e Author: kuhn Date: Fri Feb 15 00:44:26 2008 +0000 turned xenoRefGene track to pack commit 24ac0422d4ea6def50ef2470bf11a9b36fc47bb3 Author: hiram Date: Fri Feb 15 00:41:07 2008 +0000 This is working fairly well. Remaining to be fixed is when a scaffold is mixed up in the GeneScaffold coordinate system commit 90349efa270749dbdebfd12379fab5f3cb225bef Author: markd Date: Fri Feb 15 00:34:49 2008 +0000 don't abort on missing genepreds commit 5043597caf7bc4c12f5e1d40f652589b819fbc99 Author: angie Date: Thu Feb 14 23:46:24 2008 +0000 Orthologous alleles from reference assemblies of chimp and macaque, for human SNPs. commit 84599d74c3e3a197e4be765968c2299ef164295a Author: kayla Date: Thu Feb 14 23:44:04 2008 +0000 took out ponAbe2 for now since Hiram is rerunning it. commit 07f46913f2b5efe5bf856ae18b64055b52ead22d Author: rhead Date: Thu Feb 14 20:22:00 2008 +0000 Added missing link, cleaned up other references. commit 22b7b0e84cfec12e49ef7b9979b0a663c81ef4a7 Author: rico Date: Thu Feb 14 20:12:06 2008 +0000 Added HG_WARN = ${HG_WARN_ERR} to the makefile commit 51d31f3bc28950fb101b07f3632aee2c36b2eaee Author: markd Date: Thu Feb 14 20:11:58 2008 +0000 deleted unneeded referenced to renamed genePred field commit 68936bfdb65657f7bcc663146cf347b1f4f0d063 Author: rhead Date: Thu Feb 14 19:45:29 2008 +0000 Added link to paper and cleaned up other references. commit 0c599d9f22454c84ce87381996b56121df635b8e Author: hiram Date: Thu Feb 14 19:31:01 2008 +0000 Orangutan has a number of names in genbank: Pongo abelii pygmaeus and variants commit b5c20a7df9abb8e08fcb91d5dab07e1e7c41607c Author: hiram Date: Thu Feb 14 18:49:12 2008 +0000 Add jkhgap library and MySQL links commit c2ba1d6d6fcecc2ee694738a7415ca244d03acc0 Author: kuhn Date: Thu Feb 14 17:52:01 2008 +0000 removed mgc machine from scripts. bye, bye, mgc commit c111b607240e43f820a6c86f9b6e565c6a9c471c Author: galt Date: Thu Feb 14 16:00:05 2008 +0000 "Encode release log update" commit be67e41f68e4763c4a1bd4d4f3007b580133e81b Author: galt Date: Thu Feb 14 16:00:03 2008 +0000 "Release log update" commit 10db1eb1acce8adbc4695061911686ba8272492f Author: markd Date: Thu Feb 14 00:38:30 2008 +0000 fixed spelling in help commit 7925316bd53729440d0897365967bb8fb738172c Author: hiram Date: Thu Feb 14 00:18:08 2008 +0000 I think this is working, but the Ensembl gtf files are broken ... commit 6fa9aeee2d6dfa1241cbf4149f87ca0ca0a89b2b Author: markd Date: Thu Feb 14 00:15:16 2008 +0000 changes to using make rules (with Kate) commit 42a1023848d80ba7a022144a11e347988628eaa1 Author: hiram Date: Wed Feb 13 23:08:27 2008 +0000 Beginning to lift gene pred OK commit 851d1de883e4262170e370068bfbe3a1953e18b4 Author: hiram Date: Wed Feb 13 19:03:33 2008 +0000 A test set of conversions commit 7f212d62d6b10c52af67aba3e7a6d9e8c920c24f Author: galt Date: Wed Feb 13 16:00:06 2008 +0000 "Encode release log update" commit 96691266a4084a9c1449a56c1252880f14dbed43 Author: galt Date: Wed Feb 13 16:00:04 2008 +0000 "Release log update" commit 866f53aeb6f90078a711de2e363efeb5e1f04326 Author: rico Date: Wed Feb 13 00:16:43 2008 +0000 Silenced compiler warnings. commit 602112dd1d8b9f68b88dce467705022111eab221 Author: kuhn Date: Tue Feb 12 23:51:38 2008 +0000 one char typo commit 78814c23c24ebdc25f3d28098acc0ea4722dfd9a Author: kuhn Date: Tue Feb 12 22:54:12 2008 +0000 added nestedRepeats to tablesIgnored commit 790908e86e072ceb342ed54e4d92d176b0f9d5c7 Author: braney Date: Tue Feb 12 22:14:03 2008 +0000 backing out rico's change commit 4ab69e69ef3b1732316aeb6726741c0fbbdcdec8 Author: markd Date: Tue Feb 12 22:02:50 2008 +0000 fixed to true similarity metric commit 171c5da861bb758c3b43fc52b016ef10416d8370 Author: kent Date: Tue Feb 12 20:47:14 2008 +0000 Avoiding negative returns on hash function. commit 282791fb0778ff5ce3d44d71ad2b0a13882cc064 Author: kate Date: Tue Feb 12 20:36:36 2008 +0000 Restoring after bad checkin commit 900c4996e8c1eee2392f62752d584843b267793f Author: kate Date: Tue Feb 12 20:33:35 2008 +0000 Fix score filter on custom tracks commit 842a7537aba049611e9d87a41e930c7373f91467 Author: rico Date: Tue Feb 12 18:31:46 2008 +0000 Added anc.h - library for dealing with anchor files. commit 2218c9c270481e4f9380b98b990407a3cf76ee2b Author: rico Date: Tue Feb 12 18:31:02 2008 +0000 Fixed memory leak in linefile.c, added anc.c (library for dealing with anchor files) and added anc.c to the makefile. commit 4786b9c2f6588bd7f963173649865b7270d14fc3 Author: rico Date: Tue Feb 12 18:28:32 2008 +0000 Code for finding alignment anchors in an argument maf file. commit a6a1bf932a610c1d08f714037c3d9ddcedf4e14e Author: kayla Date: Tue Feb 12 17:49:11 2008 +0000 added anoCar1 commit 52e1fba5071b39b78f074ad09da19038c62a010f Author: galt Date: Tue Feb 12 16:00:08 2008 +0000 "Encode release log update" commit 9621ca5f1b81eecd785157710d8d59cc85d2303d Author: galt Date: Tue Feb 12 16:00:05 2008 +0000 "Release log update" commit 743fdcc651e5239e3ecbf7e71a12e4de90025e0f Author: galt Date: Mon Feb 11 23:44:08 2008 +0000 give each instance a unique cookie commit 19115f6da645114ae4e65c3daf126cd80b972d02 Author: hiram Date: Mon Feb 11 23:07:11 2008 +0000 Adding in MySQL file download business to do the GeneScaffolds liftAcross commit e000f89fb63ec148c41aaead09f3ad85d5426840 Author: hiram Date: Mon Feb 11 23:06:10 2008 +0000 I think this reads in the lift spec file commit 484edf120ca3cebd13bf034a54429926632150bd Author: galt Date: Mon Feb 11 23:01:12 2008 +0000 make user be local scope- we were seeing a side-effect commit ef5855355e6bcfd31842b294a03fbf42c73914db Author: angie Date: Mon Feb 11 22:22:09 2008 +0000 Oops, adding intialization to NULL to avoid -O warning/error. commit 2097c3a33ddf599c50827b577e0de27c488a5018 Author: hiram Date: Mon Feb 11 22:14:48 2008 +0000 Initial empty source commit d60104899f874175f5704bb1ebcae3291d2b396c Author: fanhsu Date: Mon Feb 11 22:04:45 2008 +0000 Updated to accomodate GSID PB. commit 02d1e5b45d6d58fa83eb267bcfc57392ca33a7ea Author: aamp Date: Mon Feb 11 20:24:39 2008 +0000 Added a re-sequencing trace experimental track. commit 5f3f39eeeb6d2b42bf3b1cae32ce1b087c652a4c Author: angie Date: Mon Feb 11 19:04:01 2008 +0000 Added anonymous ftp username hint to bigZips/README.txt. commit 8332245d579aad4bc2d03eb0b4a28920ec1ff680 Author: angie Date: Mon Feb 11 19:01:40 2008 +0000 Updated settings for ortho display (snp128 and snp126). commit e748b3401d7a4db8ba6e9c409d1ade710ada5404 Author: angie Date: Mon Feb 11 19:00:25 2008 +0000 Added snp128. commit 5d4ee6869ab406a7ee6fa34b6cecf357e74bb70e Author: angie Date: Mon Feb 11 18:56:14 2008 +0000 Added better error reporting for incorrect coords passed to snp details (from manually constructed links). commit 4e1ffa5b72d32e5954c9e6bd4bda84f1dfa13e59 Author: braney Date: Mon Feb 11 17:49:48 2008 +0000 oops... I didn't add my name to this mess commit 6514f38debb7bf17fe9615ada0ce7659666984a7 Author: kent Date: Mon Feb 11 17:10:58 2008 +0000 Committing this source file that was part of a paraflow experiment a year back, but slipped through the cracks. commit 4c093b734de9742c8c46c62e74f72989af602e18 Author: kent Date: Mon Feb 11 17:08:48 2008 +0000 Adding dupeOk flag to cope with some duplicated data in latest SwissProt release. commit ea5de9400f9d69ed411862842fc5ffede8dcd605 Author: kent Date: Mon Feb 11 17:08:15 2008 +0000 Making it ok for index to have multiple reasons why a protein exists. commit 59f41112e114fee8b0222fb43fe8c2ce917967a7 Author: galt Date: Mon Feb 11 16:00:07 2008 +0000 "Encode release log update" commit a2b778b18b2f60347789aa22fd4f5943cc2c92af Author: galt Date: Mon Feb 11 16:00:04 2008 +0000 "Release log update" commit deb07df559e0b4683700a653bb8775ecc8b22022 Author: braney Date: Mon Feb 11 03:14:39 2008 +0000 add multizPrimate frames and phastCons track commit 83016e9765acf908e46f6d2068902de2c5b59ad6 Author: galt Date: Sun Feb 10 16:00:06 2008 +0000 "Encode release log update" commit 2bd79d1451e74ca2564b4f4aa99eeb3c1ba04b25 Author: galt Date: Sun Feb 10 16:00:04 2008 +0000 "Release log update" commit 625885a3f6d4b1c2c68af2df7a8c84d83498d4a1 Author: kate Date: Sun Feb 10 02:29:43 2008 +0000 Tool for changing project statuses in the ENCODE pipeline commit 458ab47eefe28639bcc14006ced015458340777d Author: galt Date: Sat Feb 9 16:00:10 2008 +0000 "Encode release log update" commit 2fe0433b8fe8a3d67c91a0d84ccd54105b3f148c Author: galt Date: Sat Feb 9 16:00:08 2008 +0000 "Release log update" commit 2a30041a7ef976f256198ef503fbaff208add4bf Author: galt Date: Sat Feb 9 08:05:13 2008 +0000 adding basic email notification to our staff for successful load commit 6177e49a921b653383a35dc94b117c098636798f Author: galt Date: Sat Feb 9 07:57:36 2008 +0000 mostly cleanup removing commented out stuff and some debugging and obsolete stuff commit bfeb591aa0ffe7d58e052f55e87e0f79576f7ceb Author: galt Date: Sat Feb 9 07:42:32 2008 +0000 adding basic email notification to our staff for successful load commit f3e4849af04b418011874629fc45996aba62b52e Author: markd Date: Sat Feb 9 05:51:20 2008 +0000 added todo note commit 0ef6b40292e2873f511b6bc9590201aaa1225491 Author: kent Date: Sat Feb 9 01:25:37 2008 +0000 Moving ucscGenes build docs to a new dir. commit 446a13fc722f4d8fb91dbb4d1ab6f29d073c016e Author: galt Date: Sat Feb 9 01:12:49 2008 +0000 fix when user auth fails commit 61a3b53e2ecfbdddc82e1fc6e97f0c745747b4fa Author: galt Date: Sat Feb 9 00:58:02 2008 +0000 using config file instead of hardwired commit cd69de165b6054edf7c9e26f35a1999e06eb8add Author: galt Date: Sat Feb 9 00:57:30 2008 +0000 adding from to config file sample commit 08a3760f1842c4eeb74388dbd135187dcf32bea2 Author: hiram Date: Sat Feb 9 00:08:16 2008 +0000 find one is actually find all commit 2ce2cb69586445688acccf6e1de6e8fd5e9fc746 Author: hiram Date: Sat Feb 9 00:07:02 2008 +0000 Fixup the pretty output commit 22dd2c4106202bee3505021ccad991588078e42e Author: hiram Date: Sat Feb 9 00:03:33 2008 +0000 Add version 47 peptide file listings commit f698932984c20c9ff72744daa6c3d411057defd5 Author: hiram Date: Sat Feb 9 00:02:47 2008 +0000 Initial source, will print out any v47 or v48 Ensembl correspondence with UCSC genome versions commit ec9f0b857be27b10368806dd5a1e73858575ccc8 Author: kent Date: Fri Feb 8 23:28:39 2008 +0000 Updating sp080205.txt for how it was actually built. commit 8af7638ff0ae717f9be42e7b8e9cdc5b96d3ab4c Author: kent Date: Fri Feb 8 23:27:18 2008 +0000 Testing new spDb function spProteinEvidence. commit 3166316d29217c93d65e343088fa2b6af9082c22 Author: angie Date: Fri Feb 8 22:58:12 2008 +0000 When looking for first . for file suffix, ignore directory names in the path (like ..). commit 81b1c18ae6ad8f60bdd6be95cb223655ae90e745 Author: markd Date: Fri Feb 8 22:48:31 2008 +0000 added geneName and transcriptName to gff object commit 3ba8bacfdd1882d7dad549e1eccf8163c6f2414d Author: galt Date: Fri Feb 8 22:32:25 2008 +0000 adding spawn plug-in commit 703cd5ec5624be449b21e62389defc39e5450e22 Author: rhead Date: Fri Feb 8 22:30:10 2008 +0000 Changed 'human' to 'mouse' in methods section commit f42f09062f733c7cfcbec84b0d1f16addfeeee97 Author: galt Date: Fri Feb 8 22:27:30 2008 +0000 re-work using spawn instead of hgEncodeScheduler commit c4b08303c876795c6348223615ddf6ee506ad3ff Author: kent Date: Fri Feb 8 21:08:01 2008 +0000 Handling new PE (protein evidence) field in UniProt flat files. commit 9bbd7dc7acde1833131f07c0bbb729f90c5725a5 Author: angie Date: Fri Feb 8 21:07:01 2008 +0000 A couple little additions to support mouse SNPs. The class=named observed values are so arbitrary, we probably don't need to check their format. commit 873bcf7452758381b53cfbc5f7f3195b0a04dc47 Author: kent Date: Fri Feb 8 20:59:50 2008 +0000 Handling new PE (protein evidence) field in UniProt flat files. commit a392a8771ef67fc4daea9ecd2f426d4e2e55d775 Author: kent Date: Fri Feb 8 19:48:38 2008 +0000 Adding intValTree, a binary tree with integer keys. commit 50a67b31469f72b7b8b78feec4386aa1079b753a Author: kent Date: Fri Feb 8 19:47:52 2008 +0000 Testing intValTree. commit 2c26bc400a20a538afa52e02dbd4e8ee9866fbd3 Author: angie Date: Fri Feb 8 17:47:44 2008 +0000 Fixed table name in snpName128 (thx Brooke). commit 8f57f4feb76e0a8fb2564d29a1099ea35e948f58 Author: kent Date: Fri Feb 8 17:07:43 2008 +0000 Moving swissProt/uniProt to uniProt subdirectory. commit b0bca06772b87c1df652df5abe667e750589e6f2 Author: kent Date: Fri Feb 8 17:01:06 2008 +0000 Moving proteins database docs to a subdirectory. commit fce05cffe34d92b8c62bf8c0b4b0c7e83c5e780c Author: galt Date: Fri Feb 8 16:00:07 2008 +0000 "Encode release log update" commit e216c8ec52a938085727a8901a63099d0aba8966 Author: galt Date: Fri Feb 8 16:00:04 2008 +0000 "Release log update" commit 3b5e0db0c32244528f09ff03b9292d5a55304140 Author: angie Date: Fri Feb 8 07:22:00 2008 +0000 1.1382, take two: fix the printf format instead of the variable declaration -- thanks MarkD. commit e9c2b370dafdba16fac8ffb73e05d543d937b107 Author: markd Date: Fri Feb 8 05:35:16 2008 +0000 added ignore entries commit 8f1028b48ffe2c2ee71f314ed7af483bb0e26d49 Author: kate Date: Fri Feb 8 00:16:04 2008 +0000 Allow local or global install commit d6ea388d2451f4cc74a8269b86bb46863566dd3c Author: kate Date: Fri Feb 8 00:01:06 2008 +0000 Make alpha target install to global location for consistency commit f3ba6de5bc1dbd341b4010da2cfbbd0713d8ec57 Author: kate Date: Thu Feb 7 23:59:25 2008 +0000 Adding whole-genome wiggle test commit 1f48eebc3264ad2cbd4db8cdee94312b03c8920b Author: hiram Date: Thu Feb 7 23:48:00 2008 +0000 Lamprey genome rebuilt as scaffolds instead of chrUn commit d26ce7443cdf94f46a3ac5506fdd90fba1aa7f8a Author: hiram Date: Thu Feb 7 23:47:15 2008 +0000 Add chain/net Lamprey commit 32a8146c77baab677c918df40926d487305257a2 Author: hiram Date: Thu Feb 7 23:46:21 2008 +0000 Add in chain/net Lamprey commit 4f53696bed759eba1c3699b8d97f72c5383c08f8 Author: hiram Date: Thu Feb 7 22:48:23 2008 +0000 No need for File::Basename here, correct a danRer5 name commit bf974143c45a95bf3bce2eec9219d045ccab259b Author: hiram Date: Thu Feb 7 22:47:38 2008 +0000 Move getSpecies() to the library commit 4be0c28427ab457bb5f8c26090b886b246660194 Author: hiram Date: Thu Feb 7 22:02:16 2008 +0000 Initial code does download, process and load of ensGene GTF and Peptide business commit 0f77b6b2fecc2d84e9253ba0ec1b23d3ee63ad15 Author: hiram Date: Thu Feb 7 22:00:41 2008 +0000 Do not try to predict Ensembl genes if there is no protein for them. They are most likely non-coding. commit 430b49f3d1e50d31c1d7d0a245e35c95a776f0a5 Author: hiram Date: Thu Feb 7 19:25:53 2008 +0000 Provide UCSC Db mappings to Ensembl versions, Gtf and Peptide FTP files commit 2c931e88bd22312b4e978faa32f7038e667bddd8 Author: kent Date: Thu Feb 7 17:47:35 2008 +0000 Moving ucscGenes build docs and files to a subdirectory. commit adbf840416b9e294ee293f2f52a160f6fba49f22 Author: galt Date: Thu Feb 7 16:00:08 2008 +0000 "Encode release log update" commit 6200dd962c220c34555825781a3f96835e590d4a Author: galt Date: Thu Feb 7 16:00:04 2008 +0000 "Release log update" commit aa346a2740f06e6ccbccc92be91e909ab68e40d6 Author: galt Date: Thu Feb 7 06:52:18 2008 +0000 cancel not implemented yet commit 8ca73bedc970570a6818fc98b3a19ae71f33349b Author: angie Date: Thu Feb 7 01:04:50 2008 +0000 Added snp128OrthoPanTro2RheMac2 (orthologous reference alleles from chimp and macaque for simple SNPs). commit 347d110763ebfe475818cc01f7f43d9701c786ab Author: angie Date: Thu Feb 7 00:57:00 2008 +0000 Updated snpOrtho128. commit 47d0db5c571675f233cd1ac6484b34ebc41e89d5 Author: braney Date: Thu Feb 7 00:11:10 2008 +0000 start phastCons for multizPrimate commit b95a3b1e1f56c5400b18bfaa74b7bb30a5ba217e Author: angie Date: Wed Feb 6 23:23:05 2008 +0000 Added display of more ortho allele info for snp125 tracks; also wrapped a table around both reference and ortho alleles so they line up for easy comparison. commit 782f1443ccbf864bed9b2effd0e5167e193c9ebe Author: tingwang Date: Wed Feb 6 18:43:44 2008 +0000 new expression difference data track commit 5f158cfb63186779213360e08fe8d531422cb230 Author: kate Date: Wed Feb 6 18:05:21 2008 +0000 Add syntax checking of perl scripts before install. Also add user vs. beta targets commit 4c48542784fd20a08002dfa8b39e82fd63bbe621 Author: kate Date: Wed Feb 6 17:24:31 2008 +0000 Remove extra slashes in file spec commit acff0719f346a1f0ad784f0b91e74580abdf5062 Author: galt Date: Wed Feb 6 16:00:09 2008 +0000 "Encode release log update" commit c89d15d62e04b8947183808fd553666d9bd0e8ca Author: galt Date: Wed Feb 6 16:00:05 2008 +0000 "Release log update" commit cbf4e1700d8ad6ff5f0a645c3412b6275f7a34c2 Author: markd Date: Wed Feb 6 07:02:57 2008 +0000 replaced unused genePred id column with score column commit 302351c93d12579f95181fb11f8b4cf5f09086c7 Author: markd Date: Wed Feb 6 05:10:21 2008 +0000 updated instructions for updated txGenbankData commit adbed8b2d69ff4e77e8fe243ebdc978ca527670a Author: markd Date: Wed Feb 6 05:08:11 2008 +0000 build subsitute for data from retired mgcFullStatus table. Don't compress files, output with desired names commit 34d2f19a0a9607b2204a06171dbc11f4cda2a304 Author: galt Date: Wed Feb 6 02:47:20 2008 +0000 getting rid of unwanted confirms on all actions except the projectdelete itself, as jim requested commit 228deca874794cf6272879978997cdb153b01203 Author: galt Date: Wed Feb 6 02:29:58 2008 +0000 change 30second autorefresh to 15sec as jim requested commit c9f44204bff90e87ef983aac98902c5724c1dd8d Author: galt Date: Wed Feb 6 02:11:15 2008 +0000 fixing bug when activation code does not work commit 65a564392afed43964d84a726dffc8fdfc95dbc1 Author: kent Date: Wed Feb 6 01:41:52 2008 +0000 First cut of ucscGenes take 11. Mostly just renaming a few things from take 10. commit 7635265fe4921debdd530bd69a2ca17945a4b0df Author: galt Date: Wed Feb 6 01:36:27 2008 +0000 cleanup sandbox using samples commit 026f7aaa97cbc56088434dcf84e3fe3d43b6bea1 Author: galt Date: Wed Feb 6 01:35:16 2008 +0000 handy stop utility commit 65f2491f057c5e5221d8b536dcd33180ed34effc Author: rhead Date: Wed Feb 6 01:34:03 2008 +0000 Removed unused variable, per markd. commit 0b3586e3e6b771e826101bbde7e599153279119e Author: galt Date: Wed Feb 6 01:29:44 2008 +0000 added sample files commit fa3a87cac462935920ab10d258eef58b1ff504a1 Author: galt Date: Wed Feb 6 01:06:07 2008 +0000 this should never have been checked in commit 7ade9c41f727ac60b60c39f6f3a78fec61cae061 Author: galt Date: Wed Feb 6 01:00:40 2008 +0000 yanking problem use of no-longer-existing objects commit 227265b5f4d5572c7527872c087920e0d5b93b25 Author: kent Date: Tue Feb 5 23:49:12 2008 +0000 A program that implements the test we're asking the potential hires to do. commit 0b16a8618046e1376f905f3dc789990ce8119564 Author: galt Date: Tue Feb 5 21:12:26 2008 +0000 unwanted redo - this one removed commit 734240207037f806d08d5a4c0a9b9c9ad121a82a Author: galt Date: Tue Feb 5 16:00:08 2008 +0000 "Encode release log update" commit 8fc86ec8078e5ed31df3b035c3ecc5dc4e597bb5 Author: galt Date: Tue Feb 5 16:00:03 2008 +0000 "Release log update" commit d69c07f1424ee9b7847f72504aab0e1ffc3c469d Author: fanhsu Date: Tue Feb 5 00:01:32 2008 +0000 Added "Select Subject" at the beginning of the page, per GSID's request. commit 5083c6ea71944a4013edae8f3781bfd0291e9cfe Author: fanhsu Date: Mon Feb 4 23:56:51 2008 +0000 Added "Table View" at the beginning of the page, per GSID request. commit 88c78a1cf44dc3f1b9d1b395b58b19585923282d Author: ann Date: Mon Feb 4 22:39:03 2008 +0000 fixed citation commit 0798cc29ccb7cb5a0479449651c36517782b94ce Author: tingwang Date: Mon Feb 4 22:36:10 2008 +0000 add expression time difference map commit 125c14bf5399ea19c464fc212579734759e42d05 Author: angie Date: Mon Feb 4 20:16:54 2008 +0000 Replacing older snp-masking programs to versions that work on input files (not db) and include FASTA headers in output: snpMaskChrom --> snpMaskSingle, seqWithInsertions --> snpMaskAddInsertions, seqWithoutDeletions --> snpMaskCutDeletions. commit 4856b8dab3616e9aa9f9af8ee9dd8b49cc68319d Author: ann Date: Mon Feb 4 19:55:27 2008 +0000 added note about HGNCs automation of their links to us commit 77f1257001e6eb4baf33a5a0a71f6420e3388049 Author: angie Date: Mon Feb 4 19:01:18 2008 +0000 Re-ran hapmapLdPh on re-released data. Added snp-masked sequences (snp128Mask). commit c31fda85013acfc56b4075089d60cfa3066a831a Author: angie Date: Mon Feb 4 18:55:57 2008 +0000 Corrected data download link. commit 5fd789d16d88972e739c8927658fa4c917375d3a Author: galt Date: Mon Feb 4 16:00:06 2008 +0000 "Encode release log update" commit 11593458c59a9e408763d5b7afa8e6df65b91291 Author: galt Date: Mon Feb 4 16:00:04 2008 +0000 "Release log update" commit 612b2ed3fb70cd68799b2ae8fb77dc8aaecc911f Author: galt Date: Sun Feb 3 16:00:06 2008 +0000 "Encode release log update" commit 0b1f646e0abcb4a331888208a7f845bde0a75ca8 Author: galt Date: Sun Feb 3 16:00:04 2008 +0000 "Release log update" commit e0ea457638e236b60a1ab587d1802eb859fce12c Author: galt Date: Sat Feb 2 16:00:07 2008 +0000 "Encode release log update" commit 616e625e82d4a47542a69e1b177bdc99dcc980da Author: galt Date: Sat Feb 2 16:00:05 2008 +0000 "Release log update" commit 497bf31f5bcadacb1c52f929fca0bbdfd56204d0 Author: markd Date: Sat Feb 2 00:14:23 2008 +0000 CCDS update commit 4c458a08bb809194b92e3a5e0d668d58403d48b3 Author: aamp Date: Fri Feb 1 18:19:24 2008 +0000 "New version number v175" commit 82213e2a3b8e99088ee31f22a106ff682bef122b Author: markd Date: Fri Feb 1 18:06:02 2008 +0000 added a bit to the README commit 2f637ef775d338681371ff5943ea2274d5211df3 Author: aamp Date: Fri Feb 1 18:04:21 2008 +0000 Some trace work. Maybe halfway done with the data wrangling. commit 7b8608620ac77532f823e988086734343d5a4699 Author: galt Date: Fri Feb 1 16:00:06 2008 +0000 "Encode release log update" commit 619a34f0ecb1eeb885b3565e4cb78475a0890781 Author: galt Date: Fri Feb 1 16:00:04 2008 +0000 "Release log update" commit 6141aff8b8d1f6131998c58d68e7655b16a3bd95 Author: galt Date: Fri Feb 1 10:36:04 2008 +0000 status logging commit 5a8e156c97c7920f5ac94a887f1a8fc4bacc38e2 Author: galt Date: Fri Feb 1 10:29:56 2008 +0000 typo fix commit e60c404118d75b0fdd3a1386608e752172434395 Author: galt Date: Fri Feb 1 10:25:51 2008 +0000 project status logging commit 60f9687ba1828d09997483e5eb0c6883774af2de Author: galt Date: Fri Feb 1 10:23:17 2008 +0000 project status logging commit 5161956ee279e5881a61e1fbdf52788c8ec3fff0 Author: galt Date: Fri Feb 1 10:11:32 2008 +0000 adding project status logging commit 9d1d8c2472e3a4b97b8d6f16eda27d58f9651226 Author: galt Date: Fri Feb 1 08:34:42 2008 +0000 creating project status log table commit b0d91472674b27293e0b6ad8e3c0a4c82a90455a Author: galt Date: Fri Feb 1 07:35:43 2008 +0000 creating project status log table commit 0aec2259e54fd73c244ebf2cfb8d150d30a66c2f Author: markd Date: Fri Feb 1 01:24:16 2008 +0000 added hack tool to look at table usage commit 254d0d5bccce0524bd4c0633616b3d0e8e659857 Author: hiram Date: Thu Jan 31 23:59:28 2008 +0000 Initial source for a cron job to watch ensembl FTP site for new releases commit 8d708f165f60922f36459644d313e42462f09489 Author: braney Date: Thu Jan 31 22:37:00 2008 +0000 working on multizPrimate commit 422f6fcef6af7dfa98f0292eef3ed8e83ac00c1e Author: markd Date: Thu Jan 31 21:30:27 2008 +0000 add option to delay update for a certain number of days commit e072f57d511f5a03dab69a2e472e9ece09a63e35 Author: markd Date: Thu Jan 31 20:49:00 2008 +0000 added option to allow for a delay before considering something out-of-date commit 8f65ad89e2b7a16b835122d099f89b4d36a07889 Author: fanhsu Date: Thu Jan 31 16:13:35 2008 +0000 Updated go database with latest release from GO. commit 75cc235d30db1432c6e06b3fe8c32c770357530b Author: galt Date: Thu Jan 31 16:00:06 2008 +0000 "Encode release log update" commit 2886da01694b0d3295def5df1c31e89847a46e19 Author: galt Date: Thu Jan 31 16:00:05 2008 +0000 "Release log update" commit 3ba25514f774c6c7ecf73898b5b6f2938c086617 Author: markd Date: Thu Jan 31 00:10:38 2008 +0000 *** empty log message *** commit a525d3463994e3ac4c8a3872dc7b5180208f59ed Author: angie Date: Wed Jan 30 23:11:27 2008 +0000 Corrected spelling error in optionSpec. commit e154333295ba0e7c805e72d95134cb25480b5cf7 Author: hiram Date: Wed Jan 30 20:11:37 2008 +0000 Clean up references to /scratch/hg/ to be /scratch/data/ commit cae137def07192252bf06b4f718710e1e4c0ca0a Author: hiram Date: Wed Jan 30 19:51:43 2008 +0000 Added petMar1 - Petromyzon marinus (lamprey) commit f3cbccdcb3aa4384b28d219f6a14d60d68ac3638 Author: hiram Date: Wed Jan 30 19:32:46 2008 +0000 Make reference to hgTracksHelp html be independent of cgi-bin directory commit 9fe63f353ca90fa11c86796630aef7aeca780744 Author: galt Date: Wed Jan 30 16:00:19 2008 +0000 "Encode release log update" commit 747a2d9d10c6e954d702b224bbf6a28d049cb116 Author: galt Date: Wed Jan 30 16:00:16 2008 +0000 "Release log update" commit fcf5caeac98fc034d7fb09a7b4886d4e544c35f2 Author: markd Date: Wed Jan 30 08:19:06 2008 +0000 use rsh for rsyncs commit 0245410f9b1475402e019498d69d4281ba36ff80 Author: markd Date: Wed Jan 30 08:15:31 2008 +0000 default to rsh, log details about transfers commit 9e72875dc8734805a0bf9197f566160fb0ec4cf2 Author: hartera Date: Tue Jan 29 22:37:06 2008 +0000 Changed longlabel to be consistent with other Ensembl tracks. commit e8437d0eee8626a7b1fed589e4be5d3a4517cdf9 Author: hiram Date: Tue Jan 29 18:26:46 2008 +0000 No lift file for petMar1 commit c12e1dfaaeb64349a24156f307843e945f132345 Author: galt Date: Tue Jan 29 16:00:06 2008 +0000 "Encode release log update" commit f0ea2c0294c41ceffbe78a4bdbc9eb8a34baff2d Author: galt Date: Tue Jan 29 16:00:04 2008 +0000 "Release log update" commit 78086c4a4363457c126c6fda073f2730110de694 Author: hiram Date: Mon Jan 28 23:48:39 2008 +0000 Properly safe SQL escape names in the select statement for custom track name items commit 9adca1c76c0b310760463afa8e5eef0c95ba5ee8 Author: kate Date: Mon Jan 28 22:49:22 2008 +0000 Customize action links based on status commit 02ec8c2470cbd5c0f98b5d76da9c6486166276ed Author: galt Date: Mon Jan 28 21:23:52 2008 +0000 typo fix commit f6f5e97fcff8ca1c9192acfafe85da8fa46cd640 Author: galt Date: Mon Jan 28 16:00:07 2008 +0000 "Encode release log update" commit e7a6114a54cbbe2154187f4a5bbc9e6eaef98cd8 Author: galt Date: Mon Jan 28 16:00:04 2008 +0000 "Release log update" commit ddb200f3caae3c20c8c74ee512a2fe4ea9c52b8d Author: galt Date: Sun Jan 27 16:00:10 2008 +0000 "Encode release log update" commit 2e54e165fe035bb8c935e4ec3e0f248ccc30933e Author: galt Date: Sun Jan 27 16:00:07 2008 +0000 "Release log update" commit 89dd0d3c9a29266c066633e212f3662f00422d5c Author: galt Date: Sat Jan 26 16:00:06 2008 +0000 "Encode release log update" commit 4de3fa7e7003eb55cd2a368e1c5638d213f0f02f Author: galt Date: Sat Jan 26 16:00:05 2008 +0000 "Release log update" commit ec8e353039f128a903b8485c83afdc94863dc4e4 Author: galt Date: Sat Jan 26 07:31:02 2008 +0000 minor typo fix commit f9a58f00183755f1c333b78800c5a52ea2839eb7 Author: galt Date: Sat Jan 26 07:29:22 2008 +0000 added "out" dir to keepers to preserve unload.ra for future cleanup use commit f7a07819388344ca357b64cc7dad61e1a08ecf68 Author: galt Date: Sat Jan 26 07:12:25 2008 +0000 removing junk left over from clone-and-modify commit 6910e46d1441acdf1ba22327f69e1a3515263a95 Author: galt Date: Sat Jan 26 07:05:40 2008 +0000 changing head -1000 into cat so we do it for real the whole input now commit a5912ae907988af55fba9d1915bb84f381b6925e Author: galt Date: Sat Jan 26 06:34:47 2008 +0000 fix bug in use of slAddHead commit aea9bf22d8910dac9e50451c177d3311bc3f8488 Author: galt Date: Sat Jan 26 05:22:09 2008 +0000 wee bug fix - only need to delete for that case, not the expand-all case or the upload case - duh commit f22a70a355d9c00460a165a0f24415ba4f2e8665 Author: galt Date: Sat Jan 26 02:42:03 2008 +0000 commenting debugging messages commit 181c10704c68c6316c59db9fdbf546ee286e2598 Author: galt Date: Sat Jan 26 02:36:57 2008 +0000 detect url fetch error and stop commit a2685e4dc1c9e072044b4290c61e0c10806140f4 Author: galt Date: Sat Jan 26 02:30:07 2008 +0000 fixing stdout,stderr redirection and flushing for waiter and runner commit 0652505a7ee1aea5938ca44a25215a5bb292f16e Author: kate Date: Sat Jan 26 01:46:36 2008 +0000 Add Bed3 tests commit 7f8f2c3c9a27e9180c4172d91ed5b0d0f3e69ad7 Author: kate Date: Sat Jan 26 01:46:35 2008 +0000 Add Bed3 tests commit aa4638f26d1b4f0690d70f8ae8081edfffbdb33e Author: kate Date: Sat Jan 26 01:46:34 2008 +0000 Add Bed3 tests commit 04539a8156bd124e55350245cfd799f2ccf8e8df Author: kate Date: Sat Jan 26 00:47:42 2008 +0000 Add gene types commit 46a4afcdef7833b9612daec13e0db3979af79936 Author: kate Date: Sat Jan 26 00:44:19 2008 +0000 Add install of new config commit 9b0bbe207e84d9ee49bf9f062eb47fe8e10b03eb Author: kate Date: Sat Jan 26 00:04:14 2008 +0000 Fix problems with error file commit 28b62f34a2a5c3e0864cccf850f826164d3f0687 Author: hiram Date: Fri Jan 25 23:18:25 2008 +0000 Add the printout of the swapped blastz alignments in other DBs commit 3244986afbaa8e3786238830dbfc9fcbdf2d5df3 Author: hiram Date: Fri Jan 25 21:07:53 2008 +0000 Running the oryLat1<->petMar1 alignments commit 5ef90a35539243f4584fb72ca0def692680df1c3 Author: hiram Date: Fri Jan 25 21:07:21 2008 +0000 Adding comments about potentially useless steps commit 064cd150215d71b4eb5137c945be068990d0f664 Author: hiram Date: Fri Jan 25 21:07:01 2008 +0000 Finish off the hg18<->petMar1 chain/nets commit f7a60c289ec771e3edf61bcae6f39a36a3de7614 Author: galt Date: Fri Jan 25 18:40:51 2008 +0000 prevent duplication of unflushed stdout/stderr messages by flushing before forking commit 002b04a8525d3f4f73106ea252f93e62dc0ae250 Author: kate Date: Fri Jan 25 18:20:18 2008 +0000 Add validation for gene data (Gencode-style GFF) commit 92d1b2d46fbe3c2ffe2d505e34aa1496ba982ebd Author: kate Date: Fri Jan 25 18:19:28 2008 +0000 Add test for GFF/genepred example commit bd0fe4089c88776c5a60246b80fd377e9fca5716 Author: hiram Date: Fri Jan 25 18:18:31 2008 +0000 http reference to genome-test instead of hgwdev commit 2df5bec787ce9bfb5103eb46f3b0a50e66407ab2 Author: galt Date: Fri Jan 25 18:13:53 2008 +0000 fix bug in scheduler that caused the cron job to wait for all children with stdout or stderr unchanged commit 6354e5eb3caee7bce73ed40bf7a20b964f8dbd1f Author: angie Date: Fri Jan 25 18:10:30 2008 +0000 In printSnp125Info, don't suppress display of reference allele when class is insertion. commit c305cc84b1241323523c0dc2f49c6eeb9eb9d2d9 Author: angie Date: Fri Jan 25 17:55:18 2008 +0000 Yet another correction to hapmapAlleles{Chimp,Summary} -- the quality score tweak for chimp chroms 21, M, Y{,_random} was performed on an unused field and did not make it into the final product. commit 00c66c1de8915172492953c188132adebbf6de4e Author: galt Date: Fri Jan 25 17:15:11 2008 +0000 little fix on array delete commit 0de2cacd9f010018af8a94d3b7876d996a5dbb1e Author: galt Date: Fri Jan 25 16:00:10 2008 +0000 "Encode release log update" commit 5dd7a6cc97863f7b8bea57d4933f7343327728e8 Author: galt Date: Fri Jan 25 16:00:05 2008 +0000 "Release log update" commit 94e736ec5a4728ffb8c8d466d3378bd172284daa Author: galt Date: Fri Jan 25 07:48:07 2008 +0000 adding auto-completion to show_user event; adding meta autorefresh capability commit 1a300b3f1454c07856aa2c2caea2ae3d268c7368 Author: galt Date: Fri Jan 25 07:46:45 2008 +0000 adding meta autorefresh capability commit dcc872c2e489e16c8701e71553f7faa13c97d834 Author: galt Date: Fri Jan 25 01:03:14 2008 +0000 minor bugfix commit 4a9e69d67bfe84a3c0e15ef566befdb14adb19f8 Author: galt Date: Fri Jan 25 01:00:07 2008 +0000 very basic unloader starting to work commit b15dd73cc63834a3c37a490b0204dc59ce0f4776 Author: galt Date: Fri Jan 25 00:59:41 2008 +0000 very basic loader starting to work commit 64c86abbbe42b0b48b11c8950ad88b93ec2321f7 Author: rhead Date: Fri Jan 25 00:13:03 2008 +0000 Added a block for hapmap SNPs. The html file has been here for months, but the trackDb.ra block was missing, so hg17 has had the incorrect description page since September 2007. commit 975a0e0c9e71119e05a290dbe2989324cd0f197f Author: galt Date: Fri Jan 25 00:09:03 2008 +0000 using verbose 2 commit b245fb691c3c419ba2bf4ead52051ae47a13b5e5 Author: galt Date: Thu Jan 24 18:53:03 2008 +0000 added some basic ruby utility modules commit 0e44353f27e57607ab7fb09a7b0485ec2c43a359 Author: galt Date: Thu Jan 24 18:38:08 2008 +0000 adding ruby utils modules commit 5896603b43e1cd7e4203a4177f21eeccb3243a82 Author: markd Date: Thu Jan 24 17:37:27 2008 +0000 used cvsStatusFilter from tree commit 1e7493159835a7d3b2489f06826318b516705378 Author: galt Date: Thu Jan 24 16:00:11 2008 +0000 "Encode release log update" commit 92fa865df9698c3da2ac01a3bd5cde908e1d290f Author: galt Date: Thu Jan 24 16:00:09 2008 +0000 "Release log update" commit e8b65603c175b11254dd09771ad5cbffea3cc29b Author: galt Date: Thu Jan 24 06:31:15 2008 +0000 changing invalid to validate failed commit 9900a58afefb8dd966a4256fbe31ffdfcb23e797 Author: kate Date: Thu Jan 24 00:55:29 2008 +0000 Add Dnase test with large data files commit 86a3b96b14853f8487f3903d1c3a73ca6a859712 Author: markd Date: Wed Jan 23 21:49:48 2008 +0000 converted from MS-DOS EOLNs to Unix commit fe13080049178be0c5ca32ae1d1e3522abd14faf Author: markd Date: Wed Jan 23 21:04:01 2008 +0000 added program to detect files checked into CVS with DOS EOLNs commit e24548865b1612b543b25d8064b36882a2c898f5 Author: ann Date: Wed Jan 23 20:06:44 2008 +0000 missing period commit 79898e0db1500975086d81ef76685321d8a978de Author: ann Date: Wed Jan 23 20:03:49 2008 +0000 adding new reference commit 72afa8797a4088048ff21834080071d9019df884 Author: galt Date: Wed Jan 23 18:33:38 2008 +0000 removing DOS newlines commit bd8faa842ef8438cf0d58875969091724e3dacaa Author: angie Date: Wed Jan 23 18:12:00 2008 +0000 Added handing of bin offset to the genePredLoad's. commit 4c0d1241adfc0a4826f8f0d6910209473fd66ae1 Author: galt Date: Wed Jan 23 16:00:30 2008 +0000 "Encode release log update" commit 10c688845aaeb2c6e46b44a35c0b7120f33e4a39 Author: galt Date: Wed Jan 23 16:00:14 2008 +0000 "Release log update" commit 7359d18cfcbf684a64129d507ca0e3d89693ac88 Author: angie Date: Wed Jan 23 05:33:45 2008 +0000 Added snp128 tables. commit 66a616fbbf86fb4f3e7b67828d86012d2388779e Author: angie Date: Wed Jan 23 05:31:16 2008 +0000 Tweak to avoid printing out some exceptions for items that we will skip, to prevent joinerCheck complaints. commit 76a4d387e1849de1521f5b566c30d4b1d1743d82 Author: angie Date: Wed Jan 23 05:24:13 2008 +0000 Wrapped up snp128 build. commit 72691ab3f15cee48131bb304b496c5248cb06dcf Author: angie Date: Wed Jan 23 03:21:38 2008 +0000 Properly handle strand '--' in baseColorOverdrawQInsert's polyA detection. commit f5f0424f80a644631f98a2a7f1623d5d6ed5f7f6 Author: kate Date: Wed Jan 23 01:51:37 2008 +0000 Fix problem with output dir commit 1020dbc6b1a6d2912cb42605fbcaf32dd20f33e8 Author: galt Date: Wed Jan 23 01:41:23 2008 +0000 more user-friendly wording commit 57995d9bbaea4412f6d509d030dd1646787fe9f4 Author: rhead Date: Wed Jan 23 01:22:49 2008 +0000 Changed links to American Journal of Human Genetics to ones that work. commit b181cc7454f40f440e3524553ef1fe55929d34aa Author: markd Date: Wed Jan 23 00:39:47 2008 +0000 use dynamic linking of CCDS to MGC commit 5584ea6fdcc87efa0c967c0ebfeac12f83c514b7 Author: rhead Date: Wed Jan 23 00:39:00 2008 +0000 Added a missing field for the .2bit format. Found by Bob Harris at Webb Miller's lab. commit 5592b35cd2279c8eefa6be6d77274011b7487ca5 Author: hiram Date: Tue Jan 22 23:05:37 2008 +0000 Properly detect no chain portion found in innerBounds commit 9e6f9c1439133da63a90631f15792b0e26548421 Author: hiram Date: Tue Jan 22 21:51:32 2008 +0000 Prevent integer overflow on center computation for zoomToCenter() commit 351605638c0ef7d12de3c4340fb81b996d67e747 Author: angie Date: Tue Jan 22 20:17:23 2008 +0000 Changed an off_t to unsigned long to avoid warning/error from %ld in printf. commit 158c0a82bd1b3b63b68be27ae72213ce0166968d Author: fanhsu Date: Tue Jan 22 17:47:43 2008 +0000 Added huge table for HuGE gene symbols. commit 8f0f1712418092150b8ff8b89efe7a35a5d3e384 Author: fanhsu Date: Tue Jan 22 17:33:00 2008 +0000 Added HuGE link. commit a26bb778cfe7efd67fde60a69744c4dab9482928 Author: galt Date: Tue Jan 22 16:00:06 2008 +0000 "Encode release log update" commit 5f995341d145c86a9e594ed370bbad80962eb4aa Author: galt Date: Tue Jan 22 16:00:03 2008 +0000 "Release log update" commit 9d100428c279523dbb7e6e97f8a230a54417656f Author: angie Date: Tue Jan 22 06:57:06 2008 +0000 Adding a proper .as and .sql for this table used in snp125+. commit 6f02ffcc0e445c46c0f875e0051fd527799f9661 Author: angie Date: Tue Jan 22 06:55:30 2008 +0000 Corrected a field name, added index. commit 319673e8ccad13351851b845e129c1ac1eef4058 Author: angie Date: Tue Jan 22 06:54:40 2008 +0000 Added bin and indexes, tweaked a couple varchar sizes. commit a49db1fac8326845bdcf2ff01a54b564ab81d326 Author: angie Date: Tue Jan 22 06:50:49 2008 +0000 First cut. Note that the exceptions have changed quite a bit since snp127 and we no longer display locType. commit 7585f36eb1223c10686d4c127d359e8b294dfc82 Author: angie Date: Tue Jan 22 06:42:52 2008 +0000 Added note about axtAffine re-alignment shown on snp125+ details page. Flip refNCBI for - strand for versions 127 and later. Don't display locType for versions 128 and later. commit 75f56053840b0fdfae68c92434a9c6c2660b482e Author: angie Date: Tue Jan 22 06:38:52 2008 +0000 Completely changed how we deal with locType -- types 1-3 are pretty much ignored (redundant with chromEnd-chromStart) and types 4-6 are displayed as exceptions. (hgc.c no longer shows locType for snp128 and later.) Changed a lot of exceptions according to new treatment of locType, added some explanatory text / hints to inspect the alignment. Promoted missing observed to error. commit 61896feae17821f481da67269c6fc43d1583d7cc Author: markd Date: Tue Jan 22 00:32:04 2008 +0000 fixed typo in cmd line option commit 90bcfb4f355e6c7c988a0f9ee84965b242632a59 Author: markd Date: Mon Jan 21 16:34:32 2008 +0000 exclude .tmp files when rsyncing downloads commit 55be33be01c3cf6d43c07d1ace8236f5a799df83 Author: galt Date: Mon Jan 21 16:00:07 2008 +0000 "Encode release log update" commit c034b5621af11a633051e3a268286527c2a940c4 Author: galt Date: Mon Jan 21 16:00:05 2008 +0000 "Release log update" commit 2cdf1c4006a870fa5d8babc175351aeb64e308ca Author: markd Date: Mon Jan 21 06:34:23 2008 +0000 checked rsync params to avoid erros with perms commit d58009e85eaadc15bea8b3ce0412c34098e42775 Author: markd Date: Sun Jan 20 18:05:03 2008 +0000 move building download files to genbank server commit ed1465ba739a706d9696b265115e0dc1564fb180 Author: galt Date: Sun Jan 20 16:00:03 2008 +0000 "Encode release log update" commit df981cdafea39165ca84e5b91460d25cb12b2ff1 Author: galt Date: Sun Jan 20 16:00:02 2008 +0000 "Release log update" commit 394481c82fe1726a45beaf2728ea5c9c7e51383b Author: galt Date: Sun Jan 20 02:07:06 2008 +0000 first cut at replacement for sqltidy script for cleaning out old cart records in hgcentral commit e230f406cd7ea7832dd69206cc779b17830db0c5 Author: markd Date: Sat Jan 19 23:31:05 2008 +0000 fixed null ptr deference with -rebuildDerive on genomes with no MGC commit 1c2fc4edeac93bc2e77a5a5ddbe870864b94848c Author: markd Date: Sat Jan 19 23:11:56 2008 +0000 added -rebuildDerived option commit a2d4af0989af24fdeef5e0b20193e05bcc2f6677 Author: markd Date: Sat Jan 19 23:05:34 2008 +0000 decouple building of MGC track from mgc tracking database; build only based on data in genbank. Fix bug where genePred tracks not updated when annotation changes but sequence doesn't commit deaa6e06dd4b3270b223780669e0fc56ef07d004 Author: galt Date: Sat Jan 19 16:00:05 2008 +0000 "Encode release log update" commit 63e2913562a4960c27b452795e443380c8ae8e58 Author: galt Date: Sat Jan 19 16:00:03 2008 +0000 "Release log update" commit 295cd5bfb32e4b471f0f4545cd37e8e571b47a34 Author: aamp Date: Fri Jan 18 23:27:22 2008 +0000 Take out a problematic warning. commit 702e37754ead48c5e3c6f69dc28dedb3b36fe363 Author: kate Date: Fri Jan 18 20:53:04 2008 +0000 Update test files for expanded track info in PIF file which is passed to loader (tableType, trackName) commit 7a98c71315a51590c99e64d0019b6789510a340e Author: kate Date: Fri Jan 18 20:45:27 2008 +0000 1. Fix directory handling 2. Add more settings to load.ra (tableType, trackName) commit 17142daecf9cffa9cf993a52dda10300ac932432 Author: hiram Date: Fri Jan 18 18:44:22 2008 +0000 Rearrange Lamprey chain and nets to before Medaka commit 3b9077f3bb6f8b8467976847895d2eb57b07f472 Author: hiram Date: Fri Jan 18 18:32:45 2008 +0000 Set Lamprey priority just before Medaka commit 65eb21a0fe2aa401cbd3664430a4c4ffdffe3ce5 Author: hiram Date: Fri Jan 18 17:40:00 2008 +0000 Adding Lamprey chain and net definitions commit 83fd999bb6d5406a35c7246c2e1433f0b001191e Author: galt Date: Fri Jan 18 16:00:25 2008 +0000 "Encode release log update" commit e846acf74dbc5d92bfd303a65055e7b9aae6badd Author: galt Date: Fri Jan 18 16:00:24 2008 +0000 "Release log update" commit 894695408608a06f2cc725c0646a8b181a26247b Author: hiram Date: Thu Jan 17 23:30:08 2008 +0000 Adding petMar1 to the build commit 7e8b22a96096542ada28af350abbda49597fa945 Author: donnak Date: Thu Jan 17 23:06:38 2008 +0000 Removed section of MAF format description implying that it is a supported CT format. commit 3b7c979ae47b7ca7778c4c31b831d0b4cb724018 Author: hiram Date: Thu Jan 17 20:49:36 2008 +0000 Sequence masked, genbank initial done, blat server on, blastz runs started commit 150b7e3924900fb32333c46c74a8af5f14e1ae44 Author: hiram Date: Thu Jan 17 20:48:36 2008 +0000 Working on petMar1 blastz commit c60b2c86597bd0c1a11d9e81160082114a3c0247 Author: hiram Date: Thu Jan 17 20:48:20 2008 +0000 Working on the pushQ entries commit 224121ad41da94a9f693b4f3cfb99b3fa8192742 Author: hiram Date: Thu Jan 17 20:47:59 2008 +0000 Some WORKING status changed to DONE commit 70344c29e91d6ed4e256333e1cb3965d8d422a5a Author: galt Date: Thu Jan 17 16:00:09 2008 +0000 "Encode release log update" commit b87fd2bc003b95de1b6f31e8c72715924abc0c58 Author: galt Date: Thu Jan 17 16:00:04 2008 +0000 "Release log update" commit 9a939059fdab4938aaa8f5244140be0bca13f4a1 Author: ann Date: Thu Jan 17 00:17:51 2008 +0000 adding link to help pages for Fast Configure mode commit 0ba2ca1cc41b96da4a5c0ec1ac455f7688e0a74b Author: ann Date: Thu Jan 17 00:15:13 2008 +0000 correcting typo commit ab63d5cf63f2b9087ea2f75161975b513585d666 Author: ann Date: Thu Jan 17 00:01:40 2008 +0000 one small clarification commit 76ba158a69c60684d1eb2c3bbe7f6092658f118d Author: ann Date: Wed Jan 16 23:59:08 2008 +0000 added tag for FastConfigure section commit ea79c269697024c3add21df3424dac7bae87a23c Author: rhead Date: Wed Jan 16 21:52:12 2008 +0000 Added notes about fast configure mode. commit eb0524dbba63e1b33a4b0ec8994b27537d8974e7 Author: angie Date: Wed Jan 16 20:39:45 2008 +0000 Removed some unnecessary mem-cloning. It was really slowing things down with our new convention of 5-base windows. commit 276a28b767ecc9a402ed7916c462bb873a6563e5 Author: fanhsu Date: Wed Jan 16 20:37:30 2008 +0000 Updated an URL to GAD. commit e9c0f7e07e334872657f1bf7a263619373785b4d Author: fanhsu Date: Wed Jan 16 19:45:00 2008 +0000 Updated GAD re-build section. commit d2fc8bdbb0818c73fe4f755f93c91584de47024d Author: fanhsu Date: Wed Jan 16 19:36:44 2008 +0000 Updated gadPos logic to avoid a blind spot if a gene symbol shows up in refLink but turns out to be a non-human gene. commit 347ea9d3aa71c3c9f907e3803b22a08a6c1dd05f Author: galt Date: Wed Jan 16 16:00:06 2008 +0000 "Encode release log update" commit 6781db284b99bf63498f6a561236d790013def4c Author: galt Date: Wed Jan 16 16:00:04 2008 +0000 "Release log update" commit 150fcd9a666c179ce88dd4a14a6c5937f3e126ac Author: galt Date: Wed Jan 16 07:39:13 2008 +0000 check to see if cleanup required commit 8f5233bdcca4edf3c63f9a9a6cd74d7eeab32c33 Author: galt Date: Wed Jan 16 07:35:13 2008 +0000 fix minor bug commit 8e2024f54369cb47a81cf493dbd0e30450290f31 Author: galt Date: Wed Jan 16 03:07:26 2008 +0000 adding unloader commit f90f3da029a2dd9e50f03cd4be14ab6e99e6ad32 Author: angie Date: Tue Jan 15 23:55:20 2008 +0000 Updated broken web link (thx Brooke). commit cd597c410c64d53a957d8eacb71819261433f018 Author: galt Date: Tue Jan 15 21:32:42 2008 +0000 adding unloader commit 8aa5cdd935b9d93362bed9d235ada53de9911840 Author: galt Date: Tue Jan 15 21:19:48 2008 +0000 adding unloader commit c9dc2e129cae1bae5c2da55b3fe45ca4c4601192 Author: angie Date: Tue Jan 15 21:13:39 2008 +0000 Browser and Email links used non-encoded user names, which causes email link problem if username has a space (or other char that should be encoded). Now using encoded names for all links. commit 292b9c7f90a8496dd0d67f5dfef6aeef7641761f Author: hiram Date: Tue Jan 15 19:58:42 2008 +0000 Adding petMar1 Sea Lamprey commit ac86f010cecd39b1c80927ee42b4e1fbe6fcd508 Author: kate Date: Tue Jan 15 19:13:30 2008 +0000 Automated testing for ENCODE validator - small DNASE HS submission commit 07565449c10c88105c9e4fb4dce6deb3287a642f Author: kate Date: Tue Jan 15 19:11:26 2008 +0000 Metadata definition files commit 00866c97c3698ac35176606fff72e429630ec06e Author: kate Date: Tue Jan 15 19:10:33 2008 +0000 File that lists errors detected by validator commit b17fd497a1a67a6377754b1d436166c99db9c220 Author: kate Date: Tue Jan 15 19:10:05 2008 +0000 Fix problems with configurable output directory commit 84f4aea2a8dcf3b98f00ceab705a7d0bbfc25eb7 Author: kate Date: Tue Jan 15 18:54:06 2008 +0000 Add configuration options commit 9a2188afa6440b09bb34445b125519a4c2e252dc Author: rhead Date: Tue Jan 15 18:52:56 2008 +0000 Fixed typo. commit c19142a30599e68ac726a0a41bfeac92e1820dd0 Author: hiram Date: Tue Jan 15 18:04:46 2008 +0000 nice in the csh scripts causes problems when running from bash shell that was nice. Don't use nice in the csh scripts commit 09225b6a9b2817991f5e341f8d95501f91cfee9c Author: aamp Date: Tue Jan 15 17:56:51 2008 +0000 "New version number v174" commit de6c9bf3b6174d22daa7fa7391fca0ecbda2efb9 Author: ann Date: Tue Jan 15 17:54:41 2008 +0000 fixed citations and prettied up table commit 4d4ab1afa8ba60a3a6318f44637857d90658863b Author: fanhsu Date: Tue Jan 15 17:37:01 2008 +0000 Updated HuGE link of GAD details page again, according to GAD feedback. commit 987a14330c564452cba2a39b7249aa520aa15328 Author: galt Date: Tue Jan 15 16:00:15 2008 +0000 "Encode release log update" commit 7bfb8a581d4248ebceec1cf7d95849650e1c1997 Author: galt Date: Tue Jan 15 16:00:14 2008 +0000 "Release log update" commit 133425ca416df687b1f32d1e7af9a269c87479f1 Author: hiram Date: Tue Jan 15 01:04:41 2008 +0000 Running WindowMasker commit 5dc4cbb984d4f30dbd98e0f15dc2363185847a45 Author: angie Date: Tue Jan 15 00:26:54 2008 +0000 Bugfix (reported by Ginger Cheng): missing test for gotAgp in the last use of acat. commit 1a14de0132800e93924dac3adf3a4c224447a955 Author: ann Date: Tue Jan 15 00:13:53 2008 +0000 fixed broken link found by link check commit b730adb6350b97d7ac35d90c21c837def06a9827 Author: rhead Date: Tue Jan 15 00:03:42 2008 +0000 Added data version to ensGene blocks. commit 0c434db0a2e754b3d241c08fec9359e161752b3e Author: fanhsu Date: Mon Jan 14 23:55:44 2008 +0000 Updated HUGE link in GAD details page. commit 3a7fec35462b9e6875afe969984ed25e5277013e Author: hiram Date: Mon Jan 14 23:41:45 2008 +0000 Initial contents for new browser commit 2e62055d1ea2f1d6a1a1d76106a9d5f75c6331e4 Author: rhead Date: Mon Jan 14 23:09:34 2008 +0000 Added dataVersion to ensGene blocks; changed build to version to be consistent. commit dc0432847963f9670c4e4499126579490d852ba7 Author: rhead Date: Mon Jan 14 23:06:15 2008 +0000 Added a note to Ensembl Genes entry to indicate addition of a stable URL. commit fca1936ac8f8598b7f6677d49e0cf3fd7b0e1d8f Author: rhead Date: Mon Jan 14 22:59:15 2008 +0000 Changed build to version to be consistent with other entries. commit f4811e6441a58d238a30534b9f3680f00f2bcb7d Author: fanhsu Date: Mon Jan 14 22:36:41 2008 +0000 Updated gad track table by using "-nobin" option of hgLoadBed. commit 07d3b36a5ee9fe3da2076297a013674046acb97e Author: angie Date: Mon Jan 14 21:44:49 2008 +0000 Updated link (thx Brooke). commit 59ddc63ca3b4bc599161ee2b804b3340cf4dec0b Author: hiram Date: Mon Jan 14 21:21:34 2008 +0000 Sea Lamprey photograph from the EPA commit cebccc05ef0ac2a825972a1c57f76a10092244b5 Author: ann Date: Mon Jan 14 21:20:12 2008 +0000 moved Jakob Pedersen to bottom commit f76587f39cec97d3afe04092372d1a5075530c11 Author: ann Date: Mon Jan 14 21:13:12 2008 +0000 fixing broken links found by link check commit a5a8010441ae1ee3cac7a91515302e9cba826c16 Author: hiram Date: Mon Jan 14 19:58:49 2008 +0000 Starting Petromyzon marinus Sea Lamprey genome build commit 86cb015e46b3c77c120a5b21a6229097992b3703 Author: ann Date: Mon Jan 14 19:45:04 2008 +0000 fixed broken links found by link check commit f34c412b7ad175bc728014c42d10f2efd66082b5 Author: galt Date: Mon Jan 14 19:33:58 2008 +0000 change "validate" to "load" commit 12f8a3407b08d900f8674c91e318b32deac71297 Author: ann Date: Mon Jan 14 17:58:26 2008 +0000 fixed broken link found by link check commit b23c2fc61f791e271234f63b59a65241e7b3b912 Author: ann Date: Mon Jan 14 17:52:56 2008 +0000 fixed broken link to wustl commit f6e76ed651f08e21d421745a038d480f8ea53491 Author: markd Date: Mon Jan 14 17:38:35 2008 +0000 changed wording commit 96e31d51abebdfcb9c440c96aacb1258368a8bd8 Author: galt Date: Mon Jan 14 16:00:07 2008 +0000 "Encode release log update" commit 0dc6f65832e2aa36b4f7b22b58e048e98fd2cc90 Author: galt Date: Mon Jan 14 16:00:05 2008 +0000 "Release log update" commit 8256602eb408fa2698a030372ff5763c2900f7be Author: markd Date: Sun Jan 13 17:54:46 2008 +0000 fixed typo in time spec commit 11ef8d660fe01dfa68a00b817e08a360443833d0 Author: markd Date: Sun Jan 13 17:43:45 2008 +0000 change polling to every hour to cut down on the number of mail messages when EST load takes more than a day commit fa41a52d60701bdb645b96b9a3ec2ad0efc04747 Author: galt Date: Sun Jan 13 16:00:07 2008 +0000 "Encode release log update" commit f3a8360e7e748ef5832ddee23095767a3c10ef2d Author: galt Date: Sun Jan 13 16:00:05 2008 +0000 "Release log update" commit 21695c3382154c775e4d63cdcba615d7b0f415fc Author: galt Date: Sat Jan 12 20:27:24 2008 +0000 initial very simple loaders for wig and bed commit 028f475b2480df187fe58027da3e0c2d0b0c9fa2 Author: galt Date: Sat Jan 12 20:24:51 2008 +0000 removing user_id from encp data path commit cdce11d092b099996d0538684bb867c23896fc43 Author: galt Date: Sat Jan 12 20:14:40 2008 +0000 removing user_id from encp data path commit fd3059bbbd1e07ded70bc4221d2ff83ae27b6baf Author: galt Date: Sat Jan 12 19:55:01 2008 +0000 removing user_id from encp data path commit 1f0bee1ea5808856639c5e98d63ef0184fed9b29 Author: markd Date: Sat Jan 12 18:07:14 2008 +0000 reenabled rsync of table stats commit cfa03561c76f8e30021c9fa6f60296eeb3008a83 Author: galt Date: Sat Jan 12 16:00:07 2008 +0000 "Encode release log update" commit db2c65bd0d853c14da8d44df252cdd6dfe72554d Author: galt Date: Sat Jan 12 16:00:05 2008 +0000 "Release log update" commit 552f49731bd341787d5d786df0f4e9915fe5e2ea Author: angie Date: Sat Jan 12 00:41:54 2008 +0000 Regenerated hapmapAllelesChimp and hapmapAllelesSummary using corrected data for chr21, chrM, chrY and chrY_random (almost fixed in June '07 but not quite -- reported by user who correctly deduced that chrY items had hg18 coords). commit b9c3f28aa95154fcf9e721c9b75c6eb75aa5c593 Author: fanhsu Date: Sat Jan 12 00:29:14 2008 +0000 Re-built GAD track. commit 84be805f54a8e54c7f5447d318a144edfd393657 Author: rhead Date: Sat Jan 12 00:18:55 2008 +0000 Added correct ensGene build information, with lines to make links go to an Ensembl archive instead of the most recent build. commit e60b0e99d4df1d403d00409bc200a49681ed5ef9 Author: rhead Date: Sat Jan 12 00:12:36 2008 +0000 Removed a defunct block of text about Ensembl Genes (noted as TBD) that was replaced by Fan's actual entry (see LOAD ENSEMBL GENES (DONE 5/12/06, Fan)) commit c7f219ac8dd2b72889983aad63e1bed26149f16b Author: markd Date: Sat Jan 12 00:08:56 2008 +0000 added mess when NCBI Clone Validation is empty commit 8703161be632ef296fcd27e95b748d9ac470064f Author: markd Date: Fri Jan 11 23:59:32 2008 +0000 fixed null pointer reference when no CCDS, RefSeq, or UCSC genes overlap commit 4b52e8c700fbc9b0f3b06a7f1699b0aad0e0f27f Author: rhead Date: Fri Jan 11 22:18:28 2008 +0000 Added some comments and fixed a typo. commit c9c43ca92da1236aab3e968a7445de2650a92e97 Author: kayla Date: Fri Jan 11 20:19:51 2008 +0000 added ponAbe2 commit 6b94dba435f9d5e1096bbe3b6c02702323ee327d Author: hiram Date: Fri Jan 11 19:58:43 2008 +0000 Fixup the example search items commit 3caac9b84a7f9eed0cc54a75089033c43dcf40ce Author: kate Date: Fri Jan 11 19:55:15 2008 +0000 Expand error messages. Move logging to separate subdir commit 7e1236bc3122c8ad1a6a1bc97865bc4df1761a90 Author: hiram Date: Fri Jan 11 19:06:03 2008 +0000 Updated assembly details, and added ponAbe2 details to multiz description commit f27d0d60520ce5696ab36350660999abfc16de9e Author: rhead Date: Fri Jan 11 18:35:39 2008 +0000 Changed dataVersion to date, as build number was redundant (it's already in the longLabel). commit b775da1ca35e7aab8c1b3a04dc498ee8511191f6 Author: hiram Date: Fri Jan 11 17:55:19 2008 +0000 Done with the 9-way alignment. On to the downloads and PushQ release. commit 9224b4ac324379ba643409c2a8d5c753c3c15ffb Author: hartera Date: Fri Jan 11 16:03:42 2008 +0000 Changed dataVersion to date of Ensembl release. commit ca843da159cc249c412770f6ab7940a73e6e65dd Author: galt Date: Fri Jan 11 16:00:13 2008 +0000 "Encode release log update" commit c9b6e32f4f77c1722f4fb073b72c214b579e5730 Author: galt Date: Fri Jan 11 16:00:11 2008 +0000 "Release log update" commit 4092330a555d06f1450bb6c0cdfdf418b5896695 Author: giardine Date: Fri Jan 11 14:20:40 2008 +0000 Updated gvPos/Locus Variants/PhenCode commit 81660bbe0b83d34c96159c2dd9659fdb918561bb Author: giardine Date: Fri Jan 11 14:02:06 2008 +0000 Added new LSDB commit e0c95d1b09db9f6e7bbf6ffbfec881a7495f9168 Author: giardine Date: Fri Jan 11 14:00:46 2008 +0000 updated PAHdb link commit ed2d9903e573c5cce2f9a975298807535f73942d Author: angie Date: Fri Jan 11 02:27:55 2008 +0000 Added note about regeneration of hapmapAlleles* tables in June '07. Also a few tweaks for emacs coloring. commit 78165c9991ce72d9c3ac2ed4eb8efe7ad3862776 Author: kate Date: Fri Jan 11 00:54:34 2008 +0000 More error checking commit c7444285ea22d43fa19915533229736d2ce9ad8f Author: hiram Date: Thu Jan 10 23:59:28 2008 +0000 Adding text for description page to the Most Conserved track commit f36464c5daaaa9926098d1ac9ff5a12817cced99 Author: hiram Date: Thu Jan 10 23:57:38 2008 +0000 Turn on the phastCons wiggle data track commit e1a09ba846a0a9f23cbd6f3166999ce1b6702195 Author: donnak Date: Thu Jan 10 23:53:35 2008 +0000 Added news item re: job opening. commit ba5c2918cd321e83a860a0c1e11b7e484e93e456 Author: galt Date: Thu Jan 10 23:35:23 2008 +0000 made safer permissions commit 52ceac13db889f6fc970891bed63892326cbb0d6 Author: markd Date: Thu Jan 10 23:34:23 2008 +0000 improved word and formatting of mRNA/EST details commit f9fc5760bfb75b50809f18b9fc5bfe1513717a02 Author: galt Date: Thu Jan 10 22:50:51 2008 +0000 added some basic .ra processing commit 9ac61b50fc263afc24b793c061640e47e0d9325a Author: kate Date: Thu Jan 10 22:24:06 2008 +0000 Changes from code review commit 6f40c0151ae8adea2176f4d2641cbea6ac9dc040 Author: kate Date: Thu Jan 10 19:58:46 2008 +0000 Change default vis of Duke track within a the supertrack, by request of Terry Furey commit fae7b1d3056895001370458bee1e1bd58082004a Author: rhead Date: Thu Jan 10 19:00:10 2008 +0000 Added a block for ensGene in order to include information about data version and archive archive links. commit e16e9547c55810befb24f3bd6568ff8889b23675 Author: ann Date: Thu Jan 10 17:15:45 2008 +0000 corrected BLAT citation commit 9a048f49b93d333a389f76319912a3b57691c2a5 Author: galt Date: Thu Jan 10 16:00:06 2008 +0000 "Encode release log update" commit 97e3f57dcc6638a2d073aa4b59e393835393a701 Author: galt Date: Thu Jan 10 16:00:03 2008 +0000 "Release log update" commit 7f20bb2b51198f8dce2e97f7e2d0a00538c0cff9 Author: jzhu Date: Thu Jan 10 06:34:27 2008 +0000 add probeAliases table for broadAffyExp track commit 38fe7f8b19a4be27ecc12720b10590484dd0ee8d Author: galt Date: Thu Jan 10 03:07:39 2008 +0000 adding simple ruby loader that uses load.ra produced by the validator commit ed4bd32f8b1eb8d66118e217e44d1c7cd28aa4c2 Author: galt Date: Thu Jan 10 03:05:48 2008 +0000 adding functionality to call loader from new project_type fields commit ce9297b30ad040e39b1937ec2652a4b5c1f46d61 Author: kate Date: Thu Jan 10 01:04:33 2008 +0000 Fix spelling in Affy EC track labels commit 3a6e65bf41e112aac3b49c1010d8a7fabe5dfb3e Author: kuhn Date: Thu Jan 10 00:45:07 2008 +0000 added TARGET = _BLANK to offsite links, changed wording in several places and fixed some typos. Also changed some very long lines to 80-char per line for readablility commit ff77d3d5041fb44ef375bfcb8f88cf22cacae689 Author: kuhn Date: Thu Jan 10 00:43:47 2008 +0000 changed groups (a verb) to combines so it reads better commit feaf1bf581e60b3cf51d239e1b8ce56f3cbb24e1 Author: hiram Date: Wed Jan 9 23:09:28 2008 +0000 Do *not* remake the table when -oldTable and -sqlTable commit 5b3a37f1394db8a4e0f08e0d9892a05aa571db5c Author: hiram Date: Wed Jan 9 22:49:03 2008 +0000 Adding the single bac end RP23-473N24 commit 656f36f1efea50be9aa687ad03e2f0a6ce68dc26 Author: kate Date: Wed Jan 9 22:12:44 2008 +0000 Revise default viewing config for Affy EC signal, by request of Phil Kapranov commit 2e7f82bd1b410cb1696a2cf4c2fa3a7d807403d6 Author: ann Date: Wed Jan 9 18:56:03 2008 +0000 added speciesCodonDefault line to multiz28way track (it was missing) commit c6a3196c67b8a7ee0bd85b6f3c0911230194f4c1 Author: galt Date: Wed Jan 9 16:00:07 2008 +0000 "Encode release log update" commit 5fdfb8c00960039a348319eeadada250e4adbf18 Author: galt Date: Wed Jan 9 16:00:05 2008 +0000 "Release log update" commit c14e64df15ccf41d8ccab945fd2aa30039872153 Author: markd Date: Wed Jan 9 09:22:22 2008 +0000 Removed dependences of MGC display on mgcFullStatus and ccdsMgcMap tables in preperation for decoupling mgcGenes from MGC tracking database. commit c05e32ab2923fe6adef74b35eac5c31a127f02f4 Author: angie Date: Wed Jan 9 01:15:54 2008 +0000 Added more explanatory text in doIntersectMore -- hopefully the meanings of the various inputs and operations will be a bit more clear. commit e31497b209f6d65321a264dd131275d593144c79 Author: markd Date: Wed Jan 9 00:52:51 2008 +0000 added comment on how to improve similarity calculation commit a0f2fc683f58727ba2b3fdcbaa568f15ad93829a Author: ann Date: Wed Jan 9 00:17:44 2008 +0000 fixed so that it doesn't refer to three wiggles commit 3cc6e5b3f900901d997dbefaa9c0174b72378f36 Author: kate Date: Wed Jan 9 00:10:42 2008 +0000 Change viewing window for Duke Dnase by request of Terry Furey commit 6dca73fe9330b7436b92f52c9968543287ded115 Author: hiram Date: Wed Jan 9 00:08:01 2008 +0000 Turn on annotation frames on the 9-way alignment commit 82553a987418e25e7876a15cb8b08ef4555f99b7 Author: ann Date: Tue Jan 8 23:39:09 2008 +0000 removed reference to two wiggles commit 44c4336e80f07bed9b66ab0c7a287a5da4ac9dfe Author: ann Date: Tue Jan 8 23:18:28 2008 +0000 generic organism commit 68fb8829caa0fb8abe4bfcdfe19fb3e39634e640 Author: ann Date: Tue Jan 8 22:26:38 2008 +0000 re-correcting the link! commit 859f7dad8c03d7a6db6f8d2c2e2395e5810e70bf Author: ann Date: Tue Jan 8 22:19:50 2008 +0000 corrected link to tree commit 48b6053162c4fd611fa9fc61b382a747650ba33b Author: kuhn Date: Tue Jan 8 21:45:49 2008 +0000 removed dependency to /etc/init.d/bottleneck since jorge made it refer to dev now instead of RR commit 813e6817078ce3c779b27235f9feb81e5e72ac1b Author: angie Date: Tue Jan 8 20:11:09 2008 +0000 In getDecompressor, use gzip -dc where possible, to minimize the number of programs that must be installed. commit ed851fbc3e54ed92cfd5b33cc4958fb902cf3ea2 Author: angie Date: Tue Jan 8 20:09:59 2008 +0000 Improved warning message for upload of 0-length (or no) file. commit bb413342b1b731950638ebb7f320983f14aa9bde Author: ann Date: Tue Jan 8 20:07:36 2008 +0000 stubbed out a section (commented out) for explanation of Fast Configure mode commit 8c50bc65910d37e02d4140d7926f352b383ba83f Author: ann Date: Tue Jan 8 20:02:40 2008 +0000 added section explaining next/previous item/exon navigation commit 667f9fa4b9f6c71417030c3342516fa246fe19d0 Author: angie Date: Tue Jan 8 19:00:00 2008 +0000 Fixed cart variable name in ldDrawLeftLabels. commit 561b071aae3343ee8816eaca0d307ea40f1cc8df Author: fanhsu Date: Tue Jan 8 18:36:35 2008 +0000 Added hivVax003Vax004 commit a83d963b976224cfa9d7b67b3b6840f6b04da560 Author: galt Date: Tue Jan 8 16:00:07 2008 +0000 "Encode release log update" commit 94204b04f60c5f13233b0a10ad3b02ece844444c Author: galt Date: Tue Jan 8 16:00:04 2008 +0000 "Release log update" commit b9745515ee930b5e76ef2bb0bde14a56c89850d4 Author: markd Date: Tue Jan 8 05:40:32 2008 +0000 Fixed printing incorrect EST strand in certain cases. Clarify description of read direction. commit 7d7163cd2cce0ef20cda48ba2e5d70329bb20573 Author: hiram Date: Tue Jan 8 00:22:36 2008 +0000 Now have iRows on commit c3efc62fc95b01af96f3212aa283cf16f8ebfe84 Author: angie Date: Mon Jan 7 23:26:11 2008 +0000 Improved utilization of TYPE=FILE CGI vars for hgsLoadLocalFileName. Removed checking of file suffixes -- linefile.c looks at header bytes to determine type, and it now supports .zip too. commit 37fd393a39eb078af15bdf10ad98965461ba74b8 Author: angie Date: Mon Jan 7 23:24:00 2008 +0000 Added .zip (PK-zip) to the list of types we can decompress. commit 5fd1820c3113b981b0709c46031ae9b10e1498cd Author: hiram Date: Mon Jan 7 23:17:15 2008 +0000 Have worked through the first part of the annotation on the 9-way alignment commit 0e197519fa0b79de3eac41581ce351eed01b7ead Author: angie Date: Mon Jan 7 22:58:56 2008 +0000 Oops, referred to hui.h when cart.h is the correct file. commit a0e193f1c3c98c95f5afbf316a72e12995e82b87 Author: fanhsu Date: Mon Jan 7 22:10:01 2008 +0000 Added itemFirstCharCase description for wigMaf. commit 02a58bd0a4d60b48636ef156a290c68be7cc5801 Author: ann Date: Mon Jan 7 21:54:51 2008 +0000 adding ponAbe2 commit f26df0494adef1a516368ab0619266f550ce66f1 Author: rhead Date: Mon Jan 7 21:50:11 2008 +0000 Corrected links to vertebrate and mammalian tree models. commit a1e10730da5d5f3065a48b8d05c1a9cefd951dc3 Author: ann Date: Mon Jan 7 21:18:59 2008 +0000 changed default codon-translation species. ponAbe2 doesn't have any translation. (Kate and Hiram both agreed to this change). commit d71bc4e3ffaf87da8867ad6ae684cf304e7a1767 Author: angie Date: Mon Jan 7 21:07:47 2008 +0000 Added correct handling of compressed uploaded files (oops). Still need to fix linefile.c so that it handles all types from textOut and has a routine to check file extensions. commit 657421421ff0a19963805768309de2ca42aaeed1 Author: kuhn Date: Mon Jan 7 18:51:10 2008 +0000 removed assembly names from conservation image commit 8ce8b995bc710d5887fb62b0bdcb6a0dae21d2f5 Author: galt Date: Mon Jan 7 16:00:04 2008 +0000 "Encode release log update" commit 3c79d788b6e4ac4fc01f58f243f23e5da71e33ae Author: galt Date: Mon Jan 7 16:00:02 2008 +0000 "Release log update" commit cd88628dc2cb94c5c79804f9e391c923a0136eed Author: galt Date: Sun Jan 6 16:00:03 2008 +0000 "Encode release log update" commit 7fdaf4f2f09c704af76a8446feea8289240d2de7 Author: galt Date: Sun Jan 6 16:00:01 2008 +0000 "Release log update" commit 75b9f65f35578b4f7ba06d4344264c806eddef40 Author: galt Date: Sat Jan 5 16:00:09 2008 +0000 "Encode release log update" commit 5aaec5d081d3cefa91329a1e193e13608c93486a Author: galt Date: Sat Jan 5 16:00:08 2008 +0000 "Release log update" commit 1a7876b8d9521bcadeecd0767c58ed9f208582a3 Author: galt Date: Fri Jan 4 16:00:06 2008 +0000 "Encode release log update" commit ffe5c8ef9e55d509f8afcb4d97b119397a00408c Author: galt Date: Fri Jan 4 16:00:04 2008 +0000 "Release log update" commit 2dcfe1502f7f253abc3df2a359ecefa17c349011 Author: ann Date: Thu Jan 3 22:45:13 2008 +0000 edited SQL statement used to get HGNC mappings commit 6251da79991f5276481964f203b57c28d0b173ab Author: ann Date: Thu Jan 3 20:45:18 2008 +0000 updated pfam link for Pfam Domains to reflect changes on the Pfam website commit c5f2f7fda5bb20a23f8b63a6ea9a89e3560fd521 Author: hiram Date: Thu Jan 3 19:44:56 2008 +0000 add FILE priviledge to db privls to allow hgLoadPsl to function without -clientLoad option commit 795d2d3bed72773eba5af79b141222fee7935b20 Author: fanhsu Date: Thu Jan 3 17:28:54 2008 +0000 Changed hConnectTcga() to hConnectLocal. commit a08fcecb3b56c09919fd6f53b267f2516b0c634b Author: ann Date: Thu Jan 3 17:21:30 2008 +0000 fixed link to omim (it had changed on the NCBI site) commit 8cd902609877d4caf1953f72209a082b19293424 Author: galt Date: Thu Jan 3 16:00:06 2008 +0000 "Encode release log update" commit 869286634a89b87353fc614786eaf8196bbf9b3b Author: galt Date: Thu Jan 3 16:00:04 2008 +0000 "Release log update" commit 7992490396740f1f43629b2feec84b843c99ebf0 Author: kayla Date: Wed Jan 2 23:56:08 2008 +0000 added a period. commit ca3b14707bed0bb3b6b1f5de7fa528fea0b91893 Author: aamp Date: Wed Jan 2 20:07:34 2008 +0000 "New version number v173" commit 93946d62fbd01d036ad241ce27f5c75bd2abfd20 Author: donnak Date: Wed Jan 2 18:45:57 2008 +0000 Removed system downtime msg. commit 900785d42391027db7f40971e11c50519aaea2a4 Author: galt Date: Wed Jan 2 16:00:23 2008 +0000 "Encode release log update" commit fc5460b6b4b959ca788ecdaaebf7c317b4a50abb Author: galt Date: Wed Jan 2 16:00:21 2008 +0000 "Release log update" commit c8443d36bd305056b03613a41583ebcb9606b1be Author: markd Date: Tue Jan 1 17:53:27 2008 +0000 added one ignore entry, deleted older ones that are no longer needed commit fd6da64057b16ff57fafed30eb0f80725b59ee41 Author: galt Date: Tue Jan 1 16:00:03 2008 +0000 "Encode release log update" commit 394cd03cb598b72a54bb105cf9dec9a353b06259 Author: galt Date: Tue Jan 1 16:00:01 2008 +0000 "Release log update" commit cab7ccdc86dd2c8a7d07d7377dc4b368a7ea1ba5 Author: galt Date: Mon Dec 31 16:00:07 2007 +0000 "Encode release log update" commit 4bb31678998af01ba3d3568c4b23c2f6d58ac5f5 Author: galt Date: Mon Dec 31 16:00:04 2007 +0000 "Release log update" commit 3705653d5b40d7ad0f1e06d9fa9495ec0b4c74c4 Author: markd Date: Mon Dec 31 01:25:15 2007 +0000 disable rsync of table stats while hgnfs1 is degraded commit e6ce79e836824b8710333241a7e89e3d525ddac1 Author: galt Date: Sun Dec 30 16:00:03 2007 +0000 "Encode release log update" commit 326cc4fc7126c07a6d201829e149b2acafd576ce Author: galt Date: Sun Dec 30 16:00:02 2007 +0000 "Release log update" commit e87947c2c69c72a6660fdc9ac41a4c4f9a78a1c2 Author: donnak Date: Sat Dec 29 23:35:17 2007 +0000 Added notice abt ftp/rsync downtime. commit f1dadba0cb0339c8fa8a7401c3ee2f3bb0a708ed Author: galt Date: Sat Dec 29 16:00:40 2007 +0000 "Encode release log update" commit b45ea50b7b453b7bfe31155b35f4073078c5015b Author: galt Date: Sat Dec 29 16:00:23 2007 +0000 "Release log update" commit b89adea59d66a21264a5870faa537bea51d1c06b Author: kuhn Date: Sat Dec 29 00:21:11 2007 +0000 removed an errant line in usage statementcatchBot.csh commit e648036be298ec54b3bf7e8c8cafd77b8008ae28 Author: galt Date: Fri Dec 28 16:00:04 2007 +0000 "Encode release log update" commit 4074d9929abe6d40624ad7d3bb3849f73bb78486 Author: galt Date: Fri Dec 28 16:00:02 2007 +0000 "Release log update" commit 04825d00811ec875c1c2ce522ae3d5f396cc47aa Author: hiram Date: Thu Dec 27 22:01:31 2007 +0000 Making downloads for 8-way conservation track commit fd35b56288fee88f7fe5fe0b19c18d542bda4611 Author: hiram Date: Thu Dec 27 20:59:33 2007 +0000 Updated procedure for mafFrags use to make upstream maf files from multiple alignment table commit d2867e1d7e8192457dc4b48df981a92352fccc52 Author: hiram Date: Thu Dec 27 18:25:27 2007 +0000 Initial source for 9-way conservation. Taken from Orangutan 8-way commit 32183b380614814f17009aa4b013c7b9e802a709 Author: hiram Date: Thu Dec 27 18:13:44 2007 +0000 Adding the 9-way conservation definitions commit b4a771f716fa2d54b4b187a8bbb096036a766dbb Author: galt Date: Thu Dec 27 16:00:03 2007 +0000 "Encode release log update" commit aeb6254f84fa72a4db186e976c524e2584411b90 Author: galt Date: Thu Dec 27 16:00:01 2007 +0000 "Release log update" commit 6084705c7a3a17c7d0e5f925a12b6dc87cba0130 Author: kuhn Date: Thu Dec 27 03:17:50 2007 +0000 added notes about notifying hgnc when there's a new proteinsYYMMDD.hgnc table commit 819d0843d24dd93f946e083abd9376bdc98abdb2 Author: hiram Date: Thu Dec 27 00:17:09 2007 +0000 9-way diagram for Marmoset calJac1 commit 46b6668c4b81b232538d3269369d07ddd937e928 Author: markd Date: Wed Dec 26 16:22:35 2007 +0000 include /cluster/data and /cluster/bin in automounter hack commit 26c219ab8a6698f2a046e541e022cd35f6defc34 Author: galt Date: Wed Dec 26 16:00:04 2007 +0000 "Encode release log update" commit 855c556a4ac8a0029faf281ad8d50a1ae8082abe Author: galt Date: Wed Dec 26 16:00:02 2007 +0000 "Release log update" commit 13169cbf044159c8c949c480a862ce5f127b4c02 Author: galt Date: Tue Dec 25 16:00:03 2007 +0000 "Encode release log update" commit 5c276e4f225c30299eae0556b46d90f0baaf3852 Author: galt Date: Tue Dec 25 16:00:02 2007 +0000 "Release log update" commit ec55a908c8497bc86a149cd01f20f30f0256bb28 Author: markd Date: Tue Dec 25 05:32:52 2007 +0000 added hack to work around genbank server automounter problems commit 7105230e95ab67bf96efce4b1dd4b2957fd16eb2 Author: galt Date: Mon Dec 24 16:00:04 2007 +0000 "Encode release log update" commit 6a323aaddd7bc02fbd551ad9354ef3bf0438d829 Author: galt Date: Mon Dec 24 16:00:02 2007 +0000 "Release log update" commit 6c5dfc9a6fa9a16d9cdf7f6f69e4323ea4c0982f Author: galt Date: Sun Dec 23 16:00:06 2007 +0000 "Encode release log update" commit 18082bae77a16a357e88963e6715b92c1fc849b6 Author: galt Date: Sun Dec 23 16:00:04 2007 +0000 "Release log update" commit 4b9535b52482539685102636c216d4e898cb5463 Author: markd Date: Sat Dec 22 19:19:18 2007 +0000 adjust some paths for /scratch/ cleanup commit ef2699943044db267fdb52775605cda3a04f3b49 Author: galt Date: Sat Dec 22 16:00:07 2007 +0000 "Encode release log update" commit 155f576895de38964c53a841588bad56972b4bed Author: galt Date: Sat Dec 22 16:00:04 2007 +0000 "Release log update" commit deba25846d00ffbafa30181247e8c5d2bc3d7352 Author: galt Date: Sat Dec 22 02:12:55 2007 +0000 added support for background unzipping commit e7a2fdebd1f455080d9c1a6443162b062a4f46c7 Author: hiram Date: Sat Dec 22 00:45:04 2007 +0000 Beginning to run 9-way alignment commit 535f0039e43493d706d0e496e6123c31e3f6d546 Author: hiram Date: Fri Dec 21 22:32:47 2007 +0000 Ready to begin 9-way multiple alignment commit d82ce12fab9729c196c3388e993ad916db81dbb7 Author: hiram Date: Fri Dec 21 20:56:36 2007 +0000 Reworking the mafFrags upstream gene creation business commit 30644a4b45a6e1a6af6bb2dd68d70634284e6250 Author: kent Date: Fri Dec 21 18:56:07 2007 +0000 Generating fake data set for testing. commit faa97a2628ed496a296618c559f1d027470c1162 Author: kent Date: Fri Dec 21 18:55:35 2007 +0000 Adding experimental unified factor/source display. commit f3ad9114ebd1cf9a698e34136280833fab40800a Author: kent Date: Fri Dec 21 18:54:56 2007 +0000 Moved canPack set to a better place. commit 76a310daff190a5013bf26f6fed455522e8039ff Author: kent Date: Fri Dec 21 18:54:18 2007 +0000 Docing small fix. commit b277ebb389f5ffc6a18c68acac21f0be54c002a2 Author: galt Date: Fri Dec 21 17:43:24 2007 +0000 fix typo bug and increase timeout for unzip commit 0e9f4da69506c910c56b9d6fad4422368f6f92ad Author: galt Date: Fri Dec 21 16:00:06 2007 +0000 "Encode release log update" commit cef693aae237cd97fa02528c1fc13a1f3e41f448 Author: galt Date: Fri Dec 21 16:00:04 2007 +0000 "Release log update" commit 40ae4bfa1e37449dc060f6c8c1cda10ccf7f7322 Author: kayla Date: Fri Dec 21 00:02:29 2007 +0000 took out a broken link commit c668e3d2e57136d9e3f31c61463d34b75b961654 Author: hiram Date: Thu Dec 20 23:35:00 2007 +0000 Adding memk to the small kluster listings commit af454abade878dbe680da7fa0bfdf56b273e9b92 Author: hiram Date: Thu Dec 20 23:34:24 2007 +0000 Ran a blastz with galGal3 to verify changes to the doBlastz script commit 0bac451f87eb84a3611ccc8a70631adb191577b0 Author: aamp Date: Thu Dec 20 22:57:03 2007 +0000 Colors graphs by the same color as in hgGenome. commit 7ba7c482250b3fd0739b47a09c3b05f1495e846f Author: hiram Date: Thu Dec 20 20:08:00 2007 +0000 Added SGP and geneid tracks to these assemblies. geneid already exists on felCat3 commit 49f66af3d74dca6dcb184581b0ed35461d9f46e1 Author: kuhn Date: Thu Dec 20 18:53:40 2007 +0000 changed over to dbDbAch when looking for archived assemblies commit a4e0e6103a8244dcc09015be2b94c83f07244136 Author: kuhn Date: Thu Dec 20 18:39:42 2007 +0000 changed link to ExonPrimer to new url commit b9a191e0346e246acced45cf1541c3854a3d7839 Author: fanhsu Date: Thu Dec 20 18:34:47 2007 +0000 # ADD LINKS TO GENETESTS ON hgGene DETAILS PAGE (DONE 12/12/07 Fan) commit cccf44d28c19c921d924c3bcdc8f0bf354cff998 Author: ann Date: Thu Dec 20 18:28:11 2007 +0000 added geneTests table to ignore list commit a4b40e2f4af11f8f9746bded9a5131dbd64b4ce4 Author: galt Date: Thu Dec 20 16:00:05 2007 +0000 "Encode release log update" commit 64b249257492e9f713f79226a2afcb6a37f7d994 Author: galt Date: Thu Dec 20 16:00:04 2007 +0000 "Release log update" commit c66923832fa53a7f3f18fd5b55ddb24e4915c685 Author: galt Date: Thu Dec 20 01:54:28 2007 +0000 fix minor but, and fix create action to redirect to show which will be easier for beginners commit 3d88aac6e547ed8fb3b7047c2db76d4c5626e681 Author: galt Date: Thu Dec 20 01:52:46 2007 +0000 fix link commit db8631a9ab72cd64bdd6729e79aa7033412947c9 Author: markd Date: Thu Dec 20 01:23:53 2007 +0000 added new MGC status field to match database; simplified some code commit c51b6074bf87fe23941fcc7112245001512c0888 Author: fanhsu Date: Thu Dec 20 01:02:51 2007 +0000 Removed two commented out lines. commit 62180a76918e5683dcb4ca5b5dc857f889e1acb6 Author: fanhsu Date: Thu Dec 20 01:01:40 2007 +0000 Removed an exttra

tags. commit aa1a3d6fc75641506ea02b7ae21395953d03ce58 Author: kayla Date: Tue Jul 10 18:27:29 2007 +0000 edited wormbase link commit 462e5969064926e49e9dd6001f1295f36cb64ebc Author: kuhn Date: Tue Jul 10 16:15:41 2007 +0000 changed output to use genome-test instead of /usr/local path commit 378a4b1cf7d6d0fc2b063cc83f9cb496ce8759e5 Author: kuhn Date: Tue Jul 10 15:57:10 2007 +0000 added dollar sign to variable commit c6e7ccf7373072e356351c7b7cd11fe3e95c2bae Author: aamp Date: Tue Jul 10 15:24:56 2007 +0000 "New version number v163" commit 1e2ce212fd8e93d834d5c0797ad1fddd8ef3e44d Author: galt Date: Tue Jul 10 15:00:24 2007 +0000 "Encode release log update" commit d48ab748a42398f6fa5a33a84d0c64543cef8bab Author: galt Date: Tue Jul 10 15:00:13 2007 +0000 "Release log update" commit e15e071c937726ca98a96032a553a31c81308972 Author: hartera Date: Tue Jul 10 07:02:30 2007 +0000 Added back in code from revisions 1.1307,1.1309 and 1.1310 that was accidentally deleted. commit bcb942b3daecf4bb62d1753e4dc52bcb5d551af1 Author: galt Date: Tue Jul 10 02:21:22 2007 +0000 fixing minor stuff for consistency commit c899e9de3c193ae98fef46aacb25019e411888db Author: galt Date: Tue Jul 10 02:09:50 2007 +0000 fixed bug in stylesheet commit e9b523bff0901cefddf9c064f3439c34322d687c Author: angie Date: Tue Jul 10 00:58:25 2007 +0000 Added generation of nestedRepeats table. commit 1893e22d9dc0eff94a28cd3171eeb1a9be048f9b Author: angie Date: Tue Jul 10 00:57:18 2007 +0000 Use the ID colum of RepeatMasker .out to join fragments of repeats into BED 12+. commit b65937b8221e6ab40e2d3b29ede8760e328ef065 Author: angie Date: Tue Jul 10 00:54:13 2007 +0000 Track showing fragments of repeats joined by RepeatMasker id. commit 0804ba6059bc419201b141951a15afa995d504ad Author: rhead Date: Tue Jul 10 00:28:45 2007 +0000 Updated references. (Copied trackDb/xenoMrna.html) commit 75289dbf869136476150f42f45ece71c177f3bc8 Author: rhead Date: Tue Jul 10 00:22:44 2007 +0000 Updated references. (Copied trackDb/mrna.html) commit 051515e13207dfb283b45a64798dbe5ec14f6b6c Author: rhead Date: Tue Jul 10 00:21:16 2007 +0000 Updated references. (Copied trackDb/est.html) commit cb5e266d5a1422baaab0caf5f12f1884857583e3 Author: rhead Date: Tue Jul 10 00:19:20 2007 +0000 Updated references. (Copied trackDb/intronEst.html) commit 8a1891d3567bfef6ef3d10ecf1be4911f8207dab Author: rhead Date: Tue Jul 10 00:17:21 2007 +0000 Updated references. (Copied trackDb/refGene.html) commit b1b9ffb7acf4d46ff825200ad264865b0b49d2f9 Author: archanat Date: Mon Jul 9 23:21:38 2007 +0000 corrected a sample position query commit 449efbadfc283d200bfc9bf66b30c44b6a3d3add Author: angie Date: Mon Jul 9 22:34:01 2007 +0000 Fixed an over-stringent check from 1.28 that was causing inflexibility in handling the different field-signatures of refGene in old vs. new dbs. commit c9ff82c831c6898de69af6955938781f7c0c335a Author: archanat Date: Mon Jul 9 22:29:45 2007 +0000 changed a link on the dm3 gateway page that was pointing to the list of chromosomes on dm2 commit 5207f1a96470e0f068e53e71b7341d919171c946 Author: angie Date: Mon Jul 9 21:06:15 2007 +0000 Moved the installation of the liftOver chain file from the net step to the download step, so that a test run with -stop net doesn't overwrite anything that affects the browser. Thx to Archana for finding this. commit 4b7590eb4ba1b51e628ef6f8c3a934772cc1ebfc Author: kuhn Date: Mon Jul 9 18:51:48 2007 +0000 made utility to run static linkChecker automatically. thanks, archana commit f2eab2ce7ad071002112c725252869f94f5fbd11 Author: fanhsu Date: Mon Jul 9 18:51:33 2007 +0000 Isolated logic for GSID specific checking into a separate function as suggested by Mark. commit a0255959b2fc2b180e2d6e5a25cc76bd8dc85595 Author: heather Date: Mon Jul 9 18:48:19 2007 +0000 change lightgray to lightgrey for better display on IE commit b8f3d1220773ffa5662e22637ae227b4254cef81 Author: kuhn Date: Mon Jul 9 18:47:03 2007 +0000 added missing endif. thanks, archana commit e5392610e44afd88a951f258401fb25438a8aada Author: fanhsu Date: Mon Jul 9 18:04:32 2007 +0000 Updated fopen, fgets into lineFileOpen and lineFileNext. commit af2221e02ab298170cbd3ad8d490d41ed4e6efd4 Author: galt Date: Mon Jul 9 15:00:19 2007 +0000 "Encode release log update" commit a8a7046b80d0c51420ccbfc5b9d19f7d4b9485b1 Author: galt Date: Mon Jul 9 15:00:11 2007 +0000 "Release log update" commit 9f83fd8b615f0608c8f18d6a709db12a936e832a Author: galt Date: Sun Jul 8 15:00:18 2007 +0000 "Encode release log update" commit 25a02bdee164207c687993442612ae63f0707df3 Author: galt Date: Sun Jul 8 15:00:10 2007 +0000 "Release log update" commit 339638d7f3b2431a279623b18021031e473a3917 Author: markd Date: Sun Jul 8 06:53:54 2007 +0000 restrict peptide check from previous change to RefSeq commit d8fb7c85b20dce95f760d4d360de2374b74363e5 Author: markd Date: Sun Jul 8 06:07:46 2007 +0000 allow empty pep.fa for RefSeq ncRNAs commit 71ba02babc12ee41c83bb8e5f7ba2980dc5c0769 Author: galt Date: Sat Jul 7 15:00:25 2007 +0000 "Encode release log update" commit 4394163b8519a758538cc695e82f4d91aee09554 Author: galt Date: Sat Jul 7 15:00:13 2007 +0000 "Release log update" commit 7aa7bfe0fcfe56a73fd5fa475a9218df51646e2d Author: heather Date: Sat Jul 7 12:01:43 2007 +0000 improved what Dave provided based on my interpretation of recent Science paper commit d781c697a0ee25b4e32217a4796ac4de539774ef Author: kuhn Date: Fri Jul 6 23:25:30 2007 +0000 removed some unnecessary ordering in early processing and added headers to output. thanks, kayla commit b298a749eaea52abbfd22b14a119226d16d4421d Author: angie Date: Fri Jul 6 22:15:31 2007 +0000 Added diff-base coloring and indel display options to hgUserPsl (blat) track for dna/rna alignments. commit 1111d921331f69634d223ab3cb6c179ee37ac369 Author: archanat Date: Fri Jul 6 20:31:45 2007 +0000 added information about the phastCons parameters. commit ca9b94736fb00455e808cefe6facff03d18022ad Author: markd Date: Fri Jul 6 19:36:24 2007 +0000 fixed typos commit 790348a0e23afea6457b5b31ae21c454c3c88815 Author: archanat Date: Fri Jul 6 19:14:41 2007 +0000 removed release alpha from droAna2 chain/net block and also changed the short label for dp3 and droAna2. commit a2fb9b3f502b1eb59de985018f195ce554cfd1d1 Author: archanat Date: Fri Jul 6 18:39:33 2007 +0000 changed short label for droYak2 net/chain commit c854a87be5d84c69d4d6c68f38fe7493db9a74e6 Author: kate Date: Fri Jul 6 15:54:09 2007 +0000 Expand to return error status commit f3fabf8dac6085f5b7686ba26c6f397d92e321af Author: galt Date: Fri Jul 6 15:00:25 2007 +0000 "Encode release log update" commit 394d1b2255c1d50610ada714e547023bc8ede942 Author: galt Date: Fri Jul 6 15:00:14 2007 +0000 "Release log update" commit 0d4f9a7b8ec101b9f41c334edaa5ae6c1ab3e4f5 Author: angie Date: Fri Jul 6 00:18:34 2007 +0000 Added script target to install refreshSledgeHammer.pl. commit e5e4289543ef5680c6c11bc1b8e422f0a77ebf29 Author: kate Date: Thu Jul 5 23:11:47 2007 +0000 webIncludeFile() now issues warnings instead of error aborts commit 53791033154b78a9c532025cd4c81b22f9a16cec Author: donnak Date: Thu Jul 5 22:27:56 2007 +0000 Added dm3. commit efe1fbc00b28a9b382af07e9810c203ecbc68a76 Author: donnak Date: Thu Jul 5 22:25:31 2007 +0000 Added dm3 to release list. commit f6f7c287683b41e199bac369a932c358dca0a796 Author: archanat Date: Thu Jul 5 21:07:36 2007 +0000 abbreviated journal name commit b56ca250b5ebbc0794f7ee8f8cc4fc3cd93ad0b7 Author: kuhn Date: Thu Jul 5 17:57:28 2007 +0000 added comment about running makeTableDescriptions commit 759b80c00f05ea07b27a03c3c5ed41a0ac685547 Author: ann Date: Thu Jul 5 16:49:02 2007 +0000 trying to make the workings of the filters easier to understand commit 0fa5657d2dd929efe1b13d7ded0787ec39a4c81a Author: kate Date: Thu Jul 5 16:45:00 2007 +0000 Remove unused variable commit 4199ff025dba86fdc9debce0f9b19758273870eb Author: galt Date: Thu Jul 5 15:00:26 2007 +0000 "Encode release log update" commit 9d9022eb256c1b5443af35a64d999bb6ff9ccfdd Author: galt Date: Thu Jul 5 15:00:14 2007 +0000 "Release log update" commit 8891453ab960ab3f7209002d0236dd8d6ca834a2 Author: pchan Date: Thu Jul 5 06:40:11 2007 +0000 add ultraConserved track description to detail page commit d8a42862f835515343158e54fe062d6d72db5eaa Author: heather Date: Thu Jul 5 05:37:15 2007 +0000 add sanity check commit 3dc1dc5dcc89c5711df89fc92f5b4ba04508c25b Author: pchan Date: Thu Jul 5 05:33:40 2007 +0000 add function to display ultraConserved track detail page as multiz page commit 5b7ec0fb8effc80a043be4aa19e4b104df669846 Author: heather Date: Thu Jul 5 05:18:53 2007 +0000 adjust chimp qual scores commit 9f7f33132c1ea9b0591142ea26ba59a657e93bf7 Author: heather Date: Thu Jul 5 04:56:45 2007 +0000 include chr21 and chrY in ortho alleles (add comments, rearrange a bit) commit 515200eaa557f7f9c4f488badaa45f7767e47655 Author: angie Date: Wed Jul 4 22:20:00 2007 +0000 Added special pattern match for caePb databases, a legit exception to our aaaBbbN pattern. commit 57f7dd6244bdfd034861d6d0c4835773f0de45c9 Author: galt Date: Wed Jul 4 15:00:28 2007 +0000 "Encode release log update" commit bfc9d3b265e22b804cc0d6cfa4785c9ba6d0cfd2 Author: galt Date: Wed Jul 4 15:00:15 2007 +0000 "Release log update" commit ab9212bee7685cb1c8776ad0b09e0dc4f098dc16 Author: archanat Date: Tue Jul 3 22:55:21 2007 +0000 changed refs to pubmed format commit 53257e8396af3af4ca8892f86cfe0ee729034e6b Author: archanat Date: Tue Jul 3 22:44:47 2007 +0000 changed refs to pubmed format commit 6cd7e6512167190bfbe3533f785df69e47bd29b5 Author: angie Date: Tue Jul 3 21:53:18 2007 +0000 Oops, don't know how I managed to check in an empty file the first time. commit 655455d283b330b890ecf21602482410f8b7cdd4 Author: mario Date: Tue Jul 3 18:51:57 2007 +0000 Display details page of ab initio Augustus track. commit 10b8599f72b71748e9a7dec81cd077ad45f55bb9 Author: mario Date: Tue Jul 3 18:20:19 2007 +0000 documentation for Augustus track commit 3385a4f2e78827f80e89674633edeaa5039ed105 Author: ann Date: Tue Jul 3 17:28:26 2007 +0000 added link to Base Position track commit 5f0ff4fd366182222303fdab10d0fe679d1dbac3 Author: markd Date: Tue Jul 3 16:25:25 2007 +0000 more orfeome IMAGE ids commit 6922019a3ba3b1340b5b6d886d3a894b5aebe7d6 Author: galt Date: Tue Jul 3 15:00:25 2007 +0000 "Encode release log update" commit b02ed10a8009a3fe5db78501b6034a622b426f8d Author: galt Date: Tue Jul 3 15:00:14 2007 +0000 "Release log update" commit caf8fe6a280bef008012fac69e7d0fc86e3394c9 Author: angie Date: Tue Jul 3 04:48:51 2007 +0000 Wrapper script to parse live filenames out of the verbose=4 output of refreshNamedSessionCustomTracks, and force their access times to be updated using O_DIRECT which bypasses the cache. commit c1f3fd2e15a085568bcd6a17739a9432e28bbeb3 Author: angie Date: Tue Jul 3 04:46:07 2007 +0000 Added verbose-4 message showing filenames that do exist, for debugging and for a wrapper script (refreshSledgeHammer.pl) to force update of access times. commit 71d66c22640fa5554601d5b59fc801f0fd6afaa2 Author: aamp Date: Tue Jul 3 00:59:23 2007 +0000 Added option to make and load chromGraph using IDs from another table like snp125 or affy500k. commit 6044df46225bc73678551e6064b89aa7961242f8 Author: mhoechsm Date: Tue Jul 3 00:52:23 2007 +0000 file was added to hg/inc commit f7bfb26a558c4d9637c743c28b830fe7cf208588 Author: mhoechsm Date: Tue Jul 3 00:51:32 2007 +0000 *** empty log message *** commit ccef763d4833066941f8865796588d6e9069a716 Author: kayla Date: Tue Jul 3 00:12:19 2007 +0000 references section fixed. commit 1431ab8e9bb70a7cbd8c759e23a458c7032de22d Author: hartera Date: Mon Jul 2 23:48:00 2007 +0000 Added data versions for some subtracks for Yale Chip Signal and Sites tracks. commit 52a5aa405c1e2bb6e0b95a9139f808de7b18e5dd Author: mhoechsm Date: Mon Jul 2 23:39:02 2007 +0000 added rnaHybridization track files, only used in lowelab extensions commit 41955de05977e05095f37fa9835332ec1261f574 Author: ann Date: Mon Jul 2 23:32:10 2007 +0000 extending the hapmapSnpId rule from just hg17 to all hg assemblies commit 0a48e9e99c6c011582bd9dfea69c872ca3937ce2 Author: angie Date: Mon Jul 2 23:30:48 2007 +0000 Enhanced liftOut() to also 'lift' the ID column of RepeatMasker output -- make IDs unique per file, so they can be used globally to identify joinable fragments. Also, allow a /dev/null liftSpec if carryMissing, so we can use liftUp to lift only the IDs. commit e3a24089759d3683e609430d1568233e4028997c Author: hartera Date: Mon Jul 2 23:25:03 2007 +0000 corrected typo in subtrack table name. commit 03d3ecdc327cbef477cdaad7378b5b41d68e68a6 Author: mhoechsm Date: Mon Jul 2 23:18:00 2007 +0000 wikibme.sql is a copy of wiki.sql to support a seperate wiki track for bme commit 90d3ff505b4094e2fd745cfb718007f2ec45d339 Author: mhoechsm Date: Mon Jul 2 23:16:36 2007 +0000 - changes are embraced by LOWELAB ifdefs - added new track handler for rnaHybridization - support wikibme as a bme wide annotation system (lowelab.c). commit c331212975e8efd4c0d1eaa156a1457f2f6d95c8 Author: mhoechsm Date: Mon Jul 2 23:12:50 2007 +0000 - added wikibme support for wiki tracks - first version of rnaHybridization track commit f0fb5912e7e7bb0693c3ba2ef3ed00d53cc82962 Author: kuhn Date: Mon Jul 2 23:02:02 2007 +0000 italicized et al. commit 14d458c50b91968907688f25ac6e2c79a80f4af2 Author: donnak Date: Mon Jul 2 22:49:56 2007 +0000 Added a bit of info to the ftp downloads section. commit 262d95a9518821274d5f089ae0838087b9234347 Author: heather Date: Mon Jul 2 22:48:19 2007 +0000 use HREF commit 8b3f57d8a5441be2acebe08bf1cf7468eb22f10e Author: hartera Date: Mon Jul 2 22:32:55 2007 +0000 Adding ENCODE Yale Chip tables to the list of human tables to be ignored. commit 9597f00ab5155f93afe212a944d3da41e7778e7f Author: hartera Date: Mon Jul 2 22:27:39 2007 +0000 Added information about display of top 20 highest scoring items (set in trackDb) on the details page for the current window. commit 7829dae82bad0ae8c28761b6f61623c683e6799f Author: hartera Date: Mon Jul 2 22:24:34 2007 +0000 Added trackDb setting to list the top 20 top scoring items (after filterin) for the window on the details page for the ENCODE Yale Chip Sites track. commit e43582477c68680de02966b0ae65da2bfd38cb8f Author: hartera Date: Mon Jul 2 22:21:58 2007 +0000 Added getBedTopScorers() function to be used by genericBedClick() and doBed5FloatScore() so that the top N scoring items in the window can be listed on the details page. commit 7906e719cac98aa8ba915f1f6507c18a758255aa Author: ann Date: Mon Jul 2 22:16:53 2007 +0000 removed old nscan track, replaced with new commit 97b6140757aa47bd00ac1f13d8adc490d93f82cd Author: angie Date: Mon Jul 2 22:16:39 2007 +0000 Added default settings for SEQ*_LIMIT as suggested by Brian. They can still be set to 0 for no-limit, but the new defaults should help prevent horrible runtimes for scaffold-scaffold runs when the developer forgets to set limits. commit 51ba924d1bdb6ef3b39315cfcf8f47e765415b68 Author: ann Date: Mon Jul 2 22:14:10 2007 +0000 added nscanPasaName rule for new N-SCAN tables (okayed by markd commit 657876c29fa36f50aa81571bd3decd21184d3d53 Author: donnak Date: Mon Jul 2 22:07:49 2007 +0000 Changed a link in Example 4 to point to uninterpreted version of the HTML doc. commit 85d2fe13508b1a1bfe02511e689624572298463c Author: donnak Date: Mon Jul 2 22:07:02 2007 +0000 Created this file to show uninterpreted HTML for Example #4 in the CT doc. commit d4911080bc6df385db274422ec55c367f3cca022 Author: kuhn Date: Mon Jul 2 21:54:09 2007 +0000 fixed CAP-G in visiGene. thanks, archana. commit aead220cf66f42d659692901df5d4576aeb2ac8b Author: hartera Date: Mon Jul 2 21:53:06 2007 +0000 Added more details about the differences in the sites displayed for different datasets. commit 5a172a9c03aa8bc8828031ba8f1e41af4d511edf Author: ann Date: Mon Jul 2 21:35:08 2007 +0000 fix up citation formats commit ce5e15db256e97375c3d13a3e80da9580b829ffd Author: heather Date: Mon Jul 2 21:18:23 2007 +0000 speed improvement; use slAddHead and then reverse commit 5be969b259476fc1ec32445a3e38e29a23744884 Author: angie Date: Mon Jul 2 18:16:00 2007 +0000 Fixed off-by-one coord error in printBand so we don't display the next band when it begins just after the item. commit 61ad98e39b22a1a535eaf2e7529e33cd4967d092 Author: rhead Date: Mon Jul 2 17:48:32 2007 +0000 Removed a leftover html tag from the no-longer-existing Regulome Corp link. commit 010dca780402c805bc860c2538633e37fc3f09f1 Author: galt Date: Mon Jul 2 15:00:19 2007 +0000 "Encode release log update" commit 93e79c94de416c93a10675deb05cd39cd9d4be7c Author: galt Date: Mon Jul 2 15:00:11 2007 +0000 "Release log update" commit 42a30ffb380da9606027da884fbe3f53de5196bd Author: lowec Date: Mon Jul 2 02:13:54 2007 +0000 the blast output format changed in either 2.2.14 or 2.2.15, and the previous version of this file doesn't work anymore. I made two small hacks, which makes it work for me with tblastn 2.2.15 and 2.2.16, as well as the old format in 2.2.13. I have not tested it with things other than tblastn, but hopefully the hack will be a general fix. commit 349a4f720184381b175c47f922f8659b703b9292 Author: pchan Date: Mon Jul 2 01:30:45 2007 +0000 check genome existence in clade table before writing blastp hits to detail page commit 90a0831962581f67e1fb298a24280f9bad10ceec Author: markd Date: Sun Jul 1 21:18:33 2007 +0000 added -statsOutputBoth option commit 34f94a58461ea2708a10f247e4a965e239f538d1 Author: galt Date: Sun Jul 1 15:00:20 2007 +0000 "Encode release log update" commit fb1a4c3972cf1122f8f99f13da67c554510fb4c6 Author: galt Date: Sun Jul 1 15:00:11 2007 +0000 "Release log update" commit b80e3f311b8ed29a1fc4c9d6e09eed5bf23ddfa8 Author: hiram Date: Sun Jul 1 01:00:23 2007 +0000 Fixup all usages of column 9 when it may be itemRgb (all except one) commit dfcad296e956e970e3211323a26aeab580cb0fb6 Author: braney Date: Sun Jul 1 00:39:21 2007 +0000 add gap tree, not destined for RR commit a92c000783a66b6fbf7fcc1209ad39befb048c6a Author: galt Date: Sat Jun 30 15:00:25 2007 +0000 "Encode release log update" commit e738ca0328a400f55786d9548f2b4d45dcde6d7b Author: galt Date: Sat Jun 30 15:00:14 2007 +0000 "Release log update" commit 7867e7334f565306d6c9bf1e27f794eba3afc2bb Author: angie Date: Fri Jun 29 23:46:36 2007 +0000 Added flyBase{Roles,Phenotypes,Synonyms} sections with notes about the old data version. Added missing method section. commit ef9d6ec92d8feec5fc4bf800abda90c5e5668cf8 Author: braney Date: Fri Jun 29 20:08:17 2007 +0000 a utility to calculate a distance matrix from a gap file from mafGaps commit e022f944285136d8abfddc17b67bd2e85ab0da85 Author: giardine Date: Fri Jun 29 18:07:30 2007 +0000 Updating Locus Variants credits to reflect new additions. Separate file so that will not go to genome until push tables. commit 1a5d078a6f611c7c53c89f1f20613222bcc7b6b0 Author: giardine Date: Fri Jun 29 18:04:50 2007 +0000 Updated text for track with Donna Hendrix words commit 166593384c94ecf2bc77bea684cb9d9000a7a663 Author: kate Date: Fri Jun 29 17:43:34 2007 +0000 Add back collapse/expand all group buttons commit ba7fee7c16e1a4e88bc0e3a381c8b62dac74b47f Author: galt Date: Fri Jun 29 15:00:28 2007 +0000 "Encode release log update" commit 359399e35061291fc3f01333dfd30c0260440ba4 Author: galt Date: Fri Jun 29 15:00:15 2007 +0000 "Release log update" commit 7d8450565d5bb20436ce590f2a186a90c12fec4e Author: heather Date: Fri Jun 29 14:56:01 2007 +0000 add note about chrM commit 45a4b698ee26d550674f0df75030d4131a5aeb2a Author: giardine Date: Fri Jun 29 12:52:02 2007 +0000 Added new attribute for Locus Variants commit 26782208845967e3c447bbe9d12f405485b4410a Author: giardine Date: Fri Jun 29 12:49:32 2007 +0000 Added new links for Locus Variants track. commit 4e75eafa0fbcbdbcd236122dff279cb0a4dcbb6f Author: giardine Date: Fri Jun 29 12:48:04 2007 +0000 Added next item buttons to Locus Variants track. commit 04b1dd13ce13f983ca8d8913fe908dd986b859a7 Author: giardine Date: Fri Jun 29 12:41:38 2007 +0000 Adding new logos for the Locus Variants track. commit 0e65221bfc73b3e18dfc08772a60db073d17cc0b Author: kate Date: Fri Jun 29 01:23:04 2007 +0000 Update of Harvard conservation for TBA commit 311cfab819b53a28d32136c21beb9020d35113c2 Author: kate Date: Fri Jun 29 01:20:46 2007 +0000 Update of conservation from Harvard commit 7b47109af30b726d89f44788a3d9a00b0f3b5bbe Author: heather Date: Fri Jun 29 00:46:57 2007 +0000 finish genscan commit 773c759945fef314b9339eee72b3766a3d2b8939 Author: kate Date: Fri Jun 29 00:41:29 2007 +0000 Update commit 55278f19b955c9887b83cc3fd73a1d7d93839487 Author: archanat Date: Fri Jun 29 00:27:54 2007 +0000 changed refs to pubmed format commit 383635f7f14a61d91fd401e666fd6546af9aa5e2 Author: heather Date: Fri Jun 29 00:21:09 2007 +0000 Jing's edits to support parallel display of multiple datasets commit 06010b419839333d84e21168c1c656d54543a062 Author: archanat Date: Fri Jun 29 00:20:21 2007 +0000 changed refs to pubmed format commit edb024b2fa4209d67b93d9d0c7071cedd1b056e2 Author: hartera Date: Fri Jun 29 00:03:01 2007 +0000 Added the rest of the code to genericBedClick(), showBedTopScorers() and showBedTopScorersInWindow() to show the top scoring N items from the window if showTopScorers is set in trackDb. It also pre-filters the list if the filterTopScorers is set. commit 96d5eec3da1de5c42b9d6fb9a2f97841bb2a1aa5 Author: hartera Date: Thu Jun 28 23:44:06 2007 +0000 Added comment that the hits files with data for the Sites track should be sorted before running the loading script for the Sites data as the script uses the comm command that assumes files are sorted. commit d934534b151d9f3f6d4f28f7a70bc3803a6a634e Author: heather Date: Thu Jun 28 23:42:06 2007 +0000 written by John Archie commit b91e780fbc4b9242facdf49751186e2edd0eb882 Author: hiram Date: Thu Jun 28 23:03:23 2007 +0000 Now including deletion comments in the wiki text article to indicate the item was removed from the wiki track commit 3a50d9c55f5d6199dad16148fea4a62f3b20a63a Author: galt Date: Thu Jun 28 22:25:58 2007 +0000 oops, dont want these committed commit 87cf56d0b603d50fe19275cdd0e5a8f7c0cad0d1 Author: kuhn Date: Thu Jun 28 21:50:08 2007 +0000 added findLevel.csh to net.csh and added split-chrom support to findLevel.csh in chain.csh commit 775b2e1567264dedaa16b6b31ee52d1276095e42 Author: kuhn Date: Thu Jun 28 21:37:30 2007 +0000 added detection that script is running on dev, changed logic in check for trackDb link at user's root, added support for split tables. commit 290cd24aafbdde1228d042601a60a3f3661dc2c2 Author: kuhn Date: Thu Jun 28 21:33:14 2007 +0000 dropped debug statement commit 5bb712b246212f33c62e2f407a7e45479952546c Author: hiram Date: Thu Jun 28 20:28:27 2007 +0000 Quick hack to fix sts Markers display commit 4e12af2d078cfe23df2e45643d7e18985e2a22d9 Author: hiram Date: Thu Jun 28 19:35:53 2007 +0000 Now adding extra tag information to the signature line commit 7bcaf64be4aaa50aeb86a819faac7e56cd6f9b43 Author: hiram Date: Thu Jun 28 19:34:35 2007 +0000 Now properly adding all isoforms and proteins to the description initial comments commit 4c4b78c94e51ded0e1e808af6d1747d04078fb8b Author: kuhn Date: Thu Jun 28 18:40:07 2007 +0000 moved some search blocks down to be bottom yo preserve chronology of oldest last commit d6d446901fbf1d5e2b34492012054b4b9c16b737 Author: kuhn Date: Thu Jun 28 18:36:33 2007 +0000 moved some search blocks out of the track section commit 218aa64330b7eb16c7d66fab24f95c6d0e3b2460 Author: mario Date: Thu Jun 28 18:27:53 2007 +0000 Added a rule for augustusAbinitio track commit 4de9f7bb6fc757f00bb3d34239ee163b9f94b076 Author: hiram Date: Thu Jun 28 16:48:35 2007 +0000 Now adding description from knownGene tables to the wiki article commit 66231cb645d785efc973a270598be3e931e60cff Author: hiram Date: Thu Jun 28 16:47:06 2007 +0000 Now adding gene descriptions from the knownGene tables to the wiki article commit 79d01e3d26e0b9c2606ee52016ab923e3a04be78 Author: fanhsu Date: Thu Jun 28 16:35:00 2007 +0000 Created trackDb.ra for vax004 DB, to be refined. commit 4f26f60834181147a0a1d9219a5bca23115004e9 Author: fanhsu Date: Thu Jun 28 16:34:22 2007 +0000 Created a temp description page. TBD. commit 8b88ce40df72fc95740083099e9b9073d0fb9399 Author: galt Date: Thu Jun 28 15:00:31 2007 +0000 "Encode release log update" commit b26d3b726b2126900d0750b3c0a51df67c52a087 Author: galt Date: Thu Jun 28 15:00:17 2007 +0000 "Release log update" commit 22fb9cddf46c1a67ca209864b18ebab9ce7acea3 Author: kate Date: Thu Jun 28 00:42:10 2007 +0000 Add image size for +- buttons; Hiram says this may speed up the browser rendering (and also, allow scaling if we want) commit 06176652c18ef4bb951534fbfcbc8f125ab335d0 Author: kate Date: Thu Jun 28 00:39:45 2007 +0000 Remove collapse/expand buttons for now. Fix navigation of +- buttons commit 0323b93f8d0fd96704b4331fd92e6bd51e957e47 Author: heather Date: Thu Jun 28 00:08:56 2007 +0000 rn4 blastz, cpg islands, genscan commit eda6fd85b9ca65e4845f75c46eb571c4b0f079f1 Author: kate Date: Wed Jun 27 23:58:12 2007 +0000 Slightly subtler (reduce black borders) versions of small += buttons commit c93bda7fa93c0c5c3294884b650159ab76067ddd Author: kuhn Date: Wed Jun 27 23:25:57 2007 +0000 removed extra "else" commit 80c922ba3a846f3a7d5e3fcb5574cca2c297194c Author: ann Date: Wed Jun 27 23:14:58 2007 +0000 correcting the number of species in the placental-only alignment (thanks Brooke) commit 1047388f456e7daa548af5fc51b0b20d3f6505d7 Author: angie Date: Wed Jun 27 23:10:58 2007 +0000 Added DroSec1 to chainDest. commit 47e730fe4061ac39421debc45c64f103d3dc34b2 Author: kate Date: Wed Jun 27 23:08:16 2007 +0000 Improved cosmetics on +- buttons, thanks to B0b commit 5f516471c0aa181f72f7968bddfb11cef6620400 Author: hiram Date: Wed Jun 27 22:49:54 2007 +0000 Initial help comments for gene annotations commit f5bd9a07ee2c5b0f75541e27eb4116dc4b5da559 Author: ann Date: Wed Jun 27 22:29:23 2007 +0000 added release alpha to sub-tracks for new nscan composite track commit b6d53fae8df0315328ce4effb829659c517e8af1 Author: ann Date: Wed Jun 27 22:02:52 2007 +0000 added back in nscanGene track as release beta. Otherwise the description page for the new n-scan on hgwdev (which hasn't been QAd yet) would have leaked out commit 37ed98641c535fb97657c3931459f1b81a818650 Author: rhead Date: Wed Jun 27 21:52:04 2007 +0000 Added note about optional BED field order being binding, prompted by a user. commit 9ae9aca3aa406ff26e0f17c64b50c263aeb2ef9b Author: rhead Date: Wed Jun 27 21:45:15 2007 +0000 Added note about optional BED field order being binding, prompted by a user. commit 94006ca2ae5cac3870c2ae13ba24f0d8224ab354 Author: hiram Date: Wed Jun 27 21:38:54 2007 +0000 Force the wiki track to find the gene specified by using the hgg_chrom=none trick commit e31e2133a547f5b1454ddea1c2e4373a72ca03dd Author: markd Date: Wed Jun 27 21:35:55 2007 +0000 revived nscanGene description until composite track is pushed commit 6ea2d6a0b573a4a1fc51c78ec79139a972f8a377 Author: ann Date: Wed Jun 27 20:24:18 2007 +0000 fixed my own typo commit 2c1d06f4bdf83d3bf076a24292ea69a4841f3174 Author: fanhsu Date: Wed Jun 27 19:16:02 2007 +0000 Updated to avoid the problem if a kg has multiple duplicated records in knownToPfam. commit 5e703c646dd4380f7bed0080e45b34fc519ad2b4 Author: tingwang Date: Wed Jun 27 18:27:05 2007 +0000 change table names for UCDavis ChIP chip subtracks commit 48009946345e2d2c41844eee3cc8453ff0c09dc0 Author: fanhsu Date: Wed Jun 27 18:10:31 2007 +0000 Added def for gsidSeqList. commit 7fe12bafdfba7b544306b2a5aaba6235227fc0de Author: galt Date: Wed Jun 27 15:00:33 2007 +0000 "Encode release log update" commit 1e7d94a2a669da9af6d81c7ed87c7fd694f0a4ef Author: galt Date: Wed Jun 27 15:00:17 2007 +0000 "Release log update" commit abf0d08146a7c42c55b4bfbdbce76362b7422828 Author: kate Date: Tue Jun 26 23:51:24 2007 +0000 Change UI for track group collapse feature, based on input from JK and DK commit 61b623e073f63d780f1e3919e4c468b0b1eef9aa Author: kate Date: Tue Jun 26 23:42:44 2007 +0000 Replace with actual small (17x17) gif commit c689dc410a9b1bbd7b6ba2c90c2e1dd623f43761 Author: angie Date: Tue Jun 26 23:10:11 2007 +0000 Fixed some looping logic in chainDraw -- when looking for a lastSf off the right side of the window, it was sometimes failing to update lastSf, so it wouldn't realize it had found it, and would insert a fake sf just off the right side. That led to double-lines where there should have been single-lines -- found by comparison with GBrowse chain plugin. commit 1be0f23d2c6bee48bbd23752faa08e87aa91f671 Author: donnak Date: Tue Jun 26 23:05:06 2007 +0000 Added article abt 28-way conservation track. commit f42dbb51b6dd5b1b14d99a0687c27923120363f5 Author: hiram Date: Tue Jun 26 23:01:56 2007 +0000 Now creating multiple entries when a gene symbol is clustered elsewhere in multiple locations commit cab12b44e1ecf53c196cec465d08b01e7955d4fc Author: hiram Date: Tue Jun 26 23:00:55 2007 +0000 Show multiple locations when the same gene symbol is found elsewhere commit 5e9a3809e39b9a0935d42916fb1b5b918c19b5f1 Author: hiram Date: Tue Jun 26 23:00:13 2007 +0000 Working on hgGene multiple entries commit befc7cc972e2b537df2cf98a494562cbed5f74f1 Author: donnak Date: Tue Jun 26 22:05:33 2007 +0000 Archived an item. commit a349ca04bb73ca27e31d074300411ed6ea27a264 Author: angie Date: Tue Jun 26 22:04:33 2007 +0000 In constrainFreeForm, allow comma so we can support queries like "where field in ('val1','val2')". commit dcedba64e6bc92f4a3a2c53cfd1fb0501c32063c Author: kuhn Date: Tue Jun 26 21:29:53 2007 +0000 utility for quick grab of orderKeys from all levels commit 63f233d5d0b59f1c49ee04405479a9bb9d757244 Author: fanhsu Date: Tue Jun 26 21:06:53 2007 +0000 Added vax004. commit af86607b3ff3960ef4c948830244cd84fb1f2b80 Author: donnak Date: Tue Jun 26 20:24:55 2007 +0000 Created this file to try to fix problem with rn1 gateway page on hgarchive -- is displaying the wrong text. commit c2f5d053c74fca77bdbf7782ea5f6e3d023b5c8d Author: angie Date: Tue Jun 26 19:38:14 2007 +0000 Fixed hash collision leading to spurious warnings in findCookieData, and clarified some variable names. commit 4df7317a4d33ed4052d2f326a8a23d2e955551ca Author: donnak Date: Tue Jun 26 18:30:56 2007 +0000 Added updated Credits section, per Kate. commit a6a6a00974b58e4601cd43783bed37f870a2cde4 Author: braney Date: Tue Jun 26 18:29:19 2007 +0000 add a link to an image of the atom tree commit 0d1c1aceb11f42bfecc7a464c0931235f8f1648a Author: aamp Date: Tue Jun 26 18:05:42 2007 +0000 "New version number v162" commit 3c4b832747cd6f06c565881147359b4a99665f02 Author: galt Date: Tue Jun 26 15:00:29 2007 +0000 "Encode release log update" commit 927edbb94d6441998a369f47aa2a18465fcfec8a Author: galt Date: Tue Jun 26 15:00:16 2007 +0000 "Release log update" commit a2b3d869969b40041020b2269ed0b9b094f23507 Author: kate Date: Tue Jun 26 06:02:17 2007 +0000 Support for collapsing track groups on configure page and hgTracks commit 4a451c89033e8592580eb2e9031f63c0608fd209 Author: angie Date: Tue Jun 26 05:56:09 2007 +0000 Added flyBaseGeneSymbolOneLetter as an exception to the rule of skipping searches on single-character strings. commit 427a0cb0a7820ed9252089d4a08e72c14c4fcec7 Author: angie Date: Tue Jun 26 05:54:37 2007 +0000 Added flyBaseGeneSymbolOneLetter for exact match of single-character gene names. commit 1e33d81170ca5572e68315e6214ca2da0f8f04c7 Author: hartera Date: Tue Jun 26 03:07:58 2007 +0000 For the release beta version of encodeYaleChipSites, removed the url and urlLabel from the trakc entry and added it to each of the subtracks entries. This is because the release alpha version uses the release beta parent track and so it will set the url even though it is not set on the parent track for the release alpha version. commit ca9ffad51029f670bce4658604975deac5f2eda8 Author: braney Date: Tue Jun 26 00:56:18 2007 +0000 update to new atom tracks (didn't I already do this?) commit 6c9edddc371f198e647ce7b5b608f35f497ba5c0 Author: kate Date: Tue Jun 26 00:38:11 2007 +0000 Companion image for the -, from Mark D. commit f5ec7b22a20757d522f81b5b1d0bfdc139abd748 Author: hiram Date: Tue Jun 26 00:25:08 2007 +0000 Add CFG_WIKI_EDITORS commit 020ad557655d96fac7f5adf9736f2aee0947402f Author: hiram Date: Tue Jun 26 00:24:11 2007 +0000 Fixup Yale DART link for the Yale TARs that don't have them commit 5fc42f6b2d562ef7a2529c3d2ab58066e51dcf2a Author: hiram Date: Tue Jun 26 00:23:06 2007 +0000 Added site number to encodeYaleAffyHELAS3 PolyA RNA and Total RNA TARS.bed commit d830d9d942a225249ae9710394af3a7308e284bb Author: hartera Date: Tue Jun 26 00:19:08 2007 +0000 Fixed typo on table type. commit 343a2f4ed9b58ce1f5c8a8d18c17931085968f88 Author: hartera Date: Tue Jun 26 00:17:59 2007 +0000 Added code to use bedMethods for bed5FloatScoreWithFdr tables used for ENCODE Yale Chip Sites data. commit e883d038ca3610285467627bafd9979b4cae9f3f Author: hartera Date: Tue Jun 26 00:16:44 2007 +0000 Added code to use doBed5FloatScore() for the bed5FloatScoreWithFdr table used for ENCODE Yale Chip Sites data. Code in the function prints the false discovery rate on the details pages if this data is present. commit 14f2769f676e1a80ed5163e4b0416f6a6b9f06d8 Author: kayla Date: Tue Jun 26 00:00:39 2007 +0000 fixed a typo. commit 4a488f424f30a10c33816aa26734fdd36916d8a3 Author: hartera Date: Mon Jun 25 23:58:42 2007 +0000 Loaded Yale Chip Sites data from Nov 2006, Jan 2007, Apr 2007 and Jun 2007 batches. commit c093a5159542e6e4c872c4252f9a211f9c8a620e Author: hiram Date: Mon Jun 25 23:53:35 2007 +0000 Allow hg.conf editor list to enable deletion rights for those listed commit f84c05ccbbda0f56741673bcc75703f432e5d12d Author: hartera Date: Mon Jun 25 23:28:03 2007 +0000 Changed description to be more appropriate for this track. Added display and configuration description. commit 3cbea818a8f28e15c1952cbf2257f232de35fa6c Author: hartera Date: Mon Jun 25 23:25:59 2007 +0000 Added configuration and display information. commit 4a72f3faab3de102d33e0e1ce08d7fb2dc2b8ef0 Author: hartera Date: Mon Jun 25 23:09:45 2007 +0000 Removed duplicates lines and made edit to Yale Chip Sites track. commit 9577465b291fb5cc49c1743166a4b09af77d9d49 Author: hiram Date: Mon Jun 25 23:08:08 2007 +0000 Proper label on the geneSymbol commit 0c50e5a77bc85cab722cd04a5e3d907e2e876d24 Author: hiram Date: Mon Jun 25 23:07:28 2007 +0000 Ready to start clustering the geneSymbol annotations commit b8c5dac570d70e20777b178321bf1d6993fe6c3a Author: angie Date: Mon Jun 25 23:05:05 2007 +0000 Use liftUp instead of cat so that ID numbers are also lifted. Also, liftUp expects header so don't strip it before lifting. commit d03344f017b26bacaa92f7e63ed60e46fd1d32d4 Author: hartera Date: Mon Jun 25 23:02:33 2007 +0000 Cleanup of Twinscan files. commit a57912728f44877cf6480f66ba4595d6411faceb Author: hartera Date: Mon Jun 25 22:57:30 2007 +0000 Cleanup of danRer2 Blastz files. commit 2c38e6f4207f7078cb8378d636536f08ff5692b5 Author: hartera Date: Mon Jun 25 22:42:59 2007 +0000 Cleanup of Acembly files and danRer2 Blastz files. commit 6c826d04365fb401ced24d95f54673a5ef7ccb9d Author: kayla Date: Mon Jun 25 22:27:51 2007 +0000 added dm3 commit 8ffb23bde9a6aa95d18ab365bda9d4f6699b7d02 Author: hartera Date: Mon Jun 25 22:01:03 2007 +0000 Cleanup of cb1 Blastz on ce2. commit 3f0e19755104bf3738118f44944d85bd3c98ee00 Author: hartera Date: Mon Jun 25 21:34:14 2007 +0000 Cleanup of ce2 BLASTZ directory. commit 31ae067b2219e20df5698c84a253d29befb8a4bf Author: angie Date: Mon Jun 25 21:33:04 2007 +0000 Typo fix in bigZips/README.txt. commit f8987f418afb599fea8d6d5ae33ebf575df9f543 Author: hartera Date: Mon Jun 25 21:12:47 2007 +0000 Cleaning up danRer1 Blastz for hg17. commit 1431b33437e863a69b94b4447299dcf32ecad240 Author: fanhsu Date: Mon Jun 25 18:10:21 2007 +0000 Created gsidGetConsensus.c to get consensus sequence from MSA result. commit 6f587ad9e5bac272fa1a4c0f6267c0220220adfd Author: fanhsu Date: Mon Jun 25 18:09:43 2007 +0000 Created makefile. commit 43ad9811fe90b1b385105e2c85011fc5d66af74b Author: pchan Date: Mon Jun 25 17:51:37 2007 +0000 add function for lowelabArkinOperon track detail page commit 81035ead748bf8628ff1501e30bf74fed76d14f5 Author: braney Date: Mon Jun 25 16:51:13 2007 +0000 fix some bugs commit 45169e1e636f21d782287c7daf918b9560cc2b6a Author: ann Date: Mon Jun 25 16:49:53 2007 +0000 added colon commit aeb2eed630d9bf451197deffd6e3d37cf5fb3bda Author: hiram Date: Mon Jun 25 16:39:45 2007 +0000 Change alignID to geneSymbol commit 56fe5a41f5a78281da44f2265ac1bb8274213eb0 Author: ann Date: Mon Jun 25 16:29:58 2007 +0000 added colon commit e3873f6064bcbdd371e9a62d49e256b953bacdb6 Author: galt Date: Mon Jun 25 15:00:27 2007 +0000 "Encode release log update" commit 1dfe7f53a90912657cf2c62e071a160e1cc621e7 Author: galt Date: Mon Jun 25 15:00:15 2007 +0000 "Release log update" commit 99258d42531b1cd8bd36e564d5e285682095d33c Author: aamp Date: Mon Jun 25 12:20:52 2007 +0000 Added switchDbTss find spec. commit e7432bc73708f2b745559d0edb3b994c8e2a4c1c Author: pchan Date: Mon Jun 25 09:32:34 2007 +0000 add lowelabArkinOperonScore commit 08046d4e22b0934eff660d4cc413e32c2c891ee4 Author: pchan Date: Mon Jun 25 09:11:49 2007 +0000 created for lowelabArkinOperons track commit fc73153042948d72ddbc0f0949e884577a9b31d1 Author: markd Date: Mon Jun 25 06:16:25 2007 +0000 handle more file compression extensions commit b12f443e821a6960ddb811934ceb1cbb678a2441 Author: kate Date: Mon Jun 25 05:33:27 2007 +0000 Slightly smaller '-' button for collapsing track group commit 5379dca08664a7b17869993798612ec52f9d0f99 Author: hartera Date: Mon Jun 25 03:00:58 2007 +0000 Removed dataVersion for the track entries for Yale Chip Pval and Signal tracks. The data versions are already on the subtracks. For the Yale Chip Sites track, changed HeLa to HeLa S3, added subgroups for cells and antibody targets, added new subtracks for Nov 2006, Jan 2007 and Jun 2007 data. For Sites track, removed the url and urlLabel from the track definition and added only to the original 5 subtracks for which there are entries in the DART database. Added filterTopScorers trackDb setting to allow the use of a scoreUi which allows the user to specify the top N scoring items only to be displayed for all subtracks. commit e14cf9bf4fa98a7a8816344157a5cfcc88cf3d1f Author: galt Date: Sun Jun 24 15:00:26 2007 +0000 "Encode release log update" commit 542b8e646c45f69c4f2cad5af378f1520b66d3de Author: galt Date: Sun Jun 24 15:00:14 2007 +0000 "Release log update" commit 241041114b53dc1656bd2b39e7b973a729d0f475 Author: heather Date: Sun Jun 24 12:56:53 2007 +0000 add check for table existence commit af4706dfc273ac1e2df810cc0dc1a49800ec83c9 Author: hartera Date: Sun Jun 24 02:07:54 2007 +0000 Description for encodeYaleChipSignal containing the updated description for the Nov 2006, Jan 2007, and Jun 2007 data. Added a table of the antibodies, target descriptions and GEO accessions for data. commit 30a4cf1288bf601ceb6b0faab4842a17979dd530 Author: hartera Date: Sun Jun 24 02:05:41 2007 +0000 Edited target descriptions. Added GEO accessions for each subtrack's data to the table. Added that there are three or four biological replicates. Other minor edits. commit 7c49da05f7b8f70d1597d635373acc8e0b5d39c9 Author: galt Date: Sat Jun 23 15:00:31 2007 +0000 "Encode release log update" commit 582503bcf8007c93c52a270b84b29da8c15adfce Author: galt Date: Sat Jun 23 15:00:16 2007 +0000 "Release log update" commit d83469389f1ecdd6c15ea1e28b0c5842a1121ae7 Author: braney Date: Sat Jun 23 02:38:24 2007 +0000 upgrade to new atom tables commit d7b43f90be98aed16caf452deb8d420c34ac3380 Author: braney Date: Sat Jun 23 02:37:22 2007 +0000 update to new atom tables commit 1ce9df418f4e7ed65ea5bc446f998895b619b955 Author: braney Date: Sat Jun 23 02:36:56 2007 +0000 fix up the printing out of atom alignments commit ef083c2a23acb0862ba19852ced443a611619322 Author: pchan Date: Sat Jun 23 00:00:40 2007 +0000 Check if database exists before retrieving gene location and product for blastp hits commit c578571a72c3848d851d742eb1183043aa483e33 Author: kayla Date: Fri Jun 22 23:54:03 2007 +0000 added a link to the Session tool. commit fe9451a220097ea27fea96cc5b0118fb3c299c5d Author: kate Date: Fri Jun 22 23:50:15 2007 +0000 SCONE conservation data update from Harvard commit a2598686c8c62c931224c5e15f96d8e4affaf2ec Author: kate Date: Fri Jun 22 23:46:44 2007 +0000 Data update from Harvard commit ed3763d28d585d416a293d8ebb0feeb4985899c5 Author: hiram Date: Fri Jun 22 23:04:42 2007 +0000 Begin to print out the geneSymbol in some places commit 3f1169aaae81e727937471a80a0671870d914589 Author: hiram Date: Fri Jun 22 23:04:12 2007 +0000 Do not allow deletion for gene annotations commit aa30883bac19f97e5e72cf798e913f9f238dd9fd Author: kayla Date: Fri Jun 22 22:36:31 2007 +0000 Added note about using a session instead of an hgsid when submitting a question to the MLQ. commit 6fc2f1537a9d092d1eca549cb4d0fb3c99d351c8 Author: markd Date: Fri Jun 22 22:15:39 2007 +0000 do cvs update before installing commit 05a53302fca5757e15a49f72b406ed3283848b39 Author: ann Date: Fri Jun 22 21:58:41 2007 +0000 added kgColor table to knownGeneId rule commit f7f439f99417e359fd4be9e39685fedfe8a08137 Author: pchan Date: Fri Jun 22 20:39:19 2007 +0000 remove hardcoded archdev url from blastp detail page commit 0a6da4d8b6309c48babc2dde6c83f1be9d1fc5f1 Author: angie Date: Fri Jun 22 20:28:40 2007 +0000 Added escape for SQL wild character _ to splitPrefix. commit 135f75a2b24be8e0584f19139272811814f6054c Author: braney Date: Fri Jun 22 20:23:00 2007 +0000 add seventh and eigth bits for dups commit 67a78133a1f2014d60236448c3fc2ffdee76a25d Author: rhead Date: Fri Jun 22 19:40:48 2007 +0000 Fixed broken link to Claes Wadelius lab. The link specific to Claes Wadelius is under construction and in German, so the new link just goes to the home page. commit dc45e30a08f3676f9b3e68dab04cf58747c655b7 Author: galt Date: Fri Jun 22 19:30:28 2007 +0000 making output be consistent between viewing and blatsearch with minMatchShown (fixes symptom where alignments scoring between 16 and 20 would be visible in hgTracks and hgc but not in hgBlat itself commit 71512875a562d040c4211feb1a8c605d1655b76a Author: giardine Date: Fri Jun 22 19:00:23 2007 +0000 Added logo for new database. commit 882abcd805dde776c40e199ba46a00ff891d2915 Author: hiram Date: Fri Jun 22 18:52:34 2007 +0000 Remove mistaken
tags. commit cf11f9cf77ac845f8c0377e245d1777c290d93e9 Author: hiram Date: Fri Jun 22 18:51:40 2007 +0000 Move encodedReturnUrl() to library, now using emailVerified() and remove mistaken
tags commit 9b389b6a8429a1c3136b671d40eb1b8c6da0586d Author: hiram Date: Fri Jun 22 18:50:02 2007 +0000 moved emailVerified() to library, cleaned up the mistaken
tags. commit 41e2a20c6de2aec76fa4c9451b93be3be9cc6c9c Author: hiram Date: Fri Jun 22 18:48:05 2007 +0000 Cleaning up experiments commit 13f89d3cd2233db9d88abbc05df9cb3a45933f3c Author: hiram Date: Fri Jun 22 18:47:35 2007 +0000 encodeReturnUrl() and emailVerified() functions move to library from hgc and hgGene copies commit 43be7ecbc61d33ce45b0b7ac90623228672bb025 Author: ann Date: Fri Jun 22 18:45:59 2007 +0000 changing Table 1 from phylo order to alpha order (per Donnas suggestion). commit 5af8997b7ad359a56f19679149c8da4075d82e5a Author: braney Date: Fri Jun 22 18:18:35 2007 +0000 add eighth line to atom display which is whether dup is present in this species commit f77efb210f050e8c985e48358c4f5a9e32566a69 Author: braney Date: Fri Jun 22 18:17:32 2007 +0000 take static off mafPrettyOut so I can use it hgc.c commit e0b4ea6ae3be397a264dc7ba697dea255ec8ed2f Author: braney Date: Fri Jun 22 18:17:05 2007 +0000 working on the atom track detail page, add alignments commit cbc19cbd66049b8fc336abb0627d4aa2e893a44b Author: fanhsu Date: Fri Jun 22 18:00:13 2007 +0000 Fixed a typo. commit 91f5d5ec236f00a5123fb27446daacac13548064 Author: donnak Date: Fri Jun 22 17:56:44 2007 +0000 Changed server maintenance window, per Jorge. commit de74c0e8b06e09e5b051c5e33cc670734ecd345a Author: fanhsu Date: Fri Jun 22 17:50:30 2007 +0000 Added struct gsidSeq for keeping track of global GSID selected sequence list. commit cf7373204b4214a18baf7e18de03e1e2cd06e3af Author: kuhn Date: Fri Jun 22 16:49:00 2007 +0000 changed capitalization commit 9afba90760f6a0932f96bb86e74650706a119c11 Author: fanhsu Date: Fri Jun 22 16:44:05 2007 +0000 Added gsidSeq structure to keep track of selected GSID sequences. commit dedb4a2ded20c6abdc6a98645997384a1079f1db Author: fanhsu Date: Fri Jun 22 16:28:16 2007 +0000 Added lines to save sequence IDs associated with selected subjects to gsidSeqList. commit 7ebddef40ec72f52bfd02727b3bf1d0743540463 Author: kate Date: Fri Jun 22 16:14:59 2007 +0000 Fix test for topScorers filter commit 26d7d93a72781f396ef5ed0cfe3d3ad169c596b0 Author: galt Date: Fri Jun 22 15:00:36 2007 +0000 "Encode release log update" commit fbdf7aa3a769564e475b8e52301fefc37442a62d Author: galt Date: Fri Jun 22 15:00:19 2007 +0000 "Release log update" commit c58b94b9b93b9f1bfbfcfc32a664520ec97f4b92 Author: kuhn Date: Fri Jun 22 01:21:29 2007 +0000 added support for internal wildcards. fixed bug that acted as if there was a wildcard at the end of the tablename if there was one in front. simplified logic when substituting list of tables for wildcard. commit 62e9224cee062ebe26b565f360b477a9ecefea69 Author: hartera Date: Fri Jun 22 01:07:08 2007 +0000 Added back Kate's code for filtering the top N scoring items in a bed track when specified in trackDb. Adds the scoreUi when bed5FloatScore or bed6FloatScoreWithFdr type tracks together with appropriate trackDb settings are used. commit 11ecd5c26db08926b6cff170645b23a870ff6605 Author: hartera Date: Fri Jun 22 01:04:04 2007 +0000 Added back Kate's code for filtering the top N scoring items in a bed track. Added code to deal with using the track table instead of a separate table for finding the top scoring items. commit a6e4ba777bc8446f41ed2f6405a877a995ee2a2c Author: hartera Date: Fri Jun 22 01:02:11 2007 +0000 Added back Kate's code for filtering the top N scoring items in a bed track. commit c3b45eab07218df3f8c9125a098d284a38297755 Author: angie Date: Fri Jun 22 00:37:45 2007 +0000 Added DHGP annotations on heterochromatin, references. commit 17a1f94947ccd7398bd6bd5634c43d5fbfb3b312 Author: heather Date: Fri Jun 22 00:36:54 2007 +0000 check for table existence commit 7ac7c60ef6f3c6413af5626f3afa60664db53bf3 Author: markd Date: Thu Jun 21 23:57:55 2007 +0000 converted N-SCAN track to a composite track and added N-SCAN PASA subtrack commit a527ad0cd9785c2f2712bcbcd943e43883606aae Author: braney Date: Thu Jun 21 23:15:48 2007 +0000 add seventh line to atoms to indicate atoms that have been dup'ed commit c4a3ba0ce83be015a1026ab017f8a196971abd94 Author: braney Date: Thu Jun 21 23:15:10 2007 +0000 add support for atom tracks, including atom table in hgFixed commit 160284c387abf09e4e02fb6d57af535d145f7aad Author: braney Date: Thu Jun 21 23:14:15 2007 +0000 add support for atom table in hgFixed commit f82f871ca3e45af2235a9fa6d0b0baef4dcaf86b Author: braney Date: Thu Jun 21 23:13:23 2007 +0000 library and include modules to support atom table in hgFixed commit 5430561f1c074c0b940d9e38605d901ee717b5ea Author: hiram Date: Thu Jun 21 23:03:24 2007 +0000 Enable wiki editing on UCSC genes commit 1e4ba015199b1bd7ea0fb1797d8969ca1ba2ed40 Author: hiram Date: Thu Jun 21 23:00:10 2007 +0000 Now creating new items when first comment is added commit 1a7b5920e0c78d125110bdd7c72a6a032699f88e Author: donnak Date: Thu Jun 21 22:56:46 2007 +0000 One more mod to MAF section. commit 490231af2b777e390c1c150c68a0bb39d61ace4c Author: donnak Date: Thu Jun 21 22:53:21 2007 +0000 Modified MAF format section per Kate. commit 51ff50129016e6ec45632c96058fce987e2d0b6c Author: ann Date: Thu Jun 21 22:48:01 2007 +0000 fixed up citations commit 1a2a9e17a7efa294b2a2d369ca5f69b610ec2102 Author: kate Date: Thu Jun 21 22:34:37 2007 +0000 Add description for 28way most conserved commit dc8cdbb62983f18b20ce44351630639b69c69b0b Author: rhead Date: Thu Jun 21 22:22:10 2007 +0000 Removed links to Regulome Corp., which seems to no longer exist. commit 7973fac20ac063eeed8a0060ca7744e8619c86cc Author: ann Date: Thu Jun 21 22:07:27 2007 +0000 corrected citation format commit 9a760d784884bd19fd0949df2b36d15ce88310dd Author: ann Date: Thu Jun 21 22:02:11 2007 +0000 changed visibility from pack for two wiggle tracks (which do not have the choice of pack) commit 007b0a58885226ce5654bf5ff0e9d83c22d726d5 Author: kate Date: Thu Jun 21 22:01:16 2007 +0000 More fixes for wigMaf commit a7b4e36096c9a02d0ff3d67cc4b1189baab2c380 Author: hiram Date: Thu Jun 21 21:59:16 2007 +0000 Moved addDescription into the library commit b6ec9654891c40c5081000ebbda95622bf9ab40c Author: hiram Date: Thu Jun 21 21:58:57 2007 +0000 Moved addDescription() to the library commit 0e6cee3b977cca73b7433e2d4415b3611fabf377 Author: donnak Date: Thu Jun 21 21:58:52 2007 +0000 Added "q" line information to the MAF format section. Need to upgrade the "Simple Example" to incorporate q, e, and i lines. commit 7e944bc37bfcf2e84209456996b54b08c633e3f4 Author: hiram Date: Thu Jun 21 21:58:21 2007 +0000 Moved addDescription() into the library commit 6845741d41af20b4f456cfbc1a5aebceeee88ed9 Author: ann Date: Thu Jun 21 21:26:15 2007 +0000 corrected links to the tree models commit 9affe6824fd92142e8143f2577368fdd562b7bd2 Author: hiram Date: Thu Jun 21 21:21:42 2007 +0000 Check for alignID == "0" - not displayed commit e06ad233b0b183ef5ae15488939ceffc48a93a39 Author: ann Date: Thu Jun 21 21:13:24 2007 +0000 reference to Table 2 commit 912b7590aa9e76deea1ea686a85b5226ab670bfb Author: hiram Date: Thu Jun 21 21:05:40 2007 +0000 Initial source under development commit 6919015edc39ae7eb76b69338a5371e29b9cbaa6 Author: hiram Date: Thu Jun 21 21:04:42 2007 +0000 Added new column to wikiTrack table definition, and transferring functions to lib/wikiTrack.c commit e275161dc05b2152860d6b190518642b7f9fc169 Author: hiram Date: Thu Jun 21 21:04:00 2007 +0000 Added new column to wikiTrack table and bringing routines into the library from hgc/wikiTrack.c commit 61e87310f41011e9a62166485de949b9d51ab3aa Author: hiram Date: Thu Jun 21 21:02:54 2007 +0000 Added column to wikiTrack table definition commit cbf698f09159a62d35d25e96aa5986662df79052 Author: ann Date: Thu Jun 21 20:33:46 2007 +0000 switching visibility for 28way (to pack) and 17way (to hide) conservation tracks. commit a1b9e4d14fb44dc94663c91127e4bcdeca12e841 Author: ann Date: Thu Jun 21 20:24:45 2007 +0000 Added to Table 2 the list of species that do not have their own codon translation. commit 4fc496c391f0f7b7afca5300e47b0818ff3c15df Author: kate Date: Thu Jun 21 19:52:31 2007 +0000 Note regarding table update commit 7128794e4ea8fce077e670c7e6d0be7efe02cfc0 Author: donnak Date: Thu Jun 21 19:37:23 2007 +0000 Range queries no longer include the 100,000-base padding on either side. commit 8f38522493d1103177a671ac66ee6fc77ed52676 Author: donnak Date: Thu Jun 21 19:00:56 2007 +0000 Moved this file back down to the monDom1 level -- not sure why it was moved up to this level(?). commit a388c4d6d11a0f95987aeb2a3d257ef2599843a9 Author: donnak Date: Thu Jun 21 18:59:46 2007 +0000 Moved this file back down to the assembly level -- not sure why it was moved up to the organism level(?). commit ec918c6914b90e556db90042e137e8e2af5645d4 Author: angie Date: Thu Jun 21 18:40:23 2007 +0000 Re-ran RepeatMasker after debugging lib problem with Robert Hubley. Re-masked dm3.2bit and regenerated downloads. Regenerated 11.ooc to be less stringent since the new chrUextra bumps up a lot of tiles over the dm2 threshold; MarkD re-ran genbank. commit bcc67ed90752506b46c256eab65d4502605af9f6 Author: ann Date: Thu Jun 21 16:29:51 2007 +0000 switching 28way and 17way Conservation and Most Conserved tracks commit ae186d34e5264c5e425f6d10fd3015821615ca4d Author: ann Date: Thu Jun 21 16:18:55 2007 +0000 reordering species in table to reflect correct order commit 19c341e62860c4a77b3c95aa9f29f4d21f320046 Author: ann Date: Thu Jun 21 16:13:50 2007 +0000 added priorities to priority.ra file to reflect correct order. commit 3445d69757a1401949e1ab03a8f30227c42b0798 Author: ann Date: Thu Jun 21 15:43:36 2007 +0000 reordered display of orgs in 28way conservation track to reflect the order everywhere else commit df1875da91a1af334c4eca3847f6ddacdfa51e4b Author: galt Date: Thu Jun 21 15:00:38 2007 +0000 "Encode release log update" commit be3b325b528a903514d5602dd37c212d7bb616a8 Author: galt Date: Thu Jun 21 15:00:20 2007 +0000 "Release log update" commit f370e0b3b44844986902f79d1511479892773a4a Author: braney Date: Wed Jun 20 23:14:37 2007 +0000 a utility that takes a list of base atoms, a base file, and an atom number, and outputs the base atoms that make up the given atom as defined by the base file commit 36d3b7b1c0bc00d114a4a97aec2b5b9ae26e8546 Author: rhead Date: Wed Jun 20 23:13:15 2007 +0000 whoops. One too many http's. commit 1741b3b63819a4924ce06e40b5daacfadb3a3379 Author: braney Date: Wed Jun 20 23:11:38 2007 +0000 a utility to iteratively choose the best atom from a set of atom files while checking to make sure the bases haven't been referenced yet. commit 8b70df940432101ef51da75294ab2e6dcafd77f9 Author: rhead Date: Wed Jun 20 23:10:00 2007 +0000 Changed Tandyman link to a working location. The site www.stdgen.lanl.gov currently has a message that reads "The STDGEN site is currently unavailable. Work is progressing to move the site to Dr Hank Seifert's lab at Northwestern University. Stay tuned, we expect the site will be back up in early 2007." commit b5b8ffd0705c9d049cb696fb7bb51e324276c356 Author: braney Date: Wed Jun 20 23:07:57 2007 +0000 change the order of libraries commit 217bc6da0a2efdc8e91d80984d2a22ddee3a86a4 Author: braney Date: Wed Jun 20 23:07:24 2007 +0000 add a few error condition checks commit 9d55433985d5ab62fd9091a5d013c1cef21dc8f7 Author: braney Date: Wed Jun 20 23:06:42 2007 +0000 add readAtom() commit f4c349ce9efb606b17d5cc1b842cc1e298b72036 Author: braney Date: Wed Jun 20 23:06:13 2007 +0000 add readAtom commit 81dafd68ad43b6c33fcfe67c3666198409823ba4 Author: braney Date: Wed Jun 20 23:04:47 2007 +0000 some changes to use mega and base files, now probably unnecessary due to baseAtoms functionality (i.e. baseAtoms piped to atomToMaf better for cluster) commit 3817ee7a64fadc0bbdbc62a73d86d282d7bf3f1e Author: braney Date: Wed Jun 20 23:00:28 2007 +0000 change to use score, hard coded for hg18,rn4,mm8,rheMac2,panTro2,canFam2 commit dda01f5947d79b6b6f17938cc6f44c1e4b2f5da9 Author: braney Date: Wed Jun 20 22:59:00 2007 +0000 specify percent to drop, allow just sorting commit cf1cfe3801abcdedafbacfd25dc2fe330a8c99ec Author: rhead Date: Wed Jun 20 22:57:31 2007 +0000 Updated uniprot data use restrictions to match all of the other known gene pages. The isb-sib link has not worked for some time. commit 47cec5f7b0149beacdedbeb7c41cdc3c71cc7d26 Author: rhead Date: Wed Jun 20 22:15:27 2007 +0000 Removed the "_fs" from the Nature article links to make them work again. commit a526195e658434dc40d30562cd9294b4a2e2da45 Author: rhead Date: Wed Jun 20 22:07:38 2007 +0000 Removed broken link to Tarjei Mikkelsen. Donna and I can't find a good replacement link. commit d0af7a499f842689c3683ae8b57d9fb12f9895a4 Author: braney Date: Wed Jun 20 22:02:41 2007 +0000 don't count dashes commit 2ed6438d5afd4c591d52e0b02b5ca98ff4681340 Author: kate Date: Wed Jun 20 21:38:46 2007 +0000 Minor changes to track labels and subtrack ordering for 28way commit 9a99b14c3e3049b709ec86daf4a102c6f6536254 Author: ann Date: Wed Jun 20 21:37:40 2007 +0000 added multiz28way tables as appropriate commit cbcfebb6d5ea2a74da07f8e81bca6958b2cc5d61 Author: angie Date: Wed Jun 20 21:27:43 2007 +0000 Added cytoBand, cytoBandIdeo. commit 6bb9bbd136847fc6d060dbdc3a453a73db40acdd Author: angie Date: Wed Jun 20 19:41:57 2007 +0000 Take ooc from same dir as .2bit to simplify fileserver usage, as requested by MarkD. commit 2596ab0188ddb05d1adb3d9601307a1f7f841d20 Author: angie Date: Wed Jun 20 19:31:24 2007 +0000 Watch out for negative coords in repeat sequence lines. commit 52e49b980a5ee90a8038b520268519ab447b01fd Author: ann Date: Wed Jun 20 19:25:12 2007 +0000 loosened gbSeq rule for altGraphX relationship commit 4b677a081ff2e83066947987b0af0e7cc3eb3b91 Author: kuhn Date: Wed Jun 20 18:53:07 2007 +0000 declared some variables at the top. reversed a confusing "if $status" conditional. moved one line out of an if-statement so it works for the case of a single machine. thanks, brooke commit 4c72ae968c3678cb7b720250bffc30a38ec4d70b Author: kuhn Date: Wed Jun 20 17:31:52 2007 +0000 changed format of output and added note that it now takes wildcards commit 34ad8aef39bf093650412b7cd6be5088c06fd137 Author: ann Date: Wed Jun 20 17:21:35 2007 +0000 editing speciesCodonDefault for Conservation track to equal this species (instead of hg18). commit 6442dad5e80a8d7c960307a59fc64321f69c2e2c Author: galt Date: Wed Jun 20 15:00:36 2007 +0000 "Encode release log update" commit 1b5382aa926d670ae10d69a0ac8921008023f5e5 Author: galt Date: Wed Jun 20 15:00:19 2007 +0000 "Release log update" commit 8ad252f6ccc9e04f7f270f89a3f606287e530ec6 Author: heather Date: Wed Jun 20 14:25:32 2007 +0000 fix typo commit 224905cb666700d2dea07f169156e5547667ff5e Author: heather Date: Wed Jun 20 14:19:12 2007 +0000 use rbest.axt not rbest.maf; add comment commit 26e34589c457dfa12e3618972944f1f86dda97ad Author: braney Date: Wed Jun 20 01:21:28 2007 +0000 modify some atom track handlers commit 97cf2543ea181cb44c6633c9c1c9e9e96eb65cc4 Author: angie Date: Wed Jun 20 01:16:16 2007 +0000 As Ann pointed out, it is wasteful to summarize when the reference sequence size is <1Mbp, because hgTracks uses the summary table only when viewing at least 1Mbp. So skip those small sequences by default (can be tweaked with -minSeqSize). commit 0a81fca77dbf161896bf0f47acdee20c2e35ada0 Author: kuhn Date: Wed Jun 20 00:43:23 2007 +0000 cleaned up logic a bit and changed usage statement commit d8ffb5a93307d2c7af9a54172350f5ab22fc617a Author: angie Date: Wed Jun 20 00:33:38 2007 +0000 A couple refinements suggested by Hiram: don't show previously pasted id's from another track in the paste form, and don't keep redundant self-mappings from alias table. commit 77f7df756fb54fd71d32dc5ac39378d5ba90a09e Author: kuhn Date: Wed Jun 20 00:27:21 2007 +0000 more borken links commit 6b18f58e5267ee768aae736c040807938e3857d5 Author: rhead Date: Tue Jun 19 23:16:00 2007 +0000 Changed longLabel for encodeYaleAffyRNATransMap. Track does not yet include HeLa cells. commit dad9e1b3fa625895dff5bbf43ecf5de18b6e9de2 Author: braney Date: Tue Jun 19 23:09:17 2007 +0000 change atom track names commit 02c086404f2333200089a3c50e270f3e4e6fa7e1 Author: archanat Date: Tue Jun 19 22:54:51 2007 +0000 converted refs to pubmed format commit d3142c0f9a843a4c8481256e046198fdf895367d Author: donnak Date: Tue Jun 19 22:21:05 2007 +0000 Added warnings to the gateway & cgi page telling users that this app is now obsolete & no longer maintained. commit 27d92d83c420e5f6e06398ccf77d09b8522897a9 Author: heather Date: Tue Jun 19 21:25:30 2007 +0000 prune multiz4waySummary commit 49f3d5e48ecbfbdc93a9460ceb1149acf8662f9d Author: heather Date: Tue Jun 19 21:07:17 2007 +0000 fixes for hapmap snps and snp arrays commit a4c93fdd7acc8f5b46bb22ee5f2cf52c335d2ec6 Author: donnak Date: Tue Jun 19 20:45:58 2007 +0000 Added links to user's guide & OH tutorial to intro. commit 8b1534fc1143ba002f08ea4098f553155bdb0adf Author: galt Date: Tue Jun 19 20:27:04 2007 +0000 cleanup - these files were long ago installed under hg/gsid/gsidSubj and development has long proceeded there commit 371e9269eabbb1fe08ef0c6033230d43ea65e946 Author: donnak Date: Tue Jun 19 19:53:56 2007 +0000 Rearranged some text in intro, per Jim. commit cbaa73ecc1fe2dbe27a969b15b9e8d85c441b948 Author: aamp Date: Tue Jun 19 19:32:37 2007 +0000 Changed shortLabels again for Affy Txn tracks: HepG2 and HeLa ones. commit c05013206bc6feaeda9b75b8dc0d53f1217d7406 Author: aamp Date: Tue Jun 19 19:29:31 2007 +0000 Backed out chromosome lists for affy txn tracks. commit 45769622bcfd140c85e71dfdee7eaae8ba792aed Author: aamp Date: Tue Jun 19 19:04:07 2007 +0000 Fixed a few more places where I forgot "chromosomes". commit cacf4f31361a4751ad0e0f0a357a6663d1532670 Author: aamp Date: Tue Jun 19 19:01:53 2007 +0000 Had to fix where I forgot "chromosomes". commit 001edfe2ebdc19a54c6bb81d9e3a4ea0c3c89cba Author: aamp Date: Tue Jun 19 18:59:49 2007 +0000 Added chrom lists to Affy Txn tracks. commit 8fe61973fa6093a4d4f202acccd213923257969f Author: donnak Date: Tue Jun 19 18:58:02 2007 +0000 Made some edits to incorporate additional info received from Affy. commit d0cab853c595046f441080869239f99d3a7364c2 Author: heather Date: Tue Jun 19 18:52:53 2007 +0000 tweaks for conservation track commit 8210f87e7e07a629ca2c9595f8438bfbea3803f9 Author: angie Date: Tue Jun 19 18:50:57 2007 +0000 Adding cytoBand, cytoBandIdeo. commit 04363f9eaa9b395c2d6e27751bff9c23be999a05 Author: ann Date: Tue Jun 19 18:17:53 2007 +0000 Changed order of organisms on Conservation description page. Should be nearest to furthest. commit 4c73514fc859b1d769f92f63c845075747629890 Author: kuhn Date: Tue Jun 19 18:17:47 2007 +0000 checked in static path list for linkChecker commit 906b57574bcc19ab73ff4e0b2ff87ecff97226b0 Author: ann Date: Tue Jun 19 18:16:02 2007 +0000 changed order of orgs in Conservation track config section. commit 70ab229dfef35dc576ef5dfc409d236595550840 Author: ann Date: Tue Jun 19 16:35:15 2007 +0000 Comment out link to Sessions Users Guide (which isn't finished yet). commit 04118c7d4d2ba6ed1a38a7f976407ea95453d976 Author: ann Date: Tue Jun 19 16:34:47 2007 +0000 fix broken link to Sessions Users Guide (which isn't finished yet). commit fc6928ad91655c69a68abec3813efe72e79fb5f5 Author: aamp Date: Tue Jun 19 16:28:16 2007 +0000 Added Affy Txn instructions. commit 1d920878e71528186e3e0ed907bf11d2226385f8 Author: hartera Date: Tue Jun 19 16:05:03 2007 +0000 backing out changes for score filter, causing error. commit a6d1b4101687ebbc963077d4c37f43036d2bfdf3 Author: kuhn Date: Tue Jun 19 15:59:03 2007 +0000 fixed links moved by Nature commit bad666fa6b88cb1dc68a9a557a388a3a3465ec4e Author: galt Date: Tue Jun 19 15:00:27 2007 +0000 "Encode release log update" commit 689c8deeff1882bd0b8d2d936306378bb718e04b Author: galt Date: Tue Jun 19 15:00:15 2007 +0000 "Release log update" commit e882522452124b99f8ec16878555c89e0ba2ba0c Author: hartera Date: Tue Jun 19 06:49:25 2007 +0000 Added April 2007 P-value and Signal data - new subtracks for Yale Chip tracks. Added a new June 2007 subtrack for the ENCODE Yale Chip P-value and Signal tracks. Started to prepare to add Sites track data updates. commit 9ce405ec7eb76ddfd0353a8bbb854983a0cb7255 Author: hartera Date: Tue Jun 19 06:26:14 2007 +0000 Added June 2007 data - one subtrack for H3K27me3 for both Yale Chip P-value and Signal tracks. commit b2993d64209cecae9016aeffb973708d39f3fb48 Author: hartera Date: Tue Jun 19 06:07:29 2007 +0000 Added information about H3K27me3 which was used in experiments from the June 2007 data. commit 7319dcc707cf9be23ac729ac2060b789122e5cc5 Author: donnak Date: Tue Jun 19 02:51:54 2007 +0000 Fixed broken link. commit 980d46f68683df24d0e87238c79123b33d5e073b Author: hartera Date: Tue Jun 19 02:22:17 2007 +0000 Added back Kate's old code to support the selection of the top N scoring items for a track. The feature is turned on by a trackDb entry. This code adds the configuration controls to the track description page. commit 0741cc03b726db5a18222f41954f5304565dbb08 Author: hartera Date: Tue Jun 19 02:20:45 2007 +0000 Added back Kate's old code to support the selection of the top N scoring items for a track. The feature is turned on by a trackDb entry. A new table can be created for selecting the top scorers or if 'self' is specified then the track commit 27beedc4252bbe8ea83ea7d3e0599cd6c838d26d Author: hartera Date: Tue Jun 19 02:17:22 2007 +0000 Added back Kate's old code so that the top N scoring items for a track can be selected. commit 46243f75ea1e8fa9dae1875fe7d2d354097f448d Author: aamp Date: Tue Jun 19 01:11:10 2007 +0000 More labeling changes. commit 83c2dbbfa77176e7e7355b73ad005229059d958c Author: aamp Date: Tue Jun 19 01:06:47 2007 +0000 Even more labeling changes. commit 1088e01842eabf8d0789ec28e7702f2b1d16ead3 Author: aamp Date: Tue Jun 19 00:30:22 2007 +0000 More label changes for the Affy Txn tracks. commit bc2b93de35e4b9d800e25ffa801531e72e6ebf3e Author: aamp Date: Mon Jun 18 23:59:23 2007 +0000 Added sRNA or lRNA to all the shortLabels and changed up the order of the tracks a bit. commit 3367c7854e243fb735e0159ed5b9d68ef214acc9 Author: angie Date: Mon Jun 18 23:47:51 2007 +0000 In customFactoryTestExistence, instead of specifically checking for wibFile and wigFile, just require that any setting whose name ends in File must specify an existing file... turned out that chromGraphFactory piggybacks on customTrack for storage, and customFactory had no concept of the binaryFile setting that chromGraph custom tracks use. This will cover future added *File settings. Added verbose(3)'s to help debug in case this turns out to cast too broad a net. commit 2856e9fc23732528bd487e1de88e4b8f3b2bddc2 Author: angie Date: Mon Jun 18 23:42:41 2007 +0000 Added trackDbSettingsLike for wildcard scan of setting names. commit 9fc569e4880caeeb2a07ba0aed55aaee3e029557 Author: hiram Date: Mon Jun 18 23:26:38 2007 +0000 Simplify the color pull-down menu, make it identical to the chromGraphs color menu. And eliminate the score as an entry item. commit fa04c25576a6c669435e08ad754c31cd34d13a6f Author: aamp Date: Mon Jun 18 22:23:35 2007 +0000 Changed some top/bottom language to plus/minus. commit 00a6acb38a38455f10245499150eb9377c1ea92c Author: kuhn Date: Mon Jun 18 22:07:44 2007 +0000 changed some links that were not working commit 88aa0f0add5184e3c413d08d7ce96e1476cfeb3b Author: kuhn Date: Mon Jun 18 21:45:32 2007 +0000 changed link and affiliation for Salzberg. commit ff49410c94c4268b4ff0f538cdc1a32a96e584ce Author: heather Date: Mon Jun 18 21:33:16 2007 +0000 phastcons downloadables commit 2db9257b20f72e97203d1ee9afe9641784505c68 Author: angie Date: Mon Jun 18 21:31:24 2007 +0000 Added DHGP's heterochromatin annotations to flyBaseGene, flyBaseNoncoding and flyBase2004Xref (though the xref in the annotations was rather incomplete). Updated hgGene/hgNear tables that depend on flyBaseGene. commit 03677e95fa806a1486809b97c8f817c44bc82897 Author: hartera Date: Mon Jun 18 21:13:46 2007 +0000 Added more information about experimental details. Added more antibody target descriptions. commit a220586a95d10079d79518b49d095a958661c588 Author: hartera Date: Mon Jun 18 21:12:56 2007 +0000 Added more information about experimental details. commit a5cbb18cd0ba6fc647d428d4fe45c8c0e621ae11 Author: donnak Date: Mon Jun 18 21:11:44 2007 +0000 Changed the short labels for the Affy Phase 3 tracks. commit 1d467186a6d44713841fbb2f6ced3f6606c6582a Author: donnak Date: Mon Jun 18 21:07:31 2007 +0000 Made a first pass at cleaning up these files. commit f379a9f6f735d49f66934d822a1d45b0eb0df2e5 Author: hiram Date: Mon Jun 18 20:40:37 2007 +0000 Take off the section header for added comments commit 20f01b154bd89f43152df803c0caf0c6b18796cf Author: heather Date: Mon Jun 18 20:21:22 2007 +0000 load phastCons commit 13f3ebb1d6b602a6ecaf908711b6508f0525c19c Author: heather Date: Mon Jun 18 19:53:57 2007 +0000 copied from ornAna1 commit 424c9d113f4ec2129f0f4e6c83e1be6b00859cfb Author: heather Date: Mon Jun 18 19:53:31 2007 +0000 add phast cons commit 9eca6779a52d3d7fc1d109753e6b40013afa8cc6 Author: kayla Date: Mon Jun 18 19:20:54 2007 +0000 Removed link to bosTau3 because it's not out yet. commit 518eb46ce7d9ce064b8c9ec57e5cebe6b7a3d8f3 Author: archanat Date: Mon Jun 18 18:50:54 2007 +0000 converted refs to pubmed format commit 31fb14f6c9b3b75a3a556098ee7282b1a6c77941 Author: kuhn Date: Mon Jun 18 18:48:52 2007 +0000 removed link to Salzberg. He seems to have moved on commit a4b45e5d8fd6ba0d64dfdc9b727f5e793fdfec2f Author: hartera Date: Mon Jun 18 18:37:52 2007 +0000 Corrected track name for encodeYaleChipPval and added updated html for the release alpha for this track. Added cell types, factors and data versions for Pval and Sig tracks. Shortened names of subtracks for each of these tracks and changed HeLa to HeLa S3 in subtrack long labels. Release alpha and release beta versions for ENCODE Yale Chip Pval, Sig and Sites tracks. commit 6043cfe45c1f0add0de7ce7f52b7fc42d00b892e Author: kayla Date: Mon Jun 18 17:49:31 2007 +0000 Added the matrix to the details page for anoGam1 and dp3 commit 8272ca0e41460c523a4cdcdd3dd03f3236d909f9 Author: donnak Date: Mon Jun 18 17:46:38 2007 +0000 Fixed capitalization in affy subtrack labels. commit 69434e7f519eed076e8d750097dc482ac4271158 Author: hiram Date: Mon Jun 18 17:42:24 2007 +0000 Properly return to add item when login is initiated from there, and take care of the case when all comments have been deleted and the header lines need to be started over again. commit 49c19135665ad220b9f81e9ecf75272118f91ba0 Author: hiram Date: Mon Jun 18 17:40:17 2007 +0000 2^31- 1 is not what you thought it was ... commit e0c72e8118c9bd3e01f145aec9ee357d699b14bb Author: hiram Date: Mon Jun 18 16:20:33 2007 +0000 Now performing the next item function on the wikiTrack commit bb9dfda092bf9a1fa9e95c05b1729d711669d72b Author: galt Date: Mon Jun 18 15:00:21 2007 +0000 "Encode release log update" commit 897976b028d24ad7b31866fc21696449a0fed803 Author: galt Date: Mon Jun 18 15:00:12 2007 +0000 "Release log update" commit bcae82e39c007acc88ce04822a3c4086e54f2a0e Author: markd Date: Mon Jun 18 01:41:48 2007 +0000 fixed bug updating gbExtFile table for genomes with no refseqs commit 9c40552c9753494b5edf9fb97858621f8497102f Author: galt Date: Sun Jun 17 15:00:21 2007 +0000 "Encode release log update" commit d731cb8c7aa8c557fe843af726e599f043eb7ad8 Author: galt Date: Sun Jun 17 15:00:12 2007 +0000 "Release log update" commit 8f91944e3c6208a7f2efbeebf3549347dbb5c8d3 Author: markd Date: Sun Jun 17 08:09:09 2007 +0000 dog organism change commit 3d8153b1f6bb61efa792c7cd835a7d8cb83e513a Author: markd Date: Sat Jun 16 19:01:50 2007 +0000 fixed bugs related to organism name changing commit ae808138f03b496ef9a74a8b30eac0c3693f7a7d Author: markd Date: Sat Jun 16 18:12:14 2007 +0000 added missing lib dependency commit 3dd66e963ef4a7fb6777c9e81efd36b7850bcf0a Author: aamp Date: Sat Jun 16 17:45:12 2007 +0000 Submitted track descriptions from affymetrix for the transcriptome phase 3 tracks. commit 240f648e02f0bd35736073419602db934bec13bd Author: markd Date: Sat Jun 16 16:40:10 2007 +0000 needed mapping for new canfam name commit 30dd3731b348418ceca399fd7392a78db1aa7c10 Author: markd Date: Sat Jun 16 16:39:47 2007 +0000 added to-do notes commit 76794606b937546dc90f5553b740ee4c7cddbe38 Author: galt Date: Sat Jun 16 15:00:27 2007 +0000 "Encode release log update" commit fae3ef5baeb75298ec4c6fd0c6a82974715f6007 Author: galt Date: Sat Jun 16 15:00:15 2007 +0000 "Release log update" commit 2be73a7591240d44465539d206044ed68d4caf81 Author: hartera Date: Sat Jun 16 00:14:11 2007 +0000 Changed minCheck value for rules in vegaPseudoGeneZfishName. commit 8112f31104a76aa00aadc41a8403a24a63b6ccea Author: hiram Date: Fri Jun 15 22:09:31 2007 +0000 Eliminate duplicate HR tag commit 85984abb84a23b59a0b8590e3d99f9814b4ec757 Author: hiram Date: Fri Jun 15 22:06:31 2007 +0000 More clean up after checking html in a validator commit f084ee5e300210f361a7b38bb6ccf55e1b067ebd Author: hiram Date: Fri Jun 15 21:16:09 2007 +0000 Cleaning up html output, labels on the color pull-down for safari, and return to tracks button on the adding comments page commit 568db47ad6fbcb381163b62291abe9d4193c4843 Author: hiram Date: Fri Jun 15 21:14:00 2007 +0000 Proper type on the stylesheet link, and no barbs on the Make New Item for wikiTrack commit 13b27779759adfc74babff0eecb0f904f79f9fda Author: hiram Date: Fri Jun 15 21:13:14 2007 +0000 Proper type on the stylesheet link commit 5efa3cc2c1d12ed28b8a7f4edecffb8267636226 Author: hartera Date: Fri Jun 15 21:09:11 2007 +0000 Description for encodeYaleChipSignal containing the updated description for the Nov 2006, Jan 2007 and Apr 2007 data. This will go with the release alpha version of the track in trackDb until it is released. commit e74c94b6d1c6102ae010e1aa630bdd4e87aefa0b Author: hiram Date: Fri Jun 15 16:38:13 2007 +0000 Clarify the inefficiency of the BED format. Recommend the use of the other formats instead whenever possible. commit f9bf1b3e372af5bdb2566244b067a5c1ad6e91ad Author: galt Date: Fri Jun 15 15:00:31 2007 +0000 "Encode release log update" commit 77942b98e3e9dda7ad5327ec8c409e7635b4911b Author: galt Date: Fri Jun 15 15:00:16 2007 +0000 "Release log update" commit abd85861201200529af7e92a8b47c8237635ab90 Author: kate Date: Fri Jun 15 04:43:48 2007 +0000 Fix problem with correlate on wigMaf tables commit c6849223ad156895da6918f70972535718434de9 Author: kate Date: Thu Jun 14 23:12:48 2007 +0000 June update commit 116c504c19a036cd3acc98a96fafdf289a2ff788 Author: aamp Date: Thu Jun 14 22:56:38 2007 +0000 A couple mapItem() functions needed the extra mapItemName param. commit 8ffc94783eacb547e08edbc4aa41f566992c5424 Author: hiram Date: Thu Jun 14 22:47:35 2007 +0000 The constructed URL in the wiki article was off by one commit 2b36c0f2c58cdacee347da2931ef011c570ff3d1 Author: hiram Date: Thu Jun 14 22:41:29 2007 +0000 That off-by-one was not correct ? commit 5a6f1782f13c0c5711f833d5c8829303362109c9 Author: hiram Date: Thu Jun 14 22:36:01 2007 +0000 Off by one error on the chromStart commit 5f32ade7f610fdf40eab8f64be3b617b3e59767e Author: aamp Date: Thu Jun 14 22:27:27 2007 +0000 Possible fix for the mapItem problem. Added another parameter to mapItem and had to change a few other files that used it. commit 872b9de191072fae46152556065fa0a23601d392 Author: hiram Date: Thu Jun 14 22:21:44 2007 +0000 Exposing linkedFeaturesName() to be used outside hgTracks.c commit 193c346996180adefa3fd709f4ea54503384dd98 Author: hiram Date: Thu Jun 14 22:21:13 2007 +0000 Now generating the hgc clicks with i=wikiTrackId number instead of item name commit d2caa1c20e21121f026b3be5c57eea9f15bfcbd0 Author: hiram Date: Thu Jun 14 22:19:40 2007 +0000 Now honoring the new wikiTrackId number from the hgTracks hgc clicks commit f9fa7dd02d97e6f8baed4db5947a2e6839b57cf7 Author: kuhn Date: Thu Jun 14 22:07:46 2007 +0000 added support for wildcards and fixed a bug that had second machine values always the same as the first. commit c9740f66fe1b6e4a19cdff7795c9d66616613e16 Author: hartera Date: Thu Jun 14 21:15:35 2007 +0000 Fixed typos. commit e4afa15ac5facf55dc32524ee0f97fb655e17edb Author: donnak Date: Thu Jun 14 20:37:00 2007 +0000 Added link to Genome Research in ENCODE news item. commit c477e9ed7981f91fcf629423ce3ae31d456931bf Author: kate Date: Thu Jun 14 20:13:56 2007 +0000 Tweak Nature paper announcement by request of Peter Good, NHGRI. He was concerned it sounded like the data had been held until now. commit 5e8c5b3b1282266b3f3842fcc26937bcbf1e99a5 Author: lowe Date: Thu Jun 14 19:25:55 2007 +0000 Using #ifdef LOWELAB to define default browser for lowelab as Pyrococcus commit b96b51affcf8dc28992a975e4f6d46ceb5153078 Author: heather Date: Thu Jun 14 19:08:52 2007 +0000 a bit more phastCons commit 1d0cce8bfdc5d3b12ecc6379a06c53792682a1b5 Author: heather Date: Thu Jun 14 18:58:59 2007 +0000 more phastCons commit b0b50375097276685f8ed374de2d4359b559322a Author: hiram Date: Thu Jun 14 17:22:11 2007 +0000 Initial wiki track add comment help page commit 909b65e85a0513a69cb828d3b91165c4f8bbc003 Author: hiram Date: Thu Jun 14 17:12:27 2007 +0000 additional comments commit 9079a9570bf421137f8214b34dfff450aa6a39f0 Author: hiram Date: Thu Jun 14 17:06:48 2007 +0000 Initial help text for wiki track create item commit 3de3e660c45530f502bf7adfc8999bc05be817cd Author: kate Date: Thu Jun 14 16:24:31 2007 +0000 Fix spelling of Rico's name, again commit e61230c4fddaf461081f5b2c1bdeaef970ab5342 Author: ann Date: Thu Jun 14 15:41:28 2007 +0000 changed Jackson Labs to Lab commit d8c6f4877e8749b7f008abcef44b5d512cc49184 Author: galt Date: Thu Jun 14 15:00:33 2007 +0000 "Encode release log update" commit 506c2ac90e07d237c6ae5b65c4b33661132c92b2 Author: galt Date: Thu Jun 14 15:00:18 2007 +0000 "Release log update" commit 18da379f482736fd96f6efd7c610f877224b9ea7 Author: heather Date: Thu Jun 14 13:53:50 2007 +0000 default assembly should be Human commit bfe7dcd0153de96409c20b154b65ad0ef1610939 Author: heather Date: Thu Jun 14 13:27:03 2007 +0000 added on behalf of Kord Kober commit 6e8c28cebc798e07328d678c30e33aaf0d9be5d0 Author: aamp Date: Thu Jun 14 08:30:40 2007 +0000 Added affy transcriptome stuff. commit ae823b45694ff4cdbf2d50c3a578d75b264c4016 Author: markd Date: Thu Jun 14 07:52:16 2007 +0000 added ignore entries commit f697bae2fb50e6780710de63dfe2e4f36ed6d6c8 Author: tingwang Date: Thu Jun 14 06:21:51 2007 +0000 modified encode UW DNase Array description commit c94db17f915851e97ed5a6f5e0cc4796696fe8e8 Author: heather Date: Thu Jun 14 01:46:17 2007 +0000 starting on phastCons commit 588b4549117c226dd01e5857c74ccb81c88ed8c1 Author: braney Date: Thu Jun 14 00:09:03 2007 +0000 add a couple of experimental tracks commit e30cdd5e72c05db42c4101e8ea67a80c685480aa Author: braney Date: Thu Jun 14 00:00:52 2007 +0000 add a few experimental tracks commit 3ca94b3bc4d8b95e1dabf147df6f95926eda562f Author: donnak Date: Wed Jun 13 23:01:00 2007 +0000 Pulled acronym out of link label. commit 2851094590ba7528b5d885262eb1ae7839b7ef83 Author: donnak Date: Wed Jun 13 22:48:35 2007 +0000 Fixed spelling of Jackson Lab. commit 60ede11c44a852fab0873f11d34bfa3ebf03c513 Author: donnak Date: Wed Jun 13 22:44:42 2007 +0000 Fixed spelling of Jackson Lab in comment sections. commit 973819066d92566bb62a66c80997b70cbb1e9e1d Author: aamp Date: Wed Jun 13 22:31:56 2007 +0000 Slight rename of transcriptome tracks. commit d5190cb83e6871eff4c2e18093e799fc8a6ba0f4 Author: donnak Date: Wed Jun 13 22:19:05 2007 +0000 Fixed spelling of Jackson Lab. commit 2882d28aa65201626293762046589aa422f1d40e Author: donnak Date: Wed Jun 13 22:14:01 2007 +0000 Fixed incorrect spelling of Jackson Lab. commit 84bcd009db9c1b731dc90207e35501dddff2f497 Author: donnak Date: Wed Jun 13 22:11:57 2007 +0000 Changed Jackson Labs to Jackson Lab. commit 39651c6a8a766093787636f5343df321ebc4257a Author: kuhn Date: Wed Jun 13 22:05:29 2007 +0000 reversed order of Mammal vs Vertebrate wiggles commit 18f675d0e3535dc6f579c10656300112848132d8 Author: markd Date: Wed Jun 13 21:05:20 2007 +0000 add beginnings of a pslMap README commit ede0fca2a57d3792abd194ab0cff1a54bbe712e8 Author: kuhn Date: Wed Jun 13 19:37:34 2007 +0000 made sequences list from Gateway page align the chrom sizes to right. made function to allow right justification in a
. commit bfbe06b90710d8c0890622cda452ed357d08494f Author: fanhsu Date: Thu Dec 20 00:54:14 2007 +0000 Updated link to Modbase. commit 93159f6b6c039c4f270a1310758dc7e5fdad92c0 Author: kayla Date: Thu Dec 20 00:46:35 2007 +0000 fixed split infinitive commit 330d4d1f1089103f38737e381a7717e51806e000 Author: fanhsu Date: Thu Dec 20 00:05:48 2007 +0000 Updated using new ModBase link. commit d99853fb5f8c2a42a5ca39cbafe4674869ebf225 Author: kate Date: Wed Dec 19 23:27:07 2007 +0000 Remove garbage commit e1635aa3f20785c0d56efa064f2ac26272cfc21f Author: kate Date: Wed Dec 19 23:26:56 2007 +0000 Add alias commit e63962fa54f2bf91a730ddc5c1a01465f45e9be2 Author: kate Date: Wed Dec 19 23:25:06 2007 +0000 Add install target commit b6be921d56c4edb4f518d54f3e4a2475b45c9ce7 Author: kate Date: Wed Dec 19 23:23:45 2007 +0000 Relocate config dir to work with scratch dir commit 801d2f0afe2940eca1e59b0d0d795b3e4f9a34bc Author: hiram Date: Wed Dec 19 23:18:39 2007 +0000 Running a self blastz with chain minScore of 2000 commit e8162db993e35437471e022daf4c2c7eed488699 Author: kate Date: Wed Dec 19 22:53:01 2007 +0000 1. Create load.ra file for automated loader. 2. Error message tweaks. commit e3448d2cb1087eef1b10766aa17d4ef8cf314b35 Author: hiram Date: Wed Dec 19 22:42:24 2007 +0000 Adding a chainSelf with minScore=2000 commit a8eb73075e42f17103229ea68ac9485061d3609d Author: fanhsu Date: Wed Dec 19 22:23:18 2007 +0000 Changed back to old state, before MODBASE updating their server. commit ce2f8a92b04a2d61c182014551bb08bc0030f62f Author: galt Date: Wed Dec 19 21:58:46 2007 +0000 fix minor bug commit 839ae952d5030e5775d1301cf46923f6ab3da77e Author: galt Date: Wed Dec 19 20:49:47 2007 +0000 added checks for NULL field values commit 17a8f3dd295532401b3eed94d5327b32bca82854 Author: galt Date: Wed Dec 19 20:40:30 2007 +0000 changed status to use 
 formatting

commit 611dcba789938f48b8c765604a7d37e08b2db941
Author: kate 
Date:   Wed Dec 19 20:13:12 2007 +0000

    Adding makefile

commit 34b90c9e3d67a410e873b066c5158271edb5a0e8
Author: galt 
Date:   Wed Dec 19 19:22:11 2007 +0000

    Make command-line usage conform to caller conventions

commit e5d616cb9521222919e7d7fe969fe5bd03958138
Author: kate 
Date:   Wed Dec 19 18:20:52 2007 +0000

    Add validation of file data format

commit 8d8b2925ad6249be419807a3cd41c3bf1502c060
Author: fanhsu 
Date:   Wed Dec 19 17:57:48 2007 +0000

    Temporarily disable Modbase images until their upgrade is settled.

commit c384bdfeec3953bc1935e1150e0ac3ef2051383d
Author: galt 
Date:   Wed Dec 19 16:00:07 2007 +0000

    "Encode release log update"

commit cef41046f674434cd82fc8ddcdd19d457cf780b0
Author: galt 
Date:   Wed Dec 19 16:00:04 2007 +0000

    "Release log update"

commit c90d02d000bf1b8fc08c4da60bff2051bbac8a17
Author: lowec 
Date:   Wed Dec 19 00:33:51 2007 +0000

    changed program to allow multiple patterns to be filtered; the same as multiple -name options

commit 5e8c192d75e91a92ffdb5f7a095d16e5c6597314
Author: rhead 
Date:   Wed Dec 19 00:14:13 2007 +0000

    Fixed broken link to wustl.

commit 9105dad85f20f6c3a1d5c87adb182ffe28d82015
Author: lowec 
Date:   Tue Dec 18 23:44:21 2007 +0000

    added options to filter out chains with large gaps

commit ea153bd5c89b95d356917110289b158356df8e7d
Author: rhead 
Date:   Tue Dec 18 23:38:53 2007 +0000

    Fixed broken link in references section.

commit 85b500b12360e00ad44458d267f3ced9589064ac
Author: fanhsu 
Date:   Tue Dec 18 23:23:43 2007 +0000

    Added hConnectTcga().

commit b129b5e665cf4bd7200b7ae71eedbf3ca049260c
Author: fanhsu 
Date:   Tue Dec 18 23:15:32 2007 +0000

    Added hConnectTcga().

commit d7d89a852e4d45b8ee6892edbc3cb44f25da74ba
Author: ann 
Date:   Tue Dec 18 22:58:16 2007 +0000

    added pga table to tablesIgnored

commit b40bad71e267750d0f892e6478ff6530d9556f7d
Author: donnak 
Date:   Tue Dec 18 21:09:10 2007 +0000

    Changed reference to gbdDescriptions (now obsolete).

commit cdbbd23994f8ff68e5292db2e4e65482b20fd3bc
Author: donnak 
Date:   Tue Dec 18 21:08:16 2007 +0000

    Moved original gbdDescriptions text to gbdDescriptionsOld and added disclaimer that info is no longer maintained. Changed gbdDescriptions to tell user abt using the TB "describe table schema" button, but also included a link to the old descriptions page.

commit 936cd527f7e0ec02e10a88f17502b034540e37a8
Author: donnak 
Date:   Tue Dec 18 21:06:18 2007 +0000

    Rewrote info abt accessing track descriptions.

commit 6c6bb6b5828df7eedde7c18390630f277427128c
Author: angie 
Date:   Tue Dec 18 20:38:14 2007 +0000

    Added a couple notes about the omission of simpleRepeat filtering -> trfMaskChrom.  The omission led to overmasking (and an inaccurate bigZips/README.txt, noticed by a user).  Also added some notes for next time to use automation scripts.

commit f3d8ee665a3d81099f4069793aaee6ad2f4964a0
Author: galt 
Date:   Tue Dec 18 16:00:07 2007 +0000

    "Encode release log update"

commit 5b51e54be2ebd97178534c12abd948b64089872b
Author: galt 
Date:   Tue Dec 18 16:00:04 2007 +0000

    "Release log update"

commit ac54f4154f5c43cad1701655ecdfb046776b4c98
Author: kate 
Date:   Tue Dec 18 06:14:12 2007 +0000

    Add cell line validation

commit edebab5452db9a67f0f132eaf060318d05e15885
Author: angie 
Date:   Tue Dec 18 06:00:27 2007 +0000

    Added snp128 track tables.  They will probably be reloaded in the near future, but the new track flow is there and I would like for it to be reviewed along with snpNcbiToUcsc.

commit 081533924a97c603b794598b3eed21f95b178d8b
Author: angie 
Date:   Tue Dec 18 05:37:01 2007 +0000

    Replaced snp/ subdirs with just snp, which now has a makefile.

commit ccc52a0ef84795a62e5c3eae8c84658e1ddb2bdf
Author: angie 
Date:   Tue Dec 18 05:36:34 2007 +0000

    Adding a makefile so that 1) snpLoad is included in the top-down build and
    2) subdirs of this directory don't have to be named in ../makefile.

commit 0049143ac0d0681d5685f73d6215b1fa9158cdec
Author: angie 
Date:   Tue Dec 18 05:27:43 2007 +0000

    Made snpNcbiToUcsc the default target, instead of the many snp* programs that snpNcbiToUcsc is intended to replace.

commit f7c83ecb6b8cb9c74940d4da0b4f3167f8485325
Author: angie 
Date:   Tue Dec 18 05:26:57 2007 +0000

    One program to replace all of the programs in pipeline.csh and several others -- in one pass through a tab-separated file of fields extracted from NCBI dbSNP tables and fasta headers, translate NCBI's encodings into our snp125+ table columns, and perform various consistency checks.

commit fe9a284be334cfd56e807066ff82c29245102fba
Author: kate 
Date:   Tue Dec 18 05:20:34 2007 +0000

    Add some validation of DDF file entries

commit 24343f4a90d69db2d62c7d2ffa23231b337e0616
Author: donnak 
Date:   Tue Dec 18 00:31:02 2007 +0000

    Added link for NAR DB pub.

commit 116b750ef0362cb81f7d4ebddf4ec3a253fc964e
Author: kate 
Date:   Tue Dec 18 00:28:48 2007 +0000

    Add parsing of .ra files

commit 081ac9da7514f716fb9675ff4b4abaa417d41b27
Author: galt 
Date:   Mon Dec 17 22:59:31 2007 +0000

    fixed overlapping tags TT and PRE so that they are properly nested now

commit b1e97a0059ea8dde10ae45cc8d4348e73bf4f2b8
Author: kate 
Date:   Mon Dec 17 19:13:36 2007 +0000

    Preliminary checkin.  This version validates PIF file and starts working with DDF file

commit 37f60b3b05263c0e52895d3cee0dafe5bc7d15ac
Author: kate 
Date:   Mon Dec 17 19:12:24 2007 +0000

    Tweak label for new feature, based on code review

commit 1c96e29a9d9d8d31aa7dcfffeadd8438e7cf7e25
Author: galt 
Date:   Mon Dec 17 16:00:08 2007 +0000

    "Encode release log update"

commit 0ae5b4133a333d109af1b63dfaead863af61e090
Author: galt 
Date:   Mon Dec 17 16:00:04 2007 +0000

    "Release log update"

commit 7a6796dd9f9cf427be82ed2d942158a021fd443d
Author: braney 
Date:   Mon Dec 17 15:42:18 2007 +0000

    back out change that was causing new problems

commit c66e6c313a3499dd22106dd5579b3ae91fa986d1
Author: braney 
Date:   Mon Dec 17 02:29:14 2007 +0000

    fix a bug in browser where blue bars were being incorrectly drawn.

commit 9d7cd33cf800e43d207befa8f15288713553e3fd
Author: braney 
Date:   Mon Dec 17 00:03:46 2007 +0000

    fix a bug causing blank alignments in regions using codon translation

commit 59b177b10ceb1c0027a2f8df9da35c8340c5d910
Author: fanhsu 
Date:   Sun Dec 16 23:21:36 2007 +0000

    Updated doGetText headers, and added special processing logic as the html table.

commit 5e30387241ae97c94916c2ef408f827fb3941937
Author: fanhsu 
Date:   Sun Dec 16 23:16:22 2007 +0000

    Changed sex into gender.

commit 820048cd15f21fda4490eb2595ac2f10f7aecfcd
Author: galt 
Date:   Sun Dec 16 16:00:08 2007 +0000

    "Encode release log update"

commit 9c708720a08cee394d8893db060c0e93077c2de1
Author: galt 
Date:   Sun Dec 16 16:00:05 2007 +0000

    "Release log update"

commit 19acb5a4095b4fbb4dc54b4e7d0235b56283ef0d
Author: fanhsu 
Date:   Sat Dec 15 18:11:11 2007 +0000

    Updated according to GSID's request.

commit 41a5bb63c6151d8f919a6ab6a0cc675632f36410
Author: fanhsu 
Date:   Sat Dec 15 18:08:28 2007 +0000

    Updated the URL to method and prototocol at GSID.

commit aef856cbc2081fbbe348662e2ca5a00a92c2479c
Author: fanhsu 
Date:   Sat Dec 15 17:49:14 2007 +0000

    Updated per request from GSID.

commit 0b5db815a247a41efd411f6b8e0549457ee85a92
Author: fanhsu 
Date:   Sat Dec 15 17:16:28 2007 +0000

    Added gsid.h.

commit 9bdfd7bf1964ac2a2c14b32e098f3592bdcb9650
Author: fanhsu 
Date:   Sat Dec 15 17:15:27 2007 +0000

    Updated according to GSID's request.

commit 6be159fb8480a44dbf753d63627cc8b22d1c8a63
Author: fanhsu 
Date:   Sat Dec 15 16:41:14 2007 +0000

    Created gsid.h.

commit 6d3807325430bb9a608d6ff1ef8b05bbef4e0917
Author: galt 
Date:   Sat Dec 15 16:00:07 2007 +0000

    "Encode release log update"

commit db9e46d576670f7987a685d72f0f655e3691147a
Author: galt 
Date:   Sat Dec 15 16:00:05 2007 +0000

    "Release log update"

commit 487253f155f7d83c25087076292f414393e0809c
Author: markd 
Date:   Sat Dec 15 00:58:39 2007 +0000

    fixed long standing strand bug

commit 5ed810ed493b71c0e56145d4382ae9a5a641838e
Author: markd 
Date:   Sat Dec 15 00:10:37 2007 +0000

    fixed warning

commit 2a6b41703c7651d249b7f2911381d9d5107753e1
Author: markd 
Date:   Fri Dec 14 23:13:34 2007 +0000

    added to-do items

commit 11073b552eabeb61f929b78443c7e5ffcc267a0d
Author: kent 
Date:   Fri Dec 14 23:00:12 2007 +0000

    Making it so that database doesn't have to be first item in org list.

commit 2f8ad5b10c7a8c8b0a4138f8a73082f44269c3f9
Author: markd 
Date:   Fri Dec 14 22:45:23 2007 +0000

    added global log file for importing CCDS

commit 5a659372fc510e729926154ef406c7691e293bd5
Author: markd 
Date:   Fri Dec 14 22:44:18 2007 +0000

    fixed clink on CCDS genes within PAR by including chromosome in selection

commit cdc2c122059bcb1a95c06912bde89900774a6c5f
Author: archanat 
Date:   Fri Dec 14 19:33:52 2007 +0000

    defined database for ponAbe2

commit 24799a47b06d0566f19d40c37327eb8e4c8078be
Author: galt 
Date:   Fri Dec 14 16:00:07 2007 +0000

    "Encode release log update"

commit 871b1e0d11fad2644031152d2f825dfdc27dd1fa
Author: galt 
Date:   Fri Dec 14 16:00:03 2007 +0000

    "Release log update"

commit 4cdeb55ec45eff40799c8f76125a0edc883bf856
Author: angie 
Date:   Fri Dec 14 04:16:27 2007 +0000

    Changed identifierHash to take a db arg in addition to table, so it can form db.table to match curTable when necessary.

commit a7d2be73ef7a5e55754577fc628903f5ec502fd8
Author: angie 
Date:   Fri Dec 14 01:20:27 2007 +0000

    Replaced a couple hardcoded POST's with cart var formMethod for easier debugging.

commit ae05c788e8438c1ecf031384a390bbbfa6c277b5
Author: angie 
Date:   Fri Dec 14 01:07:42 2007 +0000

    Added a separate vs_list args2 for vaWarn in qaStatusSoftError.  The reuse of args was resulting in bogus text in the final message.

commit 36be683a9f0033ba043c6e8c21a74ff792999643
Author: hiram 
Date:   Fri Dec 14 00:21:15 2007 +0000

    Finished off the calJac1 blastz and swap

commit 2e0057860f8675483c50283543768658efbae657
Author: hiram 
Date:   Fri Dec 14 00:10:36 2007 +0000

    use chooseFileServer correctly from HgAutomate, and use the fileServer for the gzip of the net file, and fixup confusion between local and global variable fileServer

commit 896820cedf1a902c363e1e1bb8af01c805902da8
Author: hiram 
Date:   Fri Dec 14 00:09:10 2007 +0000

    Running a galGal3 blastz to verify changes in the doBlastz script.

commit 7cf7190998f54da120e0ade0c5b5327b062855c9
Author: hiram 
Date:   Fri Dec 14 00:08:31 2007 +0000

    Finished off ornAna1 blastz swap.

commit 37792acd2eadfb9031536f08808734ff45eecb75
Author: hiram 
Date:   Fri Dec 14 00:01:02 2007 +0000

    Finished calJac1 blastz with a manual load of the enormous chainLink table.

commit 88b8c62074b913268e7dddc37978f84a53457047
Author: hiram 
Date:   Thu Dec 13 23:59:43 2007 +0000

    Make downloads for calJac1 swap blastz

commit e833c0320c6429da40e117856ce3389b6d074cc8
Author: donnak 
Date:   Thu Dec 13 22:15:28 2007 +0000

    Added microarray CT format.

commit 99eb3d0e02343ccda6da8b7ef55b2896b99c8451
Author: fanhsu 
Date:   Thu Dec 13 22:09:51 2007 +0000

    Added links to SeattleSNPs PGA genes on hgGene details page.

commit a0ebf47bbf8d5180f469327d9a7472b863a3dce8
Author: donnak 
Date:   Thu Dec 13 21:48:59 2007 +0000

    Added section on microarray track format.

commit 00902b2a894d0948013aa2d01a55e2d738a47c3d
Author: fanhsu 
Date:   Thu Dec 13 21:48:48 2007 +0000

    Added pga table for SeattleSNPs PGA.

commit 6d08a0ade348799c954f0a3feb39c0d1a3c10fc5
Author: galt 
Date:   Thu Dec 13 20:30:15 2007 +0000

    adding support for archive undelete and restoring previous state

commit 4166a265484a0d3a6b8b57304e17b588629f83a9
Author: archanat 
Date:   Thu Dec 13 20:04:02 2007 +0000

    Limited text to 80 characters and fixed the references

commit 9442d1449b7e5cd0a0cdd457a73aef82c762b29f
Author: archanat 
Date:   Thu Dec 13 19:34:44 2007 +0000

    Limited text to 80 characters and also fixed the references.

commit 130574f30cf19ef3bbf75cad49e2e3219b7d4326
Author: fanhsu 
Date:   Thu Dec 13 19:29:42 2007 +0000

    Added SeattleSNPs PGA link.

commit f2609009d5e884b512a715e6e3575d879cdf8ea9
Author: galt 
Date:   Thu Dec 13 16:00:12 2007 +0000

    "Encode release log update"

commit 0344010b426febeb87ca7fca4f65d2df2604569b
Author: galt 
Date:   Thu Dec 13 16:00:09 2007 +0000

    "Release log update"

commit 7a91a086c1512104d0651a892deb652ae263c9bf
Author: donnak 
Date:   Thu Dec 13 00:34:18 2007 +0000

    Archived an item.

commit 4e0fa5c9e2c3b284bf144d3a31e1dcbc9ee9ceb1
Author: donnak 
Date:   Thu Dec 13 00:32:37 2007 +0000

    Added news item abt job openings.

commit 30c8a9ae38afaf908576b4b4f47b47fb224702b6
Author: hiram 
Date:   Thu Dec 13 00:00:58 2007 +0000

    Made the pushQ entry.

commit 40ab4342f642714b267080c00e7e49213d57fdca
Author: hiram 
Date:   Wed Dec 12 23:46:09 2007 +0000

    Done with the phastCons experiments.  The 8-way track is completed.

commit 1ae9af1a561552aee348b23d082c4ec300c8e4fc
Author: aamp 
Date:   Wed Dec 12 23:30:12 2007 +0000

    Supertrack description page for EC tracks.

commit 6136df4c2f789b288cd57da0529a5d3b5d245f4e
Author: aamp 
Date:   Wed Dec 12 23:28:52 2007 +0000

    Supertracked the Affy EC tracks.

commit fcf59982ed846586ec37559c408e02daab2b67c9
Author: hiram 
Date:   Wed Dec 12 23:27:56 2007 +0000

    Proper priority on the Conservation vs the most conserved tracks

commit 3200faa6565fb613136a92bb321ca0337bf0ae96
Author: hiram 
Date:   Wed Dec 12 23:27:34 2007 +0000

    Initial source

commit ae3ceefebf7ea2934820e6a05f34505d68ec3f65
Author: markd 
Date:   Wed Dec 12 23:24:59 2007 +0000

    fixed link to CCDS site to function when a CCDS is delete in a new assembly, but still valid in an older one

commit a027248950e7747c83eeac616c349ab3855e34cc
Author: kuhn 
Date:   Wed Dec 12 22:58:00 2007 +0000

    punctuation

commit 0b4d2f42f3f7e253d07078b288b1306c989de8a5
Author: kuhn 
Date:   Wed Dec 12 22:56:48 2007 +0000

    punctuation

commit 6974fe795692de536c43893d03aced169ed6c72e
Author: kuhn 
Date:   Wed Dec 12 22:54:49 2007 +0000

    removed the extra links to the same affiliation

commit b0da87f00b1e0540436c03e08bab49c2e39fdbbd
Author: fanhsu 
Date:   Wed Dec 12 22:39:55 2007 +0000

    Updated contact info.

commit cb33b7e17b5b85d3acf9b78b6251d8ec185523b6
Author: rhead 
Date:   Wed Dec 12 21:25:15 2007 +0000

    Puncutation.

commit dc76674768fb6946291dfa9644b00deaac3822e0
Author: aamp 
Date:   Wed Dec 12 21:15:08 2007 +0000

    Descriptions mixed up a bit.

commit 57cacc3c1477a6008f8f2924470986f1523cffc2
Author: galt 
Date:   Wed Dec 12 20:43:30 2007 +0000

    removing dependencies on old settings

commit 9a444c1e453cf5d0b103e419c5bd7dfcdcd0efbe
Author: galt 
Date:   Wed Dec 12 19:59:40 2007 +0000

    fixing shell issues

commit 4faf040b5837e6fa36e4970b579644262bd291cb
Author: angie 
Date:   Wed Dec 12 19:49:04 2007 +0000

    Added local def of snp127, with snpSeq setting so it doesn't default to snp126's snpSeq table.

commit ab087a376dcf5efe4508b383eb67d1d2993f0a7c
Author: angie 
Date:   Wed Dec 12 19:47:47 2007 +0000

    in doSnpWithVersions, don't display the MultipleAlignments exception -- redundant with display of other mappings below.

commit 7804ca3e40141c5df46b197f78a725f2b9f9bd9c
Author: angie 
Date:   Wed Dec 12 19:42:09 2007 +0000

    In snp125Color, instead of treating ignored function types as unknown, really ignore them (unknown could have an interesting color).  Also fixed the way I was invoking the color comparator.

commit e6ccabb38e9d2c83b222e2388c37b6e3dc4acc21
Author: kuhn 
Date:   Wed Dec 12 19:25:24 2007 +0000

    put the Most Conserved composite tracks behind 'release alpha' to keep it from leaking out to the RR

commit 34a83aeba5e996b4aa6aec729e4cfb49631e260e
Author: markd 
Date:   Wed Dec 12 19:24:53 2007 +0000

    updated ccds tables

commit c1a979768c0d877e1cbf62b17320a9f4ec4bc7d6
Author: markd 
Date:   Wed Dec 12 18:47:56 2007 +0000

    handle new table dumps without quoted columns

commit 316586e694fb802a8a4f4852b7dd587bb46f3b71
Author: fanhsu 
Date:   Wed Dec 12 18:43:01 2007 +0000

    Added geneTests links for hgGene details page.

commit f2c324e0eaa97d11a0e89c822974c10539e52a42
Author: fanhsu 
Date:   Wed Dec 12 18:23:53 2007 +0000

    Added link to GeneTests.

commit 0198b6330976e0498932768eefc4ad53677a80ff
Author: markd 
Date:   Wed Dec 12 18:21:26 2007 +0000

    build mm9 swap chains

commit c3a5edb0d3e353dfa1973a9d15919830eb748b39
Author: markd 
Date:   Wed Dec 12 18:21:18 2007 +0000

    build monDom4 swap chains

commit 9c688a06b7ddc8cc9da3ff6dfa6fb1d7736a3054
Author: markd 
Date:   Wed Dec 12 18:20:13 2007 +0000

    build canFam2 swap chains

commit 81d5866e9ff6fc2bdbca779f123608d1d23cd363
Author: fanhsu 
Date:   Wed Dec 12 18:18:55 2007 +0000

    Created geneTest.sql.

commit eafb28aefb41a382b8bfc001d36cda65c26d7f53
Author: markd 
Date:   Wed Dec 12 18:17:28 2007 +0000

    build hg18 swap chains

commit 30b57e2c9d4c5ba33b44e479c85fe12c63f0c4b2
Author: hiram 
Date:   Wed Dec 12 17:30:17 2007 +0000

    No need for the second graph and most conserved on the 8-way, and turn on mouse

commit d9dd5ae3be1263e3ed66063f49449b67970dfc3c
Author: hiram 
Date:   Wed Dec 12 17:17:21 2007 +0000

    Proper link to WUSTL sequence center

commit 9a59ab4a7a7f1569bce2c6c759ee912599c96d70
Author: hiram 
Date:   Wed Dec 12 17:16:33 2007 +0000

    Properly remove and copy this script to the scripts directory to maintain ownership and date/time stamp properly

commit 9fd69af98a870b50d60435306e7fa3d7fa5674f1
Author: hiram 
Date:   Wed Dec 12 17:13:55 2007 +0000

    Test for fully qualified kk name too

commit 292dc6c3b72739996c470a5a0822035af2ac0dfb
Author: galt 
Date:   Wed Dec 12 16:00:06 2007 +0000

    "Encode release log update"

commit 07b63fcec1fa0de8864715998b9f4e26e0faf065
Author: galt 
Date:   Wed Dec 12 16:00:03 2007 +0000

    "Release log update"

commit bc9b192c66d6dce3015b10899d934b3b707324fe
Author: galt 
Date:   Wed Dec 12 02:41:47 2007 +0000

    added status field to project_archives

commit c2f4b682ed126eea3193f23920bdd043ad09f13b
Author: galt 
Date:   Wed Dec 12 01:58:07 2007 +0000

    added status field to project_archives

commit 03222a26f5cc5bbf9f256932f4bf792f228fedb7
Author: rhead 
Date:   Wed Dec 12 01:42:49 2007 +0000

    Deleted the copy of affyTxnPhase3* blocks (revision 1.252). Andy also made this addition in revision 1.253.

commit f9b2c2915e1aa33dde9d4b12e2632eeb5ab3eec8
Author: aamp 
Date:   Wed Dec 12 01:15:09 2007 +0000

    Supertracked the Affy Transcriptome track.

commit 52fbb008ede5b198c49792e10d4f31331563494f
Author: hiram 
Date:   Wed Dec 12 00:34:06 2007 +0000

    Fixup chainMergeSort situation for too many chains in one directory to work in the shell expansion

commit f08874515ebf72afa48bff0ce56f75fef3214fdf
Author: rhead 
Date:   Wed Dec 12 00:01:04 2007 +0000

    Copied affyTxnPhase3* blocks to assembly level in order to add an origAssembly line (as these tracks were lifted from hg17).

commit d8201a39c9ad50fec66809af8349b5b1f8c752d9
Author: angie 
Date:   Tue Dec 11 23:18:17 2007 +0000

    Improved filtering by snp125Func -- ignore types we don't care about if other types are listed.  Still coloring those types as unknown (but they can be overridden by more interesting colors if other types are given).

commit a829a95066c5f19d385587241e429a5178f58d7a
Author: angie 
Date:   Tue Dec 11 23:15:01 2007 +0000

    In snp125FuncDataSynonyms, map the no-op types to ignore for better filtering.

commit 03fb1e602a12d6873a12e62a252ced7ac2d010c5
Author: galt 
Date:   Tue Dec 11 22:21:51 2007 +0000

    added the local file upload back

commit 98ffe67eabbe4367497a930c08452c2df85c0f12
Author: angie 
Date:   Tue Dec 11 21:35:08 2007 +0000

    Preparation for snp128: replaced hardcoded ortho table name with trackDb setting; more general snpNNN track name match.

commit abbc1bf425782f5fd5f63bdea751ce8acce3d5f5
Author: angie 
Date:   Tue Dec 11 21:21:00 2007 +0000

    Added relative priorities to snp12* so they appear newest-first.

commit 63ef235dba8e24ae644edee07b11f42d45cec7d7
Author: angie 
Date:   Tue Dec 11 21:14:01 2007 +0000

    Registered snp128 track.

commit 3f5b967e343fca34118c8319edcdc657a1a5eb9a
Author: angie 
Date:   Tue Dec 11 21:04:17 2007 +0000

    Added a mapping of newer, more specific NCBI function types onto the older, more general types.

commit a8056c61621d4ef9c16d3d7498c85aee2f719c75
Author: angie 
Date:   Tue Dec 11 21:03:45 2007 +0000

    Extended the snp125 coloring code to deal with new function types from NCBI.  Replaced hardcoded ortho table name with trackDb setting.  Removed some orphan code.

commit d82767a9354b142332fbfaf598907b832e38d830
Author: hiram 
Date:   Tue Dec 11 19:55:18 2007 +0000

    Reloading genbank alignments

commit 12e81e76da9244c4053605777939653060d5de7b
Author: aamp 
Date:   Tue Dec 11 18:54:33 2007 +0000

    Added chrY fix for short HeLa signal track.

commit 31dcf7f3d08c6ffd30790e428ace240bdea1bb37
Author: galt 
Date:   Tue Dec 11 16:00:08 2007 +0000

    "Encode release log update"

commit eb2449aa77be194abb6904034b4c863e4076ce7c
Author: galt 
Date:   Tue Dec 11 16:00:04 2007 +0000

    "Release log update"

commit 6b474a80c7b096b2fab5368a695d3fe3c59b93ee
Author: giardine 
Date:   Tue Dec 11 14:02:33 2007 +0000

    Added some more IDbases

commit 5b26de52dba03577d5aa4d29311c6d7c1eba8e9a
Author: giardine 
Date:   Tue Dec 11 14:01:36 2007 +0000

    Changed globin to phencode

commit 0ad5a5fd7389f670943f28d17357db712c5f7364
Author: giardine 
Date:   Tue Dec 11 14:00:47 2007 +0000

    Switch to relative url for Genome Graphs, and globin to phencode

commit 5f2e95cd96be714b5bcd6c76d3fa18f4c1864b18
Author: giardine 
Date:   Tue Dec 11 13:59:15 2007 +0000

    Change globin to phencode in link

commit c59e7719f84aad4935ed41924c1aa99c1ee34eb6
Author: angie 
Date:   Tue Dec 11 08:33:15 2007 +0000

    Cleanup of code for snp12*, in preparation for snp128: added trackDb settings and smart defaults in order to avoid hardcoded names and needless dependency on extFile; removed a lot of orphan code.

commit 95949ae5a904e764ad62178acadb4763c50d5257
Author: angie 
Date:   Tue Dec 11 06:17:45 2007 +0000

    Added url and urlLabel to snp track.

commit a95e25b7d6ae05e3adb3a3b7f3405a9e43e90be1
Author: angie 
Date:   Tue Dec 11 06:13:48 2007 +0000

    Added snp128 searches.  Put snp12x searches in order and added relative priorities so they will be performed in the correct order.

commit 9bb0fa966cdaaab3f3f31528c25310833b1db892
Author: angie 
Date:   Tue Dec 11 05:57:26 2007 +0000

    Added local definitions of snp126, snp128 with new chimpMacaqueOrthoTable setting.

commit c3142d7bab2c2de2da29701ace324398483035a1
Author: angie 
Date:   Tue Dec 11 05:55:39 2007 +0000

    Added snp128; added url and urlLabel settings to snp12*.

commit becf61c7943574eba746da32b6ef1de4506c8fda
Author: hartera 
Date:   Tue Dec 11 00:35:26 2007 +0000

    Added hArchiveDbExists() to check that a database name exists in dbDbArch. Added hDbDbCmpOrderKey() to sort a list of dbDb objects on orderKey.

commit 857fe100ac2593407a9a55b638ae3222bb3cc452
Author: hartera 
Date:   Tue Dec 11 00:30:50 2007 +0000

    Added a sort function to sort a list by orderKey for a dbDb object. Added a sort to both hGetLiftOverFromDatabases() and hGetLiftOverToDatabases() so that the concatenated list of databases from dbDb and dbDbArch are sorted by orderKey. This results in the correct order of assemblies in the dropdown menus for hgLiftOver and hgConvert.

commit fa5b0dfdec086e84db8853677634bbe087d77ab7
Author: ann 
Date:   Tue Dec 11 00:19:39 2007 +0000

    relaxed ensInfo part of ensemblTranscriptId rule (OKd by Rachel)

commit 966fdbf4682e649316bb8edda8f5ceaed9afd5c1
Author: fanhsu 
Date:   Mon Dec 10 23:52:52 2007 +0000

    Adopted from pbGlobal.c.  Initial check in.  To be refined ...

commit bf54633c8da8a5431a439523afd901acf240eced
Author: fanhsu 
Date:   Mon Dec 10 23:51:56 2007 +0000

    Created makefile.

commit ff96afa86ea56123646aecf59d66b3ffa83dc3cd
Author: kate 
Date:   Mon Dec 10 22:36:54 2007 +0000

    Add fast configure option to configure page.  This will cause track config submit buttons to navigate to configure page.

commit 8e0f2a3cc58889b44fe836a298d34226207b901a
Author: ann 
Date:   Mon Dec 10 22:13:49 2007 +0000

    added mm8 to less-strict locusLinkId rule

commit 8927b91f0fadd727943fc5c90d68bdd0d76ad342
Author: ann 
Date:   Mon Dec 10 22:07:22 2007 +0000

    moved mm5 down to less-strict rule. as dbs get older they drift further.

commit 0162789fb064f2997a7a003ff101fca6c1f7d051
Author: ann 
Date:   Mon Dec 10 22:03:31 2007 +0000

    slightly more relaxing of the flyBase2004Xref rule

commit b0c7bb324d09d352b38ec36cba871991ace7a5a6
Author: ann 
Date:   Mon Dec 10 21:59:38 2007 +0000

    slight relaxing of the flyBase2004Xref rule

commit 5936de3ac37a7ab4470de257ad5bb8107aa4de2d
Author: kuhn 
Date:   Mon Dec 10 20:04:13 2007 +0000

    added some descriptive methods

commit 403c9fd964ad24bd88cc93a1e14fb82141f4e114
Author: ann 
Date:   Mon Dec 10 18:46:51 2007 +0000

    removed hg17 from part of hapmapSnpId rule

commit 19940b506d0a78a03a8ac6ce011eed7e6ec152da
Author: galt 
Date:   Mon Dec 10 16:00:05 2007 +0000

    "Encode release log update"

commit 5d253db4e15d004ad6b7d45e92b53b9399b97ce0
Author: galt 
Date:   Mon Dec 10 16:00:03 2007 +0000

    "Release log update"

commit 7f4659ba1578476adacdd9a2ff06d549bff84500
Author: galt 
Date:   Sun Dec 9 16:00:05 2007 +0000

    "Encode release log update"

commit 50ba32ca2767f80b8e586271cd6b7b25d3148aa2
Author: galt 
Date:   Sun Dec 9 16:00:03 2007 +0000

    "Release log update"

commit 1387d4e6064e8e3e2d304802ec64f49f89eb7e6a
Author: galt 
Date:   Sat Dec 8 16:00:06 2007 +0000

    "Encode release log update"

commit 01c7261e20d641b6f154c8498bc9c6ba87382d87
Author: galt 
Date:   Sat Dec 8 16:00:05 2007 +0000

    "Release log update"

commit ebe1d2de9102a7dbda5fa91a81ab160a596c0574
Author: angie 
Date:   Sat Dec 8 00:31:34 2007 +0000

    Removed some unnecessary subTrack-off's and n/a subtrack entries from hapmapLd and hapmapLdPh.

commit 07f60f98b5f7f711586813ee2c626196f80b605f
Author: angie 
Date:   Sat Dec 8 00:28:39 2007 +0000

    Added per-chromosome RepeatMasker .align downloads -- user request.

commit 67fbf597c4fd857f96f7af7e8631575a366148de
Author: angie 
Date:   Fri Dec 7 23:17:30 2007 +0000

    Added per-chromosome RepeatMasker .align downloads -- user request.

commit 4222cc22e6e69dfe208498cb354d0011572ff8fe
Author: galt 
Date:   Fri Dec 7 20:33:33 2007 +0000

    adding miniBlat.c

commit 70257e4d0c25a90728dbdf9355259f243d554d77
Author: angie 
Date:   Fri Dec 7 19:32:58 2007 +0000

    Added soft-masked chromosome fasta downloads.

commit 8dc170cbb62312efc7acf79135679a26e224125b
Author: aamp 
Date:   Fri Dec 7 18:20:17 2007 +0000

    Changed EC tracks.

commit 70964f84e8f08e3bd420b795a784f94c5b32d22b
Author: galt 
Date:   Fri Dec 7 16:00:05 2007 +0000

    "Encode release log update"

commit 11e012b51efcf64b16cdc7be3ea9f8ab3bc22e55
Author: galt 
Date:   Fri Dec 7 16:00:03 2007 +0000

    "Release log update"

commit d7329c8483edf7fd69529c65fac40eb963d42d78
Author: markd 
Date:   Fri Dec 7 01:45:50 2007 +0000

    removed vi swap file JK committed in some 20001 coding frenzy

commit 08093f166da876050683cbbc775fbca5a2f6d04e
Author: rhead 
Date:   Fri Dec 7 01:27:05 2007 +0000

    Added url for hgFindSpec instructions.

commit d8aadf9b85d93a7c0c17133b8f22e6164e8819d0
Author: markd 
Date:   Thu Dec 6 16:25:20 2007 +0000

    added ignore entries

commit c111d76ceec1fd43bc7230a8664c415f67621c93
Author: galt 
Date:   Thu Dec 6 16:00:06 2007 +0000

    "Encode release log update"

commit 58a792b37a8ac61da332d143929fe384eca32c87
Author: galt 
Date:   Thu Dec 6 16:00:04 2007 +0000

    "Release log update"

commit 5808b53d485853f154faae462a995d9d93fb4ac1
Author: galt 
Date:   Thu Dec 6 02:37:38 2007 +0000

    adding encode Yale RACE

commit a0ea28d1e16911a527af8e76b2d123902c3a30c3
Author: mhoechsm 
Date:   Wed Dec 5 23:10:34 2007 +0000

    removed coloring for alternative startcodon CTG. LOWELAB browser only!!

commit fbfc9f50e7565f690a0fda477218f5fefa113c73
Author: mhoechsm 
Date:   Wed Dec 5 21:01:20 2007 +0000

    fixed a problem with color coding alternative start codons

commit c2dc56a6ecf64182240417258403f2c04c77e636
Author: ann 
Date:   Wed Dec 5 19:25:26 2007 +0000

    changed reference to Genome Browser to GSID HIV Data Browser

commit 56fb484ff01e61f349d20b67ee3c09df2cc53666
Author: ann 
Date:   Wed Dec 5 19:19:57 2007 +0000

    fixed link to credits page

commit 2489d13580d9f334e1f40b03303976e8e9e180ff
Author: jzhu 
Date:   Wed Dec 5 18:29:03 2007 +0000

    add more groups for the instinct project

commit 6d50882599fc1add90b99f053e1157b216fa831c
Author: jzhu 
Date:   Wed Dec 5 18:27:57 2007 +0000

    update trackDb.instinct.ra

commit d60247f6320793e02c33884ced11fbd0b85ec488
Author: galt 
Date:   Wed Dec 5 16:00:05 2007 +0000

    "Encode release log update"

commit 0c3cc7501ab52cc7e7237a54d125bcd239bf198e
Author: galt 
Date:   Wed Dec 5 16:00:03 2007 +0000

    "Release log update"

commit d5514a033c8af5628b72a4e4302cd3e9a73b11e2
Author: kuhn 
Date:   Wed Dec 5 14:51:01 2007 +0000

    changed name and priority of 30way multiz to match connvention

commit 701123d68b7f36fde9e91182e27843287c5ecd9a
Author: kuhn 
Date:   Wed Dec 5 12:25:55 2007 +0000

    changed to 2 sec delay

commit ff9f1ac6f4d7902ff00ff81417bc1511d8d4ff96
Author: hiram 
Date:   Wed Dec 5 06:47:53 2007 +0000

    Do not put the self species on the pair-wise list, causes hgc to go crazy

commit 08a10021d6fa61bd03f75fe126b0a5dc43d1061f
Author: kate 
Date:   Wed Dec 5 01:35:52 2007 +0000

    Update Duke Dnase entry prior to adding to pushQ

commit 08fe060d615ada5f0eafee39078ef470d1b825ca
Author: kate 
Date:   Wed Dec 5 01:29:46 2007 +0000

    Change default wiggle config per request by Terry Furey

commit d1091967cf4d0cecf5005e4129ce45cf01053515
Author: kate 
Date:   Wed Dec 5 00:19:17 2007 +0000

    Expand buffer for track name

commit d3c72e15b40929b205000226d65687a6dc2c2490
Author: hartera 
Date:   Tue Dec 4 20:19:54 2007 +0000

    Adding dbDbArch table for download. This table contains information about archived databases and was previously unavailable to mirrors.

commit e37739a6c5100723b217c0a5a9b7a900e2d8de84
Author: angie 
Date:   Tue Dec 4 19:05:26 2007 +0000

    Shortened longLabel for JPT+CHB subtracks of hapmapLd and hapmapLdPh.

commit a7a6669c6499576c095aa60551e5cfe0d40f5524
Author: ann 
Date:   Tue Dec 4 17:30:19 2007 +0000

    using the newer-style googleForm request

commit 0f4c98d2da8162709ad5750d880f7e6237a4d2cb
Author: aamp 
Date:   Tue Dec 4 17:27:20 2007 +0000

    "New version number v172"

commit a94e084828dd3e97f66383b6520b95b0c95e7b1e
Author: aamp 
Date:   Tue Dec 4 17:24:55 2007 +0000

    Affy transcriptome instructions.

commit 2b65dad6f57aed132a7fccfa70624c2f9421f888
Author: aamp 
Date:   Tue Dec 4 16:19:35 2007 +0000

    Added missing '>' to  tag.

commit c772478d74ea1233db670d079995a3d1510e14f3
Author: galt 
Date:   Tue Dec 4 16:00:05 2007 +0000

    "Encode release log update"

commit 5f6d01dd70eac030d3e341eb2edac605c221aead
Author: galt 
Date:   Tue Dec 4 16:00:03 2007 +0000

    "Release log update"

commit 02428836756262699f18353883b398cfb6e190a3
Author: angie 
Date:   Tue Dec 4 01:01:19 2007 +0000

    In ldDrawDense and ldDrawDenseValue, avoid subtractions that lead to unsigned underflow.

commit 73ea65184757d7a00df862683fe9a195a3fe5ef3
Author: fanhsu 
Date:   Tue Dec 4 00:41:29 2007 +0000

    Removed ispyTables.as.  It is replaced by ispyTableDefs.as.

commit 30b257f819e8d82a514fc1baa56b2e02fd7bdc10
Author: angie 
Date:   Tue Dec 4 00:27:09 2007 +0000

    Added the older of two dupes (ispyTables.as older than ispyTablesDefs.as) to %autoSqlIgnore.

commit 390bcaa1de9e3d11e413856712df9c557e36af05
Author: kuhn 
Date:   Tue Dec 4 00:15:23 2007 +0000

    reduced sleep to 5 sec and added reporting to see state of delay before reset

commit 7ca90fc67fed69002d9304f20bd5c5ec4002ab1f
Author: angie 
Date:   Mon Dec 3 23:37:46 2007 +0000

    Added another historical note about automated updates to igtc (Gene Trap).

commit 2317603f5deab222eb2170f774baa2cb9e96c5f5
Author: angie 
Date:   Mon Dec 3 23:32:09 2007 +0000

    Added note about monthly automated loading of igtc (Gene Trap).

commit 7f39d1b353deee275b30c5b2157f5162d949146b
Author: hiram 
Date:   Mon Dec 3 23:23:32 2007 +0000

    Turning on primates and vertebrate phastCons tracks on 8-way

commit 5d962fbb6bc8d313a13c3c62c410cf2a51984f3a
Author: fanhsu 
Date:   Mon Dec 3 22:50:43 2007 +0000

    Turn on PDF/PS.

commit 4b28257f880cd8c00ed2b02835806eb32fd7e53a
Author: donnak 
Date:   Mon Dec 3 20:48:28 2007 +0000

    Added 2 pubs.

commit 69b45cc8df08d10cca311c39711e5913e706d1e7
Author: galt 
Date:   Mon Dec 3 16:00:04 2007 +0000

    "Encode release log update"

commit 39213e620b44fcdecbc21ed4ca11e943241e78b4
Author: galt 
Date:   Mon Dec 3 16:00:02 2007 +0000

    "Release log update"

commit 2dfde8ad08a4968425b1ebad7274e867b01b4020
Author: baertsch 
Date:   Sun Dec 2 19:26:47 2007 +0000

    move organutan and marmoset chains and nets to the proper place in the comp geno track group

commit b1b06bc0911efce55a7fff6f0b005407a7d48dd1
Author: galt 
Date:   Sun Dec 2 16:00:03 2007 +0000

    "Encode release log update"

commit ed512574eeaa85effe198fe4347878861e182eb0
Author: galt 
Date:   Sun Dec 2 16:00:01 2007 +0000

    "Release log update"

commit 3eaa4f143ccec90aae7b28c1db659da4dd604b8c
Author: galt 
Date:   Sat Dec 1 16:00:06 2007 +0000

    "Encode release log update"

commit 9d1684dfea0d91584bc12c9fce61287872816a9a
Author: galt 
Date:   Sat Dec 1 16:00:04 2007 +0000

    "Release log update"

commit 55d0947b8ba3d2311358418ca087902457071e17
Author: kate 
Date:   Sat Dec 1 00:55:58 2007 +0000

    Add entry for wiggle coloring

commit 7afb08e5540295e8799e17685110ce83e6fc6b45
Author: hiram 
Date:   Fri Nov 30 22:25:03 2007 +0000

    Working on phastCons 8-way

commit 36e229a4c671d571155497a69bbd1973e9bece74
Author: hiram 
Date:   Fri Nov 30 22:24:35 2007 +0000

    Done with calJac1 Marmoset blastz and swap

commit 810606b9e0048e9280de3231b089082f3af51a37
Author: galt 
Date:   Fri Nov 30 16:00:05 2007 +0000

    "Encode release log update"

commit 43d717cde12426f51d532874e48e696e1464c47b
Author: galt 
Date:   Fri Nov 30 16:00:04 2007 +0000

    "Release log update"

commit 62a1cf43d063887d790c4481fd633b98ef9c283a
Author: kayla 
Date:   Fri Nov 30 00:07:48 2007 +0000

    Added cb1

commit 89ec42ef4cd3a6ce438f5787dbe030b8eda17956
Author: rhead 
Date:   Thu Nov 29 19:54:08 2007 +0000

    Added a section for genePred tables. Prompted by a user question.

commit 7237856e1b8f41f2b3e31ee3fa89fde7882e7ef6
Author: donnak 
Date:   Thu Nov 29 19:41:58 2007 +0000

    Added some more pubs.

commit b4f7a529b8837ed04666c4b3dd6c9192b492cceb
Author: ann 
Date:   Thu Nov 29 18:17:38 2007 +0000

    I think there's a security problem with using scp as qateam.  until I resolve that, I'm exiting if it can't find the report

commit b9a220f9956aaad3ee6434462e26df04180cbef6
Author: donnak 
Date:   Thu Nov 29 18:06:26 2007 +0000

    Added 2 new NAR pubs, updated link on 1 pub.

commit c027316fffd8cceffcbcacc02574452328600764
Author: archanat 
Date:   Thu Nov 29 17:47:55 2007 +0000

    added an entry for all_est and all_mrna table

commit 6372009fa9ec75bec025b8fcdf147f9bfbe0c3e7
Author: ann 
Date:   Thu Nov 29 17:44:21 2007 +0000

    supressed output from the safe copy call

commit c7af753f8dc6264d9bc42f44dacd41135eb7a094
Author: galt 
Date:   Thu Nov 29 16:00:05 2007 +0000

    "Encode release log update"

commit 7073470c7c45ce0e1343c1dc8f9d93c41284583d
Author: galt 
Date:   Thu Nov 29 16:00:03 2007 +0000

    "Release log update"

commit 7a213919c45c1a93e64a9d8a232f92c7809e9e47
Author: hiram 
Date:   Wed Nov 28 23:13:46 2007 +0000

    Starting calJac1 Marmoset blastz run

commit 0938dcd69f24bb4bb44fe071307d77b13a380e91
Author: hiram 
Date:   Wed Nov 28 23:13:32 2007 +0000

    The calJac1 blastz did not work, too many chainLinks on calJac1

commit d858db6b3328280da8eee0c65d054e34d7ee0de4
Author: angie 
Date:   Wed Nov 28 20:21:38 2007 +0000

    Updated hgSession Help link to point to new user's guide.

commit f58168cddd79416f12511fb3bf3a2366ea30ddbd
Author: jzhu 
Date:   Wed Nov 28 20:01:17 2007 +0000

    add proteomics ispy data, TCGA gene expression data

commit b95e6abc7a0a6a8f9be998af34017c2c156c6960
Author: angie 
Date:   Wed Nov 28 19:11:23 2007 +0000

    Folded hapmapLdSnpId into hapmapSnpId so checks would be performed; added some new hapmapLd tables.

commit 03131312fba04cd75718473c6a84c3c1e3c9a987
Author: ann 
Date:   Wed Nov 28 18:21:51 2007 +0000

    cleaned up supertrack entry

commit b6ffc1199730815d410d8930961aae169d008453
Author: galt 
Date:   Wed Nov 28 16:00:08 2007 +0000

    "Encode release log update"

commit 08336b6a6bc0a4cd12519baec74aed972d34f3f0
Author: galt 
Date:   Wed Nov 28 16:00:05 2007 +0000

    "Release log update"

commit ca1ff302036fb5ecdb0b7b00a3336e8b83263b9f
Author: hiram 
Date:   Tue Nov 27 23:14:44 2007 +0000

    8-way conservation track beginning to appear on Orantutan, with frames and iRows annotations

commit 3d7cc828b0e00d169415178585c076303387f51f
Author: hiram 
Date:   Tue Nov 27 23:10:01 2007 +0000

    annotated frames and iRows are on for the 8-way conservation

commit 81e449868329f2c3f279cd0ec8426504b6cd6fcc
Author: ann 
Date:   Tue Nov 27 22:51:40 2007 +0000

    adding google search of Genome ML archives now that there are some questions there on this topic

commit bf16e65d3972477ed4f0a487600a9595eaf807cf
Author: ann 
Date:   Tue Nov 27 22:43:57 2007 +0000

    details about archives

commit 021f28a67c4011ebb3ee9ed666a50eb966bb790d
Author: ann 
Date:   Tue Nov 27 21:51:25 2007 +0000

    now that there are some MLQs in the archives, I am enabling this search

commit 7a32331ed46c82132952731be1f0c248b8caf58b
Author: ann 
Date:   Tue Nov 27 18:43:43 2007 +0000

    added cb1, as MarkD has rerun genbank and added it to the nightly updates

commit d832f50298e288a6633ca7935f896e493205fea3
Author: hiram 
Date:   Tue Nov 27 17:47:42 2007 +0000

    blastz runs for Marmoset calJac1 and Orangutan ponAbe2

commit 64837e12acee4dd37dde3b8d55b74a858247a7b1
Author: hiram 
Date:   Tue Nov 27 17:43:55 2007 +0000

    blastz run swaps to prepare for 8-way alignment, syntenic nets, starting 8-way alignment

commit 9eb53123f64eedfa91d3cbebab2479508dabdd32
Author: hiram 
Date:   Tue Nov 27 17:41:44 2007 +0000

    Attempted Platypus vs Marmoset blastz, ran into a bug

commit 197b6f5b3e4b050a0cdd8a6748b8293652fafae1
Author: hiram 
Date:   Tue Nov 27 17:40:41 2007 +0000

    Orangutan ponAbe2 and Marmoset calJac1 blastz working

commit 230c7b205d4655bb76d3c969dc0aad72ff878a4f
Author: galt 
Date:   Tue Nov 27 16:00:08 2007 +0000

    "Encode release log update"

commit 460b0366b5b90c667624aaaaee4fa52202418270
Author: galt 
Date:   Tue Nov 27 16:00:04 2007 +0000

    "Release log update"

commit 580be0854a576a23ef76f47ebc42023f2a5a6181
Author: angie 
Date:   Tue Nov 27 05:24:22 2007 +0000

    Added Scaffolds track.

commit f936757c47c9d80aa2795ea4cd1d2f0b86b35c23
Author: angie 
Date:   Tue Nov 27 05:10:37 2007 +0000

    Added Scaffolds track.

commit e3862d737ea0677a8ec4a05a3199ace4b557f457
Author: kent 
Date:   Tue Nov 27 01:57:18 2007 +0000

    Making factorSource type tracks packable.

commit 4c459c6937e3a9fb61c2b957da12a1e028c195b6
Author: angie 
Date:   Tue Nov 27 00:45:41 2007 +0000

    Wrapped a check for track!=NULL around the gvPos track disclaimer code, to avoid SEGV when All Tables.

commit 669c467e9e7f585f8a3af8368622a409adc8bc5b
Author: aamp 
Date:   Mon Nov 26 23:41:05 2007 +0000

    Jim's code review suggestion to add "Transcription" to the longLabels

commit 7ce09d00dae7272ef53270f0ae4ac17b604c5294
Author: hiram 
Date:   Mon Nov 26 22:52:24 2007 +0000

    Adding 8-way conservation track

commit a66d1c2503d77634397a9836ca5da7c1e6703380
Author: hartera 
Date:   Mon Nov 26 22:45:57 2007 +0000

    Removed chromSeqFileExists() function - it was added to the chromInfo.c library. Added an include for chromInfo.h so that this function can still be accessed by hgc.

commit aa9c44e5d947cb8ecd9e94c2278a9f38f2b39827
Author: hartera 
Date:   Mon Nov 26 22:43:43 2007 +0000

    Added a check for the existence of the toDb and whether the chromosome sequence file for the result exists in the location specified in the chromInfo table of the toDb in addition to checking if the toDb has active set to 1 in dbDb. A link to the toDb is only printed if these conditions are true.

commit 09026ebeffbefcaa64407da3a495011ff61cf42d
Author: hiram 
Date:   Mon Nov 26 22:43:21 2007 +0000

    8-way alignment tree on Orangutan ponAbe2

commit 5c324a7bce1d12af08e6b15c950cdc162b53135d
Author: hartera 
Date:   Mon Nov 26 22:40:02 2007 +0000

    Added chromSeqFileExists() to check for the sequence file in chromInfo for a chromosome and then check the file exists in that location. Moving this function from hgc.c so that it can be used by different CGIs.

commit 9ea858486501a8af4529d92735bbe02780ed3235
Author: angie 
Date:   Mon Nov 26 21:55:42 2007 +0000

    Removed CHB and JPT subtracks of HapMap LD Unph -- Daryl says they're not necessary since we have JPT+CHB.

commit a9effaef1896d9eaafaef621e8cb0a7801ba1fa9
Author: ann 
Date:   Mon Nov 26 19:38:32 2007 +0000

    more cleanup

commit 5bc52e9ac22ea977095960221df08323a534876c
Author: ann 
Date:   Mon Nov 26 19:33:16 2007 +0000

    general cleanup of orignial text

commit 3c5aa3829f75c68534b1e05fffa2da5680c2a519
Author: aamp 
Date:   Mon Nov 26 17:32:26 2007 +0000

    chip-seq tracks.

commit 9e2384f4708a18bcc7ebebdfa22de456dada395f
Author: donnak 
Date:   Mon Nov 26 17:10:05 2007 +0000

    Uncommented link to Session User's Guide.

commit d9b9063ad917cdd96f4ca82400ffb7fe3370a793
Author: galt 
Date:   Mon Nov 26 16:00:08 2007 +0000

    "Encode release log update"

commit 37d782615b730a279f42d9727f054b5a189c4e16
Author: galt 
Date:   Mon Nov 26 16:00:04 2007 +0000

    "Release log update"

commit 983345d7a325de810d61407cf95e34550470944f
Author: kent 
Date:   Mon Nov 26 15:51:07 2007 +0000

    Moving test dir to be tests, so can do 'make test'

commit df6347713fb789f641a854d712a99e1ab94b31f3
Author: kent 
Date:   Mon Nov 26 15:50:44 2007 +0000

    Swapped two columns in bed output.  Removed debugging statement.

commit 9232b377945664ea91b1513059e617f178d32a01
Author: kent 
Date:   Mon Nov 26 15:46:52 2007 +0000

    MOving from test to tests.

commit f343b4160f2aa13aa52e1fa6c986635e58ce2e5e
Author: kent 
Date:   Mon Nov 26 02:15:30 2007 +0000

    Not drawing label to right in dense or squish mode.

commit 293bc270e0dadcbdceb7a8d5bde5aa6865dcfef5
Author: kent 
Date:   Mon Nov 26 02:11:23 2007 +0000

    Adding new factorSource type.

commit e4466505867d9ddab8b79fc93453ade0d8fe67de
Author: kent 
Date:   Mon Nov 26 02:09:52 2007 +0000

    Adding rbTreeFreeList

commit b8092c0057cdc60bff35d27bfbf286d48b603b34
Author: kent 
Date:   Mon Nov 26 00:18:46 2007 +0000

    Seems to work, what's implemented at least.

commit f380d589aba48e0c14e56894de93fa8869b5afec
Author: kent 
Date:   Sun Nov 25 17:20:35 2007 +0000

    Improving usage statement.

commit fba63439a6192d2de9c458be2285095a997765ed
Author: kent 
Date:   Sun Nov 25 17:19:53 2007 +0000

    Bumping version number

commit b4247d67987771d195e604675db56461691b06ad
Author: kent 
Date:   Sun Nov 25 17:17:55 2007 +0000

    Reporting total query sequence as a long-long to avoid overflow when people using really long query files.

commit 195cfe2f6dd66fe5ef5bea2970312c4a42626d15
Author: galt 
Date:   Sun Nov 25 16:00:17 2007 +0000

    "Encode release log update"

commit b1557af770d16032ea8d6dd786827b48e0276616
Author: galt 
Date:   Sun Nov 25 16:00:15 2007 +0000

    "Release log update"

commit 81acc1b334f6af5f1bef49994574b7af30ea5a4d
Author: donnak 
Date:   Sun Nov 25 01:19:59 2007 +0000

    Removed msg abt system downtime.

commit d9fe18da6c8092d28e83312938ebc3aac32c36f3
Author: markd 
Date:   Sat Nov 24 18:15:15 2007 +0000

    added ignore entry

commit 09de6d4b3d7224bfce3a0971b55519377a61f1ec
Author: hiram 
Date:   Sat Nov 24 17:58:02 2007 +0000

    turn calJac1 updates after fixing genbank.conf

commit 001795cf8cfd1ab61bd3906f8d50ec682a0538b5
Author: hiram 
Date:   Sat Nov 24 17:55:45 2007 +0000

    calJac1.perChromTables = no

commit 207bae813607df03ee4c788d0a1b27170e41eb57
Author: markd 
Date:   Sat Nov 24 16:46:54 2007 +0000

     disabled calJac1 load

commit b45f0e3a60774fed417320f402dd5573bface396
Author: galt 
Date:   Sat Nov 24 16:00:04 2007 +0000

    "Encode release log update"

commit cfde6363b2eb859c12b0df5ea297b68dc3d7516e
Author: galt 
Date:   Sat Nov 24 16:00:02 2007 +0000

    "Release log update"

commit d3c5162796da229dd2634597fc2aa903ecec1142
Author: galt 
Date:   Fri Nov 23 16:00:06 2007 +0000

    "Encode release log update"

commit 181114ab196202b55371c97bb2721a9f0c2c67e6
Author: galt 
Date:   Fri Nov 23 16:00:03 2007 +0000

    "Release log update"

commit 511b86c7de17f60299a1d83f1eec3408d026c0c1
Author: galt 
Date:   Thu Nov 22 16:00:06 2007 +0000

    "Encode release log update"

commit 6f9e3cbe13b9ebbea2ae3e3bdafc563ddcb9d119
Author: galt 
Date:   Thu Nov 22 16:00:04 2007 +0000

    "Release log update"

commit 441455ff4cf94cc0aca5766144cd26f919a6b98e
Author: ann 
Date:   Thu Nov 22 00:43:19 2007 +0000

    added new browserUsage script

commit 1ae1d4db0bb835480b6d8fff0f7c50a84f492609
Author: ann 
Date:   Thu Nov 22 00:42:36 2007 +0000

    script to track browser and o/s usage by website visitors

commit e4f4d25fd6b8fa489ea796857d83bb8a6cff3de3
Author: hiram 
Date:   Wed Nov 21 20:20:35 2007 +0000

    Finished Orangutan and Marmoset blastz runs (ponAbe2 and calJac1)

commit e42dd04f5cc6b8a575fa5d1124ea9ada2b25e7ab
Author: hiram 
Date:   Wed Nov 21 20:19:42 2007 +0000

    Finish off ponAbe2 and calJac1 alignments (Orangutan and Marmoset)

commit 9399122d37ef6a888467288ce9dfe5d4fa845fae
Author: hiram 
Date:   Wed Nov 21 20:18:58 2007 +0000

    Running thorough some of the temporary DB table loading

commit a55a4c83dcda2550b8d7998b4d802091739ad6b4
Author: hiram 
Date:   Wed Nov 21 20:18:29 2007 +0000

    Finished genbank run, abandoned Platypus alignment

commit 483b60527daba4fab08e15c5102b1537a095d67f
Author: hiram 
Date:   Wed Nov 21 20:17:01 2007 +0000

    Added calJac1.

commit 997ac74611530731993974fecc71f09aaa059ac7
Author: kuhn 
Date:   Wed Nov 21 19:14:43 2007 +0000

    tweak

commit 89ef7ba13e49395f4eb9f5b945cccecedea776c8
Author: ann 
Date:   Wed Nov 21 16:57:13 2007 +0000

    directed link to contact page instead of to genome email list

commit ae3dca498176add48caac3d86b422dab71f0675a
Author: galt 
Date:   Wed Nov 21 16:00:06 2007 +0000

    "Encode release log update"

commit 0a9bce41f8b3a87f4dc037b273815276a6a4387d
Author: galt 
Date:   Wed Nov 21 16:00:04 2007 +0000

    "Release log update"

commit 7bae05bee5a5779e15f65038b73d9c6d29310fc1
Author: donnak 
Date:   Wed Nov 21 08:48:42 2007 +0000

    Edited this file, updated some information to match recent mods to the hgSession tool.

commit 6656c90d7a14fe75af3ab02c054a6e11d4aed8c5
Author: kuhn 
Date:   Tue Nov 20 21:57:51 2007 +0000

    extended count of source to include previous release on beta

commit d2bc227db58cc12a8d21df231afcc0c2169eccb8
Author: ann 
Date:   Tue Nov 20 21:32:07 2007 +0000

    adding information about the new built-in data sets

commit cc65439758a88c713aa0c29612c9c632a7175110
Author: kuhn 
Date:   Tue Nov 20 20:50:10 2007 +0000

    removed assembly names from image as they are listed twice in text and image looks cluttered

commit 4d7ab4c62067b6b35bf6efe66a2ba5fa8d23a62b
Author: galt 
Date:   Tue Nov 20 19:47:21 2007 +0000

    noting move to new location for cleanup

commit 09677e4a2a2f23223d74032194d9afb4f7b0b2bc
Author: aamp 
Date:   Tue Nov 20 19:22:16 2007 +0000

    Fixed groups.

commit 560fe5842936db8b25451d3a548aa32b77e85cef
Author: kuhn 
Date:   Tue Nov 20 19:12:01 2007 +0000

    added chunk for counting number from each contributing lab

commit ab195ea360327b0486498d59be025c01f7a93ffb
Author: hiram 
Date:   Tue Nov 20 19:11:35 2007 +0000

    Properly locate calJac1/11.ooc

commit eb098296046f9661e34322501ac507affaa169d2
Author: angie 
Date:   Tue Nov 20 18:40:27 2007 +0000

    Add rcsid line to .c even if no -cvs -- it may well be checked in later anyway.

commit 5d70b7d7e16ce294ef070f546cde5f3b466faa30
Author: aamp 
Date:   Tue Nov 20 18:00:42 2007 +0000

    Initial trackDb for Yale ChIP-seq`

commit eb2c2b9219087a60504241e20bf0b20668cabf53
Author: aamp 
Date:   Tue Nov 20 17:58:38 2007 +0000

    Initial track descriptions for Yale ChIP-seq supertrack.

commit b156aeccb822757865a2b135831a689f2ec5b72f
Author: ann 
Date:   Tue Nov 20 17:50:19 2007 +0000

    one more addition suggested by Fan

commit fb310712b6a87a95c38c0c5ca8ad17e5769560cd
Author: ann 
Date:   Tue Nov 20 17:35:05 2007 +0000

    corrected the name of the study.

commit 38eae9fefea6cd40423063b0baf6aab9f76cd378
Author: kuhn 
Date:   Tue Nov 20 17:17:24 2007 +0000

    added some knownAlt checking

commit ed4f38f9fe30a145920777d744da815aa93f1046
Author: kuhn 
Date:   Tue Nov 20 17:16:02 2007 +0000

    added new dbDbArch table to monthly backup

commit fe26454cca52b3763c24f7787f8e805ef1e44d8a
Author: hiram 
Date:   Tue Nov 20 16:25:57 2007 +0000

    Finished genscan, working on genbank, attempted Platypus blastz

commit 624baf4f999d028d4f7bd74d0ba52f7b9951c6ea
Author: galt 
Date:   Tue Nov 20 16:00:08 2007 +0000

    "Encode release log update"

commit 4f47fada07fd4ad4a99ffd879adb15c50f5fd492
Author: galt 
Date:   Tue Nov 20 16:00:04 2007 +0000

    "Release log update"

commit 54c2550736f022c0940d8e07cd328ce871514249
Author: donnak 
Date:   Tue Nov 20 04:59:47 2007 +0000

    Added temporary warning msg abt system down time.

commit 8dfe920026e55afb94f1b63c5ea89dbb01f966a8
Author: fanhsu 
Date:   Tue Nov 20 03:52:43 2007 +0000

    Put out "N/A" if ESDI is -1.

commit 1723ba53a495f258e6876fa0c5ad065c4e002bb5
Author: hiram 
Date:   Tue Nov 20 01:05:28 2007 +0000

    This was run up to the point where tables would start loading.  Took 3 hours wall clock time to run, including some side steps to prepare other tables it needed.

commit bc5beb60a2d4cb7ebbf0242bb00123862e850649
Author: galt 
Date:   Tue Nov 20 00:55:25 2007 +0000

    purely semantics: renamed submission to project everywhere

commit 8f0c07fb3cb96a648342cbf4d14852dc245e1cd9
Author: hartera 
Date:   Tue Nov 20 00:46:29 2007 +0000

    Report if no conversions available from an assembly in the fromDb list.

commit ad77a40b11b259b9264fb2a567460c84d5a6a20a
Author: ann 
Date:   Tue Nov 20 00:45:53 2007 +0000

    commented out link to Sessions UG

commit c3d90d6f3c97e858d010724c70909228a3e4ef3a
Author: fanhsu 
Date:   Tue Nov 20 00:45:39 2007 +0000

    Updated the html title.

commit 0e7cad46b7d99ab4df3f94f903a50362e877203d
Author: galt 
Date:   Tue Nov 20 00:43:43 2007 +0000

    purely semantics: renamed submission to project everywhere

commit 80a0629fe3928594194fabefdf596179c3000c03
Author: hartera 
Date:   Tue Nov 20 00:38:50 2007 +0000

    For convert results, print a link only if active is set to 1 for the toDb and if the database exists for it otherwise just print the coordinates with no link.

commit d4d29dc6273dbfdee89ccb525a6c791e7c916c31
Author: hartera 
Date:   Tue Nov 20 00:35:45 2007 +0000

    Changed functions that use the dbDb on the archive server to use a new table, dbDbArch, that is in hgcentral.

commit 2998f739256bc59ca68563aa5196f7ed9865ba00
Author: hiram 
Date:   Tue Nov 20 00:23:27 2007 +0000

    genbank daily alignments enabled, genscan genes done, playtpus and marmoset alignments running swap

commit 5d30a784fa398e149a97f0b0b82b2f2f42c3022d
Author: galt 
Date:   Mon Nov 19 23:34:36 2007 +0000

    cleaning out old rails tutorial stuff on categories and classifieds

commit 88e92ace9755a71a63db007fe1a1ba8aa3755939
Author: hiram 
Date:   Mon Nov 19 23:34:14 2007 +0000

    Lift exoniphy business from Hg18 to here for UCSC gene create experiment

commit dce73a6d0e6b6abfd01707041a8a42ed982307f4
Author: galt 
Date:   Mon Nov 19 23:21:43 2007 +0000

    bug fix missing path to sh shell

commit 11e76ec440d289ea619aba2bb24deda92c15ce71
Author: kent 
Date:   Mon Nov 19 22:42:50 2007 +0000

    Describing new knownToEnsembl build

commit 7330eacfee7bf7e0c901b93b341274e1d941aca3
Author: kuhn 
Date:   Mon Nov 19 22:25:34 2007 +0000

    added total of index + main tables and set default to print index

commit 3502c807d70dde247e85ddea4960618d27803082
Author: kuhn 
Date:   Mon Nov 19 21:33:13 2007 +0000

    removed automatic email to user

commit 960ed860c43c97a5fbe7976025688b14922c63e4
Author: markd 
Date:   Mon Nov 19 20:34:23 2007 +0000

    moved cb1 to genbank update

commit 4b60c73faf8a90e57fdd977d2063b200dcdc7a4b
Author: galt 
Date:   Mon Nov 19 19:30:11 2007 +0000

    bob wants the CGI_VERSION removed

commit 41435a847545e9b68517b3eaa64773e508496b93
Author: fanhsu 
Date:   Mon Nov 19 18:08:45 2007 +0000

    Change data used for ESDI to Days of collection relative to the estimated HIV infection date.

commit df0c082b6270de477d2b04fe77e9f4b16ff3f53b
Author: giardine 
Date:   Mon Nov 19 16:39:17 2007 +0000

    Added disclaimer for Locus Variants track (gvPos)

commit 9be537838b2006773e4f03534abeb2b28a10ed99
Author: giardine 
Date:   Mon Nov 19 16:38:49 2007 +0000

    fixed spacing

commit f6c3ace650e5e1043180edd2505b5385d156cceb
Author: galt 
Date:   Mon Nov 19 16:00:08 2007 +0000

    "Encode release log update"

commit f5086ff6dd08df7eb966e191092e77abd2a26081
Author: galt 
Date:   Mon Nov 19 16:00:04 2007 +0000

    "Release log update"

commit 958bf67b78add104d4300e15e2aa8ae078f66c58
Author: giardine 
Date:   Mon Nov 19 14:55:42 2007 +0000

    Changed OK button to Agree, Disagree.

commit c34aa0ec031d436d7d3abeee7bf95d2231225d25
Author: jsanborn 
Date:   Mon Nov 19 06:12:48 2007 +0000

    Fixed a typo

commit 4e207a8329fb792d854ccd3e9ef6a9be49ba138f
Author: jzhu 
Date:   Mon Nov 19 04:58:29 2007 +0000

    add ispyAgiExpT1 track

commit f8dcd4ef613895455ad5ed31c8f3f3ace31dc26b
Author: jzhu 
Date:   Mon Nov 19 04:57:05 2007 +0000

    add uncAgiExp
    ispyAgiExpT1 info

commit e705a18f44a8384d107f2cf57f90675e169d053c
Author: jsanborn 
Date:   Mon Nov 19 02:35:11 2007 +0000

    Updated trackDb file for specific fields to generalize feature sorter for both TCGA and ISPY data

commit 4069d017c23363d361185a82e577da5527e84ecc
Author: fanhsu 
Date:   Mon Nov 19 01:41:07 2007 +0000

    Changed "HIV VAC" into "GSID HIV Data Browser".

commit 8c6cb594cfc91ab2dc603afff304de12655786fb
Author: galt 
Date:   Sun Nov 18 16:00:05 2007 +0000

    "Encode release log update"

commit 7b9d15e1d87f312871b9516290d5757969f1ab46
Author: galt 
Date:   Sun Nov 18 16:00:04 2007 +0000

    "Release log update"

commit 8d546ce37b5adc21b11e2c629307f4a56b6bc90d
Author: markd 
Date:   Sat Nov 17 22:33:36 2007 +0000

    deal with bug caused by same version being included twice in one update

commit c421c36562a73af4cfd91c724b1fce6e99600ed7
Author: fanhsu 
Date:   Sat Nov 17 22:16:45 2007 +0000

    Added special logic to display special conditions of CD4 and viral load.

commit a3315edef83b17b435f972148f6ada8d64075f18
Author: fanhsu 
Date:   Sat Nov 17 20:18:25 2007 +0000

    Corrected the unit of viral load.

commit 0434e29078c21188f86c88874d66dde9554cea26
Author: fanhsu 
Date:   Sat Nov 17 20:16:48 2007 +0000

    Updated logic for viral load display.

commit 533d1d52d639be37ea945f4b46ffe469af615746
Author: fanhsu 
Date:   Sat Nov 17 20:04:31 2007 +0000

    Updated unit for CD4 and some special logic.

commit d66ec085b88e66f5bfacaf67f9baf41fe35779bc
Author: fanhsu 
Date:   Sat Nov 17 19:59:32 2007 +0000

    Corrected units for viral load and CD4.

commit 4790b7a833d2905e043af68778122e245af33082
Author: fanhsu 
Date:   Sat Nov 17 17:38:56 2007 +0000

    Updated CD4 and HIV-1 RNA column to get values from gsidClinicRecWithSeq table instead.

commit c8f2ba00d7b414576abd658a31f07d630a307c18
Author: fanhsu 
Date:   Sat Nov 17 17:37:00 2007 +0000

    Updated cell value function to return "N/A" if the field is NULL.

commit 6169409e0b28e3c3a1702fd3b499a1d6fc994d3a
Author: galt 
Date:   Sat Nov 17 16:00:05 2007 +0000

    "Encode release log update"

commit fdf15f47b3a0014840c230315cd83433c37f7e1d
Author: galt 
Date:   Sat Nov 17 16:00:03 2007 +0000

    "Release log update"

commit e13f954a55f26a426a300e7a6ef1da9fc9bd0b46
Author: fanhsu 
Date:   Fri Nov 16 22:21:13 2007 +0000

    Added subject ID.

commit 850dbe84e343c125818001c626bcfe820adb3926
Author: kate 
Date:   Fri Nov 16 21:44:50 2007 +0000

    Howto setup development sandbox

commit 290d034656478ff91d7a41ee3eb88f751a8b41fd
Author: ann 
Date:   Fri Nov 16 20:04:11 2007 +0000

    removed reference to Gates Foundation (per GSID request)

commit 2d3290da950bc017b39e1bbaf22074b733c65716
Author: markd 
Date:   Fri Nov 16 18:19:50 2007 +0000

    increased size of several hash tables

commit 7056bd4272db2e2f2a3b609cd6babadc6239093f
Author: galt 
Date:   Fri Nov 16 16:00:05 2007 +0000

    "Encode release log update"

commit 57f1810fcc00eb0ef55da7a5976bb13010a5c220
Author: galt 
Date:   Fri Nov 16 16:00:04 2007 +0000

    "Release log update"

commit 31d41a0d0146439616d0e25aa259c2c94371dee1
Author: aamp 
Date:   Fri Nov 16 14:52:55 2007 +0000

    Hopefully fixed hgGenome problem where graph persists after changing assembly.  This fixes nothing on hgTracks though.

commit a50c80b8eb9ef6a3c72eaac436dc9684915f15e4
Author: fanhsu 
Date:   Fri Nov 16 07:04:27 2007 +0000

    Added ESDI note.

commit 1dd059343d8d3c8088a8765a7217af59a2f7295c
Author: fanhsu 
Date:   Fri Nov 16 00:33:38 2007 +0000

    Added warning message for GSID.

commit e9c3395172829394cd8f42a83eb671bbfb5801cb
Author: ann 
Date:   Fri Nov 16 00:29:39 2007 +0000

    edited sentence to reflect agreed-upon name for GSID browser

commit 9e3e2ebe3bebeca5b6940dd92c5df44bc7b100a4
Author: markd 
Date:   Fri Nov 16 00:29:37 2007 +0000

    enabled cb1 xeno refseq

commit bffa08e7c84c396f33450ad48ba58f4667ab5e23
Author: ann 
Date:   Thu Nov 15 23:50:55 2007 +0000

    inserted variable where extFile was hard-coded (should alternate on seq/extFile variable)

commit 3425e9490813c4f12c7e2392413d83342124b62b
Author: angie 
Date:   Thu Nov 15 20:46:37 2007 +0000

    Tweaked labels of HapMap LD subtracks.

commit 4dede96db705a6c94c7d839efa455892894888dd
Author: markd 
Date:   Thu Nov 15 20:41:53 2007 +0000

    commited info on partially completed ensembl update

commit f942088d05d51041d8956d50816aaa380c2e65e8
Author: angie 
Date:   Thu Nov 15 20:41:46 2007 +0000

    Tweaked HapMap LD priorities so HapMap SNPs doesn't appear between them.

commit ddd556e72cac1edc5558b19cab5bd95f8786dbd4
Author: ann 
Date:   Thu Nov 15 20:25:11 2007 +0000

    changing background color of hotLinks top navigation bar to match all other nav bars

commit 1fe94f837c6486af05d8c5ac541d85e13b73a69b
Author: angie 
Date:   Thu Nov 15 19:56:38 2007 +0000

    Added new consortium member.

commit c5d471434594ec28a6f4eb877f5e24a93364dc3d
Author: angie 
Date:   Thu Nov 15 19:54:49 2007 +0000

    Added a color to igtcColor for a new consortium member.

commit e77fd14d6a3a2433eed5b18c6f52e0c32bd97e3d
Author: giardine 
Date:   Thu Nov 15 19:52:16 2007 +0000

    Adding UniProt variant track

commit 87bd18dcd7d9b07e3851811d81971d3d3f1a1603
Author: fanhsu 
Date:   Thu Nov 15 19:41:27 2007 +0000

    Updated per GSID users feedback.

commit d109bdb4fc0fcca2115acdde1d6996fb93c66ec0
Author: fanhsu 
Date:   Thu Nov 15 19:34:56 2007 +0000

    Added ";" after nbsp.

commit 0ffc37f7f065995e2436f146a0b099f095e9600a
Author: fanhsu 
Date:   Thu Nov 15 18:42:57 2007 +0000

    Updated with a few changes per GSID users feedback.

commit d4eea2aa8b5d943ecc75014af414cb3fe449c47f
Author: fanhsu 
Date:   Thu Nov 15 17:54:49 2007 +0000

    Added ";" after "nbsp".

commit 336eff8d4ae61af6fd338e1af3e659184fecfc9b
Author: fanhsu 
Date:   Thu Nov 15 17:01:09 2007 +0000

    Removed the item of "Days of infection relative to last negative date".

commit bbc7f92ab5a2ef49f74e3ed1bd59826005e06933
Author: giardine 
Date:   Thu Nov 15 16:45:41 2007 +0000

    Commented out parts of code not wanted currently.  May be permenant, may not.

commit dd45a6fea53acc8f7bb716751102c99190c00d63
Author: giardine 
Date:   Thu Nov 15 16:44:16 2007 +0000

    Added UniProt variants, and disclaimer on first use of Locus variants

commit f9f16d4035fd11326a4a9f06004173086d97c8f4
Author: giardine 
Date:   Thu Nov 15 16:42:15 2007 +0000

    Added UniProt variants, added disclaimer on first use of Locus Variants

commit 037a7a46696b3aac6934374d63d64b07bf9ed73b
Author: giardine 
Date:   Thu Nov 15 16:40:50 2007 +0000

    Add / edit links

commit 4bbffb1daca24d833fd91ecee019b7e27fc9174a
Author: giardine 
Date:   Thu Nov 15 16:39:33 2007 +0000

    Added disclaimer

commit 1ac12bdfbeeae7b67f2a8196d1c131d5f18d809b
Author: giardine 
Date:   Thu Nov 15 16:38:47 2007 +0000

    Added UniProt Variants file

commit d537f7e03dd3ff471a4c99b7f8c6e978c804490a
Author: giardine 
Date:   Thu Nov 15 16:38:15 2007 +0000

    Changed reference to disease, added disclaimer

commit bafb6ed3c2b3735c94035eaa273f5d5f37091931
Author: giardine 
Date:   Thu Nov 15 16:36:11 2007 +0000

    Added links for new UniProt variants track

commit 494a8a1463afd00e5f32e3ba508eb0c838c68a31
Author: giardine 
Date:   Thu Nov 15 16:34:59 2007 +0000

    Separated out UniProt (Swiss-Prot) variants, added new LSDBs

commit 241c5592b8fdeda3421f35668a6ee51129c27d1a
Author: giardine 
Date:   Thu Nov 15 16:34:22 2007 +0000

    Changes to Locus Variants and UniProt variants to make them less "scarey"

commit 07ee9e4f599889dd500f1bcdf4ef0d24ae455932
Author: giardine 
Date:   Thu Nov 15 16:32:18 2007 +0000

    New file for UniProt (Swiss-Prot) variants.  Separated out from Locus Variants
    track.  This is just a stub, needs work.

commit 26793b31ce58860840afac5e618b367c31aa846b
Author: giardine 
Date:   Thu Nov 15 16:27:56 2007 +0000

    updated text

commit 57bc0972f0fd6fddc861307baf8dc9d7b0f57241
Author: galt 
Date:   Thu Nov 15 16:00:08 2007 +0000

    "Encode release log update"

commit 2b46e36a3ed622bd9ce95a0f66802804d700ed5c
Author: galt 
Date:   Thu Nov 15 16:00:04 2007 +0000

    "Release log update"

commit 6a0a9530ba9a99f587009a31321c35c0de949aab
Author: rico 
Date:   Thu Nov 15 15:11:06 2007 +0000

    Added check to make sure gap fits.

commit 736242276a31606d0882ade4dcf63bb28c34d739
Author: rhead 
Date:   Thu Nov 15 03:25:10 2007 +0000

    Updated link to English version of www-lbme.biotoul.fr to one that works. Also changed www-lmgm.biotoul.fr to an English-language link.

commit 9324071382b21bf8eb758300c12727d51be81a2f
Author: jzhu 
Date:   Wed Nov 14 23:51:02 2007 +0000

    add unc agi gene expression data

commit fa837ae59b27fcd313e138bad1797efd7452f623
Author: donnak 
Date:   Wed Nov 14 23:10:08 2007 +0000

    Added Ting's pub.

commit 95b8f8922ad69d3fd15efddcf5c2ad8d4e69bd64
Author: angie 
Date:   Wed Nov 14 22:35:32 2007 +0000

    Added scaffolds -> chr liftUp file jkStuff/scaffolds.lft.

commit a6b9a9719db054e117263eb0ddf52b5b29a7e63d
Author: kayla 
Date:   Wed Nov 14 19:52:17 2007 +0000

    Changed the mention of the default species to reflect which are actually the defaults.

commit 119f964be06f55a49b8e4cc0ca569d64358527bf
Author: jsanborn 
Date:   Wed Nov 14 19:49:21 2007 +0000

    Changed patDb from 'ispy' to 'ispy1', the new ISPY clinical database

commit 83867c7f46179ea4acf8d8a61f7eb06486e6ba0b
Author: donnak 
Date:   Wed Nov 14 17:22:13 2007 +0000

    Added 3 new pubs.

commit 7d9dacba0a33a884b44f566ebe2b95203953f477
Author: galt 
Date:   Wed Nov 14 16:00:05 2007 +0000

    "Encode release log update"

commit 306ee37686e4807c3f5e6ad7b55eda292458aadc
Author: galt 
Date:   Wed Nov 14 16:00:04 2007 +0000

    "Release log update"

commit da54a268678e90b83e4d48ff15e0dfba44d243c5
Author: jzhu 
Date:   Wed Nov 14 01:22:23 2007 +0000

    correct names for harvardCGH track

commit c8925c4c3f9d8049d1a7e996a1e0f0c7a0a29702
Author: markd 
Date:   Wed Nov 14 00:51:57 2007 +0000

    reenabled canFam1/2, which were forgotten after the species rename

commit fa42daa5998d3ead3390d21c0d74f7b053e96a0c
Author: jsanborn 
Date:   Wed Nov 14 00:36:04 2007 +0000

    Added fields to INSTINCT's trackDb.ra specifying tables to get sample/patient Id's

commit 7186b4852716cf224e38115d56ef2833a8866276
Author: jsanborn 
Date:   Wed Nov 14 00:34:52 2007 +0000

    Fixed harvard 'names' field to match tcga1 database

commit 28e2d87fec0a5d40a494e0b3947551892bd60a1d
Author: fanhsu 
Date:   Tue Nov 13 23:21:41 2007 +0000

    Changed "file" into "text (ASCII) file" in advFilter.c.

commit 24f39aa48681d012fee11a003fed0492cb60dae7
Author: ann 
Date:   Tue Nov 13 23:21:25 2007 +0000

    cleaned up error found by track check

commit 60e312f391f63766de34be9eab33668461e522c7
Author: hiram 
Date:   Tue Nov 13 23:02:18 2007 +0000

    A Marmoset chain and net.  Already done before by Kate in October.

commit 4173cc44088e8768521b06de752b445a0f1d4449
Author: fanhsu 
Date:   Tue Nov 13 20:23:16 2007 +0000

    Included logic to test if it is GSID before put out "Sequence View Gateway" in the top bar.

commit 5924b33df3063057b5d088d9a0ff1aad6e01fe5f
Author: fanhsu 
Date:   Tue Nov 13 20:17:42 2007 +0000

    Changed "Genomes" in the top bar into "Sequence View Gateway".

commit 6966195254f57cd753a7607d7f3e6b60fe6af10d
Author: fanhsu 
Date:   Tue Nov 13 20:09:37 2007 +0000

    Updated page title.

commit 8f135b1fe3669704898510787101cb6537a2ca69
Author: fanhsu 
Date:   Tue Nov 13 19:59:49 2007 +0000

    Changed "User's Guide" into "Tutorial".

commit de6cdf0e30c604b812cc7e78c536777fcd6c8c74
Author: genbank 
Date:   Tue Nov 13 18:17:57 2007 +0000

    added dump subcommand

commit 6adeb0a9d457c723fb02b73de1bc3db35b553a19
Author: aamp 
Date:   Tue Nov 13 17:59:22 2007 +0000

    "New version number v171"

commit ee8da1af04d0947e71d00a2221eb8bc1850aa966
Author: fanhsu 
Date:   Tue Nov 13 17:40:22 2007 +0000

    Remove version number from HTML title.

commit f2f1b0db023245f79fd8e1ce926aae5918cf764f
Author: fanhsu 
Date:   Tue Nov 13 17:29:46 2007 +0000

    Added Subject ID display and edited search text.

commit 97030881a137fcf06865b0bdfc83373aa349974a
Author: galt 
Date:   Tue Nov 13 16:00:04 2007 +0000

    "Encode release log update"

commit 35cadcd12c022634bd073dc90c31a8755e2235f2
Author: galt 
Date:   Tue Nov 13 16:00:03 2007 +0000

    "Release log update"

commit bf642c774d2d1bba59c4ffb21efda728e6366d1a
Author: rhead 
Date:   Tue Nov 13 01:43:12 2007 +0000

    Corrected capitalization on affy txn table names.

commit d2957e0c4fca2efc261e3d4af71458683aee5bb7
Author: rhead 
Date:   Tue Nov 13 01:39:10 2007 +0000

    Added Affy Txn Phase 3 sRNA signal tables to tables ignored.  These used to have underscores in the names.

commit 66536f1e70651cab4a593f6a2b7a27939c8f5da7
Author: galt 
Date:   Mon Nov 12 16:00:04 2007 +0000

    "Encode release log update"

commit f7fad283a013e9670a745e62ddcbc78dbcef4d99
Author: galt 
Date:   Mon Nov 12 16:00:02 2007 +0000

    "Release log update"

commit a2b4702d3d5779075817c3cb0161f96abc3b8417
Author: fanhsu 
Date:   Mon Nov 12 00:08:54 2007 +0000

    Updated for Beta release special processing..

commit 6023f69b87bba3b33d8aba9ef5ac97abe055f634
Author: fanhsu 
Date:   Mon Nov 12 00:08:05 2007 +0000

    Original version of gsidMember.c, before change into temp Beta version.

commit a4da5f2309022698aa876b4b1e9127c2b4f49dc5
Author: fanhsu 
Date:   Mon Nov 12 00:07:25 2007 +0000

    gsidMember.c version for Beta phase release.

commit c3542e99311bbc0421e5fffc8f563c4f4d5e6dce
Author: fanhsu 
Date:   Sun Nov 11 21:33:34 2007 +0000

    Added a blank character before "of".

commit 56a32d2038faac4dfad011885492fdf17108f45b
Author: galt 
Date:   Sun Nov 11 16:00:05 2007 +0000

    "Encode release log update"

commit 2500a01791688685781476c56e03a56815079a42
Author: galt 
Date:   Sun Nov 11 16:00:04 2007 +0000

    "Release log update"

commit 12e2eb684bade4c7430b6ccef7def36786a879be
Author: donnak 
Date:   Sun Nov 11 07:36:37 2007 +0000

    Fixed incorrect info abt Blat.

commit 1e7c85772ccfe3dff4c61a1e7b2ef2d4c1aa421d
Author: donnak 
Date:   Sun Nov 11 07:35:04 2007 +0000

    Fixed incorrect info in About section, per Jim.

commit f9d3eb31ba40fd745ba442916ba1fe0a77255466
Author: galt 
Date:   Sat Nov 10 16:00:05 2007 +0000

    "Encode release log update"

commit 831d83c02bb41d8484aafd9d345201d578a6643a
Author: galt 
Date:   Sat Nov 10 16:00:03 2007 +0000

    "Release log update"

commit fd435e373b9bd09833e2ce2af87e54d5412e490c
Author: markd 
Date:   Sat Nov 10 03:53:11 2007 +0000

    added ignore entries

commit 06dc509bd1834567437b40348b7e7260f14d31f0
Author: hiram 
Date:   Fri Nov 9 23:42:57 2007 +0000

    Added Callithrix jacchus (Marmoset).

commit 5d94eb822573293d268b1522bb3cb45c1a2a72c9
Author: hiram 
Date:   Fri Nov 9 23:40:16 2007 +0000

    Added calJac1.

commit b3f6008711300b67d294f3ec93c884951bb3c835
Author: hiram 
Date:   Fri Nov 9 23:22:40 2007 +0000

    Added ponAbe2.

commit ad9846787a7a61591f27e5e042fa1b4f21f72c0f
Author: archanat 
Date:   Fri Nov 9 22:57:00 2007 +0000

    added an echo statement

commit a5a6fef94dadc8c8ca9b717ac2902bf9ad4ee804
Author: aamp 
Date:   Fri Nov 9 17:20:43 2007 +0000

    Fixed table names.

commit c66f38d2b130cd8865232fc21d45ee91c0134370
Author: aamp 
Date:   Fri Nov 9 17:20:26 2007 +0000

    Changed max height for EC Affy track.

commit a9c82b06f3de8892b37fbfd8ad26fe89cdf5c090
Author: rico 
Date:   Fri Nov 9 16:18:50 2007 +0000

    Add gap data to a qa, ssave it as a qac with corresponding index.

commit f75c561c608bf734a0f05735b3bf6f2748ea161f
Author: rico 
Date:   Fri Nov 9 16:03:49 2007 +0000

    Add gap data to a qac file and index it.

commit 6d1e899c7f59a56ff5f567cccf100392fc8844c0
Author: galt 
Date:   Fri Nov 9 16:00:10 2007 +0000

    "Encode release log update"

commit d02ec5bfa23f23c256d31ef2b240dc3feb329c4c
Author: galt 
Date:   Fri Nov 9 16:00:05 2007 +0000

    "Release log update"

commit 66e23df396235681f8615e41c646eada5f966ecd
Author: markd 
Date:   Fri Nov 9 01:30:06 2007 +0000

    don't assume tclsh location

commit 79ed7eb7f88af273fe8501beeab3400a30476a14
Author: ann 
Date:   Thu Nov 8 23:40:22 2007 +0000

    added note about dropping wig files from the download sever

commit 353998e7bfac518aa694cf08f04abb4d2639e0a2
Author: hiram 
Date:   Thu Nov 8 20:03:59 2007 +0000

    No need to warn about gaps at end of chroms that are telomeres.

commit 4b397fbf1c3102d61bfd18e731a33009e40b48bc
Author: ann 
Date:   Thu Nov 8 16:33:25 2007 +0000

    edited MAFFT sentence -- OKd by Keith Crandall

commit 973236bf8dc6d061d36b323b50be43cdc1685adf
Author: galt 
Date:   Thu Nov 8 16:00:06 2007 +0000

    "Encode release log update"

commit 84d3c0156b4a796d1c83be3101dda8be961c4729
Author: galt 
Date:   Thu Nov 8 16:00:04 2007 +0000

    "Release log update"

commit b00afdcc5eb41ca22d0977dda6a8204d36be522e
Author: aamp 
Date:   Thu Nov 8 08:26:48 2007 +0000

    Cleaned up Affy Transcriptome track labels a bit.

commit 38914baae50f0f70fd062531370e98faa41b8e25
Author: rhead 
Date:   Thu Nov 8 01:58:09 2007 +0000

    Took out extra commas, removed a typo.

commit e1779667ac58389d6fa03660c9e6f5030c6d1e9f
Author: aamp 
Date:   Wed Nov 7 23:48:24 2007 +0000

    Needed an autoScale option for a wiggle composite track.

commit 61345ccd16c2fc603e6086f624f15aa9a74edf66
Author: galt 
Date:   Wed Nov 7 23:45:51 2007 +0000

    fixed archive expansion processing so it creates the subdirectories being processed correctly as it moves the files from the temporary "upload" expansion subdir into the real working dir

commit 758b81fd6035074abd9b1b6223f3a603dc11b8da
Author: ann 
Date:   Wed Nov 7 23:33:37 2007 +0000

    added tables to tablesIgnored based on output from running joinerCheck with  -tableCoverage param

commit 8a843360d72294522d22e04dcbfc183a2be0038e
Author: hiram 
Date:   Wed Nov 7 23:07:11 2007 +0000

    Done with 30-way, and the blat.mm8 dropunder

commit 927c39b8d538930c6508d6d9baad07e70a2d56a5
Author: markd 
Date:   Wed Nov 7 22:54:19 2007 +0000

    added to-do

commit 78ab1a49415bf726e2a1e43993047cd4b457e205
Author: hiram 
Date:   Wed Nov 7 22:30:32 2007 +0000

    add note about zlib-devel rpm

commit 269d092fd388a84d3dedb9beef75bf6d1d5e78b4
Author: ann 
Date:   Wed Nov 7 19:58:41 2007 +0000

    adding snp12xExceptionDesc to tablesIgnored

commit 6a9551af89ca212dbdae20c456c2dc7cd9153117
Author: ann 
Date:   Wed Nov 7 19:51:35 2007 +0000

    added tables to tablesIgnored based on output from running joinerCheck with  -tableCoverage param

commit 2848fa6f1e80a92a5c89d9dc37b8abb69b5b58ca
Author: jzhu 
Date:   Wed Nov 7 19:45:44 2007 +0000

    change TCGA color intensities

commit e3cc7d9b17485430c3328ebd08de7a0b28c08232
Author: jzhu 
Date:   Wed Nov 7 19:36:50 2007 +0000

    add TCGA CGH info

commit 7afcd89fed854e84e9490318a9c3f682f7debb0a
Author: ann 
Date:   Wed Nov 7 19:26:56 2007 +0000

    removing bogus snp125 rules that have never run correctly (in fact, never even run at all -- they are malformed)

commit e0171f19b05ee201b376f7bb7e716a38d2b9782d
Author: hiram 
Date:   Wed Nov 7 19:20:06 2007 +0000

    Now with annotation to indicate the three groups

commit 4586efd7f88257cd4a66b3789c264cf64c3f0efc
Author: ann 
Date:   Wed Nov 7 17:58:35 2007 +0000

    added correct output file name

commit 8618d8ae873e619d28f6cd0eb691f76627bcfc60
Author: aamp 
Date:   Wed Nov 7 17:27:51 2007 +0000

    Changed Affy EC trackDb naming and made 4 tracks into 2.

commit 75f2dfd5ab5b020e99cc561fe1b054774164743f
Author: galt 
Date:   Wed Nov 7 16:00:07 2007 +0000

    "Encode release log update"

commit 204219c31bc907e999824ab0a0f2e24d8f51f955
Author: galt 
Date:   Wed Nov 7 16:00:04 2007 +0000

    "Release log update"

commit d04b3e7ee4f043382d1a70f46e4b62e2833636fe
Author: rico 
Date:   Wed Nov 7 14:34:18 2007 +0000

    Added documentation for adding quality data to the mafs

commit b266a18bbdbc0087bad6c6f7382385f3d66776b2
Author: galt 
Date:   Wed Nov 7 07:22:53 2007 +0000

    making URL uploads run in background using the scheduler

commit 6360e4a0b504050e24a64f5d7ff3b6a29d2d4416
Author: hartera 
Date:   Wed Nov 7 05:07:54 2007 +0000

    In genericNetClick, removed part of condition as chromSeqFileExists already checks for the database. Only put the details page link to the other browser if the other databas is set to active in dbDb.

commit 9b036d5b44e7c3dd49ebca563129f3b930f31d46
Author: ann 
Date:   Wed Nov 7 00:20:07 2007 +0000

    making changes suggested by running joinerCheck with the -tableCoverage param

commit 0c96dcb05a2f14aea108eaaeed77481c487fbe6c
Author: hiram 
Date:   Tue Nov 6 23:42:25 2007 +0000

    Finalizing the text of the description pages, and arranging the composite mostConServed tracks

commit b54483a7da068692ff9dcccff2bb5e8a8ee21b1b
Author: ann 
Date:   Tue Nov 6 23:27:01 2007 +0000

    Bob wordsmithed the introductory sentence.

commit cec7498af135210194ec09adcf2dfc7c82fba789
Author: hiram 
Date:   Tue Nov 6 23:10:13 2007 +0000

    Initial source

commit cce3840b4a8f49fe1eea54e54d998241685cea07
Author: ann 
Date:   Tue Nov 6 22:08:05 2007 +0000

    fixed broken links found by Xenu Link Sleuth.  Mostly extra internal HREFs or NAMEs.

commit c061e014b995e9bad398a7c4323be50b36d1f9a5
Author: aamp 
Date:   Tue Nov 6 20:45:12 2007 +0000

    Got rid of doubled track description.

commit d717beee0767d64b3f2b1af3662b13244cf4b1b7
Author: markd 
Date:   Tue Nov 6 19:39:28 2007 +0000

    work around make clean not working

commit 664bcbb6e3d10b999f6d4efd43abfa43a3af7585
Author: galt 
Date:   Tue Nov 6 16:00:07 2007 +0000

    "Encode release log update"

commit e33ab407224abd4fa7a65339f5820cca81db5cd3
Author: galt 
Date:   Tue Nov 6 16:00:03 2007 +0000

    "Release log update"

commit b3c9e3b24116dc7d8f317611610520ad45f63076
Author: angie 
Date:   Tue Nov 6 04:33:00 2007 +0000

    UI improvements suggested by Donna and b0b: show save options before load options; checkboxes instead of share/don't share buttons; a bit more horizontal space in My Sessions table; show Browser and Email links (if applicable) after loading a Session.

commit cbb02ee67790a652a253674c8e51da0433479af2
Author: rhead 
Date:   Tue Nov 6 00:32:56 2007 +0000

    Added settings line to hg16 and hg18 evofold blocks to indicate data were lifted from hg17.  Copied entire block from human level to hg16 level to make the change on hg16.

commit 6c4e976dbf3454d35a2e1d0a84b5082f44bdfc8c
Author: angie 
Date:   Mon Nov 5 23:34:57 2007 +0000

    Handle stdin data input gracefully.

commit a3ac91f02047b49d5d621f5d592e77d92122108c
Author: markd 
Date:   Mon Nov 5 22:47:53 2007 +0000

    fixed warning on gcc 4.1

commit a90db3b616ab76ab19eba9ca503b1a41b767e272
Author: markd 
Date:   Mon Nov 5 22:07:18 2007 +0000

    fixed incorrect use of toupper() macro, found by newer version of gcc

commit 3b66b8b62058a3fa2fd55ab2de6c545bb8d7c38d
Author: markd 
Date:   Mon Nov 5 21:39:50 2007 +0000

    fixed typo in last commit to cvs checkout instructions

commit a4de2092e2d05067df96c232959be4f18b871986
Author: markd 
Date:   Mon Nov 5 21:28:16 2007 +0000

    correct anonymous cvs checkout instructions

commit 875091ca266f08b082c4459081112f532ff642f9
Author: kuhn 
Date:   Mon Nov 5 19:12:52 2007 +0000

    added a ref and reformatted the other.  changed and author's name

commit 429580befbe378c11c656b8431b04bb31d1f188e
Author: hiram 
Date:   Mon Nov 5 19:07:11 2007 +0000

    Straighen up the long list of assemblies used in this 30-way alignment

commit 20bc3d0e0d40a780be0d19b798ea38a1c786467c
Author: markd 
Date:   Mon Nov 5 18:49:06 2007 +0000

    don't check count of intronPsl, as not tracked in dbs

commit bd67fe0543275221e1d7ed6bf009e53df083a899
Author: fanhsu 
Date:   Mon Nov 5 18:28:01 2007 +0000

    Updated message again for GSID.

commit daeac4b3e39586ccd400f55af8b637f7f9f0afb9
Author: fanhsu 
Date:   Mon Nov 5 18:15:50 2007 +0000

    Updated the message for GSID.

commit 2a31ab20432728348551c78a19cf153d2f7bd663
Author: fanhsu 
Date:   Mon Nov 5 18:15:14 2007 +0000

    Updated Help link on the top bar for hgBlat.

commit 34e08b7fe69d6495bccb157c83af850353f8cca3
Author: hiram 
Date:   Mon Nov 5 18:00:05 2007 +0000

    targetScanS track done

commit 1ba4e41215cfdacb82cac70a84a173fc1c7921ab
Author: galt 
Date:   Mon Nov 5 16:00:07 2007 +0000

    "Encode release log update"

commit 5724461467985d33f047169c845bd81fcbf16294
Author: galt 
Date:   Mon Nov 5 16:00:03 2007 +0000

    "Release log update"

commit ff1005b7f24899eecf13d18499f0812bd59ab2d8
Author: giardine 
Date:   Mon Nov 5 15:32:12 2007 +0000

    Added new species for ORegAnno links

commit 05951a29795b6f9950e6c5be2276f16f80951aa2
Author: giardine 
Date:   Mon Nov 5 15:22:54 2007 +0000

    Documented the most recent update for the ORegAnno track.

commit de3abc83e55dd6235c50e5ed3da1a43c5d626de9
Author: fanhsu 
Date:   Mon Nov 5 14:12:47 2007 +0000

    Added Help link for GSID on top bar.

commit e06adddb2ace36f3047371d00d26648399c0ae5f
Author: fanhsu 
Date:   Mon Nov 5 14:11:50 2007 +0000

    Added Help link for GSID.

commit ed442318716322ebb98f0886937f4e3bf866a74c
Author: fanhsu 
Date:   Mon Nov 5 01:50:02 2007 +0000

    Add/Updated Help on hot links.

commit ea002efddd2c2fc6599e93f6fae040275b956e8e
Author: fanhsu 
Date:   Mon Nov 5 01:42:15 2007 +0000

    Added help to hotLinks.

commit 3f203ddad294a34e2875bc77ee6219be0676b5e4
Author: galt 
Date:   Sun Nov 4 23:16:59 2007 +0000

    change system to use background validation (we had already begun doing background loading)

commit 89b7f09e2eab24cdbdeed804766a9ff52ce84904
Author: kate 
Date:   Sun Nov 4 22:08:09 2007 +0000

    Further work on Duke Dnase HS

commit d35f9a0f87f86bd09e39bbe3c07aec53a5323e6d
Author: kate 
Date:   Sun Nov 4 21:22:34 2007 +0000

    Shorten label to 16 chars

commit 6e2e45d65b864f6a636ad53084228d3bd39c1979
Author: kate 
Date:   Sun Nov 4 21:19:26 2007 +0000

    Fix format of viewlimits setting

commit d6549a324f3426bb6f46289f99e841f9fbef95af
Author: kate 
Date:   Sun Nov 4 21:16:22 2007 +0000

    Genome-wide DNaseI hypersensitivity data from Duke

commit fa7fede36b9689cbd15a50cf3ae95c84e8487002
Author: fanhsu 
Date:   Sun Nov 4 17:38:55 2007 +0000

    Changed Subject into subject, per Bob's suggestion.

commit 22aef761047b6181f5a53b26c075a85d35a14d66
Author: galt 
Date:   Sun Nov 4 16:00:08 2007 +0000

    "Encode release log update"

commit f833937b4d4e93afff714d0ee692b4cb4b6f2528
Author: galt 
Date:   Sun Nov 4 16:00:06 2007 +0000

    "Release log update"

commit 481d12dbce09d349563bace955ad1cb25c551c20
Author: fanhsu 
Date:   Sun Nov 4 01:55:01 2007 +0000

    Removed Help link from makeTitle().

commit 237c1956f970c71b7c294100d813009870bc0f26
Author: fanhsu 
Date:   Sun Nov 4 01:51:57 2007 +0000

    Added hotLinks().

commit 2813e85f24f0eaf58c0cfacc9d852d4f4d813021
Author: fanhsu 
Date:   Sun Nov 4 01:50:44 2007 +0000

    Updated top bar.

commit 56d1d4102c9227dcbf95b7d9864ba5f2ee9e49e4
Author: fanhsu 
Date:   Sun Nov 4 01:35:08 2007 +0000

    Updated top bar per Bob's suggestion.

commit 1599d31208d6611ab0946d322554f55c0a7ac304
Author: galt 
Date:   Sun Nov 4 00:17:20 2007 +0000

    changes to enable other jobs besides "loading" to be scheduled

commit 7c8837b99d5c5ee4513f80a0fe5057c3209c0fee
Author: galt 
Date:   Sat Nov 3 15:00:15 2007 +0000

    "Encode release log update"

commit ec66b8d51112173b4e48ecacd08777eee386d4ad
Author: galt 
Date:   Sat Nov 3 15:00:11 2007 +0000

    "Release log update"

commit b1fd6b1895d4d8bc05f531cb54ccde1f689f0685
Author: galt 
Date:   Sat Nov 3 07:18:36 2007 +0000

    changing from using submissionTypes.yml to submission_types table because this will make it easier to share the config info between Rails and C-code

commit a7adaa692d48467f0381fd96fb75146516e6bd12
Author: fanhsu 
Date:   Fri Nov 2 23:47:56 2007 +0000

    Removed some sentences for GSID server.

commit 5cfb6af67fb77cd31c8d447209661af293952217
Author: rhead 
Date:   Fri Nov 2 22:26:36 2007 +0000

    Added a rule for snp127 tables (just copied snp126 entry). Also added a definition for the databases that contain a snp127 track, and added bosTau3 in addition to hg18.

commit 32ca656932d426c0c134b0321c8d3df1054b0fbd
Author: hiram 
Date:   Fri Nov 2 21:37:33 2007 +0000

    Determined that the annotations needed to be reloaded into the correct table.

commit 38a48bf692cda2f3d989418545e9eefb5389b659
Author: hiram 
Date:   Fri Nov 2 20:26:50 2007 +0000

    Disable nucleosome tracks until a final set of data is ready

commit cf3051e72f222199e34d48a08aa367cf107683b3
Author: angie 
Date:   Fri Nov 2 17:57:28 2007 +0000

    Added Ensembl Genes ('bout time!).

commit 56e7d0469c007f6ff80c0749534c829db14c6669
Author: ann 
Date:   Fri Nov 2 17:55:16 2007 +0000

    added example of usage

commit 99477e3d07847cefb14fab03bf42b29dc16f5e6f
Author: rhead 
Date:   Fri Nov 2 17:36:28 2007 +0000

    Added an origAssembly line to the evofold block to show that the data were lifted from dm2.

commit 6eb2e54402d6e648e2f0057935e12430ff45d33f
Author: kuhn 
Date:   Fri Nov 2 16:51:25 2007 +0000

    prettied up a little.  thanks, ann

commit 656825acd5f6a7e6c95f3f9444dc7da663c07a3f
Author: kuhn 
Date:   Fri Nov 2 16:01:56 2007 +0000

    added dupeOk.  OK?

commit 8b480b5cf938308fa51667e5a78ee2dda8f125d7
Author: kuhn 
Date:   Fri Nov 2 15:59:44 2007 +0000

    removed a dupe.  thanks, ann.

commit a2c846062731589037932fe972f542c8d84fdb88
Author: galt 
Date:   Fri Nov 2 15:00:07 2007 +0000

    "Encode release log update"

commit bbed288f3add75c41bb04e833a377aeaf88eda63
Author: galt 
Date:   Fri Nov 2 15:00:03 2007 +0000

    "Release log update"

commit 357071ca00b36dc138855508382e4f4f7c3f8900
Author: jsp 
Date:   Fri Nov 2 13:09:24 2007 +0000

    rnautil.c

commit ece3cb97c988c3e6c616adfc9e9044575982a71e
Author: angie 
Date:   Thu Nov 1 23:11:28 2007 +0000

    Added latest HapMap paper and updated format of references.

commit 44bfc65628110a322f7723dd6b8b79bc7fc20356
Author: kuhn 
Date:   Thu Nov 1 22:14:35 2007 +0000

    added relationship recently discoverd, but it is betw two dbs and the rule doe not work. thanks, kayla.

commit 515746d28a704b240a720dd7ddd00eebec25367a
Author: archanat 
Date:   Thu Nov 1 22:08:09 2007 +0000

    fixed a typo, fixed references and number of characters in a line

commit 983c6b12d3369ca6b5d8bcda229462fb43494f11
Author: fanhsu 
Date:   Thu Nov 1 21:34:51 2007 +0000

    Remove .o file accidentally checked in.

commit 79c50186bc5b231db1236eb740accb9587be6ed9
Author: fanhsu 
Date:   Thu Nov 1 21:33:59 2007 +0000

    Added files for pwdtest to test password generation.

commit 23f479e317afbe03e661a0eeaee62c10db603103
Author: ann 
Date:   Thu Nov 1 21:31:43 2007 +0000

    added check for encodeRegions table

commit 79044f7de49c3feab991a520036ab0bddadf79be
Author: kuhn 
Date:   Thu Nov 1 21:03:20 2007 +0000

    added a path to ls of directories to drop every month

commit 220c8c340621f5624868ec173db1354691ed1324
Author: aamp 
Date:   Thu Nov 1 20:50:43 2007 +0000

    Changed details for chromGraph clicks.

commit 8813e990c8e04407eb23a780aaee5638372a5b92
Author: hiram 
Date:   Thu Nov 1 20:40:36 2007 +0000

    hgWiggle isn't getting into the utils build since it exists here has a binary after the CGIs have been built and thus is not rebuilt.  Prevent it from being left here during the CGI build

commit 37004edcc5165593667211a21951402d18a7ab46
Author: ann 
Date:   Thu Nov 1 20:11:21 2007 +0000

    fixed broken links

commit 113c5e80967f9705abf024cbd0965df7e1732d52
Author: archanat 
Date:   Thu Nov 1 19:52:42 2007 +0000

    fixed a typo

commit ccaf0007107a80fcaa07c56ee2b0dc4ed9f3d015
Author: fanhsu 
Date:   Thu Nov 1 17:31:13 2007 +0000

    Removed help link on 0-based for GSID.

commit e4db941d5dd3784e7df4829635d6bc7be2a646eb
Author: ann 
Date:   Thu Nov 1 17:16:20 2007 +0000

    minor correction.

commit 8305770383853a68b47f4331fe345f6d11ae767c
Author: galt 
Date:   Thu Nov 1 15:00:07 2007 +0000

    "Encode release log update"

commit 980d05d6097c6af1bf91b7512bb1fdfe515c5268
Author: galt 
Date:   Thu Nov 1 15:00:05 2007 +0000

    "Release log update"

commit 241bf9b05999796838b3abf30efd13ac4f3ac30c
Author: angie 
Date:   Thu Nov 1 03:53:55 2007 +0000

    Restored faster & more specific url to jaxQtlMapped.

commit 0e5378eac1640d639ee6aca40632ef22cc923351
Author: kuhn 
Date:   Wed Oct 31 23:30:58 2007 +0000

    added  tags

commit 895d708b98f217b4dbf0f4dc0e028ab1e466d2af
Author: kuhn 
Date:   Wed Oct 31 23:30:14 2007 +0000

    added additional disclaimer

commit 50e46bcd42d0908aff2d3a6a6eae7f4b69e5bc1a
Author: kayla 
Date:   Wed Oct 31 22:58:06 2007 +0000

    fixed PhD --> Ph.D

commit 8a75e22498058d44e7888fe3b083bd4b399aff2c
Author: kayla 
Date:   Wed Oct 31 22:39:03 2007 +0000

    added TARGET=_BLANK to two links.

commit fe5fce59295f44e3c1b0e3e0654f0cfacfc375d8
Author: kayla 
Date:   Wed Oct 31 22:20:08 2007 +0000

    removed "release alpha" from the GAD block so that I can see the track on beta.

commit 6b20d7f9c3c593e372bb496eccb83759ed04e782
Author: angie 
Date:   Wed Oct 31 18:42:11 2007 +0000

    Changed type of hapmapLd from bed4+ to ld2.

commit b780e48b1b9f9e8282cd5856f7ff31370ec9d020
Author: angie 
Date:   Wed Oct 31 18:41:28 2007 +0000

    For type ld2 tracks, added an hgTrackUi checkbox for whether to shade gaps by tInt in dense mode.

commit db98ff7cae234929413b3b2afe4450fd40c27f18
Author: angie 
Date:   Wed Oct 31 18:03:44 2007 +0000

    Oops, removed a dangling reference to handleDbChange.  hgText is not in the top-level build!

commit 3dc252d7840870e05fa25b872591275c35648c11
Author: giardine 
Date:   Wed Oct 31 16:59:28 2007 +0000

    Updated divergence track

commit 7e03539c1469d256d9005e4b859d51df6c9d391c
Author: giardine 
Date:   Wed Oct 31 16:55:11 2007 +0000

    Added coloring by type to ORegAnno track.
    Changed coloring for Omicia track.

commit f6934a0caf542ea11a039550730241eeeaf9851f
Author: fanhsu 
Date:   Wed Oct 31 16:45:39 2007 +0000

    Fixed a typo.

commit fa84a2ff4788038d69b6ace18a7593fed5b8fe13
Author: fanhsu 
Date:   Wed Oct 31 16:44:37 2007 +0000

    Updated description of proteinID field.

commit 0ae3c5db128747e9de1228ad83392496c4919819
Author: fanhsu 
Date:   Wed Oct 31 16:42:41 2007 +0000

    Define proteinID more precisely for KG II and KG III difference.

commit 2298834d6977bd5afd7b437a44c8389c58dbb3cb
Author: galt 
Date:   Wed Oct 31 15:00:06 2007 +0000

    "Encode release log update"

commit 6a9fc75c82c5fa2239d5e6522c99c696d6c04d2f
Author: galt 
Date:   Wed Oct 31 15:00:04 2007 +0000

    "Release log update"

commit 4904ef940d1e4691fe214063af45b3454e022dfa
Author: angie 
Date:   Wed Oct 31 05:44:37 2007 +0000

    Code review feedback: removed unused variable/arguments (thx Daryl).

commit 7d9f2051866371fcb1168ca1572418a07f891198
Author: markd 
Date:   Wed Oct 31 04:06:08 2007 +0000

    added more verbose message

commit d03e41875a2c0c869af6e3f9a3cb6c1c54d7ddf5
Author: angie 
Date:   Wed Oct 31 00:28:56 2007 +0000

    In ldDrawLeftLabels, use (subtrack-specific) tg->shortLabel if available, for more flexibility, instead of parsing table name first.

commit ce862013ee94a9e72eb4e177419926e383ee2754
Author: angie 
Date:   Wed Oct 31 00:25:44 2007 +0000

    Improved shortLabel for subtracks of hapmapLd and hapmapLdPh.

commit ebb7f49258d324db0622fddf9c37d34230d0c988
Author: kate 
Date:   Wed Oct 31 00:02:23 2007 +0000

    Chip-chip from Sweden

commit b66258f78cb2b63e29399000768c81d3e852d759
Author: angie 
Date:   Tue Oct 30 23:56:39 2007 +0000

    Tweaked hapmapLdChbJpt shortLabel for consistent spelling.

commit 0c212445f3940e9da2f378689c193fa2218dea18
Author: hiram 
Date:   Tue Oct 30 23:45:53 2007 +0000

    Correct names on phastCons plots, remove unused instructions for phastCons construction

commit 5e0ce7f1add5abd108eb7466620522dba592e7e8
Author: angie 
Date:   Tue Oct 30 23:30:59 2007 +0000

    Fixed default vis for hapmapLd, hapmapLdPh.

commit b044bc6f7080117917b10e49a9e7a2482810d4fd
Author: angie 
Date:   Tue Oct 30 23:20:18 2007 +0000

    Correction to hapmapLdPh chromosome list: no data on chrX.

commit 2d09678831ea441859101c5c06b9d2988b35bb81
Author: angie 
Date:   Tue Oct 30 23:14:14 2007 +0000

    Descriptions for HapMap LD on unphased and phased release 22 genotypes.

commit 302b00c4b7c4e20ea968eb2231f191f52b8f8231
Author: markd 
Date:   Tue Oct 30 23:06:30 2007 +0000

    added mm9 to list of supported CCDS databases

commit 49d7d350e774be6ec8a587b917f705d4ff45bdb5
Author: hiram 
Date:   Tue Oct 30 17:41:08 2007 +0000

    Turn on phastConsElements30way track

commit 83b5cc89c0e5e159a5ed03df4dc474f0847b7abb
Author: kuhn 
Date:   Tue Oct 30 17:22:32 2007 +0000

    adding block to quit if error.

commit aa788b8daccfb870d9575b9e8f30e7a650479ca2
Author: kuhn 
Date:   Tue Oct 30 17:21:06 2007 +0000

    removed some text from first column of output that was interfering with sort on percent

commit a7b0f2b3ca865f83b086360432f85e233fd23cd0
Author: hiram 
Date:   Tue Oct 30 17:02:38 2007 +0000

    Added two other phastCons wiggles to the 30-way multiz

commit f3e9c1353ff8000ab91944c64e04e08fc88676b3
Author: kuhn 
Date:   Tue Oct 30 16:51:27 2007 +0000

    pluralized the verb for data

commit 5ad059e121119f7c4c3dc5f13c8496abb4912900
Author: kuhn 
Date:   Tue Oct 30 16:42:03 2007 +0000

    added TARGET _BLANK to offsite links and encoded emails to discourage spammers

commit 9bc59b6bf40813d10c8e3c2f446997d4f6d71b52
Author: aamp 
Date:   Tue Oct 30 16:32:12 2007 +0000

    "New version number v170"

commit d9555ac14141a0f483b6ab775685fe9f5e609176
Author: ann 
Date:   Tue Oct 30 16:23:18 2007 +0000

    fixed typo.

commit 34059885bdbb39821317355701c2f2b402d36034
Author: ann 
Date:   Tue Oct 30 16:16:25 2007 +0000

    corrected link to User's Guide.

commit 7c66916c32727295946afece7f451f8e95ce9a1d
Author: galt 
Date:   Tue Oct 30 15:00:05 2007 +0000

    "Encode release log update"

commit efa50df5ac072cc6d28a705f96327a115407f1a6
Author: galt 
Date:   Tue Oct 30 15:00:03 2007 +0000

    "Release log update"

commit 2e0d6b02e1d6e45ecf71dad2b4fd9d980d29183e
Author: aamp 
Date:   Tue Oct 30 10:09:02 2007 +0000

    Bug related to "db: " prefix.

commit 391813b0490d2360de2a97aff96ca4d1f0f1194d
Author: aamp 
Date:   Tue Oct 30 10:07:55 2007 +0000

    Supports composite track/graph configurations better.  Seems to work and cart vars travel across CGIs (hgTracks/hgTrackUi/hgGenome) OK... I think.  Also got rid of "db: " and "user: " cart var prefixes in favor of "" and "user_" respectively.

commit 79bf1a2e82c5aada0dc72cf41d82d2d183aadd35
Author: daryl 
Date:   Tue Oct 30 05:56:32 2007 +0000

    fixed slReverse call by passing a pointer to bedRegionList

commit 9a2676e07895b0e2d1ae4ad33e38392113432ee9
Author: angie 
Date:   Tue Oct 30 02:36:28 2007 +0000

    Added hapmapLd and hapmapLdPh (LD scores computed on unphased and phased HapMap genotypes).

commit 28a535ae6f949b14ed8c3eff4588b6a8bfa8a53a
Author: angie 
Date:   Tue Oct 30 01:24:44 2007 +0000

    Added ld2 trackDb type support in fillInFromType so specific track names don't have to be registered.

commit b3ebcccf679d945475f5c3dde7c527ecc468bad0
Author: angie 
Date:   Tue Oct 30 01:23:42 2007 +0000

    Added new arg (tdb->tableName is composite track name if mapName is a subtrack) to currently unused mapDiamondUi.

commit 6addba43e5af2658257b8d3214cb7d7cadb66567
Author: angie 
Date:   Tue Oct 30 01:19:16 2007 +0000

    Extended ldDrawItems to handle the new extended ld2 format in addition to ld.  ld2 contains precomputed average scores for faster dense mode display.  It also contains tInt shading which probably will be replaced with some other gap-shadin method.  Also replaced tests for hapmapLd in table names with general support for composite tracks' cart settings in ldDrawItems.

commit 21c15b7433cf25f307d20b750dd87aeaf022fe8f
Author: angie 
Date:   Tue Oct 30 01:16:40 2007 +0000

    Added ld2.{as,sql,c} -- a new superset of ld.{as,sql,c}.  Removed ldUi.c because it no longer contains code.

commit d019f7a384c294b1b6801c29e211c1b8672aa73a
Author: angie 
Date:   Tue Oct 30 01:15:23 2007 +0000

    In ldUi, replaced tests for specific table names with general support for composite tracks.  Also hooked up ldUi for new track type ld2.

commit 0eda7a86fc53b548343bea803701fe17f611ef43
Author: markd 
Date:   Tue Oct 30 00:41:29 2007 +0000

    done core dump on misconfigured base color settings

commit db9c4e166f0ac485493bc1087cfcceed276e2f2c
Author: fanhsu 
Date:   Tue Oct 30 00:08:40 2007 +0000

    Disabled complement toggle for HIV.

commit 745acb81ec09eea8c632a9dd40258329fd1c95ce
Author: hiram 
Date:   Mon Oct 29 23:59:55 2007 +0000

    Add two other phastCons wiggles for Euarch and Mammal

commit 16b77b454901299f5cb1f3c9e827eeea668e314e
Author: markd 
Date:   Mon Oct 29 23:51:59 2007 +0000

    rsync from genbank to hgnfs1

commit 0543a8bde891ffbb61d550dadb66ce541b58d42c
Author: angie 
Date:   Mon Oct 29 23:48:21 2007 +0000

    Cluster job script for PHASE input files.

commit 9eb2a4ece7498b344903194692c826f30c1e53d7
Author: angie 
Date:   Mon Oct 29 23:47:39 2007 +0000

    Cluster job script based on Daryl's in makeDb/doc/hg17.txt.

commit cb447d4401bd447f9a8a4ab8df079992ea2ca263
Author: angie 
Date:   Mon Oct 29 23:47:21 2007 +0000

    Merge the Haploview LD files resulting from a cluster run on inputs split by splitGenotype.pl.

commit d669fc4521f0a5e12ae5b1c76c6af8d6315679a3
Author: angie 
Date:   Mon Oct 29 23:46:58 2007 +0000

    Split HapMap genotypes_*.txt.gz download files into 10M chunks, overlapping by the 250k window size both before and after 10M boundaries for a total of 500k overlap at each boundary.  In addition to chunks, writes a map file that tells which SNPs have complete window-coverage within each chunk, for merging results.

commit cac4fc64839dfcb38b133e8385fc3aa91e4fa35b
Author: angie 
Date:   Mon Oct 29 23:46:06 2007 +0000

    Based on Daryl's makeDcc.pl and makeLdBed.pl in makeDb/doc/hg17.txt.  Outputs both files in a single pass, and adds precomputed average scores for faster dense mode display.

commit bda8ea65f8b85f351a9863dd440ac25d4a2754e5
Author: angie 
Date:   Mon Oct 29 23:45:05 2007 +0000

    For making PHASE format files palatable to Haploview.  If any ? characters are found in the .phase file, remove the columns of .phase and rows of legend.txt for which any SNP in the .phase column has a ?.

commit 0deffb6636abcf80459a8641770adfb70bbe69dd
Author: angie 
Date:   Mon Oct 29 23:44:41 2007 +0000

    Test assumption that the LD output of Haploview contains pairs of consecutive SNPs with no gaps or order-swaps.

commit 09fcf4db5e4c9a2da612d98d0c33dc63bacebe3d
Author: angie 
Date:   Mon Oct 29 23:43:49 2007 +0000

    Loaded both phased and unphased HapMap LD scores.  Had to employ some new tricks: split unphased data before cluster run to avoid running out of mem; remove ? characters from PHASE files to avoid Haploview crashes.

commit ea5cf3751a8f8b7d3eb6ceea6dccdb15ba8de668
Author: jsanborn 
Date:   Mon Oct 29 23:31:37 2007 +0000

    Added key to ispy tracks to get access to alias table

commit 6ba01c90991867305f2f2e9c10b2f12d3f4a3422
Author: fanhsu 
Date:   Mon Oct 29 23:07:07 2007 +0000

    Enlarged array size for maf species count from 256 to 2048.

commit cd31a77ab542ed309194c888bff59d050206b44c
Author: hiram 
Date:   Mon Oct 29 18:08:27 2007 +0000

    Turn on the phastCons30way graph

commit 832ccbbe0bb1c5f1dcba608fb92d61d11e05fa01
Author: fanhsu 
Date:   Mon Oct 29 18:01:18 2007 +0000

    Added "onlyVisibility full" to maf tracks.

commit 90ebff3f38088fb5d0b8a16f876386ad38ffdc81
Author: rhead 
Date:   Mon Oct 29 17:22:14 2007 +0000

    Changed shortLabel on danRer4 nets and chains to $o_db name, as they are being replaced by danRer5 nets and chains.

commit ce7911313bc5d9f3adadaddd6e33a7e08736a4f0
Author: markd 
Date:   Mon Oct 29 16:55:49 2007 +0000

    move build workdir to genbank server

commit 11369cd32cead5c51d3fa69e6b4ac6094e1d33ec
Author: markd 
Date:   Mon Oct 29 16:54:29 2007 +0000

    move build server to genbank

commit 5fd0a317f14847f53908ed03fb81733eafa8f2c1
Author: galt 
Date:   Mon Oct 29 15:00:04 2007 +0000

    "Encode release log update"

commit 57a46935b39caa30c45a11e05214f5b540ef9735
Author: galt 
Date:   Mon Oct 29 15:00:02 2007 +0000

    "Release log update"

commit 50ab4e91103cbc7b66aeb4c89976f598d6d46b81
Author: markd 
Date:   Mon Oct 29 03:20:28 2007 +0000

    add check for running on build server

commit 6edd6462ac5948212a32097f8b1a0aec9b399ff2
Author: galt 
Date:   Sun Oct 28 15:00:04 2007 +0000

    "Encode release log update"

commit 08940f34d4736ec563d6de2e097873daa1e61ea0
Author: galt 
Date:   Sun Oct 28 15:00:02 2007 +0000

    "Release log update"

commit 0141be83606e7876a8847f0d2b7faef5dfb8896d
Author: galt 
Date:   Sat Oct 27 15:00:06 2007 +0000

    "Encode release log update"

commit ef95bf15891e7bbd9dbc925deb2d49f59703c7ea
Author: galt 
Date:   Sat Oct 27 15:00:04 2007 +0000

    "Release log update"

commit 96f28bf9b26f61a5bc5ea990c8acccadc9edab2e
Author: galt 
Date:   Fri Oct 26 22:10:43 2007 +0000

    added encode pipeline scheduler for loading

commit 9033f483493aea22faecae93c81e15b5850b70b8
Author: fanhsu 
Date:   Fri Oct 26 20:51:51 2007 +0000

    Sorted disease class codes for GAD track.

commit cf6929f81473e89bbbbf8d85a1362d27abfb79f7
Author: ann 
Date:   Fri Oct 26 20:23:08 2007 +0000

    added note about the evofold track using the multiz15way table.  This is
    because once we accidentally dropped an old multiz table on another
    assembly that evofold was using.

commit b6012af1c05df281e1c461aea14a7d2ca275d7f5
Author: ann 
Date:   Fri Oct 26 20:21:53 2007 +0000

    cleaned up a little bit

commit 03d42e6d2a53c6395eb07d2fb350b2175ae66f44
Author: rhead 
Date:   Fri Oct 26 19:39:11 2007 +0000

    Added a not about fixing corrupted bigZips file.

commit 4d62e2359e506af669e0ba7ecda0a79b1986e21d
Author: ann 
Date:   Fri Oct 26 19:23:57 2007 +0000

    fixed typo.

commit 0e93dac7c9ec356b899d1e197d9e4bd505c55236
Author: ann 
Date:   Fri Oct 26 19:23:50 2007 +0000

    fixed typo.

commit e24ab5390b8f6e7b7cf56ce84a0e973de91ee863
Author: ann 
Date:   Fri Oct 26 17:29:41 2007 +0000

    made changes so that it would correctly find trackDb.ra entries for
    chains and nets (and not be tricked by the commented lines "#" that
    are in place to note that there is an entry in the priorities.ra file).
    This fixed the problem, however it introduced a new issue.  The output
    now contains a 'grep: no match' warning when there is no trackDb.*.ra
    file present (that is, no encode trackDb file).  I have not been able to
    fix this problem by adding either a -q or -s flag to the grep, nor by
    directing such errors to /dev/null.

commit a3c4df85ecd02415bc51887d258065207f95d589
Author: galt 
Date:   Fri Oct 26 15:00:06 2007 +0000

    "Encode release log update"

commit 723113ba73cadc7d33c5b8ab459035792efab5ea
Author: galt 
Date:   Fri Oct 26 15:00:04 2007 +0000

    "Release log update"

commit 8b586fb69d8d55d5360be53a283915ff3a245032
Author: fanhsu 
Date:   Fri Oct 26 02:25:31 2007 +0000

    Limit GAD disease code list to those with association='Y' only.

commit 0260133ebfb9547d63e27659a325138ae53ab23e
Author: fanhsu 
Date:   Thu Oct 25 22:46:14 2007 +0000

    Make disease class unique.

commit 089ccf2c9249975add3aa022f3d99db254db90ae
Author: rhead 
Date:   Thu Oct 25 21:34:06 2007 +0000

    Fixed a typo.

commit a85be6abb4ecf7562eac6fec2a458a8d26e28517
Author: rhead 
Date:   Thu Oct 25 20:50:24 2007 +0000

    Fixed conversion formula for axt minus strand coordinates. Also changed axtBest to axtNet (thanks, Angie!)

commit 498783617dac40a02d1001e68f77a42b91d1bfa5
Author: fanhsu 
Date:   Thu Oct 25 19:11:25 2007 +0000

    Skip "Components not displayed" section for GSID GB.

commit 1f2adfa979f5dfb43beabf7f5c270cfe1defeb73
Author: hiram 
Date:   Thu Oct 25 18:38:56 2007 +0000

    Added CpG island track build

commit bbe57c52d0430bda94443b8e1473334520d594bb
Author: ann 
Date:   Thu Oct 25 18:30:39 2007 +0000

    replaced some code with a call to the new getMatrixLines script

commit a474e065fd16aa4a4e7f73383b2fc2c519e7bd4f
Author: ann 
Date:   Thu Oct 25 18:10:41 2007 +0000

    fixed for the case where the line is non-standard

commit c28b307d92ba2ceb48d6aa3f26aab79a891495d7
Author: ann 
Date:   Thu Oct 25 18:06:25 2007 +0000

    added getMatrixLines.csh

commit 8c4ddcce0e10f208fcbd7f1a2d684e7f11375d95
Author: ann 
Date:   Thu Oct 25 18:05:12 2007 +0000

    this script creates the two matrix lines needed for chain blocks in
    trackDb.ra files.

commit 1b1480ea19e9160c9e81566aa6bc4474a105d6bb
Author: fanhsu 
Date:   Thu Oct 25 15:48:48 2007 +0000

    Added disease classes to GAD details page.

commit 6a73adba03ed1225f8cb25361eac9950abf5d8fb
Author: galt 
Date:   Thu Oct 25 15:00:06 2007 +0000

    "Encode release log update"

commit f4efe840f112f1667f4b11ba693ba735cfde0e66
Author: galt 
Date:   Thu Oct 25 15:00:04 2007 +0000

    "Release log update"

commit 5df87223e38f8ba621912fa1ba2b7386ecd43d77
Author: markd 
Date:   Thu Oct 25 01:17:31 2007 +0000

    added mm9 nscan

commit f13ab2ccf95b02c676747a493eda6f610f2c3c7c
Author: galt 
Date:   Wed Oct 24 22:40:11 2007 +0000

    customizing list.rhtml for both list and show_user; adding rescue for routines that read the validate_error and load_error files

commit 8bebc174c8af30020d28e50e15dd7999ba296463
Author: daryl 
Date:   Wed Oct 24 21:01:41 2007 +0000

    moved bitsToBed to the library

commit fc115e71d56a6ff3fec6a2e16370e4706d888e5d
Author: donnak 
Date:   Wed Oct 24 20:57:36 2007 +0000

    Removed spurious "." in title path name.

commit c195b8f2d2995fd5776e4edb839c1f9bba271ddf
Author: archanat 
Date:   Wed Oct 24 17:52:40 2007 +0000

    changed some wordings and added reference section. Reviewed by Donna

commit 82f55fb2323db6991b90425aa89d602c9df7d7ad
Author: archanat 
Date:   Wed Oct 24 17:41:14 2007 +0000

    changed some wordings and added references section. Reviewed by Donna

commit 76016193298abf3db16cce54d7c068bd2fa4b3fb
Author: ann 
Date:   Wed Oct 24 17:21:38 2007 +0000

    added databases that were completely missing to 'databasesIgnored' list

commit 400e18e20ff9881ba9cc95adb764f39cc2dddff5
Author: galt 
Date:   Wed Oct 24 15:00:08 2007 +0000

    "Encode release log update"

commit 1b33b7aeea413173f426e7169e85a35a490992ee
Author: galt 
Date:   Wed Oct 24 15:00:04 2007 +0000

    "Release log update"

commit 4e7473dbfff6d58891a5aecdcbf9e08c95cd214d
Author: kate 
Date:   Wed Oct 24 05:33:29 2007 +0000

    Sep-07 ENCODE MSA sequence freeze and TBA alignments

commit 6ddfa11fd31fdb092e1d96e2b5711357efb413e2
Author: kate 
Date:   Wed Oct 24 05:24:13 2007 +0000

    Spelling

commit d822c64e6cb8496a0615babfbf3bfff8e695322c
Author: kate 
Date:   Wed Oct 24 05:20:39 2007 +0000

    Fix name of Uppsala super-track

commit 99c6a8b92a8fe846c7d6cb1f249550502e455a57
Author: kate 
Date:   Wed Oct 24 05:14:17 2007 +0000

    Genome-wide ChIp-chip data from Sweden

commit 4a0dbb54ce7f463f041d4731f7705125bb609fcd
Author: kate 
Date:   Wed Oct 24 05:13:15 2007 +0000

    Genome-wide ChIP-chip data from Sweden

commit a5911ab6d536b8154d336ae5cf420f0031e24b6e
Author: rhead 
Date:   Wed Oct 24 01:14:29 2007 +0000

    Changed priorties in priority.ra files for danRer5 <-> hg18 nets and chains.  Added note at same-level trackDb.ra files.

commit a21b2c748f7c8ca209169972832ae243633b3140
Author: kate 
Date:   Wed Oct 24 00:28:54 2007 +0000

    Add latest ENCODE TBA alignments from Elliott Margulies

commit 8ad72ad75462cce7eeb6eba94cd2c47071e217d1
Author: kate 
Date:   Wed Oct 24 00:28:10 2007 +0000

    Adjust priorities to move in the direction of alphabetical ordering

commit a43f58fc34a33d5480965138bd56e1d772bc1d4f
Author: conodera 
Date:   Tue Oct 23 23:39:57 2007 +0000

    Edited info for vistaEnhancer tables.

commit 3cca3539ffb62b73d5927d31f82b7c54c6bb67b6
Author: rhead 
Date:   Tue Oct 23 21:41:28 2007 +0000

    Tweaked references a bit more.

commit 6c46eb0da39b9edef5e779dd37848b64de62e362
Author: ann 
Date:   Tue Oct 23 18:00:54 2007 +0000

    added link to citation.

commit d4164139b628e6cbdd1c1b7288e509bf4fe2ae18
Author: fanhsu 
Date:   Tue Oct 23 17:34:14 2007 +0000

    Added trialId col.

commit 65ed0babf6e4108b2b3356f3769735bdd0bc6e6d
Author: ann 
Date:   Tue Oct 23 16:59:48 2007 +0000

    fixed details because these other regions don't map to this genome

commit 9ac1873624c3a81add5eeed8a725cce2f7c1bdf9
Author: ann 
Date:   Tue Oct 23 16:24:16 2007 +0000

    fixing table structure (HTML was malformed)

commit 9ea1d79b7bd393ec6d6740976e812e008b6cda43
Author: aamp 
Date:   Tue Oct 23 16:06:09 2007 +0000

    A program similar to liftUp but more designed for converting from gene coordinates to genome coords.  It handles multiple copies of the gene on the genome too.

commit 3d519ec4365cfb9885b47c9d38d607bfc8de4203
Author: aamp 
Date:   Tue Oct 23 15:59:13 2007 +0000

    Added a couple functions more for convenience than practicality.

commit 1d5e7c2e4ab004dcad91e24c797f9fb531522100
Author: ann 
Date:   Tue Oct 23 15:16:16 2007 +0000

    fixed two typos

commit 9016248489555681a76be67d080ae6c930e854d6
Author: galt 
Date:   Tue Oct 23 15:00:05 2007 +0000

    "Encode release log update"

commit 872d963924e349179a3ad4a2f672b72e79293ec3
Author: galt 
Date:   Tue Oct 23 15:00:03 2007 +0000

    "Release log update"

commit c6a95ec64ed68b5b436f0b93b634a7ca52735c67
Author: hiram 
Date:   Tue Oct 23 00:09:21 2007 +0000

    Continuing adjustments to phastCons 30-way run

commit 4ad7e8d8a7d1a67fcedda667ca2b21d2b5326dbf
Author: donnak 
Date:   Mon Oct 22 23:57:30 2007 +0000

    Temporary patch (changed relative paths to full paths) to get error pages to display correctly from all subdirs. Currently they don't seem to display correctly from any subdir that is 2+ deep (such as htdocs/goldenPath/help).

commit 532a92e607cc692e97aee5888d33c9833a6dd9ee
Author: archanat 
Date:   Mon Oct 22 23:40:48 2007 +0000

    changes refs to pubmed format

commit f6912ef36cd6d978603ef5ab9382645055ae7967
Author: ann 
Date:   Mon Oct 22 23:19:39 2007 +0000

    added text for case/color option page in GSID browser.

commit cf75e7eaa277486f84503f0be7d8cdeb501bf1d3
Author: fanhsu 
Date:   Mon Oct 22 22:42:22 2007 +0000

    Added if statment to differentiate descption for GSID.

commit 9edb6501962dbc3e28c34f1ae5e3604c93f24633
Author: kate 
Date:   Mon Oct 22 21:13:41 2007 +0000

    update

commit c98a88f776cfa62f029140f09ecbf2390c5e89c9
Author: kate 
Date:   Mon Oct 22 21:03:25 2007 +0000

    Add NHGRI DIPs track to combined compgeno+variation group

commit b1eb5211446e42f0ae695d3ad4835b5e470f633d
Author: kate 
Date:   Mon Oct 22 21:02:02 2007 +0000

    Add info to NHGRI DIPs entry

commit 14e2173673ec087504ba85466e552e69bd0b5d70
Author: kate 
Date:   Mon Oct 22 21:01:23 2007 +0000

    Lift NHGRI DIPs track

commit 9ae3a24dfd4241be890fd12199bf49b5e10f0afb
Author: angie 
Date:   Mon Oct 22 19:26:30 2007 +0000

    Added support for future name change jaxQTL --> jaxQtl.

commit 83ce8963f36b7afae05d5dcb0920dcd6dc371314
Author: fanhsu 
Date:   Mon Oct 22 18:40:58 2007 +0000

    Updated URL to NCBI/BLAST.

commit 41dedaed5d4a52a8f779d6c7d9cce8e4cfaf36c2
Author: galt 
Date:   Mon Oct 22 15:00:17 2007 +0000

    "Encode release log update"

commit 669756647ddc42f5d38c743cd3e320f626952bae
Author: galt 
Date:   Mon Oct 22 15:00:15 2007 +0000

    "Release log update"

commit 2314e995850a62a03928828973be319071e72510
Author: galt 
Date:   Sun Oct 21 15:00:23 2007 +0000

    "Encode release log update"

commit 05b18c841d8be006ea8f469d09dd8ec7eb934b4e
Author: galt 
Date:   Sun Oct 21 15:00:21 2007 +0000

    "Release log update"

commit 6f4f9b3d524f2f66881594e99c062b30864f2f4a
Author: angie 
Date:   Sun Oct 21 04:11:28 2007 +0000

    Made identifierHash() safer by making it check whether the requested table is curTable.  Added support for custom tracks to identifier stuff -- except it doesn't check whether names are valid (CT data not loaded up).

commit 06efc4a429baa1c9ca176e123c6c47a1204ec08b
Author: galt 
Date:   Sat Oct 20 15:00:14 2007 +0000

    "Encode release log update"

commit a43564fa8f14ce93dbd9e12fc6da4348a749396e
Author: galt 
Date:   Sat Oct 20 15:00:13 2007 +0000

    "Release log update"

commit 8c448c39d6fd02b06ff09ff273c81ff767eb6171
Author: ann 
Date:   Fri Oct 19 23:34:37 2007 +0000

    fixing citation error found by Brooke

commit c417524c5d32a0654d6e031acf95a0548316d3b0
Author: ann 
Date:   Fri Oct 19 23:26:46 2007 +0000

    two typos found by Brooke in code reivew

commit 0bab8123076eb6be3983541c214a9dd2533f6c17
Author: ann 
Date:   Fri Oct 19 23:22:29 2007 +0000

    tidied up based on code review comment from Brooke

commit 76435f6f16510fd317b69983b46d51640a10a0b6
Author: fanhsu 
Date:   Fri Oct 19 22:16:44 2007 +0000

    Changed GNE8 to MN.

commit 428248a81c03b320e85c9872672893ee9316d8c8
Author: galt 
Date:   Fri Oct 19 21:52:34 2007 +0000

    added a new status file for load errors, and gave a new name to the old validate error status file

commit 273be5c681a1e0c30fe1b3229f2e85018f9cc26e
Author: ann 
Date:   Fri Oct 19 20:41:56 2007 +0000

    several rule changes based on problems found by the bi-monthly joiner check for all assemblies

commit 647c49a8e5537aa44005448e7adbd40a0ea98eaf
Author: donnak 
Date:   Fri Oct 19 19:55:32 2007 +0000

    Mods suggested by Brooke.

commit cf567674a37493458f17f9da26498f65ff8ac712
Author: fanhsu 
Date:   Fri Oct 19 18:22:26 2007 +0000

    Created hivMn1.txt.

commit 777eaa10217dd7a0aff4da1868da31d309974914
Author: fanhsu 
Date:   Fri Oct 19 18:14:37 2007 +0000

    Changed GNE8 to MN.

commit 08ce5db0c3fca08d81c097c935b1729cce2b6f4b
Author: giardine 
Date:   Fri Oct 19 16:58:20 2007 +0000

    Updated links for LOVD database

commit 24ea855ae68805ce782252451d66f663b3ddfaf2
Author: fanhsu 
Date:   Fri Oct 19 15:37:26 2007 +0000

    Created for hivmn1.

commit ecf3d4b6ee856f33b5ea94343008e965ecc7e7ca
Author: galt 
Date:   Fri Oct 19 15:00:08 2007 +0000

    "Encode release log update"

commit 802dc4fe034502d7b1a56787e9393ba05a18227f
Author: galt 
Date:   Fri Oct 19 15:00:04 2007 +0000

    "Release log update"

commit 0f060e923f062fb3f99c88217bc54eb3f6dcb94b
Author: conodera 
Date:   Fri Oct 19 05:38:11 2007 +0000

    Added info regarding updated vistaEnhancers tables for hg17 and hg18.

commit 7276d5eed080f9446a4ef206a0bd84b71602bef4
Author: hiram 
Date:   Thu Oct 18 23:53:32 2007 +0000

    Have mostConserved data from first pass phastCons run.  And have annotated the multiple alignments with genes

commit 2672a731b9c0523049de1a363195dfbe46a8c024
Author: kate 
Date:   Thu Oct 18 23:43:49 2007 +0000

    Replace SCONE cons with update

commit 4e7c168f690a9079329735272756a1b1fa1fb490
Author: hiram 
Date:   Thu Oct 18 23:27:22 2007 +0000

    Annotation gene coding frames and Irows turned on for 30-way multiz

commit b15f9408378b6386d2a3b0d236253fa3979e5668
Author: daryl 
Date:   Thu Oct 18 23:27:15 2007 +0000

    Added check to make sure twoBit chrom is same as bed chrom for bedRegionIn option

commit 6dd15b3f7e561311a7716cd49abb12c5584fc56a
Author: jzhu 
Date:   Thu Oct 18 23:06:33 2007 +0000

    remove files in subdir

commit 045027b9bca39982027d78fc23e6d9b7cb5fc695
Author: jzhu 
Date:   Thu Oct 18 23:05:04 2007 +0000

    remove .c .h makefile

commit c2e8b32e62a4385101cb7bcebb5b935541c5cf8a
Author: hiram 
Date:   Thu Oct 18 21:53:02 2007 +0000

    danRer5 blastz done

commit 302445e878a4e162dd84b538285ab4ba60d5873d
Author: archanat 
Date:   Thu Oct 18 21:02:18 2007 +0000

    fixed references

commit a01db4c24a67337779e90648c52b0d57e6d403fd
Author: kuhn 
Date:   Thu Oct 18 20:36:25 2007 +0000

    changed usage statement a little

commit 3db3d974a05a003480fb286fcb1fc03a38f2d448
Author: angie 
Date:   Thu Oct 18 20:09:14 2007 +0000

    Quick fix: Don't use identifierHash() for a table that is not curTable.

commit ff42b2dc5b650872bc88c78febffa944201f4c8e
Author: kuhn 
Date:   Thu Oct 18 18:47:20 2007 +0000

    added link to affy

commit 34559cd15637f5f3872250771e6e622850780f44
Author: fanhsu 
Date:   Thu Oct 18 18:39:05 2007 +0000

    Fixed a bug caused by negative offset value.

commit e10d070f65cb6f0e2a4aa17872fa58ddacf1064c
Author: galt 
Date:   Thu Oct 18 17:40:27 2007 +0000

    display validated status

commit e04f2e1b8438428c0bb33077838bf7c0a88ab4a3
Author: galt 
Date:   Thu Oct 18 15:00:07 2007 +0000

    "Encode release log update"

commit 113fbe5f43dce3ae549dec64636ba83d40d1b6f3
Author: galt 
Date:   Thu Oct 18 15:00:05 2007 +0000

    "Release log update"

commit ef01cfa25508a3d9f3b8b4d59f4f942f6f261de3
Author: braney 
Date:   Thu Oct 18 14:28:35 2007 +0000

    added Human Proteins (hg18) track

commit 07418728d187616445bffffecae992af92e1a96e
Author: galt 
Date:   Thu Oct 18 00:40:14 2007 +0000

    trivial

commit 858d3bd6f334996b6c37e46548991a1b167ca322
Author: kayla 
Date:   Wed Oct 17 23:35:31 2007 +0000

    added matrix values to the strPur2 block

commit 66adb7705c7dee8bfdd9ea505818e7f39fe2e582
Author: hiram 
Date:   Wed Oct 17 23:18:45 2007 +0000

    Content contained in the composite track affyMouseExon.html

commit 5b79f0a8c42d4758384124828e668595725a45d7
Author: hiram 
Date:   Wed Oct 17 23:18:04 2007 +0000

    Content is contained in the composite track container affyRatExon.html

commit e0539ff3500b788d2d83cabf3f7d1eae00ff3384
Author: hiram 
Date:   Wed Oct 17 23:16:55 2007 +0000

    Add score vs. classification listing

commit 6cc170818c581d486b0d148e17bbde88ced17035
Author: galt 
Date:   Wed Oct 17 23:10:57 2007 +0000

    adding link to show results of status invalid

commit c48e3f65e7041bae524d984c16c2fbbdc3166a88
Author: galt 
Date:   Wed Oct 17 23:07:28 2007 +0000

    no longer used, redirects to list.rhtml instead of show_user

commit be8e92d1bfd6af2c882acd0e8952f41f70416a7d
Author: donnak 
Date:   Wed Oct 17 22:31:14 2007 +0000

    Added hapmap pub.

commit 5b6eb445a8a940a84508baaafaf93a4d6a1fe83f
Author: fanhsu 
Date:   Wed Oct 17 21:57:54 2007 +0000

    Added two lines about adding miRNA section to trackDb/mouse/mm9/trackDb.ra.

commit f0157c02656578f7d740ce288e1fd9a12abcc494
Author: fanhsu 
Date:   Wed Oct 17 21:53:58 2007 +0000

    Added miRNA section.

commit ceb6fda497ce3ff95f48124f1a35d4d498bf4968
Author: ann 
Date:   Wed Oct 17 17:41:06 2007 +0000

    removed duplicate wording.

commit e0b1f9c34f9211a89c6eb1e5dac230f0b259714e
Author: hartera 
Date:   Wed Oct 17 17:19:51 2007 +0000

    Edits and formatting changes.

commit 500de6f08832ef1d3381649e3a4a9b70bd298eb9
Author: hiram 
Date:   Wed Oct 17 17:18:04 2007 +0000

    Starting hg18<->danRer5 blastz

commit 84f28a65a804af1998a72c9ed4262b959bc39a62
Author: kuhn 
Date:   Wed Oct 17 16:39:52 2007 +0000

    fixed bug in file name

commit 7cccda9ee1cefb2d89074605cf1007673e2d3fab
Author: galt 
Date:   Wed Oct 17 15:00:06 2007 +0000

    "Encode release log update"

commit 9b332298af02c7cd008a912240a6a3ff6b09cbad
Author: galt 
Date:   Wed Oct 17 15:00:04 2007 +0000

    "Release log update"

commit 01b5c986610bb4815709c81a2d5a747b457ebf06
Author: kate 
Date:   Wed Oct 17 00:55:59 2007 +0000

    Additional work on Duke Dnase submission

commit 80d07fed5a87e5a631bffd0150e263d3a64f9044
Author: kate 
Date:   Wed Oct 17 00:55:34 2007 +0000

    Cleanup UCSD Chip track

commit b024d277fe2d912df73b9a96c020901edacfd076
Author: kate 
Date:   Wed Oct 17 00:55:09 2007 +0000

    Cleanup UCSD Chip tables

commit 2938c24bc66d55ae29c23256fb1a1cbdc625583d
Author: kate 
Date:   Wed Oct 17 00:54:22 2007 +0000

    Adjust priorities on UCSD Chip tracks

commit faf15b5cb415f2499fc37358ca486d64e342ec5e
Author: galt 
Date:   Wed Oct 17 00:20:24 2007 +0000

    added warning when non-chrom assembly chosen

commit 94c24d718c75bac06a6d5fc4c852bf4097d0b7a3
Author: aamp 
Date:   Tue Oct 16 23:58:51 2007 +0000

    Added better details to coloredExon clicks.

commit 2d47156b6280fdf5f03211b8d89ffd1d9b32d38f
Author: fanhsu 
Date:   Tue Oct 16 23:56:24 2007 +0000

    Documented removal of about 25K records from the snpArrayAffy6 table per Affy's request.

commit 71093c4ae63c072c89e80cbfb2b3df0da0b4f685
Author: ann 
Date:   Tue Oct 16 23:49:53 2007 +0000

    fixed citation.

commit 50fe83e6f5315cc7d118445b29f4068f49c7eb31
Author: ann 
Date:   Tue Oct 16 23:40:35 2007 +0000

    fixed citation

commit 2e5af50f9c95779554eafa6a78b0f5224216670e
Author: kate 
Date:   Tue Oct 16 22:48:24 2007 +0000

    Fix for custom track management screen issue when organism is selected and it's default database has not custom tracks

commit ba1c746372f41c953987fe6a6553158f74c96471
Author: rhead 
Date:   Tue Oct 16 21:04:07 2007 +0000

    Added a comment to output to indicate that we're checking the introns against unbridged gaps.

commit 172762124a7573687a036e76d01edf98bdc22e87
Author: rhead 
Date:   Tue Oct 16 20:40:31 2007 +0000

    Corrected spelling of contributor's name; fixed up last reference.

commit a061748cb7714075609b70b0be98074e3ea1fdf5
Author: ann 
Date:   Tue Oct 16 20:33:51 2007 +0000

    Cleaned up.  Added 'Display Conventions' section.  Fixed citations.

commit 9abc9dc85848e2f3d34bb98c41849668f8fd15ca
Author: ann 
Date:   Tue Oct 16 20:31:29 2007 +0000

    Removing this file so that hg15 will use the /human verison of the file.

commit 151bf625f825a24dd6e35720ec9b606d76625689
Author: braney 
Date:   Tue Oct 16 20:24:09 2007 +0000

    move to braney CVS archive

commit efdf944c5fab596c6fb0bb60ac1a8a2cb7e085fe
Author: ann 
Date:   Tue Oct 16 20:23:47 2007 +0000

    Removed so that hg15 will use the vegaGene.html file from the /human level.
    The only difference was that this one specified which chroms the genes were on.
    I edited the /human level file to be more generic.

commit ab9b2c5d4a5d2361a755cfda8c154ff3e70df5c2
Author: ann 
Date:   Tue Oct 16 20:17:44 2007 +0000

    cleaned up grammar. added Dispaly Conventions section (approved by Rachel).  fixed citations.

commit 4d53f29efd10b197b0613f33469181fd57f8ff01
Author: braney 
Date:   Tue Oct 16 20:05:55 2007 +0000

    moving over to braney CVS archive

commit 1f39ef5bc0084bc64c309b170d34dccd831d1836
Author: braney 
Date:   Tue Oct 16 19:59:22 2007 +0000

    moveed to braney CVS hierarchy

commit 4d2a26ab0d2c94b10f24da1da641501d12722024
Author: braney 
Date:   Tue Oct 16 19:15:50 2007 +0000

    clean up drawing code

commit 4b89ad432afaf5d391e14dfac81c53968a078c53
Author: braney 
Date:   Tue Oct 16 19:15:25 2007 +0000

    some long forgotten changes

commit a915ef56ec3f2fbb570dbc937877bfe915cbed38
Author: braney 
Date:   Tue Oct 16 19:14:59 2007 +0000

    call read tree correctly

commit 1a43f55bf3363227f390fdbf3a7f07f775b670d3
Author: braney 
Date:   Tue Oct 16 19:14:21 2007 +0000

    added code to add leaf nodes for lost genes

commit 1fb05fb3f8df15269ffa189a5cba7b32e60b83cd
Author: braney 
Date:   Tue Oct 16 19:13:44 2007 +0000

    add source/dest logic to the element file

commit 1b4a6e0f248836844c8cac79ae5278280827b661
Author: braney 
Date:   Tue Oct 16 19:13:09 2007 +0000

    add option to swap rows

commit 23fe8c3d0e5a46b98fc8e72c6d01b157d017706b
Author: braney 
Date:   Tue Oct 16 19:03:39 2007 +0000

    add an option allow overlap

commit 9a5b342079fe01efdbb45e0934589a0dabbab679
Author: braney 
Date:   Tue Oct 16 19:02:21 2007 +0000

    add option to build mafs using mega atoms

commit 94e9297efa8707b6883bc15ee3049c0b0dac5a4b
Author: braney 
Date:   Tue Oct 16 19:01:32 2007 +0000

    add an option to add instance name to bed name

commit d8cf4f52d95246731c991f560b02cc77b585b110
Author: braney 
Date:   Tue Oct 16 18:55:37 2007 +0000

    remove printf

commit ba7ef83399c374705cfe430237e1a391ca371e45
Author: braney 
Date:   Tue Oct 16 18:55:09 2007 +0000

    some new test results

commit d9ae1cb8f83e1a2d8ad0596790f8562f85aee305
Author: braney 
Date:   Tue Oct 16 18:54:24 2007 +0000

    add an option to pad out atoms rather than generating new ones

commit 2fcba05ff9532754b97a445df5262544841d4b29
Author: braney 
Date:   Tue Oct 16 18:44:18 2007 +0000

    add flags to use different scoring methods, or to just drop dups

commit 1127424a38654ff5c31ae22adc793fdbaca99dde
Author: braney 
Date:   Tue Oct 16 18:43:27 2007 +0000

    allow two different scoring methods

commit aace93ffaff6e5276c79ea91f1f0aaf508063b70
Author: braney 
Date:   Tue Oct 16 18:41:23 2007 +0000

    add strand to 5' and 3' atoms

commit b792830fae20592f28c39244a959deae712e61f4
Author: kuhn 
Date:   Tue Oct 16 18:35:53 2007 +0000

    added ital to an 'et al.' and reformatted refs to new standard

commit 9e69556272e716b61cd7ba1ef767c71cd93def7c
Author: ann 
Date:   Tue Oct 16 18:32:24 2007 +0000

    html clean-up based on output from tidy program

commit d8f08a670f60432ed3a09d18a46fc0650fdd3c96
Author: fanhsu 
Date:   Tue Oct 16 18:29:01 2007 +0000

    Added hivmn1.

commit 84da68c7794a30f0abfa01a8fd2d8ee7324d0c29
Author: kayla 
Date:   Tue Oct 16 18:24:48 2007 +0000

    changed mm9 to $o_Organism

commit 6e756946bc50f9923381e70aa0448dc55f48b133
Author: hartera 
Date:   Tue Oct 16 18:16:09 2007 +0000

    Removed almost duplicate function, printCustomUrlWithLabel(), and rename printCustomUrl as printCustomUrlWithLabel(). Add a wrapper function printCustomUrl() to use this function when there is a single url in the url setting of trackDb with label in the urlLabel setting. Another wrapper function added is printOtherCustomUrl() which uses url2, url3 etc. settings. The new printCustomUrlWithLabel() was modified to handle multiple urls and labels being set in trackDb. Functions that used the old printCustomUrlWithLabel function were modified to use the new functions - these were doEncodePseudoPred(), doWgRna and doZfishRHmap(). printZfinCustomUrl() was used as it is no longer needed. Moved code in genericChainClick() so that the chains to other browser link is only added if the database exists for it and if the sequence files exist. Also check for the existence of the database in chromSeqFileExists() before checking for the chromInfo file.

commit ad3744a34ab7a6f12059783e343b72e5db375539
Author: angie 
Date:   Tue Oct 16 18:06:01 2007 +0000

    Fixed sqlTableWildExists which was always returning TRUE (oops!) because unlike sqlTableExists' count(*) query, a show tables query should never fail but might return 0 rows.

commit a52c235d4cb5637ea54ae5c79385253112d84f72
Author: hartera 
Date:   Tue Oct 16 17:52:24 2007 +0000

    Added a url label for the rhMap track to be used by hgc for display on the details pages.

commit 6990fbebf4f6e426044d8cd7b827f8c8e9ea53e3
Author: hartera 
Date:   Tue Oct 16 17:50:45 2007 +0000

    Changes to url and ulrLabel settings for a subtrack of encodePseudogene.

commit 2e62931cee371652ee15b858444930ca71fad72c
Author: hartera 
Date:   Tue Oct 16 17:49:19 2007 +0000

    Added urls and url labels for the wgRna track - to be used by hgc to display the correct urls for the details pages.

commit a0b0bc4dbf640bcd40ee01c24ab63f0a3383c589
Author: hartera 
Date:   Tue Oct 16 17:48:24 2007 +0000

    Added a url label for Ensembl non-coding genes.

commit 505003f5b6bd8104c9a4a772e81e7fefd78ec03f
Author: hiram 
Date:   Tue Oct 16 17:47:55 2007 +0000

    gcc version 4 errors out complaining about possible use of uninitialized variable

commit b494808c78050327355b064c7b314cfa6f8b68e0
Author: hiram 
Date:   Tue Oct 16 17:44:50 2007 +0000

    gcc version 4 errors out with complaint about possible use of uninitialized variable

commit 8fa83a0f7c31b421e02dad286d99832a72362fc1
Author: hiram 
Date:   Tue Oct 16 17:33:36 2007 +0000

    gcc version 4 errors out on a warning about potentially using an uninitialized variable

commit 5255b93e0d08e8ad987063c55e05bf52e89abbb7
Author: hiram 
Date:   Tue Oct 16 17:31:51 2007 +0000

    gcc version 4 errors out on a warning about potentially using an unitialized variable

commit 3374f68c6445f6dc38cc85af11150023fb6db70c
Author: kuhn 
Date:   Tue Oct 16 17:02:12 2007 +0000

    removed hg17- and hg18-level blocks for wgRna.  human level covers them.  this standardizes the longLabels

commit 2333dee4ea15c60d07887df9d300148a4d2d5e14
Author: ann 
Date:   Tue Oct 16 16:45:41 2007 +0000

    fixed table structure (missing a set of
tags). commit 7808aec6c18e5d2abb7ad7083c75bb18db61d7ee Author: galt Date: Tue Oct 16 15:00:05 2007 +0000 "Encode release log update" commit b0d45f07c48bda709f7aa45b6ac014f4cb1ee74c Author: galt Date: Tue Oct 16 15:00:04 2007 +0000 "Release log update" commit e0df6f8095e5c17f759f1827bd142ea22c8b60bb Author: aamp Date: Tue Oct 16 12:44:09 2007 +0000 "New version number v169" commit 2435625fc71668771d2c7e02c1ef052dac9b1366 Author: aamp Date: Tue Oct 16 09:49:51 2007 +0000 Took out some code Angie said was a duplication of stuff in hdb.c and changed hgGenome accordingly. commit 775e66c7ab6e506bd03877bdf7d01017e3b4a0f8 Author: kate Date: Tue Oct 16 01:09:47 2007 +0000 Restore track lost during ENCODE migration reorg commit a279f6512d0a0b903f8a52c1812aaec833a0f947 Author: galt Date: Tue Oct 16 00:37:19 2007 +0000 changes to allow archives to expand subdirectories -- this was not previously allowed commit 0b5ceb5385eab107467e382cb61a130aeb562e68 Author: kate Date: Tue Oct 16 00:24:30 2007 +0000 Add dataversion to SCONE tracks commit a1b71954b3776db617a171ed816c791f7bb0e0d0 Author: markd Date: Tue Oct 16 00:22:49 2007 +0000 added .as file for contrastGene commit 5d259a5bb6911f0c6fb96c81f57cca04637dded8 Author: angie Date: Tue Oct 16 00:02:14 2007 +0000 Remind developer to make pushq entries for other dbs' chains to this db. commit e20d28e1a890a2de1fdc273a023ffda8d2edc4ac Author: hiram Date: Mon Oct 15 23:42:08 2007 +0000 Annotated the 30-way mafs with I-row information commit 4018ac26d71e7406a791b234e22ba05f5258ff99 Author: kuhn Date: Mon Oct 15 23:38:34 2007 +0000 fixed logic. off-the-end chroms were wrapping around top of numberspace instead of reporting negative. commit 85767844e2d6f25359b5ca1e8aea243f57b78cbe Author: kate Date: Mon Oct 15 23:30:42 2007 +0000 Updates commit f06e0b27a37db1a57f530d063cc5ba16a59ecfd8 Author: galt Date: Mon Oct 15 22:54:44 2007 +0000 getting rid of unused sf_type and status fields in submission_files table commit a293c51f30809392aa6ab3c140aa59ce087ae7ea Author: kuhn Date: Mon Oct 15 22:19:12 2007 +0000 added some comments to locate multiple rebuilds of wgRna track commit f9f9d507377a94110daa0cca2d21dc0025d14c29 Author: angie Date: Mon Oct 15 21:39:23 2007 +0000 Added notes for next time building MGI QTLs -- use table name jaxQtl instead of jaxQTL (b0b's request). commit 52dd1ac8fc9fc3b93394be0793196e11204ba7ed Author: angie Date: Mon Oct 15 21:38:27 2007 +0000 jaxQTL --> jaxQtl name change requested by b0b. commit 608378579353b9447ec7d3a5c6b7ae9da5ef537f Author: kuhn Date: Mon Oct 15 21:27:48 2007 +0000 removed comment about measuring directly in humans. still don't like that it sounds like rat QTLs here.... commit afdffc68c5d799d2c2fe6d2f916ac77733ea96ef Author: angie Date: Mon Oct 15 21:21:34 2007 +0000 Removed unnecessary sqlNextRow's from sqlTableWildExists (Hiram code review suggestion). commit 1a00bab818764b245f38e363bc4e4315489e5646 Author: angie Date: Mon Oct 15 21:10:28 2007 +0000 Tweaked $clusterSeq to be distinct from the filename used by doRepeatMasker, so if both use the same cluster-storage simultaneously, the one that finishes first will not clean up the file that the other is still using. commit 2beed0c9e0a2d184141c10cbac8ef8cb4962792e Author: kayla Date: Mon Oct 15 20:37:41 2007 +0000 added danRer5 commit 1c04493537fa0e2e8a921955e36049d68d9f4e68 Author: angie Date: Mon Oct 15 19:49:45 2007 +0000 doSimpleRepeat.pl -- run TRF and filter results for masking. This doesn't do the actual 2bit masking because it might be concurrent w/doRepeatMasker. commit a6d1da6e2ae53144378d5ade26ee9c8559a0a585 Author: ann Date: Mon Oct 15 18:54:38 2007 +0000 corrected for release date of danRer5 commit 478e440131c066a213b4fbb88184c74d234c2566 Author: ann Date: Mon Oct 15 18:12:15 2007 +0000 finished sentence commit 1c754a431928f15190c4e15ffc5eefc2f849460a Author: kuhn Date: Mon Oct 15 17:56:53 2007 +0000 changed the link to MGI for QTL details. commit 44479bc2878bb1076625651b9ac5b5beb7726d25 Author: rhead Date: Mon Oct 15 17:05:43 2007 +0000 Changed two link to their English versions from their French versions. commit 37e5b9d5051b5314417d4420fa4ac37c5ab4efe7 Author: hiram Date: Mon Oct 15 17:04:07 2007 +0000 Do not include the : in the suffix $p string commit a5f78d0f5a14c19edd31a5dadadb134164b91816 Author: galt Date: Mon Oct 15 15:00:08 2007 +0000 "Encode release log update" commit a998f963fb75e27520f9bffae3677132ab17ca5c Author: galt Date: Mon Oct 15 15:00:04 2007 +0000 "Release log update" commit 0c21785b2527bbcf3b5b4962c53a8d17f5756cb0 Author: donnak Date: Mon Oct 15 04:50:09 2007 +0000 Added this file (created by Branwyn) showing results from the 5/07 GB users' survey. commit e415277eeaec5235b7a962a6cd78b6ca206babf3 Author: donnak Date: Mon Oct 15 04:49:10 2007 +0000 Added link to GB user survey results. commit 440b5ae6e48f71f204b64564f9b2382171cd30ca Author: galt Date: Sun Oct 14 15:00:06 2007 +0000 "Encode release log update" commit 9be7b58f7e7f9c9746fbfef3990b1fa6c5779f3c Author: galt Date: Sun Oct 14 15:00:04 2007 +0000 "Release log update" commit 93d9c84bd9e5f4fc2b89cdacd6a99a05b7abf40d Author: galt Date: Sat Oct 13 15:00:08 2007 +0000 "Encode release log update" commit 18717ea26d33b16f536c5a0e4e50d4872eb90b3b Author: galt Date: Sat Oct 13 15:00:04 2007 +0000 "Release log update" commit cbae3d2d3435764794ebb16adb0abd11673a36fd Author: kuhn Date: Fri Oct 12 23:54:26 2007 +0000 changed tableNames of jaxQTL* tables to jaxQtl to match convention commit 3b9bbc46c242b1d50eade2ff5a75e971778bfeb7 Author: kuhn Date: Fri Oct 12 23:40:32 2007 +0000 changed tableNames of jaxQTL* tables to jaxQtl to match convention commit 137dba98ca815d4cdb3dc9ff05b5183c70ef9afc Author: galt Date: Fri Oct 12 23:22:41 2007 +0000 added handler for a few signals that will log the errors commit b4f29ec383a481f80ca8913d8a4051c7f5b6e3c3 Author: kuhn Date: Fri Oct 12 23:19:48 2007 +0000 added 'Human' to short label to match mouse and rat QTL tracks commit 3d7695a2a6cc672c3094694246fd497fa789bffd Author: kuhn Date: Fri Oct 12 23:10:31 2007 +0000 made the rgdQtl.html human-specific to reword the description slightly commit 383ab06f098de15925f6d54b9d7702f97ef74c5e Author: kuhn Date: Fri Oct 12 23:08:33 2007 +0000 reworded on sentence slightly commit b77131f04cf0c62d99163f14f36af189acf4897b Author: hiram Date: Fri Oct 12 22:57:25 2007 +0000 targetscan.org works better commit 2562e886dad2e9eb7d9896dff187d60f330ed4f2 Author: hiram Date: Fri Oct 12 22:52:32 2007 +0000 Update url link for target scan commit 3597b6fabe1688758579398385042ea926f36e12 Author: jzhu Date: Fri Oct 12 22:30:11 2007 +0000 add min value thresholding to column set up, similar to what i did for max value thresholding, anything beyong the cutoff will be set as null commit 9e12a023067f5bcbc20f44c3bd422a0d59a7f493 Author: kuhn Date: Fri Oct 12 22:29:37 2007 +0000 changed usage statement slightly commit 98d0115fb73a9477937e28b1b96148a4f2cac5fc Author: angie Date: Fri Oct 12 22:11:00 2007 +0000 Use the new printLiftOverGenomeList -- don't check database existence. Even if a db doesn't exist, we might still have liftOver chains to/from it. commit 44b6531cb1cbf145acba81a092f5b8b94674348e Author: angie Date: Fri Oct 12 22:10:30 2007 +0000 Changed hGetDatabaseRank, hGetLiftOverFromDatabases, and hGetLiftOverToDatabases (currently used only by hgLiftOver) to disregard whether a database exists. Even if it doesn't, we might still have liftOver chains for it. commit 4549d4ab6f3f067ca0738a705af6100b1b32bbec Author: angie Date: Fri Oct 12 22:09:39 2007 +0000 Added printLiftOverGenomeList, a variant of printSomeGenomeListHtmlNamed that doesn't require the databases to exist. commit 0dc64892947e1579abb93bbe5508e3c1908da614 Author: kuhn Date: Fri Oct 12 21:10:07 2007 +0000 fixed incorrect file name for what gbdb to drop. commit 2d2d3a44d0fd4c1a8a591a20585b4b618290dba0 Author: fanhsu Date: Fri Oct 12 20:53:39 2007 +0000 Updated logic to only include genes having 'Y' in the association field. commit 7ad614e336516aea811d18cb32b1fd72f03a4006 Author: ann Date: Fri Oct 12 20:53:28 2007 +0000 more verbose statements and one logic addition commit 3fd44464d6e04724cefae9ed037089a5107b230b Author: jzhu Date: Fri Oct 12 20:12:20 2007 +0000 add feature labels, fix a few bugs, introduce max setting in column.ra file commit 99c3b26fe770c043aacc17ec7e3ec96115c2a0bd Author: kayla Date: Fri Oct 12 19:38:20 2007 +0000 copied from netGasAcu1.html commit b2d278f0b350c6b935b153f93c4882550a4af294 Author: kayla Date: Fri Oct 12 19:37:53 2007 +0000 copied from chainGasAcu1.html commit c23329b182708e5ac9f22ab63937cd2abf809f38 Author: kuhn Date: Fri Oct 12 19:16:11 2007 +0000 added ting's name to his RACEfrag block commit b5513c83edeb154d93709c41fb1a60c54c6d6667 Author: kuhn Date: Fri Oct 12 19:07:54 2007 +0000 removed a space in the middle of '5-prime' commit 10c846a9b47cdb366653cefd3d7fb3b67dc1e228 Author: ann Date: Fri Oct 12 18:03:33 2007 +0000 added note about the matrix parameter possibly being in the other README file commit 15711e819d901ca0492accdf83d88877c5d77a5e Author: ann Date: Fri Oct 12 17:22:20 2007 +0000 a few grammatical changes. commit 32f562643f183f30d3f7e4258814e61585026831 Author: kuhn Date: Fri Oct 12 16:06:43 2007 +0000 oops. removed some debugging stuff. commit 2810fc4ae405593be168a7239bc8a7c5baa294c7 Author: kuhn Date: Fri Oct 12 15:57:31 2007 +0000 refactored to use arrays for stepping through mouse assemblies instead of using same code three times. commit 492dbc45f313d7d34e3fbbd477ebdd9ae804f5e6 Author: kuhn Date: Fri Oct 12 15:56:53 2007 +0000 changed format of usage statement to match most of our other scripts commit 37e27d1bfed707dec7645e2d76800b6ce0846f18 Author: galt Date: Fri Oct 12 15:00:06 2007 +0000 "Encode release log update" commit 891894e2bfbd11e3928b4c9bae28104ff0d88917 Author: galt Date: Fri Oct 12 15:00:03 2007 +0000 "Release log update" commit 0d1b5c5dc4836653210bbd8d88f89854e4c49d07 Author: daryl Date: Fri Oct 12 06:27:17 2007 +0000 added support for the bedRegionIn/bedRegionOut option for 2bit files commit cf2b2cf91da03c9bcf43e413d55751f3bc3ad5cd Author: hartera Date: Fri Oct 12 04:08:07 2007 +0000 Turned off the autoTranslate setting for vegaPseudoGene. commit b4cdd13bc8305ceb0fef4c01d10d9b75cb85b35d Author: hartera Date: Fri Oct 12 04:04:32 2007 +0000 Added vegaPep table to vegaGene track definition and also turned off the autoTranslate setting for vegaGene. commit 6e400db8b67537a07d7030969d8d057202a23f71 Author: braney Date: Fri Oct 12 03:09:37 2007 +0000 added blastHg18KG track (Human Proteins) commit 9ba00c7fc75e3e38bb5b64df27885716f10a105a Author: angie Date: Fri Oct 12 00:08:03 2007 +0000 LiftOver chains to ce5. commit 5fd6375d6427b95da6c9bcc21acfc92c02178c02 Author: angie Date: Fri Oct 12 00:07:23 2007 +0000 WS180 -- Masked sequence only, no database, plus liftOver chains to ce4. Did this for modENCODE -- we don't have the resources to build a new database for each WS{N*10} release every 4.5 months, but can produce liftOver chains so that our browser can be used with data from newer assemblies. commit 491e7db266e266f2ab073178132dae10b552c51d Author: fanhsu Date: Thu Oct 11 23:43:27 2007 +0000 Updated gad track. commit 3dae92fdc24afbbc5351cce4e82a058a3d2cdfdc Author: hiram Date: Thu Oct 11 23:31:18 2007 +0000 Update targetScanS track data commit 15d706419233bc67c6434d73fa51d7ba376c8ddb Author: hiram Date: Thu Oct 11 23:30:49 2007 +0000 Finished off the blastTab loadings into the other organisms. commit 096a81a286c06a1653f52a8454d4b6849955b79e Author: hiram Date: Thu Oct 11 23:27:19 2007 +0000 Update otherOrgs to mm9 commit 868b796ae010fe1f3a8f93f86b70c6798b9b5bce Author: hiram Date: Thu Oct 11 23:23:10 2007 +0000 Initial file to correspond with mm9 updates commit dc2168af1f55f7eb550214171f47be2a045886c8 Author: fanhsu Date: Thu Oct 11 23:19:34 2007 +0000 Updated according to latest data from GAD. commit 7fbfb85d9f732836f6531150edcc127d8a55e02b Author: hiram Date: Thu Oct 11 23:05:58 2007 +0000 Add url link for Affy Exon transcripts commit 7dd8cc2b9a86c0378bfd0cf259f8298968890b4b Author: hiram Date: Thu Oct 11 22:56:10 2007 +0000 Fixup link-out for affy Exon array transcripts commit 6a7b2b31c798fc1a024c38e5fe7241ef57fc380d Author: ann Date: Thu Oct 11 22:55:27 2007 +0000 many, many changes. commit 5f0bee232dfa7b76806b5aff6e68bfaeeb7e4aad Author: jsanborn Date: Thu Oct 11 22:51:37 2007 +0000 Cleaned up some code as per Galt's suggestions. Significant changes/improvements made to sortFeatures.c commit 71614404d635408f40a2ab251745633eb5d53cf4 Author: hiram Date: Thu Oct 11 22:46:12 2007 +0000 Adding exoniphy track display commit 397c6e03d07782a7434555310983bc48b096db48 Author: hiram Date: Thu Oct 11 21:56:48 2007 +0000 Introduced an error by not doing this completely properly. Rework it a bit. commit 398bab8206e2514bcba841ec3c7cef194e67d068 Author: aamp Date: Thu Oct 11 21:51:07 2007 +0000 CCC note. commit 580183b4959c2b243737dbbaa39773c9c0016413 Author: hartera Date: Thu Oct 11 21:32:09 2007 +0000 Updated to reflect the new default display for the array data. commit 848e3684d4a2179806a00493c38e9b16727c53e4 Author: hiram Date: Thu Oct 11 21:23:46 2007 +0000 Update blast tab comments to indicate newer procedure commit 59866d9ba606fd562f8eeacc62f8d4fe2f4f1337 Author: aamp Date: Thu Oct 11 21:18:27 2007 +0000 Fixed another bad link... needs to open new window. commit 1d4c24680fe09b365aaf3f9d18e71b25e4239c76 Author: aamp Date: Thu Oct 11 21:16:55 2007 +0000 Fixed bad link. commit e6f5185a1692f0da6cdbcd9c111c91593a340066 Author: aamp Date: Thu Oct 11 21:14:21 2007 +0000 Fixed bad word. commit b84870306efb90645811e5a1f53604633af52ffe Author: hiram Date: Thu Oct 11 21:14:09 2007 +0000 Update to danRer4 and ce4 commit e9b2af341ce7d12e511eb1cd96636b92c54f7512 Author: jzhu Date: Thu Oct 11 21:01:43 2007 +0000 communicate hgheatmap with configureFeatures using active column setting (old method: hghPersonOrder), remove sort pateint button, sorting get effect after submitting from configureFeatures commit b4a2211c15464506c21847ce05f448a870799789 Author: kuhn Date: Thu Oct 11 20:59:36 2007 +0000 fixed search for consIndels tracks commit cd77eb87364815a6e665a9788cd352b5f540ec3a Author: angie Date: Thu Oct 11 20:57:38 2007 +0000 Added chooseSmallClusterByBandwidth. Added $setMachType constant: a csh command that correctly sets $MACHTYPE. For csh scripts that run on other machines, esp. cluster nodes. commit c120085a021c0d67445d2a13fb2d19dd7982a09d Author: angie Date: Thu Oct 11 20:54:32 2007 +0000 Added -noMask to the faToTwoBit commands that make $db.unmasked.2bit, in case the original sequence has lowercase letters. commit d0eb15676fb51df567b077d03f1cc3984796f568 Author: archanat Date: Thu Oct 11 20:38:59 2007 +0000 fixed link commit e55ebe2f8766b5c90d1f1ff08f72cef2649af704 Author: ann Date: Thu Oct 11 20:07:08 2007 +0000 added to tablesIgngored those tables in support of the Genome Graphs built-in data sets commit 812d784a81f33febd96decf85405ff54320faa21 Author: hiram Date: Thu Oct 11 20:03:04 2007 +0000 Recognize a new trackDb setting of scoreFilterMax commit 67d99e04993e92aae4e00c07862210e31679fefa Author: hiram Date: Thu Oct 11 19:54:50 2007 +0000 Fixup short and long names for targetScanS track commit e6cfac521f757f17f70e37f154590c221b24953c Author: kuhn Date: Thu Oct 11 19:53:35 2007 +0000 changed consIndel* table names to have consistent name in both asemblies commit 5f49c16be655564f7992aa12ccf41eb991bffa4e Author: hiram Date: Thu Oct 11 19:50:04 2007 +0000 Update the target scan track html and url substitutions commit a080da36b2a687d18cbb56d89b74492ab8511ffb Author: hiram Date: Thu Oct 11 19:49:21 2007 +0000 Add a scoreFilterMax variable, and document the substitution strings available on a url link commit a91373b26e05c740f884021d0321849aec8a11ce Author: hiram Date: Thu Oct 11 19:48:50 2007 +0000 Fold in the special case for targetScanS into printCustomUrl() with a couple of new substitution strings commit f652f72ade1c906feb1690ffb416b240d5f0adab Author: kayla Date: Thu Oct 11 18:57:24 2007 +0000 added strPur2 commit 281e71d9a029f2135e5c1d76dfa777c70a427071 Author: hartera Date: Thu Oct 11 18:05:43 2007 +0000 Removed redundant text, moved text and changed the default display so that it is the replicate means as for GNF Atlas. commit 27dcc39136b4043f66cbeb9c1730fb22f1d8435c Author: hartera Date: Thu Oct 11 18:04:37 2007 +0000 Changed default for Affy Zon Wild Type arrays to be median replicates as for GNF Atlas. commit bf50bb75c7fc7e0a84ab6cf147a25dd583d59c80 Author: fanhsu Date: Thu Oct 11 18:03:34 2007 +0000 Updated ipsyTables.h. commit 7549806fc7c72363365b5ce9a0753225fb21dd89 Author: fanhsu Date: Thu Oct 11 18:02:33 2007 +0000 Updated ispyTables.c. Generated with the additional -dbLink option. commit 40fcc79b1738e605ca65e03e33ca12428ea476e9 Author: fanhsu Date: Thu Oct 11 18:01:27 2007 +0000 Updated ispyTables.as. commit a98a5274b7c11e38e41b204683a9031d608c87c8 Author: ann Date: Thu Oct 11 17:25:24 2007 +0000 lots more cleanup commit 22e591d62abc46aedc4296c0e86d8f45f079e43c Author: rhead Date: Thu Oct 11 17:23:11 2007 +0000 Updated link to Fish and Wildlife endangered species page. commit a00544f22681685a730b34190f393e30e0b90772 Author: ann Date: Thu Oct 11 17:12:38 2007 +0000 shortened the too-long long labels even more! commit 6e1ea9889b7502e952f4e0a09124c30b4cc0c8d8 Author: ann Date: Thu Oct 11 17:07:30 2007 +0000 shortened the too-long long labels commit 44064ef7ac91f0c9192101fbb34885a2d23419b8 Author: kuhn Date: Thu Oct 11 16:47:09 2007 +0000 util to get last month in yyyy-mm format commit 92a256c75a3577a473753f4543c48ecb35da352e Author: ann Date: Thu Oct 11 16:28:14 2007 +0000 a little clean-up commit 0b382d4515ca307da1852ad026e91bb40e87eec1 Author: hartera Date: Thu Oct 11 15:02:45 2007 +0000 Removing affyZonWildType.html to be replaced by affyConsensusAndTargetZonWildType.html. commit 28f2596b9bf68df925fe39357d7b7a4b697056ae Author: hartera Date: Thu Oct 11 15:01:10 2007 +0000 Description for Affy Wild Type expression track with consensus and target sequences aligned for the Affy Zebrafish chip. commit 9172c137d35947356b47433f023beae2c52baa4d Author: galt Date: Thu Oct 11 15:00:07 2007 +0000 "Encode release log update" commit 7e3793a52bcec346efc71117cfa21fd14404a6eb Author: galt Date: Thu Oct 11 15:00:03 2007 +0000 "Release log update" commit fbdea4d5a14b92f50d0d9549540ca3ea3fabb6fa Author: kent Date: Thu Oct 11 14:14:13 2007 +0000 Adding bottleneck to makefile. commit 31f33d4b5be65e91d4bc7b54fce458afc2957132 Author: donnak Date: Thu Oct 11 06:19:34 2007 +0000 Edited this file. commit 9cac4a3bb70bfdd988d90edc41843da03dd0214c Author: donnak Date: Thu Oct 11 06:08:36 2007 +0000 Made some edits to these files. commit f285b394d351d05e41101779964bee137e405123 Author: donnak Date: Thu Oct 11 05:40:14 2007 +0000 Uncommented danRer5 entry in release table. commit 964107e51c309d244c6efc1f3270ccd3aba2b384 Author: donnak Date: Thu Oct 11 05:39:01 2007 +0000 Uncommented news item abt danRer5, archived an item. commit d56ead0c3d71a6dffdcfdd48ddb070eec2949a6a Author: donnak Date: Thu Oct 11 05:38:07 2007 +0000 Archived 2 items. commit 3a698f38db14e6c7d1619c311e1cda4e11fd7b30 Author: jzhu Date: Thu Oct 11 05:28:12 2007 +0000 improve speed to do configuration in dispatchPage, fix bug when no sorting columns are selected commit a0bd423a2b25066c6ed96b6a344be0d6c912b7aa Author: kent Date: Thu Oct 11 05:08:32 2007 +0000 Trimming a few lines by using cgiMakeIntVar instead of cgiMakeTextVar for score. commit 920782770e90d26e18292d603c442c5ae53f00b4 Author: donnak Date: Thu Oct 11 05:03:54 2007 +0000 Updated date for strPur2 release. commit 67a4c2ea0e19de44c0670397a45415df2d3b0532 Author: kent Date: Thu Oct 11 05:01:13 2007 +0000 Removing ensGeneName which no longer does anything. commit a1a2d8f430369a5827b919f42a65c3305a342e5f Author: galt Date: Thu Oct 11 01:14:50 2007 +0000 re-worked it to use the new slPairFromString function commit 4d532622bd648488abee479e171c795e9048a72e Author: galt Date: Thu Oct 11 01:14:12 2007 +0000 adding a function to create an slPair from a string commit 85e9181a0c2a01f7c068bdbe31ee66e0502f9a1b Author: kuhn Date: Thu Oct 11 00:40:08 2007 +0000 change text slightly commit a04925db7af827875cc98d475b57fd1c92e49990 Author: kuhn Date: Thu Oct 11 00:03:06 2007 +0000 changed 'data' to plural commit d0338bb55d9431e2211197524a3fe84bf7efc9f9 Author: hiram Date: Wed Oct 10 23:44:41 2007 +0000 Initial source from Venu commit 4e822e3eca4f35e95dbf8359ab7d97997bfd1d07 Author: galt Date: Wed Oct 10 23:18:21 2007 +0000 added missing celltypes commit 1dfaba55e377efe104823e94c7b38107b3c0a0f6 Author: galt Date: Wed Oct 10 23:13:59 2007 +0000 added missing celltypes declarations commit 38ecf8707537234960933857d5276666d38945a0 Author: galt Date: Wed Oct 10 23:03:13 2007 +0000 added missing celltype k562 to parent composite commit 4f5e6772703d66dfcb66a66ecc177c0175609d6b Author: hiram Date: Wed Oct 10 22:56:26 2007 +0000 Add link to genomewiki parameter page for Mm9 alignments commit f5dc7dd7b53a47ea57f75e8a172e4fd4eb0afebc Author: kuhn Date: Wed Oct 10 22:52:42 2007 +0000 fixed link commit 3e57df11da083a3005745217726878d9b6fa1192 Author: ann Date: Wed Oct 10 22:48:33 2007 +0000 cleaned up rules for danRer5.affyZebrafish commit b667def5b9a2b4d5ca588964e4096d91620f7842 Author: rhead Date: Wed Oct 10 22:32:19 2007 +0000 Took out an extra quotation mark. commit f8f1a4da8bbb378d3abd12e92e5441405ae36c1b Author: archanat Date: Wed Oct 10 22:01:44 2007 +0000 changed refs to pubmed format commit 252b69a17611345831bd82de28b8f34c5207b710 Author: ann Date: Wed Oct 10 18:32:40 2007 +0000 minor edits commit 76ce5233e34f3b3f9eba33ebc6cce44e88a8195c Author: hiram Date: Wed Oct 10 18:10:45 2007 +0000 Added knownAlt table for Alt Events track commit 9c9d7b23a7aea49155d1ce4e3350e96766e8ea74 Author: angie Date: Wed Oct 10 17:58:54 2007 +0000 Ran makeDownloads.pl -- user request. commit 715ddc22074e8faea315c465bc8fccb748cabf1a Author: angie Date: Wed Oct 10 17:23:56 2007 +0000 Added note for rgdRatQtl to use mergeOverlapBed4.pl next time. Re-ran mergeOverlapBed4.pl (with name sorting) on jaxQTL* and reloaded. commit 3f3f24b6a6f1aba777b35cb778408b9a2fe60c8e Author: angie Date: Wed Oct 10 17:21:13 2007 +0000 Adding mergeOverlapBed4.pl, which merges overlapping bed4 items with the same name and sorts by chrom, chromStart and name-descending (so names appear in ascending order in hgTracks). commit e90cb7ece98c40caf65d23d70057fa4bb570a15f Author: angie Date: Wed Oct 10 17:03:43 2007 +0000 Small explanatory note about the \ in our splitPrefix. commit fbfb5b5a8edc6eae5024ab5f4657fc477a57ee5c Author: galt Date: Wed Oct 10 15:00:08 2007 +0000 "Encode release log update" commit 1a9c56df5690992cdd564596359354c6ceb96c8c Author: galt Date: Wed Oct 10 15:00:05 2007 +0000 "Release log update" commit 5af493136d04808a7ef7ca221b9da74764c5be91 Author: donnak Date: Wed Oct 10 05:44:10 2007 +0000 Initial edits to the gateway page text. commit c607291d149c4f91fb9ad4dc644267067df75fda Author: angie Date: Wed Oct 10 05:41:41 2007 +0000 Fixed jaxQtlMapped settings to catch up with hgc.c mods. Added searches for subtrack tables of jaxQtlMapped. commit 88d2645d291b359bf8cee7fae059e04da176aaa5 Author: angie Date: Wed Oct 10 05:38:09 2007 +0000 Extended doJaxQTL to handle the cross-species-mapped bed4 case. commit f7524286d17f91b44ec5287d27df677f775303da Author: donnak Date: Wed Oct 10 05:22:53 2007 +0000 First pass at the danRer5 news item. commit 4164df12f3c33ff01679b086a6ed92723166698d Author: angie Date: Wed Oct 10 04:55:02 2007 +0000 Quick fix to keep jaxQtl bed6+ handler from triggering on the bed4 jaxQtlMapped subtracks. commit 20828668efd01a1324ae2263524d5b4b3ecfd365 Author: angie Date: Wed Oct 10 04:45:11 2007 +0000 Mapped mm8 MGI QTLs to hg18, using filtered .over.chain, liftOver, and padding QTLs with marker-only coords to ~100k as Jim suggested. commit 9293425b7bc3dd99c3148655b6d0d57ceaee038f Author: angie Date: Wed Oct 10 04:43:15 2007 +0000 Added jaxQtlMapped track, for MGI QTLs mapped cross-species via filtered .over.chain and liftOver. commit a566467599e0f5c7e97b190edb799f4ff7640d57 Author: kate Date: Wed Oct 10 03:24:33 2007 +0000 Marmoset alignments, requested by Elliott Margulies commit d0f388954a3942229fdea9af074e81a68e91de77 Author: kate Date: Wed Oct 10 03:16:58 2007 +0000 Fix subgroup errs commit bd0821a70d9e87003ffb579bd127502441757378 Author: galt Date: Wed Oct 10 01:01:20 2007 +0000 kate requested verbose level 2 for this warning commit 2d4aa9176aadaae8703bd1a0ced9130c8d65dace Author: kate Date: Wed Oct 10 00:15:19 2007 +0000 Fix subgroup settings commit 24cf3b3b91f0187001b9f6c72b0e4cc7c402db68 Author: kate Date: Tue Oct 9 23:45:35 2007 +0000 Make DNA extended case/color feature understand supertracks commit 02f5e56579af15b904fe5f8db59b329471a582f4 Author: galt Date: Tue Oct 9 23:37:36 2007 +0000 adding checks for subGroup data between subtrack and composite parent commit 18e23fb06ccb40c8a6391205d942b4c61b620cad Author: angie Date: Tue Oct 9 22:49:57 2007 +0000 Bumped up priority of FB Noncoding so it stays next to FlyBase Genes (thx Brooke). Also, hide the liftOver'd dm2 FB genes. commit dd12b3d15ce710389e286fe85245ebeb35aaa6b9 Author: angie Date: Tue Oct 9 22:39:45 2007 +0000 Removed the link for BDGP accessions (no longer supported by FlyBase) and added a FB transcript ID column (what the BDGP IDs used to resolve to). commit 85e29c73ec2a582a508fbbf0dad56c0d4358165f Author: ann Date: Tue Oct 9 22:16:28 2007 +0000 removing danRer4 (covered in top-level), and adding info about priority.ra file commit 162f071ce06444cb509f5779671dc680879a0c42 Author: ann Date: Tue Oct 9 22:15:29 2007 +0000 adding this file to accommodate chain/net priorities commit 49b8f7877bdf0975784ba5d9d8ffcc694fc68774 Author: angie Date: Tue Oct 9 21:35:59 2007 +0000 Added noScoreFilter for flyBaseNoncoding. (thx Brooke) commit 67dac691f9967bd4e80d5ad0f3322c1f47006eea Author: angie Date: Tue Oct 9 21:21:29 2007 +0000 Rephrased a conditional-execution statement to avoid warning in GCC 4.1.2. commit e4f188051af2df1b6db5deea8014bcce6b62b4f6 Author: ann Date: Tue Oct 9 20:36:19 2007 +0000 moved danRer5 chains/net blocks up from species level to organism level commit 4d866a4e49be95f45127c43418ce1f78b2da75ab Author: ann Date: Tue Oct 9 20:20:19 2007 +0000 adding danRer4 chain/net to this level (from top) commit 20d45ed5ed4a7b9599ced2020a7db69593415fb7 Author: ann Date: Tue Oct 9 20:13:07 2007 +0000 moved danRer4 chains/nets down from top level commit f7083789be4f704e53e19c64c69e07a867546cca Author: ann Date: Tue Oct 9 20:04:58 2007 +0000 making danRer5 the dominant chain/net (instead of danRer4) commit c53b9a28620f704268aefeac7501600dcae8029f Author: angie Date: Tue Oct 9 20:03:25 2007 +0000 Added hasBin for correct loading of genePred query in showMrnaFromGenePred. commit 45894d43011211aea43cfb1d4c872b32d8cce054 Author: angie Date: Tue Oct 9 20:02:26 2007 +0000 Use the more specific FBtr ID to link to FlyBase instead of FBgn. commit 374303bcaf1964fc3ffa9e4d82325d084d0c33b4 Author: angie Date: Tue Oct 9 19:39:12 2007 +0000 Added droWil1 to $droMult and $chainDest. Added Ci1,Ci2 to $chainDest. commit e32aed21ee2ffd94fcb37f56c14ec71af814757a Author: kuhn Date: Tue Oct 9 19:36:06 2007 +0000 updated scripts for KG3 commit 5f93b46b8b16b1b2185c5a4d8abc428efeffcb7b Author: kuhn Date: Tue Oct 9 19:34:41 2007 +0000 removed unused variable commit bf4726ae9177f3303d7a1b7063995740ba19530d Author: ann Date: Tue Oct 9 18:33:17 2007 +0000 removed dollar-signs, as the script wanted to treat them like variables, even though they were in an echo statement commit 87ff71d1c46078f796916b7b7e471c655793b48f Author: ann Date: Tue Oct 9 18:16:04 2007 +0000 changed priority of VegaGene and VegaPseudoGene to cause protBlat to move out from between them commit 8c5b91bd114360868c02274e2410b580954d9bf2 Author: kate Date: Tue Oct 9 18:01:08 2007 +0000 Marmoset alignments commit dad3e4c0f925db82bcbef8d1072a19cd0281629a Author: ann Date: Tue Oct 9 17:53:04 2007 +0000 made this page consistent with the /zebrafish/danRer5/vegaGene.html page commit 22b78143411cd74cfa233dc207be0012cf071954 Author: ann Date: Tue Oct 9 17:16:21 2007 +0000 more clean-up to these VEGA pages commit a5f51f83c1856c7800e9df94cf15f441cf2bc8dc Author: galt Date: Tue Oct 9 15:00:05 2007 +0000 "Encode release log update" commit f0b7aa0f13b073201df6462ea8a3deea1cb1750f Author: galt Date: Tue Oct 9 15:00:04 2007 +0000 "Release log update" commit e3e537937fd84c86c50a4da6541cb0d23c2aae7a Author: angie Date: Tue Oct 9 06:58:33 2007 +0000 Enhanced tableExists to pay attention to splitPrefix. If splitPrefix is given, we check with and without it, and use sqlTableWildExists when checking with it. commit bbbb6172006988c196df9054eadf2cd1a747e01f Author: angie Date: Tue Oct 9 06:56:02 2007 +0000 Removed redundant unsplit chain and chainLink lines. Added a few jaxQTL variants to tablesIgnored. commit 450c4c1ab2f5ac233ca47f85882a818d7c6cd877 Author: angie Date: Tue Oct 9 06:54:52 2007 +0000 Added sqlTableWildExists, to detect whether any table matching a pattern with SQL wildcards exists. commit 9408465c274ec3949727c0791e5993b7680fe42f Author: kuhn Date: Tue Oct 9 00:38:37 2007 +0000 added comment about fixes to stsIno2 and stsAlias table. thanks, archana commit 5fe92df1ec15293b13a189504e03fe1d162f2ff2 Author: galt Date: Tue Oct 9 00:26:41 2007 +0000 changed misleading name p-value to prob-value commit 7a5bfff3842e6eff2ac16caf3207e67588b57792 Author: hiram Date: Mon Oct 8 23:55:47 2007 +0000 Complete Orangutan swap, add targetScanS track from George Bell commit 729f756bea07b13a83e01bc79fe1d3516298ca90 Author: hiram Date: Mon Oct 8 23:46:53 2007 +0000 Special case the targetScanS table on hg18 for its URL link commit fd0e450c42f0c81c548dbd01c846a2dd2799d189 Author: markd Date: Mon Oct 8 22:58:05 2007 +0000 fixed coloredExon drawing in CONTRAST track commit b4644d6d1ce187fed1c3a82982dd5692d04b4895 Author: kuhn Date: Mon Oct 8 22:53:38 2007 +0000 added some whitespace aroung image to keep text from crowding it. commit 15385148cae707d80e8085c5885c93848e70adce Author: hiram Date: Mon Oct 8 22:49:32 2007 +0000 Add note about modification to the Affy Exon Transcript score column to accomodate useScore for the Probe track commit 07e46ff05f641d979f4626f15e5c21eac9a47dd2 Author: hiram Date: Mon Oct 8 22:28:58 2007 +0000 Default wiki track hide until it is further developed commit c0b7e264fa378253337d3de9b8978a911a4094a0 Author: hiram Date: Mon Oct 8 22:22:12 2007 +0000 Add noScoreFilter to affy exon track, it does not work in this composite track commit e7cda0f07ecf454f94ccfe16ee945f883901a637 Author: hiram Date: Mon Oct 8 22:05:01 2007 +0000 Fixup the affy Exon tracks so they cooperate in their composite commit 72b507b2b47e080e328479cdb6734bddd91d527b Author: hartera Date: Mon Oct 8 21:40:12 2007 +0000 Cleaned up section about the gene and transcript types. commit faa2a3893f7580848d4c723c2f48d412990e1dad Author: hartera Date: Mon Oct 8 21:34:58 2007 +0000 Updated Vega tracks to v28 and updated chrom and scaffolds lists for the tracks. commit 77ae17740caec185d7cc8da88fed5aa09d3755e2 Author: hartera Date: Mon Oct 8 21:24:38 2007 +0000 Added a comment to describe the track. Added more details about the gene and transcript classification. Added missing word. commit 208c7ca1e4059e3a98202ff0b5f104ca2556b6e6 Author: hartera Date: Mon Oct 8 21:23:20 2007 +0000 Added a comment to describe the track. Added more details about the gene and transcript classification. commit ab1a614a21f6c909669b3989633a2481b524d2fd Author: hiram Date: Mon Oct 8 21:07:00 2007 +0000 Make the affy exon tracks function independently of each other while in the composite track commit e7f0393157b0fd5875e1cdd1b709e0e16ccdd92b Author: kate Date: Mon Oct 8 21:05:27 2007 +0000 Remove spurious schema link from supertrack UI pages (occurs when first member track is a table (not a composite)) commit f2e918f65e1714ffbb635874065a1445a8f027f6 Author: ann Date: Mon Oct 8 20:36:22 2007 +0000 a little clean-up commit f4ec11b5ff8570ffbe4735e13e1ef7533f828dc6 Author: jsanborn Date: Mon Oct 8 20:36:18 2007 +0000 Fixed heatmap/features not being re-ordered prior to drawing. commit c7944a2e32b3492dfd56e57a23398e98319ed0dc Author: ann Date: Mon Oct 8 20:28:24 2007 +0000 a little clean-up commit 486a0953bb7789b4a0b3e3a293ae65bd0250e03e Author: jsanborn Date: Mon Oct 8 20:13:14 2007 +0000 Updated to setup ascending/descending sorting on columns commit 6014bd9d24fe01fbef790ad748788f4c22ef7825 Author: jsanborn Date: Mon Oct 8 20:12:21 2007 +0000 Updated hgHeatmap to setup ascending/descending sorting on columns commit ef0d061c380ae3179635f3dc3834fbd72f177f49 Author: jsanborn Date: Mon Oct 8 20:10:49 2007 +0000 Updated configure page to configure ascending/descending sorting on columns, also fixed changing priorities commit fe521a48fa6a308f957c7cf7940c623d0373de4f Author: archanat Date: Mon Oct 8 19:10:23 2007 +0000 References section: added a total of 10 authors to author list, and standardized everything to match Pubmed exactly. commit 7ee7b44b09086be2e1c9816e6cd81ebd16009544 Author: hiram Date: Mon Oct 8 18:16:45 2007 +0000 Not much of interesting having the empty gap track on by default commit 044dbdff7cb20b11c3d15a68f5a99287de709f25 Author: hiram Date: Mon Oct 8 18:06:44 2007 +0000 Organize the 30-way tracks commit 332206577c1d33e326308e0c8560f629ef9db43d Author: hiram Date: Mon Oct 8 17:33:59 2007 +0000 Remove the Rn4 test chain and net entries commit 2746107e604787c70d9350872b60fca2714ec838 Author: hiram Date: Mon Oct 8 17:33:25 2007 +0000 Reorganize order for organisms to match distances to 30-way tree, and adding Affymetrix Exon array tracks commit 6b9d7f5db63fb539d1f3732d94032d3bd83322e2 Author: hiram Date: Mon Oct 8 17:32:25 2007 +0000 Add Shrew, hedgehog and guinea pig chain and nets commit ac4e27755c0248d8da2f9a6869b213efbe81a85a Author: kate Date: Mon Oct 8 17:00:27 2007 +0000 Correct subgroup for Sanger track commit 3801cc35d22b7a5a5286fef5dff3e01fef5b2325 Author: galt Date: Mon Oct 8 15:00:10 2007 +0000 "Encode release log update" commit 82ed39b549eab326e0ec105a7e3fc67cb201a70b Author: galt Date: Mon Oct 8 15:00:04 2007 +0000 "Release log update" commit c3e2129b145e2f350b3c3477acb6038c814131f9 Author: jsanborn Date: Mon Oct 8 05:37:19 2007 +0000 Updated sort feature commit 6abf2bedb0cb1fe2310a73325fab45e47b80f846 Author: jsanborn Date: Mon Oct 8 05:36:06 2007 +0000 Updated sort feature commit 0b1ba97c018628eed2dbce106c02167621e780cf Author: jsanborn Date: Mon Oct 8 05:02:32 2007 +0000 Fixed something in hgHeatmap that I changed to test something. A mistake to commit it before I had changed it back commit 1b5fa1d8df44e82ab018b26c949a7ff708004fea Author: jsanborn Date: Mon Oct 8 04:59:24 2007 +0000 Added tree-based sorter for feature sorter. commit 37fae7dac55d38a59f88f0d36ed6b922fc5e8be0 Author: braney Date: Sun Oct 7 18:41:43 2007 +0000 more changes commit 51fa5d2b211a8317511c4cf8af1067c4e17155af Author: markd Date: Sun Oct 7 17:11:36 2007 +0000 added ignore entry commit 2f50f555636cb50218b0050ab7b304779d3f104c Author: galt Date: Sun Oct 7 15:00:05 2007 +0000 "Encode release log update" commit 67ee0928d45fe2e9be11ae55e4b29f7a0609f97a Author: galt Date: Sun Oct 7 15:00:04 2007 +0000 "Release log update" commit 71b9157bae4511f66b86db968250e86905494bec Author: galt Date: Sat Oct 6 15:00:05 2007 +0000 "Encode release log update" commit 798f99872a5ac2b7504a31fa5f6179c71cd380a7 Author: galt Date: Sat Oct 6 15:00:03 2007 +0000 "Release log update" commit 5b6814b4e67488b005368c597495e1cbbfa952da Author: hiram Date: Sat Oct 6 00:29:28 2007 +0000 Initial 30-way alignment up and running. Reloaded allenBrain data. commit c3b2fc3335852bd4c69c9517f473b2a57eee6fa6 Author: hiram Date: Sat Oct 6 00:27:56 2007 +0000 Turn off the 4-way conservation commit 7b90fd6d831a40d85ca00cdb2b6c60877c0d8fba Author: hiram Date: Sat Oct 6 00:17:54 2007 +0000 danRer4 is danRer5 commit 3ae5b2583752100e7e077387cbdda5fb07626ccc Author: hiram Date: Sat Oct 6 00:15:03 2007 +0000 Need to straighten out the order of these species on this 30-way alignment commit b873391cb7f7f2744643de392e2109ffa2e57713 Author: hiram Date: Sat Oct 6 00:11:58 2007 +0000 Initial Mm9 30-way diagram commit f91fb9a353178f743caa00cc453af72d803d0a62 Author: hiram Date: Sat Oct 6 00:01:49 2007 +0000 The Affy Rat Exon array tracks as a composite commit 8fc621b56f013219f2d00f158f5d4ce7c537b046 Author: hiram Date: Sat Oct 6 00:01:29 2007 +0000 The Affy Rat Exon array track as a composite track commit 79831e1ccc10bb86007f1c468960984a3ab082d8 Author: ann Date: Fri Oct 5 23:17:05 2007 +0000 rolling back these changes (1.11) as they caused more problems than they fixed commit dddd28f63b90d78445dfe7272ab0f35623115cc1 Author: angie Date: Fri Oct 5 23:13:04 2007 +0000 A better fix -- don't pass over anything that has tName,tStart,tEnd, and look for whatever specifics we know about. commit d8771156864076f136c19605cac0bd8a19ce345f Author: aamp Date: Fri Oct 5 23:07:24 2007 +0000 Fixed bad download link. commit ab1471e6241ec0ec315276d7764f447d2c7a0447 Author: markd Date: Fri Oct 5 23:02:24 2007 +0000 renamed easter eggs due to SHH gene rename commit 70a6d7848064b4552e9be4748ab0afbeb90e7117 Author: donnak Date: Fri Oct 5 22:21:21 2007 +0000 Fixed problems with sea urchin image. commit b2e31594efcfbdb9c13a458b95abcbacce94d469 Author: angie Date: Fri Oct 5 22:17:14 2007 +0000 Added recognition of chainLink fields to hFindBed12FieldsAndBinDb, so featureBits can find the chromField and TB recognizes it as positional. commit a8aa4add8694d8cbcd44ef3d631cfd779b976ca5 Author: donnak Date: Fri Oct 5 21:54:49 2007 +0000 Added danRer5 browser credits. commit e858d7594aa2c2c53442920e991595d65010ae3c Author: donnak Date: Fri Oct 5 21:52:31 2007 +0000 Added danRer5 release (commented out). commit c147fb2170bf3a1ba169c77315883f2ac621e2e8 Author: donnak Date: Fri Oct 5 21:43:48 2007 +0000 More updates to strPur2 news item. commit 65ed30ea64cfe50f0dc60f1a8c3e00ae803a5e72 Author: donnak Date: Fri Oct 5 21:31:02 2007 +0000 Edited & updated this description, fixed the sample queries. commit 77b54f85c783ed5e8c38b0af6fbefd31796cf299 Author: hiram Date: Fri Oct 5 21:25:38 2007 +0000 Adding targetScanS track from George Bell commit 4b51f4d414a775c960a91bf5b17d02879e0e5294 Author: kayla Date: Fri Oct 5 21:21:44 2007 +0000 added blocks for chainStrPur2 and netStrPur2 commit ffbea73a3189678298f34a56204271e2026d09ab Author: aamp Date: Fri Oct 5 21:21:13 2007 +0000 Removed some stats from the hapmap SNP details. commit dac911e1b24e79f593e25709a3b52359bc243f46 Author: donnak Date: Fri Oct 5 20:18:41 2007 +0000 Added a bit more assembly information to strPur2 news item. commit 19c43c6a0e2f0b432f29f04655931619a1524069 Author: archanat Date: Fri Oct 5 20:17:55 2007 +0000 added mm9 to gdbPdb pointing to proteins070202 commit 5a75b6673e70daa104365e2e5a01fb893795aeda Author: donnak Date: Fri Oct 5 20:02:37 2007 +0000 Added announcement for strPur2. commit 505933fe4dddda05e4be05b2dccc4b3c4a2e8ed3 Author: hiram Date: Fri Oct 5 19:12:18 2007 +0000 Description for the 30-way multiz commit af515158afb0f1d56cbfbc12dececb9d8b66dcf4 Author: hiram Date: Fri Oct 5 19:09:51 2007 +0000 Add multiz4way which was used for UCSC genes construction, and multiz30way in preparation commit ed09bf3741988d10da9047499bcc1218b832bad3 Author: donnak Date: Fri Oct 5 18:55:42 2007 +0000 Added strPur2 credits. commit 85b1f8b31c24ecef3883a214df8164cc36370380 Author: donnak Date: Fri Oct 5 18:34:02 2007 +0000 Added strPur2 to release list. commit 81a33804042aa0f106b0be6f6f66c40c541d5877 Author: jzhu Date: Fri Oct 5 18:25:10 2007 +0000 typo commit da159bedd5ca3e7cc7677a5d3bd949f466c0303d Author: ann Date: Fri Oct 5 17:58:47 2007 +0000 it was erroneously finding commented lines starting with 'track trackName'. I edited so that this no longer happens. Also sent error messages to /dev/null. commit 147eebeeab0eb1266304d51fbe44b43042055571 Author: jzhu Date: Fri Oct 5 17:39:43 2007 +0000 add alpha option to makefile commit 8df14db12eb3f6aa4a0d03ca522faba2ad8468e2 Author: kuhn Date: Fri Oct 5 17:07:39 2007 +0000 changed the matrix to check different combinations of machines commit 70742a0f1eef82635f5b42aa28cb397131d1f7cc Author: hartera Date: Fri Oct 5 16:22:42 2007 +0000 Edits to the contigs track description. Removed unnecessary text. commit e60a7bff6fe565d1d5e6d26adb0bc4c1bd35df8c Author: galt Date: Fri Oct 5 16:15:54 2007 +0000 name change commit fd1f65be3de991f025ab7d0b23f280eeaff8a4ef Author: fanhsu Date: Fri Oct 5 16:13:34 2007 +0000 Added miRNA track. commit 8872f43b94cd7f4942f838340f65697813f648f6 Author: fanhsu Date: Fri Oct 5 16:00:34 2007 +0000 Updated wgRna track. commit e40abb3f85ba68d1a647025e979c1293f77c693f Author: galt Date: Fri Oct 5 15:00:08 2007 +0000 "Encode release log update" commit 04a4e4d60286b0ec9f3b6ab0101d1566c8935d4c Author: galt Date: Fri Oct 5 15:00:04 2007 +0000 "Release log update" commit 1f53da490513456641d068883bd4756fb4101c46 Author: jzhu Date: Fri Oct 5 06:03:14 2007 +0000 add patDb patTable patKey to ispy tables commit b3da5c8cf93e3cb423dbcf494e874145d0110bc0 Author: jzhu Date: Fri Oct 5 01:28:11 2007 +0000 more generic code not rely on ispy db in hgHeatmap commit 7b0e93c55869274e85099be630050489d9639456 Author: kuhn Date: Fri Oct 5 00:55:53 2007 +0000 added support for split tables, so runBits.csh does not break on chains commit 724311ed2c545de5304ca9047b7547188d741e26 Author: kuhn Date: Fri Oct 5 00:55:26 2007 +0000 tweaked output commit 1e316da11d4b7d48b245bd7747514b201911d37a Author: jzhu Date: Fri Oct 5 00:54:48 2007 +0000 change feature color to light yellow based, add patDb, patTable, patKey in trackDb.ra file so that only tables with clinical features will be displayed commit 24a048b2c88532ceae89153ad44ffc1bbda82e41 Author: donnak Date: Fri Oct 5 00:25:37 2007 +0000 Fixed a tag. commit c857afdf8d6c3d0a55a36661f616b6e8e2ee1c53 Author: kate Date: Fri Oct 5 00:13:43 2007 +0000 Fix link commit b8442eb8e099a4018ee63009bb9d09a5d69ca67c Author: donnak Date: Fri Oct 5 00:13:28 2007 +0000 A bit more editing on the ENCODE announcement. commit 12c0bbb902897ce58ceb90b063c8a8be136071b8 Author: kate Date: Fri Oct 5 00:01:35 2007 +0000 Fix typo commit 58671a39a98e5852445ea4bb789199e914488041 Author: kate Date: Thu Oct 4 23:40:20 2007 +0000 Erase trailing spaces on ra record values commit 4cb705a7b05969a4c23de976f42a2567af5c76ad Author: kate Date: Thu Oct 4 23:34:41 2007 +0000 Add to credits commit ec7870e4489881fc2e07779c99676d2c7c7fb542 Author: ann Date: Thu Oct 4 23:26:18 2007 +0000 added blocks for danRer5 nets/chains commit 00742aa572e80167994bf79d93f32c9e06b50e76 Author: kuhn Date: Thu Oct 4 23:20:12 2007 +0000 added link to hg16 commit 71b2792ac827060124de4dba31d4b0712d0c2861 Author: jzhu Date: Thu Oct 4 23:07:27 2007 +0000 change color commit e91de45c832ee12cf4532acddd52cb92cdef26b1 Author: ann Date: Thu Oct 4 22:42:03 2007 +0000 removing spaces from the ends of the lines in this file, as the program cannot handle them commit 3aff745513eff21b6f98cb3e041fc7783063a95b Author: galt Date: Thu Oct 4 22:40:41 2007 +0000 jim requested rename commit 9d64d5c2463a166eea2a5c32e5120adc73e8f738 Author: galt Date: Thu Oct 4 22:39:14 2007 +0000 renaming as jim requested commit e0943f77ed2906f4ea9b25108d0df4e05bc4f52a Author: donnak Date: Thu Oct 4 22:06:04 2007 +0000 Archived 2 items. commit 9ffda232cb3fb25d7d38fc541e3fe57106650ff6 Author: donnak Date: Thu Oct 4 22:05:53 2007 +0000 Added item abt ENCODE hg18 migration. commit bca95dde802785dc6e385d905697e77bd1086236 Author: archanat Date: Thu Oct 4 21:35:19 2007 +0000 removed the link to GeneLynx. This site no longer exist. commit 4494809fc94b528a17638ff2419e9dd02f546f77 Author: donnak Date: Thu Oct 4 21:29:48 2007 +0000 Removed ref to GeneLynx. commit 24e5c3cc6527b7485e7577b6df89b1020be9e5cd Author: kate Date: Thu Oct 4 21:26:39 2007 +0000 Correct a few numbers commit 21266cd4863be536e07b4c8c07b0626c804117ce Author: ann Date: Thu Oct 4 21:16:35 2007 +0000 added section for printing the blastz scoring matrix (to be used in the matrix variable on the chain description page). commit cb41e41b92687492ed8f86f9069faaae835e6c50 Author: ann Date: Thu Oct 4 20:55:21 2007 +0000 added danRer5 chain/net blocks commit 951a3796dbe3114f5f1dbc85b90574ec33e94017 Author: kuhn Date: Thu Oct 4 20:45:14 2007 +0000 added Zv7_ to list of acceptable scaffold prefixes commit 872859e4dbe08b4e41041ed6689cd5b465c204a8 Author: donnak Date: Thu Oct 4 20:16:52 2007 +0000 Minor edit to 10/4 news item. commit ab98e3171cafda39e626fa7eae49d35b0b96d6df Author: donnak Date: Thu Oct 4 20:12:43 2007 +0000 First pass at 10/4 news article. commit 5900a6e99c36199e35e76f49711dc3be86003dba Author: donnak Date: Thu Oct 4 20:12:26 2007 +0000 Archived an item. commit 2c6ddf1c2fb0772ba572b1e52d31e700b2484cc8 Author: jzhu Date: Thu Oct 4 20:07:19 2007 +0000 fixed bug commit 3c367139d491831160c28533d0b893b4d0ad8d33 Author: jzhu Date: Thu Oct 4 20:00:55 2007 +0000 *** empty log message *** commit ba38710daa6dc34105f7556c939ca8b912695733 Author: kuhn Date: Thu Oct 4 19:55:33 2007 +0000 removed tablename variable, fixed usage conditions to require two arguments exactly, removed two rm statements for files not yet existing, made a filename longer to avoid accidently clobbering some other file, and dropped an echo statement to plese brooke. commit a9555296012b1011d3d556bee4c3b6e7a87fa1c5 Author: hiram Date: Thu Oct 4 18:58:09 2007 +0000 Added Affy Exon probe and transcript tracks commit 8e51b25d38528ad67ee7e3493dcecefa227336d3 Author: hiram Date: Thu Oct 4 18:51:13 2007 +0000 Add affy Exon probe and transcript track commit 730a0b1a6384202044f5779ddc2ef85157dbab9f Author: hiram Date: Thu Oct 4 18:50:43 2007 +0000 Adding Affy Exon probe and transcript tracks commit 762501966ca77d6138386390c5e5ca0324821949 Author: hartera Date: Thu Oct 4 18:27:26 2007 +0000 Added danRer5 as an MGC machine database. commit 3262eb99b6c1cc577338279397a87de86f53519d Author: kayla Date: Thu Oct 4 18:09:54 2007 +0000 added danRer5 commit 4010605add8d6b5f74b7a046eea07f8f029bf00d Author: jsanborn Date: Thu Oct 4 17:35:19 2007 +0000 Fixed adding integers to heatmap hash using correct function hashAddInt commit b56a14656df4c39f661b02f4e2ec95a1fe351ba4 Author: jsanborn Date: Thu Oct 4 17:30:23 2007 +0000 Temporarily fixed adding integers to heatmap hash commit 4c18e80b6572429e83a0cfae0e51afca5f2fa035 Author: jzhu Date: Thu Oct 4 17:14:42 2007 +0000 use table labTrack, add index to db table labTrack commit 144fd711ccb5e9a8d6d6ed27273630c341aaf508 Author: ann Date: Thu Oct 4 17:02:29 2007 +0000 added notes about placing chain/net priorities in the new priority.ra file commit 49909058070e8622b61e5402552073f8ca7e94cd Author: ann Date: Thu Oct 4 17:00:23 2007 +0000 adding this file to organize the order of the orgs in the track controls and display commit 87425529e5c3a7f8f89a572c44b0e441743c009e Author: jzhu Date: Thu Oct 4 16:51:22 2007 +0000 temporary fix just to make the code to work, there still problems with hash sampleOrder commit 65bca81a960ecaf183e494717cd48ab7cde11364 Author: ann Date: Thu Oct 4 16:46:27 2007 +0000 changed priority of mm9 chain/net commit 5a72435792bcab527de630c087a0aca9145c9e50 Author: jzhu Date: Thu Oct 4 16:38:48 2007 +0000 getId takes char * argument commit 5f75eb428060e0eeeb1da3246c593fa7b67cd6cb Author: jzhu Date: Thu Oct 4 16:20:42 2007 +0000 fix three pointer conversion errors commit 99121dba33af39f803a57c8e65bd533d519e1108 Author: hartera Date: Thu Oct 4 15:27:01 2007 +0000 Modified vegaGeneName rule. commit 000f4aa46b099430026057d1e4a861849ca93c1c Author: hartera Date: Thu Oct 4 15:20:42 2007 +0000 Added rule to vegaGeneName for danRer5. commit 5c3b83abf651225cbf23333b28ff75236dd18a12 Author: galt Date: Thu Oct 4 15:00:07 2007 +0000 "Encode release log update" commit 9a8dab88a25a532d861436adaf374ef6e4859a3f Author: galt Date: Thu Oct 4 15:00:03 2007 +0000 "Release log update" commit 1b479d6ba1f3acce5577f98fe142bd576360c634 Author: hartera Date: Thu Oct 4 14:54:39 2007 +0000 Added clarification about the 5036 fragments mentioned on the Sanger Sequencing Project page for zebrafish. commit f20b1c1df3a5172eaabe8e02f667f552fc8d91a0 Author: jsp Date: Thu Oct 4 14:28:42 2007 +0000 Added genus and italized some species names commit d135ced23361d28a1278b6ef54d6bfd8c4cd9cbc Author: jsp Date: Thu Oct 4 14:22:10 2007 +0000 corrected a recurrent typo in some comments commit 70821036743214021084681619978efe4047f600 Author: galt Date: Thu Oct 4 08:46:27 2007 +0000 NIMH Bipolar description page commit e7cad2b66f0dc964f0d901b8f798eadc988f4c1c Author: galt Date: Thu Oct 4 07:49:43 2007 +0000 NIMH Bipolar built-in for Genome Graphs commit 95c9bc8fa9c3dd32212de39e72acfdf64f233f36 Author: markd Date: Thu Oct 4 07:41:33 2007 +0000 commented out info on codon coloring feature commit 907ce58a61048bd20097284e56f994b525197634 Author: hartera Date: Thu Oct 4 04:29:04 2007 +0000 Added an include for ensInfo.h. Modified showGenePos so that if name2 is noXref in ensGene then the Alternate Name on the details page is displayed as none. Added code to doEnsemblGene() for dispalying information from ensInfo on the Ensembl Genes details pages. commit 7fe1f237227362025dff8f584c5e5a27ca7572a1 Author: kuhn Date: Thu Oct 4 01:58:50 2007 +0000 made util for converting block-structure tables to uniform filled-intron bed file, and used it in runBits.csh to catch unbridged gaps in introns. thanks, brooke. commit f3bdd4bdbb9700136e64c3bb009b89b83d7f1a97 Author: donnak Date: Thu Oct 4 00:46:13 2007 +0000 Corrected Conditions of Use statement. commit 679d375b5527f9306a9d2db537776c28e792d7ea Author: galt Date: Thu Oct 4 00:36:24 2007 +0000 preventing null in printf for SOLARIS mirrors commit 4e4d7e17422be1dbf1d02707d87a9dcd9e0b4d74 Author: galt Date: Thu Oct 4 00:32:47 2007 +0000 typo fix commit a8ab2b80167268cf94890612e52a32870fd63433 Author: donnak Date: Thu Oct 4 00:19:08 2007 +0000 Added warning about using the "all" parameter setting in browser lines. commit 220fa0219ce0e2d27ae36799ec960c9ec1ea1d9d Author: donnak Date: Wed Oct 3 23:38:09 2007 +0000 Added info abt uploading from a URL. commit ca4547a610816214ce8a6ae97de87377da06ca41 Author: angie Date: Wed Oct 3 22:26:20 2007 +0000 Mapped rn4 rat QTLs to hg18. In order to prevent being swamped by unnecessary detail, used stringently filtered .over.chain, and liftOver instead of pslMap. commit e4791124564d8537b3b96762b13cee9fe08d0296 Author: donnak Date: Wed Oct 3 21:04:44 2007 +0000 Made a few minor edits to the Upload file formats section. commit 64f6d0e68ef43729851b1621b6763ee7279ae8b7 Author: hartera Date: Wed Oct 3 21:02:14 2007 +0000 Changed the frag name in the gold table from gi number to accession for chrM. Documented the re-creation of the Nested Repeats track (by Angie). Added autoSql code for ensInfo and documented the addition of code to hgc to print out the details from ensInfo on the details pages for Ensembl genes. Update the Vega Genes and Vega Pseudogenes tracks to Vega version 28. commit 81337c61b73dbb018dfa6069e83997d765c4a7e2 Author: angie Date: Wed Oct 3 20:08:58 2007 +0000 Updated description of score field. commit 75093831a443e364f6a70733b4be98fe4eb1addf Author: hiram Date: Wed Oct 3 19:13:02 2007 +0000 Done with all the blastz runs, starting on the 30-way alignment commit 01cb0f19049b9f6671206fd5da2a31842a8c396e Author: hiram Date: Wed Oct 3 19:11:32 2007 +0000 Updated hg18 SGP genes, and started ponAbe2 alignment commit 2803e71e1436f313bd48c7b64112cfba0598cb80 Author: hartera Date: Wed Oct 3 17:50:11 2007 +0000 Removed unnecessary text. Also re-worded text to make it more comprehensible. commit 155a2b38f66a94965235c851cc04704f325733a1 Author: hiram Date: Wed Oct 3 16:51:32 2007 +0000 Add hgKnownGeneList to the build commit b30e79673f3af718c7434acf565223ce57ec867b Author: galt Date: Wed Oct 3 15:00:06 2007 +0000 "Encode release log update" commit 20b01685eb23ea5127612286fec6ec81d985738b Author: galt Date: Wed Oct 3 15:00:04 2007 +0000 "Release log update" commit 70a5da82b946ac4c36e7b0fdab2eac9fa3342e44 Author: angie Date: Wed Oct 3 00:25:21 2007 +0000 Added genericNameValue.as to cover simple name,value tables (e.g. those created by hgMapToGene) -- buildTableDescriptions.pl was previously picking up orfToGene.as for those, which isn't right in most cases. commit 98cb7cf4e9c571dfe5cf07c9bc760f69dc80399d Author: markd Date: Wed Oct 3 00:01:44 2007 +0000 added CONTRAST gene predictions commit 4c7b5326ad9f6feb0bdbedc4fd2458691ca476b6 Author: ann Date: Tue Oct 2 23:18:34 2007 +0000 two more small tweaks commit f43fd8cd985a85277f4811d988a3ddb29740b3c4 Author: ann Date: Tue Oct 2 23:14:02 2007 +0000 changed wording to make it more clear? commit 1106018f999332d4a11301e423597a653c9e0183 Author: jsanborn Date: Tue Oct 2 22:32:43 2007 +0000 Updated code to draw features aside heatmap commit bfea679195510e8af46479c175af6e173a665e1c Author: archanat Date: Tue Oct 2 22:28:39 2007 +0000 changed the priority of netRn4 commit 4e863f6fbc314c23589a0069720e629482eabd72 Author: hiram Date: Tue Oct 2 22:25:09 2007 +0000 Have mm9 participate in the KG-III business commit f9bc3f06d47f110e427dfd132cbdbca95303bfa3 Author: angie Date: Tue Oct 2 21:28:54 2007 +0000 Updated Pfam url (thx Brooke). commit 8ff50daca90585c964cd91b1f349cd3d93f8c8ea Author: angie Date: Tue Oct 2 21:07:18 2007 +0000 Added tbSchema (thx Brooke). commit 0c9b39ede44b59653baa72b73e99a4bba098aa9c Author: ann Date: Tue Oct 2 21:07:16 2007 +0000 Fixed citation format for Ensembl paper. commit c25e3fa66dc1f4191b21b77ef91da856e1a10dab Author: angie Date: Tue Oct 2 21:04:44 2007 +0000 Added cytoBandIdeo to tablesIgnored. commit 3fc7f64a6996d2a4e05f636ba0e8d42253141013 Author: ann Date: Tue Oct 2 20:56:17 2007 +0000 fixed citation commit 10f7d7d6a3d173874a7fc338cde57a5412c60b77 Author: kuhn Date: Tue Oct 2 20:53:34 2007 +0000 added underlines to headers in output table commit 6852dd765a281b5e969d556f0bc58bb883c9c19b Author: kuhn Date: Tue Oct 2 20:41:17 2007 +0000 new KG3 process requires new name and new html file commit d15e8c89408a96ce20600427ae19f41d55ce8e44 Author: hartera Date: Tue Oct 2 19:26:58 2007 +0000 Minor edit to update the description specifically for the hg17 version of the indel-based conservation track. commit 94d75ed971aa132fe17252874125ce4288650913 Author: hartera Date: Tue Oct 2 19:24:41 2007 +0000 Added indel-based conservation track for human hg17, mouse mm5, and dog canFam1. commit 9a436d86d052db616ffe5ec7a160244a67e4793b Author: angie Date: Tue Oct 2 19:00:15 2007 +0000 Changed priority of RGD QTL tracks so they appear at the end of the human phenDis group. commit 013483c55e368a3f1d192bcce1f2f03f80f8f86c Author: hartera Date: Tue Oct 2 18:49:08 2007 +0000 Corrected the name for the consIndels track. commit 87cc49ee70415ece700ae9c4051033f1703ca150 Author: ann Date: Tue Oct 2 18:40:20 2007 +0000 added note about mytouch to geneidPep table (it was failing -times but not -keys joinerCheck rule) Kate said OK. commit c5fd2f75013baba0a7c954239680a4f0536a8382 Author: hartera Date: Tue Oct 2 18:34:52 2007 +0000 Changed search priority for consIndels track. commit a12bdf79908e59b30c64c82116d64542278d42e2 Author: hartera Date: Tue Oct 2 18:34:05 2007 +0000 Added search for consIndelsHg17Mm5CanFam1 track. commit 30a43ddab029ac154d215cb912da2b9a0a60feba Author: hartera Date: Tue Oct 2 18:30:23 2007 +0000 Added description for indel-based conservation track for hg17/mm5/canFam1. commit e7865b1c9e472959482e7eabd8bdbe44ee154d24 Author: hartera Date: Tue Oct 2 18:29:44 2007 +0000 Added indel-based conservation track for hg17/mm5/canFam1. commit 3d0228a59543c43a3e3a08e1def28ba4abd0a325 Author: archanat Date: Tue Oct 2 18:16:47 2007 +0000 copied the blocks for mm9 net/chain to organism level and changed the short label commit 7dbc25a1e88461d1239d092d79f6c69d4da83436 Author: archanat Date: Tue Oct 2 18:06:29 2007 +0000 changed refs to pubmed format commit ca8678d06277270f5131b31ff324460fb92ec8ca Author: archanat Date: Tue Oct 2 17:53:33 2007 +0000 changed refs to pubmed format commit da53a96a7b9e0e6cf37605af058a948ceb3d3785 Author: kayla Date: Tue Oct 2 17:31:32 2007 +0000 This file didn't exist, so I copied from netGasAcu1.html commit 21465d28275a92052cdd234d8485dd3b26724585 Author: kayla Date: Tue Oct 2 17:31:07 2007 +0000 This file didn't exist, so I copied from chainGasAcu1.html commit fe57feb33f7adcccb5486774b1df5a93012d6986 Author: aamp Date: Tue Oct 2 17:29:34 2007 +0000 "New version number v168" commit 418db16e2cf548827f67ece62ef08364d72e18b5 Author: galt Date: Tue Oct 2 17:23:58 2007 +0000 added ability to specify url for upload file commit 0211518f6e85437a737f7ec73cf1c514360d7f5a Author: aamp Date: Tue Oct 2 16:47:54 2007 +0000 A start to the CCC track description. commit 10cdb3895dd6ba22a9094d4197b242def0c17d6b Author: aamp Date: Tue Oct 2 16:27:48 2007 +0000 Silly little program that yeah duplicates the job of grep, uniq, sort, and other UNIX cleverness... but is easier for working with 3+ files. commit 1500f8aac3c6d89e487b9adf550d4a08abdb79ff Author: ann Date: Tue Oct 2 16:15:30 2007 +0000 added mm9 net/chains to this level (because mm9 is still not the default mouse everywhere) commit fbd903997921e9724534b98f76c832b4c77a59cd Author: aamp Date: Tue Oct 2 16:02:42 2007 +0000 Forgot to commit the makefile. commit 56ebc69985eeb2e4c6732138d6936576cee4dd4a Author: aamp Date: Tue Oct 2 16:02:13 2007 +0000 Just a one-shot program for the all-exon gene sorter column. commit 629f39372440d0eb9854e2cdaf664b6a11c76b1f Author: kuhn Date: Tue Oct 2 15:51:16 2007 +0000 reversed track and db in call to getChromFieldName.csh commit b658f59a86516700b63dce953fae7c98cd5afef8 Author: kuhn Date: Tue Oct 2 15:45:42 2007 +0000 added comment commit 93b2e0af050c66e79552393254bcd02fa5a8a932 Author: galt Date: Tue Oct 2 15:00:07 2007 +0000 "Encode release log update" commit afe91b1cc00143ebfad56c569753a7ab79f32d83 Author: galt Date: Tue Oct 2 15:00:04 2007 +0000 "Release log update" commit 010d015b98254c40e56daba490d98e2a4e5e7913 Author: jsp Date: Tue Oct 2 09:35:56 2007 +0000 small changes to EvolFold description page commit cd9ea063b706cc8804fc8899fd6809cb592c81fb Author: jsp Date: Tue Oct 2 09:04:05 2007 +0000 Added EvoFold track to dm3 (lifted from dm2) commit dc7faabc379687fbb98893982f95fc26866dd85c Author: jsp Date: Tue Oct 2 08:59:21 2007 +0000 Added documentation of EvoFold tracks commit 97ca92f643cc7f0eabda9b2e03c22aca34b610a5 Author: aamp Date: Tue Oct 2 05:25:15 2007 +0000 Human normal groups? I thought they were here already. commit 722281b7a12286b79ac0d430e7c051bb7fce70ab Author: angie Date: Tue Oct 2 05:20:58 2007 +0000 Test whether a gi number or accession is passed in for mitoAcc when making the fake gold table entry. commit 2b1e0ce876db1f1d9baf1e795da4fb53356ffe1f Author: angie Date: Tue Oct 2 05:10:56 2007 +0000 Added optional config.ra setting targetAbbrev, so when using a temporary database for target, the other databases are loaded with the correct target-BlastTab table name. commit a531208cc67cd4bef14899550f5f7c418acfc0ab Author: donnak Date: Tue Oct 2 05:04:47 2007 +0000 Uncommented the link to the Sessions User's Guide. commit 212bedca45b7302f67648009aa79e2a81c81072f Author: angie Date: Tue Oct 2 04:47:47 2007 +0000 Changed group of rgdQtl and rgdRatQtl to phenDis at Jim's request. commit e0d38cc28b62a219797d9f46152ff09d5bcab49d Author: angie Date: Tue Oct 2 01:25:34 2007 +0000 Ran makeDownloads.pl -- README.txt files still need edits. commit 4d79f69d1af6e1d4149ce5baaaad8572093cb991 Author: angie Date: Tue Oct 2 00:31:55 2007 +0000 Don't quit if there's no trfMaskChrom/chrM.bed. commit 9809472178d4c5c99c94ce0149f300a6be72544c Author: hiram Date: Mon Oct 1 22:22:52 2007 +0000 Only three pair-wise left to go commit 6f2ee4c1371768176cde88dd13224700bf9fcb5b Author: angie Date: Mon Oct 1 21:32:55 2007 +0000 Make strand '+' if it is neither '+' nor '-', so the output is legal PSL (readable by pslxFileOpen). commit b05539477a8d321ad73af73958e275a6231a6088 Author: angie Date: Mon Oct 1 21:31:13 2007 +0000 Fixed duplicate rgdQtl ID w/correction from RGD. commit 83653807fdc503198840359c586d99cf1b8b2d14 Author: angie Date: Mon Oct 1 21:23:58 2007 +0000 Added rgdRatQtlId and dropped rgdQtlIdRn4DupeOK -- the dupe has been fixed on hgwdev (email correction from RGD). commit 14352e95d61e18bffeac23da838c4bf06a8eff1d Author: ann Date: Mon Oct 1 20:15:33 2007 +0000 corrected list of chroms on which vegaPseudoGene elements are found commit 2a77057018e484cb46078513a9aa997169831a6f Author: ann Date: Mon Oct 1 20:14:19 2007 +0000 changed assembly date commit a7f43bf797e043f8049923a8d6ffbeee1bbbb9cc Author: ann Date: Mon Oct 1 17:50:28 2007 +0000 added note about mytouch to ECGenePep table commit ce85e6268b0627562e5a43909893e6d265b529d1 Author: markd Date: Mon Oct 1 17:46:06 2007 +0000 added dm3 nscanPasa commit 8f3186c82591c0751d7b0891a0b6bbf5bd6b103d Author: markd Date: Mon Oct 1 16:50:38 2007 +0000 reload nscanPasaGene to fix naming and search commit 2ee5653d4c8bedd40eeaac0f57462a26c7c71815 Author: hartera Date: Mon Oct 1 16:17:08 2007 +0000 Adding ensInfo object code generated by autoSql. commit eb8d1184ef593ede30170413e89c54a55badf168 Author: hartera Date: Mon Oct 1 16:16:20 2007 +0000 Adding ensInfo object definition for autoSql. commit 02e415812669b8f59e93c3e91cdde1ebaa7dcb73 Author: jsp Date: Mon Oct 1 15:06:02 2007 +0000 Added support for additional color markup of alignments annotated with RNA secondary structure commit 974e3a604cf0ff57a3e8fdca131c27f436129470 Author: jsp Date: Mon Oct 1 15:04:45 2007 +0000 Added additional color markup of alignments on the detail pages of the EvoFold track commit 19fa2b969bee5c3db6670705d732cc43fc1f0484 Author: galt Date: Mon Oct 1 15:00:05 2007 +0000 "Encode release log update" commit afad6adc33fce334a595f2dfe80dfa9a5ef784b0 Author: galt Date: Mon Oct 1 15:00:04 2007 +0000 "Release log update" commit b6f83e38a899e007cd149346a057220cd5dcae25 Author: jsp Date: Mon Oct 1 14:56:45 2007 +0000 Added EvoFold track and description page. commit a7ca743395d9491a1453d9b0782ee7e42859365f Author: galt Date: Sun Sep 30 15:00:05 2007 +0000 "Encode release log update" commit ff01a593beb9b2f504396fc041ef72d37a842887 Author: galt Date: Sun Sep 30 15:00:03 2007 +0000 "Release log update" commit b76ca2d822076a53a6e9c92c164d0575d322bee8 Author: galt Date: Sat Sep 29 15:00:05 2007 +0000 "Encode release log update" commit 73d789ea3fa492b57067aa02fdaa889ba12f697b Author: galt Date: Sat Sep 29 15:00:03 2007 +0000 "Release log update" commit 50c6987074fa5a83e1cef4a3243e5ab60e774795 Author: hartera Date: Sat Sep 29 06:24:20 2007 +0000 Added rule to ensemblTranscriptId for the ensInfo table. commit 859e204af762bb949321f458442af77f77db08cf Author: hiram Date: Sat Sep 29 06:15:41 2007 +0000 Almost all of the rest of the blastz runs done commit 144607be711375a98ba8e504fcb9e405e5e29de3 Author: hartera Date: Sat Sep 29 04:51:22 2007 +0000 Fixed minor error. commit e8bb825878bffb252f1ce5405f7edd4adbf9d212 Author: hartera Date: Sat Sep 29 04:22:40 2007 +0000 Added ensInfo object. commit cf9d230030364e048edd206705adb13423bfa519 Author: markd Date: Sat Sep 29 00:37:37 2007 +0000 reload strPur2 genbank to fix various problems commit f91bcce58d56d56bd242337b23d905f94b2ac16c Author: kayla Date: Fri Sep 28 21:13:29 2007 +0000 added a chain and net block for ci2 commit 5cfd1e328b874105362b6a987f6c79bb98fc8cdd Author: angie Date: Fri Sep 28 20:24:53 2007 +0000 Instead of just putting goldenPath/db/liftOver/* and /gbdb/db/liftOver/* in the 'supporting tables and files' entry, put the specific liftOver files in the Chain+Net entries. (but if there happen to be same-species liftOver files already, do include those in the supporting-stuff entry.) Also fixed duplicate detection of Net tracks. commit 849e99bf4839a8e0c8eed32f0889a5585afc2864 Author: hiram Date: Fri Sep 28 19:09:41 2007 +0000 First failed attempt at Venter alignment commit cc9642bf75b233576f006bf34394f2e8b48fd7bd Author: hiram Date: Fri Sep 28 18:23:22 2007 +0000 Add more about the assembly description. commit 8149459ec2e814d1e5f8e1470d58358d2b941ef8 Author: ann Date: Fri Sep 28 18:20:27 2007 +0000 Changed order of sub-tracks in affyZebrafish track. commit 6ffce2915966a32cf86f318bfa6343e384f1b2c4 Author: galt Date: Fri Sep 28 15:00:06 2007 +0000 "Encode release log update" commit 322a9c870f481d32d33a4a9137c6abf5a439f8b1 Author: galt Date: Fri Sep 28 15:00:04 2007 +0000 "Release log update" commit 568a214c984f26210995e6089dfe7dce6b70a3ce Author: kuhn Date: Fri Sep 28 02:01:23 2007 +0000 removed comment commit 12affbf430a7b1860fa9b00662c7e5418610c174 Author: kuhn Date: Fri Sep 28 01:57:41 2007 +0000 added logic to process databases that are not assemblies. can only do those using STATUS dumps, not in real time. commit d9af24ed3660af5ec1be66816699f18a6c085878 Author: hiram Date: Fri Sep 28 00:01:28 2007 +0000 Now with approved photograph commit 472fd8f2fea92cd710790b5ffa455d3b8e2413e7 Author: hiram Date: Thu Sep 27 23:59:32 2007 +0000 Courtesy Evan Hurd - J. Craig Venter Institute commit d3591c6e5f48c47e717da00cc7f46a57b54f4f56 Author: aamp Date: Thu Sep 27 23:58:33 2007 +0000 Modified release/build. commit bfdb7f6fc92eabeec13edcb3a1e21602040d101e Author: hartera Date: Thu Sep 27 23:25:25 2007 +0000 Removed extra line which would free a structure for the second time. commit e95ce72df97f76fe4b02abaf6e707241f75ff1b5 Author: galt Date: Thu Sep 27 23:15:11 2007 +0000 making the cgi logging re-usable commit 3c71e3ebcc7f15ff4ca29a59ebcbc6368ad6459e Author: galt Date: Thu Sep 27 23:12:57 2007 +0000 replacing errAbort with simple html commit e332189bc24a97f91d747c8569cfc2f0ed93744e Author: hiram Date: Thu Sep 27 23:01:30 2007 +0000 Add the option -noDbNameCheck to avoid difficulties with oddly named genomes commit 217b639e3e3fa04bfd2f2f080d32f570805d39b8 Author: jsanborn Date: Thu Sep 27 23:00:12 2007 +0000 Integrated Feature Sorter data access to hgHeatmap commit 561ca626eea35a911e660c804b6c36851c401eca Author: jsanborn Date: Thu Sep 27 22:58:48 2007 +0000 Column DB data for ISPY feature sorter commit 6219fa54dddd250a7b0d2f7a3f3b9b3868b2da0f Author: jsanborn Date: Thu Sep 27 22:57:57 2007 +0000 Added user settings header file commit 295bb45c9cd1635f51fcbd375b28e89f044e2d19 Author: jsanborn Date: Thu Sep 27 22:57:47 2007 +0000 Added user settings, copied from Gene Sorter commit 69915c5e096ede83653eee6b6d35b060dc63bf81 Author: jsanborn Date: Thu Sep 27 22:56:55 2007 +0000 Added ISPY specific feature access to database commit 899ad32efb15c3b6d7cd1bf60e54e3d79a11978c Author: jsanborn Date: Thu Sep 27 22:55:52 2007 +0000 Added file for Feature Sorter configuration page commit 7983ca8d642b8335c08ac0cf36b4f47851df4e0a Author: angie Date: Thu Sep 27 22:25:17 2007 +0000 Make carefulTrackOpenVis more careful -- cart does not always exist! commit 6df149e4a8bfce9906feb0eb9b4478660419733d Author: hiram Date: Thu Sep 27 22:20:10 2007 +0000 Better reference links, and fixup species name ... commit ca52a549f2495276c52e521202992295e66c0436 Author: ann Date: Thu Sep 27 22:07:55 2007 +0000 Correcting URL to Sanger data use policy. commit 50a0567ff6c7a43e40428f56373ca8ea23e2b971 Author: hiram Date: Thu Sep 27 22:02:14 2007 +0000 Add venter1 to the build commit d826e52303c68ef55126c9f0b40f97ce51afa717 Author: hiram Date: Thu Sep 27 22:00:37 2007 +0000 Initial contents commit 07fa5bd2a9d7ecb302362d40fcdb8cd5f32687c3 Author: ann Date: Thu Sep 27 21:44:35 2007 +0000 adding link and image size commit c4a74f62b249c73b4c35ba6abbe0c0a5651a4e9a Author: angie Date: Thu Sep 27 21:28:24 2007 +0000 Moved the contents of printRgdQtlCustomUrl into doRgdQtl because the former did the whole item-info section, not just the url. Made it able to handle track tables with other names and hooked in rgdRatQtl. Since there can be many cross-species mappings for one item, show the clicked-on position first, followed by a list of other mappings, sorted by decreasing genomic size. commit b349de47edc39473419afb0bfbb4f28db7fff867 Author: ann Date: Thu Sep 27 21:15:40 2007 +0000 adding danRer5 as new assembly commit 3e5eaf07b7db1268262c9f2ca5d44e574e073610 Author: tingwang Date: Thu Sep 27 20:56:04 2007 +0000 documents for adding strand information for RACEfrag data commit ee7d9d7bd3abe1f4073b7c0b1b0d9a1df6f464ea Author: galt Date: Thu Sep 27 20:02:14 2007 +0000 adding hgsid variable to debugging output commit ca995f4e6864225f88410e1658eac17d8fd76003 Author: kent Date: Thu Sep 27 19:49:31 2007 +0000 Freen creates a test.bed. commit fd924db4d6c44883caef9e328fe003b08116c675 Author: kent Date: Thu Sep 27 19:46:57 2007 +0000 Shortened some comments to fit on slides better. commit 041b0a8e5784df14d196a33648f1873be0be93c3 Author: angie Date: Thu Sep 27 18:22:02 2007 +0000 rgdRatQtl = rat QTLs mapped to $Organism (just hg18 at the moment). commit 3605a11c678e9f7b345f06c12fbb54ca0f074072 Author: angie Date: Thu Sep 27 18:14:34 2007 +0000 Added rgdRatQtl, tweaked longLabel of rgdQtl, and changed Nested Repeats --> Interrupted Rpts. commit 7158e689c61e057c978d535b1296a73d84af4877 Author: angie Date: Thu Sep 27 18:05:32 2007 +0000 MGI tracks data update. commit a6e6b940ab653bbf0080da23c64d5f2ec3a066aa Author: angie Date: Thu Sep 27 18:03:17 2007 +0000 Terminology: nested -> interrupted. commit dc1e7afa97d9c2999940b6c2f9202d5e0ad8465e Author: kuhn Date: Thu Sep 27 17:01:31 2007 +0000 simplified logic for supertrack handling commit 7f86af0b91f38d5aeda0af60e453093c3306b6eb Author: galt Date: Thu Sep 27 15:00:07 2007 +0000 "Encode release log update" commit ab72cd33e3544b87865d3eaaa31f0e168ac5756c Author: galt Date: Thu Sep 27 15:00:03 2007 +0000 "Release log update" commit a59d69ea278756399f5da6c83a06d0e136d6ab14 Author: angie Date: Thu Sep 27 03:42:49 2007 +0000 Made rgdQtlDrawAt able to handle other table names and registered rgdRatQtl. Also fixed text drawing (was overflowing on the right when box width was 0.5 to 1 times text width) and refactored to move variables closer to where they're used. commit 2f26de7214219977864df844dedf30188456fa61 Author: galt Date: Thu Sep 27 03:09:42 2007 +0000 another fix commit c93350e6ec0d679925aab86804219a50457f5c44 Author: galt Date: Thu Sep 27 03:00:33 2007 +0000 oops variable had wrong old name commit 6e0f1e1d6a5a1b7246d99b2d930a31fc03fc3b93 Author: kuhn Date: Thu Sep 27 01:01:01 2007 +0000 added links to three biggest breaks in coverage commit ea07b17650739134d43b5511cec015728126a685 Author: jzhu Date: Thu Sep 27 00:15:43 2007 +0000 sort by ispyId (cgi variable hghPerson) working for multiple tables as long as they share the same patient ids commit 9f2f916a3e0d1f7ed35648f56edf2c04f571d027 Author: hiram Date: Thu Sep 27 00:07:57 2007 +0000 Remove chrM gold table before reloading, it may be in the way commit c1a952d8bf646b2dc9a60fe26a7aae1269ceebd1 Author: hiram Date: Thu Sep 27 00:04:48 2007 +0000 Properly cloneString static items during creation of the track commit 91a9ea3c8167de5b4c99dc9b801ca29354bead15 Author: hiram Date: Thu Sep 27 00:04:20 2007 +0000 Properly cloneString the "other" name for the group name commit 49b745cf2754ad68166edb280de155252c094918 Author: hiram Date: Thu Sep 27 00:03:38 2007 +0000 Properly clone string static items in the cutter track commit c9af42dc882279a15faf124979c4c0f05523c3ba Author: jzhu Date: Wed Sep 26 23:43:57 2007 +0000 agilent whole genome array 44K annotation file is confirmed to map to hg18 commit 6daf10e0020fa7689eda84d775c4fe3d1ef93b0c Author: kuhn Date: Wed Sep 26 23:43:06 2007 +0000 simplified logic for handling case of limiting chroms commit 6b16f922347d9d6118a826a3e4f4305cc2108866 Author: hiram Date: Wed Sep 26 23:34:02 2007 +0000 Shorten things down with printf tricks commit 1d8d9e2dc3f13fa965d65ae7d449174133b8f33c Author: jzhu Date: Wed Sep 26 23:07:06 2007 +0000 Removing unused usage.c module. Using slCount instead of reimplementing it. commit 9f3e77666de10ea83693fdebf61bd9948bb3421f Author: galt Date: Wed Sep 26 20:54:53 2007 +0000 improvement to backwards compatibility - allocates the same copySize ram regardless which is the old behavior commit 3c9efb784186498ee84aaed8902404588bf3f82d Author: galt Date: Wed Sep 26 20:32:55 2007 +0000 undoing accidental commit commit f5409342088bc4cd1045fd05c686278ebba43a71 Author: galt Date: Wed Sep 26 20:28:16 2007 +0000 fixing problem with cloneStringZ and code cleanup commit f98d0af4cb17969305df72c36f414856edf25dc8 Author: galt Date: Wed Sep 26 20:26:11 2007 +0000 added check to cloneStringZ so it will not choke on strings shorter than you request commit 569214d2b1fc614ad0818eb504cb23bfcedea295 Author: kuhn Date: Wed Sep 26 18:26:12 2007 +0000 simplified the output to make it a litle easier to read at a glance commit 58ac1140a748b602e1ea490df8be99f7431ceb0b Author: galt Date: Wed Sep 26 18:02:47 2007 +0000 adding support for logging with better memory handling against attack commit 393ea9cf934f3bc3acf4adf71a9a277557f4c4bf Author: angie Date: Wed Sep 26 17:11:14 2007 +0000 htmlVaWarn: Enlarged timeStamp buffer size to avoid buffer overflow leading to recursive calls (buffer overflow -> errAbort --> htmlVaWarn...) ending up in stack overflow with nothing printed to stderr. timeStamp still has finite size... but if errAborting because of mem alloc problem, dyString might cause infinite-barf too. commit c576302461af5f22d23edc7d321bfcdec1831f8b Author: ann Date: Wed Sep 26 17:02:29 2007 +0000 Added logic for searching the new type of trackDb.*.ra files. commit cfe8e90687520602b891fe9330e6db9e4f7d694f Author: ann Date: Wed Sep 26 16:27:05 2007 +0000 added International Gene Trap Consortium script commit 0769b627a7fbf13d24d893c388d02efff83c479f Author: jzhu Date: Wed Sep 26 16:24:57 2007 +0000 add ispy Agilent gene expression track commit c8ed5692fe92f8b256663f168dab4869ae2e4e6c Author: jzhu Date: Wed Sep 26 16:21:17 2007 +0000 add menu entry for ispy Agilent gene expression dataset commit 6e8448dceae196ddb591c688caf4da6ae54de36f Author: aamp Date: Wed Sep 26 16:20:05 2007 +0000 Removed caseControl from hg18 and put it in human. commit 5b1f69fa7d4442bfc7d4467f18951e437d6071bf Author: jzhu Date: Wed Sep 26 16:19:54 2007 +0000 add Agilent gene expression track commit 1d8f0abd229f832b375b8e0a3f82a6320758770a Author: galt Date: Wed Sep 26 15:00:06 2007 +0000 "Encode release log update" commit d1ebf9dd701527d1b776f393ff9f556516834be5 Author: galt Date: Wed Sep 26 15:00:03 2007 +0000 "Release log update" commit aca8d9fec581b66425183d811dd9fbfde617ab9d Author: angie Date: Wed Sep 26 02:59:44 2007 +0000 Updated FlyBase version (thx Brooke). commit aa76ecc9591a578ea121839ddc9e6fca9086bc4e Author: hartera Date: Wed Sep 26 01:31:42 2007 +0000 Added new zebrafish assembly, danRer5. commit 79b8d22e30bf1d9ece4a96531a54c094399ffb33 Author: hiram Date: Tue Sep 25 23:42:25 2007 +0000 some WORKING status cleaned up to DONE and working through the blastzs commit 7ff62322d500e2d38192bdad467a1786d5805c1a Author: hartera Date: Tue Sep 25 23:03:31 2007 +0000 Added release alpha and release beta versions for ensGene with correct build number and archive setting so the link goes to the correct archived Ensembl build. This is because hgwdev and the RR have different versions of Ensembl genes sets. commit cb6a3937157525187a04c298b94b1e812d820bbc Author: hiram Date: Tue Sep 25 22:53:36 2007 +0000 Fix priority for Mm9 chains and nets commit eb406f49e1f3bec4e3f0e9a3db2bb73af6ca4d0e Author: ann Date: Tue Sep 25 22:26:07 2007 +0000 A few more sections sketched out. commit 3e8ae0e016b6b801d784ddc4dafa52018d6bb922 Author: jzhu Date: Tue Sep 25 22:02:12 2007 +0000 R output uisng quote=FALSE commit 50c408bb95d4b27b37f37b4f1b9212aa33b89212 Author: angie Date: Tue Sep 25 20:52:23 2007 +0000 Updated url for rgdQtl. commit b528193e0ce2b37920776c9b3ee52a1c400991db Author: angie Date: Tue Sep 25 20:50:01 2007 +0000 Allow duplicate name for rn4.rgdQtl only. commit 1951a16030c47b6be168dae4fe248ac187dc029d Author: angie Date: Tue Sep 25 20:47:28 2007 +0000 In printRgdQtlCustomUrl, if there are multiple item matches, print all. commit 4c05aaa3fe14198df20f7716d2542e90d1106706 Author: angie Date: Tue Sep 25 19:36:14 2007 +0000 When forming result URLs, if a track is already in full mode, don't force it to hTrackOpenVis because that might step it down to pack mode. commit fbda2422c096eafd6ecf6ab77aa94697a46f1772 Author: angie Date: Tue Sep 25 19:18:38 2007 +0000 If search item's track is already in full mode, don't force hTrackOpenVis because that might step it down to pack mode. commit f68d90018eb604bfe32e218b4f04e456d84668b0 Author: jzhu Date: Tue Sep 25 18:55:01 2007 +0000 add function setSampleOrder to sort sample using Patient Id order change setOrder to setSampleOrder add defaultOrder for reset commit 1b58062e01987576899f49ff87b3a99d3740c1fe Author: jsanborn Date: Tue Sep 25 18:52:07 2007 +0000 Fixed R object extraction section commit a6ff6e456dbad4da8b19150382829eef1fad4702 Author: jsanborn Date: Tue Sep 25 18:23:43 2007 +0000 Updated R object extraction to txt file commit 807dfa82677716e87031354cde1912bb73b3ed72 Author: ann Date: Tue Sep 25 17:29:28 2007 +0000 Corrected citation format. commit d84b5c2229eacb5d416ed3f2d1898aee221e227e Author: jzhu Date: Tue Sep 25 16:45:15 2007 +0000 *** empty log message *** commit 1e2829310f57b59b458f7758056b36b0f0e6dbe3 Author: jzhu Date: Tue Sep 25 16:43:38 2007 +0000 include trackDb.instinct.ra in hg18 commit 9359746a608a848ec108be0a76171a9942eb0350 Author: markd Date: Tue Sep 25 16:40:05 2007 +0000 fixed bug in last commit commit f4ac58e837a5e5cfa75bfa8a5e0ef9ce7f3e75bf Author: jzhu Date: Tue Sep 25 16:39:53 2007 +0000 add ispyMipCGH track commit ccf58c620e8255d0a6226e37fb8802dc91fde69a Author: jzhu Date: Tue Sep 25 16:39:15 2007 +0000 add trackDb.instinct.ra commit ca948aab57713cd70fb22f9a4faf5cd2dce93938 Author: fanhsu Date: Tue Sep 25 15:27:01 2007 +0000 Updated to accomodate the fact that qName in kgProtMap2 is no longer the protein ID, but the KG III gene ID. commit feacee21b60d8d3bf6faa3dfcdef2f1bad7a3d8a Author: galt Date: Tue Sep 25 15:00:05 2007 +0000 "Encode release log update" commit 2dfe82e6aefe7a5c1aab1ab27a12fc86057248f7 Author: galt Date: Tue Sep 25 15:00:04 2007 +0000 "Release log update" commit 325619dfc2e6894d9e1af35e8c3604b8e25fc06c Author: jzhu Date: Tue Sep 25 07:30:51 2007 +0000 ispyMipCGH - trackDb.instinct.ra and microarray.ra commit c06969337bd3015e72629f122d4756e5ce2cf7c4 Author: tingwang Date: Tue Sep 25 06:03:01 2007 +0000 convert MIP CGH to hg18 commit 973f2aa6345b05118fae9769710f822790f92c76 Author: tingwang Date: Tue Sep 25 05:08:05 2007 +0000 fixed error on STAT1 ChIP-PET counts commit e5bb54f11ea8b50d99a6ac87813fd4508f040a99 Author: tingwang Date: Tue Sep 25 05:06:45 2007 +0000 added more references commit bb026442598840242dc52ae5b61662312edfed6f Author: angie Date: Tue Sep 25 04:19:26 2007 +0000 Updated wssdCoverage with corrected data from Ginger. commit 68555553fedd44fb660081825ed5cde880f6a679 Author: angie Date: Tue Sep 25 04:17:15 2007 +0000 Added nestedRepeats, rgdQtl. commit 41b1d04d47eec80fa658d5b742c7b8ca5331583e Author: hartera Date: Tue Sep 25 02:16:10 2007 +0000 Minor edits. Downloaded Ensembl protein-coding genes' peptide sequences from BioMart and compared to the translation from the genome. Loaded BioMart peptide sequences into ensPep table. commit b29e2d468b327ec1bb72ec051830e0b57fdc26c7 Author: hartera Date: Tue Sep 25 02:11:37 2007 +0000 Added data version for ensGene track. commit b6b349bca0dd186eb99f397943a573df7178e809 Author: jzhu Date: Tue Sep 25 00:24:44 2007 +0000 data source and instructions to build ispyMipCGH table commit 0c95a5b1029fc1f280c235656d7d1dc872b98571 Author: jzhu Date: Tue Sep 25 00:04:56 2007 +0000 display only a subset of the experiments in the order that is set by function setSampleOrder commit 202f2f42cf5ce4ad38102275d85a870658005284 Author: hiram Date: Tue Sep 25 00:03:20 2007 +0000 Started panTro2 and equCab1 alignments commit caa232069b180f75d0202ace13331a5a78af1953 Author: angie Date: Tue Sep 25 00:03:16 2007 +0000 Include common.mk and use its ${BINDIR}. commit e7bafd59813502d248fece88d2217d4204181e93 Author: angie Date: Mon Sep 24 23:59:29 2007 +0000 Build into $BINDIR instead of leaving extra copies in this directory. commit b27cbd04087696e2892d567341baec0f0ca2d6d1 Author: angie Date: Mon Sep 24 23:30:25 2007 +0000 Updated rgdQtlId to include all human assemblies. commit b7633a0784ed8805f736d97dc8f1ee1c46ad814e Author: galt Date: Mon Sep 24 23:24:43 2007 +0000 fixed bug in allTables for snpArrayAffy500, a table with no corresponding track commit c0b1b1b05b47cbc4cee3cb4ced921bfa1f358e3d Author: markd Date: Mon Sep 24 22:36:04 2007 +0000 handle mitochondrial codon translations commit 3a01718b81b4d01afd63ce1ed3f946b07f97e8da Author: markd Date: Mon Sep 24 22:18:30 2007 +0000 don't stop at first difference, added peptide option commit 82f0b702d0722f6a7439361a99f72dd04729ed41 Author: jzhu Date: Mon Sep 24 22:17:02 2007 +0000 set up cancer1.txt documentation on how to set up tables, tracks, data analysis, convertion, and everything related to make the data tracks on cancer1 commit 61bb42500db5b0ea55df10aec5d84f384b82277d Author: hiram Date: Mon Sep 24 22:11:37 2007 +0000 Done with second run of known genes on mm9 commit d8f294ee43003660ca953b89e6f404b887ddd116 Author: hiram Date: Mon Sep 24 22:10:17 2007 +0000 Clean up WORKING status commit 44e729863a3701dee35d03dc95653e16c567e1f4 Author: hiram Date: Mon Sep 24 22:10:01 2007 +0000 Done with mm9 swap commit c5bb95c879160f8674ecaba6349cef0ab386d681 Author: hiram Date: Mon Sep 24 22:09:30 2007 +0000 Done with genbank and mm9 alignments commit 86a6c3ac4b5698d2cf9646a3aec4bba4d2470424 Author: hiram Date: Mon Sep 24 22:08:51 2007 +0000 Done with second run of known genes, done with Orangutan ponAbe2, Allen Brain Atlas, xenTro2, anoCar1, working on galGal3, ornAna1 commit 9e060c8a0b968fcba82b06a4ef18312c3fc3cc7a Author: angie Date: Mon Sep 24 21:48:47 2007 +0000 Some tweaks to RGD QTL parsing, after closer examination of RGD's details pages. commit b592bea70743463250874016e517dabc8e2f84a4 Author: angie Date: Mon Sep 24 21:30:45 2007 +0000 Loaded RGD QTLs. commit e1983a2577c30e89c3b19e7d041d42d9e710965b Author: angie Date: Mon Sep 24 20:36:09 2007 +0000 Fixed segv in rgdQtlDrawAt. commit 47df85dd8f68252891765042148c3630bedb49f0 Author: rhead Date: Mon Sep 24 18:29:40 2007 +0000 Replaced broken Exogean link. commit a81201d7bf90f5310d753d9105f86ae2769e6f45 Author: rhead Date: Mon Sep 24 18:05:32 2007 +0000 Moved the cbseweb address up a bit and added a note about Genome Browser questions at the bottom of the page in an effort to prevent misdirected emails to the cbse webmaster. commit 640b68e2331972b52040e8b758f81bddd5aecc6b Author: galt Date: Mon Sep 24 17:49:39 2007 +0000 adding REQUEST_URI on error commit 49e43d5e33e9ebcde2ad149dda5c15569233fe05 Author: galt Date: Mon Sep 24 17:43:23 2007 +0000 trying to suppress build-as-util when target is alpha commit 495789a88d5f04b80b50f3849b03c9aed548ada5 Author: galt Date: Mon Sep 24 17:22:57 2007 +0000 adding knownToVisiGene to utils build to keep it up to date commit 4ca47e06d4d64e6fc1abc82073facb289ac22cb1 Author: hiram Date: Mon Sep 24 16:48:35 2007 +0000 Include cgi binary name in the warning messages to the Apache error_log commit 8ad227e797f275caff44f273322a6ed4a9ebeb34 Author: donnak Date: Mon Sep 24 15:55:51 2007 +0000 Added J. Ma et al. pub. commit d7fc1f07a4716bfeb46372e21438946f28c7fd67 Author: galt Date: Mon Sep 24 15:00:06 2007 +0000 "Encode release log update" commit bcf489a9050a56ef7215dbe1bdb736f3743ab0c7 Author: galt Date: Mon Sep 24 15:00:03 2007 +0000 "Release log update" commit e110d58bc2cf22d362f342977629ca10f4b3a063 Author: hartera Date: Mon Sep 24 01:15:43 2007 +0000 Updated description of assembly methods. commit 18d387ee051a64eb76d069fcd6d2419d694bf4ea Author: galt Date: Sun Sep 23 15:00:06 2007 +0000 "Encode release log update" commit 2af56fcd873e24316eeb353e22c681bd068c8a1f Author: galt Date: Sun Sep 23 15:00:04 2007 +0000 "Release log update" commit f30b259ac9cb06f699d1c72c1c7737284320af3a Author: hartera Date: Sun Sep 23 02:24:06 2007 +0000 Expanded credits section. commit f71384222fa1be57c4a0257d0e3b689f4db38326 Author: hartera Date: Sun Sep 23 02:04:58 2007 +0000 Modified the sourceName in the dbDb entry for danRer5 and added Sanger's full name. commit 5131e47d38769e3f44c9ad55e04b97da739046f6 Author: hartera Date: Sun Sep 23 01:48:54 2007 +0000 danRer5 blastz swap to create zebrafish danRer5 chains, nets, axtNet, mafNet and alignment downloads. commit d6e11355e50601646ed2dee6b64eb2a4969da402 Author: hartera Date: Sun Sep 23 01:42:55 2007 +0000 Freed dynamically allocated itemConf object. Added include for itemConf. commit c24029a70474bc1a2406398b896c52176e58cce2 Author: hartera Date: Sun Sep 23 01:38:10 2007 +0000 Add code to display details of items in an indel-based conservation track. commit 5304e0c08993f19425b3d0d3a97a47d4c5168047 Author: hartera Date: Sun Sep 23 01:23:19 2007 +0000 Minor edits and formatting. commit cf06d1fce2a68394d1cb9a0f9a98a270d9862420 Author: hartera Date: Sat Sep 22 23:57:56 2007 +0000 adding itemConf. commit a2aba685547fb39b2662d700a6c69c94de699699 Author: hartera Date: Sat Sep 22 23:55:18 2007 +0000 Adding itemConf object to support additional information (probability and false discovery rate) for a track. commit 018ad34f8d103e6e9f812facb6da377ee6afec76 Author: hartera Date: Sat Sep 22 23:53:30 2007 +0000 Autosql generated library functions for a track item, probability and false discovery rate. commit 9194177ef10f67d990059e5e878f9e938314d476 Author: hartera Date: Sat Sep 22 23:52:52 2007 +0000 Autosql generated table definition for a track item, probability and false discovery rate. commit 851a584dc408363228b654788521c62d330ff42c Author: hartera Date: Sat Sep 22 23:51:59 2007 +0000 Autosql definition for table for a track item, probability and false discovery rate. commit cf8e4678b9df2f3e340947eb40f6b55a01d0604f Author: hartera Date: Sat Sep 22 23:49:50 2007 +0000 Minor edits to track methods. Blastz and create chain and net tracks, axtNet, mafNet and downloads for Fugu (fr2). Creat liftOver chains from danRer5 to danRer4. commit fa8f49c1839cda8124e96e1fd8aba6426b068311 Author: hartera Date: Sat Sep 22 23:47:40 2007 +0000 Reordered track display for wild type expression data. Created danRer4 to danRer5 liftOver chains. commit b53f70179cd7207ea175a18b5cf3bcbee984dadd Author: galt Date: Sat Sep 22 15:00:05 2007 +0000 "Encode release log update" commit 3749b91fdf1e114e7c98c50eaca0fd0224df3281 Author: galt Date: Sat Sep 22 15:00:04 2007 +0000 "Release log update" commit 6c74e786ff86a4b5826fadcebf990b4828a791b4 Author: hiram Date: Sat Sep 22 03:29:56 2007 +0000 Beware of undefined REMOTE_HOST variable commit 53c632b128a5789564422551c701ac569c3ab49c Author: kate Date: Sat Sep 22 00:27:51 2007 +0000 Temporary patch around memory problem commit 5f58b105520e16af32e4b34a0ced7aebc4597c9d Author: hiram Date: Fri Sep 21 23:59:25 2007 +0000 Add time stamp and remote IP information to warning outputs from CGI binaries commit 9b1a8e08a9eb68c93388cd467308c21585f16606 Author: angie Date: Fri Sep 21 23:31:01 2007 +0000 Added recognition of altGraphX fields in hFindBed12FieldsAndBinDb. commit c12b93be418f68321d0b4fbbc0ca3548a09a6733 Author: kayla Date: Fri Sep 21 23:13:46 2007 +0000 added StrPur1 and StrPur2 to the chainDest block. commit 60a1167866e9e09fed8490f8508e82bd02dd44b8 Author: kayla Date: Fri Sep 21 22:31:36 2007 +0000 added strPur2 to both the blastHg18KGPep04Id and blastHg18KGRef04Id blocks. commit f057bd5148691fa45530611228d05fdede3443e0 Author: kayla Date: Fri Sep 21 22:29:41 2007 +0000 Added strPur2 commit a9114596ce3460a39794ff6a488d2abe4d5de07a Author: rhead Date: Fri Sep 21 22:28:55 2007 +0000 minor edits commit c243a262f4d45d9dba7bdf892718ec0eeb8c15d5 Author: kate Date: Fri Sep 21 22:23:48 2007 +0000 Guinea pig alignments commit b1d22a8c3b8d9cd662ecec6ebbbb0d213e83da24 Author: rhead Date: Fri Sep 21 22:13:15 2007 +0000 added 'the'; punctuation commit 598fae9fa2bc6cd203c2379724607168eb9d289e Author: hartera Date: Fri Sep 21 22:12:37 2007 +0000 Updated the reference to the PubMed format used now. commit ed9e31886ce003b555bbfabcce14d5268f4bbdb0 Author: rhead Date: Fri Sep 21 22:00:54 2007 +0000 typo, punctuation commit 0ff15502c0f365be3eb43243f4d0fbe21374600d Author: rhead Date: Fri Sep 21 21:56:04 2007 +0000 punctuation commit d9c2ceba819b4f1a37b4ea0c24c1657129c7301e Author: rhead Date: Fri Sep 21 21:38:20 2007 +0000 punctuation commit 499ccae2ebb6e3a90fb030df8867c70b5edc97bd Author: rhead Date: Fri Sep 21 21:30:14 2007 +0000 A tiny bit of rewording. commit 277af013b07672b3a44812f9e109447aa2f42322 Author: kuhn Date: Fri Sep 21 20:41:57 2007 +0000 made a util that detects that regions not covered by a table and reports the bigges such regions orderd by size commit 08267d9b7e15acf536b10e9286529c3c82cf15bf Author: kuhn Date: Fri Sep 21 20:40:22 2007 +0000 pulled from checkOffend.csh the routine that finds out what a chrom is called: genoName, chrom, tName, and made a util that does only that commit 63ec9b254d4ad6eefaa7b0f3289dc255aac7d43f Author: donnak Date: Fri Sep 21 20:38:38 2007 +0000 Updated in press refs, fixed formats. commit 96cfbb84dad23f07f3bbd4293a91c9dc7bd3f361 Author: donnak Date: Fri Sep 21 20:33:25 2007 +0000 Updated in press refs, fixed formats. commit 72c9e60c6bac7c7593fcc02d9be47b1fbb9f1c83 Author: hiram Date: Fri Sep 21 20:23:39 2007 +0000 Add chain and net ponAbe2 commit 9bc26c4bffb82234418078e0b3c06e7a59c5b90a Author: hiram Date: Fri Sep 21 20:20:17 2007 +0000 Clean up batch.bak files during cleanUp, and mark kluster run directories with the hub in use commit 2e6998b74cfa7f8792642b20c902ab394aa2604c Author: donnak Date: Fri Sep 21 20:13:53 2007 +0000 Updated in press pub, fixed formats. commit 09e4556bff290e017f4be0fe5a6c076558635b26 Author: donnak Date: Fri Sep 21 20:09:39 2007 +0000 Updated in press ref, fixed formats. commit 451dd9f54fc685e39d0457704e15769693bb763c Author: donnak Date: Fri Sep 21 19:54:22 2007 +0000 Updated refs. commit 9e93329bcd2c31c4dd37af91822d8be30c220336 Author: donnak Date: Fri Sep 21 19:50:49 2007 +0000 Updated in press pub, updated ref formats. commit 7e050ff441b08fff0201740316ac729d5f973233 Author: donnak Date: Fri Sep 21 19:38:32 2007 +0000 Updated in press pub, fixed formats. commit b6a31a8344f8510935d922b9fad6d57609d46c88 Author: kate Date: Fri Sep 21 19:28:02 2007 +0000 Update intro and blue bar for hg18 migration. Still need News commit 421270b774c4cd0eaa2f2bdd6e94ea74653d89c4 Author: donnak Date: Fri Sep 21 19:08:47 2007 +0000 Updated a few refs, fixed formats. commit 632e6919f5baeed329bc1370d7b4648ff1c5208d Author: donnak Date: Fri Sep 21 18:48:32 2007 +0000 Updated some refs previously listed as "submitted", fixed other ref formats. commit c65142f433eaf518faf30645aa0d9e7979f0ab0c Author: donnak Date: Fri Sep 21 18:23:23 2007 +0000 Removed Epub from refs. commit d21985b0c5310af8923c49067b959d289802f2d7 Author: kate Date: Fri Sep 21 18:21:35 2007 +0000 Downloads for ENCODE hg18 commit ba478ae6d70b6d67c17a54e7f0babc08182b69e8 Author: donnak Date: Fri Sep 21 18:21:07 2007 +0000 Fixed reference. commit 83b77a4c17f10706bdc25d29a026cb2ffbc11e24 Author: donnak Date: Fri Sep 21 18:14:30 2007 +0000 Added links for Yeang & Dreszer pubs. commit 5130452f4648091a9046b629b3986f3b0c866b3d Author: kate Date: Fri Sep 21 17:59:03 2007 +0000 UCSD Chip data from 2006 commit f6b40f42b918960fa3546eb740a35cfe269542d3 Author: kate Date: Fri Sep 21 16:34:28 2007 +0000 GIS table rename for whole-genome track commit b76cfeceb02a1b40ec04a5e658f7ab3e7a455bd6 Author: galt Date: Fri Sep 21 15:00:07 2007 +0000 "Encode release log update" commit 3b4469dd9c7909a73c4578c15e2902587acb7b59 Author: galt Date: Fri Sep 21 15:00:04 2007 +0000 "Release log update" commit 077cee4ed10905e7bbcbbbb92fd63c7ec4eb0107 Author: kent Date: Fri Sep 21 14:13:02 2007 +0000 Fixing typo in comment commit e9d87d778e2131b0f85698e0369cd4eddce57580 Author: kate Date: Fri Sep 21 05:24:42 2007 +0000 Rename tables, composites, and supertracks for GIS whole-genome ENCODE tracks. Add supertrack commit 47917ef291d38982b88ec43eac9b87c234eb7294 Author: angie Date: Fri Sep 21 04:38:15 2007 +0000 Updated FlyBase annotations to 5.3 (flyBaseGene, flyBaseNoncoding and many related tables). commit 01a86b1ddfbd51217c4d9c5ad91361f56ba3f6c6 Author: angie Date: Fri Sep 21 03:50:54 2007 +0000 Updated FlyBase annotation version to 5.3. commit bf907ae75deef8060b608da6e858637af0a14f35 Author: kayla Date: Fri Sep 21 00:32:06 2007 +0000 added strPur2 commit 1a713abf3bc70969c4f809fa3026573a8a91e5ea Author: donnak Date: Fri Sep 21 00:17:40 2007 +0000 Fixed some typos & edited. commit 7b750c17b9e04db8bfe7a111e9e1f9f6808bdd50 Author: rhead Date: Fri Sep 21 00:16:43 2007 +0000 Changed Exogean link to one that works (thanks, Kate). commit 0bc68523642ecccd29c9fc8b00c71bbceac5b84f Author: rhead Date: Thu Sep 20 23:45:46 2007 +0000 Wording change to be more consistent. commit 4364bb7b8406e006cfdfcfc7c0c764f1bbe09d52 Author: aamp Date: Thu Sep 20 23:33:03 2007 +0000 Added CCC genome graph build instructions. commit 9465ce0c3816ec44841e4d4b093874ffb4a9025b Author: hiram Date: Thu Sep 20 23:27:56 2007 +0000 Added Pongo pygmaeus abelii (Orangutan). commit 84977b3c75d29595daa28fc9e763597a2e7b435d Author: aamp Date: Thu Sep 20 23:26:35 2007 +0000 CCC genome graphs and Human Normal microarray. commit 27151fe1e680943cfe8d30c17653d3ebf0e45e03 Author: hiram Date: Thu Sep 20 23:24:34 2007 +0000 Added ponAbe2. commit 681a54d01d28dcd3d4defad86ac4dec784d71c8d Author: kate Date: Thu Sep 20 23:09:07 2007 +0000 Change spelling of supertrack (cosmetics) commit 17c0fd5ad09520c59e0b2c665fb305ab579b1bcd Author: rhead Date: Thu Sep 20 22:48:21 2007 +0000 Added a hyphen to 'super-track'. commit 781f08c219cd2b8c308635f07af7c952cf615c6b Author: ann Date: Thu Sep 20 22:39:56 2007 +0000 big editing session commit 7d12bafa89bbbe6491f839ead9407f5dcc274bbf Author: kate Date: Thu Sep 20 22:20:22 2007 +0000 Cosmetics commit 526a7ab9affda97d9599b9166025a28efbcca42a Author: markd Date: Thu Sep 20 21:54:15 2007 +0000 fixed bugs with stop codon location and other GTF stupidity; added tests, wasted time commit dc2bf5b7b5b15271005d4f2b4626d28b35a7a116 Author: angie Date: Thu Sep 20 19:58:06 2007 +0000 Added description of BED score and shading. commit 93a3db96fdd293b2a237368274204a2fea949587 Author: kuhn Date: Thu Sep 20 18:44:23 2007 +0000 made usage statement a bit easier to read commit a4e49c91bdbda7755ff2f31c0d041b45322da3f4 Author: braney Date: Thu Sep 20 17:38:10 2007 +0000 add a couple of fields to atoms (threePrime and fivePrime) commit 3df789211401ad0a8201a6b564bb81f438146ed0 Author: galt Date: Thu Sep 20 15:00:05 2007 +0000 "Encode release log update" commit 256630d38d5dfd719200c7b4785edcbc06be28b4 Author: galt Date: Thu Sep 20 15:00:03 2007 +0000 "Release log update" commit 71c7549c6cea53aa4e5382d82aa9e70f9ac94a1d Author: angie Date: Thu Sep 20 07:43:37 2007 +0000 Added useScore to nestedRepeats for shading of items by identity score. commit a681b2f4ae34b6fa1584f494637ca9744c539c33 Author: angie Date: Thu Sep 20 07:42:30 2007 +0000 Transform identity score to bed score, and average across fragments, so that shade of items in nestedRepeats will be similar to the fragments' shades in rmsk. commit c6f9aec99b67f4de554887b071bac9154340fd54 Author: lowec Date: Thu Sep 20 03:24:14 2007 +0000 changed the way that a bed list is put into a hash commit 1578d5c7837c8c2a41beee2ebf1c0e5a1f5f7d52 Author: donnak Date: Thu Sep 20 02:24:07 2007 +0000 Noted that multiple search terms can be entered at once. commit 4fe2cabd2c0e07ff09f2a0a015e3a61190fbda0c Author: donnak Date: Thu Sep 20 02:20:06 2007 +0000 Fixed some grammar problems, added note that multiple terms can be used. commit c5caf915648985a6659cbec2ed87b81ecf8e4475 Author: angie Date: Thu Sep 20 00:33:33 2007 +0000 Merge overlapping fragments to make legal BED12. commit 203c751c9a1117a7de30d450d7e7ce0e243d0880 Author: kuhn Date: Thu Sep 20 00:05:02 2007 +0000 added support for supertracks commit ec5aa2a1c70a736286628199e556217289fd71d9 Author: kuhn Date: Wed Sep 19 23:08:26 2007 +0000 shortened two lines to fit into 80-char commit 7ee1fc044a89e507abc9cd00c380db6f3db4b5ce Author: markd Date: Wed Sep 19 23:01:47 2007 +0000 don't blame OS/X bash our problem commit f07caf9d42375dc855a8dca3c635653d6ca0d282 Author: angie Date: Wed Sep 19 22:15:07 2007 +0000 Added an add/manage custom tracks button at the end of the group/track line. commit c5d07f46162e9afb2a7467829a094c2e8d4d3d6b Author: hiram Date: Wed Sep 19 21:45:46 2007 +0000 Done with RepeatMasker and simpleRepeats. commit 2380ebd6818673bb1b146a154e6371fd54a7a092 Author: kuhn Date: Wed Sep 19 21:38:40 2007 +0000 dropped mm6 and added mm9 commit 4f11eecb8f1fe5a7893e4340276677203ae2e175 Author: kuhn Date: Wed Sep 19 21:25:00 2007 +0000 Expanded some sections, especially the MySQL commands for extFile/seq handling. Made some output clickable by adding links. commit f3c97e23ddbb9fb661f02f988afed473a579bed2 Author: kate Date: Wed Sep 19 21:15:15 2007 +0000 Enable supertracks when using -strict option commit ae37cf952201ba9c106e214087e99080d419de01 Author: hartera Date: Wed Sep 19 21:05:31 2007 +0000 Minor correction. commit 11f7e8c57ee0d2b16356d88003a2d3e20bac8828 Author: ann Date: Wed Sep 19 20:54:54 2007 +0000 script to QA International Gene Trap Consortium track commit 28ffcb094c62ccf55b6cc06a986afcf5c7d568c8 Author: hartera Date: Wed Sep 19 20:44:35 2007 +0000 Corrected database name in danRer5 blastz section. commit be17a845a59b3c644fac5ddf65ab3f9ca2f44633 Author: angie Date: Wed Sep 19 19:31:07 2007 +0000 Updated db list: IGTC now processes mm7-mm9. commit 43f11a2266a407bf2e1a699742636287ddc11629 Author: donnak Date: Wed Sep 19 19:12:14 2007 +0000 Added link to ref. commit 3a68df2383bdc0f5f838693946d54b9d72d740cb Author: kuhn Date: Wed Sep 19 18:59:21 2007 +0000 removed variable, today (unused) commit 0fefdb86b8c4dd0c4e6f79f0e81811d9959cb675 Author: angie Date: Wed Sep 19 18:48:44 2007 +0000 Fixed creation of outRoot. The gratuitous nfsNoodge used to be harmless, but now that nfsNoodge includes touch, it was actually preventing the subsequent mkdir. commit 33ac73765936b0ea63ad3bbfd3804669fcfeadd8 Author: hartera Date: Wed Sep 19 03:55:05 2007 +0000 Added search for consIndelsHg18Mm8CanFam2 track. commit 99454b4391b64a76a6fbb302fc8708e58607caaa Author: hartera Date: Wed Sep 19 03:40:56 2007 +0000 Added searches for Affymetrix Zebrafish array consensus sequences and target sequences tracks. commit a79adf9f144e105d3d1c3f7906023c04ea426e79 Author: hartera Date: Wed Sep 19 02:23:51 2007 +0000 Added Ensembl Genes v46 track for protein-coding genes. Added search for contigs track. commit 85fa22a2976b02809eb7788850875aa9beb67db3 Author: hartera Date: Wed Sep 19 02:21:30 2007 +0000 Description for Ensembl protein-coding genes track. commit dbef26eba330b3e38fc01333deb8b9702c8a4a18 Author: braney Date: Wed Sep 19 01:27:37 2007 +0000 an autoSql file for atoms commit 7311ec15e660297d21166b588c8b3424b38903f0 Author: kate Date: Tue Sep 18 23:10:39 2007 +0000 Fix typo commit b002329483c40e5cdb5231f037695c8006043e3d Author: markd Date: Tue Sep 18 23:00:58 2007 +0000 made pslChain compile, although I live in fear of the results, so it wasn't made part of build commit ed82b6ff83d4a32b3724bc20990d2314854dbbf5 Author: hiram Date: Tue Sep 18 22:53:29 2007 +0000 Note about fixing STS aliases next time commit fc5252395ee8fece061cfed62552a3db0e91ef10 Author: kate Date: Tue Sep 18 22:04:39 2007 +0000 Remove files needed for transition of html on Affy tracks commit 7e4a57323d8e2eb2ef57dc22745f23dd3ba85b0e Author: kate Date: Tue Sep 18 22:01:53 2007 +0000 Update Affy Chip tracks to include ME-180 cell line in labels and descriptions commit 048cbc4c10ffd32d9c85db2bbee0a90582bb4f11 Author: kate Date: Tue Sep 18 21:57:56 2007 +0000 Correct Affy Chip descriptions to include ME-180 cell line commit 979f720aa10e5b49e133141837f08316c86944b8 Author: kate Date: Tue Sep 18 20:49:37 2007 +0000 Remove release alpha from supertracks commit 55d9fd7c6395bdd77018ecdfaa975fc4e10db41c Author: archanat Date: Tue Sep 18 20:19:10 2007 +0000 correct the value for the default upper range commit f6826483b25f36052ff1e6b11ef1213a39966596 Author: archanat Date: Tue Sep 18 20:18:01 2007 +0000 corrected the value for the default upper range commit 97ddf11c015570759daeca18f65188f384b2d4a1 Author: angie Date: Tue Sep 18 20:13:51 2007 +0000 Minor tweak to clean up after self upon successful test. commit d51e95458298569bce0ed718fa70be405ddcfa0f Author: angie Date: Tue Sep 18 20:11:36 2007 +0000 Updating to match whitespace changes in output. commit 7311ace28926823e9d25560878cfbfa26bf242f2 Author: markd Date: Tue Sep 18 19:43:22 2007 +0000 ignore some private sequences commit 417a321de8472acb5c56570a9b57e0f49a5eee93 Author: ann Date: Tue Sep 18 19:10:22 2007 +0000 added note about significance threshold only pertaining to the first graph commit 312ddecab93ed11f11003155de46c43b3235f12c Author: braney Date: Tue Sep 18 18:38:46 2007 +0000 some changes to the atom track handler (show 5' and 3' atoms) commit a3c16daedeab7eadc47588bc218860747ac88646 Author: hiram Date: Tue Sep 18 18:23:35 2007 +0000 When on hgwdev, fixup any directory /gbdb/db/html/ to be a symlink to /cluster/data/db/html commit 7cfa2939651aacf1e6cd29a87cf0fe634a456eec Author: hiram Date: Tue Sep 18 17:44:40 2007 +0000 Do not require mm9 when 'make alpha' since it is not yet on hgwbeta commit 8cefe2a9f47699343a332325df310c8b5ce7be7a Author: hiram Date: Tue Sep 18 17:42:52 2007 +0000 Do not remove the description.html symlink from the /gbdb/db/html/ directory commit c4092bbf1c1f6f5b53b4a7e13ccc74e195fdec89 Author: kuhn Date: Tue Sep 18 17:23:36 2007 +0000 replaced some code with call to getMonthLastYear.csh for removing old files commit 4252a59fce2999404f50d3d352f10af578a2a102 Author: hartera Date: Tue Sep 18 17:14:45 2007 +0000 Added more people to the credits. commit 02d08b419978682d40d21a0657e439900966a70c Author: aamp Date: Tue Sep 18 16:42:16 2007 +0000 "New version number v167" commit d9b4148c2e71152f8fc555283f085d9d27df9b78 Author: galt Date: Tue Sep 18 15:00:30 2007 +0000 "Encode release log update" commit 9695ed90203a31423384530a5996a1be4ebbbe58 Author: galt Date: Tue Sep 18 15:00:28 2007 +0000 "Release log update" commit 2a0b3008b128935f37c2a243d96bad55c4c1697c Author: pchan Date: Tue Sep 18 10:56:43 2007 +0000 add tigr operon track commit f3c9a4ba1468e9f0be5cfe82baea5ac855ba7583 Author: pchan Date: Tue Sep 18 10:27:58 2007 +0000 add lowelabTIGROperonScore.o commit 3bdee8c8348cee93ee34715687782a274448e717 Author: pchan Date: Tue Sep 18 10:27:09 2007 +0000 add lowelab TIGR operon track commit 3720419131ae2c4ee99183833ab9fc285614973e Author: tingwang Date: Tue Sep 18 06:04:32 2007 +0000 update .ra to move GIS tracks from ENCODE to regular track group commit d112be0cce8bd4b0a5e583e08d63a08fbc6f3f17 Author: hartera Date: Tue Sep 18 05:36:44 2007 +0000 Added track for indel-based conservation between hg18, mmm8 and canFam2. commit 21c170c98fd68d0b6294429dc344f57d6bcc0c96 Author: kate Date: Tue Sep 18 04:23:30 2007 +0000 Rename whole-genome tables and tracks to include prefix 'wg'. commit df03af2ba4296b6238ef33c67a81b980076fa932 Author: kate Date: Tue Sep 18 03:40:42 2007 +0000 Change names to 'wg' (whole genome) commit a3de5f5e2c4a3c63e776ae77edfb360f25ec3078 Author: angie Date: Tue Sep 18 03:24:45 2007 +0000 Reloaded acembly with new data. commit b0f1ec2ada762400be5acb2bcc8039a93f036022 Author: hartera Date: Tue Sep 18 02:04:24 2007 +0000 Changed default position for danRer5 Genome Browser. Re-run RepeatMasker, processed simple repeats into a mask, made ooc files for Blat. Created lift file separated by non-bridged gaps for Genbank run. Set up Genbank mRNa, EST and ZGC genes run. Added Ensembl protein-coding genes track (done by markd). Made blatserver entries in hgcentral. Added Vega genes track, created Medaka (oryLat1) chain and net tracks and axtNet, mafNet and alignment downloads. Split genome sequence 2bit file into chrom and scaffolds FASTA files. Added Affy Zebrafish track with alignments of both consensus and target sequences. Added assembly downloadable files. Added contigs track. Created wild type array expression track with consensus and target Affy Zebrafish sequences. Blastz for tetraodon (tetNig1) to create chain and net tracks, axtNet, mafNet and alignment downloads. commit a9857f93106f0ce121791b62350eb2cdefbf0a52 Author: hartera Date: Mon Sep 17 23:58:47 2007 +0000 Added paragraphs and a link to the article cited and link to data and added citations. commit 25c7ac4264247681cbf214ce12c254cb34c59be9 Author: angie Date: Mon Sep 17 23:41:44 2007 +0000 name can be >11 chars -- broaden primary key limit. commit 92f443c6d9990116558326976f712e26ee6a8ff4 Author: kuhn Date: Mon Sep 17 23:41:41 2007 +0000 added file removal to keep archives from growing beyond a year commit 55ec2a3cefc57198d73632c146e1f01a50ab14cf Author: kuhn Date: Mon Sep 17 23:31:53 2007 +0000 added util to get last year year-month for cleaning out old monitoring data commit fbbe081f22a7cf3fbf112532a0914d6986e62db5 Author: hartera Date: Mon Sep 17 23:24:48 2007 +0000 Description of indel-based conservation data provided by data contributor, Gerton Lunter. commit 72aca8b2817234198fea732e9a1c23fc319db675 Author: hartera Date: Mon Sep 17 22:03:45 2007 +0000 Blastz swap to get danRer5 chains, nets, axtNet, mafNet and downloads for tetraodon. commit 35bbe25d992d0d2c195bd826d776044e82f53c83 Author: hartera Date: Mon Sep 17 22:01:21 2007 +0000 Corrections in danRer5 blastz section. commit 22537849b045ed6e5120e979011047c2e8792655 Author: rhead Date: Mon Sep 17 21:37:36 2007 +0000 Moving a copy to assembly level so that information about the hapmap release can be maintained separately for each assembly. commit bdf4f9a63cbe5db8d959a57daad26acb6d4d6bba Author: fanhsu Date: Mon Sep 17 21:13:21 2007 +0000 Updated per Jim's input and added withNull logic for SaveToDb functions. commit b1ca18be7e83fbe7e485dedc28f8e802e0d680ca Author: hartera Date: Mon Sep 17 20:29:21 2007 +0000 Corrected section heading. commit 982df83b0fa7f5abead958647d02e660819f1dc7 Author: hartera Date: Mon Sep 17 20:26:36 2007 +0000 clean up and create blastz.danRer5 directory to link to blastz results. commit df60c0218100c1e1b2d3550a5c4236472a8fd638 Author: kate Date: Mon Sep 17 19:35:47 2007 +0000 Move genome-wide UCSD Chip tracks from ENCODE to Regulation track group commit f49e7114e6caa35dfa880492ab901b711f571c9e Author: kate Date: Mon Sep 17 19:33:14 2007 +0000 Reorganize genome-wide UCSD Chip data in supertrack commit 222114b73a24b61f68ee669a48b281796188be2d Author: kate Date: Mon Sep 17 19:32:19 2007 +0000 Add new trackDb file for genome-wide ENCODE, and include UCSD Chip tracks commit 720d6cf72377a5f4c86111a4ca508f532c264389 Author: hartera Date: Mon Sep 17 04:17:48 2007 +0000 Added danRer5 chains, nets, downloads and syntenic nets. commit d22bac13e83c0340ddff7e316a71f5951e1b5da7 Author: kate Date: Mon Sep 17 03:44:08 2007 +0000 Allow visibility control for supertrack members using custom track browser lines commit a969254d99993e07a111d34da6cb69542c67067b Author: hartera Date: Mon Sep 17 02:45:38 2007 +0000 RepeatMasker track description for Zv7 zebrafish assembly (danRer5). This describes the use of an additional repeat library of unclassified zebrafish repeats and the omission of some of these repeats since Sanger found that they mask out real genes. commit fd2becdf0275afd255ce1f1a94ab98c4451171a9 Author: hartera Date: Mon Sep 17 02:33:52 2007 +0000 Added contigs track, Affy Wild Type expression data composite track, Affy Zebrafish composite track and RepeatMasker track. commit 618ad9b49e242757fb217ebe1475f6de22eea480 Author: hartera Date: Mon Sep 17 02:31:16 2007 +0000 Added a section on display conventions and configuration. commit 35f6af48a1f95ac08610c321e5ab3c98ca91cf9c Author: hartera Date: Mon Sep 17 02:29:58 2007 +0000 Changed title of secton on display conventions and configuration. commit 75ec56bfeeb57ee9580cdf797b54f5ddf0de2866 Author: hartera Date: Mon Sep 17 02:24:14 2007 +0000 Expanded description of assembly track with details specific for the zebrafish Zv7 assembly (danRer5). commit 2b3056e254dee480aae9d04ee596ee26cbd301d4 Author: hartera Date: Mon Sep 17 02:13:52 2007 +0000 Description for contigs track. commit 17351fc5b881a954d0dd91cebd9ec3798e19da85 Author: hartera Date: Mon Sep 17 01:53:53 2007 +0000 Updated gap track description so it is specific for the zebrafish Zv7 assembly. commit 90ac1f3ad20dfcc964280abbc73c82050b72317b Author: hartera Date: Mon Sep 17 01:43:23 2007 +0000 Corrected assembly coverage. Added information about the mitochondrial sequence and removed extraneous text left over from description template. commit a2853f4a797c83aadcf3cdf902fe93f9c925b05e Author: hartera Date: Mon Sep 17 01:01:16 2007 +0000 Corrected date of assembly data freeze for Zv7. commit 8f9eb5576d82656428704cc21341314b2c17424f Author: hartera Date: Mon Sep 17 00:54:44 2007 +0000 Corrected typos. commit d0c7dfcd0cdefb77990360090a381e91cd80b663 Author: hartera Date: Sun Sep 16 22:08:48 2007 +0000 Added more information about subtracks for this track. commit c012b8eecc0a1e7112d61182afd33486d84674a8 Author: hartera Date: Sun Sep 16 22:02:19 2007 +0000 Added more details specific to the Zv7 zebrafish assembly. commit 78c42fc39775fff6ee63f6a16a020b4156529ae7 Author: hartera Date: Sun Sep 16 20:54:14 2007 +0000 Description for Zon wild type expression data track using Affymetrix Zebrafish GeneChip. commit dbdd901fda6d965042bf146f493a2c32a306896c Author: galt Date: Sun Sep 16 15:00:06 2007 +0000 "Encode release log update" commit b442ecee8c37a4049f53b8963cdd63eae583b8f3 Author: galt Date: Sun Sep 16 15:00:04 2007 +0000 "Release log update" commit 9985d9dd25f0f9c8ff6492fea54b23be10079295 Author: galt Date: Sat Sep 15 15:00:09 2007 +0000 "Encode release log update" commit 0feda86077a9b86bbf2512635b05691a9d8e218f Author: galt Date: Sat Sep 15 15:00:06 2007 +0000 "Release log update" commit 5f8e24d0f6b2bdd187a1127f8fe7eb1ceaac92c7 Author: kate Date: Sat Sep 15 00:31:52 2007 +0000 Move UCSD TAF1 CHIP tracks from ENCODE to genome-wide track group commit 6e31c46d514a2cfd0bca81e318e4617a5b09237a Author: kate Date: Sat Sep 15 00:31:02 2007 +0000 Move UCSD TAF1 IMR90 tracks from ENCODE groups to genome-wide commit 654859670d49dbff4db084594550b8759e199e90 Author: galt Date: Sat Sep 15 00:28:34 2007 +0000 currently we have no action for clicking on a filename commit 8f0b7738de90928bbe8bb40d278b1b9611a18031 Author: galt Date: Sat Sep 15 00:25:25 2007 +0000 minor trapping/reporting for invalid mime upload type commit 938e288360516f3beeb18741b17057036709bc11 Author: galt Date: Fri Sep 14 23:59:12 2007 +0000 adding error handling for http fetch commit 8184294024add4db507bba4efe50e721273483db Author: galt Date: Fri Sep 14 23:38:09 2007 +0000 trying to keep the status up to date as things change such as archives being added or deleted commit 7b9815c2392ef487fa021334c665aca031ad81f2 Author: galt Date: Fri Sep 14 23:36:54 2007 +0000 removed individual file status as the we will probably not use it and we need the display space for other stuff commit a5a607b4bdde836c2900922546c8f54f7e599725 Author: galt Date: Fri Sep 14 23:34:28 2007 +0000 added note about the extensions allowed commit 7150a4adefbbeeed759c10bb2366ea1a7691d807 Author: angie Date: Fri Sep 14 23:09:34 2007 +0000 Don't require gbMiscDiff. commit ccba79871bf1c0cbd6d75b0ce13f160a78fdab43 Author: angie Date: Fri Sep 14 22:50:54 2007 +0000 Added -noGenbank option to make the script tolerate lack of genbank tables. commit ea63d7f7a168831c97e72e0310999ae774d49db2 Author: kent Date: Fri Sep 14 22:36:42 2007 +0000 Seems to work for fixedStep wigs and bed4s. commit 3c6716e2a6413fe5f1d1ab4b6421faf487fb61e9 Author: kuhn Date: Fri Sep 14 22:33:13 2007 +0000 broke long line into 80-char chunks commit 41c25a010be74b27aafc476e024d512f1906cc2d Author: galt Date: Fri Sep 14 22:21:56 2007 +0000 added ability to delete archives, with clean out of upload dir and re-expansion of remaining archives in the submission commit 2f995597a7f1ab665c06fd74a7585d0a1235e0e2 Author: kent Date: Fri Sep 14 21:52:52 2007 +0000 Freen does sizeof(double) commit 00579b1da8155a8fb2032eb157c671cc196dca1a Author: angie Date: Fri Sep 14 21:15:06 2007 +0000 Adding Jim's intronSize.c for a happy build. commit 1d003b0fc1211a259ed121170fd17e34c9567ff6 Author: kate Date: Fri Sep 14 19:29:14 2007 +0000 Reorder subtracks of new UCSD chip tracks. Fix cell and factor settings. Add subtrack colors by cell type commit 7234398bc7d1c080033e5c862c5d9ca16153dc34 Author: hiram Date: Fri Sep 14 18:40:20 2007 +0000 Fixup comment about resolution download reference when on gc5 tracks commit 22b57b44e4469409d5a4948168bee22d85388fcf Author: kayla Date: Fri Sep 14 17:50:57 2007 +0000 moved chain/net mm9 blocks down to /fugu level. commit 84e6c4f45368a3b1e2dfe23fd8946caf391838c2 Author: archanat Date: Fri Sep 14 17:20:56 2007 +0000 fixed a typo commit 1a77489e65bf40e61c882026cdfe4bd6f7cd734a Author: hiram Date: Fri Sep 14 16:27:53 2007 +0000 Adding Marmoset, Orangutan, danRer5 chains and nets commit 340df155f009c3591ab4d0f1fb7e2d65d336c79f Author: galt Date: Fri Sep 14 15:00:05 2007 +0000 "Encode release log update" commit adbde095a68086890dd44e304eed293f68e71bd1 Author: galt Date: Fri Sep 14 15:00:04 2007 +0000 "Release log update" commit 0da97ab93c723efed944b615103f63cc63719cda Author: jzhu Date: Fri Sep 14 07:05:23 2007 +0000 fix a few bugs found at code review with Galt. commit 964a6963ea0ef92e36971365fd1acf7925aca9b2 Author: donnak Date: Fri Sep 14 06:57:43 2007 +0000 Fixed spelling typo. commit c53bfeebab7f518fd5226188bbc0f698b5cc0f01 Author: kent Date: Fri Sep 14 03:47:49 2007 +0000 C version of a SQL query. Bigger code but faster. commit 8b8a560c276de6ed61b6ac6c0333dc6ae7119601 Author: kuhn Date: Thu Sep 13 23:53:44 2007 +0000 fixed logic for parent track to account for case where there are multiple settings. commit 142ed2221d3a1c74128e60dd430567ca7e5d5cdc Author: hiram Date: Thu Sep 13 23:27:40 2007 +0000 Add ponAbe2 to the build commit 53ab7a87967fba6aa9a30774785a4e91471d3ca5 Author: hiram Date: Thu Sep 13 23:27:18 2007 +0000 Initial contents of files, somewhat accurate at this time. commit e2b0645f72d276164b173871e50e69d9ce118080 Author: galt Date: Thu Sep 13 22:52:16 2007 +0000 moved submission_files to be children of submission_archives instead of submissions commit f7c91cb6faba97411a3d019d0c5363a4f3f34b2b Author: kayla Date: Thu Sep 13 22:32:41 2007 +0000 Fixed the matrix numbers. commit 29aec7e235d4de475bc4e56062b4f19b4a056b7c Author: hiram Date: Thu Sep 13 22:32:19 2007 +0000 At long last, probably now have the nfsNoodge() function where it will work commit 83f4e57098614b3e9bd5627b89b446cc798b3ed2 Author: hiram Date: Thu Sep 13 22:26:20 2007 +0000 Other knownGene tables should be loaded after the primary knownGene table commit 18c6806499003d4c41b82ae9859fc7acff3e5075 Author: galt Date: Thu Sep 13 21:49:49 2007 +0000 added ability to validate commit 296989859988b97a7e8bb0075801289d62b05702 Author: kuhn Date: Thu Sep 13 21:30:33 2007 +0000 simplied logic and dropped a variable. thanks, brooke. commit 3d083032e7208bff0f57a67d43ea54e00bf4e985 Author: kuhn Date: Thu Sep 13 20:54:12 2007 +0000 adjusted spacing on if-blocks and simplified output. thanks, brooke. commit 8646ae4b6c59200fbc0506359e4d8fcfde6b7705 Author: kuhn Date: Thu Sep 13 18:33:32 2007 +0000 added a reference and reworded the descrption a little. commit ef4f3bd56aff958a218c0f1122ca6e047f2dbe73 Author: hartera Date: Thu Sep 13 17:20:52 2007 +0000 Description for zebrafish Vega Pseudoenes. commit b2ca6b9b3c98af24a2e548f540e356360b1bd816 Author: hartera Date: Thu Sep 13 17:20:20 2007 +0000 Description for zebrafish Vega Genes. commit dcdc32be365ce59a9cd3189f8fc097cb69ec22d7 Author: hartera Date: Thu Sep 13 17:19:44 2007 +0000 Description for composite Affy Zebrafish track of alignments of consensus and target seqeunces. commit 3d039d9da23d0540ecf2c6e2a816cbfb42b2591c Author: hartera Date: Thu Sep 13 17:18:39 2007 +0000 Added Vega Genes and Vega Pseudogenes tracks and a composite track for Affy Zebrafish of consensus and target sequences' alignments. commit 4284189c965955535892836c97d0493742a57d06 Author: galt Date: Thu Sep 13 15:00:05 2007 +0000 "Encode release log update" commit 67a777e0bd86d73ff3bcc56991da06ba5c67a7b9 Author: galt Date: Thu Sep 13 15:00:04 2007 +0000 "Release log update" commit 71ac6d7c9640b60040024e862f574b88d77d519a Author: rhead Date: Thu Sep 13 00:25:43 2007 +0000 Added note to output to remind us that the total size includes the size of the index. commit f27ec37c8863ab1ab558dd95b838ef7df4621d9c Author: kent Date: Thu Sep 13 00:05:08 2007 +0000 Adding description html files for cdsScore and geneCategory. commit 5025bb594b738c5d023bbda59fd9121e6edc941d Author: kent Date: Wed Sep 12 23:47:20 2007 +0000 Correcting label text for intronSize. commit d8e82b9819a17cf9aa4d1177e0eebb709e644401 Author: kent Date: Wed Sep 12 23:41:45 2007 +0000 Adding intronSize column. commit 5274b13f5b025862d1a614546b314c53f802fe2b Author: kent Date: Wed Sep 12 23:41:37 2007 +0000 Improving template a bit. commit 8d6fda2e7cedae8b6e6ca9e5d0c27dc0f76ba2fc Author: kate Date: Wed Sep 12 22:56:05 2007 +0000 Adjust pri for ENCODE Genes supertrack commit 9bc7051bce33ad6313cc184eb323cb4279d4089b Author: galt Date: Wed Sep 12 22:52:56 2007 +0000 support for submissionTypes.yml reading-in, sorting by displayOrder, UI dropdown list, display in list, show_user, and show events - our types are now better defined, and easily extended in the .yml commit c98b1bf5d42c89dd4576ec6f2405ecd4d7927227 Author: kent Date: Wed Sep 12 22:49:02 2007 +0000 Adding knownToCdsSnp table. commit 80199018de10863097fff94b04d071077f5938fe Author: kate Date: Wed Sep 12 22:45:25 2007 +0000 Minor revisions commit 08cfa41366601c076fd5200959d7a6db112fd36f Author: galt Date: Wed Sep 12 22:43:24 2007 +0000 moving the delete button to the end where it commit 9601096d9a4b6bb01c6d4e5cb1c145affc70f91a Author: galt Date: Wed Sep 12 22:42:57 2007 +0000 straightening out the cancel button from the lockbutton and fixing a spelling error commit 69c23de35de984d451df10bb58f8cfc9d6d0d639 Author: kent Date: Wed Sep 12 22:41:41 2007 +0000 Removing intronSize column. commit cd1387cd5b41ebe5ea8b73c6dc3640b32159c802 Author: galt Date: Wed Sep 12 22:41:39 2007 +0000 fixing dependency definition commit f4541f91229f2d904cc667f799d494fc5b631d6a Author: kent Date: Wed Sep 12 22:40:13 2007 +0000 Simplifying xyzExists routine. commit 4dbcbfb7b8c9cb7557a6fa7d0e97d061e8d5c4d2 Author: fanhsu Date: Wed Sep 12 22:39:49 2007 +0000 Updated synonym.c to show non-coding RNA, per Mark's suggestion. commit ea6a7dd28590d33dbe5ff45a6700525eaf6b45db Author: donnak Date: Wed Sep 12 22:34:47 2007 +0000 Made a few minor edits. commit 18849a125d713cbc82d3be4a9f176e5ce89c9f08 Author: kent Date: Wed Sep 12 21:44:19 2007 +0000 Adding geneCategory and cdsScore columns. commit 1ee7ba1fdff8efb764dc2b78699dbab88a57d899 Author: kate Date: Wed Sep 12 21:01:00 2007 +0000 Minor revisions commit 34487170f36e13d41bb9752ad500f630149f2396 Author: hiram Date: Wed Sep 12 20:55:56 2007 +0000 Last tables of knownGenes/geneSorter/Proteome browsers done commit 0d703241bd7e8b964e060385a5d25e1b4957ced2 Author: kate Date: Wed Sep 12 20:48:02 2007 +0000 Minor revisions commit 7261120e95e866b5ed835f17f17768f96d351be0 Author: hiram Date: Wed Sep 12 20:47:11 2007 +0000 Add hmmPfamToTab and scopCollapse to the build commit 5a5baba22be3abba5651c83bd7c090a1003900c5 Author: kate Date: Wed Sep 12 20:37:37 2007 +0000 Minor revisions commit 50f11f8e6a24f25c94f6ff11f513c963fd305e69 Author: donnak Date: Wed Sep 12 20:31:23 2007 +0000 Made a tiny edit. commit cca00ba94cdf1e12903491ef67335cdd98dc23a4 Author: donnak Date: Wed Sep 12 20:25:12 2007 +0000 Fixed typo. commit 1573dcd384490d743047bec63049a213868285ad Author: donnak Date: Wed Sep 12 20:25:02 2007 +0000 Made a few edits. commit 0263fe3b5544285f416e89375cf90d646e3e0465 Author: donnak Date: Wed Sep 12 20:18:16 2007 +0000 Made a few minor edits. commit c0accd73487c75929eab41c0b154156e647d92e3 Author: donnak Date: Wed Sep 12 19:52:49 2007 +0000 Made a few edits, mostly to the ref formats. commit e36621b8946dd012f37f325306339f3708f545f2 Author: kate Date: Wed Sep 12 19:46:46 2007 +0000 Minor revisions commit 5228bab017fa60b20597d3fafc2c5fcf00c68a10 Author: hiram Date: Wed Sep 12 19:42:03 2007 +0000 Remove the temporary if() statement that was skipping business already done. This procedure has been continued to completion in mm9.txt commit c265c129e1b2177da70198460c82d989b35eb8f1 Author: kate Date: Wed Sep 12 19:41:01 2007 +0000 Minor revisions commit 5afb5de09dac0e1263acd863aa00c6d34dc841c7 Author: hiram Date: Wed Sep 12 19:40:49 2007 +0000 Swap blastz mm9 to rn4 commit b61ffc78cc273a07ee0584cd7ccb3a8739315a5f Author: hiram Date: Wed Sep 12 19:40:30 2007 +0000 Finished danRer5 blastz, and almost done with UCSC genes. Proteome browser and gene sorter now enabled. commit 72fc1f3b225c4a11392141541a33efbf85487c8c Author: hiram Date: Wed Sep 12 19:40:00 2007 +0000 Swap blastz mm9 to danRer5 commit ec69bd7bc2ebe1b215ee30a6aaea13966f691164 Author: donnak Date: Wed Sep 12 19:37:02 2007 +0000 Edited this file. commit 3b74a139596a92c728ee294dcbcb296837d15249 Author: kent Date: Wed Sep 12 19:28:16 2007 +0000 Making a colTemplate file for people making new types of columns. commit a5b0ac025ef351911e38907978d2ce6f4c381314 Author: hiram Date: Wed Sep 12 18:50:15 2007 +0000 kgProtMap table is now kgProtMap2 in KG-III commit 18eac580e177f8254f30a78d487a8b9d023fffce Author: hiram Date: Wed Sep 12 17:38:56 2007 +0000 The URL for pfam references has changed. This should probably be in a .ra file commit d6faac62a5f25095ecc378afa12ade225a1ca8b6 Author: markd Date: Wed Sep 12 17:13:21 2007 +0000 added new image ids commit 51c6e63af992ad1f9a3f8f9ac66bb95fcc874da3 Author: hiram Date: Wed Sep 12 16:49:59 2007 +0000 Add raToTab to the build commit 0455845d10de67dbd992344bff4b2a274c393957 Author: hartera Date: Wed Sep 12 15:54:18 2007 +0000 Added Affy Zebrafish track with consensus sequences used in probe design. commit 45b83e15d7f596fc016e44b027defb542dfbfeec Author: galt Date: Wed Sep 12 15:00:07 2007 +0000 "Encode release log update" commit 84f6a0ba3931834e015ec41420a08605cacdc4d9 Author: galt Date: Wed Sep 12 15:00:06 2007 +0000 "Release log update" commit 898d5e6d415aa346352783a42d02b44a5d26bb9b Author: hartera Date: Wed Sep 12 03:16:27 2007 +0000 Added Indel-based Conservation track for hg18,mm8 and canFam2. commit 72b3115c11bb28df973ab9b4e524b466ffb4e4f1 Author: rhead Date: Wed Sep 12 00:22:15 2007 +0000 Changed some encodeAffyChipHl60* longLabels and shortLabels to reflect the fact that the experiments were done in ME-180 cells, not HL-60 cells. (per Kate, per Philipp Kapranov.) In fact, just copied Kate's previous changes to the labels, which were only done on release alpha entries at the time. commit df6eccffbcd28a462749e624466d7972d2010b56 Author: kate Date: Wed Sep 12 00:04:35 2007 +0000 Update supertrack descriptions and enable supertracks for ENCODE Chromatin track group commit a2d9d575d64a95bdd29ab6d5155b18ce47cde02c Author: markd Date: Tue Sep 11 23:51:47 2007 +0000 adjust height in base/CDS difference overdraw bars when drawing in UTR commit d42901f2787a89e354c8c2e13301a7df2c2c8120 Author: kate Date: Tue Sep 11 23:44:31 2007 +0000 Refine supertrack descriptions and enable supertracks for ENCODE Transcription track group commit 553cddba722d91ddb3d7859cf68efc0e072ea269 Author: kate Date: Tue Sep 11 23:15:23 2007 +0000 Tweak visibility of EGASP track in supertrack commit 1baa8e9a98a37dd05ea068a4053fd21ef501b071 Author: kate Date: Tue Sep 11 23:11:44 2007 +0000 Add Introns track to Gencode supertrack commit 61c07151fabd6a249a8537f8ebfbf1e32bbad562 Author: kate Date: Tue Sep 11 23:05:02 2007 +0000 Update supertrack descriptions and add supertrack entries for ENCODE Genes track group commit 456a097ba93f82fc8cd9bb4ecb5ffd3636facb84 Author: kate Date: Tue Sep 11 22:43:05 2007 +0000 Tweak priorities and visibilities in Gencode supertrack tracks commit e8628e8e40dc3d1273c8ee661639b23d322cdc58 Author: archanat Date: Tue Sep 11 21:27:30 2007 +0000 changed the short label for mm8 nets/chains to '$o_db' commit 7204d41313e79b6d1c127993be8090b227aabfc7 Author: archanat Date: Tue Sep 11 21:02:01 2007 +0000 added blocks for mm9 nets/chains commit bf6e06741e606a9735f3795ec90f3d968847f0cf Author: kate Date: Tue Sep 11 18:45:24 2007 +0000 Add liftOver annotation to Yale Sig track commit 595c78a77469e5de720c2b8a3c5912c777bfdccc Author: kate Date: Tue Sep 11 18:12:34 2007 +0000 Add data version settings to some tracks commit 51f9c2fd72b994e753c2469c364bce41b3856a78 Author: hiram Date: Tue Sep 11 17:34:28 2007 +0000 Add mm9 blastz swap commit 0b8331356ef64b578e69db3af79b96cf864c7670 Author: kent Date: Tue Sep 11 17:09:49 2007 +0000 Removing MYSQLLIBS from makefile. commit 03c7d7c1f1248a7ad37e88d09ae4e76501703bd1 Author: braney Date: Tue Sep 11 15:19:57 2007 +0000 fixed up base usage commit 598c4496b820de091f1c274cc8bceb29765d3bd0 Author: galt Date: Tue Sep 11 15:00:06 2007 +0000 "Encode release log update" commit ea485db4b0f90b05a8bc31e08ba76d84bfc530c5 Author: galt Date: Tue Sep 11 15:00:03 2007 +0000 "Release log update" commit 446c5a46b92fff97de68ca0ac798307d45ab3d4a Author: kent Date: Tue Sep 11 00:24:09 2007 +0000 Getting rid of mapsSelf flag to fix full mode label click behavior. commit 3333b0117eb9909c1b7a50c2851429d3b5c7b54c Author: hiram Date: Tue Sep 11 00:13:05 2007 +0000 Adding mm9 to the visiGene.text commit cde30c97d1a7ca5c36473dc597f593ac249212ab Author: hiram Date: Mon Sep 10 23:49:04 2007 +0000 Initial files for mm9 blast tabs commit 39c66f2be4261727ae6ccb8562da3000dade8e76 Author: kate Date: Mon Sep 10 23:41:31 2007 +0000 Mispelled setting commit 65b7e01fc5f8664ae0ea930e5a639b071cb01206 Author: hiram Date: Mon Sep 10 23:21:40 2007 +0000 Working through the numerous number of tables to get gene sorter knownTo tables done commit d264f35a69a9f55828263cd7c6e183e0501c613c Author: kate Date: Mon Sep 10 23:08:43 2007 +0000 Remove uninformative setting commit e65b5fb1fdff2cc8f0422f8b7e9f49fa98a2735a Author: kate Date: Mon Sep 10 22:53:15 2007 +0000 Prune over-long Affy Chip track short label corrections commit 01d519576b3fc11346fd385ae30e995660ce9b7f Author: donnak Date: Mon Sep 10 22:39:47 2007 +0000 Changed this to a redirect to OH website. Current accessed via Training link on home page. commit 838bdee5b64fbcfb24917257442ef636fec09a52 Author: donnak Date: Mon Sep 10 22:39:20 2007 +0000 Changed training link to local link that currently redirects to OH website. commit 86b57113d8687b1b03db6b9b91a2e0cea61cc820 Author: galt Date: Mon Sep 10 22:34:47 2007 +0000 improve wording of comment and help output commit c8c9b2cd283e2e4ec2e17f1835027dfe2b010f42 Author: kate Date: Mon Sep 10 22:24:56 2007 +0000 Fix liftOver message for track details and UI for subtracks so that it uses subtrack setting rather than always using composite setting commit a5a8ed002383e7716b515828b225b089baf6169a Author: archanat Date: Mon Sep 10 18:37:35 2007 +0000 changed the short label for mm8 net/chain to "$o_db" commit 5cff97ea4dfe4baa5fb9d54bf524cfba94c29b0d Author: archanat Date: Mon Sep 10 18:29:23 2007 +0000 added blocks for chain/net for mm9 commit b7258d26a2a80e9c29df2494784d85ebb6de7286 Author: hiram Date: Mon Sep 10 18:17:57 2007 +0000 Add mm9 swap blastz sequence commit 2b755efdd9328c5151f7c5cea0938aaab60051e8 Author: kate Date: Mon Sep 10 18:04:35 2007 +0000 1. Add supertrack info. 2. Adjust priorities on Affy Strict tracks commit 972684e0521fefcbf9bbc041133a8051daf188eb Author: archanat Date: Mon Sep 10 17:06:16 2007 +0000 changed refs to pubmed format commit ff64847767e3d3b3e83dc28dac1918dccbe36876 Author: galt Date: Mon Sep 10 15:00:07 2007 +0000 "Encode release log update" commit 421558d69705454bf6b91d0ece9981efecfa572c Author: galt Date: Mon Sep 10 15:00:04 2007 +0000 "Release log update" commit 1afe7c5829faacf94eb0848ab1154c212f7c5399 Author: jzhu Date: Mon Sep 10 05:15:12 2007 +0000 update for instinct commit ab703561447d6a98dd67c5fc9ca3605d09b2c555 Author: jzhu Date: Mon Sep 10 05:06:20 2007 +0000 update trackDb.instinct.ra commit e2f4ba7477064950ead33c9b7ec4dfec29cc32ef Author: kate Date: Mon Sep 10 03:54:44 2007 +0000 Add UCSD 2007 Chip-chip data commit 31755921ba27764ddae258b65331bbfc37a75e94 Author: hartera Date: Mon Sep 10 03:23:31 2007 +0000 Documented renaming of the gencodeGeneClass tables for Gencode Genes Oct05 and Mar07 to include the 'encode' prefix. Added some information about Gencode Genes from an e-mail from the track contributor. commit 11b395a95bf6b59cc43ffaeea80334bcb0b80c53 Author: hartera Date: Mon Sep 10 03:18:12 2007 +0000 Updated the itemClassTbl for Gencode Genes Oct05 and Mar07. The table name was changed to add the 'encode' prefix. commit 480bccc855a396cb692be3aca7413149eb97ef81 Author: jzhu Date: Sun Sep 9 21:42:39 2007 +0000 add functionality to use cart variable to pass sample reordering information. the corresponding cart variable is hghOrder_tableName, in which tableName is the name field in struct genoHeatmap. commit e398e7fcc0c652f983e3fcd44950dbeb2d2dca59 Author: jzhu Date: Sun Sep 9 20:02:26 2007 +0000 add data fields in struct genoHeatmap to provide functionalities for re-ordering of samples in display, these data fields are: struct slName *sampleList; /* List of names of samples, sampleList position matches sampleOrder hash */ struct hash *sampleOrder; /* Hash of orders for samples, key is the sampleId, value is the order position */ int *expIdOrder; /* ordering of expIds for display of bed15 format */ the default ordering is defined from track setting by the "order" variable. "order" variable is optional. commit f2aee2788fe07543bc215d53c18879d55b702413 Author: jzhu Date: Sun Sep 9 19:53:34 2007 +0000 add variable "order" : ordering of the samples in heatmap display commit 92e9fd8a579ae8debf2f3d7f6a1e9706c6595d62 Author: galt Date: Sun Sep 9 15:00:06 2007 +0000 "Encode release log update" commit d43fc394974302aa41efef53fa4137395267faa2 Author: galt Date: Sun Sep 9 15:00:04 2007 +0000 "Release log update" commit 872e9fa6ac14d35102b43c5fba67e280948f2b0a Author: galt Date: Sat Sep 8 15:00:15 2007 +0000 "Encode release log update" commit 8898b55fdd120bbef0291807c2016bc81767a231 Author: galt Date: Sat Sep 8 15:00:14 2007 +0000 "Release log update" commit 83b6191c268a657116c0741920bbbbb941fccfa4 Author: kuhn Date: Sat Sep 8 01:12:00 2007 +0000 removing link t hg18 accidnetly pushed commit 0d44ad726c8c3a5310138f5d9e0b8de9e21da1c2 Author: kayla Date: Sat Sep 8 00:06:44 2007 +0000 gave rhesus its on chain/net mm9 blocks commit 17f0c664162273f9bf58856e9b5827f07ea1417f Author: hiram Date: Sat Sep 8 00:03:36 2007 +0000 Got to the point of creating xref tables for the geneSorter commit 8b24fcc2b971f8be4b69dd4361639a11dfc99b14 Author: hiram Date: Sat Sep 8 00:03:05 2007 +0000 Add a blat server commit f8727aa3e98e785226b12183704b09b8487ecc1b Author: hiram Date: Fri Sep 7 23:29:57 2007 +0000 Done with Stickleback, Marmoset, Fugu, Tetraodon blastz alignments commit 527273f3f6f47ee7c1986d4836dfbefd38e69ced Author: hiram Date: Fri Sep 7 22:39:47 2007 +0000 Add the txGene directory to the build commit 4ecb45977e8718a4b3a45b6df5945eabfe56e5f3 Author: hiram Date: Fri Sep 7 21:43:05 2007 +0000 Add a makefile to create everything in the sub directories here commit 0dd66d7efbb6ef8d5336c89a78517ebadd15b4dd Author: hiram Date: Fri Sep 7 19:12:18 2007 +0000 Working through this on mm9. commit 7b47558f3cd79bb1a38dd93d184f4af267666fd5 Author: hiram Date: Fri Sep 7 18:43:36 2007 +0000 Now have a 4-way conservation and exoniphy, so can now see if the UCSC gene build will proceed further commit c2efaee8cb4e4a522bdac2170d95b49b52563875 Author: hiram Date: Fri Sep 7 18:27:06 2007 +0000 For the Mm9 4-way alignment commit 49174a73ad5ca2f7bf2814030760f395cbe568b9 Author: kent Date: Fri Sep 7 18:17:35 2007 +0000 Adding cgiSpoof line for cgi's. commit 0a8ccf726fadcbac148d4b5eddde5af3d14ba3a1 Author: hartera Date: Fri Sep 7 18:04:24 2007 +0000 Finished RepeatMasking, added quality scores, Genscan track, Blastz/chain/net for hg18, Blastz chain/net ci2, human proteins track. Tracks added by and doc checked in on behalf of Kord Kober. commit 4d2bac91126ad054286f721cc9d87b6d59be52df Author: fanhsu Date: Fri Sep 7 17:36:29 2007 +0000 Added ispyTables. commit 08e2e6746634fa72a19f33eb777cd6e424cce635 Author: fanhsu Date: Fri Sep 7 17:35:20 2007 +0000 Added to support ISPY tables. commit c554bf1edbe739d37152ca269d716c7aadc6e06f Author: hiram Date: Fri Sep 7 17:35:19 2007 +0000 Change nfsNoodge wait time to 20 seconds from 10 commit ae86868db9c2b1a620bf8b467aab4ea2a444c77f Author: fanhsu Date: Fri Sep 7 17:34:57 2007 +0000 Moved to ../inc. commit 2f2e6aa3a35757996dd3e491789daf52e87d4271 Author: fanhsu Date: Fri Sep 7 17:32:35 2007 +0000 Created to support ISPY tables. commit 4b78c968f0b6acc63b726581411197e171656b5f Author: fanhsu Date: Fri Sep 7 17:30:01 2007 +0000 Added "-withNull" option to generate .sql, .h, and .c files to support processing of "missing value" (NULL in SQL) situations. commit 381fefdafeb5a5e3079144db6d92421596c8d095 Author: galt Date: Fri Sep 7 15:00:07 2007 +0000 "Encode release log update" commit 8c7ca2b003d9a1fcbc92f3406130ce2f3aa6f557 Author: galt Date: Fri Sep 7 15:00:03 2007 +0000 "Release log update" commit dc4db8dacb3880dd9937301b996b58f976073f5e Author: rhead Date: Thu Sep 6 23:10:07 2007 +0000 Removed an extra space in sanger ChIP-chip longLabel. commit 724c622a2c19f66ba5155407b2624adc1c14373e Author: donnak Date: Thu Sep 6 22:19:51 2007 +0000 Removed Heather, Yontao, Phoenix. commit a24a05b5732fe8a8d43d9c02388bc2b27a06c0bd Author: kayla Date: Thu Sep 6 22:04:19 2007 +0000 gave mm9 nets/chains it's own blocks at this level commit 5e1175f42f1c89abacf2870652030bf3cff8b889 Author: ann Date: Thu Sep 6 18:33:59 2007 +0000 Fixed URL and citation. commit e200c491ab228d9bb62293399cc03804ba67d3ae Author: galt Date: Thu Sep 6 15:00:05 2007 +0000 "Encode release log update" commit 3babc1bbd442038334a947c4890bd16554aba305 Author: galt Date: Thu Sep 6 15:00:03 2007 +0000 "Release log update" commit 7ee24e91e784235ebff1e787509fcbd28ea7aecd Author: markd Date: Wed Sep 5 23:33:39 2007 +0000 fixed bug just introduced involving setting cds start/end status in genepreds commit 67ef43256598b7d7e5273aad1816c5d95880a146 Author: kent Date: Wed Sep 5 23:03:23 2007 +0000 Restoring forgotten check in. commit b45494507e7eedcd392a0caf5b77deb9a90316eb Author: kent Date: Wed Sep 5 23:03:22 2007 +0000 Moved axtOutPretty to library. commit 70a1209921122886d43e2d98c34f491f25db8249 Author: kent Date: Wed Sep 5 22:59:47 2007 +0000 Seems to work. commit 2d07ab368dc007f21db006499737b7a90d6ced74 Author: galt Date: Wed Sep 5 22:57:55 2007 +0000 adding -fine as a requirement commit 5102fae5f3a30bae3cade385e8f5da2e57f7b0ef Author: kent Date: Wed Sep 5 22:36:10 2007 +0000 Added session id in hidden variable and new line for some browsers. commit 94d2a1ecd9891b174a4c494b1668134b16fc3fbe Author: kent Date: Wed Sep 5 22:35:49 2007 +0000 Seems to work. commit 0b12bb740d36bd7ef5db07920b0d7ddcac29147a Author: hiram Date: Wed Sep 5 22:15:42 2007 +0000 Finished with simple repeats. Now have fully masked sequence. commit 5b3cb2adc375c17372442478cb8527dcc29489b8 Author: kent Date: Wed Sep 5 22:06:18 2007 +0000 Seems to work as a basic demo. commit a3f1d60bab99b6e0c4dd02b309c669042d3e62fa Author: kate Date: Wed Sep 5 19:35:04 2007 +0000 Fix problem with track/group reordering when difference from default < 1 commit 6a92a402ac9557a6a2de734968ea88d9662dbbde Author: rhead Date: Wed Sep 5 19:28:12 2007 +0000 Replaced broken link to Nikolaus Rajewsky lab. commit ab7791d9a27fe355cf41756f35799e1b7f03a0c7 Author: kayla Date: Wed Sep 5 19:03:13 2007 +0000 changed $o_Organism back to mm9 at root level. I noticed a comment in the pushQ that says the top level should stay as mm9, since it needs to be mm9 on other assemblies. commit 93a06cc7daa19322b1a829c447ba48e80c468ede Author: hiram Date: Wed Sep 5 18:57:34 2007 +0000 Rework the fishClone track commit d4837a30a322f2260a5b83e9411f048c8fece2eb Author: kayla Date: Wed Sep 5 18:54:27 2007 +0000 Edited priority so the nets and chains will be in the correct order commit 7ec4aab445490c779e75b0b55af219a2db894705 Author: fanhsu Date: Wed Sep 5 18:47:13 2007 +0000 Skip NR_xxxx as representative mRNA. commit b370a325af990fe2ef7f0f106b75e962de1832a4 Author: rhead Date: Wed Sep 5 18:21:41 2007 +0000 More wording changes on the BLAT maximum sensitivity section. The -minScore change was suggested by Galt. commit 5fbf4e61e0f5ab8d2e94b10094731ac24badfaf1 Author: kayla Date: Wed Sep 5 18:20:44 2007 +0000 changed mm9 to $o_Organism commit 8ede3b001cae53ffe6a672feb66caa16ad581bfa Author: kate Date: Wed Sep 5 18:05:28 2007 +0000 Fix Blat track to work with cleaned-up track reordering (and restore fallback code to accomodate non-standard track creation) commit 9117bb3a4cec056eb5c2be7ac16f0e9d741112f5 Author: ann Date: Wed Sep 5 17:41:26 2007 +0000 loosened refSeqId rule for mm8 (it's drifting) commit f4ac616b41525702a91019e295cd523ed6612f55 Author: hiram Date: Wed Sep 5 17:31:57 2007 +0000 Try something different in nfsNoodge() commit f84c5ea8ce007485ad0579955e8f052364dbc798 Author: hiram Date: Wed Sep 5 16:38:05 2007 +0000 must set a variable to NULL at time of declaration to avoid an error exit during compile on gcc v4 commit ccc846a21d3aedbbe87dfcf65ee719ab4e831489 Author: galt Date: Wed Sep 5 15:00:13 2007 +0000 "Encode release log update" commit 10ff8940bab8d8eb08142e99bedf3ed4dcd4e57a Author: galt Date: Wed Sep 5 15:00:09 2007 +0000 "Release log update" commit 2b18c39303757b91dd5c7e0eb95d9505c10fb378 Author: jzhu Date: Wed Sep 5 08:15:24 2007 +0000 *** empty log message *** commit 91e4ca0b76105b2f25e7f68f0c2d38c05cfdca43 Author: markd Date: Wed Sep 5 05:02:50 2007 +0000 added notes for building tests for tandem dup handling commit 91992a805526ed1fb33d5afa9be36fdd5d13a37d Author: markd Date: Wed Sep 5 04:30:58 2007 +0000 added support for PSL track coloring for entries that are not in the genbank tables commit 398e933069bc4d2184d21904027f2b9ba1653dce Author: markd Date: Wed Sep 5 04:27:35 2007 +0000 improved error message commit 188c2b4dca700eb8a377b42295b259435c13499b Author: angie Date: Tue Sep 4 23:41:32 2007 +0000 Another clarification from Danielle Thierry-Mieg. commit f428b292991c2ebe9f28a1b107f233f60deafa8f Author: kate Date: Tue Sep 4 23:28:07 2007 +0000 Allow free-format for 'origAssembly' setting (used by hgc and hgTrackUi), used to generate the 'Data coordinates converted via liftOver from...' message commit fc4fe9ff5c5681da4ffe97e099c7fc079a62ef64 Author: rhead Date: Tue Sep 4 22:32:41 2007 +0000 Changed links for public mailing lists so that they either gave a warning about the fact that they are public or so they redirected to our 'contact us' page, in an effort to keep people from being shocked that the questions they ask are made public. commit c1a4d9ad8bd63948926c3759f9b8264c8e8e17f6 Author: ann Date: Tue Sep 4 22:02:50 2007 +0000 loosened up refSeqId rule for hg17. it is drifting, as they tend to do. commit 3a5ebe398fcc37866df283c57e34487e7605f655 Author: kate Date: Tue Sep 4 20:38:36 2007 +0000 Fix problems with custom tracks with track reordering on. Also, base position track with custom tracks commit e7385465df472b842e717cb36ad1ae35d1aec944 Author: angie Date: Tue Sep 4 20:21:42 2007 +0000 Make the removal of ctfile_ cart var's that point to nonexistent files optional, so that if there are any new expirations, we can investigate and then manually run -hardcore to clean up. commit a780e1166e912a96d8a3a780cb61d3005a9ef622 Author: hiram Date: Tue Sep 4 20:18:26 2007 +0000 Temporary rn4 alignment chain and net test commit 5241eb42a9e780627352db521fdb8d2973d93568 Author: hiram Date: Tue Sep 4 20:16:34 2007 +0000 Temporary doc pages for an Rn4 chain and net alignment test commit 47425365c6b6e50553a11a9a090bf0f8a7e54e0d Author: rhead Date: Tue Sep 4 19:30:42 2007 +0000 Changed links for public mailing lists so that they either gave a warning about the fact that they are public or so they redirected to our 'contact us' page, in an effort to keep people from being shocked that the questions they ask are made public. commit 1cbca4d3fc1b7f8ae21b40ed9c99d91f766958c0 Author: angie Date: Tue Sep 4 17:53:37 2007 +0000 Instead of separate drop table command, do a 'drop table if exists' in the same script that creates the table. Saw some errors that indicated that the commands weren't executed in sequence as intended. commit fded45bbc9b245283798fbadebc9edcbc4c4968a Author: kent Date: Tue Sep 4 17:43:38 2007 +0000 Adding identifiers for affyHumanExon track. commit fce4219bf8039666f002c4a891b3d1a78d23cdbc Author: ann Date: Tue Sep 4 16:49:53 2007 +0000 added rat to list of databases that have a Gene Sorter commit 262faf63c607bb2077cde46a94447c6202139a72 Author: galt Date: Tue Sep 4 15:00:05 2007 +0000 "Encode release log update" commit df83e23cd49caace042674e6848c4657ac6616d0 Author: galt Date: Tue Sep 4 15:00:03 2007 +0000 "Release log update" commit d6526e937acd87a35b6bb6d27183c12537728bd4 Author: kuhn Date: Tue Sep 4 03:09:35 2007 +0000 added hyphen commit e91d4aa3715761e63f3098a5516c5a2c7b9a8f40 Author: hartera Date: Mon Sep 3 19:32:11 2007 +0000 Remove colur by codon drop down for Ensembl NonCoding genes track. commit e166aa8357e4de75d5b65c08926e0555ad5fe773 Author: kent Date: Mon Sep 3 15:33:18 2007 +0000 Revising a little to correspond with changes in atgTable. commit 6a4c01bbeb3931301d47778e3c80f3323e74d032 Author: kent Date: Mon Sep 3 15:32:40 2007 +0000 Shortening label of oldKnownGenes. commit fc8aa993407581216891d86c2bb41ce532391360 Author: kent Date: Mon Sep 3 15:31:48 2007 +0000 Testing sibTxGraph. commit 098888c97f5c92aaf1943c3a5254c39186e63695 Author: galt Date: Mon Sep 3 15:00:07 2007 +0000 "Encode release log update" commit 544a1f7c24f6ae6ce7ce20fe8e03706b5d9c555d Author: galt Date: Mon Sep 3 15:00:03 2007 +0000 "Release log update" commit 04557f092d3caeaa676549f55b6b9ab56e8fa164 Author: jzhu Date: Sun Sep 2 18:51:49 2007 +0000 *** empty log message *** commit 46ef986c46bae221911f8412945be82c2856c374 Author: galt Date: Sun Sep 2 15:00:06 2007 +0000 "Encode release log update" commit fd354d2b6c2b3cf3f2fa767ae32cca5ed8ac8194 Author: galt Date: Sun Sep 2 15:00:05 2007 +0000 "Release log update" commit 9ba7ab00dac92eed3b94c0f7ec7258dd5cfef0d3 Author: galt Date: Sat Sep 1 15:00:06 2007 +0000 "Encode release log update" commit 8e3a01ccbdb7ff801bb2820ffd49a4f213a696dc Author: galt Date: Sat Sep 1 15:00:04 2007 +0000 "Release log update" commit 37bbefa3183351ea0ca88a173159f0c6c7857a16 Author: markd Date: Sat Sep 1 02:37:14 2007 +0000 exclude haplotype chroms unless explictly requested commit c18b926098f2bc886684eef299ebb821be4bdb92 Author: ann Date: Fri Aug 31 23:10:22 2007 +0000 added functionality to provide (in addition to the shortLabel) the group name. commit 9e537cfeefcc5d75dd18a7d826168473db85aeaf Author: angie Date: Fri Aug 31 22:44:57 2007 +0000 If a ctfile_hg18 cart variable refers to a custom track that doesn't exist, remove the cart variable so it doesn't get propagated from session to session. commit c07223e73eb4a98905a748ae550afca2515e59c8 Author: angie Date: Fri Aug 31 22:42:58 2007 +0000 If a saved session has a ctfile_hg18 setting for a custom track file that does not exist, remove the setting from the session so it doesn't get propagated and so that new session-CT disappearances are easier to identify. commit edc3fa1408934573e07d214e62f0aacb25882c45 Author: hiram Date: Fri Aug 31 22:40:17 2007 +0000 Running a third run of Rn4 alignments. And need to get an exoniphy track for the ucscGenes10 business. commit ca4f345bd42da920e6dae92fc94204a794bbba42 Author: hiram Date: Fri Aug 31 22:14:22 2007 +0000 Actually, oryLat1 is HoxD55 matrix ... commit 17dd010764a9e2f4a803aec89edc95b0d602f2ac Author: angie Date: Fri Aug 31 21:37:30 2007 +0000 Added 'autoTranslate 0' setting to acembly, so acemblyPep is used and hgc doesn't offer protein links for the noncoding genes. commit 01966cc996e27a0ad6266e2059ebc3281ce908cd Author: hiram Date: Fri Aug 31 21:24:58 2007 +0000 Special chain parameters for oryLat1 chained alignments commit 07235ed13ea9101e2ad497268c3d130c16ff13b2 Author: hiram Date: Fri Aug 31 21:18:17 2007 +0000 for Mm9, axtChain minScore is 5,000 not 2,000 commit 89c6ec37f4feaac5abdec994a81751f0dd3cdfe0 Author: hiram Date: Fri Aug 31 20:46:19 2007 +0000 Add bedOrBlocks txCds txGraph directories to the build commit 3ce8728ae4b83f932d021c9ddc647517894a1632 Author: hiram Date: Fri Aug 31 20:45:47 2007 +0000 Add bedWeedOverlapping to the build commit 458b56a3b56cc6d45884917eba31eeaa2c13601f Author: hiram Date: Fri Aug 31 19:24:59 2007 +0000 Add clusterPsl to the build commit d9d9581dce4ff767caae415a54372be562600573 Author: hiram Date: Fri Aug 31 19:23:27 2007 +0000 Fixup build of lower level directories commit c0f1c35d65967c0b32659c95b48614c934516890 Author: kate Date: Fri Aug 31 19:16:33 2007 +0000 Temp fix for custom tracks crashing reorder feature -- assure no null default fields in track struct commit 444a5fc0696a4e6692e82f89dfccc82aec1e16e5 Author: markd Date: Fri Aug 31 19:00:45 2007 +0000 switch to using actual genbank root commit f0ff95c1245087c0ab711a0bbb247832eac918dd Author: kuhn Date: Fri Aug 31 18:57:31 2007 +0000 made outlinks spawn new browsers commit 5872bef9af7d0fdc5aa66be7bf3951a846d4f7e0 Author: kayla Date: Fri Aug 31 18:54:24 2007 +0000 edited references section commit ae3164c30f3574ecbcf546dd09298ec24a6d8f59 Author: kayla Date: Fri Aug 31 18:52:40 2007 +0000 edited references section commit b9511fb2bc5a7a2f9cf9043779668d381dca447d Author: hiram Date: Fri Aug 31 18:34:13 2007 +0000 Working through repeat masker and starting simple repeats commit a23e25d416c797d14d848fba38faba9eff97764a Author: hiram Date: Fri Aug 31 18:33:17 2007 +0000 Done with self blastz and Medaka oryLat1 commit bca672edeb3b89f31184b6ac09c4982a3f8fb8ab Author: galt Date: Fri Aug 31 15:00:06 2007 +0000 "Encode release log update" commit 1199fff1c7b368578c946dc9a3f7ab550f54312a Author: galt Date: Fri Aug 31 15:00:04 2007 +0000 "Release log update" commit 84df48bef0f84e90588dafb6b027d899760bdf9d Author: kent Date: Fri Aug 31 11:59:31 2007 +0000 THrowing an altGraphXVertPosSort in front of the altGraphXEnlargeExons, since this routine does expect the sorting to happen, and the SIB ones are not necessarily sorted. commit cc77fd65e99b94156235816dedd6014675c7deb4 Author: kent Date: Fri Aug 31 11:58:42 2007 +0000 Changing altGraphXEnlargeExons to make it so that largest intron and largest exon are the same size, which seems to produce visually pleasing results over a larger variety of genes than the older scaling factor. commit f4b637af29bb130389863d76a905c2ab98bbd421 Author: angie Date: Fri Aug 31 04:23:49 2007 +0000 Fixed suffix-grabbing regex. commit 1a8663eab016f069acad0f6e82a758087445ea7c Author: angie Date: Fri Aug 31 04:17:25 2007 +0000 More descriptive urlLabel for acembly. commit 46227a6c9a1a22e18c64c209d7eb81cfc7e465bd Author: angie Date: Fri Aug 31 04:01:33 2007 +0000 More descriptive urlLabel for acembly. commit 76a7fd4c36796ca8ac17fb36c8d29068a89cfb58 Author: angie Date: Fri Aug 31 04:00:53 2007 +0000 Update from Danielle Thierry-Mieg so that the text applies to both human and mouse. commit 8dd19a808e5f6a46cb62c10e563b962dd2744ed0 Author: hiram Date: Fri Aug 31 00:21:52 2007 +0000 Finishing up selfBlastz, re-running rn4, started oryLat1 commit 3dca7ddbd73635925024c2697b5d968382cab232 Author: kate Date: Fri Aug 31 00:06:46 2007 +0000 Copy html for lift commit f00c9f0c12b0ff757d13ed5491e46cb4dda18cc1 Author: kate Date: Fri Aug 31 00:03:50 2007 +0000 Fix pri on Davis Chip Hits commit 97775c38203b0dddcf966cdfbb51e7b49cb2e2c5 Author: kate Date: Fri Aug 31 00:02:32 2007 +0000 Fix priority on UC Davis Chip hits commit f3c972225083999a5801d836c487b677ee3a3836 Author: kate Date: Thu Aug 30 23:47:16 2007 +0000 Shrink overly long Sanger Chip long label commit 53a8ba665c965b51b3dd87aca4d94763eb6202d9 Author: kate Date: Thu Aug 30 23:44:16 2007 +0000 Add data version and correct lift info for GIS PET track commit bc57364e56f300c06dd8c694deee276531b6b65d Author: kate Date: Thu Aug 30 23:30:22 2007 +0000 Tweak priority of Affy track commit 71371ae270757a21d2370c6a90fdff1d2e873522 Author: tingwang Date: Thu Aug 30 22:39:09 2007 +0000 new super track description for encodeUtexChipSuper commit 705822f27f3963d567f757a25c84c0408daa7e47 Author: tingwang Date: Thu Aug 30 21:08:16 2007 +0000 added notes for building new GIS tracks commit 843ebe3c09b1a27f341e80627129d4c0c1991908 Author: tingwang Date: Thu Aug 30 21:03:49 2007 +0000 add new subtrack info for GIS CHIP-PET on hES3 commit c07371d4a14757c48762f70c05783df136f54dd1 Author: tingwang Date: Thu Aug 30 21:02:21 2007 +0000 modified description for new hES3 data commit a784b96983ca35a7eb4f3118da029fd9f7722d5e Author: tingwang Date: Thu Aug 30 21:00:37 2007 +0000 add new subtrack info for GIS RNA-PET on hES3 commit 1d34b444be38257240a2d2367eba04a730392fad Author: donnak Date: Thu Aug 30 20:59:10 2007 +0000 Made a first editing pass at this file. commit dbb13eaa465917ac3942affa8e2bac8e040eca96 Author: angie Date: Thu Aug 30 20:43:46 2007 +0000 Restoring older acembly description for older assemblies. commit 7d1bd8d1fed027ed20613dd2d0e59c36de71680b Author: angie Date: Thu Aug 30 19:20:50 2007 +0000 Finally added doc for baseColor* and indel* settings (thanks MarkD for the prod). commit a88a9678d1edf063899897b6a2c3143ceecaec7c Author: donnak Date: Thu Aug 30 19:20:44 2007 +0000 One more change to Katzman links. commit 001378c6501d2bf46eb2241615331c313b23e496 Author: donnak Date: Thu Aug 30 19:05:40 2007 +0000 Did a few more link mods to Sol's entry. commit b37fdcdf2686874c9e93acf89f938776b5407b63 Author: kuhn Date: Thu Aug 30 18:53:50 2007 +0000 made outlinks sawn new browsers commit 73f5713f57456b6f03f77ceaa273627fa3c81205 Author: kate Date: Thu Aug 30 18:19:05 2007 +0000 Fix priority of UCSD Chip supertrack commit fded60fb09eb5f6b67f8e79e43f704d1875f5370 Author: angie Date: Thu Aug 30 17:55:35 2007 +0000 Loaded acembly. commit 7af89dd905c5c015c415d515c6c5b9f7660d2734 Author: angie Date: Thu Aug 30 17:53:28 2007 +0000 Loaded acembly (replacing prior liftOver from hg17). commit 51b5c3fec6eed5282dee7665d6c4913c587ab153 Author: angie Date: Thu Aug 30 17:45:00 2007 +0000 Rewritten by Danielle Thierry-Mieg. commit c8848a753d11c32c60e8c34eb56286bb8f9b170d Author: fanhsu Date: Thu Aug 30 17:43:47 2007 +0000 Re-built Gene Bounds track. Identical process. commit 54345d34c7e45f88df6d818d233e21709dc39e87 Author: rhead Date: Thu Aug 30 17:32:45 2007 +0000 Changed wording. commit 525b747221363391febae73535a0b29093d27bca Author: donnak Date: Thu Aug 30 16:25:47 2007 +0000 Added 2 articles by C-H Yeang. commit 27995cf000f67458f94e99c4231d475edde16760 Author: donnak Date: Thu Aug 30 15:47:40 2007 +0000 More editing to article submitted by Galt & Brooke. commit f76ea8b0c31fb3943fb73d8d5a271b68609cfb0b Author: galt Date: Thu Aug 30 15:00:06 2007 +0000 "Encode release log update" commit ec782b57747cd9fe45aa4a3bc8217df91bef6e1a Author: galt Date: Thu Aug 30 15:00:05 2007 +0000 "Release log update" commit e964c6c6f197a2aea00b0d479a144fe113a45275 Author: tingwang Date: Thu Aug 30 06:42:08 2007 +0000 add one line to include trackDb.instinct.ra commit e372e0b78ca2986169b6c315d2b2409d140c455f Author: tingwang Date: Thu Aug 30 06:41:33 2007 +0000 new .ra file for INSTINCT project commit 1a66462203dbbc2f520b61ccef246fcfdcdcb04f Author: donnak Date: Thu Aug 30 06:35:05 2007 +0000 Edited FAQ item created by Galt & Brooke. commit 7847cf20a6e525bf8b62585574ff012544b5fb09 Author: angie Date: Thu Aug 30 05:45:46 2007 +0000 Fixed strand values for genomicSuperDups. commit f410323a4656cdbfb09035abc2737c6308d3606d Author: kuhn Date: Thu Aug 30 02:50:59 2007 +0000 added utility to keep an IP alive if someone is running a class and we can expect a lot of hits. commit 7b2667164a4d2afbbc036d5b0205672dfe333973 Author: kuhn Date: Thu Aug 30 02:49:17 2007 +0000 tweak to usge statement commit f2439b1dcfd06789deb3dd6769e4b4ed4179a53f Author: kent Date: Thu Aug 30 00:55:56 2007 +0000 Adding cgi option. commit 8261538a3d5e6691fc7a8c3a595f2b482573ab0f Author: galt Date: Thu Aug 30 00:34:26 2007 +0000 using Blat for short sequences with maximum sensitivity commit e0f5837c6af512cd213720c7da0b047604619af8 Author: hiram Date: Wed Aug 29 23:46:21 2007 +0000 Add gc5Base download files commit ae0ad31a94c18fb5b753a7d5c9db0c1e45659d2a Author: hiram Date: Wed Aug 29 23:46:01 2007 +0000 Create gc5Base download files commit acc6fb50905becd11e57290207d31835df09a4ac Author: ann Date: Wed Aug 29 23:28:59 2007 +0000 readme file for liftOver utilities on hgdownload server commit 12bb50080a88d75fb6c3ab30c7b3050234411f44 Author: kent Date: Wed Aug 29 23:28:34 2007 +0000 Moving SIB Alt Splicing from top level to human/mouse level to accommodate URL links to SIB. Changing color of SIB genes to orange. commit ac550c4d4930391e3b523448189719bd0310d2ee Author: kate Date: Wed Aug 29 23:15:44 2007 +0000 1. Cleanup on hideTracks 2. Fix supertrack group change from config page commit fc8e013abe47af24b1e67ce64941db43177a569d Author: hartera Date: Wed Aug 29 23:12:37 2007 +0000 Added line so that genbank tables are not split by chromosome. commit 901d75ba532d75b85414e08ee2cb2b388f8b3036 Author: ann Date: Wed Aug 29 23:06:19 2007 +0000 fixed up citations commit dffba678ac4671870fe884a6963ff69cb62a1006 Author: kent Date: Wed Aug 29 20:49:06 2007 +0000 Adding SIB Transcriptome. commit ce3eb83a3ec7f12bb47bd7057aca7dd064b15a9f Author: kent Date: Wed Aug 29 20:48:34 2007 +0000 Finishing up SIB Transcriptome. commit 774a1f3269b4d649e09a08e74ebdf87152a732df Author: kuhn Date: Wed Aug 29 20:25:51 2007 +0000 added terse mode commit 7c8667a8fe4b44375c26f941bdcc3c33bf513f96 Author: angie Date: Wed Aug 29 19:37:53 2007 +0000 Append "Group" to anchor name for each track group. The map group anchor was clashing with the main image map (both named "map"). Caused a tidy warning, but no apparent malfunction. commit e53fed1a9e535747572db73e4feca080485667bb Author: kent Date: Wed Aug 29 19:15:22 2007 +0000 Making altGraphX tolerate edges with no evidence a few more places. commit ceae58d45d389c8f6657e56dadd07650780cf269 Author: angie Date: Wed Aug 29 19:07:27 2007 +0000 Fix to doTrackMap: account for height of nextItemCompatible tracks in full mode. Before fix, mapboxes for non-mapsSelf tracks below full tracks were put in the wrong places. commit cdfcff48d4de9ad81235f10a3d7713dac62de988 Author: kent Date: Wed Aug 29 19:00:18 2007 +0000 Making altGraphXLoad tolerate edges with no evidence. commit 9091664074c3cb73b98da01478c0f18e589af11d Author: ann Date: Wed Aug 29 18:18:17 2007 +0000 added getTrackName.csh script commit d8d3ab281b8aaff804d58a5ee4594747ade6fe29 Author: ann Date: Wed Aug 29 18:17:18 2007 +0000 returns Short Label of track given a table name commit f711d5b226c61cce7446e0a3a0b8f2e3b0838074 Author: ann Date: Wed Aug 29 17:43:14 2007 +0000 removed Heather from list of users to email. commit 909c093ddddfb648fff1fbd64156bec6187406b3 Author: galt Date: Wed Aug 29 15:00:05 2007 +0000 "Encode release log update" commit 596c0d0ab6512a0736b4c71a10b1bdac615d3a88 Author: galt Date: Wed Aug 29 15:00:04 2007 +0000 "Release log update" commit bf347cd8ac9da8d67d9078ac4eb40bf43adea51f Author: markd Date: Wed Aug 29 06:28:08 2007 +0000 dont include word "warning", as some script checks for it commit dff12bfc658ac5037f34f7805f4b22d8d2b6bb1e Author: hartera Date: Wed Aug 29 06:11:42 2007 +0000 Added danRer5. commit bc0b7949cfeb2be2001a37edbf1ce2b810e66a3b Author: markd Date: Wed Aug 29 04:28:24 2007 +0000 removed hack put in to work around my stupid bug commit b9d2a9d92f4b3c04a8b332ff4df39ef34bd13962 Author: markd Date: Wed Aug 29 04:26:30 2007 +0000 check if databases does not exist for use on hgwbeta commit 5a58cfbf5514f8a9f8744f561648cf8e0f4ec6a5 Author: rhead Date: Wed Aug 29 00:30:37 2007 +0000 Added a note about affyRatio so that it will be able to have tableDescriptions built properly in the future. commit 8daa5f02288587f073f7e276de1dbd539b6a410f Author: kate Date: Tue Aug 28 23:53:07 2007 +0000 More fixes to track reordering with supertracks. Looks pretty good now commit 4c58b69cd29cd13a37065a233a913da125e2b2e3 Author: galt Date: Tue Aug 28 21:25:25 2007 +0000 adding column user.pi and updated_at to list-ing commit e56c29345a26b3181e12612d4acd3c930a2889f0 Author: galt Date: Tue Aug 28 21:24:53 2007 +0000 adding a comment commit bae275c30202cfcc6000ff717ee7d85b3195d0af Author: mhoechsm Date: Tue Aug 28 21:18:33 2007 +0000 added coloring for alternative start codons GTG and TTG. This is only active when LOWELAB is set. commit 5a4fe3c778f6644d9f5be88f2f6a32a504476e22 Author: angie Date: Tue Aug 28 20:39:56 2007 +0000 Moved acembly from top-level down to human and mouse so that url's are correct. commit 1e6c1fac75e8f935e104fa214d7b4cb08cb2bbf6 Author: angie Date: Tue Aug 28 19:59:37 2007 +0000 Corrected type of wssdCoverage track. commit e640289e07987e03e3f0b753e8cc03e02eb87500 Author: angie Date: Tue Aug 28 18:04:38 2007 +0000 Updated acemblyName for new data in hg18,mm9. commit 8cc06078ead671477757ca39007165973dbd2f8f Author: galt Date: Tue Aug 28 17:22:51 2007 +0000 changes to accomodate non-tcsh users commit 07e4de703ccf3a29bea28267c6c688ae592a1ee2 Author: galt Date: Tue Aug 28 17:19:26 2007 +0000 message cleanup commit fe4ae6e0b199d9a60905f17f7a36219e03b83d59 Author: galt Date: Tue Aug 28 15:00:07 2007 +0000 "Encode release log update" commit 93731498851c74bc8da12aa537acd6bbfd9c19b4 Author: galt Date: Tue Aug 28 15:00:03 2007 +0000 "Release log update" commit 9332e11b7daaa4022685e0cc43c2458a5ed1aced Author: galt Date: Tue Aug 28 05:08:30 2007 +0000 adding note that data moved from panasas to sanvol1 commit 9babeecfbe6f7afa567f7f8772965f626548a675 Author: hartera Date: Tue Aug 28 04:54:55 2007 +0000 Removing hg13 from DBS list as it breaks on hgwbeta with make strict as no hg13 db there. Adding a HGWDEV_DBS variable. commit 58b1a9848160ef6ec9b8781ab1676cc32753fafa Author: hartera Date: Tue Aug 28 03:29:17 2007 +0000 "New version number v166" commit 0ddabe7600b0374dba895595cd75fe15c41af901 Author: kate Date: Tue Aug 28 01:29:36 2007 +0000 Improvements to track reordering with supertracks commit 65b01c23053d1c577efc84444048dc62c877bf00 Author: galt Date: Tue Aug 28 00:21:43 2007 +0000 changing static public/index.html to welcome/index.rhtml and now routing to it commit 900573ce0f6321855197f722e9489ab69a82d379 Author: galt Date: Mon Aug 27 23:53:21 2007 +0000 added config/database.yml setting to make title ENCODE or modENCODE very easy commit d60e13c519fee97f36dc63304e2bb3bc54c209f5 Author: galt Date: Mon Aug 27 23:35:38 2007 +0000 removing hardwiring of config to use RAILS_ENV instead commit 091d863eeb7b7513edcf09da67feede1740348c5 Author: galt Date: Mon Aug 27 23:23:54 2007 +0000 dealing with returning to show instead of to list now in many places commit cd1fdb79ce0f6417bc16a15769d17e96d975bf5a Author: angie Date: Mon Aug 27 23:10:11 2007 +0000 hg18 no longer needs its own acembly description. commit a525920fda9ff4a478e74b8ad9a90b09a97df01a Author: kent Date: Mon Aug 27 21:59:17 2007 +0000 Seems to work. commit 2e98918b106b8d2f5b855fcca1f60886c505f683 Author: kent Date: Mon Aug 27 21:45:04 2007 +0000 Compare SNPs shared in Affy 250k and Illumina 300k platforms. commit 972de9d447b61cf578a1ea98f910c2d3cfb681c4 Author: kent Date: Mon Aug 27 21:44:55 2007 +0000 Compare SNPs shared in Affy 250k and Illumina 300k platforms. commit 723c1ee5547a5e9b31db5c06c187d017eb675bf8 Author: kent Date: Mon Aug 27 21:42:11 2007 +0000 Made it read from file by default. Database takes explicit -db option. commit 0ba951be6f282bdd7f900096c466eae2f00148a1 Author: kent Date: Mon Aug 27 21:34:00 2007 +0000 Seems to work except on ensGene. commit b798cc497b1f0688d7bad79b45f48acffe708feb Author: angie Date: Mon Aug 27 21:29:03 2007 +0000 Added extractNestedRepeats.pl target. commit b16a69d1f9fb8ff0bb03687966c52d15ba771bb5 Author: angie Date: Mon Aug 27 21:25:40 2007 +0000 When .out has a * instead of a numeric ID, print a warning and continue. extractNestedRepeats.pl will die if run downstream. commit 9d33bee8813dde7dea730d0b8f061f171ce198f6 Author: angie Date: Mon Aug 27 19:43:46 2007 +0000 If input has missing or malformed IDs, report all of them and then exit with error so developer knows to send a bug report. commit da52433bcaef9cb5eb1c48eb9fb85675f4978b2c Author: archanat Date: Mon Aug 27 19:25:25 2007 +0000 minor edit commit 8ebde3f43b7350ee6dbb120ad242040d73aeb840 Author: archanat Date: Mon Aug 27 19:24:51 2007 +0000 corrected the reference commit 9ef1362ac9a0304b437815395fad6f73f3551cc3 Author: angie Date: Mon Aug 27 19:02:40 2007 +0000 Oops, run extractNestedRepeats whether we're chromBased or not! commit 09bae0b2542059c96594de5ed1ecce43dc1df604 Author: galt Date: Mon Aug 27 18:37:00 2007 +0000 allow other users to see a submission commit 801fcab075deb39db40407a41f6e9b087f5768dc Author: ann Date: Mon Aug 27 18:29:42 2007 +0000 switched short labels for chain and net on mm9 (from mm8). commit fb03dd8c4cdcacbd342f81aa197db1f10b4f424c Author: ann Date: Mon Aug 27 18:26:58 2007 +0000 switched short labels for chain/net for mm9 (and mm8). commit 2d50857d84d2f5c33b2bb7aa069033d7cbd2baea Author: ann Date: Mon Aug 27 18:18:15 2007 +0000 cleaned up citations commit 2d6354c8f9cadfd3c99df561de68658147ce1d75 Author: hartera Date: Mon Aug 27 16:50:04 2007 +0000 Added more description of what makeGenomeDb.pl does. Documented how long makeGenomeDb.pl took to run. commit f11242df766a03613d94d95e62fb5ec2fce089ae Author: hartera Date: Mon Aug 27 16:43:14 2007 +0000 First processed AGPs to create an AGP with gaps between scaffolds for the randoms and tried to process the contigs to chromosome AGP for the chromosomes 1-25. Then decided to base the assembly on scaffolds as before and also to use only the scaffolds for the unmapped sequence (no random artificial chromosomes for these). AGP for the unmapped scaffolds was created and an AGP of the scaffolds to chromosomes was created. AGP files and FASTA files were checked for content and size consistency. The genome db, gold, gap tables, GC percent track and hgcentraltest entries were made by running the makeGenomeDb.pl script. Gap table was rebuilt with all the gaps within contigs and scaffolds as well as between scaffolds. RepeatMasker run is in progress. Simple Repeats track created. commit a9f1955f32fcf1c77cc5824ffb5a9cde9510b916 Author: jzhu Date: Mon Aug 27 16:31:28 2007 +0000 In order to prevent overflow on long_max on a 32bit machine, change variable totalBases from long to unsigned long in function "genoLayNew" (allOneLine configuration). commit 112c1b18f366f3e7155fba376f41152e9858e622 Author: hartera Date: Mon Aug 27 16:22:32 2007 +0000 Makefile for agpAddCtgNamesAndGaps program. commit ba76f6b249d134e2c6da763455ff9b58421db3dc Author: hartera Date: Mon Aug 27 16:21:13 2007 +0000 Makefile for the createScaffoldsAgp program. commit 370964680d310b53713ec39f34c52d7fd039b407 Author: hartera Date: Mon Aug 27 16:19:27 2007 +0000 Program written for the zebrafish Zv7 assembly to take a contigs to scaffolds AGP and a contigs to chromosomes AGP and output a scaffolds to chromosomes AGP. commit 0ea022d823c872d74c6ae560b3cd74a4cc82666f Author: galt Date: Mon Aug 27 15:00:07 2007 +0000 "Encode release log update" commit a4b011e16a7bdb02d9313bb8f5ac5548182b23f8 Author: galt Date: Mon Aug 27 15:00:04 2007 +0000 "Release log update" commit e1d1a61b4d39e8cf5ea75eeda6ca1920951a700b Author: galt Date: Sun Aug 26 15:00:07 2007 +0000 "Encode release log update" commit 3d4f938dee9fe01fd348419a7520849bea1e1acd Author: galt Date: Sun Aug 26 15:00:06 2007 +0000 "Release log update" commit 90fe0591a842f34217e965d0e8cdf7f75908c1c4 Author: galt Date: Sat Aug 25 15:00:04 2007 +0000 "Encode release log update" commit 9787f8c855663c68fe1dce87677ec817dc5a6ed7 Author: galt Date: Sat Aug 25 15:00:03 2007 +0000 "Release log update" commit 3a852c79eafce1c69e83c5f62df3b77b71ff727f Author: hartera Date: Fri Aug 24 22:27:58 2007 +0000 Updated the URL for wget for the mitochondrion genome sequence. commit 462155c3ff02e4426c9afad1d5aa561214bdc159 Author: hartera Date: Fri Aug 24 22:17:44 2007 +0000 Initial description for danRer5 gold (scaffolds assembly) track. commit db9031ead28cb626005a17ff48a9983eca5ec9ff Author: hartera Date: Fri Aug 24 22:17:28 2007 +0000 Initial description for danRer5 gap track. commit 2e5b5a88c68bc72888dee1ccb24e5eb8f089669d Author: hartera Date: Fri Aug 24 22:16:26 2007 +0000 Initial descriptions for danRer5. commit 5032d6e44e2965b65fc3fd795be8f411e3af38a1 Author: hartera Date: Fri Aug 24 22:14:51 2007 +0000 tracks for zebrafish Zv7 assembly (danRer5). commit 71a34cdba6753982e7a34fb44e85b05bf25a144e Author: hartera Date: Fri Aug 24 22:13:51 2007 +0000 Added danRer5. commit 66017e4f6475adafc748f2ad86a0992b937bdecc Author: archanat Date: Fri Aug 24 21:32:44 2007 +0000 combined the all.joiner rules for the oreganno tracks for hg18 and dm2 to include all $hg and $dm databases and also changed the identifier commit 2d83677e738a2e69194b69420d070467bfd24b9b Author: jzhu Date: Fri Aug 24 20:59:22 2007 +0000 *** empty log message *** commit 3b40e84268c4b31e0e40a929aebbfb2bf923d03f Author: galt Date: Fri Aug 24 15:00:03 2007 +0000 "Encode release log update" commit 77850040ae2fb8cd9f92d38f0c31ed84331773d0 Author: galt Date: Fri Aug 24 15:00:01 2007 +0000 "Release log update" commit a55b6476867558fe9c4e4dfacb6fcb9ab4e8fdcb Author: markd Date: Fri Aug 24 01:16:59 2007 +0000 fixed literal % in fprintf that were not escaped commit 071a12c164d13d3317a79432636446a3e38fddc9 Author: kuhn Date: Thu Aug 23 22:51:56 2007 +0000 changed link to wormbase after Bob Waterston found a bug during SAB meeting. commit 54e801410c57d6f48f000ff0f1c856412040443f Author: hiram Date: Thu Aug 23 19:37:24 2007 +0000 no-long-double for darwin Mac compile commit 415a026e59028520ea797cb797d7787a6b1e72a8 Author: donnak Date: Thu Aug 23 18:40:54 2007 +0000 Added links to apps mentioned in intro paragraph. commit cf37f4f10cf7b2346a2fd4fa565ef78e29b6f4e7 Author: hiram Date: Thu Aug 23 16:53:47 2007 +0000 Include note about OSTYPE export on the Mac commit 2b7a211475bab4b920ad50dc7e4319d8d3b22278 Author: galt Date: Thu Aug 23 15:00:05 2007 +0000 "Encode release log update" commit 18c477d3167a9d7ed998a2a46d5f2848866e7820 Author: galt Date: Thu Aug 23 15:00:04 2007 +0000 "Release log update" commit 748f517967e7c23f641322c03e518ac8058880d1 Author: donnak Date: Thu Aug 23 00:42:58 2007 +0000 Updated mm9 announcement. commit 924145e192d6e099120d620368fa30eb72a5c79f Author: donnak Date: Wed Aug 22 23:56:45 2007 +0000 Fixed a few inconsistencies in mm9 article. commit 076467a85a1c097cd86f77bcfa05e6716af89553 Author: donnak Date: Wed Aug 22 23:41:46 2007 +0000 Fixed minor inconsistency in mm9 news item. commit e6cbecdb50ae95663161a545f483e3ac8bcd1169 Author: galt Date: Wed Aug 22 23:19:10 2007 +0000 minor typo fixed commit be0e47c01910faa826f3846abd3cce0382ec6853 Author: kayla Date: Wed Aug 22 21:05:00 2007 +0000 adding bosTau3 and mm9 commit 2ddec1961b3474f1c739488c5368adbc4081bb97 Author: mhoechsm Date: Wed Aug 22 19:06:53 2007 +0000 fixed an issue where the track name can be drawn over the next track... commit 162eb89ea3447da67b33b6ed2046e8f9c9d358c4 Author: donnak Date: Wed Aug 22 18:51:54 2007 +0000 Updated bosTau3 news item. commit 1ef322a6c499680a51f4715075a7ca5ff64cbe09 Author: donnak Date: Wed Aug 22 18:46:37 2007 +0000 Edited & updated this file. commit 94e5f65308ca3ee80b26b1d6e5f7cb422e260a43 Author: hartera Date: Wed Aug 22 18:18:19 2007 +0000 Added more assembly details. commit 6f35a04703798fbf93ef4fecd8c55c0ef1de1754 Author: donnak Date: Wed Aug 22 16:41:39 2007 +0000 Archived 1 item. commit 9e01d2edb09e2f961bb79ab5bc1b3fb2bd8cd36e Author: donnak Date: Wed Aug 22 16:41:24 2007 +0000 Edits to the cow & mouse sections. commit 34a4286f9e03b1bd62ecc7333685670a4ac898b7 Author: donnak Date: Wed Aug 22 16:40:52 2007 +0000 Edits to the mm9 & bosTau3 news items. commit c37acfe68f2bf2589d8b44e3fb39b31228237f61 Author: donnak Date: Wed Aug 22 16:33:31 2007 +0000 Regenerated this release for the archive server. commit bdb0490a2d82e148646a4a12a0c0f401c7a74f5b Author: galt Date: Wed Aug 22 15:00:06 2007 +0000 "Encode release log update" commit 4badb09e4181810aeca9019f41654a69c3892857 Author: galt Date: Wed Aug 22 15:00:05 2007 +0000 "Release log update" commit d669534b395b0b260376942fedf75bde4ef005b0 Author: markd Date: Wed Aug 22 02:49:48 2007 +0000 fixed bug computing match/mismatch counts commit 02d4c6ed36f742a922d9f45f888bed5233d85a00 Author: hiram Date: Tue Aug 21 23:54:19 2007 +0000 Allow output to san filesystem for kk kluster commit 842709d79e629c5706135ba9549c10ee15456d35 Author: hiram Date: Tue Aug 21 23:44:40 2007 +0000 Sort the chrom.sizes file by size commit 60c2e288bbfe7d81eb386309db65f811195284d7 Author: hiram Date: Tue Aug 21 22:50:29 2007 +0000 Add Orangutan and Marmoset commit 5b35ba77cbed1ca60abb5eb6e7927c58a7d22b2b Author: hiram Date: Tue Aug 21 22:50:03 2007 +0000 Initial contents from makeGenomeDb.pl commit 136b7d75fc42c83ba4de51d77b8b98ac999db9de Author: galt Date: Tue Aug 21 22:23:31 2007 +0000 undoing, the BED cannot use the simple method the wiggles did for missing data. Need to add gap info sometime soon to do properly commit a48310e6daee5e3c758ca6215b4e03acddf1fbc6 Author: galt Date: Tue Aug 21 22:11:14 2007 +0000 Handling missing data in Depth/Coverage BED imports. commit 6dccdd771017b340101e433a53b1d1d07dafd501 Author: hiram Date: Tue Aug 21 21:27:29 2007 +0000 Fixed up photo link and references commit 1933ceee66ca9587b5204d13d64bb14efbbd03ed Author: hiram Date: Tue Aug 21 21:21:45 2007 +0000 Orangutan and Marmoset photos from NHGRI commit f0033792af10b37ac2f98a6180610af698915d71 Author: donnak Date: Tue Aug 21 20:13:19 2007 +0000 Added credits for mm9 & bosTau3 browsers. commit 7fc6ce2f7f2f9385c1702bcfc245ab24c2fa4d41 Author: donnak Date: Tue Aug 21 20:03:04 2007 +0000 Added bosTau3 & mm9 to release list. commit a4162cde329d4a6088588b29bc6631569b5c2cc5 Author: hiram Date: Tue Aug 21 20:03:00 2007 +0000 Also initialize local library copy of Repeat masker for each hub commit 16949d2fa7638c38d7f1dedba232669577dfe5d4 Author: hiram Date: Tue Aug 21 19:59:40 2007 +0000 Use local RepeatMasker now from /scratch/data/RepeatMasker, and remove all references to panassas commit da1837f0d38962e46700c99ff8817ad29e524dc6 Author: kent Date: Tue Aug 21 18:55:04 2007 +0000 Handling missing data in Wiggle imports. CHanging status message for imports. commit 93dfb5c4cf076aa955161df3038af79f77252e18 Author: markd Date: Tue Aug 21 18:33:20 2007 +0000 added check for match/mismach count sanity commit 62e4d59cf1ba5b49ebdd657f757797d795f76ccf Author: hiram Date: Tue Aug 21 17:30:07 2007 +0000 Initial files from makeGenomeDb.pl commit 56eb841f176e412fac1fa6108bb20d24f0edeea4 Author: tingwang Date: Tue Aug 21 16:27:07 2007 +0000 fixed reference link commit 64609f6e26a7dc905cd5882a79d27bf340a581d6 Author: hiram Date: Tue Aug 21 16:18:19 2007 +0000 Initial contents, beginning Orangutan build commit 8f0c37281fa24b96a266066f2fe363ed6320d2c7 Author: galt Date: Tue Aug 21 15:00:04 2007 +0000 "Encode release log update" commit 5230925255dbfb59524dbb26cd8c0ecb1b75d87f Author: galt Date: Tue Aug 21 15:00:02 2007 +0000 "Release log update" commit ee7b195e9fd5aadaad0abf637ca7acc9067125f6 Author: hiram Date: Tue Aug 21 00:16:06 2007 +0000 Update entrez fetch of mitoAcc sequence. They changed their interface commit f3466c87e855cc7d557b8edc4cd2656d82d30b2b Author: angie Date: Tue Aug 21 00:12:22 2007 +0000 Fixed call to vgTextCentered to use left coord and width instead of center coord. commit ecdf1b4629ca567bb6872b9d45bb32bbae3a65c3 Author: hartera Date: Mon Aug 20 23:24:36 2007 +0000 Added brown as the colour for pseudogenes in the Ensembl non-coding genes track. commit 30fd348710f05615e17e0632b6c2b452eeb8a2c8 Author: kate Date: Mon Aug 20 23:18:36 2007 +0000 Fixes for track priority reordering of supertracks commit b70a8f06309e8cac10e907542bc6607a2db28ec4 Author: hiram Date: Mon Aug 20 22:32:01 2007 +0000 Done with Mm9 blastz alignments commit 25ea8d606b3cdaf3e0f819279fa107c9d1c8a29e Author: hartera Date: Mon Aug 20 21:31:58 2007 +0000 Added back variable initialisation. commit f9a53ccf41b18376ead48baae27b4c1241217cc0 Author: hartera Date: Mon Aug 20 21:27:48 2007 +0000 Added code to doEnsemblGene to handle Ensembl Non-Coding Genes. commit f1f8fb9ad63e95185fc43d1c4b0ec4f092971c89 Author: rhead Date: Mon Aug 20 19:08:07 2007 +0000 Removed broken link after checking with angie. commit 31090b74881314d6de237b2b9a9a8eeed8a50951 Author: galt Date: Mon Aug 20 15:00:05 2007 +0000 "Encode release log update" commit 71d88d9eae1584da406b174f51ad03d5b6edb783 Author: galt Date: Mon Aug 20 15:00:03 2007 +0000 "Release log update" commit 81ddf49165d3a2286106e3d26b434e662e410603 Author: donnak Date: Sun Aug 19 17:42:19 2007 +0000 Updated some entries, added 1 new one. commit 74dd44d3aec7270cd51c762294038e37d3d24c92 Author: galt Date: Sun Aug 19 15:00:05 2007 +0000 "Encode release log update" commit 957bda0b95fa591ec5ad2b25e8c118d732726767 Author: galt Date: Sun Aug 19 15:00:03 2007 +0000 "Release log update" commit e968f0b12499452331bec65aa74cc683e627ee4d Author: galt Date: Sat Aug 18 15:00:06 2007 +0000 "Encode release log update" commit c048dbc933e95bcc9d31f3ba27641c2471e2b5a2 Author: galt Date: Sat Aug 18 15:00:05 2007 +0000 "Release log update" commit b455938389d1928a294c744f15c5bcfc3dc32d6c Author: galt Date: Sat Aug 18 02:26:55 2007 +0000 added ability to upload multiple archive files into the same submission set commit 36d7063dbdcd13443e9fa71a65f1e14c1f652608 Author: kuhn Date: Sat Aug 18 00:08:32 2007 +0000 added note about renaming directories for regPotential7X tracks commit e4216132cee581336627ec8d93c9eb8813a1383b Author: markd Date: Fri Aug 17 21:42:23 2007 +0000 work on polishing off ensembl/vega load scripts; not perfect yet commit 08551f7897584ed7bb43012ec988af59d880076c Author: hiram Date: Fri Aug 17 19:55:37 2007 +0000 Properly obtain machtype from uname -m instead of the potentially missing MACHTYPE environment commit 496021262b5690ab4425e6dbf4913201cca4c388 Author: donnak Date: Fri Aug 17 18:39:13 2007 +0000 Added link to supporting materals for Katzman paper. commit 2ccd871dead47be733193661e8766ea9bbc1a0d5 Author: angie Date: Fri Aug 17 18:32:19 2007 +0000 Needlessly re-ran doSameSpeciesLiftover to bosTau3 (oops). commit 478ff71a5bae51476654ec2ebaa09cb7cc9aeb1e Author: angie Date: Fri Aug 17 18:16:21 2007 +0000 Handle either split or unsplit files when making download links (oops). commit b342cd83eaa6386bb055925e25a072920c01c37d Author: kent Date: Fri Aug 17 17:58:53 2007 +0000 Improving usage statement, updating test set. commit 584daad13abe934cb95f32b28178d7c8de7a8304 Author: donnak Date: Fri Aug 17 17:51:45 2007 +0000 Added one of the links to Katzman Science article...still waiting on link for supplemental materials. commit 75d811fb6600552fe94273ae315242bd97054a72 Author: galt Date: Fri Aug 17 15:00:08 2007 +0000 "Encode release log update" commit 1f28eff89feabd8df1faa200be49609f525f7ea9 Author: galt Date: Fri Aug 17 15:00:04 2007 +0000 "Release log update" commit ba8198471f4b7e0f0f2ee7a69518845f8799eb70 Author: kent Date: Fri Aug 17 14:43:31 2007 +0000 Documenting output better. commit 21900be272c43bb60b0e3c7c679d7eec3fc4b8a0 Author: kate Date: Fri Aug 17 04:37:25 2007 +0000 Mouseover of supertrack member on config page shows supertrack label (helpful if member track is reordered) commit de8f79655f8505afe6498d8fa43d21a61e319b1d Author: kate Date: Fri Aug 17 04:36:35 2007 +0000 Fix to supertrack priority reordering commit c7c52a59b9d4407a287ff53177492b53614cdcea Author: kate Date: Fri Aug 17 04:14:44 2007 +0000 Fixes to hide/show dropdown (hidden text) for supertracks commit 1b5f0e7b729279cfac7a2edf3c18955fa3bd04f7 Author: kate Date: Fri Aug 17 03:55:24 2007 +0000 Make track reordering work better for supertracks commit ddddfca06b9853d784e4162688ca91fc5cf800a5 Author: markd Date: Fri Aug 17 01:22:23 2007 +0000 added tetNig1 N-SCAN commit bcdd45fab2f5534785fd6e164eaeba642c35824f Author: markd Date: Fri Aug 17 01:15:44 2007 +0000 added program to find gaps and blocks in a fasta file commit 507f34eb4811d58e9d79e8061cfd639cec5e4f4e Author: kent Date: Fri Aug 17 00:54:49 2007 +0000 Removing duplicate description in altGraphX types. commit eff71ce00e308a4f9a940258f15e3e6c17b69c58 Author: kent Date: Fri Aug 17 00:54:11 2007 +0000 Improving phrasing in sibTxGraph description. commit f5ce554ddca0e278196e364c22cf2d2cea2c46bb Author: galt Date: Thu Aug 16 23:25:50 2007 +0000 moving location of upload to database.yml upload setting commit 58a0007d1f996b79c5c86512ce63a0e1041c9158 Author: hiram Date: Thu Aug 16 23:17:36 2007 +0000 Add chain and net for Mm9 for all organisms commit dd015ded824ddb11543706c3b56a8f9a6bc81d9f Author: hiram Date: Thu Aug 16 23:16:40 2007 +0000 Do not copy description.html during -strict commit 156d6dea6942ba2c30576997723c185869f1d9e6 Author: galt Date: Thu Aug 16 23:14:54 2007 +0000 removing dummy test table (actually thru db:migrate of course) commit 3f1d74fb8482d440f63ec2eca2065cd6bd6a3639 Author: hiram Date: Thu Aug 16 23:07:14 2007 +0000 remove before copy and copy with permissions copied commit 91c87e810accd4fe90354832bab07c58399edf62 Author: rhead Date: Thu Aug 16 22:57:45 2007 +0000 Added note about request for rhesus nets and chains. commit 344f6654e6688c6de3c956432d7099d369e1a7c2 Author: galt Date: Thu Aug 16 22:41:32 2007 +0000 removing unneeded test change after reverting to previous version with rake db:migrate VERSION=12 commit 401fbd0a24e4aa4885eb3fcb388bcaddf8472e9e Author: markd Date: Thu Aug 16 19:39:42 2007 +0000 don't report parse errors via assert commit 88ad712abae999cca06c245ca3ff3269cfe27a9a Author: galt Date: Thu Aug 16 18:09:56 2007 +0000 updating section on reproducing our hgBlat results commit da33cf9e47baf33f144c9059db47467c8a8b6cd3 Author: kayla Date: Thu Aug 16 17:40:48 2007 +0000 added a block for bosTau3's snp127 track commit 6f932d5bb6a2711f9a4a7fd9da637fb3b4ec06ad Author: kayla Date: Thu Aug 16 17:33:20 2007 +0000 changed 36_2 to 3_1 Because this is cow, not human. commit 3e53b6bbdca1710a84234092ca35008c477b15c0 Author: kayla Date: Thu Aug 16 17:30:07 2007 +0000 bosTau3 gets it's own copy of this file. commit 967ba92bdeb147eb98f4e92bd2dd29238761b07d Author: kuhn Date: Thu Aug 16 17:27:21 2007 +0000 made "databases" plural commit 6618c829e94acfb1411e9371172d342e2493064a Author: rhead Date: Thu Aug 16 17:24:54 2007 +0000 Added a link for axt format. commit e3a2b0d6dbf242cf8aec6517c75858c0e1712fb4 Author: kuhn Date: Thu Aug 16 17:22:50 2007 +0000 added two proteinsYYMMDD to the db list and added instructions to make all spYYMMDD dbs and to make a uniProt symlink to the most recent commit cfac1f93e2e3b05c75b86185b3c6e91a5731c05c Author: tingwang Date: Thu Aug 16 17:16:31 2007 +0000 description of encodeBUORChID commit 9d463de4beb1c5e2574f7949937dd6111025e084 Author: tingwang Date: Thu Aug 16 17:12:54 2007 +0000 modified description for encodeBUORChID.html commit 31ce854e1905ae266b3f1434ebdbabf09cd36db6 Author: kent Date: Thu Aug 16 16:56:02 2007 +0000 Improving opening comment. commit 60fde0e8d2f83d0147abecf3dae5e5e0b69607aa Author: ann Date: Thu Aug 16 16:11:28 2007 +0000 fixed journal names. commit 7a394cb5b036282804936f5ebb3f58b19f293839 Author: galt Date: Thu Aug 16 15:00:05 2007 +0000 "Encode release log update" commit aa0493ce48efbf5f1fc3f1b1d966883eebac8245 Author: galt Date: Thu Aug 16 15:00:04 2007 +0000 "Release log update" commit a3e56dee806c9db46e8d4c332fde51cbfb5d527b Author: hiram Date: Wed Aug 15 22:55:10 2007 +0000 Adding chain and net mm9 commit 4b329790092ff0c845d779ac75572f993891b9e9 Author: hiram Date: Wed Aug 15 22:49:04 2007 +0000 chain and net html pages for Mm9 to apply to all other genomes commit 660e6dd01aa822d108de2bb36cf0976b08ab3d57 Author: hiram Date: Wed Aug 15 22:47:08 2007 +0000 Use the chainMm8.html file in the top-level trackDb directory commit 675ea3781d1fb0e0775f21ccfb7b0b7449721dfe Author: hiram Date: Wed Aug 15 22:17:17 2007 +0000 Add in chain and net for mm9 commit cd28610e72248a8a1ddc8a7787c1defb15e00366 Author: hiram Date: Wed Aug 15 22:15:33 2007 +0000 Add in chain and net for self alignments commit 72a5b70120c2c4dfea805439c323844fa43b03d1 Author: ann Date: Wed Aug 15 22:12:17 2007 +0000 Clarifying explanation of gap annotation line for MSA protein tracks. commit 0d4cf873b82ec59309f3dde19a117d710c91ebe4 Author: fanhsu Date: Wed Aug 15 19:21:31 2007 +0000 Divides number of bases by 3 to get number of AAs for insert line dispaly. commit 59882b63953c58c3f009a5194f040f763954e7d7 Author: hiram Date: Wed Aug 15 18:55:11 2007 +0000 Ideogram build fixed up. Rn4 blastz done. Self still working on. commit d5c8358b2d1b7015b3e5207b1d02e5e6c8b4cb3a Author: hiram Date: Wed Aug 15 18:52:45 2007 +0000 Eliminate error line from mm9 ideogram file from NCBI commit e7fc1398a613aa2ff6e75720074de2640709293a Author: hiram Date: Wed Aug 15 18:50:11 2007 +0000 Initial source to check a cytoBand.bed file against chrom.sizes commit a6336975c6986cb49bbd8cf8dde968de6426772d Author: fanhsu Date: Wed Aug 15 18:39:58 2007 +0000 Added "maxItems 2000" to vax004. commit c9d04dc69dcdeb8e19f5ab389cd75af838719e9e Author: fanhsu Date: Wed Aug 15 18:24:58 2007 +0000 Added "maxItems 2000" to vax004 track. commit 7732e1c5e9ff359e3ec0c1cf9e53228e2bd888c2 Author: fanhsu Date: Wed Aug 15 18:21:57 2007 +0000 Added maxItem of vax004 to 2000. commit ef57ac35e357e1364894d3426c6fe3f04cbd682a Author: hartera Date: Wed Aug 15 15:54:17 2007 +0000 Add code and new functions, ensemblNonCodingTypeConfig() and ensemblNonCodingUI() for the Ensembl Non-coding track filtering for the track UI. commit f9bf0c51be97254d89ce90a1e83ba2eb87c84477 Author: galt Date: Wed Aug 15 15:00:03 2007 +0000 "Encode release log update" commit 8b3d906ae8f5e953640156494c3f1801a5906461 Author: galt Date: Wed Aug 15 15:00:01 2007 +0000 "Release log update" commit 20ebb38655d12f9ea3e90646c55d5e50a8df8961 Author: kent Date: Wed Aug 15 14:23:39 2007 +0000 Adding support for idInUrlSql to give finer control of outside links. commit d7640d7b718a4011d7dc94b2ae14ce5d2d42495b Author: kent Date: Wed Aug 15 14:23:04 2007 +0000 Adding outside URL links to SIB tracks. commit 1ac980915544d3f57a83746ad6d82b7cdb623854 Author: kent Date: Wed Aug 15 14:22:25 2007 +0000 Documenting idInUrlSql and urlLabel tags. commit f9cafbfba5faa317a9dd14355338a60e3d503af4 Author: fanhsu Date: Wed Aug 15 05:40:09 2007 +0000 Removed the temporary fix of limit to 200 sequence for GSID sequqnce list. commit 34cee4249b863720845cdf453ec19a4a901fa779 Author: hiram Date: Tue Aug 14 23:09:09 2007 +0000 Add ignoreSelf option to doBlastzChainNet and fixup null sequence check in blastz-run-ucsc commit b562fc3d4d29004fc56d2f1ff194eaaf264200ba Author: braney Date: Tue Aug 14 22:46:17 2007 +0000 backing out a change that is causing problems with the GSID browser commit c16d800199e2dd4187be2c3dc481ce2476e18556 Author: ann Date: Tue Aug 14 22:21:02 2007 +0000 put back down on species level. commit 850f41ccb009626faf70da0f887f7cd82dcbd7fd Author: ann Date: Tue Aug 14 22:20:33 2007 +0000 re-added from up one level (I guess the bi-level trackDb-building doesn't work) commit 2435d656f3093ea355f74a4ee946a41e4e50a485 Author: ann Date: Tue Aug 14 22:12:44 2007 +0000 Moved up from species level. commit b563960131c10212021a89e747078ad718b53fa4 Author: ann Date: Tue Aug 14 22:11:15 2007 +0000 Moved up a level. commit df7bde7b5f21796486190e52ffbf13012b6b3d82 Author: kent Date: Tue Aug 14 22:09:45 2007 +0000 Adding some test tracks. commit 0f1c186161c779e2a72955f4a9eebdfd8fe7a8dc Author: fanhsu Date: Tue Aug 14 22:09:00 2007 +0000 Updated to include several track builds. commit a5c1f733f6d96c9e66004113bac669363277e2ef Author: kent Date: Tue Aug 14 22:06:04 2007 +0000 Adding sib html files. commit 88d97a94397acbc5b15df8d4323c170a9a26064c Author: fanhsu Date: Tue Aug 14 21:12:12 2007 +0000 Checked in hivGne8.txt. commit 9be66463c087d5744d1e0e28a84a05f7061faa3a Author: braney Date: Tue Aug 14 20:42:29 2007 +0000 if there isn't a wiggle, and you're in dense mode, draw graph with only the selected species (also set speciesOrder cart variable so hgc know the proper sequences to display). For Fan/GSID commit f000a5ad611fa9640af8351c2bf8e20c61b86a9b Author: donnak Date: Tue Aug 14 20:00:48 2007 +0000 Updated version # for dm1. commit c6239eec89164798db694948dc8d205b0b51d9de Author: aamp Date: Tue Aug 14 18:53:08 2007 +0000 Moved caseControl to hg18 to avoid error on alpha. commit c5d064473fe69e7f2c0544c959ea0f045a086e0a Author: fanhsu Date: Tue Aug 14 18:17:14 2007 +0000 Changed "base" into "amino acid" for wigMafProt. commit 49f581338726f1678c0627df2a0f22e0138d4a3d Author: ann Date: Tue Aug 14 18:16:07 2007 +0000 changed references from base to protein/AA. commit 27064cd12a8b0cebf8b13c8c5f9c02729ceb9164 Author: fanhsu Date: Tue Aug 14 17:11:37 2007 +0000 Created for hivmn. commit 0b5815b2986f0f098e7f4c3391392f7c6eb5d73e Author: fanhsu Date: Tue Aug 14 17:09:44 2007 +0000 Created trackDb.ra for hivmn. commit bcc5e1ce1ad2a7af3eb9938f990886b37677bbae Author: fanhsu Date: Tue Aug 14 17:08:32 2007 +0000 Added "maxItems 2000" to vax004Maf and vax004AaMaf tracks. commit 946a4c2880200a09f54c365f39211c1278339c32 Author: fanhsu Date: Tue Aug 14 16:59:06 2007 +0000 Updated max number of wigMaf sequences to 2000. commit a9435af2a603d3aa83165a041f5e9de99d2d0fb9 Author: fanhsu Date: Tue Aug 14 16:57:06 2007 +0000 Increased the max number of sequences to 2000. commit 6ba23902ef195ec8e1b00d2a1f8c12d977158140 Author: hiram Date: Tue Aug 14 16:24:09 2007 +0000 Properly use a here-is print instead of multiple individual print statments commit 6249136255dac6b2f3f9ab1e724f26a8bb8bee17 Author: fanhsu Date: Tue Aug 14 15:44:17 2007 +0000 Added vax004AaMaf.sql, generated by autoSql. commit f7aa110bb3c5d2270a9d0b2ba2d672e78d0c5ec5 Author: fanhsu Date: Tue Aug 14 15:43:43 2007 +0000 Created vax004AaMaf.as. commit 3a5efa4d5b77427ec32d665900c695f2c3fbfdff Author: fanhsu Date: Tue Aug 14 15:41:23 2007 +0000 Added vax004Maf.sql, generated by autoSql. commit f861cad9eeec21b47357f160305b623c940d4865 Author: fanhsu Date: Tue Aug 14 15:41:01 2007 +0000 Created vax004Maf.as. commit 55af71f4da4f950f5738f5a83e66600806bc1a85 Author: fanhsu Date: Tue Aug 14 15:37:43 2007 +0000 Forgot to change vax004Cons.sql. commit 9bd77a9ec458356089b205c9f0e03588e75b198e Author: fanhsu Date: Tue Aug 14 15:36:37 2007 +0000 Forgot to change table name. commit 534aa116837d57a9ebe5c9fa1df1156fa95cf015 Author: fanhsu Date: Tue Aug 14 15:18:06 2007 +0000 Added vax004Cons.sql, created by autoSql. commit 2276faf0075ee35de6e76b0436280f80ec8d5c6e Author: fanhsu Date: Tue Aug 14 15:17:34 2007 +0000 Added vax004AaCons.sql, generated by autoSql. commit b33af52cac9fbb537804801254f0927fdb23c89d Author: fanhsu Date: Tue Aug 14 15:16:55 2007 +0000 Created vax004AaCons.as.Created vax004AaCons.as.Created vax004AaCons.as.Created vax004AaCons.as. commit 2f97ecbac1a6bb009fa02cc669f624e9291332aa Author: fanhsu Date: Tue Aug 14 15:16:26 2007 +0000 Created vax004Cons.as. commit 9d63cff3223632a3c56cd00a88754927e9d97a50 Author: aamp Date: Tue Aug 14 15:11:21 2007 +0000 Composite chromGraph compatibility. Click in hgGenome turns on track/subtrack in hgTracks. commit 011ffcf99ee8eebf4e13447c5d07903c4ddbb8bc Author: galt Date: Tue Aug 14 15:00:05 2007 +0000 "Encode release log update" commit ef1e3bbb027fd04dfe8e3a83c12d71cd38ff7530 Author: galt Date: Tue Aug 14 15:00:04 2007 +0000 "Release log update" commit 8496e623cb10b5773b29cd21301d3f8dba34a68b Author: hartera Date: Tue Aug 14 06:37:36 2007 +0000 Added trackHandler and methods for Ensembl non-coding genes (ensGeneNonCoding). Added filterNonCoding() to filter items on biotype. Added loadEnsGeneNonCoding() to load track and ensGeneNonCodingColor() function to colour items by biotype. commit 9f366911767a08ab84f3a56ef88924387d0866d7 Author: hartera Date: Tue Aug 14 06:27:51 2007 +0000 Added nonCodingUi. commit 53638713b094a56e90431e285fccd49b4601f57d Author: hartera Date: Tue Aug 14 06:26:13 2007 +0000 Code to allow filter for non-coding genes track from track UI. commit 2195784dc25da66d19e5df655a9ac6d7fa87fe5d Author: hartera Date: Tue Aug 14 06:25:23 2007 +0000 Code to allow filtering for non-coding RNA in the track UI. commit 76332cda260c78bb0ad94025a0050777d061e0a6 Author: tingwang Date: Tue Aug 14 06:23:39 2007 +0000 supertrack description for encodeYaleRnaSuper commit 4bda9533ed09efb9777fe062290a1dc4ab81e1d4 Author: tingwang Date: Tue Aug 14 06:23:25 2007 +0000 supertrack description for encodeYaleChipSuper commit ad1ab1062e2a99661b2f2f783286191986bf1ee2 Author: tingwang Date: Tue Aug 14 06:23:14 2007 +0000 supertrack description for encodeUwDnaseSuper commit a35a8f9539c91b0ddbee004ac5de021a8657838a Author: tingwang Date: Tue Aug 14 06:23:02 2007 +0000 supertrack description for encodeUvaDnaRepSuper commit 053ba612456470db211bdf100b941a3410cc7c8b Author: tingwang Date: Tue Aug 14 06:22:47 2007 +0000 supertrack description for encodeUppsalaChipSuper commit 67f570386576a70f3fe886272ce609a666d149b1 Author: tingwang Date: Tue Aug 14 06:22:33 2007 +0000 supertrack description for encodeUcsdChipSuper commit f20c0c028c1bd41a7534ad6daa07151d129d9feb Author: tingwang Date: Tue Aug 14 06:22:13 2007 +0000 supertrack description for encodeUcDavisChipSuper commit 73163595f9f54a855227f9d4295eaa2d6c15f8da Author: tingwang Date: Tue Aug 14 06:21:55 2007 +0000 supertrack description for encodeStanfordChipSuper commit a9318281ef7fb2410a5b5aaa6a8c7eafbd713c24 Author: tingwang Date: Tue Aug 14 06:21:39 2007 +0000 supertrack description for encodeSangerChipSuper commit 4f323a47f3d73f4e81e2663ff172ebcd7b2c255e Author: tingwang Date: Tue Aug 14 06:21:24 2007 +0000 supertrack description for encodeGencodeSuper commit fd0d074c98ce4ebd1190dbd020f1a072f9389b0a Author: tingwang Date: Tue Aug 14 06:21:07 2007 +0000 supertrack description for encodeEgaspSuper commit ab19bf36f767927c594eb2722807c3429611e0e5 Author: tingwang Date: Tue Aug 14 06:20:45 2007 +0000 supertrack description for encodeAffyRnaSuper commit 5bcccc9f7007dcefeb29dc166fbaa7fcb324d755 Author: tingwang Date: Tue Aug 14 06:20:24 2007 +0000 supertrack description for encodeAffyChipSuper commit a076790d3a5b54ab2cebeb5ca3a2dd071762980d Author: angie Date: Tue Aug 14 03:54:49 2007 +0000 Added exception to non-genome-db-skipping logic for hiv1. commit 7f5dc296bb37a58ccb1e5cbd8b3bdb0207b21299 Author: baertsch Date: Tue Aug 14 01:14:53 2007 +0000 added genePredCheck commit a0c79884da87e22494e41be9cb14f088d093a8a1 Author: baertsch Date: Tue Aug 14 01:10:41 2007 +0000 fix hap names commit 2978a64f6ff26a27a4f9a1c97ff039e13ca586c5 Author: markd Date: Tue Aug 14 00:56:17 2007 +0000 use BINDIR variable rather than $HOME commit 3d587938a09d1182aae1b1d9f063602f61e9bc96 Author: baertsch Date: Tue Aug 14 00:55:41 2007 +0000 initial version commit e0b782a44b9f444dd3a01a4245c8a01a526a427b Author: galt Date: Tue Aug 14 00:01:30 2007 +0000 added section for reproducing hgBlat results with standalone blat commit 6cf63e76419e8b4bb6bc7fe0310a645f3e614c81 Author: markd Date: Mon Aug 13 23:29:49 2007 +0000 added missing newline in message commit 7d0f5f79820439b5e2ab3378acaa5f6bf630ca99 Author: hiram Date: Mon Aug 13 23:13:41 2007 +0000 Protect against target or query containing too little sequence to be worth the trouble commit dec6271e741be7c65ec1c6f26ef57a48f2b94aea Author: fanhsu Date: Mon Aug 13 22:43:51 2007 +0000 Fixed a subtle bug due to misunderstanding of startsWith() syntax. commit 9312245d78bae917f57ca0060dec9bc8747cdb63 Author: kent Date: Mon Aug 13 22:07:33 2007 +0000 Adding note about uc accessions being permanent. commit 93ff6bd0100e8cf01500fd1118f57cd8e040384e Author: markd Date: Mon Aug 13 21:33:40 2007 +0000 echo cmds to stdout rather than stderr to kent autoload cron happy commit bce37a228327c12e568ef6b40005e8fefb8db757 Author: angie Date: Mon Aug 13 21:00:29 2007 +0000 Resolved -Wall warning: unused variable. commit 6007959e970ff808889035976f7aaa6d1bac2ba1 Author: angie Date: Mon Aug 13 20:48:24 2007 +0000 Made HgAutomate::getCommonOptionHelp more flexible: instead of demanding defaults for certain options whether or not they're applicable to the script, now it takes a hash of relevant option names and optional-defaults (can be empty). Got rid of getCommonOptionHelpNoClusters. Updated scripts to use the new hash spec, and to include only relevant options. commit 1c2ea57090da7d44541e5fa02c597b9a659c0975 Author: angie Date: Mon Aug 13 20:47:00 2007 +0000 Added oligoMatch so top-level build will catch it. commit ba12ef9fe86ad3224a97e694a2e40e4bdbfa0ea5 Author: giardine Date: Mon Aug 13 20:21:11 2007 +0000 Added code to support ORegAnno track lifted from hg18 to mm8. commit 54d286534d22983dffac712710d41c3ac75c0188 Author: giardine Date: Mon Aug 13 20:19:54 2007 +0000 Added track for human ORegAnno regions lifted onto mouse build. commit c07c4a98e3b9605e730e9cf8705bb9d41a425daf Author: markd Date: Mon Aug 13 19:52:50 2007 +0000 removed zoo files commit 2a18228b761c571ebbdd1fcc396e2dfb323226d6 Author: markd Date: Mon Aug 13 19:52:32 2007 +0000 removed unused defs commit e711b85ab4776bb39ad88d50ea7ff22d2c1aee17 Author: fanhsu Date: Mon Aug 13 18:55:52 2007 +0000 Updated logic to calculate mafOrigOffset. commit fc4d94170cc92165a697473b6b56f8c5bce96b80 Author: fanhsu Date: Mon Aug 13 18:53:58 2007 +0000 Added a new parameter to spreadAlignStringProt(). commit f94ff31eecf22240e5927533c30061cf6b6938cd Author: fanhsu Date: Mon Aug 13 18:52:25 2007 +0000 Updated logic to display protein MAF. commit c9d9a9e615369ed411e6e092c9034273be646b71 Author: kpollard Date: Mon Aug 13 18:50:31 2007 +0000 Generated hg18-rheMac2 reciprocal best nets commit 63b7d9f4f2ada5196d5868ed39a7000f4dce6694 Author: kate Date: Mon Aug 13 18:38:23 2007 +0000 Remove duplicate entry for baboon in TBA entry commit bf1cdaa814cc1eedb9889348cbe6db2f84aed640 Author: kayla Date: Mon Aug 13 18:12:11 2007 +0000 fixed typo commit 032e7ba44ea511b5af42df8aa30d6fe842ed0512 Author: hiram Date: Mon Aug 13 16:56:01 2007 +0000 Add gapToLift to the directory build list commit 20c9d4af12b5f37633e6ddf376b060477cab4614 Author: hiram Date: Mon Aug 13 16:31:03 2007 +0000 During clean, also clean the tests directory commit 7938f2a3a3e2c14d9c034584e5d01853b0423998 Author: markd Date: Mon Aug 13 15:59:41 2007 +0000 fixed going past end of memory block when counting match/mismatch commit 113bfce870aaa635e99083adfcf723c58773f069 Author: galt Date: Mon Aug 13 15:00:07 2007 +0000 "Encode release log update" commit 2eda09e80a708c18f29d4b79dfcc2860576c2c9b Author: galt Date: Mon Aug 13 15:00:03 2007 +0000 "Release log update" commit c226a4f2bd7be3184ac4b427c688a51655c88ebc Author: fanhsu Date: Mon Aug 13 00:57:42 2007 +0000 Corrected a hard-wired bug. commit 10ff663bb0e9215a351eebfb3b8e6e1bfb932572 Author: markd Date: Sun Aug 12 19:20:09 2007 +0000 moved duplicated code to bash script commit 11a657dc36cddaee09c9de491420b121217a4e66 Author: markd Date: Sun Aug 12 17:51:41 2007 +0000 updated expected results commit 87f58d5321307a2ad2de94e1513ad8be22350794 Author: fanhsu Date: Sun Aug 12 16:30:22 2007 +0000 Added a period. commit f2343e7dc6d82b45e787ba6caac67934856f8821 Author: fanhsu Date: Sun Aug 12 16:27:29 2007 +0000 Polished the wording. commit d8d98f2cd123c9a6d142d4964e9c777fb7a1e0a5 Author: galt Date: Sun Aug 12 15:00:05 2007 +0000 "Encode release log update" commit 11bf2075cc95d2c907d1cd1ea49382990117c99e Author: galt Date: Sun Aug 12 15:00:03 2007 +0000 "Release log update" commit 206a276cae27109bfa22d251b10cca6bc74a0a45 Author: markd Date: Sun Aug 12 06:07:46 2007 +0000 add support for parsing TBLASTX output commit e4fa0f9e73de9c6b6564b1e8d89440b979e1806d Author: fanhsu Date: Sat Aug 11 23:23:50 2007 +0000 Added a temp fix to limit total number of sequences in selected sequence list to no more than 200. commit cd2671e8118c6e5c72b5b44e6c18e8a8239d2665 Author: fanhsu Date: Sat Aug 11 20:56:27 2007 +0000 Created VAX004 MSA track. commit ed7c0bb89d05ccdaa3faebf3cf0c12902be825e3 Author: fanhsu Date: Sat Aug 11 20:55:59 2007 +0000 Created VAX004 Conservation tracks. commit a64d956c78b9dced713cd5a1c909670e875d65c2 Author: fanhsu Date: Sat Aug 11 20:38:13 2007 +0000 Added conservartion and MSA tracks. commit e761ce542a6b787dc00067ba3532f38f015b3fdf Author: galt Date: Sat Aug 11 15:00:05 2007 +0000 "Encode release log update" commit cfd39064e969cab83643d14a4f9d50279cc8925c Author: galt Date: Sat Aug 11 15:00:04 2007 +0000 "Release log update" commit 1e95dd59f50e114398ef1f9c294eae72bbbd8498 Author: markd Date: Sat Aug 11 04:55:10 2007 +0000 report reason for ignoring CCDSs commit 31d802600cd4e5f0e053d1d69d6194016be789b5 Author: fanhsu Date: Fri Aug 10 23:14:45 2007 +0000 Created vax004.sql, generated by autoSql. commit 9902520fd4261739b3683079366dc2df9982d9d7 Author: fanhsu Date: Fri Aug 10 23:14:20 2007 +0000 Created vax004.as. commit 17b710dea7df120c1032106f849c92613bf3346e Author: fanhsu Date: Fri Aug 10 23:04:28 2007 +0000 Updated interPro.sql, using the one generated by autoSql. commit eea008d4d77672a3351278df4ebcfe882483dd8f Author: fanhsu Date: Fri Aug 10 23:03:20 2007 +0000 Changed key of hivGene table. commit 4a30e580991e18844ecfcdb91f7e614476cf8ff4 Author: fanhsu Date: Fri Aug 10 23:01:49 2007 +0000 Created interPro.as. commit d0a14e8c503794012427d4f5b0bb335aa69249ad Author: fanhsu Date: Fri Aug 10 22:58:03 2007 +0000 Created hivGene.sql, generated by autoSql. commit edb23f3b07216f3f32f84c1b246365ee445e90cc Author: fanhsu Date: Fri Aug 10 22:57:37 2007 +0000 Created hivGene.as. commit 75bd535d0a9e53149499f73069acdca1a8198b0d Author: fanhsu Date: Fri Aug 10 22:28:22 2007 +0000 Disable motif highlighting for protein maf display. commit 8826e1e298f29a49d30284c705794ab6c680abc0 Author: hiram Date: Fri Aug 10 21:32:56 2007 +0000 Started blastz mm9 commit dead5baf4b0eaf1d2be42afa5dc1484b3d2aead7 Author: hiram Date: Fri Aug 10 21:31:58 2007 +0000 Cytoband done, genscan done, lineage specific repeats made, blastz self running, blastz rat running commit 06bc065713fa583524d4211478031780515887f7 Author: fanhsu Date: Fri Aug 10 21:31:48 2007 +0000 Added logic to supprt GSID wigMaf and wigMafProt type of tracks. commit 50afd30ab9ba3cf89a7dc39d443eca119e4647be Author: fanhsu Date: Fri Aug 10 21:30:47 2007 +0000 Added wigMafProt handle. commit 02c3475dc8577def212caf6c7e02d0ce97a15cb2 Author: fanhsu Date: Fri Aug 10 18:23:12 2007 +0000 Updated the array sizes for wigMaf processing. commit 6587750a6b952a3dfbaab087ff8c193782d97e7d Author: fanhsu Date: Fri Aug 10 18:05:47 2007 +0000 Updated array sizes used for maf processing. commit a091b211737996c30c3375ef2559d67d6c217bca Author: hartera Date: Fri Aug 10 15:40:26 2007 +0000 Create a directory for the AGP and FASTA files. Start processing randoms to create an AGP for the virtual chroms for NA_random and Un_random. commit 7ada0a7e503f300f024ad65132f4fc3e7d55699a Author: galt Date: Fri Aug 10 15:00:05 2007 +0000 "Encode release log update" commit d275d2bc966d0be468081c6e780d310113edd4dd Author: galt Date: Fri Aug 10 15:00:03 2007 +0000 "Release log update" commit 10a2b6aed8e41b8751fadb0987733bd8193a949d Author: kent Date: Fri Aug 10 14:03:37 2007 +0000 More SIB stuff. commit 5a13dee0db7906cd3d8d37ebc072b29bd817a6cc Author: ann Date: Fri Aug 10 03:35:00 2007 +0000 changed wording commit fc620d4f25096fabc361471bc7f894eb39ca2d76 Author: ann Date: Fri Aug 10 03:14:01 2007 +0000 a few small changes. commit b1b9e744be1979c1dccf798bd5a58d0a96b1f2bf Author: kent Date: Fri Aug 10 01:49:14 2007 +0000 Adding SIB gene tracks from Christian at Bucher lab. commit eb91b0b91d2b33a292bece6bb80a55b745656a56 Author: donnak Date: Fri Aug 10 00:08:37 2007 +0000 Updated spec from Jim. commit 9f69043ff61d2207bd62f38a055b759de00d3576 Author: hiram Date: Thu Aug 9 23:21:18 2007 +0000 Up to date for build 37 information, with appropriate URL reference links commit 06357d89c6dac9063b8bc15c1fa5eb42501dc09b Author: fanhsu Date: Thu Aug 9 22:57:03 2007 +0000 Created trackDb.ra. commit 29a9a5f943d447ee4ecab085f8abf32e7a9143d0 Author: fanhsu Date: Thu Aug 9 22:56:36 2007 +0000 Added interPro. commit b3b893a0b88cf4c0324d752b8c82a0df29cfd6f4 Author: angie Date: Thu Aug 9 22:54:15 2007 +0000 Added missing cloneString. commit 1fe6a67da002c8030b19b50c148e38dfb003b5cb Author: fanhsu Date: Thu Aug 9 22:50:21 2007 +0000 Created interPro.html. commit 24533cfcb197d6d0dba70ee245a08976b7fb7b75 Author: fanhsu Date: Thu Aug 9 22:49:51 2007 +0000 Updated interPro.html. commit c07f481588bf2167feed4f573e125a747e56531a Author: fanhsu Date: Thu Aug 9 22:38:44 2007 +0000 Created interPro.html. commit 77ca50b059909a35451cc975bd249391d64655c9 Author: fanhsu Date: Thu Aug 9 22:14:53 2007 +0000 Created description.html. commit 1d0fed26678d9e1590818c16e05687d011decffa Author: kayla Date: Thu Aug 9 22:09:38 2007 +0000 added mm9 commit 9954d65584659dd31eba8017799cd6a140e336d5 Author: fanhsu Date: Thu Aug 9 22:08:02 2007 +0000 Updated to latest version by Ann. commit 974bd01756b75884169fac7cbebab51c126c6197 Author: fanhsu Date: Thu Aug 9 22:06:47 2007 +0000 Edited hivGene.html. commit a82b015de80160da9a606b0e54447d252b73262e Author: kate Date: Thu Aug 9 21:48:27 2007 +0000 1. Fixes to Base Position track control cosmetics 2. Indent supertrack vis control on config page (Brooke request). commit ebbd634a96aeefa3c6f82e7fc20fc12cea9aecc9 Author: fanhsu Date: Thu Aug 9 21:41:48 2007 +0000 Created hivGene.html. commit 80c4b1909874e0d0b1ac20f7b2e2f1626b6252f2 Author: fanhsu Date: Thu Aug 9 21:29:54 2007 +0000 Created vax004.html. commit c257ac2c237fe1ff20c3734205420b9f97beb05f Author: kate Date: Thu Aug 9 18:59:13 2007 +0000 Restore original name for method (Dnase-array) pending agreement on standard commit dc5d4a5e911691ba8eb8e17e5e9da41f25c8586c Author: ann Date: Thu Aug 9 17:43:26 2007 +0000 fixing citation commit 0af30071552c99ac819b304cf2c236b65e0213f0 Author: ann Date: Thu Aug 9 17:38:15 2007 +0000 Added organism variable as needed. commit e076b8beb516bf31e814b282287f9549bcbde74e Author: ann Date: Thu Aug 9 17:17:28 2007 +0000 two small typos. commit b26c920275f4c9fca8e40d65a9440cd079632d5b Author: ann Date: Thu Aug 9 17:12:58 2007 +0000 lots of edits. commit 59bedb215f66fd3d9af9c4ffaa8b505abc2aab46 Author: ann Date: Thu Aug 9 16:57:30 2007 +0000 added information about how to choose subjects to view commit 76f45065905dfe9ec6054aa9d3dd6da9136d5be9 Author: ann Date: Thu Aug 9 16:48:12 2007 +0000 Cleaned up methods section. commit f175d9308c26148c48b8c41b3ed482b363e032d5 Author: kate Date: Thu Aug 9 16:39:07 2007 +0000 Restore 1.3 changes in hg17 commit 4ec2f61b74502cd428c7f5939f0fde18f824746d Author: ann Date: Thu Aug 9 16:38:57 2007 +0000 removed line about default subjects being displayed (this is now covered in the Display Conventions and Configuration section) commit 83d88ffcb3af1b345eab7f2d56dc2af873a3d502 Author: ann Date: Thu Aug 9 16:36:22 2007 +0000 Added Display Conventions and Configuration section. commit 30e01f44a8aa35727289167f6b4bea446d071cbe Author: kate Date: Thu Aug 9 16:18:27 2007 +0000 Move GIS description to hg17/hg18 commit 95328a97e17d65fd78898fb5614ae60f420e3ed1 Author: markd Date: Thu Aug 9 16:10:41 2007 +0000 validated command line options commit bb0e73ecaebaf5528447d3c24acf55c4f4ab2ddd Author: galt Date: Thu Aug 9 15:00:05 2007 +0000 "Encode release log update" commit 419d4e1c7063f414d84c3cb6f0c5c3cd9d142517 Author: galt Date: Thu Aug 9 15:00:04 2007 +0000 "Release log update" commit 2d721ec6917b2759dee2c30226c1ac2e89aad9c0 Author: giardine Date: Thu Aug 9 13:32:08 2007 +0000 docs for latest ORegAnno update. commit 694b7eed1889e1f273504231e80c37e6e57fe9b5 Author: kate Date: Thu Aug 9 03:33:49 2007 +0000 Add supertrack info commit 21d307c60b04f906077c492b17e073bb52009825 Author: fanhsu Date: Thu Aug 9 00:07:47 2007 +0000 Changed Sequence View in the top bar to go to hgTracks instead of hgGateway. commit c6d09a30a154b9f14794263ad87af027045717ac Author: hartera Date: Wed Aug 8 23:30:26 2007 +0000 Fixed error. commit a45aea7a2b5e4c4813445974d2bc293ee42fb5e2 Author: fanhsu Date: Wed Aug 8 23:20:38 2007 +0000 Added logic to bypass codon highlighting if the track type is wigMafProt. commit 7d33dc6660bf02917871cc4800ed6736b838a0cf Author: ann Date: Wed Aug 8 23:19:28 2007 +0000 wording and format changes. commit 3c34838144f7c8d10ef4ee701da3e0c4e91b86ec Author: hartera Date: Wed Aug 8 23:18:09 2007 +0000 Added more usage comments. Added code to handle the fact that there is more than one chrom type in the apg and prevent adding a gap line between them. commit 9f270f67df189b817bd6d179f9a1aa9b4a8eebd4 Author: fanhsu Date: Wed Aug 8 23:04:55 2007 +0000 Put the conditional logic in for GSID server. commit 8c2fade5c71ff830ee55bf26d30cc7d823b390f2 Author: fanhsu Date: Wed Aug 8 23:03:02 2007 +0000 Added a section about Sequence View. commit 5e4a62ebbe0ba0106043f8a97574a3f51025a6a1 Author: ann Date: Wed Aug 8 23:01:29 2007 +0000 Italicised journal names. commit 44d07e931719cb6b0c3072951101b23adc7d8788 Author: hartera Date: Wed Aug 8 22:40:29 2007 +0000 Initialized hash and list variables. Removed unused options code. Removed printfs for debugging. commit 11f6fddd6c9367101747398b8ed4f84bc8954be5 Author: fanhsu Date: Wed Aug 8 22:31:01 2007 +0000 Added breaks for every 6 items in the species not displayed list. commit f1e5d1de210ec4edf5c1587b5c71c1e4af8fc824 Author: hartera Date: Wed Aug 8 21:29:18 2007 +0000 Program for adding new fragment names to agp file and to add gaps between scaffolds. Developed to use for the danRer5 (Sanger Zv7) assembly. commit a21c4985d2af09bc70c3f3025cf6f4f10aad8155 Author: fanhsu Date: Wed Aug 8 21:28:12 2007 +0000 Changed number per row from 5 to 6 for GSID maf details page, per Ann's suggestion. commit e37486816191b1456f5676cf3abf5a8ded51a02e Author: fanhsu Date: Wed Aug 8 19:31:01 2007 +0000 Updated HGNC link. commit 2698747f8f1c9864ddfcf361ae49369ad6b85e01 Author: fanhsu Date: Wed Aug 8 19:01:11 2007 +0000 Removed a fflush(), per code review with Kate. commit f83d1370fc0023fdffbb602a73afa200b556aad3 Author: fanhsu Date: Wed Aug 8 17:42:35 2007 +0000 Created two functions to do specific mafClick processing for GSID MSA track. commit 16a1a279afb607e967e232730c0331f7b34b5266 Author: kent Date: Wed Aug 8 16:58:02 2007 +0000 Adding SIB transcriptome splicing graph and splicing events tracks. commit 39ab1ebd60908754c3d2db028a15a8b4b152cdaa Author: galt Date: Wed Aug 8 15:00:05 2007 +0000 "Encode release log update" commit 70683ef61d325fee3f16071d232680921f8593a9 Author: galt Date: Wed Aug 8 15:00:04 2007 +0000 "Release log update" commit 03d56142e55235594a1f795a7b399dd065db0a9b Author: kate Date: Wed Aug 8 00:48:11 2007 +0000 Updates commit 79c43b86ca5bec1f8c7d2c38f4d642748ca874bd Author: kate Date: Tue Aug 7 23:49:08 2007 +0000 Remove HTML format error commit cbb1fde9c8c6acde74301cb621a63542d89dd071 Author: kate Date: Tue Aug 7 23:38:02 2007 +0000 Adding for hg18 commit 68164e2b7e877504bd7c824f3bee09ae4a925f3a Author: ann Date: Tue Aug 7 23:32:13 2007 +0000 prettied up commit b79c4fe017921d9578df953d5f8fc1d142b496dc Author: ytlu Date: Tue Aug 7 23:27:55 2007 +0000 correct: hc to hgc at the first comment of code commit 874e7a757ddbd687c6666ece724ae53437bcf29c Author: ann Date: Tue Aug 7 23:12:09 2007 +0000 prettied up commit 1570c5ad4e192bc2006d174fb544ebf61ba76582 Author: aamp Date: Tue Aug 7 23:05:15 2007 +0000 Injured this file on the last commit... putting the '#' back. commit 0eb813eab6bca45164d17c18bf26359148013b13 Author: aamp Date: Tue Aug 7 23:03:05 2007 +0000 Uh oh, I named some files wrong. commit e6eb84de59f4ef0387184627e5f003dbcd592d95 Author: ann Date: Tue Aug 7 23:02:36 2007 +0000 cleaned up citations in Reference section. commit 35f58db11810e405775d303db2cd4d06596ee851 Author: aamp Date: Tue Aug 7 22:58:29 2007 +0000 Added descriptions. commit 4c3d46b67278d17c41988a1f3d4730d39624cd33 Author: aamp Date: Tue Aug 7 22:42:57 2007 +0000 Table name changes. commit aba6cdb1646f12b142c00a2c61be0fa92ae40568 Author: archanat Date: Tue Aug 7 21:18:29 2007 +0000 added mm9 to chainDest commit 2c5a55d40c6e6fc7b4794cef7c071f4a8091825e Author: ann Date: Tue Aug 7 21:15:48 2007 +0000 edited citations in Reference section commit e247d908c63598d4ac9310eb1c952314844f65d6 Author: fanhsu Date: Tue Aug 7 19:32:50 2007 +0000 Added doVax004(). commit 38aaffbfaca0619459c87dde4721efd522e080f5 Author: kate Date: Tue Aug 7 18:44:27 2007 +0000 Restore file commit 260556515ba16e198fe01691864265c58ecdbf1b Author: hiram Date: Tue Aug 7 16:58:35 2007 +0000 Add more files to the clean target, and replace () with {} commit 10a0aebbc2918dfe18e4e347e106b2115505dc10 Author: fanhsu Date: Tue Aug 7 16:48:37 2007 +0000 Updated search expression of hivGene. commit 33dc3fe938a83342372e080933890b48bc51e270 Author: hiram Date: Tue Aug 7 16:48:23 2007 +0000 Safe rmdir becomes rm -fr commit e21f2592673335990ff585cc6def46d7ae56ce13 Author: fanhsu Date: Tue Aug 7 16:40:56 2007 +0000 Updated some wording. commit 0fa2d2a9aa384db25d43e37b9efbb4e257d0e399 Author: aamp Date: Tue Aug 7 16:35:17 2007 +0000 "New version number v165" commit a9abdd32694afbf082ab44f3a7330821d96726de Author: hiram Date: Tue Aug 7 16:34:55 2007 +0000 add clean target to get lib and altSplice directories cleaned commit a02702826253ad3d2e987952ffde22ed8c329624 Author: hiram Date: Tue Aug 7 16:32:08 2007 +0000 Initial source to support ce4 orfToGene track commit d256b4727ab005f19f7d639f9aac5a1240138e91 Author: hiram Date: Tue Aug 7 16:27:05 2007 +0000 Do not need a on the first protein commit 23edb24ef0b7b793a7894e81dadb853cacd7c8b4 Author: aamp Date: Tue Aug 7 16:18:21 2007 +0000 Yale PolII stuff... not done. commit e258c46065ed6f3b3ef2442bc0763d76ef0287d9 Author: fanhsu Date: Tue Aug 7 16:11:07 2007 +0000 Created vax004.html. commit 0d53376eb9cf491d941daa026fc7d63db0eaf361 Author: fanhsu Date: Tue Aug 7 15:51:44 2007 +0000 Created vax004AaCons.html. commit 05af3aa9bd04f3e082898e11914998b7ac11f641 Author: fanhsu Date: Tue Aug 7 15:37:34 2007 +0000 Created vax004Cons.html. commit 41784ec19a7d6d3e127a35eec830943cc524a181 Author: galt Date: Tue Aug 7 15:00:10 2007 +0000 "Encode release log update" commit 6bcd909ff88790306506216ec917293622f69e3c Author: galt Date: Tue Aug 7 15:00:05 2007 +0000 "Release log update" commit 4cafaad662ebf6da987d2777eac8d0fdd8650403 Author: hiram Date: Mon Aug 6 23:50:22 2007 +0000 Completed reload of regPotential7X track commit 9f34de1e3356cc425b1c573d401dca1463a79208 Author: hiram Date: Mon Aug 6 23:49:40 2007 +0000 reworked STS markers to eliminate the "-" named items, and completed BAC Ends track commit e018972c3762f2ca9196c1940ef1480c8a3342c1 Author: fanhsu Date: Mon Aug 6 23:40:52 2007 +0000 Reversed one previous change (that disabled custom track for GSID). commit 2f28e02da5035e7baa2b98bb4ac7fb36fb96f3b6 Author: fanhsu Date: Mon Aug 6 23:34:31 2007 +0000 Reverse previous update (that disabled custom track for GSID). commit 672b6e888f0dd84dec9063978140b8445f215a4d Author: hiram Date: Mon Aug 6 23:26:04 2007 +0000 Properly parsing mm9 lift and agp files commit fc768d513ebf2734b9dbd4efca289b14135b31b6 Author: kate Date: Mon Aug 6 22:26:50 2007 +0000 Label tweak for supertracks commit 9b8b9480690ddadb84434d8a55cef2307323e87a Author: kate Date: Mon Aug 6 22:26:01 2007 +0000 Header tweak for super track page commit 86bfcbebb3149155203390fd92423b79d73c69bf Author: kate Date: Mon Aug 6 22:24:10 2007 +0000 Layout tweak commit 6b29020be245475c6a6705367beefc27d5c6070e Author: kate Date: Mon Aug 6 22:23:24 2007 +0000 shorten track label commit b753a00af4e0b9fa763a963e13254e8ebe5cb094 Author: hiram Date: Mon Aug 6 22:14:07 2007 +0000 Source used in mm9 processing commit b5070c930dc209d10fa9bb89e59ce13cdf19aa8c Author: hiram Date: Mon Aug 6 22:09:39 2007 +0000 Better garbage sorting, and name mangling to eliminate the - names commit 0b50040fd28cdf40e98c1f3c9ec25340da122cda Author: ann Date: Mon Aug 6 21:53:55 2007 +0000 correction to usage statement commit af94b5c2c63aa0380876dd36b0f2d86d6bb50b6d Author: ann Date: Mon Aug 6 21:50:37 2007 +0000 edited joinerBatch* scripts to accept a fourth parameter (extra) which will work on 'other' types of databases (e.g. protein and go databases). I did NOT mean to commit the checkEncodeRegions.csh script with this check-in. I'll see about un-committing that file! commit 477910e2079c6fdfb23e8f3d9a99821016250028 Author: kate Date: Mon Aug 6 21:49:12 2007 +0000 Fix show-all for supertracks commit ff142879c3c4abb72d74f46f8414b871985229e1 Author: hiram Date: Mon Aug 6 21:35:03 2007 +0000 Initial source, patterned after ancient split.pl used in bacends processing commit 49b86e0aee03437e3e00ec1567db2fecafa2233c Author: fanhsu Date: Mon Aug 6 21:12:22 2007 +0000 Created vax004AaMaf.html. commit b27a1063ab4318810d7d2f9fce91bcab86b5aebb Author: kate Date: Mon Aug 6 21:09:59 2007 +0000 Move to encodeTxLevels group commit bf67143185147cbbce5f9fddfa95b961d3df4cf2 Author: fanhsu Date: Mon Aug 6 21:05:35 2007 +0000 Created vax004Maf.html. commit aa229ac0651139e482ec6dd41f17c2d4e38e4445 Author: angie Date: Mon Aug 6 20:04:35 2007 +0000 Updated to use doHgNearBlastp.pl instead of manually blasting everything. commit 7eb4f0234193a6ea8adb940f946ad524d68ba10b Author: ann Date: Mon Aug 6 18:52:43 2007 +0000 added description about the display of black codons at the end of chromosomes commit 78beeb94be9d6436c2d790ac3c85f8f7c7fd0c4d Author: angie Date: Mon Aug 6 18:34:00 2007 +0000 Updated refs to PubMed style. commit 99d0d310b1a465335d449eb2a7e9dcbd0f03308d Author: angie Date: Mon Aug 6 18:33:05 2007 +0000 Added other authors to references. commit c56e69cb506fce5bea7b145c370a39e4889ea55f Author: angie Date: Mon Aug 6 18:28:41 2007 +0000 Converted references to PubMed style. commit 6865faf93750f828d0ff4b6ac0649261c422a3fc Author: angie Date: Mon Aug 6 18:17:41 2007 +0000 Loaded up genomicSuperDups and wssdCoverage from Eichler Lab. commit bfc636d67afe78020c56154116f81c461da0627b Author: kate Date: Mon Aug 6 18:12:51 2007 +0000 Add phastCons paramerters to 17way track description commit 263c773772813f7b0ae0738b7eea4b398e3edf78 Author: galt Date: Mon Aug 6 15:00:06 2007 +0000 "Encode release log update" commit 53c1208a5dfc895c08afe475eb742a205b2b135e Author: galt Date: Mon Aug 6 15:00:04 2007 +0000 "Release log update" commit e8e0d1135f4a18353e99d9919145e3c66c85e2e0 Author: kate Date: Mon Aug 6 04:11:08 2007 +0000 Add supertracks to ENCODE ChIP group commit 3a553ac18fc84db8aec6a11435f5985f692f37e7 Author: fanhsu Date: Sun Aug 5 16:12:31 2007 +0000 Disable custom track for GSID. commit 4123bda16ddc047bde313ca7a33e9e1a592245a2 Author: fanhsu Date: Sun Aug 5 16:02:09 2007 +0000 Disable custom track for GSID. commit 1c01433f154a83cabb8cda7a80a8f8202220ef1e Author: galt Date: Sun Aug 5 15:00:06 2007 +0000 "Encode release log update" commit 015769a24ab744dd8ef2a55f1831a89f8951a77f Author: galt Date: Sun Aug 5 15:00:03 2007 +0000 "Release log update" commit 609ee9eeebb17e29a1df60a2c8daaac444d9529c Author: markd Date: Sun Aug 5 01:10:19 2007 +0000 prebuild downdirectory commit cf99c9198aba1d8645f0ab76b826d050cfe2de58 Author: fanhsu Date: Sun Aug 5 00:50:53 2007 +0000 Added def for gsidSubjList and gsidSeqList. commit e9d77f5962538744156f851a7489a06f5aa25cca Author: kate Date: Sun Aug 5 00:45:09 2007 +0000 Add supertracks commit e9071f2e69055ac46f9aab3780516d8b291ec4b5 Author: fanhsu Date: Sun Aug 5 00:38:04 2007 +0000 Updated tittle for GSID. commit 6ada5a2798b7a9969dc2bd15d88c2cca54d0b135 Author: kate Date: Sun Aug 5 00:33:25 2007 +0000 Improvements to supertracks: 1. Fixes to hide-all, and in custom tracks browser line. 2. Readability improvements from code review commit 5e38a73766d6ef4b2b9ccf13433edaabc7d11527 Author: kate Date: Sun Aug 5 00:28:42 2007 +0000 Fix supertrack show in menu to be normal text, as it doesn't update in response to other menu item changes, so can be misleading commit 005e74003d855021fc3513a74c817abd4690448f Author: fanhsu Date: Sun Aug 5 00:18:41 2007 +0000 Updated trackDb.ra for Milestone 3 deliverables. commit dc4f18243079d8159b87138f22966553b9156e42 Author: fanhsu Date: Sat Aug 4 22:52:40 2007 +0000 Change tittle if the browser is for GSID. commit 39f018eccf78c4ffc0a9ebde727a3631aad8f90c Author: fanhsu Date: Sat Aug 4 17:29:07 2007 +0000 Added logic to bypass message about TB during Get DNA. commit 14a127022ee31c67b9addb562f4cfcd58827006d Author: fanhsu Date: Sat Aug 4 16:25:20 2007 +0000 Added saveDefaultGsidLists() and associated logic to initialize lists of selected GSID subjects and sequences if the user haven't select them. commit c14ce4a89d1a8580926af2af0ade4a52fc089771 Author: galt Date: Sat Aug 4 15:00:05 2007 +0000 "Encode release log update" commit 23c9c39f6632eb4b157a4b6fda45324bbcd3e90c Author: galt Date: Sat Aug 4 15:00:04 2007 +0000 "Release log update" commit 3479dc6d5a2ae9473f4bd37e1783fdc6017887dd Author: angie Date: Sat Aug 4 00:20:31 2007 +0000 Added wssdCoverage from Eichler lab. commit 4dd955b7acc8d2fefc76a15165fdc16fb1ed4658 Author: kent Date: Sat Aug 4 00:06:42 2007 +0000 Adding biggestAtg option. commit 37472d3b538c7b9912a45f31881980f144b3dedc Author: kent Date: Sat Aug 4 00:06:11 2007 +0000 Adding -anyStart option. commit 838eca1a7b8e2885fd32bb43150fa33b807d951f Author: hiram Date: Fri Aug 3 21:42:07 2007 +0000 Reverse meanings of TJ,TK and S,T end codes commit e0d3bd4e3c55a907e611276f00bb07d41bffe5d4 Author: donnak Date: Fri Aug 3 20:56:13 2007 +0000 Added more dummy links for Sol's Science paper. commit a110cc7d4382bdbf32260a5c550733b48d90f9b9 Author: giardine Date: Fri Aug 3 20:28:34 2007 +0000 Add 2 new LSDBs to credits. commit 90cafb0b5eb8adf9d1431f60cf90c517d6ffad64 Author: giardine Date: Fri Aug 3 20:27:03 2007 +0000 For ORegAnno track links, make it handle cases where url requires 2 "accessions" commit e5cb507c384801075e7f650d9ae2b0a5a186b950 Author: archanat Date: Fri Aug 3 18:51:21 2007 +0000 relaxed minCheck for mm9.all_sts_primer.qName for identifier mouseStsTrueName commit 7a6f573bb97ec7b85f2b8f352c20ee423e47367d Author: hiram Date: Fri Aug 3 18:31:36 2007 +0000 Reset default position, start genbank daily updates, starting BAC END build commit b783b4d1514a53989907459979f2ca02b084c6d9 Author: hiram Date: Fri Aug 3 18:30:38 2007 +0000 Added mm9 - Mus musculus commit 85d0382ae667b25e8e5a3ef7cd2260fb2520bebf Author: ytlu Date: Fri Aug 3 18:25:40 2007 +0000 correct off one base error for putative pseudo/coding element page commit d686799afc5f7320997cc6534fc29408614c53bb Author: donnak Date: Fri Aug 3 16:52:44 2007 +0000 Minor change to news item. commit 6e64c26d1b8a3299e56edeb5afe26fe0cbfa5570 Author: hiram Date: Fri Aug 3 16:46:12 2007 +0000 Correct spelling commit 7abd0f04e5143eceb0fb3082f5f30d54bb7239db Author: hiram Date: Fri Aug 3 16:45:40 2007 +0000 Minor fixups commit 64543f4e21cdb786a094e64ea2ea7147149fc818 Author: hiram Date: Fri Aug 3 16:45:12 2007 +0000 Properly closing DBSTS instead of FILE commit dee487f9ff63694e18e8aac32d01f18f11880afd Author: hiram Date: Fri Aug 3 16:44:33 2007 +0000 Now properly specifying 2bit file, was previously pegged to mm8.2bit commit 68895f07da6a1715ca6927272ae51b1b326d2a9b Author: hiram Date: Fri Aug 3 16:42:51 2007 +0000 Change parens to brackets, add compile and clean target commit 4b65cb6080034ba0a26e96da38ce3d856c3ad0ed Author: hiram Date: Fri Aug 3 16:41:12 2007 +0000 More extensive name checks commit 0ab2074afcf17f6597c323e4f60c7b0d61a50e98 Author: hiram Date: Fri Aug 3 16:39:51 2007 +0000 Properly processing only the C57BL/6J strain commit ef67fc868bc875efcd0281b87ecfd45653425210 Author: hiram Date: Fri Aug 3 16:33:17 2007 +0000 Reformat a long if() statement, and a better error message printout commit 0aac3b0d24230979ba3308ce442935ae26f97c47 Author: galt Date: Fri Aug 3 15:00:06 2007 +0000 "Encode release log update" commit c829c283720152bdbafd14cf784ea75114368100 Author: galt Date: Fri Aug 3 15:00:04 2007 +0000 "Release log update" commit 6ed43115fd26332e26200b0c0393c23034f39e8d Author: fanhsu Date: Fri Aug 3 13:32:48 2007 +0000 Changed HGNC URL per HGNC's announcement. commit d8d25aa14f753fd65ab3152de95c7f90515f1ff4 Author: markd Date: Fri Aug 3 05:07:20 2007 +0000 enabled update of bosTau3 commit 5ecf2496c34efc71a596e354ea70c458b30fb94a Author: markd Date: Fri Aug 3 04:58:19 2007 +0000 added error detection for cases where there is nothing to validate commit c556670a46387124dc6d76c4772e5eff03a2061b Author: braney Date: Fri Aug 3 00:48:46 2007 +0000 a slight change in atom track display commit c2f0ac6f51c81599c2a2111963b056069093fe8f Author: hiram Date: Thu Aug 2 23:44:25 2007 +0000 Improved ctgPos search commit 6a5a85954452e7c72dbba483c97cee11ceee1f1e Author: heather Date: Thu Aug 2 23:36:07 2007 +0000 handle if count1 == count2 commit c6fe04c98668c13cc2183b145c7ed3976b0dc5ef Author: kayla Date: Thu Aug 2 23:05:27 2007 +0000 added 5 worms. commit bfa82ef7df494caaae47170e2908003982e2b22e Author: ann Date: Thu Aug 2 23:04:46 2007 +0000 made several small changes -- mostly based on feedback from Bob during code review commit f1d446de5b47f21686f92c7aaadd3a992cf977f4 Author: hiram Date: Thu Aug 2 22:48:12 2007 +0000 Stray line at the end commit c7e361d9148d3f2b90f644445ae75f9941e010c7 Author: hiram Date: Thu Aug 2 22:46:00 2007 +0000 Can have four of these tracks together in one commit 56b7d64c8202a36474c86e86b1e1e5ebca836366 Author: hiram Date: Thu Aug 2 22:03:06 2007 +0000 Split up the nucleosome track into three different tracks commit b4c143eaf7e144f57e8ce63d21648f780f902a27 Author: archanat Date: Thu Aug 2 20:57:24 2007 +0000 added srpRNA to the list of RNA repeats commit d8e6d94c9690a4e908e9dd21e84656bbd11df59b Author: hiram Date: Thu Aug 2 19:18:42 2007 +0000 Creating all the xxBlastTab tables commit 14c644ba10771a988afa50f6547e7740e08d574e Author: galt Date: Thu Aug 2 18:39:21 2007 +0000 undoing change 1.1323 (except for renaming psRcBoth to psRc) commit 7e144a4defd40002b2aca55e29378115f57b9432 Author: giardine Date: Thu Aug 2 18:04:28 2007 +0000 Added new EnsemblGene link for the ORegAnno track (dm2 and rn4). Should be able to remove old ones once all data is switched over to new. commit 89c94ea11d9b65e0a3364cf9b108f4fc965f14c4 Author: kayla Date: Thu Aug 2 17:06:42 2007 +0000 Changed the date on the ce4 description page per Donna. commit b59591d3ba5d0bfb2bf10ab10d3460b00878d762 Author: fanhsu Date: Thu Aug 2 17:00:45 2007 +0000 Added vax004 track. commit d4c2df407a41f6fdf88e5fea8a1290f226db2da1 Author: kuhn Date: Thu Aug 2 16:36:07 2007 +0000 removed heather from output list commit 7588c9134d6ce77de49a2da64b5ef2543b06f79c Author: galt Date: Thu Aug 2 15:00:05 2007 +0000 "Encode release log update" commit 10235b5c3865d8ded02f47ffef74cb3606377ded Author: galt Date: Thu Aug 2 15:00:03 2007 +0000 "Release log update" commit 03379fc725c35da7532267cd3c0249eea1d0ff4e Author: donnak Date: Thu Aug 2 14:31:42 2007 +0000 Added more people to worm credits. commit 5899c8801851cf58f4a88d9072fa5327be162070 Author: donnak Date: Thu Aug 2 07:58:11 2007 +0000 Edited this file. commit 10d29812bbb3db4ba567f17bdc75ab4710f8cf53 Author: donnak Date: Thu Aug 2 06:44:29 2007 +0000 Added announcement about worm browsers. commit 052b4a5d65d870d577bd0dce3b9bdf826193cc38 Author: donnak Date: Thu Aug 2 06:44:11 2007 +0000 Updated worm credits. commit fa0d09cb42c89a331be6709c8ca94175319e2a6f Author: donnak Date: Thu Aug 2 06:43:49 2007 +0000 Archived an item. commit 831ff6d5428e0a0e4db28ffce6f5df9f9efe2a65 Author: donnak Date: Thu Aug 2 06:43:34 2007 +0000 Updated caeRem2 entry. commit 53669e18cabb80ab0712500a5b513ff67fc29ac4 Author: galt Date: Thu Aug 2 01:35:03 2007 +0000 refactored psl.c combining pslRcBoth and pslRc so that pslRcBoth is gone commit aa48ad34f566c18ec7823e1a52a865ac8e10a238 Author: galt Date: Thu Aug 2 00:54:01 2007 +0000 removing unneeded variable tRcAdjustedStart, now that the bug in psl.c for pslRcBoth has been fixed commit f462cbfe71ec8601b96521d0247ec3e321e25b6e Author: galt Date: Thu Aug 2 00:52:58 2007 +0000 fixing bugs - the tStart and tEnd do not need flipping. also cleaned up unneeded casts. Also fixed minor bug in Marks version of pslRc commit 6b0a9216f6108021f6f8b6fc83da7a50e14176f2 Author: hiram Date: Thu Aug 2 00:05:48 2007 +0000 Shorten nucleosome map short names commit 87c2b3985c227a79adf6aebd92883fb9dce9213b Author: hiram Date: Thu Aug 2 00:04:49 2007 +0000 rearrange nucleosome map tracks commit a3ac2f7eba64437d5e6473cec41a77470a8f553c Author: kate Date: Wed Aug 1 23:55:24 2007 +0000 Tweak label of supertrack link (suggestion from Galt) commit 0d277a7176c298598109fb71f5d3dcb3244c4787 Author: kate Date: Wed Aug 1 23:53:35 2007 +0000 Remove unnecessary Group table header when track group is collapsed commit 3b5e7a7e53215c3c6ba0baf1885a84b5941ca3ef Author: ann Date: Wed Aug 1 23:03:32 2007 +0000 prettied-up formatting commit 0d45fb22502b426ee94bd640468488917c44a6c2 Author: kuhn Date: Wed Aug 1 22:31:37 2007 +0000 remove versioni-checking, as it is brokeninstall commit b527c10bcacaabf62f9a1dfb79566f039965d905 Author: fanhsu Date: Wed Aug 1 20:45:55 2007 +0000 Added "(log in required, registration is free)" to Affy's link. commit 2a267191560d76d1799a901e66260953fb74fa8c Author: kate Date: Wed Aug 1 20:01:55 2007 +0000 Move GIS RNA from Genes group to Transcription, by request of Ting commit 789c1366f529a75b8d579821b21fe98db2547191 Author: donnak Date: Wed Aug 1 19:46:16 2007 +0000 Added 5 worm assemblies. commit 30738ae81bf08470de3eaea1ed8da2e011e4ac81 Author: kate Date: Wed Aug 1 19:30:32 2007 +0000 Fix problem with fat blue bars on config page that appeared on Firefox for collapsed track groups when track reordering was turned on. Thanks to Ann for the fix! commit b12b302981e8d3a11f58c31d90ce27a393908388 Author: jzhu Date: Wed Aug 1 19:24:26 2007 +0000 Lightly refactoring code for better readability and simplicity. commit 899e33263262cc69102aca8e1a917591513d9573 Author: jzhu Date: Wed Aug 1 19:23:52 2007 +0000 Updating makefile so that it actually makes. commit 39536d07346f9fe868924025ea20ee66b60465da Author: jzhu Date: Wed Aug 1 19:23:11 2007 +0000 Adding a little test program for Jing. commit 9480394b8e8e561096188091cdbaa7e38ae4c4d4 Author: ann Date: Wed Aug 1 19:21:03 2007 +0000 changed user to whom email gets delivered from hardcoded name to $USER variable commit e21b263512b1e711c84c80f738576a57e58bcd66 Author: kate Date: Wed Aug 1 19:19:19 2007 +0000 1. Change group names. 2. Copy class table for pseudogenes track commit e4cec1807debb3c9cbe568592bbec4ac9aebeea3 Author: angie Date: Wed Aug 1 19:03:38 2007 +0000 oops, quick formatting fix for jaxRepTranscriptAlias.alias (thanks Archana). commit 12d79a5a80ccbfffe634c8510b5151d4529ab6ab Author: ann Date: Wed Aug 1 18:07:42 2007 +0000 changed searchPriority of snpArrayIllumina* tables from 13 to 14 so that they would show up after the HapMap SNPs in the search results page. commit 15546bb84f14e1ea6abeeee1feda075900acd36e Author: archanat Date: Wed Aug 1 17:42:09 2007 +0000 removed 'Clone' from the types of gaps. commit 792febd67dba13106def911fde77e6325dd0432e Author: donnak Date: Wed Aug 1 17:07:05 2007 +0000 Added entry for Katzman pub, commented out for now. commit df331bfc3a6ea833aae0dec7df2b7485b6e5290d Author: galt Date: Wed Aug 1 15:00:08 2007 +0000 "Encode release log update" commit 047c19366851a6f57355de7e4a589dce5c81c9ce Author: galt Date: Wed Aug 1 15:00:04 2007 +0000 "Release log update" commit 525622bd5b4db9ad71da1dc1db354f785c3e2767 Author: mhoechsm Date: Wed Aug 1 01:14:16 2007 +0000 checked back in after recovery steps taken by browserstaff commit 06ce7743ffa6be3b6fd9258e5cb3f1489fbfb4be Author: mhoechsm Date: Wed Aug 1 01:04:45 2007 +0000 added new features for rnaHybridization commit e7b5ba2ddb27d915d1a143aa8287e47ac1a2a0b0 Author: donnak Date: Wed Aug 1 00:57:25 2007 +0000 Added link to GARField browser. commit 0dee8de61966bf2aeab9ed43d083028d81baae5f Author: kate Date: Wed Aug 1 00:30:01 2007 +0000 Move STAGE track out of this track group (to encodeChip commit adecf594dbeae6667e0a0d60512d284abbd0a48e Author: mhoechsm Date: Wed Aug 1 00:29:21 2007 +0000 added new fields commit 9dcbb9821f2f910ffe676af73636f422ca6dbd70 Author: kate Date: Wed Aug 1 00:15:11 2007 +0000 Fix regexp for matching subTrack and superTrack settings -- this was broken in 1.326, attempting to accomodate tabs (not needed, as these are stripped from settings) and simplify commit b9d7eafe5e5a54eafd5b913f9df1f911d357f60f Author: galt Date: Wed Aug 1 00:12:53 2007 +0000 removing stuff that broke the build because the .h file was not checked in commit a6da1690a97e85a3771786404411bcf53ebfc96f Author: hiram Date: Wed Aug 1 00:11:11 2007 +0000 group map for the nucleosomes commit 370ede5e7807a310e3915b3d1b333c00eca13aaf Author: hiram Date: Wed Aug 1 00:09:37 2007 +0000 Adding nucleosome data from Andrew Fire and Anton Valouev commit f72d59a63e6138d4461dcf2bee9b4cf142e196bc Author: ann Date: Wed Aug 1 00:01:39 2007 +0000 fixing up links and adding new links commit 80d91e991397d22d2d58638346ed68c5a1ca928a Author: ann Date: Tue Jul 31 23:34:41 2007 +0000 fixed typos and formatting commit 471cd5e0053ebd5fdbfc2b2e8efec1f1daf1e55d Author: hiram Date: Tue Jul 31 23:34:08 2007 +0000 Add $ce.sangerGeneToWBGeneID.sangerGene to the sangerGene name checks commit 99b5f9849609ec1690c5ed28bcf9d9fda78b775f Author: kate Date: Tue Jul 31 23:13:40 2007 +0000 Add assembly to config page commit 59fb2f171748b095f2b989bfc1653f3a1a85e512 Author: kate Date: Tue Jul 31 22:49:09 2007 +0000 Expand liftOver message to accomodate arbitrary note commit 8bfd9435dc16b6190bca937a6127214926864e20 Author: fanhsu Date: Tue Jul 31 22:43:23 2007 +0000 Created hivGene.html. commit 724841e643a3acb8e434a291043935ef2bd94c97 Author: kate Date: Tue Jul 31 22:04:07 2007 +0000 Add genome assembly to section title of configure page commit eba1e9fad60c146a773b99f9d6cb4c01e714be11 Author: fanhsu Date: Tue Jul 31 21:11:51 2007 +0000 Explicitly show the content of old.bed. commit 8ba0e0a4531f009f596b059d3065ed3d926d815d Author: fanhsu Date: Tue Jul 31 21:09:17 2007 +0000 Created hivGene track. commit faaefacc3e8444dc134a87fdaddfa909a064764d Author: ann Date: Tue Jul 31 20:29:32 2007 +0000 added two tables to snpArrayHg18 rule commit 95ae996e123be56722573e3ac9fa339784633b9f Author: donnak Date: Tue Jul 31 20:09:39 2007 +0000 Edited the references in these files, fixed a few typos, did some other format changes. These probably need another pass after Ting makes further edits to content. commit 4bc4949b5018fa8c6f204666d81d01aeb02164b0 Author: angie Date: Tue Jul 31 19:23:04 2007 +0000 One more straggler that needed to use getDbAndGenome. commit 77226efa1bb22a3bcbd70fca5c39e3c6a672d808 Author: angie Date: Tue Jul 31 18:34:13 2007 +0000 More jaxQTL* track label updates. commit 92c5e9ced050037ce502e09eef3c81833d1104f6 Author: angie Date: Tue Jul 31 18:33:34 2007 +0000 Spelling correction. commit 2f86c1e4c4fa65267d621d9c5dacdced72865429 Author: angie Date: Tue Jul 31 18:24:53 2007 +0000 Updated jaxQTL description. commit 7be1fba640b6fd8f33eb047b65d82971c3cda5f9 Author: tingwang Date: Tue Jul 31 17:54:41 2007 +0000 new track, encodeBUORChID commit 9cef764c7b2d59f2cfc4263b65e1d41d6e3f62af Author: archanat Date: Tue Jul 31 17:15:31 2007 +0000 removed Pre-Draft from the list of clone type key commit d42d84d584aebf6d740cb3d3ee03624f186cddd3 Author: archanat Date: Tue Jul 31 16:47:26 2007 +0000 added mm9 to the list commit d65eee34d7e55a86f85ecad818ded267a6efd252 Author: aamp Date: Tue Jul 31 16:40:24 2007 +0000 Wiggle lift notes and Affy EC data. commit 697347e4b0dbc8c51c71049f6bd3bf51129865c2 Author: galt Date: Tue Jul 31 15:00:05 2007 +0000 "Encode release log update" commit 2300ce79b64af1828933deb5d3be445989499bd9 Author: galt Date: Tue Jul 31 15:00:03 2007 +0000 "Release log update" commit 6e17db06e159964719ae37b7eaf94554e6647ac9 Author: aamp Date: Tue Jul 31 09:48:57 2007 +0000 EC tracks. This'll probably be revised a few more times. commit 650c431884bbe8d6d60c49722487bc66b38bf024 Author: kate Date: Tue Jul 31 01:08:57 2007 +0000 Reimplement supertracks for improved visibility control features commit 2ae016ad7e73e65bfd99c0d0056f10338fdc7b5d Author: tingwang Date: Mon Jul 30 23:17:35 2007 +0000 description of super track encodeYaleRnaSuper commit a694094bfcea1a0fcd4cdede4a127547391e1ad8 Author: tingwang Date: Mon Jul 30 23:17:20 2007 +0000 description of super track encodeYaleChipSuper commit be5e12ea6b78ca2ba72778ccb75a3a5a6255ca0e Author: tingwang Date: Mon Jul 30 23:16:48 2007 +0000 description of super track encodeUwDnaseSuper commit e7ce63e30cf8149d57e406ede275d62031f5ed07 Author: tingwang Date: Mon Jul 30 23:16:22 2007 +0000 description of super track encodeUvaDnaRepSuper commit 2796959719a82220c8ba8277cf9daf71b5a95c50 Author: tingwang Date: Mon Jul 30 23:15:49 2007 +0000 description of super track encodeUppsalaChipSuper commit 87daed4e1c4e22ab9fbdc005147edae5351e6dcd Author: tingwang Date: Mon Jul 30 23:15:10 2007 +0000 description of super track encodeUcsdChipSuper commit b5b0cd9d7b47038e2094a57df3c928566016d5ee Author: tingwang Date: Mon Jul 30 23:14:36 2007 +0000 description of super track encodeUcDavisChipSuper commit 583d2745d6dabec667740903133f4a6a1653c1fa Author: tingwang Date: Mon Jul 30 23:13:54 2007 +0000 description of super track encodeStanfordChipSuper commit 89a63b8f67708071e2f579c9b790f2f625e1b4cf Author: tingwang Date: Mon Jul 30 23:13:21 2007 +0000 description of super track encodeSangerChipSuper commit 4f7022552ce30518757712bd3b2acc1762b2afd8 Author: tingwang Date: Mon Jul 30 23:12:29 2007 +0000 description of super track encodeGencodeSuper commit 2e5e978c957e6a2eb9b50cf4f194e0eae17393dd Author: tingwang Date: Mon Jul 30 23:12:05 2007 +0000 description of super track encodeEgaspSuper commit 98b35c383d02d4a35dc337eea808e53d13f2e75d Author: tingwang Date: Mon Jul 30 23:11:42 2007 +0000 description of super track encodeAffyRnaSuper commit f0aea3d0ae3293b985501b8748adbaacde733124 Author: tingwang Date: Mon Jul 30 23:11:04 2007 +0000 description of super track encodeAffyChipSuper commit 5be5828d984c1a17cf51112fdfd66eb12225080c Author: tingwang Date: Mon Jul 30 23:09:44 2007 +0000 description page for encodeBUORChID track commit 922cee91be167478ce4f443c4473ba8503a29748 Author: fanhsu Date: Mon Jul 30 23:00:10 2007 +0000 Changed interPro track from psl to bed format. commit ba56ebe94ddcf6a8e2156a9358cee212b56f0872 Author: fanhsu Date: Mon Jul 30 22:57:01 2007 +0000 Added InterPro track for hiv1. commit 56284c1f525c1ccdfe73efd774e7d4db6392e110 Author: tingwang Date: Mon Jul 30 22:56:16 2007 +0000 document on building new encodeBUORChID track on hg18 commit 864e054c2e7cb8ab64965fbf3f9805a88ea54bfa Author: hiram Date: Mon Jul 30 22:51:59 2007 +0000 STS markers done commit fe98c687331c6c6c8abecb2bb9ed9a79ab0071a2 Author: hiram Date: Mon Jul 30 22:42:58 2007 +0000 Fixed orfToGene table. commit c251287284e2842beb2579dce786f472be49ea8e Author: hiram Date: Mon Jul 30 22:35:12 2007 +0000 Needs same entry as was for ce2 commit f3abdffdba3180e799d85e6136d710d2116f5a84 Author: galt Date: Mon Jul 30 15:00:03 2007 +0000 "Encode release log update" commit 62cccd6401bcac4816563a249620071ab2e15f6f Author: galt Date: Mon Jul 30 15:00:01 2007 +0000 "Release log update" commit cc5d8067fcd717547b28d6fe87e915ff3f17242d Author: fanhsu Date: Mon Jul 30 02:08:28 2007 +0000 Created makefile. commit d7b5b36398c2033096ea039129599e824118596e Author: galt Date: Sun Jul 29 15:00:05 2007 +0000 "Encode release log update" commit 497b25d49e014a196494640eda25a03e72af6be1 Author: galt Date: Sun Jul 29 15:00:03 2007 +0000 "Release log update" commit ffe9e011adeb10623788b2cd636849651839b247 Author: fanhsu Date: Sun Jul 29 04:18:15 2007 +0000 Added hivgne8 to hiv. commit 44eb6a2ef46667a19dc1688572612c3e7d7be2e2 Author: braney Date: Sat Jul 28 21:22:19 2007 +0000 a working version commit d8b00819ccb761b8baa641d18a473618dddcfa5e Author: fanhsu Date: Sat Jul 28 20:08:24 2007 +0000 Updated interProName() to use bed instead of psl. commit 4b1f7285e8b0d87529d270b14f352c88e6b152af Author: galt Date: Sat Jul 28 15:00:05 2007 +0000 "Encode release log update" commit 4a76afe83189700b6a8c22dde1b639aaafd15dd0 Author: galt Date: Sat Jul 28 15:00:03 2007 +0000 "Release log update" commit ab3b150f3a8b007c4cb89f5f1b007720b56cd445 Author: heather Date: Sat Jul 28 00:14:31 2007 +0000 add notes for bosTau3 blastz commit 0ceb73a3231be9dfa7f58d4aa365602d3117f987 Author: heather Date: Sat Jul 28 00:09:12 2007 +0000 fix typo in previous commit commit eaeafd5c2061b70be44bf72991741063a2742c03 Author: heather Date: Sat Jul 28 00:03:03 2007 +0000 add notes for bosTau3 blastz commit f6dfc6ebb3a6fe1c8cc90a27dc9922157ead71c2 Author: angie Date: Fri Jul 27 23:55:18 2007 +0000 liftOver'd MGI tracks from mm8 (Jim's request). commit 0eded2c2ed4dcf5f87458d1bc56ece27968b3eac Author: hiram Date: Fri Jul 27 23:32:08 2007 +0000 Done with genbank a second time, working through STS markers commit 29942eb72e0cc9d3490fc14ae49db52ac72d652d Author: archanat Date: Fri Jul 27 23:14:44 2007 +0000 added BosTau3 to chainDest commit 75b3c338c9083861c76ec9fc5bcb2a67d3b0168b Author: angie Date: Fri Jul 27 22:17:50 2007 +0000 Updated D. mel. db to dm3. commit 85bbcdef5da94f72460c3231ee585d6c6efff2ec Author: archanat Date: Fri Jul 27 21:51:09 2007 +0000 added entry for hg18 and mm8 chain/net. Needed to add at this level because the default matrix was incorrect. commit 6779a0bd4519d16f87dd1564539be16c9609928c Author: heather Date: Fri Jul 27 21:51:08 2007 +0000 move stanford chip to genome-wide commit f162deeac5d1cbbc981585cca40ca93fe2a5dc63 Author: heather Date: Fri Jul 27 21:50:00 2007 +0000 remove stanford chip (moved to genome-wide trackDb.ra) commit fedf12a17300e6cecb1124b9275880efa4bd08b7 Author: braney Date: Fri Jul 27 21:49:06 2007 +0000 a meaningless intermediate version commit b0cf4134930769c6d9bf9ff11e52da58c8338015 Author: heather Date: Fri Jul 27 21:48:57 2007 +0000 add stanfordChip commit 8a986f1273585512d6e7065eae4a2d4ed350c81b Author: heather Date: Fri Jul 27 21:48:24 2007 +0000 initial draft commit ff7264d7fb313e9c3cb87172562ec8d5b1e8c681 Author: mhoechsm Date: Fri Jul 27 21:26:11 2007 +0000 Lowelab wikibme links now to microbewiki commit 86f27dfe208d9861a4dd9ff6575ec5f6c1838938 Author: giardine Date: Fri Jul 27 20:39:42 2007 +0000 logo for RISN commit 3e7853c38a34a7790184a1728a727fb7bb0aff2a Author: giardine Date: Fri Jul 27 20:26:30 2007 +0000 Added new LSDB source to links. commit b9752e48bc25e18b40f66bec8b4b38fcbbd450fb Author: heather Date: Fri Jul 27 20:25:27 2007 +0000 add snpArrayHg18 commit ca802c660a4705ff5b1dcd8aef8e6e46744fc78b Author: giardine Date: Fri Jul 27 20:20:10 2007 +0000 Added new LSDB to credits and tables. commit 38be40fdfaf5fd0c784418564584ba393baf7687 Author: heather Date: Fri Jul 27 20:19:00 2007 +0000 just use rsIds and pos from illumina commit 07fbce4fd055c1d1a1550d47ecac3afb2c709754 Author: heather Date: Fri Jul 27 20:13:03 2007 +0000 tweaks for snp arrays commit 93c8e9d19b4d36a2a9354c2c13e0307fbfddcc19 Author: giardine Date: Fri Jul 27 20:09:45 2007 +0000 Adding next/prev item option to ORegAnno track. commit 1bed0fe1bba1ac4b3c6a9fd5d5121ac0b65d8529 Author: heather Date: Fri Jul 27 20:08:24 2007 +0000 search terms for snpArray track commit a0478344d67ffeec90510706b844e2e48dacf9e6 Author: archanat Date: Fri Jul 27 20:04:53 2007 +0000 copied the entry for net/chain bosTau3 to organism level and changed the priority commit e9ab9400fa320a1053017fc172132b42a4a485cc Author: archanat Date: Fri Jul 27 19:48:25 2007 +0000 initial file (copied from Hg18) commit c9b3f99b8c6eb02d321ad0982274a3eafde57f66 Author: archanat Date: Fri Jul 27 19:47:48 2007 +0000 initial file ( copied from Hg18 ) commit 14f37d4a6adf1ef4682a549ffa1f7d63784a84ae Author: heather Date: Fri Jul 27 19:45:19 2007 +0000 bi-alleleic only commit a2e20be174d0f2695a6077bd7225d6ad2ddcc315 Author: angie Date: Fri Jul 27 19:31:13 2007 +0000 Cleanup: removing the last vestiges of hgNear's oldDb and oldOrg (db-switching now handled by getDbAndGenome). commit 89e44c4acfdf1119873ca876e3a8beb0ea449b62 Author: donnak Date: Fri Jul 27 19:12:53 2007 +0000 Added db= attribute to track lines section. commit 8f036286e722c0ba7b81d4f632f4cdc748c7351a Author: angie Date: Fri Jul 27 19:09:54 2007 +0000 Correction to comment about kent/src location of file. commit d8c94d9e4f304a94a41239e5fe7368384f249de1 Author: angie Date: Fri Jul 27 19:08:44 2007 +0000 Moving cvsup from utils/ to utils/cvsTools/ where it belongs. commit e7e04297dd7ac74de6b7ac23a5baf33cddd2fbfe Author: angie Date: Fri Jul 27 19:03:52 2007 +0000 Removed nonexistent dumpDb.pl from SCRIPT_FILES. Ignore cp -p errors. commit a41198a4efd0ec68427b128ad9e2434c41681a2e Author: angie Date: Fri Jul 27 18:31:53 2007 +0000 Adding cvsup to utils/ scripts. commit 68d4227c7b390f04ded98205f084af0925e6e889 Author: galt Date: Fri Jul 27 18:02:49 2007 +0000 added missing close-block curly-brace that Kate forgot that broke build commit b57f66be580d0a26ae263fea9ec97455c6bbd95c Author: archanat Date: Fri Jul 27 17:59:54 2007 +0000 added entry for chain/net bosTau3 commit 62488d25c5d3c3f776ce49865debfd86a55565a7 Author: galt Date: Fri Jul 27 15:00:29 2007 +0000 "Encode release log update" commit f718197835c56f7f9bfce1a96046c0e364240920 Author: galt Date: Fri Jul 27 15:00:16 2007 +0000 "Release log update" commit 530304f56047aadf8ff16c225debce451897b1da Author: markd Date: Fri Jul 27 05:41:48 2007 +0000 fixed typo commit 3262d98581d50d5d05217e2b3147784c60c34aa3 Author: markd Date: Fri Jul 27 05:26:19 2007 +0000 added -simplifyMappingIds and -swapIn options commit 86b1188a800f3fb295c970f3c7ec2e030092844d Author: hiram Date: Fri Jul 27 04:53:27 2007 +0000 Set mm9 2bit file for an iscratch filesystem commit b59331b67a275cc5f36a4c103abe4b0446f416a1 Author: heather Date: Fri Jul 27 02:25:38 2007 +0000 edits for illumina snp array commit 78b11296199418edcd3ec73ca02200d7c6808a65 Author: angie Date: Fri Jul 27 02:24:03 2007 +0000 Added support for xrefLookup and xrefOrg settings, to allow translation of names in columnDb.ra lookup queries. Added those settings to flyOrtholog specs for databases whose dmBlastTab table has CG* IDs instead of FlyBase's preferred FBgn* IDs. commit 5e0f3b8426c8a693894febb979e528d549232f5c Author: heather Date: Fri Jul 27 02:22:13 2007 +0000 tweak commit 5dcbb1b13fe37332c26ed0fc30de16b93954cd76 Author: heather Date: Fri Jul 27 02:02:55 2007 +0000 cleanup commit 2b1bd058bf1c5d70f8cbad12edc1b4fab213a387 Author: heather Date: Fri Jul 27 00:59:26 2007 +0000 not using func commit 4909560d92a41f15500e86585de55ff60065fa07 Author: uid2578 Date: Fri Jul 27 00:24:33 2007 +0000 tweak error message commit 3a20682efc5835a608f3b76355fd508006370691 Author: hiram Date: Fri Jul 27 00:06:46 2007 +0000 mm9 should be finished, not just ordered. And limit non-bridged breaks to only the chr*_random chroms commit 5e6a2dc71667edee1aa23f95a8f8e99cb8afd1de Author: heather Date: Thu Jul 26 23:58:44 2007 +0000 add illuminaLookup2 commit 140a4386096c98c180fd5843005a8c298cfa77e1 Author: heather Date: Thu Jul 26 23:55:25 2007 +0000 don't use strand and observed from illumina commit 0fdcc65565b5faf34b2ee081c29c37c88c48b49e Author: ann Date: Thu Jul 26 23:50:27 2007 +0000 Adding new script that is used to ensure that all elements in ENCODE tables fall within the ENCODE regions for that assembly. commit ab31d0dd4c26d9759777768d340ef18dc884dc7e Author: angie Date: Thu Jul 26 23:08:51 2007 +0000 Bring back the onchange clearing of near_search. Swap " and ' to make the javascript work (tested on Win FireFox and IE). commit 01014902333d2ea68c1eec1b068f49e2f25cf138 Author: fanhsu Date: Thu Jul 26 22:15:33 2007 +0000 Created interPro.sql. commit 03bb846cd62550a18c53e293f0a9ba252e4d6076 Author: angie Date: Thu Jul 26 22:06:56 2007 +0000 Oops, don't clobber hgNear search term from CGI when switching databases. commit 384761eb7c31c4a9110a89556b4235dd8a31d2a2 Author: angie Date: Thu Jul 26 21:53:39 2007 +0000 Removed yet another bit of db-switching logic from hgNear (hgGene had a link that didn't use the right special var) and moved it into getDbGenomeClade where it belongs. commit 812c3a4af9a4c2c626d041edd45948d4e6ae08ba Author: kent Date: Thu Jul 26 20:56:03 2007 +0000 Adding back links here and there, and some minor changes just to get to know Ruby on Rails. commit 252ba887f6d0caad303911662a2b935c88d6203c Author: kuhn Date: Thu Jul 26 20:13:21 2007 +0000 removed commas from usage statement commit 8475ee36ff62ea30a0941e7ba7ca3c5115a90370 Author: aamp Date: Thu Jul 26 20:08:11 2007 +0000 Added a composite-track-related function for use of composite tracks outside of hgTracks... starting with hgGenome. It's not as complex as what's in hgTracks, but it covers the basic functionality and fills the data structure out a bit. commit 01eb17a62904205b0d24d2a93ff8af3888eafe1e Author: aamp Date: Thu Jul 26 20:01:21 2007 +0000 Added Case Control trackDb. commit f2d83ca307f93445b3c4b794f13091477ac0a338 Author: kate Date: Thu Jul 26 19:46:16 2007 +0000 Redo supertracks to change default vis behaviors. Probably an intermediate implementation to be cleaned up commit 0e37da0c5f34332464f30847911aa05c61ddb7ce Author: angie Date: Thu Jul 26 19:40:56 2007 +0000 Updated jax* handlers for recent MGI tracks, to support liftOver'd *Lift versions. commit e220b4c09743b2107480bd32e6f8a23c70a9fae7 Author: angie Date: Thu Jul 26 19:37:21 2007 +0000 Added jax{Allele,Phenotype}Lift for liftOver'd versions, and moved out of the ENCODE related section. commit cb944f01485aa6f6105f3f2545790a2680f5c6f2 Author: galt Date: Thu Jul 26 19:34:26 2007 +0000 putting login link first commit f81ade0a743ad7ccadcba5e5cc81545f82836964 Author: angie Date: Thu Jul 26 19:33:16 2007 +0000 liftOver'd MGI tracks from mm8. commit c2ad10165a43a78fb6d378898e79cd667f66aa88 Author: hiram Date: Thu Jul 26 19:16:47 2007 +0000 Add to README files alternate methods to FTP access, rsync and wget, with example uncompress commands and database loading commit 4d8935402c251eb69f2cb8736b822223589df137 Author: hiram Date: Thu Jul 26 19:03:04 2007 +0000 Added gbMiscDiff to required genbank table list commit bd44206e3cec222594b9bf9f272420f4caf16b1d Author: hiram Date: Thu Jul 26 18:47:03 2007 +0000 Have made downloads and now in the pushQ commit 095d718257ef27588c550b983f8f058b8920c29c Author: angie Date: Thu Jul 26 17:20:25 2007 +0000 Added MGI phenotype-allele relationships for display in details pages of MGI Phenotype & Allele tracks. commit ebc1d48890d8b628ac42615bc33e6da52258b8d4 Author: angie Date: Thu Jul 26 17:18:45 2007 +0000 Added MGI phenotype-allele relationships for display in details pages of MGI Phenotype & Allele tracks. Fixed QTL off-end-of-chrom coords. mm8 -> mm9 liftOver. commit 3e4d0ee948cb5735983b1a5d4641b1baaa0dabe1 Author: galt Date: Thu Jul 26 15:00:35 2007 +0000 "Encode release log update" commit 8ea181eb89a33b045f22e5d37f29092b463a3ad9 Author: galt Date: Thu Jul 26 15:00:18 2007 +0000 "Release log update" commit 6bf428b5fbce9f7c5d7013027cf321a766e65311 Author: archanat Date: Wed Jul 25 20:17:35 2007 +0000 changed refs to pubmed format commit 53aae282d0bf6f1efd540fc30d9e01acc0f30174 Author: archanat Date: Wed Jul 25 20:09:42 2007 +0000 changed refs to pubmed format commit 12e29353d226a217c095d5c8806d5db2044ff01f Author: hiram Date: Wed Jul 25 19:48:23 2007 +0000 Done with genbank run, and now making downloads commit 5f94a0db35799abbe8614fc4ed20ff176c602818 Author: hiram Date: Wed Jul 25 19:48:00 2007 +0000 fixed sangerLinks and sangerCanonical tables to avoid the one dot vs. two dot name problems. And make a sangerGeneToWBNameID table for cross reference and hgGene WormBase links commit 8cebd7cf5515daf3b0ccd5c67b8877a3f32167c1 Author: hiram Date: Wed Jul 25 19:23:49 2007 +0000 More specific URL references to ws170.wormbase.org commit bd2f1811f3fc3e54cfc311927c4ad05a0266c620 Author: hiram Date: Wed Jul 25 19:20:41 2007 +0000 Add in ce4 link references commit 6daee4d345a23ef774b97ffefece2ff6fbae248e Author: hiram Date: Wed Jul 25 18:50:37 2007 +0000 Add sangerGeneToWBGeneID to the library commit 45af17473aa2085990b441f62feb83b4e64d66c7 Author: hiram Date: Wed Jul 25 18:49:26 2007 +0000 for sangerGeneToWBGeneID.c commit e042ed9be73134155bf00dc4716e8ad6fa430ba3 Author: hiram Date: Wed Jul 25 18:49:03 2007 +0000 On second thought, maybe yes, let's have the .c and .h files commit 2f74eec6859864c83b52b66bdb1ab6817d40bcfe Author: hiram Date: Wed Jul 25 18:48:10 2007 +0000 May not need the .c and .h files for this simple xref table commit 5a980d90f35f20a6829b2271440527c62806ac45 Author: heather Date: Wed Jul 25 17:33:08 2007 +0000 details on 6.0 array commit 1e573bc03c784470f9dff6c0863f47e5cadea943 Author: heather Date: Wed Jul 25 15:45:53 2007 +0000 rename an affy snparray table commit a372164d370b45804bda44541bba5b66a5f7b825 Author: galt Date: Wed Jul 25 15:00:33 2007 +0000 "Encode release log update" commit 712c422083c2b2b7aae2c900c8b62c42ad8d8d6d Author: galt Date: Wed Jul 25 15:00:17 2007 +0000 "Release log update" commit 925e190a3d47171023500a9d09d11e52dde56767 Author: kuhn Date: Wed Jul 25 00:07:12 2007 +0000 simplified that output paths commit 08ec76f8f15fc93d56a334e1fcb9780f9411ca50 Author: kuhn Date: Wed Jul 25 00:05:59 2007 +0000 prettied up the output format a little and some minor tweaks commit 8fe4ce9455840a73498b5c0ce5aa973ed6a67aba Author: hiram Date: Tue Jul 24 22:51:49 2007 +0000 Recovering the genbank alignments commit 30bf4256b7889f84d0fdc46a326bccf1c598a500 Author: tingwang Date: Tue Jul 24 22:24:44 2007 +0000 release notes on encodeUCDavisChip tracks commit 569a9a24927414c42282a11b58930c0f22ba9a08 Author: angie Date: Tue Jul 24 22:17:26 2007 +0000 Don't blow away liftOver -- just regenerate the README.txt. Especially when re-running, liftOver may have links that this script doesn't regenerate. Thx to Archana for noticing when I blew away dm3/liftOver. commit 63df7d1e67c598a9f05061d7f9750bfb1d9f56a0 Author: angie Date: Tue Jul 24 21:43:28 2007 +0000 Re-masked sequence, regenerated bigZips after RepeatMasker beta re-run. commit 3f310e14a60a94162fac03f7549a4ecd25251dfd Author: heather Date: Tue Jul 24 21:31:59 2007 +0000 finalize commit 0e2e0b97511d67ddcf4faf18d3283851bd91558f Author: angie Date: Tue Jul 24 18:43:20 2007 +0000 Added note about new practice of recipBest for distant species pairs. commit ee064e267f4aa31e2c078c95b3243f9207688c14 Author: aamp Date: Tue Jul 24 17:16:04 2007 +0000 "New version number v164" commit e12c910162772ec93a5522ad28c9718447769a9e Author: tingwang Date: Tue Jul 24 15:53:17 2007 +0000 update make doc for releasing UCDavis Ng ChIP track commit 754ba06484f5d9479b7afa041527c23c244e0692 Author: galt Date: Tue Jul 24 15:00:23 2007 +0000 "Encode release log update" commit 8028ccefb589608185913a399ca56234e0250d4b Author: galt Date: Tue Jul 24 15:00:13 2007 +0000 "Release log update" commit 81b28c253b91d790e015af77e52f02b2cae76602 Author: galt Date: Tue Jul 24 09:19:56 2007 +0000 adding submissions tests commit a343d359d499ff4f328ab62953891b1e81ec8453 Author: galt Date: Tue Jul 24 09:17:52 2007 +0000 adding some fields expected by show method commit 8f04c181f992a36263ce32346b0b40884e0e2c00 Author: galt Date: Tue Jul 24 09:16:42 2007 +0000 adding check for directory exists commit 6f7f2bef5c3d93fe06ba9eaf1b10b28db4e40ff5 Author: galt Date: Tue Jul 24 08:20:19 2007 +0000 sf_type is required (now that field name collision has been fixed) commit 6f7ee2d8564e8e47522dc3db959c0b551fc2e46f Author: galt Date: Tue Jul 24 08:12:45 2007 +0000 adding fixtures and unit tests for submissions and submission_files commit 718db124ee2715246b34633d292ea57534de6f7b Author: galt Date: Tue Jul 24 08:12:05 2007 +0000 trying to keep rake tests from trying to send email commit 4fef355636a5a14c858fa36d2116ac29fd8feaa7 Author: galt Date: Tue Jul 24 08:11:32 2007 +0000 user_id should be required commit fa3cd0657b2a6ac892c20bf351a3f3f007fe503a Author: galt Date: Tue Jul 24 08:10:38 2007 +0000 changing field submission_files field name "type" to "sf_type" since type is a magic name commit ff930ff41e4b5b30c062fbef82f03c53eee43e82 Author: kuhn Date: Tue Jul 24 01:14:48 2007 +0000 added a ping to a full unit to help ensure that the du will work commit 5915185f082cf1e2a62a16a74e45968ddf0acb5d Author: heather Date: Tue Jul 24 00:09:33 2007 +0000 implement filters for CGHBreastCancerUCSF commit 73ca0a7db669b1201dd1ba69fa1364076d862b29 Author: hiram Date: Tue Jul 24 00:04:42 2007 +0000 Got genbank started with a non-bridged gap lift file, and map contigs track up commit 5b70eec61502ce3db423ea696ee7653a8628d821 Author: heather Date: Tue Jul 24 00:04:36 2007 +0000 expose maximumTrackHeight so expRatioTracks can use it commit fced2adc5edca59385361c656aa86a6b18373c81 Author: heather Date: Tue Jul 24 00:03:53 2007 +0000 add ucsfdemoUi for CGHBreastCancerUCSF table commit 885ea011f4e914763ac68d57c240556aa4988184 Author: heather Date: Tue Jul 24 00:03:11 2007 +0000 add cart vars for UCSF demo commit 5b5f716ec7398eb30d26b54529af603c6f5660e9 Author: hiram Date: Mon Jul 23 23:43:14 2007 +0000 Trying out the nonBridgedGap.lft file for mm9 commit 740fab40b87d10b20607dd20d140261f4019155b Author: ann Date: Mon Jul 23 23:20:45 2007 +0000 cleaned up citations commit d6a5ae56593fcdf61f734b6852b74e6e02a20606 Author: ann Date: Mon Jul 23 23:18:27 2007 +0000 removed authors from paper link commit e3ccd52a9adf23744a2f68774b70925986a17366 Author: ann Date: Mon Jul 23 23:11:10 2007 +0000 fixing citation commit 15b46a86bb83bfd71734afdede437d4bf04be9ec Author: heather Date: Mon Jul 23 23:07:30 2007 +0000 move NRSF from encode to regular commit db1685eb1082567653dccf136fbede9a46b42172 Author: hiram Date: Mon Jul 23 23:06:31 2007 +0000 Reverse the meaning of sane and replace it with insane commit 1f7e3b416691d73a7632024c680656592b214981 Author: hiram Date: Mon Jul 23 23:00:27 2007 +0000 Fixup the sanity check so it functions on a properly ordered gap list commit 8fd561e5f1236ae8d4eedc1349d85a95e0802335 Author: hiram Date: Mon Jul 23 22:38:57 2007 +0000 add to usage message to indicate what types of segments it makes commit 8745f7db48ff1b59f1b63cf5a5860aa33a29be28 Author: kate Date: Mon Jul 23 21:46:17 2007 +0000 Update links to newly published papers commit e97286e0f90008b2c42178e280e8c5335c3c65d2 Author: markd Date: Mon Jul 23 21:35:40 2007 +0000 added -clusterTxBed option commit 0192aa5d3575be41caa91044924e5c10c1f9d1c4 Author: heather Date: Mon Jul 23 21:33:28 2007 +0000 not using chrom commit 0ee0c380a87cf91ee292cdb431f0ff494d853143 Author: hiram Date: Mon Jul 23 21:18:08 2007 +0000 Proper overlap detection, and option to output segments to bed file so they can be seen in the browser commit aeabd26e1ae1ada1ba0a4a18cc5d54b28d8e9c12 Author: hiram Date: Mon Jul 23 21:01:23 2007 +0000 Initial source commit 76b0c81fa30b99b8fc15beb280ec92111c863d41 Author: ann Date: Mon Jul 23 20:41:07 2007 +0000 cleaned up grammar commit 29e206cebe023d219ddaf18c5a5c77b50a3c9e9c Author: ann Date: Mon Jul 23 20:36:58 2007 +0000 removed extra space in link commit af56e898b72b71547a5ccf70c447b9b02de951a4 Author: ann Date: Mon Jul 23 20:35:01 2007 +0000 corrected name of cell line commit 14c7afdbdf1d4c0dd1b4ab3f08c4bd614a210539 Author: ann Date: Mon Jul 23 20:33:23 2007 +0000 corrected capitalization of c-Myc antibody commit 3172b696a958f1361815305ddd86eb70484723f2 Author: ann Date: Mon Jul 23 20:28:10 2007 +0000 corrected typo commit 76c64d5e791a637114616744432d2e260e730371 Author: heather Date: Mon Jul 23 18:49:07 2007 +0000 renamed from encodeStanfordNRSF commit bfbde85b18adc98a186d4b51d623a0b4534323c9 Author: ann Date: Mon Jul 23 18:06:15 2007 +0000 fixed typo commit b857d6fcb3fc4e240ca8bdd3dbfd19b42705d47f Author: heather Date: Mon Jul 23 16:32:57 2007 +0000 move ChIP-seq track from encode to regular file commit fec8d60c4e092b9c8673eca6d0fca9e622391f4f Author: heather Date: Mon Jul 23 16:17:45 2007 +0000 move ChIP-seq notes from encode to regular file commit f270cf016b64b734801d701308a29516de7077a6 Author: galt Date: Mon Jul 23 15:00:18 2007 +0000 "Encode release log update" commit 44b0a5e82ca05d2e3313b9949841b0de3fcced5a Author: galt Date: Mon Jul 23 15:00:10 2007 +0000 "Release log update" commit a6d563254aec1225c8e5fe1e05d5fb2027a1b221 Author: galt Date: Sun Jul 22 15:00:20 2007 +0000 "Encode release log update" commit 7e1d3026005fd2d956afbc8ae186419d1c4bcf48 Author: galt Date: Sun Jul 22 15:00:10 2007 +0000 "Release log update" commit c9e92461b3554364c93ecc4034260376b7980b0c Author: braney Date: Sat Jul 21 15:19:47 2007 +0000 a utility to build an eltree out of a species tree and a gene tree commit d819052ccbe268e3521d08ac8ce704662f681998 Author: galt Date: Sat Jul 21 15:00:24 2007 +0000 "Encode release log update" commit 4fc2d81fb06a891844393cde512a351fcd0fae90 Author: galt Date: Sat Jul 21 15:00:13 2007 +0000 "Release log update" commit 97adb0ae642ed8c1407fbb08b6e7027e67c7e03e Author: pchan Date: Sat Jul 21 03:42:04 2007 +0000 add gc content to refseq track detail page commit 4365a7e72e9ca8337db00c9eabd9036736bea42b Author: galt Date: Sat Jul 21 00:36:21 2007 +0000 changing permissions to be executable commit f32aff5cb43d1a4d6d9fc0f3c268c8b07ab3acdc Author: kate Date: Sat Jul 21 00:13:39 2007 +0000 Suppress wrapping of rows on configure page -- needed for lengthy ENCODE tracks commit e92db959e6fea32347b92f99bd87f0a6f06c87e7 Author: galt Date: Fri Jul 20 23:48:24 2007 +0000 testing support for change_email commit 189da1480d6732d41baa48f97e5656260b7ca593 Author: galt Date: Fri Jul 20 23:47:45 2007 +0000 deal with any immediate problems with email address commit 6f770639d93d2c376326589f3ccfa189945e7b6f Author: hiram Date: Fri Jul 20 21:14:05 2007 +0000 Initial source commit 5adec6bdb248e36b8cde4084ca0cf60bffd9696e Author: kate Date: Fri Jul 20 20:39:08 2007 +0000 Support for style attribute (e.g. width) in dropdowns commit 95e23dd33129f54fa587eec6142b30df63add3a3 Author: angie Date: Fri Jul 20 20:03:14 2007 +0000 Details page improvements for MGI Phenotype, Allele and QTL tracks. Show allele-phenotype relationships when available, and skip over missing data (empty columns) in QTL details. commit 3994fca6aa9c408d2d0882843fb4fb906d785194 Author: angie Date: Fri Jul 20 19:11:51 2007 +0000 Regenerated rmsk with new & improved platypus lib from Arian and Robert. commit f9825f96736d648bf02ef1544d5e12fd46aa100e Author: angie Date: Fri Jul 20 18:43:06 2007 +0000 Adding Nested Repeats track. commit b1b6957cb940d66cc5b128444b284ee8dd3527f5 Author: angie Date: Fri Jul 20 18:42:24 2007 +0000 Added RepeatMasker website reference at Robert Hubley's request. commit 30f324e3163555c97993f0912ec9d0930c509687 Author: kate Date: Fri Jul 20 18:30:47 2007 +0000 Enforce uniform width of visibility dropdowns commit 6b67557b96cf0cf4665a075679db6552596f288b Author: hiram Date: Fri Jul 20 18:24:23 2007 +0000 Final mm9 release now underway. TRF done, RM running. commit cd62826357e170e505bcf0313b082bf3731ffe0e Author: angie Date: Fri Jul 20 17:54:45 2007 +0000 Added jaxAllelePheno to mm6. commit c8a675c89616388544b2f71cd873a873b6e3aa7f Author: hartera Date: Fri Jul 20 17:04:36 2007 +0000 Make document for the Genome Browser for the Sanger Zv7 zebrafish assembly. commit c2d303912a53dd97c5506ebfbdb417c70d684dcd Author: galt Date: Fri Jul 20 16:59:23 2007 +0000 added tests for change_profile commit e49465cebbbfe20b596c311f32e99ea284eb369e Author: galt Date: Fri Jul 20 16:58:52 2007 +0000 trivial change for consistency commit 4cb37e3c3d66ec8cf9d57b77dbe58f078fa06548 Author: galt Date: Fri Jul 20 16:58:20 2007 +0000 added test for list and show_user commit d6719b5939ab208a5e5c35d4d48874911eb947f5 Author: galt Date: Fri Jul 20 16:33:16 2007 +0000 adding institution to rhtml views; making name, pi, institution be required; adding corresponding support for these changes in the test harness commit 1b7d29312d1a29bfee561344154fef9737c2bfda Author: kuhn Date: Fri Jul 20 16:29:25 2007 +0000 expanded ref to ten authors and formatted to PubMed commit 3f2988ea07a7666cf837a520706cd4c06587710d Author: galt Date: Fri Jul 20 16:07:33 2007 +0000 add test for change_profile commit 602ac8e0470717e57d17c22e7546540a91998ab0 Author: galt Date: Fri Jul 20 15:00:28 2007 +0000 "Encode release log update" commit 051e9962d3017962eedcfe0f6416e93455c09019 Author: galt Date: Fri Jul 20 15:00:15 2007 +0000 "Release log update" commit 7d5422026c5c3432754ae0315ed5a9c0919f4879 Author: pchan Date: Fri Jul 20 09:48:34 2007 +0000 add detail page for primer tracks commit 204c4b677568593b8b630b5769e947ccd299f276 Author: galt Date: Fri Jul 20 06:17:25 2007 +0000 trying to get the test harness NOT to really send mail by moving the settings, even though the test.rb is supposed to over-ride the environment.rb commit e89664817b389ca0cc5a9e637e1b3ef969b6051b Author: galt Date: Fri Jul 20 03:05:31 2007 +0000 making Rails test harness work with the login-security layer commit 24bf2a660a3ea8fd9739e30a63fc272b19c8e848 Author: hiram Date: Fri Jul 20 00:41:11 2007 +0000 Remove the note about the pre-release build status commit 389f9fe819bd2a46ee5f673fe2a03a0e92bb0f1c Author: heather Date: Fri Jul 20 00:01:44 2007 +0000 add bosTau3 commit c593831ade5c239d09471970cb1ecf634660625e Author: fanhsu Date: Thu Jul 19 23:57:57 2007 +0000 Refined some logic to make it more robust. commit 15a74c67949602b78243805e1313ac1c15c2824b Author: angie Date: Thu Jul 19 23:38:21 2007 +0000 In cartCopyCustomTracks, get database from getDbAndGenome, not straight from the cart. This allows the cart db (from saved sessions) to be overridden by CGI params if appended to the link for loading the session. commit 0836a9ffc84489c60231daa56f9a5204b9077068 Author: fanhsu Date: Thu Jul 19 22:48:02 2007 +0000 Updated logic of saving sequence IDs to get rid of "ss." part. commit 3681a2db6caac020def84ca26e17ae9a1be9e433 Author: kayla Date: Thu Jul 19 20:27:18 2007 +0000 fixed formatting of references commit 869ffeba5fe34cf0c6ad95ff9614f071445d75c4 Author: hiram Date: Thu Jul 19 20:26:38 2007 +0000 Initial source commit 0e8089d02cfc1039d822b015c3875d2218e1b356 Author: donnak Date: Thu Jul 19 20:25:56 2007 +0000 Another small mod, per Bob's request. commit dde05c78ded43450065c8ed1e8c7cb6d2d2f82a2 Author: donnak Date: Thu Jul 19 20:16:53 2007 +0000 More & more mods from track author (sigh). commit b9243575fec63793c7bc6085c6b0a161b50ae764 Author: heather Date: Thu Jul 19 18:49:49 2007 +0000 improve format of doUCSFDemo() commit d084c5d50d301f70516d3043c0ebaa1631a9b57c Author: hiram Date: Thu Jul 19 18:44:53 2007 +0000 Initial source commit 3fd6ca8c61c92df8a736292bdaaf3fa0ec0d4200 Author: hiram Date: Thu Jul 19 17:12:46 2007 +0000 Slight reformat commit 79f14348df1ab87efbbcf9cc7428be60b00f7267 Author: kate Date: Thu Jul 19 17:10:00 2007 +0000 Add supertrack display to configure page commit 722da16cbfb447c23d44132841dd91b242e64546 Author: hiram Date: Thu Jul 19 15:52:53 2007 +0000 Initial source commit f9fd5d562263c2bc16f1ad2b6d680c54d0a876a3 Author: donnak Date: Thu Jul 19 15:38:57 2007 +0000 Removed "PolyA" from some long labels, per author. commit bc6ef2f64854b56442c1a003f1c5c5be77550fdf Author: galt Date: Thu Jul 19 15:00:29 2007 +0000 "Encode release log update" commit e8802cce4367f86c2a542995bf17bae13f584673 Author: galt Date: Thu Jul 19 15:00:16 2007 +0000 "Release log update" commit 3ee858a0ba9b41912010f97df9298d648992dfd6 Author: donnak Date: Thu Jul 19 04:34:16 2007 +0000 Changed PolyA+ to PolyA at the track author's request. commit 5dd6508a81bc510220b8e1de7de3752ccf39575f Author: donnak Date: Thu Jul 19 04:19:33 2007 +0000 Made some mods, per Bob. commit 2dc753d2017804e2a20b734333490fa1152bc06a Author: jzhu Date: Thu Jul 19 01:40:24 2007 +0000 Various things Jing has done. Jim tweaks colors and clipping a little. commit e9c3d67a118487fc83ef398f20c2cd4a6be5fc12 Author: kayla Date: Thu Jul 19 00:30:55 2007 +0000 fixed typo commit 601e4184d96c7f1c20a884e24cd0305d32ae50c6 Author: jzhu Date: Wed Jul 18 23:38:26 2007 +0000 *** empty log message *** commit 9b6b625937b387c4f072f01aa416782b00ddeeb8 Author: hiram Date: Wed Jul 18 23:36:54 2007 +0000 Add all_est entry to trackDb to get spliced and unspliced ESTs to show up commit 2c80a93da3fd05bca0cd56c4fc1ac0d43c24685a Author: angie Date: Wed Jul 18 23:32:21 2007 +0000 Performance fix -- very necessary for large scaffold-based assemblies. commit f99fc310a6609c170279d5f0a6e6f6ac3dca6bc8 Author: hiram Date: Wed Jul 18 23:08:14 2007 +0000 Turn off native refSeqs for cb3 and caeRem2 commit 97f47d7bb63948d8cf4643df9a6387c8b062a8a3 Author: galt Date: Wed Jul 18 23:00:52 2007 +0000 adding placeholder for log directory, required for running rake tests commit 10db596a48e3dc2b2bb46b9c2d1f2992d9e42a65 Author: kate Date: Wed Jul 18 22:34:05 2007 +0000 Supertrack implementation commit 6c58790c9cf5869d7a1ae84c5dd2460182c7c35f Author: angie Date: Wed Jul 18 21:59:41 2007 +0000 Added jaxAllelePheno. commit 19aa66d7435bb0ecb26a4b5604fde062e475923c Author: heather Date: Wed Jul 18 19:40:59 2007 +0000 change priority of stanford NSRF ChIP-seq so it appears at the end of the regulation section commit 263b3ebee34955eedfee85c082cb1b1b6b54f2db Author: heather Date: Wed Jul 18 19:36:08 2007 +0000 move stanford NRST whole-genome ChIP-seq to regulation group commit 563f91d7509e8a7f2f229662ffc358fe70b71277 Author: heather Date: Wed Jul 18 19:02:27 2007 +0000 correct chromosomes list for Stanf NRST ChIP-seq track commit 9a0e6805f7de99cdd85debc96fcb9dc1466985d4 Author: hiram Date: Wed Jul 18 18:50:24 2007 +0000 Adding new data sets to existing set poly(A)+ and Total RNA for HeLa S3 (3 biological replicates for each) commit b00c1c7152613bdb9207ca7046a9700cac446836 Author: heather Date: Wed Jul 18 18:50:23 2007 +0000 remove cost comparison commit da5e7267f6f90657ca31c9220a6ee0f676746324 Author: heather Date: Wed Jul 18 18:14:15 2007 +0000 add 2 references commit 84e9939cde094a3362c486f102ba0907c7f5788e Author: heather Date: Wed Jul 18 17:53:57 2007 +0000 moved up a level commit 7099d9a3f4af44ba429e5a185b657f8a757b9116 Author: heather Date: Wed Jul 18 17:53:28 2007 +0000 move Stanf NRSF up a level; remove Stanf NRSF overlaps commit 9d793ba01855bbcb5c418184df658f7da44b89f4 Author: heather Date: Wed Jul 18 17:51:54 2007 +0000 tweaks for Stanford NRSF ChIP-seq commit b18f59a785bc904dbd9abfa94397b2c20796c2dc Author: heather Date: Wed Jul 18 17:47:33 2007 +0000 edits suggested by Kate commit 7159ee6e4b893ca9deaad08b01653cd1ce807301 Author: heather Date: Wed Jul 18 17:28:57 2007 +0000 tweaks to Stanf NRSF ChIP-seq commit 7a8152bd6bf4c0f09c376b700e81cab93ba3c87e Author: angie Date: Wed Jul 18 17:11:48 2007 +0000 Another spurious negative number to watch out for when pattern-matching. commit 1845dae2e5c03fbea08e608f96dc487b69378ba9 Author: heather Date: Wed Jul 18 16:42:31 2007 +0000 remove bosTau3 commit 719602b2f689d0978757d54d6c6318870afb96c9 Author: markd Date: Wed Jul 18 16:40:31 2007 +0000 fixed typo in comment that had been copied to several files commit f99648baac4526e9d3f5f05b923062da799b391c Author: galt Date: Wed Jul 18 15:00:28 2007 +0000 "Encode release log update" commit a5bdd9139793cee18975f6e172971b1c84ab839e Author: galt Date: Wed Jul 18 15:00:15 2007 +0000 "Release log update" commit 65c141f42398408cca235ed097e4f9c69b9c689b Author: galt Date: Tue Jul 17 23:51:34 2007 +0000 initial addition of encode pipeline ruby source commit fef0a3740ba581c25e3f3e83f48ef8f72f0fb5d4 Author: fanhsu Date: Tue Jul 17 23:26:24 2007 +0000 Add Table View link for GSID server. And added gsidWigMaf, gsidWigMafProt handles. commit 0e0e377de8cb79eebc40644fec07290cf36b7d4e Author: markd Date: Tue Jul 17 23:15:53 2007 +0000 use same naming convention for flat BED records as for bounds BED records commit 438e845d2bf2c4896c10657071be67b901f2548e Author: angie Date: Tue Jul 17 22:58:27 2007 +0000 Added help text to doUserPsl (Blat Sequence track, hgBlat results) and replaced strings with new constants from hui.h. commit 43d2a552ca2b77a4775eda4f0bfdf6f690fdba45 Author: angie Date: Tue Jul 17 22:57:04 2007 +0000 Added defines for Blat Sequence track (hgBlat results). commit 1e05a7c0fd1be7fce7c1fa9ba799a961700ecb23 Author: hiram Date: Tue Jul 17 22:29:20 2007 +0000 Add local ctgPos2 commit 93aa6e6e7b2c1f54bb0e98efdca36b018ab2ea87 Author: hiram Date: Tue Jul 17 22:28:54 2007 +0000 Minor addition of a comment here commit 553c823960e01b0a937ca5b806216db0fb93a808 Author: hiram Date: Tue Jul 17 22:28:25 2007 +0000 Add ctgPos2 so local ctgPos2.html is picked up commit c19fbb6b67c689147179e86e90d73c1b49105ad6 Author: hiram Date: Tue Jul 17 22:19:48 2007 +0000 Add Credits section commit 1e1b80e1210ce2241f4bf2e3b102b1c3ac5477a9 Author: hiram Date: Tue Jul 17 22:18:00 2007 +0000 Correct text for scaffold gap on chrUn commit 71f4c84c43b49d60141bfad0fa2a362bf2af1e44 Author: hiram Date: Tue Jul 17 22:15:09 2007 +0000 Updated gold and gap, added ctgPos2 commit 3246d3ea102472507cd70c9f7b735d10545c82fa Author: hiram Date: Tue Jul 17 22:14:04 2007 +0000 Updated gap and gold commit 8bb131bb508c63405d6b2b1abedc1335bfa8479c Author: hiram Date: Tue Jul 17 22:12:53 2007 +0000 Added ctgPos2 and updated gold and gap commit 3058de5288caeddc759239992605bcd589f006f7 Author: hiram Date: Tue Jul 17 22:11:41 2007 +0000 Updated gap and gold, added ctgPos2 commit be1098d8c7acffc3ec792aaae955b77a68c34100 Author: fanhsu Date: Tue Jul 17 21:57:37 2007 +0000 Filled in content for the description page. commit 48cf72e9b5f24b30976c121fb50657701b770e8a Author: hiram Date: Tue Jul 17 21:38:23 2007 +0000 Updated tfbsCons track commit a2bb917f6fda689204e8b931722c200d0308dd76 Author: heather Date: Tue Jul 17 21:34:55 2007 +0000 add bosTau3 commit c827d9dd8cb5bd893078584f1d3bde70fce621a5 Author: angie Date: Tue Jul 17 21:23:09 2007 +0000 Added -q to $CVSUP so "make alpha" output won't be so verbose. commit e0067a4fdf6c36a9617c94d1927c784270605afa Author: angie Date: Tue Jul 17 21:20:46 2007 +0000 Description for Blat Sequence track. commit 5aef3d350d749b8ead6593637a89235cf0743665 Author: jzhu Date: Tue Jul 17 21:15:20 2007 +0000 *** empty log message *** commit bd7ac03053b29122b838f457eab51b4f4c514928 Author: hiram Date: Tue Jul 17 21:06:50 2007 +0000 Updated tfbsCons track commit a2edcfa345e9eddb71ac3579c28329f4c1a289c3 Author: jzhu Date: Tue Jul 17 20:16:21 2007 +0000 *** empty log message *** commit 48a05e32cf6b25062f9fc2817196e01ed4f0b0df Author: kate Date: Tue Jul 17 18:28:22 2007 +0000 Remove release alpha entry to change vis on UCSD Chip track -- its not dense enough to be interesting at all positions commit 1e68960e80e46e9af7926e5ed8293169a8d37c4b Author: fanhsu Date: Tue Jul 17 18:10:05 2007 +0000 Start to filling details of the descripton page. commit c3b722839709d9feee8d2ab9f4b2c09984b0b793 Author: braney Date: Tue Jul 17 18:03:02 2007 +0000 add a trackDb variable that says maf displays should get their order from a file name that's in a cart variable who's name is in a trackDb entry. commit 173df7e9a36950d11b0d0fe7fe2561df16d7c8f9 Author: braney Date: Tue Jul 17 18:00:15 2007 +0000 add a trackDb variable that says maf displays should get their order from a filename that's in a cart variable who's name is in a trackDb entry. commit 435086f92dbaa7322c1933f08d8a51934328e3b1 Author: braney Date: Tue Jul 17 17:58:06 2007 +0000 add a routine to read a cart variable for the name of a file to get a list of names from commit 91ae0acd845e109ddccda2ae8a1908a8dd948d2f Author: braney Date: Tue Jul 17 17:46:48 2007 +0000 add a trackDb entry to say maf's should be ordered by the contents of a file commit 7e4019d64d1e1bdfc3f5310a88da14127e6d62fe Author: braney Date: Tue Jul 17 17:46:13 2007 +0000 add a routine to get a list of species names from a file named in a cart variable commit b63a6ea1506371911b5741bcc3b11401e3dfc3b5 Author: angie Date: Tue Jul 17 17:27:28 2007 +0000 Oops, forgot include of web.h. commit af4b9d7612dbf1c71ce116cabebfa156f5923c68 Author: galt Date: Tue Jul 17 15:00:23 2007 +0000 "Encode release log update" commit 9b6a3466609f09543eefd9bd4e6f085e0da64a45 Author: galt Date: Tue Jul 17 15:00:13 2007 +0000 "Release log update" commit 6f5e05c0b5c20e365a9a54dcf3f3ec1a7b63599c Author: aamp Date: Tue Jul 17 08:31:49 2007 +0000 Made load behavior more like hgLoadWiggle and removed the parts making directories and soft links automatically. commit 0d067f8b5f2a8e790f5b51c00d977afab2bab089 Author: angie Date: Tue Jul 17 01:14:47 2007 +0000 Get database from getDbAndGenome, not straight from the cart. This is good practice in general, and absolutely necessary when looking up the database prior to cartWebStart -- now that getDbAndGenome stores its results in the cart, the old cart values are clobbered! commit 49eb161fb7017e628d9d5bd4557cfcf487d55db1 Author: angie Date: Tue Jul 17 00:10:23 2007 +0000 Set database by calling getDbAndGenome, not from the cart before getDbAndGenome resets the value of db. commit 0ac52e562cb2004a317a925edb51293a21958726 Author: angie Date: Tue Jul 17 00:07:05 2007 +0000 Fixed webStartWrapperDetailedInternal to get db only from getDbAndGenome, not from the cart before getDbAndGenome resets the value of db. commit 6c0031acfe03f21d6d8490e0f0001d3512f777b2 Author: hiram Date: Mon Jul 16 23:47:30 2007 +0000 Add liftOver to Ce4 commit 466eff150ab694fca85020de76c2a5bcd40a58b4 Author: hiram Date: Mon Jul 16 22:46:53 2007 +0000 This is WS170 not WS120 commit 10be5fc9bea0bbe7d4b74540c2a80b5ec840a021 Author: hiram Date: Mon Jul 16 22:42:19 2007 +0000 Provide a WormBase blue bar link for cb3 briggsae commit ea69e3b6790e6e674c2f12f75fd04573cfb59d01 Author: heather Date: Mon Jul 16 22:38:53 2007 +0000 remove clone of encodeStanfordChip commit fd0b7ec885e3f196932a9224f8a07bce9475ec1d Author: jzhu Date: Mon Jul 16 22:35:18 2007 +0000 UCSF demo commit d67024f1049bd7c0daaf45ed64f26f5bee214a30 Author: hiram Date: Mon Jul 16 22:31:53 2007 +0000 Added description from wormbase commit 3dae9960c4529409881ea89e98de071c752bed10 Author: heather Date: Mon Jul 16 22:20:31 2007 +0000 add dataVersion for Stanford NRSF commit d742ee63db8b149e812fa552c3cae5f3af4326f1 Author: hiram Date: Mon Jul 16 22:06:09 2007 +0000 Add in WS170 blue nav bar link for ce4 commit 0fafc47e64fa1c961c1c3ea36ca4c44ddd1af733 Author: hiram Date: Mon Jul 16 22:05:01 2007 +0000 Initial set of comments for assembly track commit 9c9f99a8ab7916ed55737e1377118d4bae1e0692 Author: kate Date: Mon Jul 16 22:03:32 2007 +0000 ENCODE hg18 migration commit 388e549c78205ea16e34fa394b322e1e87c5e560 Author: hiram Date: Mon Jul 16 21:22:58 2007 +0000 Fixup for missing photograph. Comment out that table. commit 6e27ed2adcd0d9134548d41fdf25380e4e7d724d Author: kate Date: Mon Jul 16 21:18:19 2007 +0000 Remove dupe section commit 1c824f42b82cfc6f3cb6e818b5fd6e90405b2d22 Author: kuhn Date: Mon Jul 16 17:26:48 2007 +0000 fixed cross links among versions hg16, hg17, hg18 commit 705e43e66f27bfa14721353db71f20f7b4dbe151 Author: kuhn Date: Mon Jul 16 17:25:35 2007 +0000 fixed cross links among versions hg16, hg17, hg18 commit 669a37452cae6a2d37de8a1740510137f40b9a73 Author: kuhn Date: Mon Jul 16 17:15:33 2007 +0000 adding link to hg18 pages commit d6185bb3cb8424e6d3b4b2105273a3f35b115ecc Author: galt Date: Mon Jul 16 15:00:18 2007 +0000 "Encode release log update" commit 9cecc20ddf077f6ca007300fb8609ce314a23924 Author: galt Date: Mon Jul 16 15:00:10 2007 +0000 "Release log update" commit 35cb78f9aa369ae80d33994c95835ddfe45fcbb1 Author: heather Date: Sun Jul 15 23:05:34 2007 +0000 draw separate mapboxes for each experiment in an expRatio track (for UCSF demo) commit f6aaa2c800cf7431a03534dd5b72e8ee0bc78263 Author: galt Date: Sun Jul 15 15:00:19 2007 +0000 "Encode release log update" commit b4d2c0e09e4597fb47a4461b1657924dc6c0a583 Author: galt Date: Sun Jul 15 15:00:10 2007 +0000 "Release log update" commit 12267255972e3704e9aff4b7c8008b9eca1cbc8a Author: jzhu Date: Sat Jul 14 23:11:12 2007 +0000 change getDbAndGenome - Jing Zhu commit 030b08045a1764a40d4a7330f368f6f25a131e9f Author: jzhu Date: Sat Jul 14 22:50:36 2007 +0000 jing zhu modification hgHeatmap 7/14/2007 commit e1fd8af0b5c9da10cffa3c36c84eafdf7c80ff1c Author: galt Date: Sat Jul 14 15:00:25 2007 +0000 "Encode release log update" commit b40739d25e1314e3cbab64b4ef8927f763e89d44 Author: galt Date: Sat Jul 14 15:00:13 2007 +0000 "Release log update" commit b17ed1ec7e014a53c240a713d60566dfb4c5354f Author: markd Date: Sat Jul 14 00:18:29 2007 +0000 renabled alignment of dog commit 1275a37de351505488d7f78a92095e1e48af8708 Author: markd Date: Sat Jul 14 00:16:02 2007 +0000 added new molecule type commit 6a6f371cb480d187b7cb526b220d5c11b04181d2 Author: angie Date: Fri Jul 13 22:56:44 2007 +0000 Added functionality to getDbGenomeClade that was implemented (or not, or not quite right) in the various CGIs: detect change of database, reset db-specific state, and save db, genome and clade in the cart. Removed no-longer-needed code from the CGIs. commit 63fa5ec802e6d13b40dd3406f30eaf1b90982db4 Author: rhead Date: Fri Jul 13 22:17:44 2007 +0000 Lowered search priority on hapmapSnps track to so that range searches on SNPs will open the main SNP track instead of the hapmapSnps track. commit ccff8b1e186f102a65d39da865d440958d366fc7 Author: galt Date: Fri Jul 13 20:10:37 2007 +0000 improving help URL to go specifically to visigene section of page commit 09675b5651be051a283108d7dba744955c341db3 Author: kayla Date: Fri Jul 13 18:19:07 2007 +0000 added dm3 commit af329714eab83a3d1b61c3114b42658253516789 Author: galt Date: Fri Jul 13 17:49:57 2007 +0000 prevent user from entering an invalid db= setting on track line commit 2f611332351e5ce158324f029329990f86555128 Author: angie Date: Fri Jul 13 16:39:54 2007 +0000 Same as used in near/hgExpDistance -- for reloading with a tweaked .tab. commit 69571e5f71cb70136be8b1515ae961ffa68874b6 Author: angie Date: Fri Jul 13 16:38:59 2007 +0000 Corrected type so correct SQL will be generated. commit 2e6d6929c6d6299ecff1a1e03237bf8be4837ee2 Author: galt Date: Fri Jul 13 15:00:29 2007 +0000 "Encode release log update" commit dd46a8f981ec2c3dc605e73dc510af7f13cd56c1 Author: galt Date: Fri Jul 13 15:00:16 2007 +0000 "Release log update" commit cc29c81514be623412d73b5fcd25f1e435d83821 Author: jzhu Date: Fri Jul 13 06:57:34 2007 +0000 jzhu modification 7-13-2007 commit 146e91f1439b40bdaaa8ef9ac905bc466c0d16de Author: angie Date: Thu Jul 12 23:40:03 2007 +0000 Adjusted kimExpDistance names to be consistent with sangerCanonical names, so hgNear doesn't have so many near-misses when ordering genes by kimExpDistance. commit a7950fa29817d3e2716c0b018a77eea0f6a130fe Author: angie Date: Thu Jul 12 19:51:24 2007 +0000 Initialize values to avoid warning when compiling -O. commit ddeeaa4c61629ec60077e1407458b83b244072d2 Author: angie Date: Thu Jul 12 19:41:19 2007 +0000 For multiTerm search, collapse multiple results to a single table+pos if all are for the same position range -- consider that uniquely determined for the purpose of multiTerm search. commit 18cb8e6a83a166bb330cc78ebec67a30c07be930 Author: markd Date: Thu Jul 12 18:37:45 2007 +0000 reenabled update of worms commit 18c98c87a74f46bc39f9529bdb5009eecb200af3 Author: donnak Date: Thu Jul 12 18:03:24 2007 +0000 Added dm3 news item. commit 7c8977e63f017636c7eb7f5887ef2d9f3f72580c Author: donnak Date: Thu Jul 12 18:03:08 2007 +0000 Archived an item. commit 984c7e2f6aab5833a2d9051e6618054a9e1090ca Author: donnak Date: Thu Jul 12 17:38:58 2007 +0000 Updated the D. melanogaster section. commit 4ad5e706ed55ab9ca5742fd6987acf8717204544 Author: donnak Date: Thu Jul 12 17:37:20 2007 +0000 Made some edits & added a bit of additional info from Angie. commit d85204c164ce21d026b9ee98bec9086719fb1ae4 Author: kate Date: Thu Jul 12 16:30:32 2007 +0000 Add anchors to group collapse/expand buttons to maintain screen position commit 8e312e07719ea9c474c52b8e4531b881996c2074 Author: galt Date: Thu Jul 12 15:00:31 2007 +0000 "Encode release log update" commit 5b11e06640442ff9177e8ba2b075d989763941b7 Author: galt Date: Thu Jul 12 15:00:17 2007 +0000 "Release log update" commit 9e36dd827ce453ec6090d6f3d1cf04f4b7e86680 Author: jzhu Date: Thu Jul 12 05:45:16 2007 +0000 replae CUSTOMDB with CUSTOM_TRASH commit bd1ddf6a06c4ddea114794036088bfe1c65e20a3 Author: markd Date: Thu Jul 12 03:01:10 2007 +0000 realigned and loaed genbank commit 4fa30d487b8aff4dcb6833803ed31f78125bae51 Author: markd Date: Thu Jul 12 01:50:35 2007 +0000 removed subspecies features and made the few that were really useful alternate names commit cc79debc7518ad2025c8d01ec568af5d2b04db75 Author: markd Date: Thu Jul 12 00:42:36 2007 +0000 disable dogs while dealing with name change issue commit e8fa14eef61e374e7335e3ac457ee343dc767d3b Author: galt Date: Wed Jul 11 23:44:06 2007 +0000 adding LanguageLevel eps comment commit 2fdaf63b0e11273c595c687129b902a1c58710c5 Author: jzhu Date: Wed Jul 11 23:41:43 2007 +0000 jzhu modification hgHeatmap commit f46ce0214a7f1eb2fbdefdc9314d1893c1bfe38e Author: angie Date: Wed Jul 11 22:44:40 2007 +0000 LiftOver chains to bosTau3. commit 5c5d9a1acb31921fd53c6e041294ee89d785aef3 Author: angie Date: Wed Jul 11 21:58:30 2007 +0000 Added some endsInLf checks to help catch out-of-diskspace truncated files. Don't know why chainSplit didn't fail... yikes. Downstream processing complained about the file format, but it's best to catch those ASAP. commit 73885fa72090bbc403a87075ee0899103b642f00 Author: heather Date: Wed Jul 11 21:54:24 2007 +0000 new chip-chip data from Dave Johnson commit be288b930cdf4f82a14b8f0c6cce237ef75bf539 Author: markd Date: Wed Jul 11 21:53:39 2007 +0000 fixed path to cb3.2bit on cluster commit 2fab0cce6c084af7923209076ce9986e342dd409 Author: angie Date: Wed Jul 11 21:47:50 2007 +0000 Added support for -lump on assemblies including non-numeric sequence names, e.g. bosTau2 which has both chroms and scaffolds. Non-numeric seqNames e.g. chrX are hashed to get the lump-bin. commit 3defc64f59bb54eeb61f72822a5aa3c80c0518e3 Author: markd Date: Wed Jul 11 21:14:00 2007 +0000 reloaded genbank commit fa924fb8b9d91ca764eef0d228651a37545d062e Author: pchan Date: Wed Jul 11 20:41:04 2007 +0000 changed by Todd; add COG code to RefSeq detail page commit 58a2531f1913132af629857df87cbcbcf328f5c6 Author: hiram Date: Wed Jul 11 20:18:54 2007 +0000 Done with the genbank alignments, now loading commit fc26d22a4199757ae92299053d2c6ae9f05b9a88 Author: kate Date: Wed Jul 11 19:38:56 2007 +0000 Whole-genome DNase array and seq data from Duke Genome Sciences (Furey, Crawford) commit 037a45278bca60a6caadc44f75cb7ee9296242d7 Author: fanhsu Date: Wed Jul 11 19:10:25 2007 +0000 Created makefile. commit ceb3ad0da6f91855623dc75f3ad022dc3f94fcba Author: fanhsu Date: Wed Jul 11 19:10:11 2007 +0000 Created gsidMsaToTab.c. commit 4300d05a314cbe94cde73d0b40ff16cc18897ddd Author: ann Date: Wed Jul 11 18:51:01 2007 +0000 Removed these files. They were created for the new subtracks added to these composites. I have moved them over the orignal files (of the same name, without the 'New'). commit 5c34b83e7d499482ecacde6d8113cdf755556572 Author: ann Date: Wed Jul 11 18:47:46 2007 +0000 updated files based on new subtracks for this composite track. commit a58f40fe18a57faac7d523f8b089457a479fe54d Author: heather Date: Wed Jul 11 18:44:25 2007 +0000 add origAssembly for Stanford NRSF commit 1891a02b53ddf1bc0ad6415b79b262ec8bdf0aee Author: ann Date: Wed Jul 11 18:40:22 2007 +0000 removed html line from three encodeYaleChip composite tracks commit 5b6e64bb068f98d5a37788f579609731760b9124 Author: ann Date: Wed Jul 11 18:22:34 2007 +0000 removed beta blocks and alpha lines for three encodeYaleChip composite tracks in preparation for staging on beta and release. commit f3972a0e9d6b619a08d4e189e33fad4566c75169 Author: kate Date: Wed Jul 11 18:20:17 2007 +0000 Change name of database variable on track line to 'db' commit 60a1163251961b398e101fd160f7f818a64ac13b Author: ann Date: Wed Jul 11 16:41:07 2007 +0000 added expected hapMap search results to rs3 search commit e7fe243d1933c740f5d47f341217bd6b62b9a737 Author: galt Date: Wed Jul 11 15:00:29 2007 +0000 "Encode release log update" commit f892c99edd2a51883aec0c0005caa90eae07d54e Author: galt Date: Wed Jul 11 15:00:16 2007 +0000 "Release log update" commit 113569ab8712b3a2914670eb126d7d3705c51ae8 Author: hartera Date: Wed Jul 11 07:30:34 2007 +0000 Added back partially deleted track name and corrected typos in subtrack names for Yale Chip Sig track, release beta. commit a47431019a8b9884d31c7b94ce491df73aa39c40 Author: heather Date: Wed Jul 11 04:51:54 2007 +0000 move from hg17 commit dcb88d342d6b077ad95645e7127a82b4b091cc8a Author: heather Date: Wed Jul 11 04:43:04 2007 +0000 add encodeStanfordNRSF (previously just in hg17) commit a0d87d375639b5517ca57d4f6bd1de8dfbc88714 Author: heather Date: Wed Jul 11 04:40:24 2007 +0000 add stanford chip-seq commit 3281f3807d881ac7da5651ce8cb6a54de42660ff Author: heather Date: Wed Jul 11 04:09:48 2007 +0000 add display conventions commit b3e1010202d50ac8123380c5fbaebdf1b18719fe Author: heather Date: Wed Jul 11 04:02:34 2007 +0000 change stanford nrsf color commit 95649e9838f13a1a481872368856ae4a7b566354 Author: heather Date: Wed Jul 11 04:01:55 2007 +0000 change colors for encodeStanfordNRSF commit 536897df2fcaf2f5ef074668b5da5568d0a1f099 Author: heather Date: Wed Jul 11 01:11:12 2007 +0000 tweaks to encodeStanfordNRSF commit 53288f995011d8c5b28204a6cfe4174ce24fdd78 Author: markd Date: Wed Jul 11 01:07:54 2007 +0000 enable ce4 xeno mRNAs commit 1e0ed521fd351ef8961bd19d0252740d8c639d7b Author: heather Date: Wed Jul 11 00:48:40 2007 +0000 change Chip to ChIP and QPCR to qPCR commit f5636f4bbf410e6dc22cbaa29da161a50b74ef79 Author: hiram Date: Wed Jul 11 00:44:05 2007 +0000 Beginning work on the released sequence commit a1ea7fceca4b450008ce7c5cc52739abfce83551 Author: hiram Date: Wed Jul 11 00:43:31 2007 +0000 Rerunning the genbank alignments to get better xeno refseqs commit c9f53801a6c001f2130de76a4b70b78a7206531a Author: hiram Date: Tue Jul 10 23:57:03 2007 +0000 cb3.genbank.mrna.xeno.load = yes commit 301c5c86d323e86ff056d291ca7efefdec94de80 Author: markd Date: Tue Jul 10 23:48:25 2007 +0000 disabled worms while realigining commit a0fc99e5625609872a0b2fc37ce240edf518b7db Author: hiram Date: Tue Jul 10 23:42:24 2007 +0000 Properly specify unplaced chrUn on the worms commit dd00843dec1af7f977c99be03389799aec9c7995 Author: hiram Date: Tue Jul 10 23:25:08 2007 +0000 Simplify caePbNames to just Caenorhabditis brenneri commit 6555e1560d3f7ff2984921f38165c2e7dbdf2986 Author: ann Date: Tue Jul 10 23:16:35 2007 +0000 fixed chromsome entry for encodeYaleChipSites track to match data. commit 474bf1237a9f52c3121ef88a7a9593770dde7b71 Author: ann Date: Tue Jul 10 22:50:06 2007 +0000 removed three links. commit fbe28540d8aa9f9494ee1296b019945d40284aab Author: ann Date: Tue Jul 10 22:46:41 2007 +0000 fixed typo. commit f05386a11358b385f6fe951fc07a526436e09f71 Author: ann Date: Tue Jul 10 22:44:47 2007 +0000 fixed typo commit e1837b6a50d9aceb4753e9e52b48a31d638e90d2 Author: ann Date: Tue Jul 10 22:44:17 2007 +0000 removed three links and fixed spelling commit 3579c4809d97db4439f3e8a98f6ec5097c68beb7 Author: ann Date: Tue Jul 10 19:24:09 2007 +0000 bringing some ENCODE Yale Chip subtracks in line with the others wrt short and long labels commit 5eefebfde21a7a41e7370693aa20b510fe57e3aa Author: markd Date: Tue Jul 10 19:23:35 2007 +0000 disabled alignment and loading of caePb1 commit d0c3c37a9637c38f7db44e235c7bb888ce477349 Author: donnak Date: Tue Jul 10 19:20:46 2007 +0000 Removed spurious character in table, fixed a few
from anywhere. thanks, kayla commit 2078b8921a1874f487e9ef73bd3b66ee12223d5c Author: donnak Date: Wed Jun 13 18:54:36 2007 +0000 Added ENCODE Nature article. commit 88a14d5c1e641ce789bd2a7f071ef2a955a21c75 Author: donnak Date: Wed Jun 13 18:37:32 2007 +0000 Added CBSE news story link to ENCODE release news item. commit a18c4a907428dc35ab2d5e3c167e68aac02e7745 Author: donnak Date: Wed Jun 13 18:37:07 2007 +0000 Fixed Nature link, added CBSE news story link to ENCODE news item. commit 3461b85cd026b25c637d5111dfe006c5f423f744 Author: braney Date: Wed Jun 13 18:22:05 2007 +0000 a utility to transform an atom list to a bed file (HMRD color bed) commit eef7dbbb306ec31c25794af288ca73fd9dff6806 Author: kuhn Date: Wed Jun 13 18:20:38 2007 +0000 oops. reversed grammar tweak commit e65067bcb1aecf279fe56dc9cdf791eeb95f2d47 Author: kuhn Date: Wed Jun 13 18:18:36 2007 +0000 grammar tweaks, typo fix in comments commit 0d5d0e70ce5f01c4f92b1fa1b029bf2d5d3df793 Author: donnak Date: Wed Jun 13 17:51:06 2007 +0000 Edited ENCODE release announcement. commit 1e764bc847e02fd3ec25ab71700a51a3d9ef8497 Author: donnak Date: Wed Jun 13 17:50:54 2007 +0000 Added ENCODE release announcement. commit 8f4961cfa3bb578c18c8c8138913cb79e998b6bc Author: heather Date: Wed Jun 13 17:35:22 2007 +0000 tweak to previous commit commit 51d0eee7ec9368e183a3c220514e179c95e16123 Author: heather Date: Wed Jun 13 17:28:04 2007 +0000 check for empty type commit 2ba017a948b464471ca3ecc58b90151664321aba Author: angie Date: Wed Jun 13 17:27:20 2007 +0000 Added missing type to ctgPos. commit 494a4fc94f6cbd9d06cacb5b503635a82a98a9ac Author: kuhn Date: Wed Jun 13 17:24:32 2007 +0000 some streamlining suggested by mark commit 7f2046fb793a7dee0a48540bbacc50fef1f96868 Author: donnak Date: Wed Jun 13 17:16:26 2007 +0000 Archived an item. commit 44aa9ff7e721c74d9710276434cf359876f9bec2 Author: donnak Date: Wed Jun 13 17:16:12 2007 +0000 Added ENCODE data release annoucement. commit df43e39836786c534e4bf9afc7561320c57dd356 Author: donnak Date: Wed Jun 13 17:15:51 2007 +0000 Edits to ENCODE release announcement. commit 480d5dfa9a5050f847ccdf2f7c4d365cd5851f0a Author: donnak Date: Wed Jun 13 17:01:23 2007 +0000 Archived a news item. commit ffa528370dea2a6db6e4d6b93dfc027eb4634c69 Author: donnak Date: Wed Jun 13 15:14:32 2007 +0000 Added first draft of ENCODE publication news item. commit 82a70eec9fa2c530bac769767e704fe47bf71bd3 Author: galt Date: Wed Jun 13 15:00:33 2007 +0000 "Encode release log update" commit 62957207db6ccd938eb74b5070cb94631da54871 Author: galt Date: Wed Jun 13 15:00:18 2007 +0000 "Release log update" commit d215dbcf8cf52fe6f3af49f0cc3e5f372b7d7c2e Author: donnak Date: Wed Jun 13 14:19:13 2007 +0000 Made some more edits to the About section. commit f0f1f0ebe64751849f6e8869d5e28185e9f8f9e6 Author: donnak Date: Wed Jun 13 06:42:41 2007 +0000 Added sentence abt Ensembl. commit fc89f88346d374ca07fc6b3d72f09cd186b9ae03 Author: aamp Date: Wed Jun 13 06:06:53 2007 +0000 Just playing with the coloring. The coloring should be someone else's decision. commit ba540ae336434a1418916123fb438e4e540ae493 Author: aamp Date: Wed Jun 13 06:05:47 2007 +0000 Fixes pointed out by Affy. commit 400b90fb91266abff40bfab261ffe0445654cebe Author: donnak Date: Wed Jun 13 06:00:43 2007 +0000 Archived an item. commit f5cef3c04916f7a55dfbcc69bea283e217e4182b Author: donnak Date: Wed Jun 13 06:00:28 2007 +0000 Added new news item from Kate. commit 5f498c2cea010ce7b8d1c9263f7880ba859ceeb6 Author: kate Date: Wed Jun 13 05:48:34 2007 +0000 Fix formatting error commit d886d40872f29a3c48bbce71997c00bda240adf8 Author: markd Date: Wed Jun 13 04:12:40 2007 +0000 removed bogus refGene trackDb entry commit 1e54a0240acb13fe9d4c5668e87f611d2d9ed079 Author: markd Date: Wed Jun 13 03:14:45 2007 +0000 enabled rheMac2 native refseqs commit a344cdafb83a4803449d930d88e042a84d6d180e Author: kate Date: Wed Jun 13 00:53:18 2007 +0000 Add Ting, and Laura Elnitski's ENCODE portal commit fcbcd32cd25ce67c8ba39e14165265e6a16c1f7c Author: aamp Date: Wed Jun 13 00:50:40 2007 +0000 Added "l" and "r" to cgapSageMapItem and made dense mode a combined TPM of all libs for a tag. commit 92853536ac94f2c5d98979c89e5af950c5f619e2 Author: hiram Date: Tue Jun 12 22:52:55 2007 +0000 The color menu works except for the initial condition commit 0d594f432e9a05ba22a943bf82f90279d571391c Author: angie Date: Tue Jun 12 21:59:39 2007 +0000 Fixed wrong type for flyBaseLiftNoncoding. commit 06b35b75d65272b9a01fb761e636bea73e9cb373 Author: hiram Date: Tue Jun 12 21:28:47 2007 +0000 Enable wiki track click processing commit 2a1f2725f2d46587ae89b4e0c5e4991fc175c2a2 Author: hiram Date: Tue Jun 12 21:24:48 2007 +0000 Allow wikiTrack function to turn on if configured in hg.conf commit bcf15fa9caa74c12c311c725ed8606238bd17e79 Author: hiram Date: Tue Jun 12 21:23:35 2007 +0000 Change group to map, turn on exonArrows, and default pack commit 21d732d8680bb2d6460bc761c34eb8eac9f33ca4 Author: hiram Date: Tue Jun 12 21:07:13 2007 +0000 Adding wikiTrack.c to the library build commit 191110990a0ade960d348c79565fddb938c88936 Author: markd Date: Tue Jun 12 18:20:42 2007 +0000 more orfeome ids allocated commit 8082f91d67f6ec5ad93e3b2749dd5a6677ef19dc Author: aamp Date: Tue Jun 12 15:42:45 2007 +0000 "New version number v161" commit 67d5d33265143607c1246706abe1cd606ce14fdc Author: aamp Date: Tue Jun 12 15:39:11 2007 +0000 Sorts pack mode by score. commit e459890c6d53879b866a244fac4c279cced5ce78 Author: heather Date: Tue Jun 12 15:09:10 2007 +0000 add new illumina snp array tables commit 77926923f87226b4c8ebd4b8e0205a857486e9bf Author: aamp Date: Tue Jun 12 15:03:36 2007 +0000 More instructions... I'll probably redo a lot of it. commit 1a30aeb470a19524fb4e2f995184399b631c8736 Author: galt Date: Tue Jun 12 15:00:26 2007 +0000 "Encode release log update" commit e1c811166c0029814f2ddc4962bd44f5f7f20420 Author: galt Date: Tue Jun 12 15:00:14 2007 +0000 "Release log update" commit 39465e1426d32990e858d6ed1d68fc4d7e9cb7c1 Author: heather Date: Tue Jun 12 02:49:41 2007 +0000 tweaks for snp arrays commit c1a4b3ae18e45326aa5d41087a0736d9b844c545 Author: heather Date: Tue Jun 12 02:48:41 2007 +0000 details for Illumina and corrections to methods commit e37ca67750ffb3696e0f8497c9147dab8416ef95 Author: galt Date: Tue Jun 12 02:15:26 2007 +0000 adding ability to crosspost from beta to dev and vice versa to support file size retrieval commit d4ee6375bce17dd2a7df1e1e8ea3d6fe8c6509cb Author: angie Date: Tue Jun 12 01:01:40 2007 +0000 Fixed a couple places that were not using mapItemName with mapItem when in full mode -- for tracks with fancy mapItemName like knownGene or chains, that resulted in broken item links. commit 76ac22329014f96c473bc27fd1d3de7a27a0ee6f Author: aamp Date: Tue Jun 12 00:49:20 2007 +0000 More trackDb additions for affy txn tracks. Still no colors. commit 9092443c0ec4488d2fe1f8a3148ecf6ac150f4ff Author: kate Date: Tue Jun 12 00:36:14 2007 +0000 Fix downloads link on top bar commit 39bdf8120d1dc6a33ade753c63860f5d0d03f6ba Author: hiram Date: Mon Jun 11 23:53:47 2007 +0000 Adding 6 new data sets for Yale TARs and TransMaps commit a74e3b3fb045775d8e875dfa6da85011f01a64b7 Author: hiram Date: Mon Jun 11 23:46:59 2007 +0000 Loaded some new Yale-Affy TransMap and TARs for HELA S3 PolyA and Total RNA commit 3779c7831f52aedb085a49575b3ff6afe2b01140 Author: aamp Date: Mon Jun 11 23:16:03 2007 +0000 First cut on Affy transcriptome phase 3 wiggle tracks. commit e95c2613fa3fa78da77f759210d9fe3cedeb17c4 Author: ann Date: Mon Jun 11 22:29:49 2007 +0000 Noted mytouch of tables to fix problems found by Joiner Check and verified by the developer. commit 93b15783e698f8b59dae5c57fd6499b15b51018e Author: heather Date: Mon Jun 11 20:39:17 2007 +0000 change order of snp array subtracks commit 2fcabb8877081cc47a7cf338502a97318c60b926 Author: kate Date: Mon Jun 11 20:06:37 2007 +0000 Fix end condition for cons wiggle setting commit 409ed5a37f34976448cdbf3acff7e90f0e576322 Author: heather Date: Mon Jun 11 19:07:10 2007 +0000 tweaks to previous commit commit d03cfc1e090f2f75c5e3e76d771a7a2aef07efdb Author: rhead Date: Mon Jun 11 18:58:55 2007 +0000 Added the five new worms: caePb1 caeRem2 cb3 ce4 priPac1. commit 4e9da8e90e52cab2adaa490ca50d88937bd91b44 Author: heather Date: Mon Jun 11 18:52:05 2007 +0000 add snp array affy 6 sv commit 85b936542383617ec4515ed97b3c232d00f7b438 Author: kate Date: Mon Jun 11 18:34:21 2007 +0000 Fix Rachel's encoded email commit c4c5e60d5f7bf77692b3ece4fd2def391a019900 Author: kate Date: Mon Jun 11 18:25:00 2007 +0000 Changing back to mailto's, as CBSE web pages have phone numbers commit c60bb7ded93267f4146fdcb6d57b6bb3bc402c04 Author: hiram Date: Mon Jun 11 18:16:29 2007 +0000 Trying to get the color pull-down menu to color itself properly. commit c04e1c87fc975c805ed3ee2f7f5c587fe0e1a51a Author: hiram Date: Mon Jun 11 18:13:50 2007 +0000 Create bigZips/chromFaMasked.tar.gz for downloads commit c55a8b678a7383c4bff3a519bbf9620712a9e301 Author: kate Date: Mon Jun 11 17:33:44 2007 +0000 Use UI label for cons stats link commit dc56de4dfe8c87611ac220c0a6a864a22c4f6d49 Author: giardine Date: Mon Jun 11 17:21:55 2007 +0000 Added methods for the Omicia track. commit e583d2bcd76fa228a19b43ee4ae111155a4853ae Author: kate Date: Mon Jun 11 17:20:51 2007 +0000 Downloads for 28way hg18.txt commit 8d20d7bcf95c99e73873302c3576dd060505a86f Author: kate Date: Mon Jun 11 17:04:03 2007 +0000 Support separate labeling of alternate conservation track on track UI and hgTracks left label commit b1093bb37033eab56e6413e763992cdee871e071 Author: hiram Date: Mon Jun 11 16:59:33 2007 +0000 Initial version, as in-use June 2007 commit d82ee6699002317b1f369c3c475b67724a573f75 Author: rico Date: Mon Jun 11 16:18:37 2007 +0000 exanded header, added comments for quality data section commit e4fab7e25d15535fcaae5937b768dded212ac0fe Author: giardine Date: Mon Jun 11 15:19:19 2007 +0000 Added display and links for new Omicia track. commit eb64e07c2c9729b1921663c7e9545b7cfe9690ec Author: giardine Date: Mon Jun 11 15:16:40 2007 +0000 Added Omicia track. Display automatically mapped variants and hand mapped separately. commit 65ecd6422aa33df2dc4b019eed128b673ee0a184 Author: giardine Date: Mon Jun 11 15:14:31 2007 +0000 Added links for new Omicia track. commit bfcf5714bf8e57289ac1353103500768e7b40b4e Author: giardine Date: Mon Jun 11 15:13:22 2007 +0000 Added start of html for new Omicia track. Needs updated before track goes live. commit fe7690ba9a82593912ecd944f04e4c6e37548939 Author: giardine Date: Mon Jun 11 15:10:52 2007 +0000 Adding track for variants from Omicia. They mapped OMIM variants partially automated and partially by hand. commit 587db5fb18ba91d95111c079ce59975f03c8232f Author: galt Date: Mon Jun 11 15:00:22 2007 +0000 "Encode release log update" commit 6a720e6d40bc41af9f505101ec43c8bd53348b8a Author: galt Date: Mon Jun 11 15:00:12 2007 +0000 "Release log update" commit 1bd70133ab2ec8af9196550cb6fa64f9a102280b Author: braney Date: Sun Jun 10 22:37:54 2007 +0000 a utility to generate a sequence file from an atom file commit a9aae584379d8eba78b6ea805030d6ea2d59ae66 Author: braney Date: Sun Jun 10 22:34:42 2007 +0000 a utilty to convert an atom file to a maf commit d3f57d04bc7ad350692a742f9ac1b41d036fa3a8 Author: braney Date: Sun Jun 10 22:06:29 2007 +0000 change over to using blocks instead of PSl's commit 524bab09f67fa09c5d69453510234af583a1bde0 Author: braney Date: Sun Jun 10 21:59:25 2007 +0000 atom header file commit 39399a4ba5eff658bd4e016ce0cdd2cd206dd439 Author: braney Date: Sun Jun 10 21:59:07 2007 +0000 add atom.0 commit 89f33952fdf532ca819b02815acf23955a9e4881 Author: braney Date: Sun Jun 10 21:58:53 2007 +0000 some library modules to deal with atoms commit fe9a8c369288d086f5154ff42ca228ee304c7bd6 Author: braney Date: Sun Jun 10 21:58:34 2007 +0000 up some buffer sizes commit 3c2704bac57634895f18c07e71a3f3ed2ac5f99b Author: braney Date: Sun Jun 10 21:55:37 2007 +0000 fix an off-by-one bug commit e3189ab35ad01f7b07333cf74ec0b9ba28005707 Author: braney Date: Sun Jun 10 21:54:46 2007 +0000 fix up some tests commit a63d1197c2afbac1aa34d8614b199e4ebf2df173 Author: braney Date: Sun Jun 10 21:53:16 2007 +0000 fiddle with tests a bit commit 0dced6d2a413f01c1d9e6f4a7bc5c81c0b02ee54 Author: braney Date: Sun Jun 10 21:52:42 2007 +0000 new algorithm. Still needs cleanup commit a695bc4ef338cfe654250480542bdc58917779d4 Author: braney Date: Sun Jun 10 21:51:54 2007 +0000 change score, drop 5% on each iteration commit 5681f59d43eaee4a1dad16056fc1f75b61397760 Author: braney Date: Sun Jun 10 21:50:01 2007 +0000 a utility to add species specific atoms in the gaps between atoms commit 0d6c6df9e50d7be72e236ff7290ab06e1a57b990 Author: braney Date: Sun Jun 10 21:48:39 2007 +0000 a utility to expand nested atom base files commit 21152c9dd4fe2a3913e0b1503debd9e57da3db30 Author: braney Date: Sun Jun 10 21:47:40 2007 +0000 a utility to annotate atom files with sequence commit fdedc764b0d16a53494dfe5dd72ef0d3f3208569 Author: galt Date: Sun Jun 10 15:00:22 2007 +0000 "Encode release log update" commit ec8a9f584b4e12a9a30eb667070268d543b7ac10 Author: galt Date: Sun Jun 10 15:00:12 2007 +0000 "Release log update" commit fca2d8ddfadc693503860710abe5ded1924fc299 Author: markd Date: Sun Jun 10 04:38:14 2007 +0000 have hTableOrSplitExistsDb return false instead of aborting if DB doesn't exist commit c63b7474bedc520fba7575a8c73bc4656e5d8473 Author: galt Date: Sat Jun 9 15:00:31 2007 +0000 "Encode release log update" commit b37f18765c472e9e7fd75355712a599d18434493 Author: galt Date: Sat Jun 9 15:00:17 2007 +0000 "Release log update" commit db62d5462ed701bcb240a968912c1b9300e87093 Author: hartera Date: Fri Jun 8 23:17:43 2007 +0000 Removed redundant text. commit 42366f01b59629ca5975868f96225a8ef619a435 Author: rhead Date: Fri Jun 8 23:17:07 2007 +0000 Corrected squish display description. Changed long description of pack shading to the more brief 'tags counts are normalized to TPM in each TISSUE OR library. commit c8e273554aae64b1198789ea77f24dd5f4f337e6 Author: donnak Date: Fri Jun 8 22:54:13 2007 +0000 Removed this section -- we now have the CBSE link in the intro section of the page. commit 6f11f1178bd5220bfcbede544ec6e9187dfedb0a Author: donnak Date: Fri Jun 8 22:53:43 2007 +0000 Revamped some of the info in the intro. commit ad2326e0c29b05432e05b05e902041e45c707b92 Author: donnak Date: Fri Jun 8 22:53:26 2007 +0000 Revamped some of the info in the intro. Still need to change info abt Ensembl. commit ffa5ccc954ac9eeeef5d94586d64594188fd3071 Author: hartera Date: Fri Jun 8 22:21:49 2007 +0000 This is v1.6 of encodeYaleChipPval.html but updated to add descriptions for data added from Nov 2006, Jan 2007 and Apr 2007 data batches. Added link to GEO database. commit 5397fce0bada9b9e714f06416410e9001ca03235 Author: hartera Date: Fri Jun 8 22:20:35 2007 +0000 Reverting to version 1.6 for release beta for this track so data update related description changes do not show up on beta until new subtracks are pushed. commit bacefb47c63392c9605f73e10354162883992d35 Author: hartera Date: Fri Jun 8 21:56:09 2007 +0000 Further addition to antibody target descriptions. commit 3741a4ff8d09b0738d68bf3663e1ea3fd3edd627 Author: angie Date: Fri Jun 8 21:32:06 2007 +0000 Added IP address to 'Cart stuffing bot' warning in saveState. commit c3b7a4cb3f685cd0b8ed283370a50c27abadfa43 Author: angie Date: Fri Jun 8 21:31:12 2007 +0000 Added cgiRemoteAddr() (useful in warning messages). Don't complain about duplicate cookies if their values are identical too. commit 53096205603f3026d0c81bbee112e0962b40e4bf Author: hartera Date: Fri Jun 8 21:30:21 2007 +0000 Added information about antibodies and cell types used in new subtracks from Nov 2006, Jan 2007 and Apr 2007 data updates. Added link to GEO database. commit 8f8d2745fdef95342a1f2df52dfccd1b72a46fd8 Author: tingwang Date: Fri Jun 8 21:30:00 2007 +0000 update UW DNase-array label commit 126ba320ffc8b60e462567c98e15dd463b7dc843 Author: angie Date: Fri Jun 8 21:29:57 2007 +0000 Added cgiRemoteAddr() and fixed some comment locations to be consistent with rest of file. commit 3bc506be212f3d591b9d31297ce0ecc9e5b48f94 Author: galt Date: Fri Jun 8 21:27:07 2007 +0000 "Encode release log update" commit ffec8c2db4b3857ff12f1f8a2b9fff4b1ac417fb Author: galt Date: Fri Jun 8 21:27:05 2007 +0000 "Release log update" commit 5d066f4c6d127e6a89cd17692d4ec04fc72a9f40 Author: hartera Date: Fri Jun 8 20:56:10 2007 +0000 Yale Chip Pval description for release beta before update when new data sets added for Nov 2006, Jan 2007 and Apr 2007. commit 7a4c2be9d3e6aeea7884a14210d887c55335511c Author: angie Date: Fri Jun 8 20:49:56 2007 +0000 Swapped dm3 chains, netted. commit a7fbd6300f167c2255f00925b234579e0a110604 Author: angie Date: Fri Jun 8 20:47:05 2007 +0000 Boilerplate descriptions. commit bd083601db6cb5069be4d86358cbc50dacdaa48f Author: angie Date: Fri Jun 8 20:46:53 2007 +0000 Tweaked priorities of {chain,net}Dm{1,2} and added Dm3. commit 5555494d1c915f5ca150fcd4ce472fe9e071caaa Author: angie Date: Fri Jun 8 20:19:54 2007 +0000 We no longer have Dm1 chain and nets, and can use top-level def's for Dm2. commit f7d16c0a759362138b3df77324f28f919143f09a Author: kuhn Date: Fri Jun 8 19:54:12 2007 +0000 hg18 pages commit e74ed01031193f6877fbdac7d7e116e0e524442d Author: donnak Date: Fri Jun 8 19:39:55 2007 +0000 Updated grad student, admin info. Also updated some of the project responsibilities. commit bb68ce34b48b80a32ab328034e11fae6153701d0 Author: angie Date: Fri Jun 8 19:15:46 2007 +0000 In order to support overriding of session settings by CGI settings, cartLoadUserSession and cartLoadSettings now reload CGI variables after loading a session into the cart, but remove the CGI variable that triggered the loading. commit acdd4bff8e7f18dbcec97d14df972688b65927b6 Author: tingwang Date: Fri Jun 8 17:45:49 2007 +0000 modified default viewing parameter and labels for encodeRegulomeDnaseArray and encodeUWRegulomeBase commit 61ab7f4ffad0b207974eefc34652bf36044b0406 Author: tingwang Date: Fri Jun 8 17:45:03 2007 +0000 modified description for UW Dnase-array data for GM cells commit 94f9ab52a663c730dad11bd336e0d8a476ebdea7 Author: tingwang Date: Fri Jun 8 17:18:50 2007 +0000 modified description for UW Dnase-array data for GM cells commit bc095b8538ef5aea200d1710ff4f9c4c37966ce5 Author: tingwang Date: Fri Jun 8 17:15:17 2007 +0000 modified description for UW Dnase-array data for GM cells commit 0ab7459ddaf2fcb25a4b4a2e91b06f7118d75d7f Author: tingwang Date: Fri Jun 8 17:12:52 2007 +0000 modified viewing default parameter and labels for encodeDnaseArray and encodeUWRegulomeBase commit 485151a1f79ae1ded04daf7f7276284987085290 Author: hartera Date: Fri Jun 8 16:41:54 2007 +0000 Added new subtracks for UVa DNA Replication Origins track. Added custom track files and table with links to the custom track files which were put on the hgdownload server. Added new subtracks for Nov 2006, Jan 2007 and Apr 2007 updates of Yale Chip Signal and P-value tracks. Addition of Nov 2006, Jan 2007 and Apr 2007 for Yale Chip Sites track is in progress. commit cd2cd1f4242d7d6918e42170a48cb8e9acace964 Author: tingwang Date: Fri Jun 8 05:59:50 2007 +0000 doc for lifting GIS PET data from hg17 to hg18 added commit dde070f08e0d7d93a2cd03ef79f213cbab43e5d6 Author: kate Date: Fri Jun 8 03:25:17 2007 +0000 Set up downloads of masked sequence for 2X assemblies used in 28way commit ca45ff63c0b96b55ef2eaa79df356f9d2d01704e Author: kuhn Date: Fri Jun 8 01:11:40 2007 +0000 fixed second-machine reporting (was giving same results as first) and added support for wildcards. commit 62b669e19c5fc9f65c61336fc343e437c83c2eef Author: aamp Date: Fri Jun 8 00:48:24 2007 +0000 Lifting 357 bed tables from hg17 to hg18, hopefully correctly. commit 9cf00a0da7c2e0e637343628addf257377072710 Author: ann Date: Thu Jun 7 23:10:17 2007 +0000 added to the regex in the grep so that it only looked at the beginning of a word. It was finding ornAna in the mm_rn run because it contains 'rn'. commit 6e227b4c797bb5ed3335fb5c7871f3a0deb15a2b Author: hiram Date: Thu Jun 7 23:05:57 2007 +0000 Do not error out in copyFile when pipeline exits commit ee3502537b951db9fb36b1ad89c64473fbac6bca Author: lowe Date: Thu Jun 7 22:56:18 2007 +0000 Incorporated lowelab-specific changes using #ifdef LOWELAB so will not affect main browser tree commit 17a2d64f6190ed6883a30bab337ad3834eb3e90f Author: archanat Date: Thu Jun 7 22:53:10 2007 +0000 minor edit commit f18626de02b2ce47625627d6377977fcf272b8d7 Author: lowe Date: Thu Jun 7 22:52:46 2007 +0000 Removed index field that wasn't unique -- old change just now getting cvs'ed commit f0b83e8f6a21ebdf7419a80ffb5c1b679d76637e Author: kuhn Date: Thu Jun 7 22:32:13 2007 +0000 removed sanvols from list of machines that would be checked through the wire if nearly full commit 3af8b9cec43215535ed1fe69b2baa02b4800215e Author: lowe Date: Thu Jun 7 22:31:39 2007 +0000 Increased upper bound on track gif size to 60K from 5K -- tested in lowelab, seems to work fine. This is change is braced by #ifdef LOWELAB, so should not affect main browser code tree commit 780770cdaf5f20b870748fa0a187cd6652ed324c Author: kuhn Date: Thu Jun 7 22:31:30 2007 +0000 removed early exit commit c1e91335afd43f228c7dcf1a03fefc139b75c097 Author: lowe Date: Thu Jun 7 22:22:57 2007 +0000 Need more headroom for more genomes -- increased menu limit to 1024 from 128 entries; needed right now for microbial genomes, but will be needed in the future for all browsers commit 856dbca01c736927127c8d0375b8058da5d1ae05 Author: lowe Date: Thu Jun 7 22:19:09 2007 +0000 Minor change to remove indexing from tRNAs table type commit ccd2888ec574747d382e7d5bc6b8703350418ce1 Author: hiram Date: Thu Jun 7 21:58:47 2007 +0000 Fixup correlate functions for custom tracks commit 050ce1ea1cdd5b742ba244b0d693ba9f3776d862 Author: kuhn Date: Thu Jun 7 21:41:12 2007 +0000 added priority checking to ease ordering of track controls commit 59a2933aed6d023433c72dd1913348451479179a Author: galt Date: Thu Jun 7 21:38:24 2007 +0000 extending encode release log to show all details (like the regular release log) commit 51aa14f87643a9a61cd1cb60242a86beeb0160da Author: archanat Date: Thu Jun 7 21:00:37 2007 +0000 updated the description commit f76ec625777d3aec152a961d1d79b628aa9b54c9 Author: kuhn Date: Thu Jun 7 20:00:35 2007 +0000 added reporting for when starting list all over commit fce0cf1f7aea9bc91adff229d2f39350d669c041 Author: donnak Date: Thu Jun 7 19:31:00 2007 +0000 Fixed some broken links. commit 6c7a539fad53055cac3c9fd3ed491dc758b933ef Author: rico Date: Thu Jun 7 19:19:42 2007 +0000 added info about adding quality data to the 28-way alignment commit a1eeaf4794cd62351c7234c5c1ebf22484b433b7 Author: kate Date: Thu Jun 7 18:48:51 2007 +0000 Update in anticipation of NHGRI press release and Nature paper commit c8f936e329a013d97cc70c3bc0e5df23091d99e7 Author: kate Date: Thu Jun 7 16:36:59 2007 +0000 Fix minor syntax err commit ffde6d182786b124d6e789b7622f51879aa70f47 Author: galt Date: Thu Jun 7 15:00:32 2007 +0000 "Encode release log update" commit 42e4894ec0714000783f4a9e0645d4a9b5a2031e Author: galt Date: Thu Jun 7 15:00:17 2007 +0000 "Release log update" commit b1b7f345a972c9cd90d9aaf220ed48f8d6b02b30 Author: kate Date: Thu Jun 7 13:55:38 2007 +0000 Add first ENCODE track for hg18 commit c30608520309f5e84ca44017886f765c484d9d78 Author: angie Date: Thu Jun 7 00:49:47 2007 +0000 Added stderr warning about duplicate cookie values to findCookieData, in order to help us identify any lingering cookie-clash problems caused by multiple hosts sending hguid way back when. commit 66ab5b1815ae10e5d06daea6f3dbaa1d7d835381 Author: galt Date: Wed Jun 6 23:49:29 2007 +0000 fixed missing sql call commit 7fb5beb6ca1c74ba9a5ae34eff9f7037b0f32df3 Author: ann Date: Wed Jun 6 23:40:53 2007 +0000 fixing config option descriptions commit 954b48ff54f023fa2bd61e8c3661df9c73fa1903 Author: kuhn Date: Wed Jun 6 23:30:47 2007 +0000 combined chain and chainLink files into single master table list and added net table to it. added tablesize checking to net script. tweaked two other scripts. commit 0aa2919b5db4149f4fa25b9a3b2a66a925b55ffa Author: angie Date: Wed Jun 6 23:27:52 2007 +0000 Updated gene credits: we now have FlyBase rel 5.1 genes (not just liftOver'd 4.2). commit bd18b39d9b3e5e74ae92dc91da88bfbe59fb3614 Author: ann Date: Wed Jun 6 23:21:58 2007 +0000 added a section for the new import feature commit 013d8580bf82b8c3139ff85382947f03c1070874 Author: galt Date: Wed Jun 6 22:48:17 2007 +0000 removed debugging statements commit 3e9ec90a9b0a43d06b18a1f0374875ce4adf97fc Author: aamp Date: Wed Jun 6 22:32:53 2007 +0000 More information about pack mode. commit dfbfe9075cc462b4fac112cfa29aa1c4a4565047 Author: aamp Date: Wed Jun 6 22:32:19 2007 +0000 Simplifying library details. commit 9bf93873e6d84aca42e968e9632759fd49db5794 Author: archanat Date: Wed Jun 6 22:08:24 2007 +0000 updated the fragment type commit ed44372dbd9993cbddf724ac8f7d0bc3e36fcc1e Author: archanat Date: Wed Jun 6 22:07:27 2007 +0000 local declaration of gold and gap so that local gold.html and gap.html is picked up. commit bb4da6cc19ebace50ac3e211f00046fb7b496fb1 Author: galt Date: Wed Jun 6 21:43:53 2007 +0000 adding support for affy 6 and 6SV commit f5d7736415f749531fd1de0eadaa028b98439cdc Author: ann Date: Wed Jun 6 21:40:57 2007 +0000 added description for new import feature commit 92844bc54401ccef7fec207b4744af9e34b6490a Author: ann Date: Wed Jun 6 21:29:13 2007 +0000 grammar change commit 31625bf43e60f602abc0aea957aed8c2842c4ada Author: rhead Date: Wed Jun 6 21:27:33 2007 +0000 Regular genemapper link was broken. Sourev Chatterji gave us a new link to use until their original link is fixed. commit 4b080d88fd3ea9b96d35bee8bf2f1bd7105a994d Author: galt Date: Wed Jun 6 21:08:35 2007 +0000 adding support for detection of illumna300,550,650 markers commit d9e9941b4b38183a1f1c85d5336ed92f23ae2d16 Author: galt Date: Wed Jun 6 20:45:05 2007 +0000 removing unnecessary lines commit d43c8f51974723607b139bff79053ae73a448831 Author: aamp Date: Wed Jun 6 19:46:58 2007 +0000 Indeces and bin changes to autosql version.` commit 6a673c53cc22a37a03107c5afcdee09f7af9fd27 Author: aamp Date: Wed Jun 6 19:46:23 2007 +0000 Forgot to add this. Just a cmp function for slSorting. commit 992b112926cf2654f8bc2089202d1d167ecdf926 Author: aamp Date: Wed Jun 6 19:45:48 2007 +0000 Forgot to add a few functions. commit dfee34b96a3bf35577ffab660defe63d8d9b00f7 Author: galt Date: Wed Jun 6 19:26:44 2007 +0000 making threshold low for coverage for sparse tracks of low density commit 91e5a08ff56b2bd2dd6db82404e353d9bf01ea5b Author: rhead Date: Wed Jun 6 17:47:43 2007 +0000 Nevermind, the rule is there in part to create a relationship between the tables. Adding the rule back, but with minCheck=0.0, and with a comment as to why it is there. commit 988a943528dff11468c0ed8856aea510a0f0c248 Author: archanat Date: Wed Jun 6 17:12:00 2007 +0000 fixed a typo commit ad07b08b3e393c66bf6cd9b844ddeed9c6e08000 Author: hiram Date: Wed Jun 6 17:11:58 2007 +0000 Added sequence for running repeat masker commit cfa1810b2559dd8c48b11c1c6521b875365cdd01 Author: ann Date: Wed Jun 6 16:48:01 2007 +0000 fixing help section typo commit 5753baa23a01063a2d43bbeac0976a2cc2320e84 Author: hiram Date: Wed Jun 6 16:37:29 2007 +0000 Properly parse tags that are delimited by single 'quotes' and not just those with double "quotes" commit ecc22b08d5ff247c3a4b48dbb02a68d73a0f9bf5 Author: ann Date: Wed Jun 6 15:55:54 2007 +0000 Made all rmsk description pages consistent with respect to the repeat classes. commit 8dcdc77f2ae121ee19d888a5c7f5d76c6425ca5a Author: galt Date: Wed Jun 6 15:00:33 2007 +0000 "Encode release log update" commit bc09a803df65c60fe22ac1c33b8b26b1e70232d4 Author: galt Date: Wed Jun 6 15:00:18 2007 +0000 "Release log update" commit cea52a90e1e1162de33e7d74af4f8e6ecabe9d1a Author: aamp Date: Wed Jun 6 08:11:30 2007 +0000 Improvement (bug fix) to clicking the sage tags. Now cgapSageMapItem is used to define the mapboxes with the lib or tiss CGI vars, and the i CGI var is set to the tag sequence itself. This removes the ambiguity when clicking on two different tags at the same locus (different SNP variants). commit 54037e179478cae9db7bdc158e8fe0563de29513 Author: aamp Date: Wed Jun 6 08:07:25 2007 +0000 generalization improvement for tracks using genericDrawItems. Now it can use track->mapItem function pointers. This definitely needs good checking in review. commit d8596c4bce92ea073de474e09a671004a55c04b8 Author: markd Date: Wed Jun 6 04:56:06 2007 +0000 added N-SCAN tracks commit 2a88a07efe9695d3178531fdb4bfb1824002aeb5 Author: markd Date: Wed Jun 6 04:38:04 2007 +0000 fixed yank-n-put typo commit 8322761dadcc0eaaab73a9f06dadca820ca5a516 Author: angie Date: Wed Jun 6 02:38:59 2007 +0000 Bugfix: added check/refresh of wibFile and wigFile settings when present, in customFactoryTestExistence. Their absence caused them to be cleaned up instead of kept alive by refreshNamedSessionCustomTracks. commit 1156d8099b90464aa4a0557e5769f494c84b96f7 Author: galt Date: Tue Jun 5 23:48:09 2007 +0000 added support for importing tables and custom tracks as chromGraphs commit 4594ab3ca6c23cff51d08a3fc2880a9fa08014a8 Author: hiram Date: Tue Jun 5 21:24:17 2007 +0000 Change blastz caeRem2 status to DONE commit fd71d0ac288a23b00af1c686f12f6f11221696fe Author: kuhn Date: Tue Jun 5 19:38:08 2007 +0000 commented out a chmod which does not work if some who does not own the file tries to run the script commit 5cefd3ee931dc406e3a14c833d8d426a7d375050 Author: donnak Date: Tue Jun 5 19:11:59 2007 +0000 Fixed a few things Rachel found in our paired review. commit d2c7917cbe48e42c0b1b506cf8df8c4cae435977 Author: kuhn Date: Tue Jun 5 17:35:56 2007 +0000 removed redundant grep commit 9df7bd2bacc1f88cf338f0b05c7841d0fd7b712d Author: fanhsu Date: Tue Jun 5 17:22:47 2007 +0000 Updated spReactomeId and spReactomeEvent tables. commit b5eeffab15406a268efaa36208c69a734aa11c36 Author: donnak Date: Tue Jun 5 17:08:14 2007 +0000 Changed hardcoded paths to relative paths. commit 7d5cc49b0b8cfcd2fb7285dfcf189b331ce254d8 Author: donnak Date: Tue Jun 5 16:59:08 2007 +0000 Changed hardcoded paths to relative paths. commit 3c5e4f230ffb69d81103f417fc82e1d80e61916f Author: donnak Date: Tue Jun 5 16:41:54 2007 +0000 Fixed hardcoded style & image paths. commit 1bdf7dc7e23caa5daa4206d8b20fda918142cb15 Author: donnak Date: Tue Jun 5 16:39:45 2007 +0000 Fixed hardcoded style path. commit 6e78bed49e00bac006b2a8e26a57e3dfc0cc8321 Author: donnak Date: Tue Jun 5 16:37:13 2007 +0000 More hardcoded path changes (/style -> ../style). commit 91b94471abaae2c7efbe9fa45fcc292530cd7da6 Author: donnak Date: Tue Jun 5 16:33:51 2007 +0000 Removed some text to make this file conform to the standard format of our other pages. commit ed92f89ceb9ec5a7c6da49913db01dd05b53af80 Author: donnak Date: Tue Jun 5 16:23:51 2007 +0000 Changed /images path to ../images. commit ff9480e4fd0567f5feebc73c98096032800ab078 Author: galt Date: Tue Jun 5 15:00:28 2007 +0000 "Encode release log update" commit 8b618faa8681fc37f89b5683fe0b9c90ae558a25 Author: galt Date: Tue Jun 5 15:00:15 2007 +0000 "Release log update" commit c933acaf057fb41d32b59f0d19e8bff66fa422e8 Author: donnak Date: Tue Jun 5 06:37:35 2007 +0000 Fixed broken downloads link. commit c9e5644060b42d962183211b75cb525c8fa7b55a Author: donnak Date: Tue Jun 5 06:34:25 2007 +0000 Fixed link broken by Galt when making links relative. commit cd9805ea20d3c6094d13ab0fe102ff07708e99ed Author: tingwang Date: Tue Jun 5 06:28:14 2007 +0000 modified ENCODE UCDavis ChIP-chip long label commit b5ce4fbb82a733cf3ada167ddf4131926829e584 Author: tingwang Date: Tue Jun 5 05:53:00 2007 +0000 modified ENCODE UCDavis ChIP-chip description page commit 0b366407aac9a5477e1004e01c7d2647378fac77 Author: angie Date: Tue Jun 5 05:05:35 2007 +0000 Regenerated flyBaseBlastTab as a test case for doHgNearBlastp.pl's use of hgLoadBlastTab's new -bestOnly. commit 1d3c4e66ba81975a353594acce7c32e35d93f9d1 Author: angie Date: Tue Jun 5 05:04:33 2007 +0000 Make use of hgLoadBlastTab's new -bestOnly when loading self (maxPer > 1) alignments. commit b575c60c49a82c8eab2730eb49d14e3be635e2f1 Author: tingwang Date: Tue Jun 5 04:28:38 2007 +0000 modified ENCODE UCDavis ChIP-chip description page commit bdb8b8cc3482537971ff4ed65db72a7450ff41fc Author: rhead Date: Tue Jun 5 01:29:15 2007 +0000 markd says this check is practically useless (also evidenced by our current minCheck=0.01 rule) commit 0baff246e3b30a461cf2c79501e691772bb18b3a Author: tingwang Date: Tue Jun 5 00:41:07 2007 +0000 modified ENCODE UCDavis ChIP-chip description page commit 732bdb41996a8ff87d9a792c80efd50228cce729 Author: angie Date: Mon Jun 4 22:57:42 2007 +0000 Added -bestOnly which causes us to keep only the first (best-scoring) hit for each {query,target} pair. This excludes extra hits/rows that are simply ignored by hgNear/hgGene. Already implied if -maxPer=1 is used. commit 119b394ba17b12e471382b0313640814964fc54f Author: kuhn Date: Mon Jun 4 22:56:53 2007 +0000 added matrixHeader for some chain.htmlpages commit e0bedf7a3b1d55f1d51c23b3c635609e6c010d6a Author: angie Date: Mon Jun 4 22:08:58 2007 +0000 ornAna1.txt commit e31be456efa237e213aa5fca0c74b60765b0b466 Author: aamp Date: Mon Jun 4 22:08:35 2007 +0000 Dense mode uses filter now. commit 1b34e400bb146ce1b4e080dc646815aad780ede3 Author: ann Date: Mon Jun 4 17:16:49 2007 +0000 added RC repeat and fixed names of other repeats commit 11dd688c7807327af416aeb9acf0fd1af2df8a44 Author: ann Date: Mon Jun 4 16:40:37 2007 +0000 fixed citation commit 6fdeb4ef7e457a594963dedf45dce44d1a9938a6 Author: galt Date: Mon Jun 4 15:00:22 2007 +0000 "Encode release log update" commit 8255a7468b1a69e93049e7cf30febb605254374c Author: galt Date: Mon Jun 4 15:00:12 2007 +0000 "Release log update" commit ed59c60ba1af521f0d8ee6f7d612fc4d50cc319e Author: fanhsu Date: Mon Jun 4 01:41:35 2007 +0000 Created getInterProFa.c to get AA sequences of InterPro domains. commit 4b64966beab92decbfb9b300a2ac9c08a9f91519 Author: markd Date: Sun Jun 3 15:25:03 2007 +0000 updated expected results for new column commit fc58d836bda6a19ad155d3a180398b5500a676eb Author: galt Date: Sun Jun 3 15:00:22 2007 +0000 "Encode release log update" commit 71dd72de2523dd6172adc60d34a0469c6554436d Author: galt Date: Sun Jun 3 15:00:12 2007 +0000 "Release log update" commit 893b2368617823d5b02694c66de8783f3ef89eb4 Author: lowe Date: Sun Jun 3 06:43:42 2007 +0000 Updated index and bin fields commit 5ca9aa4643f049b3ce372cf94e4a3387caf8a2a7 Author: pchan Date: Sat Jun 2 23:06:20 2007 +0000 Cosmetic change in displaying clade on Blastp detail page commit 208bd868ef90f5085c1cd89951167102ecceafc4 Author: markd Date: Sat Jun 2 21:57:19 2007 +0000 added computation of target coverage stats commit 56ac2ea2db71797e32e3d902e1cabd6f5e080666 Author: lowe Date: Sat Jun 2 20:52:44 2007 +0000 Added object file for new lowelabPfamHit type commit ceeadf6390f516dbef8bf612f34af87b4d0e9945 Author: lowe Date: Sat Jun 2 20:51:22 2007 +0000 include file for new Lowe lab Pfam Hits table type commit 641bbb47a557264dc827861a71ee762f09ca6ed4 Author: lowe Date: Sat Jun 2 20:50:32 2007 +0000 Added new data type for Pfam Hits track for Lowelab microbial genome browser commit c5bb440ab728644957e2ec2f4f84c12f6a150bd0 Author: lowe Date: Sat Jun 2 20:43:33 2007 +0000 Added custom Pfam hits details page commit 0947d4794849b92f623023c80ebb2eb4d362a553 Author: markd Date: Sat Jun 2 18:29:37 2007 +0000 change cvsStatusFilter output to match help, added additional columns commit e5fb00ba2e932641d9221ea6aab233ac5720802c Author: galt Date: Sat Jun 2 15:00:27 2007 +0000 "Encode release log update" commit ec48ecb78d716a523544ec93626e86780db4fd95 Author: galt Date: Sat Jun 2 15:00:15 2007 +0000 "Release log update" commit 38d6b9fc72a85b4733989247f8551a75b3d3dcec Author: markd Date: Sat Jun 2 07:13:17 2007 +0000 more dog organism changes commit e1ae6e716a449348048341cf5a88c4f6e23a1460 Author: heather Date: Sat Jun 2 00:12:39 2007 +0000 add a line to previous commit commit 4c6e35a837c8ae27ef93dc7c3156a045971530d7 Author: heather Date: Sat Jun 2 00:11:18 2007 +0000 new snp array data from Affy (and a couple of tweaks) commit 3212a95ef413f185b6376436782cd727b48fde83 Author: heather Date: Fri Jun 1 23:54:03 2007 +0000 add strPur2 commit b11968809c758f6878019661c821c4c09ae29a6f Author: hiram Date: Fri Jun 1 23:04:38 2007 +0000 Begin to make the color pull-down menu commit e09239f60f050d4b1a84a09bc077769973b32550 Author: hiram Date: Fri Jun 1 22:36:53 2007 +0000 Now using linked features to get color drawing (do we really need that ?) commit c33f81165adc7e9e2f373f08c798ad909852400b Author: donnak Date: Fri Jun 1 20:25:07 2007 +0000 Fixed path for images dir reference. commit 0966bb791c888fb50469117e9efdbdda02f58e4b Author: archanat Date: Fri Jun 1 20:05:59 2007 +0000 changed the wordings of a sample positon query commit 6ea8ce7b272085df66c0211aa7eb8026745c8483 Author: galt Date: Fri Jun 1 19:40:11 2007 +0000 fixing relative paths commit 446e380945f88b0cb981e972928c096740ee99c7 Author: archanat Date: Fri Jun 1 19:26:42 2007 +0000 converted refs to pubmed format commit 14103da7a9add14f93f921f96bb70c960449eb35 Author: hartera Date: Fri Jun 1 19:17:03 2007 +0000 Changed URL for sequences table as we are now hosting it plus custom track files locally. commit dadc278d59d5a14881205b1d8affbcef981c9ade Author: hiram Date: Fri Jun 1 19:08:42 2007 +0000 Now allowing deletion of items. And checking for email verified before allowing edit forms. commit bc9658cfbb29140e35085653b87f9d54aa5159d0 Author: hiram Date: Fri Jun 1 19:07:21 2007 +0000 loadWikiTrack is better named addWikiTrack commit 4ff9b8f1b2ca2fd25e2ed38f2867076e569687b8 Author: hiram Date: Fri Jun 1 19:06:38 2007 +0000 Add the delete item function, and a cfg variable for browser return URL commit ffc698bc159c23de8b9ac8bcd3535fc9b28d572c Author: kuhn Date: Fri Jun 1 18:30:48 2007 +0000 added checking for index size and reformatted output. changed getRRtableStatus.csh to fail more gracefuly when db is not in STATUS dumps. thanks, brooke commit 125883e06040967ec69b70fc995c97e452233335 Author: donnak Date: Fri Jun 1 15:25:16 2007 +0000 Removed survey link. commit 913a38c5bbb6c03534a14c937b3c137d1322c208 Author: donnak Date: Fri Jun 1 15:22:58 2007 +0000 Removed UCSF mirror site, per Paul McKenna's request. commit 20dd94c30dbdc4abc9314338558d3faba3b227c8 Author: galt Date: Fri Jun 1 15:00:32 2007 +0000 "Encode release log update" commit 29652362f77717cc878780d11d001b61bac1399a Author: galt Date: Fri Jun 1 15:00:17 2007 +0000 "Release log update" commit 8b52cdaeb3ac981fbb95693894bc2d2d1a8c618c Author: kuhn Date: Fri Jun 1 00:15:55 2007 +0000 changed Pb1 to CaePb1 in chain list commit 1e8e8910e0f8cbe15abc70ba702d305fbf15f0a4 Author: kuhn Date: Thu May 31 23:55:51 2007 +0000 rearranged priorities for nets and chains commit fd8387fba9280c2b4d21eb3e256f9f01d7c13a74 Author: kuhn Date: Thu May 31 23:11:45 2007 +0000 rearranged priorities for nets and chains commit d36bd2da5f3b8d45c37afcffed47ad24ce9ddd99 Author: hiram Date: Thu May 31 23:04:08 2007 +0000 Properly link back to hgwdev-hiram commit c3be1161b02e9518742b672d1fe966d329c3bc3d Author: hiram Date: Thu May 31 23:02:17 2007 +0000 Starting to add the delete function commit 23c7bd58c138600f18c7ab8c497467061ef40d0d Author: hiram Date: Thu May 31 22:01:33 2007 +0000 Better definition of checking for logged in status commit aa5979dfb4ab884466cadf78b889dadd0d008ad5 Author: hiram Date: Thu May 31 22:01:02 2007 +0000 the htcAddWikiComments define commit 27ac4c6f21e226c36b17fafbfac2ee0c07876ea9 Author: hiram Date: Thu May 31 22:00:09 2007 +0000 Now performing additions to comments correctly. commit a6f26a0e56ebdb50c2a07f721091247438762193 Author: kuhn Date: Thu May 31 21:14:26 2007 +0000 changed the aspect ratio a bit and added periods after the genous names commit 361a607fc1871859e93592521be9951d614ea96b Author: heather Date: Thu May 31 21:02:03 2007 +0000 add snpArrayAffy6 commit 9c66702448e7d3d6c5209655b7d11f5194e60806 Author: heather Date: Thu May 31 21:01:26 2007 +0000 update for snp arrays track commit 2cb5ddc10da998df7fcef31dcbbabfe6753d056c Author: donnak Date: Thu May 31 20:37:35 2007 +0000 Made an initial editing pass of this text. commit b0d7423b27fddb639834bdbe4c56bb263e2a4f80 Author: kuhn Date: Thu May 31 20:15:44 2007 +0000 added matric header to all the new worm chain tracks commit 2a4324d56cecde73c7b07420f8d9fca10cfb1b28 Author: kate Date: Thu May 31 20:01:46 2007 +0000 Fix spelling of Rico's name commit 4fd8d364c118874f83309dac7029d94575f80b81 Author: kuhn Date: Thu May 31 19:58:25 2007 +0000 added matric header to all the new worm chain tracks commit 8c20972342a7bb179137bf5a0b71c674a2426a81 Author: markd Date: Thu May 31 18:54:32 2007 +0000 fixed signed/unsigned gcc complaints for stuff pulled from psl commit 95a54bfad6d7ee951562f6baa8fa8f4ead663378 Author: hiram Date: Thu May 31 18:44:32 2007 +0000 Correctly label the blastz swap cb3 commit 6d11209b1811f78627a35a5b1a21d6eddfc1c3c7 Author: hiram Date: Thu May 31 18:42:31 2007 +0000 WORKING status is actually DONE commit 190de29c1082e1f627b30122ba7dbd18b6afe72d Author: heather Date: Thu May 31 18:19:46 2007 +0000 don't include self in multiz species list commit 20a50dde32457dc85514b97d875775f690e821e1 Author: hiram Date: Thu May 31 18:12:21 2007 +0000 Add simpleRepeat build sequence commit 94ebf1b2308d3e53ad3452caf2f7a24f2a1d26dc Author: kuhn Date: Thu May 31 18:05:07 2007 +0000 added logic to stop processing if no overlap to unbridged gaps. no need to print empty links commit 1e8ae6314d537a0e046634e0229587f1281f3dde Author: fanhsu Date: Thu May 31 17:32:40 2007 +0000 Updated miRNA track, using latest data from Michel Weber. commit a516cba069898205bc3648c9a1c25462be2c7c46 Author: heather Date: Thu May 31 17:09:27 2007 +0000 copied from platypus commit 66dc9a9b01365b237f47543cd4187b1db0f8944a Author: fanhsu Date: Thu May 31 16:55:35 2007 +0000 Updated wgRna track using latest data from Michel Weber. commit f9ec63d767338c585f62b8d0c25b50aa1fea7dbc Author: hiram Date: Thu May 31 16:48:41 2007 +0000 Add clean target commit 19deca71bb54d80844827d80537cf3945ae3ad61 Author: hiram Date: Thu May 31 16:47:54 2007 +0000 With advice from Peter Schattner, fixup relative paths in makefile and add jkhgap option commit 374d4e2905609592479af421ddc5a8c131781315 Author: galt Date: Thu May 31 15:00:32 2007 +0000 "Encode release log update" commit 26fcb5d96f5e5d57f43025eac0b19bc8c191f5b3 Author: galt Date: Thu May 31 15:00:17 2007 +0000 "Release log update" commit 4ef0c83a6b17df9ccd25a3fd64b3642bd5e98309 Author: heather Date: Wed May 30 22:59:58 2007 +0000 added strPur2 commit c4655f691f771a267aa7f92b03dcc37b47546c60 Author: kuhn Date: Wed May 30 21:31:59 2007 +0000 removed Dm3 from chain list commit b9d67bcd4162308874b6aa5b100edbabfbce70ec Author: kuhn Date: Wed May 30 21:23:00 2007 +0000 added some missing commas commit 9d0b181ff2988783af567252f1a29f90b7c5fdbc Author: kuhn Date: Wed May 30 21:21:52 2007 +0000 dropped a number that shouldn't be there commit f595b53a6bf2b8057014243a15d181f669e294ed Author: heather Date: Wed May 30 20:50:28 2007 +0000 add multiz4wayFrames commit 1c6ac44d2ed4861334346d2b3fccabb0b8db6bc2 Author: kuhn Date: Wed May 30 20:47:16 2007 +0000 added worms and added worms and dm3 to chainDest list commit 94a32230b06e7144319a78b6c0c108eed8a29e4b Author: heather Date: Wed May 30 20:39:43 2007 +0000 multiz downloadables and frames commit 94616b6104c39133095b6e6f63a90459a0a7f66b Author: ann Date: Wed May 30 20:34:47 2007 +0000 cleared up language commit 0bd8fa2f5446c5829cf45d72cf5a0fdf4d1bfd5b Author: kate Date: Wed May 30 20:14:23 2007 +0000 Rename 28way multiz table commit d2e0acf90a96a03e78428b4acce3ee7761b10a32 Author: kate Date: Wed May 30 20:12:04 2007 +0000 28way multiz commit 771a50c35eecde159607330cc0210207e1a6cbd5 Author: kate Date: Wed May 30 19:34:58 2007 +0000 Suppress 'Data last updated' for wigMaf as it is currently misleading commit 2a80a57f24384f358832d1309f152ae8faf49e23 Author: heather Date: Wed May 30 18:03:49 2007 +0000 rerun multiz (with corrected split filenames); change tree; add treeimage commit 8efe33202bd9ef779e8160d3eadcfa67e3cd14e7 Author: galt Date: Wed May 30 15:00:29 2007 +0000 "Encode release log update" commit 9ee4551ebbec61a20774a2b466c7ecf36282c97f Author: galt Date: Wed May 30 15:00:16 2007 +0000 "Release log update" commit 52dcdbcb84ed5739f1bd3cc1e286f83c6d8f55d9 Author: heather Date: Wed May 30 02:13:48 2007 +0000 correction commit 3cd0979aa23e335907b5ab00f0a52a4b2e934a52 Author: kate Date: Tue May 29 23:50:08 2007 +0000 Add track of phastCons restricted to high-quality assemblies, for evaluation commit 3dc3e1995cd122e30a2a93de27fed9078f13ea7d Author: ann Date: Tue May 29 23:04:44 2007 +0000 one more release alpha to remove for encodeUvaDnaRepOrigins track commit f5f67c9299256da4d367fc0a67437dc5b2083d26 Author: ann Date: Tue May 29 22:57:58 2007 +0000 messing with release alpha and beta for encodeUvaDnaRepOrigins track commit 63a9243278149bcdcc43cc648a19434e121e44c7 Author: ann Date: Tue May 29 22:31:53 2007 +0000 minor edits commit 20a68e668265d7560226269755122774a32b76bf Author: heather Date: Tue May 29 22:27:06 2007 +0000 add treeImage for multiz4way commit 4c58a12096cf95270f484a236e747fd7e31e42d8 Author: heather Date: Tue May 29 22:19:58 2007 +0000 new image commit cb39a05a5d3cabc35f356d97d1349ce646d3685d Author: aamp Date: Tue May 29 21:23:00 2007 +0000 "New version number v160" commit 8ba4adee89c22ab2733c33152147f39c7a8bae1d Author: rhead Date: Tue May 29 18:08:18 2007 +0000 Removed note about library filter (andy removed the filter). commit 6d23652039826312fdb3322603be671cc34f9d35 Author: markd Date: Tue May 29 15:12:45 2007 +0000 dog organism change commit f679aabe8f55f5ad6c056991e5641317f50a1533 Author: galt Date: Tue May 29 15:00:23 2007 +0000 "Encode release log update" commit edd758b2629f00f6a1dcbb5c91211c582abdb48f Author: galt Date: Tue May 29 15:00:13 2007 +0000 "Release log update" commit 1a858e1222bb932f939502eb770c3423b3fdddbc Author: markd Date: Tue May 29 05:33:20 2007 +0000 fixed my stupid broken commit commit b4c09ee91d8cfd8fbfd249386b92458375b809fd Author: kate Date: Tue May 29 05:01:06 2007 +0000 Correct wiggle item height in dense mode. commit 4d7d94f3f052526f4160baa7fb63e5d22e5c4828 Author: kate Date: Tue May 29 00:14:38 2007 +0000 Tweak label for conserved elements commit 9d2d1aa7a4e78bb1a2b231bf141de89b7410a417 Author: rhead Date: Mon May 28 21:52:32 2007 +0000 Removed broken link to Tarjei Mikkelsen. Couldn't find a good replacement. commit 726d9c85e2f910e8d4755c7ec281f4de8a023da5 Author: galt Date: Mon May 28 15:00:20 2007 +0000 "Encode release log update" commit 1852a39494324281916b4f3f35dc75cfa23290b2 Author: galt Date: Mon May 28 15:00:11 2007 +0000 "Release log update" commit cb48b0077b6784fbf818902ae2c8cdf75de1c701 Author: markd Date: Sun May 27 21:23:07 2007 +0000 fixed signed/unsigned problem commit 0c45f669883f16bf3c20b97fc1c1484deb050d98 Author: braney Date: Sun May 27 16:17:19 2007 +0000 another version. Experimental. commit ba0dced2766fa13c6df1a5978e06de9639b587ec Author: braney Date: Sun May 27 15:58:29 2007 +0000 add rheMac2 alignments commit a93ee8d640f1b129a591150d3d111bd10b3e2600 Author: braney Date: Sun May 27 15:57:59 2007 +0000 add monDom4 alignments commit 477d66b05566fbb703f914f43311f9f2431fa6a6 Author: galt Date: Sun May 27 15:00:22 2007 +0000 "Encode release log update" commit db56fa8fc0f49f4c4b5c61f2ad0f7d7d19b168f4 Author: galt Date: Sun May 27 15:00:12 2007 +0000 "Release log update" commit 74f3ea48cb5770966cd799081aaa0b3fbbca6221 Author: markd Date: Sun May 27 01:24:01 2007 +0000 dog organism change commit 89f4112dcf2273a814e975692d20894f88c01618 Author: angie Date: Sat May 26 17:42:15 2007 +0000 In presentProteinSelections, watch out for rows of kgSpAlias that have empty spID (which won't join up with spXref3. Also moved around some sqlConnects to avoid multiple connections without disconnection. commit cd2b57a0c6ad43a57c371455fface03c0b0d1aad Author: galt Date: Sat May 26 15:00:26 2007 +0000 "Encode release log update" commit 39bbfce29490fe17be0ae7c3646523ad7ead8f3c Author: galt Date: Sat May 26 15:00:14 2007 +0000 "Release log update" commit 793f13ba6029b605b3a18b78c0ab5def9dd44bcd Author: markd Date: Sat May 26 06:04:01 2007 +0000 allow -statsOutputAll to work without -aggregate commit a348e8771db5d39170d2043f16cc4e0bc779a4c9 Author: kate Date: Sat May 26 01:28:32 2007 +0000 Add placental mammal conservation for 28way commit 066fe12742413147774070efe3aa6a71b3517c41 Author: rhead Date: Sat May 26 00:19:44 2007 +0000 fixed target=_blank commit 40bb8ce0389662492ef949b6ef6599568be5fbb0 Author: rhead Date: Sat May 26 00:17:17 2007 +0000 Reworded methods section. Thanks markd. commit 09c6df557b12ac61314f9b2f20729bc9329fe397 Author: kayla Date: Fri May 25 23:13:54 2007 +0000 Added ornAna1 commit d14cff171d3a3c800598775d1272b44912bec13f Author: aamp Date: Fri May 25 23:06:30 2007 +0000 Took out library filters. commit 73ad084e54882edf08781c4ed7eef8eb17fab2e4 Author: aamp Date: Fri May 25 23:02:26 2007 +0000 Better way of printing out track html because it includes the schema. commit a0f10fcfe54e612e161ec4f33c24dd19b973f0c5 Author: hiram Date: Fri May 25 22:55:19 2007 +0000 Adding a session cookie variable commit 76e3d0ea1eb46db20a05eb23f66ce28574f76f63 Author: hiram Date: Fri May 25 22:54:54 2007 +0000 Adding an auto-increment id field commit 1dc67df6e87f557afc351c28c812c390fb53170b Author: hiram Date: Fri May 25 22:41:52 2007 +0000 Cleaned up, debugging removed, will now properly add a new item. commit 5338316b2c8184747dcd0f0763f559e238618dc6 Author: donnak Date: Fri May 25 22:06:55 2007 +0000 Updated a few entries. commit aaf6bd8ca5bf5fd40e113b89564d367e05a69a8f Author: rhead Date: Fri May 25 21:43:16 2007 +0000 Removed broken links to flyBase. They have redesigned their site, and this information seems to be no longer available. commit c2a888ce31e1b0fe12ac58a0782b9c489aac7678 Author: hiram Date: Fri May 25 21:33:37 2007 +0000 Is now creating initial content in the wiki. With lots of debugging statements. About to remove all of that business. commit 66cc455d4c452b24ba06fb95be68ec264847842e Author: aamp Date: Fri May 25 21:26:48 2007 +0000 Add back in the dense-mode coloring. I thought I already did this. commit 3389297f1ba5e35e94f9d8f4f42e03237c8a2ef1 Author: hiram Date: Fri May 25 20:56:24 2007 +0000 Reset HELP_DIR relativity. No longer ../ needed commit b9c0363157942f51fd9ed9a1a2c40cc4653b3b9c Author: donnak Date: Fri May 25 20:06:15 2007 +0000 Uncommented platypus release. commit 5c9e88c9b54de1632e82f06826f6b56db094f28e Author: aamp Date: Fri May 25 20:03:38 2007 +0000 connector lines wasn't being drawn on linkedFeaturesSeries tracks. commit 6d385f6af01bb8a7ca7cded64d6abfe6cea99319 Author: donnak Date: Fri May 25 19:46:01 2007 +0000 Uncommented platypus credits. commit 00cc316bbb6e8aad58204beda03c6baf7e339574 Author: donnak Date: Fri May 25 19:44:34 2007 +0000 Archived an item. commit e41888f09d652145870d40f252e97a4eb4053b2e Author: donnak Date: Fri May 25 19:44:25 2007 +0000 Uncommented platypus announcement & archived lizard announcement. commit d9e310123937dd92c793c26a65878d8fe780a547 Author: kuhn Date: Fri May 25 19:06:02 2007 +0000 simplified logic while checking chroms with no chains commit c02d337ea5b48445cbc34c3efb64b5ac8f5a04aa Author: kuhn Date: Fri May 25 18:57:00 2007 +0000 set getSplit to look at gap track instead of input track, fixed file name, and added one to start coord for browser url. thanks, kayla commit e816b7e4a68cd5df1aa8e706d88726d9e9f58aaf Author: archanat Date: Fri May 25 18:10:57 2007 +0000 updated the description commit bbcfcab9f501e9f2bf925f05294bf9b669d5c0e7 Author: markd Date: Fri May 25 18:08:50 2007 +0000 move grepIndex to /data/tmp commit 1e3ec4bee3157b3492ebaa734fe869bb56e2d648 Author: kuhn Date: Fri May 25 17:42:25 2007 +0000 added comment about committing binary files commit 4b4be98728f1d4fc916de82d96b948a9010117a1 Author: galt Date: Fri May 25 15:00:30 2007 +0000 "Encode release log update" commit 74ba910fd5aa8161211ad1d4479488a625186a74 Author: galt Date: Fri May 25 15:00:16 2007 +0000 "Release log update" commit c2031cc653981f3e483aa17eb33241ef36447498 Author: pchan Date: Fri May 25 03:10:14 2007 +0000 combine all blastp hits into the same table on detail page commit 342561a2a6aca78946bf2f7b5316fc14b3ebac28 Author: heather Date: Thu May 24 23:57:10 2007 +0000 maf summary commit 2bcbf841256fe3049d118f259f3a59265cc5ffc5 Author: heather Date: Thu May 24 23:47:12 2007 +0000 starting on multiz4way commit 4863af58ee2fadd4ddc2d1232b8af3194f06d699 Author: heather Date: Thu May 24 23:22:19 2007 +0000 concat, filter and load (hopefully the simple concat is okay) commit bb8acba4fc61b5873f63509df589bd6ff6eb0290 Author: heather Date: Thu May 24 22:08:44 2007 +0000 tweaks to previous commit commit 925ef842c7ed9a0f900de8e924a3bc789778123b Author: heather Date: Thu May 24 20:44:57 2007 +0000 progress on maf annotation commit 28ce177a48443bdbc354ac61ae631fffd7fafce8 Author: angie Date: Thu May 24 18:51:29 2007 +0000 RT 1485: the main page "clear list" button should also clear the previous form input value. commit a7a537f8f218a7b1604ead4e09693507616a9f36 Author: braney Date: Thu May 24 16:36:28 2007 +0000 dog and rhesus alignments commit 51405b34cfd2b85068f27ceeca610b560a724d2c Author: aamp Date: Thu May 24 16:15:04 2007 +0000 Added indeces to all the hapmap SQLs. commit d28af93f6c2586a136d413b5e58316e6b28e695a Author: aamp Date: Thu May 24 16:13:49 2007 +0000 Added hapmap SNPs instructions. commit 999df4a325859236a9bdd4a83bafb794c9fca068 Author: galt Date: Thu May 24 15:00:30 2007 +0000 "Encode release log update" commit e183fb4ced2f800d4a0f1adb24e3908129d27a3e Author: galt Date: Thu May 24 15:00:16 2007 +0000 "Release log update" commit 0367e7ed87c712e9d16f66353877358d8787d25b Author: markd Date: Thu May 24 07:37:09 2007 +0000 added more doggy organism change ignores commit a6c32e20d6721cfb1a8d2b4eacdf3d3789a76698 Author: markd Date: Thu May 24 04:36:44 2007 +0000 allow blat to read compressed files commit ea770a210b80a5ccd1e63eb00badef8c4b07206c Author: galt Date: Wed May 23 23:19:03 2007 +0000 trying to fix relative paths commit eb747f695dfdcd38076e2c5c54c716e721ca2483 Author: galt Date: Wed May 23 23:16:02 2007 +0000 removing unneeded old cgi commit 71ae9c3515487a0a05873557682a79b298399a16 Author: galt Date: Wed May 23 23:09:44 2007 +0000 trying to fix relative paths commit cbcd026271122b2f2637b9a911c8efdca766a78d Author: galt Date: Wed May 23 23:03:31 2007 +0000 fixing relative paths commit 0b6e2ad6d109aeafb4b8b58b6316ef0ea6734050 Author: galt Date: Wed May 23 22:48:58 2007 +0000 repression hgSession link in top blue menu bar when hgSession itself is the cgi commit bc6f8977ce7b8fb08fc158ff30b1229c5aa55821 Author: donnak Date: Wed May 23 22:02:54 2007 +0000 Updated pipermail address from cse to soe. commit 0ceabd2b3eb3c8b7b3b42ac7390838e5a4384610 Author: donnak Date: Wed May 23 21:57:53 2007 +0000 Updated pipermail address from cse to soe. commit 84598b1846f9384244d91e4a0a9a1688ed2880f5 Author: donnak Date: Wed May 23 19:33:25 2007 +0000 Added pub by Giardine et al. commit 9ab6bece52455a7c64b1e0c880626d8aaad5e3da Author: galt Date: Wed May 23 15:00:29 2007 +0000 "Encode release log update" commit d9efe2660efcde0c41e7b8602309b336b5781e7c Author: galt Date: Wed May 23 15:00:15 2007 +0000 "Release log update" commit 11202dcc5fa9e51bdd0f7b0916c5a705af0279dc Author: galt Date: Wed May 23 01:37:38 2007 +0000 trying to make links be relative commit b66e90253e5193f78806ed572aa9046d227ec5ae Author: galt Date: Wed May 23 01:28:09 2007 +0000 trying to make links be relative commit 814c5539d0869bbdb572bd2115f214b90e8157a5 Author: galt Date: Wed May 23 01:05:56 2007 +0000 trying to make links be relative commit eddb81cf6e5ca927c8675e0eddc3ae861a82acd3 Author: galt Date: Wed May 23 00:48:11 2007 +0000 trying to make links be relative commit 16c4e718857a3a7d69a59c455e519b49086d5b02 Author: galt Date: Wed May 23 00:30:47 2007 +0000 trying to make links be relative commit 5dcb6f7bbf8c60870dcccf25dba058a228955c9c Author: galt Date: Wed May 23 00:25:14 2007 +0000 trying to make links be relative commit f7b514870165641e8d451f9581d40091357c21fe Author: galt Date: Tue May 22 23:58:58 2007 +0000 trying to make links be relative commit 29e139da71302055cb12bb022640b597a766a63f Author: galt Date: Tue May 22 23:12:12 2007 +0000 trying to make links be relative commit f9cdf582eaa3aa6b35dfa7d49dd5570b8353ee73 Author: galt Date: Tue May 22 23:03:31 2007 +0000 trying to make links be relative commit 39c111ba4e9985584e614a3071b78e05b0b60df2 Author: galt Date: Tue May 22 22:52:13 2007 +0000 trying to make links be relative commit 04dc6a9bc2366c8f8bc303a8db8a7fd2fb9145af Author: rhead Date: Tue May 22 22:40:54 2007 +0000 Wording changes and small edits. commit 57499dd52970a4ca0cb92abc1d5955d941120527 Author: galt Date: Tue May 22 22:36:05 2007 +0000 trying to make links be relative commit a607ae3dcbfaf5f83ef889163b2b69058d445b99 Author: galt Date: Tue May 22 22:30:23 2007 +0000 trying to make links be relative commit 5cd1a998250141c222861f25d89a155b93e75de4 Author: galt Date: Tue May 22 22:26:21 2007 +0000 adding new wigFetchRawStats commit e8e7c14af527884823e10d607c892698a69740dc Author: galt Date: Tue May 22 22:19:26 2007 +0000 trying to make links be relative commit e396ad1e6507cb1ef3124291b54f6cbca2a2a981 Author: hiram Date: Tue May 22 22:18:30 2007 +0000 Now with initial comments entry text area, and classification group pull-down menu commit ae010aac357f82636273b9a3418a68e7dd50fa00 Author: hiram Date: Tue May 22 22:17:45 2007 +0000 Initial contents commit 9e6cc5c592aee408b3d7a5a47feeabd775ce7330 Author: hiram Date: Tue May 22 22:14:45 2007 +0000 initial contents commit 2bec07528d576aaeb15f2c1ca3048c6fc8ed14b0 Author: galt Date: Tue May 22 22:08:45 2007 +0000 trying to make links be relative commit 1fb1c7165d3c148320416906fa52c99b2d4d6eb9 Author: galt Date: Tue May 22 21:58:46 2007 +0000 trying to make links be relative commit 9981f4e929f8cd491adaa916d4a3bc9295f0aead Author: galt Date: Tue May 22 21:56:34 2007 +0000 trying to make links be relative commit 085f1ccc211330d27d3983f7d2a67a031acf8cda Author: galt Date: Tue May 22 21:49:45 2007 +0000 trying to make links be relative commit 80764244d073386283095331cb8f088312c26b23 Author: archanat Date: Tue May 22 21:13:43 2007 +0000 updated the assembly release date for the Lizard assembly commit 6f9747cf0238e21b0f3aa1f38665d5ce3a2dde6c Author: archanat Date: Tue May 22 21:08:41 2007 +0000 updated the assembly release date for the Lizard assembly commit 767bec529e549db7446d74df23320bffed943a04 Author: hiram Date: Tue May 22 19:10:12 2007 +0000 Initial contents for wiki track item edit and display commit fa9066d79d285c9bfeddac8c175f7f49d1d869f1 Author: markd Date: Tue May 22 15:30:20 2007 +0000 ignore a lost dog commit 20dd9aab63ac48ede8d193b2063028d98ffd6953 Author: galt Date: Tue May 22 15:00:26 2007 +0000 "Encode release log update" commit 0e648e5549292f8a7d903cd4259826513c040597 Author: galt Date: Tue May 22 15:00:14 2007 +0000 "Release log update" commit a0e9e1d18611f0c49788e27d390aaa748045f048 Author: heather Date: Mon May 21 23:58:20 2007 +0000 redo multiz with mafSplit useHashedName ala ornAna1 commit 106fac98b7813ab7d7c561d962dce10efe8936fd Author: aamp Date: Mon May 21 23:50:29 2007 +0000 Performance bugfix. Full chrom view sucked. commit a7abd1745dc1ebc4417c1746459fad027da56976 Author: ann Date: Mon May 21 22:29:55 2007 +0000 removing html line from encodeNhgriDukeDnaseHs track, to allow it to use the newly-updated html page commit aba4a33a887be9788ba91e7cecfee22f20dd2510 Author: ann Date: Mon May 21 22:26:27 2007 +0000 updating description based on changes to track and sub-tracks with new data commit bec4e4c984578da179ae554a3c27301212552b38 Author: ann Date: Mon May 21 22:16:54 2007 +0000 removed beta blocks and release alpha for encodeNhgriDukeDnaseHs track and sub-tracks commit db0691349a4c425011e7635591e7568c00e5e6d2 Author: aamp Date: Mon May 21 22:00:49 2007 +0000 Added strand to display in CGAP track. commit fe580007e09e97f43e3c8e9f93f00ef74eafc493 Author: rhead Date: Mon May 21 20:27:13 2007 +0000 Removed journal name of unpublished article. commit 1f407cd7b7af367d639630df14b58eeade3c23a7 Author: braney Date: Mon May 21 20:11:19 2007 +0000 changed this test a bit. Experimental commit 776d75e3252a1da9cac053f7551a12c43b08b783 Author: braney Date: Mon May 21 20:10:22 2007 +0000 add some more input files. Experimental commit 70e75228ab8e2b7c8e3a46f25096b860f1b5c253 Author: braney Date: Mon May 21 20:09:50 2007 +0000 add some more expected files. Experimental commit be0450ab9f8ea9d20426faac701e6fcf0f38edd0 Author: angie Date: Mon May 21 19:47:52 2007 +0000 Minor typo fix: restore missing quote that throws off editor-coloring. commit 7e88771869e859f057dc917bf93cac38fe98fa29 Author: angie Date: Mon May 21 19:47:12 2007 +0000 RepeatMasker: for - strand items, repStart and repLeft columns are swapped (it's a cross_match thing). Swap them back so the displayed numbers make more sense. commit 810000e6a90f13b88d7ba6b29794ebb8ffdd84f3 Author: rico Date: Mon May 21 16:08:12 2007 +0000 Updated to use lineFile library. Now uses a species list file which has the species name and a directory which contains the .qdx and .qac files. Now takes a divisor option which is used to scale the quality values. commit 1e5165503aed73c23dc92ba8a64940d8a4e1a6f3 Author: galt Date: Mon May 21 15:00:21 2007 +0000 "Encode release log update" commit a24d2a1c6efc42af6d32553ff10ac88bcaa50b24 Author: galt Date: Mon May 21 15:00:11 2007 +0000 "Release log update" commit 0693c58971cf3a2a9c1e7088417d9bba286cf7ff Author: galt Date: Sun May 20 15:00:21 2007 +0000 "Encode release log update" commit 00e09461fb6c1deaf8a8030d9ad0f02fb88939b4 Author: galt Date: Sun May 20 15:00:11 2007 +0000 "Release log update" commit f3db68e790521a95c8c0b6203e9df3bf581ef865 Author: mario Date: Sun May 20 14:02:00 2007 +0000 Replace the previous Augustus gene prediction track with a composite track with three subtracks based on different evidence. commit 9fd052f437448fa95260b59c99c9dac8101dba2d Author: braney Date: Sun May 20 14:01:28 2007 +0000 input files for atomString test commit 3cd6d9e4af674216c432e95b4cd34948ee5aec70 Author: rhead Date: Sun May 20 00:28:29 2007 +0000 Added a target=_blank to an outside link. commit d4fe676aa77853ea4b7a094761ab9cb13e4473bc Author: markd Date: Sat May 19 15:55:03 2007 +0000 added ignore entry commit 936b99d8524075c2b323fb4757c028bd3ccb8c20 Author: galt Date: Sat May 19 15:00:27 2007 +0000 "Encode release log update" commit d2d28c5c2a32b6370acf7a72521727d1b0eaf537 Author: galt Date: Sat May 19 15:00:14 2007 +0000 "Release log update" commit 0d5380df1c2d9ea546a9bf06e5b759a0bf871557 Author: ann Date: Fri May 18 23:26:02 2007 +0000 changed line length. commit 09b1b6a7c91dc0d636360bcddcb48dd83d1b23c6 Author: ann Date: Fri May 18 23:10:31 2007 +0000 added link to instructions for loading a track via a URL. commit c782b79d01c2e4067934c253eb493ef7a505e5dd Author: ann Date: Fri May 18 22:54:54 2007 +0000 changed all caps to bold. commit 9c79d2977903dfca82fb2672c04924eff29a64d9 Author: hartera Date: Fri May 18 22:16:27 2007 +0000 Updated description with new colour scheme. commit 94f30e77b825f23a9e95c49d2f8be0fd8d80d46f Author: hartera Date: Fri May 18 21:36:28 2007 +0000 Corrected typo in RH map long label. commit 6b45649ef19df28a6619d561033ff82092df4d83 Author: hartera Date: Fri May 18 21:02:56 2007 +0000 Removed new subtracks from release beta version of UVa DNA Rep Ori track and added release type to the subtracks for release alpha and release beta versions. Added colours for subtracks. commit 9a6d748889cfb7abcf4171800270a8d3295bb215 Author: archanat Date: Fri May 18 20:31:57 2007 +0000 changed the assembly release date and some sample position queries for the Lizard asembly commit 37dedd5c159da8bea679b423b171a2c8c062ca29 Author: hartera Date: Fri May 18 19:59:03 2007 +0000 Re-ordered method descriptions and re-named the original method to Ori-TR50. Some editing of description. commit e79ba5513922e4a2b8c9792dcf488f2ac157e112 Author: galt Date: Fri May 18 18:26:54 2007 +0000 making current pushQ appear in gateway list as requested; resetting month to "current" when going through the gateway as requested commit a7d6fee3e1cdc26dbcd6dc617016acbda65939ab Author: angie Date: Fri May 18 17:44:24 2007 +0000 One more fix for baseColorOverdrawQInsert, strand +-: forgot that psl->tStarts[] (though not psl->tStart) are reversed, and the gotPolyA flags refer to q not t. commit 9a0fce759f065fc62884418d518c37cf6487300f Author: rhead Date: Fri May 18 15:50:44 2007 +0000 Removed the word 'abbreviation' from the abbreviations. commit dee99360bde680c984bd595a550473f928aa77ae Author: galt Date: Fri May 18 15:00:31 2007 +0000 "Encode release log update" commit 767c1cd8f9cf4b776dc454f84746a17e0bc74570 Author: galt Date: Fri May 18 15:00:17 2007 +0000 "Release log update" commit 8fa45b8a63950c1e61a31b43660396de7520e653 Author: galt Date: Fri May 18 01:27:40 2007 +0000 making high-resolution chromGraph in PS output commit 91631d4482a711554f32451ae8685cddcd8db560 Author: galt Date: Fri May 18 01:18:46 2007 +0000 bug fix pscmDot should be calling pscmBox, not psDrawBox - fixes half-pixel dot alignment issue commit efd691299acc1711000af8c258b889f1f80bae3e Author: galt Date: Fri May 18 01:17:09 2007 +0000 expose interface for setting color commit fb7a16c764b234b725dfe071c99b88e2c8a1c0dc Author: galt Date: Fri May 18 01:16:14 2007 +0000 expose interface for setting linewidth commit 6c854e8cd87a6883c661ef17febe4e16e303dd72 Author: hiram Date: Thu May 17 20:11:20 2007 +0000 Verbose argument now requires a zero to stay quiet commit 9289f74f2ff5836868477efc786bc4dc890ab729 Author: markd Date: Thu May 17 18:59:51 2007 +0000 don't let gbSanity try to check non-protein-coding RNAs for now, since they are not loaded commit a43f8d2ee13559eb92c89b23ab1841cafe5edca4 Author: hartera Date: Thu May 17 18:48:26 2007 +0000 Added back a blank line between track definitions. commit 8f47c75cc738ae26df76ce1bfa11ffceb372d083 Author: rhead Date: Thu May 17 18:35:06 2007 +0000 Truncated author lists to 10 authors. commit bea67122616be0d956da3d97d7c5743bc82a9934 Author: rhead Date: Thu May 17 17:49:28 2007 +0000 Fixed some names, took out the 'and' in name lists, changed some capitalization in references. commit 699049bde251cecf32319d0b17007f6515f90c37 Author: rhead Date: Thu May 17 17:31:28 2007 +0000 Fixed some names, took out the 'and' in name lists, changed some capitalization in references. commit 1b1eaf1f5e79782ad4872d7298a4fdc7bf149a34 Author: galt Date: Thu May 17 15:00:30 2007 +0000 "Encode release log update" commit f14a7088899079e70a59e343d54605a9de0fd624 Author: galt Date: Thu May 17 15:00:16 2007 +0000 "Release log update" commit 42b4e22e7b444586eb88c72edb531a662db20536 Author: markd Date: Thu May 17 00:42:23 2007 +0000 fixed typo commit 122d62ba2eadff4c3dff04ab1b0334b76bded55d Author: markd Date: Thu May 17 00:36:33 2007 +0000 removed request for native refseq alignments commit dcc2e58fa1cebad2f31bb48f28dacd25a106b7a7 Author: markd Date: Thu May 17 00:35:58 2007 +0000 fixed typo commit 865654a01081f2224fe3fc8342b75fefe8c033eb Author: markd Date: Thu May 17 00:34:33 2007 +0000 disable native anoCar1 refseqs, as there are none commit a311c9d52d0d31a077e190ca7f88cf78b350e7b4 Author: galt Date: Thu May 17 00:15:26 2007 +0000 spelling paypal as PayPal in messages commit 3bcccc17a1fbdc56c1bffc8eafc7093668b1061c Author: heather Date: Thu May 17 00:11:04 2007 +0000 duplicate Trinklein entries; use release beta (original) and release alpha (new) commit 4d4987b9c23447814c4f1a9dae3775f14bc4be86 Author: kate Date: Thu May 17 00:08:19 2007 +0000 Add more description of the 'release' setting commit a8fe465fecad3b0ebdad1f261c98dea82442dd15 Author: heather Date: Wed May 16 23:57:20 2007 +0000 tweak qual scores for chimp chr21 and chrY commit 4f2a3c25bfc77fe13f9efebbbc5ed66364d3a712 Author: heather Date: Wed May 16 23:50:11 2007 +0000 tweaks for hapmap SNPs and SV commit a95683794eedf73727195d4fc2a9794733a44bcf Author: donnak Date: Wed May 16 22:38:05 2007 +0000 Archived news item. commit 4ba69aea02ec92a5d35fd82904b87785c6da0162 Author: donnak Date: Wed May 16 22:37:49 2007 +0000 Re-prepared file for lizard release. commit 72a71f1fdcb086f46371055357c20393f295a00e Author: donnak Date: Wed May 16 22:15:31 2007 +0000 Removed outdated OH seminar announcement from archives. commit 18c5ca7564daa7004e5f2eeaaf627a6ddf2fd864 Author: donnak Date: Wed May 16 22:14:53 2007 +0000 Added OH announcement. commit ed55ad4c18eae33c7c8eb7216da2cbda57a41710 Author: angie Date: Wed May 16 20:51:37 2007 +0000 Added clarifications to field descriptions. commit 47e5180aa854c35cb6f8caa7b65fc9b3a97357b7 Author: kayla Date: Wed May 16 19:49:44 2007 +0000 added oryLat1 commit 704fc415335e15033ab9efa32f077dd8c325826f Author: donnak Date: Wed May 16 19:47:58 2007 +0000 A few updates to platypus & lizard announcements. commit 2c4d4020af0c8b350e74b6377dbe028f5b3608de Author: kuhn Date: Wed May 16 19:47:50 2007 +0000 added -countGaps flags to featureBits. added exit if no overlap to gap. thanks, brooke commit 7093e130e775b770d29ef0c57174146a8b8fbb0a Author: donnak Date: Wed May 16 19:47:19 2007 +0000 Updated lizard & platypus credits. commit dfaf82ee297cc3cc7b8edc0271221b2e696236a2 Author: kayla Date: Wed May 16 19:38:02 2007 +0000 added ornAna1 and anoCar1 commit 515867cdaa6b15609af5f823f9ee115bcbaaf4e2 Author: kuhn Date: Wed May 16 19:26:21 2007 +0000 added warning to usage about normal output going to stderr. thanks, brooke commit fe7427aa3d5adefaf40a9054c1b9d62d71133e8c Author: hiram Date: Wed May 16 18:51:02 2007 +0000 Change 5-way Multiz label to Conservation commit 263dd16bc7a8569a56f6ca56eeadf07a4408dad9 Author: kuhn Date: Wed May 16 18:05:54 2007 +0000 added EM tags to an 'et al.' commit 06f920b2c30a8e0fa854fbddf198ed9f9043a134 Author: kuhn Date: Wed May 16 18:01:49 2007 +0000 fixed a ref and added a link for it commit ddc00f08d8490fe5e49289349d25aff9448fc5f9 Author: aamp Date: Wed May 16 16:54:10 2007 +0000 Added more CGAP SAGE instructions. commit 049a68e6e86acbf59ab114b8a87ea32b78174d6a Author: rhead Date: Wed May 16 16:45:28 2007 +0000 Wording change re: ortho allele filters. commit 95cda6b4815927ff9aed2ab9fc1f5ba33e675abc Author: donnak Date: Wed May 16 16:26:52 2007 +0000 Made some edits to the sample queries & text in this file. The Assembly Details section could use some work (way too dense). commit 43c87a19f22249b05fc4630bd1303f867f0e1d25 Author: galt Date: Wed May 16 15:35:20 2007 +0000 "Encode release log update" commit a0fce9dc08549a8131701ff609ddf5acad5d4a26 Author: galt Date: Wed May 16 15:35:18 2007 +0000 "Release log update" commit 7008a3ff3ce639212a09117c11dbad84ecbfa281 Author: markd Date: Wed May 16 14:55:24 2007 +0000 added ignore entry commit e8b3bee3a2465b831a54f76950c46244931fbba8 Author: donnak Date: Wed May 16 14:17:51 2007 +0000 More work on lizard & platypus credits. commit 5634effc05e1cde3ef7bec37204adabbea07ab7c Author: donnak Date: Wed May 16 13:33:43 2007 +0000 Added Bob to platypus credits. commit 586978f1ab344b8f14785d696462744f8c7a233a Author: donnak Date: Wed May 16 07:31:51 2007 +0000 First drafts of lizard and platypus news items, platypus commented out until release). commit 77e61baf672399c725bf50e62a271d860329af91 Author: donnak Date: Wed May 16 06:25:52 2007 +0000 Archived an article. commit 8e88cf7bfa9ed033e8b5ab8db1e2a81635dc76f9 Author: donnak Date: Wed May 16 06:21:35 2007 +0000 Uncommented lizard credits, added commented-out platypus credits. commit 196629d0e302a3214b63a5e230ffff210091bf37 Author: donnak Date: Wed May 16 05:54:11 2007 +0000 Uncommented lizard release, added commented-out platypus release. commit 85cecaf0f98415fbec4fd84f3fff042d3f95b3ac Author: kuhn Date: Wed May 16 04:48:54 2007 +0000 changed refs to 'in press' commit e8e3fa0ca8c3e8501d52b851b443148bc57dd805 Author: donnak Date: Wed May 16 04:14:56 2007 +0000 Removed journal name from Margulies et al article at authors' request. commit 48c750e2c96493eb302e42900370e0024ea3c546 Author: hartera Date: Wed May 16 01:35:30 2007 +0000 Removed reference to journal until ENOCDE analysis paper is published. commit 620e8a041b4ab7a079b73435c50c1f97bb943513 Author: hartera Date: Wed May 16 01:30:11 2007 +0000 Removed reference to journal until ENOCDE analysis paper is published. commit 3547b813ff60aa2a01e0715dc97547975ee3f67c Author: aamp Date: Wed May 16 00:07:56 2007 +0000 Added CGAP SAGE instructions. commit 7b3af1f5ae184a28f80087bda9bf2aaa91c9618b Author: heather Date: Tue May 15 23:36:58 2007 +0000 exonArrows off for hapmap snps commit 208991aef6b438d15535e36a805162cc6e853979 Author: rhead Date: Tue May 15 23:14:02 2007 +0000 References section: put et al. in italics, swapped publication information on last two papers, made other small edits. commit ecb6670ba00c7040787d49adfd4c026d0c07a2ad Author: heather Date: Tue May 15 22:55:19 2007 +0000 add filter details commit 4ba09a29f15e6f56a429bb0751fae8acf96673c2 Author: rhead Date: Tue May 15 22:14:49 2007 +0000 Whitespace changes. commit f462ad3a3a6f4658dd042ec6a47a19d8e0a61319 Author: heather Date: Tue May 15 21:15:43 2007 +0000 use single base position for hapmap snps commit 995a07b27f9467f8ba919d1900b9131f2de5ae9f Author: heather Date: Tue May 15 20:21:37 2007 +0000 remove unused line in hapmap display commit 4f3ca1c0572ce99c476fe65d5acd7714bdd3eac4 Author: heather Date: Tue May 15 19:51:26 2007 +0000 trackDb.ra revision 1.407 gets rids of KG matches commit 63913455c272b96bdc5ec5903310895431534a12 Author: archanat Date: Tue May 15 18:24:15 2007 +0000 added anoCar1 to the xenoRefGene definition commit b6591db4bd409db0dc71741249c363f16b3a3bab Author: aamp Date: Tue May 15 15:24:01 2007 +0000 "New version number v159" commit b818b503762b28b7b5df14a915feba07b9fe039b Author: galt Date: Tue May 15 15:00:27 2007 +0000 "Encode release log update" commit 44d0131fe6e99910903ce83ca2f1080cc4601aec Author: galt Date: Tue May 15 15:00:15 2007 +0000 "Release log update" commit df9dc444aa0ca3fa219fba28e60c2778f1d9b039 Author: galt Date: Tue May 15 09:29:07 2007 +0000 fixing bug in use of sizeof on array parameter commit 26a69c2c85486fcc5d78cf9838b8910e893bb6e3 Author: heather Date: Tue May 15 07:42:35 2007 +0000 fixes for ortho strand commit c80e161a25ad403388e3217d2662f53ab3ee5422 Author: donnak Date: Tue May 15 07:03:06 2007 +0000 Changed ChIP/Chip to ChIP-chip, per Kate. commit d1eb668f7bad3812bd059ac8ada512b10d12720b Author: donnak Date: Tue May 15 06:55:24 2007 +0000 Changed ChIP/Chip to ChIP-chip, per Kate. commit 4651f25e50ab96c046bd871000fc2c590a0d80dc Author: heather Date: Tue May 15 06:16:14 2007 +0000 improve hapmap ortho alleles commit ad03ceab344b1bcb7e6cf40ea846c309d31b084d Author: hartera Date: Tue May 15 05:28:14 2007 +0000 Added new TR50 method subtrack for HeLa cells to UVa DNA Rep Ori track. Removed original subtracks to be replaced (UVa DNA Rep Ori and UVa DNA Rep Conf). Changed long and short labels and re-ordered tracks as suggested by data contributors. commit a81224640e3e39209b13cabea0aea63dc288ddf3 Author: rhead Date: Tue May 15 01:12:29 2007 +0000 Changed horse net priority so that the net would be next to the horse chain. commit 85ce3584e01e74c0ed5cd10e0646d3c2898a6e75 Author: hartera Date: Tue May 15 01:11:42 2007 +0000 Added a release beta version of the UVa DNA Rep Ori track that uses the old html description associated with this track before new subtracks and methods added. commit 917bdd9e50abebaa1dac3d8a7d826c42f0d59a03 Author: hartera Date: Tue May 15 01:08:25 2007 +0000 UVa DNA Rep Ori description for old set of subtracks. Use for release beta until new subtracks released. commit a6e40b85f640eef29aa86d333a919500e7ea8786 Author: kate Date: Mon May 14 23:40:40 2007 +0000 Remove debug comments commit 5f2f5884a42253163d9f26c4a66e753039a32866 Author: kate Date: Mon May 14 23:38:33 2007 +0000 28way phastCons work commit 87f9070e2cdf83f104e6798856ddc9785b97e178 Author: kate Date: Mon May 14 23:34:15 2007 +0000 Add exec perms to scripts before installing commit bbde30a7e0b0ee5c256a4c719a0d30b44b9f7c48 Author: angie Date: Mon May 14 23:05:25 2007 +0000 Added a comment to explain hardcoded bin for fake chrM_gold per Kate code review. commit 7615a1cca6a8ae65d073f40ee4bb810b9f7b2f77 Author: angie Date: Mon May 14 21:34:45 2007 +0000 Removed index on chromEnd. commit 4aa84060042b8f940edad02e64c4f17e7e424404 Author: donnak Date: Mon May 14 20:14:03 2007 +0000 Commented out another lizard reference. commit 9e10433983810fa97ce9bf697cf5a530350524a1 Author: donnak Date: Mon May 14 20:11:05 2007 +0000 Added lizard credits (commented out). commit d5914c3827d07b7db28e574e72d236f558f60f5d Author: donnak Date: Mon May 14 20:04:51 2007 +0000 Added lizard to release table (commented out). commit 946903ed400b2bfa1a50c159218c3538df13d081 Author: donnak Date: Mon May 14 17:27:02 2007 +0000 Changed date on horse announcement. commit d122f4219e49aba30d0dfee31870190e32716936 Author: kuhn Date: Mon May 14 17:01:28 2007 +0000 fixed refs to match PubMed format commit f753f104bfc97d29fde737e9477c366f415ab959 Author: lowe Date: Mon May 14 16:58:32 2007 +0000 Fixed omition of #else for #ifdef LOWELAB for increasing MAXPIXELS. commit e6f600c2b3cd7d903cf8bfa6322c8aabd1157d3e Author: galt Date: Mon May 14 15:00:22 2007 +0000 "Encode release log update" commit c76b76bd54abb05ae1778be3f99093ef6a48020e Author: galt Date: Mon May 14 15:00:12 2007 +0000 "Release log update" commit 62b9384ad4d98b459b0f49942e255f41e8077ee7 Author: galt Date: Mon May 14 05:34:43 2007 +0000 cleaning up the hprintf escape commit aee9488e3e9e8eed5f6466dbf1e135a6417c5cbd Author: angie Date: Mon May 14 04:52:01 2007 +0000 Added an hSetDb to cartCopyCustomTracks to prevent customFactory parsing from setting it as a side-effect of hGetMinIndexLength. commit e69eb0a01d529e5c9f929fa9eb132cf8130878d6 Author: fanhsu Date: Mon May 14 01:42:46 2007 +0000 Fixed a bug seems only show up on 64 bits machine. commit 03834ef5bd76ef82f4b7311b65f20bc4dd74a2a6 Author: lowe Date: Sun May 13 19:16:24 2007 +0000 For LOWELAB, increased max pixel width of browser window to 60,000 from 14,000 (tested, and works OK in firefox) commit bf85626ef5981ce625cc82695348cc47c2404cc2 Author: galt Date: Sun May 13 15:00:22 2007 +0000 "Encode release log update" commit 34262a576a91799639bbfcc4ca57edd9a45531cc Author: galt Date: Sun May 13 15:00:12 2007 +0000 "Release log update" commit 1116a504119969903a46f4fecbafe9547d67e3a3 Author: angie Date: Sun May 13 05:39:41 2007 +0000 Added semiShortCircuit refGeneAcc search so knownGeneAcc won't eclipse NM_'s. commit 2e8c7e8b94b0827c4d8a97ea93fa42443ed622c5 Author: galt Date: Sun May 13 01:45:09 2007 +0000 removing unneeded and duplicate lines commit 2bb74abf105820a2e2d050941b6216fd32d287e1 Author: fanhsu Date: Sat May 12 18:03:17 2007 +0000 changed visibility of DNA and protein conservation tracks. commit d0028a8409a303e956fe15e41014cf5cd7673791 Author: fanhsu Date: Sat May 12 16:58:14 2007 +0000 Changed title and color of HIV Genes track. commit a291bc94bcaca40cc55e380380b213506bd9e973 Author: galt Date: Sat May 12 15:00:28 2007 +0000 "Encode release log update" commit f1d2fabd6591bcea0a50e80295635b661d0e60c3 Author: galt Date: Sat May 12 15:00:15 2007 +0000 "Release log update" commit c1b2b0a41b9efd8f5600be5d1791c72dc4aacd7b Author: kent Date: Sat May 12 06:34:10 2007 +0000 Updating my email address and mentioning the UCSC Genome Bioinformatics Group as authors as well as myself. commit 56340c4c1b6ed5b71c4c000626f7f0ed88ba613c Author: angie Date: Sat May 12 06:13:18 2007 +0000 Fixed baseColorOverdrawQInsert to correctly handle ++ and +- strand alignments. commit 959c44de82fe83c4c4f85ec451088c2cebcc73a5 Author: donnak Date: Fri May 11 23:57:04 2007 +0000 Fixed year for Siepel/Haussler book pub. commit 6b30054602a523ad87ee9730b5866329c43141e8 Author: donnak Date: Fri May 11 23:50:50 2007 +0000 Fixed typo. commit 1c8841499f99b2a2df162f5de589275835aa1641 Author: kuhn Date: Fri May 11 23:44:28 2007 +0000 converted refs to PubMed format commit c2cca86ed3ef204ea737606b0fdba32b1ac41b53 Author: archanat Date: Fri May 11 22:59:06 2007 +0000 minor edit commit 295fb25c647275c1a313ef1cc3cf9a308e426e46 Author: heather Date: Fri May 11 22:47:39 2007 +0000 include strand in ortho filter matches neither human commit 344645fbda7811888c3f11d68605c74ec88e75f5 Author: heather Date: Fri May 11 22:10:43 2007 +0000 correction to getMinorAllele() commit 3595d54b5a0b035c49c211502134a38ed01a3914 Author: heather Date: Fri May 11 21:51:41 2007 +0000 only reverse complement for population snps commit 94473d09f5dc8f3ab5ec3bca96ef15ea0e0d0553 Author: hartera Date: Fri May 11 21:07:52 2007 +0000 Added names for the two Gencode RACE frags primer searches. Added searches for the rest of the subtracks of this track. commit 3f4e5dae438bfad58773761cfe528a8427870542 Author: kate Date: Fri May 11 20:49:36 2007 +0000 Get ready for hg18 migration of ENCODE, and load TBA alignments commit 60f34472f9a42206e4c89e36d6654c1e50b7b461 Author: kuhn Date: Fri May 11 20:25:06 2007 +0000 added runBits.csh to chain and net scripts. took commas out of usage statement between arguments commit c24deac05cb27e81934a86d75e1566e19fccd4b3 Author: angie Date: Fri May 11 20:22:36 2007 +0000 Added explanation of yellow error color. commit 9478b53c4b1ee3731426c4828ffab0938b5a526f Author: kuhn Date: Fri May 11 20:17:46 2007 +0000 oops. uncommented some debugging bypass commit b5ef2059d123a7c5a795020235f84d5861a7ce00 Author: kuhn Date: Fri May 11 20:15:59 2007 +0000 added runBits.csh to get featureBits info and gap overlap for tracks commit 2cf8399fcf99e93e14c6e83ce8fe182b82326814 Author: angie Date: Fri May 11 20:11:10 2007 +0000 In convertCoordUsingPsl, tStart was unsigned but then we subtract 3 from it in a comparison; if tStart < 3, that results in a large positive (unsigned) number, so the comparison failed and -1 was returned, causing the block to be colored yellow (error). Fixed by using int instead of unsigned. commit 9e1df2a205a4ac7af14cd2ba455bcc9b9946418b Author: pchan Date: Fri May 11 19:52:09 2007 +0000 add #ifdef for calling lowelab specific code occurs in doMiddle() commit b167da39beaa2eed0aa846cb47ffa13df71e0fa4 Author: donnak Date: Fri May 11 19:28:38 2007 +0000 Changed date on horse announcement. commit 776c2c6e8ab8159e838a21c733e7f1651a7dc797 Author: mhoechsm Date: Fri May 11 19:08:04 2007 +0000 renamed RNAlPfold to RNAPLFold commit ec96728a86efa140623e556647d233c5677b67dc Author: heather Date: Fri May 11 18:49:32 2007 +0000 tweak for hapmap ortho alleles commit 075de338d6e4d350c534956b63091fe040a5a823 Author: heather Date: Fri May 11 18:16:38 2007 +0000 fix for hapmap ortho position commit 2c0f1de57d210e329030df51439b67ae1eeeb74e Author: rhead Date: Fri May 11 17:32:33 2007 +0000 Turning on horse on both hgwbet and rr, after pusing from beta to rr. commit c0f7af18468814a0014e5ba45699081252029e24 Author: kayla Date: Fri May 11 17:18:35 2007 +0000 added ornAna1 commit 8fcc74342642f6a133b57dbcb54f2632a2a22ed8 Author: kuhn Date: Fri May 11 17:10:03 2007 +0000 changed output for assemblies to in progress from "hgcentralErr" to "dbDbErr" as it could be either beta or RR commit a51d34046f1a9eae97f6fe89aca83e61d8847f3c Author: kuhn Date: Fri May 11 16:22:38 2007 +0000 changed output for assemblies to in progress from "err" to "hgcentralErr" commit ea5b4cc9d699563872a485d72847bf7d2aa38322 Author: galt Date: Fri May 11 15:00:34 2007 +0000 "Encode release log update" commit 9291b24e79eb8f867ad776f395302460af03b2b2 Author: galt Date: Fri May 11 15:00:18 2007 +0000 "Release log update" commit 11c9fdbbf4594ca3d8a3b2c662e41fc33f6c2de3 Author: galt Date: Fri May 11 07:21:51 2007 +0000 knownToVisiGene utility now supports symbolic and both xeno and self probe matching commit 29ff921052b1de71d6a620dc4b386fe4b68e7d0e Author: galt Date: Fri May 11 06:37:26 2007 +0000 making automatic use of vgProbes and vgAllProbes, because mm8 now has frog as well as native alignments commit dace62b4b4b7ade3502ffade4eebbb73119482e6 Author: hartera Date: Fri May 11 06:00:00 2007 +0000 Added code so that the track configuration for item label and the codon coloring does not appear for the ENCODE Gencode RACEfrags track as they are not applicable for this data. commit 829be538be9f6bc7633e7d1588af294356df2092 Author: hartera Date: Fri May 11 05:57:39 2007 +0000 Removed unnecessary trackDb settings and added a setting to stop the link for protein translation being displayed. commit cce730f37739ee918b1d0d76da9511feb165fb96 Author: hartera Date: Fri May 11 05:56:21 2007 +0000 Fixed the strand for the Gencode RACEfrags Primer subtrack. Removed some configuration settings and the protein translation for items in this track as they are not applicable for this data. commit 5c43d8da74952e61a0b593b93ee8dbc73eea6157 Author: hartera Date: Fri May 11 02:53:16 2007 +0000 Fixed typos in comments. commit 71782d7b71a8f4e16fad2bc5f093dd17245450e4 Author: fanhsu Date: Fri May 11 02:36:13 2007 +0000 Added a warning about not to load chrUn for 3rd party data. commit 1c5aa3d7f178a2bd7157ecf610a1c0b0c464d34f Author: rhead Date: Fri May 11 01:08:53 2007 +0000 Formatting tweaks to reference section commit 202e0f307c7332f6eadbbbea28cfa9d0224dc5ef Author: heather Date: Fri May 11 00:06:44 2007 +0000 figuring out multiz run commit 05cc26eaf1b899157d3772a467eb0b83cc0b0bc9 Author: mhoechsm Date: Thu May 10 23:45:48 2007 +0000 rnaPLFoldTrack displays base pair probability matrices on a genomic scale. wiki(Track) highlights regions which have an annotation in a wiki system. An extension in hgc/lowelab.c handles clicks on wiki track data and directs the browser to the corresponding wiki article. commit 2996f4a517cb9e095d3892455f3bf854ec309f8f Author: mhoechsm Date: Thu May 10 23:38:27 2007 +0000 wiki.as and wiki.sql describe bed6 like structures for storing wiki annotation positions rnaLpFold was renamed to rnaPLFold in correspondance with the tool RNAPLfold, which generates this track data commit abfaf1dba48fddffcc554d3ee7559657fe6caf47 Author: kuhn Date: Thu May 10 22:09:22 2007 +0000 made choice of records to display randown instead of choosing last chrom and renamed the variable commit 7cf24e3f447ad9559942c1f5f5810de9dee71a37 Author: hartera Date: Thu May 10 21:58:52 2007 +0000 Finished Gencode RACEfrags track. Added new subtracks for the UVa DNA Rep Ori track. commit 413e672fd4dfcdb35b7c3c69de63a668a71994c5 Author: hartera Date: Thu May 10 21:24:46 2007 +0000 Added release alpha and release beta versions for Vega tracks so that colour does not change on RR until next build. Removed old test track for Vega. commit 4e1965d3f0735a2608a6666cd75ee7d087ade781 Author: hartera Date: Thu May 10 21:20:06 2007 +0000 Added release alpha and release beta versions for Vega tracks so that colour does not change on RR until next build. commit dd0272a67efd405916baeda4ce56bd0e1833c8f1 Author: hartera Date: Thu May 10 20:44:56 2007 +0000 Minor edits. commit 59b9c1dcb582a28490c67b7f0b63739a43e26c90 Author: hartera Date: Thu May 10 20:30:03 2007 +0000 Added abbreviations for methods in the description to reflect those used in the subtrack labels. commit 35993bab165d4e8e427ebccb7f0bfd2d83959013 Author: hartera Date: Thu May 10 20:29:00 2007 +0000 Updated the data versions for subtracks for the UVa DNA Rep Ori track and also added the method type to the subtrack labels. commit 7c8d59e157787cfff87962899524e79a849623e1 Author: heather Date: Thu May 10 19:26:28 2007 +0000 correctly handle strand commit 466e7973760450df0cab0753bbc210295142800e Author: angie Date: Thu May 10 19:15:39 2007 +0000 Make the knownGeneAcc termRegex pickier so it doesn't trigger on symbols like TP53; also, make it handle the new UCSC Genes IDs with or without the dot-version suffix. commit 1fc9606548350ecffcf5a4e9013891aaebd02063 Author: archanat Date: Thu May 10 17:21:59 2007 +0000 whitespace changes to make lines 80 chars or less commit c0ebc046ba06b0b30743196a0bda42e098e49219 Author: archanat Date: Thu May 10 17:12:25 2007 +0000 changed wording slightly commit 917fb02ebda882c0ad9921a298d9e65ed58a9e5e Author: hartera Date: Thu May 10 17:02:07 2007 +0000 Added colours to subtracks for Vega Genes instead of parent track. Added entry for Compugen zebrafish oligs and a search for this track. commit ba0b9a9065a02833eac276a745b55bc763d70e1b Author: kuhn Date: Thu May 10 16:27:30 2007 +0000 recorded drop of chromEnd index commit 66528b0ce68f955b0b6f4ccea5c74c3b8b63f37e Author: fanhsu Date: Thu May 10 16:20:12 2007 +0000 Added a caution paragraph about the simplistic approach taken on constructing the chrUn chromosome. commit 19fbb9b2a688b442b60cb3e3028a965d7fb9591f Author: kent Date: Thu May 10 15:41:45 2007 +0000 Fixing kg1ToKg2/kg2ToKg3 renaming issue. commit f5b9f2ebfbdbcaf6e8233b4f57d83fba25210224 Author: galt Date: Thu May 10 15:00:34 2007 +0000 "Encode release log update" commit 6a185fbd6f14053d7d10d4f62631896db4ece7d6 Author: galt Date: Thu May 10 15:00:18 2007 +0000 "Release log update" commit 5fd43df7ea7a5261a8538f404c04a567a7948dd7 Author: galt Date: Thu May 10 01:46:01 2007 +0000 adding steps to bring frog probes to mm8 and self probes to mm8 and update knownToVisiGene vgProbeTrack commit ac356ad796d4efb9ae2ec468eb008bfc15b5781d Author: galt Date: Thu May 10 01:32:01 2007 +0000 added SELFMAP command to migrate vgProbes psls to vgAllProbes commit bc41b9092a726f97f4d8e20a41b7af32cacd9f43 Author: angie Date: Thu May 10 00:00:51 2007 +0000 Removed index on chromEnd. commit b43eccea5a5a384b85c8fbe63da41c373ce452f7 Author: angie Date: Wed May 9 23:47:21 2007 +0000 Removed index on chromEnd. commit 40eef5277ac690c7a9d45a2e0693e9211418e50e Author: hartera Date: Wed May 9 22:56:08 2007 +0000 Remove old default colours for Vega subtracks. commit 4f50b70087b11a40fc6a2731e2f2ca68ad3dccd5 Author: markd Date: Wed May 9 22:10:17 2007 +0000 fixed typo commit de37890912e41012399c40746f47bf05dd227f8b Author: hartera Date: Wed May 9 21:54:07 2007 +0000 Changed default colour for Vega tracks to be the same as that used for RefSeqs. commit 46aac2a439f30421e8cf3400c983ade3a28d03f7 Author: hartera Date: Wed May 9 21:51:08 2007 +0000 Changed Vega gene colouring to a similar as that for RefSeqs. commit 1339bc8b530a63157fc0cb970dae2572e40d4ddf Author: hiram Date: Wed May 9 21:37:16 2007 +0000 Remove the warning, verified matches current assembly. commit 0c277dc66a647d25cf0c53d310b3734457d12f7d Author: hiram Date: Wed May 9 21:34:08 2007 +0000 Reduce content to match reality. commit 0ccf12f2c0b6d337c0a084f0b89782a84ac21c32 Author: ann Date: Wed May 9 21:24:29 2007 +0000 randomizing the list of databases (so they dont come in the same order each time) commit fa48d267af059f9fbf2e8b5097be33ad4e233ffb Author: hartera Date: Wed May 9 21:08:44 2007 +0000 Made changes to vegaColor to check for whether a table contains the confidence field which should be used for the coloring else the method field should be used if it exists. This avoids having to track which assemblies have this column. commit e49d7a97b28cda0072824141951fe377ec3165ad Author: archanat Date: Wed May 9 20:54:58 2007 +0000 changed the link form the picture of the lizard commit ef884c6ce5e2dacbc4f09f0d6ab3cc2ae18dcdf7 Author: galt Date: Wed May 9 17:46:26 2007 +0000 fixing bug - link should go to displayAccountPage, not displayAccount commit be47bea697833d0666e85bb3aaa9fd917a362d99 Author: kate Date: Wed May 9 16:59:16 2007 +0000 Add support for custom track database to DNA coloring feature commit bcd95ea88bada346bcf621b20b5d0188da98e378 Author: donnak Date: Wed May 9 15:44:59 2007 +0000 Added horse browser credits. commit 9730c0c8c1aa4d9d1db45dce65a11b40f2e9710a Author: donnak Date: Wed May 9 15:41:40 2007 +0000 Added Kate to horse credits. commit 589725a627293d8faba8d8935d6b83b388fe7250 Author: galt Date: Wed May 9 15:00:32 2007 +0000 "Encode release log update" commit ba687a6b1cf117a367cac9cc68743f9e8f98b21f Author: galt Date: Wed May 9 15:00:17 2007 +0000 "Release log update" commit e8313389bd54d4bd3b53769478367eeea4af91df Author: kent Date: Wed May 9 14:22:22 2007 +0000 Making refSeq accession appear by summary when summary is available. commit 5d873956e691049e2c251d83d9ca35344a30d0ca Author: markd Date: Wed May 9 07:59:30 2007 +0000 fixed error messages commit 787820ab1c00e4a22912487f17373a8b00de642d Author: markd Date: Wed May 9 06:16:41 2007 +0000 added options to include unaligned in stats commit afca5059a1a6a4f226a058e81166906e67ef0dd4 Author: markd Date: Wed May 9 06:15:35 2007 +0000 added function to get number of entries in a hash commit bc189b23fd0668419c46b854bb71b64cecf5bda4 Author: heather Date: Wed May 9 00:41:21 2007 +0000 tighten up ortho allele filtering commit 0e2ea3ecc5a033d558cb0044d1b8469c6cb0e801 Author: hartera Date: Tue May 8 22:22:43 2007 +0000 Added a space. commit 72eb1b99fb71994a3203c4213f0310889c8485e3 Author: hartera Date: Tue May 8 22:10:18 2007 +0000 Edited description for new methods supplied by track contributors. Reformatted references and added links to abstracts. Added links for cell lines. commit 34419f6d82f59ac96c83e44ae9182b0886933f50 Author: heather Date: Tue May 8 21:54:33 2007 +0000 make monomorphism filter for hapmap snps specific to each population commit 9dc99ee1b5c2aee17cb0e01cff31b9a09659bfe5 Author: galt Date: Tue May 8 21:53:14 2007 +0000 trying to offer a better explanation to the user about paypal payments commit 0ee48c2a439572f4ee62ed586d4f80dad687cef3 Author: hartera Date: Tue May 8 21:51:28 2007 +0000 Added descriptions for new methods used in track as supplied by track contributors. commit 19c79de519addb20d8eff8501dd76e0c2a734427 Author: aamp Date: Tue May 8 21:18:41 2007 +0000 Added mapping stuff to description. commit 0a55c9b8e5c4fc6408fd2bd40ba258da08ac7677 Author: hiram Date: Tue May 8 21:11:25 2007 +0000 Fixup mime parsing to eliminate bad Internet Explorer behavior of full path names, with spaces, being passed where not expected commit c0e45bdcb94aa9c97e9ec4de2187e1f5db80537e Author: aamp Date: Tue May 8 20:45:39 2007 +0000 More hg.conf survery var stuff. commit 9b25a70d0951310229eb3fd9318afd3dbb7228fe Author: rhead Date: Tue May 8 20:44:41 2007 +0000 Turning off horse updates while we rsync to RR. commit a0cc2fd2f015dc80de658cfc4434daf41057917b Author: donnak Date: Tue May 8 20:12:35 2007 +0000 Made a few more edits to horse news item. commit eb58762ef12e93ab66a7d11e6aa315849ba227c7 Author: donnak Date: Tue May 8 20:12:03 2007 +0000 Made a few more updates to horse credits. commit a749ce302c17fc263ea68deb0963c30f9b2ce3b7 Author: donnak Date: Tue May 8 19:56:52 2007 +0000 Updated sample queries, edited some of the gateway text. commit 6aab3926da2da8ccac96b57f22ec83cf6b315ca9 Author: aamp Date: Tue May 8 19:51:08 2007 +0000 Added survey=on config option to hg.conf commit 9d69c12af7e8de681313982544b74e2ca8e5f0c3 Author: heather Date: Tue May 8 19:35:21 2007 +0000 one more reference commit 4e0e6d6457611605823a747dbe19200309d2f814 Author: donnak Date: Tue May 8 19:33:43 2007 +0000 Added horse GB article. commit cbfd814848f9bbc041bba34c7ec6242b2f311819 Author: donnak Date: Tue May 8 19:33:28 2007 +0000 Archived an item. commit 267be44299b4e7a3df05a0971035533560cedddb Author: heather Date: Tue May 8 19:22:59 2007 +0000 add example research; change suggested by Daryl commit a9936299744114b53e4153b0d6edbd80fb3c6839 Author: donnak Date: Tue May 8 18:56:56 2007 +0000 Uncommented horse release. commit e5fada28368e5f265acbbb4a8393a5fad4c90210 Author: donnak Date: Tue May 8 18:56:24 2007 +0000 Updated horse credits, reordered links at top of page. commit 21e89684c0383b0b66e7bd7592c7105cbc17db41 Author: angie Date: Tue May 8 18:33:44 2007 +0000 Another assembly clarification from LaDeana. commit 2e8c2ab9ddf717ace726a4eafce56cb559f4eaa4 Author: rhead Date: Tue May 8 18:23:50 2007 +0000 Tweaked Ponting reference. commit 461fdb65fe6d2df27dfb9edce37ee599d6544bd9 Author: hartera Date: Tue May 8 18:15:09 2007 +0000 Changed the priority for the June 2005 Gencode Genes and Introns tracks so that these appear after the March 2007 Gencode Genes and the Oct 2005 Gencode Genes and Introns tracks. commit ebefb64a96f9b7217a3e4d70fb392f502056eb27 Author: hartera Date: Tue May 8 18:13:48 2007 +0000 Added new subtracks for the UVa DNA Rep Origins track. Reordered the Gencode Genes track so that the latest version is first, followed by the October Gencode Genes and Introns tracks. Gencode RACEfrags are after all theh Gencode Genes tracks. commit 5c85d4f6da777b7aa98c95237ca95caf5eda9014 Author: heather Date: Tue May 8 18:11:09 2007 +0000 add Ponting reference commit cb7d1f1322e2915fe56dd93a34a52e4e1c50c680 Author: rhead Date: Tue May 8 17:58:46 2007 +0000 Fixed typo, tweaked format on Fuek reference. commit cdb31258cf188048accbc86339584a09fdbc3554 Author: hiram Date: Tue May 8 17:42:08 2007 +0000 Allow bed graph tracks to output all or selected fields commit 929e1c613a18fdbefc9500314fd3d8a9400c9847 Author: kuhn Date: Tue May 8 17:36:16 2007 +0000 broke line into shorter lengths commit 0673721ffd569e288d5d70cf3528d9b9f364fe4f Author: hiram Date: Tue May 8 17:26:46 2007 +0000 The gateway page calls configure with a different "value" ... commit 781aca641d91ff4594e0ed2f23d18e2d17e188e1 Author: hiram Date: Tue May 8 17:19:15 2007 +0000 Make the checkbox on the configure page for track reordering do that job and return to the config page immediately upon click, using javascript commit d28c1e4713466128265fd136d58c31208dc81f54 Author: hiram Date: Tue May 8 17:16:11 2007 +0000 Add hCheckBoxJS() function commit 12c4b529ab884b4d4d026699a03563476f59b40e Author: hiram Date: Tue May 8 17:15:31 2007 +0000 Add cgiMakeCheckBoxJS() function commit 5729aa126b98ac906b1792145f059cd2c5a6ce76 Author: heather Date: Tue May 8 16:19:13 2007 +0000 tweak to hapmap snps UI commit e3713744fa0c815836fddad0de83129a771b4943 Author: galt Date: Tue May 8 15:00:27 2007 +0000 "Encode release log update" commit 23bfc632e03b0a4dea658657821ca33008e6f825 Author: galt Date: Tue May 8 15:00:15 2007 +0000 "Release log update" commit 3c3b578c4ff462656788d316ef15a681f69df47f Author: galt Date: Tue May 8 06:09:55 2007 +0000 oops undoing accidental checkin commit 3114711d37cb7d87bf76bbbd7cfcf85c396b11c4 Author: galt Date: Tue May 8 06:06:23 2007 +0000 fixing paypal code - can not free both p7bio and memBio if they are intertwined. Found out we dont even need memBio commit da08d715c7449877bb71d2a1d1032f03b9d26108 Author: kent Date: Tue May 8 03:07:26 2007 +0000 Polishing some of Fan's instructions for the protein oriented parts of the UCSC gene build. Also fixing a few typos here and there. commit e0ced9d35976be568c71191d846020e7380cc19d Author: rhead Date: Tue May 8 02:43:07 2007 +0000 Removed '_fs' in Nature article links to make the links work again. commit f43a24268b0421cccd8713135fed9533d0559f5f Author: kent Date: Tue May 8 02:32:20 2007 +0000 Downgrading verbosity on a warning message that is common now that there is so much noncoding. commit 7c907ee2f5b691a65319d128d3a21657ef3fed85 Author: rhead Date: Tue May 8 02:29:47 2007 +0000 Changed link to paper to pubmed, as old link was broken. commit 1fe903c4473688ee76f6d2302a7e5a6fdfeddfaf Author: kent Date: Tue May 8 02:28:54 2007 +0000 Adding pbCalResStd to makefile. commit e57264383ae4b6a087b1042376c66ab02010e81a Author: kent Date: Tue May 8 02:28:41 2007 +0000 Removing unused variables so will compile without warnings. commit 568fc21f9fc5732f549ff89b58bdc2bbd3adceed Author: kent Date: Tue May 8 02:23:19 2007 +0000 Adding pbCalDist to makefile commit a36f73fa75218e1672624a2404fdf54808f0ed77 Author: kent Date: Tue May 8 02:22:46 2007 +0000 Getting this to compile without complaint by removing a bunch of unused variables. Also initializing a variable that looks like it really was hiding a latent bug if the garbage on the stack was non-zero. commit 8f29b7028ddd1e6ce90c6fc710ba9ad3c23d28af Author: heather Date: Tue May 8 01:56:31 2007 +0000 include font height in y size for allele commit e8d3e3ff032d5f9cfb35b69cf5da7fa000938270 Author: angie Date: Tue May 8 01:13:37 2007 +0000 Updated some numbers to reflect the final release that ornAna1 was built on. commit 796e6ed4dfa05dca72d5ae6ceaa998928d7e86b4 Author: heather Date: Tue May 8 00:18:22 2007 +0000 add notes for stanford/johnson March 14 data commit 1c0da2c5c8626f196d54566b4736191eb0a4b404 Author: tingwang Date: Tue May 8 00:01:54 2007 +0000 operation for adding new UCDavis Chip data logged commit 4af90f3a75433d549695f71fa01b4944bcd92216 Author: angie Date: Mon May 7 23:29:39 2007 +0000 WUSTL now refers to this assembly as Mar. 2007, 5.0.1 so update dbDb. Since we got the data in Feb. not Mar., make sure it's the same. commit 1ab223a6c693d822cef4e506675405470fc75086 Author: krish Date: Mon May 7 23:10:42 2007 +0000 added homIni14 to the list of dbs commit 3d068471a0007947d69c07c789b26369694d91cf Author: fanhsu Date: Mon May 7 21:15:25 2007 +0000 Changed GP120 into gp120. commit 4ce0b0d62273f6b64619b1ea38d57a91057ae363 Author: rhead Date: Mon May 7 21:06:46 2007 +0000 Fixed spelling of author's name (Argarwala --> Agarwala) and added two periods to reference. commit 0c8ab93519bfd69eebdd064bc3222b78cbb6f13c Author: rhead Date: Mon May 7 20:57:40 2007 +0000 Added chromosomes to description, changed wording slightly and mentioned gaps between scaffolds. commit fdebf1bcb7dcc2c2fca869fb0b53197ba1c13488 Author: galt Date: Mon May 7 19:31:24 2007 +0000 removed text describing a requirement that no longer exists commit 53adac28653e65b08f4b68f2e89597ea44c6a5c4 Author: lowec Date: Mon May 7 19:30:43 2007 +0000 changed the entry for my exaptedRepeats track to make it shorter and easier to re-create. commit 1498b3d56a08d9fca9abb6f817d414f8a07869f4 Author: braney Date: Mon May 7 19:25:23 2007 +0000 fix a fix to correct a problem printing garbage passed the end of a string commit 55bcfb3aa7e3d8bc3da4362f7aeccb436d12088e Author: fanhsu Date: Mon May 7 19:22:07 2007 +0000 Changed "DNA Sequences" to "GP120 Sequences". commit f2bd9db8cc32519d640cab2facdf80a89d166411 Author: hiram Date: Mon May 7 19:21:17 2007 +0000 create mafDownloads directory for annotated mafs commit c9a281a7133257a47e30a830a53f2e704fe60c66 Author: rhead Date: Mon May 7 19:09:10 2007 +0000 Fixed spelling of author's name; added two periods. commit 3fae5678f5a354b0893a1e7ab1500c430a2dfe02 Author: kate Date: Mon May 7 18:59:45 2007 +0000 Fix base-level display in wigMaf tracks, when looking at 1bp window commit 194cbe24057c53a768b660eb3f86a226db2f8300 Author: rhead Date: Mon May 7 18:34:21 2007 +0000 Added horse gold tables to tablesIgnored. commit e6f79827abee6438cf4dd04ec190eb57024febad Author: hiram Date: Mon May 7 18:20:44 2007 +0000 Update sanger gene annotations descriptions commit 41a07642b48cf8c5c530360a706bfe600b0ec79b Author: kuhn Date: Mon May 7 18:11:48 2007 +0000 renamed ucsc10.txt to ucscGene10.txt and added note in hg18.txt about the UCSC Genes track commit 3a644a92bbb7108a4dba07a31798b24cc42c509e Author: fanhsu Date: Mon May 7 17:55:23 2007 +0000 Added search definition for gold track. commit d6d470de29f5926b6f2d3bebc84011562aa4557b Author: heather Date: Mon May 7 17:47:48 2007 +0000 add a general reference commit ae9eee2e8e63489a24a8a5f424d49f194552c5ba Author: hiram Date: Mon May 7 17:34:00 2007 +0000 Add SOCKETLIB to the link line to fix a problem in SOLARIS commit 37c6216a128a67163ee169063805e68c5895f342 Author: hiram Date: Mon May 7 17:30:52 2007 +0000 Add limits.h to avoid compile problems on SPARC commit a682e7f14c0d83428d3b2f8fae81924a0a8e89da Author: hiram Date: Mon May 7 17:28:03 2007 +0000 Change name of single variable, was a clash in SPARC floatingpoint.h commit a53cb4cfa60095e274eb16d12d3cd69f8933af60 Author: hiram Date: Mon May 7 17:26:10 2007 +0000 Change name of extended variable, was a clash in SPARC floatingpoint.h commit ef2b4490f40fece16031f5a65866f57fb65b37cb Author: hiram Date: Mon May 7 17:19:01 2007 +0000 Add reference to genomewiki, update hg.conf example, and the rsync stats commit 9a87fa2bac5104f6b8b784bf84f1bcd462a2dbf3 Author: galt Date: Mon May 7 15:00:23 2007 +0000 "Encode release log update" commit d9cd4a175e34f08dcc9f6e0f7a4a4e65dd38c900 Author: galt Date: Mon May 7 15:00:13 2007 +0000 "Release log update" commit 795fc55f0b92dcf1a0848e8cbacfb2dba0580ef5 Author: fanhsu Date: Sun May 6 21:57:09 2007 +0000 Took out "(under development)". commit 679027a3082a276417ece4fd5bb671f9d98a1a5c Author: braney Date: Sun May 6 21:41:18 2007 +0000 add a maf track built from atoms commit f926771dabdc7101d650631045ef93130685cbeb Author: kent Date: Sun May 6 15:07:45 2007 +0000 Adding nibbImageProbes. commit b67b77373a8d8e8b95a26618c2ab65229c5e0f75 Author: galt Date: Sun May 6 15:00:22 2007 +0000 "Encode release log update" commit 121a9468954c13994497494bed36930f97e616c6 Author: galt Date: Sun May 6 15:00:12 2007 +0000 "Release log update" commit 08a6bcb76b00dba61cae628c594794c718bc418e Author: pchan Date: Sat May 5 18:35:33 2007 +0000 fix problem for blastp detail display when gbProtCodeXra does not exist commit f7394dde9f14858b1d180ef1c838622f39329d6f Author: pchan Date: Sat May 5 18:25:04 2007 +0000 fix problem in blastp detail page when refSeq table does not exist for retrieving target gene's positions commit e4aa7deabee11f29f80ca6ee212198908ff2b64a Author: galt Date: Sat May 5 15:00:28 2007 +0000 "Encode release log update" commit 90dd47b7648dd53f024a3affdb5ec1b8501f1275 Author: galt Date: Sat May 5 15:00:15 2007 +0000 "Release log update" commit ae0607292011ca4144268f371420ae3054a2fc7a Author: lowe Date: Sat May 5 05:28:28 2007 +0000 Changes to blastP table display: Adjusted Column names and fixed % length of protein column numbers so identity hit is now 100% commit 461c95d3876d80718fd8e0374a32ad87341b0f2e Author: galt Date: Sat May 5 05:19:21 2007 +0000 adding more illumina choices to upload types commit 8ae5d669468df2b60084a8dcd0ed7fc0e81df456 Author: galt Date: Sat May 5 01:59:38 2007 +0000 fixed missing close quote on area-tag href commit cdfc42329bab36cdb32f25da174309168cf6a7f6 Author: galt Date: Sat May 5 00:49:28 2007 +0000 adding Illumina 550 and 650 beadchip support commit 6cb4e1a27af16be7f6c8bcf5c79042ee833e98d9 Author: heather Date: Sat May 5 00:37:54 2007 +0000 ChIP/chip track from Dave Johnson (Stanford) commit 8e7ca6fa7ff8a95ea932a4566249d10d9039ce82 Author: heather Date: Sat May 5 00:21:40 2007 +0000 tweak for encodeStanfordChipJohnson commit bebf3e698e9ac32f9fab7d4b7b46d27c4c494b07 Author: angie Date: Sat May 5 00:19:40 2007 +0000 Swap chain, net ornAna1 for symmetry. commit b05670a5ef4447f2e30dd2a0edebc8ff6443f5f2 Author: angie Date: Sat May 5 00:19:14 2007 +0000 Redid {chain,net}OrnAna1 (back in April). commit e92c9dd8467911183c8fed6bb7c96b88fb52da53 Author: galt Date: Fri May 4 23:58:47 2007 +0000 3 more KGIII fixes for association type commit f26817025c912a544aa198fb52ee84caf3be5cc8 Author: galt Date: Fri May 4 23:36:43 2007 +0000 fixing GO Similarity for hg18 kgIII commit ba14dce19b745112ed154acac8db4c636e32c423 Author: galt Date: Fri May 4 23:29:15 2007 +0000 at bobs request - making listQueues show self in list, as long as its not a transfer operation commit 00d8200984a08bd0596c4554e2a7f9ff3491b664 Author: angie Date: Fri May 4 23:20:30 2007 +0000 Added {chain,net}OrnAna1Pre for comparison with the corrected {chain,net}OrnAna1 -- the *Pre were used in the 28way Conservation. commit df3ba35271da69c2e7636fa8d71f85dc54b1f8f7 Author: kuhn Date: Fri May 4 23:20:08 2007 +0000 added comment stearing users to the hg18 Old Known Genes track as source of Human Proteins alignments commit 0c9ed0d7b29cff23e38ff8c538b0f526b7a44767 Author: galt Date: Fri May 4 23:16:09 2007 +0000 at bobs request commit 2b037df07454eab6d120a42aae903ec0b96dcb30 Author: kuhn Date: Fri May 4 23:04:35 2007 +0000 changed the phrasing of invitrogen disclaimer slightly (again) commit 1f374cf69f3f8be448bf1f65fe5d14976e63c504 Author: kuhn Date: Fri May 4 22:56:54 2007 +0000 changed the phrasing of invitrogen disclaimer slightly commit 4afee2276351ce2925db027e4f93203e3eeca1af Author: kuhn Date: Fri May 4 22:24:00 2007 +0000 added comment about our filtering the onerous Invitrogen clones commit 3877efc12aa7e598f3dadbdb315cf1c269faa5e5 Author: tingwang Date: Fri May 4 22:05:23 2007 +0000 new tracks for UCDavis ChIP-chip data commit f1030d6a4df3ef2c563ddb55b47362cd6e71c1a5 Author: fanhsu Date: Fri May 4 21:32:43 2007 +0000 Added defensive logic to deal with empty query string. commit 6e65dc4b696bf0c988229531483458a61c77124f Author: pchan Date: Fri May 4 21:21:18 2007 +0000 move columns in blastp track detail page; add percentage of full length and anchors to each gene commit 7a2e43a614d1d38b2dfa447fec80b88229bc7bd2 Author: tingwang Date: Fri May 4 20:30:01 2007 +0000 new tracks for UCDavis ChIP-chip data commit 39822a774e93a02efd63e1cad11cc4fa9d6b40f1 Author: donnak Date: Fri May 4 19:26:44 2007 +0000 Added pub by Craig Lowe et al. commit 331dce4b394ca9eb4ab985a07698fa4b134ce202 Author: kuhn Date: Fri May 4 19:13:56 2007 +0000 changed table to knownGeneOld2 for the blastHg18KG rules commit df73a96b49400bbfe2b73bb45c2b561d3d880b6c Author: rhead Date: Fri May 4 18:51:59 2007 +0000 Changed wording slightly. commit a5e821e7a4b563ecf4dcb4441d7b5ddb628a8e02 Author: kuhn Date: Fri May 4 18:49:49 2007 +0000 added bosTau3 to dbsChecked commit df53e32b9c9841dff222a6d7c1479d8628f4ae43 Author: donnak Date: Fri May 4 18:37:31 2007 +0000 Made a few small edits. commit 2ae7b8e445e1b0adc03045ff288524ca13bc688c Author: kuhn Date: Fri May 4 18:25:35 2007 +0000 added ce4, gasAcu1, bosTau3 to HumanProteins commit ad5f888de26dea03b00accf26790c6c86429edc4 Author: kate Date: Fri May 4 18:19:12 2007 +0000 1 new submissions: Univ Virginia DNA Replication Origins (new methods in 2 cell lines). 1 new in-progress: UC Davis Chip/chip Mar07 batch. 2 sent to Q/A: Gencode Genes, Gencode RACE Frags commit 03ffeb4c6d007db2e0a9165a6453e3ca2f1f666b Author: kate Date: Fri May 4 17:51:24 2007 +0000 DNA replication origins data from U. Virginia (new methods, in HeLa and GM cells commit 3ffc1e0490ae6db1cd30dbdd8cc9a1e8f4c2db60 Author: kuhn Date: Fri May 4 17:18:51 2007 +0000 added mm8 to HumanProteins commit 301879debc3422058311e94f93fedbe8fddca89f Author: galt Date: Fri May 4 15:00:30 2007 +0000 "Encode release log update" commit 253fac2958d2430304c04d235b4add2dd4e1309e Author: galt Date: Fri May 4 15:00:16 2007 +0000 "Release log update" commit 2589cfd895b061e995af591af4baec0d1395b530 Author: markd Date: Fri May 4 07:23:51 2007 +0000 disabled cb3, as genome files are missing commit d461babb4e46d855b9fabaa72f3c381bc63872f3 Author: pchan Date: Fri May 4 06:22:24 2007 +0000 add functions to post blastp track detail page with all blastp hits commit e274b5917e06377169ad4a6252d5f5c615f0513c Author: galt Date: Fri May 4 06:09:43 2007 +0000 calling the correct set-clip routine commit ad1164ddf9a341e6db737a2c3009a81859042189 Author: galt Date: Fri May 4 06:08:45 2007 +0000 adding a hack to help ghostview 4.x commit 571cd9a4fffb62c30f329b9c66b11491b2809e14 Author: hiram Date: Fri May 4 05:54:11 2007 +0000 Clean up multiz5way, now with frames, and set default visibilities commit 605bccc0d9ee0507da84a0128947e38d194ee5b6 Author: galt Date: Fri May 4 03:24:58 2007 +0000 adding support for hgBlat results to htcCdnaAliInWindow() commit 0c6eda6c0ce01b3fa2644c85448d054b8fa68eb1 Author: heather Date: Thu May 3 23:39:44 2007 +0000 add new Stanford ChIP/chip track (Dave Johnson) commit a6428968a44fd1c6ff5ab707580250f1134fcaaf Author: kuhn Date: Thu May 3 23:23:41 2007 +0000 added horse and liard to Human Proteins commit 7eb16c6471998416445aaedf0ff7ffcaa8e14f1d Author: fanhsu Date: Thu May 3 23:19:29 2007 +0000 Fixed a crashing bug. commit 83781b05282a7315a7d40bb8dd78b47daaa1932b Author: hiram Date: Thu May 3 23:18:37 2007 +0000 Ran a 4-way multiz, and a 2-way multiz, corrected the phastCons runs, adding annotation to multiz5way commit 6bb0ec3b2037ba5a93c4e473d2d6424df3e8d9e7 Author: hiram Date: Thu May 3 23:18:03 2007 +0000 Done with C. elegans gene mapping commit 1998f5875cc52c5c0a54cf77d5125041aa80ec98 Author: kuhn Date: Thu May 3 23:00:15 2007 +0000 added platypus Human Proteins commit 57753b58e95936911beabae4f91726c9efe75648 Author: fanhsu Date: Thu May 3 22:43:37 2007 +0000 Corrected the logic for KG III specific processing of looking up protein. commit 743501d164a682f77dd80e4c4d931ee9751f4292 Author: kate Date: Thu May 3 21:48:15 2007 +0000 Improve TB correlate support for type wigMaf tracks. Currently, supports correlation of any wiggle table in the track, but only the wiggles commit 5b8f78620d338f46995e9d495ab48118146be302 Author: fanhsu Date: Thu May 3 21:31:58 2007 +0000 Fixed a problem with GO for KG III. commit 01035fd28e38c01229a2b02d3c6fa48e5dbb4ab1 Author: donnak Date: Thu May 3 21:07:44 2007 +0000 Slightly changed wording abt track mini-buttons. commit 48a3c7d62a8e4488385fa2d4c483214cf396a198 Author: angie Date: Thu May 3 19:19:45 2007 +0000 Fix: in linkedFeaturesLabelNextPrevItem, update position in cart so that links using only hgsid (like PDF/PS) will correctly get the new position. commit f5242e518c8bca22c7fb07e962c1a8e044a0836f Author: hiram Date: Thu May 3 19:18:31 2007 +0000 Adding modern description for conservation track commit 405c06935bf30bf6b6b50e780456bdefbbe2f1e5 Author: hiram Date: Thu May 3 18:58:24 2007 +0000 rearrange order commit ef003d11bcf8add8c7f4d21229542e7ea738ab23 Author: hiram Date: Thu May 3 18:56:26 2007 +0000 The C elegans 5-way alignment tree commit 091cbdcd156cfbdb4df218b3689ea6231cdc2c52 Author: hiram Date: Thu May 3 18:31:38 2007 +0000 indicate maximum gap size of 50,000 commit 128a8372f9c06a9d16cdd3f933d1e8e3cb8fe6d3 Author: fanhsu Date: Thu May 3 18:18:17 2007 +0000 Added type Contig definition. commit 5142738fe21fd2d2ee0546ef04632a4aef5bbeb5 Author: ann Date: Thu May 3 18:14:10 2007 +0000 fixed typo. commit 3ea7146c75ec89b5037077caa70d9c2e06b9a08c Author: rhead Date: Thu May 3 17:47:23 2007 +0000 Removed untrue line about horse clone gaps. commit 385fcc8467df1bfeb6913ca96f26d5978d6c69b8 Author: hiram Date: Thu May 3 17:20:45 2007 +0000 Moved blastCe4SG up one level to be on all nematodes commit d5ec4a86ecf63c5d53f2185cdce987379ad07487 Author: hiram Date: Thu May 3 17:20:14 2007 +0000 Adding the blastCe4SG track to all worm browsers commit 0a147a1b11b6f244a79f7de9f567903e21c8e597 Author: galt Date: Thu May 3 15:00:32 2007 +0000 "Encode release log update" commit 6da466f3eb849bb1bbbe093635cee770d6cd3a14 Author: galt Date: Thu May 3 15:00:18 2007 +0000 "Release log update" commit 94abb2f77fa21c2ca44c65a495258b92118bb223 Author: lowec Date: Thu May 3 08:03:32 2007 +0000 fixed spelling mistakes commit 1cf7cffd90801907c26b8e8638255d9ec16589c5 Author: rhead Date: Thu May 3 00:49:43 2007 +0000 Added fragment type F to include chrM. commit f43e45b204ec92ad7d6ab74d3fcf28b9b77c54e0 Author: kate Date: Thu May 3 00:17:16 2007 +0000 Remove 1 pixel adjustment to wiggle track height, as it results in misplaced map boxes. Watch out for affect on chromGraph and sample tracks commit 079519ca02cce9ee85f29fd5df7b402f55189b3b Author: kate Date: Thu May 3 00:01:19 2007 +0000 Remove defaults button from MAF tracks that don't have default species off set commit 0a25de2ee0ff2a453cb59304f132be5318927da6 Author: galt Date: Wed May 2 23:54:51 2007 +0000 Carter Lee requests password requirements of 3 classes of chars be reduced to just 2 commit a6065c84bfbd5c4d5c5f1e78a040f56d83cb4c3d Author: kate Date: Wed May 2 23:45:15 2007 +0000 Remove inadvertent header file inclusion commit 659334e86b8c1b96904d00e6d9a58bf42c812890 Author: kate Date: Wed May 2 23:44:42 2007 +0000 Better implementation of test for maf tables -- the table name is the track name for maf type tables commit 745ac1552352cb0c3d2022c416b593e128577758 Author: kuhn Date: Wed May 2 23:32:22 2007 +0000 change to make mention of priority.ra all consistent commit fcc4802de2c91e797b0374c7857b2295e3469ffc Author: angie Date: Wed May 2 23:29:42 2007 +0000 Oops, avoid redundant net track entry. Also removed the reminder to update track sizes since b0b said QA does that anyway while checking indices. commit c4b782cded63bb22df635c143ec05bf5dad74835 Author: kuhn Date: Wed May 2 23:27:41 2007 +0000 added priority.ra and rearranged chains and nets to better reflect evolutionary relationships commit 633b3b2a610653f11e62d2baaba2da95ac8cfd2d Author: angie Date: Wed May 2 23:22:01 2007 +0000 When an assembly includes AGP but we fetch chrM from GenBank, make fake gap/gold entry to avoid featureBits anomalies. Also, include all_est in template trackDb.ra for scaffold-based, in case it's needed. commit cb3d59a630758fab07af5a2730cba17a9dd81c57 Author: kuhn Date: Wed May 2 23:08:37 2007 +0000 added priority.ra and rearranged chains and nets to better reflect evolutionary relationships commit 42d756c59e405fc082a4593eeebde98df608a9b0 Author: kuhn Date: Wed May 2 22:56:05 2007 +0000 added priority.ra and rearranged chains and nets to better reflect evolutionary relationships commit 0a8ce463563d56ece30544e7367b2c6702a1c7a3 Author: markd Date: Wed May 2 22:52:47 2007 +0000 enable auto-update of orfeome tables commit 876fa34c8228ca876c4ac1998a9a4ff6db7af11d Author: markd Date: Wed May 2 22:52:05 2007 +0000 enable orfeome autoupdate commit 7cb166f42121f59e5f28e24ea343a299ce0a6d0b Author: angie Date: Wed May 2 22:33:09 2007 +0000 Oops, all_est was missing. commit 978a0335b0c582d7aad024322854805b974d9157 Author: kate Date: Wed May 2 22:26:48 2007 +0000 Fix problem with base-level display of wiggle-less wigMaf tracks, introduced with the multiple wiggle feature commit b8be3194152dccad924329f4860c4a87de59c622 Author: fanhsu Date: Wed May 2 22:07:20 2007 +0000 Added 1 record to chrM_gold. commit 8c76d3ca8257b7939b8a3349638612e8f48d8856 Author: ann Date: Wed May 2 22:05:56 2007 +0000 cleaned up one sql statement commit 55eef3c9a47000680c8c3cff7bab55e45c5aa88f Author: kate Date: Wed May 2 22:05:21 2007 +0000 Fix problem with correlate on Conservation tracks introduced with multiple wiggle feature commit e4352d6d8e43b9dbff847bbacfb221669885f5ab Author: kuhn Date: Wed May 2 22:04:46 2007 +0000 added priority.ra and rearranged chains and nets to better reflect evolutionary relationships commit 9c6a6f10fa915419c1d52a88fdbf813c20b44ae6 Author: ann Date: Wed May 2 21:45:40 2007 +0000 cleanup up usage statement commit 34039112b0d8d7b14bb302b67589e9a309f532ef Author: markd Date: Wed May 2 21:38:56 2007 +0000 enabled orfeome tracks commit 63b0b1c49495d8f74dbe08ac0f1d2125f0eb5b4e Author: galt Date: Wed May 2 21:35:57 2007 +0000 removing htcCdnaAliInWindow for hgBlat type="user" alignments commit d7cc54156164a77bd0e30ce4126295f955878c39 Author: galt Date: Wed May 2 21:34:52 2007 +0000 updating the README regarding adding new users so that the role dev or qa is specified commit 58e1cc4c00b377c0003cf29c90d8be98be9a9feb Author: kuhn Date: Wed May 2 21:34:40 2007 +0000 added priority.ra and rearranged chains and nets to better reflect evolutionary relationships commit ccac8ed92f12cc4bb1768ec555b029f2b8c5426f Author: hiram Date: Wed May 2 21:07:37 2007 +0000 Fix error messages when chrom names are case sensitive and that may be the trouble commit 6eb205fa31b87dd32b918fdbf0e67bc5ebd61ad9 Author: archanat Date: Wed May 2 21:00:47 2007 +0000 updated the medaka contigs description, per request from NIG commit 776d7bbf3bab4997c228dac96960400a7707e4c7 Author: kuhn Date: Wed May 2 20:53:55 2007 +0000 added priority.ra to rearrange the chain and net track controls commit dca8870b712b69ed60f8477ac2d90b4289bde320 Author: hiram Date: Wed May 2 20:46:49 2007 +0000 Indicate chrom name case sensitivity when can't find size commit 876b2e3993584019976119c5ca811fe986d5e883 Author: hartera Date: Wed May 2 19:16:40 2007 +0000 Changed colouring for cell line subtracks for encodeGencodeRaceFrags tracks. One of the colours was rather pale previously. commit 25e36fd7457cb22c522067ae895a20483abcc1d1 Author: kayla Date: Wed May 2 17:34:07 2007 +0000 fixed the references section commit febe75e4a549ef0984150ffbf5225b6ceac82b56 Author: kate Date: Wed May 2 17:26:17 2007 +0000 Add support for priority.ra commit 1b2ba4211dfa31487113dc548ddda52c1e9d8890 Author: ann Date: Wed May 2 17:20:58 2007 +0000 corrected definition of BED 9 line commit b6eae260c454edc53564c8f4794e493510cd44e8 Author: hiram Date: Wed May 2 17:13:16 2007 +0000 Finished with C. elegans tblastn track commit 739ec80afdec92ed1cc1b206092b1f5094502313 Author: kate Date: Wed May 2 16:27:44 2007 +0000 Add priority.ra handling to hgTrackDb commit a52b5295bff97069f9e91845266427064b6a0a5e Author: donnak Date: Wed May 2 15:52:31 2007 +0000 Changed a few things in medaka announcement, removed outdated OH announcement. commit e9384378f7447a58a343905b1dbe9cf5968cf7fb Author: donnak Date: Wed May 2 15:48:12 2007 +0000 Reworded a sentence. commit 171277ad8ff9509e4eb94e7e7eddbcf864545e39 Author: donnak Date: Wed May 2 15:46:16 2007 +0000 Updated release date & some of the statistical info, per NIG. commit 333379d3b10fbff3ec582e00441eba13800063b9 Author: galt Date: Wed May 2 15:00:32 2007 +0000 "Encode release log update" commit d996d93417e8263fccb3634ac2a5a583fd084150 Author: galt Date: Wed May 2 15:00:17 2007 +0000 "Release log update" commit b92e83c4c2d9b28529460fda181e626a3f02e037 Author: kent Date: Wed May 2 07:59:02 2007 +0000 Adding kgTxInfo table. commit d1b66248fcc55aae7ad9b32bfc8680da9bc0c6a0 Author: kate Date: Wed May 2 01:20:06 2007 +0000 Tweak survey link cosmetics commit 8365643cbec9d9dc146450b3f454075679c1568b Author: kuhn Date: Wed May 2 00:41:23 2007 +0000 using kate's priority.ra to rearrange chain track controls commit 6ab39a8197eb02b85cdab5f1df843e1cbfe8a561 Author: kate Date: Wed May 2 00:20:00 2007 +0000 Add support for priority.ra files that override trackDb in the same fashion as visibility.ra files commit eb166b25b7982f111f64f232a7fa0702d83702f0 Author: rhead Date: Wed May 2 00:07:52 2007 +0000 Added line about display IDs changing between assemblies. commit d836168575c732d7aea44240bb1e37023ee51a7b Author: donnak Date: Tue May 1 23:53:03 2007 +0000 Made a few edits to horse credits. commit 6c57e30edc20b01010121c49e5b3311915bd7098 Author: hiram Date: Tue May 1 23:14:58 2007 +0000 Reset date of assembly on request from the Medaka group in Japan. commit 0693f53e6a08225e9e2fe7a7b79763f863617138 Author: donnak Date: Tue May 1 22:59:39 2007 +0000 Added horse (commented out). commit f9a1ab87149b5a372d94ae311f913fa0ac322eb8 Author: donnak Date: Tue May 1 22:58:20 2007 +0000 Fixed date & a few other things. commit 6fbccbadbb49476a68bc764b0d119e5b734bda2a Author: donnak Date: Tue May 1 22:45:19 2007 +0000 Made a few edits. commit 295872ee72fdcb26aa5ecb3784582ab45a90c225 Author: rhead Date: Tue May 1 22:40:33 2007 +0000 Changed author lists in references section to list first 10 authors only. commit c4a8c72f8bc306c49cd072e79bb30bdb531ebc7d Author: hiram Date: Tue May 1 22:34:25 2007 +0000 Make downloads and enter into the pushQ commit 80767b4f8edf99e00e3074ed67e23be361800d24 Author: hiram Date: Tue May 1 22:33:52 2007 +0000 Finished with the 5-way experiment. Tried a 4-way experiment, no improvement in coverage commit 01596c9b38d5319baa1a77c28de59094dec5ef15 Author: heather Date: Tue May 1 22:29:06 2007 +0000 tweaks for SV track commit 05e66675a0ad258aef70277b85bdb863dbcea17d Author: hiram Date: Tue May 1 22:27:10 2007 +0000 Add 4-way conservation, and the phastConsElements for both 5 and 4-way commit 312707f253de068ff8bf5f68e88bb8f4bbf763bb Author: angie Date: Tue May 1 22:08:38 2007 +0000 Ensembl Genes, Conservation, Most Conserved. commit 0f2c898dce58d2fb226c6044203829cad569382a Author: kuhn Date: Tue May 1 22:03:49 2007 +0000 more bug fixes commit c7127cd6140c475dfc462e599a24a7d7b02b659d Author: kent Date: Tue May 1 22:00:44 2007 +0000 Seems to work. commit dbb724e71f889f8aa2b7c3af56e476d152b28484 Author: rhead Date: Tue May 1 21:19:32 2007 +0000 Changed the number of conrad cnps to match newly loaded cnpConrad table. Also fixed several typos found when QAing hg18/cnp.html. commit f90142eebef49ae68d4527af2cbce146b974ad5e Author: kuhn Date: Tue May 1 21:12:18 2007 +0000 added matric headers for chain{Mm8,Hg18} commit b52edf1d5f34d78a6e38e7798f2b04e243f60c1e Author: hartera Date: Tue May 1 21:12:04 2007 +0000 Fixed typo. commit 70aa5bd376c266c1f0ddd72a173d860cd8649505 Author: archanat Date: Tue May 1 21:07:19 2007 +0000 updated RH Map table name commit e9cfbfed7245dbd3891641a65e3e3664eff0a526 Author: rhead Date: Tue May 1 21:00:56 2007 +0000 Added a missing period. commit 68310fe2579ca03947c34d804d57fbe4c5b853fc Author: heather Date: Tue May 1 20:03:25 2007 +0000 fix typos for SV track commit 5e3a63b13a2e2172d8fd1c8d9dbe7db6255152f2 Author: donnak Date: Tue May 1 19:16:35 2007 +0000 Updated medaka date & information, per request from NIG. commit cbdd4df5b6f2356bd1162bd80f94c2cdc797774a Author: hartera Date: Tue May 1 19:04:11 2007 +0000 Updated rhMapName rules to work with danRer3 and danRer4 RH map tables. commit 080454e7c152728d54488fdab73e3bbe8dea8be3 Author: donnak Date: Tue May 1 19:04:03 2007 +0000 Updated medaka release date, per NIG's request. commit 7265686e31a68679226075cd50cec39d756ed033 Author: rhead Date: Tue May 1 18:21:22 2007 +0000 Added a note about IDs not being preserved between assemblies. commit 6a82234743ba1104778ee8c2bd19b25b58e22bbe Author: angie Date: Tue May 1 17:44:30 2007 +0000 Added Dm3 and OrnAna1 to chainDest. commit aefcd7bb5ea9a35094363ca9e0983ff6bae25a7c Author: galt Date: Tue May 1 15:00:27 2007 +0000 "Encode release log update" commit 303a0c26d7fb92deca08fb4753c7da0dd0e93696 Author: galt Date: Tue May 1 15:00:14 2007 +0000 "Release log update" commit 726b2955afa8b0787670537c54d2b69db226e52b Author: aamp Date: Tue May 1 14:56:37 2007 +0000 "New version number v158" commit 79015295b253c9487bb900aab82cf543c51a8573 Author: kate Date: Tue May 1 05:11:12 2007 +0000 Link to survey commit 17f7ed25e748aacdcad1a33c69f93923f2d6ba48 Author: lowec Date: Tue May 1 05:01:59 2007 +0000 I added a section for the exaptedRepeats track commit 1db1316f6e5c443502df632b274239a120692ef1 Author: rhead Date: Tue May 1 02:19:37 2007 +0000 Wording changes and typo fixes. commit 2a01ec15147ea41e9b549de3167994a01c2e56a3 Author: kate Date: Tue May 1 00:28:39 2007 +0000 Fix HTML syntax on temp survey code commit 4d02ec9c3f661a18727b26be572818cf5e8c87a4 Author: galt Date: Tue May 1 00:23:42 2007 +0000 undo remapping of vaccine/placebo and make fuller descr of HIV Quan commit 2aab70a43d33c20df49b712786a9b4688fcfc62a Author: galt Date: Mon Apr 30 23:56:29 2007 +0000 Making it say when nothing passes the filter so the user returns to filter page commit 1125688d78a00acc6b298e2f3e980f8bd30092c3 Author: galt Date: Mon Apr 30 23:53:57 2007 +0000 changing "membership" to "access" commit 357753da9e22aa9e6e07ef8b5f8e0f88595da74b Author: angie Date: Mon Apr 30 23:51:01 2007 +0000 Added reminder to add db to all.joiner. commit 255e59d75dd6479320ba990be8b18d2e49f6b6e1 Author: galt Date: Mon Apr 30 23:49:55 2007 +0000 changing "membership" to "access" commit 1d30a7aaba9e6149fd45f4deaff43d0944828d2f Author: angie Date: Mon Apr 30 23:47:49 2007 +0000 Lump in net track with chain track entry since QA tests them together. commit d98993a5e312d4d3d2883e2897a50fe72ca50262 Author: kate Date: Mon Apr 30 23:42:59 2007 +0000 Add link to survey commit 5fb7d64ab218f4ca229707aede2105a09fc7561a Author: ann Date: Mon Apr 30 23:30:18 2007 +0000 added a Using the Filter section. commit 5d58e0d32ec45d09526737dd204f07762796936d Author: hiram Date: Mon Apr 30 23:20:12 2007 +0000 set defaultDb to cb3 commit e5a805e31a6123d73a67fbdc018a17d1cc032575 Author: rhead Date: Mon Apr 30 23:18:48 2007 +0000 Whitespace changes to make lines 80 chars or less. commit c187ee53f49b084304463993eddc6b5252e74cd1 Author: kent Date: Mon Apr 30 23:15:44 2007 +0000 Making singleExonMaxOverlap a command line parameter. commit d935ad90c61987b1a55b0b0904b576c962486c64 Author: kent Date: Mon Apr 30 23:14:59 2007 +0000 Adding a couple of columns to output. commit 7aa0a15a973b6fc31f536bf93243d7eaee854ea9 Author: hiram Date: Mon Apr 30 23:14:58 2007 +0000 Done with 5-way phastCons and protein blat commit 8f68bb41ceb64ee5c6104d3e2fd14253ca5db264 Author: kent Date: Mon Apr 30 23:14:28 2007 +0000 Tweaking output format for Webb's paper. commit d9bad30f295378e0eb7d0366b11f45638f7aa0a4 Author: kent Date: Mon Apr 30 23:13:54 2007 +0000 Adapting procedure to build UCSC genes to mouse. commit 0a851ab5d6d793c27d4636843bf90a106fedb285 Author: kent Date: Mon Apr 30 23:13:33 2007 +0000 Minor updates to database load for temporary known gene QA tracks. commit eb7f6903d7e1648f21b10587c7cd0080f1d68044 Author: kent Date: Mon Apr 30 23:12:02 2007 +0000 Adding UCSC id to title. commit ba0f3e786a89e26636c80d28a252022b4f01a100 Author: hiram Date: Mon Apr 30 23:11:20 2007 +0000 Done with mapping C. elegans genes commit b411e61cf342fe56f7d30f2185ff7427b1a0f627 Author: hiram Date: Mon Apr 30 23:09:07 2007 +0000 Add blastCe4SG commit 4d3b4d23155e82baaa818406a10718c27e462613 Author: hiram Date: Mon Apr 30 23:08:43 2007 +0000 Now functioning for ce4 protein alignments on cb3 commit 7011dc81a9dfbd6f22e200b201172663913f110e Author: angie Date: Mon Apr 30 23:00:21 2007 +0000 Added dm3, ornAna1. commit affba519c6c553899150d49b5b6b5f758832d6e5 Author: rhead Date: Mon Apr 30 22:55:13 2007 +0000 Edited Locke CNP number, and changed CNV to CNP. Also fixed a typo. commit fc952741471f5673b1206490f7ebc61dbe944a20 Author: kuhn Date: Mon Apr 30 22:52:22 2007 +0000 more tweak ts that came up during testing commit 425e0330cd4599fd4ec7e755b5d69da9b81b7900 Author: ann Date: Mon Apr 30 22:51:27 2007 +0000 general cleanup commit 9338205f4536b1ee25cf0d7b8f51f8862ac4cc81 Author: angie Date: Mon Apr 30 22:38:47 2007 +0000 Fix: look for unsplit gold table first. commit 2fdc565663657a5a70d9d0031257d3c959d7df75 Author: angie Date: Mon Apr 30 22:24:04 2007 +0000 Bumped up verbosity of complaint about NULL update time. commit fd07e2b5aabae4a486e1e95aa7a3b04dedb2d69b Author: angie Date: Mon Apr 30 22:23:18 2007 +0000 Added -useHashedName for splitting by target when we need a repeatable many-to-one mapping of sequence names to split file names (e.g. scaffold-based assembly with multiple sequence naming patterns). commit 6e50bba26fa437a4522981aaae16861a7a62cd56 Author: angie Date: Mon Apr 30 22:16:19 2007 +0000 Added CREATE TEMPORARY TABLES to required privileges for CGI user (now needed for jksql::sqlRandomSampleWithSeed which is used by TB paste/upload page). commit d1180374c4ca66d08e6a3ed31f72bbc42b9439b5 Author: ann Date: Mon Apr 30 22:05:35 2007 +0000 hyphenated nonexonic commit 1d3b920196295f109a88eca11ae546dbf9f205eb Author: lowec Date: Mon Apr 30 22:03:50 2007 +0000 changed uppercase yes and no to lowercase in doExaptedRepeats commit 599297fe5447c0ff068ce68c7cf055f6708908c8 Author: lowec Date: Mon Apr 30 21:43:13 2007 +0000 added search lines for exaptedRepeats commit 1a756758cac99b274123456f5146bda71b74499b Author: lowec Date: Mon Apr 30 21:37:05 2007 +0000 added the exapted repeats track to the list of ignored things for $hg commit 693a05e198b3ddbeff4600b46b8cd4cdbccf2bca Author: kuhn Date: Mon Apr 30 21:34:46 2007 +0000 added some more whitespace around image commit 7ee3fc79e855ce140aa869d5e2d52e1745714275 Author: kuhn Date: Mon Apr 30 21:33:52 2007 +0000 added some whitespace around image commit ffe2f6858101e1166fb79ebef21ca45d2e6e31df Author: kuhn Date: Mon Apr 30 21:20:45 2007 +0000 added entry for chicken chain/net tracks to get order of track controls right commit 7115c2fe0f14eba9f9b7ae67c09e74ce3be10564 Author: ann Date: Mon Apr 30 21:16:03 2007 +0000 re-added link to Craigs webpage. This should be removed when the link becomes available for the paper (which is currently in press). commit 9b72621268e65a9b81d3588bf901f472ace6f423 Author: ann Date: Mon Apr 30 21:12:30 2007 +0000 fix up citations and line length. commit f81dec6c7c10ef8133d49664d269425fb25737de Author: galt Date: Mon Apr 30 21:04:08 2007 +0000 added real contact phone#; added "to activate" and reminder to click link to return to merchant commit f6ff8d41947640fbebe27ae990be564657d597b3 Author: galt Date: Mon Apr 30 20:40:52 2007 +0000 minor title change promotes use of filter page for more than just table view itself commit 21db7320661a5a7dd62b1525b085441641e51e3d Author: donnak Date: Mon Apr 30 20:10:40 2007 +0000 Updated medaka entry. commit 0deb9fd18afb2f1459c9413d517f2f6c4c616dad Author: donnak Date: Mon Apr 30 20:10:13 2007 +0000 Archived some items. commit 45d941e0ccc653fcb2981f7f88a1d54be85991a3 Author: donnak Date: Mon Apr 30 20:09:52 2007 +0000 Added announcement abt medaka, archived some items. commit 5feb8607379ce57ab1aa67b4edbaad410dedf728 Author: donnak Date: Mon Apr 30 20:09:05 2007 +0000 Added period in survey portion. commit 2d41ddbd81b19ba5c67802e8d08079298fff6927 Author: giardine Date: Mon Apr 30 19:30:08 2007 +0000 Updated ORegAnno docs to reflect latest reload commit df38f5b39123b7860daf67cb61e9bd061ec9f46d Author: markd Date: Mon Apr 30 19:14:51 2007 +0000 added new orfeome ids commit 8cc3358fef3c9ef90cdc43bbd9cd6a38af6ef5b6 Author: hiram Date: Mon Apr 30 16:48:17 2007 +0000 Add matrix for chainGasAcu1, chainMm8 and chainHg18 commit 0629cf7e0cb6708f90cb01ce55c4b91871a4c097 Author: galt Date: Mon Apr 30 15:00:21 2007 +0000 "Encode release log update" commit 7fe7be56cf1b98bee5b8c770a85b072b7cd0183f Author: galt Date: Mon Apr 30 15:00:12 2007 +0000 "Release log update" commit 9fd15ae3c189d74f009f4be1dff5d9dedc661c72 Author: giardine Date: Mon Apr 30 13:24:36 2007 +0000 Make sure Locus Variants searched items are displayed even if category is hidden. With Swiss-Prot hidden by default, searches not displayed can cause confusion. commit 0aaef290dd6c25170cb8a37d1c8f12eff4900b6c Author: galt Date: Sun Apr 29 22:44:33 2007 +0000 using new pixel-fattened polygons for a good-looking centromere commit 95a199ab24c7d66abad1498d488f24aaa1bdc683 Author: galt Date: Sun Apr 29 22:42:43 2007 +0000 adding pixel-fattened routines for line and polygon including stroked outline commit ab21ebb4fa020197e27c5e02991ee75fd629d087 Author: kuhn Date: Sun Apr 29 20:41:03 2007 +0000 needed to rename variable (again) commit c060fbfd364bd881dbe9962ef96f0f06b561f4f1 Author: kuhn Date: Sun Apr 29 20:26:13 2007 +0000 removed a hard-coded db name, fixed capitalization issue and modified some output text slightly. commit 44c9608b710e2c09720e7b048b49a501fad70d81 Author: galt Date: Sun Apr 29 15:00:22 2007 +0000 "Encode release log update" commit 4167b83f3caacfda42c4ae7d2bf77f14d1d91408 Author: galt Date: Sun Apr 29 15:00:12 2007 +0000 "Release log update" commit 780ba8a2ef2447b4844f9b8f88000e39437a03d1 Author: kuhn Date: Sun Apr 29 07:04:35 2007 +0000 mods to debug the conversion to allow non-split chain tables and some output tweaking commit 305af3d73c69fe5dd4dea06882f77658e50a24cf Author: kuhn Date: Sun Apr 29 00:34:11 2007 +0000 needed to rename variable commit 98c658479020baa4b36951381349d14cf1fc5f7d Author: kate Date: Sun Apr 29 00:33:39 2007 +0000 Update for new consWiggle type commit 0b0d7497b798f0ea26f74bb0c2da57969d6c16c8 Author: kate Date: Sun Apr 29 00:30:07 2007 +0000 Remove test tracks. Adjust defaults on 28way commit 77f49ce42bc1b8209bfd2d3b0a9e4392260678bb Author: kuhn Date: Sun Apr 29 00:28:29 2007 +0000 adjusted to accomodate unsplit-chrom assemblies commit dc93c112ecd8ae645d2bdba266128bfd2aff7b6e Author: kuhn Date: Sun Apr 29 00:25:15 2007 +0000 removed some redundancy commit eeaad2c442711c6830367b0bf2ceb4bb4eccaba5 Author: kate Date: Sat Apr 28 23:59:41 2007 +0000 Support for multiple conservation wiggles in wigMaf tracks commit e28775dda8ad0b6506cf09688ff484398b5ac140 Author: kate Date: Sat Apr 28 23:13:16 2007 +0000 Prep for multiple alignment commit 520786e78e1dff294c68a4bb660f9bdb2cc4ff62 Author: kate Date: Sat Apr 28 22:53:24 2007 +0000 New data submissions. Post MSA conservation wiggles for download commit 91f2b3e32c926e97e861f31872695da8948d4b43 Author: kate Date: Sat Apr 28 22:51:51 2007 +0000 Replace dropped table commit 6646422b6958310a0773b77654bf5d0a91231517 Author: hartera Date: Sat Apr 28 19:36:43 2007 +0000 Added definition for lfNoIntronLines which is used to flag that no lines should be drawn between exon blocks. commit 44d6664fd3e580e95042461f20190845004929f8 Author: braney Date: Sat Apr 28 16:02:52 2007 +0000 added human proteins track commit d890a6f48fac7908984370e2579473c823f0f573 Author: kuhn Date: Sat Apr 28 15:11:14 2007 +0000 extended to handle unsplit chains tables commit e9f056d624a5b5b742cc394abae3eb4a13ec1370 Author: galt Date: Sat Apr 28 15:00:27 2007 +0000 "Encode release log update" commit 181fe72ef29460943e5691345b5847fa011d29d7 Author: galt Date: Sat Apr 28 15:00:15 2007 +0000 "Release log update" commit d64544709dc4990c8e89f71b7181b1e8521743ff Author: kent Date: Sat Apr 28 08:33:30 2007 +0000 Seems to work. commit 2deae09c4b6c05d96a9fee9322c8adea94431961 Author: pchan Date: Sat Apr 28 05:47:18 2007 +0000 updated by Todd in Feb 2007 commit 7ee11fb96b17d54a8baab720207876a12f656bdf Author: heather Date: Sat Apr 28 02:57:16 2007 +0000 split up delConrad and delMcCarroll to properly handle delConrad thickStart/thickEnd; embed other scripts commit 8fc8e2ec7bed18ec7c7578dd3c362df8e784f01a Author: fanhsu Date: Sat Apr 28 00:16:20 2007 +0000 Updated for KG III specific processing. commit 2af815180bb403880dab3ad31c817a148735b7ac Author: fanhsu Date: Sat Apr 28 00:15:28 2007 +0000 Updated for KG III. commit 4ef203a59745e18f4ab54293fcb1af6ca1fd0133 Author: fanhsu Date: Sat Apr 28 00:10:50 2007 +0000 Updated to fix the problem that for KG III, the protein field in knownCanonical table is no long UniProt ID. commit aeb840e0a3c613c25e4179ffdb837105ac58b49d Author: hiram Date: Sat Apr 28 00:00:20 2007 +0000 May have the sangerGene track now done correctly. And created the exon set from the sangerPep data for the tblastn runs against the other worms. commit 6102248e1ec6bc2673d524655e21fba84e13e7df Author: hiram Date: Fri Apr 27 23:59:28 2007 +0000 Starting ce4 sangerGene proteins tblastn run commit 8f1be18937fc8c2fb627b4ee5088f3604aa9d513 Author: hiram Date: Fri Apr 27 23:58:49 2007 +0000 Set default position to 16S ribosomal RNA, and add photograph from Eric Haag commit d9b941352d553cd2baee862bba04293d12ccbe59 Author: kuhn Date: Fri Apr 27 23:58:41 2007 +0000 dropped unused variable commit 938476b3c4cb8dfba6c69d80e6bf305754d41023 Author: hiram Date: Fri Apr 27 23:58:15 2007 +0000 Change name to C. brenneri commit 043cad1197e88d11a0ae83f23a5389751da9e6a2 Author: hiram Date: Fri Apr 27 23:57:43 2007 +0000 Set default position to 16S ribosomal RNA commit 822c6c2489389a9c6d64451b02745b35c63e8e02 Author: hartera Date: Fri Apr 27 23:34:08 2007 +0000 Fixed typo. commit b2afa7e0927af0e3bb77992b911b037e1bf05b02 Author: angie Date: Fri Apr 27 23:31:48 2007 +0000 Don't apply split table $prefixPattern when n/a. commit e940fc076b6dcd9688c64f8847bbfeabcde3cbf6 Author: ann Date: Fri Apr 27 23:28:49 2007 +0000 removed this temporary file. The real file is gvPos.html. commit 13812bc49252e134ed7ec6cb85a96b74b7292d76 Author: hartera Date: Fri Apr 27 23:09:29 2007 +0000 Added code for methods for the ENCODE Gencode RACEfrags track and added a track handler for it. Also, added code that will hide intron lines in transcript displays under a defined condition. commit a5396c388e68a143e382fcb31b066c7ed4bcc13f Author: hiram Date: Fri Apr 27 23:02:24 2007 +0000 Adding RNA and pseudoGene tracks commit 3caa55da953c576adcdf0ac0666e1f56e789b7cb Author: hartera Date: Fri Apr 27 23:01:37 2007 +0000 Fixed a sentence. commit f1f4a6a6f5bc85c52ca17f8ac34f4c0f2fd771b6 Author: hartera Date: Fri Apr 27 22:54:21 2007 +0000 Added information abou the colouring scheme used in the track. commit 7e951e777df4c2613c9590b6ad27fc9baffc2dcf Author: angie Date: Fri Apr 27 21:55:00 2007 +0000 Updated mRNA and EST examples to native sequences; tweaked version back to 5.0. commit fbb457397833c7ef9071488c752d837dcd26b2d2 Author: ann Date: Fri Apr 27 21:28:18 2007 +0000 dropped release beta block for gvPos and removed release alpha line in the block that is staying commit 9e0da849d99ccfcd712cf947107bb846cb4c6720 Author: angie Date: Fri Apr 27 21:08:06 2007 +0000 Added multiz6way Conservation and phastConsElements6way Most Conserved. commit 35fdd0e6c543ef78916d441fca03409ad37a44d1 Author: heather Date: Fri Apr 27 20:45:31 2007 +0000 edits for Locke commit 819bc99fa15dd94108fe1b1547e6415658997209 Author: angie Date: Fri Apr 27 20:35:39 2007 +0000 phyloGif for platypus 6-way. commit 31c66fd5b56913f2aea6837d84dc968f07d169a7 Author: angie Date: Fri Apr 27 20:28:36 2007 +0000 Changed a cartUsualInt to cgiUsualInt in a !useCart section of code. commit 73d3751f36e9c4d0773c1ed77707346945a9b3e6 Author: aamp Date: Fri Apr 27 18:30:22 2007 +0000 switchDbTss track updates include a struct change and a description fix. commit a103b8a42b876633186eafc73e2a5816fe6068dc Author: heather Date: Fri Apr 27 17:55:35 2007 +0000 edits to validation section commit 884e4196dda23fda7790838b33ff4e5f6e798efa Author: kuhn Date: Fri Apr 27 17:53:05 2007 +0000 fixed some bugs. commit 7fe414acfb9494dfa94f7d5b1b1adb696d8b9229 Author: hartera Date: Fri Apr 27 16:35:36 2007 +0000 Converted URL to hyperlink. commit 94cd5d0aa20ecb8c7bd9a9bed00b6cd66677ff8c Author: hartera Date: Fri Apr 27 16:04:37 2007 +0000 Minor edits. Correction to the Credits table. commit 70bd5ba8c081edf26eef9339674b978c3e472fc2 Author: galt Date: Fri Apr 27 15:00:32 2007 +0000 "Encode release log update" commit cbd92574dc7085f98ceb07b04049e543d2e4b5f5 Author: galt Date: Fri Apr 27 15:00:17 2007 +0000 "Release log update" commit a732ba45b772da165241dbc0ccb6f212c18a25d9 Author: giardine Date: Fri Apr 27 12:02:17 2007 +0000 Change in wording for Locus Variants detail page. commit 0e63906163c5990a6d0698c00cc281375097e062 Author: kuhn Date: Fri Apr 27 06:10:40 2007 +0000 fixed a block that wasn't working for unsplit tables commit 81fc6f593f1bcee49b81a492194a4a3bd69d8e48 Author: kuhn Date: Fri Apr 27 05:49:15 2007 +0000 refactored to accept non-split chain tables commit 6769891402054bb3ac93853e7b77ece1d255b8db Author: markd Date: Fri Apr 27 04:04:38 2007 +0000 added tool to help with updating cdnaInfo columns commit 23cc7ada627054406f01ee3a6ef94b9e1b46857b Author: heather Date: Fri Apr 27 03:49:07 2007 +0000 indices for snpArrayIllumina550 and 650 commit 2b8ad3948ca648fab8ab9cb1a1f302305b39cd89 Author: heather Date: Fri Apr 27 03:47:14 2007 +0000 indices for snpArrayIllumina tables commit 0b6412a2442e99b9c643fe841d0ae44dec7f59d4 Author: heather Date: Fri Apr 27 03:19:56 2007 +0000 add new Illumina arrays to SNP Array track commit 8d7241de6bff5482d6b37c739b6912cfa2fa74c3 Author: heather Date: Fri Apr 27 03:19:36 2007 +0000 transfer Illumina 550 and 650 arrays from hg18 (and fix typo in HapMap SNPs) commit f6f9bb8349d44438f00b6eca8a1d3be8972fcb6d Author: kate Date: Fri Apr 27 00:54:35 2007 +0000 Correct temporary html setting for Affy Chip Strict track commit 0c5a3f8c206efb94f2aec855066be7e2588e9a41 Author: kate Date: Fri Apr 27 00:50:35 2007 +0000 Correct release setting on Affy Pval Strict track commit 1eb79eca251f29256c238d600d11219b8659af46 Author: kate Date: Fri Apr 27 00:46:00 2007 +0000 Add syntenic net subtracks commit da080bb77b2f73a87a0734fac42c2357ad02ec23 Author: kate Date: Fri Apr 27 00:45:11 2007 +0000 Correction to 3 Affy Chip/chip tracks (Strict versions) for hg17. For p63 experiments, the cell line was ME-180 commit aed4769619b7d3312e0a00d3421fd4f85c69cc83 Author: ann Date: Thu Apr 26 23:31:06 2007 +0000 added acronyms for new databases commit d26e1bba28936983f027ed5ed0cff2499491cf9b Author: hiram Date: Thu Apr 26 22:52:39 2007 +0000 Fixup search examples so they all work, and assembly details commit c32c25d3caf97139abb143afe627c4964ec77298 Author: hiram Date: Thu Apr 26 22:52:09 2007 +0000 Fixup search examples so they all function commit 1b500d70cc05075b3fac3b7d6db3508b80e4a150 Author: kuhn Date: Thu Apr 26 22:33:39 2007 +0000 grammar correction 'like' --> 'such as' commit a93f78b79c914aad9941f3355c995a444b4eda8c Author: lowec Date: Thu Apr 26 22:31:46 2007 +0000 add the exapted repeats track commit 6bc1b64d1ee808228130099c53a0d5937f283e4b Author: galt Date: Thu Apr 26 22:23:27 2007 +0000 redirect capability to return to a specific cgi after filter page runs and updates the shared subjList commit eccfae2e6ec64df16d47a9fbee78b7457d9e06e5 Author: galt Date: Thu Apr 26 22:22:11 2007 +0000 adding alternate entry point to support additional optional header info, e.g. can use for META tags commit a012ea79ea280ba07766f55ba5a69c7bae24599a Author: hiram Date: Thu Apr 26 22:18:40 2007 +0000 Fixup search items, and complete assembly details commit b73c018aa381605a92253adb40c2fde338dc71dc Author: lowec Date: Thu Apr 26 22:15:50 2007 +0000 This is for the exaptedRepeats track on hg18. commit 3f1f95ffb7e2e973a674eb13b5682ddb67aa730c Author: lowec Date: Thu Apr 26 22:14:34 2007 +0000 I updated hgc.c to handle my exaptedRepeats track. It is similar to a bed track, but uses the score field for a confidence metric. commit e75a705a05d81f9b521aa00601940675841d9947 Author: hiram Date: Thu Apr 26 22:12:29 2007 +0000 Fixup search terms so they are accurate and will function commit a413bbed53226ab0047a995e34dc4bd3cfc4959a Author: kate Date: Thu Apr 26 20:59:29 2007 +0000 PhastCons for 28way. Get chain stats commit 3cc6b2547a0b9aad5c8ec604cc86a36e6ac9c379 Author: kate Date: Thu Apr 26 20:49:45 2007 +0000 Released tracks: 1. UC Davis Chip 2. U Virginia DNA Replication update. Tracks now under development: 1. Gencode RACE Frags. Tracks sent to Q/A: 1. Gencode Genes Mar07 batch commit 4992ec5198975327587d7928a55ba094f95678f9 Author: kate Date: Thu Apr 26 20:46:40 2007 +0000 Update commit 576e7c71d7e822372d50b988c647f02278f8b024 Author: hartera Date: Thu Apr 26 20:33:48 2007 +0000 Added more information to the Verification section and re-wrote part of the section. commit 2a446b154135aba35f68a6eae073ee0b987ce11a Author: hartera Date: Thu Apr 26 19:45:05 2007 +0000 Added searches for the Gencode RACEfrags primers. commit bcf8c1de4b93d6d323c262fb20f09a58bf64731d Author: rhead Date: Thu Apr 26 19:36:49 2007 +0000 Changed genethon link again; old link gave a 404 message. commit 61878177d6a34b148d53ab1ab220eda3c461699d Author: rhead Date: Thu Apr 26 19:27:46 2007 +0000 Changed genethon link again; old link gave a 404 message. commit ca2674947f01386ad74f657c35017bf21da5689a Author: hartera Date: Thu Apr 26 19:08:56 2007 +0000 Added encodeGencodeRaceFrags tables to the list of tables to be ignored for human. commit dcd70db4ad61f5e34f76e66e35703411dd14e5bd Author: hiram Date: Thu Apr 26 17:06:29 2007 +0000 Adjusting description commit 7849393bde3a4a4ddb430ec72fca47f1b2ab378b Author: hiram Date: Thu Apr 26 17:05:56 2007 +0000 Adjusting desciption commit e78e02dbb6f9d34cf3f802e94fcd380e94d3d09b Author: ann Date: Thu Apr 26 17:05:50 2007 +0000 added missing period. commit 04fe070714b304ef0ba78589503a2018682c7886 Author: hiram Date: Thu Apr 26 17:05:21 2007 +0000 Adjust chain and net positions, update description commit b66c3585461f13594582eb01bfd4f83a61636172 Author: giardine Date: Thu Apr 26 16:08:06 2007 +0000 Added note about recent reload for Locus Variants track (gv* tables) commit 55ed4d5287dd40ff62c43de9cd290c32ff3b6b5f Author: giardine Date: Thu Apr 26 16:04:29 2007 +0000 Moved exclude by source higher up in the track details page for Locus Variants. (so Swiss-Prot being excluded by default more obvious) commit 30ee1bffd9eaaae42140c0fd3a25bbeccf54c03e Author: fanhsu Date: Thu Apr 26 15:51:59 2007 +0000 Edited horse section. commit bc1a03a3364db6ce9fd3e338551cb9b87cfea96f Author: kuhn Date: Thu Apr 26 15:13:45 2007 +0000 made survey open in a new window commit 3e4bcef17d42d7a046f290970a80d0d1989527c7 Author: kuhn Date: Thu Apr 26 15:12:22 2007 +0000 made survey suggestion (not serving suggestion) more prominent commit 6f750df6610ee0422cc4ba4aa1416abc05a622da Author: donnak Date: Thu Apr 26 15:03:36 2007 +0000 Added link for survey. commit ea876ede63894af4cc2a31c958813742259fc613 Author: galt Date: Thu Apr 26 15:00:33 2007 +0000 "Encode release log update" commit fa1ae65c2bfc549e488330c181c7cdf28b4f857d Author: galt Date: Thu Apr 26 15:00:17 2007 +0000 "Release log update" commit 46e2486337619a3c25a7aa7aa9c66beee6c84b17 Author: fanhsu Date: Wed Apr 25 22:23:50 2007 +0000 Added BLASTZ with horse. commit 3b4d1222da8b11c8a943b70a788c419657cd3e21 Author: fanhsu Date: Wed Apr 25 22:21:40 2007 +0000 Added BLASTZ section with horse. commit f997f9836c6cee8f63e6b9f49f0349fc26191af4 Author: heather Date: Wed Apr 25 22:21:07 2007 +0000 set color to gray for cnpTuzun (hg18) commit 07d6b9f96615d8f0dcb8c3544273f042522030d4 Author: fanhsu Date: Wed Apr 25 22:16:45 2007 +0000 Added BLASTZ with horse. commit b0e1a831818c5572d361e3f8d0cca4ec9d333c17 Author: fanhsu Date: Wed Apr 25 22:14:36 2007 +0000 Added BLASTZ with horse (equCab1). commit d3b1564f8cad135119b8a2064f37d6784b713b28 Author: fanhsu Date: Wed Apr 25 22:09:44 2007 +0000 Added horse (equCab1) BLASTZ section. commit 39283474c720c3e995c1314714fe0731ab5ed345 Author: hartera Date: Wed Apr 25 20:10:14 2007 +0000 Added links for cell lines. commit b714c39865d18cbed1377d8cf3df510556795d58 Author: hartera Date: Wed Apr 25 19:39:20 2007 +0000 Re-ordered subtracks and changed colouring for Gencode RACEfrags track as requested by contributor. commit 39dc4cfaa78ec0a4daa3ae165532885b5feb943d Author: archanat Date: Wed Apr 25 17:53:43 2007 +0000 added matrix to chainHg18 block commit b93339568ee307bbad1e9a782d77f75029d349fb Author: heather Date: Wed Apr 25 17:43:59 2007 +0000 add color for cnpLocke commit 39c0ebd761d183f572f765da7f033457622e187c Author: heather Date: Wed Apr 25 17:43:11 2007 +0000 add method for Locke; delete display for Tuzun (no longer available) commit 034c47002581d123c203e4c2775df0080901736c Author: angie Date: Wed Apr 25 17:30:37 2007 +0000 Instead of directly connecting to the central db named on the command line, use hConnectCentral so that the hg.conf file's main connection info is still for the genome db's, which may be required for hGetMinIndexLength when reading in custom tracks. We still need a command line arg to suppress usage message, so keep the arg and compare it to the central db specified in hg.conf. commit 5fd4b5222d41d68a261a6f06f41dfa78d8f63882 Author: hiram Date: Wed Apr 25 17:23:44 2007 +0000 Add entries for chain and net OryLat1 to eliminate data display on chrNA_random and chrUn_random commit 75f1d74eb5360a0ed454fd596cdb8373124960d4 Author: hiram Date: Wed Apr 25 17:09:41 2007 +0000 Added phastCons5way commit 7c8d75b7f314dcd725fb93a7bc870a6304a4d235 Author: hiram Date: Wed Apr 25 17:09:08 2007 +0000 Finished genbank, and added blatServer commit 68163f1b96b67172528b158877e6f2031b075dc5 Author: hiram Date: Wed Apr 25 17:08:33 2007 +0000 Enabled daily alignment of cb3 commit bcbdb65895bca3623b92908260cfa662d00c1cab Author: hiram Date: Wed Apr 25 17:05:52 2007 +0000 Added genbank and blatServer commit 9eb0ae4629897e8976272079ef1332be533f9c98 Author: hiram Date: Wed Apr 25 17:05:21 2007 +0000 Added caePb1, caeRem2, cb3 commit d0c2c8985b01cd2531546ebdd51fca0271d38d82 Author: hiram Date: Wed Apr 25 17:02:55 2007 +0000 genbank done, and added blatServer commit ee1257be9315ba1f6a7fa968c25e3ffa192e73e6 Author: hiram Date: Wed Apr 25 17:02:08 2007 +0000 Added priPac1 - P. pacificus commit ecc4669048d65139a3b27710d343ff174d444543 Author: hartera Date: Wed Apr 25 16:49:05 2007 +0000 First draft of ENCODE Gencode RACE frags track description supplied by track contributor. commit c99cce4a7addcd930c6f0107a72a239cc9a31277 Author: galt Date: Wed Apr 25 15:00:34 2007 +0000 "Encode release log update" commit fcc2a79fa1f24c7e0dec133a5b19b1ef6b42f917 Author: galt Date: Wed Apr 25 15:00:18 2007 +0000 "Release log update" commit 91c39737efc9f68c514d32b23fb19d5ca3ee68dd Author: angie Date: Wed Apr 25 05:24:49 2007 +0000 Added counters for live and expired CTs; at default verbosity, only the counts are reported. commit b8a152c70603941ee11d2da5c18c2a138f70cf7d Author: heather Date: Wed Apr 25 03:34:25 2007 +0000 switch to pubmed format; correct counts commit ab8ed1fc40eb945d2234f3e75064a71b032716c6 Author: heather Date: Wed Apr 25 02:40:19 2007 +0000 tweak cnpLocke longLabel commit 1aaf4be2f8d7402c012b10231f14d8de3c3c98fc Author: hartera Date: Wed Apr 25 02:01:55 2007 +0000 Removed unused variable. commit 7a543f27509c58a4673f53962348385347621b7d Author: hiram Date: Wed Apr 25 00:02:50 2007 +0000 Turn on phastCons5way graph on the multiz5way track commit de658ff892af4c39b00e54b7c92496d4b7ac9ed1 Author: archanat Date: Tue Apr 24 23:35:39 2007 +0000 minor edit commit 427a1dfa8245fe6708607854c0dace4307ff2bfa Author: archanat Date: Tue Apr 24 22:49:37 2007 +0000 changed the name of the author to be consistent with the name in other places commit 2d944ded76ffa78adcde9a9d2ba06f3618145c05 Author: aamp Date: Tue Apr 24 21:58:13 2007 +0000 Just a little utility for coloredExon track making. Seems to work so far. commit 98a6e54e39a2f8b97a359d6816a3eb82e0e15dc1 Author: ann Date: Tue Apr 24 20:30:37 2007 +0000 typo commit 37d4f4d8eeabb2a5484cd8edb71951703daf111d Author: hiram Date: Tue Apr 24 19:37:45 2007 +0000 Fixup the problem of recognizing autoScale=on from custom tracks commit 62477ddefe0a8109019e3202a3fe8742242aca42 Author: heather Date: Tue Apr 24 19:01:06 2007 +0000 alphabetical order by author last name commit 14fa7d4ac5f6b405770c7ec7e405e824f6854fbf Author: heather Date: Tue Apr 24 19:00:49 2007 +0000 alphabetical order for SV track commit ed950172cc6f7eba86386127b8d8ac0cd4b58c48 Author: braney Date: Tue Apr 24 18:57:41 2007 +0000 an exmaple genome tree for tubeTree drawing commit 99a0eb8138e9afd1e4b6f6c0d738cca4f73e55ca Author: heather Date: Tue Apr 24 18:53:39 2007 +0000 add link for liftOver commit 813d0255e771fd32313b20269e17815832dd1c1f Author: hiram Date: Tue Apr 24 18:37:46 2007 +0000 fixed mispelling commit 17a5e1450d9313a870d8accbe51757af57bad4ae Author: hiram Date: Tue Apr 24 18:35:43 2007 +0000 show errno on failed malloc calls commit 16f595f95e2554ca534c971c14a0fb589fa2e17a Author: braney Date: Tue Apr 24 18:31:14 2007 +0000 a clean up. Experimental commit ecb52a096c0274ac20ed2ada58bf5b13f2022ede Author: rhead Date: Tue Apr 24 18:22:47 2007 +0000 Changed NCBI link to BACPAC Resources Center link. Whitespace changes. commit ca4379a39363c3fed98b039e4892b67be1fcb4f1 Author: braney Date: Tue Apr 24 17:23:52 2007 +0000 make psLineTo a global commit 19bc51adb01c0250bb651dec685f7ff56562c9d8 Author: braney Date: Tue Apr 24 17:23:02 2007 +0000 add human proteins track commit 3bbda029c245992af07312f5a8c007bf2d950b24 Author: braney Date: Tue Apr 24 17:00:56 2007 +0000 the source used to draw the PRAME tree. Experimental. commit 779a83b75f60cc57440ec5b040b3ad528e13633b Author: galt Date: Tue Apr 24 15:00:29 2007 +0000 "Encode release log update" commit 7d78550a065066e76646a990e2179cbb764e7931 Author: galt Date: Tue Apr 24 15:00:16 2007 +0000 "Release log update" commit efcf895fb339a6c1520d4d05fe72c923de75e088 Author: aamp Date: Tue Apr 24 13:59:29 2007 +0000 SAGE track description changed for human. Mouse SAGE track doesn't use SNP data. commit aaff8d7bbffa8972957197233d390b461684bae0 Author: angie Date: Mon Apr 23 23:13:06 2007 +0000 Mention indel coloring options and link to help/hgIndelDisplay.html. commit 80c42dfaca88ac14a5c14ed91a1e118517c31820 Author: markd Date: Mon Apr 23 23:09:56 2007 +0000 trim spaces from GFF gene names commit 7017ac114485830ab56a6ac67b58591521c69923 Author: hiram Date: Mon Apr 23 23:09:29 2007 +0000 Completing all combinations of blastz and swap between oryLat1 and tetNig1,danRer4 commit 51385030ff405e33ba10843d0c881aa350fe4ceb Author: heather Date: Mon Apr 23 22:58:47 2007 +0000 edits for SV clone links commit 11e28a923c4fe9012b7423f6ea0f316461ac42b5 Author: heather Date: Mon Apr 23 22:58:00 2007 +0000 new SV data commit 0edc0a207d1170f6597f96e55094a79a621fc869 Author: heather Date: Mon Apr 23 22:57:15 2007 +0000 add cnpLocke commit d46b0ea0ae45589e955d0cad2bb14c6568588f32 Author: kuhn Date: Mon Apr 23 22:45:55 2007 +0000 moved cat and horse chains and nets down here to properly set prioirty to reflect the evol distance commit bb05380a98348eedaa1f74feed268705ae341ab3 Author: markd Date: Mon Apr 23 22:45:42 2007 +0000 removed spurious comment commit 871675c8ca59bcbde9c044a764b0d6e75f795167 Author: angie Date: Mon Apr 23 22:37:21 2007 +0000 Self chains (special req. back in March). commit 8905601f7df93ad4b6ad7407e4d1e863b0f3b614 Author: angie Date: Mon Apr 23 22:36:56 2007 +0000 Re-swapped galGal3 and hg18 chains/nets. Swapped monDom4 chains/nets. Blastz/chain/net anoCar1. RepeatMasker beta test (will redo in a couple weeks when new platypus lib is available). commit 41d1d8faea8a5e6264ee0b36b65bdb29c168edb8 Author: angie Date: Mon Apr 23 22:09:55 2007 +0000 Appended date to sequence file name so pushes aren't so dicey: hgwbeta shares /gbdb with RR, but has its own seq/extFile, so reusing a sequence filename is a problem. commit 042a11571af4f98dfd580a9f39911785ef8bc772 Author: angie Date: Mon Apr 23 22:06:48 2007 +0000 Added some verbose's for debugging. commit 7e8f924f246061533f797a80832f6bdb0dad5c82 Author: kuhn Date: Mon Apr 23 22:04:05 2007 +0000 moved dog chain and net next to cat commit 18d789f8b7fefb723e962eb14f6b3ebf378982df Author: galt Date: Mon Apr 23 20:58:15 2007 +0000 added way to detect protein-psl customtracks even if the psl header is missing commit b1d8c5204202bfbce6260b8ecd61277205f3cd66 Author: rhead Date: Mon Apr 23 19:58:16 2007 +0000 Commented out horse credits section, as it is not complete and has errors commit 741d9708a7c980d844af45e536d547588890d95e Author: ann Date: Mon Apr 23 19:16:48 2007 +0000 lots of small fixes commit 9834f4c84180fab5f987ff1d05570ea526753a41 Author: ann Date: Mon Apr 23 19:16:09 2007 +0000 changed max and min for encodeNhgriDukeDnaseHs track commit bc6c29989cb04e78099694a8a4d0c4e97a493599 Author: heather Date: Mon Apr 23 18:23:12 2007 +0000 correction to name label commit f458897df804618c90f1d66dfacfd6b885782311 Author: hiram Date: Mon Apr 23 18:18:23 2007 +0000 Beginning genbank alignments commit 4cbb13474329b0dbb5f3070ee46bfd192a9a08e5 Author: archanat Date: Mon Apr 23 18:09:29 2007 +0000 changed refs to pubmed format commit 5986d377e7401ef9d32e4ea455ade5b39a098bc8 Author: heather Date: Mon Apr 23 18:02:34 2007 +0000 SV subtrack commit 45a4c074137b36cb133cfe30c91277c8fff15961 Author: heather Date: Mon Apr 23 17:18:34 2007 +0000 correction to name label commit 53da560ba9c89d584f0fd67ce7aa006ccf64d2a2 Author: hartera Date: Mon Apr 23 17:17:58 2007 +0000 Added Gencode RACEfrags track. commit 376fa809c1aa520cf37783eecf8976bc85e8543d Author: hiram Date: Mon Apr 23 17:08:44 2007 +0000 Move cb3 and ce4 files to iscratch, tweak priPac1, caeRem2 and caePb1 commit 8ee0edb3813f858173a74b66ad8aa53da0ad8cc0 Author: markd Date: Mon Apr 23 17:00:57 2007 +0000 added another test cases for db before query, with test disabled until it is handled commit 88a9fb9ad1a0ac9169e64a0a45a25dd6f98f89c3 Author: hiram Date: Mon Apr 23 16:56:19 2007 +0000 Adding priPac1, caeRem2 and caePb1 commit fb7b3825759576896650c638d6348c0bd46ee2db Author: hiram Date: Mon Apr 23 16:17:22 2007 +0000 Adding two nematodes caePb and priPac commit bdf9bb92351b66069d3042ff3454929523fb5f00 Author: galt Date: Mon Apr 23 15:00:23 2007 +0000 "Encode release log update" commit d3a0a399d9ed4bbf252f1f206fc9ff123a57783b Author: galt Date: Mon Apr 23 15:00:12 2007 +0000 "Release log update" commit 146dbd8fb926d8725f1eabf026131899467a268b Author: galt Date: Sun Apr 22 15:00:24 2007 +0000 "Encode release log update" commit 2c766d8275d0f294e4e20bdc19094c3a1e59f566 Author: galt Date: Sun Apr 22 15:00:13 2007 +0000 "Release log update" commit ec628b107608bdde00280a44eda9fc38b6c3baa1 Author: hiram Date: Sun Apr 22 05:16:32 2007 +0000 Initial view of multiz5way conservation track commit a0a2a1c4701d6d319fb8079532b299bb0973fd8b Author: hiram Date: Sun Apr 22 05:09:37 2007 +0000 First run at a multiz5way commit d5acbd1dec07a8d0fcdb640d740e67cb614d122c Author: hiram Date: Sun Apr 22 03:41:24 2007 +0000 Swap to caeRem2 complete commit 7bff042a7d2ac1a457b098dbda333aec77e3836a Author: hiram Date: Sun Apr 22 03:41:07 2007 +0000 All blastz runs are complete commit eaa6dc0c4a9fbb12cc1db60d157833010ba83fc0 Author: hiram Date: Sun Apr 22 03:40:22 2007 +0000 All possible pairs of blastz runs are complete commit cd53c71611618a87ea60eb48ec1c5b1ae81009e5 Author: hiram Date: Sun Apr 22 03:22:25 2007 +0000 All four blastz runs complete. commit 5802ac7dca59cb61559e2ff1d16e58dbf935485b Author: galt Date: Sat Apr 21 15:00:29 2007 +0000 "Encode release log update" commit 87d4a63d8f1c44ca6897a92ece2b320087df00fa Author: galt Date: Sat Apr 21 15:00:15 2007 +0000 "Release log update" commit 18fdc0e98d2230c48b6f86f80ddb798bc833487c Author: pchan Date: Sat Apr 21 04:49:38 2007 +0000 add function to support JGI gene track; add Matthias's function for wiki track commit 38453e5075089cff08c705e4f98cc6ce472e13aa Author: angie Date: Sat Apr 21 00:00:48 2007 +0000 When hgFindSpecFromRa recursed on include files, hgFindSpecPolish was called multiple times on the included records, causing too many backslash-escapes. Added a flag reEntered which is set during recursive calls, to prevent multiple-polishing. commit 5137469ce1367e947d4088a6e792fb0c474c02c3 Author: ann Date: Fri Apr 20 23:48:47 2007 +0000 added chromosomes line to encodeUcsdNgChip track commit 7f007414ca0a0ffbe2e9cfca1718ab239ea1ba6b Author: kent Date: Fri Apr 20 23:46:03 2007 +0000 Documenting latest change to blat. commit af62193cff27c54a7bd2222dbc8fd6e05589a43d Author: kent Date: Fri Apr 20 23:40:53 2007 +0000 Bumping version number. commit 82bc595e17822f28b11added63b635cd5ad5463d Author: ann Date: Fri Apr 20 23:28:17 2007 +0000 added chromosome list for encodeRna track commit 7c497129adecf8b689023a8ff600358ff0d7402c Author: ann Date: Fri Apr 20 23:24:13 2007 +0000 added chrM to chromosome list for encodeGisRnaPet track commit c7d0f8818f00321730992147c0d868bcf841b623 Author: markd Date: Fri Apr 20 22:54:58 2007 +0000 added new molType commit ff41647ddd141179a2648fbbca380049cbcceeeb Author: kent Date: Fri Apr 20 22:47:03 2007 +0000 Bumping blat version. commit eb9e4c09f6929d0dba137758cb91d436b9603a61 Author: kent Date: Fri Apr 20 22:44:11 2007 +0000 Taking out some debugging code. commit 069ae4469971846a6949d4380b831f62e4d0b4db Author: kent Date: Fri Apr 20 22:43:37 2007 +0000 Fixing a missing x3 bug in protein/dna alignments. commit 086df2e1dbeb7bba31a715629b430a947441cbbc Author: archanat Date: Fri Apr 20 22:31:08 2007 +0000 moved chain/net block to the organism level and added matrix to the chain block commit 5d9d00cdec6efd31b776b75f11f3c4040044279b Author: galt Date: Fri Apr 20 22:05:32 2007 +0000 fixed jax levels 5,6 commit 09f382c2b821342a33ccc37423789a015360ef1c Author: fanhsu Date: Fri Apr 20 22:03:26 2007 +0000 Updated to create non "-" consensus sequence. commit 1b5d92e73895795140b40d944ad36855e3634b9e Author: galt Date: Fri Apr 20 21:59:10 2007 +0000 fixing missing jax levels 5,6 for 13000 pix commit 6b7c3a037945b4a7de09e6d4057168541ca621e5 Author: fanhsu Date: Fri Apr 20 21:52:42 2007 +0000 Updated to generate none "-" consensus sequence. commit 4f3910c3910701824e92c46fcb007efe05758fb2 Author: fanhsu Date: Fri Apr 20 18:34:01 2007 +0000 Created gsidAaMsa.c to generate conservation wig file for GSID protein MSA. commit 3bc746def22b83e9b22176d9e37514fa7d086e93 Author: fanhsu Date: Fri Apr 20 18:32:49 2007 +0000 Added makefile. commit f7f7d0c91a29fe4ca4fffa06b030632bab5871a2 Author: ann Date: Fri Apr 20 17:20:40 2007 +0000 added line about how we run the web-based blat servers commit 549c54f6a2cd84cc4a6d18327f0d0feba3af8f14 Author: braney Date: Fri Apr 20 17:15:03 2007 +0000 added human proteins track commit bd46799d435a5d13f53be37983920a72b4f48745 Author: donnak Date: Fri Apr 20 16:29:04 2007 +0000 Updated medaka credits. commit 22310ca5ccc85fc2482880ecb46f39e027c41876 Author: galt Date: Fri Apr 20 15:00:33 2007 +0000 "Encode release log update" commit 0d3285dd9c0560f778f81d20ee5084362c61b4f2 Author: galt Date: Fri Apr 20 15:00:18 2007 +0000 "Release log update" commit 2d6b5b86c6942a957d30fd5b1508d6260c6f12a2 Author: braney Date: Fri Apr 20 14:42:44 2007 +0000 generate postscript from atoms. Experimental commit 7299398d4f5cb9f41f47448f4f27c1720789dcfb Author: braney Date: Fri Apr 20 14:39:40 2007 +0000 a utility to convert atoms into chains. Experimental commit 422b55999f73346e75fa5cd30c080f62fcb2e4e2 Author: braney Date: Fri Apr 20 14:38:42 2007 +0000 a utility to drop low scoring atoms. Experimental commit 77e7a5b1b0fb46995869d22fa23aa1608c9331e3 Author: braney Date: Fri Apr 20 14:36:33 2007 +0000 no more spanning gaps. Experimental. commit e94b051d970438b9d62e399b12ecc51e130e93f6 Author: braney Date: Fri Apr 20 14:35:14 2007 +0000 some more changes. Experimental, no review necessary. commit 27fb2e590039189cd5435f2e8dd9fa48e174d292 Author: hiram Date: Fri Apr 20 05:43:55 2007 +0000 Finished off cb3, now working on caePb1, and catching up some older ce4 business commit 5738051a11f2e4e4d756e26820fbea136e292cd3 Author: markd Date: Fri Apr 20 04:37:44 2007 +0000 move filtering of non-coding to load time; filter invitrogen bogus cDNAs, don't let STS into mRNA track commit d5f26df7394fb9f91ba39b276bf1f10fd1ad0627 Author: hartera Date: Thu Apr 19 23:22:11 2007 +0000 Added track handler for encodeGencodeGeneMar07 track. commit 7062a6d4e6ca062bb4ad571989529e11590a02f5 Author: angie Date: Thu Apr 19 23:08:07 2007 +0000 Instead of passing accession as position to hgTracks (genomeUrl), look up the actual coordinates and pass those along with track visibility and hgFind.matches. That zaps us straight to the intended ortholog, instead of digging up all search results for the accession. commit b66e84358c8f64fb2465953f4eea64dadda2af60 Author: angie Date: Thu Apr 19 23:05:19 2007 +0000 Added geneTable setting for querying position for genomeUrl (hgTracks) links. commit 7f586a149804d05c0d7a16526613ae30d2d7ba34 Author: fanhsu Date: Thu Apr 19 23:00:13 2007 +0000 Created gsidMsa to generate wig file from GSID MSA sequences. commit 096b3c8a0e658d1fcb51c5a928e202bb29c2b429 Author: fanhsu Date: Thu Apr 19 22:59:30 2007 +0000 Created makefile. commit 00dd89c5d4d1600413b09cdf8877dfd4e2c69a9a Author: archanat Date: Thu Apr 19 22:44:52 2007 +0000 added matrix commit 36e32dc22625bc247dbfb628a5e060c8e500ecfa Author: archanat Date: Thu Apr 19 22:38:45 2007 +0000 changed refs to pubmed format commit 12189c858fa05b043b8a83fa5e03945951be8f34 Author: donnak Date: Thu Apr 19 22:06:05 2007 +0000 Fixed up a URL in OH announcement. commit ca9c3baedc9a5eb2403b7a8f6907a8c70c4fad81 Author: donnak Date: Thu Apr 19 21:46:56 2007 +0000 Made a few edits to this page. commit 0d57f2cdd3de857a4e77bf69104b0eda7ec65e26 Author: hartera Date: Thu Apr 19 21:36:55 2007 +0000 Corrected an identifier name. commit 1e9dd298e72b2d1eef592d18a12b6197d9867fe3 Author: donnak Date: Thu Apr 19 21:25:51 2007 +0000 Edited medaka credits. commit 2a61c63ae8a82fd1a0dd1851a330ee7601185dda Author: donnak Date: Thu Apr 19 21:25:07 2007 +0000 Added Medaka to release list. commit 8dedb82b22ebdc70a40c26380b06173360f350f0 Author: donnak Date: Thu Apr 19 21:04:57 2007 +0000 Archived a few items. commit 07c1498b11070601c7830b7035bfac4ce5daee0d Author: donnak Date: Thu Apr 19 21:04:42 2007 +0000 Added OH seminar on GB at Experimental Bio 2007. commit 9f3abbf326a104c64b0e37bdcd06629219af8b31 Author: ann Date: Thu Apr 19 21:03:40 2007 +0000 changed one of two duplicate identifier names commit 5760bd0e154c572a35cfc112031a14c99553ae08 Author: markd Date: Thu Apr 19 20:22:59 2007 +0000 change mm8 to use global near-best filtering commit de8ab5ac01d060a68718ea2669cd4b3ecfae4677 Author: rico Date: Thu Apr 19 19:13:52 2007 +0000 Added mafAddQRows commit 37bf0d24ac6795c102de22847aaf595a3b96d92d Author: hartera Date: Thu Apr 19 18:48:16 2007 +0000 Minor edit. commit 9cd9e73510bfa7a3db0350c1391087f26294a802 Author: hartera Date: Thu Apr 19 18:37:13 2007 +0000 Removed duplicated line. commit 2bfd264ff241fd8de756921744c90673c6c53017 Author: fanhsu Date: Thu Apr 19 16:45:02 2007 +0000 Moved hiv1 to under GSID_DBS. commit 3ebe43b328bb80785475b15b8aa579a899049fca Author: fanhsu Date: Thu Apr 19 16:37:20 2007 +0000 Changed logic to search kgXref table instead of knownGene for mrnaID for KG III. commit 66c4c1c827b34128691df554d3a605d9f0bc0649 Author: archanat Date: Thu Apr 19 16:02:37 2007 +0000 converted refs to pubmed format commit 5ca7f0b1670f6f59bffb4ad8d459ff9879059804 Author: galt Date: Thu Apr 19 15:00:34 2007 +0000 "Encode release log update" commit 9eeb6505dca1ccb4dd7714e43fbbfb23902028b3 Author: galt Date: Thu Apr 19 15:00:18 2007 +0000 "Release log update" commit 91c47922dfc4cac65cfc23c21a64eeb6e6ee27f5 Author: fanhsu Date: Thu Apr 19 00:11:04 2007 +0000 Removed a debug fflush() statement. commit 824fe040a6ccae7cb8ca72873a56a14ecd2f331c Author: kate Date: Thu Apr 19 00:06:30 2007 +0000 Remove unused function commit b15e122bddee081cabc277861ee04111aaa08fac Author: archanat Date: Thu Apr 19 00:03:09 2007 +0000 converted refs to pubmed format commit cc85706470ad2a507f718eafac929694af0135ba Author: hartera Date: Wed Apr 18 23:20:54 2007 +0000 Changed short label for encodeGencodeGenePolymorphicMar07 subtrack. Added searches for the ENCODE Gencode Genes Mar07 update track. commit 1148b8a188fb6d6621c43c4b3c3d0891d42de47e Author: hartera Date: Wed Apr 18 23:04:19 2007 +0000 Added rules for the ENCODE Gencode Genes Mar07 (encodeGencodeGeneMar07) update track. commit a22a3f46523061f8793b037b01ba9a2442974116 Author: kent Date: Wed Apr 18 22:25:11 2007 +0000 Fixed spelling doner -> donor. commit 6f0c6ce72d68842461d9e5e0d6ce7f99ad4ff1df Author: hartera Date: Wed Apr 18 22:18:07 2007 +0000 Corrected typo for Gencode Gene Mar07 subtrack. commit d88386b3e61b524aecc72a61169a6a0cc956f4db Author: hartera Date: Wed Apr 18 22:16:10 2007 +0000 Clarified the origin of annotation software. commit be62db2acd1bebc15dbe33459469a949b33d21e8 Author: angie Date: Wed Apr 18 20:50:25 2007 +0000 Fix to spacing for sequence names that keep the -end suffix. commit 0d64c97ed0698d0256b24a3850fe890d22c2e1ac Author: lowe Date: Wed Apr 18 20:24:51 2007 +0000 Added jgiGene.o for new data type (for lowelab archaeal browser) commit 92d7798979f5847749baa095538a0e0303d39335 Author: lowe Date: Wed Apr 18 20:19:19 2007 +0000 New data type for lowelab browser: JGI track gene information commit 45a617c156636a61318f4635c692a5786fd27212 Author: lowe Date: Wed Apr 18 20:18:03 2007 +0000 New data type for lowelab's archaea browser: JGI gene annotation track commit 85d45ae6eee14e956a976f8edc535b8480311024 Author: angie Date: Wed Apr 18 18:55:19 2007 +0000 Added liftRMAlign.pl. commit d2a9b245cd9e622b12e8876c86bc79b6178dc092 Author: angie Date: Wed Apr 18 18:54:46 2007 +0000 Updated to handle output of RepeatMasker open-3-1-7. commit 555c6f27c4555ef231d4823faf02c0556abc51eb Author: angie Date: Wed Apr 18 18:49:35 2007 +0000 Rescuing from /cluster/bin/scripts/; this version worked up through RepeatMasker open-3-1-6. commit 8b6f0fbc84ddd1f58dc8986ebd13318502073640 Author: donnak Date: Wed Apr 18 18:35:35 2007 +0000 A few more edits... commit b234a66bb1d0b13ac1a165c7553d02f5094a865d Author: rhead Date: Wed Apr 18 18:32:09 2007 +0000 Added equCab1. commit dc65a5180397bb0ade5202d6a34f6aab9e1e2dbb Author: kent Date: Wed Apr 18 17:41:13 2007 +0000 Fixing link to proteome browser in mouse to stay in page and be green. commit d2230f3c8b867409f0877ec5513609d6c35bb827 Author: fanhsu Date: Wed Apr 18 16:56:46 2007 +0000 Minor adjustments. commit 1f0ba074edd71c121e17c9b29e0b79c2c8d8413f Author: markd Date: Wed Apr 18 16:31:15 2007 +0000 enable orfeome update on hgwbeta commit b5e8d05d8a5e08fac1d25015fa2ef2b504c9871c Author: markd Date: Wed Apr 18 15:50:16 2007 +0000 added new orfeome IMAGE ids commit e2240104620c27ceec7d32870191caa385aff9dd Author: galt Date: Wed Apr 18 15:00:36 2007 +0000 "Encode release log update" commit 7c1dc0acfb99fcaa334a7d673c3f186b840c6968 Author: galt Date: Wed Apr 18 15:00:19 2007 +0000 "Release log update" commit 6702c3504a242c92b482c9585b1c362dfb667edf Author: aamp Date: Wed Apr 18 09:50:50 2007 +0000 -bedPlus=5 was necessary for to lift hg17->hg18 switchDbTss. commit b6b0efedfe46bc53c89787a77d87d9e288f4dd15 Author: aamp Date: Wed Apr 18 09:42:41 2007 +0000 Mostly UI changes plus addition of pseudogene TSS classification column. Also, Switchgear should be SwitchGear in trackDb. commit 43d91dbb7ec0117d83d23692f03694ac2c259aad Author: donnak Date: Wed Apr 18 06:38:17 2007 +0000 Made a few more edits to this file. commit ab9933326df9a5d24d7a5e2b663458f562e50ddc Author: markd Date: Wed Apr 18 05:54:50 2007 +0000 prevent gbSanity from reporting errors about partations that are not being load commit bbf92b1eebdfd9b6e01fb5ded02dad28c08ca85c Author: markd Date: Wed Apr 18 05:21:17 2007 +0000 disable oryLat1 native refseq commit a2272810b81f06c396ef93e82c72c377c8bb832c Author: kate Date: Tue Apr 17 23:56:08 2007 +0000 Include update time for data in table for the track commit cf939a2707e73726fb3f974be6703df53d06d443 Author: hartera Date: Tue Apr 17 23:51:07 2007 +0000 Further edits to FAQ on EST orientation. commit 0059a19a19d3b58b9f1f8409e1c482d461c48b07 Author: ann Date: Tue Apr 17 23:16:42 2007 +0000 fixed up citations. commit 87024d87918fee19acd6a83376823fb26b2c3b51 Author: kuhn Date: Tue Apr 17 23:13:09 2007 +0000 hide EST track by default commit 7b89125ad91503fdb9a6e2aabb37d7df2498d21b Author: fanhsu Date: Tue Apr 17 22:29:22 2007 +0000 Changed knownToTreeFam to knownToTreefam. commit 3c438b97544b2223f4707afc775f756fd1e6b7c7 Author: fanhsu Date: Tue Apr 17 20:53:46 2007 +0000 Updated trackDb.ra for hiv1. commit 862b972325a85c37cabf6da7b775fa97b3e6c3f3 Author: fanhsu Date: Tue Apr 17 20:52:54 2007 +0000 Hide InterPro track by default. commit 180d13daf05b1fa42e22e5ba12fabb2e9492975d Author: rhead Date: Tue Apr 17 20:26:17 2007 +0000 Reordered the cnp subtracks so that all of the copy number polymorphisms will be grouped together. commit c466e3cfaf0ab8f7fcfafe87299a1aac95403d26 Author: rhead Date: Tue Apr 17 20:16:08 2007 +0000 Added one more table for the structural variation track. commit cd7812a0b693a45455d1e7a8488c89b4248be340 Author: fanhsu Date: Tue Apr 17 19:27:56 2007 +0000 Updated logic of checking subject. Do not turn on checkSelected unless the user has selected subjects. commit 07df8aa3d800205683d1c6066d4810734a230948 Author: fanhsu Date: Tue Apr 17 16:41:21 2007 +0000 Changed gsClinicRec to gsidClinicRec. commit 3bac1044c196eaee580ff744e66ca4056fbfb2df Author: fanhsu Date: Tue Apr 17 16:25:39 2007 +0000 Added a ";" after  . commit b122be2bf76f136eaf2a1b45d4d6f3cc7308060d Author: aamp Date: Tue Apr 17 15:08:26 2007 +0000 "New version number v157" commit 2d7620e585c039635fbb7f7617a0b767db71e8c7 Author: aamp Date: Tue Apr 17 15:04:00 2007 +0000 More improvements including a bug fix for minus strand SNPs. commit 43f8b18bd954df6e4c1a78373a29bca2bad24c90 Author: galt Date: Tue Apr 17 15:00:35 2007 +0000 "Encode release log update" commit aad00b864c7f87d586890499f0cff72e98970a8d Author: galt Date: Tue Apr 17 15:00:19 2007 +0000 "Release log update" commit a2923e76f9a3a2c73b40fbce9a1982c48ffdb539 Author: fanhsu Date: Tue Apr 17 00:07:08 2007 +0000 Added "Select Subjects" to the top bar for GSID. commit 40eadcbd3d3a06a74d3b9190a78921b83e17bf48 Author: galt Date: Mon Apr 16 22:55:12 2007 +0000 escape stuff for mysql commit c11bfaa1f39a97490e699dcbe36d5801db15b72a Author: angie Date: Mon Apr 16 22:38:46 2007 +0000 Added idXref setting to refGene. commit 0efa399b7cdc4b93a6fba034ba403db76ea25570 Author: angie Date: Mon Apr 16 22:34:30 2007 +0000 Updated FlyBase links to point to flybase.net not indiana. commit 10de87f28bc34edf35ea3eb7c20d147085379a03 Author: angie Date: Mon Apr 16 22:33:06 2007 +0000 Added -nobin to ldHgGene because the Bad test case causes the bin code to barf. commit 312f02db5e17628478be7508fbe7534c1ebc5e2f Author: tingwang Date: Mon Apr 16 21:22:38 2007 +0000 Label change for UCDavis ChIP Hits tracks commit 9378adb413400cb64e888fd1d391f5c8b76fe240 Author: angie Date: Mon Apr 16 20:28:33 2007 +0000 When warning user about pasted/uploaded terms that don't match anything expected, mention the alias table (idXref setting) if applicable. commit 185310cb9f5568716247e7b786dadb1d5a160c54 Author: angie Date: Mon Apr 16 19:40:08 2007 +0000 duh, forgot a cloneString. commit b16c9f584be9d175eab7442c351a832270920651 Author: kate Date: Mon Apr 16 17:35:45 2007 +0000 New tracks in progress commit 6f7d7080018406cd7c013270b0fc5b51240648ee Author: hartera Date: Mon Apr 16 17:33:44 2007 +0000 Added missing data for ENm011 region for the Mid, Late and Pan-S subtracks of the UVa DNA Rep Seg track. commit 7cc01c4039be305e8e5febf7b8ca7e7570b6e17c Author: galt Date: Mon Apr 16 15:00:33 2007 +0000 "Encode release log update" commit 1e49d388b4833851c5c7647542725d6c179ae9c8 Author: galt Date: Mon Apr 16 15:00:18 2007 +0000 "Release log update" commit ef9e205236e90fcfcdfaf28bd000aafe2a44b910 Author: fanhsu Date: Mon Apr 16 01:59:48 2007 +0000 Enhanced the logic of checking if subject selection is needed. commit d39c3dec49bbcc06fad1d28871faba3ea571bf47 Author: hartera Date: Sun Apr 15 21:51:26 2007 +0000 Gencode Genes track update in progress. Started notes on updating the UVa DNA Replication with missing data for the ENm011 region. Started an entry for the Gencode loci RACEfrags track. commit 807b166d8e029026128c426049201b4c8ef3c2ae Author: galt Date: Sun Apr 15 15:00:33 2007 +0000 "Encode release log update" commit 68fa49503ae9db4a7532293c6f27bb5d5498b416 Author: galt Date: Sun Apr 15 15:00:17 2007 +0000 "Release log update" commit ff8f0cbd8f3f80b3576b5013b3f2d3693e3d2566 Author: galt Date: Sun Apr 15 00:43:41 2007 +0000 handle special case polygons better commit 3f959a25e9fc879d264c092056a920f40dc7a137 Author: galt Date: Sun Apr 15 00:33:53 2007 +0000 adding hints to guide postscript output commit d43cc2df4eb21d49cac364d94ff3d063daacfe89 Author: galt Date: Sun Apr 15 00:29:47 2007 +0000 fixing closepaths: apparently it IS needed for strokes, but must not be used for fill commit 7656ce16142c8147f82a14ba6c2b7027db441995 Author: galt Date: Sat Apr 14 22:51:44 2007 +0000 added special case for horizontal or vertical lines which draws better - see hg17 hapmap LD dense where 4 lines are drawn to make a black outline around a colored box - also using the box routine to draw these lines fixes a minor problem of color-halo-ing caused by stroke-width of line not being exactly the right width at high zoom commit 14ebeaf530803a8aa2d5dd4176475c984003da9c Author: galt Date: Sat Apr 14 22:38:21 2007 +0000 moved pixel-specific code from psGfx to pscmGfx, made psGfx use doubles consistently,added new polygon psPoly of type double commit c8ae67ccc49693d91d8016277b9228d630ea5470 Author: markd Date: Sat Apr 14 17:07:27 2007 +0000 added hashMustRemove, removed warning, removed duplicated code commit 04118fe35ac7126fad4831d31aa55d1af0a840cb Author: markd Date: Sat Apr 14 16:38:52 2007 +0000 wrong script being used on sat updates commit 2e4cefd583f74864d8c3d54db4fedbfda7a243e2 Author: galt Date: Sat Apr 14 15:00:36 2007 +0000 "Encode release log update" commit ed91b3500ad684a1c642f0ab2f12cb4c96c10b34 Author: galt Date: Sat Apr 14 15:00:19 2007 +0000 "Release log update" commit bcbceb759b496a32440bc0cf6b897305868db913 Author: hiram Date: Sat Apr 14 04:22:55 2007 +0000 Finish off the re-work of the annotated maf's commit d169ee3a5af39dc0a43d3c891c617f630bed8027 Author: kate Date: Sat Apr 14 04:12:49 2007 +0000 Fix Mammal Cons entry commit a19e255c00ab43c02103c58c44cbbfc25a70853a Author: kuhn Date: Sat Apr 14 03:50:53 2007 +0000 swiveled tree branches to put medaka on top commit 35951a982b40d71a227c09b897c333e070ace116 Author: markd Date: Sat Apr 14 02:42:59 2007 +0000 force reload missed gbSeq entries commit 608792f3b4adde9bf108e1cf4c20268d6bb32444 Author: kate Date: Sat Apr 14 01:10:55 2007 +0000 Add phastCons for 28way commit a130f031e2ec908cb010a23714e2b4cbc0a880e3 Author: kent Date: Sat Apr 14 00:29:47 2007 +0000 Adding a blank line at bottom to make things look better to Donna. commit 8426297f8994383f1bc83fbfd85abbd129a2b2fd Author: donnak Date: Sat Apr 14 00:16:30 2007 +0000 First pass at editing this...a bit more to do after the weekend. commit 00de61fd2b15e6dedbb3f2baa9c06a752d3a5d28 Author: hiram Date: Sat Apr 14 00:15:26 2007 +0000 genbank reload done commit 6205ed55bf422ffb7b91894332fa9601610b0290 Author: hiram Date: Sat Apr 14 00:14:10 2007 +0000 Properly annotate multiz5way mafs, fixup ctgPos2 and gold tables. Fixup ensemble tables so everything matches commit d19f7947c699407a868089443e34b7bced386213 Author: hartera Date: Sat Apr 14 00:13:11 2007 +0000 Added rule for affyZonWildType table for affyZonWildType identifier. commit 21449e84ef9092d859c2dde0d2c5844c85abc6d7 Author: hiram Date: Sat Apr 14 00:12:07 2007 +0000 Adding a blat server commit 5b6e3b532fe07d06e73852f5865017be429748f0 Author: hiram Date: Sat Apr 14 00:11:22 2007 +0000 Create liftOver from fr1 to fr2 commit 26dc332dca1335b3fd060bbacc38aac575ed5ee4 Author: hiram Date: Sat Apr 14 00:11:04 2007 +0000 Made 11.ooc file for blat to do liftOver to fr2 commit 6c89c1200928c581a252b11ab9a15a361df3d3d0 Author: hiram Date: Sat Apr 14 00:10:41 2007 +0000 Making downloads directory commit 26cd4a0dfe0bb0a50872cb82bffecd05f340d275 Author: hiram Date: Sat Apr 14 00:10:09 2007 +0000 Genbank rerun to get xeno refseqs, caeRem2 chain and net, downloads, fixup chrM_gold commit a24b095c78c1f2230f64a05c8e15b2c3859defe9 Author: hiram Date: Sat Apr 14 00:09:02 2007 +0000 cb3 swapped chains and nets placed on caeRem2 commit 2472eb2eff5050255b1f18f0c6b61f62a1eb7fe2 Author: hartera Date: Sat Apr 14 00:02:25 2007 +0000 Don't need to free this item here. commit 3e5d9c4f48b22101d2ccfd06cc7097d469d7c09e Author: angie Date: Fri Apr 13 23:36:04 2007 +0000 Use flybase.net instead of old indiana address (thx Ann). commit 0d5e3cb22f53249b04e4ad57de9cc4b07d41b96b Author: kuhn Date: Fri Apr 13 23:25:16 2007 +0000 adding html files for chains and nets back to horse commit 2c66f981bff4708403ea5e25829eabbda8997837 Author: hartera Date: Fri Apr 13 23:24:05 2007 +0000 Added rules for the affyZonWildType and other Affy Zebrafish associated tables. commit ae8651b1b0d5c3c23625b097bddc015b44ead3fb Author: aamp Date: Fri Apr 13 23:13:58 2007 +0000 SNP information outputted on CGAP SAGE track. commit 034052373fe800bd993f559cafb5a32f09181f9a Author: hiram Date: Fri Apr 13 23:05:57 2007 +0000 briggsae cb3 can benefit from the refseq.mrna.xeno sequences commit 877a0c7d2e6945c02b9b00a319310d08de0041bd Author: kuhn Date: Fri Apr 13 22:58:29 2007 +0000 forgot quotes arount 'gap' commit 199e79400f7f3f75f7d51db5404c2ff4392e0c39 Author: hartera Date: Fri Apr 13 22:39:40 2007 +0000 Added Gencode Genes March 2007 update. commit 8d14936282fb37055555b66dbb12ec209d56b49c Author: hartera Date: Fri Apr 13 22:38:39 2007 +0000 Reformatted the citations. Minor edits. commit 9977e3ef76706f6f6d26689ab751b1531ee09980 Author: kuhn Date: Fri Apr 13 22:37:27 2007 +0000 added some examples that are not gap commit f1549bc7faea5eb0801420192dd79f5a8d9b55d8 Author: kuhn Date: Fri Apr 13 21:57:38 2007 +0000 added type to list of fields in output for manual checking commit b0430294aa8fb336cb28361be860ce05a54e8cce Author: kuhn Date: Fri Apr 13 21:54:07 2007 +0000 added level to list of fields in output for manual checking commit 33adf0769bfae090b3d3ff55a3059203c44ad081 Author: kuhn Date: Fri Apr 13 21:33:29 2007 +0000 fixed a capialization error on lizard commit d279f3f19a4ed0e0731a78998f5b53e30b41c07a Author: kuhn Date: Fri Apr 13 21:31:46 2007 +0000 fixed a ref to horse by dropping the 'one' at the end and added lizard and the new worm, ce4 commit f43ed925fe23a4ae9076fce060e417b1c04c312d Author: archanat Date: Fri Apr 13 21:20:25 2007 +0000 changed the order of organisms commit 995462f17817026c812b281ead004f38d9859308 Author: kuhn Date: Fri Apr 13 21:14:20 2007 +0000 added horse to the lists commit 5da5459e7fc7d7f76ed4bbb7eef524c018b07522 Author: hiram Date: Fri Apr 13 21:03:01 2007 +0000 Reduce vertical space, using imagemagick display to chop vertically commit 89b05d5d23f44c63487d41a7b4bb0ed275eacb3a Author: rhead Date: Fri Apr 13 20:56:25 2007 +0000 Fixed broken link to Robert Geisler at Max Planck Institute. commit 8aadc0ac133660df237cb3662cac0067474c1e55 Author: galt Date: Fri Apr 13 20:47:55 2007 +0000 removed redundant closepath that is creating artifacts when viewed at high-res. The artifact looks like a little hook at starting vertex of the polygon. It is redundant because we have already closed the path by returning to the EXACT starting point. commit 9f0832d9780a86e549b9e9c9b73ae4b16c8123fb Author: hartera Date: Fri Apr 13 19:55:15 2007 +0000 First draft of Gencode Genes March 2007 update description submitted by contributors. commit 269a140f763832a9f3aa5e89b9e60d51e884679b Author: hiram Date: Fri Apr 13 19:19:01 2007 +0000 Initial file contents commit 8ba815e472b56dd8e3bc34ddacf8385c8e2d744a Author: kate Date: Fri Apr 13 18:55:39 2007 +0000 Change diagnostic output to go to standard error commit 12a1ac39698d7fb412f08e2499a28929b191b857 Author: giardine Date: Fri Apr 13 18:55:05 2007 +0000 Updated McDonald Kreitman track, will delete old after comparisons done. commit 69814fc49383875352b44a90824badbfb1129f95 Author: markd Date: Fri Apr 13 18:32:47 2007 +0000 fixed type cases that caused GCC optimizer to complain about breaking strict-aliasing rules commit d63b812284786566bbc2d2dcb48452ab2d67f146 Author: donnak Date: Fri Apr 13 18:24:05 2007 +0000 Added rhesus macaque paper. commit d26c430bcb1e161428e74c3a4271288962d3c44e Author: ann Date: Fri Apr 13 18:20:28 2007 +0000 Cleaned up titles (they were appearing twice). Cut off lines at 80 chars. Fixed broken links in D_melanogaster file. commit fc212a7f4f33781c9b3517dc204e42e9def053b0 Author: fanhsu Date: Fri Apr 13 18:00:27 2007 +0000 Added EquCab1 to chainDest. commit 3b36bc5f471dedc4c47f5ae7e4fff7f85fd9110b Author: ann Date: Fri Apr 13 17:28:37 2007 +0000 added link to flyBase commit 365f10cef213234c9497362bc759c3cf91747f3f Author: ann Date: Fri Apr 13 17:26:10 2007 +0000 updated link from flyBase 4.2 to 4.3 commit 9fcf6c67f4ad29ba381b2f595cfe49c1c9cdc7a7 Author: markd Date: Fri Apr 13 16:36:02 2007 +0000 made -bin the default on genePred tracks commit c62414f94a49a86b34321060da3f07043febcfdb Author: archanat Date: Fri Apr 13 16:32:35 2007 +0000 added oryLat to xenoRefGene definition commit 4f4aefe64ec840cf0205ae9abd6870d55a428bae Author: rico Date: Fri Apr 13 16:30:58 2007 +0000 added info about "q" lines commit 27fb1dcad48c166abb52508b6a4b0207348c5722 Author: fanhsu Date: Fri Apr 13 16:21:13 2007 +0000 Added Treefam links. commit f54e8b341e19f5a156470462f02ec441aa62dc90 Author: fanhsu Date: Fri Apr 13 16:16:01 2007 +0000 Added Treefam links to KG details page by creating the knownToTreefam table. commit 3790f392992de60c092bf82ee5ca08c9d7f03916 Author: galt Date: Fri Apr 13 15:00:38 2007 +0000 "Encode release log update" commit 307fac365e87799799e0d527f2c27a56057b520f Author: galt Date: Fri Apr 13 15:00:20 2007 +0000 "Release log update" commit 51d0a31e46ed19eb1e67bb4b404e5fc334b11cc6 Author: markd Date: Fri Apr 13 05:58:24 2007 +0000 removed end index and key length restrictions on genePreds commit ae8f701054e838d00a1c925566c2ea06ccf807f0 Author: aamp Date: Fri Apr 13 05:50:38 2007 +0000 Fixed bug where switchDbTss track wouldn't load anything on a clean cart. Setting the score filter to anything > 0 would load the items. Also added code to warn if the score is negative and delete cart var in that situation. Since this is a general function, it'd probably be best to allow negative score filters at some point. commit 06bffd4632fe53deafb7c6a5e5c18e325a23a464 Author: markd Date: Fri Apr 13 05:26:30 2007 +0000 fixed off-by-one setting frame from gtf commit ff0d55d457c0dd54a990571379584874164ca015 Author: kent Date: Fri Apr 13 03:19:31 2007 +0000 Separating model info from methods section per Chuck's suggestion. commit 492ae5cb09fdc27c1522368fbab672bb139ed972 Author: angie Date: Fri Apr 13 01:20:58 2007 +0000 When making a View Table Schema link, if parentWigMaf has been passed in directly by CGI, use that as the track name for hgTables. commit ca0e54be15538f00ee324d6d5db108be5cc593ca Author: kuhn Date: Fri Apr 13 01:19:45 2007 +0000 added hosre chains and nets commit fd8150ef35916c25212fb88b16280fe979bd382f Author: markd Date: Fri Apr 13 00:10:57 2007 +0000 renamed orfeomeMRna to orfeomeMrna commit 0cdecc5c1caa9033bc1b6db91beca917534a84f2 Author: markd Date: Fri Apr 13 00:05:32 2007 +0000 use genbank-specific BIN/LIB dir make vars commit 0da9104227d830f8e5ca2d458799dadba1114464 Author: hiram Date: Thu Apr 12 23:52:20 2007 +0000 Ordering of chains and net properly (for ce4) according to http://www.its.caltech.edu/~wormlab/briggsae/phylogeny.html commit fc0806ca789588ceaf406d6fde6248ed92117837 Author: hiram Date: Thu Apr 12 23:48:25 2007 +0000 Properly position the chain and net tracks according to http://www.its.caltech.edu/~wormlab/briggsae/phylogeny.html commit 922d7582b2441fa5472a13a8f45604d1c4eb43dd Author: hiram Date: Thu Apr 12 23:31:53 2007 +0000 Correct stats and correct links out from the photograph commit ab5bfa4d3dae0a6fbaf9931dd458131e56f7209a Author: hiram Date: Thu Apr 12 23:30:52 2007 +0000 More correct statistics on this one. commit 2a03bdb1d6ebd91c41bbcc1bd3a91c3eaff25121 Author: aamp Date: Thu Apr 12 23:25:35 2007 +0000 Forgot to initialize sr. commit 44c16324a1087ff06e0382f22b9794b309bbf48f Author: kuhn Date: Thu Apr 12 23:24:03 2007 +0000 made refGene track visiblity = pack so default position looks better. commit 7a03885cb6543dee95f5419be6949f3aaa988e0f Author: heather Date: Thu Apr 12 23:15:54 2007 +0000 temporarily comment out printCnpSharpSampleData commit 190190a6ec8f60580934e61f4f8a42048927b60b Author: tingwang Date: Thu Apr 12 23:10:25 2007 +0000 new description page for UC Davis ChIP Hits commit 4e2b78deb6c462d44b6c6ca6cdfae020855a6096 Author: aamp Date: Thu Apr 12 22:57:30 2007 +0000 Added a comment. commit fdbe77eedb3c9e67bb5863517e2368e0c225f317 Author: aamp Date: Thu Apr 12 22:54:05 2007 +0000 Utility to find annoying SNP clusters messing up SAGE analysis. commit 624588a2b245332676c23f40446ff0e5707e85a7 Author: ann Date: Thu Apr 12 22:53:18 2007 +0000 changed score for negative items in tables from 100 to 200 (so we could actually see them in the display) commit 3a5dc50ba8f9eca2d048b0de5b38420bba88dc42 Author: ann Date: Thu Apr 12 22:52:16 2007 +0000 edited entry for vistaEnhancers track. I changed the score in the table from 100 to 200 (so I edited this doc to coincide). Galt agrees that this is a good change. commit dedbd2378591cec54d8ac16c526ffffc362c2d1a Author: angie Date: Thu Apr 12 22:48:33 2007 +0000 In sqlRandomSampleWithSeed, perform the uniquifying and randomizing on a limited-size temporary table to avoid thrashing on mega-row tables. commit 68389c4c018f7181f9fe72236eecd3c94d412a90 Author: ann Date: Thu Apr 12 22:44:35 2007 +0000 adding vistaEnhancers to tablesIgnored commit 5123c133c3812c04ea7f8b76ec3bafad8777e9e9 Author: kuhn Date: Thu Apr 12 22:27:21 2007 +0000 added some whitespace around image commit 19e607679b212fe2418bd7d4704aa806bb8f59ae Author: kuhn Date: Thu Apr 12 22:25:13 2007 +0000 beefed up the description commit b5335c8d6edea263fee7e65e75bfb3a11593e39d Author: markd Date: Thu Apr 12 22:24:45 2007 +0000 rename orfeomeMRna to orfeomeMrna for consistency commit b96f6f5738d05436b1b5797ab09a16cd77acfc3a Author: fanhsu Date: Thu Apr 12 22:24:14 2007 +0000 Added "assert(exCount > 0);". commit cf762147f6e88a518bc0d52cdec81b31f336b6c3 Author: kuhn Date: Thu Apr 12 22:23:22 2007 +0000 slight rewording to include idea of training set. commit 6c45a5878031fd7213ff104f2ae582210dd0c847 Author: fanhsu Date: Thu Apr 12 22:22:29 2007 +0000 Added " assert(*exonCount > 0);". commit 2fb94494b4492f7963ee9631d64aea62fe23e43a Author: markd Date: Thu Apr 12 22:21:18 2007 +0000 added oryLat1 xeno refseqs commit cec6f126672799c022ab9b403bb67438c4fbe7ec Author: fanhsu Date: Thu Apr 12 22:17:57 2007 +0000 Changed sprintf() to safef(). commit 07192f0ba55e74f0623ef2fde7d3a4f2ed67c1a8 Author: angie Date: Thu Apr 12 22:12:25 2007 +0000 Added new setting idXref to tell hgTables to look here for identifier aliases that may be pasted/uploaded. commit ae0ab02eaf80baaa43f69054c24b7edb67650559 Author: angie Date: Thu Apr 12 22:04:00 2007 +0000 Enhancements to support search on gene symbols: 1) On the paste/upload pages, tell the user what table & field their terms will be searched in, and show examples. 2) Check the submitted terms and warn the user if some of them don't exist in table.field. 3) Support a new trackDb setting, idXref, so that another table can be specified as a place to look up alias terms and map them to terms found in table.field. commit 0b63ca2c707b1288e151f298f336d30096b9bcb6 Author: angie Date: Thu Apr 12 21:57:30 2007 +0000 Use getIdField() (instead of duplicating some of its logic) to determine whether or not to offer identifier paste/upload. commit bb5dea98a98803eaa8af44c4060729d864d04a20 Author: angie Date: Thu Apr 12 21:55:54 2007 +0000 In getIdField, default to first field if this appears to be a non-positional table. commit 2cae082ac49bd8f71f21871a18e854dcf50b9337 Author: ann Date: Thu Apr 12 21:46:44 2007 +0000 minor edits. commit f4d0724af8c1e78a9bf1f117f2f0db7deb0ab6ed Author: angie Date: Thu Apr 12 21:36:56 2007 +0000 Prevent segv for wigMaf tracks-in-progress that don't yet specify wiggle table. commit e3e08c476c4124c928e839e81b688ba6c177cdee Author: markd Date: Thu Apr 12 21:28:15 2007 +0000 enabled oryLat1 xeno refseq commit 164aa5fd0e4baa388abb08a58de60133e9e478f1 Author: ann Date: Thu Apr 12 20:51:19 2007 +0000 added chopBefore to two augustus rules (OKd by Mario) commit 0ea46ad9e320adca8ea7585c77444e54722da2b9 Author: ann Date: Thu Apr 12 19:51:19 2007 +0000 Fixed citations, grammar, subtrack headings, and display conventions. commit a6d6cfb29b11de730d57002cb1ab506383573957 Author: rico Date: Thu Apr 12 18:54:23 2007 +0000 Modified error message when "q" or "i" lines don't match the previous "s" line commit 2ef7848b2032d9712281d13b9052444ccf714327 Author: heather Date: Thu Apr 12 18:44:59 2007 +0000 add sv tables commit 4725b3a07015217750e9d2bebd29810edb0ef911 Author: heather Date: Thu Apr 12 18:37:57 2007 +0000 alphabetical order; encode at the end commit 00b3bcd8ae2dfc5e2cabe075301bcc6af4f9f2ba Author: heather Date: Thu Apr 12 18:28:30 2007 +0000 if ortho data not available, then filters aren't used commit 5cf58e3aeaf12f82cf703428265f978c3a6e346e Author: kuhn Date: Thu Apr 12 18:18:04 2007 +0000 fixed the drop-old-directory part, which was choking on the wildcard. didn't choke on the command line, only in the script commit 5af04bec7d09c6f330cf250f84c8fe7a5a718690 Author: markd Date: Thu Apr 12 18:15:26 2007 +0000 added oryLat1 commit 44e1aaf9083fa249adf141d6238cdf9c5f6609be Author: markd Date: Thu Apr 12 18:15:14 2007 +0000 remove commented out entry commit 9e267b3d284dde82eefaed6dcfff0368dba7afa4 Author: heather Date: Thu Apr 12 17:53:41 2007 +0000 tweak commit 19cbe45bc09da9d0976e708ba52628c884642447 Author: rico Date: Thu Apr 12 17:40:06 2007 +0000 index a qac file commit 57e1f29516435001603d9cf06a85af47145fde60 Author: giardine Date: Thu Apr 12 17:34:41 2007 +0000 Added description of last updates to Locus Variants track commit f0cc2f32bef12b8d1c21b57a931d35662a226fff Author: fanhsu Date: Thu Apr 12 16:59:29 2007 +0000 Added knownToTreefam.sql. commit d902a9132d1352ab12890b2157d6efdf196719f0 Author: rico Date: Thu Apr 12 16:56:04 2007 +0000 Added comments, attempted to transform code to follow UCSC style guidelines commit f5514fb94b6390d23832a8d531c224652f496731 Author: ann Date: Thu Apr 12 16:42:50 2007 +0000 Done messing around with Conservation track. Set visibility back to pack. commit 28ef4223a4afd1c061b98a44d1279cbec4cc11b2 Author: heather Date: Thu Apr 12 16:41:36 2007 +0000 color tweak for hapmap snps commit 8083b02e914e35642159278be13359536ef7808f Author: galt Date: Thu Apr 12 15:00:38 2007 +0000 "Encode release log update" commit 74ed5a26bda781b8aa521d0ba5eb7fc8d24021fa Author: galt Date: Thu Apr 12 15:00:20 2007 +0000 "Release log update" commit 52b0744e80d32add10696a1a3d10124482759ac3 Author: aamp Date: Thu Apr 12 10:00:33 2007 +0000 Forgot another makefile. commit e0e6612dfec3a7038fd2c9dc6861b6f75c33ec34 Author: aamp Date: Thu Apr 12 09:53:34 2007 +0000 Stuff for SwitchDB TSS track on hg17/hg18. Forgot the big lib makefile again. commit 3e4f78e1c94da69cb9acb87d0bb6411f209b10bd Author: aamp Date: Thu Apr 12 09:52:42 2007 +0000 Stuff for SwitchDB TSS track on hg17/hg18. commit 19097624ff209edc3250be2a960a6ee55ab06eb4 Author: kent Date: Thu Apr 12 09:12:28 2007 +0000 Restoring line between bacEndPairs in squished and dense mode. commit 0cd245576d99496ae80ffcab4418280452b11291 Author: markd Date: Thu Apr 12 05:12:38 2007 +0000 fixed bug were frame is incorrectly convert from GFF/GTF files commit dc87b1d5cda650dd0a7c62d8eda6edd2aaa0e8f7 Author: hiram Date: Wed Apr 11 23:53:19 2007 +0000 Use gamma 1.7 instead of 1.5 for a lighter image commit ee1fd5743227c8f508c2059b2417a52fba7dd7fc Author: hiram Date: Wed Apr 11 23:50:53 2007 +0000 Reset default position instructions after they were all lost from hgcentraltest dbDb commit bf1aafb6702203b67ae1e9406ac1f5e6c80e08dd Author: kent Date: Wed Apr 11 23:50:38 2007 +0000 Removing bogus line in the middle of connection of bacEndPairs. commit 32ec4f9c4b1ae29ffb40ea97e85738d62141602a Author: hiram Date: Wed Apr 11 23:50:18 2007 +0000 Reset default position instructions added after they were all lost from hgcentraltest dbDb commit be609806d191f09dae7ce5de46830ac223a40187 Author: kent Date: Wed Apr 11 23:50:01 2007 +0000 Updating BAC end pairs and fosmids to make connecting arrowheads darker. commit d755b0cf97b8e2a38056f77e92bc28627c922705 Author: donnak Date: Wed Apr 11 23:49:23 2007 +0000 Added Cory to fr2 credits. commit e265a7f52061bc46c29351334a0fada50b11ea90 Author: donnak Date: Wed Apr 11 23:41:33 2007 +0000 Fixed typo. commit 1deef3bb4009676cb523df92c68d19f68134e011 Author: ann Date: Wed Apr 11 23:27:45 2007 +0000 temporarily set visibility of Conservation track to hide (while I mess around with it on hgwbeta) commit d38f2a148552bf3fa039fad3939790f4aefca566 Author: hartera Date: Wed Apr 11 22:51:19 2007 +0000 Organised table so that the strains and time points are in the same order as the track display. Removed time point numbering. commit eae20181a8973ab8cad782022e9951b29f132e4b Author: galt Date: Wed Apr 11 22:47:33 2007 +0000 adjust to use pixel-centered coordinates with explicit pixel-fat commit e5bd3de087c40a1233c02b39a4887b6b95934a7b Author: galt Date: Wed Apr 11 22:43:40 2007 +0000 bug fix - set initial clipping region only AFTER the EPS header has been written commit d871291bb17f6faf8e18de89502a3e2e919cbe88 Author: kent Date: Wed Apr 11 22:43:12 2007 +0000 Seems to work. commit 727a0e28bce8d7cde97086175d5dbcf5a6f8451f Author: donnak Date: Wed Apr 11 22:05:21 2007 +0000 Uncommented fr2 announcement. commit dfcaa178ed803de1ad2c0ebef15e335377b1bccf Author: kuhn Date: Wed Apr 11 22:03:22 2007 +0000 move link over to title of paper rather than the reference itself, to conform to our standard commit 1ca78500d030fcdaa68b1f5c598f55fd0b1b9f71 Author: kuhn Date: Wed Apr 11 21:58:34 2007 +0000 slight rewording and fixed wrap on encoded email address to remove a space before the edu commit ec350ae2db36652f04a545c5be9594878f0abf9d Author: heather Date: Wed Apr 11 21:33:32 2007 +0000 edits for SNP array commit 4413a9a685dfa2c1aa97e88c4b601c611f39ce08 Author: heather Date: Wed Apr 11 21:32:58 2007 +0000 split affy SNP array; remove illumina (expecting better data commit 6f12419543669f9f2067926ea14756a5fdfc1e32 Author: kuhn Date: Wed Apr 11 19:14:27 2007 +0000 oops. had to remove the .html from the file name for gvPosOld release beta commit 0a722efe6c906151c602011055153a00951a44a3 Author: kuhn Date: Wed Apr 11 19:11:23 2007 +0000 removed latest changes (r 1.26) from gvPos.html andcopied into gvPosOld.html to support beta while waiting for data to catch up commit b82f5678f80931a8abf8697564a6eb0557d29ac5 Author: hiram Date: Wed Apr 11 19:06:07 2007 +0000 Correct scaffold and contig count on chrUn and clarify number of bases on chrUn commit c2c409c3960312503b8dcaf4092030e4dcc54250 Author: kuhn Date: Wed Apr 11 18:56:04 2007 +0000 added beta block to keep gvPos.html diffs from going out. will be using gvPosOld.html on beta commit 690907748bfb4fa7cb2bf734f3d3f2ed5475724c Author: hiram Date: Wed Apr 11 18:34:55 2007 +0000 Only two simple types of gaps on this fish commit 23629e3bf057f07bc4b8351e7c0c4b9c68e9cefd Author: heather Date: Wed Apr 11 18:25:10 2007 +0000 move encodeRna commit a530df85a182a8d2e72313bc91a5fa0c38cae7ee Author: aamp Date: Wed Apr 11 18:24:05 2007 +0000 Put the functions unimportant to the basic algorithm in a separate module. commit c93a2f8b3e4bd87969d2b472feb1efb2fdb23bda Author: aamp Date: Wed Apr 11 18:11:26 2007 +0000 Pretty much a rewrite of much of the big algorithm parts. commit 5100e4906f006fe8af2f7b0bd7b6b17d8ae1cff4 Author: rico Date: Wed Apr 11 17:59:08 2007 +0000 New code to add quality data to mafs commit e6debc94ee4f6b890819d1679ecfed4c7e5944ea Author: rico Date: Wed Apr 11 17:56:45 2007 +0000 Added support for "q" lines commit 176d74af1cb1fd0d6805dd174ae23bd8c0e25891 Author: rico Date: Wed Apr 11 17:56:29 2007 +0000 Added support for "q" lines; added error message when "i" lines are out of sync commit f98d58d85343696e24fc5e2325565d9119aa7138 Author: heather Date: Wed Apr 11 17:34:56 2007 +0000 encode stanford NRSF color by strand commit 110b4d7e2324fdf62ba745526e2fac823eeaf08b Author: kayla Date: Wed Apr 11 16:58:05 2007 +0000 added fr2 commit 74413cb4c8829210e935efe4f46d2e79793321fa Author: markd Date: Wed Apr 11 16:53:42 2007 +0000 loaded N-SCAN track for equCab1 commit 57779be362d6cde7477076b01de6e030caa94230 Author: markd Date: Wed Apr 11 16:09:04 2007 +0000 added public orfeome track commit d47f847c88f790e0822268847adf20fc236a8d3f Author: galt Date: Wed Apr 11 15:00:37 2007 +0000 "Encode release log update" commit b3df5d714208f4c80d5e5f9899fa722bf25712f9 Author: galt Date: Wed Apr 11 15:00:20 2007 +0000 "Release log update" commit fc8c70cb82f6e1395aa62e6a8fadbe70ab4ba9b1 Author: markd Date: Wed Apr 11 14:17:48 2007 +0000 enable orfeome load on hgwdev commit 38f0e3ae47c6a98311c13d212a0132451ef3368b Author: markd Date: Wed Apr 11 14:17:35 2007 +0000 specify tmp dir for orfeome load commit b498ce8088510c88a5076e491008c246185b11ed Author: markd Date: Wed Apr 11 14:16:46 2007 +0000 even more todo commit 8f427bd8a8ab5710b48301520cd4e903dc7a112f Author: markd Date: Wed Apr 11 14:16:33 2007 +0000 use correct db list for mgc commit a62b15b7226a9a9f684108b32f1ff89d7192e9b5 Author: markd Date: Wed Apr 11 13:53:11 2007 +0000 removed stray spaces causing parse to fail commit 7a2121d18b0e9a78243e8a85bc35fa67743e4782 Author: kuhn Date: Wed Apr 11 03:43:43 2007 +0000 set so it removes directories a year old, one month at a time commit 22431748135f01936985926120559f640e06a78a Author: donnak Date: Wed Apr 11 03:20:19 2007 +0000 Made a few initial edits to FAQ on EST orientation, but item still needs work. commit a9adda7fce3c1889ab288bb6d52c43e42fdb80d0 Author: rhead Date: Wed Apr 11 02:25:06 2007 +0000 Changed broken link to paper to a pubmed link. Updated citation format and standardized so that all pages look the same (changed 16 pages total). commit 7037628dd576d3f69bb5b36f8094b3fbdf29d539 Author: heather Date: Wed Apr 11 01:40:56 2007 +0000 cloned from hapmapSnps commit 56f9b8a06356177d9bce98cc6654c22efd674f5e Author: heather Date: Wed Apr 11 01:36:43 2007 +0000 correct comment commit 5ac02503dcc7994c4577956d3bd415f2160f9385 Author: heather Date: Wed Apr 11 01:34:23 2007 +0000 cloned from hapmapAllelesOrtho.as commit aabae4bada55eed5fcf37ca32c07acf57ed653bb Author: heather Date: Wed Apr 11 01:22:44 2007 +0000 small edits for hapmap snps commit 3be5d200a6afb20028add9f14dc3242522fbaef2 Author: donnak Date: Tue Apr 10 23:49:44 2007 +0000 Added announcement abt OH seminars. commit 9462b6e6ea647fdbb9926aa504af3e37e9301f3d Author: kuhn Date: Tue Apr 10 23:48:27 2007 +0000 fixed reference format. added TARGET=_BLANK to reference. added text describing the track and method more fully. expanded ACE acronym at first use. encode email address. italicized et al. and added period. commit ddb1fe727fcd8dc793b659f2aaa24a545d86922b Author: donnak Date: Tue Apr 10 23:47:39 2007 +0000 Uncommented fr2 release. commit 1a90b066b5424bcc3740a7a610c3a279293e0c0c Author: heather Date: Tue Apr 10 23:38:34 2007 +0000 change source URL commit 792510c6d8d8ac90ea5cf7964d90a12f1efcc47a Author: hiram Date: Tue Apr 10 23:16:01 2007 +0000 Remove references to the CleanTrash script and instead show the find commands commit 68be03725137f19ead5d4e418c35e99c0348c9da Author: donnak Date: Tue Apr 10 23:13:52 2007 +0000 Fixed typo. commit cd97edc42e69a132580326eeed9bd6e1fc416639 Author: heather Date: Tue Apr 10 22:36:41 2007 +0000 change some menu labels for hapmap snps commit 12ab781c09ad70082ec1260a3f3da0f76069d176 Author: heather Date: Tue Apr 10 22:36:14 2007 +0000 change some menu labels commit 7ed81395fdc7e0be23a468ac6d2b3732efbb8194 Author: heather Date: Tue Apr 10 22:00:03 2007 +0000 change from 'any' to 'no filter'; other edits for Brooke commit b51e5f32dd1b687ce7fb02adea03fdaa01737364 Author: heather Date: Tue Apr 10 21:59:47 2007 +0000 change from 'any' to 'no filter' commit 41a8d8ea62098b9b95e38c82912b98a7c9fe0987 Author: heather Date: Tue Apr 10 21:34:10 2007 +0000 ortho alleles in brown commit a81e87094f393456f44adb934e6bef339723eb79 Author: heather Date: Tue Apr 10 21:32:49 2007 +0000 use brown for ortho alleles commit 7a98551fabda8c336a210f1f1465ca630a6b1e61 Author: ann Date: Tue Apr 10 21:23:10 2007 +0000 added matrixHeader as needed commit a8b0bb6da53847162c22b1cad5fc90ec3afe4544 Author: kuhn Date: Tue Apr 10 21:12:51 2007 +0000 enforcing 80-char per line. explicated acronym, ACE. commit 0186432c6fa116cd9224abe5cdd0a5a497ccebd4 Author: heather Date: Tue Apr 10 21:06:47 2007 +0000 use http instead of sftp commit 28ec5c40369e712ed32af4c984113d6a8338cf5f Author: donnak Date: Tue Apr 10 19:45:33 2007 +0000 Attempted to rewrite an awkward sentence (tho the resulting sentence isn't particularly a work of art either!). commit 9d268bbb1e858a10bd63698a67d08aa30ee1ffd6 Author: donnak Date: Tue Apr 10 19:24:14 2007 +0000 Fixed up a few html tags and added a
at the bottom (for some reason, this page was hugging the bottom margin w/no padding...don't know why. commit f2652688904c420260125a1cfdf10b8148d5561c Author: kuhn Date: Tue Apr 10 19:18:41 2007 +0000 speeled 'addition' correctly commit 6f296d3e487113934bc6511f70205f817eade825 Author: heather Date: Tue Apr 10 18:46:03 2007 +0000 edits from review with Brooke commit 27ce2fad322665111f73b3aa67ade17927125413 Author: hartera Date: Tue Apr 10 18:42:41 2007 +0000 Added new subtracks for H9, IMR90 and K562 cells to the Duke/NHGRI DNase track. Removed two subtracks created by the old method. Started Gencode Genes update. commit aa84923d32afc0de4fe45deaab3fc9c68e8fb305 Author: kuhn Date: Tue Apr 10 18:38:02 2007 +0000 added hyphen commit d2ae88fa89a338635601cc89a5b0a34cbb232ceb Author: archanat Date: Tue Apr 10 18:17:33 2007 +0000 added oryLat to wgs definition commit 5fabe6d6e5b1b642403c7b388fbfd09def46e281 Author: ann Date: Tue Apr 10 17:28:19 2007 +0000 removed extra space commit dfdb5c8cff93fda167f97876a2152505c8785349 Author: kuhn Date: Tue Apr 10 17:22:14 2007 +0000 removed redundant assignment of urlPath commit e303670614074ec5ae045fa1ed78815aa5ec78f5 Author: hartera Date: Tue Apr 10 17:19:46 2007 +0000 Removed Old Method subtracks for GM06990 and CD4+ T cells and removed New Method label on remaining subtracks for the release alpha version of the Duke/NHGRI DNase track. Also added release alpha and release beta to each subtrack as appropriate for this track. commit ed363bec1278c43406091dddf1b75a68f481de31 Author: kent Date: Tue Apr 10 16:49:46 2007 +0000 Hiding dm2net and exonWalk by default. commit d080b23bb4e66052dc80b3e8fdf391b544a0e0d8 Author: kent Date: Tue Apr 10 16:47:20 2007 +0000 Hiding GAD track by default. commit a4b48e25d83636add26bf639fae9fd82a701f893 Author: kent Date: Tue Apr 10 16:45:52 2007 +0000 Hiding Eponine by default. commit f35ed510d65d230093235a8ba3d6986d100de258 Author: markd Date: Tue Apr 10 16:32:42 2007 +0000 added add/remove icons commit 18614c731a7bea94f555d2c0e3df20a5151132cc Author: markd Date: Tue Apr 10 16:29:53 2007 +0000 added add/remove icons for hgGene commit e07d3b0a74b7732f6fb61a3fba67acd8c65f903c Author: kent Date: Tue Apr 10 15:40:38 2007 +0000 Making a bunch of Fan and Galt additions use $db and $tempDb rather than hg18 commit cb1e0b3d4f12d52e32956a0b3b825f3b27105ce6 Author: hartera Date: Tue Apr 10 15:24:33 2007 +0000 Removed all references to Old Method as removing subtracks done by the old method. The New Method is now the current method. commit 348651bf1dcc9168cea2a8360f419db969f3b8c6 Author: galt Date: Tue Apr 10 15:00:30 2007 +0000 "Encode release log update" commit e556396b414f43539fd2dfc7cabd7ef2f2c4e109 Author: galt Date: Tue Apr 10 15:00:16 2007 +0000 "Release log update" commit daf040cea0c6de710e8c238aac20a6da690a2f94 Author: galt Date: Tue Apr 10 07:57:15 2007 +0000 moving text up by one pixel - not as much better as hoped, returning to original behavior commit 8d36b9d6bf874f08c71b8d21b7229eb4dba02fe9 Author: galt Date: Tue Apr 10 07:51:18 2007 +0000 moving text up by one pixel seems to improve the appearance commit 869f2b67ab5b772046bc2b879105432dfc528099 Author: kent Date: Tue Apr 10 07:48:47 2007 +0000 Moving description of txInfo fields to a separate page. commit 5547910bc315af6999610c714ddacbe669a1c869 Author: galt Date: Tue Apr 10 07:48:33 2007 +0000 a little more cleanup of clipstack stuff commit ee8ef41169cec7671497ce5e9bd76ea32831029a Author: galt Date: Tue Apr 10 05:46:46 2007 +0000 removed unneeded clipstack since we should be able to just use the cliprestore command which is part of the Postscript Level 3 standard commit fcd3ef2fc180e1753f5e3d641058e2dda2eb6141 Author: heather Date: Tue Apr 10 05:06:19 2007 +0000 distinguish old and new KG commit bdf9da6caee8aa9589d3ae635992abed8fbb9eef Author: hartera Date: Tue Apr 10 00:21:48 2007 +0000 Reordered the experiments in the display for the Affy Zon Wild Type data track. commit c09189d66dfc7e2967851a56c85c850dc288918d Author: heather Date: Tue Apr 10 00:17:29 2007 +0000 improvements commit 0b5266de0974ebe59d3bc6676bbe86f5eb59c0e2 Author: hartera Date: Tue Apr 10 00:17:23 2007 +0000 Reordered display of experiments for Affy Zon Wild Type track. commit 3c01021a0f3e0a0a37b6b984223053e1f165a972 Author: heather Date: Mon Apr 9 23:53:32 2007 +0000 enhancements for hapmap snps commit ca00ce8d0154eed5346a3352f7017734eb25a72b Author: hiram Date: Mon Apr 9 23:36:38 2007 +0000 Adding photo from Eric Haag commit 8d9f642f3f734a660c1f8594c2fc61c5e074381c Author: heather Date: Mon Apr 9 23:36:00 2007 +0000 tweak label in hapmap snps commit e6dd9e359a183a216e95efb88efc6dfd869ed53f Author: heather Date: Mon Apr 9 23:35:10 2007 +0000 correct heterozygosity display for hapmap snps commit eb1ba35dd12ed7c942349d9d7732090614a43614 Author: hiram Date: Mon Apr 9 23:28:29 2007 +0000 Photo obtained from Eric Haag in email 2007-04-07 commit d329da21c83566acd02aad179a5b8d52ea1050c0 Author: hiram Date: Mon Apr 9 23:23:54 2007 +0000 Brought in from the images directory commit 19f8ef795c32eaff85ee591485ea199ef6dba5d0 Author: hartera Date: Mon Apr 9 22:55:44 2007 +0000 Updated the EST orientation FAQ to include further explanation. commit 8720d7a108e8488b2c14738443a876413053bb9d Author: ann Date: Mon Apr 9 22:55:41 2007 +0000 fixed up citations in Reference section commit 45e746612fcc6c0330a2d2845928a5bcc5692a74 Author: ann Date: Mon Apr 9 22:48:20 2007 +0000 fixing citations in References section commit fa447b2b1237d61f156f540c8f5bb0f824990748 Author: hartera Date: Mon Apr 9 22:42:47 2007 +0000 Updated script to include all transcripts in the vegaInfoZfish table. Updated all Vega tables. commit d268a114ce47c7e737ccd0cf0a0e2d9308d4f060 Author: fanhsu Date: Mon Apr 9 22:35:19 2007 +0000 Simplified a logic. commit 23c0c56e499328be61cd5db37de9a31bb0790908 Author: donnak Date: Mon Apr 9 22:29:10 2007 +0000 Added announcements for upcoming OH seminars & fr2 release, both commented out for now. commit 20c411e3e3e0eceb8940a892760457ea72398ee0 Author: ann Date: Mon Apr 9 22:03:18 2007 +0000 Fixing up citations in References commit 2a1575e63d03b880a8d325124ad959f3ec146392 Author: ann Date: Mon Apr 9 21:56:41 2007 +0000 giving chain/net for fr1 the o_db shortLabel commit 046847a5b28c41dd533c2bf6596e96afd61af8c7 Author: donnak Date: Mon Apr 9 21:56:38 2007 +0000 Fixed caps in UCSC long label -- "GenBank". commit 8283b773ba41a76d658fe1a4e5212e60603ad177 Author: ann Date: Mon Apr 9 21:53:54 2007 +0000 fixing chain/net for fr1 and fr2 commit 8b40e6e2f2f208a74433ccecb54f8a35e28fd3ed Author: hiram Date: Mon Apr 9 21:53:34 2007 +0000 Set defaultPos to HMGB1 gene commit d28d27faf82c48ed05546e8c033534d302afd198 Author: ann Date: Mon Apr 9 21:52:33 2007 +0000 added blocks for chain/net for fr2 commit c4faace19e5aed60cb2ccd76ea73778b083d9736 Author: ann Date: Mon Apr 9 21:46:14 2007 +0000 added blocks for chain/net to fr2 commit 911efd5d6b975fcd2694b4701bbe5f96be1dcfad Author: ann Date: Mon Apr 9 21:40:11 2007 +0000 fixing hard-coded shortLabel for fr1 chain/net commit 22bae6c6134d572f42d05b5e73bc05f134d7dfa8 Author: ann Date: Mon Apr 9 21:35:54 2007 +0000 Fixed citations in References section. commit b92018acc1f89a6b59bf9fb94f840b1272bcd74a Author: heather Date: Mon Apr 9 21:28:51 2007 +0000 update to UCSC Genes commit db74d11b95d52e6b707b3a5f9d068ffb31ced624 Author: ann Date: Mon Apr 9 21:28:37 2007 +0000 added matrixHeader line as needed commit 714ec4e22adc76adabdb4ea0c30138b79d89a58b Author: angie Date: Mon Apr 9 21:17:09 2007 +0000 Regenerated ornAna1 blastz/chain/net -- first time around, the ornAna1.2bit used was from the pre-release, doh! commit 7aabf8ee4f5dc1614e47f57f049aae8797cd18ea Author: ann Date: Mon Apr 9 21:16:22 2007 +0000 switching short label for chain/net of fr1 and fr2 commit 5ff0a624d10d65ba6e40c6f36603927d0569b93d Author: angie Date: Mon Apr 9 21:14:11 2007 +0000 Added recipBest config keyword and -noLoad. commit e9d34edf05f3f50a68006c2d9f6500c08b5f7522 Author: giardine Date: Mon Apr 9 21:12:48 2007 +0000 Added logos for LSDBs dbPEX, RettBASE, and IPNMDB commit 614d871b86fdbea7554fdd55fc7969e74c1145e7 Author: angie Date: Mon Apr 9 20:54:18 2007 +0000 Added flyBaseGene, flyBaseNoncoding (rel 5.1), and hgGene/hgNear tables. commit f5caa7f60720c9c29fd9843aaac2bf6ff18c6a97 Author: angie Date: Mon Apr 9 20:52:21 2007 +0000 Updated hgGene/hgNear tables that depend on flyBaseGene since it has been updated to 4.3. commit e2f4f03340131eecb4191333e6aa27545722fa03 Author: angie Date: Mon Apr 9 20:49:40 2007 +0000 ornAna1 (platypus) blastz/chain/net. commit 3179d455f8c91ce838bf31f9856dc8d84f0b3974 Author: hiram Date: Mon Apr 9 20:47:53 2007 +0000 Add $Bin to the running of partitionSequence.pl commit f0167b9815f4c490ff387473e48392cd648f5e11 Author: angie Date: Mon Apr 9 20:45:54 2007 +0000 Updated termRegex/dontCheck for CG*-R* IDs which can now include -R followed by two letters. commit c57390253cb1dd3bc39b971667542be21af5429e Author: angie Date: Mon Apr 9 20:44:06 2007 +0000 Broadened bdgpExprLink to other dm (though somehow it was hit anyway) and added minCheck to flyP2P since its rows are for dm1 (rel3) genes, some of which are not in later releases. commit a2869089473d5a8d8fb4882b28093071c0be9aae Author: ann Date: Mon Apr 9 20:43:27 2007 +0000 switched old fr1 blocks to o_db commit ccb565243a49349243d2334f2eafbf4d82d55ecc Author: angie Date: Mon Apr 9 20:42:08 2007 +0000 Added hgLoadNetDist and hprdP2p to default target so they will be included in top-level make. commit 914de3f7807096fa380f9003e9906539ca71e52e Author: ann Date: Mon Apr 9 20:41:40 2007 +0000 added blocks for chain/net to fr2 commit 31e64b54dabf6eb01f2dc1aa6f9a07daaa15f740 Author: kuhn Date: Mon Apr 9 20:36:57 2007 +0000 utility to copy hgcentral* from all three levels to qa/test-results for backup commit 5d405bec0aa6bbd77f2a9772fb7fcb1f6a633712 Author: donnak Date: Mon Apr 9 20:33:16 2007 +0000 Removed extra
s that were causing extra spaces on home page. commit 5f3dafe99cdac4187dd8a6fa909f7f22cc36dadd Author: ann Date: Mon Apr 9 20:31:32 2007 +0000 fixing citations in Reference section commit 0d73194ff1914fa26ca34a1a3c1beeb4d2ceb9c7 Author: hartera Date: Mon Apr 9 20:26:39 2007 +0000 Removed duplicate hgBlastTab rule from ensemblTranscriptId. commit 46fcfb95028d7c66b6fc72945294d7197755df6a Author: ann Date: Mon Apr 9 20:25:01 2007 +0000 fixed up citations in References section commit 72c796c2063df3c40ea784f853ac371ed73e14bb Author: ann Date: Mon Apr 9 20:22:04 2007 +0000 Fixed citations in References section. Added $matrix in chainDanRer4.html file commit e7e0c69bb47f3e641f73a810dcf569c5fb426590 Author: giardine Date: Mon Apr 9 20:06:11 2007 +0000 Added several new LSDBs. Also fix for terms link that was going beyond the text. And fix in alt for image. commit 7649f24a66a4418de2e4c51401eab7d1b19f865a Author: donnak Date: Mon Apr 9 19:57:39 2007 +0000 Added info abt Alt Events track. commit cd271f7f001f991309e34d343bc1799e10bdbbb9 Author: galt Date: Mon Apr 9 18:48:18 2007 +0000 balancing pixel-centered polygon and line coordinates (versus box coords) commit 2ced18390f5756cd95bda2881a48fbb47d131f54 Author: galt Date: Mon Apr 9 18:44:19 2007 +0000 fix pop clip call - someone forgot to do this commit 1e0bcad972df9e0f4558a0e786e54624503561a1 Author: kayla Date: Mon Apr 9 18:41:38 2007 +0000 added fr2 commit 43840e863ea6123108ff65b67143ecf5da98ffb6 Author: heather Date: Mon Apr 9 18:11:41 2007 +0000 fix bug found by Brooke: match from subtrack needs to send parent to open track (single match case) commit 636f48a1e34499aff045032a3bce21fb6f257c51 Author: heather Date: Mon Apr 9 17:55:45 2007 +0000 provide reference commit 55799eeb6bfaf456d8adcf1575cc0848784588fb Author: hartera Date: Mon Apr 9 17:43:55 2007 +0000 Added rules to ensemblTranscriptId for ensZfishBlastTab, ceBlastTab, dmBlastTab, mmBlastTab, rnBlastTab, scBlastTab. commit 92229d3a267585edf3baf2a7b6342ed5cf451281 Author: hartera Date: Mon Apr 9 17:36:41 2007 +0000 Added rule to ensemblTranscriptId for hgBlastTab. commit 23bfaa4311e7d255264cdb565baedcce82f7ca07 Author: kent Date: Mon Apr 9 17:15:23 2007 +0000 Removing careful memory checking, which was tripping up mouse. commit b9272f7d499b7cd5dd56d10075b322ecb764b1b3 Author: ann Date: Mon Apr 9 17:09:55 2007 +0000 fixed up reference commit 89bf68e0bc4d5c9836ad25dbc4a902e30b478973 Author: heather Date: Mon Apr 9 17:03:48 2007 +0000 provide reference commit a7d78f48f8657af2dc9322e44d9ed65c5d50d20e Author: kent Date: Mon Apr 9 16:55:52 2007 +0000 Hopefuly fixing bug involving methods link and going to other species. commit 420a1acee45688401e4fd0b833fafa6b93786678 Author: braney Date: Mon Apr 9 16:52:59 2007 +0000 clean up commit 0278514b25419eb296647634da76697ab25fba05 Author: braney Date: Mon Apr 9 16:45:33 2007 +0000 a first pass at an atomizer commit 186d05b493aa749fe06129610c0be19e5214d2b5 Author: braney Date: Mon Apr 9 16:45:02 2007 +0000 clean up commit 0939f8bd09b717817150ede2aa9cb531e3af8cfd Author: braney Date: Mon Apr 9 16:39:53 2007 +0000 a first cut at an atom stringer commit 7a87fd135cdc3c5e955b9cd34de1d8fbe67c0804 Author: markd Date: Mon Apr 9 15:57:23 2007 +0000 output mRNA sequences commit c5163f7fe950bad3a1e0f35d05b37c6b9f2a0586 Author: galt Date: Mon Apr 9 15:00:23 2007 +0000 "Encode release log update" commit aa8ad41964f0de9fb73a6a545987e22e889d9aeb Author: galt Date: Mon Apr 9 15:00:13 2007 +0000 "Release log update" commit a41f7e082c8d9d4a640096103c7865a86df1d0bd Author: kent Date: Mon Apr 9 06:54:13 2007 +0000 Adding a few more flexible ways to do tables. commit 9310ef092e6416184c0b019e968dcf0d1ac398c4 Author: kent Date: Mon Apr 9 05:53:10 2007 +0000 Making it more blue. commit 360e301b0cf7dfea260f25c37c541c0c57b41d30 Author: kent Date: Mon Apr 9 05:50:11 2007 +0000 Making it more blue. commit d9bf8280d85e1de0da099f3bc49dfab5a301cbaa Author: kent Date: Mon Apr 9 04:41:30 2007 +0000 Stripping out some repetitive text. commit 5dc94737c0f8f1d7f76e6c2b6069066a72e4610c Author: kent Date: Mon Apr 9 03:11:25 2007 +0000 Made it look a little better for noncoding genes. commit 91948df26a6c87dd35068c0fedf839cfd63a28b9 Author: kent Date: Mon Apr 9 03:03:58 2007 +0000 Adding gene model info. commit 11cf83cb4310bf56bc05c6ab0a71c7511f5c9e1a Author: kent Date: Mon Apr 9 02:31:19 2007 +0000 Merging sequence and links table. commit f2805929f03996917df97731d9ee05ac48c958a4 Author: kent Date: Mon Apr 9 02:10:58 2007 +0000 Rearranging page a bit. Moving most of the database IDs to a new section near the bottom. Merging sequence and links sections. commit 56529e50c9f024d89d8248ed10c6726faca74253 Author: kent Date: Sun Apr 8 19:37:03 2007 +0000 Some rearrangements to layout of first section of hgGene. commit 20f5f1604dfd86251bfca9334c1e9e05fd99ae4b Author: kent Date: Sun Apr 8 19:06:50 2007 +0000 Fixed problem in knownAlt instructions. commit 69a9266083ca038d541c25b4f5150b9fced23e05 Author: kent Date: Sun Apr 8 19:05:54 2007 +0000 Enabling filtering out of non-coding and splicing varients of known genes. commit 4f2fb049457f263dfb99db29968a87f32847e83e Author: kent Date: Sun Apr 8 18:55:35 2007 +0000 Adding bigBlue style of links. commit 4c59bbb8d2cf86d7d60347feb4019be8395263e5 Author: kent Date: Sun Apr 8 18:43:21 2007 +0000 Making connnects to other database in otherOrgs section more reliable, particularly with KG3. commit acd7c939e2ef9ea4267a257206b8925a2311a026 Author: kent Date: Sun Apr 8 18:42:17 2007 +0000 Making sections closable. commit c43e73457be4ee4dc4a872183cf9b7b124caf876 Author: kent Date: Sun Apr 8 18:41:01 2007 +0000 Tightening up section layout a bit. Removing required blank line at end of all sections. commit cd4e7b84d762cf184b77772c5ac63829236ef181 Author: sugnet Date: Sun Apr 8 16:43:17 2007 +0000 Initial draft of program for cleaning up splicing graphs. commit 497ced380cda91602eb6b60ff2e49a874c31db73 Author: galt Date: Sun Apr 8 15:00:24 2007 +0000 "Encode release log update" commit 4077dfd317095017a5ec6ca7c33a315eb444ebf3 Author: galt Date: Sun Apr 8 15:00:13 2007 +0000 "Release log update" commit 8d713c3e8a1df17634028a56d5b8465d0a3e3d62 Author: acs Date: Sun Apr 8 14:29:45 2007 +0000 added exoniphy commit 6645b573dd72c91dad601d6ae1050c8e8da5c284 Author: acs Date: Sun Apr 8 14:29:03 2007 +0000 added exoniphy lift from hg18 commit 93301bdaa42bf989d00e3e2647cafe3b21a50b52 Author: hiram Date: Sun Apr 8 03:04:38 2007 +0000 Adding mm9 definitions commit 15a6c2294b11083211817ef9f31e5c7434b0b717 Author: markd Date: Sun Apr 8 00:35:23 2007 +0000 added option to compute overall stats, plus add means to query stats commit c5996aebd9a8ea8f06c1aa794ae6bd9d44ee64a6 Author: heather Date: Sat Apr 7 21:41:13 2007 +0000 tweak commit 56aab295a554155aa46efcbbe107131448c1d321 Author: hiram Date: Sat Apr 7 20:00:54 2007 +0000 Re-run TRF with randoms included now in the 2bit file commit 7762996f785d934dd4979c0dd61c1e15406201f8 Author: heather Date: Sat Apr 7 15:39:06 2007 +0000 first draft (Dave Johnson) commit 12da34a219c118abc4da2b78e2b4f9c88885868e Author: heather Date: Sat Apr 7 15:38:37 2007 +0000 add stanford NRSF (Dave Johnson) commit 03670be307b05cd48a4f4e24a0bbe809b1057877 Author: galt Date: Sat Apr 7 15:00:32 2007 +0000 "Encode release log update" commit ce18ce9e4b85fb3798a8d37630cb0b9e4dc717c4 Author: galt Date: Sat Apr 7 15:00:17 2007 +0000 "Release log update" commit a612b1dab5df43258829cd4788cc4a7a4502de9f Author: galt Date: Sat Apr 7 03:34:11 2007 +0000 cleanup removal of old unused code -trivial commit ab9ef2ecca9a2075eaf6134bedd0c55ba4c01547 Author: galt Date: Sat Apr 7 03:32:42 2007 +0000 typo fix in comment -trivial commit 1b7f955ad08546c7999125215bc2f176aaf7cdea Author: kent Date: Sat Apr 7 03:19:52 2007 +0000 Making some of the hgBlastTab joins less picky. commit f317c93e999cc62ab73a1316de98d8f8dc97f9c2 Author: kent Date: Sat Apr 7 03:03:44 2007 +0000 Hiding uniGene_3 track by default. commit 1b4acbc7175a1b7805701f3cda5c6f3f14b0df61 Author: heather Date: Sat Apr 7 02:42:53 2007 +0000 add notes for SV commit a10297617b3f2999ad5f79c77f70b73955d0556e Author: heather Date: Sat Apr 7 01:45:42 2007 +0000 tweaks commit 68530b17ad7b7c7571d1fe8ad3cc640a02fd6a6a Author: heather Date: Sat Apr 7 01:42:40 2007 +0000 info on affy genome-wide array commit 8be9c13bcb0cff9aa8c7947e88fdabd54dc4838b Author: heather Date: Sat Apr 7 01:19:46 2007 +0000 newest first commit 3c4f1c887e77d6ea9010f0602165d81923ab094b Author: heather Date: Sat Apr 7 01:17:23 2007 +0000 add snpArrayAffyGenomeWide (and a couple of other old tweaks) commit fbce2abb5d20448a8ff35481b6c88b288ff0a051 Author: rhead Date: Sat Apr 7 00:08:43 2007 +0000 Removed comment-lines from the ce.xxBlastTab lines. commit 1f4f0a4544cd00863d57fe31d61c4ccac3e39519 Author: angie Date: Sat Apr 7 00:06:19 2007 +0000 In linkToDetailsCellPrint, print out the link to hgGene even if we get a NULL description (n/a). commit bb2d0162f259fdfb360f814421d26d33f48a9ad0 Author: kuhn Date: Fri Apr 6 23:49:05 2007 +0000 added some space around image commit a8ac9c3f1caa8e8b7e20b64770fb765b9145cd74 Author: heather Date: Fri Apr 6 23:39:24 2007 +0000 add snpArrayAffyGenomeWide commit 8dce401fcf43d92c29a5a9337939715854575cf4 Author: kuhn Date: Fri Apr 6 23:22:44 2007 +0000 fixed to make distinction between archived and staged commit 7364f1038b57727df54b9221bb01fb3283af516e Author: heather Date: Fri Apr 6 22:57:44 2007 +0000 extend log message commit 6f538adfff0e86c08fc9ee33c66ad396214a4b05 Author: baertsch Date: Fri Apr 6 22:21:40 2007 +0000 remove reference to knownGeneLink commit ec23b34c1af772b8daeedcfdb4eb485a6fced338 Author: baertsch Date: Fri Apr 6 22:21:09 2007 +0000 removed reference to knownGeneLink commit 67685f218f0d6fa26f64867a786dbd048dc20be7 Author: angie Date: Fri Apr 6 22:17:27 2007 +0000 Added cytoBand, cytoBandIdeo, flyBaseGene and flyBaseNoncoding. commit f62ecbfd4a64cea20f15345601662633280adf20 Author: donnak Date: Fri Apr 6 22:00:18 2007 +0000 Removed padding from release table to condense size. commit 053da7e3196d06760840e3cd56cba94d885078e5 Author: angie Date: Fri Apr 6 21:48:54 2007 +0000 Adding dm3 (for now, just like dm2). commit aa798f3967486df0a77da4cb418ab4b910160803 Author: angie Date: Fri Apr 6 21:46:21 2007 +0000 Adding dm3 -- for now, just like dm2 but without the fb* tables (no acode from flybase). commit ca8e28b04e29007eb991b818f40c370061bf0a7a Author: hartera Date: Fri Apr 6 21:31:57 2007 +0000 Free structure in doVegaGeneZfish(). commit 4c3d9f3318217d4abe4708d028ec9138092ae4d4 Author: galt Date: Fri Apr 6 21:21:21 2007 +0000 removing unneeded conditional, works now that pscmGfx.c is correctly calling the right routine in psGfx for unclipping commit db9db72f97a829868b1730fb417a759f129b4f9f Author: donnak Date: Fri Apr 6 20:26:12 2007 +0000 Added categories to release table. commit 412e1a13c440aba9debcb2218e5c72c09c656194 Author: donnak Date: Fri Apr 6 20:10:59 2007 +0000 Made a few mods to KGIII announcement. commit 32bfe74849de41aaacf377a4a2ec9f7d131a5f41 Author: donnak Date: Fri Apr 6 20:08:32 2007 +0000 Made a few edits to this file. commit ba9f223cd55c0cdb57535c08eb46722879beb46a Author: heather Date: Fri Apr 6 19:46:39 2007 +0000 fix suggested by Angie: don't trust trackDbIsSubtrack commit 9b0bcb32db869d96e482fc6f8aa4e466a9e6d4b2 Author: donnak Date: Fri Apr 6 19:23:08 2007 +0000 Edited this description page. commit bda6430259393084f22b9c2e07d06e5c2dc38d9a Author: baertsch Date: Fri Apr 6 19:20:14 2007 +0000 added -branchMultiplier requested by Tom commit a88a014b3f953f2d6f7de5192b4a1f9660c679a0 Author: galt Date: Fri Apr 6 17:42:17 2007 +0000 removing pscmVerticalSmear entirely as it was intended to be static and thus should not be in the interface. I tested the change this time by doing a complete make clean and then make libs and make cgi with no errors commit c5cfee37570e936f0b9e09e806a08333383cd7a7 Author: ann Date: Fri Apr 6 17:36:04 2007 +0000 typo commit e83a6a4a6388cfa3d6c8bf1c4d0cd2babc102f4b Author: kuhn Date: Fri Apr 6 16:02:41 2007 +0000 utility to check the table-time sync for the db o' th' day commit e23a25d16ca89be6d5d2128fa5d302f6efa507a8 Author: galt Date: Fri Apr 6 15:00:38 2007 +0000 "Encode release log update" commit b7d71d034bc2728a1b779345dbc7e0ecf1f9829c Author: galt Date: Fri Apr 6 15:00:19 2007 +0000 "Release log update" commit 2938225d16ddd550e3dd250471059134466c1318 Author: hiram Date: Fri Apr 6 05:13:59 2007 +0000 Initial pre-release test sequence, chroms only, no randoms. Running RM and TRF commit 0f9e3d3a14079e8f8fca3ab89657b629ea57dc0e Author: hiram Date: Fri Apr 6 04:56:20 2007 +0000 Add mm9 to the build commit c8b46aee4ef1a367a7b657a2fb09d4f87f79c639 Author: hiram Date: Fri Apr 6 04:55:56 2007 +0000 Brought up to speed with Mm8 contents commit c90d6dcf8c04c215eb1481386144f92413e8f156 Author: hiram Date: Fri Apr 6 04:52:29 2007 +0000 Added appropriate pre-release test build comments commit fe194d2c6b6935a3327aa37445eff3f47c51891a Author: hiram Date: Fri Apr 6 04:49:12 2007 +0000 Initial files directly from the makeGenomeDb.pl run on the chroms only, no randoms yet commit f3b4a7e7b34382d9a8fa8f4588b6da5f1a135e61 Author: hiram Date: Fri Apr 6 04:24:56 2007 +0000 faSize has changed, try grep for bases to get just the first line commit 40f43f3aedf67c53ea70e41835bd49f68a0cf257 Author: hiram Date: Fri Apr 6 03:55:10 2007 +0000 Add special search for gold and ctgPos2 commit b538d65a265658412955eed09beb37adc0e8ac5c Author: markd Date: Fri Apr 6 03:54:58 2007 +0000 added option to igore strand in clustering commit 1a37b145d8e97b15cd6d4d2c3906ea1cd55a4e37 Author: hartera Date: Fri Apr 6 03:48:14 2007 +0000 Added functionality to vegaColor() to color items according to confidence level for databases other than hg15 and hg16 whose info tables for Vega have a different format to info tables for later assemblies. Zebrafish has an info table with a different name. commit 160c7af056dfd126a3673b8c8e47a3b344b63d42 Author: galt Date: Fri Apr 6 02:38:37 2007 +0000 change link to the real site (not test site) commit 824a146626fcca8710cfd9a9279c53b3c4070a72 Author: galt Date: Fri Apr 6 01:24:52 2007 +0000 fix bug in clipping. if box to draw is entirely outside the clipping region, then the width and height can be 0 or negative, and postscript draws negative height boxes just fine, which makes for weird errors commit f24205b4b8de69ead1d9f7c1565601697d043945 Author: kent Date: Fri Apr 6 01:19:20 2007 +0000 Removing curType global variable and replacing it with calls to genomeSetting('knownGene') which looks things up properly in the .ra file. commit 2b84fe0f40c63e702d104dbde80dc664cfcab968 Author: hartera Date: Fri Apr 6 01:06:53 2007 +0000 Added new subtracks for the Duke/NHGRI DNase track. Made a release alpha and release beta version for this track. Only the release alpha version has the updated html description - trackDb setting html is set. commit 170e1675542abdcf78645c63dd02d0753f12dfd3 Author: kate Date: Fri Apr 6 01:02:02 2007 +0000 Lots of new data commit 647470f600c4b76bafae7f2fcfee7199b523dc02 Author: galt Date: Fri Apr 6 00:55:15 2007 +0000 removing unwanted static declaration in a .h file commit ffc7af3da5cbf8a82310431dc8450cc4f72ca304 Author: hartera Date: Fri Apr 6 00:36:22 2007 +0000 Description for updated Duke/NHGRI DNase track in Feb 2007. Updated publications format. commit be9010c4f76d9e5e895009d01949f88ac3a6b7a5 Author: heather Date: Fri Apr 6 00:27:58 2007 +0000 extend labels for cnpLocke commit f1411be6436152810dc4b6d460c9fcf16960501e Author: heather Date: Fri Apr 6 00:25:08 2007 +0000 add reference for Locke commit 2fdf588dab466749333e391077d038447ed3cb7e Author: heather Date: Fri Apr 6 00:10:07 2007 +0000 copied from hg17; credit Lars for hg18 coords commit fdff245d3689acf1aa73ab5a6a79d398c06a9174 Author: tingwang Date: Thu Apr 5 23:47:44 2007 +0000 Adding description page for UC Davis ChIP array hit data commit 095955a64648dee629ddbb63aef137519548acb2 Author: kate Date: Thu Apr 5 23:40:35 2007 +0000 Phylogenetic tree with branch lengths derived from 4d sites for 28way phastCons commit b3e1edf581c99ba7aa7b03b877da18cacd1e07b0 Author: kent Date: Thu Apr 5 22:29:06 2007 +0000 Removing direct connection between knownGene and the UniProt accession/displayID identifiers. commit 9fb576e9a13bf28fb79a224f247bfa979dc9d8f0 Author: kent Date: Thu Apr 5 22:26:50 2007 +0000 Suppressing joining on empty fields commit 88f77372fc356249e47e1fd85c22ea4f1972d826 Author: galt Date: Thu Apr 5 22:16:16 2007 +0000 made a note about a possibly substituting strptime for getdate commit 6c83ab7bb18b655a09fb55d23641d6c72bf354ab Author: galt Date: Thu Apr 5 21:04:37 2007 +0000 had to add the blasted PDT for Pacific Datelightsavings Time commit a2921c96d8aa4c6165ef24f15c73860401d6e8a6 Author: angie Date: Thu Apr 5 21:01:23 2007 +0000 Expanded name index size because now we can have CG\d+-R\w\w (not just -R\w) when there are >26 transcripts for a gene. commit 8b6371c7d0d948dcee2ad53694d82227f4b0f326 Author: kent Date: Thu Apr 5 20:59:44 2007 +0000 Fixed misspelling of 'reduce. commit f7931c7c94d1a659673ee71f6ca5902e1493788f Author: donnak Date: Thu Apr 5 20:47:14 2007 +0000 Archived an item. commit 63331777bf3568d80691a7f77b30e2609f41b74e Author: donnak Date: Thu Apr 5 20:47:02 2007 +0000 Added KGIII announcement. commit 1887c10a38e3685bb6e38c558f6880fcbde3b951 Author: hiram Date: Thu Apr 5 19:51:47 2007 +0000 Fixup the sample queries, and assembly comments commit 4a02ad56767f7f612733cfc3cdf887344c195bda Author: mario Date: Thu Apr 5 19:50:58 2007 +0000 added two augustus tracks. de novo: table augustusXRA using all kinds of evidence: augustusHints commit 1f381759738bb3e578ab1e2fa564551dd5320903 Author: galt Date: Thu Apr 5 19:24:20 2007 +0000 post coderev, fixed bug in looking for blank spID and improved hash loops with for() commit 7f77c87cc64f89b0f73ec4a9734710d2729d9016 Author: galt Date: Thu Apr 5 19:11:07 2007 +0000 removed word test as misleading commit 683e966e3aefeb4c0d65377821fa09799651a1a1 Author: galt Date: Thu Apr 5 19:08:09 2007 +0000 changed to carefulClose() commit 43a57fffb0b9314ceb9357d4022c9ed3c4704db5 Author: galt Date: Thu Apr 5 19:06:53 2007 +0000 splitting out some code as handleMissing() for clarity based on Jims coderev feedback commit 4d4444031238c5a0d46052a6e98ca974bfaa13dd Author: hiram Date: Thu Apr 5 16:54:04 2007 +0000 Add a lift file for cb3 commit 4404e2508ebd43eb8e83532fb8cb6d2e28c68a65 Author: hartera Date: Thu Apr 5 16:15:26 2007 +0000 Minor edit suggested by Ann. commit 230c5c89a9693fb78e098c4f8a3170d3b2a3ec0b Author: galt Date: Thu Apr 5 15:00:35 2007 +0000 "Encode release log update" commit 9a058704b56dc1f740c33036460b6f32c71514bd Author: galt Date: Thu Apr 5 15:00:19 2007 +0000 "Release log update" commit 1fd6e61b7679f8011eb7ba898010177cf25ce4cc Author: kate Date: Thu Apr 5 14:59:54 2007 +0000 Fix CVS merge marks. Start phastCons for 28wsay commit 6288c2cb57caaebddbf477d5cfeb7c6f0fce2a8d Author: heather Date: Thu Apr 5 14:59:13 2007 +0000 add delConrad2 commit ef2f0f29e932ea592b0e23645b4bb617ef20aec7 Author: markd Date: Thu Apr 5 07:30:14 2007 +0000 added option to create genePred with no CDS annotation commit 48bac93d9488700a28a8068871a10da7c4c28e8d Author: heather Date: Thu Apr 5 05:35:49 2007 +0000 add delConrad2 commit c27583949d3ba2cd67800f3b0122a311786510d9 Author: heather Date: Thu Apr 5 05:33:38 2007 +0000 new format commit 56e3c2aca4a39275376a928ec0704b5c6b2bf4a7 Author: donnak Date: Thu Apr 5 03:31:27 2007 +0000 Updated this description. commit a8771d4fc79ac4477994d0ffe48194f99b3499f3 Author: donnak Date: Thu Apr 5 03:28:14 2007 +0000 Updated Fugu data release info. commit ddd2d0a0719f19befe86bd27c3a10e7ad2513873 Author: hiram Date: Thu Apr 5 00:41:32 2007 +0000 created 11.ooc file and start the genbank alignments commit 5abe89c882142c5d3f97ac526bd6729fef4bc7f5 Author: hiram Date: Thu Apr 5 00:39:35 2007 +0000 Added blat server commit 760070e9aa7c00ff53a887fafa134d48909fcbda Author: hiram Date: Thu Apr 5 00:39:18 2007 +0000 Finished caeRem2 blastz, added blat server, reset default position commit 3d3bdda9ba879d9a268ee87027849100e65ff17b Author: hiram Date: Thu Apr 5 00:36:25 2007 +0000 Added cb3. commit 4eb94bde4519b631d3df8821fe867888a50044bd Author: fanhsu Date: Thu Apr 5 00:13:22 2007 +0000 Changed max of 4 to max of 3 for PDB 3D pictures per row. This helps to avoid text not wrapping around in lower resolution PC display reported by Brooke. commit 0a5e9bcbb8fd2c2fc803135e256a8fb7db524f2b Author: angie Date: Wed Apr 4 22:31:39 2007 +0000 In customTrackUpdateFromSettings, if the track line does not have tdbType or wigType, look for type as well. It may appear in fresh-from-user CTs that have not previously been parsed and rewritten (with tdbType). Also, in wigRecognizer, recognize the wig (parsed) as well as wiggle_0 (unparsed) types. commit 083f64b0d0a3b7472a65614aa3f03c7ddfdfb067 Author: heather Date: Wed Apr 4 22:15:37 2007 +0000 minor refactoring (no actual changes) commit 6eb496be7c74a884890c8718a7d2d276045e19fa Author: mario Date: Wed Apr 4 21:53:57 2007 +0000 dependency between augustus tables and the correcponding peptide tables commit f5e1bcfff304f30663afda117d132e3d8ff8d1f2 Author: mario Date: Wed Apr 4 21:50:55 2007 +0000 make augustus tracks searchable commit 1f60621b808c842315a2c559bdee4688f7e8fba4 Author: ann Date: Wed Apr 4 21:46:41 2007 +0000 changed priority of knownAlt so that UCSC Gene track and old Known Gene track appear next to one another commit 0466cf78907f3596b14aab957a6ebc69b6d8b1a2 Author: rhead Date: Wed Apr 4 21:31:52 2007 +0000 removed release alpha line from knownGene track so that we now use KGIII info. commit ecf0da17cb66c1e48c6ff5838dd8d608c2089d1d Author: galt Date: Wed Apr 4 21:12:45 2007 +0000 changed it to real gsid city and site and remade gsid_cert.pem commit 1a3f601b03396bab98f81f894fbe3c0999e9f99e Author: giardine Date: Wed Apr 4 21:12:39 2007 +0000 Fixed problem with having 2 PubMed links with same name. commit 9193944ec2b04f937cc1f26f66f1d6d1f939e836 Author: kuhn Date: Wed Apr 4 21:11:21 2007 +0000 added some spacing after print of ProteinID for consistency commit 328494154b54ee22c7335a2b414b74074328a90f Author: donnak Date: Wed Apr 4 20:22:33 2007 +0000 Fixed broken link. commit 6ce66762edb3317a7e87e23802f70cf68d2f6795 Author: fanhsu Date: Wed Apr 4 19:27:47 2007 +0000 Removed hgKnownGeneList, where it does not belong. commit d041eaf2b748bb858452e6148e2f337ee95880bf Author: hiram Date: Wed Apr 4 17:39:16 2007 +0000 Appropriate comments for WS170 gene set commit 3482d15c55395434027e4e7a3bcfac096c4afe50 Author: hiram Date: Wed Apr 4 17:35:56 2007 +0000 There are no gaps in WS170 commit 04fac96d71fbc5bdc4de4959e6e446ace988e291 Author: hiram Date: Wed Apr 4 17:15:53 2007 +0000 Fixing up sample position queries, add link to data usage policy. commit b240271c26366704594d158807cb008ebe356bee Author: angie Date: Wed Apr 4 17:01:33 2007 +0000 Test oldDb for empty (in addition to NULL) so it can be reset via CGI. commit 9bf48395885b8658c42544a31d49820a50921836 Author: angie Date: Wed Apr 4 16:59:55 2007 +0000 Reset near.oldDb instead of near.oldOrg in Gene Sorter links. commit 6de4917be919cd7d545e7f1bfb1501423afd4a5e Author: fanhsu Date: Wed Apr 4 16:45:00 2007 +0000 Minor update to change some sprintf() into safef(). commit fd47ce8453272a414a5e91a78f2c6e65d9ffbc58 Author: ann Date: Wed Apr 4 16:38:54 2007 +0000 Flipping to ExonPrimer back to real site. commit ebf09b68745719f447823d7c5ed07073ea7c6c4a Author: galt Date: Wed Apr 4 15:00:33 2007 +0000 "Encode release log update" commit d83263195a86f842304e8854a9b411ac8b349d6f Author: galt Date: Wed Apr 4 15:00:18 2007 +0000 "Release log update" commit 0a4cc8c61ca5a65c64b3965defadcb38bb2ce34c Author: hiram Date: Wed Apr 4 05:48:12 2007 +0000 Correct comment about chrM. There is none. commit 69419e55298e4c9040035059579b782bce1aa2d4 Author: hiram Date: Wed Apr 4 05:43:37 2007 +0000 Added link to WUSTL GSC commit c0c40f5813bae48828bfd6eca1a6a30aac81f0a0 Author: angie Date: Wed Apr 4 04:09:44 2007 +0000 Added blastRecipBest so it's built by a top-level make. commit 7dfb737989552a665e635df9602d04c61108476f Author: hiram Date: Tue Apr 3 23:34:15 2007 +0000 Added photograph from Juergen Berger and Ralf J. Sommer, www.eb.tuebinging.mpg.de commit ace5d3d08c3961c51c523c8db706ba86b83c1ed8 Author: hiram Date: Tue Apr 3 23:33:06 2007 +0000 Photo from Juergen Berger and Ralf J. Sommer, www.eb.tuebinging.mpg.de commit 0eace4f1e9a309ac5bae353658bb8b91aee73c5f Author: rhead Date: Tue Apr 3 23:32:41 2007 +0000 Fixed citations more. commit c5495645e236445ebea3a056e5639eeb75c5ef29 Author: rhead Date: Tue Apr 3 23:12:25 2007 +0000 Fixed citations more. commit 43ca1b590ddef65218139f2f2ff90e746378ab1a Author: fanhsu Date: Tue Apr 3 22:38:47 2007 +0000 Updated logic in handling KEGG links. commit d6da2432094259a00238b13280e0f48694f69f88 Author: kent Date: Tue Apr 3 21:28:26 2007 +0000 Updated expected output for new uniProt. commit ae6f0259ff8b82ab6c44ec344769669e3979028e Author: galt Date: Tue Apr 3 21:12:31 2007 +0000 added explicit path ./ so will work even if current directory is not on the users path commit e3ff68bdd12187510ca91283bec3baeeb707c808 Author: ann Date: Tue Apr 3 20:52:24 2007 +0000 bringing this down to the hg18 level from the top because it is now based on UCSC Genes commit f4a10f8476260671947c03977d05eb2ba2159aeb Author: kuhn Date: Tue Apr 3 19:22:22 2007 +0000 grammara mod commit cf7cb2d3243e738f6869495dea2a30556ca9cfd1 Author: fanhsu Date: Tue Apr 3 18:59:17 2007 +0000 Updated to handle KG III. commit 7b4932206e2edf360309680f7b6aafde2d184364 Author: ann Date: Tue Apr 3 17:53:05 2007 +0000 added space in AltEvents shortLabel commit 9bd2063b1a39ca7fcac9b80ac6f5341e3eb49e17 Author: ann Date: Tue Apr 3 17:51:23 2007 +0000 added full English words for cryptic splicing events commit 6713043f35fb46d6b4982d1c4f8c0cb0c95d6aa9 Author: markd Date: Tue Apr 3 17:31:51 2007 +0000 ner orfeome image ids commit 13644ca0482f9c01dc9e9689548285ba407eb2b6 Author: fanhsu Date: Tue Apr 3 17:25:50 2007 +0000 Updated to include searching on RefSeq in addition to mRNA. commit f4df50a172b15c4b626f990cd08aca0c2e3896b3 Author: ann Date: Tue Apr 3 16:52:42 2007 +0000 minor wording edits commit b077f683de226d7d586da0d2d535a36da2d355e9 Author: kent Date: Tue Apr 3 16:45:59 2007 +0000 Fixing CDS Exon Count for non-coding genes. commit 9565498d9bd49f4bbb82bb54c36e6e6c4a8baab3 Author: kent Date: Tue Apr 3 16:40:00 2007 +0000 Updating test set to cope with uniProt change. commit 580bee3e83e37e9077ead597f903f1b1e57e4462 Author: kent Date: Tue Apr 3 16:24:50 2007 +0000 Made it so that score is max of overlapping features, not max of all features. Making test set work again. commit 526d99c93e030386d405230e603834d06809a9e4 Author: aamp Date: Tue Apr 3 15:16:37 2007 +0000 "New version number v156" commit a3160941171790a1d2a61727a03b5b889e161e40 Author: galt Date: Tue Apr 3 15:00:29 2007 +0000 "Encode release log update" commit bedf23237775c958395273c8861b8454ebf070fc Author: galt Date: Tue Apr 3 15:00:16 2007 +0000 "Release log update" commit 54a115477f58ac78f476a591792a729a71bfd225 Author: heather Date: Tue Apr 3 05:28:33 2007 +0000 add cnpIafrate2 commit bc2d57c009334c33cf714febe6522b54ad450bd3 Author: heather Date: Tue Apr 3 05:28:02 2007 +0000 changed format commit a5356e311f6515f29ecccbceee23d945d47fa98c Author: kent Date: Tue Apr 3 04:24:11 2007 +0000 Dealing with kgProtMap not always being around. commit 4b8a0b3a018172ab3f124361ae4950e5229ae3e5 Author: kent Date: Tue Apr 3 04:12:36 2007 +0000 Making it so that it clears settings when you switch assemblies as well as organisms. commit 69f371c1a9cc13f2755e4b69008ae9ddac76b52f Author: kent Date: Tue Apr 3 04:06:32 2007 +0000 Fixed typo. commit cbb897504476ba244e9592b687ad6625077ec50f Author: kent Date: Tue Apr 3 04:05:34 2007 +0000 FIrst cut of knownAlt (aka AltEvents) description page. commit 904400d050f73e2190ed38a40a570bb9dce7e973 Author: kent Date: Tue Apr 3 03:51:39 2007 +0000 Adding altFinish. commit a50153972f9e21d933b2a28f66fb2498623a256e Author: rhead Date: Tue Apr 3 03:35:21 2007 +0000 Changed zebrafish pointer from danRer3 to danRer4 and changed the otherUrl ensembl link for zebrafish from apr2006 to dec2006 commit 7e77b47a99b90f23c4bb33a4379db803d4a2908c Author: hartera Date: Tue Apr 3 03:30:50 2007 +0000 Removing otherOrgs.ra as moved to danRer3 subdirectory. commit 277ab36fde754d78f0e146fd5d0b85ae0b6d6987 Author: kent Date: Tue Apr 3 03:24:10 2007 +0000 Adding knownAlt. commit 8e6e1bef4ca2e2847d0cbe9929f41d3499d8244a Author: hartera Date: Tue Apr 3 03:22:13 2007 +0000 Links specific to danRer3. Added Ensembl Genes link. commit db056f884f1936b1c4db66883b61fbba20eb280f Author: hartera Date: Tue Apr 3 03:21:31 2007 +0000 Removed the Ensembl Genes entry and moved it to a danRer3-specific links.ra in the danRer3 subdirectory. commit ccea437f803548e4af5070b880da85993001f7ad Author: kent Date: Tue Apr 3 03:17:44 2007 +0000 Removing some debugging code. commit f01088666d6ff6567d7bd2f601fa50f71ff1dbfe Author: hartera Date: Tue Apr 3 03:17:28 2007 +0000 Moved otherOrgs.ra from Zebrafish level directory to the danRer3-specific subdirectory. commit 76ea4e9a5c42a329ac493eea75b56dcbb58b9a40 Author: kent Date: Tue Apr 3 03:12:19 2007 +0000 Adding rudimentary gene name and description for antibodies. commit 9817a0099aa122a5aa4e20bc5f24dddec5db49fa Author: kent Date: Tue Apr 3 03:11:58 2007 +0000 Adding some more protection against NULL results to refSeq and mrna accs. commit ec076f40e682acd92d90979178b0da35c1418c77 Author: kent Date: Tue Apr 3 02:13:29 2007 +0000 Adding knownToRef setting, and using this to find refSeq rather than kgXref. Protecting mRNA lookup with check for kgXref existence. commit fba43a6691a12211aa1eb7d1526b88a77b6f54f4 Author: kent Date: Tue Apr 3 01:54:50 2007 +0000 New utility to get only the thick parts of a bed. commit b2f7c0cc4781bab74c637baf1f3934d596ba91d7 Author: kent Date: Tue Apr 3 01:50:52 2007 +0000 Moving bedThickOnly to library. commit c526bfcf1e76801d7fd0ca4566c9a09c91d55a4a Author: kent Date: Tue Apr 3 01:50:29 2007 +0000 Adding notes from chuck. commit 1a60d37f15036c611950f958f72e0e250c825e7b Author: kent Date: Tue Apr 3 01:50:06 2007 +0000 Simplified pipeline in docs. commit c63f37aa29f1c0b345d5d3e19a8c2ec707c0a6bd Author: kent Date: Tue Apr 3 01:43:38 2007 +0000 Fixing bug where start/end boundares in canonical table were those of the gene, not the canonical transcript. commit 25a9cf7dbc28da8380fd46264a1a65c78959862d Author: kent Date: Tue Apr 3 01:18:26 2007 +0000 Adding back pfam column to dm1. commit 68fa8590076cb21d4736c47cd257ecae976172c8 Author: hartera Date: Tue Apr 3 00:07:41 2007 +0000 Changed type for description to longblob. varchar(255) is not long enough for some descriptions. commit 19e6e78fa203bc89de10490ba8794feeb1c1d7ff Author: hiram Date: Tue Apr 3 00:03:06 2007 +0000 Proper links and credits on the photograph commit 73f033aa76e2ebdecbc61fb8a96c7973072a14ad Author: hiram Date: Mon Apr 2 23:56:51 2007 +0000 Rearrange chain and net track to approach correct order commit 6221498d3b8abda8a484f8d4da5a754592e12c45 Author: hiram Date: Mon Apr 2 23:20:56 2007 +0000 Adding ce4, cb3, caeRem2, priPac1 commit 16e807dd1a89230e560df714ac2488b6a22748fe Author: ann Date: Mon Apr 2 23:15:08 2007 +0000 removed extra spacing in long label. commit ecfda4138f5b08c3f240aac13bc9f4c97d5839d1 Author: hartera Date: Mon Apr 2 22:58:45 2007 +0000 Added ensXRefZfish. commit f0fcd0cbfa49311834633bbc1b063381f807d7f3 Author: hiram Date: Mon Apr 2 22:53:51 2007 +0000 Continuing with the worm building commit c2158ad28b0e1e30c4456d0a2d1831239bbef2b0 Author: fanhsu Date: Mon Apr 2 22:53:42 2007 +0000 Added PB tables build. commit 27f98f08ccb35da0aacbf360dc6e6696169aa5fd Author: rhead Date: Mon Apr 2 19:46:37 2007 +0000 Added a rule for the old (KGII) knownGene and kgXref tables, which are being kept after release of KGIII. Also put the new kg2ToKg3 table in the ignored list. commit 7ea94c088c15b3cba298ee1ab51b3d32fa50041c Author: fanhsu Date: Mon Apr 2 18:05:48 2007 +0000 Added kgSpAlias table. commit 9e38c70cb01e9f095e9baca415ff5186cd880262 Author: fanhsu Date: Mon Apr 2 15:52:39 2007 +0000 Added myExp10(), using powf(), to replace exp10(). commit be814a35c1fec1c931358ba1217cee28961263f3 Author: braney Date: Mon Apr 2 15:02:14 2007 +0000 oops, fix DONE date commit 9dff8a6b996ef014f109636d457f261c88fc0c52 Author: galt Date: Mon Apr 2 15:00:22 2007 +0000 "Encode release log update" commit 0c54bbd221aabe89ff12eca3044987c9f958b201 Author: galt Date: Mon Apr 2 15:00:12 2007 +0000 "Release log update" commit a8788310bb4ff538dbdfac8d7b90644e5267d15e Author: braney Date: Mon Apr 2 14:46:52 2007 +0000 add human proteins track commit 47fbd79b77e030627c8f47cc3f612bc68cab2212 Author: galt Date: Sun Apr 1 15:00:22 2007 +0000 "Encode release log update" commit ffb33d8ced0a77f1c8e7cdc205288e0c3adf5194 Author: galt Date: Sun Apr 1 15:00:12 2007 +0000 "Release log update" commit 28b35ae4dc93d907ba690c175bab2134744dadff Author: kent Date: Sun Apr 1 09:29:27 2007 +0000 Adding bedThickOnly. commit 5095a337211e4615ee679c4fe811f26afe9b74fb Author: markd Date: Sat Mar 31 19:38:16 2007 +0000 fixed various issues detected by GCC 4.3 commit 7c1c4d72e6cabb2a56fc75d35dff56b29bb5002e Author: braney Date: Sat Mar 31 18:47:19 2007 +0000 add ellipse routines commit bd01b7d48612e0de0d178cc626a92c637332572e Author: braney Date: Sat Mar 31 18:47:00 2007 +0000 add routine to find all components commit 306ab82966a7d31b2ec8615f2b504aca9b1a4d19 Author: braney Date: Sat Mar 31 18:46:04 2007 +0000 added ellipse routines, take static off psLineTo commit c59393bbc9a0791956ce8923c9b3fd445f4487f2 Author: braney Date: Sat Mar 31 18:45:27 2007 +0000 add new routine to find all components commit b270ff9dd1097a27433f33426fc85d43a7a40274 Author: braney Date: Sat Mar 31 18:44:54 2007 +0000 add ellipse again commit ff67dcc5459a4f2458699048bc58500ae841079c Author: braney Date: Sat Mar 31 18:44:35 2007 +0000 add ellipse commit 0c41cc853cb0c7f0a795eb349a9e65387686f541 Author: braney Date: Sat Mar 31 18:41:42 2007 +0000 update to be 64 bit compatible commit 8fee4a79d92f484d5b632c34c0b7f9d232ffac5d Author: markd Date: Sat Mar 31 16:48:10 2007 +0000 fixed C portability issues commit d62039fee0308557569bc750ff6ed953585c99dc Author: markd Date: Sat Mar 31 16:45:49 2007 +0000 fixed C protability problem (side-affect expressions generate warnings in gcc 4.3) commit bee3668a51b5f8bee93020adf46ca3b8527f0bba Author: galt Date: Sat Mar 31 15:00:26 2007 +0000 "Encode release log update" commit c33e2fd243fa16fb6c09f7faec2537c000ccab49 Author: galt Date: Sat Mar 31 15:00:14 2007 +0000 "Release log update" commit a86a9b65fe09173946bf67d6b80ed5bdeaf6faf5 Author: markd Date: Sat Mar 31 04:32:28 2007 +0000 fixed unix portability issues commit 114e178f200d9cc8ab3de2355e166f6b99219bd3 Author: rhead Date: Sat Mar 31 03:51:25 2007 +0000 Changed GRIB link again -- last fix was not successful. commit 5e6b8d2a7ce0f8e9b244cb7bfbc170418acb2478 Author: kent Date: Sat Mar 31 00:45:54 2007 +0000 Seems to work. commit 5b27f9f19a55770780bdf7c83d980967de97103e Author: heather Date: Sat Mar 31 00:01:01 2007 +0000 add cnpSharp2 and delHinds2 commit a66c496373b8eb3b7f8e18807396cebab9b0df4d Author: heather Date: Fri Mar 30 22:48:48 2007 +0000 add cnpSharp2 commit 83a1815fa7f48fd905a059caef6ebb11fd965e12 Author: heather Date: Fri Mar 30 22:44:29 2007 +0000 add cnpSharp2 and delHinds2 commit 0d038f50d41656e39030a2dd1cfcfa26a0a2f0de Author: heather Date: Fri Mar 30 22:44:13 2007 +0000 fewer columns commit 08221d3eaf4d3351140bfb8321c5bf8e0d83f5c0 Author: hartera Date: Fri Mar 30 22:42:16 2007 +0000 Re-created the gzipped downloads for the agps files, hard and soft repeatmasked sequence and RepeatMasker out files for bigZips to include NA_random and Un_random which were missing. commit 5963b9fade2bf461d11b4d992240c4c99eb18be3 Author: heather Date: Fri Mar 30 20:35:56 2007 +0000 add delHinds2 commit 1fec9d3c3639b367d6a12f09d05f352a33c9ab92 Author: heather Date: Fri Mar 30 20:35:28 2007 +0000 one extra column in hg18 commit 10ad1ae6df4feda786d956ff8e980bde0576438c Author: heather Date: Fri Mar 30 20:12:09 2007 +0000 add track handler for delHinds2 commit ba33168b40d791973c97c42d02afb38fce50faf2 Author: markd Date: Fri Mar 30 19:52:43 2007 +0000 removed explite use of HOME in makefile, use common.mk defines instead commit b0180444b0c443055f8785b356157a9e196c179f Author: kent Date: Fri Mar 30 19:32:04 2007 +0000 Updating user docs to reflect change from bestOrf to txCdsPredict. commit 9cbc0880a4f9d17d2a65d71a3c7b3495f9276cc7 Author: kent Date: Fri Mar 30 19:05:19 2007 +0000 Flipping to ExonPrimer test site for a few days. commit 9a17b4b6ccd4a44a94e24469a5da44881b6d1c07 Author: kate Date: Fri Mar 30 18:36:22 2007 +0000 Add codon framing to 28way commit 24ed68d88e7ca273c4f49262fa9688f119950048 Author: kate Date: Fri Mar 30 18:33:37 2007 +0000 Add gene framing for 28way commit da4ed2d5184efbe3719423bebf9d4ab47235b501 Author: markd Date: Fri Mar 30 17:59:40 2007 +0000 specify -verbose=0 on genePrep/PslCheck in tests commit 79e8b702fdab81fa1d06362d0d58706c0571ae4a Author: markd Date: Fri Mar 30 17:58:37 2007 +0000 allow overriding HG_WARN and BINDIR commit cc7df97ba6bf0a3508387ccd727db8b9db2bd7de Author: markd Date: Fri Mar 30 17:57:40 2007 +0000 use BIN_DIR instead of HOME commit 192a982a8ae94f8078e9235a0b6eedea73a137f0 Author: kuhn Date: Fri Mar 30 16:25:34 2007 +0000 removed commas from usage commit c7e14fe85b6bba273d54dcdbe1442ee866efa1d5 Author: kuhn Date: Fri Mar 30 16:23:52 2007 +0000 added clarification in usage statement commit 71f46ae45c41ff8c9f423d2666b8329031110ffc Author: kent Date: Fri Mar 30 16:11:05 2007 +0000 Adding another few ideas for next time around. commit f2eb042651fbaa46011ac4f5cbc8da80830b8f05 Author: kent Date: Fri Mar 30 16:10:16 2007 +0000 Adding -miss option. commit 2600b0dd28f2144ed362b73e1b880e0224482d5f Author: kent Date: Fri Mar 30 16:09:39 2007 +0000 Adding some scop analysis. commit 88d9113f8a52ea6ba5c7d7658eeda27b78433b0c Author: galt Date: Fri Mar 30 15:00:30 2007 +0000 "Encode release log update" commit e04b6ad1b6559e640b6efd773ccb32ac155d3989 Author: galt Date: Fri Mar 30 15:00:16 2007 +0000 "Release log update" commit b212e3e4ad361f6f878f609986314c862fb4ba17 Author: markd Date: Fri Mar 30 05:54:41 2007 +0000 output orient info data too commit 667a421004d3456abbbe4a79f63d00186715603e Author: fanhsu Date: Fri Mar 30 04:00:43 2007 +0000 Updated to fix some problems and adapt it for KG III. commit f8044031ee2a2c4f0e3acecdacf03abe291ccfc3 Author: fanhsu Date: Fri Mar 30 03:54:02 2007 +0000 Updated BioCyc related tables. commit 0d06ba67ab00b7678f71f2d10117d9b7f255f2bb Author: aamp Date: Fri Mar 30 03:47:22 2007 +0000 I forgot to commit these. The module is updated to store SNP info. commit dec16620f57edcfc8dff9d05f5b3bb4ce4a6f6fa Author: aamp Date: Fri Mar 30 03:44:56 2007 +0000 Seems to work. Plus added the functionality of cgapSageBedAddFreqs... so that program can be destroyed now. commit f951cba087b5421f023d3f15bbbdc2d78e7bf62d Author: kent Date: Fri Mar 30 03:11:14 2007 +0000 Printing protein accession in visible part of link when it is used in invisible part of link. commit 748b46f7aebe3440421ac5091629e9aaa6b90346 Author: kent Date: Fri Mar 30 02:59:09 2007 +0000 Avoiding setting position in cart to null:null-null. commit 17549bd5529074a26cdc6531c4ca25e01a9be93b Author: kent Date: Fri Mar 30 02:43:08 2007 +0000 Added comment. commit e68955bc269f112ef699cf2caf7c97625db22b11 Author: galt Date: Fri Mar 30 01:01:16 2007 +0000 added human p2p incremental build instructions commit 3ddccfb921fcef8c7a32fe3eba3ea881583ec243 Author: galt Date: Fri Mar 30 00:54:59 2007 +0000 added steps for redoing human P2P for hg18 kg3 upgrade commit 3a215a77ec23c5f4faf2a9ca286a4743f088e637 Author: hiram Date: Fri Mar 30 00:37:44 2007 +0000 Reload genbank to see ESTs commit daf7b399d7d9d0122f304978e78b64711e66856a Author: galt Date: Fri Mar 30 00:26:26 2007 +0000 added example builds for humanP2P commit 77c37b03cb93c6609770896b801114301e715e95 Author: markd Date: Fri Mar 30 00:24:06 2007 +0000 verbose option to output number of alignments check and number that failed commit cce49ec5a0490a46e1bd977945d54e2cc9b3e868 Author: markd Date: Fri Mar 30 00:23:16 2007 +0000 brain damange resulting in confusing python and C commit 6852c12b2e971fbc0909167cc7c7a56244eb7d1b Author: markd Date: Fri Mar 30 00:20:12 2007 +0000 added verbose option to output number of genes processed commit 71c4a9a533b3d325739ae3f3b46ed2a2d33c43a7 Author: markd Date: Fri Mar 30 00:16:54 2007 +0000 don't lose empty columns commit 9b9e7278f684b4e89f57094a06a6c8f381eff9e0 Author: hiram Date: Fri Mar 30 00:13:13 2007 +0000 Adding sangerGene track, selfChain, chain and nets for several other worms commit eab13fb2e0b08e05013471568ed061cf1b2a9b5d Author: markd Date: Fri Mar 30 00:12:11 2007 +0000 modify chopByChar to allow NULL output array to get number of columns that would be produced, just like the other chop functions commit cfb622c644894741531b483fbbbfb838028cc327 Author: galt Date: Fri Mar 30 00:11:29 2007 +0000 cleanup commit d8be150a23b81c899779415856076a1fec06e940 Author: galt Date: Thu Mar 29 23:53:57 2007 +0000 cleanup moved to proper doc/directory commit dcc1f2961227846fbc30fd890352804bd0bbd309 Author: galt Date: Thu Mar 29 23:30:23 2007 +0000 split hgNetDist.c into hgNetDist.c and hgLoadNetDist.c to facilitate faster incremental kg3 building commit 1a13ea13fc62a74df89d1807b720d531d32c7d19 Author: hiram Date: Thu Mar 29 23:20:04 2007 +0000 Initial sequence for caeRem2 commit 20dbf9ee923b3fcb073cc972fc0f09010773915d Author: hiram Date: Thu Mar 29 23:19:32 2007 +0000 Continuing with sanger gene track, and self blastz chain/nets commit 043a031e72e8f4f276577f30649c0d90a100418d Author: fanhsu Date: Thu Mar 29 22:41:47 2007 +0000 Updated KEGG related links for KG III. commit 615ff241c8b16edc70274ebf3c92d8f02255cc3f Author: fanhsu Date: Thu Mar 29 22:37:21 2007 +0000 Updated to work with new entrez data. commit f0b5e0bc2c4b73df48f7fcffc47cf59e7a8cee70 Author: fanhsu Date: Thu Mar 29 22:32:10 2007 +0000 Updated KEGG link. commit ae5c22216447caa91334f6f06da3895cb2962ea8 Author: hiram Date: Thu Mar 29 22:18:00 2007 +0000 Add sizeof to the utils build commit 96bd4ead285c579f8842c1a8471897de769e2943 Author: fanhsu Date: Thu Mar 29 22:10:26 2007 +0000 Updated entrez DB. commit 632073fd2af6c8523142070b685ab14b14f367a3 Author: hiram Date: Thu Mar 29 21:49:35 2007 +0000 Proper credits and label on the photo commit 899a8ee611b2c42785eed3c84c070f360e30c137 Author: galt Date: Thu Mar 29 21:36:02 2007 +0000 cleanup commit 93dc311f680e9ef17246e408b216a547643d19b0 Author: kuhn Date: Thu Mar 29 19:35:08 2007 +0000 edits for readability and grammar commit 397c99646d1fd38b2a679fa2b9cb35eeeafae70d Author: fanhsu Date: Thu Mar 29 18:25:50 2007 +0000 Rebuilt knownGeneList. commit a68e87060c25a22f542add221ac11b9758cb7114 Author: fanhsu Date: Thu Mar 29 18:14:22 2007 +0000 Updated to handle KG III. commit d2b1f035829b84b649798cfaf8f2cb9c2e1d2802 Author: ann Date: Thu Mar 29 17:25:43 2007 +0000 Fixed citations. commit 65dd73270cd5f83a74ae64b08698a6370aeb43f9 Author: ann Date: Thu Mar 29 17:15:56 2007 +0000 Fixing citations. commit 706744d6b14e33759ac1ef226e13512042eadcd0 Author: ann Date: Thu Mar 29 17:07:01 2007 +0000 I got tired of deleting old archived messages off the pipermail server for users, so I edited these instances of information about how public your message to genome is going to be. commit 0ca100b559b146b8fc7a2c096a51987c554df700 Author: baertsch Date: Thu Mar 29 16:17:51 2007 +0000 add nscan commit 9f7801e1f17393142233f541bf19b4fc5fb0b288 Author: baertsch Date: Thu Mar 29 16:17:09 2007 +0000 add nscanGene commit 9e000554c842930f2d8465e681a45ed80a4ed9a9 Author: baertsch Date: Thu Mar 29 16:16:20 2007 +0000 *** empty log message *** commit 1ed580484998d3eaab69236317922f8f943b0f88 Author: kent Date: Thu Mar 29 15:50:00 2007 +0000 Adding test case for next version of known genes. Nice one Galt found. commit 3c050d6b19b380c76d33b6748fc513c45fd45dd2 Author: kent Date: Thu Mar 29 15:49:29 2007 +0000 Minor adjustments to ucscGenes build instructions. commit fc8e6ab4291935a9991404f24aab0dfeb0170260 Author: kent Date: Thu Mar 29 15:48:02 2007 +0000 New object for more or less generic protein annotations. commit 8e69f62b4382d2fa8eea1def04bc0dd9c1eb86d3 Author: ann Date: Thu Mar 29 15:31:25 2007 +0000 Removing human/hg18/knownGene_1.html -- the table was renamed, so I renamed the html file accordingly (knownGeneOld2). It appears that this is also going to commit fugu/fr2/gap.html which just has some small changes. commit 8893694976806c33a42788899409c4d10d85f254 Author: ann Date: Thu Mar 29 15:23:50 2007 +0000 Renamed from knownGene_1.html (the old Known Gene table was renamed). commit 7c96105286665558dfd66427ab9d2e396a16d4e1 Author: fanhsu Date: Thu Mar 29 15:13:38 2007 +0000 Updated to exclude non-coding genes. commit 6ee5ab8127b22910842aee59e1aabec2b56789b5 Author: galt Date: Thu Mar 29 15:00:32 2007 +0000 "Encode release log update" commit ee7be45851e984ec8a80255ac488af7abe7bdf71 Author: galt Date: Thu Mar 29 15:00:17 2007 +0000 "Release log update" commit 150d514609a3087bc8c909bca09346938d2fd3c6 Author: fanhsu Date: Thu Mar 29 14:53:08 2007 +0000 Added hgKnownGeneList. commit 4b393618a023b4ae2722e61f45f461dff16687d5 Author: kent Date: Thu Mar 29 11:08:51 2007 +0000 Bumping pfam list from top 10 to top 20. commit 8d53ab0553bee8121ec01191b7fd882587437057 Author: kent Date: Thu Mar 29 11:08:33 2007 +0000 Adding paper outline. commit b4504d4ca884367b1c2c576351873445dbb79634 Author: kent Date: Thu Mar 29 09:41:11 2007 +0000 More analysis. Saving email to mine for paper text. commit d6b737606d3320c81bf17beea2bfd8962e79f260 Author: kent Date: Thu Mar 29 08:58:31 2007 +0000 Seems to work. Some more analysis to go. commit 827e863ecc4a039c8219c73858ece3b0847aec28 Author: kent Date: Thu Mar 29 08:04:08 2007 +0000 Adding protFeat object. commit 3445e918a3ab92448b917fbf299a7fe3d2a7d61a Author: kent Date: Thu Mar 29 07:45:20 2007 +0000 Adding table on start/stop codon conservation. commit a87800ebf57999bc8db5885a765dd87134722f27 Author: kent Date: Thu Mar 29 07:41:38 2007 +0000 Starting on directory for gene set analysis paper. commit fea6e25aa49c6dbc4a8b49e6f4258d565c65c54a Author: kent Date: Thu Mar 29 07:06:10 2007 +0000 Updating to handle dashes and dots. commit 533eb810d27a4f1caf6dfff4c13a14aa03732c29 Author: kent Date: Thu Mar 29 07:05:52 2007 +0000 Saving dashes and dots separately. commit 826dbd1fb1dc35fe052cb3db8cd88c8e34449fcc Author: galt Date: Thu Mar 29 04:28:24 2007 +0000 added utility for processing HPRD PPI and Complexes in flat file format to make the p2p input for hgNetDist commit ff2f2d7d188946351e1cafed78ffd87a20ddef0b Author: galt Date: Thu Mar 29 04:17:14 2007 +0000 fixed to use lineFileRowTab, fixed hashLookup when using NULL values as existence hash, added -keepTab option to ease debugging commit 66bdc031d08113222c35655fcf7fca8e8550096a Author: galt Date: Thu Mar 29 03:15:59 2007 +0000 cleanup commit 5af085446caea528dd0b6d560b87bd1087d8175e Author: galt Date: Thu Mar 29 03:05:00 2007 +0000 cleanup commit 199c021c7c340952b60bbcd3552b879f0abe50a2 Author: galt Date: Thu Mar 29 02:43:50 2007 +0000 removing comment-out from debugging commit e402c508b1548843395b9beef1e79548bb86d5a6 Author: kent Date: Thu Mar 29 02:28:41 2007 +0000 Renaming knownGene_1 to knownGeneOld2, and related stuff. commit cc72c8afd9b60380d5c9747d89890d2abf665a6c Author: galt Date: Thu Mar 29 01:42:39 2007 +0000 adding utility to create knownToHprd commit c5b2b7a0b260685a22d2c6bf345073603f983d0f Author: hiram Date: Thu Mar 29 00:00:46 2007 +0000 swap to braFlo1 done commit ddf9db0c17e19e62f4f3af8debee277dfccc14e4 Author: hiram Date: Thu Mar 29 00:00:06 2007 +0000 Chain and net for braFla1 / Lancelet done commit 4ca278755f265fd2a78a5adf88036c5d13b18c09 Author: hiram Date: Wed Mar 28 23:59:43 2007 +0000 Beginning sangerGene track commit f7116930866f2a359cb2e4140ffbaf1e6e387017 Author: hiram Date: Wed Mar 28 23:59:15 2007 +0000 chain and net for Hg18 done, genbank done, photograph added commit 0203fea315fed122a134cb71d943d7282b96e550 Author: kent Date: Wed Mar 28 23:52:42 2007 +0000 Fixed misspelling. commit 1ee286176d7632354333a5efcbe62a98953b971f Author: kent Date: Wed Mar 28 23:48:52 2007 +0000 Fixing missing refSeq link. commit 23f85d4959be56ad050e5513665989fbf78ee735 Author: donnak Date: Wed Mar 28 23:14:07 2007 +0000 Made a few minor punctuation mods. commit 2f6fa5ef01fc5c70f4ecb14331384e50f9c6ab2f Author: hartera Date: Wed Mar 28 23:07:12 2007 +0000 Update of Vega with problems. Feb update of Vega Genes track. Statistics on RH map collected for the map data provider. commit 0be70e4b2958e00932b7b71a05e18181fc738505 Author: kent Date: Wed Mar 28 23:04:21 2007 +0000 Change uncoding to noncoding. Added Exoniphy. Smoothed out explanation of graph traversal a little I think. commit c769ca266bc3d5ae0297db2e8db53269e34d8542 Author: donnak Date: Wed Mar 28 22:48:32 2007 +0000 Edited one of the refs. commit cec01811d179123dac48fe21b85e46d8bc07c050 Author: donnak Date: Wed Mar 28 22:48:22 2007 +0000 Made some edits to the original text. commit d67e30597418a9e67fb3c4430aad971e5bfbf079 Author: hiram Date: Wed Mar 28 21:59:37 2007 +0000 Fix annotated mafs on the multiz17way to mark gaps properly in other species commit 63b3cadb2e3fcdc7417a9267c9ce66b19b08a01e Author: angie Date: Wed Mar 28 21:14:24 2007 +0000 Added a couple gates with wikiLinkEnabled() to make prevent errors when hg.conf does not have wiki settings. commit cb7c42b48db7697fecdb1f167a89d9d6f819404a Author: donnak Date: Wed Mar 28 20:40:21 2007 +0000 Fixed typo. commit 9e70e89cfccc3094b5c4836eb1e286d2ad691b13 Author: kent Date: Wed Mar 28 20:19:51 2007 +0000 Improving usage message. commit a29a905bba82d84dd4e1be190208ededccef0cb9 Author: kent Date: Wed Mar 28 19:28:22 2007 +0000 Changing
    to
commit 12e26e506ed6b7bdcc2a3b6f22eeb851437634b4 Author: kent Date: Wed Mar 28 19:27:04 2007 +0000 First cut of new known genes description. commit 9c67e19209efc0874248d7b43950edb2724edee2 Author: fanhsu Date: Wed Mar 28 17:48:19 2007 +0000 Fixed a bug on setting kgVersion. commit 76f712e675246aa872ea6cd3b7a229e1d8752549 Author: kate Date: Wed Mar 28 17:40:46 2007 +0000 New data submissions from Yale and Gencode commit b9b87fc4b2410687510b7c47b41e49be500bd814 Author: hartera Date: Wed Mar 28 17:36:37 2007 +0000 Ensembl Genes in progress. Cleanup of BAC ENDS files. commit 12741519909f24befc19ae31628103d30b8dc94c Author: hartera Date: Wed Mar 28 17:35:39 2007 +0000 BAC ENDS files cleanup for danRer2. commit 3adb5f40c72e4135b80432b6082cf366a957b7fa Author: hartera Date: Wed Mar 28 17:35:01 2007 +0000 File cleanup for danRer1. commit fcacc8debd22bd2341fc184862ba4fa322e90be7 Author: heather Date: Wed Mar 28 17:33:13 2007 +0000 match on coords commit 29efab578faccac46ec63ccce53343800ec14c73 Author: ann Date: Wed Mar 28 17:31:50 2007 +0000 remove release beta from known gene (we still need it on hgwdev too) commit 79a04deebbc261c07336c708077e9ffafc1e9088 Author: hartera Date: Wed Mar 28 17:29:39 2007 +0000 Added track handler for vegaGeneZfish track. commit 79b5102429448b8e6c919415206fd64e63a0bdf7 Author: hartera Date: Wed Mar 28 17:27:18 2007 +0000 Changed label for Zebrafish Vega Gene details. commit afe5836ec925fc63f65a46d06d28a9e6f9e8ce16 Author: ann Date: Wed Mar 28 17:26:25 2007 +0000 making release alpha & beta for Known Genes tracks commit e7ffd6683ef3338b76acfb8d10f529816d3cd678 Author: kate Date: Wed Mar 28 17:18:55 2007 +0000 Restore 28way with gap annotation now that mafAddIrows is fixed. Demote 25ways to the experimental group before retiring commit c6f61ef2bd5ca9010cc10a6e34075a3bdf4c982a Author: kent Date: Wed Mar 28 17:13:55 2007 +0000 Making raFoldInOne do a little error checking. commit 9e615ec52d12061b723ffb25a28abea956a9df10 Author: kate Date: Wed Mar 28 16:39:22 2007 +0000 Add references to raw datasets deposited at EBI ArrayExpress commit 4f28de1d91f7b5f6e67e8451566c250f6f666e7c Author: braney Date: Wed Mar 28 16:03:30 2007 +0000 take out some unused variables commit 875f3b1b7aec43e4d233dfb02913fe6375f3cdd6 Author: donnak Date: Wed Mar 28 15:42:03 2007 +0000 Added pub by Ni et al. commit 520a860a566180811315e6c2820b0c1430d13bab Author: galt Date: Wed Mar 28 15:00:32 2007 +0000 "Encode release log update" commit b777bce01cf4564d89eea40876b373e4fbcf37c6 Author: galt Date: Wed Mar 28 15:00:17 2007 +0000 "Release log update" commit 18371389264b51e88a4827488a98c0e938f6fcef Author: kent Date: Wed Mar 28 06:19:55 2007 +0000 Taking genePred file as argument, so as to be consistent in protein assignments. commit 5a233c4ad29ea3cdba96460d4ee2d6fe63c19d8c Author: kent Date: Wed Mar 28 06:06:19 2007 +0000 Chopping .version from NP_ proteinIds. Making it use uniProt ID in favor of refSeq protein ID. Treating exact matches to protein in preference of other matches. commit 44a1099252bebd0aa07ee2ceb821d22840283588 Author: kent Date: Wed Mar 28 02:18:58 2007 +0000 Changing handling of acc column a bit. It was causing problems before from the changes I made last week in some organisms. commit 786dc4f83c5f74ddd70539693087bacf9741e731 Author: hartera Date: Wed Mar 28 01:03:41 2007 +0000 Changed expStep for log ratio display of Affy Zon WT track. Added chrUn_random to Vega Gene track. commit d779ff9395acc353f4ffeffbee614ebbe90e0f7c Author: kent Date: Wed Mar 28 00:50:04 2007 +0000 Making it say 'no ortholog' instead of 'no homolog' for missing data. commit 30b6cae7aa56047d7d2da5c41a171fb11e9cf459 Author: kent Date: Wed Mar 28 00:46:38 2007 +0000 Making the filter use the knownToPfam table as well. commit 43ac70ae087fa4d26e9ddcdfedc636d8e4f526ba Author: kent Date: Wed Mar 28 00:30:26 2007 +0000 Making the pfam column use knownToPfam (and sangerToPfam etc) rather than taking a long trip through the proteome database that sometimes ended up ending badly. These XyzToPfam tables actually have been around since 2003, since they were needed to *sort* by pfam. commit 5238e955b963b947d574ce6d924cba3fa9ce400a Author: markd Date: Wed Mar 28 00:24:44 2007 +0000 added program to get genbank data for UCSC genes pipeline commit fa666f3f7dce7ab9e177d1d4c1bd275de1d260d6 Author: kent Date: Wed Mar 28 00:17:55 2007 +0000 Adding a bit more docs. commit a060db38a47732e05ab6e05738582c398afc42db Author: hiram Date: Tue Mar 27 23:59:39 2007 +0000 Turned on genbank commit 540db813758ba84f4a2ea68fe750b4ada4da73a4 Author: hiram Date: Tue Mar 27 23:59:14 2007 +0000 Added ce4 - C. elegans WS170 commit 2642ca3683dc3d2119d16041e79dd19e89146c68 Author: donnak Date: Tue Mar 27 23:47:52 2007 +0000 Updated release date for stickleback browser. commit fbc3bb514e795860fdfb63f1641fa9a313a45144 Author: heather Date: Tue Mar 27 23:43:09 2007 +0000 fix error check commit 93e5aea0c712b7b033cf92cd4c68c5a7f2d561e3 Author: angie Date: Tue Mar 27 23:21:25 2007 +0000 Another reworking of partial aligment display to fix a bug found by David: edges of region were colored as alignment gaps even if they shouldn't be. Morphed ffShAliPartPart back into ffShAliPart with an explicit range in haystack coords, and only one input alignment. commit 598ecb6bc33ba939264b28e29acf3b49446fa6b1 Author: heather Date: Tue Mar 27 22:45:15 2007 +0000 fix bug found by Brooke: match from subtrack needs to send parent to open track commit fbfa68dc177819ee81d085ae381a6f561dd5cb64 Author: heather Date: Tue Mar 27 22:44:02 2007 +0000 add hTrackIsSubtrack and hGetParent commit 4093e86e71db6d1e4f74a72823fa9a89e8b9ff16 Author: hiram Date: Tue Mar 27 22:39:00 2007 +0000 Added ce4. commit 9ee8f2e86e47a2f41f277ed3a23dfea9b7ba31aa Author: hiram Date: Tue Mar 27 22:23:58 2007 +0000 Initial tracks for chains and nets on the other nematodes commit 5d58dde0311bc5b02f7a0e89da8b1580210c1614 Author: fanhsu Date: Tue Mar 27 22:13:21 2007 +0000 Use proteome_pfamDesc.sql for proteome DB to avoid conflict definition of pfamDesc table in genome DB. commit f6704a308b49b66061fa7d3d5c16442ab65e39bb Author: fanhsu Date: Tue Mar 27 22:05:34 2007 +0000 Added proteome_pfamDesc.sql. commit 917ca66fc0a9127ee74b4a47a8cb7dbb5ea7cc5b Author: fanhsu Date: Tue Mar 27 21:58:13 2007 +0000 Updated to handle version numbers in UniProt AC. commit 9f24f14ff4c42887f87cc940b28b5c1f3d96fac9 Author: heather Date: Tue Mar 27 21:49:09 2007 +0000 upgrade java version commit 301a73213cc50036a53b8ce0b5b8e88406c4f113 Author: donnak Date: Tue Mar 27 21:27:59 2007 +0000 Added 3 new pubs from ENCODE. commit cb3fc9c480cc67b88c3c5a35b9e39e1110cd20ec Author: donnak Date: Tue Mar 27 21:13:05 2007 +0000 Added 2007 pub by Jakob et al. commit a40fc50b0ba04e67db8e3b6e05bb8845c5ce8607 Author: hiram Date: Tue Mar 27 21:06:11 2007 +0000 Proper name on Scaffold (==Assembly) track commit 3830b0a87e02b1fd02fee3210ba5d65362b4f189 Author: hiram Date: Tue Mar 27 21:05:16 2007 +0000 Rearrange location of Assembly track commit d7fcbed5a2afa0bb27f12efce29cc45297501b76 Author: heather Date: Tue Mar 27 21:04:25 2007 +0000 fix typos commit ea06c81936ae90459bddae919fd1fb2b12a1fc33 Author: donnak Date: Tue Mar 27 20:58:31 2007 +0000 Added fr2. commit 2366bbd36d2abe064bd0556dd60c8ac5c26f4775 Author: donnak Date: Tue Mar 27 20:46:38 2007 +0000 Added fr2 to releases list (commented out til release time). commit 1eec917153971bdc7a44b7e91ccec54190044478 Author: hiram Date: Tue Mar 27 20:31:54 2007 +0000 Corrected multiz8way annotations commit 3fc7a5e5cdb62d52d1e2dd2853c9140505457a55 Author: hiram Date: Tue Mar 27 20:31:30 2007 +0000 Corrected multiz5way annotations commit ac27e2cc6e7c8fcf780cbaadc58415322223048c Author: galt Date: Tue Mar 27 20:19:12 2007 +0000 added correct mapping to psl with vgPrbMap.vgPrb as the id commit 2fd9cd2c5f3efc535bbfe0bf8aa6873f9f040ba3 Author: donnak Date: Tue Mar 27 19:51:42 2007 +0000 Fixed broken html found by Jim. commit ab09969f55dde9ad75638975fe9f93c536466bc8 Author: kayla Date: Tue Mar 27 18:45:34 2007 +0000 adding gasAcu1 commit 8e097e93953efdcaefa9c5ffa02743f7843f2bc3 Author: fanhsu Date: Tue Mar 27 18:37:33 2007 +0000 Updated the logic to set kgVersion using existence of kgProtMap2 table now. commit 9a539788d8a901ca4a3a94832adbfd9bc8b71e64 Author: kate Date: Tue Mar 27 18:01:39 2007 +0000 Back out annotated 28way for now while Brian reloads commit 4ffedd424403b1f239b7cf85e99a0fdd2c9a28fd Author: heather Date: Tue Mar 27 17:54:13 2007 +0000 fix typo in comment commit 37efc724a37aa3d729c0827b91d7da81d668a949 Author: braney Date: Tue Mar 27 17:51:08 2007 +0000 fix to not use memory intensive binKeeper library commit e8809d09eee7e6faeaa8a3d8851f994db6e28758 Author: fanhsu Date: Tue Mar 27 17:40:05 2007 +0000 Updated logic to require doExonTrack flag be turned on before offering the "DNA" button for user. commit 9ca0dd329817f0c5ed339626992c1ab1e03bc3b0 Author: ann Date: Tue Mar 27 17:06:42 2007 +0000 cleaned up citations commit 4bb081af2c221414b51fa0a4e1641727ca31b7e5 Author: hiram Date: Tue Mar 27 17:00:28 2007 +0000 Add chain and net for braFlo1 - Lancelet commit d9c453bfd4fabcf18c5ec32d30e8f21abe655b7a Author: ann Date: Tue Mar 27 16:56:55 2007 +0000 changed verb tense, cleaned up citations commit 1a00768a96117eb2c9789f7f9fd3fc7e2e92ba85 Author: hiram Date: Tue Mar 27 16:50:47 2007 +0000 Added braFlo1 - Branchiostoma floridae (lancelet) commit a72ace243b21fc3d5e13fff8b4ccaea9ff85e27f Author: hiram Date: Tue Mar 27 16:48:15 2007 +0000 OK for native ests - no to native refSeq for braFlo1 commit ebbf52a3e2dd7871ae0304f570039416a6e89d48 Author: aamp Date: Tue Mar 27 15:03:20 2007 +0000 I think Jim forgot to commit these after adding them. This autosql module is needed for hgc to compile. commit 391cda0c80dc2b390493d6b0f0c6e66038ec6666 Author: galt Date: Tue Mar 27 15:00:28 2007 +0000 "Encode release log update" commit e9476fb04ad8b3d12d8e1b1d2121ad9de55a8c66 Author: galt Date: Tue Mar 27 15:00:16 2007 +0000 "Release log update" commit 69dc821f366e762fa14f19fd5ca644ee4ff56e1f Author: aamp Date: Tue Mar 27 12:36:08 2007 +0000 "New version number v155" commit ef55d0d7addc46f9f350d374575d528d5a6f7839 Author: aamp Date: Tue Mar 27 12:25:42 2007 +0000 Utility to find SAGE tag locations and also taking into account SNP data. It sorta works. commit bcfc94ed3b8dc8cfd3f5e937905e9b4dadc868ec Author: kent Date: Tue Mar 27 07:18:47 2007 +0000 Fixed Stanford SOURCE link. commit 2ddeb44c266dd8c8a0f19fc09bacb651a3f6fd6a Author: kent Date: Tue Mar 27 07:17:18 2007 +0000 Fixing ExonPrimer link. commit 0490e74bb6cda38752dc7cbf15b0808c6d55b7df Author: kent Date: Tue Mar 27 07:09:52 2007 +0000 pdating knownGene description. commit 5f62a944cd3a4caa0b4a1d877151204f758e5a70 Author: kent Date: Tue Mar 27 07:05:39 2007 +0000 Adding in UCSC Gene ID. Also bringing CCDS into same line. commit 9eb5be08ec9a8951467df6d361b1039b9ec3a058 Author: kent Date: Tue Mar 27 06:00:52 2007 +0000 Adding html page for Old Known Genes track. commit e247f511917ae716b4acb59e4d38dd6cfdd10399 Author: kent Date: Tue Mar 27 05:54:28 2007 +0000 Adding in a bunch of knownGenes 3 stuff. commit e2661f009b08049feaa8e30b1b2ec5eac251d0fc Author: kent Date: Tue Mar 27 05:50:33 2007 +0000 Adding info on old/new mapping to knownGene_1 track. commit 1a88093074e6d6da6685d04086a8d0e38b89a770 Author: kent Date: Tue Mar 27 05:21:09 2007 +0000 Seems to work. commit a2b4367a431e16aab35fcf8191cfa97247416ad2 Author: kent Date: Tue Mar 27 05:20:54 2007 +0000 Adding object to explain fate of old gene in new gene set. commit 14fcf41aaff1ab62ae80e62d4f337cd3645137a5 Author: hiram Date: Tue Mar 27 04:52:51 2007 +0000 Added braFlo1. commit fc7c75b8b066507c473e5bebd521803ffb49d290 Author: hiram Date: Tue Mar 27 04:32:33 2007 +0000 Adding braFlo - Branchiostoma floridae commit 155bfd4057c3a4be9d342ed443d294e1a6d717b6 Author: kent Date: Tue Mar 27 03:58:16 2007 +0000 Updating test set for versioning. commit d22605d0cf55382954f09686179950ef67d53764 Author: kent Date: Tue Mar 27 03:58:07 2007 +0000 Moving bedCompatibleExtension and bedExactMatch to library. commit 9baa146a99c8cf5cec2aa8d50b36affdc67dd032 Author: kent Date: Tue Mar 27 03:20:52 2007 +0000 Adding knownToSuper.tab output. commit cca1b29595f0dfd7dd67072457203e991eae88b3 Author: kent Date: Tue Mar 27 02:01:56 2007 +0000 Adding eValCol and scoreCol options. commit b5fcbeff9085c986ff41c69c565f8f35b22551ea Author: kate Date: Tue Mar 27 01:05:52 2007 +0000 Add temporary entry for gap-annotated 28way commit f4e1a4bbe0a32dcfd563a343d1be77cb5ae4e29f Author: galt Date: Tue Mar 27 00:29:53 2007 +0000 checked visiGene stuff and added vgGetText call commit 2548089ee731dc57d7f703ed015b26d1bfdb7d72 Author: fanhsu Date: Tue Mar 27 00:11:40 2007 +0000 Updated CGAP tables. commit 724eb2e2adbc7f9226a447c9b1f2124685d0f035 Author: galt Date: Tue Mar 27 00:09:18 2007 +0000 fixed case-issue with new kgIDs commit 92ecb930b1267c4921d14648ce704dfb0a2dde4c Author: hiram Date: Tue Mar 27 00:07:20 2007 +0000 Properly get the quality track loaded, truncating values over 99 commit 648d0cdc0d44a49f4116741a92b9a7bee47bee9d Author: hiram Date: Tue Mar 27 00:06:56 2007 +0000 Fixup chrM_gold table commit 11356662713848cb8ec2e0f9cd5609e4c9bf9198 Author: hiram Date: Mon Mar 26 22:44:55 2007 +0000 Add comment about chrM for the Assembly track commit a266860b4257c091faa482dca2b36110bb80beee Author: hiram Date: Mon Mar 26 22:29:33 2007 +0000 Reload rmsk table to take care of empty chrM rmsk commit 5f2a71e2a54c22954ad9f0980487a5f7d5f5b1a4 Author: hiram Date: Mon Mar 26 22:23:12 2007 +0000 Initial sequences for Lancelet genome commit 32bb3c34006f9ffc67df5982abc938ac7c413fd9 Author: fanhsu Date: Mon Mar 26 22:21:28 2007 +0000 Updated to show Pfam and SCOP links for KG III. commit 3645404e8411e94f175b63b1bfd5a0d4aee98782 Author: angie Date: Mon Mar 26 19:51:36 2007 +0000 Handle isRc when printing out target coords in alignment title. commit 8a76f9eaef2f72a6a2e3e6c03124b3e83421ed54 Author: angie Date: Mon Mar 26 19:37:05 2007 +0000 Oops, don't emphasize haystack bases unless we're just showing a part. commit e07c4cce390517d50ea66dd93038199f351126bd Author: kent Date: Mon Mar 26 18:48:45 2007 +0000 Suppressing internal databases in sqlHashAllDatabases. commit 9e70a9a0e9fc6b2d790632f72e105d03144ab540 Author: angie Date: Mon Mar 26 18:41:19 2007 +0000 Remove link to htcCdnaAliInWindow where it is not yet supported (translated alignments). commit 57525443dccf2b17ae4d797d70fa5d051b055ae7 Author: kent Date: Mon Mar 26 18:28:17 2007 +0000 Updating for KG3. commit 18341d77f9bf9fce1605f49a78b28208bafe5725 Author: hiram Date: Mon Mar 26 18:16:23 2007 +0000 Add caePb1 and braFlo1 commit e99905848b573bbbcc1d5c39b2700d9891496e71 Author: heather Date: Mon Mar 26 18:15:11 2007 +0000 a bit friendlier error message commit 8cc7aec831b5660d9e5dc42e471cec917877ea88 Author: heather Date: Mon Mar 26 18:14:52 2007 +0000 update for new KG commit 284e7973bed714245632d77973b85c22a88b99ae Author: angie Date: Mon Mar 26 18:14:09 2007 +0000 Added error message for unsupported case (htcCdnaAliInWindow for translated alignment). commit 93597556e4769adc1e4e5ac7330b22f1395c8b89 Author: hiram Date: Mon Mar 26 18:13:39 2007 +0000 Initial contents commit 54aa19992aa2aa4a4ed9479a18f32430c0c103c9 Author: angie Date: Mon Mar 26 18:12:52 2007 +0000 Tweaked description and added emphasis to haystack bases in partial alignment view. commit ca7f3f08d22633e98a5183ed3f24a6176af860cc Author: angie Date: Mon Mar 26 18:11:48 2007 +0000 Pop the formatting for whitespace and lineNumbers -- it looked bad when underlining extended past the bases. commit 8aec6280a13c41279f38ffae903a769e3add6a32 Author: hiram Date: Mon Mar 26 18:03:55 2007 +0000 Added some assembly comments commit 7212522f02091115a8d5d2ae07e1bbc2f03e5c2f Author: angie Date: Mon Mar 26 18:02:05 2007 +0000 Updated to use common.mk definitions for portability to cygwin. commit 07e43d25eaac42ca2562186613a0e367bcfd0934 Author: angie Date: Mon Mar 26 17:37:15 2007 +0000 Resolved -Wall warning: unused variable; main return value. commit dd8133f03a425ed8a4cf8d46b85675d04f21987d Author: angie Date: Mon Mar 26 17:36:39 2007 +0000 Updated to use common.mk definitions. commit 7db6f70aee176e3aace5fe751858b9eeb406ecc4 Author: hiram Date: Mon Mar 26 17:33:42 2007 +0000 Starting new ce4 sequence commit 4e6339c84fbab16cd8bd2d1e88c7b559d6040541 Author: heather Date: Mon Mar 26 17:14:12 2007 +0000 make the het calc clearer commit 53ce51a7e7a4446eb336b60a0c241111ad5dbc9c Author: hiram Date: Mon Mar 26 17:07:56 2007 +0000 Avoid final useless gap output commit 85a4f1756f5d0c798aa0e52147484a0c487d27b2 Author: hiram Date: Mon Mar 26 17:06:47 2007 +0000 Updated tests to match current code behavior commit 2d355064602e83b34457cfc578c34d87001ff9be Author: hiram Date: Mon Mar 26 16:45:21 2007 +0000 These are actually in src/utils/scaffoldFaToAgp commit e982a41168958f262fc1081f38ed75a2815bf35a Author: hiram Date: Mon Mar 26 16:44:48 2007 +0000 These are actually in src/utils/scaffoldFaToAgp/test commit a85f3a6037a38025181e46eee24811bbb12c69c9 Author: kate Date: Mon Mar 26 16:40:54 2007 +0000 Restore 28way after reload commit 6ccecc3581aa47964ec4ccdb2c32ce75df568bd1 Author: kate Date: Mon Mar 26 16:08:00 2007 +0000 Remove 28way temporarily, extFile fixes needed commit 4aa8a30b0319d0949c3bc42362f747c9763ad543 Author: kent Date: Mon Mar 26 05:47:00 2007 +0000 Adding how to make pfamDesc.tab commit 25e6ca094f4b599a89863d3c2d99a26261d83d4e Author: fanhsu Date: Mon Mar 26 01:08:40 2007 +0000 Added SCOP links. commit 8101179822244818ad819f05a0e88c8f96b9de8e Author: fanhsu Date: Sun Mar 25 21:56:05 2007 +0000 Added pFam processing for KG III. commit adda588172af4d2a80c73bb550275e2de234b83d Author: fanhsu Date: Sun Mar 25 21:55:35 2007 +0000 Added kgVersion. commit 14c55bc047ea0b292ec1596899f32fa0f7fc7c7b Author: fanhsu Date: Sun Mar 25 21:37:27 2007 +0000 Added a ";" commit 37b9fedec3dac62abe243ff5792eead18f72e9e4 Author: fanhsu Date: Sun Mar 25 21:36:24 2007 +0000 Added getDomainList() commit 6d30393fac7e84bae1ff389834d85aa1fb6d3964 Author: fanhsu Date: Sun Mar 25 21:35:00 2007 +0000 Added getDomainList(); commit d8488069f12379401693883c90869a8dc8c0e0a2 Author: kent Date: Sun Mar 25 18:44:47 2007 +0000 Adding -eVal option, and setting default to 0.0001, which seems to be where the SCOP/Ensembl run was set. commit b699018eacdd83930caac4d2c030906975a74bd8 Author: kent Date: Sun Mar 25 18:23:11 2007 +0000 Adding more info on knownToPfam table. commit e25d2f529abf8cac9d0b7c837ee4304d27f2249a Author: kent Date: Sun Mar 25 18:22:42 2007 +0000 Adding another index. commit 0fed735295782c6e81aa71b35134be868fd11656 Author: fanhsu Date: Sun Mar 25 17:08:53 2007 +0000 Fixed a typo. commit f1d00acf5299ab1675cfcc4ce9661cf935870b88 Author: fanhsu Date: Sun Mar 25 17:06:52 2007 +0000 Created scopDesc.sql. commit bce12eebb946e1483bb39539c62910c5b9490482 Author: fanhsu Date: Sun Mar 25 17:05:53 2007 +0000 Updated to make it more generic. commit cfae4eea6dd6d89bbbb93ae5728051fb806a03e1 Author: fanhsu Date: Sun Mar 25 17:04:35 2007 +0000 Created domainDesc.sql, a generic domain description table. commit e89334da6338ec54c2e7901598deb6866f5a4a23 Author: fanhsu Date: Sun Mar 25 16:58:06 2007 +0000 Created ucscPfam.sql. commit 1e4d178ff485ddbb9896fbf7f1c2b57ec0f70eb7 Author: fanhsu Date: Sun Mar 25 15:55:51 2007 +0000 Created ucscScop.sql. commit f7d68d8aebac30351ce3493ed795aec67243fb50 Author: fanhsu Date: Sun Mar 25 14:21:08 2007 +0000 Added kgVersion. commit 9f0c491a38e73ff09c9510088ddfe9772e74c8a1 Author: kent Date: Sun Mar 25 06:25:58 2007 +0000 Seems to work commit 0343eee70f9f3454237bd84843e1a58d36aa3c48 Author: angie Date: Sat Mar 24 04:03:29 2007 +0000 ifdef'd out the whole thing for cygwin - can't find exp10 in libs. commit c831475bd042b10a29cb6b3344136ed0bc3ebf85 Author: fanhsu Date: Sat Mar 24 03:34:30 2007 +0000 Added logic to handle KG III. commit ae4da3b04ab602adc1de63d461e3dd4a552bb1a0 Author: kuhn Date: Sat Mar 24 02:59:09 2007 +0000 no need to worry if gbDelete_tmp does not match commit 27511a52e2895f8c4e116c62e208ce430a081175 Author: kent Date: Sat Mar 24 01:27:59 2007 +0000 Adding a generic knownTo.sql. commit eb016b3c35b541b94dc47fa15aee2f40df6b1a79 Author: rhead Date: Sat Mar 24 00:50:50 2007 +0000 Changed references to pubmed format, changed links to html rather than pdf, and provided links to the HapMap Project. commit ad5c1290ac466e5ebff701ad5c68474842731f9c Author: rhead Date: Sat Mar 24 00:17:34 2007 +0000 whitespace changes commit f88e4a8b5ac6b08960ecd09ce79e36642fd77c76 Author: kate Date: Sat Mar 24 00:11:19 2007 +0000 Hide experiments for now commit b7d759ec9d8f654a40aaa3d19b06378d90f10d9a Author: kent Date: Sat Mar 24 00:00:55 2007 +0000 Adding info on SCOP run and fixing bug of csBlastTab where should be scBlastTab. commit b75e6aaf31756f0a80a41a8fe913a46162c40bfe Author: ann Date: Fri Mar 23 23:55:44 2007 +0000 added fr to wgs alias commit 7d5dae29d479f7c62764233eca8d00ef47cc065e Author: ann Date: Fri Mar 23 23:50:09 2007 +0000 personal preference commit 76a68823467ebbad73d17e87ca6d3f4ac0602477 Author: galt Date: Fri Mar 23 23:37:24 2007 +0000 removing unnecessary argument-requirement commit 84ab6885de2005788f237cb254ba374aaa80e384 Author: hiram Date: Fri Mar 23 23:36:29 2007 +0000 Eliminate duplicate definition of convertEpsToPdf() function, now in src/lib/psGfx.c commit 37117ad6e9921f908fb43966fa46e36bc5025254 Author: fanhsu Date: Fri Mar 23 23:28:21 2007 +0000 Added declaration of kgVersion. commit c2e07f5004e0f10cc1cd3d1bba01e088b1245c2d Author: ann Date: Fri Mar 23 23:24:01 2007 +0000 fixed link to wustl commit 8dd4cefb5c854d5d8a130bf23cf83785ef104c7d Author: hiram Date: Fri Mar 23 23:13:47 2007 +0000 The Assembly track is called Scaffolds commit 94948a793e35681cbb0dcb59108bcb0113aa2600 Author: hiram Date: Fri Mar 23 23:10:26 2007 +0000 Eliminate duplicate convertEpsToPdf() function now in psGfx.c commit f43e0d700a2848654dd7ce904630da8cfdbb20df Author: hiram Date: Fri Mar 23 23:00:54 2007 +0000 Updated to represent reality. commit b3065e77dd1a1271c6f88db7fbae21ca58ddda25 Author: kate Date: Fri Mar 23 22:53:04 2007 +0000 Another test track for multiz commit f4ca6be4a14f29311edd803448b0295d933ede92 Author: kate Date: Fri Mar 23 22:52:45 2007 +0000 Repair 8way, for dev purposes commit 31300999b34a9f37744c845d11cda21f4ddcd6fa Author: galt Date: Fri Mar 23 22:26:59 2007 +0000 added topbar help link to hgGenomes own help page commit 2a033c43a57f95ae205f4a9ecd2fcf1e2579410e Author: hiram Date: Fri Mar 23 22:07:03 2007 +0000 Special quality track, no data on chrUn until scaffold/ultracontig mapping is figured out commit 65722ba3a4c487b8c9917da121beb3e1b202add0 Author: ann Date: Fri Mar 23 21:56:48 2007 +0000 added disclaimer about haplotype and mitochondrial chromosomes not displayed commit f2760c579db79684fead52e692384f49cfbb91fe Author: angie Date: Fri Mar 23 21:28:19 2007 +0000 Added more explicit usage of custom track db instead of relying on hdb routines that call hGetDb, so we can recognize sequence names as valid for the custom track's db which may not be hGetDb. Fixed the way that tdb->type is passed in to the fac->recognizer routines, and the way that they compare type strings. commit 4fff85ffc8414d2bad6ef8942988b3bae36ce922 Author: angie Date: Fri Mar 23 21:11:58 2007 +0000 Removed customFactoryCheckChromName because it was used only internally to customFactory (and has been replaced). commit f9c460a0e328e254e772fa41038a1989e6f506a1 Author: angie Date: Fri Mar 23 21:10:16 2007 +0000 Added hgIsOfficialChromNameDb. commit b37b62ea3bf03399d8ca6d5bd944baa934508358 Author: galt Date: Fri Mar 23 20:36:25 2007 +0000 added   for cells that are blank so table cells get their separating border commit 9f3fd7c9f1a910e67fea25ac96faf620687845c4 Author: rhead Date: Fri Mar 23 20:26:56 2007 +0000 Moved the chimpParalogy trackDb.ra entry and html file up to human level from the hg17 level. commit a81747412755c64cd9498d4d202fd667c414911f Author: rhead Date: Fri Mar 23 20:23:04 2007 +0000 whitespace changes commit ad4ac59b4c47bcfe1e7abe2bf81111c4de9dedd8 Author: hiram Date: Fri Mar 23 18:22:49 2007 +0000 Cleaned up old references. commit b88f86116cdf641528c01795bf27e4bc35a537cd Author: heather Date: Fri Mar 23 18:02:36 2007 +0000 remove extra line (not needed) commit bd0f02bf54935bbb62b72264d766314d76c46792 Author: rhead Date: Fri Mar 23 17:56:51 2007 +0000 Changed refs to pubmed format. Corrected page number on second reference. commit 1c27ff5f471a9e3f4f4f5a166383afd2d580d754 Author: fanhsu Date: Fri Mar 23 17:50:22 2007 +0000 Updated to work with KG III. commit 75da2934fb69c800a4259add7075750e4d67f67d Author: hiram Date: Fri Mar 23 17:48:22 2007 +0000 Add additional notes about two week updates, and src/product README files commit 8f066074812e2c3967ab12b6bc5ddfa98d5f6851 Author: fanhsu Date: Fri Mar 23 17:32:11 2007 +0000 Commented out debugging code. Might need it later. commit f8fce1791e0190c4089988915e16af2a096ce3d0 Author: fanhsu Date: Fri Mar 23 17:15:06 2007 +0000 Updated to work with KG III. commit f9cff26edb2324b9d839d745cb6276ae0df641c3 Author: kent Date: Fri Mar 23 16:38:40 2007 +0000 Fixing rare bug from keeping pointer into lineFile buffer past lineFileNext. commit 6b0b055f5daa9947a230987f6bed98e9d5e074ee Author: kent Date: Fri Mar 23 16:14:46 2007 +0000 Bumping up a sanity limit so as to handle titin and SCOP commit 7911f2957d7e32175f52286da3d02985527726a9 Author: kent Date: Fri Mar 23 16:00:56 2007 +0000 Adding -tToo option. commit c7d6027882ebfc7af910374133b7387087dbdabc Author: fanhsu Date: Fri Mar 23 15:34:35 2007 +0000 Added declarations needed to support KG III. commit cb674effec27f8eec8f3616e950b475a50d24b5e Author: galt Date: Fri Mar 23 15:00:30 2007 +0000 "Encode release log update" commit edb41d5d0096499183a46a568e09940a43315edc Author: galt Date: Fri Mar 23 15:00:16 2007 +0000 "Release log update" commit 2f5be54ff914b5f3f25d77a6415943d28e716050 Author: kent Date: Fri Mar 23 11:11:02 2007 +0000 Writing up pfam, and some of SCOP stuff. commit fa72726a92345c71ee86e6006abc196b3886ad45 Author: kent Date: Fri Mar 23 10:43:14 2007 +0000 Seems to work. commit 958a709af592bcce313e18f8e36269a3a84084db Author: kent Date: Fri Mar 23 08:21:15 2007 +0000 Seems to work. commit a043bcae8c1d52f6b56651ec610c054b4489a2dd Author: kent Date: Fri Mar 23 08:12:42 2007 +0000 Adding lineFileSkipToLineStartingWith commit b11d1078ba0435f0511db5e8c9f3ed638e63db8b Author: kent Date: Fri Mar 23 08:12:18 2007 +0000 Adding module for parsing hmmpfam output. commit 62f8551e3ede1c8c228e7dac688580e18a4b2ebf Author: kent Date: Fri Mar 23 06:29:51 2007 +0000 Moving spacedColumn stuff to library. commit 19a4b171ed45baac2ec2d3621c6f98addd72b6ff Author: kent Date: Fri Mar 23 06:21:28 2007 +0000 Adding -sizes flag and a test case for it. commit d8064db983cc87cdecdf22922fdc974de44c9f01 Author: daryl Date: Fri Mar 23 06:04:39 2007 +0000 correction to recombination rate data format commit e763f5620961b918acaedfa3ad8bb085991a448e Author: kent Date: Fri Mar 23 06:03:13 2007 +0000 Making compiling, not testing the default make target. commit 36997ba8dc5acc70cef76d957c1681534f19c214 Author: kent Date: Fri Mar 23 06:02:42 2007 +0000 Refactoring and adding a test case. commit 4f7560827a7c654412a66c0f501198419800313e Author: kate Date: Fri Mar 23 03:33:31 2007 +0000 Reciprocal best filtering of pairwise alignments for use in multiple alignment commit 7ffce08bcd49085d57e8d544098226da47b6da39 Author: kate Date: Fri Mar 23 03:33:07 2007 +0000 More multiple alignments commit a033cbbee7f074c18c131d3f35a657ba8e5544c9 Author: galt Date: Fri Mar 23 03:15:09 2007 +0000 added PDF/PS topmenu bar link and supporting output page commit 0a10977fdd78931e30c4c22faaeb01775a6e0e00 Author: galt Date: Fri Mar 23 02:20:58 2007 +0000 moved utility routine to convert eps to pdf over to the share-able library commit ad5114ac4d95e4a8d8c4c47df1462df1dd7b3f79 Author: galt Date: Fri Mar 23 02:19:06 2007 +0000 utility routine to convert eps to pdf commit 37effc9a635d7d3c9393e2af7fcf7c50322372c8 Author: fanhsu Date: Fri Mar 23 00:32:43 2007 +0000 Updated to adapt to KG III. commit 4197a7ead52e8b4e64eaf1b9cb99ec81ff159aa1 Author: hiram Date: Thu Mar 22 23:38:08 2007 +0000 Proper use of hgtaTrack define instead of string "hgta_track" commit 86640a86b74fa5f9a0ff1efe0df51c03e758119b Author: fanhsu Date: Thu Mar 22 21:46:36 2007 +0000 Updated gdbPdb table record for hg18 to point to proteins070202. commit ed6046c5941a1d9edfe95fbd39df0622457f90d6 Author: ann Date: Thu Mar 22 21:43:13 2007 +0000 added steps used to create 4 missing tables (chains to fr2) commit 9bf2f3cfeaab2edf0904259d7a946c2a56f0c38e Author: hiram Date: Thu Mar 22 20:46:59 2007 +0000 Properly disconnect from custom track db when in use commit 0c3b768cb5a839bac37e66a2526aaf24643722a2 Author: hiram Date: Thu Mar 22 20:33:03 2007 +0000 Properly free result and disconnect after custom track db query commit b67bd16c33c588052ebe491b71de918fb8153f23 Author: kate Date: Thu Mar 22 20:13:14 2007 +0000 Add 28way conservation commit 615ec3b10d375d94fbed507fb7aa383ba15ddd98 Author: hiram Date: Thu Mar 22 20:11:31 2007 +0000 Missing an sqlFreeResult after custom track query commit 8e1b25d1e7dd39227458f00f28fc542d46d27696 Author: heather Date: Thu Mar 22 20:07:27 2007 +0000 remove getCfgValue commit 0c59d48ee413e9a808d30f9d678c21f50f7b0519 Author: hiram Date: Thu Mar 22 19:50:57 2007 +0000 Can print out Data last updated: status for bed 3 custom tracks too commit 938486575683cb1b823085d997d9bfb923fc03c8 Author: fanhsu Date: Thu Mar 22 19:32:09 2007 +0000 Rewrote isSelected() logic to reduced many SQL calls into just one. commit 867792b8af01e99fa1cdee67c9e7e2a4d8b30fbf Author: ann Date: Thu Mar 22 18:22:01 2007 +0000 added matrix lines to chain blocks commit 56e990c8bfde86a8cfd16a2d6f6defb2144d7c39 Author: galt Date: Thu Mar 22 17:39:42 2007 +0000 making comment available again commit 7d3672dc7a27de42081cedb31f54d42f4b42d801 Author: fanhsu Date: Thu Mar 22 17:38:17 2007 +0000 Added special processing to check if an entry belongs to a subject before inclusion in the display (special processing for GSID). commit d7931242d94b3a1fba334559fbeaedda875fbd13 Author: fanhsu Date: Thu Mar 22 17:28:18 2007 +0000 Set gsidSelectedSubjList initial value to NULL. commit 074487a72202cb3555271e2b03bad8eb7120d85c Author: fanhsu Date: Thu Mar 22 17:21:30 2007 +0000 Added gsidSelectedSubjList. commit 3422fa891e1efe634ff4a748844ae5a3c18b3ea3 Author: fanhsu Date: Thu Mar 22 17:20:35 2007 +0000 Added gsidSubjList. commit 7521f0a3af145a490a5f264aa679585debe410db Author: fanhsu Date: Thu Mar 22 16:35:09 2007 +0000 Replaced writeString() with fprintf() for gsidSubjList file output. commit 0cb5d25a99939483ecd63aa008199c690e2b9dcd Author: heather Date: Thu Mar 22 16:26:51 2007 +0000 add all_est commit 713e84c8476ed77155f780e0f7865e7145686367 Author: heather Date: Thu Mar 22 15:26:01 2007 +0000 getCfgValue is now public commit 8a49878cd8a70da726d1ab84a6d9662fe2c271a1 Author: kate Date: Thu Mar 22 15:06:43 2007 +0000 1. Add support for scaffold-based target 2. Remove use of DEF file commit eb599276de77dbd75cb8482c912f428c10892d08 Author: galt Date: Thu Mar 22 15:00:31 2007 +0000 "Encode release log update" commit 4dec691326dd8a96f380792a75ba7c9d782c6c09 Author: galt Date: Thu Mar 22 15:00:17 2007 +0000 "Release log update" commit 3d92f3462cf5808c79c7bf698cec9c58d2588602 Author: kent Date: Thu Mar 22 06:59:14 2007 +0000 Removing version suffixes. commit a0af7b5b5c5d8f7520f492a3b094afe0b0d183f2 Author: kent Date: Thu Mar 22 06:58:43 2007 +0000 Adding -tweaked option. commit 6c55d77a2dd048bccce2114186ec0fd38054a5c7 Author: kent Date: Thu Mar 22 06:58:04 2007 +0000 fixing warning. commit 79d633265f70d3aabd3f517d0a791f825c0c0bb2 Author: kent Date: Thu Mar 22 06:57:04 2007 +0000 Not yet working. commit 18d9cddff777bfb34fe36c8004a460ff3121b3f1 Author: kent Date: Thu Mar 22 06:55:35 2007 +0000 Seems to work. commit 2d9556dd22f343c22283b2ecef1bfc755a1c2f42 Author: kent Date: Thu Mar 22 06:55:22 2007 +0000 Adding a few new utils to makefile. commit 5b8740fc813015ac24f8c71013e9f3eb616ab22f Author: kent Date: Thu Mar 22 06:39:22 2007 +0000 Adding in a bunch of stuff to load the database, and a little bit of proteome browser stuff. commit 9fa6ce796e20e40ee45352a63b43a40e1b1e0f68 Author: kent Date: Thu Mar 22 06:38:29 2007 +0000 Seems to work. commit fd84d25fef670f347f961959408d9420f28aee62 Author: baertsch Date: Thu Mar 22 01:33:22 2007 +0000 add lift and superfamily options to sample download script commit d043f257211fc58e55ba021e489668f4d3638c48 Author: baertsch Date: Thu Mar 22 01:32:47 2007 +0000 remove unused tables from download commit d64ad8dea28a38c8b45795ae497337dd695cb4da Author: baertsch Date: Thu Mar 22 01:32:03 2007 +0000 add -f and -p options for pseudogene track and superfamily tables commit c91533dd5585c697cb2e803553bfa7ca38419053 Author: baertsch Date: Thu Mar 22 01:31:15 2007 +0000 remove unused tables from download, fix bug with randoms commit 9d6e3e4ed982637a8f1f171e99e9b1f93e047ceb Author: rhead Date: Thu Mar 22 01:00:04 2007 +0000 Removed links (from trackDb.ra and the track html) to the Genoscope comparative genomics browser, as it no longer exists. Rachel confirmed this with Olivier Jaillon at Genoscope. commit 5577070759c1e35b096537f535d5578cbcc6046e Author: heather Date: Thu Mar 22 00:03:06 2007 +0000 add chimpParalogy to tableIgnored for human commit c6dd708526d7b5288d40cacdede65330bea743df Author: ann Date: Thu Mar 22 00:01:33 2007 +0000 adding chain and net blocks so that I can get the ordering correct commit c59cd00fd29c54b254eca60510287417a8cdb69b Author: hiram Date: Wed Mar 21 23:51:22 2007 +0000 Rework the gold tables, and add ctgPos2 to show contigs and scaffolds properly commit 301d22e4fb9b1452fe17a348497f505a026124a0 Author: hiram Date: Wed Mar 21 23:42:02 2007 +0000 Adding ctgPos2 track commit 4409c547f0e3ff0f9333319a305951f39db4a668 Author: hiram Date: Wed Mar 21 23:40:34 2007 +0000 For the contigs track commit 8c352f184db23731b2544dd7704c373eca25a1f4 Author: rhead Date: Wed Mar 21 23:33:53 2007 +0000 Removed links (from trackDb.ra and the track html) to the Genoscope comparative genomics browser, as it no longer exists. Rachel confirmed this with Olivier Jaillon at Genoscope. commit 57eadbd1a69d5e55fab96cf8fd63478dd8aea328 Author: rhead Date: Wed Mar 21 23:18:35 2007 +0000 whitespace changes commit 8f7c53a92ffc5813c13d9eae474fb50b27c9db9d Author: kent Date: Wed Mar 21 23:09:54 2007 +0000 Making program alert you to unknown source, so hopefully something like the trembl/tremble mixup won't happen again. commit 39260663708b7549ef82fc89187a8f55f60ff92c Author: kent Date: Wed Mar 21 23:01:59 2007 +0000 Coping with chanage from bestorfScore to cdsScore. commit 6829ab3f514df6d0fa9d3a2cb51a2d33e06a00cb Author: kent Date: Wed Mar 21 23:01:39 2007 +0000 Got rid of some of the obsolete info. commit ca09d81288ba29773fe3eb93a1f1572faf6ef019 Author: kent Date: Wed Mar 21 23:01:15 2007 +0000 Adding a makefile for all the txCds programs. commit eba19e3837cecf93dcc77b06684559fc8c338bba Author: fanhsu Date: Wed Mar 21 22:44:52 2007 +0000 Defined DB source where the protein comes from. commit 1dbcdc131fbd965d9a3be209a54c8d321e06b0d7 Author: hiram Date: Wed Mar 21 22:07:57 2007 +0000 Add Repeat Masker and Downloads directory. commit 25dd91f50986535d9809403d2fe278c456a39fe1 Author: galt Date: Wed Mar 21 21:31:19 2007 +0000 fixed link missing hgsid and some other commented-out cleanup commit 2cab0048b379df3b84f92801f17acf58b65ef1d9 Author: heather Date: Wed Mar 21 21:17:55 2007 +0000 typo in comment commit d5e0688efd7a986673ca264478542e1192d1205e Author: hiram Date: Wed Mar 21 21:04:04 2007 +0000 Eliminate duplicate function getCfgValue() - make it public from jksql.c commit 08c8cdc120ad664a98ddeddba297c7f39b13122e Author: archanat Date: Wed Mar 21 20:29:24 2007 +0000 added oryLat1 to all.joiner rule. Also added the new track WM+Sdust to the tables ignored section commit 423bee7950d9d532c963609fc7baba17d42bc856 Author: galt Date: Wed Mar 21 19:53:13 2007 +0000 adding saveSubjList() function to save the filtered list of subject gsids for other applications to use commit 4abe8d8b7356bcdcfa8e53ac830cab7ccb63f028 Author: galt Date: Wed Mar 21 19:51:38 2007 +0000 removed "comment field" by commenting it out. commit b70cfaa5d928b1c6f954e0b0a87376caf2c3eeaf Author: baertsch Date: Wed Mar 21 19:06:31 2007 +0000 add lift for fugu commit bf0f0c530d5c04024eb8422bcf5a57c0a11ca981 Author: baertsch Date: Wed Mar 21 19:03:39 2007 +0000 add -p load pseuodgene track option. Not loaded by default. commit 169249f4bb48f0aff8c77597c8d2a41d64e6e5e7 Author: donnak Date: Wed Mar 21 18:26:38 2007 +0000 Added tag for stickleback data use section. commit a449ec402a8a212910e7f19ce425154a39b2d494 Author: heather Date: Wed Mar 21 18:26:27 2007 +0000 use iSync alternative commit ef288c92aa917bd460f5e01db6efea698c017697 Author: donnak Date: Wed Mar 21 18:26:00 2007 +0000 Added announcement for stickleback. commit f54fc445a25b8bd819a89f00cbe888b6914bf331 Author: donnak Date: Wed Mar 21 18:12:46 2007 +0000 Edited this page. commit af80f6603331a20ec60ecc2fe8f287f1804dd93e Author: hiram Date: Wed Mar 21 18:08:48 2007 +0000 Finish off measurements for WindowMasker commit 5efb4b738daf4ce03b28c8fdafd6931e32316064 Author: ann Date: Wed Mar 21 17:55:45 2007 +0000 added ensGene search (because the naming scheme changed since fr1) commit 2e7c1d5c885484431b7ee861245a4fad41740163 Author: heather Date: Wed Mar 21 17:36:13 2007 +0000 small cluster files commit 374152e2f8a2bf511157335b6c40ebdf5a208c2d Author: hiram Date: Wed Mar 21 17:33:44 2007 +0000 Complete oryLat1 alignments commit f8dc3e98f45e8797065f38766b6e317a6a323f3e Author: hiram Date: Wed Mar 21 17:32:57 2007 +0000 Add repeat masker track and data, add mrna.fa and xenoMrna.fa to downloads commit 0ca5f73ba001d1f20b538ebcf5120f17bc4d2371 Author: hiram Date: Wed Mar 21 17:32:20 2007 +0000 Add the mrna.fa and xenoMrna.fa to the downloads commit 64d964ceb90ad5a2faf01d69f88f8534504250bf Author: heather Date: Wed Mar 21 17:31:23 2007 +0000 never mind about ooc, it's fine commit efc58acdff20f32a668668ce246d96699bdb7a9b Author: heather Date: Wed Mar 21 17:27:53 2007 +0000 ooc to iserver commit f18e5c090002068dcde588ea8fcf396a4ee04c1e Author: donnak Date: Wed Mar 21 17:11:18 2007 +0000 Added gasAcu1 credits. commit 5c1724296d9e3ba5c62b9756df3357c62466d172 Author: heather Date: Wed Mar 21 17:10:17 2007 +0000 first attempt at bosTau3 commit 16cacea7bce58fe5e33be91e5b4624dcac2de658 Author: ann Date: Wed Mar 21 17:07:05 2007 +0000 added some details commit 73b0b58d5a82151f1a454d4a259c3044c48a7230 Author: kate Date: Wed Mar 21 16:46:11 2007 +0000 Allow missing genome setting in custom track input commit fe10c75a4057acf791fe9dd6353beadd5c4524c8 Author: donnak Date: Wed Mar 21 16:19:05 2007 +0000 Added gasAcu1. commit 446533c90e01e33eb5e09dbf842f9dd69bb9390f Author: galt Date: Wed Mar 21 15:00:32 2007 +0000 "Encode release log update" commit f20ae29f48e2d9e21925053e332202881536921f Author: galt Date: Wed Mar 21 15:00:17 2007 +0000 "Release log update" commit 7df3b173280e83be336f995fff005d35e1590b5b Author: kent Date: Wed Mar 21 07:09:58 2007 +0000 Describing what we do for the homologous genes, which is sufficiently improved that it is now labeled orthologous genes. commit 4f72dc8a01ed158187131b73d93c34984a76241f Author: kent Date: Wed Mar 21 07:04:13 2007 +0000 Connecting to refSeqSummary via knownToRefSeq since it doesn't have the .version in it while kgXref now does. Mark. Grrrr. Maybe better in the long run, but will break much now.... commit 236819bd9cdd75a5a587db57a514651906b61c50 Author: kate Date: Wed Mar 21 04:25:32 2007 +0000 Remove Gene checks from detail page -- no longer needed commit 88253e0d9b87e8b78e0b9f4dc9e36ca3549e3df4 Author: kate Date: Wed Mar 21 03:43:07 2007 +0000 Add Gene checks to Gencode Genes details page commit 0c100d0552a956973e4c1310cb4e22d18fd78c59 Author: heather Date: Wed Mar 21 03:03:33 2007 +0000 add cnpSebat2 commit 1c59c1755c8648f57517b536924fd999d98e12d4 Author: heather Date: Wed Mar 21 03:00:38 2007 +0000 one less column in hg18 commit ba7947e84681d192657d769d9b7d0a11982e6891 Author: galt Date: Wed Mar 21 00:07:18 2007 +0000 resurrected! commit c0eb4500800c75dd57d895efaec6ca46108c2ce3 Author: rhead Date: Tue Mar 20 22:35:10 2007 +0000 Added a 'target=blank' to a link so it will open in a new window. commit 4e0e3ebb33573a3c67df3080d3e3f1e91b54d041 Author: galt Date: Tue Mar 20 22:26:59 2007 +0000 removing possibly troublesome columns commit d3de07834a534f823148fceabf4201880d1bc813 Author: rhead Date: Tue Mar 20 22:26:29 2007 +0000 Fixed broken links to several Nature papers by removing '_fs'. commit 25a56ad2e453d690a3343d2b166857cce07d6810 Author: angie Date: Tue Mar 20 22:23:09 2007 +0000 Use hGetMinIndexLengthDb instead of kludging around maxChromName when loading a custom track that might be for a different db than hGetDb. commit b06a95b21f5e3c20c679a1469e21508541406d32 Author: angie Date: Tue Mar 20 22:20:10 2007 +0000 Added hGetMinIndexLengthDb. commit ea31a49570c684f52fc7bf1db82033ab0bf4d2d7 Author: rhead Date: Tue Mar 20 22:15:57 2007 +0000 Looks like Genethon changed their site from www to w3. Changed link accordingly. commit 80cfece4368945e069e1bd5da5c64f8134a7061a Author: rhead Date: Tue Mar 20 22:10:38 2007 +0000 Fixed broken link to Nature paper by removing '_fs'. commit 5250ba70c3d8e3b47d82761a99eaed050dd5d415 Author: rhead Date: Tue Mar 20 22:09:08 2007 +0000 Fixed broken link to European Institute of Oncology. commit 7fa0de2279ab17d945762c520c992a0dd913e86b Author: rhead Date: Tue Mar 20 22:01:44 2007 +0000 Looks like Genethon changed their site from www to w3. Changed link accordingly. commit e7bd77aa677eb9cfcb513ce1e0e522156af35c7e Author: rhead Date: Tue Mar 20 21:54:01 2007 +0000 Fixed broken links to Nature paper by removing '_fs'. commit 8a35fe1e2df94df6ebd44c040d8fd61d4e6b4f64 Author: rhead Date: Tue Mar 20 21:42:18 2007 +0000 Removed part of the a link to Gish lab that was causing it to break. commit 4a67226a2f05e9bf77d1c568513cd69d689f8f5e Author: rhead Date: Tue Mar 20 21:35:43 2007 +0000 Fixed broken links to Nature paper by removing '_fs'. commit c628ce24b7c16fc5f044b7f0984de69a3e620717 Author: rhead Date: Tue Mar 20 21:25:03 2007 +0000 Fixed broken links to Nature papers by removing '_fs'. commit e06853777812519c2bba971903e6346002fb78f6 Author: rhead Date: Tue Mar 20 21:07:55 2007 +0000 Fixed broken link to GRIB. commit 71421ec9cd082439f10cbcdfd80c36591be75ac7 Author: angie Date: Tue Mar 20 21:04:19 2007 +0000 At David's request, underline the cDNA sequence in window, add a jump link to start of cDNA sequence in window, and open the frameset there. commit e64ceb1708c65614a7605472b4e3bef4d55e0405 Author: heather Date: Tue Mar 20 21:01:45 2007 +0000 add a tweak commit aa9c7e90919291b67b5c2dfd85d8bbd2c938174e Author: rhead Date: Tue Mar 20 21:01:42 2007 +0000 Changed a broken link to a paper. commit 1ac6fe67c6251fd78bdec3ce1a40b01828080432 Author: rhead Date: Tue Mar 20 20:53:39 2007 +0000 Added 'nemo' to a broken link to restore its function commit e152b3ad5901307dd6c0788de8ef4661743cb689 Author: baertsch Date: Tue Mar 20 20:05:55 2007 +0000 move debugging statement commit 91e3abc3fe041a3ec99ad7326df76cbc30986423 Author: rhead Date: Tue Mar 20 19:44:31 2007 +0000 Removed the 'index.html' off the end of a link that was causing the link to break commit c2931facd86af160cdc97f28e64589e420568d5c Author: rhead Date: Tue Mar 20 19:27:57 2007 +0000 Fixed broken link to Nature paper. commit a19a6c4d3d0322be2741916c985192fb1be2f6a2 Author: rhead Date: Tue Mar 20 19:08:56 2007 +0000 Fixed broken link to Nature paper. commit 79bfb00b3bff4460c63150cf7b7186eeb7f5d665 Author: ann Date: Tue Mar 20 16:28:06 2007 +0000 typo commit 695088acc733cf70a7b3d866c00327545248de2e Author: ann Date: Tue Mar 20 16:22:04 2007 +0000 added fr2 assembly where appropriate commit f07f768a4fe934f1ac69404d888c498a413da80a Author: kate Date: Tue Mar 20 16:09:38 2007 +0000 Temporary experiments with multiz, marked alpha commit a3fa9b2917cd71410e8b49edf619fa16d9edd798 Author: ann Date: Tue Mar 20 16:01:38 2007 +0000 edited searches to values that work in this assembly commit b6abc1f71d867162ff4ac03af1db8140fe189c04 Author: fanhsu Date: Tue Mar 20 15:22:42 2007 +0000 Updated to fix a bug that is causing RR crash. commit 568ca879a11a4b20329d9d3da19d2a185530ae21 Author: galt Date: Tue Mar 20 15:00:28 2007 +0000 "Encode release log update" commit a5dcf9dd9946120877408f8b7a94bda5e3387eff Author: galt Date: Tue Mar 20 15:00:15 2007 +0000 "Release log update" commit 28fc28f583244ebeb5b9d71a9402011c95986f76 Author: mario Date: Tue Mar 20 06:52:48 2007 +0000 The right augustus.html is now one level up in the human directory. commit 477939b4af100b68f3ddeee717ff33168c593eb8 Author: angie Date: Tue Mar 20 02:57:13 2007 +0000 Added new -noStrict option to hgLoadBed so tests of *Bad bed tables won't abort. commit 0af01341a3dc203f658912458e9366d3374d1133 Author: angie Date: Tue Mar 20 02:56:33 2007 +0000 Since strict and allowStartEqualEnd are now the default behavior, removed -strict and -allowStartEqualEnd and updated usage. Added -noStrict option for test loads of tables with coord problems, to test checkTableCoords. commit 68bd47ddb713b5d4cbca5a316fc8cc82a853d681 Author: angie Date: Tue Mar 20 02:54:59 2007 +0000 Added a new view-ali-in-window link to the GenBank details page. Link goes to htcCdnaAliInWindow. Uses new ffShAliPartPart to do the actual display. commit 48826576434538e8a6f82b919d46a199b1881825 Author: angie Date: Tue Mar 20 02:53:04 2007 +0000 Added ffShAliPartPart, which extends ffShAliPart by accepting two lists, partial and whole, and displaying the whole needle but with the partial portion in bold, plus the partial haystack and blocks. commit d69fd04ed6d7349eb53f32239f70fe164d4811ba Author: galt Date: Tue Mar 20 00:15:29 2007 +0000 allow it to pick up subdirs too, in this case the loader subdir has 3 utils Hiram made for use by the custom-track database system and since that has finally been activated, we now need the subdir. commit 9be461a91173924ff8dfa5b10a4eec3b022dfa4a Author: ann Date: Mon Mar 19 23:53:00 2007 +0000 backing out Heather's change in -r1.7. commit 855d321c8e19d7cecb0168b183ad0486627ca057 Author: heather Date: Mon Mar 19 23:18:39 2007 +0000 change error tag commit 1c2f22f6643d40066b9cb18b0368eb9a49911e75 Author: heather Date: Mon Mar 19 23:18:02 2007 +0000 make error message more consistent commit d22b6b917f76188c0a8c23e65ea0ad6c90850d0c Author: hiram Date: Mon Mar 19 23:15:30 2007 +0000 Added note about using ssl libraries if mysql needs them. commit 96eec374558aa3b5a3d4cf85d36f59625414236e Author: heather Date: Mon Mar 19 23:15:21 2007 +0000 sample input for testSearch commit 46cf55b6ae16c608620926ec55d71cedf264ae79 Author: heather Date: Mon Mar 19 23:02:38 2007 +0000 add call to doSearchRobot commit c9d0b6f441aa5360894e28c12176b63793831d26 Author: heather Date: Mon Mar 19 23:02:24 2007 +0000 new robot commit 09d50a7f43f407938bfd54293f75a76f63a4a1a2 Author: kayla Date: Mon Mar 19 22:51:05 2007 +0000 Changed o_db to o_Organism for the nets/chains to fr1 commit eca6f859703f0a5f56bf9e93feb726887913f662 Author: angie Date: Mon Mar 19 22:50:56 2007 +0000 Oops, file existence must be tested before calling customFactoryParse* functions. commit b5c42f72097a817a051bf921aa7cc345bfdeae88 Author: heather Date: Mon Mar 19 22:45:30 2007 +0000 standardize commit d8c14340a1c685475ad22fab737abb535e3e8d1d Author: heather Date: Mon Mar 19 21:37:12 2007 +0000 tweak verbose statements commit 780ed0d62024ea5e79d600a3eec744643b7aada7 Author: heather Date: Mon Mar 19 21:29:06 2007 +0000 make downloads commit d9a6aa75da546e5140ded17a880920c0a06680d1 Author: hiram Date: Mon Mar 19 21:03:06 2007 +0000 Properly 1-based on the position example commit e2151f4ce501d292e3bb05eb61c4983ae7305186 Author: heather Date: Mon Mar 19 18:45:39 2007 +0000 better way to get cart commit 4b4362978c31f202a7c5d19be6e7a604454fc920 Author: heather Date: Mon Mar 19 17:26:55 2007 +0000 fix typo commit 36800d9a171a98ab3287661bdc860d85fdd1a852 Author: galt Date: Mon Mar 19 15:00:23 2007 +0000 "Encode release log update" commit 66d6dc337b348b193d25bc5c800b706d8030b137 Author: galt Date: Mon Mar 19 15:00:12 2007 +0000 "Release log update" commit ab7471ca34faaea5aebc710681ba4ecaa995571c Author: mario Date: Mon Mar 19 07:21:27 2007 +0000 Made the AUGUSTUS tracks a compound track with two subtracks. commit 0fe67572e01954ab86604e5f4362948bd33546b9 Author: mario Date: Mon Mar 19 07:19:42 2007 +0000 Made AUGUSTUS tracks a compound track with two subtracks. commit aae5b0cf047b5a19b87642c206a66b2cba660c9c Author: lowe Date: Sun Mar 18 21:55:08 2007 +0000 Added field hmmScore to data type snoRNAs commit 2700f5aa16217d5735802248c24cea9a1f659027 Author: lowe Date: Sun Mar 18 21:53:56 2007 +0000 Added new field "hmmScore" to snoRNAs data type commit eec9b30539e968fe3fb440593b900767d28d4d5e Author: kent Date: Sun Mar 18 21:09:59 2007 +0000 Seems to work. commit 03cc6d18a88742920202d24d59680fa14e99c8bc Author: markd Date: Sun Mar 18 19:05:56 2007 +0000 fixed bug not reversing the query range when orientation is changed commit 510997383eb3265a5f06c259138f28ff98910749 Author: markd Date: Sun Mar 18 18:19:41 2007 +0000 added option to drop alignments completely contained in the exon of a another alignment commit 46e677cd11d5555cadf8f5ba8c0cccb26616e8ad Author: markd Date: Sun Mar 18 17:24:53 2007 +0000 added -exclude option commit c279021530e23199a388727edc34226205323f26 Author: galt Date: Sun Mar 18 15:00:22 2007 +0000 "Encode release log update" commit aa58fdcbf461df56b587189cae34b5f71e1f757c Author: galt Date: Sun Mar 18 15:00:12 2007 +0000 "Release log update" commit bd9417dd55bce44690904a7c986a1379e87019b1 Author: kent Date: Sun Mar 18 02:42:39 2007 +0000 Creating versio of kgNotes.txt that just contains the build procedure. Making it use variables rather than hard-coded paths and db names, so should be easier to make into a script that can be used on multiple organisms/databases later. commit 5e2b16b1beab4506a6366d327f1606eda8f6dd4c Author: kent Date: Sun Mar 18 00:10:14 2007 +0000 Adding uniProt option to specify a particular uniProt database. commit a01e0a8b850f3f7dc5cbbb6eb1662631d3aa5d88 Author: kent Date: Sun Mar 18 00:04:19 2007 +0000 Adding tempDb option to help build hg18b without having to do the messy sym-link from hg18 first commit 1bff9a4e1dae294a8b0ac28ad6bedb9f8b82783a Author: kent Date: Sat Mar 17 23:12:08 2007 +0000 Adding summaryTable option. Making it try looking up refSeqs with and without the .version commit 31d5cabe771b0e7b55fd06b5e3e4e9cc1f80d192 Author: kent Date: Sat Mar 17 23:10:59 2007 +0000 Giving refSeq proteins a chance to be in the proteinId field. commit 0f80ae34c59885de41ebe6008da93de6da3ed4ad Author: kent Date: Sat Mar 17 22:40:25 2007 +0000 Adapting to accession.version rather than just accession. commit bda3f1a7c845e87370ae15887bbab3fea8f2f91c Author: kent Date: Sat Mar 17 22:38:40 2007 +0000 Adapting this to using txCdsPredict instead of the old mishmash. commit 03ceff5c97ede71a2948db386e13d74d1c652d7e Author: kent Date: Sat Mar 17 22:37:36 2007 +0000 Adding a few more notes on KG3 build. Most of this stuff is now going in the somewhat slimmed down ucsc10.txt commit f8b31bca783c9c3cb7e9cffb38d5a8ee68851547 Author: kent Date: Sat Mar 17 22:36:06 2007 +0000 Changing bestorfScore to a more generic cdsScore. commit 4ec270f91571a8ab978542db57614ce81b31ae77 Author: kent Date: Sat Mar 17 22:35:28 2007 +0000 Getting rid of genbank and wBorfScore fields. commit 983b5205676c60a4af3799f334356b39cf6e3a9b Author: kent Date: Sat Mar 17 18:54:29 2007 +0000 Allowing genes without mRNA evidence to get antibodies through. commit 40ea3a170f3b0b287a12b59469b14aed3f23b44a Author: kent Date: Sat Mar 17 18:44:44 2007 +0000 Adjusting to handle antibodies, that have no mRNA. commit 34568832341a060c9f474918e28d9e6c0d04e50d Author: kent Date: Sat Mar 17 18:12:41 2007 +0000 Adding support for varSplice in description, gene, and gene logic tables. commit 57fb195f7dc33cdd7f6d96c079a7d8d7cf747347 Author: kent Date: Sat Mar 17 18:10:27 2007 +0000 Adding var-splice accessions to some additional tables. commit ca758bf84b6a9cfe44853bfdae252e07d129eec9 Author: kent Date: Sat Mar 17 17:57:12 2007 +0000 Bumping size of SpAcc to accommodaate alt-splice varients. commit 3823be30e379fd07cffd6c8a2000fb96d98fc429 Author: markd Date: Sat Mar 17 17:45:05 2007 +0000 added support for obtaining orientation info files commit f96763ebab592fd2441cf34081f65fc4e91b7517 Author: galt Date: Sat Mar 17 15:00:26 2007 +0000 "Encode release log update" commit d890a0e8e6c4455fd9aad033081786b169d4aae5 Author: galt Date: Sat Mar 17 15:00:14 2007 +0000 "Release log update" commit d2db652b48d57af66545bc66a3fd433463f06dd7 Author: heather Date: Sat Mar 17 06:07:18 2007 +0000 read input cases and compare commit edefe44b68386378e4e138295f06806054f22208 Author: kent Date: Sat Mar 17 05:37:28 2007 +0000 Using new accession format: uc123abc.1 commit 81416cc31179b10c3c64ca30d63ec1d7ac2f3050 Author: markd Date: Sat Mar 17 05:28:12 2007 +0000 more image ids commit 8908e1cad1209eae62952aaeed287ab5d23f1b48 Author: kent Date: Sat Mar 17 04:20:58 2007 +0000 Adapting to antibody name change. commit 333ad0041060bb790995fb13ecf07d210b7ac33b Author: kent Date: Sat Mar 17 04:14:08 2007 +0000 Removing orthology from this step, since it now happens upstream. Adding a little accounting. commit 832672c7bdc08709e779cf54019289217a9bdefb Author: kent Date: Sat Mar 17 04:04:15 2007 +0000 Adapting to using txCdsPredict score instead of bestorf score. Also coping with accession.version rather than just accession. commit 9389114614c9b3aa25e4451473f1eb6365b55ad0 Author: kent Date: Sat Mar 17 03:31:22 2007 +0000 Avoiding fractional last codon in fragments. commit 950d06f9993183d677d239e07ac88a63bf60ab40 Author: hiram Date: Sat Mar 17 00:21:21 2007 +0000 Proper order for Assembly(gold) and Contigs(ctgPos2) tracks commit 94782e945d47e6558bb4ab646e6ba81262d4bc61 Author: hiram Date: Sat Mar 17 00:18:39 2007 +0000 Adding ctgPos2 definition for contigs track commit de1eb42ad194b9d06b56f8e0fc52a71e25bce49d Author: galt Date: Fri Mar 16 23:50:19 2007 +0000 support reporting multiple missing values as a warning instead of just errAbort commit 0b83a28405cfc2cd1c3dfed6d459a530397c3f0e Author: fanhsu Date: Fri Mar 16 22:53:35 2007 +0000 Updated GO URL. commit c77ef816849a42f2279d3b22a76a986d3c2502e1 Author: fanhsu Date: Fri Mar 16 22:52:17 2007 +0000 Updated Amigo URL. commit 121472d8e58ff442a10c981937889b4e44ab7298 Author: fanhsu Date: Fri Mar 16 21:56:35 2007 +0000 Updated URL to GO page. commit 5c49aeb644449791f8f2c62a41f3b3aeff60e4b0 Author: galt Date: Fri Mar 16 21:17:28 2007 +0000 fixed err caused by previewing lines: later reuse has no access to the original linefile object, so segfault when it tries to use it in some input error reporting errAborts. Fixed by making alternate versions that check first if the lineFile is found, and if not then does NOT use that info in err msg, i.e. line 35 of test1.data, commit 8747f73082877e8ea8ce79654b0791c1cfa1334d Author: kent Date: Fri Mar 16 19:00:51 2007 +0000 Bumping max size of acc.ver commit afbf801d1f8a5a04f03758738a3cb0e28406028d Author: kent Date: Fri Mar 16 18:53:29 2007 +0000 Adding txCommon module for stuff that many txXxx programs need to share. commit ab3ff8e2ac27a4b1fb0dbcc9e57a8328d6107edd Author: ann Date: Fri Mar 16 18:48:12 2007 +0000 adding info about saving a loaded session commit 7d30e7e74e639560fea92a840453412a1f22ef03 Author: archanat Date: Fri Mar 16 18:30:26 2007 +0000 corrected an example that has positions out of range on the chromosome commit 199fc23fb9fbd41c06225bb3aaecb7b8650954c0 Author: kayla Date: Fri Mar 16 18:18:01 2007 +0000 added gasAcu1 commit 3b7d4a3eb931861754db863e058df6f751102b33 Author: kent Date: Fri Mar 16 17:48:40 2007 +0000 Changing output from orfInfo to the cdsEvidence other programs are using. commit 8bd56ad96e664ae42e9d42d6789a661f635083b6 Author: kent Date: Fri Mar 16 17:34:49 2007 +0000 Adding cdsEvidenceCmpScore. commit f1865977c9f5c9e0690baa8bacd6c6248a74cb51 Author: kent Date: Fri Mar 16 17:31:02 2007 +0000 Adding to test set a case that caused a crash before fix. commit 15b8c310dc6a698988dca2795abdc1d930abd5a0 Author: angie Date: Fri Mar 16 17:14:53 2007 +0000 Added formMethod cart var for debugging. commit 6321382dea0212fbb23680cea516e2be3cb77251 Author: hiram Date: Fri Mar 16 17:08:48 2007 +0000 Why not check the input as it is being read rather than after the fact ? commit 81b691ec757097777d29f944beb77e018b6ad9bb Author: hiram Date: Fri Mar 16 17:07:15 2007 +0000 Better error reporting on bad bed chrom coordinate input commit 90d33a77d64491c2f7610e49894d1c991a3f1283 Author: kent Date: Fri Mar 16 16:51:30 2007 +0000 Improving comment commit 0d61b3eca7ad390c7570cdb978a53253dc335a39 Author: kent Date: Fri Mar 16 16:51:13 2007 +0000 Adding -bad option to print out info about misses. commit 076f5b3ae4acf4c21d79f24b2fa60b896dff0bcd Author: galt Date: Fri Mar 16 15:00:29 2007 +0000 "Encode release log update" commit 62c90a94d5c8c831e0d3f090a91c4cf2891f95a5 Author: galt Date: Fri Mar 16 15:00:15 2007 +0000 "Release log update" commit df75738fb5be2489edd59a793036f2703666e99f Author: kent Date: Fri Mar 16 09:19:42 2007 +0000 Adding .version to all accessions. Also making and accVer.tab file to help translate between data with and without versions. commit adec71671fd4bc5a847a939965684e934492d3a9 Author: kent Date: Fri Mar 16 05:37:31 2007 +0000 Seems to work. I hope... commit 0c768f65d6b322885d9de3e608f7f47c6708b9c2 Author: baertsch Date: Fri Mar 16 03:32:54 2007 +0000 lookup orthlogs in other gene sets using maf commit df8faae1a9a1183d990e6c2275e937813167c409 Author: kent Date: Fri Mar 16 03:09:07 2007 +0000 Debugged a write-past-end-of-array problem. commit 0e7d96737f6bd74f6760182be3de2d83a4b0dd64 Author: kent Date: Fri Mar 16 02:30:57 2007 +0000 Maf flag seems to work on little test set commit 0e20c8f5b900177e677b9f120c0c5da43d38f97f Author: hiram Date: Fri Mar 16 00:07:52 2007 +0000 Properly handle bedGraph column, it can be anywhere, and check for chromEnd of 0 commit 53b6bfabe39b9f32b8d13f347cce3f491033f1b8 Author: angie Date: Thu Mar 15 23:31:31 2007 +0000 Fixed slurpAutoSql to recognize enum fields. commit 1fa4470b05da3d5d064d85798703bba6e7b23022 Author: angie Date: Thu Mar 15 23:25:09 2007 +0000 Added formMethod cart var for debugging and errAbort in a situation caused by out-of-sync gene and canonical tables that would lead to a later segv. commit eaf1d891e20203bdaefd74fc273a30115650659c Author: heather Date: Thu Mar 15 22:53:53 2007 +0000 simpler solution to previous commit commit 6015c11d76c3e981f26f15451f4404821b8ad182 Author: markd Date: Thu Mar 15 22:45:05 2007 +0000 added more image ids commit bd847fbe82d72fe596f23ecfe2def7dd7c22115f Author: heather Date: Thu Mar 15 22:44:50 2007 +0000 provide link to open HapMap track from SNP track commit 12f5c5b9d6bb89daa6de88a295087bedb260a5d4 Author: angie Date: Thu Mar 15 22:33:11 2007 +0000 Added cartCopyCustomTracks to cartLoadUserSession and cartLoadSettings, so that a user who loads a session that contains custom tracks cannot modify the original session's custom tracks. commit 2b97824c6317149da139d97e48362e50f3b87376 Author: angie Date: Thu Mar 15 22:31:39 2007 +0000 Added customFactoryParseAnyDb, a variant of customFactoryParse that doesn't die if the tracks are for a database other than hGetDb. commit 69d91817ab547732a5186f2ca94cba268d237a15 Author: aamp Date: Thu Mar 15 21:49:50 2007 +0000 Added to the methods description on the ACEScan track. commit 0171d71c14386c7a76e590ce72f3d172f05c5e36 Author: aamp Date: Thu Mar 15 21:46:46 2007 +0000 Made ACEScan track purple and fixed some HTML. commit 1950c383fa9bca59094b11c17a71e5d06b14ab36 Author: heather Date: Thu Mar 15 21:28:21 2007 +0000 add syntenic nets commit bb72c2370912f7a8414449bf2f06f8704a5701a4 Author: heather Date: Thu Mar 15 21:15:01 2007 +0000 syntenic nets commit a4ea3401851b05a22ae37c2fe45b273bc695291b Author: heather Date: Thu Mar 15 21:12:10 2007 +0000 tweak to previous commit commit 9119f68fe0a7df173dee3e41f51002d856ab4ce7 Author: heather Date: Thu Mar 15 20:52:08 2007 +0000 add blurb on minimum totals per population commit d6079bfa2cf587018eb2588305f54793b4d2ec0d Author: hartera Date: Thu Mar 15 20:20:45 2007 +0000 Added generic header for doBed6FloatScore(). commit 4e7a2f533d03030ad3f500155b590cd3f404e65b Author: kent Date: Thu Mar 15 19:52:28 2007 +0000 Starting to implement -maf option for comparative genomics weighting. It just produces copious debugging output at the moment, but the debugging output is starting to look good. commit a9583d7cb78e2fef429046d95f718a1e55e569c3 Author: ann Date: Thu Mar 15 18:06:37 2007 +0000 adding kayla, brooke, and archana to email notification list commit 63b59202eca08562d6ec4476b2a13f2983c12b41 Author: fanhsu Date: Thu Mar 15 17:49:35 2007 +0000 Removed hgNotYet from BROWSER_BIN. commit 1074044a1a652518b9f6c0a6f3b496c8b87c342e Author: fanhsu Date: Thu Mar 15 17:00:20 2007 +0000 Added subject ID into header line of FASTA output. commit 9d1a5510d9f2cfee69dddb2173f88eda578c1dde Author: fanhsu Date: Thu Mar 15 16:56:18 2007 +0000 Added subject ID to FASTA file header. commit 3a4b7315e7fbd4748d90a73de7a6e2b7eccc1cb1 Author: ann Date: Thu Mar 15 16:53:06 2007 +0000 typo commit 19f106ac6c03c9a81beefe12cc829bc6531ba5fb Author: galt Date: Thu Mar 15 15:00:31 2007 +0000 "Encode release log update" commit 8bcd9d0ac37018d77f9398ea64b6041c8dba7728 Author: galt Date: Thu Mar 15 15:00:17 2007 +0000 "Release log update" commit a850a31bb0a6ff7702b75f2a36fa89bad9262d1f Author: aamp Date: Thu Mar 15 09:46:02 2007 +0000 Added first cut of ACEScan track. commit 407bbc549718be210d68e33b8b02935c3abfe5d5 Author: kent Date: Thu Mar 15 08:16:33 2007 +0000 Adding -nmd option. commit b3469dd5cca626ac4877a99efdedf553735c2d94 Author: kent Date: Thu Mar 15 07:42:43 2007 +0000 Oops, forgot to check in this autoSql-generated module. commit a202b8f4e53376d49487e5793e10ee76449e99b7 Author: kent Date: Thu Mar 15 07:41:36 2007 +0000 Adding test set. commit bf920b8e5bdcf184ec3bccf5f6b1633a096e87d7 Author: kent Date: Thu Mar 15 06:49:16 2007 +0000 Improved accuracy 0.4% and sped up about 100x commit 3ca8db30044d879385e89b2ed202086522522bf2 Author: baertsch Date: Thu Mar 15 06:27:36 2007 +0000 automated ensemble build commit 87b82f49e0466ef6d1ef8faee81b205ec811f7a6 Author: baertsch Date: Thu Mar 15 06:16:49 2007 +0000 add -d option to drop temp database commit fc9bea350cfec68cad2cfa108dc3f904f81ee858 Author: baertsch Date: Thu Mar 15 06:13:42 2007 +0000 update usage commit 1c1e453a159821d5da9a2be41392589acbb5f1ae Author: baertsch Date: Thu Mar 15 06:01:22 2007 +0000 no change commit 68df0a4397d79b6dae61b4e16a5a7a1cc46b86f3 Author: baertsch Date: Thu Mar 15 06:00:40 2007 +0000 add mkRandomGoldLift mkRandomNTLift ensemblVegaMap ensemblSuperfamily commit 224d6836be7b3570825901df9219ea10baff4e74 Author: baertsch Date: Thu Mar 15 05:56:58 2007 +0000 add lift to mouse commit 9268366142c59bb5afcf3b5d3703cacc64e0b6d9 Author: baertsch Date: Thu Mar 15 05:55:48 2007 +0000 add -s option to skip download , -d to drop temp database at end , and -l for lift file commit 1482485ae386e492ebae8a9710c9adf154621c37 Author: kent Date: Thu Mar 15 05:53:48 2007 +0000 Works surprisingly well. Slow for some reason though on certain transcripts. commit c83c6efa27c761a445ac615c2df39593c28b3f3c Author: kent Date: Thu Mar 15 03:23:17 2007 +0000 Seems to work commit a6f28259e2f4a6dcffd0dca6d3c5eaee7902b55f Author: kent Date: Thu Mar 15 02:28:11 2007 +0000 Seems to work commit c533b55cb735d143bcedc34ae122f15dc04b9051 Author: angie Date: Thu Mar 15 01:45:17 2007 +0000 Added description of optional liftSpec strand column, and more errAborts where it is not yet implemented. commit 2762b00ab6940f52bd83a2fbb8f609acfe72c1a3 Author: angie Date: Thu Mar 15 01:44:08 2007 +0000 Added -type=.bed8 to the bed8 tests and updated expected/bed8.bed so that the last 2 columns are lifted. commit 45ba58cdb83ed0cdaf57a4bf1e325a9a45effed2 Author: angie Date: Thu Mar 15 01:36:32 2007 +0000 Updated acc and FlyBaseId links to latest FlyBase gene query format. commit 42ce41e667243098f460da6e62acd088437b1571 Author: galt Date: Thu Mar 15 01:32:13 2007 +0000 updated getSeqFromBlob to use the new gsIdXref table for mapping gsId to dna and aa seq ids commit f17d1d39bc178baf4cc5f80ffe88a8a5a4d4f2c7 Author: kate Date: Thu Mar 15 01:21:23 2007 +0000 Add development track for reciprocal best nets commit a409e0ee4637cc9b24ee356536fec61122e1c033 Author: kent Date: Thu Mar 15 00:57:53 2007 +0000 Adding cdsOut option. Modernizing handling of command line options. commit b0ed85ee4cb438be81efd5748004b4eb78981ad1 Author: markd Date: Thu Mar 15 00:48:10 2007 +0000 added comment to keep mgc in sync commit 6dccd3c098bfacb4239a66af7703caa9eda90651 Author: angie Date: Thu Mar 15 00:26:26 2007 +0000 Added chainSelf (Gill's request). commit 3f675fc96918be67124c90b5462ab3ba916447e4 Author: hartera Date: Thu Mar 15 00:12:03 2007 +0000 Added eponine to the list of tables to be ignore for human. commit aea995c2c39a8aa5b2f132f1920cc8f4621bbc99 Author: kent Date: Wed Mar 14 23:47:31 2007 +0000 Adding option to output .ra as well as .tab file. commit 0727d431a2beb6369e5e38d89aed554735d70966 Author: kent Date: Wed Mar 14 23:46:51 2007 +0000 Moving gpPartOutAsBed to library. commit 79dea0c7fe8e9ae3154fc479805d8973969cd5b7 Author: markd Date: Wed Mar 14 23:29:14 2007 +0000 add mol column commit 62673fdf325fc057eab870df7c92c44029e3798a Author: heather Date: Wed Mar 14 22:51:17 2007 +0000 add helper functions commit 8ca8a4fdfa548ebfd94eece149f3c7d01502923b Author: galt Date: Wed Mar 14 22:24:23 2007 +0000 fixed missing password file update for lost password function commit 7207dcedb648a78d8bf2344eef849b06f7136d99 Author: galt Date: Wed Mar 14 22:22:32 2007 +0000 fixed quoting around lost password email commit 6e0e7da1eb7be0deb8f592d13548ca3b38205f56 Author: angie Date: Wed Mar 14 22:17:07 2007 +0000 Include portable.h which defines struct tempName. commit bfd7d2394fb9830ef949c20dabcd06c01f01a2c3 Author: heather Date: Wed Mar 14 22:13:47 2007 +0000 add strPur2 commit 8f877e83596c7ae3411ee2e75f2262e1cbe05928 Author: heather Date: Wed Mar 14 22:13:19 2007 +0000 initial revisions commit c94ab3c1d25c1852e17199adfdbef43109b7b3b4 Author: galt Date: Wed Mar 14 21:47:42 2007 +0000 added minimum password length check to change password function commit bcea4fdf110745cc96e51c8a89854375fc9720bb Author: hartera Date: Wed Mar 14 21:44:12 2007 +0000 Removed commented out code that removed hgSession as it is now released. Removed line that removed the loader directory - this is now needed for the custom track loader that is being released. Remove old cgi-bin-32 directory and recreate each time. Uncommented line so exits if errors are found. commit 40fc4a8f7b4975116be056ec8557ea537ca5418f Author: heather Date: Wed Mar 14 21:20:09 2007 +0000 functions moved to kent/src/hg/lib; name changes commit 5d64d6b2f0edba432c8caad681befae3d77869e7 Author: heather Date: Wed Mar 14 21:19:36 2007 +0000 functions moved to kent/src/hg/lib commit 226047da957b1cf980f4e016171a9d774e8f04fd Author: heather Date: Wed Mar 14 20:33:56 2007 +0000 name changes commit a2bfca3859de66903b7b3e94a9baa205608ff9b4 Author: hartera Date: Wed Mar 14 18:49:22 2007 +0000 Changed some text to from upper to lower case and vice versa (Bob's suggestion). commit 59489409c98023f0cc90e7e6c500dcdf8d36fcc0 Author: heather Date: Wed Mar 14 18:49:19 2007 +0000 edit comments commit 38626df68df01b396af1d44b6c81ca10173bed26 Author: hiram Date: Wed Mar 14 18:25:43 2007 +0000 Better management of environment variables while pipeline loaders are being run commit c1111a6b1c7e6007ce1762cfd3bf64152f264200 Author: hiram Date: Wed Mar 14 18:16:32 2007 +0000 Beware of environment strings coming back empty from getenv() commit 4501f2a178aef5e7e9540c0dd23132af15c87e7b Author: kent Date: Wed Mar 14 17:09:27 2007 +0000 Removed 'search exact' on acc column for backwards compatibility. commit a8d870d7b68920eeca9d95990e40c579ad63f87b Author: ann Date: Wed Mar 14 16:56:13 2007 +0000 fixed missing quote found by TrackCheck commit 5ddd2aa2a6e4560fdbe6b4e8920797fb9f08b00c Author: fanhsu Date: Wed Mar 14 16:48:29 2007 +0000 Updated to accomodate structural change of gsidSubjInfo table. commit c001390d3618d7da87def2ce2c6710cd79b2bee4 Author: fanhsu Date: Wed Mar 14 16:45:23 2007 +0000 Created gsIdXref.sql. commit 3b8b9ad3c40e36be2fc13468e791fa49c8284fbf Author: fanhsu Date: Wed Mar 14 16:44:46 2007 +0000 Removed machine generated comment lines. commit d5ac71c53c8d2a4970c0c950e28aa3e457841851 Author: fanhsu Date: Wed Mar 14 16:43:28 2007 +0000 Created gsidSubjInfo.sql. commit d9dbb24f3a421dbc5dc895c153b19f95dfa672c8 Author: fanhsu Date: Wed Mar 14 16:42:50 2007 +0000 gsClinicRec.sql is replaced by gsidClinicRec.sql. commit 9f399d4a549b996058806ced3a2d53e8a54a217b Author: fanhsu Date: Wed Mar 14 16:41:47 2007 +0000 Created gsidClinicRec.sql. commit 69d9418f4a4ae62d8cb4e05a4fe6062668b59db8 Author: fanhsu Date: Wed Mar 14 16:38:32 2007 +0000 Removed seqAvail field and added comment field. commit 13bf988f66e38e0dfe06b4a40f7741c7807402d5 Author: fanhsu Date: Wed Mar 14 16:37:39 2007 +0000 Added "(under development)" to title of the page to indicate that this is not officially released production level code. commit 4dca349720dee39a22e1c347543fe6b61bc15dff Author: galt Date: Wed Mar 14 15:00:31 2007 +0000 "Encode release log update" commit 2f0ef8e5b9fa4db347241396bc4ae6b2a933ae88 Author: galt Date: Wed Mar 14 15:00:16 2007 +0000 "Release log update" commit 010a749bb3619dbed350ad7779d71589ea138b36 Author: galt Date: Wed Mar 14 10:12:01 2007 +0000 added sqlRandomSampleWithSeed function to allow specifying seed for reproducible random numbers during debugging commit d7f9dc4c07e648ce1e5b440b9489a4d59c165a38 Author: galt Date: Wed Mar 14 10:10:17 2007 +0000 added -seed option to aid debugging; fixed pattern-matching in ACC column (now ucsc id) commit 4182f03da18f74e7172a67f5e8d93adb7391a63a Author: kent Date: Wed Mar 14 05:56:14 2007 +0000 Seems to work. commit 975fffe06d119842aaa4e22309af3fe2c23f66be Author: kent Date: Wed Mar 14 04:55:16 2007 +0000 Moving isKozak to library. commit 4e2d435b66c8c71c1fe1598fb4f9fb1f2303b756 Author: kent Date: Wed Mar 14 04:54:55 2007 +0000 Adding isKozak to library. commit 563cc06671d2227b7ed75324871514ac1a0473fd Author: kent Date: Wed Mar 14 04:16:16 2007 +0000 MOving mafStripEmptyColumns to library. commit e7af9834934cf42e28852def7ec09f40c700eb40 Author: kent Date: Wed Mar 14 04:15:04 2007 +0000 Bringing up to date with current coding standards. Separating out -stripDb as an option. Making 'first' be a special tName. commit 40a243ec00ebf7fbb510c6780b81041c1b5f3969 Author: kent Date: Wed Mar 14 03:06:15 2007 +0000 Adding gpPartOutAsBed commit d154981fa0b7f79843f6426b87de647ec7679477 Author: kent Date: Wed Mar 14 03:05:38 2007 +0000 Addign mafColumnEmpty and mafStripEmptyColumns. commit ced47d02b87c8e46968045fabb8f2dceb498771f Author: kent Date: Wed Mar 14 02:21:26 2007 +0000 Fixed minus strand problem on cds output. commit 17a4fc93f5ef8da701a2fb4fba27ce766ebffd72 Author: kent Date: Wed Mar 14 01:41:58 2007 +0000 Adding test set for -various option. commit 7e8955c38aac1f348078ec07f55a8e0ff74f807f Author: kent Date: Wed Mar 14 01:41:34 2007 +0000 Adding a bunch of new options. commit 44487c2dc07ac3a74e0a75e0315afa32f05848be Author: rhead Date: Tue Mar 13 23:56:03 2007 +0000 Moved Gene Trap track to Genes group (okay with Angie and Jim) and put it right after miRNA track. commit e5f93ec75bf7864af10049d0eb073eaa5208dd16 Author: heather Date: Tue Mar 13 23:49:44 2007 +0000 add hapmap snps commit d5464985c64884dc5ce8159dfb8304eb67b1f7f2 Author: donnak Date: Tue Mar 13 23:31:58 2007 +0000 Added Galaxy link to left sidebar menu. commit a522707a1e8cc172e54b2a2f2f8610809600c10f Author: heather Date: Tue Mar 13 23:30:15 2007 +0000 protect against wacky input commit 0b289b71d3c25519b3901d74722e43802c3f4c3b Author: hiram Date: Tue Mar 13 23:10:11 2007 +0000 For the customTrackLoader, do not error out on loader warnings commit 680662c8b133b7434319bf6e56bdf829c9a9ba5d Author: heather Date: Tue Mar 13 23:09:04 2007 +0000 hapmap tweaks commit 44bad29dd9f3825f0c26275fa4f452469b4e77da Author: kent Date: Tue Mar 13 23:01:33 2007 +0000 Adding cdsOut option. commit 111f199532272a9c4a6bcc076bc5ad4b20d49163 Author: heather Date: Tue Mar 13 22:51:57 2007 +0000 tweak commit 0804de174ccc902c93f61103b10192a78dbe9325 Author: heather Date: Tue Mar 13 22:40:15 2007 +0000 don't need A for allele2 commit bc66ec72e0976d513dc20da7d6b5442350031057 Author: galt Date: Tue Mar 13 22:37:25 2007 +0000 fixed threshold type commit 37a70cfeec476bd8451a7127749bbea2fe006fad Author: kent Date: Tue Mar 13 22:27:24 2007 +0000 Adding meFirst flag. commit c831bef2133ca3840181c8df783b9f502eafa040 Author: rhead Date: Tue Mar 13 22:25:21 2007 +0000 minor spelling and punctuation changes commit a13f7661b4f5acc133dc1e37d991a70a33ab912d Author: kent Date: Tue Mar 13 22:21:50 2007 +0000 Seems to work. commit 0f78234d98d9c9d70e757f139593842763893b26 Author: heather Date: Tue Mar 13 22:19:11 2007 +0000 don't need double quotes commit 4a7e542be933f6b685b7dd71afd18c5ae0aaea21 Author: heather Date: Tue Mar 13 22:16:20 2007 +0000 add some hapmap sanity tests commit 2ab66076080083d3bcba3ffba2015aca4ea99b6f Author: heather Date: Tue Mar 13 22:14:40 2007 +0000 cleanup commit 1c15aa4a8c2372be99ab1a4b2f19d7083593a926 Author: heather Date: Tue Mar 13 22:13:32 2007 +0000 not needed commit 5b4a3676b9facd3d642abd3dc8e055b51ae35184 Author: heather Date: Tue Mar 13 22:07:19 2007 +0000 use none commit d1e715a2c1bd76cf37440ced066fa02262fe4981 Author: heather Date: Tue Mar 13 22:06:31 2007 +0000 tweak commit a893ec978c819e4f0683a020745cb8e4ebdfa9fb Author: hiram Date: Tue Mar 13 21:47:16 2007 +0000 Ignore empty lines in input, add new options to usage message commit dfd0c16208cb6312048cd5232703b1856068ed4e Author: heather Date: Tue Mar 13 21:38:54 2007 +0000 tweak commit 5c234bda636319c855d15122d30db4fe866e919c Author: ann Date: Tue Mar 13 21:38:11 2007 +0000 added dp2 and dp3 to the bogus (needs serious work) refSeqId rule commit 06b8adffb7277150269c59a567c1300abad810f9 Author: kent Date: Tue Mar 13 21:35:53 2007 +0000 Adding genbank.html to go with genbank column. commit 916119b1de92abe7f95487c39d731cd83aa2db65 Author: kent Date: Tue Mar 13 21:31:05 2007 +0000 Making id handling more likely to be consistent across files. commit 99850c9dfd3cf000d1d01ab9a61f432b8ca8fd7b Author: heather Date: Tue Mar 13 21:28:12 2007 +0000 still tweaking commit 2ed386e51323f33b3b37b2adaaecc1825aac8797 Author: heather Date: Tue Mar 13 21:23:45 2007 +0000 yet more tweaks commit bb5decb71fe80f029df3a9e265638ebfe6b84d0f Author: heather Date: Tue Mar 13 21:22:19 2007 +0000 more tweaks commit e38a1223f8e711a3e5347ddf3e3ac1936e976eca Author: heather Date: Tue Mar 13 21:21:06 2007 +0000 tweak commit 2c32bc31ab0c2a89a9d63da8421da5791b6cd235 Author: heather Date: Tue Mar 13 21:19:09 2007 +0000 new implementation based on genotypes commit da55edf80b243507c4b9b304090b5cbdfb7bdfc4 Author: heather Date: Tue Mar 13 20:56:36 2007 +0000 tweaks commit a3d29137a7ff38c1356ff68ff26c8bde5458b048 Author: rhead Date: Tue Mar 13 20:56:08 2007 +0000 Updated Data Use Restrictions section to match later known genes versions, since the links in the old section no longer work. commit cfed1dd76f63a36629cd8fa384a62475d63e135f Author: kent Date: Tue Mar 13 20:43:05 2007 +0000 Closing file. commit 32b6a6bc3763203fc4e79d346d36f71090ee2290 Author: kent Date: Tue Mar 13 20:26:17 2007 +0000 Fixing bug in cds output. commit ce46086b1552e858642f82c059dd525d609a8c9f Author: galt Date: Tue Mar 13 19:29:51 2007 +0000 oops, forgot moving a branch tag is considered dangerous, therefore requires extra -B flag commit 05a4ce2d3ef7389eb500aed8f83c06edd774b461 Author: angie Date: Tue Mar 13 18:26:30 2007 +0000 Moving cdsOrtho object to library. commit 30cfcb7d14aa7a5008876adaef989c091f23676f Author: rhead Date: Tue Mar 13 18:15:06 2007 +0000 Changed link for Colin Dewey to his current location at University of Wisconsin-Madison commit e5fded8e4c1e3a0eac3299752d21f02f5fea88af Author: galt Date: Tue Mar 13 18:08:08 2007 +0000 added -F force option so that retagging would move to the current head commit 48cfdd1b1dc391a4ebfecc6c685181a4387c1884 Author: ann Date: Tue Mar 13 17:51:50 2007 +0000 cleaned up wording and Reference commit 31a769a0f5ae3b44a597e478df4498f5119df7d1 Author: kent Date: Tue Mar 13 17:10:14 2007 +0000 Removing selectTrainedHits (a stub of a program) from makefile. commit a43cc9a9acc926a358fa1fadf199c33eef4465e1 Author: kent Date: Tue Mar 13 17:09:24 2007 +0000 Seems to work. I wonder how useful it will actually be. commit 38f03d0b86759bb2296763118e414a9382ecef0c Author: baertsch Date: Tue Mar 13 15:09:46 2007 +0000 add -bin field to ensGene and ensPseudo commit 4d05beee8958489258e0d1e1e927653587265620 Author: galt Date: Tue Mar 13 15:00:26 2007 +0000 "Encode release log update" commit 0a5148d4cc1c5dd7f6083fcde008c2c425541cbb Author: galt Date: Tue Mar 13 15:00:15 2007 +0000 "Release log update" commit 23b7c1ef206616b278a08a035c3b5a0a837b9920 Author: baertsch Date: Tue Mar 13 14:10:53 2007 +0000 don't display error if we can't find ensembl gene check entry commit cec142bdd7002d1c9cb4e55b3c3b6c291f93043e Author: baertsch Date: Tue Mar 13 13:30:04 2007 +0000 convert utr to lower case, cds in upper commit aedd26b3425225fcadaa483a240206bfaede7ebe Author: baertsch Date: Tue Mar 13 12:22:10 2007 +0000 convert genePreds to mrna using genomic sequence commit 5b0b113665d754d85fe50ad60c5bfef963c79e27 Author: baertsch Date: Tue Mar 13 12:21:00 2007 +0000 added -sortName option. commit a3b0400cfd827000c99016f04daf44e8e153bf09 Author: kent Date: Tue Mar 13 08:31:31 2007 +0000 Committing this set of results from the orfStats program, since it is a little bit of a pain to set up to run it. commit b2f059667944bb8e3cb9460a8f7d97b01322edf4 Author: kent Date: Tue Mar 13 08:28:27 2007 +0000 Removing this little piece of cruft. commit 563ed6fff35966308ac24731f82c9c34f2f1e639 Author: kent Date: Tue Mar 13 08:00:43 2007 +0000 Adding cds output. commit df52544abf49b73d6d6b9e1b6a0271410a650628 Author: kent Date: Tue Mar 13 05:33:28 2007 +0000 Seems to work. commit 5e44a02ccd2ea2c1ad8a50be889957b56f04e395 Author: kate Date: Tue Mar 13 04:44:39 2007 +0000 Fix typo commit 9fa56edf833a264853f98cee3cb123067c75ccd7 Author: kate Date: Tue Mar 13 04:37:56 2007 +0000 Remove debug commit e9669a40a704ab2d50474655402b8877551d78d1 Author: kate Date: Tue Mar 13 04:37:11 2007 +0000 Wrong -- not a typo commit 96a4de438d5ef0e7a96cbc17000f75a1eea32449 Author: kate Date: Tue Mar 13 04:35:50 2007 +0000 Fix typo commit 9f3822f9c68251d0cfc66e3b43e5c553c0da6e61 Author: kate Date: Tue Mar 13 04:33:29 2007 +0000 More alignment work for 25way commit 8575684402192cb93cda505d0bb37c19ec0c00db Author: markd Date: Tue Mar 13 04:30:31 2007 +0000 added HMS ids commit 1a822610dbd2eb4f5e79aab412facb2d20dbdee5 Author: heather Date: Tue Mar 13 04:28:17 2007 +0000 more display tweaks for hapmap snps commit 202c528ddd0b21cd9e0e6f9b76dc1c69fe581215 Author: heather Date: Tue Mar 13 03:55:35 2007 +0000 use table for hapmap ortho alleles commit 090dc33ffd4e3212fa3e874d979405e5913a3498 Author: heather Date: Tue Mar 13 03:43:00 2007 +0000 display tweaks commit b5bc4aba43d3c99590217d8417c519d08c88bcc6 Author: kent Date: Tue Mar 13 03:26:36 2007 +0000 Seems to work. commit 0709c375b35eb4d57d294ce7e0f93a4eb25db391 Author: baertsch Date: Tue Mar 13 03:25:37 2007 +0000 don't print ensembl gene check details if there are no details. commit e57f0449f3b15af4b0b431cc45f4a30942341094 Author: baertsch Date: Tue Mar 13 03:19:54 2007 +0000 add -l option for lifting contigs to random chroms. add -extGenePred optino to liftUp commit 901c713d525bbc8b934a508288a63465cf425ebe Author: baertsch Date: Tue Mar 13 02:59:35 2007 +0000 added -extGenePred option to support extended genePred format. commit 1337bc944ca7b00b700fb598a4e8cacff9539c9b Author: angie Date: Tue Mar 13 02:57:23 2007 +0000 Added igtcName because igtc sequences are in seq. commit 7acc09ca511ec9cb158e5697db8ada73f00908d7 Author: kent Date: Tue Mar 13 01:41:53 2007 +0000 Editing usage statement. commit 65eed5b0f2710b1c5507e08d0f4084fec4e03ac9 Author: kent Date: Tue Mar 13 01:41:20 2007 +0000 Improved usage statement. commit f7d8ca06b42d95d605a0442bd0e4fdc235b80423 Author: kent Date: Tue Mar 13 01:36:35 2007 +0000 Seems to work. commit 1db370dca38ea18fdf3dd1cbc1918477c015876f Author: kent Date: Tue Mar 13 00:51:27 2007 +0000 Seems to work. commit 861077f260f0ecb14a38b163e1a7db204e5e43fe Author: heather Date: Tue Mar 13 00:06:57 2007 +0000 refactor display of hapmap snps summary info commit 6a16d817c654871c27f6ac51aa16d923d983717e Author: markd Date: Mon Mar 12 23:44:34 2007 +0000 fixed nscan search spec commit 0329975cc933c7355affe216091c277627f04c2d Author: heather Date: Mon Mar 12 22:59:42 2007 +0000 remove hapmapAllelesCombined commit b2f7bd742ea015ec909d353c17e48ee3c100f87f Author: heather Date: Mon Mar 12 22:56:47 2007 +0000 name changes commit 2a9d13f5fda6dbed38f2fe11cc0fd0c9f965497c Author: ann Date: Mon Mar 12 22:52:41 2007 +0000 edited links in Reference section for *scan*.html files. The links used to go to PDF files -- now they go to the Journal websites. commit 557251d75469c324c2c87d7c75dbecbaf32b86d9 Author: aamp Date: Mon Mar 12 22:51:25 2007 +0000 "New version number v154" commit c59eda22e4e8f8d64caa1f94acd8b2fc923fb429 Author: heather Date: Mon Mar 12 22:28:19 2007 +0000 change hapmapAlleles to hapmapSnps commit 55d77231f5026166c1b28a3d9e0f4859e963804b Author: hiram Date: Mon Mar 12 22:22:48 2007 +0000 Indicating Chicken chain/net swap in Fugu make doc commit dc857530412399c71839454817709b271d7dfbad Author: heather Date: Mon Mar 12 22:22:40 2007 +0000 remove hapmapAlleles and hapmapAlleleFreq; rename hapmapCombined commit 2fc9bfce61bc53503d9f197e4873aa2588e2353a Author: heather Date: Mon Mar 12 22:22:05 2007 +0000 previously hapmapAllelesCombined commit 517f156b4c2289148b0233442ea002d00116eead Author: markd Date: Mon Mar 12 22:20:34 2007 +0000 added Kazusa ids commit 2ad91738e65ab6a023523953fa74b874dd7344b1 Author: angie Date: Mon Mar 12 22:12:02 2007 +0000 Special tweak for mrna-->all_mrna in findSelectedTrack to match what is done in getFullTrackList. commit fa2aae6232c022ba3c8351bcc376f31ed12ed745 Author: hiram Date: Mon Mar 12 22:00:23 2007 +0000 Alignments with fr1 and fr2 complete commit 2a59aba175f01caf42da944710dde97d1a115b56 Author: angie Date: Mon Mar 12 21:57:10 2007 +0000 Added history comment. commit f1d291769edab867b573aef5f8e1ede5a0490d3c Author: hiram Date: Mon Mar 12 21:46:32 2007 +0000 Free the limit text string when it is not used commit b7800f67d71df326cfca0ad5d371dd32a13ec875 Author: heather Date: Mon Mar 12 21:40:51 2007 +0000 don't use ushort commit 934cf65370aa7bd16869ad8a62687e46c8724011 Author: angie Date: Mon Mar 12 21:22:22 2007 +0000 swap chain/net galGal3. commit 6f6fb2546b1635ab96d56d93976eb3647785150c Author: angie Date: Mon Mar 12 21:21:59 2007 +0000 blastz/chain/net ornAna1. commit 7405cdca3514ff9c42b196a22f7a091d1c9b7bc8 Author: fanhsu Date: Mon Mar 12 21:20:32 2007 +0000 Removed kkr8u00. According to cluster admin, this rack is off and will no longer come back. commit 6b33e52274ced916e48b742d766423f4fc63e379 Author: heather Date: Mon Mar 12 21:18:00 2007 +0000 increasing MAX_EXONS; adding func commit e2eb301a5602a8a031a8bbe80ba64862dba6388a Author: hiram Date: Mon Mar 12 19:03:03 2007 +0000 Add note about allowing parsing chrN:start-end coordinate types commit f82b8a9f51a5fc7271c8357896aabb80da8ec626 Author: hiram Date: Mon Mar 12 18:59:49 2007 +0000 Now allowing chrN:start-end format entry of data points commit 720f93babf31b635a3649ed3063b38afcf006b16 Author: kate Date: Mon Mar 12 18:50:34 2007 +0000 Add an optional syntenic net step. This generates additional maf files from the syntenic net; suitable for use with multiz (recommended for high-coverage placental mammals aligned to each other) commit 59d9030ded8ad770aaa9404a2769a7067e095467 Author: heather Date: Mon Mar 12 18:19:34 2007 +0000 name change commit 771e05ff1a95dc3dfb71d2ef57bfa640be798bdd Author: hiram Date: Mon Mar 12 18:13:14 2007 +0000 Prevent unusually long inputs, issue warning commit acd93413e980ae3205d40355abe4d8d5ef0161b0 Author: heather Date: Mon Mar 12 18:10:48 2007 +0000 name changes commit ab1470e75ce9642486673fe93c4d329a55611d8f Author: kent Date: Mon Mar 12 17:36:32 2007 +0000 Fixed missing reserved field. commit 64c8fda1042f5bf75ca2e9edaa8e86c296165b72 Author: heather Date: Mon Mar 12 17:34:54 2007 +0000 name change commit 3afced30bbb2dd0e2968b90a46ddb34978d6d5c1 Author: heather Date: Mon Mar 12 17:28:31 2007 +0000 name change commit c9ce838af8534fbb6fee4c0c804434eb9d579e04 Author: heather Date: Mon Mar 12 17:11:43 2007 +0000 new implementation using genotype summary commit f6e2a3255e7b094b91f10b3cf0689b24479d3427 Author: kate Date: Mon Mar 12 17:11:26 2007 +0000 Revert multiple conservation wiggles until issues with TB are resolved commit 5b4805d4d49ea80efda741bef8d6d504e5ded948 Author: heather Date: Mon Mar 12 17:03:52 2007 +0000 remove hapmapAlleleFreq commit 3c17d8f3a753fab9cbf5eddb23133ab4c5d13a4a Author: markd Date: Mon Mar 12 16:57:09 2007 +0000 added -oppositeStrand option commit f2b8256c7be543a0136481e01a52e22f890e2d18 Author: heather Date: Mon Mar 12 16:47:37 2007 +0000 remove old hapmapSnps commit d782eb08c3b4cc051958ce624bd8e1688bdac446 Author: galt Date: Mon Mar 12 15:00:21 2007 +0000 "Encode release log update" commit 0255234f95f4d646ca42f6400613da94d83d91a7 Author: galt Date: Mon Mar 12 15:00:11 2007 +0000 "Release log update" commit f4e538e8b3dbdd87716e959aeb9b536e3468a215 Author: kent Date: Mon Mar 12 08:27:05 2007 +0000 Seems to work. commit 80801a3ad3ff55bf8a4af4bb864ad306f2048bcf Author: kent Date: Mon Mar 12 06:09:21 2007 +0000 Moving cdsOrtho object to library. commit 902b001aa347716581fe1e0b1482d3dccdbf6914 Author: kent Date: Mon Mar 12 06:08:18 2007 +0000 Relaxing size limits on some of the knownGene index fields, and on the alignId field. commit 08f09db26cea206c42b3fb103c927ba2d4fb0d40 Author: kent Date: Mon Mar 12 05:37:38 2007 +0000 Putting in very week weeding for orthology. Need to have 60% ORF size in two of chimp, rhesus, dog, mouse. commit 275d2f0bb0d4afac8a76fbe421756a69b6e90428 Author: kate Date: Mon Mar 12 05:08:42 2007 +0000 Add summary tables for 25way cons tracks commit d59a68bef7aabe5e9dc1de8ab05a7d81f18732f0 Author: kent Date: Mon Mar 12 04:34:42 2007 +0000 Making dodgeStop (and frameShifting) only apply to refSeq. commit 6a6efd75d3f77e4a7511dc639ac73e6c9dd2a49d Author: kate Date: Mon Mar 12 04:31:36 2007 +0000 Test 25way with reciprocal best and syntennic net commit 1929bfe34b5273c9b201e40eeefe05024cdb2ec7 Author: heather Date: Mon Mar 12 03:36:59 2007 +0000 add snp127 commit ae8d40c7aefef78a712e917ecd5f143a48c7696b Author: heather Date: Mon Mar 12 03:26:08 2007 +0000 add snp127 commit 70df0d657498bc7dc8dc76e87a953090c25d1a7e Author: heather Date: Mon Mar 12 03:25:36 2007 +0000 initial revision commit 8811396043149637f4fa622936f4bdd9b4bd3548 Author: kent Date: Mon Mar 12 03:06:52 2007 +0000 Fixed bug that was letting 80 minus strand NMD candidates not be flagged as NMD. commit 7478759ff06ccbd59abdda50613dde207a8fda3a Author: kate Date: Mon Mar 12 02:57:05 2007 +0000 *** empty log message *** commit f77efc90e6133d9935008292ce05e07ebd0d2bb2 Author: kate Date: Mon Mar 12 02:56:23 2007 +0000 Continue 25way alignment -- use reciprocal best and syntenic net pairwise alignments commit 94b4edbd2b5c28c85ca16b38d861d9fd0ac743fc Author: baertsch Date: Sun Mar 11 23:21:49 2007 +0000 remove stderr redirection commit 1bf59a74e555c7e8459d3c55033bfc61e88c3ff9 Author: markd Date: Sun Mar 11 16:05:17 2007 +0000 changed include order commit ad193fdb61478ebb937b70a33cfda43bbf952dc3 Author: baertsch Date: Sun Mar 11 15:58:11 2007 +0000 add ensGeneXref support to superfamily track commit 82417abb9dd1ccc259888ec417674cd6506c9646 Author: galt Date: Sun Mar 11 15:00:22 2007 +0000 "Encode release log update" commit 7fcabcdc5214c4343022ba367bb7d96f4aa24cbf Author: galt Date: Sun Mar 11 15:00:17 2007 +0000 "Release log update" commit 576d6e80cd5496e7b33d54c217ad3c2ee7c70a58 Author: braney Date: Sun Mar 11 14:24:41 2007 +0000 added a correct version from Cory (cmclean ) commit 0a0da5c8861071ccaeea57e0a47c8ca7848b4f7c Author: heather Date: Sun Mar 11 04:40:01 2007 +0000 fix typo commit 831996c39005405188d56e139f400bb2ecaf9ad6 Author: heather Date: Sun Mar 11 04:02:21 2007 +0000 tweak commit 728b08fdd99374f471b8fc92ec42bfc255a8de75 Author: heather Date: Sun Mar 11 03:59:40 2007 +0000 fill in details commit 267c769ac44f83a92a00b435c2eb8f131399db26 Author: heather Date: Sun Mar 11 02:44:02 2007 +0000 name change requested by Evan Eichler commit be24fe2cb33dee04243f642acf9ae85fd6e8b574 Author: kent Date: Sat Mar 10 18:02:14 2007 +0000 Starting to put in stuff about orthology in CDS region and also SVM stuf. commit 02459816f7edd0d3d83b308f8b8b79c61d772b37 Author: kent Date: Sat Mar 10 17:57:24 2007 +0000 Adding missingSize field. commit 26df60def970dbb78fc691b003cf7a961a2b3c84 Author: kent Date: Sat Mar 10 17:56:05 2007 +0000 Looks like it works. Will no doubt be adding to it over time. commit 8b414c43c82ace06ab937bceec281bec55eac474 Author: kate Date: Sat Mar 10 16:47:21 2007 +0000 Add timestamp to stepper message commit 07ac5a12289c874434a8c006ebfc83569f986a56 Author: galt Date: Sat Mar 10 16:00:26 2007 +0000 "Encode release log update" commit d75802d28629e87acf242821a3254380ff0696d6 Author: galt Date: Sat Mar 10 16:00:14 2007 +0000 "Release log update" commit 4aea91d3ce3079f05b7b1a27d617241519f84553 Author: kent Date: Sat Mar 10 07:21:37 2007 +0000 Seems to work, very specialized, almost one shot tool though. commit 8280a8b5da8aec01ec1432eb3d22bba345537048 Author: heather Date: Sat Mar 10 06:18:33 2007 +0000 add histogram of heterozygosity for hapmap snps commit 448854415e03c4c2c870859ca7e51e621b1863e5 Author: heather Date: Sat Mar 10 05:37:45 2007 +0000 hapmap summary commit 415796ecf1c3085a4096efd872b43a9617c09e42 Author: heather Date: Sat Mar 10 05:36:40 2007 +0000 get the sum right! commit bef528bc0a758d9636c521369e14e7d068bb7b80 Author: heather Date: Sat Mar 10 05:13:35 2007 +0000 remove calcHet (now done in hapmapSummary) commit 68614f8086af93f66aaaeeeb955219dec103a718 Author: heather Date: Sat Mar 10 05:11:24 2007 +0000 put calcHet here commit d92b0e0b31ff3a625092b3be12aa5dd74bff857a Author: heather Date: Sat Mar 10 04:21:32 2007 +0000 disqualify mixed items when freq filter is set commit c4adbc74580aa0763e81f8f4c1c63b2d79d062d3 Author: heather Date: Sat Mar 10 03:03:13 2007 +0000 convert from count of individuals to count of allelescvs diff hapmapSummary.c Duh. commit 54c395650118f93c1cb80548d9b715b227e2cf28 Author: markd Date: Sat Mar 10 02:18:37 2007 +0000 added TARGET=_blank for external links commit 5878615cac2f981b2ba2e7566b264c6e84dd4a71 Author: rhead Date: Sat Mar 10 01:52:12 2007 +0000 Fixed typos, reworded commit dba7b0605f379254f763c829c439997115b5d89d Author: baertsch Date: Sat Mar 10 01:31:18 2007 +0000 fix broken html tables on ensembl details page commit f52b050e852d6b00b350486043ef8366179b19a4 Author: baertsch Date: Sat Mar 10 01:11:23 2007 +0000 add support for ensGeneXref commit e854277efb3ba4a802d9cb776161742b379faa41 Author: hiram Date: Sat Mar 10 01:07:07 2007 +0000 No real need to make the percent display be an option, just do it. commit 53cf9f472474bb035091ce62b4a6e6ffdfeda55e Author: baertsch Date: Sat Mar 10 00:45:35 2007 +0000 use a makefile instead of dump script to install scripts commit 560b5b1f6382eab23e175769928acae87d7c9330 Author: fanhsu Date: Sat Mar 10 00:00:10 2007 +0000 Finished proteins070202 build. commit 2a2d5f9c76a3505fa71897d519929fdafec4c67f Author: rhead Date: Fri Mar 9 23:56:26 2007 +0000 Fixed broken link to BACPAC Resources Center. commit 11190cd3746adbcfa57bbc9d5e8bf979d265de74 Author: hiram Date: Fri Mar 9 23:42:16 2007 +0000 Ensure userRegion choice is allowed only when there is actual input commit 416377620a49630bf80f90df7cc0f26a20ac5009 Author: hiram Date: Fri Mar 9 23:40:28 2007 +0000 Allow 1000 region display for wiggle summary data output commit dfdc9cf6f0cbec6162311eacfdd5342c628df4f3 Author: hiram Date: Fri Mar 9 23:24:44 2007 +0000 Add coordinate verification commit 9514b956c69f93ba83b48850594a17ccccef9503 Author: hiram Date: Fri Mar 9 22:55:31 2007 +0000 Perhaps this is the correct situation, it is hard to tell. commit 58381c97c3cd4a94c659c173211773c748a929a8 Author: kayla Date: Fri Mar 9 22:44:32 2007 +0000 creating chainGasAcu1.html commit 29badb879f218f1fb962bad544018497dc65218b Author: kayla Date: Fri Mar 9 22:41:17 2007 +0000 creating netGasAcu1.html commit 2c04e4bf8c74995d0ba165cf6df3dbf1c2759d47 Author: archanat Date: Fri Mar 9 22:20:14 2007 +0000 relaxed the check for hg18.ccdsInfo.mrnaAcc for identifier refSeqId commit a09c0703b973541d15eee516d2e4b4388e92074b Author: giardine Date: Fri Mar 9 21:09:10 2007 +0000 Added fix for when there is a intersection and all fields selected and Galaxy output. Made Galaxy in text links, and removed if that kept the Galaxy connection on genome-test. commit 3414b2f0f48fa1b4ecd8aaac910e6b8ee4d43b50 Author: baertsch Date: Fri Mar 9 20:24:58 2007 +0000 quote syntax error commit 2112e765ba529519d152749b1e9fb46d569db804 Author: baertsch Date: Fri Mar 9 20:24:08 2007 +0000 more remapping chrom changes commit faa53f489a2f83cf9ec180ef8c68fc96e8c70a7a Author: baertsch Date: Fri Mar 9 20:20:10 2007 +0000 prepend "chr" on X, Y,Z,W,Un commit 6f74580b08936b59587da9255324194da028837c Author: ann Date: Fri Mar 9 20:02:48 2007 +0000 removed usage restrictions (the dog sequencing folks at Broad said it was OK) commit 50ec4be767877e656a219e9ba7ee8d58c2d7182d Author: baertsch Date: Fri Mar 9 19:58:48 2007 +0000 rename chroms in ensemblDbImport instead of here. commit a9ffa5685818c54aba0623fb25393963c2161525 Author: baertsch Date: Fri Mar 9 19:58:15 2007 +0000 rename chroms here instead of exportEnsembl commit 79b917deec334d02e49ab53f22041dc63e7ae88e Author: archanat Date: Fri Mar 9 19:57:23 2007 +0000 converted refs to pubmed format commit 27aa360cd14836a8cbd701347d371afed9fbc019 Author: ann Date: Fri Mar 9 19:57:10 2007 +0000 removed usage restrictions (the dog sequencing folks at Broad said it was OK) commit a9f3f1658d674ceb545a640f4f3cdd7f2f778adc Author: ann Date: Fri Mar 9 19:53:13 2007 +0000 updated dog usage restrictions because the paper is out now commit 747bf5acdb444e27092410619cab10ea2c708cd3 Author: hiram Date: Fri Mar 9 19:33:49 2007 +0000 Allow use of Kates defines for prefix names in trashDir files commit 80c07dd7ad3a1d961c681af58d2740e5a8d4939a Author: angie Date: Fri Mar 9 19:29:00 2007 +0000 Cleaned up the perl so that -revStrand is recognized when passed in; also so that it adds a strand column to the output instead of modifying sequence names. Would be even nicer to use GetOpt so that input doesn't have to come from stdin, but this works. commit 4e92520ac7834c05c14246b297a74abf3db506db Author: baertsch Date: Fri Mar 9 19:10:12 2007 +0000 add geneCheck details page to ensembl commit 9a44bfd605d45d89aabea2062d2d709d69beb968 Author: baertsch Date: Fri Mar 9 18:59:44 2007 +0000 add -compat to output 23 col format commit 2149ae5b338fb86ce682b24d7d56af5491f4a651 Author: fanhsu Date: Fri Mar 9 17:54:59 2007 +0000 Created spDeleted.sql. commit 0a4b74fdd4a794d0e3df9acd29880508b999753a Author: donnak Date: Fri Mar 9 17:07:08 2007 +0000 Made a few mods to Hiram's previous mods. commit 92138e72c0b425e3f418eee25212233bdf755717 Author: baertsch Date: Fri Mar 9 16:05:48 2007 +0000 fix MACHTYPE commit 283f3aadf4d20e69760013d5e6b09d3ac684d16c Author: fanhsu Date: Fri Mar 9 16:02:33 2007 +0000 Updated to avoid a warning. commit 61efe380f46a27cafc8f217a3b86aa0b44b0b491 Author: galt Date: Fri Mar 9 16:00:33 2007 +0000 "Encode release log update" commit 2b89533994e84d294534b7bced3e33ab880621f8 Author: galt Date: Fri Mar 9 16:00:18 2007 +0000 "Release log update" commit f04d6f30fcfafbed833d5ee5d4c1d41b128dd526 Author: baertsch Date: Fri Mar 9 15:57:59 2007 +0000 docs commit ba714611caf64fa56c5aea63f262514e23db191d Author: baertsch Date: Fri Mar 9 15:56:44 2007 +0000 remove cleanGeneTable commit 5104def6643c63e64af5fa59bbdc0fa50d7d0dec Author: baertsch Date: Fri Mar 9 15:55:31 2007 +0000 change -nib-dir to -genome-seqs for marks new gene-check commit 99b6d1e4fe8fabd4c71a19d3d8ab9569ddfd8db9 Author: baertsch Date: Fri Mar 9 15:53:45 2007 +0000 force frame to 0 for the first coding exon. Ensembl bug. commit a79b6bc9901b97a69c7ef4727d1ab6785551e81a Author: baertsch Date: Fri Mar 9 09:21:22 2007 +0000 make working directory commit d99c23c2e84c13aa6cfa7293e27ca0451b9fa7e4 Author: baertsch Date: Fri Mar 9 09:17:26 2007 +0000 a very stupid install script commit f8b92c6563341e22e328c60509df4e2bd057f0b9 Author: baertsch Date: Fri Mar 9 09:16:46 2007 +0000 add ensemblSuperfamily commit cdb7f935cc502b1212ef513e42cb5af24190f2e0 Author: baertsch Date: Fri Mar 9 09:15:30 2007 +0000 add superfammily loading commit 46f1c4c8c11105aa5ca3ecea267969a01a3b8dcb Author: baertsch Date: Fri Mar 9 09:15:08 2007 +0000 remove cleanGene , filter out hap genes until we get the offset commit 9a4cf716b4b3809816de2a4e4f97436ee8592d87 Author: baertsch Date: Fri Mar 9 08:57:50 2007 +0000 add dog to superfamily commit 0dedcbdf5b5fa086cf8542740f1ce4203d7b1167 Author: baertsch Date: Fri Mar 9 08:43:05 2007 +0000 add support for ensGeneXref cross reference. check for table existance. commit 1b2728a4917ef4be1bf149987062a2b18ee78a4c Author: baertsch Date: Fri Mar 9 08:09:35 2007 +0000 set working dir commit 70515357f8a1f1161d9c9c2a1853602a7816c2b3 Author: baertsch Date: Fri Mar 9 07:46:21 2007 +0000 add details to geneCheck and fix bugs commit a4b5d7633a04fe4e556333ed181e3563f6b583d6 Author: kent Date: Fri Mar 9 07:29:00 2007 +0000 Fixing out of frame bugfrom using relFrame instead of bestFrame. Adding to test set. commit f5d24b33a21199f2eb4a2c250a2a889dcde24265 Author: baertsch Date: Fri Mar 9 07:02:58 2007 +0000 fix arg count check commit b041b423a1ca7e348ad55e63e16025337bb11165 Author: baertsch Date: Fri Mar 9 06:59:17 2007 +0000 initial version commit 5d337342cda92149e4e8f7a3b36b58cc0320488e Author: baertsch Date: Fri Mar 9 06:43:13 2007 +0000 added geneCheckAndLoad commit 49793b979270b73c8f5a0086f33471dadbf252a8 Author: baertsch Date: Fri Mar 9 06:41:30 2007 +0000 sample script to load all browser databases commit 11a5c92cddc13da6d281c60ad2a20d50d1e32bb7 Author: baertsch Date: Fri Mar 9 06:37:11 2007 +0000 drop old ensemblXref3 commit 881062308d8083677d19eaa1c97313a2ca29be58 Author: baertsch Date: Fri Mar 9 06:35:59 2007 +0000 add call to geneCheckAndLoad commit b5accf83699897e6baa4e45872f7808a380b9959 Author: baertsch Date: Fri Mar 9 06:31:20 2007 +0000 run gene-check on genepred and load tables commit dea5f8c886a0ceac5bdb3ecd67bf3e4dc8035d6a Author: kent Date: Fri Mar 9 06:24:02 2007 +0000 Seems to work commit 589c534297e1c1675f2417d6e45418d2252a4ae4 Author: baertsch Date: Fri Mar 9 06:23:42 2007 +0000 run gene-check on ensembl predictions and load database tables commit b9045a6f6c4fed050ea3e7b338f36f2c572bc0ed Author: baertsch Date: Fri Mar 9 06:20:25 2007 +0000 move export code to exportEnsembl. This script only loads the databases. commit 0175d1c16fcfeb838f6a4bdb9fb479214dbab108 Author: baertsch Date: Fri Mar 9 06:17:54 2007 +0000 split loadEnsembl into two scripts exportEnsembl and loadEnseml. commit 84af49e0ec08ef5806ec8d927306bce439e5f652 Author: hiram Date: Fri Mar 9 04:50:02 2007 +0000 function customTrackTrashFile removed, now using trashDirFile commit 484d20140f9126c76e855e4a9044e3db6d66b805 Author: hiram Date: Fri Mar 9 04:49:30 2007 +0000 Now using trashDirFile instead of customTrackTrashFile commit 481d5e6c2189ae3a7793b8eb1eb9307270fe6382 Author: heather Date: Fri Mar 9 04:40:43 2007 +0000 tweak allele freq commit 2e0a30784b7079325f2d5739fe4894ed0971997c Author: baertsch Date: Fri Mar 9 04:20:47 2007 +0000 add if exists to database drop commit 3ab61a12e937e17392442aacc8152af93c8b7d73 Author: baertsch Date: Fri Mar 9 04:17:54 2007 +0000 set frome to 0 for single exons genes to overcome ensembl defect commit 1321843d35a77ed0af2708e588773a402019abbf Author: heather Date: Fri Mar 9 04:15:21 2007 +0000 tweak comments commit 97d42312a0735a49f14e89ffa5f20eeea31cfb32 Author: baertsch Date: Fri Mar 9 03:39:02 2007 +0000 fix frame bug. Single exon genes still have no frame commit be88058715b6aabb0c55aa3764b755eae4dec89b Author: heather Date: Fri Mar 9 03:14:52 2007 +0000 GUI tweak commit 0de6afbaf61ad736673185b7450ec7e4dc4019c8 Author: heather Date: Fri Mar 9 03:12:07 2007 +0000 use consistent default commit c20e240f9688d834a7a4ca02b041ef5ba33af61c Author: heather Date: Fri Mar 9 03:11:48 2007 +0000 use consistent default for hapmap snps commit 4f67076985748e6568ee9ee639a646d8026c8055 Author: heather Date: Fri Mar 9 03:02:11 2007 +0000 refactor ortho allele filter commit 79bd89f15e1775a81cfd4971c659d2892467387c Author: heather Date: Fri Mar 9 01:54:48 2007 +0000 use sameString for isMixed; return FALSE for isMixed/ortho filter; use mismatch for fixedDiff commit f09d8b5888fe85cd629a08696f1a6b49dbfc783f Author: heather Date: Fri Mar 9 01:35:22 2007 +0000 rename ortho fixedDiff option commit ff827fafb3d9608258725ce12e2d8aa85e4b0fb7 Author: galt Date: Fri Mar 9 01:25:59 2007 +0000 replaced code with ct library calls on Kates advice commit a0eb26592e7c27e881cda67bc71e5f21d2545766 Author: hiram Date: Fri Mar 9 01:13:25 2007 +0000 Description of new custom tracks database implementation commit 6a9e5bb2ebeeae6e3615ed4e09942f7f47c0cb62 Author: hiram Date: Fri Mar 9 01:13:00 2007 +0000 Add documentRoot, wiki, customTracks, and indel options commit 39b110712b87ff1b86081e60beb72324df72b316 Author: hiram Date: Fri Mar 9 01:12:28 2007 +0000 Add documentRoot, wiki, custom tracks, and indels options commit d214e6754d45c674bd2266a510b3a64b3d003941 Author: heather Date: Fri Mar 9 00:48:37 2007 +0000 fix typo commit 630e55de60c076547ea100b735b2c62f28ea37dd Author: heather Date: Fri Mar 9 00:40:05 2007 +0000 fix typo commit 80f462088ee155eab526c0ebf8ad07e3515e2a7d Author: baertsch Date: Fri Mar 9 00:30:25 2007 +0000 rename temp table commit 9d39c70107a401c4abb0fc7327c5cc70746430c1 Author: galt Date: Fri Mar 9 00:08:17 2007 +0000 moved location of search results tempfile to trash/vg subdir to keep things tidy commit 349063a6b1480882d172627a59f41d0ea21b117b Author: hartera Date: Thu Mar 8 23:59:30 2007 +0000 Added search for Eponine TSS track. commit 9fcb320ba15f7dc2cd34106ebe36610b1d36f60a Author: baertsch Date: Thu Mar 8 23:55:24 2007 +0000 add script to delete invalid gene models commit e0bf7805b86f068a3d7e851abc24985e5932c512 Author: hiram Date: Thu Mar 8 23:53:47 2007 +0000 Improve the parser to allow a wider variety of garbage input without failing commit 3e4d730eb84691ac7fab3c5090b55013e3faff96 Author: hiram Date: Thu Mar 8 23:46:43 2007 +0000 Fix broken processing for a file with no line termination on the last line commit 6f4d923affb459acba44986edf92d28c4ca502ba Author: hiram Date: Thu Mar 8 23:34:04 2007 +0000 Add the note about accessing the public MySQL server with a username and password combination commit 8a6e2294170093e798371061f43a10befe6d601c Author: ann Date: Thu Mar 8 23:33:05 2007 +0000 Call three existing scripts instead of reinventing them here; better SQL statment for empty fields; tightened up if statement; remove three duplicate SQL calls. commit 3c496c03d907f6de08dcedb1b120774043eef942 Author: baertsch Date: Thu Mar 8 23:23:50 2007 +0000 add ensGtf ensGeneXref to load process commit dcefac0694e251f2d3b6e880ac930267f3d10205 Author: baertsch Date: Thu Mar 8 23:19:27 2007 +0000 bring back old ensGeneXref commit 39918f3242be92b9b09da9698d6406205ca7305d Author: markd Date: Thu Mar 8 23:13:36 2007 +0000 added function to check for a table commit 41d17f2efa07ac666ed3369b58b893fe97ebfafe Author: markd Date: Thu Mar 8 23:08:53 2007 +0000 template for program to modify tables commit 90031a2ed86acc309237a31d6c81c9702c89f0d7 Author: hartera Date: Thu Mar 8 22:58:43 2007 +0000 Added Eponine TSS prediction track. commit 92b8a71011c00813113e4604a2056e872a5f5e61 Author: heather Date: Thu Mar 8 22:54:43 2007 +0000 use CloneVar; return simpleItemsFiltered commit 7bbb481ed1cbe9b1a859a95870ab779d6c99108c Author: markd Date: Thu Mar 8 22:47:40 2007 +0000 work on non-coding loading commit 5cb4ca23cc38fec56ab80a8e2f9d6f31660f511d Author: ann Date: Thu Mar 8 22:31:11 2007 +0000 point to newly checked-in version of getChromlist.csh; display actual counts instead of just saying that it's OK; call on commTrio to compare tables. commit 01b8d8e57fdda15e05cfbc4d11baae9d46c7687a Author: fanhsu Date: Thu Mar 8 22:21:50 2007 +0000 Updated to remove junk causing warnings. commit 953470f16b3265df35064c756c31f2ec608ba795 Author: hartera Date: Thu Mar 8 22:12:56 2007 +0000 Added version number and date for Eponine software. commit 6bea6e85837980b110f9e2373f5d2e06661e1aa5 Author: markd Date: Thu Mar 8 22:04:00 2007 +0000 added felCat3 N-SCAN commit a2fed636fb5727949c9e779860f64ac83bea8d0e Author: markd Date: Thu Mar 8 21:56:02 2007 +0000 added felCat3 N-SCAN commit 512a47eb5cfee4ac4c2d79fff8900c5455ed5af5 Author: baertsch Date: Thu Mar 8 21:44:22 2007 +0000 change back to using type for coloing commit 8081037561ab6e0a3f80281b9f3b3262c9e4653a Author: markd Date: Thu Mar 8 21:22:28 2007 +0000 removed whitespace that caused match failure commit 19de4a2c3fef73afd697e476e02d2a62345c3999 Author: baertsch Date: Thu Mar 8 21:06:56 2007 +0000 increase documentation, remove echos and add redundant field to avoid silly outer join limitation in mysql 4.1 commit 8cca5a2b87deb006227202f4fe8a54fda6c67320 Author: fanhsu Date: Thu Mar 8 20:55:08 2007 +0000 Added pbCalPi. commit 889e63a048e4556a05044663407464f32807012f Author: fanhsu Date: Thu Mar 8 20:52:49 2007 +0000 Get rid of the first comment line. commit 37f3b002e25ac654ab0a557f4c023e96bc49164f Author: fanhsu Date: Thu Mar 8 20:04:58 2007 +0000 Added interProXref.sql. commit 1e87421110737ea752548465ca3b67cc931aaea8 Author: fanhsu Date: Thu Mar 8 19:53:42 2007 +0000 Added spDisease.sql commit 9b93a8cfa732e0c07de93e6ba8cb342091f130e1 Author: fanhsu Date: Thu Mar 8 19:47:31 2007 +0000 Added pdbSP.sql. commit 9f2e990d7886216dc8b9b21de96dce749e1e31c5 Author: ann Date: Thu Mar 8 19:44:45 2007 +0000 small tweaks commit d6b8e2ff46298b69d06c53f1468ee53b0c0daf72 Author: ann Date: Thu Mar 8 19:37:12 2007 +0000 the hg16 genbank is drifting from the KG set. Loosened the rule by one percent commit e66065837b45596b67972e7122338557b33afbef Author: baertsch Date: Thu Mar 8 19:10:35 2007 +0000 remove redirecting of output commit 670060b6d33d4bbbbd2c456b6ccb9f80bd1fea42 Author: baertsch Date: Thu Mar 8 19:08:28 2007 +0000 remove commented code and echos commit e06de65016597665b0acff8a72a91286fe18118f Author: baertsch Date: Thu Mar 8 19:00:50 2007 +0000 fix bug to remove first blank line from output and last record with duplicated exon. Neaten code. Thanks Mark. commit 13805397f9d505daf6e604a7e48da30a4b79a5b7 Author: angie Date: Thu Mar 8 18:52:32 2007 +0000 Reloaded Ensembl genes using latest BioMart interface. commit 01eafb8135aba47cc9f442b3540d6df52b268b88 Author: fanhsu Date: Thu Mar 8 18:43:46 2007 +0000 Added spSecondaryID.sql commit 02d345a9bc38a31a19d1823b3b831e2679dc1ac8 Author: fanhsu Date: Thu Mar 8 18:37:02 2007 +0000 Added spOrganism.sql. commit 848a686be00d960f3966fdfcbf2114c7a7576ebb Author: kent Date: Thu Mar 8 17:31:19 2007 +0000 Adding the bits for fetching the human/chimp/rhesus/mouse/dog bits of the multiple alignments that cover the transcripts. commit fdccca3970842f9cf0cea142d6743a6b070160c9 Author: kent Date: Thu Mar 8 17:29:32 2007 +0000 Saving a fake srcSize so mafLoad is happy. commit 49cf742cb9335b767d4c0e921b5251f48a2cdf43 Author: kent Date: Thu Mar 8 17:28:50 2007 +0000 Making mafWrite a little friendlier in case where leftStatus not set. commit 5264d2fa293f6ad93f97ae86b204775e4d8a50e2 Author: kate Date: Thu Mar 8 16:57:16 2007 +0000 Update email notification to reference new alias. commit 981a9620919f5175ee62581c58ac01ec6b730cf4 Author: galt Date: Thu Mar 8 16:00:36 2007 +0000 "Encode release log update" commit 1bc787fdbc78509d28de17821a9d16355824cce9 Author: galt Date: Thu Mar 8 16:00:20 2007 +0000 "Release log update" commit 7c1cd18fbc61911829e2d7ccccd9d5a9e8ad729f Author: kent Date: Thu Mar 8 09:34:39 2007 +0000 Seems to work. commit 248341316ab08f784aab862b5250b7bf733e57fd Author: kent Date: Thu Mar 8 08:41:38 2007 +0000 Adding bed12 and thickOnly option, to deal with beds that have blocks. commit 31451728cab3727d1eabc28c4ad4fdabcb0b0c38 Author: markd Date: Thu Mar 8 07:24:23 2007 +0000 added support for non-protein-coding mRNAs commit 65da61928b4fbcf6ad337adc104dd8bbccbcf3f9 Author: markd Date: Thu Mar 8 05:56:56 2007 +0000 switch finished assemblies to globalNearBest filtering commit f3a9d4918208647ed79df9fb61b778b54c39c215 Author: kent Date: Thu Mar 8 05:45:20 2007 +0000 Softening up compatible extension criteria for single exon genes. commit 37086d4bb3f4bf4b6effdac7fa77d2ee3fd51413 Author: kent Date: Thu Mar 8 05:31:25 2007 +0000 Seems to work. commit 710240bae3d6d348f6f1b1ea159cf85e30e0e626 Author: heather Date: Thu Mar 8 05:08:26 2007 +0000 use homoCount, correct het calculation, use none for monomorphic commit b0363a65b092a4cc43903175f9b30fa3f9b20ee3 Author: heather Date: Thu Mar 8 04:55:11 2007 +0000 UI feedback from code review commit c5cc1456f5febc2d27b934e7634a757737b1d82d Author: hiram Date: Thu Mar 8 01:20:03 2007 +0000 Proper hgg subdirectory for the cgp files commit 11d2bf15e0471f49e81750c7480aa374f2115824 Author: hartera Date: Wed Mar 7 21:41:04 2007 +0000 Now using USER variable instead of a defining BUILDPERSON in buildEnv.csh. commit 60f0868a1479027adcbf0fc3659bc656ce726c5d Author: braney Date: Wed Mar 7 21:35:25 2007 +0000 fix to get the right bases to calculate the score. commit 8471819c5cdc2ff88160db39ad63a6057fcf678b Author: hartera Date: Wed Mar 7 21:34:27 2007 +0000 Remove BUILDPERSON script. Using the USER variable instead in scripts that send e-mail. commit 59dca981618d60dcfd50aa326ce07b541211a019 Author: baertsch Date: Wed Mar 7 21:19:37 2007 +0000 add gene type to gene attributes table commit c12e7648d5ab48037ed21510d9d6f912137e17ec Author: baertsch Date: Wed Mar 7 21:12:00 2007 +0000 initial commit 4a8d9347f5a89ef21f54b904e81717da30750148 Author: heather Date: Wed Mar 7 21:07:09 2007 +0000 bug fixes commit 811cea3c078f9d64bacb1db5832a7b4e21674cfb Author: baertsch Date: Wed Mar 7 21:07:07 2007 +0000 reformat awk for readability commit 74caae3f5d59579a7db9502f9bd08ac92316c78e Author: baertsch Date: Wed Mar 7 21:02:36 2007 +0000 rename tables to tables.tmp commit 762d59e52a05e1087ff83009271fa74c8aa0e819 Author: baertsch Date: Wed Mar 7 21:00:32 2007 +0000 write usage to stderr commit 20771edda030df755ab9670518078e7fe26c6536 Author: baertsch Date: Wed Mar 7 20:56:06 2007 +0000 add bash to header and -e option for better error handling commit 36191ca99311228033462c592c3650d299df5ddc Author: baertsch Date: Wed Mar 7 20:53:39 2007 +0000 add support for gene description int genePred ItemClass tables commit ed8317e89154726955446a2b6743a3a34f86fa30 Author: baertsch Date: Wed Mar 7 20:49:10 2007 +0000 rename field confidence to class and class to type for compatibility with kate's itemClass close commit e3492412b149418469242f8d62398c6951940384 Author: baertsch Date: Wed Mar 7 20:20:10 2007 +0000 change desc to blob commit bd15e75557dc11b0dc0d6f3ba604cd6e444e4bf0 Author: baertsch Date: Wed Mar 7 20:14:57 2007 +0000 longer description commit 728bbfa1b8215171059ebc78230e209ebcf9036b Author: baertsch Date: Wed Mar 7 20:09:29 2007 +0000 fix primary key name commit 1bb0dd1f2235369f48d7893a0c49e0f767c18b2f Author: baertsch Date: Wed Mar 7 20:07:24 2007 +0000 rename transcriptId to name for Kate's code commit 7ecf41dccca9a4db5b44d67894c3fb410cfd2630 Author: baertsch Date: Wed Mar 7 20:02:22 2007 +0000 rename method to class commit 02fa42c99c81459ecec21e55d36508b8f49abdee Author: baertsch Date: Wed Mar 7 19:29:23 2007 +0000 add novel transcripts to ensInfo commit 2202066d8b5c910454512cfda215b120819bf7c7 Author: markd Date: Wed Mar 7 19:13:52 2007 +0000 template for MGc hg.conf commit 9a900e9df8284b4064b5a66aa30349a822c7ae66 Author: kent Date: Wed Mar 7 18:10:54 2007 +0000 Some special case code to get the 4 Antibody fragment genes into system. commit 51cb5e207d4fe7dc6353ead77312325411d316ec Author: kent Date: Wed Mar 7 18:09:54 2007 +0000 Adding how separate anticoding, and the new weeding steps into kgNotes.txt. commit 9de377823abe17a8a5bf6f0984cc581641796d39 Author: kent Date: Wed Mar 7 18:08:50 2007 +0000 Adding a info about antisense to details page. commit 75f8e7ce72ab162dbff7b50f3e733cd45f586129 Author: baertsch Date: Wed Mar 7 06:48:00 2007 +0000 cleanup by deleting temporary ensembl database commit f6b01f5c36919b565ade2843521dbf6f9d0ac7db Author: baertsch Date: Wed Mar 7 06:45:58 2007 +0000 add support for scaffolds by mapping GeneScaffolds -> scaffolds commit a4345ab16aa9a8a5b5f8cb58c935644e699eadd9 Author: baertsch Date: Wed Mar 7 06:03:35 2007 +0000 fix typeo commit ce22db7768a413b8cd3262282f90cd06c68aa7ac Author: baertsch Date: Wed Mar 7 06:02:42 2007 +0000 add organism paramter to loadEnsembl commit cf38042238ca67f9a9a6fb6633d8b21158f78896 Author: baertsch Date: Wed Mar 7 05:54:29 2007 +0000 move cd earlier commit cb1227002bb5b6a89e31d1103db1cfd2149954e1 Author: baertsch Date: Wed Mar 7 05:44:12 2007 +0000 typo commit 7fff922a1db195c167c39e993477c5f5d71023ab Author: baertsch Date: Wed Mar 7 05:36:43 2007 +0000 hard code exception tables that should not be imported commit a977fd6b4fda33778197de685d01b4f1fb0962a7 Author: baertsch Date: Wed Mar 7 05:34:39 2007 +0000 hardcode exception tables commit 7118c74446f70cd7cdeda1e6c5b6c04f28bc5f8f Author: baertsch Date: Wed Mar 7 05:24:49 2007 +0000 add messages commit f5d0fae4097a3f0b0db8bbe3db223223650ef1ec Author: baertsch Date: Wed Mar 7 05:23:19 2007 +0000 add pseuodgene table ensPseudo commit d38ac3057095650233b75ea3702bebf6c6ab79cb Author: baertsch Date: Wed Mar 7 05:21:21 2007 +0000 make temp database more unique commit aafcb5cf43b49836d4d576158b65eefaad7f444b Author: hiram Date: Wed Mar 7 05:16:56 2007 +0000 Leave the regions in the order of entry commit bd9ff4094c409a2e0c6d430fe714dad44eb87737 Author: kent Date: Wed Mar 7 05:16:29 2007 +0000 Adding in nearCodingJunk output. Putting in bit on antibody. commit cb5c75bafd1d3892ffc5d91c41e52252a8fc38a2 Author: baertsch Date: Wed Mar 7 05:06:32 2007 +0000 ensembl additional info commit e8d2588ce02dc7d487ead5e6e397c886b80167ba Author: baertsch Date: Wed Mar 7 05:04:27 2007 +0000 typo commit fddbec3c35354d5f098549b3563d3b7b408a2502 Author: baertsch Date: Wed Mar 7 05:03:19 2007 +0000 awk script to convert ensGene to genePred format commit 8583ea42ab85d7b3e92eb3fa3d9830ccff13a881 Author: baertsch Date: Wed Mar 7 05:00:28 2007 +0000 embed seql in script. remove processed pseudogene filter (for vega only) commit 246c5b3916f4e16d64418c738c3883a2285a3a91 Author: kent Date: Wed Mar 7 04:49:38 2007 +0000 Adding prefix option. commit d9855d2243b9aa17fc5492f88d9c7ca29903261d Author: baertsch Date: Wed Mar 7 04:41:21 2007 +0000 move renaming chroms to end of script. commit 1e3e88ade2e58752187c3097b821946c055ba2de Author: baertsch Date: Wed Mar 7 04:31:45 2007 +0000 fix chrom names to match ucsc standards commit d1df345bcc6868068eba172942b373e06e4c6dee Author: baertsch Date: Wed Mar 7 04:28:01 2007 +0000 add cd commit 90999572e2afed585342610ee1e45ebf3c545ae2 Author: baertsch Date: Wed Mar 7 04:24:43 2007 +0000 initial scripts to load ensembl data from any species into browser ensGene track commit a2af582fe42317c8973a6056f7c2ed67537c61a1 Author: baertsch Date: Wed Mar 7 04:11:37 2007 +0000 updated to ensembl gene build 43 commit 63c1083404082dcc167ad0f1c31058d550442824 Author: rhead Date: Wed Mar 7 02:59:59 2007 +0000 Fixed one typo; added punctuation. commit b4bd48b5c9b5c040e050b57c40f88d2c60e9fb00 Author: rhead Date: Wed Mar 7 02:35:24 2007 +0000 I noticed that this image was in /usr/local/apache, but I could not find it in CVS anywhere, so I am checking in a copy. commit 75ee7971f68ee487711842090c87bbd5ea31076c Author: angie Date: Wed Mar 7 01:47:32 2007 +0000 Clarified an option description. commit a72edfb3a36aec70499f904a7e305f56b3845ee3 Author: angie Date: Wed Mar 7 01:46:43 2007 +0000 Increased memory usage limit as suggested by Mike Pheasant. commit 5dcfd68e7bab13dc62721c25bf6c200af8f4295a Author: heather Date: Wed Mar 7 01:22:25 2007 +0000 implement filters commit e19fe2069197026caaf9350ce96de36f1239e333 Author: heather Date: Wed Mar 7 01:21:47 2007 +0000 tweaks to hapmap snps commit 0a8b030ce37d5d40990cde073a92894007c13eae Author: heather Date: Tue Mar 6 23:51:40 2007 +0000 keep it simple commit 5cdcbd744ee44aa01b30fc803aa231d4ab6e47b7 Author: heather Date: Tue Mar 6 23:51:00 2007 +0000 fix typo commit 2a1badb906ba2002b5c8be95c81d27acb65eb269 Author: hartera Date: Tue Mar 6 23:32:14 2007 +0000 First draft of description of Compugen Oligos track. Includes a Disclaimer from Compugen regarding the oligo sequencees. It was copied from the Ensembl Compuget oligo track for human. commit 880c1b268505545fa867dfe6b89e7f17632ed8c0 Author: kent Date: Tue Mar 6 22:41:50 2007 +0000 Separating out antisense from the rest. commit 3fe1b30a5657bb2ffbed3abd8dbcf7546c3ba1f6 Author: hiram Date: Tue Mar 6 22:39:17 2007 +0000 No more top-level trash names, everything properly contained in sub-directories now commit 23044e7ab2da8377af09bec69c28c16fbd1e6674 Author: hiram Date: Tue Mar 6 22:25:24 2007 +0000 Better clearing of everything on each possible clear button. commit 90726285fd39967c1907e1d4438badd57291aae9 Author: hiram Date: Tue Mar 6 22:17:24 2007 +0000 Properly default to genome region after messing with userRegions and they are cleared commit 2c88cf5ee12599dd4a364e3e9d89ef4696b80011 Author: hiram Date: Tue Mar 6 22:14:35 2007 +0000 Properly remove region type if nothing to do with userRegions commit 0819a1c83a4201c6a6998009284996fba8f5c8fc Author: heather Date: Tue Mar 6 22:05:50 2007 +0000 change mono default commit 0d99f498a3f1cdef665a42e282bbf1829b356527 Author: fanhsu Date: Tue Mar 6 21:56:53 2007 +0000 Replaced by spXref2.sql to reflect case sensitive name. commit 8fad2046972faf605123c637258db83b2c802e29 Author: fanhsu Date: Tue Mar 6 21:55:37 2007 +0000 Copied from spxref2.sql to reflect the spXref table definition. commit e8e8df9029a80b9e8ebca3b985a13d3ccaf6f97d Author: hiram Date: Tue Mar 6 20:46:16 2007 +0000 More complete help text commit 0d0efc6264f3badd288082f20938b55f8651e161 Author: galt Date: Tue Mar 6 20:43:47 2007 +0000 fixed evil key length limit on primary key commit 24765340729867de346bd450d258c06dacb7e269 Author: hiram Date: Tue Mar 6 20:41:28 2007 +0000 Adding definition of user regions function commit 6972556f8a0bf3c3b86e30d5a1df11df11e6a5f4 Author: hiram Date: Tue Mar 6 20:40:17 2007 +0000 Adding function of allowing arbitrary user region settings commit e3a6ef56294771b1598d105b7174fca1ea3eae46 Author: heather Date: Tue Mar 6 20:22:04 2007 +0000 remove hapmapAllelesCombined commit 83ff59233355c23342a676c80fbb7090feb0eeab Author: hiram Date: Tue Mar 6 19:32:53 2007 +0000 Help text for table browser define regions option - used in hgTables/userRegions.c commit 804c24051d7face45996730c52b8dd9a833595a7 Author: heather Date: Tue Mar 6 19:12:05 2007 +0000 kludgy checkin to keep things building...work in progress... commit e164daa448e373b7253cc545e76e2e838ab43b91 Author: kuhn Date: Tue Mar 6 19:01:11 2007 +0000 fixed commit 0e4e04416c4c24b3dbd5602948f5ee000e917a3b Author: kuhn Date: Tue Mar 6 18:58:35 2007 +0000 added back outfile unitl chain.csh is refactored to use std output instead commit b5234c28094e23db6d4c70314b73339354603a68 Author: kuhn Date: Tue Mar 6 18:53:16 2007 +0000 removed two echo statements commit 34a2aaa11fecfd5726e99acdffba0d5d0efa00b6 Author: kuhn Date: Tue Mar 6 18:51:53 2007 +0000 added getChromlist.csh for use in other scripts commit 0b61f7a3c80d368a7f8caa6feb97c3c40b254400 Author: fanhsu Date: Tue Mar 6 17:51:08 2007 +0000 Added BLASTZ runs and HUMAN PROTEINS. commit 70202cf00373eba226fccd686b15bdfc57bc3a94 Author: kent Date: Tue Mar 6 17:09:36 2007 +0000 Swapping Reviewed and Validated. From what I understand this is the real heirarchy. commit 72762a115b3bbdd3a021a39685438a844a2c11b0 Author: kent Date: Tue Mar 6 17:08:50 2007 +0000 Adding pbHgnc to makefile. commit 0084a85ce2b098c99eebe2f8f8eb07d1f73d6431 Author: kate Date: Tue Mar 6 17:00:41 2007 +0000 Common shrew 2X for multiple alignment commit 0eaea4f8a7cf08395edc4dc4656575a72d8c6aae Author: fanhsu Date: Tue Mar 6 16:36:38 2007 +0000 Added equCab1. commit 8d15377f668b1eb07fa2936573fe799d188333a4 Author: galt Date: Tue Mar 6 16:00:32 2007 +0000 "Encode release log update" commit b8364e736de854ecdacbb544facae8ebd25854d8 Author: galt Date: Tue Mar 6 16:00:17 2007 +0000 "Release log update" commit 495e8a5537b76621a3b49c02dd9323bf38b2dd48 Author: kent Date: Tue Mar 6 09:33:32 2007 +0000 Making refSeq's immune to CDS stripping from nonsense mediated decay. commit 08d8e5162425a1a6eb34a3e6df077c2e54853206 Author: kent Date: Tue Mar 6 09:31:50 2007 +0000 Notes on take 8 and 9. commit 6a9211e3e0e3d3a7713a4793e68e60f9339f9bde Author: kent Date: Tue Mar 6 09:31:08 2007 +0000 Adding a little more varSplice processing commit a960073485aed4e45689de36d4889cf0f6abe65c Author: kent Date: Tue Mar 6 08:25:57 2007 +0000 Adding exceptions. commit 1b07eb19b3f5486aa48df5cf917739b8c40e2213 Author: kent Date: Tue Mar 6 06:25:55 2007 +0000 Seems to work. commit a16c1c5d38c890e79991eab7122603a566613b82 Author: kent Date: Tue Mar 6 05:55:06 2007 +0000 txReadRa Read ra files from genbank and parse out relevant info into some tab-separated files. commit c94c1defc86324cfa27ce4a68ec08517cdaa7e2e Author: heather Date: Tue Mar 6 05:28:57 2007 +0000 change filters for hapmap snps commit b09cf4897c0260dc2c21f8363c23c272578f045f Author: heather Date: Tue Mar 6 05:28:06 2007 +0000 cart variables for filters commit c8d2e11e4a8f7e630d1b963e70ff5298ffd0f014 Author: kent Date: Tue Mar 6 04:38:10 2007 +0000 Adding support for the accToTaxon table. commit 518a55448b9c959f78911cab4a903fd5c0c9ad03 Author: kent Date: Tue Mar 6 03:45:54 2007 +0000 Added constExon option to help with a user request. commit 902164bdef6c764991475c3475370403953afe87 Author: kate Date: Tue Mar 6 01:55:54 2007 +0000 Exclude special table browser setting from original track line used by update screen commit 8198d8ce65aa72bd6dedb7703358fb32ec50583d Author: kent Date: Tue Mar 6 01:52:20 2007 +0000 Adding an additional output, and doing a better job of matching up exact matches before going on to 'compatible' ones. commit 8c2d3a395c2c0b702c86533e9559eb87767f9c2a Author: galt Date: Tue Mar 6 01:46:01 2007 +0000 updating link commit f5ccd70f24dca8ee2a0f4a8d0e08110b6934c1de Author: kate Date: Tue Mar 6 01:08:38 2007 +0000 Mark table-browser-generated custom tracks to indicate they have not been through the factory parser although they are written to the trash file. This notifies customTrackSave that they need to be rewritten; assuring they will land in the database commit a6bbbe72998fa13ee37e7675201a7aaec0712b78 Author: kate Date: Tue Mar 6 00:52:58 2007 +0000 Mark table-browser-generated custom tracks to indicate they have not been through the factory parser although they are written to the trash file. This notifies customTrackSave that they need to be rewritten; assuring they will land in the database commit 1721e46027596ea896de50f965e2706092aabfd2 Author: fanhsu Date: Tue Mar 6 00:37:03 2007 +0000 Updated to put out accession IDs as variants' displayID instead of parents' displayID. commit 47a9c00e111a503ce50627928830e9212960e8a2 Author: heather Date: Tue Mar 6 00:17:59 2007 +0000 use hapmapAllelesCombined.h commit b77a04c655b6839cd0d92842b6ba68d5ba4193ea Author: kent Date: Tue Mar 6 00:07:35 2007 +0000 More work to do all exact matches before any approximate matches. commit 67be211479970d37bc00bf69c60f99a92f33e19a Author: kate Date: Mon Mar 5 23:57:56 2007 +0000 Update tests to work with database implementation commit e2722ef86719a8592c7c24e40eefbffe2eb7c139 Author: ann Date: Mon Mar 5 23:36:03 2007 +0000 fixed up HTML error found by TrackCheck (during CGI push). commit 8c3ce74ab74c38d005b3f7e6f691ccba0020cd3b Author: hartera Date: Mon Mar 5 23:32:22 2007 +0000 Using build person variable to send automatic e-mails to buildmeister. commit 8a42828953cf3431b016b6c8620111905ebfe8de Author: heather Date: Mon Mar 5 23:30:44 2007 +0000 for filtering commit 891fe34b165d77ba191188fe42bd45d62243cb41 Author: hartera Date: Mon Mar 5 23:30:20 2007 +0000 Add a new variable for setting the new build person conveniently in one place. commit 46328f72b33a72b05ad78738d100e782a7c9dfb7 Author: heather Date: Mon Mar 5 23:30:00 2007 +0000 add hapmapAllelesSummary commit 970d43a89a3e21cb05adbf6a903efcd3c6cdcd96 Author: heather Date: Mon Mar 5 20:17:54 2007 +0000 use binRange commit f992b77400e55e87c047b0375c8f014c7d09d8af Author: angie Date: Mon Mar 5 19:58:41 2007 +0000 swap chain/net hg18, mm8. commit f118abd398f5077fba2af2135fcf4db201e2e95f Author: angie Date: Mon Mar 5 19:58:15 2007 +0000 Added note about automated updates of igtc (Gene Trap) track. blastz/chain/net Platypus (ornAna1). commit eddc1cc7bb612dd29286f725c85a8241abf8bb44 Author: angie Date: Mon Mar 5 19:57:42 2007 +0000 Added note about automated updates of igtc (Gene Trap) track. commit 28577c5ba5255086433475fc74f92f4b7464f5d0 Author: kent Date: Mon Mar 5 19:50:26 2007 +0000 Changing code to examine all possibilities for exact match before going on to compatible matches. commit b9f2e8d5a25ae27c0078e7bdd5def89ccc908a35 Author: kent Date: Mon Mar 5 19:35:12 2007 +0000 Fixing it to allow soft joins in non-refseq at non-intron gaps seems to cause more problems than it solves, so no longer allowing that. commit 6b34aaaa9ad1870daf246703b2235cea52b46fd9 Author: kent Date: Mon Mar 5 18:56:56 2007 +0000 Oops, backing out change from TX to UC accessions. Didn't mean to put that in quite yet. commit 2add9bac337169cb4094ac1614f76e73d20946b6 Author: kent Date: Mon Mar 5 18:55:52 2007 +0000 Adding a test case. commit 6dcefe1e700d124698036040f8ed1ca345fbad56 Author: kate Date: Mon Mar 5 18:32:33 2007 +0000 Preliminary run of 25way alignment commit e8409c125d6f14aaf3673fed96e294eff9da28f8 Author: kent Date: Mon Mar 5 17:51:16 2007 +0000 Changing library paths in makefiles of rnaStructure to be relative like the rest of the system. commit 4ac557e51e63c92e8de27e7fc043e7c23055e0dd Author: ann Date: Mon Mar 5 17:43:52 2007 +0000 Fixing broken link to WUSTL website. commit 3c6dc5b86f144877c5d34bbb6ae525d4f86ff6f3 Author: kent Date: Mon Mar 5 17:41:32 2007 +0000 Removing bogus test target commit 2c8e3967e1aa9c1592dc584342902a19c51235af Author: kuhn Date: Mon Mar 5 17:18:42 2007 +0000 changed so it will do the du through the wire if machine cannot be logged into. ok with erich if not frequent commit a6ee5b147b5713cfa9fd85ad62dd5a6179426f51 Author: kuhn Date: Mon Mar 5 16:47:00 2007 +0000 added aping to each store unit to load the mounts commit e90362e5da987b9156001039aed24c09cc115244 Author: markd Date: Mon Mar 5 16:15:21 2007 +0000 work on CGAP SAGE track description commit 88c46077d7d78603b3e146cce093796917357d64 Author: galt Date: Mon Mar 5 16:00:24 2007 +0000 "Encode release log update" commit 0e86a98bb8945cbe30e8e785475572a8a969b4a1 Author: galt Date: Mon Mar 5 16:00:13 2007 +0000 "Release log update" commit 894a76be2b5bcd5956398341d5ad28af3c8f12c6 Author: giardine Date: Mon Mar 5 14:52:52 2007 +0000 Changed default URL for galaxy connection. commit b82fc3d6b0e491be9a269e6cdf79c7e803565516 Author: kent Date: Mon Mar 5 09:12:32 2007 +0000 Fixed bug that was causing breakup at non-refseq funny introns. commit 88f8d084d81a05c56d3dd655e18f9431c231901e Author: kate Date: Mon Mar 5 05:02:08 2007 +0000 Adapt custom track tests to support database implementation; show them where track loaders are commit 277c0143bb90095ba1f5d2f83271ab4313a4401f Author: kate Date: Mon Mar 5 04:44:28 2007 +0000 2X mammals for 28way alignment commit 28118fdad8bd3f408453f8267d5ea015b5ce550c Author: baertsch Date: Mon Mar 5 04:40:15 2007 +0000 add fields for dog orthlogy commit 51f2149b0da10f8fc299345a01463327075963e0 Author: baertsch Date: Mon Mar 5 04:34:24 2007 +0000 retrogene details page commit 6dd1a1a4b0e40e043f8dd4da4b434f22ecfcba7e Author: kent Date: Mon Mar 5 03:49:56 2007 +0000 Starting on docs for new proteins database. commit ac655c1d86099a18585469241c069ec33b102fd1 Author: kate Date: Mon Mar 5 03:47:31 2007 +0000 Fix CVS conflicts commit 831387a5aa69ef4388098a74721fe27370b69a13 Author: kent Date: Mon Mar 5 02:30:03 2007 +0000 Removing some unused vars so it compiles clean. commit 4b0dacaed83f5321b65e37a01420d44eb4ae8a00 Author: kent Date: Mon Mar 5 02:27:56 2007 +0000 Adding some make files to higher level visiGene directories. Correcting some warnings. Still won't completely auto-build, so not yet calling hg/visiGene/makefile form hg/makefile. commit 0c7814c4ea101f5030f82b397a369ca0b600ba23 Author: kent Date: Mon Mar 5 02:23:32 2007 +0000 Adding autoSql-generated .h file to get it to compile. commit e5d3b2a34d7bdb69051d330a2aab3f358aa9d836 Author: kent Date: Mon Mar 5 01:43:20 2007 +0000 Getting rid of curProtId as separate entity. It just was gumming up the works. commit d2bfed4914d4757f45cba88c58bb46eafd6e686e Author: kent Date: Mon Mar 5 01:41:21 2007 +0000 Suppressing protein browser link when no protein. commit a6b3e9e68f6cbf742c44f28a961e79dbc01cf372 Author: hiram Date: Mon Mar 5 00:10:39 2007 +0000 Add WindowMasker, simpleRepeats and creation of masked contig sequence commit c0d43d0bdab9db2cce6f0c4f206eb9f7486a66b5 Author: hiram Date: Sun Mar 4 23:41:54 2007 +0000 Initial sequence to get gold and gap tables established properly on chrUn commit fbad34b12836606c86640cdc5817a97ed63b2173 Author: kent Date: Sun Mar 4 20:57:54 2007 +0000 Further work on hgNear & hgGene for hg18a. commit 13cd177883944cd1429fb164f2539e407086e3bc Author: kent Date: Sun Mar 4 20:56:34 2007 +0000 Adding -warnEmpty flag to bypass rare problems in RNAfold. commit dc7cc9a3002429c1c89bb478a181e4ed4af23b1f Author: kent Date: Sun Mar 4 20:26:28 2007 +0000 Made the fromProbePsl case more precise and about 1000x faster. commit 0ce0f4339b8a73b2cd7ece4fc312e831f06831be Author: kent Date: Sun Mar 4 20:25:21 2007 +0000 Adding genePredToRangeTree. commit 3d9758a115f6b88bc46f1360c023221062dbd15f Author: kent Date: Sun Mar 4 20:24:19 2007 +0000 Adding pslRangeTreeOverlap. commit 325dc68063c5fa29a796b36e940f3ebda94b5ec1 Author: markd Date: Sun Mar 4 18:18:17 2007 +0000 use dynamic buffer for update SQL commands commit 324db378b6d896e9b8630399db53fea80442201b Author: kent Date: Sun Mar 4 17:53:58 2007 +0000 Defining a makefile for the rnaStructure directory. commit 3d32174e6f39f3aa4e18d40e752fa92d25d9be21 Author: kent Date: Sun Mar 4 17:53:40 2007 +0000 Adding rnaStructure to src/hg/makefile. commit 350d6ed1510b7413d2c155ff3cedd7ab27fd5c1c Author: kent Date: Sun Mar 4 17:39:23 2007 +0000 Adding note on synteny filter. commit b7922c8cbe71bd41acc0d8fbf3c31724bc4cb1cd Author: kent Date: Sun Mar 4 17:19:07 2007 +0000 Ranaming struct range to struct simpleRange to avoid name conflict with rangeTree's range. commit c6ce2282a949d8fb33046ac96715ff89cfd4be75 Author: kent Date: Sun Mar 4 17:09:52 2007 +0000 Ranaming struct range to struct simpleRange to avoid name conflict with rangeTree's range. commit a81249e3d474d32329155b94d583c4c856cf3990 Author: kent Date: Sun Mar 4 17:04:46 2007 +0000 Renaming struct range to struct liftRange to avoid name conflict with rangeTree.h's new struct range. commit a4a4620fc49fb3d3c5397e95b8a0ee383f4436fd Author: galt Date: Sun Mar 4 16:00:26 2007 +0000 "Encode release log update" commit 71a483b6e901e0d9324515af76d02bb7144deb9b Author: galt Date: Sun Mar 4 16:00:14 2007 +0000 "Release log update" commit 6ae15386df1d6c5b234b2a4d021ccb265e5aadb4 Author: kent Date: Sun Mar 4 10:43:42 2007 +0000 Reading protein from file rather than recalculating it badly. commit edd61eb2dbdb1d43d99add2fa124c4391114cdd9 Author: kent Date: Sun Mar 4 10:41:59 2007 +0000 More work creating the various Gene Sorter tables on hg18a. commit ae0d1e76530a858fec34cd8f1a6c336c55aed248 Author: kent Date: Sun Mar 4 07:08:56 2007 +0000 Adding a comment. commit e84f0c7621851255142731d1dbaabf1e89c3d0f3 Author: kent Date: Sun Mar 4 07:07:20 2007 +0000 Recalculating best protein pick ourselves rather than relying on tab-separated file, that ended up generally being out of sync. commit 0c8051e53d06318542895e6393ba645036f77ab9 Author: kent Date: Sun Mar 4 06:54:40 2007 +0000 Moving txInfoCodingScore to library commit 3385e36e3d2fefa633865a03cf4615fee7718af3 Author: baertsch Date: Sat Mar 3 22:49:15 2007 +0000 new retroGene table retroMrnaInfo commit f4ab7c797e25f35d85cb351de77263c8ffa954bb Author: baertsch Date: Sat Mar 3 22:26:15 2007 +0000 add exonArrowsAlways to show arrows always in the retroGene track with small insertions commit d329389fb46595345c0eccdc079388df3c730bc7 Author: kent Date: Sat Mar 3 22:05:08 2007 +0000 Creating a separate UCSC column, and reworking GenBank column to be read from kgXref rather than relying on it being the same as the UCSC Known Gene ID. commit 5cce4ef53d91d3cb9eb085ed0abfca4faecbcee3 Author: baertsch Date: Sat Mar 3 21:50:20 2007 +0000 add retroGene click handler for new table retroMrnaInfo (replaces old pseudoGeneLink), also remove orphan function getSequenceInRange() commit b1c4a9a02e24cbf581d65f307d697bc720e0dfa7 Author: baertsch Date: Sat Mar 3 21:45:48 2007 +0000 new retroGene details page to for table retroMrnaInfo that will replace table pseudoGeneLink commit c8b7c5b405a360bf7db02f93ae70a24009f1bf5f Author: baertsch Date: Sat Mar 3 21:35:16 2007 +0000 show arrows in retroGene track even when there are small gaps in the annotation commit c26a5abfb57402fae86a396a8aee7cea4b51c883 Author: kent Date: Sat Mar 3 21:26:02 2007 +0000 Maintaining proper strand on cluster. commit cc488f8b7ecf12d4cedce6bb982215bea5b1b4c1 Author: kent Date: Sat Mar 3 21:25:22 2007 +0000 More progress on hg18a build. commit 72fc81c93fd13c0c6c078f07c8b4e91026cfaa3b Author: kent Date: Sat Mar 3 21:17:19 2007 +0000 Making cluster ID a number again, the way knownCanonical likes it. commit 1a833b01239603c64cfab2702070089d9f6d299c Author: kent Date: Sat Mar 3 21:16:22 2007 +0000 Getting rid of some chars in gene symbols that tend to mess with html and SQL. commit 9f2aac29734fd81f2c9f4a901cc3c21b178932d9 Author: kent Date: Sat Mar 3 21:05:52 2007 +0000 Replacing some strdup with cloneString. strdup bypasses our memory handling. commit 0c166da12147188d0fcff2e1803a6722fb4d355d Author: kent Date: Sat Mar 3 20:45:55 2007 +0000 Adding sql files for knownCanonical and knownIsoforms. commit 22a81d004e0ac60b64a44ae3ffbdf76cd2a8b186 Author: kent Date: Sat Mar 3 20:34:17 2007 +0000 Adding bedRangeTreeOverlap, bedToRangeTree, and bedIntoRangeTree. Moving bedsIntoKeeperHash from minChromSize to bed module commit 04cef61c8ee222b74714354dd7c89e0f14573721 Author: kent Date: Sat Mar 3 20:32:05 2007 +0000 Seems to work. commit 68c4485408a025b79f1f6ec59344ce3705ae716b Author: kent Date: Sat Mar 3 19:45:15 2007 +0000 Testing refactored bedSameStrandOverlap. commit 436578de24286461a002a48bba8ea14396968993 Author: kent Date: Sat Mar 3 17:55:37 2007 +0000 Wrapping in define to prevent multiple inclusion problems. commit 5c7d23a7fb8fe142e5afea166445ec931e58e2ca Author: kent Date: Sat Mar 3 17:24:00 2007 +0000 Moving stuff to make a binKeeper for each chromosome, and one filled with beds, to new library module minChromSize. commit 1d2e2194b3a3155601318a657f93e976c8e6ac79 Author: kent Date: Sat Mar 3 16:25:34 2007 +0000 Suppressing empty string aliases. commit 45f726f8b25a2f460abd0d1830e26f28a6305689 Author: galt Date: Sat Mar 3 16:00:32 2007 +0000 "Encode release log update" commit 553c395c6b1dd894ddad72dcaf8e775bd63c7204 Author: galt Date: Sat Mar 3 16:00:17 2007 +0000 "Release log update" commit b6717d8eccf396c0972560eccf5a0144297da7b2 Author: kent Date: Sat Mar 3 05:09:00 2007 +0000 Adding -list option to subColumn. commit a0d7518c8e0b993727a293bc40a6f52f13557a35 Author: heather Date: Sat Mar 3 01:17:38 2007 +0000 smallint is acting weird. Also give up on shorter chrom/chromStart/chromEnd/name for now. Single quotes in allele2 enum. commit 4e5f9bf72ef05aa804945ac219b860dd34a12ee9 Author: galt Date: Sat Mar 3 01:14:54 2007 +0000 fixed format bug commit 2897403df8470b09f25d05a85242fd0b646a86a2 Author: galt Date: Sat Mar 3 01:09:26 2007 +0000 more date fixing, this time the month. just re-arranged the date by YYYY/MM/DD as more logical and sorts alphabetical is also chronological commit 491851c8cca38c9f342adc47df1d4d58035eed4e Author: galt Date: Sat Mar 3 00:58:50 2007 +0000 vista enhancers commit 509020971c0b2714ccaad5c0277fccc7974b369d Author: galt Date: Sat Mar 3 00:58:11 2007 +0000 typo commit b52408f60bd696e64e3bd08bb87652810f028cb9 Author: aamp Date: Fri Mar 2 23:41:54 2007 +0000 Added windowmasker auto-script to /cluster/bin/scripts copying. commit dc07b6d032b3a6d1c7e74a9f69ca7dae222d435d Author: fanhsu Date: Fri Mar 2 23:30:38 2007 +0000 updated equCab1 lines. commit 6df8b541b02cde479ea41a614e68781a9abecbc0 Author: aamp Date: Fri Mar 2 23:26:03 2007 +0000 Build instructions for mm8 CGAP SAGE commit 4a52879de99640f5dde646865b4cb58720235601 Author: ann Date: Fri Mar 2 23:16:06 2007 +0000 added -w to grep command so that it looks for complete matching words only commit 913e7f22507016dfa4e0ab68d8243e7d8309e73e Author: angie Date: Fri Mar 2 22:53:01 2007 +0000 Added quality scores track. commit 207ab6292bd5a93fde3807d2558bdbc6c8ec67c8 Author: braney Date: Fri Mar 2 22:35:09 2007 +0000 fix base position zooming so can't go to zero width commit 24ac0f8f70e197b7cb0a001113f0bcf49b1ed36e Author: hiram Date: Fri Mar 2 22:34:56 2007 +0000 Update the use of the hgLoadBed for the loader to streamline the argument passing, and now handling negative scores in bed files submitted for custom tracks commit efa122ff3ab44bde99cf74518db9c76ab06a7839 Author: hiram Date: Fri Mar 2 22:04:18 2007 +0000 Add -verbose=0 to -customTrackLoader set of options commit 30096786a580cea6e80930a9261cf1bd26688361 Author: hiram Date: Fri Mar 2 21:59:30 2007 +0000 Implement -allowNegativeScores option commit a75c2b000260926ef002d8b725b79ba8f2d321f7 Author: aamp Date: Fri Mar 2 21:32:40 2007 +0000 Made position linkable on cgap sage details. commit 3bf42df59013264a3d8d7eb272fdf8088fb78703 Author: markd Date: Fri Mar 2 21:00:55 2007 +0000 CCDS update commit 8a611fa5bbc12dd6a25ee0c08118c439bc1d6dd3 Author: markd Date: Fri Mar 2 20:46:46 2007 +0000 add hg18 to ccdsDb commit dc890b8593b8026545b0705cf904a03f5fa847c3 Author: braney Date: Fri Mar 2 20:43:51 2007 +0000 double ugh. take out a printf commit ffe2388522f70a8e96cdabf02e96b95ce7a2f1c7 Author: braney Date: Fri Mar 2 20:39:33 2007 +0000 ugh... today is not my day. Fix this right this time. commit 7603d6a7d5b6fffbd4e0947b20b8cc10091c091d Author: braney Date: Fri Mar 2 20:31:31 2007 +0000 fix zoom in problem resulting in 2000 base pair view, used to default to 30 commit 71c1fda2f5156f6f2aef6bf2e3400807b49ea25a Author: angie Date: Fri Mar 2 20:14:42 2007 +0000 In linkedFeaturesDrawAt, don't draw each codon if we are zoomed out past the codon-per-pixel level. lf->codons might still be non-NULL so that we can OverdrawDiff later, so gate it with zoom level. commit adc9069edc566e0447343f099f93b47194cb4803 Author: kate Date: Fri Mar 2 18:49:09 2007 +0000 Back out reference to unfinished help doc for hgSessions commit 72d19bb82243e7421a75d3ba933d2d005027bb05 Author: markd Date: Fri Mar 2 18:47:04 2007 +0000 added verbose output for ignored CCDSs commit 164e715cf586de4d151db1496639da26f7820c67 Author: kent Date: Fri Mar 2 17:14:19 2007 +0000 Fixing typo in string, and renaming a variable. commit 6bbed58901972669da71cadd56f2d138cfa219fd Author: kent Date: Fri Mar 2 17:13:29 2007 +0000 Improving unmapped output in too divergent case. commit 8acf26286e4b8cc4510a401c04992d69bb9781a0 Author: kent Date: Fri Mar 2 17:12:53 2007 +0000 Testing pslCalcMilliBad. commit 09940356cf1c0b7206c579038dee39a522fc0632 Author: kent Date: Fri Mar 2 17:12:12 2007 +0000 Fixing name conflict between range defined here and range in src/lib/rangeTree.c commit 3a757b0e20c428724beff20ae052317535e080b4 Author: markd Date: Fri Mar 2 17:10:35 2007 +0000 support for hg18 human CCDS commit 5d77a6f6c7c409f51109305c9ee618581d64c097 Author: galt Date: Fri Mar 2 16:00:33 2007 +0000 "Encode release log update" commit 705ade72c559f023994ff48780765ccdad53b106 Author: galt Date: Fri Mar 2 16:00:18 2007 +0000 "Release log update" commit 57bcbf4ed1baff19068f45bfc0c002b9fa1acced Author: giardine Date: Fri Mar 2 14:25:44 2007 +0000 Changed name check so Galaxy output should be available for genome-test? commit 1670a9fe33a570c628e1a34d53e7eb72b7e095bc Author: kent Date: Fri Mar 2 12:09:10 2007 +0000 Seems to work. Should run it by Fan. commit c946b36b6d1622867b3b819113528c455537b3d0 Author: kent Date: Fri Mar 2 10:41:25 2007 +0000 Starting to build and write up actual knownGenes table and relatives. commit 3c628ba87f7fc5ceb8ed7bf81af3f189c2e9d19f Author: kent Date: Fri Mar 2 10:32:54 2007 +0000 Putting in an alternative way for known genes to get it's color simply from a table, rather than adding additional complications to existing scheme for KG3. commit aeb19bd43fff13cce6f452013be6f32717b570d3 Author: kent Date: Fri Mar 2 10:31:48 2007 +0000 Seems to work. commit ebb456125f6ee5fbb4f2b8f7327876d61f4d8a1f Author: kent Date: Fri Mar 2 09:39:33 2007 +0000 Tweaking index sizes. commit 0ed67538070c54166461f338880e0919bc9ff18f Author: kent Date: Fri Mar 2 09:36:07 2007 +0000 Adding txRnaAccs and kgColor tables. Making kgXref.description handle more than 255 chars. commit 9f684c5f8e3cdd1bce5314bc0cf736040e3571bb Author: kent Date: Fri Mar 2 08:54:36 2007 +0000 Making it handle missing protein data better. commit d4102dd899902c5c0b5205836214b595d11eff2e Author: kent Date: Fri Mar 2 08:46:48 2007 +0000 Not assigning UniProt accessions to stuff we consider noncoding. commit 6900a44e7b24e7536c480d3dc0da10b463a31a76 Author: kent Date: Fri Mar 2 08:35:48 2007 +0000 Seems to work. commit d094aba4a9c12984d48c3f51efd1534466866119 Author: kent Date: Fri Mar 2 06:59:41 2007 +0000 Seems to work. commit 3a8735f93854ec1d441868da811bcdb528ab0648 Author: kent Date: Fri Mar 2 06:48:13 2007 +0000 Expanding size of alignId field a little. commit 9ec624c5fbe2a5c4a2a16261f1650f16890995cd Author: heather Date: Fri Mar 2 06:23:26 2007 +0000 don't need bin; do need observed commit c706c3bf1fc613b48e71a0f049260e23a608b907 Author: kent Date: Fri Mar 2 02:34:27 2007 +0000 Seems to work. Needs more testing. commit 6e41a7a4b8b98c46dda684b5ad0920d9078aef8a Author: kent Date: Fri Mar 2 01:39:37 2007 +0000 Making this update the txInfo file. commit cf2a70ca34ff6b3bd58a02935b2adad0d430aa00 Author: kent Date: Fri Mar 2 01:25:03 2007 +0000 Added bedSameStrandOverlap. commit 16d88a9d5b632856a69e5dba8e611e65c69a54ad Author: kent Date: Fri Mar 2 01:20:38 2007 +0000 Added test input and fixed a bug test unvieled. commit a4e578cea482e2f2140bbbbb3fb57bd734a9b6ba Author: kent Date: Fri Mar 2 01:00:04 2007 +0000 Fixed bug, and now have verified that it maps new transcripts to identical old transcripts correctly. Still need to write test case to see if mapping of extended new transcripts to old transcripts works. commit 2ae630cffae9648a382b092bf298f6461d5cfacf Author: kent Date: Fri Mar 2 00:51:52 2007 +0000 Initial coding done. Works in case where no old genes. commit b046f77a4d2e738b99cffb86e51d21206e074543 Author: kent Date: Fri Mar 2 00:49:31 2007 +0000 Adding subColumn utility. commit 0daffc0fe265cffc5ab8d2d6ccdc9978b9fc466c Author: kent Date: Fri Mar 2 00:48:49 2007 +0000 Removing hashTwoColumnFile since this is now in library. commit e71a6837e5724a4543dbe750660603ea43da595d Author: kent Date: Fri Mar 2 00:45:01 2007 +0000 Adding hashTwoColumnFile commit bcbf817e52bf2c46cfcd54cbd5f564e2a1e4d291 Author: kent Date: Fri Mar 2 00:44:26 2007 +0000 Seems to work. commit 9a87c9237eb87aab869388eaf6ca99b01afd46f0 Author: heather Date: Fri Mar 2 00:21:13 2007 +0000 fix bug commit cb945b389c1709292260b441300ec42ba1f81304 Author: kuhn Date: Fri Mar 2 00:09:40 2007 +0000 fixed it so that when units can't be logged into, it doesn't try, but simply notifies. commit 029147eb0831492878eab33c218c0eabc67fbb69 Author: angie Date: Thu Mar 1 23:59:01 2007 +0000 Made multiz9way hidden by default because it has been replaced by 15way on hgwdev, beta and RR. commit 2f937a9ac01c8ddebcfe07192effec9d8ad07422 Author: kuhn Date: Thu Mar 1 23:45:33 2007 +0000 moved Table Schema priority so it comes after visiGene, which should be grouped with the other utilities from ucsc commit ef1cf4ea285e4b3c4bb12f6537af58dda86ed27c Author: kuhn Date: Thu Mar 1 23:28:23 2007 +0000 oops. had to remove my private # on the cvs up for beta commit f05432290757cefb07b73fa619cc12b66cd0b137 Author: kuhn Date: Thu Mar 1 23:27:11 2007 +0000 moved danRer1 out of the make targets for MGC and strict. added to ARCHIVED_DBS list commit 0ceb780f130dd7efd1ed4f4bfd3b4faccae04a5c Author: angie Date: Thu Mar 1 23:16:22 2007 +0000 Removing link to hgSessionHelp.html temporarily. commit 0f90065a0e4407cbea41299d51739df6bd82b7fc Author: kuhn Date: Thu Mar 1 23:10:04 2007 +0000 fixed handling of archived assemblies so that those still around with chromInfo table are listed. commit 3f6a31d621f5ce41eeed4787a72e4df5e7e854d3 Author: heather Date: Thu Mar 1 23:04:32 2007 +0000 create table of summary data for filtering commit 8aa7ac2fec3e83ba95b42db6a9132fe46f29ce63 Author: heather Date: Thu Mar 1 23:04:00 2007 +0000 rename hapmapExtend to hapmapSummary commit fccafefba2d0f0d5deb3db4dc698811083752f68 Author: heather Date: Thu Mar 1 17:57:49 2007 +0000 change allele2, restrict sizes, use enum for strand commit db1d8971e58766317227edd559e138aae61da649 Author: heather Date: Thu Mar 1 17:55:16 2007 +0000 change allele to string, use ushort, update score comment commit 4b26a8f239d57da36a5b478afe03db6933213d3b Author: heather Date: Thu Mar 1 17:53:51 2007 +0000 change allele2 to char * commit f33d2eafa231b1fa0ecaac18675593e9cae75700 Author: galt Date: Thu Mar 1 16:00:33 2007 +0000 "Encode release log update" commit c0edecbe386e353c54f9ca8eeaac6c8b60d102d5 Author: galt Date: Thu Mar 1 16:00:18 2007 +0000 "Release log update" commit e6f4d5330cd24cad690de7d83789732b6240971e Author: kent Date: Thu Mar 1 00:12:30 2007 +0000 Making it so that table browser genome/encode/position radio button doesn't get automatically set to position when following tables link from hgTracks. commit da0939174820998a54f19aa535a2f987946900c7 Author: baertsch Date: Thu Mar 1 00:02:28 2007 +0000 add retroMrnaInfo commit 5a8b4d2290aa6f1f0b7533ff977f294e3e580ad1 Author: baertsch Date: Thu Mar 1 00:01:47 2007 +0000 new retro tables commit 4d4899b340819d0a0a820b0cde41044adc134f7a Author: baertsch Date: Thu Mar 1 00:00:11 2007 +0000 retroGene name, new tables (retroMrnaInfo) commit a135fa756d4f2b5665360a709952dea0dac36b69 Author: markd Date: Wed Feb 28 23:44:17 2007 +0000 fixed reference format commit f229a891cac35da864044a6bee18a75261059576 Author: angie Date: Wed Feb 28 23:43:36 2007 +0000 Added updateIgtc.pl and monthlyUpdateIgtc.csh to SCRIPTS. commit 9d4f9f48f0cb59d01ca85780ba60b52dcfcd6490 Author: angie Date: Wed Feb 28 23:42:21 2007 +0000 Updated trackDb settings for all_mrna. commit f06e42cdc2e1ff57174c211ddd35da8dc94a8888 Author: angie Date: Wed Feb 28 23:41:17 2007 +0000 Scripts for cron-driven monthly update of IGTC (genetrap.org) track in mm6, mm7 and mm8. commit 2c8ac2d260eecec05d5ce4d6121ce56eca0e95b1 Author: heather Date: Wed Feb 28 21:53:28 2007 +0000 tweaks for hapmap snps commit 322f0f09b0af5fdfe0372520fcd1c4aeb8849f08 Author: heather Date: Wed Feb 28 21:46:42 2007 +0000 use grayscale for quality score for ortho alleles commit 0266edf7c41cc1bb3ca33057955a63bd2c48aa54 Author: heather Date: Wed Feb 28 21:33:34 2007 +0000 tweaks for hapmap snps commit 05717132c09bdffa0a2adb069f16b7a03b3d1d35 Author: giardine Date: Wed Feb 28 20:39:08 2007 +0000 Change galaxy connection to galaxy2. Allow all output formats to be sent to galaxy. Only provide Galaxy output option on genome-test and my dev site for now. commit bb1072842b18ce4a10c1ae59ea066378ddb0bc19 Author: heather Date: Wed Feb 28 20:37:55 2007 +0000 change hapmap allele2 to char * commit 950f8683bde59da6594d07959e16eb55abe3a0b0 Author: galt Date: Wed Feb 28 20:04:08 2007 +0000 paraHub - fixed bug in year. needed to add 1900 to tm_year commit a0e803f5e3e47635ef57735a7415bf3cf9b85332 Author: heather Date: Wed Feb 28 19:49:52 2007 +0000 alleleCount change to homoCount for hapmap snps commit 0178936aa24b54dda3b38f376a440aaf77ce893b Author: heather Date: Wed Feb 28 19:49:13 2007 +0000 alleleCount changed to homoCount commit 261ea84198685c19f7ad0d96417b4e17a9f43788 Author: heather Date: Wed Feb 28 19:48:25 2007 +0000 use char* for allele2 commit 9dfe9e74e851076ab03e46d67b0e73c799c94c71 Author: hiram Date: Wed Feb 28 18:31:49 2007 +0000 Add percent masked printouts with -showPercent argument commit d5921c1b0533f1b3f63b79aa0591abd365c223d4 Author: heather Date: Wed Feb 28 18:00:28 2007 +0000 rename alleleCount to homoCount; use none rather than ? for monozygous; limit length commit b7fe9deea72bffc7d90e53e0a61a9c978454e6e4 Author: ann Date: Wed Feb 28 17:55:52 2007 +0000 added 4 scripts: chain, chain2, net, chainNetTrio commit 0bc2ebc3deb860cc6fa73c60923dd918da0dce03 Author: ann Date: Wed Feb 28 17:53:42 2007 +0000 Initial checkin. chainNetTrio calls: chain, chain2, and net. These all work together as a suite to ensure that chains and nets meet certain requirements. commit 9b093511593fb19a29a97d8864f3841c7ae2ba36 Author: galt Date: Wed Feb 28 16:00:33 2007 +0000 "Encode release log update" commit c25e25dbfcd8c2d74af7c0c6db8f9835090323a4 Author: galt Date: Wed Feb 28 16:00:17 2007 +0000 "Release log update" commit 2b1084a2b7b9f7c217ab092fb0820b4c9aa6ff38 Author: kent Date: Wed Feb 28 08:50:54 2007 +0000 Making the CDS single description more accurate. commit b5fad2192850b1ab9023790404e709bbcf5d753b Author: kent Date: Wed Feb 28 08:46:43 2007 +0000 Adding atacIntrons field. commit 2260b278f9685e02f2e83b12bd72e5d94da3128b Author: kent Date: Wed Feb 28 08:46:10 2007 +0000 Including bed.h since have a bed. commit 121716f6de8ef190775fd1abd5f7d39753cf853f Author: kent Date: Wed Feb 28 08:44:33 2007 +0000 Added a few new fields to txInfo. commit c73bd2c0998d3f537159b9d57ddb957a0ac9546d Author: kent Date: Wed Feb 28 08:36:16 2007 +0000 Fixed typo. commit 79a1cee77facfbe2f1e424ea39c04a020325824b Author: kent Date: Wed Feb 28 08:26:47 2007 +0000 Writing up explanations of fields of the big txInfo table. commit 55ea7bcbc9d94f69eef4b70ddd7cc212de237319 Author: kent Date: Wed Feb 28 07:12:53 2007 +0000 Separating out kg3 bits into new file. commit c03c64b5ae7589ef15f3c47bcaa50229ead5ae24 Author: kent Date: Wed Feb 28 01:57:43 2007 +0000 Seems to work. commit 46a1d5b6d759e3b27adc66009780aa61a832735d Author: kate Date: Wed Feb 28 01:11:44 2007 +0000 Duke Dnase data submitted. 4 newly expected commit 2ae584236c648984aa17e8fd45c57e4112371fe4 Author: heather Date: Wed Feb 28 00:51:37 2007 +0000 read combined tables for isMixed and isAllPops commit 14129972f1d595de01b991510bb8d0b8cbdfbcf4 Author: heather Date: Wed Feb 28 00:51:10 2007 +0000 add hapmapExtend commit 85ecfb948b06264092e1083ebac46f7d91325e14 Author: kent Date: Wed Feb 28 00:44:47 2007 +0000 Adding updated txInfo output. commit a0e77a1a4167f6806d301268b7ccad864cc11347 Author: angie Date: Wed Feb 28 00:32:42 2007 +0000 Tweaked customFactoryTestExistence so that it now touches custom tracks that are live. commit dec6b2a01e8495644c542d37c1acfde93386d401 Author: kent Date: Wed Feb 28 00:31:46 2007 +0000 Adding additional explanitory text. commit 5785d716f5ab7d792fc738ba24f45527195d60f2 Author: angie Date: Wed Feb 28 00:28:15 2007 +0000 Cron robot for keeping alive custom tracks that are referenced by saved sessions. commit c0895d623cf6af943fff30e42affe0d43ec5e0f4 Author: kent Date: Wed Feb 28 00:25:55 2007 +0000 Seems to work. commit f0ce328d271bb1dd261cf36f82064fdc36acefc2 Author: galt Date: Wed Feb 28 00:03:09 2007 +0000 added change password capability commit a3b056b1201529d120c3302b1868f6005884766d Author: kate Date: Tue Feb 27 23:56:28 2007 +0000 DnaseI HS data in IMR90, K562, and H9 cells from Duke commit 5c976b74c4a441da90c3b6b6e5dfe8e79a671730 Author: kent Date: Tue Feb 27 23:56:16 2007 +0000 Adding stuff to collect strange splice sites and bleeding exons. commit 388740ac09f7062d3cb3fd1c3b53729b492ad51c Author: kent Date: Tue Feb 27 23:22:59 2007 +0000 Making this flag introns with strange ends and exons that bleed over into introns. commit 17011d93add0298cbfd4f743211a3c5321b36e97 Author: heather Date: Tue Feb 27 22:55:49 2007 +0000 add chimpParalogy from Eichlers lab commit 52d9cb42bdaf5e7f6c635f5902dca94fc86555c9 Author: ann Date: Tue Feb 27 22:55:19 2007 +0000 added bosTau2 to two blastHg18KG rules commit d13cda8823eb78416f4918501b82d177ad822993 Author: heather Date: Tue Feb 27 22:52:01 2007 +0000 new data from Eichlers lab commit bf7df9c0c90c13e702ac23f67bd1fa814dce6b79 Author: heather Date: Tue Feb 27 22:51:42 2007 +0000 add chimpParalogy commit 8ea55a38b569a3cab1ae6dec9e8d88cbf7e87702 Author: heather Date: Tue Feb 27 22:36:53 2007 +0000 adjust priority of snpArray commit 236c8b8eb355ca904ab940126d2e8a5d9df783f5 Author: heather Date: Tue Feb 27 22:33:04 2007 +0000 adjust priority of snp track commit 0c2257402f6e20658243b6087388f906ffd64d96 Author: heather Date: Tue Feb 27 22:23:57 2007 +0000 adjust priority of RIPs commit a49089bfcc2753a16384abc08b1f6dc0bc50ae61 Author: heather Date: Tue Feb 27 22:21:52 2007 +0000 adjust priority of chainSelf commit 516cdcb250f4feeafb403f0e277085eddb0effe4 Author: kent Date: Tue Feb 27 22:00:46 2007 +0000 Adding bedTotalThickBlockSize function. commit 73d593703acdf48df2230bac77b924aac8c3ec1e Author: kent Date: Tue Feb 27 21:59:43 2007 +0000 Reworking pipeline description a little. commit f8f985792a466740e35cfa61df258583d41c12aa Author: kent Date: Tue Feb 27 21:58:53 2007 +0000 Handling stop codon better. commit 2f5e4806368872cdb2c74d20983fcca400ae76a7 Author: kent Date: Tue Feb 27 21:58:30 2007 +0000 Adding more info to txInfo, still some more needs to go in here. commit 7b402ecbb85ae36881c6cae981452b27b6c5f136 Author: kent Date: Tue Feb 27 21:58:00 2007 +0000 Adding some more info to txInfo. commit d9c30fa0d7c4f9cc37428d59e6fa9cc5e77837b4 Author: heather Date: Tue Feb 27 21:50:54 2007 +0000 adjust priority of selfChain commit 0414b1521a5b02e6fa869483ce1b66eb70a6c08d Author: kent Date: Tue Feb 27 21:04:36 2007 +0000 Seems to work. commit 536788d9b240b7b94bea41708c2e36145dd66201 Author: rhead Date: Tue Feb 27 19:39:36 2007 +0000 Changed 'Meyers' to 'Myers' . . . this is actually spelled incorrectly in the linked paper -- everywhere else online it is spelled 'Myers', including Pubmed commit c7919ab3592aa6f891644993031330cb19b617d3 Author: heather Date: Tue Feb 27 19:15:04 2007 +0000 finish hapmap ortho load commit acc7627c59ff4c9f585c0f3c304cd65243f0eab4 Author: heather Date: Tue Feb 27 19:12:32 2007 +0000 skip lift if not size 1 commit ad32da550ac0eed68e61a1cfb81c098c826661f1 Author: ann Date: Tue Feb 27 19:09:06 2007 +0000 split up the very long URLs into two lines each commit 19c8b92fb340281fb58a0d5d1ad30c2085b776d0 Author: kent Date: Tue Feb 27 18:57:49 2007 +0000 The program seems to work as designed. Testing indicates though that this is not the best approach. I'm committing it just to keep some of the useful functions contained herein in the source tree. commit 71ca92d585d8ec1bc002afa1df2a9474d55274fb Author: galt Date: Tue Feb 27 16:00:27 2007 +0000 "Encode release log update" commit 30437fdfceeeff70f25d3f01e7c1b46db7e44b02 Author: galt Date: Tue Feb 27 16:00:15 2007 +0000 "Release log update" commit f2231af34796fb41249dcfca13a868e72c5d98a9 Author: hartera Date: Tue Feb 27 15:43:07 2007 +0000 Adding missing quotemark to URL under credits section. commit 5d9767e8a545bc1d57531d24f383f1562cb4e6a6 Author: kuhn Date: Tue Feb 27 03:48:25 2007 +0000 tweak commit efb75239f5ae55542cfdbfddf006dada72aae915 Author: hartera Date: Tue Feb 27 03:48:06 2007 +0000 "New version number v153" commit 7ff1af1732c6d897db64a1d31d4801bd176080ba Author: kuhn Date: Tue Feb 27 02:47:42 2007 +0000 made log base 10 use a subscript commit 433b3fd2bd150c9e61616179ca26d8b704eb3081 Author: angie Date: Tue Feb 27 01:37:23 2007 +0000 Removed obsolete settings cdsDrawDefault, cdsDrawOptions and pslSequenceBases. Upgraded the baseColorDefault to diffCodons for native mRNAs (ran this by Jim a while back). Added some recent settings from the top-level to lower-level definitions that were missing them. Added new indel* settings (which are invisible unless hg.conf has browser.indelOptions set), so that native mRNAs will have double-sided insert, query insert and polyA display on by default; other GenBank tracks will have double-sided insert and query insert on by default. commit 2214259be1e562e32414430f26e3c5ae1d20a8e7 Author: heather Date: Tue Feb 27 01:10:22 2007 +0000 add notes for snp ortho alleles commit 5633310cadc8a3ffa2468ec8ac40f76ab1fbd227 Author: hiram Date: Tue Feb 27 00:58:55 2007 +0000 Initial files from makeGenomeDb.pl commit cc962ec34de254903b2f573fe67feed7baa88bed Author: hartera Date: Tue Feb 27 00:18:27 2007 +0000 Changed long label for encodeRegulomeDnaseArray track. commit 380f9d4fb072a53ab2022a07408f74309c3d5c7e Author: galt Date: Mon Feb 26 23:41:52 2007 +0000 now storing hashed-passwords in members table instead of plain, for greater security commit fb0bff021c0919b622532dc05b7c7023d1bc3f88 Author: angie Date: Mon Feb 26 23:22:31 2007 +0000 Added new indel display options requested by David & MarkD. Double-sided inserts can be highlighted with double horizontal lines (as in chain tracks), query inserts can be highlighted (blue vertical line for insert at end of query, orange in middle), and when query sequence is available, valid polyA tail query inserts can be indicated by green vertical line. Did some more refactoring of cds.c code along the way. The query insert options use the baseColor setup and psl-reading code to get the psl (and for polyA, the mrnaSeq) needed to identify query inserts. commit f4ea472c13e06aec8a2ac4b55bd15b83df713440 Author: angie Date: Mon Feb 26 23:10:08 2007 +0000 Added indelShowOptions to mrnaUi, so that if hg.conf has browser.indelOptions enabled, the GenBank tracks will offer the new indel options for double-sided or query inserts. commit 89672527a4daa526321e1fb79712f143c6ce1447 Author: angie Date: Mon Feb 26 23:05:06 2007 +0000 Added routines for indel display options (double-sided gaps, query inserts). commit 3cf17d74b5a6f827f4fef7ce937933f185cf19fa Author: angie Date: Mon Feb 26 23:02:18 2007 +0000 Changed the new polyA/T sizing routines to be looser than the masking routines (they're applied after blat, so it's not as important to be conservative). commit 23e4a73ec573d6f034a6b76488498b42b7f123a5 Author: hartera Date: Mon Feb 26 22:41:35 2007 +0000 Shortened rhMap track short label. commit d2c6b6a611633da679ffb9c79f6f05e9a004222a Author: donnak Date: Mon Feb 26 21:41:01 2007 +0000 Added a news item about archiving danRer1. commit cc4da2d51d3a03f64bc4b7613da8ede6be8e7acc Author: donnak Date: Mon Feb 26 21:40:36 2007 +0000 Archived a news item. commit 35c628215ddc09f92d0abd7f3fc00364aeb48dce Author: kuhn Date: Mon Feb 26 20:46:37 2007 +0000 clarified about index in usage statement commit 414e0527a80d895d3446007f8d229521764f62e7 Author: hiram Date: Mon Feb 26 20:23:49 2007 +0000 Added division boundary commit 2c067776708f2607ded0c70ff29a654c96d3eb05 Author: braney Date: Mon Feb 26 19:41:54 2007 +0000 should have checked this in long ago commit 226c0630de17c9276b83e3057820f0e622efa14d Author: hartera Date: Mon Feb 26 18:45:07 2007 +0000 This is the renamed rhMapInfo.h file to indicate that it is specific for zebrafish. Thie file contains code generated by autoSql for rhMapZfishInfo which contains Radiation Hybrid map marker information. commit 1468a54e1398ef0f77053bdb0365b6bb5b4e7d25 Author: hartera Date: Mon Feb 26 18:43:37 2007 +0000 This is the renamed rhMapInfo.c file to indicate that it is specific for zebrafish. Code generated by autoSql for rhMapZfishInfo which contains Radiation Hybrid map marker information. commit 3ccb9a12de2a73d51977b3e1db7659a71dbc04cb Author: hartera Date: Mon Feb 26 18:42:06 2007 +0000 This file is the renamed rhMapInfo.sql file to indicate that it is specific for zebrafish. Table definition for rhMapZfishInfo which contains Radiation Hybrid map marker information. commit 6f3c2670d4d31723c6322eea7882a0b1a1cc0988 Author: hartera Date: Mon Feb 26 18:40:45 2007 +0000 Definition for rhMapZfishInfo which has marker information for the Radiation Hybrid map. This file is the renamed rhMapInfo.as to indicate that it is specific for zebrafish. commit ef1804b6fad0c457a61ee54e146d2154a137ac95 Author: angie Date: Mon Feb 26 18:33:06 2007 +0000 Platypus (ornAna1) chain, net. commit 63bf488abfbc51fb3ea69d20a11f1138f5798e79 Author: angie Date: Mon Feb 26 18:24:43 2007 +0000 blastz/chain/net ornAna1. commit b7d9f56e2159056cc4e1cbd4bef19fb2a7c349b0 Author: hartera Date: Mon Feb 26 18:23:13 2007 +0000 Renamed rhMapInfo to rhMapZfishInfo as it is specific for zebrafish. commit e23489589a79344730035c3b8a5d5f979c0769d5 Author: hartera Date: Mon Feb 26 18:21:24 2007 +0000 Renamed the doRHmap function to doZfishRHmap as it is specific for zebrafish. Added new code for processing the info table (rhMapZfishInfo) for this track which now includes a ZFIN ID. Function added for creating a ZFIN custom URL to link to the ZFIN site via the ZFIN IDs. commit e216be49a1b4bb4609e2b3fad76ff4f1d66b50ed Author: galt Date: Mon Feb 26 18:21:22 2007 +0000 darkened color; cleaned up help page commit 65546f34a0535972d8e0bfbfe2dd404f22c34218 Author: kent Date: Mon Feb 26 18:09:08 2007 +0000 Ifdefing out Galaxy link on table browser main page until next release cycle at Anton's request. commit 59b92f53a8c59f7975f1c3437abf4ddcf34c7982 Author: hartera Date: Mon Feb 26 17:56:39 2007 +0000 Changes to long labels for encodeUWRegulomeBase and encodeRegulomeDnaseArray tracks. commit 98e88ec333bbef220cf55c2d3af3b629cc6d2b50 Author: hiram Date: Mon Feb 26 17:54:33 2007 +0000 Display contig/scaffold count and total genome size on chromInfoPage display commit 7fa1f36990411f2c9215159e16805e63e12b5365 Author: kent Date: Mon Feb 26 17:02:33 2007 +0000 Moving betTotalBlockSize and setBedCds (now cdsEvidenceSetBedThick) to library. commit a8b0feef9c6c6b55c0bb4c0709d40103da69cf88 Author: kuhn Date: Mon Feb 26 16:22:43 2007 +0000 added gbLoaded to genbank list, as it is never in sync, either. commit 955c7d34784ad9f158917822cc680a92a8a2c386 Author: kent Date: Mon Feb 26 16:14:12 2007 +0000 Making the table passed in on the command line override the table in the file. commit 9b28767ce9c4fa68b15921af665f78f169d2a3c3 Author: galt Date: Mon Feb 26 16:00:22 2007 +0000 "Encode release log update" commit 0d2c75094ae76229d6981be7487bed3975968d09 Author: galt Date: Mon Feb 26 16:00:13 2007 +0000 "Release log update" commit e5d989cbaa4e889ecbc1010180f18d56cfee612a Author: archanat Date: Mon Feb 26 15:14:53 2007 +0000 changed short label for blastHg17KG commit 04fca1ed4552d677476457253ac8c6c69b1bda42 Author: kent Date: Mon Feb 26 10:29:01 2007 +0000 Adding txCluster data structure. commit d1b1f9f4c15c528608d8b11d4c25141ec2e338a0 Author: kent Date: Mon Feb 26 10:28:20 2007 +0000 Outlining more of the pipeline. commit c13d52d8ffe514d046c1984ef56753b5e1b37eaa Author: kent Date: Mon Feb 26 10:28:03 2007 +0000 Reading input, doing some processing. Need to do a bit ore processing before producing output. commit 2f6602cc2e077a8f0d1c1d2d4d1cf9376432eabb Author: markd Date: Mon Feb 26 08:28:46 2007 +0000 added intromation about display modes commit 0003678f479d9f7f58a6ca8da25eb67f98816859 Author: aamp Date: Mon Feb 26 07:54:07 2007 +0000 Put a 3 megabase governor on the CGAP SAGE track. Zoomed out more than that is dense if anything. commit 5980fc950bfb8980c389a930678923764584e90c Author: kate Date: Mon Feb 26 07:36:02 2007 +0000 Test twenty-something (23-way) multiple alignment with split mafs commit 3ac4f623e0118f783e9962259ad75a278ec5e0be Author: kent Date: Mon Feb 26 06:39:30 2007 +0000 Adding bedCmpChromStrandStart commit 943037df402702eb78e0619a1b3fef752d04c5a9 Author: kent Date: Mon Feb 26 06:21:23 2007 +0000 Reducing verbosity. commit 7145c01246b4b32292de5a200a166ed9dcc3bdf3 Author: kent Date: Mon Feb 26 06:10:32 2007 +0000 Making bounds of clusters follow cds rather than tx boundaries. commit 5d697986f8f475413f74de2532f34518e008553f Author: galt Date: Mon Feb 26 05:43:46 2007 +0000 darkening the foreground a little commit 1aaeba843adc6ac7d59990f7ebd92451a57aad45 Author: kent Date: Mon Feb 26 05:21:57 2007 +0000 Seems to work. commit 33e0391274587b309b11a9c527d2d46da0f6a3b5 Author: kent Date: Mon Feb 26 03:10:07 2007 +0000 Clarifying that coverage and identity are percentages. commit ac83628a7aed55d7da07e6a5f203f8283cba3b99 Author: hiram Date: Mon Feb 26 02:25:20 2007 +0000 Allow difference in standard naming scheme for caePb1, and do featureBits after load commit b46347c4b4c5ef90345068dd8be3b676f6f67abc Author: heather Date: Mon Feb 26 01:17:52 2007 +0000 hg18 blastz commit 382bccd984b5acbdad7aa4e1309b5a54bd4870d2 Author: kent Date: Sun Feb 25 23:30:45 2007 +0000 Further notes on KG3 work. commit cb0a8dfb79bd9bf2d8f01f0b846775708cee91b8 Author: kent Date: Sun Feb 25 23:29:55 2007 +0000 Adding information about alignment of source rna to genome. commit f728697367ff9a0ea31f1865a9695e310988246e Author: kent Date: Sun Feb 25 23:29:21 2007 +0000 displaying txInfo in details page for kgIII temporary genes page. commit 98213f639ca8ad5ace40f105476bc439f737cc3e Author: kent Date: Sun Feb 25 23:28:20 2007 +0000 Adding hashNameIntFile commit a9f436ef21d9ebfe8b353132fb2f334277bf8ba3 Author: kent Date: Sun Feb 25 23:27:47 2007 +0000 Adding alias for rangeTreeFree. commit 4872a82b36713ea9398add8061e75e40b212f22c Author: kent Date: Sun Feb 25 23:27:07 2007 +0000 Adding more fields to txInfo. commit fabd633416d0314e95c0cb1848ce2e55abb864c0 Author: kent Date: Sun Feb 25 23:26:37 2007 +0000 Adding webPrintDoubleCell commit 0cc4687da83a5603c321617aa5c5f307d17c6b09 Author: galt Date: Sun Feb 25 22:33:10 2007 +0000 VISTA Enhancers track commit 84df6c9cfb7c794ff1735f7ea02d54b11bb8f57f Author: baertsch Date: Sun Feb 25 21:28:29 2007 +0000 test commit b95c46acac1bff683a3d22821f1894580be4a3dc Author: markd Date: Sun Feb 25 17:17:06 2007 +0000 added needed parameter to a ftp function commit c973626f52c5f68f04238be0c45614741a6a3aa0 Author: galt Date: Sun Feb 25 16:00:23 2007 +0000 "Encode release log update" commit f6569a01092fd4ca7539b9d441eebd16fdc077b9 Author: galt Date: Sun Feb 25 16:00:13 2007 +0000 "Release log update" commit d0b9f9ac202430d66c59f6f06a624879f1228c8e Author: kent Date: Sun Feb 25 13:06:35 2007 +0000 Adding txInfo data structure. commit 1777856e2ea2b4f1279318b9ac4a2899b09deee6 Author: kent Date: Sun Feb 25 13:05:08 2007 +0000 Putting some distributions that help rationalize scoring in README. commit 58e212ee3762331514841ee46695219145017d8a Author: kent Date: Sun Feb 25 13:04:32 2007 +0000 Tweaking score function. commit 0b5b4a5817a3cf8fe6e8c8ca7aa3ffaf8725ceae Author: kent Date: Sun Feb 25 13:03:08 2007 +0000 Seems to work. commit b639dd0270ed73169f86cd597d0fdcdf88450dc3 Author: kent Date: Sun Feb 25 08:18:07 2007 +0000 Tweaking scoring scheme. commit c6005147cb7b59b7cf5395a07c2da642342a81dd Author: kent Date: Sun Feb 25 02:57:36 2007 +0000 Seems to work. commit d88ae77788db0a754949aa1e24e9660be7f8eb1e Author: markd Date: Sun Feb 25 02:44:06 2007 +0000 added option to warn instead of aborting if the size of a file on the ncbi server differes from the size of the file that was downloaded commit a9a2f2cfbd67fa40603b1ebfb375a2ad63507495 Author: kent Date: Sun Feb 25 02:27:48 2007 +0000 Fixed problem in defrag logic. commit 2121fa93b4b24fc8cd7e026fbf82f1ade6ce63e7 Author: braney Date: Sat Feb 24 22:39:15 2007 +0000 added locus variants track commit 8eca351e4647870c80cbb669b0e848b8bf37ee09 Author: hiram Date: Sat Feb 24 22:32:31 2007 +0000 Running Medaka again to get the human randoms covered correctly commit 7d484b92a37cd44d802e2098e10e1a7b4eece3d9 Author: hiram Date: Sat Feb 24 22:18:58 2007 +0000 Completed blastz of anoCar1/Lizard to xenTro2/Frog commit 436ea28441f188c9d0f480eb0137504a57fbe606 Author: kent Date: Sat Feb 24 20:51:56 2007 +0000 Adding exceptions flag for dealing with selenocysteines. commit 0c177923beb9ed196c907f2ce62d9d23342ae799 Author: kent Date: Sat Feb 24 20:49:19 2007 +0000 Adding exceptionsIn and exceptionsOut flags. commit ef2fb516fc9e95d3fd7f90f4196708ec183bf27b Author: kent Date: Sat Feb 24 20:06:56 2007 +0000 Moving gbExceptionsHash to library. commit 5e3306bc3100b9af74f3bd0eb2bdf51a6b941703 Author: kent Date: Sat Feb 24 20:04:57 2007 +0000 Adding genbankExceptionsHash. commit ac75a347096f9a58ac3dcd5a76028e077b3a9659 Author: kent Date: Sat Feb 24 19:32:12 2007 +0000 More work on take 6. commit d8f7a71e951d5cd212cb25d7404d80e8970f43d2 Author: kent Date: Sat Feb 24 19:29:01 2007 +0000 Refactoring selenocysteine handling and adding altStart support. commit 5e46dbba214007d42a6735936901f6e7be4faad1 Author: kent Date: Sat Feb 24 19:27:59 2007 +0000 Adding dodgeStop and minCoverage options, for use with RefSeq where we *really* want to follow their protein in the CDS! commit d95e4cd0dd80fcc484ec7cbbda3959f841334975 Author: kent Date: Sat Feb 24 17:31:13 2007 +0000 Adding isReallyStopCodon to cope with selenocysteine. commit 53b5870813d83907cceb8ef1302882e3640432dc Author: kent Date: Sat Feb 24 17:07:59 2007 +0000 Processing genbank exceptions, particularly selenocysteines. commit f11f5e1f2d7cea0e5fb3d7b3f7eb7a5ba4a05be5 Author: galt Date: Sat Feb 24 16:00:28 2007 +0000 "Encode release log update" commit 8fbdd7f147c637033c67d9ed935631c3acebcef6 Author: galt Date: Sat Feb 24 16:00:15 2007 +0000 "Release log update" commit 8081c91de3a13a74a9c0aa59a62c444d009e123f Author: kent Date: Sat Feb 24 15:59:29 2007 +0000 Improving some comments. commit 541311a99e18745e6e805f122eb7d1794713abe3 Author: kent Date: Sat Feb 24 12:32:08 2007 +0000 Getting rid of some debugging stuff. commit 3b0d4fa89d8ccba3a9eb5e6ec1023d5dbb084287 Author: kent Date: Sat Feb 24 12:30:57 2007 +0000 Making it do near best. Hmm. commit 674bfa24f98166482deca1007f35556198f99e26 Author: kent Date: Sat Feb 24 11:49:34 2007 +0000 Adding refToPep option to help keep refSeq's attached to their own CDS. commit aa91c2733098d9dac9488ca37a3bf6cb4a0aa721 Author: kent Date: Sat Feb 24 11:42:56 2007 +0000 Seems to work. Is it really necessary? commit 89509f270f43cb3ebdb7bd9c3d0ec1b9d2acb265 Author: kent Date: Sat Feb 24 09:28:39 2007 +0000 Seems to work. commit d401bc6a2c7ba52b2309a8f66b998f6c60413875 Author: kent Date: Sat Feb 24 08:34:22 2007 +0000 Adding defrag option, and sizes option to support it. commit 7cb6587c7648f3bed73157def17aa4dee677895a Author: kent Date: Sat Feb 24 07:30:43 2007 +0000 Backing out change to add source->size. commit 2634e98dc18ee9d8edcb44aaf3b0ba0122854cdb Author: kent Date: Sat Feb 24 07:23:04 2007 +0000 Removing txSource->size, looks like just too much trouble. commit f5015b1d7b7731992010c268b97d029ba85c268e Author: kent Date: Sat Feb 24 07:14:27 2007 +0000 Adding source->size field. commit 93e7434e89def31f53010ed8bfe41f9d612dac27 Author: kent Date: Sat Feb 24 07:09:54 2007 +0000 Adding size to txSource. commit 18ed3f11562b3d7e442c57d82c841da947493e4f Author: kent Date: Sat Feb 24 06:36:48 2007 +0000 Improving subset detection logic so that don't need to have same # of exons. commit c26c5e38846b8e8b115ff27ede835432c441cf37 Author: kent Date: Sat Feb 24 05:39:21 2007 +0000 Adding next field to rbTree, so you can easily have a list of them. commit 47c2ce4539c554fe4561aae2080cc46005d7f32d Author: kent Date: Sat Feb 24 05:27:58 2007 +0000 Updating test sets for changes in code. commit 1325afdf1f28ab103825cdde9444523afb002c5e Author: hiram Date: Sat Feb 24 05:25:53 2007 +0000 Remove unused sequence of events in an oryLat1 experiment blastz commit 787302ef809fc344a4210188f8ec9bce114b0841 Author: kent Date: Sat Feb 24 04:31:14 2007 +0000 Fixing bug in refJoined code and adding test case for bug. commit 9bbae2f15c9f19c36d0f86dabbba06efe5b82a9e Author: kent Date: Sat Feb 24 04:17:35 2007 +0000 Adding checking for disjoint refSeqs in same graph. Making test set. commit 4079994a72c25857f91f89aa27c300e51c506937 Author: kent Date: Sat Feb 24 03:01:02 2007 +0000 More notes on pass 6. commit f75573ba175f973507ce74a16f2a7c96679ca790 Author: kent Date: Sat Feb 24 02:26:26 2007 +0000 Changing edges field to be edgeList to help clarify it is not an array really. commit 2adb4c3f06a638b91796f78e06748fbdcc79b1bc Author: kent Date: Sat Feb 24 02:25:55 2007 +0000 Making it do bedLoadNAll rather than bedLoadAll so that it works in a pipe. commit a47f9a8b5fd2f01614b4ff1e283ea67c653fe387 Author: kent Date: Sat Feb 24 02:22:11 2007 +0000 Seems to work. commit 3538aaa61b3a334a3cd88deebc0435b788f13dbb Author: kent Date: Sat Feb 24 01:54:33 2007 +0000 Changing edges field to be edgeList to help clarify it is not an array really. commit 16684796ae52982c33b3fb61252b6da195899f39 Author: hiram Date: Sat Feb 24 01:47:49 2007 +0000 Initial set of files from makeGenomeDb.pl commit e4cc5f06e9c1929c3f2896d4c59e36dc6970ae33 Author: hiram Date: Sat Feb 24 01:14:41 2007 +0000 Initial files from makeGenomeDb.pl commit 70db7f0f4fad849061a1760b8cab10ea4d01da86 Author: angie Date: Sat Feb 24 00:50:50 2007 +0000 Moved bgiSnp description's reference to BGI gene annotations down into galGal2. commit 1d391bae6d23f0258a7d56d5a15e340287057143 Author: heather Date: Sat Feb 24 00:42:42 2007 +0000 finish TRF commit 8a25a7289ef6124a0bf5bdc14e434e10e93bf8ee Author: ann Date: Fri Feb 23 23:42:21 2007 +0000 edits as suggested by Bob commit ce39c624422720ef0ca1cac4e63eaff72aa3ecf8 Author: angie Date: Fri Feb 23 23:22:26 2007 +0000 Added tailPolyASize and headPolyTSize to measure size without masking. Tweaked the trimSize calculation for headPolyT (was off by 1). commit 6cdfa5047e059fea8fb5fd362bc72a01e2315824 Author: ann Date: Fri Feb 23 23:20:30 2007 +0000 added sentence about Genome Graphs commit 303e49b8c268dc1100b73e003300ed169f9bd0b6 Author: angie Date: Fri Feb 23 23:18:12 2007 +0000 Fixed empty ; statement that caused problems for bash users. Added creation/update of liftOver/md5sum.txt in download step. commit 380b1e2e7bc45181290dbcfe7c536d2447e1b211 Author: angie Date: Fri Feb 23 23:16:22 2007 +0000 Decreased the verbose level of info messages in execute (Kate's suggestion). commit 51d8502bf46eeb203be68cd173b7dfef8bd255f9 Author: hiram Date: Fri Feb 23 23:06:49 2007 +0000 Initial set of files commit 0b3b48cfe424e51e27284b21a0babd32f9b9d6d2 Author: aamp Date: Fri Feb 23 22:04:45 2007 +0000 Forgot the CGAP SAGE track details at the bottom of the page. (from the trackDb). commit 1168614b3f4764517ad1555a5cd508320276a0e8 Author: hiram Date: Fri Feb 23 21:51:12 2007 +0000 Add notes about typical build failures commit b13f060ad0c391fe6f2ef370fac18703175bbb8b Author: aamp Date: Fri Feb 23 20:38:44 2007 +0000 Fixed a small bug involving overlapping tags on the browser. Clicking one would display details of another. I constrained the range query more. commit 97a590da187261ea9fec0e2aab1b05a4e90d1d25 Author: kuhn Date: Fri Feb 23 20:15:28 2007 +0000 added support for Roman numerals up to XXI for stickleback. Except that chrX is called chrX, not chr10. Stickleback has no sex chroms. thanks, kayla. commit 2b45341216d2a9cc410044e76a2a14a3ade5719a Author: kent Date: Fri Feb 23 20:15:17 2007 +0000 Adding a factor of the length of the overlap with the evidence vs. the length of the edge. Making single exon transcripts score 1.3x what usual transcripts score to pass. commit 7bcf0960826864edeee61ea13619ca27c04e7954 Author: aamp Date: Fri Feb 23 19:40:45 2007 +0000 Added the CGAP SAGE joiner stuff. commit 16d074e030e3b0e21e98b9f75d0f22080bf0a45c Author: rhead Date: Fri Feb 23 18:50:06 2007 +0000 Removed references to strPur1.blastHg17KG and replaced them with strPur1.blastHg18KG entries. commit 8091f10515cc5941afcc2c1f137df722a7f3bb0d Author: kuhn Date: Fri Feb 23 18:28:08 2007 +0000 added support for multiple files of same name and added total to get number of lines commit e77a419063511ee50d17b0839506df801db5fa0a Author: kent Date: Fri Feb 23 18:22:42 2007 +0000 Making placement more exact, particularly when mixing soft and hard ends. commit 65526ab7b4408a244aa001755d3eb3a6965d1447 Author: kuhn Date: Fri Feb 23 18:02:13 2007 +0000 quick util to find a file in the src tree and see who wrote most of it commit dc90003b38c739d50b2006b79d2d27cd7fe67c12 Author: aamp Date: Fri Feb 23 17:26:10 2007 +0000 UI options seem to work for the CGAP SAGE track now. commit 5c89f8f904a245ca10628d5eb156a58e1c648b15 Author: archanat Date: Fri Feb 23 16:33:32 2007 +0000 added dm2 to blastHg18KGPep04Id and blastHg18KGRef04Id commit e1ea6434cb8630be8140656e3c99cd42572e1024 Author: galt Date: Fri Feb 23 16:00:30 2007 +0000 "Encode release log update" commit d0358a4ab2438732273fdb7f2c8979bfe23533c8 Author: galt Date: Fri Feb 23 16:00:16 2007 +0000 "Release log update" commit b6c1257367ec10c0ff8b843242e2adbfd0582c4c Author: hiram Date: Fri Feb 23 05:31:13 2007 +0000 Beginning Lizard/anoCar1 swap commit 098c226c24c3200f2249825b08ceabf2cab951c1 Author: hiram Date: Fri Feb 23 05:29:11 2007 +0000 Running xenTro2 swap commit 0875b887add56b1ae97380815ccd75474c34c8c5 Author: kent Date: Fri Feb 23 04:57:05 2007 +0000 More progress on take 6 of KGIII. commit 3309572f7f2e40081289af083a8460d2eab9dcdc Author: kent Date: Fri Feb 23 04:37:19 2007 +0000 Removing unused options part of usage statement. commit 00c16d98ebc712b34a9cf58c1b17100c90f0aa2a Author: kent Date: Fri Feb 23 04:37:03 2007 +0000 Adding txPslFilter and txgGoodEdges to txGraph makefile. commit 4baf50f23d42653a6dabe32b7b2bac96bc090761 Author: kent Date: Fri Feb 23 04:36:37 2007 +0000 Seems to work. commit 31e1bc88840960cfb0407a12a19c91e8ff28f069 Author: heather Date: Fri Feb 23 04:16:22 2007 +0000 tweaks on previous commit commit c86519e5b1c82b62aabc1f043c49ad873a67b178 Author: heather Date: Fri Feb 23 03:47:19 2007 +0000 use bedGraph for snpRecombRateHapmapPhase2 commit f2d539ac510d3bb60ca5ea5cfb90d2e8fdc6c2b5 Author: kuhn Date: Fri Feb 23 03:29:58 2007 +0000 made Indel Confidence print 'High' or 'Low' instead of 'H' or 'L' commit 518e39393473f7c62dc737311cee6462df76b5b8 Author: heather Date: Fri Feb 23 03:25:07 2007 +0000 add snpRecombRateHapmapPhase2 commit 39b632735392da0ae78192fbe1e0a488de5c3bd3 Author: heather Date: Fri Feb 23 03:24:18 2007 +0000 add notes for snpRecombRateHapmapPhase2 commit bc8aa45f3cdd5be4190f8e1fade58e67a2009657 Author: kent Date: Fri Feb 23 03:19:47 2007 +0000 Adding -embedded option. commit 4eb0597e99b785d4de6af6a7eba5cd2cb4c402fd Author: kent Date: Fri Feb 23 02:40:58 2007 +0000 Changing xml format a little to include sources. commit c1722acecbc2dc3a3a08928ec44b608a08d29c88 Author: kuhn Date: Fri Feb 23 02:25:37 2007 +0000 made use of 'data' consistently plural commit 6a359adcff0bd6ddb1081c01d74893f03a1224a7 Author: kent Date: Fri Feb 23 01:35:52 2007 +0000 Added rangeTreeOverlapSize. commit 74a61574dfad1c4d47f24d55eaa5f861c6fb3eb0 Author: kent Date: Fri Feb 23 01:35:25 2007 +0000 Seems to work. commit 2ab7f85edba4f8359b1f8ed2e2afc042d63df901 Author: angie Date: Fri Feb 23 00:50:31 2007 +0000 bugfix for cartLoadSettings: I mistakenly thought that chopString would stop chopping at the last element of its outArray, but it does chop after that word so I was losing words from multi-word cart settings. commit 4ed94dbba1ffefd2044ae6ea2091f7841ae6e5cb Author: kent Date: Fri Feb 23 00:24:26 2007 +0000 Added -weeded option, and test case. commit 220c33240ecf9609afd73ec81ce169c66e9824b4 Author: kent Date: Fri Feb 23 00:14:50 2007 +0000 Seems to work. commit 20196319626388e88c66d442e29ee6468491e91d Author: hiram Date: Thu Feb 22 23:37:19 2007 +0000 Initial set of files, not yet edited commit 3825e9aee2df8a5e498f93c78a2abbdef22afefd Author: donnak Date: Thu Feb 22 22:59:48 2007 +0000 Fixed reference to Uppsala -- should be Uppsala Univ., not Univ. of Uppsala. commit fbaf4214ce3f62c55d7f688d0ddb0b20042a2a65 Author: kent Date: Thu Feb 22 22:57:38 2007 +0000 Adding some notes for take 6. commit e45be65b1cc74ca22a18aa5271a043460e66f20e Author: donnak Date: Thu Feb 22 22:45:16 2007 +0000 Corrected a few things in the 8/31 archived news item. commit d0deb55e1b5f76cf48cc113ca0b914456d0cb17f Author: donnak Date: Thu Feb 22 22:43:54 2007 +0000 Changed date on 9/1 item to 8/31...this item already exists under the latter date on the archived news page. commit aeff5325ac95d135b811f277807378260d96f5c0 Author: hiram Date: Thu Feb 22 22:43:31 2007 +0000 Added Lizard blastz commit 3cb49d0ce3c868995ca70da43cc47cccc7c1fad3 Author: kuhn Date: Thu Feb 22 22:42:38 2007 +0000 changed link to english version commit 0d70233a5c4393869007f7bcb7fd573306197335 Author: hiram Date: Thu Feb 22 22:38:49 2007 +0000 Got genbank done, blastz frog running, swap mm8 done, blat server set up. commit 1d2f4b7e079ce33d8a588444ff7bafb7091a414e Author: kuhn Date: Thu Feb 22 22:37:11 2007 +0000 added a link for the image commit aca08ebaca1b79e2d07acebe857228db23fbcf65 Author: kuhn Date: Thu Feb 22 22:36:47 2007 +0000 updated link commit 19aa746b817938e906247009b7b08d9f82ecfa6e Author: braney Date: Thu Feb 22 22:36:38 2007 +0000 added multizMetazoan commit 3e0cd711edc05d6ec156a98da112fcb92c5145ed Author: donnak Date: Thu Feb 22 22:33:58 2007 +0000 Added 2 news items, per Kate. commit b9d17aac5fa9bdbab3f57f8ddd1b2ef258f55608 Author: kuhn Date: Thu Feb 22 22:32:18 2007 +0000 added another link to BGI commit ca83beca4cd6ac20afade038de531c10c3a2fe1a Author: ann Date: Thu Feb 22 22:13:38 2007 +0000 added Example section commit c08aa281d38704a493bc43ad5139f5d8d404912a Author: hiram Date: Thu Feb 22 22:07:47 2007 +0000 Adding photo to xenTro1, same as xenTro2 but reference previous release at JGI commit 610504ece8df4a9ea1900bae3ae1ac9393c48052 Author: kuhn Date: Thu Feb 22 20:20:34 2007 +0000 added some whitespace around images commit a53ac617c3f5ba9782db1f9fc924a64bd3361a6b Author: hiram Date: Thu Feb 22 19:51:19 2007 +0000 Add photo from Kathrin Holzer, www.hobbygarten.com commit 8e2243a1659f60594f0711754a525ea562aa6428 Author: kuhn Date: Thu Feb 22 19:51:18 2007 +0000 slight rephrasing commit 7a4a0f42ebeea8ffd26c6694ae5477ce277c4f7f Author: kent Date: Thu Feb 22 19:48:51 2007 +0000 Adding pslSplitOnTarget to utilities automatically built. commit 8546eaa2d234386217cdd562f46ae1ed3cab6224 Author: hiram Date: Thu Feb 22 19:37:47 2007 +0000 Add all rights reserved for Venkatesh commit e611bdb2f3026e11eb1d8ae31ed4cde4d562baf7 Author: hiram Date: Thu Feb 22 19:31:20 2007 +0000 Customize blue bar link to U. Tokyo Genome Browser for Medaka commit 7d29cf14c4456b8bd3970f6ffa57cd0156b1cb0e Author: galt Date: Thu Feb 22 18:46:15 2007 +0000 do not need to change value of CVSROOT commit 04e0ac3c50eb1a8f8ebf522d4a397761bee7121c Author: angie Date: Thu Feb 22 18:19:31 2007 +0000 Fixed description of saved session Browser and Email links (thanks Ann). commit ddded1adad3b8a3c556e1d0442bb577aa1a3fe70 Author: hartera Date: Thu Feb 22 17:31:01 2007 +0000 Re-made the RH map track using Blat filtering parameters as determined for RH map markers on danRer4. commit b168b77773c46e515acd40afbf042abc5bdcc000 Author: hartera Date: Thu Feb 22 17:29:57 2007 +0000 Re-made the RH map track as one of the marker sequences also had a primer sequence added to the beginning. Also, removed spaces from the primer sequences and re-made the rhMapZfishInfo table. commit 0a6f95502a4c998bfce021115fb7baeb6aac7893 Author: ann Date: Thu Feb 22 16:30:54 2007 +0000 small edit commit 73cf69098a8627af9749a6458f3b16414506b44e Author: galt Date: Thu Feb 22 16:00:31 2007 +0000 "Encode release log update" commit e51eb38ccdbda9569cc777ec79f784ce1120e2bc Author: galt Date: Thu Feb 22 16:00:17 2007 +0000 "Release log update" commit dc4d457b36aab2c6f5fe675d82e0864f52f2c137 Author: hiram Date: Thu Feb 22 02:36:01 2007 +0000 Photo from Kathrin Holzer, www.hobbygarten.com commit 62266f15e087b5c35146dd7c419685e7ffba62cb Author: hiram Date: Thu Feb 22 02:23:38 2007 +0000 Correct html error commit d86ad7273a64d059cc5aaa7c79c62f4081f03ac3 Author: hiram Date: Thu Feb 22 02:19:48 2007 +0000 Add photo from Chris Showell, UNC Chapel Hill commit ad70e5d2187f6e6876bfa65263eac80bfe2951e4 Author: markd Date: Thu Feb 22 02:14:46 2007 +0000 added title for ESC paper commit 978420f1846b833d49deda342c17d2f40c56346e Author: hiram Date: Thu Feb 22 01:54:47 2007 +0000 photo from Chris Showell - UNC-Chapel Hill commit 07febef6ca382a2b2fa17aed369188f3137aa77a Author: braney Date: Thu Feb 22 01:31:18 2007 +0000 allow zooming out to ranges less that 30 bp (good for codon viewing). commit f97926c3579ff77412d7174cddb3ac83e3c3412d Author: heather Date: Thu Feb 22 01:19:23 2007 +0000 swap order of orthoStrand and orthoAllele commit 463e55f862dbb2224b7dcd0c127b8173ac02e077 Author: heather Date: Thu Feb 22 01:13:12 2007 +0000 add notes on trial run without quality score for hapmap orthos commit cfc18afc9585b9c01944a1f0069f03b794b617ab Author: heather Date: Thu Feb 22 01:04:29 2007 +0000 get hapmap orthos from all orthos commit f9b7ff3d4e9c38fb5d8e17323214699c173d6f9f Author: heather Date: Thu Feb 22 01:04:13 2007 +0000 create table for all snp orthos commit ee422bb62ea3ac20faa6fd63d126883263b3d20f Author: heather Date: Thu Feb 22 00:59:57 2007 +0000 add hapmapOrtho and snpOrtho commit efe2fd1b9042a7166db681b3f970a547938883a6 Author: ann Date: Thu Feb 22 00:55:30 2007 +0000 added several sections. Upper-cased Session throughout commit 84e6332402889d1c22076f8225ffef8f1350d301 Author: kuhn Date: Thu Feb 22 00:39:58 2007 +0000 added a method to get yesterday's db commit 04c86eaffdad7a228dd9eb9cfb8dbd707ee0ff10 Author: kuhn Date: Thu Feb 22 00:29:50 2007 +0000 removed two methods that were replaced by parameterized doMetaData method commit 25784ec7f4acfb2feac085d22ce0ed9451145909 Author: kate Date: Thu Feb 22 00:28:47 2007 +0000 GO similarity for ce1 and ce2 must be configured differently due to differences in underlying tables commit f00abadbae7c3c88f590ae53083480bedbed52de Author: kuhn Date: Thu Feb 22 00:00:56 2007 +0000 removed dependency on file commit d89d0de4649e3bd69a473d925d509b52a4a9f818 Author: kuhn Date: Wed Feb 21 23:45:19 2007 +0000 changed a comment commit 4223ebad35b80ac8d40cc8f72c1aef1834841f17 Author: heather Date: Wed Feb 21 23:45:03 2007 +0000 add refUCSC and observed commit 2faf34a84e297bee2af08540806f7db87251aa83 Author: heather Date: Wed Feb 21 23:40:07 2007 +0000 use enum for strands, shorter varchars and ints, remove extra orthoAllele commit c8643ca049ca2a69634ae9c07d5989e20310ca07 Author: kuhn Date: Wed Feb 21 23:39:54 2007 +0000 added checking for correct db name commit e8627a7701710d71d34355f88c7da1419bc6b0f7 Author: angie Date: Wed Feb 21 22:55:04 2007 +0000 Updated hgSession help link to Ann's new detailed help page. commit bc80d1a7b936d818fa60331a8ad6a8c0b48c9e62 Author: angie Date: Wed Feb 21 22:37:39 2007 +0000 doh -- typo fix for last rev. commit 1217b8096dc6f2849449864d33c2bfff827797b2 Author: angie Date: Wed Feb 21 22:32:31 2007 +0000 Added hgSession-specific help link to hotlinks. commit 2ec349e0e62d1939774322ea0732b6acf454b99f Author: angie Date: Wed Feb 21 22:32:02 2007 +0000 Added link to help doc. commit c17b682ff8b052b970d0f8d7b61b43a9ce80a938 Author: ann Date: Wed Feb 21 22:23:02 2007 +0000 added links to GG User's Guide and Sessions User's Guide commit 11af8b1931937dda78882216d4c0eab1aa5beb8a Author: kuhn Date: Wed Feb 21 20:30:18 2007 +0000 added semiShortCircuit to blastHg18KG commit 90f2edefe628b7980ad26f1d40554c975c491d60 Author: donnak Date: Wed Feb 21 20:28:55 2007 +0000 Moved NAR 2007 DB issue pubs to 2007, now that they're available in hardcopy. commit d3de3c717031d214d2699dcfd71e08d030367304 Author: kate Date: Wed Feb 21 20:26:41 2007 +0000 Revert GO ordering to use the protein ID in genomes having canonical tables containing the id rather than the symbol commit 14caf694919a8d6fe468c962d4aa6acd3a70cc1c Author: angie Date: Wed Feb 21 20:12:55 2007 +0000 Added link to hgSession (Jim's request). commit c1e8782c16eee7207884b3cc9c72c4509a741be9 Author: heather Date: Wed Feb 21 19:31:29 2007 +0000 update notes for snp orthos commit a462aeb87f3c730dfd32b1a7b0ef7b26b248c1a6 Author: kuhn Date: Wed Feb 21 19:21:09 2007 +0000 refactored to use getField.csh commit 56e875a72b6550f58398e46cb9f520faa87ba897 Author: kuhn Date: Wed Feb 21 19:20:11 2007 +0000 added warning that even in realTime mode, uses genome-mysql for settings and html fields commit 16160bb01707c74cc723e8a64048d05871842948 Author: ann Date: Wed Feb 21 19:18:22 2007 +0000 Introduction section commit c8da6360ebd4e70f58d3191f83437b4100478489 Author: kayla Date: Wed Feb 21 19:15:32 2007 +0000 I removed the "release alpha" block and the "release beta" line of the encodeSangerChip track. commit 772ee5516406b6936c0af8243daff33fb56360e4 Author: kayla Date: Wed Feb 21 19:04:55 2007 +0000 This version is for the update which includes 5 new subtracks. I am copying encodeSangerChipJan07.html over the existing file and checking it in, per Rachel's instructions. commit 32291da3812c4ea60a0d39a9c257a8a5af753603 Author: ann Date: Wed Feb 21 18:58:38 2007 +0000 cleaning up internal doc links commit 826db649b01f5cda70950093ae6f9f0ab075360a Author: ann Date: Wed Feb 21 18:54:50 2007 +0000 Sessions User's Guide -- initial stub commit 2482e46c67e3235d148f08a28bf9d5143fc023a0 Author: kuhn Date: Wed Feb 21 18:36:45 2007 +0000 changed output filtering to cleaner sed command for removing header commit a939352ed29d4df9dfd69bad52bce062a9441aea Author: fanhsu Date: Wed Feb 21 18:03:50 2007 +0000 Added equCab (horse). commit c68a20587b645fe9a3331cc9ad4509c8dd9573ac Author: fanhsu Date: Wed Feb 21 17:43:30 2007 +0000 Removed a fflush(stdout); statement. commit 0299767223c44f168e9903ffc4d3a264b1a2d2f4 Author: ann Date: Wed Feb 21 17:16:30 2007 +0000 Changed User's to User for Genome Graphs section (to comply with others) commit f65630c6a0ec4b20aba1eef620e577672d2013d2 Author: ann Date: Wed Feb 21 17:09:52 2007 +0000 small format changes commit 6e8150572ff29ce46ec5cc1e8799cbf02849893d Author: ann Date: Wed Feb 21 17:07:43 2007 +0000 a few tweaks commit fc40237a40ec6ff27009c59bc8663e0a82ea5aa7 Author: ann Date: Wed Feb 21 17:01:17 2007 +0000 added info about sessions commit 4629a2f879c21bee334d8551fba8f737dc47b9ca Author: kuhn Date: Wed Feb 21 16:50:53 2007 +0000 rearranging program blocks and deverbosifying error output commit e79bb18aa5ff4fd8040ffa013f246c248580a6ad Author: galt Date: Wed Feb 21 16:00:29 2007 +0000 "Encode release log update" commit 7a6e5e5c6a6df6ecbeca0a169123be7a1fefc829 Author: galt Date: Wed Feb 21 16:00:16 2007 +0000 "Release log update" commit c55c0ea151539ec3b66a38aeaddda3c1b4b5a1eb Author: fanhsu Date: Wed Feb 21 14:05:10 2007 +0000 Added equCab1. commit 02d1e5cc7ab54bd1e6410b46cd96a6a436ce0a15 Author: fanhsu Date: Wed Feb 21 14:01:50 2007 +0000 Added equCab1.2bit to iscratch. commit fdc9a7a5d2b2171e5999b17acc747c2d791a8271 Author: kent Date: Wed Feb 21 05:16:08 2007 +0000 Outputting phase rather than frame as GFF demands. commit db7372be7c264eeb879f2de4f4680164d697fccf Author: kent Date: Wed Feb 21 04:22:32 2007 +0000 Fixed a bug that led sometimes to monster exons when an exon was split. commit 5875926305a32e541eb930729ea39897c295c2d5 Author: kent Date: Wed Feb 21 03:21:46 2007 +0000 More notes on kgIII process. commit 71effcd2baf1ee3bbda48aeb5fe28d7286deda7a Author: aamp Date: Wed Feb 21 02:26:30 2007 +0000 Added CGAP SAGE one. commit cb906c58ad961006cc96c38d8a9d2d5e1aa70e2b Author: markd Date: Wed Feb 21 02:17:59 2007 +0000 removed ESC LongSAGE track commit 04d3501479a8d10a8415c94bb1588c4f81927b3e Author: markd Date: Wed Feb 21 02:16:29 2007 +0000 added cgapSage track descripition commit b273216f0a8346e0e0d9ce67ea39bd2c85b98dcc Author: fanhsu Date: Wed Feb 21 01:23:55 2007 +0000 Added 11.ooc. commit 706abf354a1f369d026b623789e345bafec95b46 Author: kent Date: Wed Feb 21 01:00:25 2007 +0000 Fixing bug that allowed stop codons in last exon. Adding 10 random test cases plus one that used to have this bug. commit ff17f3e8a63380b1b6ede40c479ac109cda2f01c Author: angie Date: Wed Feb 21 00:50:28 2007 +0000 Initial description of new options for highlighting transcript alignment indels requested by David and MarkD. commit 9dd092f21c5d86053e548e9f41dfa440eedca6c7 Author: hiram Date: Wed Feb 21 00:42:20 2007 +0000 Initial contents of script that creates photo gateway page from dbDb and images in /usr/local/apache/htdocs/images/ commit 9769ea162ad3aa48e089a0a21183a223d9611a8e Author: fanhsu Date: Wed Feb 21 00:33:43 2007 +0000 Added BLAT server. commit 72ac282c6eab27305f12c176540cc4167e1d540a Author: kent Date: Wed Feb 21 00:28:30 2007 +0000 Minor tweak on cdsSource handling. commit 30e20912858dd6cd2010efb3693fb678d7d3fe1d Author: rhead Date: Wed Feb 21 00:28:29 2007 +0000 Moved phenotype association explanation from methods section to display section. Changed wording slightly to reflect the fact that disease association is no longer shown for every variant. commit daec80d2d8202f9026470013241b73eeff689a01 Author: kent Date: Wed Feb 21 00:20:25 2007 +0000 Making source field of GTF a little more meaningful. Refactoring bedToGtf for future use. commit b43490d060e2a2d26380ca3dffd203a434716e4d Author: kent Date: Wed Feb 21 00:05:30 2007 +0000 Refactoring a bit. commit 8a267dbf148e168ee016b8112fcdccbb32d81244 Author: fanhsu Date: Wed Feb 21 00:00:44 2007 +0000 Added initial section for horse. To be further polished/updated later. commit e258fac3b8dbbf3d397fca1a003c60653dae4661 Author: kent Date: Tue Feb 20 23:50:34 2007 +0000 Making bed output option. Fixing bug in cds output in case where cds is split. commit 86e58686788572d654aeb62b80d371c0759e4e06 Author: giardine Date: Tue Feb 20 23:43:46 2007 +0000 More edits to fix Galaxy connection for Galaxy2. Also added MAF output. commit 362323eba3cd4bb138ac2af3c621cd2a73a72370 Author: hiram Date: Tue Feb 20 23:40:58 2007 +0000 Added photograph from Wikimedia Commons user Gorgo commit b4620dad36632914230a44a5ff5f69f7597e8ae1 Author: hiram Date: Tue Feb 20 23:36:06 2007 +0000 Added Elephant photograph from Wikimedia commons user Gorgo commit f2aa2079b3d26870b74dfc1c7b73025d9c9d9573 Author: hiram Date: Tue Feb 20 23:23:43 2007 +0000 Add Lizard to the daily updates anoCar1 commit 4d4efa161dc51ea8f5282a3db0d5664829ac4f19 Author: hiram Date: Tue Feb 20 23:21:40 2007 +0000 Allow native mRNAs to be used even though there are only 5 now. commit 965f2dbcc6729a787c4e3224fc0d36e5a961d0cc Author: kent Date: Tue Feb 20 23:15:16 2007 +0000 Adding comments, removing debugging statements. commit 4b205ab9742ace9761cec6d61982b5aaee09762a Author: kent Date: Tue Feb 20 23:04:12 2007 +0000 GTF output is starting to work. Still includes lots of debugging code, and needs more testing. commit 9b31916158d0858f57d475301a51f17dfe7364c1 Author: donnak Date: Tue Feb 20 22:48:32 2007 +0000 Changed EXON to lower-case to conform to the code & spec (per Jim). commit ed9540c68e9d8179157254e321e482fee0091cb1 Author: fanhsu Date: Tue Feb 20 22:41:18 2007 +0000 Updated gold.html. commit ab2f2f2a4f07ad3739593533a2f24ea9e0763747 Author: fanhsu Date: Tue Feb 20 22:40:11 2007 +0000 Updated gap.html. commit 239092b9f7a6010da0a6985a0d16f22efdf8eaa2 Author: fanhsu Date: Tue Feb 20 22:38:19 2007 +0000 Updated description.html. commit 5f4b4e3a02303f294e2723118db16ec83e39f826 Author: galt Date: Tue Feb 20 22:23:14 2007 +0000 noting the knownToVisiGene table updates commit be781b4c9fa4bf35f4d8a8fce25d2f46d9182359 Author: hiram Date: Tue Feb 20 21:52:03 2007 +0000 Better formatting commit 7fa625b7578955eb04855a1f01ce48cb443a48a2 Author: hiram Date: Tue Feb 20 21:50:30 2007 +0000 Photo obtained from Digital Media Library - Jerry Segraves commit ca46e5d3972d241a3c7ce9c20232095bc4e1aa33 Author: heather Date: Tue Feb 20 21:35:43 2007 +0000 3rd arg is outputfile name commit b24ea2fda9471c957963d312e3b823dac52cb1e7 Author: hiram Date: Tue Feb 20 21:26:28 2007 +0000 Adding photograph from Wikimedia Commons, Kralik Divorky commit 77b44c86e48715dfbb754bbf09c942e2318c7787 Author: hiram Date: Tue Feb 20 21:22:57 2007 +0000 Added photo from Wikimedia commons, Kralik Divorky commit 0f1c9265d0a423da58c076020563b9055d3fccb4 Author: hiram Date: Tue Feb 20 21:03:55 2007 +0000 Added photograph from Wikimedia Commons - Jonathan Beilby commit c14cfdda9cd9e584c4686615c0570b24fbd180d4 Author: hiram Date: Tue Feb 20 19:53:25 2007 +0000 From Wikipedia commons, Jonathan Beilby commit e73cb7bedd79b56ffcd1eb16a79f58a12fa76cac Author: kent Date: Tue Feb 20 19:52:25 2007 +0000 Starting to describe txCds pipeline in README. commit b06d0c8fe360270704a98f819b7fb0c0c4be06d0 Author: kent Date: Tue Feb 20 19:49:36 2007 +0000 Adding cdsPick data structure. commit c0672c60c40adbcc293d8c2eb9c012959d1ea61f Author: kent Date: Tue Feb 20 19:49:07 2007 +0000 Adding macro to define number of columns since borf.h predates when autoSql automatically generates it. commit 1d276e3254438eb17f8dff9dda5f9aec565597fb Author: kent Date: Tue Feb 20 19:47:15 2007 +0000 Looks like protein output is working. Still to go GTF. commit 607aaf89c1bb9d48ea1a5d6942ef09a750067260 Author: hiram Date: Tue Feb 20 19:39:34 2007 +0000 Add photograph, and doing WindowMasker commit 1772e64ecda358d3105936999776bb1ed0f3b473 Author: hiram Date: Tue Feb 20 19:29:07 2007 +0000 Do a WindowMasker run to get more sequence masked commit c990aae6dc7f522ef3ed854379fc4d98457ca7f4 Author: kent Date: Tue Feb 20 19:23:35 2007 +0000 Parsing input. Created test case. Crashing on output. commit ecb5123c5ae53e55df6eac0868448557a2add42d Author: fanhsu Date: Tue Feb 20 19:20:39 2007 +0000 Initial part of horse genome build. commit aaa0b5b455f7bbe6a4ac773b8d1f72f2329b39f4 Author: kent Date: Tue Feb 20 18:51:51 2007 +0000 Moving faReadAllIntoHash to library. commit 74145f4f85bfb87402ad355404883ca7e5b3c431 Author: kent Date: Tue Feb 20 18:50:21 2007 +0000 Adding faReadAllIntoHash function. commit 4e18b843a1c8dfcd73767023987a0c19040849b5 Author: hiram Date: Tue Feb 20 18:50:01 2007 +0000 better formatting commit 186576f316640b780c1ed1fa5f2d685a7f900887 Author: hiram Date: Tue Feb 20 18:47:58 2007 +0000 Add Twilight's name commit 600827281761c4491a33dcfd3ddfdbd5013f048c Author: hiram Date: Tue Feb 20 18:45:07 2007 +0000 Added photograph of Twilight commit 2a1e3879d2f09643d89787953c16f06c2c90aabc Author: hiram Date: Tue Feb 20 18:40:01 2007 +0000 Press photo of Twilight from NHGRI commit bb6bf4edd1b073658b433bb7001be26a763cea58 Author: hiram Date: Tue Feb 20 18:32:04 2007 +0000 Changing order key to fit in lizard commit 3190e2ca694c827e8b883b5e978d1a74ad6cb115 Author: kent Date: Tue Feb 20 18:28:02 2007 +0000 Adding cdsPick data structure. commit c6d9bb7044c91295478cb0e67f7e9e63cf613b26 Author: kent Date: Tue Feb 20 18:27:30 2007 +0000 Moving cdsPick.as and generate files to library. commit 6d4522b0ffefbb58b42aa8818af1b4a5e6df8a0a Author: kent Date: Tue Feb 20 18:24:50 2007 +0000 Working on real output. commit 9f32fa3f0f46bbad90ae7543ce82be1b19b11084 Author: kent Date: Tue Feb 20 18:24:25 2007 +0000 Suppressing alignments if they include stop codons. commit b83c6921ce3ea10eb9698a44ea11ae16df70cade Author: hiram Date: Tue Feb 20 17:56:17 2007 +0000 Properly turn on mrna.xeno.load for anoCar1, and no native.load anything commit 9a7b8e09ab242012eef136d61876b2e4b476cc08 Author: kent Date: Tue Feb 20 17:02:08 2007 +0000 Moving cdsEvidence module to library. commit bd4638151a655ad734ed8462ab6ef26a742db052 Author: kent Date: Tue Feb 20 17:01:23 2007 +0000 Adding cdsEvidence data structure and autoSql-generated i/o routines. commit 70b38d1906268e1bf6f29e65f1937c6ea7e4830f Author: kent Date: Tue Feb 20 16:53:28 2007 +0000 Saving a weight file that seems to work reasonably. commit 07eea53d83b09dc02ff040bffe3b010bc931033f Author: kent Date: Tue Feb 20 16:52:40 2007 +0000 Downweighing split CDSs commit bb944ef90f3e974b10b314e463a206f4c614d42d Author: galt Date: Tue Feb 20 16:00:26 2007 +0000 "Encode release log update" commit 05d57d5bfd91ed33fa7d88d156d21468b41e7332 Author: galt Date: Tue Feb 20 16:00:14 2007 +0000 "Release log update" commit 890438e7a92a1cab762131e41c182828933b4dc1 Author: kuhn Date: Tue Feb 20 14:57:12 2007 +0000 tweak commit 9384190be5808e6fc2bb527c0ea71c096073bd5a Author: kuhn Date: Tue Feb 20 14:55:41 2007 +0000 added warning about new sessions overriding existing commit 89f3e413c3a2492008d5948b6c42f6a059a6bd0b Author: baertsch Date: Tue Feb 20 14:00:17 2007 +0000 transfer from kent tree commit a7ca0ab4c0a719d60a2b749156663735405621ed Author: kent Date: Tue Feb 20 09:18:21 2007 +0000 Removing extra 1 in all output lines. commit 8302c768fe6d923737c9b2d21b8d404b18c9b8aa Author: kent Date: Tue Feb 20 09:16:29 2007 +0000 Improving stop codon handling a little. commit d396a16a11014f9471aacf0c3956d91143254b32 Author: kent Date: Tue Feb 20 09:14:57 2007 +0000 Basically works. Will be fiddling with score for quite some time. commit 93a3a5a7fcde803c9fd5d421456966a188f87aa3 Author: kent Date: Tue Feb 20 09:08:49 2007 +0000 Reworking score a little and not mapping some with higher sequence divergence or lower coverage. commit 007d8a2db6885d30c5fec88521976503856fd4eb Author: kent Date: Tue Feb 20 08:47:13 2007 +0000 Adding test cases. Fixing handling of stop codon. Slightly tweaking score. commit f5b37ea9062e26cee73e1d2acf2eaa1131c3fd23 Author: aamp Date: Tue Feb 20 06:38:33 2007 +0000 Added code for the CGAP SAGE track in hgc, hgTracks, and hgTrackUi all of which have their own module for the code. This is almost ready. Just the track options don't do anything yet. commit e2ccb172187963678f743696694bcddf38514614 Author: hiram Date: Tue Feb 20 06:09:11 2007 +0000 added Anolis carolinensis (lizard). commit 8d18ffef63ab5037785c497747955c0cc7331ea0 Author: hiram Date: Tue Feb 20 06:02:55 2007 +0000 Proper ooc file for anoCar1 commit 38be72c4322dd69ca714f1ed202464c58e5de53d Author: kent Date: Tue Feb 20 03:36:32 2007 +0000 Seems to work. commit 156cf07de4c75f91fccf23f24010d167bc526088 Author: kent Date: Tue Feb 20 02:52:46 2007 +0000 Seems to work. commit 0c99c3ba2034614c2eaf068a43ce100df6f04299 Author: kent Date: Tue Feb 20 02:40:34 2007 +0000 Fixed bug in start codon sequence. commit 40fa9169a85d69164f92698b992acb8bc4d9bd5b Author: kent Date: Tue Feb 20 02:14:34 2007 +0000 Converting list of end coordinates to list of sizes. commit d05b5a6d97acd72cd0888147d8f069b8c21ac90d Author: kent Date: Tue Feb 20 02:02:46 2007 +0000 Adding isStopCodon function. commit 6de05d398bc315a272c5cffe49d0acf7f57616ba Author: kent Date: Tue Feb 20 02:02:27 2007 +0000 Moving isStopCodon to library. commit c0b3a3ca8815a0cddd1075bd06713739d932d77f Author: hiram Date: Tue Feb 20 01:59:26 2007 +0000 Adding Lizard/anoCar1 commit 52440d5f795c53e084c5d4ec6201ed100a81bbf5 Author: kent Date: Tue Feb 20 01:26:44 2007 +0000 Fixing bug in processing of source command line option. commit 765b07c907d78c54803a20ebfe404cd3f013366b Author: kent Date: Tue Feb 20 00:58:07 2007 +0000 Saving unmapped CDS info in a separate optional unmapped file. Creating a test set. commit b9b8731e377d876f46403f91a65f811ec40ac65c Author: kent Date: Mon Feb 19 23:57:59 2007 +0000 seems to work. commit 75b4753e2324d017191f51bc116ca2836a8c4175 Author: giardine Date: Mon Feb 19 23:44:08 2007 +0000 Added link for protein searches at RettBASE commit fe20222645d80d0ccc11f3cc953541176edd6be7 Author: giardine Date: Mon Feb 19 23:29:39 2007 +0000 Added RettBASE to links in prep for new data. commit 91f5ecf4fe6b24969e8345f64e576c112600a002 Author: giardine Date: Mon Feb 19 23:28:37 2007 +0000 Switching output option for Galaxy from Galaxy1 to Galaxy2. commit 3af0407e09f4a2a2e87761fd59e9c029ad2dd36a Author: hiram Date: Mon Feb 19 23:17:00 2007 +0000 Done with gasAcu1<->anoCar1 blastz and swap commit 4fd4c58914695c9b55f25c1f607395c5af667d9e Author: hiram Date: Mon Feb 19 23:15:20 2007 +0000 Done with galGal3<->anoCar1 blastz and swap commit 00386eb6f3cbd495aea1015911bde68ff34bbf69 Author: hiram Date: Mon Feb 19 22:58:25 2007 +0000 Running stickleback swap commit 057396a81a30d65fff8772b114e84939ff899ee7 Author: kent Date: Mon Feb 19 20:51:08 2007 +0000 Parsing inputs and checking input CDS vs. sequence. commit f6f059b993c70000c4c792e88fbfebc15ba6da95 Author: braney Date: Mon Feb 19 19:09:13 2007 +0000 added Human Proteins track commit 2165539b584ebc06850549375a13dbd92daaa350 Author: kent Date: Mon Feb 19 18:30:21 2007 +0000 Make rangeTreeAllOverlapping return forward sorted,not reverse sorted, list. commit 045d5c2d591c67cc13c8ad82b018cb250d26c1cd Author: kent Date: Mon Feb 19 18:29:32 2007 +0000 Adding chainFastSubsetOnT. commit aa40fc9b47ae66f89ab7a028ff4519db0c7f4ecf Author: kent Date: Mon Feb 19 18:28:42 2007 +0000 Freen tests rangeTreeAllOverlapping. commit 3aee59d6de854a97cd57dbefef71eea30d30bf47 Author: kent Date: Mon Feb 19 18:28:07 2007 +0000 Adding Galaxy link to main page. commit 50ea7033ed80061750ca940ad20be56f54a799c4 Author: kent Date: Mon Feb 19 08:28:34 2007 +0000 Starting on allowing all paths except for proper subsets. However still need to bring in weights into it, so it's commented out for now. commit cb57f9ef2cf01bf5105721dd5057cb479b3b905a Author: hiram Date: Mon Feb 19 08:07:31 2007 +0000 Done with genscan commit 97fd71251409f1737b5c9d7230ca9e2eb3d76fd6 Author: kent Date: Mon Feb 19 07:25:38 2007 +0000 Adding evidence optional output. Including trancript id no. commit 85e11c1ab938ceca0fa18ad6a28c622382e3dd89 Author: hiram Date: Mon Feb 19 06:57:51 2007 +0000 Reordered in dbDb to get between frog and fish, finished swap from hg18, and running genscan commit b72b3970866c0459a6715fd3a056d57f8b41a44d Author: hiram Date: Mon Feb 19 06:57:06 2007 +0000 Done with swap for Lizard/anoCar1 commit 822a3e71db2ec211554f927bb7bde386a535f7ac Author: hiram Date: Mon Feb 19 06:06:42 2007 +0000 Finished with blastz to anoCar1/Lizard commit fed5444f17e777ba2b3ec42cd0a701967a22efdc Author: hiram Date: Mon Feb 19 05:59:24 2007 +0000 Started Lizard blastz commit e599b765e92970a9f93bd3f72278ad728524ce83 Author: hiram Date: Mon Feb 19 05:45:51 2007 +0000 Starting Lizard blastz anoCar1 commit d6428c8cfc53ea66256ce6e4e722e9a75eadcc05 Author: hiram Date: Mon Feb 19 05:06:09 2007 +0000 Turning on blastz Lizard track, as ordered on the hg18 browser commit 437bf61de399c1b6656e496c911aeed180fa0543 Author: kent Date: Mon Feb 19 03:16:33 2007 +0000 Indexing chains via a rangeTree. Uses a bit more memory, but is more than 10x faster. commit bde181ca077e713e2d54dfe60e23565945ba2ee6 Author: kent Date: Mon Feb 19 02:06:19 2007 +0000 Making rangeTreeAdd return the added range. commit 40f84106bb6add8ef37027e1a04d9d4e8361f15e Author: kate Date: Mon Feb 19 02:05:10 2007 +0000 Add wiggle downloads commit 025f691cb553e44c8642a8d4a4b0fb0e7c43c871 Author: kent Date: Mon Feb 19 01:54:32 2007 +0000 Adding rangeTreeAllOverlapping commit 46ef71a5045e47cb9684a81d36d717b917d0a06c Author: markd Date: Sun Feb 18 22:13:33 2007 +0000 added ability to get refseq peptides with gbGetSeqs commit 1f03b7477ad8d1c06d28178a61d48927e2f4bdb0 Author: kent Date: Sun Feb 18 19:34:18 2007 +0000 Reworking reporting of unusual alignments. commit 4783096bbbb2bef30d9991fa0fa04ac7c380fb35 Author: galt Date: Sun Feb 18 16:01:20 2007 +0000 "Encode release log update" commit 0acbcee934ac4cb03d9ec1b89cf2e889d87a0a22 Author: galt Date: Sun Feb 18 16:01:19 2007 +0000 "Release log update" commit fad162d3e22dfed217fc82b27ddc5fb685e8e452 Author: hiram Date: Sun Feb 18 08:25:32 2007 +0000 Have Lizard properly masked, started hg18 blastz with anoCar1 commit 05fdc2cb8e6e94941c61407ed1515720c3f07a65 Author: baertsch Date: Sun Feb 18 05:48:43 2007 +0000 increase buffer size to allow up to 64 col bed file. commit 4e5cec500a0a9261d4ae7558c60385d34e174010 Author: galt Date: Sat Feb 17 16:00:27 2007 +0000 "Encode release log update" commit c95619e80ffb52f33d55b18c676024662a3198f9 Author: galt Date: Sat Feb 17 16:00:15 2007 +0000 "Release log update" commit 07f16900abe0b3bb94b0a3108f5f2e330f614299 Author: heather Date: Sat Feb 17 08:00:25 2007 +0000 rewritten. Read from file, use 2bit commit 6cb1bb07692903cbc3030ab139edb6629aad7187 Author: hiram Date: Sat Feb 17 07:24:03 2007 +0000 Done with WindowMasking - started simpleRepeat commit fec25e5a26d7b76244feef63928c72a486b9eab0 Author: kent Date: Sat Feb 17 06:27:40 2007 +0000 Saving 'mapInfo' table, which is mostly about reasons why the CDS doesn't map. commit cbaa2348d2fc247d3c751cbce6a5364beefde01c Author: kate Date: Sat Feb 17 02:54:00 2007 +0000 Protect against NULL protein ID's in worm canonical tables -- caused filtering to crash gene sorter commit 6d36e8e74272dce8a193963e4d2ca166a3acb5e1 Author: kate Date: Sat Feb 17 02:53:24 2007 +0000 Remove vintage 2003 OLD code ifdefed out commit 4e8e1f7140de97d07ed9a40b3cb7e46f66640e86 Author: kuhn Date: Sat Feb 17 00:23:08 2007 +0000 added my name, per Kayla and Angie commit 6dded62bcf24d007fc7e0b2b0f591f42f7bd2eb7 Author: hiram Date: Fri Feb 16 23:53:41 2007 +0000 Fixup reference to ../cgi-bin/ - doesn't work when in trash sub-directory commit 71fafabf7635884e00f70d58c5ef443b522a478c Author: fanhsu Date: Fri Feb 16 23:53:40 2007 +0000 Created makefile. commit 229c521e30e7d3ddd515265a4a6e2c6f42e303de Author: fanhsu Date: Fri Feb 16 23:53:25 2007 +0000 Created gadPos.c to generate genomic positions for GAD entries. commit a0cd9c9086d4c38d2e08b9a8153c0e8ac5627eb2 Author: fanhsu Date: Fri Feb 16 23:52:46 2007 +0000 Added gadPos. commit 403395c1c5afdc3e31cc4b0fcf108707c7aec7b0 Author: galt Date: Fri Feb 16 22:48:37 2007 +0000 added remove for hgSubjData commit 11314259657462096e8058a1900b4bbbfe96289b Author: rhead Date: Fri Feb 16 22:25:52 2007 +0000 removed release alpha/beta for gvPos track commit 586f290585ad2af660c7fd77054935d840761d87 Author: rhead Date: Fri Feb 16 22:20:44 2007 +0000 made LOVD link open in a new page commit 63f7302d2951eadc8794567cfe9a675536d132e7 Author: hiram Date: Fri Feb 16 22:12:06 2007 +0000 Made downloades, started genbank auto update commit 3ff71ce576a68a7887dd19eceef2824fb19dfd34 Author: hiram Date: Fri Feb 16 22:11:42 2007 +0000 Added oryLat1 commit 8389855aabb79aaeae5766b650744b78ea9a843b Author: hiram Date: Fri Feb 16 22:09:25 2007 +0000 Made downloads and added photograph commit 7594134c6989028534008bdbfb75375319f7e169 Author: hiram Date: Fri Feb 16 22:08:40 2007 +0000 Started WindowMasker commit bd1362a42defaa6e915ad15ba4eaac6cf2b90e3b Author: hiram Date: Fri Feb 16 22:03:55 2007 +0000 Initial browser up, photograph added from R. Steven Rainwater commit 15e37af88c826f35e96078f6dde2f138d4e717cc Author: kent Date: Fri Feb 16 21:34:34 2007 +0000 More testing and a couple of fixes to CDS handling. commit b581aa632a033a04f218a606d0b1590cab099dc3 Author: hiram Date: Fri Feb 16 20:58:38 2007 +0000 Adding Lizard anoCar1 commit e232ec1743562d699113df661807cda5b43218db Author: hiram Date: Fri Feb 16 20:58:21 2007 +0000 Initial set of files commit 06f757dc666f6b3e80ff79b355fc0783e998bd49 Author: kent Date: Fri Feb 16 20:56:10 2007 +0000 First pass at adding cds processing. Needs more testing, but looks like it might work. commit ac9f4f53c78663f40e3fe96bf2ee7321273d0075 Author: galt Date: Fri Feb 16 20:53:47 2007 +0000 probeTrack processing for ABA update to visiGene commit f6000bd71e0364c25311bac2cf100c03babaf5b1 Author: rhead Date: Fri Feb 16 20:32:13 2007 +0000 changed quoted terms to italics commit 1cfe9015b07a119e270981f81465cd3c4efe2ffe Author: hiram Date: Fri Feb 16 20:14:35 2007 +0000 Photo obtained from R. Steven Rainwater commit 464e3ddc36c06907301f2fd913fbe556c531ddf1 Author: angie Date: Fri Feb 16 19:55:35 2007 +0000 Added gi field to keep up with the database tables. commit 35bc179f444b9210feee535b7501e1f72d07d211 Author: angie Date: Fri Feb 16 19:55:04 2007 +0000 If we have partial autoSql, but no perfect match by fields, don't overwrite with the match by fields so we can correctly complain about the partial autoSql later. commit 324509e369bd59a166ee07d342915fd62eb35be0 Author: ann Date: Fri Feb 16 19:52:34 2007 +0000 changed link for HAR1 paper to Nature journal commit b99ae7c6db76038c1d3858d0f2e9769be8264fa8 Author: kent Date: Fri Feb 16 19:41:58 2007 +0000 Renaming annotateCds to genePredAddGenbankCds, and making it public for use in txPslToBed. commit 42ba7479f9209a49839aafcdd1c07ac67531df67 Author: hiram Date: Fri Feb 16 19:24:12 2007 +0000 Stumbled upon the newly released Lizard genome and decided to pick it up commit cbaa7b0c014e5af19c9f64ddd5be5b44b19a6a65 Author: heather Date: Fri Feb 16 19:04:55 2007 +0000 extra stats commit d3e3a8cadd3e603d8b23c52738f03dc9c0c4d02b Author: heather Date: Fri Feb 16 19:04:41 2007 +0000 add hapmapMixed commit 3cabca52c8e4c99519793f0d392b0b56c55f5c21 Author: kate Date: Fri Feb 16 18:24:15 2007 +0000 Adapt GO filter so it can use the protein accession as the GO id column. GO similarity still uses protein name, since this uses generic code -- to use id's here would require changing the semantics of the key protein identifier field, and making sure this worked everywhere. commit 6fa84de45b675eec89a0780ed623d6ce91a23a95 Author: kent Date: Fri Feb 16 16:48:29 2007 +0000 Freen tests the range tree. commit af5872f2b85029c069bad6b817a7d83cb74df0c5 Author: kent Date: Fri Feb 16 16:47:49 2007 +0000 Starting on the CDS mapping section commit 34159d31cb2ab35ac8bf592f9a94476be608724a Author: galt Date: Fri Feb 16 16:00:29 2007 +0000 "Encode release log update" commit 7ec5bb8e4a6427a06cd367d3af2beebb42343e34 Author: galt Date: Fri Feb 16 16:00:15 2007 +0000 "Release log update" commit f42fc055b60316cebcce83e095642dd81fe64540 Author: kuhn Date: Fri Feb 16 09:20:48 2007 +0000 tweak commit 9503b995aa937017e938bab528263c733f210778 Author: kuhn Date: Fri Feb 16 09:12:55 2007 +0000 replaced all tabs with spaces. want to reduce left-side whitespace next. commit c3eb0455c6647eeab7cef4e52ad509521346c9fe Author: kuhn Date: Fri Feb 16 09:05:00 2007 +0000 added more detail about hgSessions commit 7da957dccc4d271b0576d7a1e33afb08616d2d7c Author: kent Date: Fri Feb 16 05:07:39 2007 +0000 Removing this earlier version of graph maker. commit 392ad6156ca4bffe35aac26273fbdc9a7afbe539 Author: kent Date: Fri Feb 16 04:15:08 2007 +0000 Fixed memory leak. commit 947234cb875f6def7a922942889a7a727b7849be Author: kent Date: Fri Feb 16 04:14:27 2007 +0000 Fixed problem where it txWalk would output overlapping blocks on some graphs. commit cc45518aec812872dc54726a4316de2f38a6edc7 Author: kent Date: Fri Feb 16 03:50:47 2007 +0000 Allowing merger of adjacent beds of same name that are immediately next to each other, no intervening base... commit 578e6a27fb793120fbb05febd8a0862b7ffd06d4 Author: angie Date: Fri Feb 16 03:19:14 2007 +0000 Removed txEdgeBed from autoSqlIgnore (duplicate-def issue resolved). commit b6e210bc8c2d497f754081e24f4d0a7f753c34bc Author: kent Date: Fri Feb 16 03:17:00 2007 +0000 Fixing name of txEdgeOrtho object. commit 889dd220ad8a2d375761186dda968bda1da8f877 Author: angie Date: Fri Feb 16 02:33:20 2007 +0000 Fix to the autoSql parser for simple reference in field descriptions. Updated autoSqlIgnore to avoid duplicate definitions. commit a838f7c5d1b40db2b3304e273d3a6e0a8545a82c Author: kuhn Date: Fri Feb 16 02:01:40 2007 +0000 added announcement for hgSession commit 213be6c681579e85097a09d53f315db9f79a586a Author: heather Date: Fri Feb 16 01:39:52 2007 +0000 tweaks to previous commit commit 6206177976aca5d0bd61e4276e5ac1c45befdd4f Author: heather Date: Fri Feb 16 01:29:13 2007 +0000 data notes for hapmap snps commit 1d5ba2a1699134e4a064252c9c88a5d47df8388b Author: kent Date: Fri Feb 16 00:47:56 2007 +0000 Redoing pipeline, take 4! commit ebe21160838efd2909acefe56aed865ee2e107c7 Author: heather Date: Fri Feb 16 00:34:25 2007 +0000 refactoring commit d6758587072dbb47bc263465e00a98f69b083f7e Author: heather Date: Fri Feb 16 00:33:29 2007 +0000 customize hapmap snps for the 600K that are monomorphic in all populations commit 49b4d15a5315121b950fffa6e9961765640ed749 Author: heather Date: Fri Feb 16 00:03:51 2007 +0000 fix arithmetic for hapmap SNPs commit fa0498e56191b8d885466025700d8f06f2708f78 Author: hiram Date: Thu Feb 15 23:55:04 2007 +0000 Incorrect TARGET specification commit c99dedc2e972b346f5143baf0ab5ac2c80e86693 Author: hiram Date: Thu Feb 15 23:52:53 2007 +0000 Adding medaka credits. commit 26ddfd40190b419e876e9badc658ce68b98a4bc4 Author: galt Date: Thu Feb 15 23:47:58 2007 +0000 compiler complains unused var commit 51b2c0e7f37b02bcf4df3382600ba072b90133cb Author: ann Date: Thu Feb 15 23:45:42 2007 +0000 fixed HTML typo found by Heather commit 3671580ea7d2d3272cb24821bd39bd2f560611dd Author: kent Date: Thu Feb 15 23:43:44 2007 +0000 Adding a removeEmptyEdges phase, since sometimes the snapClose can create these. commit af5a4ed22cffc3a3adb35da7f062f8bbfc62393e Author: hiram Date: Thu Feb 15 23:40:35 2007 +0000 Better position examples in the search examples commit 56de79519a9fed9a90f8f7f679b2d9d960e971cf Author: hiram Date: Thu Feb 15 23:36:03 2007 +0000 Fixup example search terms to be accurate commit 0ea7c32503a10f084bc8c165eeecd09bb93892ed Author: hiram Date: Thu Feb 15 23:24:50 2007 +0000 Updated links, photograph added properly, statistics mentioned commit 6393be6deaf18c23882d94747461779478e9488b Author: heather Date: Thu Feb 15 23:11:51 2007 +0000 add snpArray (and move 2 searches for other tracks) commit 3ab5a70bd13a8c3b53a344f4805accf3f2fe607f Author: heather Date: Thu Feb 15 23:11:17 2007 +0000 similar to hg17 commit 1927ffd5ddd168866c3cc3169bafc12664c1386a Author: kent Date: Thu Feb 15 23:08:57 2007 +0000 Fixing bug that caused infinite loop, and adding test case for the fix. commit 5cc732433f8141e16f96136dc763eb41e507fd20 Author: markd Date: Thu Feb 15 22:50:18 2007 +0000 added option to skip validation of psl commit 160b97934f58e45be98caff20af68720d3259f09 Author: hiram Date: Thu Feb 15 22:47:14 2007 +0000 Processing the photograph. Robert needs to obtain permission for this photo. commit 6c7084c3fec58ef429488ffff195aec11c0d14e3 Author: kent Date: Thu Feb 15 22:39:08 2007 +0000 Removing some debugging uglyfs. commit 78e2dbef169792b821fa178b7c47669d6fb49103 Author: kent Date: Thu Feb 15 22:37:10 2007 +0000 Adding removeEnclosedDoubleSofts phase. commit cc8abd37adad35e8d78f880fc61d0fc658d65a0f Author: heather Date: Thu Feb 15 21:31:38 2007 +0000 extend observed filter to include transition and transversion commit 9c5be10bf9820b6d3307f00d6f93a183ffb27e7e Author: heather Date: Thu Feb 15 21:30:56 2007 +0000 extend hapmap observed filter commit cbda5d8afdcc84111d66299d68dc690e3930fcc9 Author: heather Date: Thu Feb 15 21:29:59 2007 +0000 add search item for hapmap track commit 34ae983f865e774f5e47a15fe1652a3851329ab5 Author: kent Date: Thu Feb 15 21:17:26 2007 +0000 Updating expected output for extra test case and improvements to code. commit 217fbc87f043e6cfae12e60fb653359e4ff517e3 Author: kent Date: Thu Feb 15 21:16:55 2007 +0000 Fixing typo in test target. commit 8070f85575b508dd5f6c9d1e7a02f5172d81227f Author: kent Date: Thu Feb 15 21:16:26 2007 +0000 Adding test case for refSeq soft end consensus override. Fixing extra zero in some coordinates in other test cases. commit 71a5b218e8f1ebb5bb3df7b1c1c83c98b4a69352 Author: kent Date: Thu Feb 15 21:15:22 2007 +0000 Making it so that refSeq soft edges will be used when available. Still form 3/4 consensus if no refSeq. commit 553ecd3751da858a5c639ab9798a1b5064428f24 Author: hiram Date: Thu Feb 15 20:47:52 2007 +0000 Processed Roberts original to smaller size and official name commit 8d75f77e13fb89b7a051cac3533ee46e6ac3040e Author: kent Date: Thu Feb 15 20:08:34 2007 +0000 Making it so that a weed can occur in any word in the input line. commit 305fb1f7d673dc6684993ef65823236183b6917c Author: kent Date: Thu Feb 15 19:57:54 2007 +0000 Adding weedlines to utilities made. commit cb7f91265bb19850dee98c40912978e2883760a5 Author: kent Date: Thu Feb 15 19:57:36 2007 +0000 Removed unused variable. commit 02d8355602bacfc720778c2fd645fe1d574c02e0 Author: hiram Date: Thu Feb 15 19:05:53 2007 +0000 Add photograph to fr1, and fixup comments in fr1 and fr2 commit 2ac85757ebffa6207843cdfdc839672d2d072a86 Author: kuhn Date: Thu Feb 15 18:57:53 2007 +0000 forgot to add exit after error detection. commit 5401d500fd9c9c56c2724927ed04f381f85b45c7 Author: kuhn Date: Thu Feb 15 18:54:49 2007 +0000 added checking for valid db commit b9326ae8287c023636071841af8b4f4502abd71c Author: kuhn Date: Thu Feb 15 18:51:56 2007 +0000 tweak commit 36e9d62329942e40b54b1ccccc8712258067d8b4 Author: hiram Date: Thu Feb 15 18:47:37 2007 +0000 Proper assembly comments and credit for a photograph from Byrappa Venkatesh commit 0b534295a445953a26cdcb619e96547001c28272 Author: hiram Date: Thu Feb 15 18:10:40 2007 +0000 Remove memory limits commit 25e2ec88497b45d84d40eeabbbd648ba79378032 Author: hiram Date: Thu Feb 15 17:28:56 2007 +0000 Takifugu rubripes photograph from Byrappa Venkatesh commit 805672b8edcf11cf1303f5a497c1a11c0b958413 Author: kent Date: Thu Feb 15 17:24:05 2007 +0000 Adding a final line to the unusual log file containing the total introns and total funny ends. commit 5b29c1cc8cfd72483278c3f4d863618aa622e8fe Author: heather Date: Thu Feb 15 17:13:16 2007 +0000 add comments commit ed419e5328f54ea9371e4f4427bbb2b7a88e34b8 Author: heather Date: Thu Feb 15 17:11:19 2007 +0000 tweak display commit fb0e375202aae78391bb8e811549f142c9506163 Author: kent Date: Thu Feb 15 16:57:16 2007 +0000 Adding logic to flip strand if splice sites indicate input strand is wrong. Adding unusual file logging option. commit b33f095ba6a5cb4bf8a13038b961b5c660699012 Author: kent Date: Thu Feb 15 16:20:46 2007 +0000 Adding intronOrientationMinSize, since smallest intron does vary with species. commit ca07f359d2172fa86f2e31a3fb1fc18aed0af4e1 Author: kuhn Date: Thu Feb 15 16:17:46 2007 +0000 reworded a sentence and expanded a reference commit fa2ba2ac8aacaef0dffc627949f900c8ab5b38de Author: kuhn Date: Thu Feb 15 16:13:51 2007 +0000 fixed zahler links commit e7e7055104eaabeb1ad4ea27ae8555db2eab93ce Author: galt Date: Thu Feb 15 16:00:29 2007 +0000 "Encode release log update" commit 96f45c304b8f2daf5456e441892dcf08ad585c58 Author: galt Date: Thu Feb 15 16:00:15 2007 +0000 "Release log update" commit 08e59cd4175839e89e1b8cbe959b971d7b735bf9 Author: archanat Date: Thu Feb 15 13:58:16 2007 +0000 coverted refs to Pubmed format and also added month and date to the reference commit 01f16b9972e27590b32e4a62ceda8e24f44a6d30 Author: archanat Date: Thu Feb 15 13:12:22 2007 +0000 added felCat3 to blastHg18KGPep04Id and blastHg18KGRef04Id commit 52d57bf1fbb2c50dd12bd9bdf220c3964c7c9be0 Author: galt Date: Thu Feb 15 00:51:16 2007 +0000 cleaning up debug msgs commit a2e1db49f4c1e446117fb88bc287a2758a2faeb2 Author: kuhn Date: Wed Feb 14 21:52:55 2007 +0000 remove reference to hgText commit 6ba6d26918d9c0a4cb11625384c43f0b74dab676 Author: kuhn Date: Wed Feb 14 21:49:41 2007 +0000 uses renamed variables per angie's suggestion commit e7b0800db8ec8f6cc17f4d4cc3ada2d27dd309f3 Author: fanhsu Date: Wed Feb 14 21:36:59 2007 +0000 Removed hgText (which will be retired soon), to prevent it from automatically being generated. commit 4a29fd848156e97eb8d753f9b5ac21ca7387e17e Author: kuhn Date: Wed Feb 14 21:26:39 2007 +0000 remove cart variables after a pass through doMetaData commit 7d03652cff8b3eafadfa1464babc277fa783e607 Author: kent Date: Wed Feb 14 20:03:30 2007 +0000 Oops forgot to add this part of test suite. commit d7c3c8b1b098be622892c356171defadd5f5d9fd Author: rhead Date: Wed Feb 14 18:40:33 2007 +0000 Removed extra comma in references. commit 36cf1f5260eb597947a5d3643d3f0363f03c3e90 Author: braney Date: Wed Feb 14 18:27:34 2007 +0000 a utility to find the closest synteny break before and after a list of beds by searching annotated mafs commit 0e47208a7a9caa4972137d4fc8a549dcc8ed1ccc Author: hartera Date: Wed Feb 14 16:28:40 2007 +0000 Added ZFIN URL and data version for RH map track. commit 926d95860a2037d9e661e22de9ecdc0045753814 Author: hartera Date: Wed Feb 14 16:26:10 2007 +0000 Updated data release date for RH map. commit 2985e914242f43304ad1348b488d195c753fb031 Author: galt Date: Wed Feb 14 16:00:30 2007 +0000 "Encode release log update" commit 71cd7d200a1ec28f75342187daa523420a5beb4b Author: galt Date: Wed Feb 14 16:00:16 2007 +0000 "Release log update" commit 2b52fc3926bd64a4840712fbc2ef1a26ffadd786 Author: baertsch Date: Wed Feb 14 15:35:37 2007 +0000 added handler for tight mrna commit 1fe85a5526057696e2ba1a578d4df184e4e87f7e Author: kent Date: Wed Feb 14 15:16:33 2007 +0000 A run up to the protein part of the pipeline with txBedToTxg replaced with txBedToGraph. commit ed7b175a76013ed445011cc7a005f82c6cba8fad Author: giardine Date: Wed Feb 14 15:13:13 2007 +0000 Changed default coloring for Locus Variants track commit 89457477840c13e2361a2ad228ebce069d52fe8f Author: archanat Date: Wed Feb 14 14:35:52 2007 +0000 minor edit to References commit 5ceff6856cbca834ce3cb6ae1b7c61cdee1009fd Author: kent Date: Wed Feb 14 14:14:21 2007 +0000 Starting a txGraph level makefile. commit 25f8f7d52bff385d9aebc5d3db2e4f9fdc2a67a0 Author: kent Date: Wed Feb 14 12:47:03 2007 +0000 Mentioning txBedToGraph in this older similar program. commit 6a9636d68274bd972cf1d02f8e9044d3871a4da1 Author: kent Date: Wed Feb 14 12:45:01 2007 +0000 Mentioning txGraph in a comment in this older, similar, module. commit abaac8e9e4b5137a8a751528aee9c4ce5f42d51c Author: kent Date: Wed Feb 14 12:44:00 2007 +0000 Deleted some unused code, and add comment recommending they try txGraph instead of this program. Updated a comment or two. commit b8b2c57096b174d9951f0b3cc0c82a81693fbca0 Author: kent Date: Wed Feb 14 12:18:07 2007 +0000 Converting graph to tgx format and saving. Seems to work. commit 8df17499d4ee3b434887eb05ad2201a0a9d2785e Author: kent Date: Wed Feb 14 11:25:47 2007 +0000 Implementing mergeDoubleSofts. commit 4c6c4afc7fc62a9f533ce18a82ac050335ce7c81 Author: kent Date: Wed Feb 14 09:50:19 2007 +0000 Maintaining evidence as merge edges. commit e98afe9c4ba6ca5a916045a079cee4a9e6b90703 Author: kent Date: Wed Feb 14 09:32:42 2007 +0000 Implementing halfHardConsensus. commit 493f212a5423242dcccc7b9e2908c935347831cf Author: kent Date: Wed Feb 14 08:41:59 2007 +0000 Adding slIntCmpRev commit 5e0963f0a29464740bd4a28da895fafab9a2dcb1 Author: kent Date: Wed Feb 14 08:06:40 2007 +0000 Implementing snapHalfHards. commit 857d94305770c96d7500d6ab708d1e132dfbb068 Author: heather Date: Wed Feb 14 05:14:01 2007 +0000 added score (avHet) and heteroCount to hapmapAllelesCombined commit f73ecd215dbb074dcb41ed485902b5c41bbe7c6c Author: kent Date: Wed Feb 14 02:41:52 2007 +0000 Adding snapVertex logic. commit 41eed3a5a5007857a398cffdc11482d5575e0a1b Author: kent Date: Wed Feb 14 01:19:01 2007 +0000 Starting to work on new graph-maker. commit 15a4d450d12d6ebe1cd511479b5caacc77641066 Author: baertsch Date: Wed Feb 14 00:53:27 2007 +0000 test harness commit 3b9f43ba5aa7b617c7804ef5852ad976c96abea7 Author: kuhn Date: Wed Feb 14 00:20:39 2007 +0000 changed variable names to be more metadata-specific commit 3d583351ce7eaa41e87687e5ded5f68036f0f8ef Author: heather Date: Wed Feb 14 00:06:46 2007 +0000 implement fixStrandAndMerge and helper functions commit 7f5c324e69adbc139479ac7bd8b0a1610267b655 Author: rhead Date: Tue Feb 13 23:12:14 2007 +0000 removed the 'full' requirement from the gvSrcId identifier per Belinda commit ccb713b4dc0282fd6de2ed14893d3d2c5198b373 Author: hartera Date: Tue Feb 13 22:43:17 2007 +0000 Corrected number of clusters. commit d90dc23346661d8d48dc51cfad041896996c9d2f Author: kent Date: Tue Feb 13 22:11:19 2007 +0000 Fixed not one, but two infinite loops. commit 53c3111911eca01c994041e132ff9170713981bb Author: kuhn Date: Tue Feb 13 22:07:47 2007 +0000 added support for index size commit 46992f88df44b00160a51a1f8a5dd4ff14747727 Author: kent Date: Tue Feb 13 22:04:08 2007 +0000 Separating out parts of geneGraph into ggTypes. commit bd5330f7dfb36f65bc86603d400619ce3543ac80 Author: kent Date: Tue Feb 13 21:58:09 2007 +0000 Parses input, and pretty much immediately falls into an infinite loop. commit b0fe3f43141630ea12cd9a94df213327262f660b Author: kent Date: Tue Feb 13 21:02:27 2007 +0000 Added rangeTreeNewDetailed. commit 137e4489efe581a0054ea7b3881417055b9ebb10 Author: kuhn Date: Tue Feb 13 20:54:28 2007 +0000 script to get size of dbs from beta commit 51c55babcd25632495464fd5ae92ddb1c05e262f Author: rhead Date: Tue Feb 13 20:24:55 2007 +0000 References section: added a total of 10 authors to author list, and standardized everything to match Pubmed exactly. commit ffd1a4743def2e4aa2d254bb4717b6ac3bc61ded Author: baertsch Date: Tue Feb 13 20:20:58 2007 +0000 clean up tests commit f2e3d872ca94257aa21d9d20b787ba0b16a3ebaf Author: hiram Date: Tue Feb 13 20:19:34 2007 +0000 Add 6Gb max mem limit to avoid memory bottlenck on WEB servers commit 273254cec3e8b7eb742f42b922b19acb74d8468a Author: hiram Date: Tue Feb 13 20:18:54 2007 +0000 Lower 8Gb max mem limit to 6Gb to avoid memory bottleneck on WEB servers commit b7ea8951b381680ef0b4aeaf5482aa0d5c24a938 Author: baertsch Date: Tue Feb 13 20:14:48 2007 +0000 test cases commit 9133dd8faf7dae245de00b81c0d24500ea9674fb Author: hiram Date: Tue Feb 13 20:14:33 2007 +0000 Add LIMIT_2or6Gb define for CGI binary memory limits commit 38ceae42bd834b86c4efb5c4003ee4080ea6baa1 Author: baertsch Date: Tue Feb 13 20:12:39 2007 +0000 *** empty log message *** commit fe39c4cf0cd3fd5ad0734a20f844e6e9e49cf513 Author: baertsch Date: Tue Feb 13 20:08:35 2007 +0000 fix -passthru issue resulting from new sort. remove clustering of alignments. commit 7053896858fcc55d240a95b18821ee2a059b13ef Author: kent Date: Tue Feb 13 19:42:55 2007 +0000 Separating out ggTypes module from geneGraph module. commit 0bb969e7d6a4ee3c3655d35f122fcd6b74b3c263 Author: ann Date: Tue Feb 13 17:52:57 2007 +0000 fixed up second reference commit 8d3533c760f8c4baf2fdae844c82226153e424b4 Author: ann Date: Tue Feb 13 17:50:33 2007 +0000 fixed up second reference commit aff94b5ec479d3c36aa66e86c52cb5c29b4bc34e Author: ann Date: Tue Feb 13 17:46:50 2007 +0000 forced new browser for external link commit 04bf0c13a379855102b3463cdc194c03d924dc17 Author: ann Date: Tue Feb 13 17:35:56 2007 +0000 put reference into new citation format commit a1b58534787fd36e5e6b54b5159f693dc4ca543b Author: ann Date: Tue Feb 13 17:19:49 2007 +0000 added tip about not including + in data values commit 6c9fbd6b1be85bda41c199fd7ebdd8cccfb62e6b Author: hartera Date: Tue Feb 13 17:15:26 2007 +0000 Corrected typo for factor in H3K36me3 subtrack on SangerChip track. commit 75faaeeee351ff8b2f925f34c223d3aeced71ac5 Author: galt Date: Tue Feb 13 16:00:27 2007 +0000 "Encode release log update" commit f7041d661f66902209a7408eaa350fba2bb24995 Author: galt Date: Tue Feb 13 16:00:15 2007 +0000 "Release log update" commit b82d96dd8d45f6ace62b719b1892c5c554ffdf50 Author: kent Date: Tue Feb 13 14:22:46 2007 +0000 Adding prefix option. commit aa06e2db1e1d9a68083574be76e5f59ec7da1f15 Author: kent Date: Tue Feb 13 14:20:28 2007 +0000 Getting rid of some unused code and fields. commit 1bae0d2dd1719002e2066c108d5ca238b944a7bf Author: kent Date: Tue Feb 13 13:35:53 2007 +0000 Discussing more interesting areas. Adding txWalk instructions. commit 2d61afbd3b255439c8b61b0ad516aed027c267f5 Author: kent Date: Tue Feb 13 13:11:28 2007 +0000 Looks like output is reasonable. commit b34c11e761cc725f24faa6076a589d9e3e7804bc Author: kent Date: Tue Feb 13 13:03:54 2007 +0000 Parses input, writes output. Output it not correct though. commit 66ce3f3aee2ed228fcf87ea445ed979e0bb11ed5 Author: archanat Date: Tue Feb 13 10:47:29 2007 +0000 converted refs to pubmed format commit 075f108ddf659a47ceb5d1133f9c20fe3826318d Author: kent Date: Tue Feb 13 10:01:37 2007 +0000 Saving email explaining algorithms a bit here. Will probably polish it up later. Maybe write a paper. Who knows? commit 805f5ade6b6983b6026b6d2664f9ad41c8e37420 Author: kent Date: Tue Feb 13 05:05:37 2007 +0000 Updating docs a little. commit b5d684cc1c2a13e324b0b7559af948dd5498a4bd Author: kent Date: Tue Feb 13 05:04:40 2007 +0000 Stripping debugging info. commit 6b28bc28d3e5021cfbe7f5615e65b6ea0763290e Author: kent Date: Tue Feb 13 04:49:37 2007 +0000 Fixing bug where first chromosome in list was always used. commit 8fde1599167e36ca466aca6fd58720cfffc6392b Author: kent Date: Tue Feb 13 04:46:07 2007 +0000 Adding trimEmptyEdges (which can result in some strange circumstances involving merging soft ends). commit 66866dfac37c98756f57cc464acf8e3900887f3f Author: baertsch Date: Tue Feb 13 03:50:36 2007 +0000 sort alignment by matches to use largest coverage as starting point commit 39dcacf2e4849a246e5d5cd28d38003f071cbd5a Author: galt Date: Tue Feb 13 03:17:51 2007 +0000 "New version number v152" commit 316a8895af677d61ab3161849eadf1181400086a Author: galt Date: Tue Feb 13 01:53:14 2007 +0000 re-ran and fixed a couple of stats commit 10a1398ef8f88bf5a9db0c00cb22b7b7b913f387 Author: kent Date: Tue Feb 13 01:47:24 2007 +0000 Adding -chrom option. commit 919541d65e498eaf3e9621bced9883407b8b6957 Author: rhead Date: Tue Feb 13 01:38:14 2007 +0000 Made some wording changes that were found when QAing hg17/encodeEvoFold.html commit cf1b5859afc70b1eaf72a57378be00d36d1a1c98 Author: galt Date: Tue Feb 13 01:37:29 2007 +0000 remove unneeded status msg commit b973e9329f48330049523cba6abf145269054fbb Author: kent Date: Tue Feb 13 01:34:38 2007 +0000 Seems to work commit 9e3c47306cb5136445794419e62ad69753d30e2e Author: hiram Date: Tue Feb 13 01:04:52 2007 +0000 Enable searching names on geneid commit cc9e3aa838be42c9009c38b3cb060b31090c3df5 Author: kuhn Date: Tue Feb 13 00:57:55 2007 +0000 removed some debugging commit 231ecf109688fe43a17fb539a162eedfe3866f3d Author: kent Date: Tue Feb 13 00:54:10 2007 +0000 Updating expected output now that are taking median of soft ends. commit c950a5484fd2c987b091667e11ed3a44627ea95c Author: kent Date: Tue Feb 13 00:53:50 2007 +0000 Bumping maxJoinSize default value from 50k to 70k after looking at histograms of real intron sizes and chr14 immunoglobulin-induced false intron sizes. commit 10200005f657160984402e3e0915dc4e5f9883c3 Author: kent Date: Tue Feb 13 00:52:18 2007 +0000 Making it so that for the double-soft-end case you end up with a median of the observed edge values for the edge value, rather than the maximum. commit fcb4f4368808ae4d6e5c1bf803b2b705061b053d Author: kent Date: Tue Feb 13 00:51:16 2007 +0000 Added intMedian function. commit 5ae15f1d7948b10adb28d7fa123e353f2b55f820 Author: heather Date: Tue Feb 13 00:46:57 2007 +0000 add notes for creating hapmapAllelesCombined commit 38018dd8e60876f324a0b1228190646613e116a2 Author: heather Date: Tue Feb 13 00:43:53 2007 +0000 add heterozygous counts commit 6ab8ef7f7bfa1b72cffa0266959789c0c721b95e Author: heather Date: Tue Feb 13 00:41:39 2007 +0000 2nd step in hapmap processing: combine population tables commit 654f5a6d1f2514d3fd225905fb2962c58a9a5e23 Author: heather Date: Tue Feb 13 00:40:14 2007 +0000 add hapmap2 commit f47be05e2cd6015a46a6b69795725a8ed0287ca1 Author: galt Date: Tue Feb 13 00:37:05 2007 +0000 fixed bug which had caused all fields after query,target to be dropped; also fixes the missing index since the original table is not dropped and replaced anymore commit ff49d89272e65eb9adaf2be551ccb81f4d375d71 Author: fanhsu Date: Tue Feb 13 00:07:27 2007 +0000 Corrected a typo. commit 6e259c631169a5bdc6e0d918fb8eb75439a3b1aa Author: fanhsu Date: Tue Feb 13 00:02:17 2007 +0000 Created for equCab1 (horse). commit cac968d5b4bae2dcf02753b732b0b14b8a7ab870 Author: galt Date: Tue Feb 13 00:00:28 2007 +0000 various changes to build commit 5d53a19906ba1ee4d525e0ed1d54e412bec8a891 Author: fanhsu Date: Mon Feb 12 23:59:55 2007 +0000 Added equCab1 (horse). commit 4c30a7470fb1fc2bafb92698d46620b47bcd2107 Author: baertsch Date: Mon Feb 12 23:43:13 2007 +0000 fix off by one error commit 552dadfca76f88d4a56021f44867139262780488 Author: hartera Date: Mon Feb 12 23:33:28 2007 +0000 Started adding zebrafish array data from GIS. commit 537c45be367d869d540d49024e13fcebf811c31c Author: hartera Date: Mon Feb 12 23:31:04 2007 +0000 Remake of Radiation Hybrid map track using alignment parameters as for danRer4. commit 8bae5e17e7920bd19c7e568638c7ac70f76f63ad Author: kuhn Date: Mon Feb 12 23:27:40 2007 +0000 removed dependency on writing an intermediate file. fixed a hard-coded path '.' to use the variable instead. removed an unneeded substitution adding newlines. commit f60fab7528e295c7e0f3420e5ed802af4677c6c8 Author: kent Date: Mon Feb 12 23:26:02 2007 +0000 Updating with txGraph pipeline. commit 0da4849870b11b590a978a503873d3624be1b403 Author: hartera Date: Mon Feb 12 23:24:52 2007 +0000 ENCODE Yale Chip RFBR track approved for release to public site. commit 541b3f25dc5ea08893cda86839438ebcbd797191 Author: kent Date: Mon Feb 12 23:24:47 2007 +0000 Added maxJoinSize option (and noForceRefSeqJoin) commit c16367126cadde8f5fd4343fd6b0e439788de6e6 Author: angie Date: Mon Feb 12 23:08:05 2007 +0000 When input is stdin, make a more unique temp file name so multiple trfBig processes can run simultaneously on a host (necessary for cluster runs). commit 3de597bb47319f004dde4de56ccc376bf483e377 Author: rhead Date: Mon Feb 12 22:57:30 2007 +0000 added encode chromosomes to encodeEvoFold track commit 7b0364fdc6d2490d02cde7cf88ddd584ae16a5ea Author: kuhn Date: Mon Feb 12 22:53:28 2007 +0000 removed dependency on qateam. added support for an alternate path for keeping the db file. removed filtering out of uneeded dbs in favor of getting the database list directly from hgcentral. added automatic re-making of list if 'today' option finds itself at end of db file. commit e434889ead78f4668a6b77f38478f127971f75d7 Author: angie Date: Mon Feb 12 22:47:46 2007 +0000 Better email wording suggested by b0b and notification of overwritten session suggested by Kayla. commit 13a973317790fea2ae38052b4d95dc722f72b104 Author: baertsch Date: Mon Feb 12 22:20:42 2007 +0000 check return status commit 8b59ad199cb4d145ca8746b9ce3e1a4e8ac8451d Author: baertsch Date: Mon Feb 12 22:10:46 2007 +0000 allow multiple top hits instead of best hit. commit db3f9ecd10ef900a0d9a749a3e30ba7403a7b443 Author: angie Date: Mon Feb 12 21:56:38 2007 +0000 Added logic to glom small sequences together into <$chunkSize groups, so that scaffold-based assemblies don't end up with one .lst per tiny sequence. commit a9a46920f6d48a63eb15b4a4d6a779bc8604bfd5 Author: hiram Date: Mon Feb 12 20:16:17 2007 +0000 Added photograph commit 948481b06fd9fb4965ae7e91467c975cb8794801 Author: rhead Date: Mon Feb 12 19:58:01 2007 +0000 Added link to Elliott Margulies, made some wording changes, added 'between a' to a sentence that didn't make sense without it commit 8c118242fdd8ba0f1125b32f19dbeed0a2713025 Author: rhead Date: Mon Feb 12 19:27:05 2007 +0000 added a note about removing hgsid from URLs commit 8ed171e94356ea99a2db2dd234a21225bd0f37ae Author: braney Date: Mon Feb 12 19:12:16 2007 +0000 a few tweaks for Wormbase track. I should move all this stuff to the trackDb entry commit f409624d856f43ede68a9b5e1316e8688f8fca53 Author: hiram Date: Mon Feb 12 18:49:33 2007 +0000 Adding Medaka fish photograph, photographer Kiyoshi Naruse, by permission from Shinichi Morishita 2007-02-09 18:25 email commit 82fec53f6112a959aff549adfa169714c855b894 Author: kent Date: Mon Feb 12 18:07:19 2007 +0000 Fixing warning/error in compile. Checking command line options. commit c5454ce5f48580f35b7059e87d8e1b247f65a61f Author: kent Date: Mon Feb 12 17:59:33 2007 +0000 Adding txEdgeBed and txEdgeOrtho modules for some of the formats that work with transcriptoin graph edges as opposed to the entire graph. commit 61bbe07ed96f80da0c3dfd807ebf04bf1d0631eb Author: kent Date: Mon Feb 12 17:59:12 2007 +0000 Adding a little protection against bogus bed input. (Also fixed bed generator separately). commit 09de6addc5a69b27032e8a41433cc192db6bac35 Author: kent Date: Mon Feb 12 17:57:46 2007 +0000 Adding #define ALTGRAPHX_NUM_COLS since back in the day autoSql didn't do this. commit 4765a78054f3c9466c7b5572d0b7dc24f4274ac8 Author: kent Date: Mon Feb 12 17:56:58 2007 +0000 Adding wrapper agxList around XML output so it is truly XML. Also removing edges and vertices intermediate objects, and moving counts to altGraphX. commit 44c0ec8665e047d56692f2f6a93ce87d72b6ff0b Author: kent Date: Mon Feb 12 17:42:29 2007 +0000 Simplifying sourceIx caching logic since it was crashing. commit 4be2937abad48d132d522eee55b0f3cc8ff02ead Author: fanhsu Date: Mon Feb 12 17:11:16 2007 +0000 Updated wgRna track again with corrected data from Michel. commit 6bb01dfe4c4ab59ce5c41a1452a37afee76e208d Author: galt Date: Mon Feb 12 16:00:20 2007 +0000 "Encode release log update" commit 6b99717138ca3ba2ce229008439937bbf3040c63 Author: galt Date: Mon Feb 12 16:00:11 2007 +0000 "Release log update" commit 4302d426d83bdd04838cdabc45d57bf76da14a43 Author: kent Date: Mon Feb 12 06:39:59 2007 +0000 Suppressing zero-length and smaller blocks. commit d16a31aace3756105df9c04e71a5bfc19243d718 Author: kent Date: Mon Feb 12 04:43:11 2007 +0000 Making tolerant of empty input. commit a5af048cb69504916fc80c86b57f987a57063b77 Author: kent Date: Mon Feb 12 04:25:06 2007 +0000 Changing command line so as not to need separate bed/type file. commit eb6029142a980f8772feefe67d9f624dfe64811f Author: kent Date: Mon Feb 12 04:15:57 2007 +0000 Changing input format to txEdgeBed. commit d73a52678749bfbff2da0ffd85dd87578a90251e Author: kent Date: Mon Feb 12 04:10:58 2007 +0000 Renaming some variables to be more intelligent. Changing output format. commit 2ffd36f72287c1ae0fd0752040aad7ce6fab1cc3 Author: kent Date: Mon Feb 12 03:37:15 2007 +0000 Adding function to convert string to vertex type. commit e801e5f1294dd92928daec002648355611828a73 Author: kent Date: Mon Feb 12 02:39:34 2007 +0000 Removing code that moved to library. commit 594da8de58bde794a9b43c7cde99cb19603b7845 Author: kent Date: Mon Feb 12 01:58:13 2007 +0000 Handling introns in absense of sequence data better. commit 77c158dba30e3cf38b5dee975f0f14698f9183fc Author: kent Date: Mon Feb 12 01:57:25 2007 +0000 Putting soft edged introns between adjacent bed records with same name. commit d2adc026177b55c8e23e3cd17709ef1c783faeea Author: kent Date: Mon Feb 12 00:39:25 2007 +0000 Removing some unused code. commit a1e762c13d0fbeceb7e669e16bd98065b6ef7722 Author: markd Date: Mon Feb 12 00:30:03 2007 +0000 added program to convert psl to pslx commit 27f9185955045e391c2b73cc45c9262c31e7b69a Author: kent Date: Mon Feb 12 00:17:51 2007 +0000 Updating status of txGraph stuff in txGraph/README. commit 9dbd0ee268c3c8d625a5935cc4cbe6514d79d1df Author: kent Date: Mon Feb 12 00:10:32 2007 +0000 Switched from agx to txg i/o. commit 585789a0a2c2ab09f83c227f8ba7d51138c6ca79 Author: kent Date: Sun Feb 11 23:57:03 2007 +0000 Seems to work. commit a0c7d6cf2465f151f7bb44f23f55e6a67799412c Author: kent Date: Sun Feb 11 23:19:40 2007 +0000 Updating txGraph format. Since autoSql handles more stuff than back in the day we can move a lot of stuff from parallel arrays to a single array of structures. commit 381ebb0d45082b875c7d4668603b6fbfb0d350f0 Author: kent Date: Sun Feb 11 21:43:15 2007 +0000 Easing restriction on simple data types in autoSql .as files. commit 747eac49cf9b7cf4524c2be5c32ff50f86d8aceb Author: kent Date: Sun Feb 11 20:58:41 2007 +0000 Adding back as binary, so string expansion doesn't mess things up. commit 7c2dd5f6894fa9d633923d765d068c22a18e709b Author: kent Date: Sun Feb 11 20:57:53 2007 +0000 Removing since needs to be binary. commit 119c55cdb7b4a480750750b4085a9600847bb79d Author: kent Date: Sun Feb 11 20:47:57 2007 +0000 Easing restriction on simple objects that they not contain variable sized array. Making simple objects handle strings better. commit 3638d5371de6c9a60680b07c441368a52fa3cf73 Author: galt Date: Sun Feb 11 16:00:21 2007 +0000 "Encode release log update" commit 2634fac6b87551ac70e4e8cd2e251efa3277f90b Author: galt Date: Sun Feb 11 16:00:12 2007 +0000 "Release log update" commit 9f94f223556acdc6dbd04ef522ce532214312108 Author: archanat Date: Sun Feb 11 14:55:02 2007 +0000 converted refs to Pubmed format commit 792e4b46f0b7f111cab42fd8691d47c1f8babb44 Author: kent Date: Sun Feb 11 08:25:52 2007 +0000 Switching to syntenic nets. commit be0b583510055935eb63c7321cf98ebc24cdb5bc Author: kent Date: Sun Feb 11 07:11:29 2007 +0000 Seems to work. commit 7bde6983a081f428d941ea2f48585b92d74a2574 Author: kent Date: Sun Feb 11 07:08:56 2007 +0000 Adding test case. Printing a little more information. commit 68431bc736ebbcb56d2bf4d7ebf10d40be419579 Author: kent Date: Sun Feb 11 07:04:40 2007 +0000 Removing some unused code. commit 5385a353e9f9a75bbbbcd6d5908faed5c1eb029c Author: kent Date: Sun Feb 11 07:03:57 2007 +0000 Removing debugging statements and refreshing expected test output. commit 86073675d4854d9bfe7bf064e17240769308f58f Author: kent Date: Sun Feb 11 07:00:23 2007 +0000 Fixed bug dealing with soft ends on reverse strand. commit 8940bb4760df8620fb90299143388ca92af32334 Author: kent Date: Sun Feb 11 06:00:42 2007 +0000 Fixing bug in ede types when converting to altGraphX from geneGraph. commit e7bdce0a7ff2a8d3de03477c4bd40b22226bc3eb Author: kent Date: Sun Feb 11 05:59:58 2007 +0000 Removing some debugging code. commit 61c02c3b424a2b4cd555888bb62753130871e876 Author: markd Date: Sun Feb 11 04:22:45 2007 +0000 added option to disable validation for debugging purposes commit 4a95c83d4b4f6647c2c49ad233018514ebb8c14b Author: kuhn Date: Sun Feb 11 03:52:17 2007 +0000 modified to use new doMetaData method in hgTables commit d6d8fbf978b35d686eea83c5006bae5a4f9872ff Author: kent Date: Sun Feb 11 03:30:26 2007 +0000 Adding ggVertexTypeAsString function. commit 53c3f7e87a28d1020b13c8947c2950975dc67957 Author: braney Date: Sat Feb 10 21:43:30 2007 +0000 added wormbase track support commit fb0daf0185e2e98ffb661f53d76decfc53151d1f Author: braney Date: Sat Feb 10 21:39:39 2007 +0000 add wormbase protein track commit 1fa2b79a8dfa2d5161567256b63db18690ac03c1 Author: braney Date: Sat Feb 10 21:36:11 2007 +0000 add wormbase track (needs a little more work) commit f89fe7bbb509a04cf9bab0781e1e82dd66ed7984 Author: braney Date: Sat Feb 10 21:35:39 2007 +0000 add wormbase track commit 133fdee80ef5cdfe68a9aad0e3bc9df78651a7b6 Author: braney Date: Sat Feb 10 21:16:42 2007 +0000 added ce3 wormbase protein track commit abde493ec1060aff4655e469402f91c8e0e3cd34 Author: ann Date: Sat Feb 10 21:16:29 2007 +0000 formatting cleanup commit 9494b662f8624332b7eb5a9cd235b2c39c1ff153 Author: ann Date: Sat Feb 10 20:52:36 2007 +0000 removed plus values from sample data commit 5948f73565e8f4f4be336e4f6815acd63e91d018 Author: kuhn Date: Sat Feb 10 19:38:26 2007 +0000 added doMetaData method for getting all databases and all tables. combined doMysqlVersion and doTableStatus into it. will drop those methods when all scripts using them have been converted. commit 369d78e5426cadbc2a7287ac123a4c5a5036c817 Author: kent Date: Sat Feb 10 18:54:48 2007 +0000 Adding some regions to look at closely. commit df18f232b383f868cf54b3605207d41d9ad3ac34 Author: kent Date: Sat Feb 10 18:53:38 2007 +0000 Fixing a little memory leak. commit dc9c68400cb46ef229de23251fb84ddae45bc7df Author: kent Date: Sat Feb 10 18:53:11 2007 +0000 Removed empty options usage statement. commit f278b84123bcd87c31116cfdf7818f6735ece63e Author: kent Date: Sat Feb 10 18:52:19 2007 +0000 Suppressing hgsid so as to create new session when user follows convert link. commit e1517f7864792a91ed8065fe51db0b164d29599a Author: kent Date: Sat Feb 10 18:51:30 2007 +0000 Fixing warning about empty format string. commit 8bed31a12b6589de7af0b6524143ca5061fb88f7 Author: galt Date: Sat Feb 10 16:00:27 2007 +0000 "Encode release log update" commit 78af69a44d39560e305d0b744b9a92b1cb657926 Author: galt Date: Sat Feb 10 16:00:14 2007 +0000 "Release log update" commit b7d8e25b9f7f01e1d9e62cbe2c4ba2f3e452a6cc Author: kent Date: Sat Feb 10 06:10:47 2007 +0000 Putting in a bunch of debugging prints. commit eac8200928bb956e71485570704d8bc7f683adaf Author: kent Date: Sat Feb 10 06:10:20 2007 +0000 Getting rid of code that flipped intron/exon on reverse strand. commit e19c9cfd8dc542be65bdccc0cdb0b7efa89a3e1e Author: kent Date: Sat Feb 10 06:09:34 2007 +0000 Seems to work pretty well for making txg into semi-readable not too bloated XML. commit 394f69b589320b43c4fcc88dca49166c1ea9c96e Author: kent Date: Sat Feb 10 03:08:11 2007 +0000 Fixed crash for altSplice running on hg18.chr22 that I put in recently when merging evidence in some new situations. commit a900c8614d8a2b57d8e68c0a4ced9b54c10e1607 Author: kent Date: Sat Feb 10 02:04:53 2007 +0000 Adding some comments. Expanding size of a hash table. Fixing warning message. Should have no run time impact. commit 6e92ee1b9e11a5fd9beffb2950cf22bb2bb85500 Author: kent Date: Sat Feb 10 02:02:19 2007 +0000 Polishing altGraphX output. commit 19e12ff1ee16bc746eacb4c27877f7c06b1f80a3 Author: galt Date: Sat Feb 10 02:01:27 2007 +0000 fixing compiler warnings commit 0a051c20207a07e4572d5649e54a75e1d7c825b4 Author: kent Date: Sat Feb 10 02:00:27 2007 +0000 Adding rangeTreeOverlaps. commit a9e02444dafbca456fb4ca81582d400db901055f Author: galt Date: Sat Feb 10 02:00:26 2007 +0000 allen brain atlas update commit 6fd35f4e24edf2eaedb29a93566451eba82383cf Author: kent Date: Sat Feb 10 01:57:50 2007 +0000 Trimming some debugging output. commit 345aa0e621e23a486668d2b0c2251029d3d90b5e Author: kent Date: Sat Feb 10 01:19:48 2007 +0000 Starting to write some output. Whittling down a reasonable sized test case. commit bf2ef3dd16bd4f3f780b3102f6998d3b2cffd111 Author: kate Date: Sat Feb 10 00:48:09 2007 +0000 Use protein accession instead display ID when looking up GO terms (accessions are less subject to change). This was changed so that older KG build works better with newer GO database. Incidentally fixes GO column in C elegans and zebrafish gene sorters -- these were not working at all. commit 7a49da469505d0ca61a8a2aeb0b479e229c027a1 Author: rhead Date: Sat Feb 10 00:34:25 2007 +0000 removed reference to /cluster/bin/i386 in FAQ commit 4ec072ae3549d7510c4b5f8e076ae60c849e015a Author: fanhsu Date: Sat Feb 10 00:30:48 2007 +0000 Added logic to generate top bar specifically for GSID. commit eacde990bcf169ff29253d332857e66f8741e98b Author: angie Date: Sat Feb 10 00:23:10 2007 +0000 Added another developer not in template description of gaps. commit a66d98000a176ad8cee5a066312a45e68e9db068 Author: kate Date: Sat Feb 10 00:21:40 2007 +0000 Liftover chains to rn3 commit e87e30afae17e8cf005f510b3636289b6d4a7a3c Author: galt Date: Sat Feb 10 00:21:37 2007 +0000 added contributors to .ra commit 3c56c78859a7c3241752d51162f8589ad2188d0b Author: hiram Date: Sat Feb 10 00:19:33 2007 +0000 Forgot one makeTempName() becomes trashDirFile() commit 565f1b70bee0d634dc716712c12dff263264ebf3 Author: hiram Date: Sat Feb 10 00:04:14 2007 +0000 null result from hashLookup means not found ... commit c159f91b9bfe0883adac6aea7a9ae39b51b1d14a Author: angie Date: Sat Feb 10 00:02:05 2007 +0000 Regenerated basic tracks after assembly re-release. Assembly changes were very minor but it's important to stay in sync with NCBI. commit 01c56237d893600d2cced93b3d6c5f5dd991afe3 Author: hiram Date: Fri Feb 9 23:53:52 2007 +0000 Don't forget the trashDir.h commit 45f61b261ed62d9a0766d2dd112e96394f64c5dd Author: hiram Date: Fri Feb 9 23:53:06 2007 +0000 Now using trashDirFile in place of makeTempName commit 29ade8c34ef0855d8e21994135a5bb0e1050e34e Author: hiram Date: Fri Feb 9 23:47:08 2007 +0000 Now using trashDirFile() instead of makeTempName() commit d688647269992a0c0218bdca7442a46c258b3741 Author: hiram Date: Fri Feb 9 23:37:36 2007 +0000 Now using dirName, base and suffix to trashDirFile() commit 23f5646e66eb6471ea53c2a01887faf3ad1fef70 Author: hiram Date: Fri Feb 9 23:19:52 2007 +0000 Now using trashDirFile() instead of makeTempName() commit 9bcf517ca78a08525df800f6ec16f8685e03a41b Author: hiram Date: Fri Feb 9 23:15:23 2007 +0000 Need to specify three items: dirName, base and suffix for trashDirFile() commit c92f401512ed90b0bcf7a569a6e8466af1f73ad4 Author: hiram Date: Fri Feb 9 23:14:03 2007 +0000 Need to specify three items: dirName, base and suffix commit c2fa9ac84382069f5e8d7cc9eb6724ed1f701c8d Author: ann Date: Fri Feb 9 23:03:54 2007 +0000 added Example 1 to Quick Start section commit 773cad84bf55012f8f5c9d350dc3eab76a741aab Author: hiram Date: Fri Feb 9 22:52:59 2007 +0000 Use generic trashDirFile() in place of specific ...TrashFile() routines commit 1d7dc876ee22e235e4bf264c9954090bcce56b55 Author: hiram Date: Fri Feb 9 22:45:50 2007 +0000 Now using generic trashDirFile() in place of specific blatTrashFile() commit 614852029300b8f6f4102b8d2d8c1b71c5637964 Author: hiram Date: Fri Feb 9 22:42:18 2007 +0000 Now using the generic trashDirFile in place of the custom TrashFile routines commit 2f192cded156e3386166e1870ee4917c6f0cd4ed Author: hiram Date: Fri Feb 9 22:38:20 2007 +0000 Add trashDir.o to the library commit c94e454e0a051fc4e68a078cbdfb1a08dfda0378 Author: hiram Date: Fri Feb 9 22:34:04 2007 +0000 Add sourceType to the ggMrnaAli structure commit f0d9dec3d09642a2ccc228e3e1112a3d68495144 Author: hiram Date: Fri Feb 9 22:32:06 2007 +0000 Add val to the range structure and the function rangeTreeFindEnclosing() commit 54812fcc469d68438e1ea06360fc4ae1e5a4f53f Author: hiram Date: Fri Feb 9 22:31:38 2007 +0000 Add val to the range structure, and the function rangeTreeFindEnclosing() commit ff72f9e9e912e42b5a186e594c45fce4774b1946 Author: hiram Date: Fri Feb 9 22:25:08 2007 +0000 Initial contents commit fc0169a8f2f1be32d9a8bab9d719805f8fc44ee2 Author: hiram Date: Fri Feb 9 22:24:45 2007 +0000 Initial source commit be841cacbebbb5cd1ea01fe238023fe90820f25a Author: kent Date: Fri Feb 9 22:14:06 2007 +0000 A little more refactoring and scaffolding. commit a85b627e1edb7d042e75eec75d57dc7ffc9d7191 Author: kent Date: Fri Feb 9 22:03:46 2007 +0000 Finds overlapping graphs in other species. commit ebe685731176d07031d20060191473991edfc4d8 Author: ann Date: Fri Feb 9 21:50:06 2007 +0000 added description for how to actually display the uploaded graphs! commit c243deec29d979509be9aa62c00b8222c03c4064 Author: kent Date: Fri Feb 9 21:14:31 2007 +0000 Reading input. Finding best chain for given graph. commit f6fcf6f5972d5ee467a1ddf1325595daa71e2dcb Author: kuhn Date: Fri Feb 9 19:07:15 2007 +0000 removed some test code commit 153d6c1530ded05689721a4a9c08fd25c492527d Author: kuhn Date: Fri Feb 9 19:03:27 2007 +0000 removed unused variables commit 0f68f7bfc5ec8dc67371a34dc2447980749d678f Author: kuhn Date: Fri Feb 9 19:00:07 2007 +0000 removed some debugging commit b311b9edb7cf8ab4c89143dd8f207588a16f7ada Author: markd Date: Fri Feb 9 18:59:24 2007 +0000 added HIP clone ids commit bff1a600c98b068df5a68bc9782793646182d1fe Author: kuhn Date: Fri Feb 9 18:15:38 2007 +0000 removing qateam ssh from scripts in favor of wget commit b4b01ff12a7ab474688c9bc49bbce8a7960ab281 Author: fanhsu Date: Fri Feb 9 16:22:56 2007 +0000 Updated wgRna track. commit 7e371d109c6288f26283e0f1e72a1d6859b994a4 Author: galt Date: Fri Feb 9 16:00:29 2007 +0000 "Encode release log update" commit e89fdb261536d8a409d78f21c583056b50612948 Author: galt Date: Fri Feb 9 16:00:16 2007 +0000 "Release log update" commit d23a863924381b1fe0c9ddfa5e8d58b27549685f Author: kent Date: Fri Feb 9 10:48:13 2007 +0000 Restricting output to sourcType refSeq, mrna, or est. commit 8557e3bb469334fe7149cae0f19ab18924ba34ae Author: kent Date: Fri Feb 9 09:25:45 2007 +0000 Adding more docs to txGraph/README. commit d33e5a88aa1ba9a3e10838cb832d90bafc282c85 Author: kent Date: Fri Feb 9 09:23:45 2007 +0000 Seems to work. commit f1f2f30c1e47c2ee56b9a01650251cdceb0399ae Author: kent Date: Fri Feb 9 08:25:20 2007 +0000 Seems to work. commit eaeb1c3c1dd59b732af0aff78091af888399b9f9 Author: kent Date: Fri Feb 9 07:54:56 2007 +0000 Parsing command line and input. Copying input to output. commit fc52aeed4e2e7aa8e51a0e94f12da7b8311dcdf6 Author: kent Date: Fri Feb 9 07:07:31 2007 +0000 Adding evidence as well as evidence source. commit ace2458c734123ab4eb9ac8029fe771c13f29487 Author: kent Date: Fri Feb 9 07:03:29 2007 +0000 Adding expected output to test target. commit 1249a3b7c90bf0b2849150f691c710509b646dff Author: kent Date: Fri Feb 9 07:01:19 2007 +0000 Writing output for first time. Actually adding evidence. Seems to work, but there is still copious debugging output. commit 048bb87c75b0f78489fd2e52fd9607a7df06ff56 Author: kent Date: Fri Feb 9 07:00:39 2007 +0000 Adding some more to test input. commit 531ac2a49f9beb0b863fbf1c084c45a1ebd3c905 Author: heather Date: Fri Feb 9 06:10:55 2007 +0000 a bit more hapmap commit fbb87c5f208c44375abfa7d05d4792212bbee78b Author: kent Date: Fri Feb 9 05:50:05 2007 +0000 A little further along in the framework code. commit 56341d32146c3f7e392aea49fc08c50b9799bc66 Author: kent Date: Fri Feb 9 05:33:21 2007 +0000 Building up a chromosome bin keeper. commit d6c490680c45c146438a0e55309b10fd4482dc09 Author: kent Date: Fri Feb 9 05:08:57 2007 +0000 Command line is working, as is parsing of input. commit 6061379055eab0dce53274c499f80b89d29a4766 Author: kent Date: Fri Feb 9 04:38:35 2007 +0000 Expanding test input. commit 3867762194955d7fc89f2770a974e3ab1e74b90c Author: kent Date: Fri Feb 9 04:33:07 2007 +0000 Making it take input from a list file (bed/type pairs). commit 9e43396e6a212e2d2cb923185e18d60e7313e5b5 Author: kent Date: Fri Feb 9 03:50:15 2007 +0000 Making genoGraph builder a little better about not having sequence available. commit d40fa71257809641237a714bd13ced4755b8b772 Author: heather Date: Fri Feb 9 03:38:41 2007 +0000 check that alleles match observed commit 4a58bd990a686136ec16f1dab482dffd2f4f2b71 Author: heather Date: Fri Feb 9 03:37:05 2007 +0000 hapmap SNPs: create base tables commit 0c4a927b2c5becdf0f24bcb768e53bc414ab5e71 Author: heather Date: Fri Feb 9 03:06:37 2007 +0000 add score filter commit 132fcb0d8a0e995990510531806e18a38ddd2cc9 Author: heather Date: Fri Feb 9 03:05:26 2007 +0000 update for zygosity commit 29e2bff24b84b97adb1b30babde8be10970fbe4f Author: heather Date: Fri Feb 9 03:04:36 2007 +0000 tweaks to previous commit commit 706bcebe6b4e16e99a7e9243256ec1cafe55a4fe Author: kuhn Date: Fri Feb 9 02:25:45 2007 +0000 added dev and beta commit a40aa3c0ac130efc07a5974490b6310974475214 Author: kent Date: Fri Feb 9 02:13:04 2007 +0000 Updating expected from sourceType change. commit 3b6cabee24cfe5f6efb86f3fc642c619d36b8143 Author: kent Date: Fri Feb 9 02:11:54 2007 +0000 Refactoring a bit so as to pass in source type to geneGraph maker. commit e731f9c7bc63e9d5604f7d891a337ef762ce0e6d Author: kent Date: Fri Feb 9 02:11:27 2007 +0000 Filling in sourceType as psl as part of refactoring. commit 6efd3e13b9b84af59d67b30c9b57397b12cfe9eb Author: kent Date: Fri Feb 9 02:10:53 2007 +0000 Adding mrnaType/sourceType to geneGraph. commit 984df16b9ee37cd83f1685e48b894d8d027222bd Author: kent Date: Fri Feb 9 01:50:16 2007 +0000 Removing exonWalk until it compiles clean on Mac. commit 28f2651a69f224707cbef83986bc86e715e1bcf2 Author: kent Date: Fri Feb 9 01:22:10 2007 +0000 Adding clarifing word to txGraph README. commit 3feb1f7232fc7330c81208f5fa82ea1a489fed4b Author: kent Date: Fri Feb 9 01:21:36 2007 +0000 Updating expected output after bug fix. commit d867ce94117309874245eb5dfc77bf7855a10ee0 Author: kent Date: Fri Feb 9 01:21:09 2007 +0000 Coping with changes to txGraph structure, change of mrnaRefs to sources in particular. commit 70e22eff87936175e9a35163a1f2d2cbd432eaf8 Author: kent Date: Fri Feb 9 01:20:24 2007 +0000 Updating comments in geneGraph.h commit 04d218a243b8c93d352bf54b8ca19deb79cba6e1 Author: kent Date: Fri Feb 9 01:19:23 2007 +0000 Saving start and end positions in evidence. commit c9cd0417fcc970336f681d113fd037c705424dc3 Author: kent Date: Fri Feb 9 01:18:57 2007 +0000 Making genoGraph system work without necessarily having genome sequence. (Can now check gt/ag earlier.) commit 04023b8c070855746f5e08ab5cb54041334de234 Author: kent Date: Fri Feb 9 01:18:05 2007 +0000 Adding mergeDoubleSofts pass. Being a little more careful about merging evidence when merging edges. commit 6b2ddcacedef8cb24ea17915f33d194f58fb2b4e Author: kent Date: Fri Feb 9 01:15:01 2007 +0000 Replacing mrnaRefs with sources commit 948dec6d9dbdbda14d016302fad9e1e258031d75 Author: galt Date: Fri Feb 9 00:51:23 2007 +0000 removed unused variable commit 8a00b3b4687b33a9c30b8ceae9edbe4e3244fc81 Author: hiram Date: Fri Feb 9 00:47:53 2007 +0000 Send tfbsConsSites constant defines to ../inc/tfbsConsSites.h commit 621a7cec1e2128a66aae7fb7d6a47d12915238ff Author: hiram Date: Fri Feb 9 00:45:10 2007 +0000 Add TFBS_SITES_CUTOFF_MINIMUM define commit 0237a97a3312e4def8749f9853af7bdf9858d914 Author: heather Date: Fri Feb 9 00:02:11 2007 +0000 oops, clobbered these commit 40a9672022bf5d8d03774fb4c83572c0acd15640 Author: hartera Date: Thu Feb 8 23:47:59 2007 +0000 Added biotype and external ID fields for the Ensembl Non-coding Gene track. Renamed the info table for the Radiation Hybrid map track to be called rhMapZfishInfo. commit 705746afd8ead9ffd5615b76c278ffb6a9382721 Author: heather Date: Thu Feb 8 23:40:13 2007 +0000 add bin commit 504917d8aeb09264fcec1b9c335b04bacee4529d Author: ann Date: Thu Feb 8 23:22:57 2007 +0000 tab clean-up. Adding some of the Quick Start section. commit f6f5370f632ff7b7a7a9915fcf232cedd263cbb3 Author: ann Date: Thu Feb 8 23:08:03 2007 +0000 uncommenting Quick Start Section commit c7ebd7f25d07b9335b6e12a06df3e6ab6bc09bbc Author: galt Date: Thu Feb 8 22:49:14 2007 +0000 implemented -cleanImages and -checkImages commit 755c19c2f5b8a377a6b20e236dfcd8eea1299b30 Author: kent Date: Thu Feb 8 22:35:49 2007 +0000 Removing mrnaTissus and mrnaLibs from txGraph. commit e29738cbb886754a778522d400f6a5df1c65abad Author: kent Date: Thu Feb 8 22:11:39 2007 +0000 Creating tgx instead of agx. Still a little rough code-wise but seems to work. commit 595eaf1a478461e63230cf2f15bb8a823b2abd4e Author: kent Date: Thu Feb 8 22:10:40 2007 +0000 Creating txGraph - a minor modification of altGraphX. commit be5288b2c51109ae1d183d840f21425a14ff4f68 Author: heather Date: Thu Feb 8 21:56:48 2007 +0000 add missing commas commit eb65b51987e4dfba9db7f7a2765313f959e7fca8 Author: heather Date: Thu Feb 8 21:39:45 2007 +0000 add heteroCount commit 5bdb4bae14f0d1d7994d02ce605873e1674e283a Author: kent Date: Thu Feb 8 21:31:47 2007 +0000 Adding test case. Tweaking verbose output. commit 040484435b881fe2a476009a2038e2741db713b6 Author: kent Date: Thu Feb 8 21:21:14 2007 +0000 Making this handle bed6 (strand, no exons) as well as bed12 input. commit 075bc45fa2ff1e79b63c282bd1b7aaedaca18b06 Author: heather Date: Thu Feb 8 21:19:43 2007 +0000 change score to minor allele frequency (not major), divide all counts by 2 commit ae634221f432350a6f31d125e61d5df5ef68693c Author: kent Date: Thu Feb 8 21:11:58 2007 +0000 Fixed +/- mixup. commit 788fa59d1cb8c73fb1cf43724f75d32b85adddb2 Author: heather Date: Thu Feb 8 21:09:04 2007 +0000 add a comment line commit f357ccc7f34046168e2d361cbc0ffc1c7fdd6009 Author: kent Date: Thu Feb 8 21:00:33 2007 +0000 Suppressing output of small beds. commit 7617bb49d3a7363dc4a704f5324566d9147dcda1 Author: heather Date: Thu Feb 8 20:36:21 2007 +0000 first step in hapmap processing commit b318366ecb27e1fe9bc6b67ef3bbf538d72b6fd1 Author: hiram Date: Thu Feb 8 19:56:56 2007 +0000 html files for chain and net Medaka commit 06ac3ff00c6a41d9d087f1067d1fea493cf5902a Author: hiram Date: Thu Feb 8 19:56:07 2007 +0000 Do not need the oryLat1 entry here. It is OK in the top level. commit e30b7f3ec0dcdd45e2b1df5d7ab041691e8a3fc4 Author: hiram Date: Thu Feb 8 19:53:19 2007 +0000 Add the matrix numbers for oryLat1 chain commit e1d834214aabee578b4333e89bb792d6501e58fd Author: hiram Date: Thu Feb 8 19:52:09 2007 +0000 Add the matrix values for oryLat1 chain commit eb215f0897a872e3a4a1b790d055ceff06b067ba Author: hiram Date: Thu Feb 8 19:40:44 2007 +0000 Allow Medaka chains and nets to show up on any assembly that doesn't have a specific trackDb entry for it commit 20fc38aac0b5719437e8e41d1085c260b4b44b38 Author: hiram Date: Thu Feb 8 19:40:05 2007 +0000 It is Ok to display the Medaka name, there isn't any other oryLat dbs at this time commit e4beba41ffccf184767f6a9098ab6b6c8968b8c7 Author: kent Date: Thu Feb 8 19:26:43 2007 +0000 Descibing overall pipeline for txGraphs here. commit 65c32b01e27d8d18250afbfe28b5344f4bb2f4f7 Author: kuhn Date: Thu Feb 8 18:23:24 2007 +0000 changing name commit a9f4d0d91021771d95bf56743a783aa6cdc2ce5e Author: markd Date: Thu Feb 8 17:53:50 2007 +0000 use STRINGIFY variable commit 54164665fe8960f2e9eaa6c6af562f42e86d1d19 Author: hartera Date: Thu Feb 8 17:20:04 2007 +0000 Shortened Radiation Hybrid map track short label. commit 4057ef3738c64a99b87320131cf1ca0451a00247 Author: kuhn Date: Thu Feb 8 17:05:11 2007 +0000 removed header from output commit d47ac21263e93b272f27f7d03c5d8bb40005c360 Author: kuhn Date: Thu Feb 8 17:02:37 2007 +0000 remove some whitespace commit dbb89bd048196baf819283db17ed4bc9a4c424c5 Author: kuhn Date: Thu Feb 8 17:00:36 2007 +0000 added method to get mysql version commit 35b19aec0c30288e028fff05221d4fca6f79bc69 Author: galt Date: Thu Feb 8 16:00:30 2007 +0000 "Encode release log update" commit 6ab0d7db8d8724dd6ab2d680b309ef7ac9d5e32c Author: galt Date: Thu Feb 8 16:00:16 2007 +0000 "Release log update" commit 578cc759e14dca24c6dc3044afee90685d0470cc Author: kent Date: Thu Feb 8 08:46:03 2007 +0000 Making clustering code less dependent on having sequence. commit db9bb75d265c571792744fae4b17f50b2d1fc381 Author: kent Date: Thu Feb 8 08:43:48 2007 +0000 Reading input and making some wacky output. commit 47d0de776e84e235986fb120010d0bc1357fea7f Author: kent Date: Thu Feb 8 07:46:27 2007 +0000 Fixing bug in intron shifting. commit a7a52f5459cb2864d77ed6346c3f88a1cbdb4033 Author: heather Date: Thu Feb 8 07:32:15 2007 +0000 feedback from code review commit 27ec021ddb0776d267cf3a527bd5e97dc2bd5d56 Author: kent Date: Thu Feb 8 07:24:04 2007 +0000 Made dnaPath a required positional command line argument. commit a341ad4e4c12e86a75c6833109629070e5e3cc79 Author: kent Date: Thu Feb 8 07:20:16 2007 +0000 Adding test case. commit cef8ddaa2a6d48321eb6700c92daf9874c7b4582 Author: kent Date: Thu Feb 8 07:19:45 2007 +0000 Splitting up where there are large non-intronic gaps. commit c8e2f79e9a5ef848ba139eca02a9488212581687 Author: kent Date: Thu Feb 8 06:07:17 2007 +0000 Removing some debugging code commit 32724790d2d61e7e41d4cc86ca2629868a128c8c Author: kent Date: Thu Feb 8 06:06:49 2007 +0000 Fixing some +/- 1 +/- strand issues on intron fixing. commit fc712ff9c315ae08aaff60e1c1acff648fe479a3 Author: markd Date: Thu Feb 8 05:35:21 2007 +0000 added ability to cleanup selectTable memory to allow checking for memory leaks commit 830745780985e2f852ac8f477bc83da36f63723a Author: kent Date: Thu Feb 8 03:06:22 2007 +0000 Program to convert psl to bed 12, merging small gaps and fixing introns, is just starting to work. commit af4a3e95ebdb448449135d86b52831cce368212f Author: markd Date: Thu Feb 8 02:48:57 2007 +0000 improved error message with track type or subTrack entry is missing commit 6d615d494a361391c0a4d486fb45552a1c96d9cb Author: galt Date: Thu Feb 8 02:11:19 2007 +0000 bob k tweaked password errmsg commit 9f9c3fca66ed84f8ad574658d397188411aee572 Author: galt Date: Thu Feb 8 01:32:32 2007 +0000 implemented -cleanImages option commit 23d6de0ec505c66d72efc0a168f0332f69e2efe0 Author: galt Date: Wed Feb 7 23:09:13 2007 +0000 made password stricter -- now requires minimum length 8 and 3 character-classes present commit 908b3acf3f6e5a323c0dfe3cabaffa266fbf6afd Author: kuhn Date: Wed Feb 7 22:51:43 2007 +0000 made stickleback-=centered image for Conservation track commit b3869d3c6d718f4d685a8ee7cfe0d5d5750de500 Author: kuhn Date: Wed Feb 7 22:35:50 2007 +0000 fixed a bug ann found. first machine total was using value from second machine commit fa555cc1976e3c416de6cf015436ddbbafef18e6 Author: markd Date: Wed Feb 7 22:00:48 2007 +0000 clean up all .o files commit 5cf2502e34721beae54602380257a3819d550919 Author: kent Date: Wed Feb 7 21:47:28 2007 +0000 Removed a couple of lines of unneeded code. commit b0d32e4eb710931cd995b2de895eeae827bf47a8 Author: kent Date: Wed Feb 7 21:47:07 2007 +0000 Fixed formatting, if somehow on line above. commit 86486f1efa67e1765d8d027ed8e3e93aaa6d9dc9 Author: ann Date: Wed Feb 7 21:02:32 2007 +0000 remove HR commit f30fa0095c99fd0a890ccffff57663eb922b3579 Author: kent Date: Wed Feb 7 21:00:14 2007 +0000 Changing output names to simpler format. commit 5f3b02cb55c17ff080de8e604536b10de501b669 Author: kent Date: Wed Feb 7 20:47:10 2007 +0000 Adding -agx option to do alt-splicing graph as well. commit 069a3e97373834a040021612da6d1ca8465f1435 Author: kent Date: Wed Feb 7 20:37:29 2007 +0000 Adding NULL check on hFreeConn. commit e51442d20ce589f676a07413e5dddaee52c1ad66 Author: kent Date: Wed Feb 7 20:37:14 2007 +0000 Adding comment commit 15bc37e2d10b7b495e706b6e0fc26d911ee72c1d Author: markd Date: Wed Feb 7 18:50:38 2007 +0000 removed use on non-posix unlocked stdio functions commit aec7c50b22328bc96e1ef2f2f83c62ae3f8494db Author: markd Date: Wed Feb 7 18:50:14 2007 +0000 used STRINGIFY variable commit 2fa20909ba5f73e996f4b5a5b4b019c500d191c9 Author: markd Date: Wed Feb 7 18:49:51 2007 +0000 added variable for stringify program commit 16d5bb3d6bce06c04472bb13c9e48d981f2fd01c Author: markd Date: Wed Feb 7 18:10:08 2007 +0000 dump format from NCBI changed, don't need to trim trailing tab commit 4a3877031b0fb813ee0c659e28729215543981e2 Author: hiram Date: Wed Feb 7 18:08:46 2007 +0000 More correct for darwin check in OSTYPE commit ed74146323b2fc356b3851baf58a2188e23d0658 Author: giardine Date: Wed Feb 7 16:28:16 2007 +0000 Changed capitilization on link to be consistant. commit 92f31f03d29ebb247735fc86790040831c6d9efc Author: galt Date: Wed Feb 7 16:00:32 2007 +0000 "Encode release log update" commit 12bcc6e178ac72b6a1ceb1d766be9da56813e473 Author: galt Date: Wed Feb 7 16:00:18 2007 +0000 "Release log update" commit 75d23770f23a214421f1af38e752457325f39dd1 Author: heather Date: Wed Feb 7 01:42:25 2007 +0000 add filters commit 797e52654a57e5034e74461c53a3a5b3186a0c03 Author: heather Date: Wed Feb 7 01:41:11 2007 +0000 add hapmapAllelesUi commit bf6d434e9956f2df856cd8108ef7282bc9040e55 Author: heather Date: Wed Feb 7 01:40:43 2007 +0000 add 3 cart variables commit f9b6e5ebdc0406ebd35c24339067c0fb5e7b73c5 Author: braney Date: Wed Feb 7 00:14:19 2007 +0000 added D. mel. Proteins track commit b6174a4cb518ab1b5f05d01e261f3e3ec1ca7754 Author: hiram Date: Tue Feb 6 23:57:22 2007 +0000 Finish up multiz5way downloadables, turn on blat server, and set default position commit 1f159fed1c2c05a0622f0d8c3ebdd61897e4dc95 Author: hiram Date: Tue Feb 6 23:56:45 2007 +0000 Better default position commit 762f6140edb4727d9276bb4a17ee75891fb069a6 Author: hiram Date: Tue Feb 6 22:43:23 2007 +0000 Now using fr2 in place of fr1 commit 3df7fef744bef1f06f2de5435712d3b25b54c3a3 Author: hiram Date: Tue Feb 6 22:43:11 2007 +0000 Proper order of chain/net tracks commit ce8bf6ebc536dded6047f59e3d3dd67dfbf50d7a Author: hiram Date: Tue Feb 6 22:21:51 2007 +0000 Now with phastCons5 and iframes on commit a9686c23443950094ab40f9fbd17aa3a08fd613c Author: heather Date: Tue Feb 6 22:12:41 2007 +0000 include N commit b6ae3178e983a9fa06483c1a3fe94d953f85775d Author: heather Date: Tue Feb 6 22:10:50 2007 +0000 companion to previous commit commit 934fc4074906e318ed4b52510f0fcd4810850399 Author: rhead Date: Tue Feb 6 22:00:37 2007 +0000 Edited refs to conform to Pubmed format. Took out one name for first paper that was not on Pubmed author list, or on our publications page. commit e702cf1ad8ea6bb772a38542d7ac0f9b2dc9f0f9 Author: kuhn Date: Tue Feb 6 21:50:05 2007 +0000 moved some newlines around commit 7375034795a90644de73ad01b924bc60017ee70a Author: kuhn Date: Tue Feb 6 21:20:23 2007 +0000 dropped a newline from doTableStatus output page commit 200e76860734481346f0ccd6a5365dab0ead9e19 Author: rhead Date: Tue Feb 6 20:41:07 2007 +0000 Edited refs to conform to Pubmed format. Took out one name for first paper that was not on Pubmed author list, or on our publications page. commit 75a62cb3f0991ebcb128dc69f46c5a99eec9099c Author: heather Date: Tue Feb 6 20:14:20 2007 +0000 handle strand commit a87848a5c12d0af019d25f9bf85f61004c385700 Author: hiram Date: Tue Feb 6 19:38:49 2007 +0000 Now with phastCons5 and proper order of species commit 3c3594982251aa15c93eb51029b05e6d49d8e3a6 Author: rhead Date: Tue Feb 6 19:33:11 2007 +0000 Added evofold tables to tablesIgnored, per Jakob commit 460ba7baaf705be78919e63949dc41332d4703d8 Author: heather Date: Tue Feb 6 19:24:36 2007 +0000 add doHapmapOrthos commit f3d9b5cbe45a2bb9ce246daa1e10636da742c709 Author: hiram Date: Tue Feb 6 18:28:39 2007 +0000 fr1 is now fr2 in the 8-way commit 1ff2b73c2f65472e6ca9698824120da73c98fd5b Author: hiram Date: Tue Feb 6 18:28:21 2007 +0000 Rearrange chain/net tracks in proper order commit c9b705c2f8b65f5e9f0cb67cc27d34b162167dd1 Author: galt Date: Tue Feb 6 16:00:27 2007 +0000 "Encode release log update" commit 5e67f79d088d6561bc030743de5143529d296c1f Author: galt Date: Tue Feb 6 16:00:15 2007 +0000 "Release log update" commit 4159ebe682c5917b22e5d3a3d384cf39c4ea7730 Author: giardine Date: Tue Feb 6 12:41:27 2007 +0000 Updated links for IDbases to new format commit e1cc5caaa6e57769ec3dc49d7ff0f0e343bb0ade Author: heather Date: Tue Feb 6 07:53:12 2007 +0000 add ortho alleles for hapmap SNPs commit 7e1feaa84a5f2b457420cc2a208fa9d706ba977f Author: heather Date: Tue Feb 6 07:52:54 2007 +0000 add ortho alleles, and switch to displaying major allele commit a2ac6df40a0af409709446be707afd68d5f490be Author: heather Date: Tue Feb 6 07:43:47 2007 +0000 add hapmapAllelesOrtho commit e080d3118cf012ecb806b96efcc916e2d7ca44e0 Author: heather Date: Tue Feb 6 07:43:35 2007 +0000 ortho alleles in composite track commit 59886f0c8a6852c8e3b864c51ca81a8f0833e00f Author: kuhn Date: Tue Feb 6 02:06:14 2007 +0000 added output line identifying database commit 33b6c873ca93fdc22dd396c22fd3633599c24d4d Author: markd Date: Tue Feb 6 01:46:10 2007 +0000 fixed bug where ESTs intron lines sometimes not drawn in dense mode commit 81f10b404cce583b099e5fcabf4237d2d3ec1bd4 Author: kate Date: Tue Feb 6 01:29:50 2007 +0000 Remove obsolete custom track code commit 3027515cf39258688a0cbc6b3fd1a999b1ea64ee Author: hiram Date: Tue Feb 6 01:14:48 2007 +0000 Redone and completed multiz5way and phastCons5 with fr2 instead of fr1 commit d6d7a4865be5f79b72d04c15665428b77b09a6f6 Author: hiram Date: Tue Feb 6 01:12:27 2007 +0000 Re-ordering buttons in Comparative Genomics commit e33e5d9eaf0d9a3bda0b7d1edeb5066a9c15c6a4 Author: galt Date: Tue Feb 6 00:56:52 2007 +0000 bugfix - need email addresses to track email (old version used invoice id as the email) commit 0b42cf8dcaa7aa79245b728168168aab6825ec10 Author: hiram Date: Tue Feb 6 00:46:30 2007 +0000 Proper order for multiz8way species commit e4c4a89b4d84c449746f4c9fe786767987b05f1e Author: angie Date: Tue Feb 6 00:34:32 2007 +0000 Temporarily removing ornAna1 while I rebuild the db (assembly re-released). commit 1b71a495fd35c67687065d975c2f9613b707befc Author: kate Date: Tue Feb 6 00:14:12 2007 +0000 Correct and consolidate GTF format descriptions, used by FAQ and custom track documentation commit ce5d32a5661d3a828f6aa15e95e0855cdea1ef61 Author: kuhn Date: Mon Feb 5 23:04:46 2007 +0000 added methods for getting TABLE STATUS. thanks, kate commit 3bd98af5e9f603fa02831dce604f76cb742542e1 Author: angie Date: Mon Feb 5 22:58:20 2007 +0000 Include referenced objects/tables in stored autoSql for each table, so that we store complete definitions (so the autoSql parser doesn't die in hgTables). commit f126765bf703d3bfb2d43650603d360bb874cbc6 Author: ann Date: Mon Feb 5 22:54:01 2007 +0000 added information about clicking on graph to go to GB commit 551b9606ab2de8422722dd0d0a38cff484eb9cad Author: ann Date: Mon Feb 5 22:40:41 2007 +0000 typo commit 6887daa887db95136a82a524decfa0fe56d267d4 Author: rhead Date: Mon Feb 5 22:34:45 2007 +0000 Fixed the genome-mirror archives hyperlink to actually point to genome-mirror (not genome) commit 7c89c57c487074cefc8e4e3203f0cb933b681b58 Author: ann Date: Mon Feb 5 22:22:17 2007 +0000 more lower case commit 403dc1cd318a852310308818ee9c983553684ac5 Author: ann Date: Mon Feb 5 22:19:56 2007 +0000 changed labels to lower case for consistency commit f581a8a09864884bd302fce5685256353e530da6 Author: ann Date: Mon Feb 5 22:15:37 2007 +0000 changed lables to lower case because code was so changed commit e14449fe28afcf5dda098d37448e330788e1c210 Author: ann Date: Mon Feb 5 22:11:14 2007 +0000 changing labels to lower case for consistency commit 0a69155d6453b1fbc77ccc42813e2a1fa103bd87 Author: hiram Date: Mon Feb 5 22:07:49 2007 +0000 Turn on genbank daily update, and finished with 5-way phastcons commit 3a26312baf441b2e1c0c4e995cce06f3fddbbf31 Author: hiram Date: Mon Feb 5 22:07:11 2007 +0000 Added fr2. commit c3dcff757b58d1aebcabda9f041c44cc63d53e67 Author: ann Date: Mon Feb 5 22:03:47 2007 +0000 changed grp from X to x. commit df13564616c1c6b34c06608cbebae392b8f775f5 Author: ann Date: Mon Feb 5 21:44:06 2007 +0000 lower-case help words to keep the same with labels commit 784f9bac8321c2b302a0e8a1475582ee2fa7d945 Author: braney Date: Mon Feb 5 20:51:56 2007 +0000 added multizMetazoan track commit e30b1ca4964d1f546266c54b87a74b2918342fbe Author: heather Date: Mon Feb 5 18:38:31 2007 +0000 add draw routine; correctly handle missing data commit 11a7f75c4800f10845103ac4a474bfff27b11d90 Author: hiram Date: Mon Feb 5 18:21:00 2007 +0000 New data for geneid track loaded commit 683d02d6ceb58856c1a08cac5771a1066f5acaa5 Author: kuhn Date: Mon Feb 5 17:51:25 2007 +0000 teaked output format, especially handling of zero tablesize commit c57f3f82d794009f401a7c4da74b114d416b67ac Author: kuhn Date: Mon Feb 5 17:40:18 2007 +0000 removed "exit 1" from output when it completes successfully commit cecc59d1299a63d8ac941961326f78677e688b86 Author: kate Date: Mon Feb 5 17:24:44 2007 +0000 Add /cluster/data reference commit 2378226a05a93335a69a24b9cf6399047269b044 Author: galt Date: Mon Feb 5 16:00:20 2007 +0000 "Encode release log update" commit ad54ef71b3ee023a88756f5604bb165296736ecb Author: galt Date: Mon Feb 5 16:00:11 2007 +0000 "Release log update" commit 21955d9bad59e8e6c6ea9107708b7436f5b0d61a Author: kent Date: Mon Feb 5 04:46:42 2007 +0000 Ifdefing out some unused code and making more sensible uniq chrom hash size (in case applied to contigs. commit ddb72d319589e4f333973ff53e45e2ba90225aa9 Author: kent Date: Mon Feb 5 04:04:47 2007 +0000 Fixing double word 'in' in usage statement. commit 1fb1c3cfe96518db24fbadf6cef8950556d1a475 Author: kent Date: Sun Feb 4 21:48:03 2007 +0000 Adding -singleExonOk option. Works in cases where splice graph is straightforward single exon. When graph is more complex but includes a single exon transcript doesn't work. I'm not quite sure what we want to do in that case yet. commit d7be4f8ab056c849a518d2c0aee78199b0fb4c69 Author: kent Date: Sun Feb 4 21:46:44 2007 +0000 Fixing some spellings in comments. commit c864500572bdcfe53399c8f0b4f1d11ef2e3d307 Author: kent Date: Sun Feb 4 21:46:25 2007 +0000 Adding -keepName option for simpler formatted fa record names. commit 3d0518f73e932ef881f6c3b16cb0c87f9f18b5cc Author: kent Date: Sun Feb 4 21:45:54 2007 +0000 Adding some more verbose debugging. Replacing call to hRangeQuery with simpler hChromQuery. commit 50207326e3c80e4e2a2749802e8d85a4be70b965 Author: kent Date: Sun Feb 4 19:06:52 2007 +0000 Keeping track of known genes III work. commit 64c34603eb313ea81ebe1035091c886732679349 Author: kent Date: Sun Feb 4 19:06:35 2007 +0000 Fixing mm8/mm7 switch in orthoSplice run. commit 64931fa148716f719be0195b00f3d6db7267a251 Author: galt Date: Sun Feb 4 16:00:21 2007 +0000 "Encode release log update" commit f1036b61630d4f60dd32d94cadc388e22094ddb6 Author: galt Date: Sun Feb 4 16:00:11 2007 +0000 "Release log update" commit 4fbdb76675ea323027bc054a24cc65addb5cba1b Author: hiram Date: Sun Feb 4 06:34:29 2007 +0000 Multiz 5-Way up and running. no phastCons yet commit f239580f2f5a74573baf58a01377925090fdab19 Author: hiram Date: Sun Feb 4 06:31:28 2007 +0000 Beginning to display 5-way multiple alignment track, no phastCons yet commit 6c96d1792d5663924cf4e3f59fc03b33b2e758ae Author: hiram Date: Sun Feb 4 06:30:54 2007 +0000 Complete 5-way html files commit 3724c5a076bc5e50767d1ec5247ebd4c5ad4afac Author: hiram Date: Sun Feb 4 06:23:43 2007 +0000 Adding multiz5way on fr2 commit e49bd8f177889288cda54b61b4834aa60e57606f Author: kent Date: Sun Feb 4 05:10:40 2007 +0000 Bumping version and documenting. commit 3d077734ebdc46a734a0b572f55080866b645522 Author: kent Date: Sun Feb 4 05:09:02 2007 +0000 Patching memory abort when database is empty. commit 1cb96be1bb82e3ed91c469d37b7e417b02af5df7 Author: hiram Date: Sat Feb 3 23:24:57 2007 +0000 Done with re-do of multiz8way and phastCons, now using fr2 in place of fr1 commit ca09b58c241c54f0da97bb955feea4d5cbaa11db Author: hiram Date: Sat Feb 3 23:15:45 2007 +0000 Change fr1 to fr2 commit e904989c3a9ef5d348e033661b42a9fca3346660 Author: galt Date: Sat Feb 3 16:00:26 2007 +0000 "Encode release log update" commit daeb6620e1e9958cba7931db64ff21a361dadf22 Author: galt Date: Sat Feb 3 16:00:14 2007 +0000 "Release log update" commit a9e01a69e0ae462688a5de12e13a1fe610330921 Author: kuhn Date: Sat Feb 3 02:39:15 2007 +0000 added support for trackDb.encode.ra and for composite tracks. thanks, brooke. commit c61f6373dbe1a9b6ea2afedfbdb54bfc75bc5f69 Author: kent Date: Sat Feb 3 02:30:38 2007 +0000 Reloading a few tables because field sizes too small initially. Adding varient splice stuff. commit ae1a3f2f9eef09d8fcd570c86ec3a03ccfbeb1cb Author: kent Date: Sat Feb 3 02:28:19 2007 +0000 Adding varProtein and varAcc tables. Making acc use 12 chars in .as file as well as in .sql file. commit a9ff5f35840bff48ef8f2a663f444ca1a99b0d68 Author: kent Date: Sat Feb 3 02:15:53 2007 +0000 Seems to work commit ef1fd5461926a540324a2f312e1c7c63f70ab23d Author: hiram Date: Sat Feb 3 01:44:56 2007 +0000 Adding the gasAcu1 chrUn blastz to make it complete commit 4d55dea470ce581334e91bc1e7f382423ed2d41a Author: hiram Date: Sat Feb 3 01:44:10 2007 +0000 Reworking the 8-way to use fr2 instead of fr1 commit e72fe52820325030fb032dc4e1d181bd8817f5ec Author: kent Date: Sat Feb 3 00:46:29 2007 +0000 Increasing some field sizes to avoid truncation. commit 97ae82ed036791358531355f6054fcc6e68bac1c Author: kuhn Date: Sat Feb 3 00:22:51 2007 +0000 added totalling when more than one table. thanks, brooke commit ce8b567fa73b7e82557d164592138f030e4765c0 Author: baertsch Date: Sat Feb 3 00:19:48 2007 +0000 remove redundant name that I just added commit ec90ed330dc887a483ebb38aea37ee2f5fd7b0ca Author: baertsch Date: Sat Feb 3 00:06:48 2007 +0000 add length to sequence display commit bfa2fff273d8ddf5c8dd3db07e6104da35c58584 Author: kent Date: Sat Feb 3 00:06:16 2007 +0000 Decribing how to build new version of uniProt. commit 4d279686893cceea62bde981e7f3422c884829bf Author: baertsch Date: Fri Feb 2 23:47:21 2007 +0000 add length to protein comment commit 45d3918e9b79554001f00cf77c1e8165dce9b93d Author: hiram Date: Fri Feb 2 23:16:46 2007 +0000 Better comment about MACHTYPE commit 8ad07ff2b0d22303c3811d7ecb7019abd4d4260d Author: kent Date: Fri Feb 2 22:53:09 2007 +0000 Downgrading a diagnostic fprintf(stderr to a verbose(2 commit d45a445121e45fb83a37db604967b0dbb31f9133 Author: kent Date: Fri Feb 2 22:52:44 2007 +0000 fixing index on pathogenHost commit 9c4c3e78f40c2409d8286114bb08c89a5e1c7b42 Author: kent Date: Fri Feb 2 22:47:19 2007 +0000 Swapped order of definitions so that main altGraphX appears first. This might help Angie's script cope. commit a85ae5b173fdb4bd03e8961c44767fcb543eb172 Author: kent Date: Fri Feb 2 22:22:42 2007 +0000 Null terminating year explicitly to cope with a date format change. commit 589a1387937856c61507db659c9c9ad8e0f8b37f Author: kent Date: Fri Feb 2 22:15:28 2007 +0000 Coping with changes in ID line that indicate curation. Tested to make sure it's backwards compatible. Also explicitly closing tab-files so they will report errors like disk full more reliably. commit 6401492e48bfe001010f6ee2c16f2b48f1e111dd Author: kuhn Date: Fri Feb 2 21:50:58 2007 +0000 formatting only commit bd061e398d3f6b6d2433f26a0c25f4733a1d3de7 Author: kent Date: Fri Feb 2 21:45:13 2007 +0000 Coping with date line format changes. Adding pathogenHost (OH line). commit 1c3d364342b21aa41b739584b49e8fd29ef1b2e5 Author: kent Date: Fri Feb 2 20:42:03 2007 +0000 Updating expected results. commit 5a2888c83a395dc18939eeba33328162ba533c7c Author: kent Date: Fri Feb 2 20:21:06 2007 +0000 Adding some experimental tracks for the KGIII project to the X group. commit 80f51bff4704cc92f6d4723db1ec55e86eb0ae63 Author: kent Date: Fri Feb 2 19:49:19 2007 +0000 Making it so altGraphX tracks can pack. commit d9f50fdac599d225b020a10c53b7fa11343d14fc Author: hiram Date: Fri Feb 2 19:24:18 2007 +0000 Add chainHg18WM and netHg18WM for Window Masker chain and net experiment commit edcd455879a3262b1ca82f8fbbbb2fc24bf5a756 Author: hiram Date: Fri Feb 2 19:23:41 2007 +0000 Add chainMm8WM and netMm8WM for Window Masker chain and nets commit a52b935f15e6d3551870258084bb2edc3787dc26 Author: hiram Date: Fri Feb 2 19:20:11 2007 +0000 Finished with chain/net mm8/hg18 with windowmasker repeat sequence commit 4a20f535aa5c8f9d20755a2b243b92d94865377f Author: kuhn Date: Fri Feb 2 16:41:29 2007 +0000 changed archive link to point to the correct archive (genome) but disabled it until there are archived items to look for. Also added search form (also disabled for now) for the archives. commit c81bb6ef856e1f345f8ed87b7c6f74225f87a196 Author: galt Date: Fri Feb 2 16:00:30 2007 +0000 "Encode release log update" commit 51d22d9aa901a925bcf7e8e2323c3b6074b5429b Author: galt Date: Fri Feb 2 16:00:16 2007 +0000 "Release log update" commit 500fe6dabfceeb477a6fd30c4331418b3d8b2110 Author: heather Date: Fri Feb 2 01:47:05 2007 +0000 cleanup previous hapmap commit commit 7aa6e658399032dac5f3facf12d16106825a616e Author: kuhn Date: Fri Feb 2 01:39:30 2007 +0000 formatting only commit fbef017f21db5d3c23f006e5e7d214185d5b9a7c Author: heather Date: Fri Feb 2 01:37:51 2007 +0000 improve hapmap display (use a table, include percentage) commit 2a8141caa211e49b261b17e6ac4568de6ac576bf Author: kuhn Date: Fri Feb 2 01:35:30 2007 +0000 mods to bottom sections commit 8553aaa44a3a243c0179479e830288bba13076f7 Author: kuhn Date: Fri Feb 2 01:31:43 2007 +0000 mods to "Displaying Data in Genome Graphs" section commit 11a360e38854e4d8b3185fe1c00299b6ddaded4c Author: heather Date: Fri Feb 2 00:38:41 2007 +0000 adding combined table to hapmap track commit 493ab7bb21c3fc2118834db11053b5da5686a6e9 Author: heather Date: Fri Feb 2 00:38:16 2007 +0000 adding code for combined hapmap table commit aa20466b6d5e854aad52c97df9f297c1e64e811a Author: heather Date: Fri Feb 2 00:37:27 2007 +0000 extending for combined table commit c6b4cd198f0c8c308abee7f753071646e228174f Author: heather Date: Fri Feb 2 00:31:36 2007 +0000 summary over all populations commit f6735219944d1d3d8fbd6d12af2b30b63e9f0151 Author: heather Date: Fri Feb 2 00:30:54 2007 +0000 add hapmapAllelesCombined commit 9a301081198b982e5413ef592cf280d63621f276 Author: kuhn Date: Thu Feb 1 23:51:43 2007 +0000 edits commit 0bf308badb536787acfab3bf9de2c2fece92ba7a Author: kuhn Date: Thu Feb 1 23:31:41 2007 +0000 grammar tweak commit 649b96a07aee14fcc01ab9763c9c8c5dbdf44e8f Author: ann Date: Thu Feb 1 23:07:13 2007 +0000 small fixes commit f1eedad3828a145bb8cf3bdafc03228269fce1ba Author: ann Date: Thu Feb 1 21:35:15 2007 +0000 typos commit fcad404114b32c24a8d21e7c09e235fc497c8c24 Author: ann Date: Thu Feb 1 21:23:19 2007 +0000 correlation coefficient commit d885a2e6cbab1c7f2ffb9543412c0046e59fc1fa Author: ann Date: Thu Feb 1 21:09:45 2007 +0000 deleting data commit 9b787f82a2fff37a8344d242b7e3baa0910abd6a Author: ann Date: Thu Feb 1 20:47:38 2007 +0000 data regions, Genome Browser, Gene Sorter commit 290b522f893d4269b69e443eb310ebea62ece328 Author: hiram Date: Thu Feb 1 20:15:44 2007 +0000 Add GENEID Genes commit 8b596310ec4c0c78e797c85b640890f062c0d789 Author: kent Date: Thu Feb 1 19:36:09 2007 +0000 Removing unused parameter. commit 2d24c0342f822752faf80ec0188e925ba1b36942 Author: kent Date: Thu Feb 1 19:31:40 2007 +0000 Patching memory leak. commit f816d37dbbcf590297be2c853bdd4d2e7ce87117 Author: kent Date: Thu Feb 1 19:15:36 2007 +0000 Fixing minus strand problem. Removing unused source files. commit 28b3243dd27ff5f2b536902efecce53ed8196388 Author: kent Date: Thu Feb 1 19:14:56 2007 +0000 Adding test target. commit aa32e22adc1a2e0a668d91d43fba5a1e6f8efd25 Author: ann Date: Thu Feb 1 16:22:47 2007 +0000 region padding and configuring individual graphs commit 285c64ace92361dad0919f92e5c3a92860666036 Author: galt Date: Thu Feb 1 16:00:31 2007 +0000 "Encode release log update" commit 24e089745d7a093961e1fd619d2cd73c09f5d37e Author: galt Date: Thu Feb 1 16:00:17 2007 +0000 "Release log update" commit a91a0cc3a33be9af3de4e7646eaa1561c0a8a76e Author: baertsch Date: Thu Feb 1 04:38:04 2007 +0000 minor bug fix if filter not specified commit 3eae1a53b298023cfb7dab4c264773b849678096 Author: heather Date: Thu Feb 1 00:45:08 2007 +0000 first draft for hapmap snps commit 8568917262bb8f0dca665d5d3a564d9c52d100ae Author: kate Date: Thu Feb 1 00:43:16 2007 +0000 Fixes to GTF processing in custom tracks (files w/o exon features were being processed to invalid BED12 so CGI's rejected them. GTF now has it's own recognizer.) commit 233b16c3433972aaa273bc060f36e0a90aa4e86b Author: kuhn Date: Thu Feb 1 00:35:21 2007 +0000 minor cleanup commit 83fa017345a4f70ed28b175c6f93acf124e8b667 Author: kuhn Date: Thu Feb 1 00:34:03 2007 +0000 removed dependency of checkTrackUiLinks.csh on qateam non-password RR access by making wgetTableField.csh commit 1c6b8553e980f109b8b30b0d461bd7911be3ec22 Author: ann Date: Wed Jan 31 23:14:40 2007 +0000 fix typos commit a7ad1016aca7c8945a30a2efd6f84ab0cae751b3 Author: ann Date: Wed Jan 31 23:06:41 2007 +0000 removed Quick Start, added Configuring and Significance Threshold commit d4fff26262aa7b16fd4b7cca6eecdac40bdc2382 Author: heather Date: Wed Jan 31 21:28:40 2007 +0000 raise everything up a level but avoid (red) overflow commit 9f5152ebc12b03de17f0193878ae0ed111376594 Author: kate Date: Wed Jan 31 20:00:53 2007 +0000 Add protection against corrupted custom track trash file commit 2b3d9e78fa0587c92129fad9f36df041ee7d5cd2 Author: hiram Date: Wed Jan 31 19:33:29 2007 +0000 Done with fr2 blastz chain/net commit a78635311dca6b6cd662a688d60b21f976ab2788 Author: hiram Date: Wed Jan 31 19:31:57 2007 +0000 Create WindowMasked sequence commit d13ba14a30e49532eefb0b5b353c3573e85473f1 Author: hiram Date: Wed Jan 31 19:31:33 2007 +0000 Testing mm8 blastz with WindowMasked sequence commit 8e7695923c34c769a06f76208d8bd85cc72fbd76 Author: hiram Date: Wed Jan 31 19:30:51 2007 +0000 tetNig blastz swap done commit f6c9e344761ed29c354b61527bb8b80023ea59c3 Author: hiram Date: Wed Jan 31 19:23:14 2007 +0000 blastz chain net to fr2 - without chrUn's commit 1d1dbdb6aadca65fb0c779753f60ba8439314c57 Author: heather Date: Wed Jan 31 18:51:00 2007 +0000 change to composite track for hapmap commit 1afc96b72154c8cc5f6da390c41246717ed9de11 Author: heather Date: Wed Jan 31 18:49:22 2007 +0000 reworked to use composite track commit e65a681b72fa774298537b6da8a5a799b8464453 Author: heather Date: Wed Jan 31 18:47:55 2007 +0000 biallelic counts for one population commit 1a3ece03758da9bcc7f21074647402c382916ab2 Author: heather Date: Wed Jan 31 18:47:13 2007 +0000 change to just one population commit 7deda048cb523aca1e966324b020bb908e625ea6 Author: kent Date: Wed Jan 31 17:29:42 2007 +0000 Adding rangeTreeNew. commit be2c08b5cbe622c324ddb1d4c269a6ef4bbbae31 Author: kent Date: Wed Jan 31 17:29:09 2007 +0000 Adding pslCmpTargetAndStrand. commit 194f746dd4a37dcf4dd28d0dc867b2433fb1b0ae Author: giardine Date: Wed Jan 31 16:26:15 2007 +0000 Updated choices for phenotype-association and changed defaults for coloring of track. commit dcbc8e75edc8f9eb646fa71336ec57c25ea0270b Author: giardine Date: Wed Jan 31 16:19:28 2007 +0000 Reloaded gv* tables for Locus Variants tracks. With updates on current data and new data sources. Also updated attributes to reflect change in phenotype-association handling. commit 42eda5811cdd485144d66c79f1a41d1b72cf90ce Author: kent Date: Wed Jan 31 08:05:37 2007 +0000 Doing local clustering rather than going through geneGraph. It's pretty simple, but isn't working on the minus strand right yet. commit ab37d4b3f41e884ec8b62a727dea145ca3d8dff1 Author: mario Date: Tue Jan 30 23:56:54 2007 +0000 Added description for creating the AUGUSTUS ab initio track. commit 4669b02e22a91fbc7aea08f244276bc82da9e1b0 Author: mario Date: Tue Jan 30 23:48:40 2007 +0000 Added description for creating AUGUSTUS ab initio track. commit 82248ff51401223186fd650267f37c54d54d62e6 Author: mario Date: Tue Jan 30 23:41:23 2007 +0000 Added description for creating the AUGUSTUS ab initio track. commit 81a5be0c803e8e87c7651238726459113d475b6c Author: mario Date: Tue Jan 30 22:47:58 2007 +0000 removed augustusAbinitio.html aver renaming it to augustus.html commit 8507acbcf08894a8de75076c3288a3d6ba00e100 Author: kuhn Date: Tue Jan 30 22:47:30 2007 +0000 cosmetic commit 78d8cbee50956a2e2aa5be9cc6e08f277e00d9ff Author: mario Date: Tue Jan 30 22:46:50 2007 +0000 Shortened the shortLabel of the ab initio AUGUSTUS track and renamed the track name. commit d5f8302bc5716ebd50d9f0dae6c34a1591c926b7 Author: fanhsu Date: Tue Jan 30 22:42:41 2007 +0000 Created makefile for gsid subdirectory. commit 0d82a2ef2b5f7ece2b7f9daa377fe22aa8bf11d4 Author: mario Date: Tue Jan 30 22:41:45 2007 +0000 Made shortLabel shorter so the html table looks nice. commit 280ac5184e80c859541be2df7f891c7e5ed433d0 Author: fanhsu Date: Tue Jan 30 22:36:29 2007 +0000 Added hgNotYet into makefile. commit aecf8e27faf9f416d0bd989fa73e79cc4434049f Author: mario Date: Tue Jan 30 22:31:26 2007 +0000 Added a new track with ab initio predictions of AUGUSTUS for mm8. commit 3abb27eb9f4337e0e9aa781c2e0f26e5ae7abc56 Author: fanhsu Date: Tue Jan 30 22:30:56 2007 +0000 Updated some wording to make it more universal. commit 77aec0ffa4d38dad4f95dfe36c84878853864f78 Author: mario Date: Tue Jan 30 22:28:14 2007 +0000 Created a new track with ab initio predictions of AUGUSTUS for panTro2. commit cb98d132b49faa97d443b95e7b53f41589d4ab6a Author: mario Date: Tue Jan 30 22:25:06 2007 +0000 Created a new track with ab initio predictions of AUGUTUS for felCat2. commit 6e8f58df89db9b0d9dc40f5b8b39785d6aa5fe5d Author: baertsch Date: Tue Jan 30 21:43:20 2007 +0000 fix missing end of optionSpecs, incorrect usage and remove unused variables commit 63244e396bc3b3f42f63e57ea3589a154e08b4e8 Author: baertsch Date: Tue Jan 30 21:41:54 2007 +0000 fix missing end of optionSpecs and incorrect usage. Added verbose message. commit c5fa65c06a416600ab12c73264210114681a8a5d Author: galt Date: Tue Jan 30 21:11:05 2007 +0000 fixed order dependency for members.o commit e5effb07a1617c5c7eca1f5d8c84c2cb4e3e8436 Author: kate Date: Tue Jan 30 20:13:03 2007 +0000 Jan07 Yale Chip/chip data submission commit e72949613b2c825d88d5dc09a73bcd5cf5953825 Author: baertsch Date: Tue Jan 30 19:55:51 2007 +0000 fix bug with passthru option - psl was reversed. also -scoreFile option is no longer required. commit 71fa2e8c7401c1534344574095a563e0bee94ef7 Author: kent Date: Tue Jan 30 19:49:42 2007 +0000 More work on next cut of exonWalk. commit 53b4c32751bea9d4abe7e8ed8ba65fc7c48f0245 Author: kent Date: Tue Jan 30 19:47:22 2007 +0000 Outputting a multi-exon bed format, with rna list at end. commit 891600b84b2ef79010079038c786d3b999aaeb26 Author: kent Date: Tue Jan 30 19:45:33 2007 +0000 Adding a few public functions to the geneGraph header. commit d3cbd130caf6e75ffe43df60bc5595dd35f43015 Author: kate Date: Tue Jan 30 19:43:46 2007 +0000 Provide filename in error message commit 99406802039e052434a9778504f5e4b1a0ba626f Author: giardine Date: Tue Jan 30 19:43:09 2007 +0000 Added missing tag commit 4479546f74c5be2c823b18b1bd88b1fc1dcfec3e Author: giardine Date: Tue Jan 30 19:40:55 2007 +0000 Fixed missing tag and made capitilization consistant commit 47668d6f2a0ead382c32e515319222a73271ec09 Author: kent Date: Tue Jan 30 19:26:50 2007 +0000 Adding rangeTree, an alternative to bitmaps for tracking non-overlapping intervals. commit d83e74d529c9ec3af0273d70597e9c5af2f2105b Author: braney Date: Tue Jan 30 17:00:27 2007 +0000 add Human (hg18) Proteins commit 9eaf5b64e3f3dc21ab8c39b0ebde40fdb3dab6f5 Author: hartera Date: Tue Jan 30 16:42:35 2007 +0000 Use our own updated version of tcl. commit e08d19b12eb3d615232dc7a47732fde9729494c5 Author: markd Date: Tue Jan 30 16:00:22 2007 +0000 added ignore entry commit 05ee099a3d42332a0888438d3ebd679986fc9c7e Author: galt Date: Tue Jan 30 16:00:09 2007 +0000 "Encode release log update" commit e66edea58af5f88274b8410750ba24d2a83ff336 Author: galt Date: Tue Jan 30 16:00:07 2007 +0000 "Release log update" commit d6049d3e131d3a551dad463c119eae7656e9290c Author: markd Date: Tue Jan 30 08:12:56 2007 +0000 use our own copy of tcl commit fd647c0f91cb77729174e8fa633a62bf0b6b2359 Author: heather Date: Tue Jan 30 06:10:56 2007 +0000 transform all rows in genotype data to 12 columns commit 817cab7d1931df39a37d1c557df8257ed10d20f0 Author: heather Date: Tue Jan 30 06:10:20 2007 +0000 add hapmapMonomorphic commit 918173bd3d1bddb863a126b8f305f51a1db7f43a Author: hartera Date: Tue Jan 30 05:23:52 2007 +0000 "New version number v151" commit 67e44703b799c7d53944c53b93733f53c9696149 Author: ann Date: Tue Jan 30 01:08:42 2007 +0000 added format and upload instructions commit eb73bbe76047811e8c718c30a2c5ac42a0d2ad22 Author: aamp Date: Tue Jan 30 00:05:40 2007 +0000 A couple library modules for CGAP SAGE tracks. commit 4fc78b7ee794c0debfd045a49e8ba615854e608a Author: aamp Date: Mon Jan 29 23:57:36 2007 +0000 Added utility for building CGAP SAGE track. commit 3df352e467c62b1b6ce884dd29d7b9d8fe7e0a31 Author: kate Date: Mon Jan 29 22:52:06 2007 +0000 Update links to data on Affy site, by request of Hari_tammana@affymetrix.com. Previous links pointed to old data commit 6c21fe5fc826bc65aee05e654d548bca37aad91e Author: hiram Date: Mon Jan 29 22:21:10 2007 +0000 Running WindowMasker for mm8 commit 08fb886374ea580952c6b91f9b0ded3928088faf Author: kate Date: Mon Jan 29 22:14:06 2007 +0000 Remove obsolete and nonsensical itemRGB info commit 27e1ddacc2b4a1cce85829bd8b4ebd86bafd59b5 Author: kuhn Date: Mon Jan 29 20:25:43 2007 +0000 added ALT tages to IMG tags commit 7a59f7e8ccbb47302a4bc6d68c4be60f21bfe89d Author: kuhn Date: Mon Jan 29 20:21:24 2007 +0000 reversed alpha and beta to get it right for gvPos commit f001704ce4e27d9118150a6519be083f3dc67825 Author: kuhn Date: Mon Jan 29 19:56:49 2007 +0000 added an ALT tag to get rid of broke-image logo if image not found commit 5d2618b74a012855f3741e2c11e4019734153856 Author: braney Date: Mon Jan 29 19:55:13 2007 +0000 added Human (hg18) proteins commit 61e62bec6a1cfa14041d0b9aa1e6fb31f1bfa8db Author: giardine Date: Mon Jan 29 19:42:04 2007 +0000 Added links for logos, changed phentype-association options, and order of colors descriptions to reflect new default. commit 484de37f2362a12404221e65ebc16d3eae41b367 Author: giardine Date: Mon Jan 29 19:40:23 2007 +0000 added links and target for links commit a81590802459ecebda15237b27ff47f05970ebb0 Author: kuhn Date: Mon Jan 29 19:10:05 2007 +0000 added old version to keep beta and RR happy til new code goes out commit 8d72bc35c2901fa63c3da3e17fb0ec2cb8566bea Author: hiram Date: Mon Jan 29 18:39:56 2007 +0000 fr2 chain/net done commit 22c2fd1d7fd41d496654477dfff95416eb62508d Author: hiram Date: Mon Jan 29 18:39:33 2007 +0000 blat servers and hg18 chain/net done commit 7e05a0d7637750f2e1a753fac51421b0df5fb990 Author: ann Date: Mon Jan 29 17:14:46 2007 +0000 Genome Graphs Users Guide - initial stub. commit 9e5567d8ab63a2296d32cf95960774f4c185c43b Author: ann Date: Mon Jan 29 17:11:12 2007 +0000 Added section for Genome Graphs. commit 7a118a75639199ef32c35e8576324e7da5728cb4 Author: kuhn Date: Mon Jan 29 17:10:58 2007 +0000 fixed typo commit b564d20abb3a94616f991773e787d84c39a4e98b Author: ann Date: Mon Jan 29 17:10:44 2007 +0000 Bumped cat news off home page to here. commit ae338689f44cb2debb4dfb5ba4e45e595ce5c487 Author: ann Date: Mon Jan 29 17:09:45 2007 +0000 Added news about Genome Graphs release. Bumped news about cat release. commit 48a8fc3181cfa25d5eef61b933b8f987ad24cc52 Author: galt Date: Mon Jan 29 16:00:05 2007 +0000 "Encode release log update" commit 3e7547012c6e250d0500d2b8c6f90598189185a6 Author: galt Date: Mon Jan 29 16:00:04 2007 +0000 "Release log update" commit 34fb332a09bd8cd0304310df9b94f45ccc163cbb Author: braney Date: Sun Jan 28 16:18:18 2007 +0000 add human proteins track commit a59f20b6d2320d33d79b5a751bb06aac818f5008 Author: galt Date: Sun Jan 28 16:00:22 2007 +0000 "Encode release log update" commit 395053369f8a7090a2d4ae0fa6bd2b033eb1723b Author: galt Date: Sun Jan 28 16:00:12 2007 +0000 "Release log update" commit 6565bb087113809c8258c0192cd7bf526b25d76b Author: braney Date: Sat Jan 27 19:21:10 2007 +0000 add Human (hg18) Proteins track commit ce7a80edff3c7229c0c791741f4767e9868d5436 Author: galt Date: Sat Jan 27 16:00:26 2007 +0000 "Encode release log update" commit 46fc47557a5e63985367710e34097bfed11834dd Author: galt Date: Sat Jan 27 16:00:15 2007 +0000 "Release log update" commit 405fd19940a822a2b08ac097e819aa2d9e6af005 Author: heather Date: Sat Jan 27 14:59:38 2007 +0000 basic function header commit 0808458faf2a2cc2d0d477d10724e0dcba2a6c18 Author: markd Date: Sat Jan 27 08:29:52 2007 +0000 added ignore entries commit 76995b26070cd5568ddeefff0dbe2b5d53fa5de9 Author: markd Date: Sat Jan 27 05:18:25 2007 +0000 added function to free hash with values using free callback commit 75ef936c000e2b6a308817ddc24d82da604587eb Author: kent Date: Sat Jan 27 04:15:18 2007 +0000 Starting to work. commit e96e638ddb3ef668dd51d8212305e03381e1bed3 Author: galt Date: Sat Jan 27 02:43:46 2007 +0000 added ability to allow expired accounts to re-activate by paying again by going to see account info, then the expired users paypal button is present. Also accounts for which the user had created a record earlier but either never pressed the paypal button or cancelled out, they too can now activate with the account info page commit 734d49f93eaf0b5583a9ecb9e3c63f3f959b14ff Author: galt Date: Sat Jan 27 02:09:10 2007 +0000 added login/account info pages commit 12dd4d4534f9a681c13602d400c94f7ecaa94900 Author: galt Date: Sat Jan 27 00:31:14 2007 +0000 added support for separate invoices table -- this helps support long-term use when expired memberships need renewing since previously using email as invoice# works only the first time commit 2364caf2ac8cdea25cd24f8f306d4a6934d2b9da Author: heather Date: Sat Jan 27 00:25:06 2007 +0000 remove debug statements commit 7af6aba23090cc10b3467048f09062aa29ec0d0c Author: heather Date: Sat Jan 27 00:11:59 2007 +0000 display just the latest hapmap track commit c666ffd1b90a23bbd78423bf3b200eb0da4feb54 Author: heather Date: Sat Jan 27 00:10:28 2007 +0000 basic description of hapmap allele data commit 7839bcc65a3abc5f0f1a70e06fbefe91454b9c7e Author: heather Date: Sat Jan 27 00:09:40 2007 +0000 new hapmap track commit 1abf9ef3fcd8032655c6fdb98fe171a7523b1f33 Author: heather Date: Sat Jan 27 00:08:48 2007 +0000 add hapmapTrack commit 08d3aa0c5fdae6a9f5afd77860bd02d311a51d40 Author: heather Date: Sat Jan 27 00:08:25 2007 +0000 custom display for hapmap population data commit 3aeff9a34408185fb7692e8a4f8586dc6dd2d08d Author: heather Date: Fri Jan 26 23:52:38 2007 +0000 hopefully stable format for hapmap SNPs commit 81d016376fae0831af7687335e0dea90e22a020e Author: heather Date: Fri Jan 26 23:51:09 2007 +0000 add hapmapAlleles commit ed2f0c82fbab750a2969b58c223eef1686160347 Author: kuhn Date: Fri Jan 26 23:24:03 2007 +0000 added images back per jim commit 3e758252f71b952d513d27a2e73477072e94411b Author: kuhn Date: Fri Jan 26 22:51:05 2007 +0000 logos for gvPos track commit efbe5f2de00abcdb64fe59457df18d141c6988a2 Author: rhead Date: Fri Jan 26 22:37:04 2007 +0000 Added notes about finding primary table names by mouseover and about not being able to display subtracks commit 6892de422e9155dfd74b9073daeed7a6772a4f99 Author: galt Date: Fri Jan 26 21:36:21 2007 +0000 added support for expires; made customized signed encrypted buttons; made https secure callback to paypal for ipn verification commit 0c75de0f0d837833c8f7ba905cb9febaa90c5e43 Author: braney Date: Fri Jan 26 19:46:37 2007 +0000 added scoreMin and scoreMax commit f10ead2ff46dea58b65de4984f9622f8c21973ef Author: kayla Date: Fri Jan 26 19:39:34 2007 +0000 Removed hot-linked images per B0b commit fe13b99266987fa5f69c00693479307ed15acaa0 Author: kate Date: Fri Jan 26 19:19:51 2007 +0000 Initial fix for score filter in custom tracks (non-db implementation) commit fdb52cb48c41a39956d0063aaa069380497075d5 Author: braney Date: Fri Jan 26 18:48:35 2007 +0000 added a Human (hg18) Proteins track commit f62d01830f6274b57885877b9b13df87ab5b5cdb Author: heather Date: Fri Jan 26 17:43:37 2007 +0000 tweaks commit 83cbc1c9e77285da9e9d69359b00bcd02f077c89 Author: braney Date: Fri Jan 26 16:29:29 2007 +0000 add Human (hg18) Proteins track commit 63919d9927db89286adc49db3a7c4c8724de3820 Author: braney Date: Fri Jan 26 16:26:32 2007 +0000 fix DONE date commit 54dbadc71560d2ca05864c0934188a4e59b5ee3b Author: galt Date: Fri Jan 26 16:00:30 2007 +0000 "Encode release log update" commit ad48bf3ea2027dd75bf0575be99ddb016c494d25 Author: galt Date: Fri Jan 26 16:00:17 2007 +0000 "Release log update" commit 57d22a71e7dabf94a6b4d154f7482f23135c314b Author: markd Date: Fri Jan 26 05:28:27 2007 +0000 prefix generated C definitions for set and enum columns with struct name to prevent name space collision. Use safecpy for copying fixed length strings commit 5135e7d008b11f7411410cce51d8d60b0d6f0404 Author: kent Date: Fri Jan 26 04:58:35 2007 +0000 Ensuring that altSplice is called on a single chromosome. Making ESTs optional. Putting in an option to allow single-exon genes. commit 1beefa64b62cf0f5034764d080d850c73c389813 Author: kent Date: Fri Jan 26 01:53:47 2007 +0000 Switching to type instead of track name to detect altGraphX tracks. commit dc2f14a37f16f6ef5ea2cbc4bcc915cef34c0ead Author: kent Date: Fri Jan 26 01:47:24 2007 +0000 Changing altGraphX tracks from type bed 3 to type altGraphX. commit 3d94eae6d5a6d34890f909a1516910eb82f8fc0a Author: kent Date: Fri Jan 26 01:46:53 2007 +0000 Adding altGraphX type, so don't have to do so many registerTrackHandlers() on oltGraphXMethods commit f1f95ddb6baa92d91a546c493bc5c7b378b8e01f Author: ann Date: Fri Jan 26 01:39:38 2007 +0000 small grammar tweaks commit 9f2c2ec9f860895317fdbccb258db7b78c2b6dea Author: kuhn Date: Fri Jan 26 01:19:28 2007 +0000 added utility to quickly get size of tables commit 0a8f43b92d48fbf2f18c860e5ade9f5ef847c66d Author: kuhn Date: Fri Jan 26 01:17:47 2007 +0000 removed need to write a file commit 47b7192cebac5257355e740d761584275f461725 Author: kate Date: Fri Jan 26 01:02:50 2007 +0000 Correct skip over file header in PSL loader commit e3dd2d9cbe3ca33ed86ccc1e9f44404c1fd33f5a Author: kent Date: Fri Jan 26 00:46:38 2007 +0000 Separating out missing data color from yellow better, and improving text about missing data on config page. commit 430b4139ecc63dba4c66ea5e6a57d8c102b1133f Author: kent Date: Fri Jan 26 00:45:56 2007 +0000 Shortening usage to avoid repeating what the previous section says about needing to upload data. commit ebca265fa70dc5a98a26e5fd458cb8e989264361 Author: kent Date: Fri Jan 26 00:35:13 2007 +0000 Making it so that by default first graph is blue. Missing data is hilight for first graph, not last. commit 8f396ca00f886bd27c8fcaa4dc1d05aebb7eba91 Author: kuhn Date: Thu Jan 25 22:44:24 2007 +0000 removed need to write a file commit fed9f32afff0fc0152de1124bf6321a2759201b2 Author: ann Date: Thu Jan 25 22:05:40 2007 +0000 added link to Genome Graphs User Guide commit 4daf162377198c3f7adc8bd35970086262964395 Author: kuhn Date: Thu Jan 25 20:52:43 2007 +0000 removed hard-coded hgw1 in gsid lookup commit a0d82b58b7596c9e36a347b99a3df3f527551642 Author: kuhn Date: Thu Jan 25 20:49:26 2007 +0000 slowed it down a little when hitting the RR commit c96c5ad2e479a4d147ff4e2f11a06c52218312b1 Author: rhead Date: Thu Jan 25 20:34:16 2007 +0000 turning off udpates on danRer1, as this is being archived commit 8fc19619269ab5c1f2e12abfa337780ca6c838e4 Author: kuhn Date: Thu Jan 25 20:17:43 2007 +0000 added utility for checking the links on details pages commit 7d1d585b6062a93a482a6b6e035f68ad92a465d3 Author: hartera Date: Thu Jan 25 18:16:06 2007 +0000 Added archive setting for Ensembl Genes track to fix broken links. The links will now go to Ensembl 31 (May 2005). commit 690671acd14bf48ad1d91ac1b0ab6ddf6957e6bc Author: braney Date: Thu Jan 25 17:56:34 2007 +0000 add human (hg18) proteins track commit deccb024808a1bb7ead5eff357173b0681d93f78 Author: galt Date: Thu Jan 25 16:00:31 2007 +0000 "Encode release log update" commit eedfad2d1ad608372b27d9fe27c6077193e98827 Author: galt Date: Thu Jan 25 16:00:17 2007 +0000 "Release log update" commit 7233690046e9e8d18b2adb942d763adb22a46279 Author: markd Date: Thu Jan 25 14:13:40 2007 +0000 added option to save information about what was changed commit 1d90fd49a0f31b394bf0a10f423642918a4fa141 Author: hartera Date: Thu Jan 25 06:02:49 2007 +0000 Added Ensembl Genes version number and the archive date for that version. commit cbd74800616e46533d1337995ac3e0ce15be1313 Author: hartera Date: Thu Jan 25 05:32:44 2007 +0000 Sometimes ensGtp has transcript ID with version number so use a more fuzzy match when querying with transcript ID without version number. commit 9dced6aef9c93d94b83ec09fcc5f19fdeb6803b9 Author: hartera Date: Thu Jan 25 01:18:36 2007 +0000 Removed url setting for ensGene as URLs are now constructed by hgc for this track. commit 3993f20ce97283fa3aa6e63b2461af5d54c673ce Author: heather Date: Thu Jan 25 01:17:31 2007 +0000 another piece of hapmap pipeline commit b283deb54765ae1d4e5f793633adfb9fa591e95c Author: heather Date: Thu Jan 25 01:17:05 2007 +0000 add hapmapCondense commit 5dd57587101aa4f4ad79a3024a67771b2ee6b8b4 Author: hiram Date: Thu Jan 25 00:16:19 2007 +0000 Starting fr2 blastz on hg18 and oryLat1 commit fbec74191560e73ecaf2e1569c7c10bface3ec88 Author: hartera Date: Thu Jan 25 00:08:08 2007 +0000 Removed url line for ensGene as not needed as now hgc constructs the Ensembl URLs. commit 96fbc3026c97db350d54ef36e3e5bafd37c5dbbd Author: hartera Date: Thu Jan 25 00:07:27 2007 +0000 Removed url lines for ensGene as not needed as now hgc constructs the Ensembl URLs using the ensArchive setting that was added. commit c2886d6ad5107fecc14fc2e6ac6a96a1a595fd00 Author: hartera Date: Thu Jan 25 00:06:11 2007 +0000 Removed url lines for ensGene as not needed as now hgc constructs the Ensembl URLs. commit a9d40fc1a7c4878c5cc45b77e15b390512cf81f6 Author: hartera Date: Thu Jan 25 00:03:53 2007 +0000 Removed urlName and url lines for ensGene as not needed as now hgc constructs the URL using the archive setting which is renamed as ensArchive. commit 8500df5485713425521c81b9b057c25a23fd1eab Author: hartera Date: Thu Jan 25 00:02:43 2007 +0000 Removed urlName and url lines for ensGene and ensGeneNonCoding as not needed as now hgc constructs the URL useing the archive setting which is renamed as ensArchive. commit db31550f6572a982e1323c95a64e679bb517863f Author: hartera Date: Thu Jan 25 00:02:09 2007 +0000 Removed urlName and url lines for ensGene as not needed as now hgc constructs the URL useing the archive setting which is renamed as ensArchive. commit 279d898d9759ccb100227ee9e80584ddab0ac920 Author: hartera Date: Wed Jan 24 23:59:59 2007 +0000 Removed urlName line for ensGene as not needed. commit c84232ae55ac919349ff193f5ea584160a587389 Author: hartera Date: Wed Jan 24 23:57:35 2007 +0000 Edited printEnsemblCustomUrl so that all Ensembl URLs are constructed in the code without using url settings in trackDb. Added code to use an ensArchive setting in trackDb to specify a particular Ensembl Archive version to be used for the URLs. commit cfe8ff1f6eba5eb31712f1bb650c4c520f164f7f Author: hiram Date: Wed Jan 24 23:56:37 2007 +0000 gasAcu1 chain/net swap, genbank run, ensembl genes added (protein_coding) only commit a6eecfabfa8e67c81df6efc10244eee3ae0515b0 Author: rhead Date: Wed Jan 24 23:54:28 2007 +0000 turning off danRer1 updates in preparation for archiving commit 2d0adf59a7a11a21fe2ea6433f69e8a0dbd74c2f Author: hiram Date: Wed Jan 24 23:53:03 2007 +0000 Done with fr2 blastz commit 3555b5fd1c45d8f2c34df2509fd9fef29fe6c6dc Author: hartera Date: Wed Jan 24 23:13:59 2007 +0000 Added urlName line to specify that the gene name should be used as the link and not the whole URL. Added archive date to be used to create URL for protein ID. commit a993873f11b2f5ba9df202d394aeeaea94f12016 Author: hartera Date: Wed Jan 24 23:10:42 2007 +0000 Removed Ensembl URL is now used by hgc but only works for human. Added urlName line to specify that the gene name should be used as the link and not the whole URL. commit a1d6d4a7e9eba037604d9b514beb3f2a4ed8f30a Author: hiram Date: Wed Jan 24 22:57:50 2007 +0000 Complete the ensGene URL reference change commit 5de77c1226284cbe959d651d7d30feaa1cf4f576 Author: hiram Date: Wed Jan 24 22:50:40 2007 +0000 Fixup ensGene external URL reference commit 3c6dd9a6fb86c4de42a60407d56b5129b029f454 Author: kent Date: Wed Jan 24 22:32:46 2007 +0000 Adding hgGenome commit acbd8d24a7141762095edf03ab0720c69a2a43c4 Author: fanhsu Date: Wed Jan 24 20:48:37 2007 +0000 Updated ncRna track name. commit 1c307df0ffda7786e7d7095aa7b5a21cd62e4c52 Author: hiram Date: Wed Jan 24 20:03:51 2007 +0000 Adding fr2 commit 36052073dc20eea51d615ec3257de60189be72d4 Author: galt Date: Wed Jan 24 19:54:33 2007 +0000 Re-added some stuff to discourage caching of CGI-generated pages (without unintended re-direct META command that came from cartReset which does need it). commit f36a3ff88a37ff6e6333654e0b154be823fdb97a Author: hiram Date: Wed Jan 24 19:18:32 2007 +0000 Adjust fr2 chain and net priority commit c1dc22ee0ed2f182732a299905ba3c288a3a2775 Author: kuhn Date: Wed Jan 24 19:16:14 2007 +0000 added new group ARCHIVE_DBS and moved rheMac1 into it. this prevents trackDb and hgFindSpec from being made on beta commit 2e25cc14a5e7f8b05c9e88c657e73a570f12bd57 Author: hiram Date: Wed Jan 24 19:15:31 2007 +0000 Adding chain and net for Fr2 commit 4f2e651cc759db367298db4e90c25b01f2121842 Author: hiram Date: Wed Jan 24 19:15:00 2007 +0000 Adding chain and net Fr2 commit 5c0c5a16d049a078c2dd3cdd54029473074e828a Author: fanhsu Date: Wed Jan 24 18:28:30 2007 +0000 Minor style update per Jim's suggestion. commit d2baff04b345cfec718ab5fa37bbd62b73177de2 Author: heather Date: Wed Jan 24 18:25:29 2007 +0000 fix typo commit 624f0fe82086911a8c52d92236b3e229c4256768 Author: fanhsu Date: Wed Jan 24 18:09:46 2007 +0000 Back out the change of 3 lines, which seems to causing a strange problem. commit 4e4a56d1ca064dd044820b74977eac5b03147668 Author: galt Date: Wed Jan 24 16:00:31 2007 +0000 "Encode release log update" commit eb8f8742c80ba3ac74068f7e2d23d9171b188bd3 Author: galt Date: Wed Jan 24 16:00:17 2007 +0000 "Release log update" commit 2abb91752943ab4055bf905eec85a1e28d2a876a Author: markd Date: Wed Jan 24 06:30:29 2007 +0000 genbank entry organsim change commit 5175c1caffd49c5f9a667a3be4d2b11918a71c6a Author: kent Date: Wed Jan 24 04:38:36 2007 +0000 Added some stuff to discourage caching of CGI-generated pages. commit 7ca3d2ba45d6dc8f76ff6a688528038fcbec7197 Author: hartera Date: Wed Jan 24 04:32:23 2007 +0000 Added rhMapInfo.o. commit a84f39a9e3f467143e63f34f23acfa73ff07a4cf Author: hartera Date: Wed Jan 24 04:24:25 2007 +0000 Finished Radiation Hybrid map track and added ZFIN IDs to the rhMapInfo table. commit ff902c3c679592edd1e22687554a5c996c6cf7b1 Author: hartera Date: Wed Jan 24 04:21:09 2007 +0000 Added a zfinId field for the ZFIN ID to the rhMapInfo definition. commit 614f1332b2d18dfa128bab5ee686bb9bd2d03560 Author: hartera Date: Wed Jan 24 04:20:38 2007 +0000 Added a zfinId field for the ZFIN ID and an index on the zfinId field. commit ce6932a712c0ab591c099c8746d4b38f4db2e63a Author: hartera Date: Wed Jan 24 04:18:51 2007 +0000 Added a zfinId field for the ZFIN ID. commit 377dd9a611eda20476c897b1c691945e72b79c14 Author: galt Date: Wed Jan 24 02:54:45 2007 +0000 making verify post slightly more secure by using https via the "bio" openssl routines commit 5bc118b6118842071829bcd9b3303ba339239b27 Author: kent Date: Wed Jan 24 01:25:57 2007 +0000 Avoiding error when min/max of chromGraph the same. commit 69109b7a3b40bef8e02a327d5ec383f8e7d340d3 Author: hiram Date: Wed Jan 24 01:00:54 2007 +0000 Add the oryLat1 danRer4 blastz sequence commit 7d2983ffefdcda6e81ba517c74705f8ca525b638 Author: hiram Date: Wed Jan 24 01:00:20 2007 +0000 Add note about what makeGenomeDb.pl creates commit 7fedec9635a2f191a8f6076a5e308899197cc9fc Author: hiram Date: Wed Jan 24 00:59:45 2007 +0000 Second day, completed masked fr2 sequence, started blastz to gasAcu1 commit ff229152decf00d382d751c0bf7bb6322f591cd5 Author: hartera Date: Wed Jan 24 00:20:40 2007 +0000 Added external URL for ZFIN IDs to rhMap track. commit fa731ba111b508d2969a0684a6199e9672b5783c Author: rhead Date: Wed Jan 24 00:13:28 2007 +0000 expanded credits section to match other net descriptions commit 73441a4ff8aac852ec3095ae37a306c24a09993c Author: rhead Date: Tue Jan 23 23:44:39 2007 +0000 added a little bit more information to references section (to be consistent with some others) commit 8bd08cd837f41d155e62a66ced3bd90f875043fb Author: rhead Date: Tue Jan 23 23:33:53 2007 +0000 added a period at end of refs commit 85c1616354b6f6417e2ad3e0ee33cd751278d81e Author: rhead Date: Tue Jan 23 23:17:35 2007 +0000 added a little bit more information to references section (to be consistent with some others) commit c235b645dd2bc12e553723f6c9008c3b1216d8d7 Author: kate Date: Tue Jan 23 22:06:00 2007 +0000 Assure that custom track file is updated when doc is changed commit d4f52b0ed8964692c87c5c7bdba5e67951bdf702 Author: rhead Date: Tue Jan 23 22:01:34 2007 +0000 added a little bit more information to references section (to be consistent with some others) commit 087000d266cdc8734599a2db6aa0e76527b95ccf Author: ann Date: Tue Jan 23 19:58:39 2007 +0000 clarifying edits commit 4c912dd042c6f3656789539ecb32a8f70f5317c5 Author: hiram Date: Tue Jan 23 19:56:35 2007 +0000 Add fr2 to the list of DBS to create commit 7e728dd7a4320b4a3299177f3ad3a76a179b1ee3 Author: hiram Date: Tue Jan 23 19:50:37 2007 +0000 Add description of the tables created with makeGenomeDb.pl commit 49ca145ab2ccbd326207d6aebee7b15243e8c671 Author: hiram Date: Tue Jan 23 19:33:36 2007 +0000 Cover Brians mistake - default vis on Atom track commit 610517be2e6ae14b58e9ec17473974ffe6f4d634 Author: rhead Date: Tue Jan 23 19:32:53 2007 +0000 added markd to cat credits commit 76389bfd1cbeded1d92d316dea21585e3ecb4a7b Author: giardine Date: Tue Jan 23 19:18:52 2007 +0000 Removed this file it has been replaced with the more general links.ra commit 4c2db7b5b2ed7675d0448f424cfa9a707e5d1a86 Author: heather Date: Tue Jan 23 19:15:24 2007 +0000 remove xenoRefGeneAnnotation commit e64311ad94610a189633c9f04a8d42c36d9ea397 Author: giardine Date: Tue Jan 23 19:14:42 2007 +0000 This explains the fields in the links.ra file commit d232c91c82ef8fc473efe9c506f0fb6a440cceee Author: hiram Date: Tue Jan 23 18:38:53 2007 +0000 trf masking done, fully masked 2bit file done. commit e69f873f3c93b7529a73bfb6e522ee09e106bfa4 Author: kent Date: Tue Jan 23 18:14:37 2007 +0000 Relaxing clipping by one pixel to accommadate very last value in chromsome in some cases. commit d2b59a7a3d1991bd51220f587885c043bd1169c2 Author: kent Date: Tue Jan 23 18:07:51 2007 +0000 Adding info on correlation page to help. commit 28c0ec7601553f34b9eb9fbdd310f43c60dc62a5 Author: kent Date: Tue Jan 23 18:04:33 2007 +0000 Decapitalizing 'Go To Gene Sorter' button. commit 8225762a769cd3a0c5c08e124294c92393356242 Author: hiram Date: Tue Jan 23 18:02:55 2007 +0000 Correct fr1 chainLink measurements commit a6a31372edb6729dfcc898aa6c1017e8828e7db6 Author: kent Date: Tue Jan 23 18:00:44 2007 +0000 Got rid of dangling 'though' in explanitory text when no built-in graphs available. commit db413fcf16a1cccac0aab84fecb894c66a684b4c Author: kent Date: Tue Jan 23 17:59:22 2007 +0000 Adding clipping to keep one chromosome's data from being displayed in another chromosome's area. Adding 'Using Genome Graphs' section to main page. commit 95d01f1d20abc16ee9b32da818d2e817b5b443ce Author: galt Date: Tue Jan 23 16:00:26 2007 +0000 "Encode release log update" commit 5267305c81f86c60fa467cf352b868965a9c1b86 Author: galt Date: Tue Jan 23 16:00:14 2007 +0000 "Release log update" commit 8e2a526fcee06c10beea020a22a1c89c7e3ff739 Author: galt Date: Tue Jan 23 06:38:12 2007 +0000 inital add of gsidMember cgi for managing GSID membership signup and paypal payments commit b7045a0df1aa81e854351664d6b63e1246a11136 Author: heather Date: Tue Jan 23 05:33:27 2007 +0000 logic improvements commit 147babe0c69db92dc0282c18383cf19f84661c48 Author: heather Date: Tue Jan 23 01:12:05 2007 +0000 compare hapmap data to dbSNP commit b8b5c948f57171267b2ceddebbc1128f8755405e Author: heather Date: Tue Jan 23 01:11:43 2007 +0000 internal consistency of hapmap data. Rough draft. Variables of interest: complex SNP, monomorphic, biallelic, missing populations commit 10e408d6c0cc6360dd8801d06652ac4ba803b770 Author: heather Date: Tue Jan 23 01:09:59 2007 +0000 add hapmapLookup and hapmapValidate commit c2e6b12d0653102258c458cecd6983a4b9c2f271 Author: rhead Date: Tue Jan 23 00:42:19 2007 +0000 changed downloads link to html commit 35c47d0baf59c5c026c84be2de69111da7e93544 Author: hiram Date: Tue Jan 23 00:42:17 2007 +0000 First day, got genome built, WindowMasker run, trf running commit 936e05c52d3d85cbf3b95ed8e8715732dc667461 Author: hiram Date: Tue Jan 23 00:41:12 2007 +0000 Indicate how windowmaskerSdust was loaded commit 80c97e659a9cb640c10b2c015d3c8078fce3acfc Author: kent Date: Tue Jan 23 00:35:13 2007 +0000 Adding missing word 'bases' to configure individual graph page. commit 4d358c7ac135b40b51e21cf0126b4890a3672218 Author: rhead Date: Mon Jan 22 23:44:09 2007 +0000 changed % sign to html code commit 5408f52a2b78a3754b5808313026be208867cac4 Author: fanhsu Date: Mon Jan 22 23:25:02 2007 +0000 Created hgNotYet.c. This is a simple dummy program putting out "...under construction ..." message. commit 53420394e21b5e60205eb4578a272eac75c2f268 Author: fanhsu Date: Mon Jan 22 23:24:05 2007 +0000 Created makefile. commit ab9d7cd1c68593d193a09596ddf1b3fb1ac5f88b Author: hiram Date: Mon Jan 22 22:45:23 2007 +0000 Initial set of files from makeGenomeDb.pl commit 44951594ab53bbe4a8a34f93c04612458b0e7be3 Author: giardine Date: Mon Jan 22 21:51:24 2007 +0000 Added logos for LSDBs where available. Also added new LSDB. commit 28bd8971e37040cc02314d328859b6e1e3986e91 Author: rhead Date: Mon Jan 22 19:36:14 2007 +0000 fixed punctuation commit ee124371cce6115ef991bc072d5abd04d287cd3d Author: rhead Date: Mon Jan 22 19:35:16 2007 +0000 Added announcement about felCat3 and abridged open helix announcement commit 09b5f815fdff72b580dd0a4a4164edd38c3d1ac6 Author: hiram Date: Mon Jan 22 19:30:38 2007 +0000 Add maxOutputSize to the argument processing commit 567374f9babdf41ff4a77baaf040d7d7ea0e0cb3 Author: kent Date: Mon Jan 22 17:54:06 2007 +0000 More work on new version of altSpliceX track. commit 79dff3b42ede0b9db782b2fab4f54738aec3a6bd Author: kent Date: Mon Jan 22 17:50:01 2007 +0000 Adding Genome Graphs link. commit b70afb6c239d7fc28cd76cdac1a9270693200d80 Author: galt Date: Mon Jan 22 16:00:19 2007 +0000 "Encode release log update" commit 0fde6a4c4420e5af3228915f7372649f449f9125 Author: galt Date: Mon Jan 22 16:00:11 2007 +0000 "Release log update" commit 8e34853719e2b719b0ef304be16b4e4c978f6a5d Author: giardine Date: Mon Jan 22 15:00:22 2007 +0000 Removed unused field from internal links commit ac9e95bdb413a12bf5e706e6d30e3edc72aa4df8 Author: giardine Date: Mon Jan 22 14:34:33 2007 +0000 Changed labels and removed unused subtracks from experimental wiggle track. commit cb3147a54af4a433ad6002d9d0a94a88f7ba9426 Author: hiram Date: Mon Jan 22 06:21:54 2007 +0000 Done with 5-way multiz commit f5519664af4dcb52f8af024738bbff9cb7a288f0 Author: hiram Date: Mon Jan 22 05:29:03 2007 +0000 Adding multiz5way track commit fced50c8f26ab1243c3b2033941b9f306f38381f Author: hiram Date: Mon Jan 22 04:32:10 2007 +0000 Adding 5-Way GIF for oryLat1 commit 9050bfab476166272b99feb51743b5fc30be7244 Author: baertsch Date: Sun Jan 21 23:27:23 2007 +0000 improve temp file handling commit ec9137e3c8e69b3ba04da257b2d6c6c7186bb979 Author: baertsch Date: Sun Jan 21 23:14:17 2007 +0000 add -maxOputputSize=N - Split file into multiple file if output exceeds N (default 2000000). commit 3610f3f06d11983e36df5fcb831b334570c417e8 Author: galt Date: Sun Jan 21 16:00:20 2007 +0000 "Encode release log update" commit 11365c1a5c82e67d138621cf7ac580fad6fed8a1 Author: galt Date: Sun Jan 21 16:00:11 2007 +0000 "Release log update" commit e2726809ff79aef3f3d1c67b8f1fffcde5f06e71 Author: markd Date: Sun Jan 21 15:48:31 2007 +0000 fixed broken code that I some how commintted commit 9a1d7fec61489f2872f0256b20637ae7398355a1 Author: markd Date: Sun Jan 21 04:20:59 2007 +0000 fixed problem with mgcFullMrna not being installed on mgc server commit 88cdbbe5bdf330f41f1ba7c00073b7705976c417 Author: baertsch Date: Sun Jan 21 01:17:19 2007 +0000 add 64 bit integer for offset commit 77d76d0bc52d173683601edeb88421a4e19f2e4c Author: baertsch Date: Sun Jan 21 00:53:46 2007 +0000 add lift file output commit 9f55d3332bec77e7fe5c1dfa89642e602350efd2 Author: baertsch Date: Sat Jan 20 23:28:52 2007 +0000 initial version commit 994afa8a76bbd1d660265938fafb873e2d11dc9e Author: braney Date: Sat Jan 20 22:53:55 2007 +0000 change name of track to Filtered Atom Maf commit 9a76b7eb7edd8a7cb19e89cb6e172e5e462b9c60 Author: braney Date: Sat Jan 20 22:44:04 2007 +0000 add atom maf track commit e32549d7c937ead9028e5730cc903d6b1d323e5d Author: galt Date: Sat Jan 20 16:00:26 2007 +0000 "Encode release log update" commit daf192850700dfe6aaf171164723568d1b7880b0 Author: galt Date: Sat Jan 20 16:00:13 2007 +0000 "Release log update" commit ad6099e32c70f88fd4af4776cbfee100d53bc7d7 Author: markd Date: Sat Jan 20 05:19:21 2007 +0000 include bin columns in orfeomeGenes and mgcGenes tables commit 95c92c550d2854e3fb681186d8d6dca4864a7a20 Author: markd Date: Sat Jan 20 04:53:26 2007 +0000 don't print link to IMAGE db if not in image commit e6299738ef077cff1531624908dc7af2f5d536a1 Author: genbank Date: Sat Jan 20 01:35:23 2007 +0000 check return of hFindSplitTable to generate a more useful error message commit 83078425e59201492004b01f0899e5567182632c Author: rhead Date: Fri Jan 19 23:47:32 2007 +0000 archived one news item; uncommented the 2007 links commit 8ad38c45f76094d461f87537e7598b0a8489f978 Author: heather Date: Fri Jan 19 23:34:52 2007 +0000 add comments, cleanup commit 80e53e9c6447066a4ce60ea9600d7c71f02f84a1 Author: rhead Date: Fri Jan 19 23:24:58 2007 +0000 moved cat above dog to be consistent with the order everywhere else commit 486fb626b5af4ab338788d48ab7f38c5fffff02f Author: heather Date: Fri Jan 19 23:18:06 2007 +0000 extension validation in it's own function commit 2fa52c2dff8342e0f8d367880aae664660e3de04 Author: rhead Date: Fri Jan 19 23:16:46 2007 +0000 changed f_catus anchors to cat commit 9954cc4e93abe7b21ea7d07c46c7746d496b9c05 Author: rhead Date: Fri Jan 19 23:04:11 2007 +0000 added Cat (felCat3) commit b9beabe36c248fa7620c45c21ca22039ae32ef50 Author: heather Date: Fri Jan 19 23:00:25 2007 +0000 add felCat3 commit 679d6b2294f78fa7834227c324f1485cfeee17b0 Author: kent Date: Fri Jan 19 22:38:34 2007 +0000 Working on an update of altGraphX track commit 9887b8d5d523ec24d30061533ebbb64128b917f1 Author: heather Date: Fri Jan 19 22:17:43 2007 +0000 input validation in it's own function commit 321b21ffc1786ffb397c78ee594e6cf8fba0536b Author: markd Date: Fri Jan 19 21:55:52 2007 +0000 fixed problem with orfeome sequence alingment using wrong psl track commit bd405c27d22bed3a35c183c269738b73027362b5 Author: rhead Date: Fri Jan 19 21:54:05 2007 +0000 added more assembly details stats and abbreviated total contig length commit 9cc7a33992d81a606857a239c4c66280d931bf9d Author: heather Date: Fri Jan 19 21:38:43 2007 +0000 reworking hapmap for files derived from genotype data commit ce4bee8268acef48917df9e376f554f87cb117b4 Author: heather Date: Fri Jan 19 21:37:59 2007 +0000 add hapmapGenotype commit f94eaf175364ba56ff4b3746767ad3a3f89d89ae Author: kent Date: Fri Jan 19 21:24:19 2007 +0000 Changed error on empty input to warning. commit bbb46747dcd34b4ba0fdd92a0f4c3bff3b600bf8 Author: rhead Date: Fri Jan 19 21:17:39 2007 +0000 corrected contig length after checking /cluster/data/felCat3/downloads/BasicStats.out commit 8fc8b630e1b851c96a766c690f559e69b0456ca6 Author: rhead Date: Fri Jan 19 21:13:29 2007 +0000 added links to Broad and Agencourt, added an example search for allergen, and added some stats in the assembly details section commit 47fb43be06dee7b08d1c038c2233058266e4f7d7 Author: genbank Date: Fri Jan 19 21:13:27 2007 +0000 fixed use of unitialized variable commit 97d5c985960fb7db772621e68412a55883286d70 Author: genbank Date: Fri Jan 19 21:13:09 2007 +0000 include orfeome code in top level build commit 031356ed59ba7a4793ed38e1becd79789056202b Author: fanhsu Date: Fri Jan 19 20:49:04 2007 +0000 Updated top bar again, now the style subdirectory is there. commit 341cc201fa98a101a263a779b8ef136506e67f4f Author: markd Date: Fri Jan 19 20:24:14 2007 +0000 added ORFeome tracks commit d447e5be66be0f486f39a19596b7550bf7799e4b Author: markd Date: Fri Jan 19 20:21:02 2007 +0000 change title on MGC browser to MGC/ORFeome browser commit 51d6f4754774006bd7951f09902a9132c62837b5 Author: kent Date: Fri Jan 19 20:20:19 2007 +0000 Adding in Chuck's altSplice dir to utilities to be made regularly. commit 3f375c57e9d307fb026a7696adcd9326f3684dec Author: kent Date: Fri Jan 19 20:18:59 2007 +0000 Adding a makefile that compiles Chuck's currently working alt-splicing programs - altSplice, exonWalk, and the borfMatcher. (borfMatcher is in the exonWalk dir) commit 238bcd153185ab0b476f9cb2bd9bf295e54a77e1 Author: markd Date: Fri Jan 19 20:16:03 2007 +0000 added support for automatic building of ORFeome tables, currently only on the MGC server commit 34ecfaf1d16074472ac4abc9c1d539fce6591300 Author: rhead Date: Fri Jan 19 20:15:32 2007 +0000 turning on felCat3 on hgwbeta and rr commit 71dd2c46915b8c78977f1ac977be3e4c6c1cb986 Author: kent Date: Fri Jan 19 20:15:14 2007 +0000 Added include to get makefile to work. commit 62fa8b3e915dbc1b193aa9478e3313746319a502 Author: markd Date: Fri Jan 19 20:01:30 2007 +0000 added ORFeome details page, fixed invalid HTML in MGC details page commit c209050a27331c96777b3bca6191928aee1b75c5 Author: markd Date: Fri Jan 19 20:00:42 2007 +0000 make webEndSection private, as it should not be used outside of web.c commit 9f6ba3c5432a8ab257623946b0aca22c68107383 Author: markd Date: Fri Jan 19 19:46:38 2007 +0000 finish code to build orfeome tracks commit 8564ee39d9ad61368fcf19de675e6c6b0b7d6411 Author: fanhsu Date: Fri Jan 19 19:41:51 2007 +0000 Updated to present top bar for GSID GB. commit 04e9bfed76f1a1d05f4d4076491a6d78bc1e48a0 Author: markd Date: Fri Jan 19 19:40:22 2007 +0000 more to-do items commit b14ed182286f4d02a9b98654e8ed4bf415cdce85 Author: giardine Date: Fri Jan 19 18:11:46 2007 +0000 Expanded check on Locus Variants links to check value of needsEncoded as well as presence. commit 4aaca109c3bf4e21af863a0c91aa0bf3e1ec1b30 Author: fanhsu Date: Fri Jan 19 17:47:45 2007 +0000 Added hIsGsidServer(). commit 2519adeca5538b7933964f54a6148bfc08ecff66 Author: heather Date: Fri Jan 19 17:22:13 2007 +0000 added reference commit f6af71e63fa70feefd50cec4f1f2a1993ffddd47 Author: kent Date: Fri Jan 19 16:36:55 2007 +0000 Commenting out fake association tracks. commit f98462016306ee0a1a114012d372d70fcd90be72 Author: kent Date: Fri Jan 19 16:33:46 2007 +0000 Beefing up a couple of comments. commit 250da1372989802455a130f08378452540c0a2c9 Author: kent Date: Fri Jan 19 16:33:09 2007 +0000 Improving error message for negative coordinates. commit 2a15b6aa28b31df256f4700db2a657cd44285d9a Author: galt Date: Fri Jan 19 16:00:29 2007 +0000 "Encode release log update" commit 580b042c068250b8546dc29a4a0736db7eec756e Author: galt Date: Fri Jan 19 16:00:15 2007 +0000 "Release log update" commit 0a62619a1b9ed20552267de6fe9378628e2a9f17 Author: kent Date: Fri Jan 19 01:31:05 2007 +0000 Fixing a few more bits of user-visible text. commit d742531ede0a4f6b47fc9c1cf541be45d5cd110d Author: hiram Date: Fri Jan 19 00:42:24 2007 +0000 Simple julian date calculator commit 4c2b4a978928bd5e1a142836e055a1c67f64968e Author: hiram Date: Fri Jan 19 00:13:29 2007 +0000 Finish off fr1, gasAcu1, tetNig1 and danRer4 blastz and swap. Begin genbank alignments commit c08b8663ab39a21e92ef1256c464126392d34e3d Author: hiram Date: Fri Jan 19 00:12:34 2007 +0000 Add stickleback blastz and swap commit 7bc7098dc5d7d1fb5674f6b416fcb72d25f1bd37 Author: hiram Date: Fri Jan 19 00:11:00 2007 +0000 Adding stickleback and medaka blastz and swaps commit 20ae863a0904055db686a4b349a871e9f7ac2b4f Author: hiram Date: Fri Jan 19 00:04:09 2007 +0000 Added Oryzias latipes - medaka commit 5affd4dd60c5be13b76b29b6c0e508747d32c788 Author: hiram Date: Fri Jan 19 00:02:14 2007 +0000 Adding oryLat1 - Medaka commit 9d65f355f04d450eaa41a83ea474e9eb6ce2eafd Author: rhead Date: Thu Jan 18 23:59:41 2007 +0000 turning off felCat3 updates in order to rsync to RR commit ee7460299b0da4b8bb369016b2069ca5d0c1c09c Author: hartera Date: Thu Jan 18 22:53:53 2007 +0000 Added five new subtracks for Sanger Chip track. Updated these subtracks with corrected data. commit 6eca8a90abb89748448508017db551bfc5f752cf Author: rhead Date: Thu Jan 18 22:36:20 2007 +0000 removed reference to xenoRefGeneAnnotation; used the encodeEmail.pl encryption for our email address commit 3fe46005d4c5cf7a7e50bd97218062798470711a Author: kent Date: Thu Jan 18 20:28:26 2007 +0000 Polishing some user-visible text on almost all hgGenome pages. Removing initial caps in button labels. commit dba478e3fc0bdbaf1acc2a3cb2861e000d4f6ed4 Author: fanhsu Date: Thu Jan 18 17:42:46 2007 +0000 Added logic to check if the extGeneId field of ncRna is "". commit bca15d1c9066535f73770813856f7f6557374782 Author: markd Date: Thu Jan 18 17:00:32 2007 +0000 fixed use of invalid point when there are multiple partitions with misc_diff update commit 50200dadf723a21677489527eb84cfef36d23113 Author: kuhn Date: Thu Jan 18 16:41:05 2007 +0000 modified output slightly commit 1bccc734556eb4affbec31e033baaf7f9240cef2 Author: galt Date: Thu Jan 18 16:00:30 2007 +0000 "Encode release log update" commit b6e985e5c000598ee4367a987b6f84512bafe142 Author: galt Date: Thu Jan 18 16:00:16 2007 +0000 "Release log update" commit 093438d36ec8f9fb18880de0dd4c821c82c93449 Author: hartera Date: Thu Jan 18 01:18:34 2007 +0000 Removed trackhandler for vegaNew which was a test track. commit 36dd1e17ba359284d0ff14aa187e88b60b80db91 Author: hartera Date: Thu Jan 18 01:16:54 2007 +0000 Added semi-colon to Ensembl Gene Link label. commit 9c3cbeebb34dbdc657fd8a181248b2b13ee9df80 Author: fanhsu Date: Thu Jan 18 01:12:24 2007 +0000 Updated one color description of ncRna. commit b18c1a4344ff5e90ba634d5c2a50efddc3765808 Author: fanhsu Date: Thu Jan 18 01:11:16 2007 +0000 Minor edit of ncRna color. commit 5fa9b5dafd632a716a5341cc58cae9c2e038ead4 Author: fanhsu Date: Thu Jan 18 00:51:29 2007 +0000 Created ncRna.html. commit 510788c1f677dabaea6a76a3657293784411f3e6 Author: fanhsu Date: Thu Jan 18 00:50:05 2007 +0000 Added display of the external gene ID for ncRnal. commit f7ac5e6800f160530e9882bb091d5823c3be4a82 Author: rhead Date: Thu Jan 18 00:44:56 2007 +0000 changed wording of NOTE and mentioned xenoRefGeneAnnotation table commit 0cf43513b3dde3d27cde0221790996cbc56dab86 Author: heather Date: Thu Jan 18 00:34:19 2007 +0000 add xenoRefGeneAnnotation commit daa5fbe0efbdfd9cddff5600587b6e65e8420fc0 Author: ann Date: Thu Jan 18 00:29:40 2007 +0000 relaxed mm8 dupSpMrna rule by one percent commit 634325eb03f22069e3f5fb819df1fdbafcb603be Author: ann Date: Thu Jan 18 00:26:40 2007 +0000 removed two redundant refSeqId rules for mm6 commit 1cbab2de74f89a154b634affd51efb812e2bae92 Author: ann Date: Thu Jan 18 00:22:03 2007 +0000 loosened up mm6 refSeqId rule commit 6d5c473b6128ddad5979e70e1a5adc69642a5cd3 Author: fanhsu Date: Thu Jan 18 00:15:12 2007 +0000 Updated doNcRna(). commit 75c99f68b4fe174511461a7b1aef198aae17e601 Author: ann Date: Thu Jan 18 00:04:01 2007 +0000 Fan said it was OK to remove the 'full' from the uniProtReference rule commit d5da4988cafc736c44736de1687994dbddc68fe8 Author: archanat Date: Wed Jan 17 23:54:46 2007 +0000 converted refs to Pubmed format commit cff54b4f189ed169db444e7d798844bc7feca2cc Author: hiram Date: Wed Jan 17 23:54:36 2007 +0000 Show featureBits on most conserved data commit ab9e863f24850f63e7864eb1ada2f2ccb09b4546 Author: hiram Date: Wed Jan 17 23:44:10 2007 +0000 Finished with 8-way conservation track commit 04f90b741af5dca428000410544f2cef688f9ad9 Author: ann Date: Wed Jan 17 23:35:31 2007 +0000 added hg17, hg18 to pseudoGeneName identifier rule commit ea16866ecd7a886f5d1bd3db925ce61c4d609fbd Author: ann Date: Wed Jan 17 23:27:38 2007 +0000 relaxed vegaName rule for hg15 commit 80f4eb873c87c0ee84635b28823d32f750a84623 Author: heather Date: Wed Jan 17 23:26:49 2007 +0000 put human last in the compGeno group commit d1c75ead7c3db21c478e085f7e0d1c04bfdd8146 Author: heather Date: Wed Jan 17 23:18:41 2007 +0000 add chainMm8 and netMm8 commit 28d8b13cda1fb8e339f7f07d00d57f070a8b286b Author: rhead Date: Wed Jan 17 22:40:33 2007 +0000 updated references to pubmed format commit 44bd556898389003edeac9bb4e7f25c86a60bf91 Author: rhead Date: Wed Jan 17 22:30:27 2007 +0000 updated references to pubmed formate commit 9e7220532fd2848597de57643fc5e945211303ef Author: kuhn Date: Wed Jan 17 22:03:56 2007 +0000 dropped one space commit c5c7bf1aecff8202cc20d78329cea21e1d7082ac Author: ann Date: Wed Jan 17 22:02:11 2007 +0000 italicized 'et al.' commit f587ee528d09b6b4e6e0ff1902e80a900af3f66d Author: ann Date: Wed Jan 17 21:58:17 2007 +0000 added tenth author to references commit f12b3b24c5704e419320230dbf1b8afad7002e9b Author: kent Date: Wed Jan 17 20:31:10 2007 +0000 Adding support for three layout types - two per line, one per line, and all in one line. commit 986eb76d779d8419005024e2ede83f912176f651 Author: rhead Date: Wed Jan 17 20:09:23 2007 +0000 added a name to authors with et al to total 10 names, added publication information from pubmed, took out spaces after semicolons commit ab9bd20d5e888093131e4421636b858cc16e0721 Author: rhead Date: Wed Jan 17 20:08:27 2007 +0000 whitespace changes commit 0889b2632f60906f3313304560c45642b641cc15 Author: rhead Date: Wed Jan 17 19:58:28 2007 +0000 added a name to authors with et al to total 10 names, added publication information from pubmed, took out spaces after semicolons commit 30ec37c3561d0ba2a4501d707167f75c0ee4499a Author: rhead Date: Wed Jan 17 19:26:16 2007 +0000 moved period outside of italics, added a name to authors list to list 10 authors total, added extra publication information from pubmed, removed spaces after semicolons commit 19faf7c92d00eeed2499ff980978041715d9e66b Author: rhead Date: Wed Jan 17 19:11:53 2007 +0000 put italics around et al. commit e7faded6dbf6e0ac90eefb9f05b940e7eb4c5ceb Author: kent Date: Wed Jan 17 18:46:11 2007 +0000 Changing title of config page from Genome Association View to Genome Graphs. commit ed60780bf6f233775122a48829798d6627dc851e Author: kent Date: Wed Jan 17 18:45:17 2007 +0000 Adding configuration for each graph on config page of hgGenome. commit bcef3409c0ea0a75741e8dce67100758edd5b274 Author: archanat Date: Wed Jan 17 18:23:14 2007 +0000 converted refs to Pubmed format commit 5a71e987ca4559e19d85d12b526e3a847a0863cf Author: heather Date: Wed Jan 17 17:56:33 2007 +0000 add a paragraph about ortho alleles commit d760bfb0f164b4b341676ee240a19d8f02ad610d Author: fanhsu Date: Wed Jan 17 17:10:17 2007 +0000 Rebuilt GO database. commit cc5236d11ac420d8aed18c1444fa5d391e593706 Author: kent Date: Wed Jan 17 17:10:08 2007 +0000 Adding back some line-breaks in form that got messed up when I moved the help text. commit 861a0449683d59a7f4ae4441775cc4ae90d3f580 Author: kent Date: Wed Jan 17 17:08:42 2007 +0000 Moving explanations of controls in Genoe Graphs upload page to a new section in the bottom, and expanding explanations. commit 0d091a12372d9d04c6e8fb25d0ac66bd419ff74a Author: galt Date: Wed Jan 17 16:00:27 2007 +0000 "Encode release log update" commit ad39612c34e5d7fe56bf997c76e18e4e3d6a6847 Author: galt Date: Wed Jan 17 16:00:15 2007 +0000 "Release log update" commit 890838a83fdc54559760e2884f8ef1d0521f10e7 Author: hiram Date: Wed Jan 17 05:01:00 2007 +0000 Adding phastConsElements8way commit f34f926e6b1d869daaccc18eacad47b903ba577e Author: hiram Date: Wed Jan 17 04:57:52 2007 +0000 Adding html for chain and net Medaka commit 573a321fc3a546ba58c8d3952799ace9ed14d984 Author: hiram Date: Wed Jan 17 04:51:03 2007 +0000 Straighten up gene selection for frame annotation commit 37552143d6115a4084a52bff2ffb5cd94b4b95f7 Author: hiram Date: Wed Jan 17 04:47:38 2007 +0000 Adding html files for phastConsElements and multiz Conservation tracks commit 84c017ed28284f1ec72ea12049a71d65a1095e17 Author: rhead Date: Wed Jan 17 01:14:47 2007 +0000 moving a copy down to felCat3 level in order to include a note about a known issue with codon coloring. Once the issue is fixed, this page can be removed and the top-level html used again. commit ad28a62a5f8a85605ef7d825037e855adb992e11 Author: hartera Date: Wed Jan 17 00:20:16 2007 +0000 "New version number v150" commit b014ade506a172820ea5a49bda83c327b6561cf0 Author: hartera Date: Wed Jan 17 00:13:51 2007 +0000 Changed the host name for the 32 bit machine (BOX32) to titan. commit 6a943de021ae6ab9d74cbf2119e572a13b23e7cd Author: hartera Date: Wed Jan 17 00:08:18 2007 +0000 Added code so that Color track by codons drop down is not drawn for ensGeneNonCoding track as it does not make sense to have it for this track. commit f3309ba9a51a368633191cd7edfb6ae750a9d85a Author: hartera Date: Tue Jan 16 23:58:39 2007 +0000 Finished Ensembl Genes tracks for protein-coding and non-coding genes. Radiation hybrid map track in progress. commit c74965f4148f4c5e1397b727015d80fc59e309d8 Author: hartera Date: Tue Jan 16 23:54:31 2007 +0000 Description for Ensembl Genes (Non-coding genes) track. commit f12d35f24d89063cd6c5cfa6eb4ff7708542fa65 Author: hartera Date: Tue Jan 16 23:52:14 2007 +0000 Description for Radiation hybrid map track for Oct 2006 release. commit c299932c8df0c473f9fc62659dc4dba41cc37c1a Author: hartera Date: Tue Jan 16 23:51:25 2007 +0000 Added tracks for Radiation Hybrid (RH) map, Ensembl Genes and Non-coding Ensembl Genes. Added search for RH map. commit be12b94062b0c84c3e24472ee299b0299b8ef36c Author: rhead Date: Tue Jan 16 23:50:13 2007 +0000 updated references to pubmed format commit 55f380dad03ec57a10e91edc8867b81031a34019 Author: rhead Date: Tue Jan 16 23:30:37 2007 +0000 updated references to pubmed format commit 868a4aeff18b67bb3e6b8d62c9c4699cfd89e5fe Author: hartera Date: Tue Jan 16 23:26:20 2007 +0000 Added ensGeneNonCoding to doMiddle. Added code to handle creating the links to the correct Ensembl archive for the ensGene transcript and protein IDs. commit 7aacd2dbac40a5f38027284ba59eca0b0a7d7abe Author: ann Date: Tue Jan 16 23:00:16 2007 +0000 added chromosomes line to encodeUViennaRnaz track commit 0ec575b83353602d8842fb76d6ada8e8f05de252 Author: rhead Date: Tue Jan 16 22:46:18 2007 +0000 updated references to pubmed format commit b1a259b43715ed6f2e6bba582c97488259cb076f Author: ann Date: Tue Jan 16 22:35:48 2007 +0000 fixed citations, and some typos commit bb283115ad67fb3ffff4cc0445debb27153b0e46 Author: galt Date: Tue Jan 16 16:00:24 2007 +0000 "Encode release log update" commit d2e0576904752face8e34c680be30659fd217a07 Author: galt Date: Tue Jan 16 16:00:14 2007 +0000 "Release log update" commit d5873ca3def9be263dba97ed6aa19222d206bcef Author: hartera Date: Tue Jan 16 07:16:12 2007 +0000 Added track handler for ensGeneNonCoding track. commit d53a96ad865f582b80525628fec8e56d09684b28 Author: galt Date: Mon Jan 15 16:00:21 2007 +0000 "Encode release log update" commit 70d1d33de6fa74f7de9478b6eb7525d176516189 Author: galt Date: Mon Jan 15 16:00:12 2007 +0000 "Release log update" commit f10ef6e99f131bfe9e04619289bcc4295687d0f6 Author: hiram Date: Sun Jan 14 23:29:47 2007 +0000 Added chrUn chain and net for all other to multiz8way. Tuning phastCons run commit 2b90c1df805e1c7bed51389089699b6a78d15b47 Author: galt Date: Sun Jan 14 23:11:47 2007 +0000 renaming gs to gsid
, and the names of the corresponding data structures commit 427ebdf284699464b6bd155938416a15acf5e48f Author: fanhsu Date: Sun Jan 14 17:04:23 2007 +0000 Added warning comment about changing HIV status logic when non-infected subjects added into DB. commit 7060b140cd9442ffc3da9f7f33b0aaf77300c9a2 Author: fanhsu Date: Sun Jan 14 17:00:55 2007 +0000 Removed "(to be verified with GSID)" from HIV status. commit 93b04aa582b366867857b33c6febddfbf34a66be Author: fanhsu Date: Sun Jan 14 16:56:22 2007 +0000 Changed example ID 3123 to 4123. (First year deliver is VAX004 only). commit ac9c82ec2f0a8a33fc054e47c9ed4d5216dff5e4 Author: galt Date: Sun Jan 14 16:00:21 2007 +0000 "Encode release log update" commit dc259fca548f73a9c39c264cc1400bf4e881816d Author: galt Date: Sun Jan 14 16:00:12 2007 +0000 "Release log update" commit 7e51827870deb773212c6963b96031f061343a8f Author: markd Date: Sun Jan 14 04:12:28 2007 +0000 more yank-n-put stupidity commit 8d388cfbfff5495be49497680e84bf2c0f20c06c Author: markd Date: Sat Jan 13 20:39:12 2007 +0000 added option to include version number commit 34b71365d340d4404564110737194c21951f0b87 Author: markd Date: Sat Jan 13 17:19:21 2007 +0000 fixed yank and put stupidity commit 492a8bb27f5559be17f72c9d5716d146f200d9a4 Author: galt Date: Sat Jan 13 16:00:26 2007 +0000 "Encode release log update" commit 87b20873142c7a1be7a5d1e37271d9fe359912b6 Author: galt Date: Sat Jan 13 16:00:14 2007 +0000 "Release log update" commit 515929eace552c2ba0d2464f8bbc9d35eaf54519 Author: markd Date: Sat Jan 13 08:18:53 2007 +0000 fixed bug from copying from rr crontab commit c09066a0b7834479510c73b43228c4d9706ce81b Author: hartera Date: Sat Jan 13 07:04:09 2007 +0000 Revert back to v1.3 for use with release beta until track is released. commit 20cb3a038e698a972396a11868d85b6e8665efa9 Author: hartera Date: Sat Jan 13 07:02:28 2007 +0000 Added new subtracks for encodeSangerChip track and renumbered existing tracks. Added new setting to use alternative html page for release alpha. Added release beta version of track. commit 15d9ce53a058f9129b0765b85babca0a079ab888 Author: rhead Date: Fri Jan 12 23:59:04 2007 +0000 updating references to pubMed citation formation commit 5d5708c5a033ae476e1edf5cf5a8cbfd829cc68b Author: hiram Date: Fri Jan 12 23:52:30 2007 +0000 Adding use of /data/tmp or customTrash.tmpdir directory for database loading commit 24a3f0fc6860bc2fe2e26ec1ef0c698c83403089 Author: rhead Date: Fri Jan 12 23:41:46 2007 +0000 updating references to pubMed citation formation commit 0e514a82fb0540e8935c5fb3edb21dbe670f62c7 Author: markd Date: Fri Jan 12 23:35:34 2007 +0000 *** empty log message *** commit 6c104ef57142a43117fe172e1386fd374ab9753b Author: rhead Date: Fri Jan 12 23:33:50 2007 +0000 updating references to pubMed citation formation commit ad58ced968fbdaf696bb263a246b584f934a4057 Author: fanhsu Date: Fri Jan 12 23:18:29 2007 +0000 Added the Ensembl non-protein-coding (ncRna) track. commit bf7bcca5e17d92359be9a9ae8f1b17af8a75a0b1 Author: fanhsu Date: Fri Jan 12 23:06:49 2007 +0000 Added ncRna.o. commit d76e06b74b186cf65a05840b49899861ea175a25 Author: ann Date: Fri Jan 12 23:02:43 2007 +0000 added databaseAday.csh script commit cd346c4780d96e727787ea7a79adc45adbd7e114 Author: ann Date: Fri Jan 12 23:02:22 2007 +0000 scrolls through all of the databases on the RR, one per day. to make them available to qa monitoring scripts on a rotating basis. commit e2da5164c8f96f830c39b3c1a80af759be2a6d1b Author: fanhsu Date: Fri Jan 12 23:02:00 2007 +0000 Added the special color needed by ncRna entry display. commit cb0f4c3634c7e3a7f8c6e3b3314f25b7e309609c Author: fanhsu Date: Fri Jan 12 23:00:15 2007 +0000 Added processing of ncRna track entries. commit 612408e867f12e8cbd258d596ad2c21db779ca30 Author: fanhsu Date: Fri Jan 12 22:56:57 2007 +0000 Added doNcRna to process ncRna details. commit 36e69b583446d2b45590e1276684aee742710938 Author: fanhsu Date: Fri Jan 12 22:50:51 2007 +0000 Added search for ncRna track. commit 7e350b743b07ccfb0062ffb1db846dd2236fda12 Author: fanhsu Date: Fri Jan 12 22:50:03 2007 +0000 Added ncRna track. commit 184e57d2bc2af0961439a91cde973a91fbaa59db Author: kayla Date: Fri Jan 12 22:14:11 2007 +0000 fixed a typo which was preventing other assemblies from checking chains to droGri1 commit 3155e76abea6c88444e8825eb5ca7ce01d68604e Author: fanhsu Date: Fri Jan 12 22:12:10 2007 +0000 Created ncRna.h. commit 7ed9857928f74a6a32eb7ebddccc2efb4070e7ba Author: fanhsu Date: Fri Jan 12 22:11:53 2007 +0000 Deleted. Move to ../inc. commit 075b00f5ac03ede109eba685831086a0f72ea41b Author: fanhsu Date: Fri Jan 12 22:10:31 2007 +0000 Added ncRna.c. commit f85b8000a7e8d6d05e7c04928fe9b5ab01cec998 Author: fanhsu Date: Fri Jan 12 22:10:07 2007 +0000 Added ncRna.h. commit 9341f3720dac54e1d52955c1ad0b39c1598f5be7 Author: fanhsu Date: Fri Jan 12 22:09:40 2007 +0000 Added ncRna.sql to define the ncRna table used for the non-protein-coding track. commit 61b567eadb07ce12cf817e5899f3f9da40c7293c Author: fanhsu Date: Fri Jan 12 22:08:50 2007 +0000 Indicate that the score field of ncRna is unused. commit d4b6933587915af22f1a36033ee69d48b7ee89f0 Author: fanhsu Date: Fri Jan 12 22:08:04 2007 +0000 Created ncRna.as. commit 9ca01248058e4cfb89a4204144bd7a0037456f86 Author: giardine Date: Fri Jan 12 20:45:08 2007 +0000 Added remaining IDbases, HGMD, and PubMed as possible links. commit c4079e6e34a5818b5ac050240a6ba11695a8e5ac Author: giardine Date: Fri Jan 12 20:43:29 2007 +0000 Only some accs should be url encoded, others shouldn't. Have flag in links.ra Added note to make clear that Get DNA doesn't not get mutated DNA. commit 826a6b73c211349f1beafc5a13b037d36e59cce2 Author: archanat Date: Fri Jan 12 19:11:50 2007 +0000 minor edit commit d931d59e8958ec02a1abc213a208a5f2b3ec7cfa Author: kayla Date: Fri Jan 12 19:04:07 2007 +0000 Removed a sentence that did not apply to this assembly. commit aa23248b9648d9e2cadc05317d6ddbb5b287f0c6 Author: archanat Date: Fri Jan 12 18:57:02 2007 +0000 converted refs to Pubmed format commit c54365559680f057c0c8c57f4a6daee7cff0d6c0 Author: archanat Date: Fri Jan 12 18:31:25 2007 +0000 converted refs to Pubmed format commit 480a9aa9efb2ab2f44dcdf2a7f0fd6a6691dc3b8 Author: archanat Date: Fri Jan 12 18:19:33 2007 +0000 converted refs to Pubmed format commit 0aadce6752720f20d805444773632184c6026527 Author: archanat Date: Fri Jan 12 17:35:14 2007 +0000 added matrix for Human chain commit 4f70d5e860fb1770e645e8fbc4e4a7062f143c0e Author: archanat Date: Fri Jan 12 17:29:07 2007 +0000 moved Human nets/chains to organism level commit d274a1e39c2a9950a5d9eebbd54231f915fb03f5 Author: galt Date: Fri Jan 12 16:00:30 2007 +0000 "Encode release log update" commit 35d4f24325e2ed972aabaf56fee4bcff07cbc435 Author: galt Date: Fri Jan 12 16:00:17 2007 +0000 "Release log update" commit 0f607da4f75d733736e577894ece67aa242b854b Author: hartera Date: Fri Jan 12 06:50:28 2007 +0000 Minor edit. commit 57908e72bbd5f252e5778c0e6f6c79acd056c52d Author: hartera Date: Fri Jan 12 03:09:49 2007 +0000 Minor edit. commit 84dbb781e53f0599e2de5324f63f3fc7fcc7aac4 Author: heather Date: Fri Jan 12 01:14:51 2007 +0000 bug fix in initCounts commit dd20b8c25fdac58a85551b9b28943ec6140d2cdc Author: archanat Date: Fri Jan 12 00:58:19 2007 +0000 converted refs to Pubmed format commit 899f8bcb6ced793373764bf7d458359fd743043c Author: kuhn Date: Fri Jan 12 00:39:16 2007 +0000 added some whitespace around the photo commit 52364cb0c7fda922396472375b139b646c7a4a54 Author: kate Date: Fri Jan 12 00:32:56 2007 +0000 Implement an 'html' setting that allows specifying an alternate .html filename for a track. commit cd3a94007c8b81fac9c43a103b9ff79ea2cde879 Author: hartera Date: Fri Jan 12 00:27:37 2007 +0000 Description for updated encodeSangerChip track in Jan 2007. commit b5e148604a37c56408d85ea7e9b59cf00e90dbb2 Author: rhead Date: Fri Jan 12 00:25:04 2007 +0000 restoring revision 1.4 after pushing trackDb to the RR commit ddaae724c6ee3ce17d3199f1f9a3b416a7a1b76b Author: kuhn Date: Fri Jan 12 00:05:48 2007 +0000 moved wiggle back in to beta version commit d8e0367195b92123ef7edf7a5d3ab83703e64a86 Author: galt Date: Thu Jan 11 23:54:04 2007 +0000 Use synteny via chains to filter blastp output (xxBlastTab). commit 570bc2170bb308c1992813fb289de9967f53df0f Author: galt Date: Thu Jan 11 23:41:29 2007 +0000 updated xxBlastTab for human, mouse, rat using new script synBlastp which uses chaining to filter out paralogs and other poor alignments turned up by blastp commit 044e4450bfcaa4348cc70a0f492d8273f9a16f11 Author: rhead Date: Thu Jan 11 23:41:20 2007 +0000 reverting back to revision 1.3 temporarily so that trackDb can be pushed to the RR commit b08394cc0c949aa1f3e75884accee6a3643927c8 Author: hiram Date: Thu Jan 11 21:57:06 2007 +0000 Turning on the phastCons8 wiggle display for the 8-way conservation track commit ad9e64ca6e83b6bedb12e45578c2589ce36347dc Author: kuhn Date: Thu Jan 11 21:56:17 2007 +0000 removed unused variables commit 48a04a15cec40a9f4ddf4a901636325a4fdf897f Author: ann Date: Thu Jan 11 19:33:06 2007 +0000 cleaned up citations. commit 41518c14414ad4eb0df2c9a4c95353275fb4ba9c Author: heather Date: Thu Jan 11 18:51:57 2007 +0000 handle multiple centers (not a big deal, we aren't putting them in output file commit f6efa724f1c9536406e97b1cb1bfdaa42054a61b Author: heather Date: Thu Jan 11 18:28:50 2007 +0000 fix logic for otherAllele commit d1cfe517b2cdcde57a8e23324d5bb8b863132607 Author: hartera Date: Thu Jan 11 16:48:56 2007 +0000 Added new subtracks for the encodeSangerChip track. commit 7dd8d31a4429f56f7d6052d7d0320465d0485ef1 Author: hartera Date: Thu Jan 11 16:47:58 2007 +0000 Added links to antibodies used in new subtracks. commit e748d9058bf5c16191a6272c1e3800013760d700 Author: galt Date: Thu Jan 11 16:00:31 2007 +0000 "Encode release log update" commit 4b0667fe033c1f816f649f954080f65f2923a4ff Author: galt Date: Thu Jan 11 16:00:17 2007 +0000 "Release log update" commit ab08d2c3a0deb8566c9d26f139d74daac499ba11 Author: markd Date: Thu Jan 11 02:33:40 2007 +0000 reload native mRNAs to get gbMiscDiff table for MGC commit 478c1cd45ea01d5c41bd29945a3ed196be160ef7 Author: heather Date: Thu Jan 11 01:16:47 2007 +0000 add hapmap commit 59156f79661c559c54eefc8d8f77844bd4297094 Author: heather Date: Thu Jan 11 01:16:32 2007 +0000 initial revision; some error logging wrong commit 84d951cde1d22c53b6824cab9562a796076792a7 Author: hiram Date: Thu Jan 11 01:16:14 2007 +0000 Starting the phastCons run for the 8-way commit 2a7a82b8181bd74d23122c9305bb7e421681f799 Author: archanat Date: Thu Jan 11 01:13:10 2007 +0000 converted refs to PubMed format and added month to the references commit 804f014e0b2f3ca87e3041e7250ae40e33e72dab Author: heather Date: Thu Jan 11 00:16:08 2007 +0000 more alphabetizing commit aefcafdaf7f50f35249bde4504ef75ec4a0d66cb Author: heather Date: Thu Jan 11 00:08:02 2007 +0000 alphabetize commit 0d96be365b8da2803327a2e3cd07241dde65c67a Author: archanat Date: Wed Jan 10 23:33:25 2007 +0000 Fixed broken link to GRIB commit 7082f7b6ee024bd468de5cb9b963e651abd40a63 Author: donnak Date: Wed Jan 10 23:23:27 2007 +0000 Uupdated info for the OH training announcement. commit 5c98e7db02d69a2826475b53a65c17c1e6a7d12b Author: hartera Date: Wed Jan 10 23:03:12 2007 +0000 QA is now running buildTableDescriptions.pl. commit ce599875583cf474a53b472ecb5d589dc882a755 Author: hiram Date: Wed Jan 10 21:05:58 2007 +0000 Frames are now on commit 4dcb61539e368e49c46101a300e1674df045c945 Author: hiram Date: Wed Jan 10 20:18:44 2007 +0000 Added the MAF Frames annotations commit f5814ac9c3644a7b4bf6962b74fcb30bfb142349 Author: markd Date: Wed Jan 10 20:04:03 2007 +0000 enabled building gbMiscDiff table commit 993505ff5366690b1cbf2118f7fabac901bc4e57 Author: ann Date: Wed Jan 10 18:37:08 2007 +0000 removed release beta blocks for encodeYaleAffyRNATransMap track, and removed release alpha lines from the other one commit 1992c2760e30ef59de95f1024a6c451657e0734c Author: ann Date: Wed Jan 10 18:21:26 2007 +0000 updated dead link to Brent Lab for GTF2 commit 49ccec8448822d8b514204610e579656fe3fc35b Author: hiram Date: Wed Jan 10 18:12:46 2007 +0000 Add a see also reference to the wiki browser install process commit 797b867ad86816bcc04218fef6283cc2c566b334 Author: kate Date: Wed Jan 10 17:56:35 2007 +0000 New Sanger chip/chip data submitted commit 70d242649a620be2d5ba02c6340eb33d7f4deacc Author: kent Date: Wed Jan 10 17:12:24 2007 +0000 Fixing typo (space that should be a comma) in uniProt display ID column. Possibly this would fix a bug in the uniProt filter. commit 03bd9f253359fb112734a81e576e94dae5ccc624 Author: galt Date: Wed Jan 10 16:00:31 2007 +0000 "Encode release log update" commit 1c513ed9455e85edcb18704d078c1693175e97c5 Author: galt Date: Wed Jan 10 16:00:17 2007 +0000 "Release log update" commit 01c3a42f6719197f9217e9a6b832887731c5eda5 Author: aamp Date: Wed Jan 10 07:53:39 2007 +0000 Added some CGAP SAGE instructions. Just the mappings. commit a03b68ae07d258e4b0b69c5718456091a50aff27 Author: markd Date: Wed Jan 10 05:10:08 2007 +0000 added hack to get ORFeome clones that were given molecule type of DNA commit 8981fb38002d18dd41fc4a41137dd74d3afdf06f Author: kuhn Date: Wed Jan 10 02:52:44 2007 +0000 added support for detection of archived databases. thanks kayla. commit 8cd6851a1e43f57ee02bfb52eb11b5c37679d84a Author: kuhn Date: Wed Jan 10 02:08:11 2007 +0000 added checking and output for case where db active = 0 on RR commit 3e409dac0dc1ca9cab2c03c3c5b7fa6767cce899 Author: archanat Date: Wed Jan 10 00:43:55 2007 +0000 Updated to include new repeat class RC commit 7721ab3b86280801b6b638032dea643f3260e3a7 Author: angie Date: Wed Jan 10 00:22:52 2007 +0000 Added info messages about saved BLAT results analogous to the messages about custom tracks. commit 2cd42e3633ef0ad8db68a35966982525bb2d1217 Author: donnak Date: Tue Jan 9 23:26:18 2007 +0000 Fixed incorrect date. commit 7f1b74b3d936701e6adcfab49038d5bdae07f453 Author: kuhn Date: Tue Jan 9 23:05:59 2007 +0000 moved Proteome Browser link up into the the group with other UCSC tracks commit c802989f45f49c9727298aa5f35e4efc96940959 Author: heather Date: Tue Jan 9 21:30:08 2007 +0000 add contigAcc commit c99bea48acf66f81a0ad16d0802f6e0fa8c8b01f Author: ann Date: Tue Jan 9 21:09:08 2007 +0000 removed subGroups from two endoce tracks that didn't warrant their use any more commit 135ecb257d3df8304803c0c183873dd25ad8c6b2 Author: kayla Date: Tue Jan 9 20:48:02 2007 +0000 added links to the References section. commit 528d36c71b47a268d1db374ba1de829c45afcb6f Author: kayla Date: Tue Jan 9 20:37:40 2007 +0000 Added links to the References section. commit 2cd9d054090f19b4c725b465b90949833864052b Author: kayla Date: Tue Jan 9 20:36:21 2007 +0000 added links to the References section. commit e7a7ba04de7db7dea6199347badd57164532294b Author: ann Date: Tue Jan 9 19:59:14 2007 +0000 a few typos, a major clean-up of the References to comply with new citation style commit a90471bd277a38d2e3418d21663fa8b2d1aec8f3 Author: hiram Date: Tue Jan 9 19:30:26 2007 +0000 Customize URL for ensGene reference commit 1d5cdcddf1b5874f6c5bf13bfb9553dfdd277cc7 Author: hiram Date: Tue Jan 9 19:27:15 2007 +0000 Customize URL reference for ensGene commit c0b5a14647fb3466afe2f205fab5472d1db15e54 Author: heather Date: Tue Jan 9 19:22:00 2007 +0000 add contig search commit ea3af56fe8204cc7da01b46f25353bd1116e973d Author: ann Date: Tue Jan 9 17:02:25 2007 +0000 changed name of output file commit 1009f49e701f584ec65e7cf6694418dc5d021217 Author: galt Date: Tue Jan 9 16:00:25 2007 +0000 "Encode release log update" commit aaf8dd9eb0194db872b8f8f9a4894afffc33004c Author: galt Date: Tue Jan 9 16:00:14 2007 +0000 "Release log update" commit 10bd7d8c6ee40fc0777f9bd74a1aeee877304813 Author: donnak Date: Tue Jan 9 10:01:19 2007 +0000 Added announcement abt upcoming OH training seminars. commit 3e4cd9de65ad570fed300d6bb5294a8f297317fc Author: donnak Date: Tue Jan 9 10:00:39 2007 +0000 Archived 1 item. commit 2a0f3f8ab145aac2051be88141aabae4f7af4025 Author: hartera Date: Tue Jan 9 04:08:05 2007 +0000 Started remaking Ensembl Genes track using Ensembl v42 dataset. commit 46d5dcb4990ab3113388eec9dcc0c9089e86e745 Author: kate Date: Tue Jan 9 01:27:12 2007 +0000 Fix incorrect label in released Yale TAR track, and update another subtrack for consistency with RNA track commit e50c102cff34a0fda4fe1bf75d979606fa81388a Author: hiram Date: Tue Jan 9 01:19:08 2007 +0000 Removed the 7-way, now using the 8-way commit bb994dcda8b675c52fabd024754953950b4f2083 Author: hiram Date: Tue Jan 9 01:18:10 2007 +0000 Got multiz8way done up to the point of gene annotation on gasAcu1, now loading Ensemble genes on oryLat1 commit 79fb20305d7229df5108ea950fda51ef12198c3f Author: heather Date: Tue Jan 9 01:08:50 2007 +0000 back out cnpSharp and cnpSebat for now commit 903f8a45e8f6f5128a53d763eb0a6cda4b7593a4 Author: hartera Date: Tue Jan 9 01:05:42 2007 +0000 Edited labels for enocodeUViennaRNAz track and added dataVersion. commit f017a8c159b3741588916cd8bcedae05e763d65a Author: heather Date: Tue Jan 9 00:52:06 2007 +0000 adding new SV data from Lars Feuk commit 46259692d0e05a41d2b02cde41cbd834c1ffa7dc Author: hartera Date: Tue Jan 9 00:23:45 2007 +0000 Fixed typo in path name. commit 8aafab6f67e401873bd1cba55d3f12b7dde76496 Author: markd Date: Mon Jan 8 23:48:07 2007 +0000 added option to output disoriented psls, plus fixed a memory leak commit 9847f6d0fec8b2dccd0b566e12c05bdcc86f5d2e Author: angie Date: Mon Jan 8 23:34:09 2007 +0000 More specific call to checkCleanSlate so this can be run with -debug and then for real. commit db8237c522766b19e481a933c1805c85371c2ba0 Author: angie Date: Mon Jan 8 23:32:28 2007 +0000 In cartLoadUserSession, give a nicer warning if user clicked submit before filling in both sessionOwner and sessionName. commit 249291d440811c927138d1f5c60d57b965bd8c24 Author: angie Date: Mon Jan 8 23:27:55 2007 +0000 Assembly & GenBank tracks. commit 769ed562d22dd65563009d77ff898f2647420039 Author: angie Date: Mon Jan 8 23:25:52 2007 +0000 Added ornAna1. commit f72bfc0709fa911db20a3e4e8600ce3de92e80f0 Author: angie Date: Mon Jan 8 22:58:32 2007 +0000 When saving a session with a custom track, warn the user about the custom track expiration policy. When loading a session, inform the user about any active or expired custom tracks in the session. commit 585f854e00871b3ed4991e37f216e6b9444b7264 Author: kate Date: Mon Jan 8 22:55:03 2007 +0000 Add check for custom track file older than config file, so that custom track files will be updated when database configuration (or any other configuration change) is enabled. By request of Hiram commit 436847f72b10c93d2967e931539f64502390c607 Author: kate Date: Mon Jan 8 22:54:37 2007 +0000 Provide last modification time of hg.conf file commit db28a3a2b99c506a21349a7d23275214a1f4f91b Author: angie Date: Mon Jan 8 22:35:41 2007 +0000 Added customFactoryTestExistence which does just enough file-parsing to be able to test existence of custom track database tables. It can be called for a file for some other database, so does not depend on hSetDb stuff. commit 0ab53e110486a041058375e394fabfd4ba3dcc1a Author: sugnet Date: Mon Jan 8 19:56:38 2007 +0000 Fixing up warnings to comply with the new -Wall -Werror compiler flags. commit 5bd067bbe26a1490a81364f27bbc25278d2c0714 Author: sugnet Date: Mon Jan 8 19:23:36 2007 +0000 Fixing up warnings to comply with the new -Wall -Werror compiler flags. commit 92fc96cb1d9449aee372ce559eabb883983b4e80 Author: hartera Date: Mon Jan 8 18:56:05 2007 +0000 Updated Affy Zebrafish Zon Wild Type array track from hgFixed data using normalised antilogged absolute values. Compugen probes track in progress commit 9a7d0f75980b58021d3f9ae75d94e00ed1172d9c Author: hartera Date: Mon Jan 8 18:55:07 2007 +0000 Updated Affy Zebrafish Zon Wild Type array track from hgFixed data using normalised antilogged absolute values. commit 824b525e3cd9439173a100089d35d9b8e0eae2f8 Author: hartera Date: Mon Jan 8 18:54:09 2007 +0000 Updated Affy Zebrafish Zon Wild Type array data using normalised antilogged absolute values. commit 09500c9491c97770ea133b18b671475dce30b765 Author: kent Date: Mon Jan 8 18:25:09 2007 +0000 Allowing search on UniProt accessions. commit c96b7c49a2710c132677fa0f5f97a92f52c5365b Author: kent Date: Mon Jan 8 18:24:28 2007 +0000 Improving comments slightly. commit 2f05982ae30d735812d3393b9856a0d596515131 Author: sugnet Date: Mon Jan 8 18:20:34 2007 +0000 Adding forgotten test files to cvs. Also changing makefile to look for latest binaries one directory up. commit cdf4d6f10966835f75fcf7a89a3feaea131d7ef8 Author: galt Date: Mon Jan 8 16:00:20 2007 +0000 "Encode release log update" commit 9818b931df25976e9113d3380429e74835c0eed0 Author: galt Date: Mon Jan 8 16:00:12 2007 +0000 "Release log update" commit 12b5855b1718cfbaba4ae8f925ae6b9ccdacdeb4 Author: markd Date: Mon Jan 8 00:48:41 2007 +0000 fix mapping of hg18 commit ed639e104b169bee957e6eae4e93355829041757 Author: galt Date: Sun Jan 7 16:00:20 2007 +0000 "Encode release log update" commit 7efde26fa80c625acbcb7a523dc110881ac3e59d Author: galt Date: Sun Jan 7 16:00:11 2007 +0000 "Release log update" commit 3e014611e968d8111a261b4a4811d2f10df707e0 Author: galt Date: Sat Jan 6 16:00:23 2007 +0000 "Encode release log update" commit 257024e3fe14d7b9f5fe7d399c03a20719c33c54 Author: galt Date: Sat Jan 6 16:00:12 2007 +0000 "Release log update" commit 092d2f1aa3d6d47ba076712d97012d862fc4fabd Author: kate Date: Sat Jan 6 01:28:13 2007 +0000 Create new composite track for Yale Chip Signal and Pval tracks to accomodate new subtracks and doc commit 5c8f45e50b32c8da16fc6d4fca11b616bf87e9a9 Author: kate Date: Sat Jan 6 01:24:11 2007 +0000 Create new composite tracks for Yale Chip Pval and Sig tracks to accomodate new subtracks and changed doc commit d6b70939be108afa9059096e322e3ab5b8e81326 Author: heather Date: Sat Jan 6 01:11:42 2007 +0000 add notes for canFam2 blastz commit 92baf5737c68611f2c795cf7a4f3a8bf53b7badc Author: heather Date: Sat Jan 6 00:57:08 2007 +0000 add notes for felCat3 blastz commit 0ae8116d160009a2aa8145c43166901a7331d09e Author: hartera Date: Sat Jan 6 00:52:01 2007 +0000 Added RNAz track from University of Vienna. commit 662585b39ce11d389eebaaa03bdbc07ac31bcc52 Author: heather Date: Sat Jan 6 00:49:32 2007 +0000 add notes for mm8 blastz commit f9eb03febe199c66cf3b7d21cd105c1460c98071 Author: kate Date: Sat Jan 6 00:41:49 2007 +0000 Fix buffer overflow commit 44eb3aa923919760d4b610a9f431c340e9e84334 Author: heather Date: Sat Jan 6 00:33:26 2007 +0000 add notes for felCat3 blastz commit 064b436c2c0f0b36a340a43924b55ed6b29edb7b Author: heather Date: Sat Jan 6 00:22:21 2007 +0000 fix typo in previous commit commit ba08053f1d05ec94b8e311e7a57a09fcd2913e3a Author: heather Date: Sat Jan 6 00:15:36 2007 +0000 remove hg18 blastz notes (moved to hg18.txt) commit 8a0893f1dfdf7c773abebf77a47f8ba4193453b3 Author: heather Date: Sat Jan 6 00:13:09 2007 +0000 add felCat3 blastz notes (previously in felCat3.txt) commit 7928d679a61ae086bb18bf7ec0fac91b7a18fdbd Author: rhead Date: Fri Jan 5 23:34:24 2007 +0000 updated link to Sugnet paper to match the working link on the pubs.html page commit e30f6cd3f57450643bcc0f6973d199465249646b Author: kayla Date: Fri Jan 5 22:44:35 2007 +0000 fixed broken GRIB link commit 44786044671a7dac1f47023c4452828efd38f692 Author: angie Date: Fri Jan 5 22:25:11 2007 +0000 Added trimSpaces() when retrieving cart variables that the user typed in, so that leading/trailing spaces are ignored as they should be. commit 121489b3ca45f18ccf457426377d49f916c2b5d5 Author: kayla Date: Fri Jan 5 22:12:05 2007 +0000 fixed broken GRIB link commit ae7282ca6d47bd5a41bf073c1f6f5f831eb222dd Author: kayla Date: Fri Jan 5 21:57:14 2007 +0000 fixed broken link to GRIB commit 267dfc56eb1418162d9e312e3eae49e664ebb8b1 Author: kayla Date: Fri Jan 5 21:54:28 2007 +0000 fixed a broken link to GRIB commit e852fe0077343288000fa37b5435e79ab1c94877 Author: aamp Date: Fri Jan 5 21:16:25 2007 +0000 Added a command-line utility for finding restriction enzymes. Perhaps a blacklist option could be added next... but no big deal. commit a18723eaadd63f39ec53f204f4425707140f4ac0 Author: kuhn Date: Fri Jan 5 20:16:13 2007 +0000 made mammal conservation release alpha only commit 539e869ca62059b58a4c581760b03155c8c1d5a9 Author: angie Date: Fri Jan 5 19:02:26 2007 +0000 Additional errors caught. commit 018c24f588ecbb3daffb2729ec7834a10a4526c3 Author: heather Date: Fri Jan 5 16:10:48 2007 +0000 handle equivalence case in sortSnp125ExtendedColorCmp -- found by Davide Cittaro commit f8866e2673a6ab6d8154f7b0f7ccd93e93f8bcf6 Author: galt Date: Fri Jan 5 16:00:27 2007 +0000 "Encode release log update" commit f51233065cdd6a465a99a74470408ef55d2980e2 Author: galt Date: Fri Jan 5 16:00:15 2007 +0000 "Release log update" commit 74a6f010d9e8b92fb07c2a342a78ffdfe66cacd6 Author: markd Date: Fri Jan 5 08:19:50 2007 +0000 reodered to put required tables together commit 8a051d12e8c3f4d053017e17d92a7f4b3e5673fc Author: markd Date: Fri Jan 5 08:18:33 2007 +0000 fixed stupid typo commit 870e4cc5fbfd6168b29846e11324eedb0e949772 Author: markd Date: Fri Jan 5 08:07:03 2007 +0000 added option to check tables commit 455215ec076fa0432cd1ddd0386fbc96ef836018 Author: angie Date: Fri Jan 5 03:08:45 2007 +0000 Oops, forgot ornAna1.perChromTables=no! commit 42f91a160d880fec3f3e7e4618092d5b3c527e19 Author: kate Date: Fri Jan 5 00:31:22 2007 +0000 Change UCDavis Chip view limits as per request from Peggy Farnham. Adjust Yale RNA subtrack label to distinguish from previous version commit 8b6807eadcdd874c69734df08a965e8390880ae8 Author: heather Date: Thu Jan 4 22:57:52 2007 +0000 change default to 1 (request from Jim) commit a62a336adc540cdfae0d4b9f9653bf780c6bab1c Author: hartera Date: Thu Jan 4 22:33:07 2007 +0000 Minor edit and rephrasing of a sentence in the Methods section. commit 84a6b84cb2c5289424751ce41fc3945aeb28f33d Author: hartera Date: Thu Jan 4 20:08:41 2007 +0000 Minor edits and reformatted the publications listing. commit df372dbba03a2bcd40e2dcfd9f2a59e315085cc4 Author: angie Date: Thu Jan 4 19:32:05 2007 +0000 Use HG_WARN_ERR for all code when compiling on hgwdev. This will keep new development tidy but should not impact mirror sites with different compilers. commit 4ae2041c9385d705c779e68a961a20c3a8b3364e Author: archanat Date: Thu Jan 4 18:49:29 2007 +0000 put the initials back in the credits section commit 432d3f801225339e6a95854a2353ccb77e0cb5a8 Author: archanat Date: Thu Jan 4 17:28:49 2007 +0000 removed the initials in the in-text referencesa(per Donna) commit c34bebf587a2d5e537933e824eb01c06e2fe915d Author: archanat Date: Thu Jan 4 17:25:41 2007 +0000 removed the initials in the in-text references (per Donna) commit 223f7ce8cbc4ae4e9d9b69e0c9dc25b064bd8f93 Author: galt Date: Thu Jan 4 16:00:25 2007 +0000 "Encode release log update" commit 2a0c54cf108a52e9dd2756e3dbc1222f18c8feb7 Author: galt Date: Thu Jan 4 16:00:14 2007 +0000 "Release log update" commit 6ddf27a90ea945b07e18778ce94df9fd5a6263e6 Author: heather Date: Thu Jan 4 01:15:05 2007 +0000 hide xenoRefGene (requested by Jim) commit a716b3e276aa98f2499c571ffccbb98980ea3952 Author: hartera Date: Thu Jan 4 01:04:02 2007 +0000 Draft of description sent by track contributors for RNA structure track from University of Vienna. commit d8fdc1fbea5a47cf4a2af55fc02bdbdfca6c26f5 Author: hartera Date: Thu Jan 4 01:02:23 2007 +0000 Added RNA structure track from University of Vienna. commit 30d7dbe9c99337c5f640e7163dbc00fa00e17d0f Author: kent Date: Thu Jan 4 00:29:34 2007 +0000 Fixing GEPIS priorities and removing redundant link in Human/hg16/links.ra. commit 7909c5f99c94cd3fc5618e57a25a87cda7efdd4c Author: angie Date: Wed Jan 3 23:45:00 2007 +0000 Pass chromEnd=0 to hGetBedRange for whole-chrom query... Querying with chromEnd=chromSize was causing us to miss some out-of-range items, doh! commit e984248aa4aec760300fdbdeedfe2a3b3ccd5ca2 Author: angie Date: Wed Jan 3 23:43:52 2007 +0000 In hGetBedRange{,Db}, if chromEnd is 0 then don't apply the range constraint (do a whole-chrom query). It would be better to replace this with Jim's version in hgTables eventually. commit b0c5f417766af74336e6d4099c1bd445812aa411 Author: angie Date: Wed Jan 3 23:14:13 2007 +0000 errAbort instead of crash when intersecting an out-of-range item. commit b473b32efaafb1524efe0242939a4caeb854a763 Author: heather Date: Wed Jan 3 20:31:03 2007 +0000 edits for weight commit 0af45fc0d4ebdb0341228e0bda8034ef77568f51 Author: kuhn Date: Wed Jan 3 19:37:46 2007 +0000 moved hgwdev and beta into loop that checks all machines via qateam so they can be tested for MYSQL version. ver 4.1 and 5.x use a different signature for the TABLE STATUS output. commit 5190963992e9a34b756369609f8120e601d6dbda Author: aamp Date: Wed Jan 3 17:20:52 2007 +0000 Added CGI data (.ra file) syncing to the "make cgi" list of stuff to make. commit 9a20a8221179b841b85c4e75ab1a5809b2dfb566 Author: galt Date: Wed Jan 3 16:00:22 2007 +0000 "Encode release log update" commit 27d02cedab64d2739ea4e52acf85c143e7d3c7d4 Author: galt Date: Wed Jan 3 16:00:12 2007 +0000 "Release log update" commit 42f9a965f6713421cf124b8c14904f8057208756 Author: markd Date: Wed Jan 3 05:15:25 2007 +0000 move back to kk commit 1bf643b34d5019d4e05a2debf9bcc489355a04d5 Author: rhead Date: Tue Jan 2 22:02:48 2007 +0000 added date to second reference and took out an extra period commit b882ee4bfdcff5d2b4dee9294c2b69c9d5e60a70 Author: hiram Date: Tue Jan 2 21:57:57 2007 +0000 Have the fundamental 8-way alignments up and running. commit e13b00d80e4bc42fb1d1c0fc7211391d085c5049 Author: hiram Date: Tue Jan 2 21:38:43 2007 +0000 Adding 8-way multiz definition commit 799812d15cb762c099763232ae920f0044165941 Author: kuhn Date: Tue Jan 2 21:26:11 2007 +0000 put in a check for ver 4.1 of mysql. this and ver 5 require a different parsing of TABLE STATUS results. also made dev and beta use the qateam access, so they can be checked for version number, too commit 385bb426b1fc49c9febda5e1bff554b2d70d3058 Author: aamp Date: Tue Jan 2 21:17:47 2007 +0000 Fixed affyRatio track grouping problem. commit 34fb5d6f6e60c029d109258b7913be54cd99c1d7 Author: archanat Date: Tue Jan 2 21:13:24 2007 +0000 Took out bold in references section to conform to standard commit 120153d8c867f81b025cc8023df2d030fc1441a5 Author: hiram Date: Tue Jan 2 21:07:17 2007 +0000 Adding 80-way phylo tree picture for Stickleback commit a51377db3eddb2fd0201d579a75d032660e602d5 Author: rhead Date: Tue Jan 2 20:45:34 2007 +0000 added date to reference to conform to pubmed standard commit 7e8352185c72cbbbb70ae4bbd6cdb19c870ec28a Author: hiram Date: Tue Jan 2 20:30:40 2007 +0000 Done with galGal3 blastz, ready to try 8-way multiz commit 30975b89cda307c656d9668e0a72595994c8ede4 Author: hartera Date: Tue Jan 2 18:33:01 2007 +0000 "New version number v149" commit 7c6178d9d837a05600546423db8ec28d18593e45 Author: heather Date: Tue Jan 2 17:02:39 2007 +0000 notes for microsat track commit 6b259c4d625b32f43e482e19a60b7e144af6ed83 Author: aamp Date: Tue Jan 2 16:22:33 2007 +0000 Fixed a bug Jim found during review. commit 075b4070917047aa9e8d2a816c241c17f280e45f Author: galt Date: Tue Jan 2 16:00:18 2007 +0000 "Encode release log update" commit c24fdf5c70cf09c5f62ee7572b52f3699b6b2aa1 Author: galt Date: Tue Jan 2 16:00:10 2007 +0000 "Release log update" commit e650a7110f323b37fa70b33a4193d54881f5d0d7 Author: markd Date: Tue Jan 2 06:08:28 2007 +0000 explictly specify psl columns to avoid need to check for bin col commit c89ff3d47d63bbb7baf763d57eb71dd38b22f13f Author: galt Date: Mon Jan 1 16:00:16 2007 +0000 "Encode release log update" commit 4116d4c1c3d99f882850ac929db10998597cb54b Author: galt Date: Mon Jan 1 16:00:09 2007 +0000 "Release log update" commit 51beee1619bdf1f32961482cf362229c86f847a7 Author: donnak Date: Sun Dec 31 22:08:36 2006 +0000 Updated w/latest version from Jim. commit 14b731845ac955709ec4ed89fd136e4761218e06 Author: galt Date: Sun Dec 31 16:00:17 2006 +0000 "Encode release log update" commit ea00090e4dbf037a6aa29e0b07d4f8cadd3da022 Author: galt Date: Sun Dec 31 16:00:10 2006 +0000 "Release log update" commit a5e8a0d44a6c345934c27f93f47623dd5e6900f3 Author: markd Date: Sun Dec 31 05:35:41 2006 +0000 don't run findUnusedReleases, it summerizes all servers commit 9b6cea07dc8478280bc114d8606ea7648f10026c Author: heather Date: Wed Dec 27 01:09:54 2006 +0000 add testSearch commit b1a15633525511abf8837b63b206eae28ab75189 Author: heather Date: Wed Dec 27 01:09:47 2006 +0000 basic idea, wrapper around hgPositionsFind commit 472a61632f80d3a1866089a1c053657e58ac3cf3 Author: markd Date: Tue Dec 26 23:55:04 2006 +0000 to-do items commit f4da6c484c9b5e264a18e282fe8d8e5ead1a2534 Author: markd Date: Tue Dec 26 23:54:47 2006 +0000 disable installing our own version of tools, they should be up-to-date commit 18d020d0311448ae713ef926fc876eeca9dc82fe Author: markd Date: Tue Dec 26 22:46:47 2006 +0000 removed old entry, sort commit 34eb467ab9b31698d771275976a1a7f4d7425a0f Author: archanat Date: Tue Dec 26 19:19:48 2006 +0000 minor edit to pubmed format commit 497dc48e5ddb3bd4d8f4a23ba644b9fd8d6db6d0 Author: archanat Date: Tue Dec 26 18:56:34 2006 +0000 minoe edit to the PubMed format commit ac2841de9694139b86cbd16d5ddd591d16e5d009 Author: archanat Date: Tue Dec 26 18:54:45 2006 +0000 minor edit to the PubMed format commit 312bbddd3150da781f4f4f32e900c17497ef1dc8 Author: galt Date: Tue Dec 26 16:00:17 2006 +0000 "Encode release log update" commit a0d3c042698da47341e7ba29f800f2700d5ffae2 Author: galt Date: Tue Dec 26 16:00:09 2006 +0000 "Release log update" commit 669df6ae3db00956119754860eaa575de440921f Author: galt Date: Mon Dec 25 16:00:15 2006 +0000 "Encode release log update" commit 698904a2f78bae2921427a1509d42d6a2cd3d519 Author: galt Date: Mon Dec 25 16:00:08 2006 +0000 "Release log update" commit ce8391bb168448223575a5c84d8c789dac9a6ae6 Author: markd Date: Sun Dec 24 20:51:18 2006 +0000 tmp switch to pk for alignments commit e513df0bcf295a7b96f1e88e235ac6b5f4a98b79 Author: markd Date: Sun Dec 24 20:48:42 2006 +0000 improved proceesed change to catch change organisms across different releases commit f8c38ba43b11baa256e2022cfe317e5d6cc593de Author: markd Date: Sun Dec 24 20:48:14 2006 +0000 work on ORFeome track load commit c39d53dd8191c770f3481dbb2f231d26016f444a Author: markd Date: Sun Dec 24 20:08:58 2006 +0000 more frog genome changes commit 54be6e7373302917973b38037e5c09531ddc5456 Author: markd Date: Sun Dec 24 17:40:20 2006 +0000 reenabled some tmp disabled entries commit ebd194dab532f5e6ec423bbf527b988d8b4d5f10 Author: genbank Date: Sun Dec 24 17:15:09 2006 +0000 tmp disable some genomes while working though alignment issues commit d722e6e490e0aec8f3e48bd7665cb31c717309d0 Author: galt Date: Sun Dec 24 16:00:17 2006 +0000 "Encode release log update" commit 7a72915f7c7bead723f25b3c6e36e1408e512f24 Author: galt Date: Sun Dec 24 16:00:09 2006 +0000 "Release log update" commit cebe5690c00d369369220831d5ca63f6d7f9ae00 Author: daryl Date: Sun Dec 24 06:31:13 2006 +0000 adding 'include ../../inc/common.mk' to fix the build commit 77c5b01eedcab33dd166addfc33aea0aacec557b Author: markd Date: Sun Dec 24 00:54:19 2006 +0000 added tool to help with extFile management commit 294e213361ef2056c4647b9527cbd12b297a029c Author: galt Date: Sat Dec 23 16:00:20 2006 +0000 "Encode release log update" commit 51a6d45d4cba1a12c84b62d959255cefe1941bd1 Author: galt Date: Sat Dec 23 16:00:10 2006 +0000 "Release log update" commit 80404ca71853b239efff06928379e4c5b81cb9e9 Author: markd Date: Sat Dec 23 04:41:20 2006 +0000 more frog organism changes commit 0a9aa105e6dc447c9d00e8f043baa1e787db8896 Author: galt Date: Sat Dec 23 04:19:24 2006 +0000 added utility to do several options to ensure integrity of allenBrain visiGene images/data commit f01ad836ab78e0a1db0757d1fa94733c6defab62 Author: hiram Date: Sat Dec 23 01:01:13 2006 +0000 Continuing with fr1 blastz alignment commit 3c585c19f1a78e3ccb5c0ba46b782fe0594e124a Author: hiram Date: Sat Dec 23 01:01:00 2006 +0000 Continuing with maf annotation commit 23f77788d41df07ca435d17cc654386c0d6d9c76 Author: heather Date: Sat Dec 23 00:04:24 2006 +0000 add cnpWong subTrack to SV track commit 2cb2f1cc559d998b755a1cabbea138a9d85e8d74 Author: hiram Date: Fri Dec 22 23:57:31 2006 +0000 Beginning the 7-way conservation track commit b1b001d8e18add11c9c37e2f4aa6557ad4b48854 Author: heather Date: Fri Dec 22 23:48:22 2006 +0000 better way to do previous commit; retains track display order commit 3f3954a9b03e4a3b4220bfe633d765b0576f7a3f Author: hiram Date: Fri Dec 22 23:43:35 2006 +0000 Reorder stickleback above Fugu commit 9e274ac6e654741e77e0ed329cd351c5a13c24de Author: hiram Date: Fri Dec 22 23:31:24 2006 +0000 Proper Net label on Net track commit 2e17c42be4980d503e4ea026a0682b919382ed87 Author: hiram Date: Fri Dec 22 23:28:19 2006 +0000 Adjust oryLat1 order commit 3389ba06cc907ec34da929f523b84cf37aa3f988 Author: galt Date: Fri Dec 22 23:25:28 2006 +0000 fixing misleading variable name inherited from old cloned program commit 2283495423258412408ee3b36de6fe6db5cf37e4 Author: heather Date: Fri Dec 22 23:19:25 2006 +0000 change order of Unknown and Other in order to correctly handle Other commit 38ba01478a98fc43b47e3a26a9cef33e7c3aeef7 Author: hiram Date: Fri Dec 22 23:12:38 2006 +0000 7-Way tree graph for gasAcu1 conservation track commit 35883544292ac37df1e139529c9b74ee35d98b82 Author: markd Date: Fri Dec 22 20:18:22 2006 +0000 specify protein psl for protBlat track commit 611658b12d90376bd209cb192c600c077a96082e Author: ann Date: Fri Dec 22 20:13:47 2006 +0000 the grep error was displaying to stdout (even though I used the -q flag), so I sent it to /dev/null commit f1a427977194c24da8f360d07f9081e4698aa84c Author: hiram Date: Fri Dec 22 19:53:34 2006 +0000 Reorder fish genomes, and running medaka -> stickleback blastz commit 0e11727671dd52b63d7742af0734b59b75b43369 Author: hiram Date: Fri Dec 22 19:52:38 2006 +0000 Reorder fish genomes in dbDb commit 2c1baa75142976638211399d60f5cf47107dc631 Author: rhead Date: Fri Dec 22 19:51:17 2006 +0000 Took out bold in references section to conform to standard commit 63ccf716b39cc1b77cb160e5147565fd2f4d2901 Author: angie Date: Fri Dec 22 18:59:40 2006 +0000 Added O. anatinus (platypus). commit 3126cd7b90200ef4a70314898e4ff56b3889069e Author: angie Date: Fri Dec 22 18:51:56 2006 +0000 Added ornAna1. commit a8de46f20247943d96a6ab6934b37b8db2a482dd Author: galt Date: Fri Dec 22 16:00:25 2006 +0000 "Encode release log update" commit ebb54aef295fd9f8c8ad4d86512a759007ac3357 Author: galt Date: Fri Dec 22 16:00:13 2006 +0000 "Release log update" commit f12ffb10a28d7206f2cfb33f487f59e37de06389 Author: aamp Date: Fri Dec 22 08:29:09 2006 +0000 Forgot colon. commit 145616983cd6b5e060bfa168ad77577cbdf2f291 Author: fanhsu Date: Fri Dec 22 00:31:45 2006 +0000 Added display of "Injection" field. commit 8cfaa1891ca8f5916ca566186d34e387c1aff97d Author: aamp Date: Thu Dec 21 23:13:00 2006 +0000 Added urlLabel for affyHuEx1 track. commit 3dbd66cb1d224f7289a5de4fde31587fe7e8a252 Author: donnak Date: Thu Dec 21 22:52:27 2006 +0000 Added mention of credits page & MySQL server to main page. commit 3debf2ed26b9a7253cf100b192cc6b023673240e Author: rhead Date: Thu Dec 21 22:46:20 2006 +0000 Added a tablesIgnored section for felCat. Heather okayed. commit 986be36d05eeed748817fed0e3e7ca3396faf5f4 Author: angie Date: Thu Dec 21 22:41:09 2006 +0000 Added W to the description of type -- thx Brooke. commit 36a87d2297d3bfa00b0b305b96921de1485aeb31 Author: angie Date: Thu Dec 21 22:23:43 2006 +0000 Edited one more reference to the location of the scripts in the CVS tree. commit e02e177e653b431c1d5bfb625818f34282e7efa0 Author: angie Date: Thu Dec 21 22:21:41 2006 +0000 Added liftOver subdir and README.txt. commit fa80c7b370dbcb18b51e4a5538512304106698d9 Author: archanat Date: Thu Dec 21 21:59:43 2006 +0000 converted refs to PubMed format commit a2035d3daa548979ae6aa21bc1f72536c0a0efde Author: donnak Date: Thu Dec 21 21:56:21 2006 +0000 Added sentence warning people to not cite our development servers in published works. commit e9931e1d3c996d9432ab57fe2b67a50bcfba1342 Author: angie Date: Thu Dec 21 21:41:31 2006 +0000 15way Conservation, Most Conserved. commit 0b4910a59e473c191a5cf83e81d848d7afaca523 Author: rhead Date: Thu Dec 21 21:17:56 2006 +0000 Added felCat, monDom, and tetNig to the wgs definition, as these are all whole genome shotgun assemblies and have contigAcc tables on hgwbeta commit 54944075379e754891f46f95144c6546a5d5bd84 Author: angie Date: Thu Dec 21 21:07:01 2006 +0000 Added Affy {Signal,Transfrags} with development timecourse data. Back in October, I reloaded flyBaseGene with rel4.3, and started to update tables that depend on it. Still need to update some more tables starting with hgNear homologs from blastp. commit 926789f9b230069afbfb3a167037776753e654d5 Author: aamp Date: Thu Dec 21 20:43:27 2006 +0000 Fix for broken links. Affymetrix changed them on their side. commit 8de79c79a6c8b44a9707319d38160bffabf3c01b Author: kuhn Date: Thu Dec 21 18:56:16 2006 +0000 some mods suggested by Ann. dropped two unused variables, declared one variable and added explanation of 'times' parameter commit c9b9518b9dc3c656cd7dc132514ee2939f967977 Author: angie Date: Thu Dec 21 18:47:29 2006 +0000 bugfix: remove hgSession action variables from cart before saving a session, so they can't hijack a newly loaded session. commit 99d492ef55c9efcc48ff40b2d28c3af81ed9d9ac Author: fanhsu Date: Thu Dec 21 17:57:02 2006 +0000 Replaced "data missing" with a temp message "Infected (to be verified with GSID)". commit f1319a9b4a00bc7c9b0a5bda2418cea4f57b6184 Author: galt Date: Thu Dec 21 16:00:26 2006 +0000 "Encode release log update" commit 758a510d3c00070ce19ad232c1f8b8368d804e14 Author: galt Date: Thu Dec 21 16:00:13 2006 +0000 "Release log update" commit 0a5772a299b6bcfbfb6eb9e89a7c4a43df950554 Author: markd Date: Thu Dec 21 08:25:13 2006 +0000 added ignore entries commit 06d7f0a96a3d5207f82d042eb949758ed1c2a253 Author: baertsch Date: Thu Dec 21 04:00:19 2006 +0000 add tupBel1 commit 63041654bda801dc659b7a41cf11e2118e764087 Author: baertsch Date: Thu Dec 21 03:15:51 2006 +0000 remove best from chain tupbel1 commit 2a74216778227f4173e88e36ae753fa20d886a6b Author: baertsch Date: Thu Dec 21 03:04:13 2006 +0000 tupBel1 chains and net commit 0b53b4dce4b4a364674028c390cd18e6d5a16f79 Author: hiram Date: Thu Dec 21 01:01:57 2006 +0000 Experimenting with various combinations of random contigs vs chrom blastz runs commit 37d9a59b3e74aeca362e8ed1863cec6eea28955d Author: hiram Date: Thu Dec 21 01:01:04 2006 +0000 Experimenting with various combinations of contigs and chrom blastz runs commit 6375daadd3b7a8b1d622cf88cc978bb51b3d0023 Author: kuhn Date: Thu Dec 21 00:12:19 2006 +0000 addressed some issues ann brought up in review: dropped two unused variables, explained teh 'times' option, checked for db name (though still a little bug in it) commit 535212f2c9c679e6bf3d84e2f0d4b17f6839befd Author: markd Date: Thu Dec 21 00:07:26 2006 +0000 added DKFZ IMAGE ids commit 31f50cc0f75a2f10af0449b34ba29a68947e2e31 Author: giardine Date: Wed Dec 20 22:40:38 2006 +0000 added new composite wiggle track of selection using the modified McDonald-Kreitman test. commit 8a1815bf3bc544ca5b4423805269ba1606731ba6 Author: hiram Date: Wed Dec 20 22:12:40 2006 +0000 Change note about jksrc.zip location commit d9e76debec9c5fffd4e6c9af460105d1c64f34d4 Author: archanat Date: Wed Dec 20 21:55:18 2006 +0000 converted refs to PubMed format commit 1c208c1341dbf0bf9d7f1c4530257689b6a1fdd1 Author: rhead Date: Wed Dec 20 20:27:58 2006 +0000 added check to make sure that all of the entries in all_mrna.qName are present in mrnaOrientInfo.name. mrnaOrientInfo is apparently not used as much as estOrientInfo, but markd says that this is a good sanity check. commit 22b624d2ced776839df30ec0ee7b0eee10cb6932 Author: aamp Date: Wed Dec 20 19:50:13 2006 +0000 It wasn't drawing expression with width 1. Set it to 1 then if it calculates out to zero. commit 4029c4c0d2d64966317581fb426a0b7c2bf1cb77 Author: kate Date: Wed Dec 20 19:37:25 2006 +0000 Started on U Vienna RNA 2ndary structure commit cbaf4cc03eec066b5025aa27f30bbcea498cc3af Author: kate Date: Wed Dec 20 19:17:54 2006 +0000 Started on newest UCSD Chip/chip data commit 8667e61539bd3387dca619b77da4f82a8cbc99e3 Author: kate Date: Wed Dec 20 19:14:56 2006 +0000 Started on new UCSD Chip/chip data commit bba9e5e8ec11ad2e4b52be35800fb4198eecd950 Author: fanhsu Date: Wed Dec 20 18:51:22 2006 +0000 Updated GO database. commit 8d62df1b55ebfdeebc339e51b610225e39995aab Author: angie Date: Wed Dec 20 18:41:54 2006 +0000 param correction from Sujit Dike. commit 555d7d1b364916758072bf32789639c16da47b4c Author: kent Date: Wed Dec 20 18:26:31 2006 +0000 Put in a var to keep track of submission status for benefit of Safari. commit f54eb9577c410e91e9e1e92ba0c6b6092119c35c Author: giardine Date: Wed Dec 20 18:22:37 2006 +0000 Documented move of oregannoAttr and oregannoLink out of hgFixed to species build database. commit a37db2487663c7ed003b411ec0bed35a19a6be7d Author: kent Date: Wed Dec 20 18:06:27 2006 +0000 Making threshold edits auto-submit. commit c086dc03818f1fd1f4071c47e9f07a1a8f84cf31 Author: kent Date: Wed Dec 20 18:03:13 2006 +0000 Adding some more javascript utility functions. commit 29419a51912d44661ae440c993367038b120fcf1 Author: fanhsu Date: Wed Dec 20 16:32:18 2006 +0000 Added logic to skip initial comment lines. commit 9d63a7d7a6401e39f4ed9442397584772f0b2bb3 Author: galt Date: Wed Dec 20 16:00:27 2006 +0000 "Encode release log update" commit 78fc54b6496c30a7ec0aa2df362092473aa7b30b Author: galt Date: Wed Dec 20 16:00:14 2006 +0000 "Release log update" commit 9aca8f4e734a5d39c29da2774a6f2aa64128f859 Author: aamp Date: Wed Dec 20 06:02:58 2006 +0000 The rendered expression items looked a pixel fatter than they should've been so this is an easy fix. I'm comparing an example: affyHumanExon (the expression track) vs. affyHuEx1 (the simple bed 6 probe track). commit 3fbfdbc09041831be4490048b40ccfede3c08933 Author: aamp Date: Wed Dec 20 05:46:23 2006 +0000 Changed because hg18 affyHuEx1 is the lifted one now (from hg17). But hg16 and hg17 aren't lifted. commit 1a60ce4d64e6cac850624dcd45707e1841424c22 Author: heather Date: Wed Dec 20 01:57:14 2006 +0000 remove reference to goldenPath/chromosomes (doesn't apply to scaffold assembly) commit 35407c19d99065e8b1d7d8cea16f5770622fb7cf Author: baertsch Date: Wed Dec 20 01:34:38 2006 +0000 bushbaby net commit 2fda179717cac69423255c88227e0e3ff3267e1b Author: baertsch Date: Wed Dec 20 01:25:01 2006 +0000 add chainOtoGar1 commit f4d115335174a511220b04475457d8fd37ce117b Author: baertsch Date: Wed Dec 20 01:05:56 2006 +0000 update priority for otoGar1 chain commit 3a6aad69e8c80242232b7a5052a6353812ce975e Author: kate Date: Wed Dec 20 01:04:24 2006 +0000 Start loading new Yale chip/chip commit 231b11bc561ab9175bb757695f0d2254a4cbbfaf Author: baertsch Date: Wed Dec 20 00:58:38 2006 +0000 update coverage commit 3d06e0a66b451b535fb4c3eefb0d6cd33ac03274 Author: baertsch Date: Wed Dec 20 00:56:56 2006 +0000 initial bushbaby html commit 18843a2b8b3e33c2646a967aa15d47ee028cc99a Author: angie Date: Wed Dec 20 00:47:41 2006 +0000 scaled-down version. commit aa4871232226ca19c426142bebce80159ba74330 Author: angie Date: Wed Dec 20 00:39:24 2006 +0000 Initial descriptions for ornAna1. commit 3e7a826c8d7b397dcae7869b453f30c0ea8e71f6 Author: angie Date: Wed Dec 20 00:39:15 2006 +0000 Added ornAna1 to DBS. commit 2b18f779a66bb28588f990238e50e35b653343bd Author: baertsch Date: Wed Dec 20 00:34:50 2006 +0000 add otoGar1 commit 632b2e706cd2b129cf1525bf615d744149db7ca6 Author: kate Date: Wed Dec 20 00:34:28 2006 +0000 Add 6 subtracks to Yale Chip/chip signal and p-value tracks: 3 factors (pol2, pol2-N, h4kac4) in hela and gm06990 commit 3819c765ba0aad357d49f9e0cad338d521cd5570 Author: heather Date: Wed Dec 20 00:27:22 2006 +0000 fix another typo commit 239ebdeb00d64c282c176f016d1a3abc9fa28358 Author: heather Date: Wed Dec 20 00:25:47 2006 +0000 fix typo commit 1cdb345a80fecabd3caf0a6efed7a671cb2a13e5 Author: angie Date: Wed Dec 20 00:20:30 2006 +0000 Photo from Wikimedia Commons (via Wikipedia). commit f1397f432a8477a1a1e96e5cb6467cec4ef7e9b1 Author: baertsch Date: Wed Dec 20 00:13:42 2006 +0000 add chainOtoGar1Best commit de239604c5ac5e722f6ebeaee762368ee41cc3bf Author: angie Date: Tue Dec 19 23:35:38 2006 +0000 Use $BINDIR from common.mk instead of hardcoding $HOME/bin/$MACHTYPE. commit 7759aa8a17af0adbd543085e99aa27ddb8c7d57b Author: galt Date: Tue Dec 19 22:49:52 2006 +0000 fixed matching allen.tab to probeseq.fasta when refseq id either had an extra [.][0-9] or needed added [.][0-4] commit 07c109424df3b79d3ead0233208dbfc69b0226dc Author: baertsch Date: Tue Dec 19 22:03:21 2006 +0000 update info commit 18a48856d98940d4b8160bfc7912f3f8cf7de83a Author: baertsch Date: Tue Dec 19 21:50:49 2006 +0000 bushbaby genome browser initial version commit 2bd01ebaf119aa5d62d874c2945d1370c30bd8ea Author: kent Date: Tue Dec 19 20:31:50 2006 +0000 Adding hyphen to 'drop-down' per Donna's request. commit 3fb86d271a4e28fd82f76191441aadf1a3c8252a Author: heather Date: Tue Dec 19 20:23:18 2006 +0000 simplify search for HapMap SNPs commit 7fa43a57ec3d465d7328d8b3df147e4b62f4aaff Author: kent Date: Tue Dec 19 20:19:16 2006 +0000 Showing help message instead of graphic when no data available to graph. Replacing blank graph drop-down with 'nothing'. Improving error handling of uploads. commit 79c2690e8e849a86774329c793c1c134bf45588f Author: kent Date: Tue Dec 19 20:16:31 2006 +0000 Jiggling around error handling for better error reporting commit d70e783d8aa03c7a536903b432d51d6a5ffe1494 Author: hiram Date: Tue Dec 19 20:02:02 2006 +0000 Working on oryLat1 blastz commit 451c56d74bd8f86534d90ddd248f1d1922741fe6 Author: markd Date: Tue Dec 19 19:43:18 2006 +0000 added Kazusa IMAGE ids commit b1bb0aa4db4e9fbef664bab7cc0633a73aa4faf9 Author: giardine Date: Tue Dec 19 19:26:24 2006 +0000 Moved ORegAnno attributes and links tables to species build rather than hgFixed. commit e70b77110c69bd95029d3199920b8ec28d19e5b0 Author: giardine Date: Tue Dec 19 19:23:44 2006 +0000 Moved ORegAnno's attribute and links tables to species build rather than in hgFixed. commit 658c183cf7a64bca9a0a5846a293cb3598fe24c5 Author: kent Date: Tue Dec 19 19:11:08 2006 +0000 Making it so that all drop-downs autosubmit. Removing Go button. commit 1142ce942f92fbc79fb51b7a34588d798c36c756 Author: kent Date: Tue Dec 19 18:49:52 2006 +0000 Making cgiMakeDropListFull use selected value rather than selected label for what is checked. Removed a half-dozen lines of workaround code. commit cd9e29bc614009ae70cce5f77131a07fc3bef676 Author: kent Date: Tue Dec 19 18:45:51 2006 +0000 Alphabetizing link list, with UCSC links first. commit 25ac7ad2b937618f993eb4782f8df5b449ddd806 Author: rhead Date: Tue Dec 19 18:38:09 2006 +0000 added the binary flags on add (cvs add -kb floretBeta.jpg) commit 2cc377ca15d552c4c78725d62f6b4ea160429edf Author: rhead Date: Tue Dec 19 18:29:58 2006 +0000 going to check this in again using the binary flags (cvs add -kb) commit 26a85f229053836ef5c1ead984b21623fa3f32cc Author: kent Date: Tue Dec 19 18:07:48 2006 +0000 Removing obsolete earlier incarnation of visiGene commit 919249283fd698c6f22b365d81c8d91d27ebdd4f Author: donnak Date: Tue Dec 19 17:07:38 2006 +0000 Modified CT update section to reflect latest changes to hgCustom. commit e1a68d9890dd11a193e12f4d3e2496bb9f629a61 Author: angie Date: Tue Dec 19 16:35:25 2006 +0000 Added ${BINDIR}/ path prefix to stringify so first-time builds can find it more easily. commit a73c6bb45c98047f05067e04a8c6238a1b6f6472 Author: galt Date: Tue Dec 19 16:00:24 2006 +0000 "Encode release log update" commit 8307ffa077a7be7bd8fbef8ef28a31b93d30b4a5 Author: galt Date: Tue Dec 19 16:00:13 2006 +0000 "Release log update" commit 10d285a4259c9e6e6ec2cb1da5afe3c675ccbeef Author: hartera Date: Tue Dec 19 03:51:26 2006 +0000 Added Yale RBFR data. Release to public site on hold. commit 6abffa32f6012083ee820f729e884b15e1789d54 Author: hartera Date: Tue Dec 19 03:45:56 2006 +0000 Ensembl genes for a known genes type track, in progress. Cleanup of liftOver Blat directories and BAC ends. Cleanup old Affy zebrafish alignment directories. Update of ensTo* tables. commit a0ca665c598959632553fe57de0465eaf2f71aee Author: hartera Date: Tue Dec 19 03:41:09 2006 +0000 VEGA genes update on hold - problems with IDs. Compugen Zebrafish array track in progress. Ensembl genes track in progress. commit 728d74c91143aaa0887b78faad0208757ed3afd3 Author: kate Date: Tue Dec 19 00:48:31 2006 +0000 New data submission: U. Vienna RNA secondary structure prediction commit f23f4707470e77985ca385944cb99efb0367a25a Author: angie Date: Tue Dec 19 00:48:11 2006 +0000 Added affyDrosDev{Signal,Transfrags}. commit fbd22974080a4ab5c326f02e08be6e423173d6d0 Author: angie Date: Mon Dec 18 23:11:20 2006 +0000 Swapped latter args to lineFileExpectWords so the error message would make sense. commit 31ea28dbc310521b63253fced9ae3e7b16047e61 Author: kate Date: Mon Dec 18 22:46:02 2006 +0000 Suppress unnecessary saves of custom track files commit 88c35dc471f74bf6deb6aa457b1b03c0253f00f5 Author: ann Date: Mon Dec 18 22:36:51 2006 +0000 added capabilities to copy html output to /qa/test-results/joinerCheck_monitor/keys/ commit 32179d296f85422fe733be60e2f86462cfc155ee Author: fanhsu Date: Mon Dec 18 17:48:57 2006 +0000 Added search for acembly track. commit d0e94898d5ae26cf7de804d41e2a0b044847c89c Author: galt Date: Mon Dec 18 16:00:18 2006 +0000 "Encode release log update" commit 8291508ca9d4654c7ae985e97b277b183c3f8edf Author: galt Date: Mon Dec 18 16:00:10 2006 +0000 "Release log update" commit 0b758abb204434983afa27efe8d2ba3f209672df Author: baertsch Date: Sun Dec 17 23:10:41 2006 +0000 move gepis down a level to handle human and mouse` commit a6e1d1e3cd5eb1c58c06da5347ca596d2d5b5737 Author: galt Date: Sun Dec 17 16:00:20 2006 +0000 "Encode release log update" commit df6d1a6eba909d0f1f218cc590b45f8d2160a7e5 Author: galt Date: Sun Dec 17 16:00:11 2006 +0000 "Release log update" commit 1cf4ec55c8400c21d13636486124cec26c507ba1 Author: fanhsu Date: Sun Dec 17 15:11:06 2006 +0000 Changed URL to GeneCards per GeneCards' request. commit cd85c192d76db9d5e348d07cc6345d92f514b4a2 Author: fanhsu Date: Sun Dec 17 15:09:34 2006 +0000 Changed GAD into "Genetic Associations". commit 0d63569719f1f982d79f30f51d51b18aea9d57ee Author: markd Date: Sat Dec 16 16:08:21 2006 +0000 added frog entries commit abcec90ab9394b10e9ef6821a4b6afb111557562 Author: galt Date: Sat Dec 16 16:00:24 2006 +0000 "Encode release log update" commit 08891251a98300057232becd62abdd88e70c29e5 Author: galt Date: Sat Dec 16 16:00:13 2006 +0000 "Release log update" commit 05b0602cdef3f3358efb4eeeba6cfe5bcfaea489 Author: markd Date: Sat Dec 16 04:25:53 2006 +0000 performance improvement to EST intron rendering commit 27947a79d5a32bebbfdc10dd8c7186d7051bc1a5 Author: kate Date: Sat Dec 16 00:08:13 2006 +0000 Fix quoting in hidden variable that caused problems with some track lines in IE6 commit 460c67260590b59d52f607a93e75267f743d2a29 Author: aamp Date: Sat Dec 16 00:05:00 2006 +0000 Separated next-gene and next-exon on the configure page. commit 09c221b6faa4b55d71020bdbb5f6e4b176c7d2d6 Author: aamp Date: Fri Dec 15 23:55:14 2006 +0000 Cosmetic changes to next-gene button. Perhaps another draft version though. commit d48afa3da88dbb3097a7bcaf2c2c3b9ad6359b31 Author: hiram Date: Fri Dec 15 21:53:34 2006 +0000 Don't output the warning message unless it is supposed to be output ... commit 5bfbb8522d8562fb8a4dbe02f69ad7c275f34aec Author: aamp Date: Fri Dec 15 21:25:22 2006 +0000 Fix for next-gene behavior not working correct that Ann found. commit d04bf6ef5f7c59cd658bad2949d105796b2bb00b Author: hiram Date: Fri Dec 15 20:36:02 2006 +0000 Fixup error for max data points eliminating all intersections. Actually stop at the limit. commit 61bf831e3c18d5bd2cc282507e17a31be3b64a29 Author: angie Date: Fri Dec 15 20:15:49 2006 +0000 Wiki description wording change suggested by b0b. commit c22b3089b8d6cac240beb00a0e9158a68aaba86c Author: markd Date: Fri Dec 15 20:11:01 2006 +0000 added cpp macro to define inline functions in a portable manner commit 3fbf54e0230b672234759bd3a315c6c5edff2090 Author: aamp Date: Fri Dec 15 19:02:08 2006 +0000 Added coloredExon track type (both regular and custom). It uses BED 14. commit 56013e7fc3cfecc8b9118723775bb63441520978 Author: angie Date: Fri Dec 15 18:48:02 2006 +0000 Update namedSessionDb.useCount and lastUse when using or modifying a session (thanks Kayla for pointing out that I forgot to do this :). commit 03d3634665b03cacb2b11c1e2fa1c1251e740527 Author: jsp Date: Fri Dec 15 17:55:43 2006 +0000 Removed erronous origAssembly entry from encodeEvoFold entry. commit bdff08177a96a9d5d20d665692cdaa9cf6f01f56 Author: galt Date: Fri Dec 15 16:00:28 2006 +0000 "Encode release log update" commit 995526e29a436cb7b8c5de9564f6e6e64eeea93b Author: galt Date: Fri Dec 15 16:00:15 2006 +0000 "Release log update" commit 51b640bacd01dc83ca932975c8921aca1cece575 Author: markd Date: Fri Dec 15 05:37:04 2006 +0000 render EST introns in dense mode upto 10mb commit 7e95f9b0ce2c400e547f5c45642e449aed9ad0b1 Author: aamp Date: Fri Dec 15 00:33:31 2006 +0000 affyHuEx1 off-by-one fixing. commit 9f5e23be1d24f6dbbee3a6d49219252c421f07ca Author: fanhsu Date: Fri Dec 15 00:30:41 2006 +0000 Redefined MAX_PB_PIXWIDTH from 30000 to 10000. commit 13a9c5a4295114ab21ce050534ca3c16c212bfb7 Author: heather Date: Fri Dec 15 00:26:32 2006 +0000 tweaks commit a41f162297b328cffd642bc965014ba00fe556ba Author: heather Date: Thu Dec 14 23:52:57 2006 +0000 add search for hapmap SNPs commit 223cd842a47a862eb960a801f0688413d3e034dc Author: baertsch Date: Thu Dec 14 23:13:42 2006 +0000 add GEPIS link for expression by tissue commit b1c27d875f9db0fd50c6c7c7ba1b0ff3b7066269 Author: angie Date: Thu Dec 14 21:58:23 2006 +0000 hgSession.c commit f5be31c14dc8dfd5069f981c8dc3e1b52ca3b7bc Author: galt Date: Thu Dec 14 20:16:26 2006 +0000 additional update keeps cart always in sync - fixes case of ?db=xx when original org differed and you cartDump immediately commit 94b5ac97866de86699ba677bc4ab5fcf8faabef3 Author: hartera Date: Thu Dec 14 18:07:22 2006 +0000 Back out changes made in 1.310 and 1.311. Remove function hMaybeConnectArchiveCentral and function liftOverChainFileExists. There is already a filtering function that does the same as the latter. These functions are no longer used in hGetLiftOverToDatabases(). Also, hArchiveOrCentralDbDbOptionalField() will now revert back to giving an errAbort if there is no connection made to the hgcentral for the archive server. commit 9b6251a69e791aab957a469ca455e1d0b5422fae Author: kent Date: Thu Dec 14 17:57:10 2006 +0000 Fixing some small compilation problems. commit afbc5a00f8cd92dc717f5544d8fffb451e81b6d7 Author: hartera Date: Thu Dec 14 17:51:24 2006 +0000 Backing out changes to check for availability of archive databases and print message if not available. commit ff1c2e78620393b4adce72b7227f19d26c73bf6c Author: archanat Date: Thu Dec 14 17:32:11 2006 +0000 Added dm2 to rules for oreganno tracks and also edited the hg18 oreganno identifier commit 62d3453d5f5456b9f5e72115b89cf4175656d55a Author: galt Date: Thu Dec 14 16:00:30 2006 +0000 "Encode release log update" commit 07af530352655e8f1f616964b8d65e2a6e21c615 Author: galt Date: Thu Dec 14 16:00:15 2006 +0000 "Release log update" commit 5867ace7cdf2e36be84ec910b50fa0409e6eb730 Author: archanat Date: Thu Dec 14 01:04:10 2006 +0000 minor edit to the pubmed format commit 866ae286cd796e013be0817bf256e28819391191 Author: galt Date: Thu Dec 14 00:22:37 2006 +0000 use for automatic Release Log updates commit a2ec649a3e04561b51916986236ec49042d41a02 Author: kuhn Date: Thu Dec 14 00:11:31 2006 +0000 added hyphen commit 5b61b411fc77ac30e2a84f9574e5f8ab692d2ff6 Author: galt Date: Wed Dec 13 23:59:56 2006 +0000 "Encode release log update" commit ee96c4d3e902c12be54d78313e7a0798e0f16e34 Author: galt Date: Wed Dec 13 23:59:54 2006 +0000 "Release log update" commit f0ef8bf1392d2875179c1069a51ecb9962eac430 Author: donnak Date: Wed Dec 13 23:22:40 2006 +0000 Added 2 NAR pubs by Daryl. commit 3aef7a4768920431d9dc134456d842e5e7560d4e Author: hiram Date: Wed Dec 13 23:18:37 2006 +0000 Add Medaka chain and net commit 797775e4b2f6cf0b0f5d9e7340feeabf160d43ee Author: hiram Date: Wed Dec 13 23:16:50 2006 +0000 Add Medaka chain and Net commit 083c1529f8b8af026182c1ff9a0a9d665ca966b2 Author: hiram Date: Wed Dec 13 23:14:28 2006 +0000 Add Medaka Chain and Net commit 7774e9dde538ffa187654e854130bb0417a56f81 Author: ann Date: Wed Dec 13 21:14:06 2006 +0000 added top-bar links to NCBI for canFam2, rheMac2, panTro2, and anoGam1 commit 881e97f2c62d4d972bd18129c4564f299de217ae Author: ann Date: Wed Dec 13 21:02:03 2006 +0000 removing Ensembl links from assemblies that are part-chrom part-scaffold (since many of them will not work) commit f27acd60746ba8e2e77d371c9134c291aa41670a Author: angie Date: Wed Dec 13 20:59:13 2006 +0000 cgiEncodeFull the userName and sessionName when storing in the database or forming variable names, in case those wacky users use quoting or punctuation characters. Also, in case they use <>'s, htmlEncode when printing out. commit cd06102d05d9882f6c4af4c3f4e8510ecf1a3826 Author: angie Date: Wed Dec 13 19:07:35 2006 +0000 Typo fix - thanks Ann! commit c20ef9aa00a29e19ddc97a01504e0283fe571622 Author: aamp Date: Wed Dec 13 18:27:50 2006 +0000 Had to fix because type="expRatio" -> type="array" change for microarray custom tracks. commit c4aa981c6a230b4916e2212512130b03447e98fd Author: angie Date: Wed Dec 13 18:17:55 2006 +0000 Added htmlEncode which does the same encoding as htmlTextOut but allocs & returns a string. commit e75f7b5908d756656e70e078ede7454d2a431db8 Author: angie Date: Wed Dec 13 18:16:43 2006 +0000 Added cgiEncodeFull which is like cgiEncode but does not use the shortcut of + for space. This was needed because at least one client (Thunderbird) did not convert + back to space in a mailto link, resulting in ambiguous + in the decoded displayed string. I felt it was a bit too risky to change the behavior of cgiEncode itself since it is so low-level and widely used in the code... perhaps we expect +'s elsewhere, or benefit from the smaller byte size?? commit adf8fe967ca6cf5e4f9c02a6e48e6e053734242f Author: hiram Date: Wed Dec 13 18:12:49 2006 +0000 Add new option to hgLoadBed to allow Start==End coordinates commit 4fb10fbc41f6727291fad10044b2c3c37e556a8f Author: hiram Date: Wed Dec 13 18:05:08 2006 +0000 Evidently it is OK to have Start==End - custom tracks on SNPs from tables browser produces these commit 898d26c52a9081002b96c24ac531c5a87a7c2a22 Author: ann Date: Wed Dec 13 18:03:46 2006 +0000 bringing Ensembl top-bar links into sync with their latest releases commit 4ba0cc26869fe13f515f30822149d4ecaeb3e4b4 Author: hiram Date: Wed Dec 13 18:03:28 2006 +0000 add allowStartEqualEnd option to be able to load SNP custom tracks from tables browser commit 63aaf8efed5dee976935944d4ad3ed2e6d7fe834 Author: galt Date: Wed Dec 13 16:00:30 2006 +0000 "Encode release log update" commit e5981232aab96bf82168d152bd75ecdbc2d6ee73 Author: galt Date: Wed Dec 13 16:00:29 2006 +0000 "Release log update" commit a0c73e962f0479d95faff42f7274cc0a3a939945 Author: kate Date: Wed Dec 13 02:32:03 2006 +0000 Streamline handling of doc files. Fixes problem where two copies were saved in trash commit f7a9536d70ac2cc66fec8dcdc61faa6c9ced7296 Author: hartera Date: Wed Dec 13 01:46:02 2006 +0000 Added JAVA_HOME variable so it is easy to maintain when Java is updated. commit 28dd78224416f8fd7f1047721b072f81a94cf413 Author: galt Date: Wed Dec 13 01:42:39 2006 +0000 fixing JAVA_HOME by commenting it out; current settings in buildEnv.csh commit 83ee6c09257404962606687bc150ee244135ff95 Author: kate Date: Wed Dec 13 01:03:59 2006 +0000 Restore newlines to parsed documentation commit 1d541bae63182aecbe232a1c7b141e9265cdcd34 Author: kate Date: Wed Dec 13 01:03:24 2006 +0000 Allow duplicate config entries if they are the same commit ad466327c9d15aa88c56f12e7e037a04d595f6f7 Author: aamp Date: Wed Dec 13 00:38:10 2006 +0000 Microarray custom track issue fixed. Look at updated wiki. Setting went from type="expRatio" to type="array". commit ed49f3880e21a923cd40d581c6b3bd21114aadc5 Author: kate Date: Tue Dec 12 22:42:55 2006 +0000 Remove Clear button on doc entry box when URL is source. Previous fix lost somewhere during reverts. commit d8ba3b57ad38c61b7ac9f31ed412555e866aa06c Author: aamp Date: Tue Dec 12 22:34:00 2006 +0000 Commit to fix an error 500. Microarray custom track functionality was lost though and will need to be restored. Perhaps the way Kate had suggested I test the track type in newCustomTrack() is ready and will work. commit 43665ffb8c253176ac2c0bb630b1adcebfb006a1 Author: ann Date: Tue Dec 12 22:33:32 2006 +0000 two suggestions from Donna at code review commit b3331ec64eccf160e2691ca667258d0acb008860 Author: aamp Date: Tue Dec 12 21:53:01 2006 +0000 Almost the right behavior for the next-gene button. commit 4717819812eda093bb19a5f18bae86c7b91f9cfc Author: archanat Date: Tue Dec 12 21:25:52 2006 +0000 converted refs to PubMed format commit 4b94a15fe43f628e5e63a4cabd0195da41361074 Author: kent Date: Tue Dec 12 20:18:51 2006 +0000 Making it so that you have to ask for the extra warnings/errors again, since this breaks the compile on so many platforms. commit 4963b42dab9362676573e16629b033701d309fdb Author: baertsch Date: Tue Dec 12 20:05:45 2006 +0000 remove hg.conf option so that reordering always appears on the config page commit 9c7ded687a399dc007796ed21b34ad2c85eeadbc Author: hiram Date: Tue Dec 12 19:29:11 2006 +0000 Allow windowmaskerSdust table as well as repeats table to fill in for rmsk table commit ec1ee4b8916c746e8821c5e1c6bee49156a4891f Author: fanhsu Date: Tue Dec 12 18:45:10 2006 +0000 Added GAD track. commit 8318e7537f0fdb92c7b8a99901dcc667b79663d3 Author: fanhsu Date: Tue Dec 12 18:34:33 2006 +0000 Removed geneComment because the latest data release from GAD removed this col. commit 46d01db772cab5dc5e82b888e49345be8c059444 Author: fanhsu Date: Tue Dec 12 18:32:29 2006 +0000 Rebuilt gad track tables, gadAll and gad, using the latest data GAD sent us. commit fcffb13aaade771f9c434f5b0ac3e759acde0d45 Author: hiram Date: Tue Dec 12 18:26:40 2006 +0000 Period . in submitted name= field of track line confuses hgTables when it is used in the table name. Strip them from the shortLabel to make the table name. commit 746a61529fff4d609211709a3e37bbeaf33e7d8a Author: galt Date: Tue Dec 12 16:00:27 2006 +0000 "Encode release log update" commit 5d090d96591fb82ccf5c3452a8ffdfa55bcbd95f Author: galt Date: Tue Dec 12 16:00:26 2006 +0000 "Release log update" commit 2c80b4df5337b068ef493c9ccf4503f8c97cbba4 Author: hartera Date: Tue Dec 12 05:31:34 2006 +0000 "New version number v148" commit 91412cb377aa280933a856a7bccdf231f3196765 Author: hartera Date: Tue Dec 12 04:15:16 2006 +0000 Changed wording of message when archive server not available. commit 494f60e7a39871bc6c9eea34b3207622f3a29218 Author: rhead Date: Tue Dec 12 02:28:07 2006 +0000 changed labels for 9way and 15way conservation for release of new track commit 15886a12a677e1a311ee51670242619f371fe339 Author: angie Date: Tue Dec 12 01:53:56 2006 +0000 Tree with org names. commit 143d814e5f58bee39955dac1a08315e3d3b7f643 Author: hartera Date: Tue Dec 12 01:09:04 2006 +0000 For hArchiveOrCentralDbDbOptionalField, if connecting to archive and no connection made then errAbort does not occur and function returns NULL commit 5c953c3b48acac684b2007ec9d2e9f8201643bf4 Author: kate Date: Tue Dec 12 00:57:49 2006 +0000 Fix handling of gzipped custom track doc files commit 3dfd049258cae224932d9e8ab03b90c3b5390627 Author: angie Date: Tue Dec 12 00:17:23 2006 +0000 oops, update to latest dbs used. commit 670a6e97d0a14d5b07d690475f3c82f51359c59d Author: angie Date: Tue Dec 12 00:15:59 2006 +0000 Added multiz15way, phastConsElements15way. commit 9dc570adcfe9b348fb55075754f96c2a23b4c314 Author: angie Date: Mon Dec 11 22:43:39 2006 +0000 Tree with org names. commit b4050182d7f32f4cec1ad3f3643274975ae1ae0c Author: angie Date: Mon Dec 11 22:11:05 2006 +0000 Added gasAcu1 (Stickleback). commit 26317bac5426cd407febc4b71c956113d89b7e71 Author: kate Date: Mon Dec 11 21:41:20 2006 +0000 Disallow configuration in both data and configuration sections of Update screen commit bf1082559f49cabefb32e47b9980454356a2074b Author: donnak Date: Mon Dec 11 20:30:55 2006 +0000 Added WUSTL version #. commit 90965289aa75547dcd7b68dfc5b3e041593fd153 Author: angie Date: Mon Dec 11 20:14:08 2006 +0000 Added example stickleback mRNA/EST IDs. commit f5d3d485daef0f000d098bfebba4e7ff3382d3b1 Author: kate Date: Mon Dec 11 20:01:18 2006 +0000 Disallow custom track update for chromGraphs commit 180a17442b8f7edc3ae55450317110fae79f008f Author: kate Date: Mon Dec 11 19:59:53 2006 +0000 Finishing touches on new Update screen commit a2be0239dd92819bfbfad456de60f0a916cf8f0b Author: markd Date: Mon Dec 11 18:56:38 2006 +0000 added header to score file commit 70f513e664d28002def95645ff76efaf26481dcb Author: angie Date: Mon Dec 11 18:14:16 2006 +0000 More pairwise in prep for Conservation: anoGam1, apiMel3 (did not complete loading because there is no apiMel3 db), triCas2. commit aa418f3b7c8f8bee157c602bfeb9f92e6601ad7f Author: ann Date: Mon Dec 11 17:57:59 2006 +0000 updated NCBI links in topbar to point to correct version (galGal2->galGal3) commit 166202599e343f677823e1c7fc2b0de7fe2fae08 Author: hiram Date: Mon Dec 11 17:46:28 2006 +0000 Finish the alignments without the randoms commit 20d31d7b651d04e91960d8831fa3ff68f8488503 Author: hiram Date: Mon Dec 11 17:45:51 2006 +0000 Add Fr1 swap alignment and measurements commit ef58567a673349b1e6001e669e23e1f4cad26594 Author: galt Date: Mon Dec 11 16:00:21 2006 +0000 "Encode release log update" commit e10535789d7ecae8dc99554090d4c68c37505307 Author: galt Date: Mon Dec 11 16:00:20 2006 +0000 "Release log update" commit 625061f5ca2a39e1bfdf784bb3bcbbe3a9271f3d Author: galt Date: Sun Dec 10 16:00:24 2006 +0000 "Encode release log update" commit 5f96d5eac55fcd1d00f8341e386ee49884858292 Author: galt Date: Sun Dec 10 16:00:23 2006 +0000 "Release log update" commit d96947f652e7b342827026e860f442c5d7e0e520 Author: galt Date: Sat Dec 9 16:00:28 2006 +0000 "Encode release log update" commit 15cf85d759309a40861a71405825b3b5221803aa Author: galt Date: Sat Dec 9 16:00:27 2006 +0000 "Release log update" commit 654907aaf158d5327695beb9008d51e3042f20a6 Author: hiram Date: Sat Dec 9 01:04:31 2006 +0000 A new set of blastz runs without chrUn and the randoms from either side commit 9c42ed4007458d1c58a5b564f01135471f5216b8 Author: hiram Date: Sat Dec 9 01:03:42 2006 +0000 Some swaps for chainLink measurements, and adding fr1 blastz commit df0975b6872eb40ac9b22c2ef6755b287bee4703 Author: kate Date: Sat Dec 9 00:17:41 2006 +0000 Fix for very early errors must maintain HTTP Set-Cookie header before Content-type commit fea95876cc7d99f3466c75b3634a7feb3f4277cd Author: ann Date: Sat Dec 9 00:16:37 2006 +0000 relaxed hg18 acemblyClass rule (due to lift from hg17) commit 690a3f8ea983dbc4ad0a848512d8e7c8b4ba6b4a Author: ann Date: Fri Dec 8 23:48:44 2006 +0000 updated NCBI links in topbar to point to correct version (hg17->hg18; mm6->mm8) commit 9eb7783237e16701b0e6959eb25078862df131fc Author: fanhsu Date: Fri Dec 8 23:28:36 2006 +0000 Fixed a typo. commit 8f74f6c8af2d8482b7d994038581a8e6fd4671bb Author: ann Date: Fri Dec 8 21:57:20 2006 +0000 relaxed aceemblyName rule for hg18 (to match hg17 from which it was lifted) commit 40140988a9dbcdd5725f790f4f659b5be2cfdbe6 Author: kate Date: Fri Dec 8 21:21:07 2006 +0000 Add very early error protection for missing hg.conf and other problems detected during cartAndCookie(), when called from some standard cart wrappers (cartEmptyShell and cartHtmlShell). Should eliminate error 500 in these cases in hgTracks, hgc, hgTrackUi, hgGateway commit a71486fc7bf720a27c82854e3f12ce9dd9dc7edf Author: baertsch Date: Fri Dec 8 21:10:11 2006 +0000 don't display mrna position if the chrom is empty or zero commit f07db21442d779e1051870023d9c8b0da5003f04 Author: baertsch Date: Fri Dec 8 20:55:50 2006 +0000 don't require t parameter when displaying the mrna detail. commit 310e1ffd466c452a66ada4dd5fd99e6035cf58d0 Author: fanhsu Date: Fri Dec 8 16:44:07 2006 +0000 Fixed a bug that caused by the new requirement that the end position of an mRNA is now needed by hgc. commit d5ffebe22ab26c5f34cee405079aab283243ce91 Author: galt Date: Fri Dec 8 16:00:28 2006 +0000 "Encode release log update" commit 0fe7bccc6bf198a6ec30cce083126973572ca471 Author: galt Date: Fri Dec 8 16:00:27 2006 +0000 "Release log update" commit f5f6a95434da6be156ef9628861a45f1113f1aee Author: donnak Date: Fri Dec 8 06:22:39 2006 +0000 Added correction, per MattW. commit ff5ff3d6ac6711c621a93613755519ac777b548b Author: kate Date: Thu Dec 7 23:57:37 2006 +0000 Can't look for url unless custom track exists commit 7277c15de2f690bae189dee9c665b234089a2315 Author: hiram Date: Thu Dec 7 23:56:46 2006 +0000 No longer need to specify ZOO_DBS="" it is already off by default commit 81417e0f4b0b0622bd1a22ce3339f143aed37a92 Author: markd Date: Thu Dec 7 23:42:37 2006 +0000 fixed bugs parsing blast files with multi-line query descriptions commit de95aae4c14aabcafe79ee55c44761a112e2a15f Author: kate Date: Thu Dec 7 23:21:30 2006 +0000 Restore Upload box for doc on Update page (should disappear only if doc from URL) commit 34fd27c949bd6b9b4a1386de0c47ab49997efc1f Author: kate Date: Thu Dec 7 23:20:41 2006 +0000 Reinstate rev 1.101 with new Edit Config box on Update page commit 4d3b4e2182e5ed473372fa439490e1f4a5979fcc Author: lowe Date: Thu Dec 7 23:12:49 2006 +0000 New data/track type: snoRNAs for ncRNA genes identified by snoscan (T.Lowe) commit 6b773d2106ed23ef2aa6d60115c111ae3e309873 Author: lowe Date: Thu Dec 7 23:11:44 2006 +0000 New data / track type: snoRNAs for ncRNA genes identified by snoscan (T.Lowe) commit 376cd5941db9832a4e741ad7fec497277b252d6f Author: lowe Date: Thu Dec 7 22:54:20 2006 +0000 Added changes to snoRNAs track type handling commit 89bd21e7d1c25b9bb0f38cf7e7476e8a1ad19a51 Author: fanhsu Date: Thu Dec 7 22:52:15 2006 +0000 Removed a useless declaration caught by Kayla and Rachel. commit ed6e66ac4a043097395ad60bcb0a733c6eb914fc Author: heather Date: Thu Dec 7 22:33:46 2006 +0000 add cnpRedon commit 4c0c0f9b95cafbd08288bc62c59e4e7c397c05c6 Author: heather Date: Thu Dec 7 22:26:39 2006 +0000 add cnpRedon commit a9972d8128639a20c00cccd8fa90ff257846ae49 Author: heather Date: Thu Dec 7 22:19:07 2006 +0000 add methods for cnpRedon commit c2c25ac93ccaa146e5201780bb4fe665a258f41a Author: heather Date: Thu Dec 7 22:14:11 2006 +0000 add cnpRedon commit c78ed6651cffab050cf703a8fff6ad67e8930507 Author: heather Date: Thu Dec 7 22:13:48 2006 +0000 initial revision commit 5476e97adf220b07c538d4f541f14ea88424c3bf Author: heather Date: Thu Dec 7 21:57:25 2006 +0000 add cnpRedon commit 18825e9ae73d569f8897e5afb3677a6cc8b22de3 Author: galt Date: Thu Dec 7 21:54:45 2006 +0000 added hidden variable to pass changeInfo - this fixes the problem of users using a url with just db=xx and wanting db to have precedence over org commit 90af5d27fe468e2256a50d44c781e2a3e1a38c72 Author: angie Date: Thu Dec 7 21:35:20 2006 +0000 Added reminder about auxiliary tables... it might be possible to find these automatically with joinableFields. commit 92d81d16665737e80da63be1df8ad90b0c4e30f2 Author: heather Date: Thu Dec 7 19:40:30 2006 +0000 cnpHurles changed to cnpRedon commit f2b95e19ab6b8cf0344f0d9cc3b02180d324c815 Author: ann Date: Thu Dec 7 19:20:18 2006 +0000 removed release alpha from encodeUWRegulomeBase track and sub-tracks. Also removed completely three tracks (that this one replaces): encodeRegulomeBase, encodeRegulomeQuality, encodeRegulomeProb. commit 3d112cdc0c1d64f756fbfbd0171c1afacea9c0af Author: ann Date: Thu Dec 7 18:04:21 2006 +0000 added key for sources, changed reference to follow new standards commit c51aed969f083b74ea8078d612534153aa10b952 Author: galt Date: Thu Dec 7 16:00:29 2006 +0000 "Encode release log update" commit 5eee9a65b8517fcdf5247066d54c1b56160b24d1 Author: galt Date: Thu Dec 7 16:00:27 2006 +0000 "Release log update" commit 89f9789a63b5470517cda47f501cb9dd06d24b57 Author: jsp Date: Thu Dec 7 05:26:42 2006 +0000 Changed maf table used by RNAfold track. commit 587ba8f68ed9b3094b0da08e0f8efc3a952e7103 Author: ann Date: Wed Dec 6 23:41:00 2006 +0000 removed two chroms from the chromsomes list for encodeUcDavisChipHits track commit bd71215b8d1ef46bde320f32c716a467076b952c Author: ann Date: Wed Dec 6 22:20:11 2006 +0000 a little cleanup commit 099d98b1e9b6ae16ae553a2392afebbaad7207af Author: lowe Date: Wed Dec 6 22:13:27 2006 +0000 Added .o objects for lowelab specific data types pLfold and snoRNAs commit adefa23d4847ff7cb7a18e24c496584beeb497e8 Author: ann Date: Wed Dec 6 21:57:02 2006 +0000 fixed up DNaseI and SD typos commit b4a19213e64aaac06afedbbc5fe2137b69c81ef3 Author: heather Date: Wed Dec 6 20:09:57 2006 +0000 add cnpHurles (SV subtrack) commit fb54be78af62ca2ab81955a859fb92875e812fe5 Author: hartera Date: Wed Dec 6 19:46:03 2006 +0000 Updated description as suggested by contributors. Added table of cell lines used and updated the Credits. commit 326968677ac2b3a5da568bd8f8ee9522ec6eea28 Author: fanhsu Date: Wed Dec 6 18:44:33 2006 +0000 Fixed a typo. commit aaa7f23479855da41475a535734150e61bc2c101 Author: fanhsu Date: Wed Dec 6 18:42:46 2006 +0000 Removed the abosulte date to guard against patient being identified by specific dates of activities. commit aff4138bafefdbca8398b284ad4713c353598bb4 Author: galt Date: Wed Dec 6 16:00:29 2006 +0000 "Encode release log update" commit b1a5ac2666e85bf1d66a7c6baf3039db933540a6 Author: galt Date: Wed Dec 6 16:00:27 2006 +0000 "Release log update" commit 4709fb228716f40da25e240db5ee8aefa31e5a8e Author: angie Date: Wed Dec 6 15:43:02 2006 +0000 Detect integer overflow in expandFaFastBuf (avoid infinite loop) and use unsigned so size can be up to 2GB instead of up to 1GB. commit 99e456548843ff8289f25c10bf98f8fe9aeb8376 Author: acs Date: Wed Dec 6 04:29:40 2006 +0000 entry for exoniphy commit ae407b2c9ad157226eb0f72021903fdfe76af1ab Author: acs Date: Wed Dec 6 04:17:26 2006 +0000 added exoniphy commit 75a799bf7b3009670fface64d8177f4ca27b0095 Author: heather Date: Wed Dec 6 01:14:09 2006 +0000 notes for getting ortho alleles for all SNPs commit 5c2172798b91566ed099d885b117789d53e640e2 Author: hiram Date: Wed Dec 6 00:49:32 2006 +0000 Add tRepeats and qRepeats options for netClass operation on genomes with no rmsk tables commit 97d24b64f254dec5e1ad9e8a1d3499e07cf448e5 Author: heather Date: Wed Dec 6 00:46:27 2006 +0000 first draft of hapmapAlleleFreq commit 1312581e370c2aa892ae9d631e09fb3071b720d6 Author: markd Date: Tue Dec 5 23:56:19 2006 +0000 recognize .bz2 and .Z compressed files commit 914cf1f1cc1ce81408b756cee4c53917c0110e1f Author: heather Date: Tue Dec 5 23:47:35 2006 +0000 add hapmapAlleleFreq commit b3fd6a6ec8940db5e65401409c2cd14434534912 Author: heather Date: Tue Dec 5 23:41:31 2006 +0000 add liftOver reference commit 8cf3c6009af4ddd11005887851398434d0154ea5 Author: heather Date: Tue Dec 5 23:35:17 2006 +0000 add HapMap SNPs (and final snp seq edit) commit 286ab12d890ec3e770e98ac1928117816672fdd9 Author: heather Date: Tue Dec 5 23:33:50 2006 +0000 initial revision commit e36c9b248b852d998be463e877238dd9c3657d7e Author: ann Date: Tue Dec 5 23:30:20 2006 +0000 typo commit a2994ffbe8f3e28854653e76349f7d77381ce0d7 Author: ann Date: Tue Dec 5 23:29:10 2006 +0000 adding felCat3 to chainDest list commit 2940bb8d0cde74b8a7bf3d84904f0b876d413c42 Author: heather Date: Tue Dec 5 23:25:51 2006 +0000 polishing HapMap SNPs commit 117a62fa23378f4cd40a308c298df8c6cde66bda Author: heather Date: Tue Dec 5 21:45:05 2006 +0000 fix typo commit 906f36391b964cbff9bed93cc19611ccf050f286 Author: jsp Date: Tue Dec 5 20:37:46 2006 +0000 Added details page for encodeEvoFold. commit 690380e666ea9ec5277dc223017aad0f30d25ef4 Author: hiram Date: Tue Dec 5 20:33:53 2006 +0000 Add option to obtain repeats from named table rather than depending upon rmsk commit 17b7ef2677962eca8bec6a735252e245e33d9eb6 Author: jsp Date: Tue Dec 5 20:32:45 2006 +0000 Documentation for encodeEvoFold update. commit 9c7d4998fd353e4acb5c63665a888bbc80e7a7f6 Author: kate Date: Tue Dec 5 19:00:31 2006 +0000 1. New submission: Chip/chip from Ren lab 2. Newly released: DnaseI from Crawford lab commit f388e3d7a2ddc0bc8fc1f880518a68f7bec98421 Author: hiram Date: Tue Dec 5 18:41:40 2006 +0000 Must use db not o_db commit 2db07afdc6596d2b7b35e4fa6196081340b7ee2a Author: giardine Date: Tue Dec 5 18:27:20 2006 +0000 Changed the way the position etc was printed so now strand is included in get DNA link. commit 4216bc626262ab293e9ac28d3a8c7b0ba32450e5 Author: heather Date: Tue Dec 5 18:24:44 2006 +0000 another comment edit commit 5aa5454867df27cbe6d8ba9916dc293ac0935b31 Author: hiram Date: Tue Dec 5 18:16:15 2006 +0000 Adding windowmasker with sdust option documentation commit 527774c2fe4c3020958cff2bfd663c833a0b709d Author: heather Date: Tue Dec 5 17:59:28 2006 +0000 fix compiler warnings commit 1b4d8a711a6506ec5b10871c5c56182ef924793b Author: ann Date: Tue Dec 5 17:46:49 2006 +0000 Updated ENSEMBL links on topbar to reflect their current assemblies commit a4d4d5f7640f013919b512bf96214ef3e091e5b9 Author: giardine Date: Tue Dec 5 17:28:30 2006 +0000 Removed include of humPhen commit 16349c445eec83f620e32e6fab4d93d3bbe8bf3b Author: heather Date: Tue Dec 5 17:26:59 2006 +0000 small edit to comment commit 824f649047d68769cf1dd501044adb310a802fae Author: galt Date: Tue Dec 5 16:00:25 2006 +0000 "Encode release log update" commit 364bc40d277909c8d605e028f3249ea0911c76f7 Author: galt Date: Tue Dec 5 16:00:24 2006 +0000 "Release log update" commit 269ec9efd5b71111c284a46f7cf29a33f79454c1 Author: giardine Date: Tue Dec 5 15:21:17 2006 +0000 Removed file from Human Mutation track commit 48e34b9902a8004fbebc34d8864a9164ed56ba42 Author: giardine Date: Tue Dec 5 15:19:04 2006 +0000 Removed files from Human Mutation track commit f7af02097c2bbbb106643138683149374d98b4c1 Author: giardine Date: Tue Dec 5 15:17:42 2006 +0000 Removing files from Human Mutation track commit eb8f0e74b7504b6a18a8ed8bc8be813080259111 Author: giardine Date: Tue Dec 5 15:15:14 2006 +0000 Removing files for old Human Mutation track commit cf08e82a363256cd652f991a6e2f6945a7f18f24 Author: giardine Date: Tue Dec 5 15:08:55 2006 +0000 Reloaded gv* tables for the Locus Variants tracks. Updates for previous sources plus added more IDbases (a set of LSDBs). commit 01c16272652ae29632a89313de07745a1ad32887 Author: giardine Date: Tue Dec 5 14:46:32 2006 +0000 This script adds likely associations for variants overlapping conserved regions. commit 84f2cee619bc0ccce9c4dab33e291cd2175d023e Author: donnak Date: Tue Dec 5 03:24:43 2006 +0000 These images are referenced by the tfbsConsSite.html track description page. Loks like they were never checked in to CVS, so I'm adding them. Matt just corrected tfbsCons7.gif, which was incorrect out on the RR. commit d7fd443a177e6408b63b9216c3a99a50f866e864 Author: galt Date: Tue Dec 5 01:54:38 2006 +0000 added count displayed at bottom of bigtable showing the # of records passing the filter commit ec8a63a7a3e4c4a8e1b12451fdd667126deac488 Author: kent Date: Tue Dec 5 01:52:23 2006 +0000 Fixing bug most evident in sort genes. commit a4bfe9dfaa2e8f77d7d72fc8a8fa78801002a76a Author: galt Date: Tue Dec 5 01:33:37 2006 +0000 removing unneeded hidden form commit 77ad1c49b96e557b21e229d6cce7407dc233ed07 Author: angie Date: Tue Dec 5 01:22:09 2006 +0000 Script for parsing BGI SNP files into our bgiSnp bed+ format. commit 2d13913e651b23229df756ad5a34b313b1e87777 Author: angie Date: Tue Dec 5 01:21:21 2006 +0000 Added BGI SNPs and Coverage. commit bfc4d412433d5b7d9f99e10de8ea154c0395f93a Author: angie Date: Tue Dec 5 00:57:55 2006 +0000 chain,net to new fly assemblies. commit cb96d367bb50b757f520be3f0b15fcbe8132a496 Author: rhead Date: Tue Dec 5 00:41:32 2006 +0000 Removing release alpha, release beta for encodeNhgriDnaseHsChip and encodeNhgriDukeDnaseHs tracks. (encodeNhgriDukeDnaseHs is replacing encodeNhgriDnaseHsChip.) commit d259c4c8797ac0f465581e1318f4a48ad4d794b1 Author: hiram Date: Tue Dec 5 00:30:11 2006 +0000 Started the blastz runs. simpleRepeat done, full masking done commit ea47947bf557ac928293c2f11b3ce08dae0bc44c Author: ann Date: Mon Dec 4 23:57:11 2006 +0000 corrected type field in two encodeRegulome entries commit 81c275b1144bb2c985bf6665efde43b8b97b7ba0 Author: ann Date: Mon Dec 4 23:48:10 2006 +0000 Added release alpha to encodeUWRegulomeBase track and sub-tracks (not ready for release) commit 2723cd89f19134b03d5987782957babb3d1af6ee Author: ann Date: Mon Dec 4 23:08:38 2006 +0000 Undid change I made in v1.91: Added back in release beta entries for three composite tracks: encodeRegulomeBase, encodeRegulomeProb, encodeRegulomeQuality (these are going to be replaced by one composite track: encodeUWRegulomeBase) commit 9c4e681bd0ef72137519cef593d3e6f7b171856c Author: ann Date: Mon Dec 4 23:00:08 2006 +0000 Adding back what I took out with v1.92: added release alpha lines from three composite tracks: encodeRegulomeBase, encodeRegulomeProb, encodeRegulomeQuality commit 19381ee6430b104e1e96fdf39510337d0d63f442 Author: giardine Date: Mon Dec 4 22:57:19 2006 +0000 Changed BTKbase reference to IDbases, in preparation for the addition of other IDbases (on genome-test now). commit 8efa200ea5bebe6e9d006552368dc0764e6fdec7 Author: heather Date: Mon Dec 4 22:32:22 2006 +0000 add printSnpOrthoSummary commit 934cc3234b5ca1f74880aa1cfbb2b17f93f1c432 Author: rhead Date: Mon Dec 4 20:21:34 2006 +0000 took out reference to floatScore field after Kate renamed it to be more obvious commit f64e8aef81a4ef540e0ae718b1abc208964b5d42 Author: hiram Date: Mon Dec 4 20:19:23 2006 +0000 According to google, should have spaces between user agent entries commit 0c1150b2cc167a8ae2782e0b846416a8f98afd31 Author: hiram Date: Mon Dec 4 20:17:22 2006 +0000 Need spaces between user agent entries. commit 355421414850c4af8855b170928c6cf15b81de86 Author: hartera Date: Mon Dec 4 19:55:56 2006 +0000 Added hMaybeConnectArchiveCentral() function prototype. Returns NULL if no connection is made. commit 3657189d113b526524131de1ed34fccdbb6df0f3 Author: ann Date: Mon Dec 4 18:59:50 2006 +0000 edited minLimit and maxLimit for UWRegulomeBase track to match data commit 3248dee75cd50c0c7f5668eaa390f18dc97b8234 Author: hartera Date: Mon Dec 4 18:06:30 2006 +0000 If no connection to the archive database is available, then print a message to state that the drop down menus only contain databases not on the archive server. commit 2245da771c5ea15d7725bdf1ba1058b5f037404a Author: hartera Date: Mon Dec 4 18:02:25 2006 +0000 Changed message printed when a connection can not be made to the archive server. commit f6dd10c3c7cf84e273cacc13cb7f2773c65637da Author: hartera Date: Mon Dec 4 18:00:04 2006 +0000 If can not connect to hgcentral for the archives server, then print a note to state this and says that the drop down menus will only contain databases not on the archive server. commit 6f7492d7cc0ffffc32fe93738737656690983568 Author: jsp Date: Mon Dec 4 17:58:54 2006 +0000 Added encodeEvoFold to details page switch. commit a1dec0c237d151b354b3a4ef108cb768927acda1 Author: hartera Date: Mon Dec 4 17:56:49 2006 +0000 Added function hMaybeConnectArchiveCentral() to check for a connection to archive hgcentral and return NULL if no connection without aborting. Added function liftOverChainFileExists() to check for liftOver chain files in gbdb. Use this function in hGetLiftOverToDatabases() and use hMaybeConnectArchiveCentral() when compiling the list of databases on the archive server. commit 58353244ed49f822ccbaa3382971c0e3feb729a7 Author: jsp Date: Mon Dec 4 17:56:07 2006 +0000 Added registerTrackHandler for the encodeEvoFold track. commit 2159aa393761d6d40ba5fc0dce2b91de7d401324 Author: jsp Date: Mon Dec 4 17:52:00 2006 +0000 Updated the encode EvoFold track. commit aa3526d2d97cd2528816e8f6445ef74034c10c9f Author: fanhsu Date: Mon Dec 4 17:17:17 2006 +0000 Updated logic to get sequence IDs from subject ID via the gsIdXref table. commit 8fb14bb382a7ddcd8219b2807c3a91803cee33b4 Author: galt Date: Mon Dec 4 16:00:21 2006 +0000 "Encode release log update" commit 6d676bee3de3875c7fc4a4f65cb2e5d7ee876e24 Author: galt Date: Mon Dec 4 16:00:19 2006 +0000 "Release log update" commit e79b6bc4664eaf5df6787fc610a41fbb6c1db2dc Author: galt Date: Sun Dec 3 16:00:21 2006 +0000 "Encode release log update" commit 1fae0bbd0912697a0cf065f80c91c7d770901d78 Author: galt Date: Sun Dec 3 16:00:19 2006 +0000 "Release log update" commit d83acd42b61ec97a7053d0f9cc3b9dc3bccb7077 Author: kent Date: Sat Dec 2 22:04:51 2006 +0000 Fixed a bug Archana found. commit 62fe185ec714ad9847f1875e9805ce50ea52ad24 Author: kent Date: Sat Dec 2 22:02:29 2006 +0000 Fixed a bug Archana found. commit bd7d4405c49356f3892b06012ec4a44d2dc1b4b4 Author: kent Date: Sat Dec 2 19:23:59 2006 +0000 Making auto-recognition of Affymetrix 500k ID's work. Putting in markerRecognizer system to achieve this. commit 5df59965f61743d5e8e9f2a4260d570718df28ba Author: galt Date: Sat Dec 2 16:00:26 2006 +0000 "Encode release log update" commit 2e714976e843baaf9682e330ec27b315cafa125b Author: galt Date: Sat Dec 2 16:00:24 2006 +0000 "Release log update" commit b0336e05a392f1f2e3eb0a89e6f098d1c32f9f1a Author: angie Date: Sat Dec 2 02:44:01 2006 +0000 Moved bgiSnp search spec up to chicken level from galGal2. commit 331a4a045e8c8be3cc76f4dd7baeb25e4f555e70 Author: angie Date: Sat Dec 2 02:33:22 2006 +0000 Moved bgiSnp, bgiCov up to chicken level from galGal2. commit 3a0edefdb15b794b569acd40fda8ff708dee3c9a Author: kate Date: Sat Dec 2 02:04:26 2006 +0000 Texas STAGE data for STAT1 released. Yale Pol2 and H3K4ac Chip/chip submitted commit 929da95d653ef6164ca8718ff93295c581f2e860 Author: kent Date: Sat Dec 2 01:32:49 2006 +0000 Making yellow background hilight for missing data an option (defaults off). commit c1ce63bf9f4ccf97245267ffd291f40ffd47cfad Author: hiram Date: Sat Dec 2 01:22:47 2006 +0000 It is Morgulis, not Margulis commit 81b3b4d6529147cac8dd12e8512807a8742ea1c8 Author: kate Date: Sat Dec 2 01:00:15 2006 +0000 Standardize extrainfo format for BED 5 (encodeNhgriDnase tracks) commit 6b45bff1258470a48c1bdbf013e7ede00362ef83 Author: hiram Date: Sat Dec 2 00:42:26 2006 +0000 Add placeholder to make directory exist during a checkout commit 3e2ec0713d6a154d98b11bdeba2ee539e058c08b Author: fanhsu Date: Sat Dec 2 00:38:12 2006 +0000 Copy over section.ra. commit f1812cd854219a04b9775871b8559f95c2fec83b Author: hiram Date: Sat Dec 2 00:35:57 2006 +0000 Do not leave hgWiggle around after a 'make cgi' commit 011fd2f271be5a895786c9251bab681aeaebdeb2 Author: hiram Date: Sat Dec 2 00:09:08 2006 +0000 Adding WindowMasker "repeats" track. commit 8f0615124e64fcd50c1177731f417c44dd272f80 Author: fanhsu Date: Sat Dec 2 00:06:44 2006 +0000 Added uniGene_3 ID. commit b8a7c1ec3027cd575302ffcb99fcbdf89bb364b6 Author: kate Date: Sat Dec 2 00:03:36 2006 +0000 Add bin and indexes commit fd95697bf13f04c78143ca16c013fe771c039514 Author: kent Date: Fri Dec 1 23:57:02 2006 +0000 Adding region pad. commit b719df5c94c61f8d14385a8790a3d9097da0336c Author: hiram Date: Fri Dec 1 23:34:57 2006 +0000 Track entry may not exist for a table that is just a table and not an actual track. commit 4153a2105e406986fa975c415b31cced3db9abc1 Author: kent Date: Fri Dec 1 23:28:25 2006 +0000 Making hgGenome picture width independent of hgTracks, though they default to the same still. commit ef69a78a68c3c5e033c598b1d1c6c342d0961eaa Author: kent Date: Fri Dec 1 23:16:33 2006 +0000 Updating name of custom track from 'ct' to using whatever customTrackFileVar returns to work with Kate's improvements that make custom tracks database-specific. commit d9055afbd33806e5fad90a7bd797b944c9bc6b45 Author: kent Date: Fri Dec 1 23:15:26 2006 +0000 Exporting customTrackFileVar. commit d814bdf82c33212155c2a9a5952510dde750daa2 Author: kate Date: Fri Dec 1 22:48:14 2006 +0000 1. CT cart parser needs to remove the 'update' uniformly (Fixes RT #1427). 2. Code style cleanup commit ca777d0e66a77eecf5a81430b98330b1f12b6e1a Author: kent Date: Fri Dec 1 22:40:45 2006 +0000 Fixing bug that made browse and sort regions buttons not work when there were two lines of graphs. commit e0a237a4917fea312b766a33a3557cc4aad590a3 Author: kent Date: Fri Dec 1 22:36:27 2006 +0000 Fixing little bug that prevented auto-submit when there were more than one row of graphs. commit 667c53312fccd245c613c2d56e6d4556d9c42c54 Author: kent Date: Fri Dec 1 22:30:12 2006 +0000 Separating out mainPage module from hgGenome module. commit 43f8e61a6aa7b11f2c1e875716501c4c70cb42c4 Author: hartera Date: Fri Dec 1 21:44:07 2006 +0000 Updated description. commit 7aed7fc32cd6110b8a70b166ea701c0b3f9d1c9d Author: angie Date: Fri Dec 1 21:34:09 2006 +0000 Resolved -Wall warning: cast to long for strlen/%ld so they jive on 32-bit systems. commit 48e741a9eb0a681a3f6772d68144c74963c06247 Author: hiram Date: Fri Dec 1 20:52:01 2006 +0000 chromStart must be < than chromEnd, can not be == to. commit da4da68c9e90297a4356179e22b2ee122bb74044 Author: hiram Date: Fri Dec 1 20:07:00 2006 +0000 doTwoBit step bossScript had incorrect name. And use csh variables that were set up rather than the longish path names every time. commit 662c6ae21437db6392199395423997d0e72840f0 Author: genbank Date: Fri Dec 1 20:01:55 2006 +0000 removed use of non-posix function commit 78362f6de194741f00fcd648b05d0f60cf4a5395 Author: kent Date: Fri Dec 1 19:36:24 2006 +0000 Adding htmNbSpaces commit d19ac79f5485dd0f6c91383bdb8ca3fb81a514a5 Author: kent Date: Fri Dec 1 19:22:50 2006 +0000 Putting in an error catcher for better recovery on bad assemblies. commit 1171c8c5c1d6496c64d50baa198d8bcc11481c2b Author: kent Date: Fri Dec 1 19:21:58 2006 +0000 Improving error message when run on assembly without chromosomes. commit b962579ad09c20cd4b10143619d83c9b2ba67d67 Author: angie Date: Fri Dec 1 18:56:12 2006 +0000 Resolved -Wall warning: cast to long for sizeof/%ld so they jive on 32-bit systems. commit abc54ba7be35a42428168b6fd07e07acb3dbf708 Author: kent Date: Fri Dec 1 18:30:43 2006 +0000 Improving -repMatch documentation. commit 0251855daa6afca469a1ce2865f0c8bcb064c69d Author: fanhsu Date: Fri Dec 1 17:00:17 2006 +0000 Added one extra record to miRNA per email from Michel. commit 17666a241135c0a36a745b57347c9cafd166200a Author: fanhsu Date: Fri Dec 1 16:52:13 2006 +0000 Updated miRNA track using new data from 3rd party. commit 702909e8dc52fa3c4d4e27b435142b8eebe963d3 Author: galt Date: Fri Dec 1 16:00:31 2006 +0000 "Encode release log update" commit 4f0b86d171dc03bad064c88e617e9a42b4ef460a Author: galt Date: Fri Dec 1 16:00:30 2006 +0000 "Release log update" commit 3e50bcdf2f670f6d39418ea6168ce3a470bc89f3 Author: kent Date: Fri Dec 1 03:20:12 2006 +0000 Adding htmlNbSpaces. commit d2c73e365e87140246557b7b04437748a112bd92 Author: kent Date: Fri Dec 1 03:18:59 2006 +0000 Fixed problem in example code in comment. commit 82303a4d6045e61b767b887d2cad85d81966fd56 Author: kent Date: Fri Dec 1 03:17:58 2006 +0000 Adding a little more explanitory text to SNP filters. commit 837634c163167e87872f8fc400b31cf0b88cc04f Author: kent Date: Fri Dec 1 03:17:10 2006 +0000 Seems to work. commit 948b597ff59250509e48e6c92e0934d35e47256a Author: ann Date: Fri Dec 1 02:12:59 2006 +0000 removed release alpha lines from three composite tracks: encodeRegulomeBase, encodeRegulomeProb, encodeRegulomeQuality commit df51cb8fc82840b3f33a4bc91531d083fd0af575 Author: ann Date: Fri Dec 1 01:59:07 2006 +0000 removed release beta entries for three composite tracks: encodeRegulomeBase, encodeRegulomeProb, encodeRegulomeQuality (these are going to be replaced by one composite track: encodeUWRegulomeBase) commit f7f6ebcdc824628757f3493339f491d34e5f88c3 Author: kate Date: Fri Dec 1 01:20:04 2006 +0000 Rollback to v146 so new Update screen can have more thrashing commit db2816f70606f17364c3419fcc23d9f091956c39 Author: heather Date: Fri Dec 1 01:09:02 2006 +0000 enable extended name display by default (ortho alleles in hgTracks) commit ad07bd0abc9db30a73e726926b0d3aa036e2240e Author: heather Date: Fri Dec 1 00:45:04 2006 +0000 only consider databases where active = 1; also print database list commit d60b7731d7d365c8e82392544b42fca32790a624 Author: galt Date: Thu Nov 30 23:55:22 2006 +0000 position-squashing fix - for when db changes commit 4dfa180be51ec9887ce967df66645f7ed5410ab1 Author: donnak Date: Thu Nov 30 23:39:05 2006 +0000 Updated the section on Updating a CT to reflect current UI. commit 0e29d44a39dc648ee337879d7f49568ad7e56f53 Author: donnak Date: Thu Nov 30 22:11:48 2006 +0000 Updated Training link to latest OH URL. commit 5ec57b5d1b524c0396fc8dd14cc7713be9fc3234 Author: galt Date: Thu Nov 30 20:51:42 2006 +0000 fixed caching problem in IE commit 757dbecf676a71daf4b11bafb628c9ebb6b7b409 Author: rhead Date: Thu Nov 30 19:29:47 2006 +0000 Added score formula and made a few minor grammar/punctuation changes commit 94cc015294a07511d9e33beb7c2e63f3794a5e90 Author: aamp Date: Thu Nov 30 18:58:27 2006 +0000 Fix for the last one about the next-exon feature. commit 852e712aeae55b3cac5ab66a2395e2c246eb4504 Author: genbank Date: Thu Nov 30 18:56:26 2006 +0000 added ignore entries commit 94316bb5ce580aa7ddf72c886928ac040dc02d0d Author: galt Date: Thu Nov 30 16:00:31 2006 +0000 "Encode release log update" commit 5f8cd617e3b0692f9866b44afbe65bcbdce3c5dc Author: galt Date: Thu Nov 30 16:00:30 2006 +0000 "Release log update" commit 1ddaf09b207d3e3fdcd464250fe4d3902010b3a9 Author: aamp Date: Thu Nov 30 11:07:31 2006 +0000 Next/Prev exon now treats UTR/CDS (thickStart/End) boundaries probably better. Before it would skip past the CDS to the end of the UTR. Now it stops at the boundary and another click of the arrow will go to the end of the UTR. commit 05f1275af83a91e7450a9f7f0398bc9806a98d00 Author: kate Date: Thu Nov 30 04:49:55 2006 +0000 More specific bed5FloatScore for Duke and others with pValue data commit cbec0bcbd2c0489bf5ac1adab55e0dcca490cb67 Author: rhead Date: Thu Nov 30 01:57:14 2006 +0000 suggested changes from Greg Crawford, as well as several minor grammar/punctuation changes commit fa0b2fa02ee8dd0e5d6bc4d7dc895897e28608ba Author: heather Date: Thu Nov 30 01:18:15 2006 +0000 add snpSeq commit 3e3d414ced112f2c7dd4526478f090c2a0dcf9ce Author: kent Date: Thu Nov 30 00:56:53 2006 +0000 Adding clade/organism/assembly controls. Now that they're there I'm not sure I like them.... They do work at least. commit cdfde7aab18f7cc2a1c4394d85cbb358990f1d5d Author: hiram Date: Thu Nov 30 00:49:56 2006 +0000 Have run repeat masker. Now trying window masker. commit 47e24e5113b9154321b3edbe2c516e056b6a94cd Author: heather Date: Thu Nov 30 00:02:53 2006 +0000 move snp seq to separate table commit 6c614de66c70cf4452ec322c9a7e39a564205d00 Author: ann Date: Wed Nov 29 23:58:30 2006 +0000 grammar change commit 0d16f33617557c62f0e69d47770da766feadecb0 Author: ann Date: Wed Nov 29 23:56:42 2006 +0000 fixed misspellings commit 6fbafc9cb69e02c2e9d04e4d5e88fd851652b7c0 Author: hiram Date: Wed Nov 29 23:51:01 2006 +0000 Worked through the makeGenomeDb.pl steps commit 577d716a121e07ec43ceed9be5cc4860a27cf84b Author: ann Date: Wed Nov 29 23:47:54 2006 +0000 changed various misspellings of "DNaseI" commit 9c5c9c36ef22c5be21659c51d19dba4cca2f97c2 Author: aamp Date: Wed Nov 29 23:44:48 2006 +0000 Seems to work now. commit 06354dbf88868d85de7f3ee6c52e7ffaff68ff65 Author: fanhsu Date: Wed Nov 29 23:09:19 2006 +0000 Added search for uniGene_3. commit 95b10a267bd51a049f10909fee1e1e06bec5fb4a Author: kate Date: Wed Nov 29 21:58:00 2006 +0000 Show previous config in config edit box correctly when error occurs during file upload commit 6989caf23aa373b18d66ec6678c27063cfb28b07 Author: heather Date: Wed Nov 29 21:53:41 2006 +0000 use separate snpSeq table for performance; add displayLength constant commit 0d3aa4f5a809073aa36f1ebd1c9986d6590ab006 Author: ann Date: Wed Nov 29 21:37:27 2006 +0000 deleted release beta section for encodeUtexStage track (and composite tracks) commit 2363dfeec94a0e617538bbfe6b487d304404ba21 Author: kent Date: Wed Nov 29 19:50:09 2006 +0000 Moving hgTables/javascript.c to hg/lib/jsHelper.c and librarifying a little. commit 5201e03ef9f1797ad061321c20d2a7a1fce03d58 Author: angie Date: Wed Nov 29 18:45:28 2006 +0000 Force HG_WARN=${HG_WARN_ERR} for the entire tree. commit 44352f7db0381748c7580531502e015983ec8d30 Author: angie Date: Wed Nov 29 18:04:35 2006 +0000 Removing local forcing of HG_WARN to HG_WARN_ERR so it can be controlled for the entire source tree in common.mk. commit a32db64efbdf0981cbeb3b91741bc3431fe1dcb7 Author: angie Date: Wed Nov 29 17:50:15 2006 +0000 Use HG_WARN_ERR from common.mk. commit b708817f23a5401de6214b79bf838ad6a105598a Author: angie Date: Wed Nov 29 17:48:40 2006 +0000 Resolved -Wall warning: unused variable; errAbort format. commit 459f6000fb85c8c046864d6613926eb2c908306e Author: angie Date: Wed Nov 29 17:44:51 2006 +0000 Resolved -Wall warning: unused variable; missing .h. commit 81be23b9eedd3a7eddb3f86b8552ed9ee15ff095 Author: angie Date: Wed Nov 29 17:41:04 2006 +0000 Resolved -Wall warning: errAbort format. commit 97c43327b6302dd348ea5369d5bce39e81478db0 Author: angie Date: Wed Nov 29 17:40:14 2006 +0000 Resolved -Wall warning: unused variable; errAbort format. commit be26468815c4cd616ccfbb0ecf99bb62caabbe38 Author: kent Date: Wed Nov 29 17:18:22 2006 +0000 Seems to work. commit 032074ec0e645fedc904952e0f8c12b94bd1b02c Author: galt Date: Wed Nov 29 16:00:32 2006 +0000 "Encode release log update" commit efac0ec44b4e5032ebd27fb1fcabab5f2a21f82e Author: galt Date: Wed Nov 29 16:00:31 2006 +0000 "Release log update" commit 3d50adce35089dffb15eba23193c93a19e3f85c3 Author: rhead Date: Wed Nov 29 01:36:38 2006 +0000 checking in a backup copy of the beta floret commit c21bb7bea680b237dade6fa9737cc06e820dc4e5 Author: hiram Date: Wed Nov 29 00:53:41 2006 +0000 Adding oryLat1 to DBS commit 93bf4ee1d0510c728402b67369ea7597694478a7 Author: hiram Date: Wed Nov 29 00:53:09 2006 +0000 Initial set of files, somewhat edited commit 5b351a3ec7bb3a78a40d5520b4bb5d4080eb275d Author: galt Date: Wed Nov 29 00:19:37 2006 +0000 fixing db when org changes and top bar menus get drawn by cart start call commit 3edfac8781d0d539619230c6772d9f795e6f704c Author: rhead Date: Tue Nov 28 23:46:04 2006 +0000 added felCat3 commit fa0e9717d267068d1cee870c2e554a0c451adabf Author: angie Date: Tue Nov 28 23:09:40 2006 +0000 Typo fix in multiz15way speciesOrder setting. commit 295d98fcbe8c7c3987e3f2607a7ebf433b7747df Author: kate Date: Tue Nov 28 22:44:07 2006 +0000 Change message on Update screen commit 3434cee53bea934bc608d5e32d28f0b63fa673fb Author: kate Date: Tue Nov 28 22:26:01 2006 +0000 Back out Save feature -- now releasing this week commit 3c87f34e9df92f89af6643322f64e089d3e1bd5d Author: angie Date: Tue Nov 28 21:42:33 2006 +0000 Added htmlTextOut for flyBase2004Xref.synonyms because it sometimes contains non-HTML markup tags -- now we show the contents verbatim. commit 38b51e04fdf4c062a74a4a4545ab1819f7cf6157 Author: heather Date: Tue Nov 28 20:23:33 2006 +0000 enable felCat3 commit 0d8b8ed25785d9ab9bddd7994254a47db29aca7c Author: angie Date: Tue Nov 28 19:07:25 2006 +0000 Resolved -Wall warning: unused variable; cast to int for char used as array subscript. commit 0293db90c0fbf8d1a17c84c679ccb4c3f3edca12 Author: angie Date: Tue Nov 28 19:06:47 2006 +0000 Resolved -Wall warning: unused variable; missing arg to warn(). commit df9a201f6aa86e9868ee6defa4485d7498942f61 Author: angie Date: Tue Nov 28 19:05:51 2006 +0000 Resolved -Wall warning: unused variable. commit 14728f3ea41409973f51791a863ebab869eed66f Author: braney Date: Tue Nov 28 17:42:51 2006 +0000 a couple of new functions: OpenTree, CountLeaves commit 8b66d80ba11b01d96938a3b855e3dbcb170c93e8 Author: braney Date: Tue Nov 28 17:42:00 2006 +0000 add a couple of new functions commit f136ba6058bf5b921f1a25c60cf12e9b45febcc3 Author: braney Date: Tue Nov 28 17:39:05 2006 +0000 add some priv pointers commit 0fd5ceaada137b0bbae4c155a80621eb3cf33cb0 Author: galt Date: Tue Nov 28 16:00:29 2006 +0000 "Encode release log update" commit 722093e90cd604b55520d9cda009e434a2ec65df Author: galt Date: Tue Nov 28 16:00:27 2006 +0000 "Release log update" commit 105b04fc51f404f45ae65f4c22c6039d9e65925b Author: hartera Date: Tue Nov 28 03:27:52 2006 +0000 "New version number v147" commit 44e04c13093b5a67a75bf22055c066d0efe46676 Author: hartera Date: Tue Nov 28 01:20:06 2006 +0000 Removed extra type field from encodeUWRegulomeBase track. commit 8cfd0b79de15d644e646cff1000e68329dcbc36e Author: angie Date: Tue Nov 28 01:06:32 2006 +0000 Added GenBank, Ensembl Genes. commit 611334156c807b3a1688a15cde4a63d942e71d8e Author: hiram Date: Tue Nov 28 00:57:42 2006 +0000 bed graph filters should work even if the table doesn't have a bin column commit 5275fa167aca714479263ef4d24ae8e52bdcf16e Author: kate Date: Tue Nov 28 00:00:40 2006 +0000 Change Duke DNase Pval tracks to bed5floatscore by assigning integer score and retaining p-value float score commit 54ac37c91600d8653c0c90368b4d3988ba0e5dbf Author: donnak Date: Mon Nov 27 23:59:01 2006 +0000 Added new staff, removed people no longer in group. commit f7bc11b1e6cb8a7a1ea55c13dcb993226febad90 Author: heather Date: Mon Nov 27 19:32:08 2006 +0000 fix comment commit 7931202c8af3256fb533cfb2b17d0921092a51ee Author: heather Date: Mon Nov 27 19:31:07 2006 +0000 skip duplicates commit c95245c961ffda8f96c8a228ad671a235d99c28d Author: heather Date: Mon Nov 27 18:15:43 2006 +0000 improve example searches commit f88f80620234fea3f9834e85c9a09ae7c98adf1c Author: angie Date: Mon Nov 27 16:54:21 2006 +0000 Resolved -Wall warning: unused variable. commit 687476e4bab684e770e76578274b0f85e57d90a5 Author: galt Date: Mon Nov 27 16:00:22 2006 +0000 "Encode release log update" commit 6a7a9c9203e910e29ad755228b7b9c59d093f756 Author: galt Date: Mon Nov 27 16:00:20 2006 +0000 "Release log update" commit aa67049815a98c39bbb43e4d3376eae7ead299f9 Author: galt Date: Sun Nov 26 16:00:19 2006 +0000 "Encode release log update" commit c6fe3619abe1daf626d5f1419ea79bdeeea23bf8 Author: galt Date: Sun Nov 26 16:00:18 2006 +0000 "Release log update" commit ed7f4abfb6e90c572a03d64b92ab0a2dbbe406ec Author: galt Date: Sat Nov 25 16:00:21 2006 +0000 "Encode release log update" commit 02e443d822502fce5fb75197acaf690456f2448c Author: galt Date: Sat Nov 25 16:00:20 2006 +0000 "Release log update" commit 5f8037bc141fc325b272cb9f9c41ed8c5dcacfa4 Author: galt Date: Fri Nov 24 16:00:25 2006 +0000 "Encode release log update" commit 41e25df910456306edefa422fab1357f16774b1d Author: galt Date: Fri Nov 24 16:00:23 2006 +0000 "Release log update" commit 6dec72af36e7b0b97bc87b2cc92cdc6455d05d44 Author: galt Date: Thu Nov 23 16:00:29 2006 +0000 "Encode release log update" commit d71b559ef106d5e1bcc710aec98d704ff0a6932a Author: galt Date: Thu Nov 23 16:00:27 2006 +0000 "Release log update" commit 05449a36aa16c099c95f0da90be90406f325dc83 Author: heather Date: Thu Nov 23 05:25:22 2006 +0000 human/neander comparison commit f6897a486ec3fbe49880a54fff1d54f08f7e6e89 Author: heather Date: Thu Nov 23 04:18:43 2006 +0000 add felCat3 commit 01283556c6a44452e9da7ddf0593330ebfb781ad Author: heather Date: Thu Nov 23 03:00:49 2006 +0000 CpG Islands commit 1f7582dcd43a62f41c6f992d03960a5cbcce5e82 Author: heather Date: Thu Nov 23 02:55:57 2006 +0000 fix typo commit bee1cc80db54d3139d6b14716784147d1756d979 Author: heather Date: Thu Nov 23 02:09:15 2006 +0000 add genscan; blastz tweaks commit 913431b3785eff20659eae778bcd4ec4f1d303ea Author: fanhsu Date: Thu Nov 23 00:53:14 2006 +0000 Added hotLinks bar. commit 06afbccbbc70848a096bf8d852a60c5fe67e8676 Author: rhead Date: Thu Nov 23 00:31:38 2006 +0000 removed the word unnormalized from the score filter, as this does not make sense in most contexts (per Adam Seipel, with agreement from Robert) commit b24b23fd7732664a0a8d05906fd75a289506f0a3 Author: heather Date: Wed Nov 22 23:59:35 2006 +0000 remove snpSeq and snpExtFile commit 43855e9cc238ff2a173b79a37a21984e84c4150e Author: kuhn Date: Wed Nov 22 22:47:48 2006 +0000 new utility, checkSyncAll.csh, is a wrapper around checkSync.csh to allow a comparison of tables of all databases bewtween two machines commit 634aac50ce8372ad2abe4fdc756dc5e1bdfe8c13 Author: fanhsu Date: Wed Nov 22 22:39:30 2006 +0000 Added weight. commit 03c29592e02ad256c3491c2ae7955c46a5e1d0a4 Author: angie Date: Wed Nov 22 22:29:12 2006 +0000 Resolved -Wall warning: unused variable. commit 44e77231313b290f79040fbfa658e029b81feb43 Author: galt Date: Wed Nov 22 22:01:28 2006 +0000 playing with filterDropDown or it may become showAvailableValues; also added link from GSID subjId column to the gsidSubj cgi commit 079a8371aa2ead08568dc8126be1bb3dd4f76dc7 Author: heather Date: Wed Nov 22 21:39:23 2006 +0000 tweaks to previous commit commit 79ffd273602fbadd69a44e9455a5a5b71799c8e2 Author: heather Date: Wed Nov 22 21:30:08 2006 +0000 handle axtAffine size limit in printSnpAlignment2 commit e50a8ea209c998f47b39ba0c13791efe2155f39e Author: hartera Date: Wed Nov 22 21:10:37 2006 +0000 Removed an unnecessary line and corrected an HTML tag. commit 7ae5fa01ee45e761bf2512599abd6a6a95477742 Author: hartera Date: Wed Nov 22 20:55:30 2006 +0000 More method details added. commit 835d348ef592bbeb23d04c671700ae61f087cfd2 Author: kuhn Date: Wed Nov 22 20:21:03 2006 +0000 streamlined the processing, pulled out some reporting from aloop to use it for the other case. reduced the number of files created commit a1b55c93f01ef185e9c671a7fb833810fa48636b Author: kuhn Date: Wed Nov 22 19:30:16 2006 +0000 removed wildcards from rm statements. tehyworking properly commit b82457ac355d0695e8e21a1c559d40d0ec0d76c5 Author: kuhn Date: Wed Nov 22 18:36:20 2006 +0000 removed an echo commit 84bf66c80a42cbaec7bec9881dd93c953d87b304 Author: kuhn Date: Wed Nov 22 18:24:51 2006 +0000 added machine-name checking and put quotes aroung an "rm" statement to avoid a "no match" return from the wildcard if file is not there commit fefba87407bf28c86cc78d74a46640c75b903c9f Author: kuhn Date: Wed Nov 22 18:07:27 2006 +0000 removed the exit statement that kept all the files from being removed. it now runs without so much junk left over. commit 0d7013685e063be00b8b3aeb1e9f751ce48c234d Author: hiram Date: Wed Nov 22 17:15:52 2006 +0000 Initial contents, URL links to data providers commit cd226cb36019ef3117647b31fdb1a047a09c5155 Author: galt Date: Wed Nov 22 16:00:31 2006 +0000 "Encode release log update" commit 23962bf57561577b96fde61fa270aecf9b0dcc73 Author: galt Date: Wed Nov 22 16:00:30 2006 +0000 "Release log update" commit f689b79530f4a6398653213db75a7c0e4a78df14 Author: kate Date: Wed Nov 22 04:31:21 2006 +0000 New GIS subtracks. Start on reformat of DNase data commit 72570494484c8b53bbd9aa4af1d92bfc5708fad3 Author: kuhn Date: Wed Nov 22 01:26:30 2006 +0000 added utility, checkSync.csh, to check the existence and update times for tables between any two nodes commit 68b398e4d43c420df2708ffe5e829e9abcadcb42 Author: hiram Date: Wed Nov 22 00:25:50 2006 +0000 And use whatever file name was given, don't enforce a .wig convention commit a0d04b94dac747808f45653f61e8670f8caeff88 Author: hiram Date: Wed Nov 22 00:07:36 2006 +0000 Can find .wib file in local directory too to simplify off-line access to .wig and .wib files commit 427e31d230a1926fdeec5cdb2225eb171fa68fa5 Author: ann Date: Tue Nov 21 18:25:39 2006 +0000 changed cgapAlias rule to join to knownGene instead of going through kgXref commit 50a82d32ddff9aa5cf2aac98428f2dbbbef3f0cc Author: galt Date: Tue Nov 21 16:00:26 2006 +0000 "Encode release log update" commit d279d788e4f1d5f67258a448966cf3233cf3cfe1 Author: galt Date: Tue Nov 21 16:00:24 2006 +0000 "Release log update" commit 1715b421eed4a7f16944aab3047c863458a1e49c Author: heather Date: Tue Nov 21 02:34:01 2006 +0000 2nd attempt TRF (in progress); ooc commit 934f1d57dd25b1d09161f3cde78e20e0acefdca0 Author: rhead Date: Tue Nov 21 00:33:26 2006 +0000 added Minmei Hou to blastz credits commit 67f73ba5d0f251aefc82bd973b2c0670923385b3 Author: hiram Date: Tue Nov 21 00:33:08 2006 +0000 More formal case on the SQL statments to customTrash commit b051eb6aaab5574bfb8f058d9d88700eda6bb8ef Author: hiram Date: Tue Nov 21 00:29:57 2006 +0000 Add affyTxnPhase2 data creation commit 53e1f1f6c010ce341e234544326268a28dfd5a25 Author: rhead Date: Tue Nov 21 00:23:28 2006 +0000 added a note about where the phylo tree came from commit 40e8d9f81213268f76f467909f455f4b65d750e6 Author: galt Date: Mon Nov 20 23:33:43 2006 +0000 now the jksrc.zip file is directly scp-d to hgdownload with full version name and jksrc.zip symlink updated automatically commit 840c62d84e7ae0de4eb57a1f3e05a8137fbdbc24 Author: ann Date: Mon Nov 20 23:31:39 2006 +0000 changed minScore for tfbsConsSites track commit 56c54331e28a2ca06216ae45444e8f41e365e4a7 Author: rhead Date: Mon Nov 20 22:50:40 2006 +0000 tidied up the Rerences section commit 2a9b0222d9a9f7e004f145c4d8cf1ab33844beff Author: donnak Date: Mon Nov 20 22:14:34 2006 +0000 Added Dr. Dobbs pub by Jim. commit 3fbd597e52e68ba7acf35b035da57f39b3d5f7f9 Author: donnak Date: Mon Nov 20 22:06:11 2006 +0000 Made a few edits, fixed up the reference section. commit 6f24480b16d630b436613e49bc2025217746f0a1 Author: fanhsu Date: Mon Nov 20 22:04:08 2006 +0000 Added uniGene_3. commit c4fac2409b0b1d14449f490598f44d3e24e87c5b Author: donnak Date: Mon Nov 20 21:57:42 2006 +0000 Moved citation into a References section, reformatted to PubMed format. commit c864fa345ae68bba3342499211f6f7748101693d Author: fanhsu Date: Mon Nov 20 21:53:00 2006 +0000 Added uniGene_3. commit 8ae7c7caf7f395e725c2c2e3ea3ebe82ccfac70c Author: fanhsu Date: Mon Nov 20 21:52:05 2006 +0000 Added doUniGene3(). commit c7ee1c7e27d8730c2941df65b7b354f0422b147b Author: donnak Date: Mon Nov 20 21:51:47 2006 +0000 A few minor edits, converted refs to PubMed format. commit 6d38a3225eb48bbb51298c3df1e0dde6c63e0123 Author: fanhsu Date: Mon Nov 20 21:43:27 2006 +0000 Created uniGene_3.html. commit 206215b08c0810fd9d584ee7b5e45a2aca2ff1ee Author: donnak Date: Mon Nov 20 21:35:40 2006 +0000 Did some editing, converted refs to PubMed format. commit 0c8ce148e87a8f10f8d591a00b7e8594a904da44 Author: kate Date: Mon Nov 20 20:13:08 2006 +0000 Add first Save to file boxes for UI review commit 0fc183ffd8e2136224a383db611c150294a2e8b9 Author: donnak Date: Mon Nov 20 20:08:03 2006 +0000 Edited the text a bit, converted refs to PubMed format. commit 493de7d1e03969ed3666476c2756d990858557c3 Author: kate Date: Mon Nov 20 19:40:52 2006 +0000 Update Davis track name commit cda2cab4e8c402b12f6b157eb407a88155a61bb3 Author: kate Date: Mon Nov 20 19:34:21 2006 +0000 Tracks ready for Q/A or ENCODE Use: Regulome, Davis, Yale commit 9858df675a582d095943d9e4068871ce54efdaf9 Author: hiram Date: Mon Nov 20 18:15:21 2006 +0000 Add the thickDrawItem option note commit 3df93ae3df88d4d9b358179e58e5253d9e80b312 Author: kate Date: Mon Nov 20 17:08:02 2006 +0000 Tweak vertical space again for DK commit f539d68a3acfa4b093ad263121bb8243dd9a7285 Author: kate Date: Mon Nov 20 16:36:13 2006 +0000 Tweak vertical space again for DK commit c688196716e024cd67fe61b612ed0eec9f2576e6 Author: galt Date: Mon Nov 20 16:00:21 2006 +0000 "Encode release log update" commit 3db35154976a19ded79fd0af10484fd70ffae2d0 Author: galt Date: Mon Nov 20 16:00:20 2006 +0000 "Release log update" commit 00726b6d069a40bb0748cdc8727b29b8145bc8f6 Author: kate Date: Mon Nov 20 15:50:08 2006 +0000 Add vertical space between text boxes, at request of DK commit d6ac03fd7757fc8f23c13c1ee50b8f059a747365 Author: galt Date: Sun Nov 19 16:00:20 2006 +0000 "Encode release log update" commit 4fcf617b60996cea79cadc0f2cf6829dd4ad834c Author: galt Date: Sun Nov 19 16:00:19 2006 +0000 "Release log update" commit 06bd0289c5e020d555aa2235354d1136d86431cf Author: braney Date: Sun Nov 19 00:18:03 2006 +0000 add Neanderthal track commit f10f67af46ed2daed5b92ad2a68ed444262c4646 Author: galt Date: Sat Nov 18 16:00:25 2006 +0000 "Encode release log update" commit 6b9036b26c0e538cb0574326deb8e486169b10fd Author: galt Date: Sat Nov 18 16:00:23 2006 +0000 "Release log update" commit 346f4f79b9249fe8a0612d9c1afd254a5c686238 Author: galt Date: Sat Nov 18 00:37:10 2006 +0000 fixed integer and double filtering commit e999e8f89b1c5737a72ce2c9165188c934f547f7 Author: rhead Date: Sat Nov 18 00:35:03 2006 +0000 shortened topology line, as it was causing text in the entire page to not wrap commit fb7528a0900cc3a3f05f4c77aacd963e7fe006c1 Author: fanhsu Date: Sat Nov 18 00:18:58 2006 +0000 Created gsidSubj.h. commit 9ff6377da9cd42069f330f79f3356de0a7f0d331 Author: fanhsu Date: Sat Nov 18 00:18:13 2006 +0000 Moved from hg/hgSubj to hg/gsid/gsidSubj. commit 2b5ab4039a82e6c418d279babf55b53353306e77 Author: fanhsu Date: Sat Nov 18 00:17:24 2006 +0000 Created makefile. commit 5b251cb6dc619d31e5319b7119d890ddaa3c571e Author: hiram Date: Sat Nov 18 00:17:22 2006 +0000 Show Data last updated information for custom tracks in the database commit f5be7ee1516d01e409c6a623501cbb70446947e0 Author: fanhsu Date: Sat Nov 18 00:16:47 2006 +0000 Moved from hg/hgSubj/hgSubjData. commit 0b6a250237ac2dfa480cb1beb56d690cd3afd402 Author: ann Date: Fri Nov 17 23:50:14 2006 +0000 added a rule for cgapAlias commit e8c92308f71701717fdf0a84ddc565712e29124c Author: galt Date: Fri Nov 17 23:13:23 2006 +0000 adding gsid main directory and gsid table view commit 94a0c6f9c83006e96dac00078dd01d231578e6c1 Author: donnak Date: Fri Nov 17 22:14:15 2006 +0000 Replaced $organism with full organism name -- substitution wasn't working correctly. commit 8b55d875ebb7cd6b804d3174918336664e7fe760 Author: donnak Date: Fri Nov 17 20:56:09 2006 +0000 Pointed users at FAQ for more information on chimp genome renumbering scheme. commit 2409465f0cd84239058cc8ae45ff98445c328aac Author: donnak Date: Fri Nov 17 20:52:19 2006 +0000 Added AceView pub. commit ff51666def98f823181eebc9e9ac6202034f7cee Author: donnak Date: Fri Nov 17 20:50:09 2006 +0000 Minor edit to refs. commit ed4feec68febe2894d0d11364cdbfd78910a6977 Author: donnak Date: Fri Nov 17 20:43:14 2006 +0000 Changed blat max intron length to 750K. commit 3950076fa7dffa3302ed555cb9ae8f22c695c64c Author: donnak Date: Fri Nov 17 20:34:58 2006 +0000 Changed max intron size allowed by blat to 750K. commit 78979e42cbf8bc45a51f337ce59d61dfdf381327 Author: donnak Date: Fri Nov 17 20:32:33 2006 +0000 Made a few edits, converted refs to PubMed format. commit 2b0f613ab5c3daa128036d862f13e0e060e2c38a Author: donnak Date: Fri Nov 17 20:03:14 2006 +0000 Added Bob's NAR pub. commit a53f06ba5c5a58da19612ebad70ed8e4bb37416c Author: ann Date: Fri Nov 17 19:45:14 2006 +0000 added matrixHeader to chainSelf commit dad66b27dc93e1c1a665151115e5e635b2991655 Author: fanhsu Date: Fri Nov 17 01:03:08 2006 +0000 Added logic to allow not lowering the first letter of wigMaf item. commit d8c559d803fb260771ad2ce87aa0285cffab8ea4 Author: heather Date: Fri Nov 17 01:01:54 2006 +0000 make sure coords fit within chrom commit 6f5ba4ff47922c2352c597466e6aa7a02fdbcdfe Author: fanhsu Date: Fri Nov 17 00:59:51 2006 +0000 Added the new trackDb variable "itemFirstCharCase". commit b96de3777f43d97d557912ecbaf8dbe0b5e23fcb Author: hiram Date: Fri Nov 17 00:25:49 2006 +0000 Properly contact the read-only database to fetch chromInfo business commit 377f44ad23198d1daeac2402443b0daca01f765b Author: hiram Date: Fri Nov 17 00:21:46 2006 +0000 Be very careful if a customTrash request is made. Use the correct connection in this case. commit 471dbe1b8d5002c168e59f35725d43206ac810c1 Author: hiram Date: Fri Nov 17 00:09:06 2006 +0000 Use differentString() instead of differentWord() commit 866ea58c6c36126ebcc844cc0e271e0b955b8db0 Author: aamp Date: Fri Nov 17 00:06:26 2006 +0000 Started a windowmasker run on cow. commit c1c474369f57cb471b807420614f4ce75f19bcfa Author: hiram Date: Thu Nov 16 23:55:45 2006 +0000 No more option for naming customTrash - it is simply CUSTOM_TRASH commit 41d2c27ff70e9c2e934015e781cf2a8c88512205 Author: hiram Date: Thu Nov 16 23:45:10 2006 +0000 No option to use any other name for customTrash db except CUSTOM_TRASH commit 8c105e936f608341af642b8debd79e018da58e45 Author: hiram Date: Thu Nov 16 21:52:23 2006 +0000 Watch out for customTrash db access, special conn mechanism commit 94731a68e0285b4730074abfd25b8dc370455e4c Author: kate Date: Thu Nov 16 21:43:53 2006 +0000 Regulome DnaseI HS update to Q/A commit 764e05fbbde30b4c601430fed3c20793d9f426b6 Author: angie Date: Thu Nov 16 19:35:31 2006 +0000 Added older cdsDrawOptions setting to jaxRepTranscript so currently released code will not offer the genomic codons option. commit 00c0aeebbd055a809c2fbce478eaeb82cfc29905 Author: braney Date: Thu Nov 16 17:39:48 2006 +0000 now works with element trees commit 422b7e277e0fb9bf4b4fe328cb89027c62c8bdaf Author: angie Date: Thu Nov 16 16:19:00 2006 +0000 Resolved -Wall warning: unused variable. commit 962af1adda73695c747c277c726ed7458f45b9f8 Author: galt Date: Thu Nov 16 16:00:32 2006 +0000 "Encode release log update" commit 11035c4bdc757219ee26eb496a79484f65b5e426 Author: galt Date: Thu Nov 16 16:00:30 2006 +0000 "Release log update" commit 4d6b4b94ed3dd03a6917cf280575e4a55dc583dd Author: angie Date: Thu Nov 16 03:24:43 2006 +0000 Added gasAcu1. commit a38429a60fc4fa6542a6b4f7c448362e6af76c69 Author: angie Date: Thu Nov 16 01:13:13 2006 +0000 Added 15way Conservation. commit aaffaf7e610dd2d474a1395a0df5dfee42efea46 Author: donnak Date: Thu Nov 16 00:47:12 2006 +0000 Incorporated edits made to human/regPotential7x.html file. commit 9667bdcd4d72fa66a8f71aa9ce8351f9cd83cf80 Author: donnak Date: Thu Nov 16 00:41:52 2006 +0000 Small edit suggested by Bob. commit a175aac9e718baaa95c7a607dcf3a10b02095c29 Author: heather Date: Wed Nov 15 23:10:39 2006 +0000 fix typo in previous commit commit 66a75a29eb2429e5556ec0b8804ceaf564742efb Author: heather Date: Wed Nov 15 23:09:51 2006 +0000 simplify process for SNP sequences commit 26c100a6cb26e0d05f217d548c432278629b60df Author: heather Date: Wed Nov 15 23:03:32 2006 +0000 simplify process for SNP sequences commit ae614a22b5d76b3f07c459f9b072a0abc0da3484 Author: heather Date: Wed Nov 15 22:55:54 2006 +0000 simplify process for sequences commit 523442583964122fc732ada5cf15bca8d75a6361 Author: galt Date: Wed Nov 15 20:41:47 2006 +0000 fixed bug curGeneId not initialized when user presses list-names button in filter page commit e397e4ae78761dfd2a9d5c28fcd4c44c52dfeedc Author: kate Date: Wed Nov 15 19:30:54 2006 +0000 Enhancements to hgCustom 'Update' screen; display separate 'configuration' entry box. Alter labels and suppress unused controls. Disable update for 'chromGraph' type tracks. commit fdfeb9deccbdb8b6208915d69023b62d8d335144 Author: kate Date: Wed Nov 15 19:25:33 2006 +0000 Remove superfluous variable declaration commit 2b09de3b9b0b5ad1bc4524e1bf42ae22e2600efa Author: kate Date: Wed Nov 15 19:19:58 2006 +0000 Remove obsolete CGI variable -- was used by Redirects in custom track code commit 198efed0384f3461da67dbb68a41be2d63138bc7 Author: fanhsu Date: Wed Nov 15 18:44:15 2006 +0000 Added hgSubj. commit 92f41b0b768355fbaa48499f665e1c4d2649ad6a Author: fanhsu Date: Wed Nov 15 18:43:17 2006 +0000 Added hPrint.h. commit 8936bb87f8a8af7de95f8a353e02d80ade9ba45e Author: kate Date: Wed Nov 15 16:20:39 2006 +0000 Pull out partial tests for now commit 30229be6e5cfc323b2deea4b78df194231587460 Author: galt Date: Wed Nov 15 16:00:31 2006 +0000 "Encode release log update" commit f3323d13862ed0daa1a0164491a042416f26101c Author: galt Date: Wed Nov 15 16:00:30 2006 +0000 "Release log update" commit 84b2158efec232e9db60d6b9010a262b13988991 Author: angie Date: Wed Nov 15 15:20:59 2006 +0000 Resolved -Wall warning: unused variable. commit c95c4ef84523123a34bfef720f2bde9479b93418 Author: angie Date: Wed Nov 15 07:59:24 2006 +0000 Added G. aculeatus (stickleback). commit 4ac2299e1ac5a35d1e81e1716ed7fbace711e4b1 Author: angie Date: Wed Nov 15 07:49:16 2006 +0000 Added gasAcu1. commit 4b0a56f2e573d83fcf9484cba4ecb609c9d966d8 Author: markd Date: Wed Nov 15 03:28:52 2006 +0000 disable felCat3 commit 4a5728f54feef480dca2f611242ab7980aea3732 Author: heather Date: Wed Nov 15 01:11:51 2006 +0000 add snpGetSeqDup commit c29f375e71eb7b91430df659a49a2b68ed0bbccc Author: heather Date: Wed Nov 15 01:11:42 2006 +0000 util for checking sequence files commit 38aecfddd4ed835889629ff2dc8cc9d29d234018 Author: angie Date: Wed Nov 15 00:49:20 2006 +0000 Added showDiffBasesAllScales setting to intronEst and xenoMrna for MarkD. Added WindowMasker and {chain,net}GasAcu1. commit d00ca50dbe0a821d9836a8468c4e384cb1ad9019 Author: mario Date: Tue Nov 14 23:40:21 2006 +0000 Shorted shortlabel and set visibility to hide for track augustusHints. commit a2d91d252944408a144cfc694f5bf9696901a8cc Author: mario Date: Tue Nov 14 23:39:26 2006 +0000 Fixed some language issues like capitalization. commit 3bb626e8dd8c312b3a1a7dab2c2bbc5353eb63f7 Author: angie Date: Tue Nov 14 23:29:55 2006 +0000 In &run, when -debug, make lines begin with "#DEBUG#" so it's more obvious that we're in -debug mode and commands are not really executed. commit f2683833d0079193bbbf80844cbbcc7fdf423a43 Author: aamp Date: Tue Nov 14 23:17:46 2006 +0000 Peer-review changes suggested by Angie that included two bugs. commit 89e8891100cea307a19adfb23512062041ab3d30 Author: ann Date: Tue Nov 14 22:21:38 2006 +0000 added qa note regarding mytouch for gold and gap tables commit 59f38bda3586ddb72a92f835f5ddeb0c2548fb99 Author: hiram Date: Tue Nov 14 22:20:47 2006 +0000 Sometimes non-existent tables are requested from trackDb, this is OK. Can only verify that trackDb table exists. commit e53aebf181b005d7438055d9af65080ec5aae332 Author: angie Date: Tue Nov 14 21:47:37 2006 +0000 Added setting to jaxRepTranscript that inhibits the codon-coloring option in hgTrackUi because CDS coords were not included in the original data. commit 9ce9258308e31dbbbd6e4d8b7389642ab0f7eb4c Author: markd Date: Tue Nov 14 21:44:56 2006 +0000 added ESC LongSAGE track commit 84cb928ce2214ce1270bb2b08dbf9fd7c9a49d83 Author: angie Date: Tue Nov 14 21:30:07 2006 +0000 Resolved -Wall warning: unused variable; cast to int for char used as array subscript; parens around && within ||. commit 16cc8b98289e00b849012cd8b899893735325df3 Author: heather Date: Tue Nov 14 20:25:07 2006 +0000 new util commit f4f8b50f04b6d910f73433d52830b8a9524c2d80 Author: heather Date: Tue Nov 14 20:24:51 2006 +0000 add snpReadSeq2, snpFreq, snpCleanSeq commit 652d9428f149af28bc29108baa8eef885f0c03f4 Author: hiram Date: Tue Nov 14 20:23:38 2006 +0000 Do the easy comparisons and the ones most likely to fail first commit b781f97a96551c7295e181c22208f6a7857276b3 Author: hiram Date: Tue Nov 14 20:06:04 2006 +0000 Just fail if sc is NULL. It is the caller's problem much before this. commit 526c02b111a6aa6f9d7adfa320065b56d72e4bd3 Author: hiram Date: Tue Nov 14 20:03:39 2006 +0000 Do not use prevConn in minSpan - it may no longer exist commit 726234c6d30bfa0b0da8704387125831dbd50e8e Author: heather Date: Tue Nov 14 19:33:40 2006 +0000 null checks in sqlGetDatabase() commit 10f28acb13178007011a3a4e74297636ae852b5a Author: heather Date: Tue Nov 14 19:33:16 2006 +0000 fix for error 500 when intersecting with wiggle track commit e2366b405188c9cf2dc0be8e2b729c20c5c04db9 Author: hiram Date: Tue Nov 14 19:06:00 2006 +0000 The error check does not work ? It is always hit. commit cb6d90a762583bf03686ad6c30cf4c5479c5bc11 Author: hiram Date: Tue Nov 14 18:59:01 2006 +0000 Better message if multiple trackDb tables commit 0ea443c7032ccf7ddec76350836af6d17c558ef5 Author: hiram Date: Tue Nov 14 18:39:13 2006 +0000 Proper error message when trackDb tables can not be found or are empty commit aff8793cbe40fbfa9a4005cb7e18090446948723 Author: braney Date: Tue Nov 14 17:55:36 2006 +0000 a utility to rescore chains with the average overlap per base commit befc92623e04d8e3bfb666967aa14eee243f6628 Author: braney Date: Tue Nov 14 17:53:51 2006 +0000 a first pass at a utility that renders tube trees (works with Newick trees now) commit ffd20f26b6c4ffeb1a9bb47c69c961ef2da7fccd Author: donnak Date: Tue Nov 14 16:52:45 2006 +0000 Fixed capitalization of short/long labels for Augustus Using Hints track. commit 6ab5fae0459af616e8d26e6ecee11683191aab9e Author: galt Date: Tue Nov 14 16:00:27 2006 +0000 "Encode release log update" commit 7575df32132f3432f65fdde7c4ef4f26fb43d414 Author: galt Date: Tue Nov 14 16:00:26 2006 +0000 "Release log update" commit 49827c06bd0003feae514bb6e66831185a4511b4 Author: donnak Date: Tue Nov 14 07:28:19 2006 +0000 Edited text, updated citations to PubMed format. commit c4ec13b56e256fdd5a01c015549d7a1f1213a369 Author: donnak Date: Tue Nov 14 07:00:41 2006 +0000 Edited this description page, converted the citation to PubMed format. commit 9365040d2d465281cf3e32aa563b36abedab67b5 Author: donnak Date: Tue Nov 14 06:21:15 2006 +0000 Changed Reg Potential 7X to 7X Reg Potential to be consistent with short labels of prior Reg. Pot. tracks. commit 180ba791e22a9be44296f5606e76642d22ec9f3f Author: donnak Date: Tue Nov 14 05:55:53 2006 +0000 Added a colon to Exclude region type. commit be1032dda41d9602647cc75bdee03c2f15a3545a Author: heather Date: Tue Nov 14 05:36:38 2006 +0000 simplify getSnpSeqFile and getSnpOffset commit 0c97323cd408fda802f022df3ce29e018503585c Author: donnak Date: Tue Nov 14 03:49:15 2006 +0000 Reworded the information link on element types to make its intent a bit more obvious. commit 01531efe5e7e11f74b5efe44b986e998a3808346 Author: donnak Date: Tue Nov 14 03:36:08 2006 +0000 Changed numbered lists to unordered, added some links, updated citation to PubMed style, removed lists from Credits section. commit 2b8a4087d9dd3dc089877846b94974a5e48ed96d Author: donnak Date: Tue Nov 14 03:15:43 2006 +0000 Fixed up capitalization in some long labels to conform to our naming conventions. commit 4d8bc4a68bb2bbbad5e9861a31a0736942045f72 Author: donnak Date: Tue Nov 14 03:04:00 2006 +0000 Shortened short label for Reg Pot 7X track, fixed capitalization of some other track labels to conform to our naming conventions. commit d22fd0a1e8e6f9f1ffd8b6d5ac86f501803792dc Author: donnak Date: Tue Nov 14 03:03:19 2006 +0000 Edited text, fixed typos. commit 706ce02b6867470c25647d7a74fd1846dbcea837 Author: donnak Date: Tue Nov 14 02:40:44 2006 +0000 Added a References section, did a bit of editing. commit df280c8973bcfc112d87a4329666696b589e1164 Author: donnak Date: Tue Nov 14 02:26:40 2006 +0000 Changed capitalization of Poly(A) labels to conform to our naming conventions. commit 1a348e471f9e420437e2c341b653f3fd27c56f80 Author: donnak Date: Tue Nov 14 02:26:01 2006 +0000 Rearranged & edited text a bit, changed refs to PubMed format. commit beee5377a586fde4e3e7a2c5c4dfee3f2941fb30 Author: aamp Date: Tue Nov 14 02:04:46 2006 +0000 Added some log-ratio'ing features for microarrays. commit 11c52af1d486c98a3c13bebfaeefd0b9ef8bd70e Author: aamp Date: Tue Nov 14 02:00:55 2006 +0000 Initial cut of this. $opt_debug = 1 still, which means it won't execute the sub-scripts. commit c491ebc6d1c2987e76f5c2407d708785bab3e4ac Author: donnak Date: Tue Nov 14 01:49:52 2006 +0000 Made a few grammar mods. commit 0e7e3f9cd9f3f485d804b6a398173f631af62085 Author: donnak Date: Tue Nov 14 01:04:59 2006 +0000 Updated the interactive use limitations, did some rewording. commit 8c7d393717450523ac518ded5f4d1b96733e0505 Author: kate Date: Tue Nov 14 01:00:35 2006 +0000 Add info about versioning settings added for ENCODE commit c2ca0b7450713bb706c576a22e48a8cc1191291f Author: hartera Date: Tue Nov 14 00:53:34 2006 +0000 Minor edits. commit be71594ec2916f9c56823390e9fa329345e52e89 Author: hartera Date: Tue Nov 14 00:48:44 2006 +0000 Added more method details provided by the track contributors. commit 3a0ad93c03770a15fe55baedb6cfeef8857f8df5 Author: donnak Date: Tue Nov 14 00:46:48 2006 +0000 Archived 1 news item. commit 28847d31d5b276a28a7612f64021577ff5ab31b5 Author: donnak Date: Tue Nov 14 00:46:36 2006 +0000 Added announcement about genomewiki. commit 8d32ba75938f7abe876091a4e6aa83a6e8829308 Author: angie Date: Tue Nov 14 00:30:25 2006 +0000 Replaced the trackDb settings and cart variable names that control coloring of bases/codons/differences: instead of cds* and pslSequenceBases vars, now there are baseColor* vars. hgTrackUi calls a simplified drop-down generator in hui.c instead of passing around small integers to signal how many options are applicable. In hgTracks, the cds.h functions have been renamed baseColor* and cleaned up to remove unused args. psl records are saved from the load phase instead of being re-queried from the db in the draw phase. Lots of general refactoring in preparation for addition of new features, but lots could still be done to clean up cds.c internals. commit a4291fe7319bed7c82670a8804a33385522766e3 Author: donnak Date: Mon Nov 13 22:58:18 2006 +0000 Fixed a few grammar things. commit 8a76cfc95f7e82b18fbbbfcb2a763b667c36c6d7 Author: fanhsu Date: Mon Nov 13 22:41:55 2006 +0000 Temporarily disable printSageGraphUrl until fixed. commit 1e066da4c8c9950cb5d44451729f9942c31cbb35 Author: kate Date: Mon Nov 13 21:40:12 2006 +0000 Add test with unnamed track commit 573b40d2a22ca7bbe6cab72488953a41c96e8046 Author: baertsch Date: Mon Nov 13 21:03:50 2006 +0000 change rna details position link to use same window instead of opening a new one. commit 566bdf8281ddb64fe33e70f4a48896913b6188d5 Author: hiram Date: Mon Nov 13 18:36:57 2006 +0000 Must use ordinary user to drop tables. commit fda8481ce73a008bc299e0a044a4bdbd8f26648d Author: kate Date: Mon Nov 13 18:23:54 2006 +0000 Tweak date commit b9e9e6b7ee13e9a90c40332b5092a43849ec6010 Author: kate Date: Mon Nov 13 18:13:57 2006 +0000 GIS cMyc Chip-Pet released commit 7c2273f97c801427c2dde2655b807b1a64bf1d0d Author: angie Date: Mon Nov 13 17:18:23 2006 +0000 Resolved -Wall warning: unused variable; assignment used as truth value. commit febf6c4b41c5a24ea9dd33b4b32a60b8efbee492 Author: galt Date: Mon Nov 13 16:00:22 2006 +0000 "Encode release log update" commit 76d64594532ae99a9cd5f022c16d78998e559fad Author: galt Date: Mon Nov 13 16:00:20 2006 +0000 "Release log update" commit 562ef3e2e53fb08f5a66c09797213db5d740fcb0 Author: giardine Date: Mon Nov 13 15:14:29 2006 +0000 removed references to old humPhen track commit 5b65af039622e589498e943b21b6a25cf894be09 Author: markd Date: Sun Nov 12 16:42:13 2006 +0000 rsync hgnfs1 from kkstore02 commit b39234f3630df4af750588c730b84bbf9f675de0 Author: galt Date: Sun Nov 12 16:00:21 2006 +0000 "Encode release log update" commit 2de78f0c0fe1e8370c0b46a0ced5c58a2910aa33 Author: galt Date: Sun Nov 12 16:00:20 2006 +0000 "Release log update" commit bdaaed76c65659df91432159b17659fb0482b3cf Author: galt Date: Sat Nov 11 16:00:26 2006 +0000 "Encode release log update" commit 1d5b6ce60465de6bd6f8c3a27a1bbf07245553f2 Author: galt Date: Sat Nov 11 16:00:25 2006 +0000 "Release log update" commit 1e24715bef9534918808b4b7277f6abfc189d393 Author: giardine Date: Fri Nov 10 19:00:08 2006 +0000 updating conversion scripts to current version commit 7342cc6611154f5cace546878872363dbd3b3888 Author: heather Date: Fri Nov 10 18:47:19 2006 +0000 hide the mrnas since we don't have very many (MarkD request) commit 05bb091cf4bf462a18556c146609378ceefcbec7 Author: giardine Date: Fri Nov 10 16:38:33 2006 +0000 removed entries for hgMut* tables commit 51e87e4e2069d7c5995fee8643513f01a820bb59 Author: giardine Date: Fri Nov 10 16:37:47 2006 +0000 removed searches for hgMut commit 007702694440802ba9256f62898efbe40bbe82b1 Author: giardine Date: Fri Nov 10 16:32:11 2006 +0000 removed code for hgMut* tables/track commit c917c90bbe48262a9350721bd57afc85f825743c Author: giardine Date: Fri Nov 10 16:24:55 2006 +0000 removed code for hgMut* tables/track commit 882a59ad3822f59ca8ca9c592fdeb48d909d40bd Author: giardine Date: Fri Nov 10 16:22:37 2006 +0000 removed code for old hgMut* tables/track commit 6a6bfbc310aa50b13a63f20e999648c8d6e34b51 Author: giardine Date: Fri Nov 10 16:15:09 2006 +0000 removed old/unused hgMut track commit f3de6049fb16778029c3157e23c0795f3b05e6b2 Author: giardine Date: Fri Nov 10 16:04:43 2006 +0000 removed unused hgMut* files commit 1cea15e1a6924843eaf34e054ecbc6ac755e57f4 Author: galt Date: Fri Nov 10 16:00:31 2006 +0000 "Encode release log update" commit d0c78f9cff74620127c3c7d1e220da38ac715a75 Author: galt Date: Fri Nov 10 16:00:30 2006 +0000 "Release log update" commit 9b57e8b13b8ed83e4a21643f7750fa4d3d097753 Author: genbank Date: Fri Nov 10 06:19:37 2006 +0000 added new A/B list track commit 3dac060a324522b1e6b902ff049ecc788476a345 Author: markd Date: Fri Nov 10 04:42:41 2006 +0000 reenabled cat (meow) commit 4fd04ffd698b5ea1cac2a575a228c8b2d872548a Author: heather Date: Fri Nov 10 01:17:35 2006 +0000 add all_est commit 266e1a89af1019783227bd9aa43b6aace3c170ae Author: fanhsu Date: Fri Nov 10 01:00:01 2006 +0000 Updated spreadAlignStringProt(). commit e4c6cf966e1aabea6af5f0a707eced7329933339 Author: fanhsu Date: Fri Nov 10 00:48:39 2006 +0000 Updated spreadAlignStringProt() to enable "dots" option. commit d7464b282de7a4af13846f97ab2e857c4ec898ac Author: kate Date: Fri Nov 10 00:37:37 2006 +0000 Texas STAGE data to Q/A commit bba5c1116a271362f7ea68c2c8bd25a97c87bdca Author: hiram Date: Fri Nov 10 00:35:57 2006 +0000 Use the CT_META_INFO define for the metaInfo string commit 64052181d15f1a1daf5060b01eacaf85ef6507da Author: kate Date: Fri Nov 10 00:24:01 2006 +0000 Methods update from Akshay Binge at the Iyer lab commit 3490c6c1c1dca1a37cce7f8369d5b23557b546d3 Author: hartera Date: Thu Nov 9 23:58:33 2006 +0000 Changed dataVersion - it is not an ENCODE freeze date. Changed track colors. commit 3c4ee52570a893c3022d14426bea9fe536a658c1 Author: heather Date: Thu Nov 9 23:58:26 2006 +0000 never mind about forcing native ests for felCat3 commit ec2bea86d24cb23a42a3801a43ac93a39b839962 Author: heather Date: Thu Nov 9 23:45:29 2006 +0000 blastz rerun for chainMinScore and chainLinearGap; previous featureBits; genbank comments commit 47bbefd866c6a19581a5ffd9983cf4a71ee88d2e Author: hartera Date: Thu Nov 9 23:43:42 2006 +0000 First draft of description from contributors for Yale Chip RFBR analysis data track. commit d74c74fae234badf271b1f81b289d7535426aeda Author: hartera Date: Thu Nov 9 23:42:20 2006 +0000 Added encodeYaleChipRfbr track for Yale RBFR analysis data. commit 92a8ff4f79a17832b5cb4555c90e086d18434dff Author: ann Date: Thu Nov 9 23:29:54 2006 +0000 grammatical changes suggested by Brooke during code review commit 66cad522fb9c0c6bb2d6ef4eb7ff64ce90020408 Author: donnak Date: Thu Nov 9 23:17:45 2006 +0000 Converted listing to standard PubMed format to standardize with CBSE. commit a73045ab672947421f784bd7cb008c81fdc11c72 Author: heather Date: Thu Nov 9 22:33:59 2006 +0000 more genbank tweaks commit 43d61f24774949a608c3b1e4840e490d7019bd14 Author: heather Date: Thu Nov 9 22:22:14 2006 +0000 force native ests for felCat3 commit 0926892c3bf88f55ac29b92e5aa19c8503e0c778 Author: heather Date: Thu Nov 9 22:05:53 2006 +0000 more felCat3 tweaks commit a4d6baeffe41f746de721c4da3deee85ba416d5b Author: hiram Date: Thu Nov 9 20:09:25 2006 +0000 Handle the case where tables and metaInfo do not match up. Clean either regardless of existence in other. commit e884b0d77a8ccfadb6ed47faf9837a698c663e1a Author: angie Date: Thu Nov 9 19:07:48 2006 +0000 Added mm8 to rules for new Jax tracks. commit 11f96f844684eebf2a5b175415541c7e33d828aa Author: angie Date: Thu Nov 9 19:04:08 2006 +0000 Resolved -Wall warning: unused variable; cast to int for char used as array subscript. commit 036a972968fe0c9f3bdd9c27f8c517c5738afeee Author: markd Date: Thu Nov 9 18:17:01 2006 +0000 disabled felCat3 until i is reloaded commit b76501eba94dcbf89c8f7e7edb9251691ac6425b Author: heather Date: Thu Nov 9 17:28:37 2006 +0000 add hg18/felCat3 chain/net commit 2523456f1d52daa9ead806096d4a179f3544f1a9 Author: giardine Date: Thu Nov 9 16:23:03 2006 +0000 removed mention of PhenCode project from description. While true not needed. commit 139c38f0598ac5d7ca81ffd4f0cb3deb1680b9ce Author: galt Date: Thu Nov 9 16:00:33 2006 +0000 "Encode release log update" commit d3b9f945b228e431b19e1569bd1138a0e3789259 Author: galt Date: Thu Nov 9 16:00:32 2006 +0000 "Release log update" commit 7267feec998866ecc9dac10bbf9eee64834c7f20 Author: markd Date: Thu Nov 9 08:40:34 2006 +0000 added ignore entries commit 2e5ef437b4846dc66d1723c2b6ca8cdd3157ec7c Author: hartera Date: Thu Nov 9 02:32:30 2006 +0000 Update to description. commit 0b50d74b42a837665dac88606c581b7dd4a5ec2c Author: hartera Date: Thu Nov 9 01:32:45 2006 +0000 Updated the criteia for a valid pair of BAC ends. commit 0d8d6c58ef63084844f3dfd720823fb7ad7dbeba Author: heather Date: Wed Nov 8 23:58:13 2006 +0000 copy ooc file commit 7287d611a32a1dcf4fbb9f449f5b1c8e4342e822 Author: heather Date: Wed Nov 8 23:49:09 2006 +0000 genbank.conf edits from Mark commit 42a9c1124b1781cc5a81c0c72a5f3c990fbbd49b Author: fanhsu Date: Wed Nov 8 23:20:23 2006 +0000 Removed some old residual code that is no longer valid. commit df3f992bb4b0147b5934c3d09cb86c890122b07d Author: fanhsu Date: Wed Nov 8 22:31:16 2006 +0000 Added calling to spreadAlignStringProt() for protein MAF display. commit 679c3b4acaae0b2c83e32a913edc5bfb436fd288 Author: fanhsu Date: Wed Nov 8 22:29:44 2006 +0000 Added spreadAlignStringProt(). commit f782393067743757afee5d373569359369c272e5 Author: hartera Date: Wed Nov 8 22:22:23 2006 +0000 Updated ensXRefZfish - added new field and altered description. commit f0859cd5c4a224c3c5f3f8a76ddf8bdba332280a Author: galt Date: Wed Nov 8 21:48:24 2006 +0000 fixes hgBlat genome list when genomes have no blatServers commit 1daa5d4535fd955767ea1c9591a80e4d75f4c7ce Author: heather Date: Wed Nov 8 21:44:46 2006 +0000 add an error check and a comment commit 08da9ab6be7d549a1845d45af5d16564ed0a2a03 Author: galt Date: Wed Nov 8 21:39:25 2006 +0000 fixed too many tabs in header line of get text commit d2e358ee8f1b6b3e73e0de0c4a7e7ff74bc3c989 Author: markd Date: Wed Nov 8 20:52:17 2006 +0000 added new ORFeome IMAGE clone ids commit c4c5ca6d176d7d445919d6cf22176147ef63ac1e Author: heather Date: Wed Nov 8 20:45:14 2006 +0000 snp tweak commit 8954d05c1e5a62b9e718a27016a366784513ee14 Author: heather Date: Wed Nov 8 19:47:23 2006 +0000 relax minCheck for snp125 sequences commit 7a13b2eaa9f092615048b5186daac681bf0dc3c5 Author: heather Date: Wed Nov 8 18:59:03 2006 +0000 another SNP alignment fix commit 3ea74a018eccebdafac05a42ed5c5adc51560418 Author: angie Date: Wed Nov 8 17:49:42 2006 +0000 Resolved -Wall warning: unused variable; argv type. commit 278abda9879427983e580cce9860be65db53ae26 Author: angie Date: Wed Nov 8 17:48:12 2006 +0000 Resolved -Wall warning: operation may be undefined (var = var = ...). commit 93d9af0a10281bb2f0acc15f06bc5babf15de97d Author: galt Date: Wed Nov 8 16:00:35 2006 +0000 "Encode release log update" commit fd241fa8e53d3a7af08af1c5a66ba694a8f15ce7 Author: galt Date: Wed Nov 8 16:00:33 2006 +0000 "Release log update" commit 373eb544cac0d674f5a14e93531f04ed0748a11e Author: markd Date: Wed Nov 8 09:46:04 2006 +0000 fixed felCat3, reordered some entries to keep file paths together commit e0743960a37a45ccaf0c40fe5329a2f24289984f Author: donnak Date: Wed Nov 8 02:34:44 2006 +0000 Fixde incorrect rhesus archive link. commit 97c9b81fd07a3bb5b4665005eb0d26b16b206143 Author: donnak Date: Wed Nov 8 02:34:15 2006 +0000 Fixed incorrect link for rhesus archives. commit f7e0efcccb38720cc31bcf3d633a133163523a71 Author: fanhsu Date: Wed Nov 8 01:00:09 2006 +0000 Removed spreadAlignString3rd(). commit 67c95942c75714df7ad4eda4c1f93651aa1ac52a Author: fanhsu Date: Wed Nov 8 00:49:10 2006 +0000 Removed spreadAlignString3rd(). commit e94f13772136cd3b016dc718edeb9bf7548b6980 Author: mario Date: Wed Nov 8 00:39:05 2006 +0000 added Augustus using Hints track on hg17 commit 7d15a3677de60e873b839710d026082e14524cac Author: kate Date: Wed Nov 8 00:30:41 2006 +0000 Dupe hidden variable with table name. It was moved to the hidden custom track form as part of redirect removal, but it is still needed on the hgTracks form to enable custom track remove commit 341b48967ce8ad5b25755beb1629a0be883f07ca Author: heather Date: Wed Nov 8 00:26:27 2006 +0000 2 bug fixes in printSnpAlignment2 commit 37b609e12cb1a121968ab19cf7b1a42fa87e1f81 Author: heather Date: Wed Nov 8 00:25:05 2006 +0000 remove debug messages in previous commit commit 6539b686e2cbf63b5c8d97ed5e01a4f82161778a Author: heather Date: Wed Nov 8 00:24:11 2006 +0000 add function isAllDna() commit 4e5798932095522eca2aa03dce84366de262c85a Author: hiram Date: Wed Nov 8 00:22:35 2006 +0000 expose ctTouchLastUse for use in dbTrash.c cleaner commit be73239eac55e569dce8feee751f3e4a4d8a1313 Author: hiram Date: Wed Nov 8 00:19:24 2006 +0000 Now using the metaInfo table only. Streamlined db connections commit c1e526ea4fb9d59e2f51a45f31bf950563c26718 Author: rhead Date: Wed Nov 8 00:14:39 2006 +0000 changed a 'which' to a 'that' commit 4fbac57c864f269122217efed2732ee2c20cd6c3 Author: markd Date: Tue Nov 7 23:57:16 2006 +0000 make sure hgFixed.mgcMBLabValid table exists before using commit c946a51ae4bc41ec148cd585ff28f7a5ff76cfe7 Author: fanhsu Date: Tue Nov 7 23:02:09 2006 +0000 Updated the last parameter name of spreadAlignString3rd(). commit 6f0c4283cc9d2a502c9c9cc203602a7bb7f5c9be Author: fanhsu Date: Tue Nov 7 23:01:04 2006 +0000 Changed initialColor into intitialColorIndex to make it clearer. commit bde765fe1507417d00decb7fca0361455268b49c Author: fanhsu Date: Tue Nov 7 22:56:42 2006 +0000 Updated spreadAlignString3rd(). commit 88885cae967e21cf61aa234593515b43662fbef7 Author: fanhsu Date: Tue Nov 7 22:55:39 2006 +0000 Updated spreadAlignString3rd() to add alternating color background. commit 7d54963c00358c06d7450294b776090f253539da Author: kuhn Date: Tue Nov 7 22:50:59 2006 +0000 a grammar tweak, added a clause to clarify one sentence and broke up a long line to fit the 80-column screen commit 22a722482559fc5e6d89c4e348930df989e35915 Author: galt Date: Tue Nov 7 22:44:21 2006 +0000 cleanup commit 1895d3855ea31695b77c2d31e22c8359f8b2396b Author: kuhn Date: Tue Nov 7 22:43:39 2006 +0000 fixed alignment so text does not collide with image commit 12a3617966e7f2c0b8adc0ca3a12a73ce849a558 Author: hiram Date: Tue Nov 7 22:09:34 2006 +0000 Fix error in resolution calculation for intersection result from Table Browser commit cf9b83dea0fb0945a6861b5845f8e11332634549 Author: ann Date: Tue Nov 7 20:34:46 2006 +0000 lower case commit 7c930f4a5b43009b4a7b513bf012609a0e09c5af Author: ann Date: Tue Nov 7 20:26:56 2006 +0000 corrected spelling, changed 'i' to 'em', chopped author list down to 8 commit c1ff69b0a54c2f442099d91c7f66da144225f725 Author: giardine Date: Tue Nov 7 20:17:07 2006 +0000 Added ORegAnno data to the fly (dm2). commit ea404b0abc6104f08c90bfe95412e0e38ad4c947 Author: angie Date: Tue Nov 7 20:03:31 2006 +0000 Resolved -Wall warning: unused functions. commit c4591401f2593ea535dfa6bc37e6157e68dd363d Author: ann Date: Tue Nov 7 19:33:36 2006 +0000 fixed link HTML (found by hgTables robot) commit a59aa8205c85dcb6d3bffc4df3b5eaf42faf74b7 Author: kate Date: Tue Nov 7 18:55:47 2006 +0000 More table layout fixes commit 2121447339b95d7247246c1500f36157b0ffb9d8 Author: heather Date: Tue Nov 7 18:44:49 2006 +0000 add felCat3 commit 735ce95f0e55289690029aeca392e954b76cb04e Author: galt Date: Tue Nov 7 16:00:31 2006 +0000 "Encode release log update" commit 9fafa8b0b6da1377f1995904834a77e4be68f8cd Author: galt Date: Tue Nov 7 16:00:29 2006 +0000 "Release log update" commit 3bc3b1a80b6627b3216ceb0c6027fab67e0bee5f Author: hartera Date: Tue Nov 7 04:23:10 2006 +0000 "New version number v146" commit 6ddc23d9b4c668fa32e14ea6355bbc4b26625b18 Author: galt Date: Tue Nov 7 02:33:45 2006 +0000 fixed typo commit c9120dba984fc9b02cc37070db741673d5d68607 Author: hartera Date: Tue Nov 7 01:14:34 2006 +0000 Added more information for the Methods and added another reference. commit 489fd3b387bca3d47eedcee69a87d0fdb8626e9e Author: galt Date: Tue Nov 7 01:07:59 2006 +0000 added dependency between knownToHprd and humanHprdP2P commit 705fba2974b27c102d23503cc65736509261d26b Author: hiram Date: Tue Nov 7 01:04:52 2006 +0000 Now updating metaInfo table in ct database commit dfca2a2516b1ae78c93bbdfa94fdcd81e12e3d8e Author: hiram Date: Tue Nov 7 00:37:54 2006 +0000 Adding definitions for metaInfo table in customTrash commit 8dee355c832db4b50fee02d8f85b820d52a1dbc9 Author: hiram Date: Tue Nov 7 00:36:44 2006 +0000 Beginning to use the metaInfo table in customTrash to remember useCount and lastUse time stamp for tables commit d6c713a83bc7140284a8eabc5a123cf669e3dbef Author: galt Date: Tue Nov 7 00:33:31 2006 +0000 added support for HPRD protein-interaction for hg18 and hg17 including adding itemUrlQuery support for link to HPRD site, and also a requested illustration under browser/images commit b5e535f6ebedf0eae881c557c985797a6942a9ed Author: kayla Date: Tue Nov 7 00:30:11 2006 +0000 Removed the "release beta" blocks for the GIS ChIP-PET track, and removed the "release alpha" lines as well. commit e78a1b7a7e963f0bdb4b63589d89ac281207f100 Author: hiram Date: Tue Nov 7 00:26:57 2006 +0000 Adding metaInfo table to custom track database commit 659fc5ee66220eeb32c31c2dd0112081509c2ea9 Author: galt Date: Tue Nov 7 00:17:32 2006 +0000 added P2P distanct network illustration as requested by HPRD commit 62215ddbb4c921ad7b3f146b120c199ed06e77d5 Author: fanhsu Date: Tue Nov 7 00:04:37 2006 +0000 Updated the logic of spreadAlignString3rd() to always display AA at the center of a codon. commit dee0aacfa71f92675af09215e68d616528f1e6dd Author: galt Date: Mon Nov 6 23:57:47 2006 +0000 added itemUrlQuery to support linking out from HPRD Protein-interaction distance to their site commit 98b95d9297631ab5ae2841e6b8b79c589b8a92b5 Author: galt Date: Mon Nov 6 23:51:08 2006 +0000 added code to JKSQL_PROF to count and report the total number of sql queries the cgi ran, and to include the connect/disconnect time in the total time commit 704f8affc6704a9ebd46bd051a5e7e753347ff97 Author: galt Date: Mon Nov 6 23:37:24 2006 +0000 added support for internal or ancestral nodes commit 1bd06419c64104f7a0d29611bbe97828d4ca0320 Author: kate Date: Mon Nov 6 23:32:24 2006 +0000 Adapt for redirect-less operation of hgCustom commit a1e2cbd8a0ef00e30a72d2defd55d567def3689d Author: fanhsu Date: Mon Nov 6 23:16:39 2006 +0000 Updated to support protein wig MAF. commit de30701cff6d16435d363e161ea6d0012a62c9d8 Author: hiram Date: Mon Nov 6 23:08:00 2006 +0000 Add the table lastAccessed to the exclude list for deletion when saving history tables commit c42aac360b90c008b764b337a7985d6b4db83005 Author: hiram Date: Mon Nov 6 22:44:21 2006 +0000 For some reason, placing a clonePos definition here makes the track stop drawing numbers on the clone bits ? commit f8f4263bb204d93658dfa8cbc3c15a1df57b8670 Author: ann Date: Mon Nov 6 22:40:50 2006 +0000 fixed typos, added commas to numbers, fixed sentences commit d13a4cdb945754a4eef9cad1b6827f9a85b95837 Author: ann Date: Mon Nov 6 22:33:38 2006 +0000 changed publication link to Science website commit 8c361873e9bb78bfa854dd33347065ae2e9727de Author: hiram Date: Mon Nov 6 22:29:44 2006 +0000 The reload of the clonePos table is complete, as good as it is going to get for now commit 0c5d0c27ec85abd90ef25290003043eef6c2d7ef Author: angie Date: Mon Nov 6 22:16:24 2006 +0000 bugfix: when drawing tickmarks for differing bases, draw them after all exons have been drawn instead of after each exon, so that non-differing exons don't overdraw when zoomed way out. commit 3e2448352f7e07e6fa5578de97c612f20bb3f5ea Author: angie Date: Mon Nov 6 21:50:26 2006 +0000 Updated trackDb settings for all_mrna. commit 8794ef0cca7520fd3d4b2a179b3e7eb5a5136c8d Author: kate Date: Mon Nov 6 21:28:35 2006 +0000 GIS track to Q/A, Yale track in progress commit a7cc4f9af45dd9f1cc6654ca96513d5f8bf1bf9b Author: kate Date: Mon Nov 6 20:36:59 2006 +0000 Fix up table layout commit 61f0965a4c9d8bd6d7c1af3b5163e1ed2a738ed9 Author: ann Date: Mon Nov 6 20:04:47 2006 +0000 cleaned up TAR types commit 397d270dbb7656e38ce5e940b6a5de0de8b980dc Author: ann Date: Mon Nov 6 19:41:19 2006 +0000 added link to DART tool commit 82d0dde7719ec40c44aae63bb60d707fbfc46bb6 Author: kate Date: Mon Nov 6 18:54:17 2006 +0000 Replace redirect to hgCustom with submit of a hidden form commit 97fb012a257745efa698f92d2c4b8d9bc087c16b Author: ann Date: Mon Nov 6 18:41:32 2006 +0000 added link to Gerstein lab commit 7b49e8565c23885300f06d5a0db21755a266bc75 Author: ann Date: Mon Nov 6 18:25:47 2006 +0000 cleaned up paragraphs commit 7ad6bb0e5aa3a9467cdb13b5e52a8f9cfa8b4973 Author: hartera Date: Mon Nov 6 18:19:02 2006 +0000 Added pslCDnaFilter parameters. commit 5a6878c1f64d6c7c295c0130fd1aa4158b01558a Author: kate Date: Mon Nov 6 18:16:33 2006 +0000 Temporary checkin of doc for soon-to-be-obsoleted ENCODE tracks commit 55d4152ae82a8ac026f1c071d11ed25e69592c85 Author: hartera Date: Mon Nov 6 18:13:28 2006 +0000 Corrected Display Conventions section. commit f40caf238ca18edbedd864d0b5f379f524f5f7ad Author: ann Date: Mon Nov 6 18:13:16 2006 +0000 cleaned up line length and HTML codes commit 52bcf2424939682cd9a23936f021b0553d8c8e02 Author: heather Date: Mon Nov 6 17:53:22 2006 +0000 fix typo in previous commit commit 5f9b298e8bfcc9c97521ca11d4932d8503a4ccb8 Author: heather Date: Mon Nov 6 17:53:00 2006 +0000 add function comment commit 8ad9e6c5a82cfd263d97a20b70903118f99b55f8 Author: angie Date: Mon Nov 6 17:33:08 2006 +0000 Resolved -Wall warning: unused variable; cast to int for char used as array subscript. commit 1aca3602745235104fa8151e8ee6d853505ed6d5 Author: galt Date: Mon Nov 6 16:00:15 2006 +0000 "Encode release log update" commit a60774b07baaf05f773ed2d02e8973c21263659b Author: galt Date: Mon Nov 6 16:00:14 2006 +0000 "Release log update" commit dcf197ae98cba0c9fb6c3be99ae811435d6ea9d1 Author: kate Date: Mon Nov 6 04:12:05 2006 +0000 ENCODE tracks from Genome Inst. Singapore commit a4537251c185bae11be7744c01f423d86a19c556 Author: galt Date: Sun Nov 5 16:00:24 2006 +0000 "Encode release log update" commit 56d86c3d2b1257b5d6d95fe40abaa641f086380a Author: galt Date: Sun Nov 5 16:00:23 2006 +0000 "Release log update" commit c7236cd4d12d0b09a6e9278c6cd97b309755a5a0 Author: galt Date: Sat Nov 4 16:00:28 2006 +0000 "Encode release log update" commit 64902f2fe2ddc4d86269f909a7a3875da5a8733a Author: galt Date: Sat Nov 4 16:00:27 2006 +0000 "Release log update" commit 96e6b5d8a01a40b9a06eaae1540cb9047a4c13d0 Author: heather Date: Sat Nov 4 01:27:37 2006 +0000 genbank: native and xeno refseq, xeno mrna commit 023e378d20662e1870aeca1838b67d2b742da183 Author: heather Date: Sat Nov 4 01:25:08 2006 +0000 native and xeno refseq, xeno mrna for cat commit 1c31545f7a6f71de29c0867c14db1fd4820e6af8 Author: hiram Date: Sat Nov 4 01:00:07 2006 +0000 Getting close to the reload of hg18 coverage track commit 3396d67106947f67a9edac3dbcec05e1e7f994b3 Author: ann Date: Sat Nov 4 00:42:16 2006 +0000 This is one of the two scripts that are run in bulk on all assemblies once every two months. commit 93cb6488863db0c04887e4ca356e1c1ede407b64 Author: hiram Date: Sat Nov 4 00:30:01 2006 +0000 Properly ignore duplicates. Rescue the removeObsoleteClones.sh script commit 54d188850d945c067e76aa2e939e443fbcf0053f Author: kate Date: Sat Nov 4 00:27:23 2006 +0000 Fix up ENCODE NHGRI entries commit a34a81c4d3b03f18bda4020ccbdfb552f3da2009 Author: kate Date: Sat Nov 4 00:25:35 2006 +0000 Add ENCODE NHGRI/Duke tables commit 3e8c790837c7d826a1567d4cf512e3d326fb2ecf Author: ann Date: Sat Nov 4 00:01:42 2006 +0000 split flyBase2004Id into two rules: one for dm and one for dp3 (per Angie) commit ec0692017527b0cacf18236289018a1b10778aad Author: donnak Date: Fri Nov 3 23:37:06 2006 +0000 Updated this FAQ to reflect some changes to the UI. commit 62550020b6aeb3068d79785c965d42224389efa0 Author: hiram Date: Fri Nov 3 23:31:21 2006 +0000 Recovering this script from the obscurity of a data build directory. Used in clone coverage track creation commit b29ee837737e2de3a6cdbca48b86c71c06ef6b12 Author: kuhn Date: Fri Nov 3 22:44:17 2006 +0000 removed assumption that a table found as split could not be also found unsplit commit 9198d73ba4d8623575a9911519bbb20d8d23050f Author: ann Date: Fri Nov 3 21:26:14 2006 +0000 loosened rgdQtl rule (per Angie) commit bb27ba78565857445671e598d1c1651e79d8c4e7 Author: kate Date: Fri Nov 3 20:53:51 2006 +0000 Remove redirects commit 0624a33701c333064f0ca3b00d81b210ae06f831 Author: archanat Date: Fri Nov 3 19:44:50 2006 +0000 *** empty log message *** commit 07a5c380e4edecb49104cbbd09d12eb6121cd416 Author: hiram Date: Fri Nov 3 19:20:01 2006 +0000 New tfbsCons tables, and continuing contig_overlaps in hg18 commit 5683515f5028823736ab9f7e8c19d36dc08c25b2 Author: hiram Date: Fri Nov 3 18:33:25 2006 +0000 Downgraded to version 7.0 of the TFLOC data commit 7c24970f4df58eecfeb4f57b8a520be89278e85a Author: hiram Date: Fri Nov 3 18:31:49 2006 +0000 Updated (downdated) to v7.0 of the TFLOC business commit 2cd31965e4c8bdd893e13fa0f9f130dd638e3aa6 Author: kate Date: Fri Nov 3 18:17:24 2006 +0000 Updates after feedback from submitter commit a2222259a8cb6f845f2181eb2f31908269182183 Author: rhead Date: Fri Nov 3 18:07:05 2006 +0000 took out extra info in reference, as this is not our standard format commit d4ea8d9b1477a4bcba67198ebf2c90e16976eee8 Author: angie Date: Fri Nov 3 17:14:28 2006 +0000 Resolved -Wall warning: cast to int for char used as array subscript. commit b567dd405057fa9bbab038cc7ccb6f1a112bd28d Author: galt Date: Fri Nov 3 16:00:30 2006 +0000 "Encode release log update" commit 89eda8ad6aaa92783685a88dfcf58998165fad01 Author: galt Date: Fri Nov 3 16:00:29 2006 +0000 "Release log update" commit 431032e25f2b99400a9c0f3d0e9b2b72e33ffdba Author: ann Date: Fri Nov 3 00:10:53 2006 +0000 added that the mail lists are public commit e9b121bfe6432122a2a47c686b2a63a2ff590655 Author: angie Date: Thu Nov 2 20:20:33 2006 +0000 Updated search specs for Jax/MGI tracks. commit 5eebaeeac33cfdfac91756e85018ff3665f167d2 Author: kate Date: Thu Nov 2 20:01:27 2006 +0000 Expand composite track explanation to include subgroups commit 349693f9324da383b70075f2a9d39e287fad6713 Author: rhead Date: Thu Nov 2 19:51:44 2006 +0000 edits after QAing track. Added disclaimer section, formatting changes, whitespace changes, rewording and several minor edits commit 6a9a5ef001176138708ddcb1141d3fa310b97cbd Author: rhead Date: Thu Nov 2 19:30:50 2006 +0000 Added a link for the PhenCode project and made terms and conditions link slightly smaller commit 5881c964d83ff72202d8d821c4729542cb15d56c Author: kate Date: Thu Nov 2 19:28:52 2006 +0000 Tumor Sequencing Project doc commit a2860181106c397f5b4f7c7301e299f6acc9b54f Author: angie Date: Thu Nov 2 17:51:09 2006 +0000 Resolved -Wall warning: cast to int for char used as array subscript. commit bb8b01828532d4f67262f8549c604082661b26d7 Author: hartera Date: Thu Nov 2 17:22:08 2006 +0000 Changed implementation of noRound option as suggested by Mark. commit dbc09adf6b31148c1fd877a2727cd5a5debb5c50 Author: galt Date: Thu Nov 2 16:00:31 2006 +0000 "Encode release log update" commit 37c526b4bc0dc381e146c952b8e3a67173873cd9 Author: galt Date: Thu Nov 2 16:00:30 2006 +0000 "Release log update" commit 3eef5a12a6665da2174a1ff553df129dde3965eb Author: heather Date: Thu Nov 2 04:26:07 2006 +0000 remove the xeno est line entirely commit c0fd3e50cfdea22f6dcbc36e270714a27326f883 Author: kate Date: Thu Nov 2 01:23:50 2006 +0000 Update for new data from Yale and GIS commit e981cc317dffa0a693ee039f2b90d56a1ddf6e77 Author: kate Date: Thu Nov 2 01:11:09 2006 +0000 Add c-Myc Chip-PET data from Singapore. Merge existing tracks into a single composite commit 12eeabaf82dc478613791ec73cd63959933f0214 Author: hiram Date: Thu Nov 2 01:05:15 2006 +0000 Continuing with the coverage track rebuild ... commit e7e92fd2cf2eb859c761a1f057d774cc4acd4e75 Author: kate Date: Thu Nov 2 01:03:48 2006 +0000 Fix misspelling commit 8cdcb6a5145126714f62b7d8094ba828631d7e80 Author: kate Date: Wed Nov 1 23:20:18 2006 +0000 New data from Duke, GIS, Davis commit 0f1ce06f7356fa2b1acfe6e710c5cb1c630537bf Author: kuhn Date: Wed Nov 1 22:24:04 2006 +0000 added support for tables of the form mz% at ann's suggestion commit e5422e4160399d0a96c6545a75487105f2c51805 Author: hartera Date: Wed Nov 1 20:35:23 2006 +0000 Added search for Bertone Yale TAR track. commit be7a7038702ba3831ec35e5d968ce012dbccd4a4 Author: heather Date: Wed Nov 1 19:57:10 2006 +0000 don't need xeno ests commit b7d1661f1a334d85f5f861c50ca2d2a3f426e92f Author: baertsch Date: Wed Nov 1 19:17:10 2006 +0000 show location of mRNA in browser. Allows user to quickly see the entire mRNA. commit 324de025877afc5bf3aab1b454983374248794ce Author: heather Date: Wed Nov 1 19:04:01 2006 +0000 progress on genbank commit 673a1041567a505903f08041b8be2e46a2256b75 Author: heather Date: Wed Nov 1 19:03:30 2006 +0000 try to get additional cat data commit d9fa030581fd8e96ffa31cb1abd93a9e72829c95 Author: ann Date: Wed Nov 1 17:40:56 2006 +0000 removed 'full' from three UniProtAccession rules (per Fan) commit ef5df26843cba72b7a6a89863b49ec7a9186c0cc Author: ann Date: Wed Nov 1 17:13:16 2006 +0000 relaxed rules for dbSnpHgId rule (per Heather) commit fcbf856203d10e7d88fbb1929ae7b9689ca114c8 Author: angie Date: Wed Nov 1 16:15:38 2006 +0000 Resolved -Wall warning: unused variable. commit 3fe7efb4c5084f7b081469a0dc8bdd6901b299f9 Author: angie Date: Wed Nov 1 16:14:58 2006 +0000 Resolved -Wall warning: missing arg in errAbort. commit 9f1f9a8ac3c5effb10d61fbf7c8e0054abdefd26 Author: galt Date: Wed Nov 1 16:00:29 2006 +0000 "Encode release log update" commit 8b7d0cb2b8cf059aae175c9da41a7cca5991fee1 Author: galt Date: Wed Nov 1 16:00:28 2006 +0000 "Release log update" commit c77cefd9f4fa1aa5c6aad22d5fff272b5931119b Author: rhead Date: Wed Nov 1 00:27:02 2006 +0000 moved oreganno track to top level of trackDb.ra commit 7d91932922f1c9c22f163b36eb17b3b6cc646cc1 Author: kuhn Date: Wed Nov 1 00:04:24 2006 +0000 fixed spelling in photo credit commit a4faa7b5048a9974a6ff420b1ba209839876243c Author: kuhn Date: Tue Oct 31 23:58:38 2006 +0000 added some space around image commit 8f46319d409c9dfadd54f8886085de1a09be965c Author: kuhn Date: Tue Oct 31 23:55:12 2006 +0000 lower-cased some more 'Catus' and added italics to specis name where needed commit a20c6993269b17c5b1f9c36e2a205b8fdaa99e45 Author: kuhn Date: Tue Oct 31 23:49:56 2006 +0000 lower-cased species name and shrunk photo to match to the space allotted on the page rather than using IMG tag to squeeze it in. commit 3f08e8a5d30945cc83b3d153e5288e95335671ff Author: kuhn Date: Tue Oct 31 23:47:59 2006 +0000 lower-cased species name and changed image size to match actual photo commit 40b2c03a8d03d24e232af9797274a4e04a0fee66 Author: heather Date: Tue Oct 31 23:24:02 2006 +0000 use genome in dbDb rather than organism commit ccc2f5bdb595e9a3a6f732c1a1cac8768a8df509 Author: kuhn Date: Tue Oct 31 23:22:08 2006 +0000 added image commit 8890cf16c37b37cc142219202af4a675dcde17e5 Author: kuhn Date: Tue Oct 31 22:37:03 2006 +0000 ciona image commit 529ac42d32c3d5d1c84ddb5382dd1579be25b6e9 Author: hiram Date: Tue Oct 31 22:07:15 2006 +0000 Beginning to show the coverage track rebuild commit 75074f98d903e9886440e71dc1c932b2584625f7 Author: ann Date: Tue Oct 31 20:17:08 2006 +0000 removing unnecessary minCheck for gvId rule commit 89f828a20f3c7582c7738c5e7531fb73fe120632 Author: angie Date: Tue Oct 31 19:21:50 2006 +0000 Resolved -Wall warning: errAbort format/argument order. commit 02cd7b053fc4ccbd814001a7f0aaec770cae21e8 Author: angie Date: Tue Oct 31 19:19:23 2006 +0000 Resolved -Wall warning: unused variable. commit 3bb8d923e6663befa0ace2610f6bf43a291b9f87 Author: angie Date: Tue Oct 31 19:18:24 2006 +0000 Resolved -Wall warning: cast to int for char used as array subscript. commit f27efb86d48e7a6bf5dbadf0161c9773c5110533 Author: ann Date: Tue Oct 31 19:01:14 2006 +0000 edited vegaGene rules to capture more table relationships (based on information from Robert B.) commit 09e5c6e09dbafc33959d9f0968ddb755f38500c5 Author: hartera Date: Tue Oct 31 18:51:40 2006 +0000 Added bacEndAlias, bacCloneAlias and bacCloneXRef tables for BAC end tracks. Also tested that the table contents are correct. Vega genes in progress. Compugen zebrafish oligos track in progress. commit 57362fb6eeaca4cddefb7a076a888c8f01e79a15 Author: kuhn Date: Tue Oct 31 18:21:25 2006 +0000 removed dependance on file writing/reading commit 0e9cc68e8119b08e6e839b78ee67896e8e6e3391 Author: galt Date: Tue Oct 31 16:00:26 2006 +0000 "Encode release log update" commit d4608cea0a992e353afc5339b7a59aaf24257f5a Author: galt Date: Tue Oct 31 16:00:25 2006 +0000 "Release log update" commit 956f0b7d5588fcbdd7375bd516ae0ab7250cbf43 Author: heather Date: Tue Oct 31 03:43:50 2006 +0000 tweaks commit 91eb219a98441220ce87ad793ccdff4c8db9a328 Author: heather Date: Tue Oct 31 03:40:30 2006 +0000 starting to take shape commit 557686b919adc5782d468a58fa21ba6521029234 Author: heather Date: Tue Oct 31 03:10:51 2006 +0000 simplify getGenomeForClade to fix hgTables clade-changing bug commit 746bc127fc4c1d6f5cfd6d11b1654a0909fdcfc7 Author: kuhn Date: Tue Oct 31 02:08:22 2006 +0000 removed some unused lines commit 82243d2e5212182ad004c32d4f80eb46172288b7 Author: rhead Date: Tue Oct 31 02:06:17 2006 +0000 improved logic for handling 'all' option, added check for valid machine name commit c59a1dc08212c1a3a581fdab54d875b78ac9664c Author: angie Date: Tue Oct 31 01:23:59 2006 +0000 Added baseColor* settings which will eventually replace the cdsDraw* and pslSequenceBases settings. commit 0f10f10bed46949f494f7fd0bca698ba63c25ee9 Author: kuhn Date: Tue Oct 31 00:22:50 2006 +0000 brooke and I added a utility that gets info about Conservation tracks - which tracks use an assembly in a multiz track commit 72946fb1776f4946d0a853c6b56a99e9386467da Author: angie Date: Mon Oct 30 23:46:55 2006 +0000 Moved redundant definitions of xenoRefGene, xenoMrna and xenoEst up one level to simplify maintenance. commit 00214c767e34140b75029242a3c3d3b017d804ec Author: heather Date: Mon Oct 30 22:59:14 2006 +0000 fix typo commit fd7bfb34f152dcc504d10a4cf38cd21eef300f6d Author: galt Date: Mon Oct 30 22:16:36 2006 +0000 galaAvail.tab no longer present, and hgCgiData subdir not desired in what is to be just cgis commit be7811332956a86580452d15a6d8e68fbdd9efd9 Author: kate Date: Mon Oct 30 22:02:02 2006 +0000 Add Hits track for UC Davis Chip commit e298146222364519f2e058515dad99f13f03c402 Author: ann Date: Mon Oct 30 21:56:16 2006 +0000 loosen up the refSeqId rule for hg18 commit 13b2549a345021f3c927f22254b6a6e5f9a838bd Author: heather Date: Mon Oct 30 21:06:12 2006 +0000 add cat commit 61b2396c8f5688515e4d8487cdcc733e867e2120 Author: kate Date: Mon Oct 30 20:59:01 2006 +0000 Add STAT1 STAGE data submitted by Akshay Binge commit 609a9e7bcee32300dcbe236613ebfd8963ee68e3 Author: kuhn Date: Mon Oct 30 18:52:55 2006 +0000 added specific tablename output for wildcard use commit 2bfe4e7e51c3da2589e4fe9386acc00f1d988413 Author: angie Date: Mon Oct 30 18:18:16 2006 +0000 Ran WindowMasker; blastz/chain/net droGri2 with both sequences WindowMasker'd. commit 60fc760d64e5691f7f84362cc5f872bdfa5248e7 Author: angie Date: Mon Oct 30 18:13:40 2006 +0000 Changed Jax -> MGI in track shortLabels at the request of Jax/MGI folks. commit 317fcdf0ddf5ac9b6584e4da70e1e166a85bcd86 Author: angie Date: Mon Oct 30 17:15:59 2006 +0000 Resolved -Wall warning: unused variable; cast to int for char used as array subscript. commit 2c6c041b38c5a9a52ced8962d55699abafad6dd1 Author: angie Date: Mon Oct 30 17:12:03 2006 +0000 Resolved -Wall warning: errAbort format. commit 95bfa2f76e09cca91bd737bf6a5afd457b49a939 Author: galt Date: Mon Oct 30 16:00:23 2006 +0000 "Encode release log update" commit d50c428a79817e7388b50362e956425690179acc Author: galt Date: Mon Oct 30 16:00:22 2006 +0000 "Release log update" commit 88c0a271ba90be464d90c252e51196d0408cee1e Author: galt Date: Sun Oct 29 16:00:23 2006 +0000 "Encode release log update" commit ea082ab369c96fffb185d194fbcd5909a09c6516 Author: galt Date: Sun Oct 29 16:00:22 2006 +0000 "Release log update" commit 7711e0f6553f6df459b351b659ba7858d075c1d5 Author: galt Date: Sat Oct 28 15:00:26 2006 +0000 "Encode release log update" commit 64f7210c443156290cc51f9e557f874f2bee6535 Author: galt Date: Sat Oct 28 15:00:25 2006 +0000 "Release log update" commit f7a8403e48e9d74d5e5ca3d7d3ab36a8af1a026f Author: hartera Date: Sat Oct 28 00:01:52 2006 +0000 Added BAC end tracks searches common to all assemblies and changed priorities on vega gene searches. commit f92ad1e3b457f89f5053e6d728381e5625f24b15 Author: hartera Date: Fri Oct 27 23:53:53 2006 +0000 Removed searches for BAC ends tracks. Moved them to highest level zebrafish directory trackDb.ra. Searches are common to all zebrafish assemblies. commit 3fb62282cc5ca5f3f12b0f3bc735185ffac19720 Author: kate Date: Fri Oct 27 23:50:42 2006 +0000 New data submissions, Duke data to q/a commit 98a66b23ba0117b2fceef857afa5504a434e29d7 Author: donnak Date: Fri Oct 27 23:20:56 2006 +0000 Another tweak to the link. commit 780f4d86929b49e600505ae085bbc07ede878ec5 Author: donnak Date: Fri Oct 27 23:20:24 2006 +0000 Fixed broken link. commit d4d818e101800bc73a8d109688e42c4a9d1ba01e Author: giardine Date: Fri Oct 27 22:17:16 2006 +0000 Changed back searches on Locus Variants commit 8b7b2ab737c8b849bac45206d9525b9ef44efeb9 Author: hiram Date: Fri Oct 27 21:45:05 2006 +0000 remove extra names in the tfbsConsFactors table commit 5f37cdf8f20333298b8a3b8afb2a47979f82e254 Author: donnak Date: Fri Oct 27 21:41:10 2006 +0000 Small tweak to text. commit 4be6c617e20fcf76802417464e4b11e129e2f11c Author: kuhn Date: Fri Oct 27 21:04:30 2006 +0000 changed logic to allow for having more than one table in output, e.g., when using wildcard commit a76379f5d110abd5584f401c7ce56ffa90f5e26e Author: hartera Date: Fri Oct 27 20:29:48 2006 +0000 Fixed bugs. Increased the values for the number of Sanger names and the maximum number of Sanger names. commit 3f492fc58769768ae337b2756d261d880fa38c9f Author: donnak Date: Fri Oct 27 20:10:01 2006 +0000 Added warning abt case-sensitivity of chrom names. commit a9ca257614b1a9aec881277c1ca571b8c6e9877d Author: donnak Date: Fri Oct 27 19:41:59 2006 +0000 Slight change to title of help section on Manage Custom Track page. commit f6a65d44e1eb1c21b769b0b4b6a26f5f211a8623 Author: galt Date: Fri Oct 27 18:52:14 2006 +0000 added support for content-location in multipart mime email commit 005341d1f67e3b7515ecb8fb02e38a1744ac6ad9 Author: hiram Date: Fri Oct 27 18:17:18 2006 +0000 Remove extra indexes from tfbsConsSites commit 8cebb4061d2a0f8f00cce0cd1e5854c20f34ec6a Author: kate Date: Fri Oct 27 18:14:03 2006 +0000 Restore previous fix commit 2d09577d22ed909a9bab3353aa3dd9a213d172ba Author: donnak Date: Fri Oct 27 18:11:57 2006 +0000 Minor edits to this text. commit 7c5d978cca678df384b6b4983cce874600fc80c2 Author: hiram Date: Fri Oct 27 18:00:28 2006 +0000 Only need two indexes, one for name, and one for chrom,bin commit a4724370facb7ae532a8be0ab1e28449eac06a8f Author: donnak Date: Fri Oct 27 17:52:57 2006 +0000 Reduced CT links in TOC to one. commit 661b832693935ada0d71ea89c2cd0c24d226d856 Author: donnak Date: Fri Oct 27 17:50:51 2006 +0000 Updated & edited this page to reflect the new hgCustom interface. commit 5d669fba439547dd0dad445277d26cc290583884 Author: angie Date: Fri Oct 27 17:08:49 2006 +0000 Resolved -Wall warning: unused variable. commit b6773244761f8f633792a4ab3504de3725fb60df Author: angie Date: Fri Oct 27 17:07:52 2006 +0000 Resolved -Wall warning: cast to int for char used as array subscript. commit d22ac7463f0aea0cae7377ad4d04d1929cb28972 Author: angie Date: Fri Oct 27 17:06:01 2006 +0000 Resolved -Wall warning: use %ld format for size_t val. commit ab921a555fee5bf5defbdc46ae572bde8e3497f0 Author: angie Date: Fri Oct 27 17:03:48 2006 +0000 Resolved -Wall warning: unused variable; cast to int for char used as array subscript. commit 100ca6ce7881271352ef1af92101de40eb41f6c0 Author: angie Date: Fri Oct 27 16:55:56 2006 +0000 Resolved -Wall warning: unused variable. commit 609869c24865d8c53a142a0f704b968eaaa87e04 Author: hiram Date: Fri Oct 27 16:35:28 2006 +0000 Add tfbsCons track instructions from Matt Weirauch commit 4bb865932964315e743d1cf339b60b0b39e5de38 Author: giardine Date: Fri Oct 27 15:23:46 2006 +0000 Fixed printing of position etc so only prints once where change is multiple, ie C>T or C>G at the same position for the same variant. commit f9d45e8f85a0488001f7e2a8d0ead56558ac9d31 Author: giardine Date: Fri Oct 27 15:04:40 2006 +0000 Changed back searches on Locus Variants commit 3142de0422b600690ec63c5f63dcbb1b289106e3 Author: galt Date: Fri Oct 27 15:00:30 2006 +0000 "Encode release log update" commit 501806f77d13ab0b0b31704f50db299f5b94d997 Author: galt Date: Fri Oct 27 15:00:29 2006 +0000 "Release log update" commit 74bf13301af16f229e2e7abeb5e0d99d787e8f3b Author: donnak Date: Fri Oct 27 02:55:36 2006 +0000 Edited this text. commit 1824761ed1e3c5d0fea0eefc5dd033ad149df159 Author: angie Date: Fri Oct 27 01:36:04 2006 +0000 Resolved -Wall warning: unused variable. commit 7565e0cbcc432356f274674c891065b704f5f073 Author: angie Date: Thu Oct 26 23:13:27 2006 +0000 Fixed an AGP name that was slightly inconsistent with sequence name, reloaded gold (and gap), regenerated missing trfMask.bed file, (re)generated downloadable files. commit 6376ae9d389c45019bcef61109475659b80e8ce4 Author: kate Date: Thu Oct 26 22:53:34 2006 +0000 Track label changes requested by Greg Crawford commit 925a18c1ab0498fb90bcb5d86f425cf07307dde3 Author: rhead Date: Thu Oct 26 22:10:08 2006 +0000 commented out gvPos search lines that were breaking all searches on hg17 and hg18 commit 19d274b1d00f81c61f73181d24f3f296147af008 Author: archanat Date: Thu Oct 26 18:47:02 2006 +0000 Copied this file to hg18 level and added Mt-tRNA to the feature type list commit fc4465332c660eccca5ea721a8ff45b608ac9f9c Author: archanat Date: Thu Oct 26 18:42:06 2006 +0000 Added block for rnaGenes commit 580be5bc3915328915032724466ac0728b54e97b Author: markd Date: Thu Oct 26 18:00:00 2006 +0000 added Brent lab MGC validation table in hgFixed commit 05415c50ae6778d44c80d214fb9bf05a6c52fa3a Author: markd Date: Thu Oct 26 17:58:48 2006 +0000 link MGC clones to Brent Lab validation database commit 18485ceed73abd3643850a175f24d43a740ea383 Author: galt Date: Thu Oct 26 15:00:31 2006 +0000 "Encode release log update" commit 834db23e434ee33ecef390cd4f26e876da19c36a Author: galt Date: Thu Oct 26 15:00:30 2006 +0000 "Release log update" commit 054e36a9081455d45781f638a679439a74c68e77 Author: rhead Date: Thu Oct 26 01:48:06 2006 +0000 added a Disclaimer section and added to the track description commit 93ac4774b5c8198cdda4ff89ec068fe5ec7fd1ba Author: kuhn Date: Wed Oct 25 23:58:05 2006 +0000 changed a variable name, the sign of usage of isChromInfo so it makes sense, dropped some logic concerning a long-dead table, added error message if not run on dev, some other trivial changes commit 3ff2c2cf6aee14f627e7349096f56ce329f9f6ee Author: kuhn Date: Wed Oct 25 23:51:44 2006 +0000 removed quiet from call to getAssemblies.csh commit 4a52e0b838ca8da07ae1ecad71e38bc9358f37bc Author: fanhsu Date: Wed Oct 25 22:25:02 2006 +0000 Added doOmimAv() and fixed a bug in OMIM links of GAD details page. commit 8bb43e9caf627a934cad0545e570bc7000da8e49 Author: kuhn Date: Wed Oct 25 22:13:40 2006 +0000 changed default behavior to quiet commit bc194b8d5a1826f1cdf44b503fcdcb3f69cbd487 Author: kate Date: Wed Oct 25 21:37:25 2006 +0000 Change position on 'goto GB' button, and do not change button label based on context commit 5161aa1eeceeeb4574d9965162b391448a4b04d1 Author: ytlu Date: Wed Oct 25 21:31:22 2006 +0000 clean some code and make the UCSC pseudogenes detail page work for multiple species. commit eb948db6a3641108f0dd694801807760407af136 Author: aamp Date: Wed Oct 25 20:38:13 2006 +0000 This was suggested in code review but it ended up making the code not work. commit 54926d9ca27e81b7cfb3eb2a61603f3f38638b61 Author: hartera Date: Wed Oct 25 20:29:55 2006 +0000 Changed expScale for affyZonWildType track. commit 7c059db8102c4d4722e0cde833ecc8f5bbe4e28a Author: kate Date: Wed Oct 25 19:07:11 2006 +0000 1. Reset cart position to default when changing assembly in Add screeen. 2. Widen buttons on Manage screen for Safari commit 2957a1ce0d254a4b9de74e03ffc5d60ef5d2de34 Author: donnak Date: Wed Oct 25 18:39:24 2006 +0000 Fixed an error in the OH press release. commit 78bc235ab9478c7200d9fab5668fdb9f23890d1f Author: kuhn Date: Wed Oct 25 18:21:04 2006 +0000 wanted to change a small typo and ended up resizing the lines to be under 80 chars as well. The refs still need to be formatted correctly commit 0ed42b529cfca7f230ebe3b9d51f6fd33a75cf14 Author: markd Date: Wed Oct 25 17:25:32 2006 +0000 link files to gbdb before copying alignments to prevent window were load of alignments fails because gbdb isn't there yet commit 454a0bf406d9ed8022967ec577bb9c1a6eea73ef Author: galt Date: Wed Oct 25 15:00:32 2006 +0000 "Encode release log update" commit 4365cca7ef4c3947ddd98a04366b22e5fcfd93aa Author: galt Date: Wed Oct 25 15:00:31 2006 +0000 "Release log update" commit 3b3bfedbaf6b42592702d27a68a2938b8a4ab253 Author: markd Date: Wed Oct 25 04:31:57 2006 +0000 added scripts to load BCGSC LongSAGE tags commit 465c296b41bd3d26aa94efb0c299ea48c3ee9833 Author: markd Date: Wed Oct 25 04:23:46 2006 +0000 renamed ESC LongSAGE tracks commit 2f19599138d0236cdc235e92decc93200ab31de0 Author: kate Date: Wed Oct 25 00:27:29 2006 +0000 Reset position to default for new database when assembly is changed in the Manage screen commit fcbb1f3c1cea124e048b357272ad20aaf399bdd1 Author: heather Date: Tue Oct 24 23:55:28 2006 +0000 add chrom argument commit 77a3d28e1066b1f61f30bfd27b4dc48c758c3f67 Author: kate Date: Tue Oct 24 22:18:45 2006 +0000 Clarifications from Greg Crawford commit af4e612094b87b59722609b202102b505965a4ef Author: galt Date: Tue Oct 24 22:18:40 2006 +0000 oops - removing stuff not yet to be checked in commit 8342d442ff912a11aceb210ea6583963e7774b11 Author: donnak Date: Tue Oct 24 19:26:52 2006 +0000 Archived an item. commit a5b16a90650aebc646f9be9fef813b9575bdbc22 Author: donnak Date: Tue Oct 24 19:26:39 2006 +0000 Fixed typo. commit 09346d0abe4f4a5420c289e6293baaf72f43a900 Author: rhead Date: Tue Oct 24 19:26:26 2006 +0000 changed mm7 nets and chains to display mm7 instead of mouse in shortLabel commit bd887757f924c65d1c1dd2d724e8d848d96be14c Author: fanhsu Date: Tue Oct 24 19:15:38 2006 +0000 Created dnaSeq.sql. commit c722e083bcad48e434bae1260020546a7590bd6d Author: fanhsu Date: Tue Oct 24 19:15:18 2006 +0000 Created aaSeq.sql. commit a6c723a33e648d3a392b4ee50a2fc3e1e76cf0db Author: aamp Date: Tue Oct 24 18:24:12 2006 +0000 Took out affyHumanExon business. commit f72fd8ab6379f7227f74688462bfb662b5dd8577 Author: giardine Date: Tue Oct 24 17:44:42 2006 +0000 provide special text for descriptions when querying Locus Variants using the position box commit 5fb323def754398688d8a18404232945d72e68da Author: donnak Date: Tue Oct 24 17:37:26 2006 +0000 Made a few formatting edits; changed a few things per Angie/Hiram. commit 573ea69d0072d6e51f9145514520b9ca7f6dc323 Author: kuhn Date: Tue Oct 24 16:01:05 2006 +0000 dropped some unused variables and changed awk to get update_time instead of incorrectly getting create_time commit ff8b9f3c74af5203f9db76aecdb61085b6d70a00 Author: galt Date: Tue Oct 24 15:00:28 2006 +0000 "Encode release log update" commit 0058ec9820ecfc2055aa96e044e3d8583ee8c4db Author: galt Date: Tue Oct 24 15:00:27 2006 +0000 "Release log update" commit 2e7a4b37cbe7100e550ec73dec5f1c7d3825cb47 Author: hartera Date: Tue Oct 24 04:29:03 2006 +0000 "New version number v145" commit c8085afda1621ac8107aa7a147edb9a35893ef47 Author: hartera Date: Tue Oct 24 00:23:06 2006 +0000 Added a check to see if active is set to 1 before printing link for position to the toDb. If set to 0, then print position only with no link. commit 260c413b8352205fcc1edbc0a1205516210f34b2 Author: kate Date: Tue Oct 24 00:07:03 2006 +0000 Display tweak commit 8748c39027a01224ff58845a33e74b1c8c96164b Author: kate Date: Mon Oct 23 23:40:07 2006 +0000 Display cosmetics: 1. Uniform button widths 2. Change label for All check/clear commit 15194e1cdd034364d6a32c08ee647773eac4b11c Author: galt Date: Mon Oct 23 23:37:56 2006 +0000 removed unnecessary #ifndef commit d680e4345448f68da13b09dda9eb1bc178129841 Author: heather Date: Mon Oct 23 22:48:45 2006 +0000 handle multiple alignments in SNP sequence display commit 6452f2b41fc76c1eddcd9e2cc9ffb813579240fc Author: angie Date: Mon Oct 23 22:45:39 2006 +0000 Ran WindowMasker for alignment vs. droVir3. commit 426a4660b52506161443a8bb35f16aa0fe85dba3 Author: kate Date: Mon Oct 23 22:29:51 2006 +0000 Restrict chrom names to proper case commit 1c222cdc4a53e8ef4d1abdb116898d1ff73308ce Author: aamp Date: Mon Oct 23 22:26:04 2006 +0000 Dumb debug code. commit 1fd4af901d9b309206313c5d403c9f4b194e96d5 Author: aamp Date: Mon Oct 23 22:25:42 2006 +0000 Recommended by Kate in review. commit 3cebaa705daf5f8c6bddafd04f6eaabe1dc36e62 Author: heather Date: Mon Oct 23 22:17:41 2006 +0000 code review comments commit 5325e5aa7e2b51eb5642e56d2e223ecbd85ac4fe Author: heather Date: Mon Oct 23 22:04:18 2006 +0000 code review fixes commit 3e5fd48163be07556fdb7ddc6b1e1d8c41c6376b Author: fanhsu Date: Mon Oct 23 21:06:12 2006 +0000 Updated omimParseAv.c to be offset/length based. commit 3196b72bd8dc215a39726534274204b67067af43 Author: hiram Date: Mon Oct 23 20:51:07 2006 +0000 formatting commit 789b5a57b7e620b9c32ea617305804f4ae6228f3 Author: hiram Date: Mon Oct 23 20:50:45 2006 +0000 Add gapSplit to the build commit 3a020e0ca492c0c8338854754b7f144ed68fe652 Author: angie Date: Mon Oct 23 20:18:38 2006 +0000 Added HG_WARN_ERR to utils so -Wall cleanliness will be maintained in top-level builds. commit b17a077088cc192f2afde79edac5c5534bcf1454 Author: angie Date: Mon Oct 23 20:09:38 2006 +0000 Ran WindowMasker for alignment vs. droAna3. commit 4b4dc418bdcab66cec5255ade2fe9c36f2601093 Author: angie Date: Mon Oct 23 20:09:02 2006 +0000 Ran WindowMasker; blastz/chain/net droWil1 with both sequences WindowMasker'd. commit 41fc115f75658554ae50861861fd4a5a10dc758e Author: angie Date: Mon Oct 23 20:06:20 2006 +0000 blastz/chain/net human, mouse, zebrafish and tetraodon. commit d9af8f5680c7d70e211073b1029aae7a55398a73 Author: angie Date: Mon Oct 23 19:57:44 2006 +0000 Added Jax {QTL, Rep Transcript, Allele, Phenotype}. Swap, chain, net gasAcu1. commit 20fea9b3fe0da5977731c4ee64ab2ac18d6ddfae Author: angie Date: Mon Oct 23 19:57:03 2006 +0000 Swap, chain, net gasAcu1. commit 17aceae4fff0dc092f036c8d68c1bc02e75ec673 Author: hiram Date: Mon Oct 23 19:33:54 2006 +0000 A simple fasta splitter to eliminate gaps of >= N and break up sequence commit 98a42d94cf76261270bbe05b1d6333a0b2bacf93 Author: kate Date: Mon Oct 23 18:41:19 2006 +0000 Prevent partial acceptance of case-insensitivematching chrom names when used in custom tracks commit d6ee078603ab600ac47a907abd447780a9f662fd Author: kate Date: Mon Oct 23 18:10:07 2006 +0000 Fix navigation issue -- show manage page when all custom tracks in the current assembly are deleted if there are custom tracks in other assemblies, but don't show manage page if navigating from genome browser commit 4dc760ba3718447a46fb0b8b533a76c5b391c6c5 Author: kate Date: Mon Oct 23 17:44:13 2006 +0000 Add stricter validation for browser line position commit 3374efd7ec7bd8684f5077b53918a24e3f63a24d Author: kuhn Date: Mon Oct 23 17:38:27 2006 +0000 removed the bolding from some names commit 3575763b8f4b865808c7d37c99476f826e5b3b18 Author: galt Date: Mon Oct 23 15:00:21 2006 +0000 "Encode release log update" commit 553dd79e5eb88995cb1692a84e72016d4fa350d4 Author: galt Date: Mon Oct 23 15:00:20 2006 +0000 "Release log update" commit 37e0a6564f3408cf2a3d0c6d067142ef69ccaa24 Author: galt Date: Sun Oct 22 15:00:22 2006 +0000 "Encode release log update" commit b9c715267afd963e61e84dde2918dbaf25bd9658 Author: galt Date: Sun Oct 22 15:00:21 2006 +0000 "Release log update" commit 57c3ae2d44ff4b0adfe7062ac8fb329792af5ffc Author: galt Date: Sat Oct 21 15:00:29 2006 +0000 "Encode release log update" commit 124cec6e383faeaf03b2881e9b387a9dfe4ecf92 Author: galt Date: Sat Oct 21 15:00:28 2006 +0000 "Release log update" commit da93f5f33ee32772e7fe67de9634a82a53c3b46d Author: hartera Date: Sat Oct 21 01:55:58 2006 +0000 Shorten long label for Yale TAR track. commit 0622bc11a8286d3650ab81651b982d594883a8a0 Author: markd Date: Sat Oct 21 00:41:49 2006 +0000 added BCGSC LongSAGE tags commit 98c5d85c8edd879ed1bcb3c9e3036005344b7386 Author: kate Date: Sat Oct 21 00:38:33 2006 +0000 Fix checking of custom track type commit 8634e339d62d4a2e2e59e7e404f3b5010634d94e Author: fanhsu Date: Sat Oct 21 00:04:47 2006 +0000 upstream maf file updated. commit 053c7395b2dae57230102c65bb7a03ab91675aa3 Author: hiram Date: Fri Oct 20 23:46:05 2006 +0000 Adding genome.sfsu.edu and URL links for all the mentioned institutions commit a1050e4336a96d751be0b5cf224742c967cb79df Author: hartera Date: Fri Oct 20 23:41:36 2006 +0000 Changed expScale for affyZonWildType track. commit d4a581a344ccd45f5fbe3736cd69aa93d8a7fe0d Author: donnak Date: Fri Oct 20 23:40:11 2006 +0000 Realphabetized list in Credits section. commit c2c9e97ce092f85dd53e14f9096670a14c42d51a Author: kayla Date: Fri Oct 20 23:24:59 2006 +0000 Added information for microRNA and MITOMAP in the Credits section. commit 7ca4c75f7c7c8f7e3b3510c98a1add3a4f977c55 Author: angie Date: Fri Oct 20 22:37:23 2006 +0000 Added urlLabel to Jax QTL tracks. commit a0ad0797befb0d8584c497a3f11b3410b4f0bc60 Author: hartera Date: Fri Oct 20 22:35:08 2006 +0000 Changed paramters for creating histogram of array scores for Wild Type data. commit 44cc1a40dc394a4083daeee41cf8787054f21dad Author: hartera Date: Fri Oct 20 22:18:46 2006 +0000 Clean up of blastz, chain and net files for danRer1. Added Yale TARs/Transfrags track for whole genome. commit a9a5af5efcdf9ef915e18d04288de388e543c0fd Author: hartera Date: Fri Oct 20 22:03:51 2006 +0000 Added Yale TARs/Transfrags track for whole genome. commit cada33eefbe870b4d84e2d4e48f77d5e74cc467f Author: hartera Date: Fri Oct 20 21:38:52 2006 +0000 Updated affyZonWildType array track with data processed by a different method. commit e3ad05e9aff6490d17a6dafd430ceddd5495d1d3 Author: hartera Date: Fri Oct 20 21:16:03 2006 +0000 Updated description for data processed by a different method. Updated description of track controls. commit 28bc6202d2d97f84eeea4b82673d74f48b143224 Author: galt Date: Fri Oct 20 20:59:33 2006 +0000 minor cleanup commit 411673a6553e6ae266510dfddb5c61ec66e0df52 Author: hartera Date: Fri Oct 20 20:46:46 2006 +0000 Adding BAC clone and alias information in progress. Tried GTF format for Vega Genes track. Updated the Affy Zon Wild Type track with the data processed by a different method. New RH map data obtained. commit e916c4b52b8fabc39559dd1942534ccacae94579 Author: donnak Date: Fri Oct 20 20:38:30 2006 +0000 Rearranged some of the links in this file, fixed up a few of the refs, tidied up the HTML to match our format conventions. commit 09f084492067e4c60b11fca4790454fc0c74d2fd Author: heather Date: Fri Oct 20 20:37:50 2006 +0000 add explaination for ortho option commit 122ac35d63ee200b0f24152b412ed069bc7e0f7f Author: hartera Date: Fri Oct 20 20:31:49 2006 +0000 Shortened long label for wild type arry data track, affyZonWildType. Changed expScale for the track. commit c7dba2fb52ee0e81608335075edcae134cbfc34f Author: markd Date: Fri Oct 20 19:21:19 2006 +0000 added warning if -allowLargeDeletes is used commit 9ed5f905284b8c57ec092967868c61e7eea09613 Author: angie Date: Fri Oct 20 18:44:09 2006 +0000 Moved jaxRepTranscript, jaxPhenotype and jaxAllele up from mm6 to mouse level because we have them for mm8 now too. commit c52312e2a18b46670d913905b86e376522c33548 Author: kate Date: Fri Oct 20 17:48:54 2006 +0000 Clarifications from Greg Crawford commit 8e1a0c45ef687923b26f21b229cbd03d39ea0a9a Author: hartera Date: Fri Oct 20 16:25:15 2006 +0000 Updated the zebrafish WT array data using the data processed in a different way. commit 100f33545a9301faf8d86d25d28aba92a0c229d9 Author: hartera Date: Fri Oct 20 16:22:48 2006 +0000 Added a new option noRound to be used when the data values are not to be rounded before loading into the database. commit ead76d59bf621f591eb03d01f7f0e33385857dc8 Author: kate Date: Fri Oct 20 15:03:51 2006 +0000 Changes to database switching for custom tracks commit 1ceba54e35ecf0af612b6125bf765997e0bbd88a Author: galt Date: Fri Oct 20 15:00:32 2006 +0000 "Encode release log update" commit fa441308c0122dcc6548190e2a20a69528b55b35 Author: galt Date: Fri Oct 20 15:00:31 2006 +0000 "Release log update" commit 9330e92fad796ee14fdfb35f3dec923ef94ed636 Author: kate Date: Fri Oct 20 14:51:53 2006 +0000 Remove gala commit fa45947f05684e2b1cc30a980b437e468e10bd93 Author: kate Date: Fri Oct 20 14:50:03 2006 +0000 Chanegs for custom tracks assembly changes commit 7103804cf738cc3f55e26ff384f332ebe93a9d63 Author: kate Date: Fri Oct 20 14:35:46 2006 +0000 Changes for assembly switching for custom tracks commit 9ebf070a3dd08752bb87b3b317f924e7e2b62644 Author: kate Date: Fri Oct 20 14:27:12 2006 +0000 1. Remove gala 2. Custom track database changes commit 26d977e79a34f8e09a1edc9124ea0b96a042d71e Author: giardine Date: Fri Oct 20 13:26:59 2006 +0000 added terms of use / disclaimer commit da3c9122898a360daa105ecf9a59cdff6c7705a7 Author: kate Date: Fri Oct 20 05:16:10 2006 +0000 Changes for assembly switching of custom tracks commit bd25d3a78fbb3e24a09776ff047af1c5f9c0ba88 Author: kate Date: Fri Oct 20 05:15:40 2006 +0000 Adapt to new custom tracks lib commit 6f820949feba0f64e02fc078fda565dc6f067e81 Author: kate Date: Fri Oct 20 05:01:14 2006 +0000 Preserve custom tracks by assembly commit 9f9f27e19b37d7077928145a7bb205650cb7188a Author: kate Date: Fri Oct 20 04:58:40 2006 +0000 Remove gala code commit 9ef943abf5f7214f11ff72fc68c68f55432958bc Author: kate Date: Fri Oct 20 04:56:54 2006 +0000 Utility function for retrieving a dbDb entry commit 5fe16cedbe423d96932d6a7a3d99ab5da2fc2112 Author: kayla Date: Fri Oct 20 01:20:12 2006 +0000 Made the journal references be italicized. commit 4ace6d2cacfbb7d7a32d0c6fa4e610ca7ca75b30 Author: rhead Date: Fri Oct 20 01:11:56 2006 +0000 changed wording commit f9ab5a6e10ff3ebf7a3b833a1d32d0b27f708ddd Author: hartera Date: Fri Oct 20 01:03:20 2006 +0000 Added more details to the methods, data analysis and verification sections. commit 1a9ed89103f772a0c2aa8ea62155c4a98d2fda83 Author: kayla Date: Fri Oct 20 00:46:06 2006 +0000 Fixed the references to be in our standard format. Added links to the papers that were listed. Removed the extra html that tries to take you lower in the page (because the page isn't long enough to warrant it). commit a80f234217e41727b8a2a92896c99451b8b08c52 Author: aamp Date: Thu Oct 19 23:04:58 2006 +0000 Added -customLib option for using custom repeat libraries. *almost working* commit 165d93f157e39f81fac5f41b4dfa0b0115836408 Author: ytlu Date: Thu Oct 19 21:35:07 2006 +0000 add a pseudogene track -- UCSC Pseudo commit 6c7015749b3ba76590e638499269947036ff23ae Author: galt Date: Thu Oct 19 15:00:32 2006 +0000 "Encode release log update" commit f4b5f08c80fc45fade2c8e6da31bbe9835e21c5f Author: galt Date: Thu Oct 19 15:00:31 2006 +0000 "Release log update" commit f9de73b0cc3062460721c4646afc195a1df5dd80 Author: giardine Date: Thu Oct 19 14:08:28 2006 +0000 Added terms of use (disclaimer) commit fb9b751b073381309c6431bb36df7d4b8b0116a3 Author: markd Date: Thu Oct 19 05:11:58 2006 +0000 added option to ignore version numbers, send information messages and happy dots to stderr rather than conditionally to stdout commit 2759d0b1d6584bda162fb33aa7e07dfe838d8383 Author: hartera Date: Thu Oct 19 00:06:37 2006 +0000 Update of Zon lab zebrafish array data. Data values were being rounded when loaded into the tables. commit 952754828f57194a94e589786bb3f924bb14daec Author: heather Date: Wed Oct 18 23:20:42 2006 +0000 use sqlFloat and sqlDouble instead of atof commit b2144bdbccf27eecc515483cd45a1e80b3443ced Author: heather Date: Wed Oct 18 23:15:32 2006 +0000 use sqlFloat and sqlDouble instead of atof commit d08d657e67a5e687c2fd48f1402519ca47a08a1d Author: heather Date: Wed Oct 18 23:09:17 2006 +0000 remove snp126 commit 07b644cf70cbbc8d0d5174644c3c05a0e3304710 Author: heather Date: Wed Oct 18 22:46:22 2006 +0000 use NULL instead of ERROR string commit 08e3d5061e389589834dea80c7ec560b3b286fab Author: rhead Date: Wed Oct 18 22:17:53 2006 +0000 changed more quotes to html quotes and changed wording commit 95f5f51577d066dc064847f5e1aa9b4949559047 Author: heather Date: Wed Oct 18 21:49:01 2006 +0000 add bin commit 8b5a3bddbd84c673900cc43d6aa86d112a736e1a Author: rhead Date: Wed Oct 18 21:20:06 2006 +0000 changed quotes to html quotes; wording change commit 5a282da3a8d39d6035603f25129799e8d2e33af2 Author: giardine Date: Wed Oct 18 21:10:29 2006 +0000 Lowered minCheck for gvLink commit 9fb22c1db72557915c288529c75a2ff32b386060 Author: heather Date: Wed Oct 18 21:10:12 2006 +0000 for dbSNP SNPAlleleFreq commit 5ffa5dc0b65cf4f1681ae6b08ca282c8b11651bc Author: rhead Date: Wed Oct 18 21:08:07 2006 +0000 took out feature ID reference and made small edits commit dc9bccf6862dcb0a53f5002f41cb89ec0c508294 Author: heather Date: Wed Oct 18 20:56:33 2006 +0000 not needed commit 3c55ae904844b4dcdfc9ef32b7b4a82c2d6617fa Author: heather Date: Wed Oct 18 19:19:45 2006 +0000 tweaks commit b2e6e1fcd89d427446aec7f5bfb883ad8406ad8d Author: rhead Date: Wed Oct 18 19:18:24 2006 +0000 added check to be sure hgFixed.gv.srcId's are in gvSrc (per Belinda) commit 566b84120596d0ac4813d3d498bdca77b98f5206 Author: heather Date: Wed Oct 18 19:08:02 2006 +0000 construct snpFreq table commit 47e89f770c32d95a35e39bec3ff06abdb3623db2 Author: fanhsu Date: Wed Oct 18 18:21:00 2006 +0000 Added hiv/hiv1/trackDb.ra. commit 58e9c68d29529c6abd79bc634b5d9f4d91fc018d Author: donnak Date: Wed Oct 18 18:17:26 2006 +0000 Fixed broken links for blat executables downloads. commit 1c2a55f595ec82eadb66a198435ede1695d70cfb Author: donnak Date: Wed Oct 18 18:12:31 2006 +0000 Fixed broken link for downloading blat executables. commit ef2762d23d8ee613cdf7cb105835da914c50e2e9 Author: fanhsu Date: Wed Oct 18 18:04:25 2006 +0000 Added defensive logic to prevent buffer overflow. commit 30ed5655c86c6e9273b37f245e4d6290840a2415 Author: donnak Date: Wed Oct 18 16:38:23 2006 +0000 Added new item on creating a GB for a new assembly. commit dad1069af8faa0b434b18a75568d643e27bfa8a0 Author: galt Date: Wed Oct 18 15:00:40 2006 +0000 "Encode release log update" commit 8c34b518dc4a15ae6985257e31f0bf0d4d80b95c Author: galt Date: Wed Oct 18 15:00:39 2006 +0000 "Release log update" commit 79e64305853a5f2aa0a621891dcf4d548d641045 Author: giardine Date: Tue Oct 17 21:50:02 2006 +0000 Added minCheck to gvPos keys commit 34c8163494f14d97ac2d5bc90671365bcfab3310 Author: heather Date: Tue Oct 17 20:33:49 2006 +0000 need position index, hgTracks is doing hRangeQuery commit 38c99a5dfbbf5fe50e4181fcfe65b30b791a419b Author: heather Date: Tue Oct 17 20:22:22 2006 +0000 never mind, put extended names back in commit 1e621e7c3dcd8172a02c9cebb4e059e39a7bf0a6 Author: heather Date: Tue Oct 17 20:21:27 2006 +0000 never mind, put it back in (this time freeing the connection) commit 85b736a2a69a6baae0300fc4d8e8bc97f91dac6a Author: angie Date: Tue Oct 17 19:54:14 2006 +0000 Moved $mkOutRoot to be executed on the same host that runs xdir.sh, to avoid out-of-sync problems (previously the xdir occasionally died because it couldn't see the result of the mkdir ) . commit ae1c926d45baf57b4173285dfcc3e926ff4028d6 Author: heather Date: Tue Oct 17 19:14:56 2006 +0000 fix mistake in previous commit commit f51b64221620db54c99b68613fcd9b57045ae363 Author: heather Date: Tue Oct 17 19:11:21 2006 +0000 remove extended name option commit d09d48c5ea277b029093fe4492a9b11c1a9e64a4 Author: heather Date: Tue Oct 17 19:10:17 2006 +0000 remove extended names option commit 050142a588f01cb635eaac924e4a58c86c188286 Author: kate Date: Tue Oct 17 16:12:26 2006 +0000 Clarify that quality scores for finished chroms were set at 98 commit 36b7ab39033e62757c6b6fa6029ef6abdcf9eb58 Author: galt Date: Tue Oct 17 15:00:39 2006 +0000 "Encode release log update" commit 5cec10948c0297af9fef68c329137e85082daa7c Author: galt Date: Tue Oct 17 15:00:38 2006 +0000 "Release log update" commit c726d699cdbbe17b55e8dfeffbc16971bf5ac471 Author: giardine Date: Tue Oct 17 14:53:31 2006 +0000 Added strand to details page for Locus Variants (gv*) commit dd54885852c28064e4a2b1aca1442a4433d1ff47 Author: giardine Date: Tue Oct 17 14:14:03 2006 +0000 Changed order in gv tables, putting gv as primary key commit 1ae532749f63eeb1e35111271f894da8e10a0ebb Author: aamp Date: Tue Oct 17 01:15:41 2006 +0000 Added microarray custom track capability. commit 77357c2a9d67da8581e8d82ad6f3ec5aacdd23bd Author: kuhn Date: Mon Oct 16 23:40:51 2006 +0000 fixed the processing of mgc. was reporting it twice. commit 0fc02d916495be0e11405d9c2a4c34978baf2e21 Author: angie Date: Mon Oct 16 23:24:01 2006 +0000 Added genomicSuperDups and wssdCoverage from Eichler lab. Generated reciprocal best chains/nets for rn4 using new script. commit 35896da2736c06f9d097c752ea534e0800c3602d Author: angie Date: Mon Oct 16 23:23:00 2006 +0000 Added wssdCoverage from Eichler Lab (analogous to hg16 celeraCoverage). commit b4d2fd6f689f5d4f9dd593ba69e5876fd771bf7a Author: angie Date: Mon Oct 16 23:16:39 2006 +0000 Added genomicSuperDups from Eichler lab. commit b94d17628a268afd2a702564ed613180320ed6d8 Author: rhead Date: Mon Oct 16 22:58:44 2006 +0000 added omimTitle to tables ignored per Belinda commit 73dce9c3362e64c396bae2bdeb77989de58c4e03 Author: angie Date: Mon Oct 16 22:17:34 2006 +0000 Resolved -Wall warning: added parens around || within &&. commit 38c48c6a51ec6c556ecca8d906f2597556a7d4e0 Author: angie Date: Mon Oct 16 22:05:31 2006 +0000 Fixed paths for scaffold-based assemblies. commit 6506d6f8572c4156ab347a1a8693d29ecb513c64 Author: galt Date: Mon Oct 16 21:21:12 2006 +0000 fixed grammatical mistake and made more legible the help messagse for twoBitToFa commit e4119f314e62da5e7e9f659b4c85c384965cea16 Author: hartera Date: Mon Oct 16 20:42:31 2006 +0000 Added new click handler for the Yale TARs/Transfrags data track. commit b24fe6f204abe80b1420d1829de9b1e0d12c44e2 Author: giardine Date: Mon Oct 16 19:59:55 2006 +0000 Changed header to print official name rather than ID for Locus Variants commit af7609e33cd5e8eca0486fa3dd2760b8dfdaa18d Author: bsuh Date: Mon Oct 16 19:47:20 2006 +0000 Initial checkin. Entropy track info. commit 1186c20dac3511b7bdad205fa8379dc0ea6d1a8f Author: rhead Date: Mon Oct 16 19:44:26 2006 +0000 Removed hyphen in description to make Locus Variants page consistent commit 340414fc149f2e5355f7e0177c34c90dbf01a87c Author: giardine Date: Mon Oct 16 19:01:06 2006 +0000 Removed ID from label options for gvPos (Locus Variants) track commit 0a3d6ad8afcb2bc485d261c4e5e0d26ecf53485c Author: rhead Date: Mon Oct 16 18:25:20 2006 +0000 Many changes after QAing track. commit a5b3cc9445dfac9f28447391128747d035172ab7 Author: hartera Date: Mon Oct 16 17:46:47 2006 +0000 First draft of a description for the Yale TARs/Transfrags data from the Bertone paper. commit 9690b6e566875ba95e9a48501db145faa97dc0cb Author: hartera Date: Mon Oct 16 17:05:37 2006 +0000 Added Bertone data for TARs/Transfrags from Yale: yaleBertoneTars. commit 637496e2908c1a172bb952a192d5beff080d9856 Author: fanhsu Date: Mon Oct 16 16:46:48 2006 +0000 Restructured and updated. Changed into offset/length based instead of text files output. commit eba775f709395382be86c996c1ed46d7493817b3 Author: donnak Date: Mon Oct 16 16:02:27 2006 +0000 Fixed some broken links to Adam's pubs on his Cornell homepage (URL changed). commit 9ec851f66a0c56bd99722586881265853938f55d Author: galt Date: Mon Oct 16 15:00:26 2006 +0000 "Encode release log update" commit 4352723d0fbc881f0cf03fe8d7a319e2a4b0d965 Author: galt Date: Mon Oct 16 15:00:25 2006 +0000 "Release log update" commit f7afaa6755d48cd629607c828bbd325c84c9c611 Author: markd Date: Mon Oct 16 06:34:00 2006 +0000 added safe version of strcp and strcat functions commit f201c5b9819bf71c19cdbdbc54c8701e5c19871c Author: markd Date: Mon Oct 16 06:06:51 2006 +0000 handle new snp table naming commit 477e339d847ea4cd6a1d9aa4dd91fee46521bd54 Author: markd Date: Mon Oct 16 06:04:39 2006 +0000 don't segv if chromInfo doesn't exist, return NULL as documented commit 93405b37a53be8da8aa5033bf934d3c4050cef1a Author: markd Date: Mon Oct 16 05:32:04 2006 +0000 fix bug with mafFlipStrand and annontations commit cd4da8a648318f03e67515c3e6512e3b1b5a82e4 Author: kent Date: Sun Oct 15 19:01:54 2006 +0000 Flipping to October and hg18 as well as hg17 commit 92497cd7066d6f269370f491ff9068c42bfac00e Author: galt Date: Sun Oct 15 15:00:22 2006 +0000 "Encode release log update" commit 124cead173342c308104d166f4239d66a38e9331 Author: galt Date: Sun Oct 15 15:00:21 2006 +0000 "Release log update" commit a18703a816412f05c86dd16f113eb2d949e84c28 Author: kate Date: Sun Oct 15 01:09:36 2006 +0000 Move custom track description handling into the library commit 841735ebfe35779ff83c424e7a2c5c10fe5b9ae4 Author: kate Date: Sun Oct 15 01:04:13 2006 +0000 Move function where it should be instead of where it might please cvs diff commit 888460c0c68446fa109fd6080ee3c1a5ca223f9b Author: kate Date: Sun Oct 15 00:54:35 2006 +0000 Move custom track description handling into the library so that URL's can be expanded by the preprocessor. Also addresses other QA requests WRT doc handling commit 5049358a1c9c7a8b4a75d357120f1b50f7f7b09c Author: kate Date: Sat Oct 14 19:41:16 2006 +0000 Abbreviate some button labels commit f3333515ecef2ee821feb2b24365b2348c130edf Author: kate Date: Sat Oct 14 19:37:28 2006 +0000 Add include file for tests commit 1e0e2d6df77b57958f357560f21dd120ac76bc0b Author: kate Date: Sat Oct 14 19:33:00 2006 +0000 Add buttons for setting and clearing all checkboxes for Delete and Update on the Manage screen commit 948f69fd63b6ed1c49ad278654f57e91b00bc482 Author: galt Date: Sat Oct 14 15:00:25 2006 +0000 "Encode release log update" commit db6534529c74db318d53b756e7e3be47a576c721 Author: galt Date: Sat Oct 14 15:00:24 2006 +0000 "Release log update" commit abecfff531aefc7e1c9f31349c758efa815d9fd4 Author: heather Date: Sat Oct 14 02:34:42 2006 +0000 tweaks (no chroms) commit c0a47616136cb7e53075829702b49a2d7aabc4f2 Author: heather Date: Sat Oct 14 02:00:54 2006 +0000 Initial descriptions commit a3b4880aa2bce2839f9d233c3609734151bd6b00 Author: heather Date: Sat Oct 14 02:00:30 2006 +0000 Added felCat3 to DBS commit 22e22837bf836fff083e07d6b3dec5360ff41091 Author: hartera Date: Sat Oct 14 01:35:12 2006 +0000 Removed ortholog table for affyZebrafish track as data not released yet. commit 0dbf924420c475d9d344a1cf55fbd02a40b4114b Author: hartera Date: Sat Oct 14 01:33:27 2006 +0000 Updated filtering parameters. commit d2d50eea027b31c736871d726eedde92fce6c45c Author: kate Date: Sat Oct 14 00:03:32 2006 +0000 Change prompt on entry box, by request of QA commit f237ffdc5a6b96a6b9f6fc253512d8a61edfd2a5 Author: kate Date: Fri Oct 13 23:15:02 2006 +0000 Add test driver and support files for custom track library testing commit fc0dd4586fe66f5b3401dd222a1785ce3c16b6d8 Author: galt Date: Fri Oct 13 23:11:25 2006 +0000 additions to support HPRD - basically improving error printing by removing duplicate messages; and handling case where there really is a self-self protein interaction, that weight will appear and take priority over the default 0 otherwise stuck in for convenience; sorting the input so that precedence is given to nearer distances when weighted commit ab052f230123f19f71d31e011cea33a80c2fc785 Author: heather Date: Fri Oct 13 19:50:04 2006 +0000 change 3 func default colors to black (cds-reference hardly used) commit 68020c653b8da7025ef9b8bcb8fe6026829ff833 Author: donnak Date: Fri Oct 13 19:13:08 2006 +0000 Added FISH mapping credits to monDom. commit 7350a9119554878e8ece83a895539a7cb24c9197 Author: markd Date: Fri Oct 13 17:24:19 2006 +0000 fixed bug with search for download files commit f8b0cb39a54d2d638296936438e49500e92e6562 Author: heather Date: Fri Oct 13 17:11:25 2006 +0000 generate snpExtFile and snpSeq using build126 commit 57667b64646f816055a5f26e6e2da4437a9a1798 Author: heather Date: Fri Oct 13 16:06:32 2006 +0000 clean up for snps commit d5045a0d9e071218f849e6ab3d9474e2bdaea6cf Author: heather Date: Fri Oct 13 15:43:13 2006 +0000 generate snpExtFile and snpSeq commit e65345e62a5570066ac3d457a58ea6f8471cac3e Author: galt Date: Fri Oct 13 15:00:28 2006 +0000 "Encode release log update" commit 7ae278324c957409d816f7ccdee8d47c627eb5a8 Author: galt Date: Fri Oct 13 15:00:27 2006 +0000 "Release log update" commit c314ce709f1867fc4d437e24a19f6ef6e8e3f8d4 Author: heather Date: Fri Oct 13 05:16:41 2006 +0000 generate snpExtFile and snpSeq commit 05b31b005a809383bf75175902f1319c33708386 Author: heather Date: Fri Oct 13 04:51:06 2006 +0000 generate snpExtFile and snpSeq commit dde574f78c87360667183f0823b93d19107241e1 Author: heather Date: Fri Oct 13 04:49:36 2006 +0000 add printSnpAlignment2 to doSnp125; stripString random commit 92e5d89f54d41a7ee5498f0a6b66b33f7ed687d5 Author: heather Date: Fri Oct 13 00:18:20 2006 +0000 generate snpExtFile and snpSeq commit 79059e54c1712c5d544c403e7d370cf7d53cb55d Author: aamp Date: Fri Oct 13 00:12:12 2006 +0000 Original assembly for affyHuEx1 was actually hg16. commit 31be2e87efdb043c3071db1bdb9d28827544e6ea Author: aamp Date: Fri Oct 13 00:10:52 2006 +0000 Added affyHumanExon to hg16. commit ccde0fb1a26755bf93e69bacc357f3790b04d27c Author: heather Date: Thu Oct 12 23:41:16 2006 +0000 tweak commit 0d6f810e813ec3f89e972acbe03128122deed603 Author: heather Date: Thu Oct 12 23:28:55 2006 +0000 remove previous method for snpSeq commit 3b6148b51f605ef6a8ab61b957360098296cd602 Author: heather Date: Thu Oct 12 23:24:36 2006 +0000 generate snpExtFile and snpSeq commit 86bcda820d906ccd5e25de76d6e668c81328dc01 Author: aamp Date: Thu Oct 12 22:53:57 2006 +0000 Forgot the
  • . commit ba8371aa9a0bc7aaa4490f25147aad4790319429 Author: heather Date: Thu Oct 12 22:53:52 2006 +0000 for SNP flanking sequences commit 1d949b6d615c705f8aa83d91d5ece0c30d5d3062 Author: galt Date: Thu Oct 12 22:50:52 2006 +0000 removed redundant hidden form, reduce javascript to minimum, made "clear" button function correctly by hitting the cgi and clearing userSeq cart var and returning a fresh page commit 6dd9c314509d36bf59bf4e9a84b7ff32a532a8f0 Author: aamp Date: Thu Oct 12 21:56:53 2006 +0000 Changes to affy human exon tracks. Put probe track right below microarray track and mention both in each others' details. commit 59e9226962154e2cff5dcce28f7463a4af4a230d Author: kate Date: Thu Oct 12 21:17:04 2006 +0000 Remove custom tracks when assembly changes (temp fix) commit 39f0907750c69e509abe14f8030b4afb72a4b7e5 Author: heather Date: Thu Oct 12 20:04:43 2006 +0000 remove old-style snp alignment commit e9c4217e884d508e6ac5f37e57f71b0e830a2b15 Author: daryl Date: Thu Oct 12 18:47:53 2006 +0000 changed description of additional name option in snp125 UI page commit 89d1ad802397c07b1407e76dcf31152c15e111d0 Author: braney Date: Thu Oct 12 18:10:57 2006 +0000 bernard's entropy track commit 01b3efad1c6c849164fe4579025ab2a9ff671fc2 Author: galt Date: Thu Oct 12 18:03:10 2006 +0000 tiny code improvement commit d46964012d16d46b8bc10b80b67098eb8b244371 Author: kuhn Date: Thu Oct 12 16:33:18 2006 +0000 added realTime.csh for getting update_time from RR machines in real time commit cfcb25aeed28585354c8b3a63ff9e93f7154ef34 Author: kuhn Date: Thu Oct 12 16:31:53 2006 +0000 simplified logic for mgc output commit d98934941219de9f0f265faa984eeb61c10fb52e Author: fanhsu Date: Thu Oct 12 16:19:40 2006 +0000 Added a new contact person. commit 7215602739ceeb5d8bd9c942c726a1c68321b34a Author: fanhsu Date: Thu Oct 12 15:57:01 2006 +0000 Created omimField table. commit 16be503669e0771715133d718a943fc788d8ebbf Author: galt Date: Thu Oct 12 15:00:29 2006 +0000 "Encode release log update" commit 52b05cfdc1d05ca686ac990d27f5dfd4f5540591 Author: galt Date: Thu Oct 12 15:00:27 2006 +0000 "Release log update" commit 228a1801ec241f4b5369fb8de8089d8e22325514 Author: kate Date: Thu Oct 12 04:20:50 2006 +0000 Remove custom tracks when genome assembly changes (temp fix) commit c8774bb397b89aab91ddd2a7c5663b633487567e Author: heather Date: Thu Oct 12 03:58:26 2006 +0000 use snpSeq with offset and snpExtFile for alignments commit 92b5fda707f8f7ce1435189325754e5981d98dca Author: heather Date: Thu Oct 12 03:34:26 2006 +0000 refactoring; don't include ortho item if chimpAllele is '?' commit b106ccd47b43f642a0d2c9b95bad11197913b3e4 Author: daryl Date: Thu Oct 12 03:03:36 2006 +0000 VERY SUBTLE pointer bug in setSnp125ExtendedNameExtra commit 5411d24b7c80ff3cabba48702bc5f89fe239e2e2 Author: galt Date: Wed Oct 11 22:25:35 2006 +0000 clean up and fix more topbar menu with no cart situation commit d10c9dc72e506962282f0868c0df3a238db4867f Author: heather Date: Wed Oct 11 21:47:59 2006 +0000 minor tweaks to previous commit commit c64cd3cee14c5e09dd71a10b4235210342695503 Author: hartera Date: Wed Oct 11 21:07:09 2006 +0000 Reprocess BAC ends and recreate track to remove replicates and start creating BAC end alias and cross-reference tables. commit 5f9fbf465294588a149acf2b5948f7a395007856 Author: rhead Date: Wed Oct 11 19:28:59 2006 +0000 gvPos.html was moved to human level to include hg18. This copy is no longer being used. commit 839cba87ac6eb70b0283a49da520be809b41a074 Author: kate Date: Wed Oct 11 19:04:27 2006 +0000 Remove custom tracks if assembly changes -- needed to till custom tracks store assembly with data commit 6aeab8f71e87335f5bd510c816f8099c07ac13fd Author: kayla Date: Wed Oct 11 18:26:32 2006 +0000 Removed the chip lines from the microarray tracks. commit c92859939a463ffdfdcf1871b0b6528500d89794 Author: heather Date: Wed Oct 11 17:54:28 2006 +0000 don't need extended names in squish mode commit 6659cba556474c43107d90b20263e143ababce91 Author: ann Date: Wed Oct 11 16:57:17 2006 +0000 typo commit 7118dfeb4dd7aa466a215a67ab61832f8eabdafc Author: angie Date: Wed Oct 11 16:48:33 2006 +0000 Added dm2.flyBase2004Xref.fbgn to flyBaseGeneId. commit fa7eb0d2b4f8cf6bd155e466ce686fffca4a84e6 Author: hiram Date: Wed Oct 11 16:34:39 2006 +0000 Fixup position printout for bed 3 items from the database commit 10dd4cea295f42162c08a89edb7a908d1673389d Author: angie Date: Wed Oct 11 15:20:22 2006 +0000 Added placeholder clean target, to avoid warning from make. commit d1032980934fe9224cd17dd2dc0de3fef4fa9c1a Author: galt Date: Wed Oct 11 15:00:28 2006 +0000 "Encode release log update" commit 209064fc606ecf9207416e778447243051b64485 Author: galt Date: Wed Oct 11 15:00:27 2006 +0000 "Release log update" commit 0883acb128a2d84ea0e0af88993cd4fcb96b573f Author: heather Date: Wed Oct 11 06:00:30 2006 +0000 Avoid sorting twice. Use estimateVisibility() to do color sort in loader. commit 0301bc4225b3e90c3858ac226d24b81495ab46a9 Author: heather Date: Wed Oct 11 05:42:54 2006 +0000 add function estimateVisibility commit 3da62492d2bb231099374719fafffcee57eaad21 Author: angie Date: Wed Oct 11 05:27:54 2006 +0000 fixed typo in multiz15way caught by Jakob. commit e3b64d3ecd09250cb0d26233250259ffcccb8193 Author: galt Date: Wed Oct 11 00:33:01 2006 +0000 using non-branch-tag tag "branch" now for cvs-reports because moving the real branch tag prevents fixes from showing up in the developers cvs reports commit a519314121b86f6946ecb7deee7d9ee9597239af Author: angie Date: Tue Oct 10 23:00:17 2006 +0000 Use verbose instead of printf for memory usage statement so output can go to stdout. Also added initialization of netList -- we were 'lucky' before but after making the verbose tweak, segv reared its ugly head. commit 0dbe7b4ed7f97f62eb22ef88ed067f7e1243b456 Author: angie Date: Tue Oct 10 22:58:03 2006 +0000 Added missing setting of isTwoBit flag when reading in .2bit file. commit 0fd54a990093b4ba81d4b47847803c2387565dc2 Author: angie Date: Tue Oct 10 22:56:35 2006 +0000 Added doRecipBest.pl (and makeDownloads.pl, oops) to SCRIPTS. commit 6608c895ee978ea4d2c4c1796e553a743c1ee181 Author: angie Date: Tue Oct 10 22:55:53 2006 +0000 Added newline to self-contained warning. commit 2afd18abd0cabf5a0ea09aabb831ee3f06ea8314 Author: angie Date: Tue Oct 10 22:55:01 2006 +0000 Automate generation of reciprocal best chains and nets (from .over.chain.gz previously generated by doBlastzChainNet.pl). commit ba07ba33849da7b498f5549a45c31e3891cc40d2 Author: kate Date: Tue Oct 10 22:35:56 2006 +0000 Switch to POST form so that huge numbers of checkbox variables can be accomodated (user with 300 custom tracks) commit fc62fce2260c50e46555632264404e17e76ed11d Author: angie Date: Tue Oct 10 22:26:02 2006 +0000 Moved browser build automation scripts from src/utils to src/hg/utils/automation (Jim's request). commit 80c085cc36542338eed331567a7233f8017229c9 Author: markd Date: Tue Oct 10 21:52:28 2006 +0000 moved CCDS search spec from human to global, for use with mouse commit 66c20828b1a23be5436400bdbedfca87776c958b Author: markd Date: Tue Oct 10 21:28:15 2006 +0000 pre-build ccdsMgcMap table commit 714ee449ca8eb9d5fee8fd161d66964c066abfc9 Author: kuhn Date: Tue Oct 10 21:10:46 2006 +0000 added hyphen commit cc4167a584d0c41112910c1a1bd7d4c7cec7858a Author: kate Date: Tue Oct 10 21:06:12 2006 +0000 Fix compile err commit 7479daa88be6852c254e94c0f2d64d20c5361ad2 Author: heather Date: Tue Oct 10 21:00:46 2006 +0000 set outputFileName commit 0db6da2c9071591a16053839281278ac15f993ba Author: heather Date: Tue Oct 10 20:58:14 2006 +0000 generate offset commit 05c11a3f3b183d6ed43ae1429b3feed55cc7bfba Author: ann Date: Tue Oct 10 20:32:12 2006 +0000 corrected ccds entry commit be717cda96ee6fec629d73dcda5c3800dd5c1795 Author: ann Date: Tue Oct 10 20:29:58 2006 +0000 added mm8 to list of ccds assemblies commit a45d5c80b841e0d8a757aaffaa4d7fb1403b6a5a Author: kate Date: Tue Oct 10 19:04:53 2006 +0000 Standardize hgsid handling -- save as hidden var immediately after declaring FORM commit 10be5a6d6bd5fb76fe43ace001e1c4382cc32c2a Author: kate Date: Tue Oct 10 19:01:02 2006 +0000 Standardize hgsid references: 1. Save hgwid as cgi hidden var with cartSaveSession(), immediately after declaring FROM 2. use cartSidUrl to add CGI variable to HREF commit a7b7d392df803947a74053c162d1bdb7f6882b32 Author: markd Date: Tue Oct 10 18:59:26 2006 +0000 added mouse CCDS commit 4d867a8ed7049c3507681cddc651f4b0a1e84846 Author: markd Date: Tue Oct 10 18:56:26 2006 +0000 added mm8 CCDS commit c1f55bc93ff6bcf51d3afdd1a354dcb5fccbb3de Author: kate Date: Tue Oct 10 18:19:36 2006 +0000 Expand references, fix formatting, add URLs commit bca6001fbb53e976d8e7c106f6729b06552928a5 Author: ann Date: Tue Oct 10 18:19:06 2006 +0000 moved erroneous line (track multiz7way had been appended to bottom of bacEndPairsBad track) commit e4eec53e36b8a8943f1c766f4cb8d96933eb0ae0 Author: hartera Date: Tue Oct 10 17:37:12 2006 +0000 Added Rachel to email notifications. commit 420c52ffbc4cfbcd7573931afba0a4269b1b16a2 Author: rhead Date: Tue Oct 10 17:28:41 2006 +0000 changed singular to plural commit 7b55b28f48b54ba780905a9c550b779c81fd0c1f Author: angie Date: Tue Oct 10 17:22:16 2006 +0000 Moved browser build automation scripts from src/utils to src/hg/utils/automation (Jim's request). commit 2ecde0f2da9548f68c37cb56869f4126df62d995 Author: heather Date: Tue Oct 10 17:07:19 2006 +0000 remove table no longer used commit aa7d0ed0f38e5b369f37ccaadab699b2e7806558 Author: fanhsu Date: Tue Oct 10 16:18:42 2006 +0000 Updated URL to GAD. commit 90a35debf8ea1a13fc09b81bded265fdd01624f9 Author: galt Date: Tue Oct 10 15:00:24 2006 +0000 "Encode release log update" commit c03727aef4466a07348aef54f6520f3822790dee Author: galt Date: Tue Oct 10 15:00:23 2006 +0000 "Release log update" commit 482f4737b5511540e88e90b1bd121c9f04e8f348 Author: angie Date: Tue Oct 10 05:34:49 2006 +0000 Added dm3. commit 5b0220b616899c0e1fba9b81cea4f8ba8f62aaa7 Author: galt Date: Tue Oct 10 04:40:25 2006 +0000 removing hgCgiData since this is run during utils build and it really makes more sense with cgi building commit 8cdbd7befb24a2b2bf541bbce0793e48fd24de56 Author: galt Date: Tue Oct 10 04:39:06 2006 +0000 adding hgCgiData since this makes more sense to run with cgi building commit 74a2b645e52285c7c818344fc271689e7027b339 Author: galt Date: Tue Oct 10 04:34:59 2006 +0000 removing hgCgiData since this is run during utils build and it really makes more sense with cgi building commit 47d7ad171f4225b219d6d4dedc3d32f9d343f222 Author: galt Date: Tue Oct 10 04:33:44 2006 +0000 various updates commit f01df91d3ac7940d102498969c8841a192e58a56 Author: hartera Date: Tue Oct 10 02:49:49 2006 +0000 "New version number v144" commit a8d566decbaeab19f8bd1e19b71cef6542cfda8a Author: kate Date: Tue Oct 10 00:21:52 2006 +0000 Add panel for help on the manager screen commit 9b479c3972448c91932da2f5799c2b6c8415945a Author: kate Date: Tue Oct 10 00:21:28 2006 +0000 A few formatting changes commit bdc27d76eee3b4eb9152533b706423d7a33301b0 Author: ann Date: Tue Oct 10 00:01:54 2006 +0000 initial doc for displaying in a section on the Manage CT page commit e7110511f2dbbb1d7c8e1c9fe9d4d5701f2fd3ac Author: ann Date: Mon Oct 9 23:53:31 2006 +0000 typo commit d823ade77cf9e49f71a17fc224e5ce12fc0a441f Author: ann Date: Mon Oct 9 23:52:33 2006 +0000 corrected information about CT details page commit 591726319c2eca1a2a2945311d17b1b13fcdaf17 Author: kate Date: Mon Oct 9 23:07:01 2006 +0000 Description for expanded Duke/NHGRI DNase track commit ac655420b473f5d05fb3af1ced63e3ce66691a22 Author: ann Date: Mon Oct 9 22:57:55 2006 +0000 corrected wiggle display for Manage CT screen commit 2c4188e3e6f436ade85305f2990cbb861dabe7e2 Author: ann Date: Mon Oct 9 22:02:50 2006 +0000 added hg18.snp126orthoPanTro2RheMac2 to snp126 rule commit cc57bc580b9e82571a3a01eacc0802b1784c6240 Author: fanhsu Date: Mon Oct 9 21:22:41 2006 +0000 Created omimCheckAv.c. commit 3c98baccdf6227dd8d5706e39eef1a6e373ee0b2 Author: fanhsu Date: Mon Oct 9 21:22:21 2006 +0000 Created makefile. commit 8c3803e28a48827a6404f4facb1f7c0b0d86333e Author: fanhsu Date: Mon Oct 9 21:21:59 2006 +0000 Created omimParseAv.c. commit ac00fd61af6cec63533f50bd913584faff21868e Author: fanhsu Date: Mon Oct 9 21:21:13 2006 +0000 Created omimParseRec.c. commit 1b67cb0ecfc2ba31cf60abbf4fca8c639ebaca55 Author: angie Date: Mon Oct 9 21:11:20 2006 +0000 Additional fly pairwise alignments requested by Mike Eisen. commit f49cf3916b1e77dcf9dc5e87dc78411c2d09870f Author: angie Date: Mon Oct 9 21:08:01 2006 +0000 Some polishing and html-fixing as suggested by MarkD. commit 03fc9597890b0c71f28f7f6c6c295d725228ab3f Author: hiram Date: Mon Oct 9 20:57:09 2006 +0000 Move tfbs sites cart variable and default value to include file commit 3432b22bca5f5242e8230c72251c90692f136bcd Author: hiram Date: Mon Oct 9 20:56:21 2006 +0000 Cutoff cart variable string and default value commit 34b8c5d6fadc2399ca0297fe7f0baa745afa1f92 Author: angie Date: Mon Oct 9 20:46:01 2006 +0000 oops, fixed relative path to inc/common.mk commit 9dd9d1cd6d8e9fa1f42c8b902408c2be672e2e5b Author: hiram Date: Mon Oct 9 20:45:00 2006 +0000 Forgot closing commit 8ce9c92b70ee457ec3fe78ef009e2343a2dc43be Author: angie Date: Mon Oct 9 20:44:34 2006 +0000 Moved browser build automation scripts from src/utils to src/hg/utils/automation (Jim's request). commit 11792fa8faf463ae18ac12c6d1cb2c4afe29b995 Author: kate Date: Mon Oct 9 20:41:30 2006 +0000 Fixes to browser line visibility handline: 1. suppress extra cart variables 2. remove superfluous code commit fe315cfdea98e3d810804d2adb437ca051a7019f Author: hiram Date: Mon Oct 9 20:36:22 2006 +0000 Adding Matt's tfbs track filter commit 4fcc93d0b365d6aafb28439b89ee4348552f3955 Author: hiram Date: Mon Oct 9 20:33:37 2006 +0000 Adding Matt's tfbsConsSites track commit 08891edb2179be0966628454a0bc154b902662fc Author: hiram Date: Mon Oct 9 20:32:43 2006 +0000 Adding Matt's tfbs track commit 5666e9288aa197d7cd95ab11ca49ac7560009bed Author: hiram Date: Mon Oct 9 19:27:25 2006 +0000 Catch errors from db pipeline loaders and display enough of the message to perhaps be useful to the user commit 4ff7bb23cb9512bfff9e4a2674d17adf75eed2ff Author: hiram Date: Mon Oct 9 19:25:27 2006 +0000 Adding stderr catch of messages from db loader pipeline commit 4b9bdffbf4e111eb8a82ebfe8ffe0f2dd855495e Author: ann Date: Mon Oct 9 17:38:50 2006 +0000 forcing links to open in new browser windows commit 8c284695cb420c0c3729fcde2daad6aa6b5c5100 Author: markd Date: Mon Oct 9 16:17:29 2006 +0000 fixed abort checking for mgc tables commit 2949142f32f527dcd75e804ddf0bacee628bec2e Author: fanhsu Date: Mon Oct 9 16:13:37 2006 +0000 Added geneid track. commit d5c7df21bfd5aec3e39165d6e904fd06cd85f885 Author: galt Date: Mon Oct 9 15:00:19 2006 +0000 "Encode release log update" commit a23de0bcf9585a299f514a7717f41b83f31225f3 Author: galt Date: Mon Oct 9 15:00:17 2006 +0000 "Release log update" commit 5fefd435ce1d83cf648ad5d3f1a74f78bb0d4912 Author: daryl Date: Mon Oct 9 03:10:19 2006 +0000 use separate loaders for snp/snp125 table formats when loading into snp125Extended commit 11278007ae4174f938c7ee888582f3cd658c4438 Author: donnak Date: Mon Oct 9 01:26:01 2006 +0000 Archived a news item. commit 5781976fe9babe340a7b6ee73453c0189be0c3da Author: donnak Date: Mon Oct 9 01:25:48 2006 +0000 Added new news item. commit abc848d3ca39c02b221c2dbe60de9b6b77aec01e Author: galt Date: Sun Oct 8 15:00:21 2006 +0000 "Encode release log update" commit a2216a4cfb6e3aa7fc32bc19de437c7cc06433c1 Author: galt Date: Sun Oct 8 15:00:19 2006 +0000 "Release log update" commit 75a76744fdb4135e3d30f5d204637cd7487677f3 Author: markd Date: Sat Oct 7 20:47:16 2006 +0000 added support for loading genbank misc_difference features commit af6e2a89b2046f304d66f89a867f4c3709d07533 Author: markd Date: Sat Oct 7 20:46:26 2006 +0000 fixed typo in message commit f51ea4b121d448724b3306f2a08f1f083cd85129 Author: markd Date: Sat Oct 7 20:37:08 2006 +0000 added support for displaying genbank misc_difference records commit acf711169bbb053324e3de1a6ff97af2ff0411d3 Author: markd Date: Sat Oct 7 20:32:43 2006 +0000 added function print int table cell commit 9bfcee15729949cdf324765d9c098492c22b9545 Author: hiram Date: Sat Oct 7 16:20:35 2006 +0000 Passing hgsid on to the next cgi when appropriate commit 7c3229c0046a7987bd8b65c0e74a5b9e9bb82b67 Author: hiram Date: Sat Oct 7 16:14:09 2006 +0000 And more passing of hgsid on the track href clicks commit 04a2349ca97004422d997369ca2746d3384d92fe Author: kate Date: Sat Oct 7 15:04:25 2006 +0000 Update for Duke and MSA tracks commit 5ce40f161be5da994e325328197c7866a4c61887 Author: galt Date: Sat Oct 7 15:00:23 2006 +0000 "Encode release log update" commit 1f6d8b0d80e06c0571e838608d89721df428be19 Author: galt Date: Sat Oct 7 15:00:22 2006 +0000 "Release log update" commit 7cbe56f9fb4a9ed39be5eb5caeabec3d51760eb4 Author: daryl Date: Sat Oct 7 06:47:34 2006 +0000 fix snp color sort so that it is ignored on older snp tracks (before snp125 format) commit 3d4f5b4809a72a5391de2aa863ec68d42d5ea116 Author: hiram Date: Sat Oct 7 03:22:06 2006 +0000 What's up with this, we can't open /dev/stderr in the pipeline ? commit f43b3de1dab4ad084a29bde9589191868bfc5209 Author: hiram Date: Sat Oct 7 03:13:44 2006 +0000 Mistakenly removed the opening to the FORM for submit commit 4952c06cc3dc69895485ae397a091694fcfe86e9 Author: hiram Date: Sat Oct 7 00:55:12 2006 +0000 Add the information about the mailto link to come commit 0c1d16645a94c2d949464ba90503eb48e504482d Author: hiram Date: Sat Oct 7 00:04:16 2006 +0000 Did not want to increase wait time to 8 seconds. It is back to 0 for the redirect. commit 389dc7b7647fb3f8df871d62d5481487f50f0a74 Author: heather Date: Sat Oct 7 00:01:19 2006 +0000 2nd location for previous change commit 0d5b1d944f72b8ac616cf34d2f1cf68c9df7fb86 Author: hiram Date: Sat Oct 7 00:00:11 2006 +0000 Maintain hgsid variable in call to hgCustom commit 979641c55e58a5b2f82f4b2298aa8ad95b09533a Author: hiram Date: Fri Oct 6 23:48:31 2006 +0000 Now passing hgsid thru on cgi forms with the hidden variable instead of in an argument query string commit 32b31fdd63eadb3320e810337a2b8ccdd8905b2c Author: heather Date: Fri Oct 6 23:47:39 2006 +0000 comment out new color sort until we can fix it for hg16.snp commit 5c48fe7f966c2d6ddb3f892c29712846eebd4773 Author: galt Date: Fri Oct 6 23:46:09 2006 +0000 fixed topbar menu for cases where user has no cart (e.g. qaPushQ) (better fix) commit 25e84d1360f14bdb34a31bb4775a6811289ed0e5 Author: hiram Date: Fri Oct 6 23:38:40 2006 +0000 Indicate failure modes for database loader failures. Errors go to the apache log commit 7f9d3c86b08d5a1b88513478527fa43df639846d Author: ann Date: Fri Oct 6 23:22:38 2006 +0000 removed absolute link commit 834d058eacb2af966ae066fdac7401ca66431838 Author: galt Date: Fri Oct 6 23:19:18 2006 +0000 fixed topbar menu for cases where user has no cart (e.g. qaPushQ) (fixed my fix) commit 2189d0d854bfaca14ac8892ed7debc132a5aae41 Author: ann Date: Fri Oct 6 23:09:15 2006 +0000 added news about new Custom Track tool commit 28eed6687b6d65b925da0153e5106fe5263d4528 Author: galt Date: Fri Oct 6 23:03:58 2006 +0000 fixed topbar menu for cases where user has no cart (e.g. qaPushQ) commit 175ddc004062cee9826ac18087748ba9e76b3b80 Author: ann Date: Fri Oct 6 22:30:22 2006 +0000 added Victoria Lin. Removed Patrick Gavin and Jennifer Jackson to bottom of page. commit 6a4488cc60e5dc65496842c43bfb10261eca13e0 Author: hiram Date: Fri Oct 6 22:17:38 2006 +0000 Need to encode spaces on an http GET filename, but no other characters ... commit 0741225fd921f5321815f34eac37e354c75e520b Author: angie Date: Fri Oct 6 21:16:52 2006 +0000 Some polishing and html-fixing as suggested by MarkD. commit 05b2a0ca7ffc7d3c4e9b856fc2fc0fbe1ad50998 Author: heather Date: Fri Oct 6 20:51:29 2006 +0000 add link to describe IUPAC ambiguity codes commit 2c55a0daa5b5374ef7b481f1c71a0b112d7a61e3 Author: heather Date: Fri Oct 6 19:38:39 2006 +0000 small improvement to error handling commit e01dad652ee563c5f7d6ab4f802a303169565071 Author: heather Date: Fri Oct 6 18:23:10 2006 +0000 repeatmasker done commit 50135a85afff6201eb8240f1545e01193e24b2c2 Author: rhead Date: Fri Oct 6 18:12:37 2006 +0000 changed tables required to draw the HPRD section commit d35d0e30ee8c5b2d1e9b58b9ce0839cdbf730652 Author: hartera Date: Fri Oct 6 17:49:54 2006 +0000 Adding searches for BAC end pairs and singles tracks. commit 01e42b93ac60729253b71805e0260410a809c8b9 Author: ann Date: Fri Oct 6 17:43:11 2006 +0000 added details about uploading multiple tracks at a time commit 39ba7a2fd849e052ec932b7afb6e31e7a339077f Author: hartera Date: Fri Oct 6 17:33:40 2006 +0000 Added BAC end pairs, singles and bad pairs tracks. commit 7033736132a7c32fb8bc1c24174e1b0fd0d49b0c Author: kate Date: Fri Oct 6 16:57:27 2006 +0000 Remove inconsistent/incomplete affiliations on MSA tracks, with agreement of Elliot M. commit f98a842ceeff20520c6b324a539bd9622eabd4aa Author: galt Date: Fri Oct 6 15:00:26 2006 +0000 "Encode release log update" commit 0064c3c230d4487cec81a73df67ece81b845114e Author: galt Date: Fri Oct 6 15:00:25 2006 +0000 "Release log update" commit c40a2abb4df35c293bc7aca7d09b1102e8cc869b Author: kate Date: Fri Oct 6 00:14:18 2006 +0000 Experiments with alternate conservation, for review by Adam commit ba00c3479f9e1e2e3106de03c86055df78b01f87 Author: kate Date: Thu Oct 5 19:06:07 2006 +0000 Label tweaks for Crawford commit 7eeb6d8dc2e218a66565562345231e67dae7d3ee Author: hartera Date: Thu Oct 5 18:50:18 2006 +0000 Added chr4 and chr10 for encodeRegulomeDnaseArray track. commit cad89343951d032faf875168897490e1509aaf1e Author: kate Date: Thu Oct 5 18:02:12 2006 +0000 Split subtrack groups by request of Greg Crawford commit 339c0c55d3d90cda8e9eab6e7267196075910537 Author: fanhsu Date: Thu Oct 5 17:50:30 2006 +0000 Updated URL to GAD web site. commit 2a1d46ad301e506f2d978a83f552e47f839fd0a7 Author: kate Date: Thu Oct 5 17:42:11 2006 +0000 Correct chromosome entries for NHGRI Dnase tracks commit d123830d7dd8cdacaa130620ea695d4a9e6cd798 Author: markd Date: Thu Oct 5 16:53:25 2006 +0000 handle changes to NCBI CCDS schema commit 098c29f2c59c1f41dc19d759b15812ed5b43bc0a Author: kate Date: Thu Oct 5 16:41:48 2006 +0000 Clean up HTML formatting commit 1821721f4a86d13c3d2d1954fd9468865db8412d Author: kate Date: Thu Oct 5 16:41:33 2006 +0000 Tidy HTML commit 8028a738f7778f8a3808498bcc6253c61b0cd71a Author: kate Date: Thu Oct 5 16:11:56 2006 +0000 Clean up HTML formatting commit e00eb232d8add0d2c2aa048e042f3ee5988a1d78 Author: galt Date: Thu Oct 5 15:00:27 2006 +0000 "Encode release log update" commit cc74f59116c7d6e89fb09edcb05813189d2321f7 Author: galt Date: Thu Oct 5 15:00:26 2006 +0000 "Release log update" commit b71c01d6fdb19750fc7b64c86ae26221c0203eaf Author: daryl Date: Thu Oct 5 05:52:49 2006 +0000 add comments; remove unnecesary NULL checks, move dyStringClear() commit 3cd2f6b604f4a66921c5cc0cbf64216a97edd2fa Author: markd Date: Thu Oct 5 01:21:55 2006 +0000 some changes for gbMiscDiff table commit b7134ed2413ba8f6e19dc7d2fbd55f9d75db6d25 Author: ann Date: Wed Oct 4 20:46:19 2006 +0000 fixing up references commit 9f0b194353411e8f45d47a5e51fdc6caaa9c5a77 Author: braney Date: Wed Oct 4 19:36:52 2006 +0000 fix usage message commit 38b2164e434f810c8b4e796e9eef1c7fd2712e5c Author: rhead Date: Wed Oct 4 19:07:01 2006 +0000 added a comma commit cf8ab262c54cf4c7d584e3d657a210f0c688926c Author: hiram Date: Wed Oct 4 18:59:04 2006 +0000 Check minor version when on version 4 - the status changed with 4.1 commit c41ffaca41543838eb0fb0fa2a1adf7693679fea Author: hiram Date: Wed Oct 4 18:58:33 2006 +0000 Adding sqlMinorVersion() commit a222343e21190cceb89831017dd1a2680a95fffb Author: galt Date: Wed Oct 4 18:51:20 2006 +0000 fixed monitor time when JKSQL_TRACE=on commit d2f213ec886c5b5bab37115eba346ead5e96ad01 Author: rhead Date: Wed Oct 4 18:50:29 2006 +0000 fixed one typo and made whitespace changes commit a87842308e72e88c519111dfeaf08e9baa8e58b2 Author: baertsch Date: Wed Oct 4 18:39:50 2006 +0000 lift eddy rnaGene track commit 3ae1effc2a674cfe7517daf21da5b3c181bb1879 Author: galt Date: Wed Oct 4 15:00:27 2006 +0000 "Encode release log update" commit 25e0062fc2d4d7754bc91cc4edb5610a14a7d975 Author: galt Date: Wed Oct 4 15:00:26 2006 +0000 "Release log update" commit 0c5a82646316571a21d272787af206ee67fd7716 Author: heather Date: Wed Oct 4 05:26:24 2006 +0000 adjust counts for snp ortho commit 95191e04a87a5e2b3904b6e77f170514519eb680 Author: heather Date: Wed Oct 4 05:17:05 2006 +0000 add comments commit a174e35c50ea67ca1bb7111fbdf3ce82d2e9f5ad Author: daryl Date: Wed Oct 4 04:55:16 2006 +0000 added code to test for presence of support table for snp125 UI page commit 249a845d765ccae11cad2d873232605f4011c6f9 Author: daryl Date: Wed Oct 4 04:49:22 2006 +0000 changed snp126ortho table to use snp126ortho> cvs diff variation.c commit 748cd6800d3dee62032ac608979513b3eac7727a Author: heather Date: Wed Oct 4 04:29:00 2006 +0000 add bin, chrom, chromStart, chromEnd to output commit 6469dbd368dfe2ac38b4dbe56eb43435735f8a38 Author: heather Date: Wed Oct 4 02:17:19 2006 +0000 fix typo commit 6d8e66fb42075ace333cbcda1cfafdfde1fd4eb0 Author: braney Date: Wed Oct 4 01:31:18 2006 +0000 add mapping chain to homIni14 commit d77d26e2090a8d3b7b0c2a344796933101c3cf03 Author: hartera Date: Wed Oct 4 00:58:52 2006 +0000 Added changes to description and extra links and credits as suggested by the Zebrafish sequence analysis group at Sanger. commit 72f3f36b6ff2c67f7f82e2ab504e7311a171b1c3 Author: braney Date: Wed Oct 4 00:51:54 2006 +0000 fix up trackDb commit aeccd6f70d0fef77fe0a3d64c171dfe1c8c0befa Author: rhead Date: Wed Oct 4 00:08:43 2006 +0000 removed hprdId identifier, as it was not doing anything (per Fan, Galt, Ann, and Rachel) commit c18002e36c927d785138c135152ed9bf6a80128e Author: heather Date: Tue Oct 3 23:17:46 2006 +0000 add counts for snp ortho data commit 30158b9538031f57de5df5554295a9ba6d853889 Author: ann Date: Tue Oct 3 23:08:41 2006 +0000 added checkTableStatus.csh commit 6f04e3f779070dd4739121682b16887b2c286485 Author: heather Date: Tue Oct 3 23:08:05 2006 +0000 table name changed commit 8f651690ed6ec353da2d62a0a83b3235807144e2 Author: ann Date: Tue Oct 3 23:07:52 2006 +0000 A script which checks to see on what date the table dumps last happened for each machine. commit 74237ac5566237c2b2fde529ed929831bf88126b Author: ann Date: Tue Oct 3 22:48:44 2006 +0000 toned down tooting of our own horn! commit 115d0aea55dd838ce73bd7b4f00adcf528842c09 Author: kate Date: Tue Oct 3 22:42:53 2006 +0000 Merge Crawford DNaseI data into a single track, by Greg's request commit 64d28b0d77966b338a1ca2049d86575e5779b1e6 Author: kate Date: Tue Oct 3 22:41:29 2006 +0000 Fix so that 'subTrack off' setting in trackDb indeed initializes the subtrack vis to off commit 5b9877370a8bc67ed4c172760aa5c471b14804ca Author: heather Date: Tue Oct 3 22:41:09 2006 +0000 add steps for snp ortho data commit bfc2d74723a9aeae266db3d574bb259ada398b40 Author: heather Date: Tue Oct 3 22:39:26 2006 +0000 use store12 for snpSeq, alot more free space there commit 7cf7829202bc4ba3ccc514933aee6b4277760710 Author: markd Date: Tue Oct 3 22:25:46 2006 +0000 added another todo commit ea71387b2f35a65e521a86270304e2941779b3b5 Author: heather Date: Tue Oct 3 22:15:06 2006 +0000 fix for splitting snpArray500 into 2 snpArray250 tables commit 6cb0f20dd3fa54feaa9448e3f4353f575ab203d5 Author: kuhn Date: Tue Oct 3 22:10:09 2006 +0000 changed description for URL-based file upload in html box. again commit 433496ffcfd0f6126cc35a8c9082b33738dca2bd Author: markd Date: Tue Oct 3 22:03:45 2006 +0000 added to-do item commit 6dea6bc9aafb2872d4e973bc1ff3bee061255630 Author: kuhn Date: Tue Oct 3 21:44:17 2006 +0000 changed description for URL-based file upload in html box commit 97177e0285914ca94683a3a2903c7afb8c1971d4 Author: heather Date: Tue Oct 3 21:36:58 2006 +0000 initial revision commit 7ea2dc64f514febe6575d70036a1e9d5da9dba75 Author: heather Date: Tue Oct 3 21:36:30 2006 +0000 generic util commit 9e9111bd1ef0b0320003ce72badcff38162d5cfe Author: heather Date: Tue Oct 3 21:36:05 2006 +0000 add trimHeader and snpOrthoJoin commit d5f5a1ea144f859cb68f0caea394d749381962bb Author: kuhn Date: Tue Oct 3 21:31:36 2006 +0000 addedc a link commit 8673be872d7307d4437266f1425c1796c9a7afd5 Author: heather Date: Tue Oct 3 20:37:18 2006 +0000 dupeOk is for base rule only commit ebc0eca64785c26689284e55d318f85d67055e0e Author: braney Date: Tue Oct 3 20:09:45 2006 +0000 a new ancestor commit 46ebd7a40e6bf8e3ed665fddb7c8cf57e1e8ebdf Author: kuhn Date: Tue Oct 3 19:53:50 2006 +0000 small wording change commit 37d586973fdff8e1448acbc89ef9604565e8d6d3 Author: kuhn Date: Tue Oct 3 19:40:33 2006 +0000 small wording change commit 39b7e73d1bd5f90478316e1738dd501734b4fdd5 Author: kuhn Date: Tue Oct 3 19:34:53 2006 +0000 small wording change commit 43ea853c10c46419fc0c3fac0f11d0c6e3c76f48 Author: kuhn Date: Tue Oct 3 19:34:08 2006 +0000 small wording change commit 23a14e25deedc6f747b51cd7414575a989b10f55 Author: fanhsu Date: Tue Oct 3 19:22:27 2006 +0000 Minor edit of NIA Gene track. commit c05df3e7d6487e8a488183876fa4703882f02759 Author: kuhn Date: Tue Oct 3 19:22:16 2006 +0000 added back NAME anchors trhat got loast. changed some text commit fb7d03689636b6b2f1c078e8de1fc61f4a770ded Author: fanhsu Date: Tue Oct 3 19:22:02 2006 +0000 Minor edit. commit 8df1847227359210a6d208ea23279851c5e7cbca Author: ann Date: Tue Oct 3 19:08:27 2006 +0000 added info about parsing HTML commit 5d9650be9409471a1c8acfb9c067833b42675ce4 Author: ann Date: Tue Oct 3 18:53:32 2006 +0000 formatting (em dash) commit bbfe1266e76664808832ea82761e112403bd1933 Author: fanhsu Date: Tue Oct 3 18:49:44 2006 +0000 Added NIA Gene. commit 0495ecf36e13cd52ff83deb394d9cce42c098392 Author: daryl Date: Tue Oct 3 18:47:40 2006 +0000 Added support for color and filter UI options to loadSnp125Extended commit 362b58a553b8e1e900eba92984aaef5c0025651b Author: fanhsu Date: Tue Oct 3 18:44:42 2006 +0000 Added NIA Gene. commit 8a9f2d875b914ecfbd986eac00ee2ac1276e6ac0 Author: fanhsu Date: Tue Oct 3 18:44:26 2006 +0000 Added NIA Gene description page. commit 6b20172b78ea3c88a5fe81f1c45e01b36644c74c Author: ann Date: Tue Oct 3 18:36:58 2006 +0000 changed references to 'html' to 'description' commit 64414fb2a948881fb96ba0ef92a37806ac0c2096 Author: angie Date: Tue Oct 3 18:31:07 2006 +0000 Adding 15way Conservation, Most Conserved. commit 9f5486099f64595c576beabd032d83c464df3cab Author: angie Date: Tue Oct 3 18:29:26 2006 +0000 Finished phastCons15way. commit f54ba870285f6af69d1edeaf752662fe0b48c679 Author: ann Date: Tue Oct 3 18:28:58 2006 +0000 added details about updating description text and the fact that it diverges from your original file commit 3f68e0304fb11299f4560265658a979c17094b18 Author: ann Date: Tue Oct 3 18:23:44 2006 +0000 added detail about updating tracks via URL commit ab31e3b882301404e9f8e917688ce4ef9ff67557 Author: ann Date: Tue Oct 3 18:20:30 2006 +0000 changes from Kate commit d5ecbe95aa0b3629a4b36e88004d8e36f77e7be5 Author: ann Date: Tue Oct 3 17:54:24 2006 +0000 refined description of how to update HTML commit cd02ebbedd8884dee66b22944de4e15ec4808827 Author: ann Date: Tue Oct 3 17:41:50 2006 +0000 added explanation about plain text commit 6b3d6b5bc5abbda1b8248b285c0bd4e1ed4a97b8 Author: ann Date: Tue Oct 3 17:25:22 2006 +0000 updated answer to 'details page' question based on new custom track functionality commit 7b58499aef782bd7324d27d9c94e9dcd7626431b Author: kate Date: Tue Oct 3 17:21:46 2006 +0000 Launch button for hgCustom wasn't correctly handling custom track expiration. Minimalist fix to expedite release commit 98afb1ffa6260b90957f20d12f4e0b26a4106835 Author: ann Date: Tue Oct 3 17:09:56 2006 +0000 typo commit 3f6b8556f1229b5a956093a7fe98c1566e98e5b2 Author: ann Date: Tue Oct 3 17:06:53 2006 +0000 *** empty log message *** commit 2f7c27bd8b370793d7b7f430f887605fa8341511 Author: ann Date: Tue Oct 3 17:04:23 2006 +0000 adding details for updating a custom track. commit c82c13e121ba043ac1ff4c4d254cee7ccf828e03 Author: ann Date: Tue Oct 3 16:33:47 2006 +0000 more cleanup. adding Update Custom Track section. commit 045ea768cd6bfe297e32639bb89cc3122b301b9a Author: ann Date: Tue Oct 3 16:06:00 2006 +0000 typos and cleanup. comment out troubleshooting section commit 19fc7594324b6e6566b1dded964abb3bf5211279 Author: galt Date: Tue Oct 3 15:00:25 2006 +0000 "Encode release log update" commit 43753800c01210481f0a0f9acd33b58419b94c39 Author: galt Date: Tue Oct 3 15:00:24 2006 +0000 "Release log update" commit 55e3994f91d951a5042466f64089974a819fbfe9 Author: hartera Date: Tue Oct 3 14:28:32 2006 +0000 Removed hgCustom suppression. commit 04c8e5587ba7220506cf9eb360a7833483cfe9b9 Author: kuhn Date: Tue Oct 3 08:25:32 2006 +0000 started the description of the Add and Manage Custom Track pages commit ed349f304ddf8804a3a8dbfddafd2aa6c8b6642b Author: daryl Date: Tue Oct 3 05:15:09 2006 +0000 sort SNP list so that it is drawn in increasing order, independent of the snp125ExtendedNames variable for including/excluding the orthologous states commit 99f4423377bebe925942e081dfeca0dabaf24ae5 Author: heather Date: Tue Oct 3 01:28:10 2006 +0000 got makeGenomeDb.pl to complete successfully commit b35846868b5610651bed59b01dcc85b0ca3ca2c7 Author: ann Date: Tue Oct 3 00:26:57 2006 +0000 bolded statement about postponed seminars commit ad370690cd84840ab749fefc883ac853f88a1768 Author: ann Date: Tue Oct 3 00:16:19 2006 +0000 editing for new CT functionality. stubbing in new sections (needs more work!) commit c5694cfdde707c06770c714d6ed35c1bc02d1293 Author: rhead Date: Mon Oct 2 23:33:50 2006 +0000 Added rule to allow duplicate values in knownToHprd table (per Fan) commit f2bb739f98b5e948d70d619a5250a9a53920b061 Author: ann Date: Mon Oct 2 23:15:21 2006 +0000 added info about new Open Helix seminar commit a4372d5d031b3354bd224832b270843b8c138373 Author: angie Date: Mon Oct 2 23:04:41 2006 +0000 Chain/net 7 new fly assemblies and triCas2. multiz15way. phastCons15way in progress. commit 200cb7b17cedfe3d0b543cdae1976f4ac43292d8 Author: ann Date: Mon Oct 2 22:43:07 2006 +0000 removed OpenHelix announcement (they are postponing the courses) commit 6264e1fad950d19a4b30e9ed273f95a955e9523d Author: heather Date: Mon Oct 2 21:34:24 2006 +0000 remove warning commit b3d8b5ae2156d31fe84aed9f25f96398e466b7b1 Author: heather Date: Mon Oct 2 21:28:16 2006 +0000 adjust image commit 876bbd53b63580a796bbacfa8c8a2b5b05ea18d8 Author: heather Date: Mon Oct 2 21:21:50 2006 +0000 add bosTau3 commit 11c244c931a7035587070d6603b6eac15498595e Author: heather Date: Mon Oct 2 21:21:28 2006 +0000 Initial descriptions for bosTau3 commit 7fa3dfe3ea6d785f2f623e0934df33ab4f8c837e Author: galt Date: Mon Oct 2 15:00:19 2006 +0000 "Encode release log update" commit 70908eb65d4bf330fc4c943224d7c162e612ad18 Author: galt Date: Mon Oct 2 15:00:18 2006 +0000 "Release log update" commit aa34ab8cf65754af46e849277c5c338a1fde7de2 Author: kate Date: Mon Oct 2 06:36:56 2006 +0000 Fixes to custom track browser line visibility settings commit cddc6c05a643ccd1adc32b892a70c4f2b9387595 Author: daryl Date: Mon Oct 2 06:15:28 2006 +0000 Added UI button to control inclusion of ortho alleles in SNP name in hgTracks image commit 91b9ab90cc597b9d5d6ddcf50b6dc174f1f68b04 Author: daryl Date: Mon Oct 2 05:23:48 2006 +0000 changed printHtmlComment to hPrintComment commit afb948df87a25e68c5ccb7c2dc1a85c6a390af2c Author: daryl Date: Mon Oct 2 05:21:02 2006 +0000 fixed memory handling in setSnp125ExtendedNameExtra; restricted ortho allele to panTro2; fixed various formatting inconsistencies commit bcb0f82d072455a8a882d2b1dea53bea1c560d14 Author: kuhn Date: Sun Oct 1 17:49:58 2006 +0000 added back the chip rows for mouse microarray tracks commit d86c97412c00abd162f30355a910ea59dcc93d8e Author: galt Date: Sun Oct 1 15:00:20 2006 +0000 "Encode release log update" commit 0252b8915255125f4873f2ce69fb2dc4df3586af Author: galt Date: Sun Oct 1 15:00:19 2006 +0000 "Release log update" commit 3a4ee91c93c98890b574eae3592b0c454a74ff91 Author: donnak Date: Sun Oct 1 05:56:54 2006 +0000 Started to edit hgTracksHelp file to reflect Kate's changes to CT UI. However, r an out of time; therefore, this file needs more editing before hgCustom is realeased. commit ddf959e298907f95bb049574e3b6e5b81c1a4202 Author: donnak Date: Sun Oct 1 05:39:40 2006 +0000 Made some initial mods to synch up this file with Kate's latest CT UI. However, ran our of time to finish it. commit 0d7bff03dc8508a8b80aa553fbda528d76c3d39f Author: donnak Date: Sun Oct 1 05:33:59 2006 +0000 Made a few updates to synch up with new information & featues available on the website. commit cd6d88c62708977e53a609938ae659144ded91c0 Author: galt Date: Sat Sep 30 15:00:26 2006 +0000 "Encode release log update" commit 7e3aa53dad77bc686cc784427a64150c31605583 Author: galt Date: Sat Sep 30 15:00:24 2006 +0000 "Release log update" commit a7ed4bdc64ea21b5e08bfba79a867fb4936e44fb Author: heather Date: Sat Sep 30 00:06:13 2006 +0000 tweak previous commit commit c50b3486545b21f50385f69557aace291b4e6c08 Author: heather Date: Fri Sep 29 23:38:18 2006 +0000 need dupeOk for rs_fasta commit 21b1e88c71de4f361ef480c11d833718d3ff9279 Author: heather Date: Fri Sep 29 23:34:12 2006 +0000 split rs_fasta files for new hgc feature: displaying SNP alignments commit 7e075993a400fc544589d7a2b1a6903cb32ca38e Author: heather Date: Fri Sep 29 23:33:08 2006 +0000 add snp126Seq commit e566feea7f84c38fb5d560d316e62ea6671dc5b2 Author: heather Date: Fri Sep 29 23:19:18 2006 +0000 cleanup: don't need inputFileHandle commit 7e5db7c9190e7941d09cc897f226d93ceebcdfc4 Author: heather Date: Fri Sep 29 23:03:38 2006 +0000 use version number for snpSeq table name; fix typo in previous commit commit cbba22bd4544551ad52a4384c354210eb7bfc5a8 Author: angie Date: Fri Sep 29 21:05:57 2006 +0000 Make use of agpToFa's new capability to handle multiple sequences, so we don't have to split and loop which was not working for scaffold-based assemblies that require agpToFa. commit ec8b50530649bffb69c02b8134badd0386e51334 Author: fanhsu Date: Fri Sep 29 20:40:03 2006 +0000 Updated link to PDB. commit c962517532633f23ffba768a22f52e78ca97e2ac Author: heather Date: Fri Sep 29 20:20:59 2006 +0000 more work on first step commit 0f87e8aac63d1e2c85ec0d7b9258f97ff1dd053b Author: aamp Date: Fri Sep 29 18:47:19 2006 +0000 This needed changing after the microarray updating. commit 6ee0d490205b132825b46bb95b6fd0f1afce5a47 Author: markd Date: Fri Sep 29 18:46:18 2006 +0000 added link to entrez commit e36b674f53c8883165876a0924df76e194caee3f Author: hiram Date: Fri Sep 29 18:37:32 2006 +0000 Print out description text custom track bed 3 type tracks commit febbd69134b26c7e26c9fceb1caf4b95e3952dc7 Author: hiram Date: Fri Sep 29 18:06:18 2006 +0000 The include pipeline.h is obsolete. Removed. commit 9a2c9f46f1abfdfe96e6ba420b7c571b4701d819 Author: kayla Date: Fri Sep 29 17:39:00 2006 +0000 Changing back to the new version of knownGene.html commit a31680742a6dc87cdc57c004515a67bc777e2b3a Author: fanhsu Date: Fri Sep 29 16:17:45 2006 +0000 Added disease class code table. commit 5d64717ad145435e0c75ef6fa41e3b30f045bda1 Author: fanhsu Date: Fri Sep 29 16:01:16 2006 +0000 Changed visisibility of GAD to pack. commit 3a458d9860c7a23714acca63e07abcef8848eee1 Author: galt Date: Fri Sep 29 15:00:28 2006 +0000 "Encode release log update" commit d2720a53de337cf60128976eefafe3299cef3ca1 Author: galt Date: Fri Sep 29 15:00:27 2006 +0000 "Release log update" commit 73a7ee5e4b35cd0e2387a0edfece6ff7812fc4d3 Author: angie Date: Fri Sep 29 14:53:47 2006 +0000 Masked sequence for alignment only -- not building a browser at this point! commit b8f567eb7782e69e4314d63e8dae020f2b258ca7 Author: galt Date: Fri Sep 29 05:09:41 2006 +0000 added script to help find stale cvs locks commit 00aefefba5d0a35259924e94824759774f03f3e2 Author: heather Date: Fri Sep 29 04:14:33 2006 +0000 needed error check commit f13556814f1a3afa18d607682af5f031fc256b5e Author: kate Date: Fri Sep 29 01:15:55 2006 +0000 Make doc file override doc text entry in update screen commit f7c5db5ae165af57ee47fe2c74e717726ffed20d Author: kate Date: Fri Sep 29 00:57:32 2006 +0000 Need to save selected table variable as the library now removes it during parseing commit 1f23409770e80afc3b8da9da5fb399f4c13380f6 Author: kate Date: Fri Sep 29 00:56:57 2006 +0000 Need to clean up the currently selected table from within hgTracks commit b187b6e96579bb8e521c16ec5d3ea65ee91782be Author: heather Date: Fri Sep 29 00:22:06 2006 +0000 handle missing data in previous commit commit 11d1df99a2a7d3113be5c524788e7671ab8bdcff Author: heather Date: Fri Sep 29 00:20:08 2006 +0000 first draft refactoring printSnpAlignment to read file defined in snpSeq table commit 9f66489fa2813c2e98e1838926541b784c5ee7c8 Author: markd Date: Fri Sep 29 00:19:21 2006 +0000 parse misc_difference fields into ra file commit 4fb727f8cc3a2444449fa321274019ea68e2c6fd Author: angie Date: Fri Sep 29 00:02:18 2006 +0000 Added support for multiple sequences in AGP and FA (agpSeq can be 'all'). Added support for compressed fasta input in -simpleMulti(Mixed) mode. commit 2dbc37f81c03b589b46096da2b1600d67a2dcd58 Author: kate Date: Thu Sep 28 23:58:46 2006 +0000 Remove extra spacing under forms added for buttons that change CGI commit c7bfb339d2f2ee1b68d77c2f2410c4dde93619c7 Author: angie Date: Thu Sep 28 23:29:58 2006 +0000 typo fix (helpAlgo --> algoHelp to match implementation). commit e97fecd9ade167e7f48322a6fb5c8b1b2a7264a4 Author: kate Date: Thu Sep 28 23:10:09 2006 +0000 Fixes to navigation when Cancel button used with error text in the entry box commit aba2bcb07199c5f500658dfc02e3192683df687c Author: heather Date: Thu Sep 28 20:46:27 2006 +0000 use arg for logFileName commit 946ef39486ec4d4d70fd4b85d9e8c914cae57f94 Author: heather Date: Thu Sep 28 20:17:56 2006 +0000 add log file commit 29badb2ef18050b4bf306fa1fa72bbd57c07320a Author: heather Date: Thu Sep 28 19:35:52 2006 +0000 fix bug in previous commit commit da0a0e06266b515f54081b5cb8ce321c5eed4919 Author: heather Date: Thu Sep 28 18:47:16 2006 +0000 use rsId for filename commit e4c53efdac222c2faf7afd28302c25f03e388d2a Author: fanhsu Date: Thu Sep 28 18:29:00 2006 +0000 Added acembly track. commit 2555fa26d0f2b1e10e057c8476962b852e7a77bb Author: fanhsu Date: Thu Sep 28 18:12:18 2006 +0000 Created acembly.html with added line to indicate that it was lifted from hg17. commit fe534a1ac75677e13e6df7c57f330b0ad8c7714d Author: fanhsu Date: Thu Sep 28 18:05:54 2006 +0000 Added acembly track (lifted from hg17). commit 53b164ea55ef1e46268180739399d395a12cbddb Author: fanhsu Date: Thu Sep 28 17:59:07 2006 +0000 Created acemblyPep.sql. commit 0a5a21dc2fba48526f5def9fc6c76edc90db964a Author: aamp Date: Thu Sep 28 17:39:52 2006 +0000 Fixed bug with trackDb html showing up twice. commit b148d96d7312ed854c35caaf03d585c3f13e6811 Author: hartera Date: Thu Sep 28 16:35:00 2006 +0000 Updated Affy Zebrafish track using new blat and filtering parameters. commit 0c2aebf1ba54962d9d8f2b2822f5a97e177a0b99 Author: markd Date: Thu Sep 28 15:43:13 2006 +0000 added missing newline commit 4c46d59805a7881ac74941e0aa0bb039df605e7c Author: galt Date: Thu Sep 28 15:00:29 2006 +0000 "Encode release log update" commit 2ac565fdd57ce54dda65069118081fb0e659a535 Author: galt Date: Thu Sep 28 15:00:28 2006 +0000 "Release log update" commit f291b8e2245b2a115d6ebf1f8858991fc75e153a Author: markd Date: Thu Sep 28 04:54:52 2006 +0000 have ccdsImport create database and tables rather than requiring doing this by hand commit f15df38550c7d5b04ff52c5bff06fcc43bc16b02 Author: markd Date: Thu Sep 28 02:59:27 2006 +0000 added options to create C variable definitions commit 253c069369bedbe350754cc111a947d94831c531 Author: markd Date: Thu Sep 28 02:41:23 2006 +0000 added support for bed8 files commit a0ae385945e06368ab458229bdca5b6083d3f337 Author: markd Date: Thu Sep 28 02:25:50 2006 +0000 added support for bed8 files commit e798875558a2ce8efdf182563233e37aae516640 Author: rhead Date: Thu Sep 28 01:28:22 2006 +0000 Added info about Illumina to Methods section and made other minor edits commit 9a5312ed1cc65673477a264fddebe2c2109e7772 Author: hiram Date: Thu Sep 28 00:30:05 2006 +0000 Add description of most generic attributes used almost everywhere commit a8426d06b43f925817ab3b8adab05c5f83fb3491 Author: kate Date: Wed Sep 27 23:14:39 2006 +0000 More fixes to HTML doc handling commit a42f73eb90dff6444a690c92290b57ded0ec6209 Author: angie Date: Wed Sep 27 22:24:43 2006 +0000 Use int instead of unsigned for comparison to coord that can drop below 0 (bug found by Adam's group / MarkD). commit 9cbf285b45e844457a64dafbe8f3444118c7fbca Author: galt Date: Wed Sep 27 19:37:46 2006 +0000 adding hgCgiData commit ae40c6f15d760eb7db670b1be0075bbe73ebb833 Author: kate Date: Wed Sep 27 18:56:36 2006 +0000 Add anchor for examples commit b1b34db871bb91aab9204ecf510f475af3d403e7 Author: heather Date: Wed Sep 27 18:44:02 2006 +0000 add score, strand, observed commit ba2b5a07a1f85e700fdd7941238520f5f5bd20e4 Author: kate Date: Wed Sep 27 18:42:54 2006 +0000 Fixes to doc updating commit 100a852c0c5d640183e1dcacd24c5453b0b54e19 Author: heather Date: Wed Sep 27 18:39:36 2006 +0000 consolidate snpArray code commit 2b42bef5d9ac18fadd81be03840740d360d55ab3 Author: heather Date: Wed Sep 27 18:23:03 2006 +0000 include score, strand, observed in output commit bc07d4df9548da3e238bdfb64f10fc639af20d49 Author: ann Date: Wed Sep 27 17:21:56 2006 +0000 typo commit 490a22b5c4456b08783dbd29f354ee8e5180d690 Author: galt Date: Wed Sep 27 15:00:29 2006 +0000 "Encode release log update" commit b7bec4c7a9c9acfa05d9ab2956a4043bd91b19ae Author: galt Date: Wed Sep 27 15:00:28 2006 +0000 "Release log update" commit 4a21216398dfd6ec7c2f32ef3806f3aa2ed681e0 Author: daryl Date: Wed Sep 27 08:12:46 2006 +0000 Commented out new snp color sort and snp ortho name changes until they are tested more completely commit 401c30a31543c4db61793a7146a41aa704c14b27 Author: daryl Date: Wed Sep 27 08:05:18 2006 +0000 Fixed performance issues for snp ortho names and snp draw order commit 9909c894c889c2656b1f7ef0b3ec84b041f5c0ed Author: kate Date: Wed Sep 27 05:40:42 2006 +0000 Repair broken form in manage page commit d68f77479eef8b2b8d5555edc230f5d92adcfa68 Author: rhead Date: Wed Sep 27 01:55:19 2006 +0000 Added reference section. commit bb72228f61b98ba4f9bf9d0eb6fb6f0e00eeda39 Author: galt Date: Wed Sep 27 01:20:02 2006 +0000 "New version number v143" commit c0d86973246e964d2253976a5660a3e9a8ea35b9 Author: rhead Date: Wed Sep 27 01:11:23 2006 +0000 Re-worded methods section; added bit about ref alelle. commit 5a6678050fc3d82cf78bc7cabb5aef128288ddd8 Author: donnak Date: Wed Sep 27 01:01:52 2006 +0000 Renamed this file from Kate's original "loadingCustomTracks.html" to conform to our naming conventions for help files. This file contains the text that is displayed at the bottom of the hgCustom page. commit 7c05951c8ad4752d7400bb41daf116a4cb415a95 Author: donnak Date: Wed Sep 27 00:50:02 2006 +0000 Changed filename for Loading Custom Tracks page to conform to other help file naming conventions. commit 98f5e6247e82700a1aec8c36e4d96526a340d175 Author: donnak Date: Wed Sep 27 00:41:29 2006 +0000 Changed capitalization of User's Guide. commit 37143bba8335dbc053d5506addf828fb4537e08d Author: donnak Date: Wed Sep 27 00:39:53 2006 +0000 Changed label on doc text box, changed text for HTML template. commit 6e0036256eb5d001788e47395841564949b630b5 Author: kayla Date: Wed Sep 27 00:29:03 2006 +0000 Reverting to old version of knownGene.html because I want to push out hg18.trackDb. I will change this back once the v143 cgis go out (which the new knownGene.html text refers to). commit f7d9b395c70f7cd0593f2016431b6b1eaa7d8bdd Author: kate Date: Wed Sep 27 00:26:35 2006 +0000 Add a text area that allows graying out. Also, mouseOver on a table field commit 5d9623ea3fe5c835ec14f81a5272dd99289fdd23 Author: kate Date: Wed Sep 27 00:22:54 2006 +0000 Suppress display of position if it's invalid for database commit 1f003002d98dcba312099fb9ea0026a0be3c111a Author: angie Date: Wed Sep 27 00:21:47 2006 +0000 Moved sqlDisconnect call outside of if/else in getRegionAsBed so it is always called. commit 74323ba0f42945887e1d6481ca45d5ee80da26d8 Author: angie Date: Wed Sep 27 00:20:30 2006 +0000 Added lineFileClose that was missing from identifierHash(). commit b935a4223829bf9e5e41e180caaeb2ea76327e8c Author: kate Date: Wed Sep 27 00:10:45 2006 +0000 Move warning message commit dabb9cf41096d70d05dbfbb2440db5dae8576eec Author: fanhsu Date: Tue Sep 26 23:49:07 2006 +0000 Added GAD track. commit 75354a6ef1c577f55e9f2f2180146543033e0757 Author: kate Date: Tue Sep 26 23:36:00 2006 +0000 Fixes to Update feature commit e3671e09dfe32ef2f4b2376179ff595b811f3b44 Author: kate Date: Tue Sep 26 23:35:11 2006 +0000 Restore comment commit 30df93b7b8cd377c966df9ff7313da2ed2d1ef73 Author: kate Date: Tue Sep 26 23:34:48 2006 +0000 Disable multiple unnamed custom tracks -- too many user scenarios that require different handling commit da386fae3f3b9a3d6f8570d5d699d571d21eb75a Author: hartera Date: Tue Sep 26 22:59:04 2006 +0000 Edited credits section. commit ceff5866388406d0e10c3730c6f43e277abf2862 Author: heather Date: Tue Sep 26 22:53:03 2006 +0000 display tweaks commit 5c14034397b2ff3c2f9838f7ffd77738d45e1a12 Author: hartera Date: Tue Sep 26 22:51:20 2006 +0000 Added to doVegaGeneZfish so that the gene type shows both the confidence and the type of gene. commit 43d3d30d34caee426ab2e029684f28e4ab14aeb6 Author: heather Date: Tue Sep 26 22:50:38 2006 +0000 change order of display commit 3c153fba1c0b263d99f0c6872c5ced78abd4b9f7 Author: fanhsu Date: Tue Sep 26 22:39:41 2006 +0000 Created gadAll.sql. commit 50e9e5130221b45a2e6dcc48afa33322d2bd6d4d Author: kate Date: Tue Sep 26 22:36:38 2006 +0000 Fix typo commit c0f09f9c322514b1a94b13f1b3a0f157a5e07c28 Author: heather Date: Tue Sep 26 22:35:20 2006 +0000 show reference allele for Affy SNP Arrays commit c999d0713a0ae8e78ddf09629aab52031a168b01 Author: fanhsu Date: Tue Sep 26 22:17:32 2006 +0000 Added disclaimer message from Kevin Becker at NIA. commit f4642a6f732fb017b3fd9d29472a52c322f92488 Author: heather Date: Tue Sep 26 22:12:05 2006 +0000 add methods commit 6310de49434cb342816e7ba93c8759d4ea2c0dc0 Author: heather Date: Tue Sep 26 22:05:38 2006 +0000 make rsId more obvious commit 1b0d8c9f424fc69313b9e5129a5a68e915670883 Author: heather Date: Tue Sep 26 22:01:12 2006 +0000 table change for SNP Array track commit 48f5089721816d3efd6be2b4fcfbc50c1cb429cd Author: hartera Date: Tue Sep 26 21:40:12 2006 +0000 Added descriptions for Vega genes. commit 0feff1fd6d2e1694a3c1e591753df2750078fb62 Author: heather Date: Tue Sep 26 21:30:30 2006 +0000 use minCheck for SNP Arrays commit 8dc37ce54be7680327785f9497fb1f8cb6aec614 Author: heather Date: Tue Sep 26 21:28:50 2006 +0000 additions for SNP array track commit 438b8e73e61b5a5497543dda2d6a582d62e33745 Author: heather Date: Tue Sep 26 21:21:49 2006 +0000 for new SNP Array track commit 16e79eaecb96d67714bf94f6e06a41c8ab7b5e1c Author: kate Date: Tue Sep 26 20:39:46 2006 +0000 Fix bad URL from previous commit commit 50f59b4be07d3477dc89b9db4731584b4f53c0ee Author: donnak Date: Tue Sep 26 20:23:02 2006 +0000 Updated links for file formats, added link for custom track doc. commit aec7d3f52bc45f544ebceeb32d192e5bdc00d966 Author: archanat Date: Tue Sep 26 20:18:11 2006 +0000 Changed two links to abstract instead of pdf commit bab6fce82a4affe7c677838e5053c88e970b535e Author: kate Date: Tue Sep 26 19:48:37 2006 +0000 1. Remove (some) redirects and improve button layout 2. Retain badly formatted text (up to 50 lines) in entry box commit 998d9f082682159921796799dac24790453d677b Author: kate Date: Tue Sep 26 19:46:33 2006 +0000 Save custom text before parsing munges it so it can be displayed if there's a formatting error commit be452c75cc0d2836b38b24207c9ff57a253de313 Author: kate Date: Tue Sep 26 19:43:36 2006 +0000 Add access function for name of hgCustom CGI commit 06e598fa5f9fee270a97aa8a739f1442cd953e0c Author: kate Date: Tue Sep 26 19:41:55 2006 +0000 Replace hgCustom redirect with a form commit 3278dcd3846ea97519bb9294b4ae224e06fa0d97 Author: daryl Date: Tue Sep 26 19:38:37 2006 +0000 sort snps only when in dense mode commit 8301dd587a1beb44cd835f5e6d19cc7165007a20 Author: ann Date: Tue Sep 26 19:34:02 2006 +0000 forced reference to open in new browser window commit 574201e6a0a10d9316be2cccc99cd53f1c84f71e Author: ann Date: Tue Sep 26 19:31:54 2006 +0000 changed two links to abstracts instead of PDF files commit d816ceabba499bff44f7fbe6d0e46a20afcbf275 Author: daryl Date: Tue Sep 26 19:28:38 2006 +0000 added sorting of snp125 tracks based on calculated color commit b62dc49c4c2dd44b4145ef38001bd618332926aa Author: daryl Date: Tue Sep 26 19:27:07 2006 +0000 adjustments to snp125Extended struct commit 2506090a664bab4f507cc27aa9d77a8193037159 Author: heather Date: Tue Sep 26 19:07:23 2006 +0000 split Affy500K into 2 components commit e57103c78af133e4e3173e9e041127e8dc8d8b0f Author: heather Date: Tue Sep 26 17:38:09 2006 +0000 changes for Affy500k in SNP Array track commit adc5a1f1df54d155462eea5a20778c991bf9fb66 Author: daryl Date: Tue Sep 26 16:53:17 2006 +0000 removed appendAllelesToSnpNames, which is now obsolete due to integrated snp loader commit 2b8678fa1e6a4233274105c4e427f8992a5eaf34 Author: fanhsu Date: Tue Sep 26 16:49:55 2006 +0000 Removed gadInit(). It is no longer needed due to new release data contain disease class code. commit 341c763311affd18550f76b868113fb4280ecd4b Author: galt Date: Tue Sep 26 15:00:25 2006 +0000 "Encode release log update" commit d7a96606f38b834223b55b7371f190c635bfb8ea Author: galt Date: Tue Sep 26 15:00:23 2006 +0000 "Release log update" commit 6a2168a94811158abbab07a852c1aaf4a9adf499 Author: daryl Date: Tue Sep 26 08:56:17 2006 +0000 removed braces for easier readability commit 928f7c52078d175072fa054c8845b1a445024ba6 Author: daryl Date: Tue Sep 26 08:53:54 2006 +0000 added snp125Extended snp loading, which supports extended names through nameExtra and will allow sorting by color through the color pointer commit 78ae82aedee8f78e112c902fcd9e01e3092b0e35 Author: daryl Date: Tue Sep 26 08:52:30 2006 +0000 added snp125Extended: nameExtra and color pointers for run-time calculation commit 2ac8d61f0743c6a3e6ba931fc5333eddba4e2e1a Author: daryl Date: Tue Sep 26 08:09:54 2006 +0000 fix typo in refactoring commit b1631767038703fd8490110f8600cf08ca9fc49d Author: donnak Date: Tue Sep 26 07:20:50 2006 +0000 Added another pub by Katie P. commit 004da6992750711f89afaa8cd95d591a89f1422c Author: daryl Date: Tue Sep 26 04:46:57 2006 +0000 cleaning up code formatting for readability commit f58a234dbc716bc73d1beb3797d59a6c3b44f5a4 Author: kate Date: Tue Sep 26 00:58:17 2006 +0000 Handle empty SCRIPT_NAME environment variable commit fae77634d12e3cb1db720a9a2491d85ebe867bf9 Author: aamp Date: Mon Sep 25 23:27:49 2006 +0000 Fix for default option for microarray combine option when nothing is set in the cart. commit 096450476200062ea334d92ac231122ba4bbba81 Author: kayla Date: Mon Sep 25 23:27:34 2006 +0000 changed "tracks" to "track", and put a period after the initials in the names of the authors. commit 34de21f6b152c0a96025270296a187dd31d1907d Author: kayla Date: Mon Sep 25 23:07:48 2006 +0000 Removing this file from /human/hg18 and replacing with a version up a level at /human. commit f83c482b3b0ec85de827255861a29b6b51c779cf Author: kayla Date: Mon Sep 25 23:04:38 2006 +0000 Moving polyA.html up a directory to /human. Incorporates changes made by kuhn. commit 806729dd98ce7d79bca7e3bb527e2aa046d76ca3 Author: aamp Date: Mon Sep 25 22:46:39 2006 +0000 Moving some microarrays over to the new method. Also added a new drawing function in hgTracks to for drawing microarray tracks with exons. commit 5c4301a5a01b107738aa39d2a8705f301096823f Author: donnak Date: Mon Sep 25 22:38:35 2006 +0000 Added news item abt OH seminars, archived a news item. commit 42031e656d5f565f6358705d4b887076d8cd0d4e Author: donnak Date: Mon Sep 25 22:38:13 2006 +0000 Archived 2 items. commit 6a96b803a7114ec8955d3effa76a9cfb8d6954a5 Author: donnak Date: Mon Sep 25 22:37:43 2006 +0000 Added pub from Bob. commit b38e7b737636fcef3903c21628c15d7ca8ad6eef Author: galt Date: Mon Sep 25 22:30:20 2006 +0000 fixing left join for mysql5 commit 9d4032670eed15a19b2009662e0b744d4d68fb7a Author: hiram Date: Mon Sep 25 21:42:46 2006 +0000 Protecting against images that are too large. 32,000 pixel height. commit acb807e7af4e99db52f807923f4fde950d5824c0 Author: heather Date: Mon Sep 25 19:16:41 2006 +0000 change sqlDisconnect to hFreeConn commit 8e392e55fa635a905e22135f58a209a602a14a8c Author: heather Date: Mon Sep 25 19:15:45 2006 +0000 don't need sqlDisconnect; using hFreeConn commit 9fd59e8223c7fe3690c42ee334b61d8039ade7c1 Author: heather Date: Mon Sep 25 19:09:13 2006 +0000 add missing sqlDisconnect commit badca76b4dce05da3d2c8c4e2bffa7a143586ac1 Author: hiram Date: Mon Sep 25 18:32:27 2006 +0000 Now using hTvDropDownClassVisOnly() to allow limiting a track to a single visibility commit 330c978161172bb8f1317e023ad56dc93d9e7c02 Author: hiram Date: Mon Sep 25 18:27:21 2006 +0000 Now using hTvDropDownClassVisOnly() to allow limiting track vis to a single mode commit b2065281dcbcb1a21db110540f443495f9a918f0 Author: hiram Date: Mon Sep 25 18:25:51 2006 +0000 Add hTvDropDownClassVisOnly() function for limiting visibility of a track to a s ingle visibility commit a9d19991895e765756d3c83400b759946b1d7f41 Author: hiram Date: Mon Sep 25 18:25:13 2006 +0000 Add hTvDropDownClassVisOnly() function for limiting visibility of a track to a single visibility commit a5a87a3439384080064d6eb06da4bf5ef13898ce Author: galt Date: Mon Sep 25 15:00:18 2006 +0000 "Encode release log update" commit 1d77d0bd8911bcd8e349571816204fc1b300e925 Author: galt Date: Mon Sep 25 15:00:17 2006 +0000 "Release log update" commit fefb9f1ab9a1714c63b063496c136369717688b2 Author: kent Date: Mon Sep 25 08:27:30 2006 +0000 Changing hPrintEnable() to hPrintDisable() to fix bogus bts in PDF output page. commit 77b126aded40fba6e89c056ea8a142c7ebb6b3fe Author: galt Date: Sun Sep 24 15:00:19 2006 +0000 "Encode release log update" commit 1490f39891bcd674f70325ada1223f1727a04305 Author: galt Date: Sun Sep 24 15:00:18 2006 +0000 "Release log update" commit f2ac23d95903fb0ad6a5b9d69af5134730398857 Author: kent Date: Sat Sep 23 23:10:02 2006 +0000 Seems to work commit a611be0335a80db5133e518bf36cf622090ebc5a Author: markd Date: Sat Sep 23 15:53:08 2006 +0000 fix warning commit 1e0d940de2f36a4feb4e05705ffd5c197fc2338d Author: galt Date: Sat Sep 23 15:00:23 2006 +0000 "Encode release log update" commit e37a8a4dfb9fcb897b3e0da46b4cbab91cccdc88 Author: galt Date: Sat Sep 23 15:00:22 2006 +0000 "Release log update" commit 6e83fe2ffd27894b0a8269e1c7da40f7bc850e42 Author: heather Date: Sat Sep 23 11:08:40 2006 +0000 add snpReadSeq commit 59edbc1ea02d8c22e5f79d1d21299fff499e01c6 Author: heather Date: Sat Sep 23 11:07:52 2006 +0000 util for splitting rs_fasta files; need to use rsId for filename commit 414cc9373e365c6932047c8840103c32fbbefbd9 Author: rhead Date: Sat Sep 23 00:05:06 2006 +0000 added ccdsKgMap table and made a ccdsDb category of databases commit dbb0dd3d928701c0fc256f117c09bed5e54b34cc Author: kate Date: Fri Sep 22 23:58:47 2006 +0000 Streamline handling of file-based input. Also corrects some problems with updates using hgCustom commit 5831fa461223dffec9d481cdb68baf470abcfd07 Author: kate Date: Fri Sep 22 23:58:04 2006 +0000 Add define for new cart variable commit 747c41e1af7be2086b694f174228c9c95f5dcf44 Author: ann Date: Fri Sep 22 23:49:56 2006 +0000 commented out description of pix browser line, as this feature does not work commit 7e94725c2912dc75baf61735a52fe74d66541b29 Author: heather Date: Fri Sep 22 23:33:39 2006 +0000 improve usage message commit 621533ef29cf54704e01458c1e58add003fc2190 Author: ann Date: Fri Sep 22 22:54:44 2006 +0000 Edited gap display description to better reflect the actual, updated display method. commit e9ee116f56e71d7e3a0cc5713c208348fa9bdb86 Author: heather Date: Fri Sep 22 22:54:09 2006 +0000 add snp126orthoMixed commit 4014a4a04ed0499f972157855d7c5853e2eca1b0 Author: markd Date: Fri Sep 22 22:45:52 2006 +0000 build hgGenericMicroarray commit 36ec79c0dbcead41fb3d3a24839bb4d89851f6ce Author: markd Date: Fri Sep 22 22:43:07 2006 +0000 changed atof to sqlFloat commit 0244ad0531ddb0c4a311a18bf1acf3144754d2d8 Author: fanhsu Date: Fri Sep 22 22:33:56 2006 +0000 Updated GAD display to show disease class codes. commit 30ab9c73937c7d19ea1ca73d9df54850323c91e3 Author: heather Date: Fri Sep 22 22:31:15 2006 +0000 comments from code review: print ortho allele after reference allele; fix bug in header for additional locations commit 6f2b2ef4b7fe85e3e3c1913986cd304b68b54a04 Author: daryl Date: Fri Sep 22 21:17:25 2006 +0000 Fixed bug in hPrintf refactorization commit 2fa36c043e5c1157a2b164d296841ab08393d405 Author: kuhn Date: Fri Sep 22 19:49:25 2006 +0000 fixed error condition if tablename matches a symlink or directory where used and fixed single-machine case to work more robustly. thanks, kayla commit cda56c13ed6d447b674515bb631018ac9234ba2f Author: ann Date: Fri Sep 22 18:55:12 2006 +0000 removed header lines (no longer used by hgCustom). commit a86a19701ae55d8d797ca863dde947cf787bc912 Author: aamp Date: Fri Sep 22 18:55:09 2006 +0000 Suggested changes from Kayla. commit 33215be03f09c68c8c509ffef7d85636b8942cad Author: heather Date: Fri Sep 22 18:05:43 2006 +0000 this is actually 3.1 for Baylor commit 81886822081805aed0f41c124623322710bc1838 Author: heather Date: Fri Sep 22 18:02:50 2006 +0000 getting started here commit 773bda2292635891a54b7fb3905a3d595ed11122 Author: donnak Date: Fri Sep 22 16:25:46 2006 +0000 Fixed 2 formatting things. commit 7920252e8961f54b4711dc6721534f6409b25efa Author: galt Date: Fri Sep 22 15:00:29 2006 +0000 "Encode release log update" commit aebd490bbc7883471747148c40c12d7307e83a8b Author: galt Date: Fri Sep 22 15:00:28 2006 +0000 "Release log update" commit 05d5ef5226f8dc841b5dada82857ce5c70209aa0 Author: daryl Date: Fri Sep 22 10:00:27 2006 +0000 reformatting to adhere to kent code conventions; fixed rnaLpFold left label; added guidelines for rnaLpFold track commit fc4444b205ce75b8fcbc4ff785265ff77ad0803b Author: daryl Date: Fri Sep 22 09:57:16 2006 +0000 fix cart.h and bed.h typo commit 8759cc4bcdf5a8e99d0997db9b3776296fa62233 Author: daryl Date: Fri Sep 22 09:56:46 2006 +0000 move htmlPrintHelper to hPrint commit ddf733529d9554a3d10c3d42e1fdc462922ae4ef Author: daryl Date: Fri Sep 22 09:12:59 2006 +0000 formatting fixes commit 6e34ab7c1df7fce7cb862463eaa343b893fb44b5 Author: daryl Date: Fri Sep 22 08:26:54 2006 +0000 moved html print functions (mostly hPrintf and hvPrintf) to the htmlPrintHelper library commit 5aa2c042a4e72069b186e91efbc1d1c813f1e20d Author: daryl Date: Fri Sep 22 08:20:03 2006 +0000 adding htmlPrintHelper to generalize the HTML printing functions commit 536d409c2ad4c1ea25f122bddbc4d5b754deb5b5 Author: daryl Date: Fri Sep 22 08:18:42 2006 +0000 added cart.h and bed.h includes to fix the build commit adeaae701dd8c737f7201a648928612f0e72a6b0 Author: daryl Date: Fri Sep 22 08:17:32 2006 +0000 Added ifdef CHEAPCGI_H commit 9392578e493e1368cb17ac26d19090381039f28b Author: donnak Date: Fri Sep 22 07:46:57 2006 +0000 Added several new pubs from Daryl. commit 6eb071f981968607dce5da78b1e4a97ccd1e3d03 Author: kate Date: Fri Sep 22 06:13:02 2006 +0000 When updating, leave default track names alone (don't create new unique tracks). By request of Mark D. commit d3723a82155e1ac776335e946b2c081de2fa55eb Author: kate Date: Fri Sep 22 05:55:36 2006 +0000 Change navigation per Mark D request -- deleting all tracks sends user to GB commit c9b33fb6611918aaa08c03a9d9a20cc9c1e27b51 Author: kate Date: Fri Sep 22 05:48:09 2006 +0000 Getting ready for release: 1. UI changes from test feedback 2. Remove interim code commit 7c0757eee4afd5e4b69a3cfb368aeb6269ba933e Author: donnak Date: Fri Sep 22 04:29:48 2006 +0000 Added 2 more pubs. commit 481a9fc5881637b3267b27716fdfd652b3779c50 Author: angie Date: Fri Sep 22 00:45:03 2006 +0000 Masked sequence for alignment only -- not building a browser at this point! commit 0deebb7f4a5fb098ebe1348654db1e58168b39f4 Author: angie Date: Fri Sep 22 00:26:34 2006 +0000 One final migration for the session-loading code: now instead of being called by hgTracks, it is called in cartNew (unless cartNew is called from hgSession, in which case it defers to hgSession). Loading the session in cartNew means that the correct page title is generated by cartHtmlShell, and the loading commands are now supported by all CGIs. commit 4bf9d0d8d0e31a6ed72c60d6fd2b01b3aa934ab0 Author: angie Date: Thu Sep 21 23:21:00 2006 +0000 One more UI suggestion from Ann. commit 81a48bf1d9da50820d50de88a1c8daaad61fb53a Author: angie Date: Thu Sep 21 23:03:32 2006 +0000 Several UI improvements suggested by Ann. commit 62d777212ac2d1414349c6bca7c0429dcfbb41e8 Author: heather Date: Thu Sep 21 22:25:01 2006 +0000 add snp125 commit 396c55fa4e0a919dd5c26ae988a2c0ac5c1c9500 Author: galt Date: Thu Sep 21 21:11:05 2006 +0000 fixed patchBranch.csh to use same log as moveBranchTag.csh since they can interleave in critical way now commit f7e93943b819b9b290068083116d3244fbc4d6da Author: heather Date: Thu Sep 21 19:11:49 2006 +0000 add snp125 commit 80a6f76ea846bd0ae6c47f0864d8e8ff52535ff1 Author: heather Date: Thu Sep 21 19:08:04 2006 +0000 copied from canFam1 commit 3a3f0ddadd7a66b89be94f5badd283f7f2a2f7ce Author: galt Date: Thu Sep 21 18:51:55 2006 +0000 updated build scripts, added new patchBranch.csh commit 6d0344ff34734285634467f37125a2bd516ece15 Author: archanat Date: Thu Sep 21 17:39:19 2006 +0000 Changed Adam's affiliation to Cornell. commit eabe56ceee03fa422bba0c23160d4d5ab376f7d8 Author: fanhsu Date: Thu Sep 21 17:30:21 2006 +0000 Added functions for InterPro tracks. commit 48e3cb21c639552b90f279645b389a73879910a8 Author: ann Date: Thu Sep 21 17:11:40 2006 +0000 edited gap annotation description to more closely describe how it is displayed commit 1db287af93a8934c2792b886abe1d5b560cdc09b Author: aamp Date: Thu Sep 21 15:30:26 2006 +0000 Added groupings for affyRatio (human), gnfAtlas2 (human), and affyZonWildType (zebrafish). commit 0d4ae21d43f4e016032ff2f23d99c43ee6a00580 Author: galt Date: Thu Sep 21 15:00:27 2006 +0000 "Encode release log update" commit 105d54620aeefc8d8ac562b1b31717cdcc1ad3c1 Author: galt Date: Thu Sep 21 15:00:26 2006 +0000 "Release log update" commit 8294ea17faff2c08102d8e3867a791fa47c71f43 Author: giardine Date: Thu Sep 21 13:39:39 2006 +0000 changed comment commit 85f5b511b207e128b507010898913cb47305e116 Author: giardine Date: Thu Sep 21 13:37:00 2006 +0000 change html linebreak format commit 4f9b386f1e157dd97a821482389767b74d215db8 Author: markd Date: Thu Sep 21 04:51:32 2006 +0000 adding need type commit 49d607b6f62b9c291e67a3b8c2e3e111212806b8 Author: markd Date: Thu Sep 21 04:45:15 2006 +0000 removed dead code commit 467e1b7d426098cc8e0b2866dcd8b54a3c731015 Author: heather Date: Thu Sep 21 02:34:49 2006 +0000 use semiShortCircuit for SNPs commit e785b02097af5c80ce27d767e84eb5a8abb48470 Author: galt Date: Thu Sep 21 01:42:07 2006 +0000 oops, real full-circle now commit 09b999f4372ac59779a13d94749a55df60b3a05a Author: galt Date: Thu Sep 21 01:40:33 2006 +0000 full-circle commit 2e230053c184778706b9b84717ac30687623b9a7 Author: markd Date: Wed Sep 20 23:54:56 2006 +0000 added new MGC status code commit 7487242f140b6366ac66580ba3aafccacdf43625 Author: angie Date: Wed Sep 20 23:31:27 2006 +0000 Several changes requested by Jim / Archie Russell: log in --> sign in; added link/email function that creates a bookmarkable/shareable url for loading the session directly into hgTracks; added another encouragement to sign in; added instructions for creating links to hgSession or hgTracks for sharing sessions. commit 664ca839b04badae367602d114d82e30f2ffc7de Author: angie Date: Wed Sep 20 23:27:12 2006 +0000 Changed the link to hgSession to just be labeled Session (not User:... or Log in), per Jim's request. commit c9b808fe27d40eab84de7ae7da4566c5a1dbbdab Author: angie Date: Wed Sep 20 23:17:19 2006 +0000 oops, need to do the session-loading before getDbAndGenome not after. commit 107eb4ebd0a0e7419ae957d7b24eb1593cfff2b7 Author: markd Date: Wed Sep 20 23:17:04 2006 +0000 reloaded CCDS commit 0778107b0ad95095ba3dc28e9d6e2e803ff397d3 Author: fanhsu Date: Wed Sep 20 23:11:58 2006 +0000 Initial .html for InterPro. commit c30efb1e7f9af7b476d24030bc27e86aa64bd012 Author: angie Date: Wed Sep 20 23:00:31 2006 +0000 Moved code for loading session from url or saved session from hgSession to hui lib, so that hgTracks could share it. Also added Session link to hgTracks hotlinks. commit 99216803d54a88f4ab7f3bbf6fe927401ba0f21d Author: fanhsu Date: Wed Sep 20 22:54:43 2006 +0000 Added InterPro Domains track. commit 8bce78d8574053b93c56bf003cbca292bf0cbb20 Author: fanhsu Date: Wed Sep 20 22:52:12 2006 +0000 Added InterPro. commit 2d210a90c055afa0bcbcd8cd1fe7ab28b5743136 Author: markd Date: Wed Sep 20 22:48:53 2006 +0000 fixed bug where multiple versions of the same RefSeq accession may end up in ccdsInfo table commit 6885c8b042185a233697c700c2461e757e030698 Author: galt Date: Wed Sep 20 21:43:55 2006 +0000 removed middle line test commented-out lines near bottom commit 08e1a6d6d17a6dd409fa2779f7b71a458f8bd390 Author: galt Date: Wed Sep 20 21:43:37 2006 +0000 modified test commented-out lines near bottom commit 8b54dcbf7b753e5a0d0f372ff7e1898fe59c5e0c Author: galt Date: Wed Sep 20 21:43:12 2006 +0000 added 3 test commented-out lines near bottom commit 72e5f8a69c026c8426da3ff45f6ed5d2deb41037 Author: galt Date: Wed Sep 20 21:41:29 2006 +0000 test rev removed 3 test commented-out lines slightly further from the top commit 3c2a812bababf94a3a2a44838c230ecb727f6b8a Author: galt Date: Wed Sep 20 21:40:15 2006 +0000 test rev add 3 lines slightly further from the top commit bb06dc16c7560b23f77321fb61393e61b037cb04 Author: galt Date: Wed Sep 20 21:39:00 2006 +0000 test rev add 3 lines near top commit e10bdf882bd8296bbbbec672b6be8dac60219f56 Author: aamp Date: Wed Sep 20 21:32:53 2006 +0000 Bug caused a 500 error when cart was empty. commit 0a7eec71562f8a00846708da52c8206ffe1c77d7 Author: markd Date: Wed Sep 20 20:58:10 2006 +0000 updated Brent lab URL commit b5fc50963cde6f093551371e7d082d43f9c8bfbf Author: ann Date: Wed Sep 20 20:22:35 2006 +0000 changed quotes to " commit 0b38f10682f30c69ca8db4d6af3d25babc3bb148 Author: archanat Date: Wed Sep 20 20:20:35 2006 +0000 Fixed a typo commit dfc5fa714c73086805d2066e351d9d9e7f23f992 Author: angie Date: Wed Sep 20 17:46:44 2006 +0000 Added simplePartition.pl to SCRIPTS. commit eff259ba576355c5d957057088f614cd0a7d6e00 Author: aamp Date: Wed Sep 20 17:25:44 2006 +0000 More changes to the .ra file. "all" grouping given the silly groupSizes field to make coding easie. commit 9504628e478ae6a7897bc81a3b804b16b32f63af Author: aamp Date: Wed Sep 20 17:16:06 2006 +0000 Changes to microarray track CGI code to use microarray lib functions that average array data defined by microarrayGroups.ra file. commit 4bb75e3621ab43d10f72612ddbf5a08f94309e06 Author: galt Date: Wed Sep 20 15:00:28 2006 +0000 "Encode release log update" commit fa69927512e4944c922f3ec071cecc8779323dfe Author: galt Date: Wed Sep 20 15:00:26 2006 +0000 "Release log update" commit 9b4662a47afca0d5ff41cacc4bc62939ff009681 Author: giardine Date: Wed Sep 20 14:30:01 2006 +0000 Changed list used for comparison. commit c702941f98edaa558f8bc3ba796f4c4265de694c Author: kate Date: Wed Sep 20 01:30:30 2006 +0000 Remove ifdef's prior to release. 2. Suppress empty url's in ct file. 3. Leave customtext on error so user can correct commit f8fa8e29e12197f18d893eea23ec17cceeb13da6 Author: kate Date: Wed Sep 20 00:16:52 2006 +0000 Fix problem that caused buffer mangling in file processing commit 20dfd7134452e230887b05376659a68db9ab74df Author: hiram Date: Wed Sep 20 00:08:07 2006 +0000 Fixup tfbsCons directions even though they refer to nothing that exists ... commit ce546da7daadb884d6a52e8f673ede6f09ceb610 Author: rhead Date: Tue Sep 19 23:58:05 2006 +0000 Changed a capital letter to lower-case. commit 242044d7a0c75cec2a50e917ac40c7db12447662 Author: rhead Date: Tue Sep 19 23:48:56 2006 +0000 Added more description of new color scheme. commit cd9ebbebe19b952010ffb00cd78e33f45a09b8c9 Author: hartera Date: Tue Sep 19 23:39:22 2006 +0000 Added absoulute expression data for wild type zebrafish arrays. commit dca88e65c48b553ec0293b99fd8701da4a068a8b Author: galt Date: Tue Sep 19 23:06:24 2006 +0000 removing unnecessary info that does not get updated when other genes are picked commit b31c0ccbc459ecdc944ea66bcb89327da338d421 Author: heather Date: Tue Sep 19 22:42:37 2006 +0000 implement search for SNP Array track commit 2cc30d4c97b99371ffcf2fcf98033a2baafcb214 Author: hartera Date: Tue Sep 19 21:54:33 2006 +0000 Added new exact search for wgRna, allows wgRna items to be found when the name is also found in a gene description. commit 6c20f7a5c480d267b310cb1d6b2fac1213ebf2d2 Author: heather Date: Tue Sep 19 21:46:14 2006 +0000 add Affy100K and 10K commit 3806bfc69b8f8e1b56613bee52d5f8417a755e2b Author: daryl Date: Tue Sep 19 21:45:23 2006 +0000 minor changes for debugging commit b0a664fe9a891b35f5cf9a146043d8b7abca08cd Author: heather Date: Tue Sep 19 20:57:15 2006 +0000 extend Affy snpArray data commit a26d2ea73c38cb106619a2d366b5dd46b46a5d49 Author: heather Date: Tue Sep 19 20:51:26 2006 +0000 add Affy100K and 10K to snpArray composite track commit 73af0c334adf2eb033604e2d4deaf3e58ce618d3 Author: heather Date: Tue Sep 19 20:47:35 2006 +0000 tweaks commit f15e44d3079aa0f749fb858b0dcdd6f4fb7641a7 Author: heather Date: Tue Sep 19 20:44:28 2006 +0000 add Affy10K and 100K to snpArray composite track commit df7d01c91903c16adf49676f49a1baa897a65c78 Author: giardine Date: Tue Sep 19 18:56:57 2006 +0000 Added new type for src link so can make sure it is displayed first. commit 43196224ec4e14c73fa5d9bfc3d7966bf3814c2f Author: angie Date: Tue Sep 19 17:34:17 2006 +0000 Added description of semiShortCircuit setting. commit 9cb4405cc7f1463699e3d7ac5f450ee63139fede Author: kuhn Date: Tue Sep 19 16:34:02 2006 +0000 removed dependency on hgwbeta. bottleneck now works from dev only. commit 68fa84d1a88fb007cd80e1a01cb698dc4717ff13 Author: fanhsu Date: Tue Sep 19 16:28:09 2006 +0000 Updated KG color scheme. commit 16abf400121a966dc876c0b6599245475a925e01 Author: fanhsu Date: Tue Sep 19 16:24:53 2006 +0000 Updated KG colore scheme. commit e9865e463c364fc5a9053a73d5c1dea7f9228fdc Author: fanhsu Date: Tue Sep 19 16:16:13 2006 +0000 Updated knownGeneColor() color scheme a little bit. commit 845701a566a7bc665f31ecd2e67b05cfc17481ac Author: archanat Date: Tue Sep 19 16:06:24 2006 +0000 Changed the URL back to the old one commit af2526c578d2934f249e403932bff088f04b55be Author: galt Date: Tue Sep 19 15:00:23 2006 +0000 "Encode release log update" commit fab3ab98da7c6a0c043880b2e1557ea178a73879 Author: galt Date: Tue Sep 19 15:00:22 2006 +0000 "Release log update" commit 5e1795ee25533cf51c8cfd01cfce361865b9ad6d Author: angie Date: Tue Sep 19 14:59:56 2006 +0000 Resolved -Wall warning: unused variable. commit 6170e7f8b971c48ae8f6c558021fa3aa6b6336cb Author: giardine Date: Tue Sep 19 13:50:29 2006 +0000 fixed gvPos searches, needed to reference database commit 1bb630e49948146415d8a2e31cc4e2a33175aa15 Author: galt Date: Tue Sep 19 05:51:28 2006 +0000 redundant call removed. on some platforms this fails confusing blat users. Hiram and Mark and Galt conferred. Seems best to just yank it. commit ad6f08bcda1e1da0ae943ca1ec3450897351b4a2 Author: daryl Date: Tue Sep 19 04:19:56 2006 +0000 right angle bracket in track name causes problems with hgc, so the function is being ignored until this is resolved commit a22aa23f6f024f0eef392197eb461a132b3fb81c Author: daryl Date: Tue Sep 19 03:11:58 2006 +0000 Added orthologous allele to SNP name when available commit a07e1fba962cf42ef3a6821893a7e385ecf268fe Author: galt Date: Tue Sep 19 03:05:54 2006 +0000 allow values/attributes with leading zeros to be treated as ids instead of integers commit d48c3bd6b752b9befd3df4e479e432d3b43500f8 Author: kate Date: Tue Sep 19 01:00:21 2006 +0000 Restore button for new custom tracks manager commit bac61667853d13716bf3e78fe8b4af49db2aa6ad Author: kate Date: Tue Sep 19 00:51:55 2006 +0000 hgCustom UI changes requested by Jim. Mostly working -- checked in for UI review commit c6235528801a483c07d69919c530b815c92132ba Author: hiram Date: Tue Sep 19 00:09:47 2006 +0000 Fix stsMapMouse.bed and all_sts_primers tables. commit 51f4069939a2859bc750a1db555ce6fa8b64a9b5 Author: daryl Date: Mon Sep 18 22:58:12 2006 +0000 Fixed bugs in alignment of SNP flanking sequence commit 3c00eb1e70306f1ec1833939f7a1036dc20399ef Author: kate Date: Mon Sep 18 22:41:53 2006 +0000 Fix mispelling commit e6fbf1353084b3730b0976256fa5e1879a658026 Author: hiram Date: Mon Sep 18 22:38:05 2006 +0000 scope difficulty with the variable score was ruining all the scores ... commit 95447e543d446a33441db1fa4a598db1d5477e42 Author: angie Date: Mon Sep 18 21:33:41 2006 +0000 Removed nonexistent database hivnm from DBS. commit c00ae38b2129d8325ace02070ab65be538d893e1 Author: donnak Date: Mon Sep 18 18:42:37 2006 +0000 Made a few minor edits, updated Adam Siepel's website URL on a few pages. commit 938c574151422a100eb395a9fd9cc55ce7bf72c4 Author: donnak Date: Mon Sep 18 18:17:17 2006 +0000 Made a few minor edits. commit 7cbac0943b4bfbd3627070315b760719ea88acec Author: angie Date: Mon Sep 18 16:31:38 2006 +0000 Resolved -Wall warning: unused variable. commit f7aa783017585a46909c68cd77174c11aa7b2c84 Author: galt Date: Mon Sep 18 15:00:18 2006 +0000 "Encode release log update" commit bac965ef911d50d33636e93076eb4e6670f9c21b Author: galt Date: Mon Sep 18 15:00:16 2006 +0000 "Release log update" commit 213048d386392163c7b1f6e9cb66af3363111176 Author: galt Date: Sun Sep 17 15:00:19 2006 +0000 "Encode release log update" commit 42569e89937d5cf966d80425950575efc2e6c908 Author: galt Date: Sun Sep 17 15:00:18 2006 +0000 "Release log update" commit 83b720088f099df3dc3e042780832abebf871483 Author: galt Date: Sat Sep 16 15:00:24 2006 +0000 "Encode release log update" commit 8927c2a46a7a3f241ef930ef4b9072fb39794eb7 Author: galt Date: Sat Sep 16 15:00:23 2006 +0000 "Release log update" commit 8427cd979b7d4d217d84b97a4f0db10a54386a9c Author: heather Date: Sat Sep 16 01:22:01 2006 +0000 add simple printSnpOrthos(); comment out calls to printSnpAlignment commit 01586947f1b76d025ab9e9a6febc4f233fc1d17b Author: donnak Date: Sat Sep 16 01:05:04 2006 +0000 Changed Adam's affilitation. commit 18621ae7a9d2b5ae370432be4cfe9ad577c245f6 Author: hiram Date: Fri Sep 15 23:30:27 2006 +0000 Done with STS markers update commit 46915466bfce741133c82aeabf3a43f0bd59c83c Author: donnak Date: Fri Sep 15 21:01:49 2006 +0000 Changed Adam's affiliation to Cornell. commit 1471f667d8ffa4305b13b5d3c53dd17209981d37 Author: archanat Date: Fri Sep 15 20:41:21 2006 +0000 Updated N-SCAN track descriptions commit 00a34684523235284d1562f92067a2598972d2cf Author: ann Date: Fri Sep 15 20:31:47 2006 +0000 added two new rules: blastHg17KGRef02Id and blastHg17KGRef01Id. added some assemblies to existing blastHg17KGPep02Id and blastHg17KGPep01Id rules. commit 72051f971627a966b9cc88b177433bb133b4823d Author: ann Date: Fri Sep 15 20:17:45 2006 +0000 added a new rule for identifier of blastHg16KGRefId commit 4becc4f91b340793906da9302261b0e0d4eb2378 Author: ann Date: Fri Sep 15 19:31:34 2006 +0000 added rule for identifier blastHg18KGRef04Id commit 6acc77416f4564c4c4771f978f3407f51282ec15 Author: ann Date: Fri Sep 15 19:18:52 2006 +0000 fixing lines in blastHg16KGPepId so they will show up in TB commit f6db90188c6390a695156a9aa261ae5afde64075 Author: archanat Date: Fri Sep 15 18:55:50 2006 +0000 Fixed a broken link commit d96de322aa70a70855aeab9766726f078adf2a0c Author: ann Date: Fri Sep 15 18:55:15 2006 +0000 cleaning up blastHg17KGPep0*Id rules commit a08aed7a15c58589adec8946cc42c16791f60a62 Author: archanat Date: Fri Sep 15 18:34:29 2006 +0000 Fixed a broken link commit 6931db872c4e8b82714131aa4a6b9691a0cac403 Author: donnak Date: Fri Sep 15 17:50:45 2006 +0000 Added template for this new FAQ page about the Table Browser. commit f47aa8cc0a7a31fd4b8a2a9794b67a6c1aeb4ea0 Author: galt Date: Fri Sep 15 15:00:27 2006 +0000 "Encode release log update" commit fc15d5b5dfc1351db86a1157b1ac20e1e6738f3e Author: galt Date: Fri Sep 15 15:00:26 2006 +0000 "Release log update" commit 33979f6e011623bbf6eecbc26c29a78864888a02 Author: braney Date: Fri Sep 15 14:37:06 2006 +0000 remove unneeded baseProb.h include commit b0e9cdb681e9389e055675d7695e5279300e71ed Author: heather Date: Thu Sep 14 23:32:09 2006 +0000 less confusing to just show the dbSNP sequence commit 3012e26525a8a4335e2e27503738efdf1917bd6a Author: heather Date: Thu Sep 14 22:53:25 2006 +0000 get the coords in reverse for negative strand commit 4a93da47086228fd76c4b3f7d6ecb99f743d7f26 Author: markd Date: Thu Sep 14 22:45:16 2006 +0000 updated N-SCAN track descriptions commit d1a8eecb374a1146f920406f32563e2bff253ec7 Author: braney Date: Thu Sep 14 21:45:44 2006 +0000 add sequence logo drawing routines commit ac2569ce689796d7c93354ef9dfb41fc5cd545d4 Author: braney Date: Thu Sep 14 21:17:34 2006 +0000 add sequence logo track and comment out the blatz tracks commit d897c41b124d4e5c76e978bef924b3f6ed2cab9b Author: braney Date: Thu Sep 14 21:08:24 2006 +0000 add stuff needed for hgTracks sequence logos commit 27c2bc3f4375a292b210e2ecb9a2cf6c47af59fa Author: daryl Date: Thu Sep 14 20:51:43 2006 +0000 Fixed typos commit e39160bbcc397bc6092ad2bfba558414184b3277 Author: daryl Date: Thu Sep 14 20:45:49 2006 +0000 Added rnaLpFold track commit 13045c30cc91faa76b8d50e86e3e2d62682aeeae Author: braney Date: Thu Sep 14 20:45:36 2006 +0000 a couple of new routines to implement browser sequence logos commit 82a77fa84821656e6d42d53a461d0f744cb63d02 Author: daryl Date: Thu Sep 14 20:17:42 2006 +0000 added support for RNA LP FOLD track commit b4f43e4e260d2cdbf448a0dc25b6ac35b353bba4 Author: daryl Date: Thu Sep 14 20:16:43 2006 +0000 added RNA LP FOLD track commit 748c66c95cc366b55e7fef6fd521dc8bcb98085e Author: daryl Date: Thu Sep 14 20:15:33 2006 +0000 Added rnaLpFold track, with test data from pyrFur2 at the beginning of chr1 commit 9810a5706f61ea305e40ebea6d9c83ccb5d6a845 Author: daryl Date: Thu Sep 14 20:14:10 2006 +0000 typo fix commit 503b5e76d75638dd03a777d456d50b26197f577b Author: braney Date: Thu Sep 14 18:49:07 2006 +0000 the beginnings of a cat browser. Just enough to build human alignments commit ec7ec593d1d330c54d35b8179fbdb39362210a99 Author: heather Date: Thu Sep 14 18:43:12 2006 +0000 display additional locations for snp126 commit 5f724303f630480219584f01e14c4cf758d92a83 Author: angie Date: Thu Sep 14 18:28:29 2006 +0000 Updated for recent apparent improvement in blat (alignment now extends right up to poly-a). commit 0a3628972d4975930b7fbc444675c60a9076e4c3 Author: angie Date: Thu Sep 14 16:44:29 2006 +0000 Resolved -Wall warning: unused variable. commit 8a7de28d971b6f9fefe39310ca6128a9d129887b Author: markd Date: Thu Sep 14 16:42:42 2006 +0000 added support for new MGC clone status code commit 352478e9a8936f98718373b62b1add51c38f2a94 Author: heather Date: Thu Sep 14 16:14:51 2006 +0000 increase gap penalty commit 3fba7933db9b66ba8548835293951be0d2fe6638 Author: markd Date: Thu Sep 14 15:40:00 2006 +0000 added opossum N-SCAN predictions commit 5ce250598ce25efcb50849226878187ecf0a7f42 Author: galt Date: Thu Sep 14 15:00:28 2006 +0000 "Encode release log update" commit 65c54b1dcbba399a8caf98490bfadbd515ba70de Author: galt Date: Thu Sep 14 15:00:27 2006 +0000 "Release log update" commit be94a15825eafe4e6678ea41889e6e174cd20fa0 Author: giardine Date: Thu Sep 14 13:46:55 2006 +0000 minor edits to text and links for ORegAnno track commit ffa08553df74eb1b7ad5fa4ea5880efb8730e365 Author: giardine Date: Thu Sep 14 13:45:20 2006 +0000 various fixes to parser commit 6bfbe755e2ff1d11771a58021bfd62468247c04a Author: heather Date: Thu Sep 14 02:13:48 2006 +0000 improve previous commit; swap order of genomic/SNP display to match alignment commit 18821b220ee548126526aa7fb94b15b96c34c6b7 Author: hiram Date: Wed Sep 13 23:16:55 2006 +0000 Less filtering, more identifiers. commit fe7ab15fda387f2f4cec44751c904ad8be13ab07 Author: heather Date: Wed Sep 13 23:06:57 2006 +0000 fix strand bug; match sequence length to alignment length commit c2cfc129f81eccb16ac0c0a59346da972fd159c8 Author: heather Date: Wed Sep 13 21:36:12 2006 +0000 fix output commit 78a652ccd714e80ca5814d3dd927226b938be23c Author: hiram Date: Wed Sep 13 21:22:57 2006 +0000 Do not put the port on the Host: line when it is the default 80, and remove the extra Accept */* commit 21724d08400a353dc9f86154c019881d1a9688fc Author: giardine Date: Wed Sep 13 19:38:17 2006 +0000 removed landmark track commit bf42a51d61a8acf521c526ae9b3a7d58bcc11f48 Author: giardine Date: Wed Sep 13 17:15:29 2006 +0000 edits based on code review commit 67e829adc7dfec8d4a8310b5dd3dee7a3633093a Author: giardine Date: Wed Sep 13 17:03:50 2006 +0000 Made missed name changes for disease-association(phenotype) commit 91ab9eee16880d117ae9f461c74a58fd89b145af Author: giardine Date: Wed Sep 13 16:52:20 2006 +0000 changed BTKbase link commit 16d79ca55cd160ccc4c6bee27defa718ffd3f6f1 Author: giardine Date: Wed Sep 13 16:33:57 2006 +0000 minor edits commit 92fca255aa568aa01028bc4321cd635b3f46b1f4 Author: galt Date: Wed Sep 13 15:00:30 2006 +0000 "Encode release log update" commit 0cba1b797aecc3dce5661dd91dc3cfb621573ecc Author: galt Date: Wed Sep 13 15:00:29 2006 +0000 "Release log update" commit 0f47f83e7951ac959539c714532cc0917c20a73a Author: kent Date: Wed Sep 13 03:15:27 2006 +0000 Fixing bugs with uploaded graphs. commit 912264646466f6f8c9cba1c55ee746f5d68fc84a Author: kent Date: Wed Sep 13 03:01:48 2006 +0000 Seems to work. commit 8540679988d8023d069f504eb1f8338a19b77964 Author: heather Date: Tue Sep 12 23:29:18 2006 +0000 use wrapper function to handle 2bit and nib commit fcbde1340b0c15dec9251f5da525cc0d3c06eb0f Author: kate Date: Tue Sep 12 20:59:16 2006 +0000 Tweaks to standardize and complete reference citations commit e31a6ab2169ae99c0a0667c6099476df4f4cc467 Author: giardine Date: Tue Sep 12 20:43:04 2006 +0000 Added to credits, description, and changed link. commit 2227567851d3c6298f1aceb2079dd49d25f33aeb Author: giardine Date: Tue Sep 12 19:26:40 2006 +0000 Updated methods and source lists, changed more disease/phenotype assoc. commit d931c1c76a04b41f4cf327baaaf4a3fccf977fe6 Author: kate Date: Tue Sep 12 19:21:11 2006 +0000 Update MSA Consensus elements labels and track description, based on input form Daryl commit 0b49117b8efab89b1e5be6e1b63fe8560df727ca Author: aamp Date: Tue Sep 12 19:08:52 2006 +0000 Color change for poly(A) track. commit 76f54ec09a39fa7fbf87c315a2d2f51d9f2d6b98 Author: ann Date: Tue Sep 12 19:04:59 2006 +0000 added minCheck to dm.flyBaseToRefSeq (per Angie) commit 101da084e9096db6776d5723cff11e6e1cfc441d Author: angie Date: Tue Sep 12 18:37:32 2006 +0000 Self chains. commit fc8406b2852f71fd77c532b180b3fca4495db4c0 Author: giardine Date: Tue Sep 12 18:28:43 2006 +0000 Changed terms used to describe disease/phenotype association. commit 70ee87596295862d656a1fea84332a008675e0ba Author: heather Date: Tue Sep 12 18:25:45 2006 +0000 fix typo commit b0b929e23c55a8f81228f5285169a0d626c61e94 Author: ann Date: Tue Sep 12 18:18:37 2006 +0000 added mm6 to list of kgProtMap dependency exclusions (per Fan) commit 2f7318b9adff93e2c79e1810c5c91de0b87c833d Author: angie Date: Tue Sep 12 16:49:52 2006 +0000 Resolved -Wall warning: unused variable. commit 443ec7a2ccecb988be45d2923096d115d0dd9726 Author: giardine Date: Tue Sep 12 15:57:44 2006 +0000 Added search on oreganno id commit d217ba72619355a295d971294bac9d38d6b15655 Author: giardine Date: Tue Sep 12 15:38:26 2006 +0000 Add oreganno commit 346d8551a9bcef0981b9ecfafbf2d4c1ae26ee48 Author: giardine Date: Tue Sep 12 15:30:52 2006 +0000 Added oreganno to docs commit b4f52f6d3e71fa6373d0364b8d9980625284c272 Author: giardine Date: Tue Sep 12 15:23:45 2006 +0000 Added strand to oreganno table commit 24183ba2c0c8506d6874494f726959e2c723ad0d Author: giardine Date: Tue Sep 12 15:23:06 2006 +0000 Added strand to oreganno table, shrunk some text fields commit 1dc7648ba1473cfaf0de032f92a5adb53d204557 Author: giardine Date: Tue Sep 12 15:21:58 2006 +0000 updated ORegAnno display and links commit fef5a286341d7668e56f0d17ba19f9d30fc5c865 Author: galt Date: Tue Sep 12 15:00:26 2006 +0000 "Encode release log update" commit 3500cd17d95735a3d0f3bda022a2f5e65c45c5f4 Author: galt Date: Tue Sep 12 15:00:25 2006 +0000 "Release log update" commit c9fb32881633a8310ac3526d86ff47f62996dddb Author: baertsch Date: Tue Sep 12 08:44:59 2006 +0000 add cpgIsland track commit dd1bf1247f44885ce7ef118abf4fe4ba01016d90 Author: markd Date: Tue Sep 12 06:51:34 2006 +0000 added to-do items commit fad52b4ebe2eebb9f01d13b798bdbc4504266ea4 Author: sol Date: Tue Sep 12 04:11:13 2006 +0000 Renamed ha_elements track to hars commit 49855bf4126f799d09b49846eae60b1f88319c69 Author: galt Date: Tue Sep 12 01:02:04 2006 +0000 "New version number v142" commit 5a896ce5c2df576813b8edb928e2fdd6c1ac89fb Author: aamp Date: Tue Sep 12 00:17:55 2006 +0000 Some functions that were needed that I forgot to check in changes for. These needed to be seen by functions in expRatioTracks.c commit e140a280dceca85874a30206b792e1d37e19bc8b Author: aamp Date: Tue Sep 12 00:08:05 2006 +0000 Constant used for new microarray-drawing code. This limits the amount of data hgc will show, since that is a giant HTML table. commit dbf4fe2739ea8ba352a111e8e1dcd0cc06a798f4 Author: angie Date: Tue Sep 12 00:07:51 2006 +0000 Basic automated tracks in place. commit 22cdf14f003ec5e0290f6a8ccf8e92181e4b1019 Author: aamp Date: Tue Sep 12 00:06:38 2006 +0000 New microarray drawing code meant to speed drawing up. With that there's some new mapbox-making code and left-label drawing code. commit 1a9f7f6d4aa8903b01aee57804ea1b33e8908fed Author: aamp Date: Tue Sep 12 00:02:09 2006 +0000 New UI interface for microarray tracks using the new .ra files. So far just the combine drop down is added. It makes a cart variable just fine it seems but that cart variable is unused by the other CGIs currently. commit 5be75ad84de2b8222e05cee056ec497b68d15c11 Author: angie Date: Mon Sep 11 23:55:57 2006 +0000 Added chainSelf (thx Kayla). commit 2acedd89906381989adfefc3373d25674c1639e9 Author: ann Date: Mon Sep 11 23:51:24 2006 +0000 added comment for mytouch for geneidPep table commit b8aa485ef2efa52f4b1f16a4fc89ef55c8ecab38 Author: ann Date: Mon Sep 11 23:47:12 2006 +0000 added comment for mytouch to geneidPep table commit d54d95f769fe1d8a981dffcc33d4973e37e24b30 Author: fanhsu Date: Mon Sep 11 23:46:46 2006 +0000 Added HPRD lines. commit e1f5a505bb1828d86aef43ecb0196b7f1124acd0 Author: ann Date: Mon Sep 11 23:44:10 2006 +0000 added mytouch comment for ensPep and nscanPep tables commit 018a2b13091cc87f210050cae8f9a076f895e5af Author: ann Date: Mon Sep 11 23:43:38 2006 +0000 added mytouch comment for genscanPep table commit 2bdb536e4425d8f0b197855b6abf20874813ec87 Author: daryl Date: Mon Sep 11 22:53:44 2006 +0000 added display for snps that align to multiple genomic locations commit b97bbbafa2f973f30ddf066b6e7e79ced91c1772 Author: daryl Date: Mon Sep 11 22:29:05 2006 +0000 Added alignments of SNP flanking sequences to the genomic sequence commit cbb7fc5ec7c7a700593311255ccfde7016018d2d Author: fanhsu Date: Mon Sep 11 21:45:34 2006 +0000 Added gsClinicRec.sql gsSubjInfo.sql. commit 8192229059800dea3f892ee82c73254c48446c84 Author: fanhsu Date: Mon Sep 11 21:44:15 2006 +0000 Created hiv1.txt. commit 559a2befaa049a89591f530556dcdbc409b6b510 Author: fanhsu Date: Mon Sep 11 21:35:23 2006 +0000 Created hivMn.txt. commit 4972f67523b9477fa8013fb23b5ace15893baf62 Author: fanhsu Date: Mon Sep 11 21:30:01 2006 +0000 Added hiv1 and hivmn. commit b1b510f9a51cbe9fe15adb439697a13b0b14fe21 Author: giardine Date: Mon Sep 11 21:28:49 2006 +0000 Description for ORegAnno track. commit eb342eed58574b34414f97fd795eb42cd2f416b0 Author: markd Date: Mon Sep 11 20:58:24 2006 +0000 added rn4 nscan track commit d534ddbc33bacba2d88997d401cd0cf987aff9c4 Author: fanhsu Date: Mon Sep 11 19:46:11 2006 +0000 Added HPRD data for hgGene links. commit 801fff6433138e87c1afc2f061c103ab0914dd2c Author: fanhsu Date: Mon Sep 11 19:33:14 2006 +0000 Created hprdToUniProt.sql. commit 831d7552113391d555edc1697774ad13f90c2baa Author: fanhsu Date: Mon Sep 11 19:27:03 2006 +0000 Added HPRD link. commit 492e0e33155ccdcd0910fd8a01e7fd96562d72f5 Author: fanhsu Date: Mon Sep 11 19:15:52 2006 +0000 Created knownToHprd.sql. commit 72681c240248616830ba387ea617a51445a2e0fb Author: fanhsu Date: Mon Sep 11 19:15:18 2006 +0000 Created hprdToUniprot.sql commit fc40680f75e7a30f9d4741ff42bc4b099abea8e6 Author: fanhsu Date: Mon Sep 11 19:14:56 2006 +0000 Created hprdToCdna.sql. commit 7a47b8c8dc1a0ce3d4fbbe1736011a35c4bf62c3 Author: giardine Date: Mon Sep 11 18:15:09 2006 +0000 Put spaces when appending multilined features. Previously the words were run together between lines. commit 7eb202bdf8ea3a23f7a2c0ba4d0de67abc7ddb4b Author: angie Date: Mon Sep 11 16:36:47 2006 +0000 Resolved -Wall warning: unused variable -- caused by multiple mustOpen(w)'s on same file! commit d3b26a77f1e410889cf166f389820c5b471883e5 Author: galt Date: Mon Sep 11 15:00:19 2006 +0000 "Encode release log update" commit 8b5f785d88794d311876f20239cc37b40c5663ff Author: galt Date: Mon Sep 11 15:00:18 2006 +0000 "Release log update" commit 1583126c1bdb0f9e6d03e796b196931200b2febb Author: giardine Date: Mon Sep 11 13:48:37 2006 +0000 Adding missed files for the oreganno tables commit cab7c3499863769f7de69eec1a9565997ebc0285 Author: kent Date: Sun Sep 10 19:13:10 2006 +0000 Documenting polyA fix and bumping version number. commit c8d96c9df905565111904e6668902272e025068f Author: kent Date: Sun Sep 10 19:10:35 2006 +0000 Fixing polyA trimming so that it handles a little noise better, and so that it leaves 2 A's to complete stop codon. commit 0783e4bbae535dba28aea4105e79e9953180aa97 Author: sol Date: Sun Sep 10 18:41:14 2006 +0000 *** empty log message *** commit 5bd64f21a93711431ea06dd645220a1b3d271fc0 Author: hiram Date: Sun Sep 10 16:43:50 2006 +0000 Checked in from Belinda's source to fix broken build commit b08c3c730e57e783e752a1ee53be1997f4974b29 Author: galt Date: Sun Sep 10 15:00:21 2006 +0000 "Encode release log update" commit 553b0f16535d3e4800081ea2c46c8fec7864be4e Author: galt Date: Sun Sep 10 15:00:20 2006 +0000 "Release log update" commit d348f27f0257155191df0d8e4019e1e64baec2d0 Author: daryl Date: Sun Sep 10 06:33:11 2006 +0000 exposing LD functions for the rnaLpFold track commit 44aea0960433f56af9f9d86589619c205ec8ab4e Author: daryl Date: Sun Sep 10 05:11:16 2006 +0000 AutoSql files for RNA LP Fold data (Matthias Hoechsmann) commit 50e7463c7333b69d363ad2e3245317e5f449c2ca Author: hiram Date: Sat Sep 9 23:50:24 2006 +0000 Now ready to check name lists to see what is new or dropped commit f68c6041781a9be89a6dcacb3e44345f55800fff Author: hiram Date: Sat Sep 9 23:38:36 2006 +0000 Recovered from oblivion from its last use in /cluster/data/mm8/bed/STSmarkers/ commit 6d5a65042aeebd8ea071711228eac7a70324de36 Author: hiram Date: Sat Sep 9 23:35:28 2006 +0000 Just about completed second running of STS markers commit b07253448ab5b1e4d0a0d84ecd059802273d8e91 Author: hiram Date: Sat Sep 9 23:32:54 2006 +0000 Is now strict and warning clean. No errors or warnings during operation and seems to have improved its output. A score column seems to be correct now. commit d58a8e3e611b68ab1b0edfb77e76b9c5ed158665 Author: hiram Date: Sat Sep 9 22:36:31 2006 +0000 Rescued from the edge of extinction from a distant copy of the ancestor from the lost filesystem /projects/cc/hg/ytlu/bin/script/perl/createStsBed commit c64c28bc5d0ebe858de0f85d97d0a6a83d141a29 Author: hiram Date: Sat Sep 9 22:31:11 2006 +0000 Removing debugging print line commit e3c64b882062103de78bd9fb1aa6c328b9fec61a Author: hiram Date: Sat Sep 9 22:30:57 2006 +0000 Now strict and warning clean, no errors or warnings, and produces output as it did before commit d8c84dee1eee2e5b42ec7d0573cc1cea726357c7 Author: hiram Date: Sat Sep 9 22:15:25 2006 +0000 Original source rescued from oblivion in /cluster/bin/scripts/ commit 5d28cae2bdc871d9ce7bf4dcaf78d87dd6edf401 Author: hiram Date: Sat Sep 9 22:13:06 2006 +0000 Now strict and warnings safe, produces the same output as before. commit f6c2db3acb7634423122523bb891f64ac4b3cfbf Author: hiram Date: Sat Sep 9 21:53:59 2006 +0000 Original source rescued from /cluster/bin/scripts/ commit 2b57ef3cd6ba0416c3824c1b7ef9c6d76ed419b6 Author: hiram Date: Sat Sep 9 21:50:58 2006 +0000 Now produces the same result as before with no error or warning complaints and is strict and warning safe commit 66c5652fd9f6979c3ecd697e53d5cb39d633b5f8 Author: galt Date: Sat Sep 9 15:00:29 2006 +0000 "Encode release log update" commit 6c78774d76861d2eaf19b36afaf982899c34840a Author: galt Date: Sat Sep 9 15:00:28 2006 +0000 "Release log update" commit 9ee4010f6ada3019c3414718a61a768b2b071a14 Author: hiram Date: Sat Sep 9 04:19:43 2006 +0000 Original source rescued from /cluster/bin/scripts commit e5a8294be6b68134c4cf30a6d265e3659ff450ce Author: aamp Date: Fri Sep 8 22:51:28 2006 +0000 Updated changes to the Poly(A) track on hg18. commit 883ad51629d85de15b89317eff28624df8888a88 Author: kayla Date: Fri Sep 8 22:22:19 2006 +0000 Fixed 2 broken links. commit 572e1eef412fced35428f4be89587670e09cbf6d Author: giardine Date: Fri Sep 8 22:17:34 2006 +0000 Changed track name from Human Mutation to Locus Variants, added strand and label to gvPos, updated data. Added gvPos to hg18. commit 27e11924a82ffd1ce038f21ba11ac22ebc0f3220 Author: kayla Date: Fri Sep 8 22:11:47 2006 +0000 Removed broken link for D. yakuba commit e768694eadf532415cb783d2add113f34c817a9c Author: donnak Date: Fri Sep 8 21:34:40 2006 +0000 Added new announcement from Kate, archived old news item. commit c44aba4e2e8a8aa44e26a820f1104446a73ff57b Author: ann Date: Fri Sep 8 21:24:50 2006 +0000 added minCheck to ce1 sangerPep for identifier=wormBaseId (per Hiram_ commit 633205ac5e4dce217b7c77eeab783a7e0073d139 Author: giardine Date: Fri Sep 8 20:00:54 2006 +0000 Moved up one level, now have data in hg17 and hg18. Locus Variants track commit 9d6d5286d0176bef45f68f37c79771efa5b2b933 Author: hiram Date: Fri Sep 8 19:17:47 2006 +0000 Cleaned up to warnings and strict safe. Produces what it did before with no errors or warnings. commit 416ed605f40eba5db97b54ee4f3b06adf11ef176 Author: ann Date: Fri Sep 8 19:15:18 2006 +0000 added separate rule for ce1 for identifier=wormBaseId (with minCheck) commit fcf647469cbd829c96f63a36cd2b04f6ddb0f7bf Author: hiram Date: Fri Sep 8 19:05:53 2006 +0000 Original source rescued from /cluster/bin/scripts/ commit c35a1af2e4d813185357d72630e224693b8b2375 Author: hiram Date: Fri Sep 8 19:02:05 2006 +0000 Now working clean with no errors or warnings. Error messages going to STDERR commit 838469c660429c91da70d5e21701e054d18b6f6b Author: kuhn Date: Fri Sep 8 17:30:46 2006 +0000 changed the name 'length legend' to 'legth ruler' for clarity in UI commit de2ddc1d10357f37dbe93d54190fa9e90164af45 Author: donnak Date: Fri Sep 8 16:51:46 2006 +0000 Changed date on rheMac1 archive announcement. commit b1705cc04a223d8d456855833e59f7f1751b484e Author: ann Date: Fri Sep 8 15:18:58 2006 +0000 excluded drBlastTab from identifier=sgdCodingId rule (Jim says OK) commit e8d819699acc3ebd079ef7a8ae4fe94b48b6616b Author: angie Date: Fri Sep 8 15:04:24 2006 +0000 Resolved -Wall warning: unused variable. commit da3f44d5376972ade564acc453d2b663b8b55a82 Author: galt Date: Fri Sep 8 15:00:34 2006 +0000 "Encode release log update" commit 186afe4e9912f346defd38de30f9834a11ba8ce1 Author: galt Date: Fri Sep 8 15:00:33 2006 +0000 "Release log update" commit 083238ad3d5609b469b53774c1e5be7c07aca0b5 Author: markd Date: Fri Sep 8 00:33:36 2006 +0000 reload of genbank commit 6ea5ec0a08ed109d03462bd19060af24a6a67dd8 Author: ann Date: Thu Sep 7 23:45:19 2006 +0000 removed dependencies for hg17 pb and pep tables on kgProtMap (per Fan) commit 8d9fc4403925e730d74ac18ff10c9a4301595d0b Author: ann Date: Thu Sep 7 21:55:53 2006 +0000 fr1 no longer has a blastHg16KG table -- removed from rule commit bac49adfd12436a2070bc344036a4505497d6196 Author: kayla Date: Thu Sep 7 19:12:44 2006 +0000 changed visibility from full to hide for the miRNA track commit c99778922340b33e79cd9034b1806e76cc6dd3f0 Author: hiram Date: Thu Sep 7 18:56:52 2006 +0000 Original script contents from mm8 first time STS markers build commit 1ab1617a0b1153741125fa074c64106b69e5e507 Author: hiram Date: Thu Sep 7 18:47:00 2006 +0000 This produces the same result as before and is now error and warning clean commit 3e075e9a340a019e9767e4fb1ef58a600fd4b8f6 Author: angie Date: Thu Sep 7 17:14:57 2006 +0000 Resolved -Wall warning: unused variable; 'operation may be undefined' from unnecessary assignment statement. commit 991a7ff2ef46ebbeebca8975bfc78e5e4e7de386 Author: galt Date: Thu Sep 7 15:00:38 2006 +0000 "Encode release log update" commit 201e078bfbea193eb4938e7df1042d2966c202ea Author: galt Date: Thu Sep 7 15:00:37 2006 +0000 "Release log update" commit f8530eff6c579344f651bf0e61414491ffc9babc Author: markd Date: Thu Sep 7 07:52:56 2006 +0000 made font on multiple alignment message bigger commit 492533a260f5fbb96f3eb97150b2c1ae892ee7ba Author: heather Date: Thu Sep 7 00:53:32 2006 +0000 add a line for snp mask commit 2369dd6c14f7a336e096dd55ddcd11e3df2d29ac Author: heather Date: Thu Sep 7 00:17:18 2006 +0000 tweaks for snp mask commit b1a585d184168928b8552d119e851bac461351a7 Author: heather Date: Thu Sep 7 00:11:40 2006 +0000 use gzip for snp masked sequence commit 0db30ee1e56c2fb0faa68468b1f8c5f143770afd Author: heather Date: Thu Sep 7 00:03:40 2006 +0000 generate snp-masked sequence for insertions and deletions commit f6cd29473238bce9157f0acfe4a0c0740fddb8c1 Author: galt Date: Wed Sep 6 23:03:02 2006 +0000 use cvs export instead of checkout to remove unneeded CVS dirs in zip commit 26711fe2b86bab1546c73ac3fe501a286b35968d Author: heather Date: Wed Sep 6 22:22:34 2006 +0000 use stripChar; remove input filtering; add asserts commit 341ee64adfd2121aec48f96a94c7a5f25c30362e Author: heather Date: Wed Sep 6 21:49:02 2006 +0000 tweaks commit 5101d5e2c4988ce0965963690520dccf7600ecbe Author: galt Date: Wed Sep 6 20:57:24 2006 +0000 removing old zoo stuff from release log commit dd197a598e2dc4bb0ed5b35381532e810b41039b Author: heather Date: Wed Sep 6 20:08:21 2006 +0000 generate filtered deletions commit 4857b926cd46dd674aaf57f0eb1e6b9166b73cd1 Author: heather Date: Wed Sep 6 20:03:08 2006 +0000 add snpGetDeletions commit 85de9708f968ca37dbed9489b4af7f00b38edaf0 Author: heather Date: Wed Sep 6 19:14:35 2006 +0000 fix comment commit 915da8f81a723130b520f4c9a96d1c9b6c73483a Author: ann Date: Wed Sep 6 18:56:09 2006 +0000 added minCheck to sacCer1 rules for identifier=sgdCodingId commit 658f1eeefa0593d020e3ccafef527fc2cf67cb46 Author: ann Date: Wed Sep 6 17:39:51 2006 +0000 added droYak2 to do not check list for mrnaOrientInfo.name for refSeqId commit 405e00402fe9f9f00704292889959688a22efcb5 Author: galt Date: Wed Sep 6 15:00:37 2006 +0000 "Encode release log update" commit c0c8a07617b03e20ae4f6cb65822a61de412953b Author: galt Date: Wed Sep 6 15:00:36 2006 +0000 "Release log update" commit 6b8819642f7fa14a73f01c3eb882933670664c41 Author: heather Date: Tue Sep 5 23:37:25 2006 +0000 add filter on weight commit 89791d23e6d5bdf59d6a031105ada796732d4a90 Author: heather Date: Tue Sep 5 20:44:29 2006 +0000 seems to work well for substitutions and deletions commit 1f357f6be414fdd62527a37c2de9017738eb0afd Author: heather Date: Tue Sep 5 20:44:02 2006 +0000 add snpCheckCluster2 commit 25f573e478d3a973c972be8e41813ef5edb369bd Author: galt Date: Tue Sep 5 15:00:24 2006 +0000 "Encode release log update" commit 0a1662df5f6775d4301f15d4d49abddf011bedd6 Author: galt Date: Tue Sep 5 15:00:23 2006 +0000 "Release log update" commit 9edea13fefdf0fa050987411d2411aee52e7df75 Author: baertsch Date: Tue Sep 5 12:31:15 2006 +0000 pass thru alignments that hit only once without passthru option, fix parens bug commit 9152bcada4e60559a99c45b45065e1da673953f7 Author: galt Date: Mon Sep 4 15:00:22 2006 +0000 "Encode release log update" commit 3785ba8d617edbb2eed1613899c002b639b2a5ef Author: galt Date: Mon Sep 4 15:00:20 2006 +0000 "Release log update" commit 50c4dd1c0ba9ad1d273d179e8db0c390bd844b8a Author: baertsch Date: Mon Sep 4 09:28:15 2006 +0000 fix big that did not passthru alignments with no misMatches. commit b21b93ce46ce217cf7e8618708435d58aa97639a Author: galt Date: Sun Sep 3 15:00:21 2006 +0000 "Encode release log update" commit c095017856b760d102befeaf4953ce12b6a1f38b Author: galt Date: Sun Sep 3 15:00:20 2006 +0000 "Release log update" commit 3dc4eca3343bc79a6c3fa942435244244ef592b4 Author: galt Date: Sat Sep 2 15:00:26 2006 +0000 "Encode release log update" commit 604f96777e154a309f54f0582bfedae9b326ca36 Author: galt Date: Sat Sep 2 15:00:25 2006 +0000 "Release log update" commit dc59c9a9c043fb7e850213b20ea442e94f0ba3e7 Author: markd Date: Sat Sep 2 00:02:46 2006 +0000 fill in variables on MGC Description and Methods link so that the hgc doesnt generate an error if the variables are not in the cart commit 75ee5a50a9966cab6283fb665edb325249a7f2b3 Author: kate Date: Fri Sep 1 23:44:04 2006 +0000 Correct names of other tracks referenced commit eb13bf4395bca06e8c3717b5fc29edf06ffe84bd Author: kate Date: Fri Sep 1 23:34:26 2006 +0000 Doc for consensus elements track commit 0c6bf9931b2d0ac59ec97acb4ad124d15ca70576 Author: heather Date: Fri Sep 1 23:20:16 2006 +0000 filter out multiple alignments and mixed observed commit c833f80d0a39341cc473a0df9bb553356dea62e7 Author: heather Date: Fri Sep 1 23:19:56 2006 +0000 add snpGetInsertions commit 68f1292048a217f3b7ebb3778320e6c9881b5c6c Author: heather Date: Fri Sep 1 22:45:16 2006 +0000 remove filtering; use twoBitReadSeqFrag commit 118a8200b3a49b3d67b38cca8eace75d6dbf4428 Author: kate Date: Fri Sep 1 21:07:09 2006 +0000 More DnaseI data commit e661a02306caab41cdaa0abdd68eaaa97d3b0a96 Author: heather Date: Fri Sep 1 20:54:01 2006 +0000 remove unused variable commit b47efb9c1141feb9b384dd074b932893f4d27c73 Author: kate Date: Fri Sep 1 18:33:13 2006 +0000 Sort input so user needn't commit e4a5879e6c52f41dc862aeb1247c0760e8591d46 Author: heather Date: Fri Sep 1 18:16:21 2006 +0000 snp126 edit: detect clustering errors for insertions commit e73badf0bfe31e8befae970a8bd7f6090af579ae Author: ann Date: Fri Sep 1 16:22:55 2006 +0000 relaxed hg17.bioCycPathway rule (Fan agreed) commit 00f46c1b96ce8e3600add380b46878b6f364d4c9 Author: galt Date: Fri Sep 1 15:00:28 2006 +0000 "Encode release log update" commit 5d7800e8ed5f32c47a09529e4869be5ee2e9eed2 Author: galt Date: Fri Sep 1 15:00:27 2006 +0000 "Release log update" commit 82d5aa376cb44a04a7dc56b3d70d55d936aaf295 Author: heather Date: Fri Sep 1 09:20:47 2006 +0000 cleanup commit de6bf22383c4ef4b67816476a74adbb845ed62b0 Author: heather Date: Fri Sep 1 09:09:56 2006 +0000 use exception output format commit b7942ed5e773d55d911a09b205105c6bd2b80c97 Author: heather Date: Fri Sep 1 08:34:18 2006 +0000 reverse complement; separate output into 2 files commit a06c6b46b44350b329c0cdf92b2209c4290c7e6a Author: heather Date: Fri Sep 1 07:32:23 2006 +0000 remove unused include commit 4867c468f59e7fac92568048266d5465fdea2cb2 Author: aamp Date: Fri Sep 1 00:37:18 2006 +0000 polyaDB->polyaDb. commit 05dc5eff591492bc5a6d308a2ca23834bf2e7721 Author: aamp Date: Fri Sep 1 00:36:28 2006 +0000 Renamed polyaDB to polyaDb. commit 042426b77dd5973dcf715ad6940ea9087ffc485e Author: heather Date: Thu Aug 31 23:27:22 2006 +0000 fix bugs, add total error count commit 641933f5d67ec7498bdf94d018ae91e554ed74db Author: heather Date: Thu Aug 31 23:10:59 2006 +0000 initially just for insertions commit 3497bff1ea73fc2974ae6e76d74a053e005ce3a0 Author: heather Date: Thu Aug 31 23:10:43 2006 +0000 add snpCheckCluster commit f45039919509c7d3d3ec17eb081baaee658172d1 Author: kate Date: Thu Aug 31 22:49:47 2006 +0000 UNC FAIRE released commit 5304a1ffbf1efde0b63084a78b06bf30b693fd7d Author: hiram Date: Thu Aug 31 22:21:32 2006 +0000 Original source from /cluster/bin/scripts commit 52d5fdb13b9af20116d688930c5ac48f364d46f1 Author: hiram Date: Thu Aug 31 22:16:47 2006 +0000 This produces the same output as the original script and without any errors or complaints. commit 5e893b6a4a5e3f882aa8679c981015a416309549 Author: markd Date: Thu Aug 31 18:40:14 2006 +0000 fixed N-SCAN search regexp to match new naming convetion commit 6e531ed7b6411d08c4c5758aaabf475991068053 Author: hartera Date: Thu Aug 31 18:37:09 2006 +0000 Only close file if it was successfully opened. commit 481d1b53aaf0ad2f3e62a623634ecdf8dc5a3156 Author: ann Date: Thu Aug 31 18:25:39 2006 +0000 relaxed hgFixed rules for affyMOE430 identifier commit 4d4cb4bc64a1450d60f742bb674d266c9c0ca600 Author: ann Date: Thu Aug 31 18:06:21 2006 +0000 added minCheck to mm6 mouseLandscapeDistance rule for knownGeneId identifier (Andy P says it is OK) commit 0dded1449da583744e5705cf2d86c88bd9117da1 Author: ann Date: Thu Aug 31 17:00:47 2006 +0000 added mm5 and mm6 to ignore list for flyBaseGeneId (the other mice are already there) commit a940ae53325ae38b3fab40fe8a7e11d671094f89 Author: ann Date: Thu Aug 31 16:59:31 2006 +0000 added mm5 to refSeqId identifier ignore rule commit 22f8730837fde915f69dcac52c994f14b51739d8 Author: ann Date: Thu Aug 31 16:32:34 2006 +0000 added usage limit statement commit 8d7785eb019e783a5969016bbf42241f0cc83e48 Author: galt Date: Thu Aug 31 15:00:28 2006 +0000 "Encode release log update" commit 95cc7261d016283fb3d887bb649d99b94fd74711 Author: galt Date: Thu Aug 31 15:00:27 2006 +0000 "Release log update" commit fd68833ab5e90abbae0b49146a03289a09a35d83 Author: heather Date: Thu Aug 31 04:18:06 2006 +0000 template without file output commit ee6c54d29f62c4d8609886abe8bf34575abc52c4 Author: heather Date: Thu Aug 31 04:17:39 2006 +0000 add seqWithInsertions and seqWithoutDeletions commit d7b1b1b142161795384f92bda4690e6eb6bc2f3b Author: heather Date: Thu Aug 31 03:19:12 2006 +0000 make chrom an argument commit eb51ac786a0046297732a2588330f8b397b472ac Author: markd Date: Thu Aug 31 00:54:01 2006 +0000 added danRer4 N-SCAN predictions commit ee9e2ca130a1622540d3d752288281fc70282969 Author: markd Date: Thu Aug 31 00:43:26 2006 +0000 forgot to add date completed commit 818d8171c21de4d23b26e966cee30a40877c2b6b Author: heather Date: Thu Aug 31 00:42:59 2006 +0000 get coords right for full chrom lookup commit b95c99800bae3debd3f72c304f4a2e294c35a576 Author: markd Date: Thu Aug 31 00:39:07 2006 +0000 added mm8 NSCAN predictions commit 4c7d49643b374d91ad0fbc08ebd37fe958deb6fe Author: heather Date: Wed Aug 30 23:50:33 2006 +0000 write to file rather than dyString commit d2f86004d9eca403b1eb7da7e277e7f80bc6288f Author: rhead Date: Wed Aug 30 23:44:19 2006 +0000 Added link to MGC references page commit 5e9140a977228a8bf15a51a1071a9598e2afab17 Author: hiram Date: Wed Aug 30 23:36:33 2006 +0000 Initial source rescued from /cluster/bin/scripts/ commit 6ee2636b899ee91902ae7722a289c873f7f4b2fc Author: hiram Date: Wed Aug 30 23:24:27 2006 +0000 This makes the same result as the original script without any errors or warnings commit b7604e48fa81ae881636e41d1a9790c279d7494c Author: fanhsu Date: Wed Aug 30 22:29:01 2006 +0000 Removed thet testing file. commit 399237f39fab145d5c09fe1dd2d9561bf3a79ad0 Author: fanhsu Date: Wed Aug 30 22:23:48 2006 +0000 testing testing .... commit a9217e6211ec416106eb14175fae30c2352457a9 Author: hartera Date: Wed Aug 30 21:56:51 2006 +0000 Moved part of code so that chain link to Browser of other organism is only shown if active is 1 in dbDb for the otherDb. commit 92851cdba89a512ea1c5b3a4011f8826c72eb68b Author: fanhsu Date: Wed Aug 30 21:56:22 2006 +0000 *** empty log message *** commit 000b568517f9e810f470424e1c458e9938409640 Author: kate Date: Wed Aug 30 21:34:49 2006 +0000 Restore Remove custom track function commit d330038de839eb40c643319fd98b7eaf04e11ddd Author: kate Date: Wed Aug 30 21:11:30 2006 +0000 Restore linefeeds to doc files commit c7325bae7c5bcc7caa78f3e5bda92f0d3ef80d3c Author: heather Date: Wed Aug 30 21:10:32 2006 +0000 generate sequence files per chrom that include insertions commit 34c14d7187ce5caee9d675ac1128fa166341bae3 Author: kate Date: Wed Aug 30 21:02:43 2006 +0000 Remove button for hgCustom until it's released commit 3c04530638fbc92e869732902433f5ebff3cba9b Author: hiram Date: Wed Aug 30 20:59:53 2006 +0000 Original source from /cluster/bin/scripts/ commit 9d07f55c801a3414face85083031cf0b11df1cf9 Author: kate Date: Wed Aug 30 20:55:07 2006 +0000 Add new string function (by request of JK) commit c8d6b193aeebfa5a35ba75015b4559d7f641bf29 Author: kate Date: Wed Aug 30 20:48:36 2006 +0000 Fix problems with spaces in custom track names when attaching docs commit 1df34303b78711b2d43e0c4e0e7ca0c8b6b6ea2c Author: ann Date: Wed Aug 30 20:36:31 2006 +0000 added minChecks to hgMut rules. Belinda has said that the percent passing are acceptable. commit ea7db1374dee11ee6adcfcf6d8866e7c16b5d8e1 Author: ann Date: Wed Aug 30 19:44:09 2006 +0000 added new rule for knownGeneId (hg15, hg16, hg17) to allow for minCheck. Added new identifier for hg18 and mm8 for knownAlignId to allow for null values commit bb54889e31f39b9d4913bb4fccac3bbed9f3e296 Author: ann Date: Wed Aug 30 18:18:53 2006 +0000 typo commit 9ecd6d0cf5216b25d52763e55376b9c69f8f4269 Author: rhead Date: Wed Aug 30 17:52:50 2006 +0000 changed wording commit 1c8807816b4e43e961771bd819322e1929892ad4 Author: ann Date: Wed Aug 30 17:27:18 2006 +0000 relaxed check for hg17 and mm5 for identifier=refSeqId commit 9be976b3917bea566ff0811db85d77e104119ce1 Author: galt Date: Wed Aug 30 15:00:27 2006 +0000 "Encode release log update" commit e0fb061734f657f9a4989291333a7393b33ec519 Author: galt Date: Wed Aug 30 15:00:25 2006 +0000 "Release log update" commit ba71a1137b0f853f0b51095aa7f81ee1043300ff Author: markd Date: Wed Aug 30 05:06:41 2006 +0000 removed unneeded indel on gbStatus commit 54c4611662726303ecfb1da7cf7fda7408f8ace5 Author: kate Date: Wed Aug 30 02:02:39 2006 +0000 Fix pattern matching so that doc loading works with hyphenated track names commit 6318e3aff06408a86d3366680e2afead6be1b04e Author: kate Date: Wed Aug 30 01:49:23 2006 +0000 Improve error handling when browser linesare incorrect commit 466a4a6130ba1b625c68be89bc77693298cae829 Author: kate Date: Wed Aug 30 00:44:53 2006 +0000 Add mouseover in Pos column that displays full position commit eb5e13db9b7978f56cc48339919ba604c5f1b128 Author: hartera Date: Wed Aug 30 00:10:39 2006 +0000 Removed comma from listing of clone IDs for zebrafish Vega genes. commit 69f9c8d915fc697515011fd160f1088cf44770aa Author: heather Date: Wed Aug 30 00:05:58 2006 +0000 translate SNP array data from hg17 commit 70a8c32a6d5f2c0074bf6dbe72dc15ec0368163f Author: hiram Date: Wed Aug 30 00:04:06 2006 +0000 Need to re-work distance when it is given as a list or KB etc... commit 13da313040bf759922a0a3ce0ebf127102111c3d Author: hiram Date: Wed Aug 30 00:03:38 2006 +0000 Second attempt at STS markers underway commit f0971189579d823dd7dc00d60ad3a13035c725c9 Author: ann Date: Tue Aug 29 23:20:58 2006 +0000 changed message about substituting your own track name commit a718b98f1b0ee16f2c7dee71b5752d534eee0729 Author: hiram Date: Tue Aug 29 23:09:03 2006 +0000 More fixups and more verbose business on steps proceeding commit dd7e4d78b504c05b8b7c00cebd1d3659d9cf6b59 Author: kate Date: Tue Aug 29 22:33:32 2006 +0000 Increase mem allocation for error msg commit 8aa944331a4646479d960e3d19def0537559a14a Author: kuhn Date: Tue Aug 29 21:54:36 2006 +0000 fixed tag commit a501bb7ab096d05aaed1873ff9da3df04a7aa3b7 Author: heather Date: Tue Aug 29 21:28:45 2006 +0000 tweak for SNPs commit 69decd791f54394fd2482368350751da43a40106 Author: hartera Date: Tue Aug 29 20:12:36 2006 +0000 In genericChainClick and genericNetClick, check for database existence before printing alignment but not by checking dbDb. commit 76263a19b2925c58f894e1e30b8eff479d260953 Author: markd Date: Tue Aug 29 19:40:17 2006 +0000 fix mapping of cow genome db name to mgc cgi organism abbrev commit ba58589163132338b0596b6f10f7b60d070af483 Author: hiram Date: Tue Aug 29 18:49:49 2006 +0000 Better error printouts on errors, and avoiding more undefined variables commit f225935e2e81f94f08f32f36c0e0468a4d35a12e Author: donnak Date: Tue Aug 29 18:35:49 2006 +0000 Clarified reference/query sequences, fixed typo. commit 0062a7499c04059cfa12cc4b3cd8291d8b02807a Author: hartera Date: Tue Aug 29 17:59:21 2006 +0000 Fixed typo. commit 7ba848a3861ab66c4377664811133ea43f0bf34d Author: markd Date: Tue Aug 29 17:39:43 2006 +0000 added -overlapSimilarityCeil and -overlapThresholdCeil options commit 3e7ff03c99bd754332f2d324b39ee53c4eab78ca Author: hartera Date: Tue Aug 29 17:39:39 2006 +0000 Changed code in genericNetClick and genericChainClick to check for the otherDb entry in dbDb and check for sequences before printing the link to the alignments. commit 587b4844b07860d37e9c2496d5f83ad73744f274 Author: kate Date: Tue Aug 29 16:31:02 2006 +0000 Roll back to rev 1.40, since the previous rev is prototype code for a new feature commit eab08981713703c258c676e8a39a983a698dfeaf Author: fanhsu Date: Tue Aug 29 16:28:31 2006 +0000 Added two rules for Reactome spID. commit 9933c1f5239b5b0f04c4e63be77d6e6cec790f68 Author: galt Date: Tue Aug 29 15:00:22 2006 +0000 "Encode release log update" commit 5a929f5281f278ea6f008f11fab7122fd60aad77 Author: galt Date: Tue Aug 29 15:00:21 2006 +0000 "Release log update" commit 0d260ba125c0c2b9e7f53563ec76e05c21bda556 Author: fanhsu Date: Tue Aug 29 13:22:36 2006 +0000 Added miRNA (bed 6). commit 4b5969683d016c8fa6105437ba6a4bb78a1fb133 Author: markd Date: Tue Aug 29 06:24:38 2006 +0000 don't add bin column if creating files commit dee53d7de1efd0a64441ed8b86575a0094f5d5cd Author: galt Date: Tue Aug 29 02:26:55 2006 +0000 "New version number v141" commit e9e2f20865b3943fa0051d8aefedfe06fd7ea8ba Author: mario Date: Tue Aug 29 01:34:24 2006 +0000 added augustusAbinitio commit 901e399c026d9e70d3389abb4048dc47855a118d Author: mario Date: Tue Aug 29 01:29:25 2006 +0000 Inserted description for AUGUSTUS tracks: augustusAbinitio and augustusHints commit 9d2d06bc8590cae44ae6df1ec4c422e1c82353e7 Author: hartera Date: Tue Aug 29 01:24:45 2006 +0000 Edited chromSeqFileExists function and added code to close and opened file. commit ec8e0a181e578eb90c36b8b38d88f6a47a8578be Author: mario Date: Tue Aug 29 01:22:55 2006 +0000 created html description for AUGUSTUS on hg18 commit 54d22ce5b88265e00c5b1fb0ed486cac6d0b4d16 Author: hartera Date: Tue Aug 29 01:13:26 2006 +0000 Added comments. Added to genericNetClick to only display the link to chain alignments if either the other database is active in dbDb or the chromInfo table and sequence file exists. commit 70b3c2ffe0d61f58d91603992cfabe07616770b8 Author: hartera Date: Tue Aug 29 01:08:06 2006 +0000 Added chromSeqFileExists function to check for a chromInfo table and then check that a sequence file exists for a chromsome. Added to genericChainClick to only display the link to chain alignments if either the other database is active in dbDb or the chromInfo table and sequence file exists. commit 5564a3785ee8ba9091ce360e96b3f8f7a9f6a3a0 Author: kate Date: Tue Aug 29 00:43:28 2006 +0000 Back out table of contents for now -- it doesn't play well in the SSI context commit 2e1ac4efc317fe3b3c7bbf9e39235aef8a827540 Author: kate Date: Tue Aug 29 00:33:47 2006 +0000 Add table of contents commit a554bd88f5ec19b52843e35eb67a1e1c48d9c6b8 Author: aamp Date: Tue Aug 29 00:22:30 2006 +0000 A couple more changes to the PolyA DB track. commit fadd83837e823c3f55c1ef9ecbf6512f0a0d343d Author: markd Date: Tue Aug 29 00:05:30 2006 +0000 added options for getting candidate CCDSs commit ff88bc64efbb282445616e7e3d1703663499fa1b Author: aamp Date: Tue Aug 29 00:05:26 2006 +0000 Added polyA DB track. commit 3e7f9c2430180fe7382ed5b1639c2fb5b2a54402 Author: kate Date: Tue Aug 29 00:04:45 2006 +0000 Remove hgCustom buttons until approved for release commit 72fb75d9975a8732f25abdd85caaeceac57e3df5 Author: hartera Date: Tue Aug 29 00:02:00 2006 +0000 Added to a Vega Gene rule and also added zebrafish specific Vega Genes idnetifiers and rules. commit a3419c3107f25461cf668bef18583b3a869dbaea Author: kate Date: Mon Aug 28 23:58:17 2006 +0000 1. Remove help panel (moving this to static pages). 2. Fix compile err commit 62a56cc5a3ebc2ef333135a1001cd6132bcd85c0 Author: ann Date: Mon Aug 28 23:51:24 2006 +0000 relaxed minCheck for locusLinkId rule for hg16 and mm5 commit 3fa7605ebd6f276834f60c16ea47b3cb4b8303b7 Author: ann Date: Mon Aug 28 23:28:03 2006 +0000 added rule for hg15.cgapBiocDesc (dupeOk), and added exclusion for hg16 knownToRefSeq.value rule (needed smaller minCheck) commit 65e7a47b1dbf4523c04c676f65167e4c2a3f2763 Author: ann Date: Mon Aug 28 23:26:03 2006 +0000 added hg15 to hg16 rule for stsInfo2 (dupeOk) commit 97d48e4efb45d0fd3816d9dd3c0d1dd0ccf21421 Author: kate Date: Mon Aug 28 22:11:39 2006 +0000 Add feature requested by B0b: when navigating from trackUi to hgCustom, populate the HTML entry box with HTML from the trackUi commit edbaeabc1521c5528d7ae530ee0e0a475ec1efa6 Author: kuhn Date: Mon Aug 28 21:53:44 2006 +0000 tweak commit 9276f9ab98ed9bb199b465ebe62fec5757b46377 Author: hiram Date: Mon Aug 28 17:36:05 2006 +0000 This is now working with mm4, to be tested with others commit eab8686009e1a67d34908462807f991862d62085 Author: heather Date: Mon Aug 28 17:27:42 2006 +0000 add a line about weight = 1 commit 4d15be8dbeac5d20d5d5d340e3f7edd4dc505c26 Author: galt Date: Mon Aug 28 15:00:43 2006 +0000 "Encode release log update" commit dfcf1899b6e54ea532a2572f16a2dc5e7d0a8241 Author: galt Date: Mon Aug 28 15:00:41 2006 +0000 "Release log update" commit 9e03f8f16ac67b524cca1a1985787ffec58f0ee4 Author: galt Date: Sat Aug 26 15:00:24 2006 +0000 "Encode release log update" commit 532764635a02bfede6280fed76abda2c4beae0f2 Author: galt Date: Sat Aug 26 15:00:23 2006 +0000 "Release log update" commit 70b0979971e12922934c07f9d30bdf459928cfd3 Author: hartera Date: Sat Aug 26 01:46:59 2006 +0000 BAC end pairs, bad pairs and singles and all_bacends tables finished. Added Vega genes track with subtracks for pseudogenes and all other genes. commit f31ab8365f0aebc21ec2053575698c22867901f7 Author: hartera Date: Sat Aug 26 01:42:00 2006 +0000 Added vegaGene track and searches for the zebrafish Vega Genes. commit a7d7dc500ab648c01d7c8d6b4fca14ea3d1eb824 Author: angie Date: Fri Aug 25 23:16:18 2006 +0000 Added check for NULL value to display of sample rows on describe schema page. commit 8cfa446222702b004995cf9d9874d67b2731afba Author: hartera Date: Fri Aug 25 22:50:13 2006 +0000 Changed field in table. commit 4662e673b7084b267aeab4da942697a2fd3aa63b Author: fanhsu Date: Fri Aug 25 22:49:58 2006 +0000 Corrected a typo. commit 79a52964c4b2571d25a8b5446964ddb4ce88ecea Author: heather Date: Fri Aug 25 21:30:45 2006 +0000 make tableName an option, hopefully speed up database select commit dfbd1b5b829a33941f2404ef07a000a2a3256044 Author: hartera Date: Fri Aug 25 20:10:19 2006 +0000 Added code to doVegaGeneZfish to handle additional information now split between two tables. commit 8a2f96d1709645b2511c81dcf141288a658b527f Author: ann Date: Fri Aug 25 19:17:48 2006 +0000 removed monDom2 (assembly does not exist) from list of assemblies and from identifier blastHg17KGPep02Id commit f413e48d91c6043467389b1f1a1714bfa0a912d1 Author: hartera Date: Fri Aug 25 18:51:09 2006 +0000 Removed clone_id field from vegaInfoZfish and added it to a different table. commit 0e126421cc7341f64cbb3f20abcf50672c044613 Author: hartera Date: Fri Aug 25 17:17:21 2006 +0000 Description for Zv6 assembly BAC end singles. commit ea25361fe4ffae6a366fa6815478d202515766d1 Author: hartera Date: Fri Aug 25 17:17:02 2006 +0000 Description for Zv6 assembly BAC end pairs. commit 08cf9e2151f1f90972ae554d602e8f01d6c7aed6 Author: hartera Date: Fri Aug 25 17:06:48 2006 +0000 Updated BAC end pairs description to reflect new selection criteria. commit 31f7ad08b3acaf03bd0495c7c262a753b60e1039 Author: markd Date: Fri Aug 25 17:05:26 2006 +0000 fixed bug with expanding number of rows when reading a bed commit b72690ad1a0c40a8bef706361ad3f1cf417aa48b Author: fanhsu Date: Fri Aug 25 16:14:25 2006 +0000 Added strand info. commit 64ac3cda8728684bcfda772e4c2fea2270d2bf01 Author: angie Date: Fri Aug 25 15:47:50 2006 +0000 Resolved -Wall warning: unused variable; cast to int for char used as array subscript; 'operation on exonPos may be undefined' (exonPos = exonPos++). commit cd96bd6bc5b66f8b4de84342299d2c3d30eae8bc Author: angie Date: Fri Aug 25 15:45:16 2006 +0000 Resolved -Wall warning: cast to int for char used as array subscript. commit 80b991e57e17d0f5df53a57561d64167e4f13219 Author: angie Date: Fri Aug 25 15:42:23 2006 +0000 Use checkAgpToFa's new support for twoBit and -exclude (seqListCmd on scaffold-based assembly is a bad idea). Added support for a single .qac file for quality score input. commit 66575cdc5657f94566f55435951cef930f980409 Author: galt Date: Fri Aug 25 15:00:26 2006 +0000 "Encode release log update" commit 3162cc9f67d06c212ce8fcc8b4baf2b4585de79f Author: galt Date: Fri Aug 25 15:00:25 2006 +0000 "Release log update" commit 8eda05addaa8add46c7ce35ad73e2f32456363ba Author: kayla Date: Thu Aug 24 23:57:36 2006 +0000 Removed 2 spaces from the snp125 block commit f76c947656b98c5fb665c2a07718827ed7b90a42 Author: mario Date: Thu Aug 24 23:56:43 2006 +0000 Renamed augustus.html to augustusAbinitio.html commit 2421b7a9ac18ea344f0af09da8bed33fc6abf656 Author: mario Date: Thu Aug 24 23:52:17 2006 +0000 Added description of ab initio AUGUSTUS track for rheMac2. commit 2ea013abab7a93f107cb62539bd4364c5be4464b Author: kate Date: Thu Aug 24 23:46:47 2006 +0000 Additional data from crawford lab commit 3f76a99b9186f21f702779a5719dcf1a5d7094ba Author: kate Date: Thu Aug 24 23:45:30 2006 +0000 Track description for new Crawford lab data commit 4240196421c8b828ef33eb5fcd043c109be95fec Author: mario Date: Thu Aug 24 22:59:33 2006 +0000 Created Track description of augustusHints for rheMac2. commit d87c952744579fd6c2fe9c2370c5cc7860b02acb Author: heather Date: Thu Aug 24 22:54:23 2006 +0000 small edit for SNPs commit 01402e22ce3e178434b936d4f8d03c1db592f707 Author: heather Date: Thu Aug 24 22:50:23 2006 +0000 handle 3 digits commit a72f904578b7aea5a7bcb0b585f55112e5ca3f50 Author: fanhsu Date: Thu Aug 24 22:16:03 2006 +0000 Added rmLf step for Reactome input data files. commit 7eaece8dd2a49729007dc0f2207c883145f1ba1a Author: kate Date: Thu Aug 24 22:12:13 2006 +0000 Reuse .html files in trash dir commit fd20ec3869749e404767606f132a48ff619ab8c2 Author: heather Date: Thu Aug 24 21:54:05 2006 +0000 bug fix commit 697d794c722b1a787397826a5f302d261a998529 Author: kuhn Date: Thu Aug 24 21:12:54 2006 +0000 made a word lower case to match convention for buttons commit 37270356ee535c0b0797cde6d57d60425dbb0b0b Author: donnak Date: Thu Aug 24 21:04:33 2006 +0000 Fixed an incorrect link. commit b162e85259e82c8222c18d27deb98a47c016bf54 Author: kate Date: Thu Aug 24 20:56:31 2006 +0000 Remove documentation from text box after it's added to track commit 13908d5e6b998b1dcf46a2a69e089c1482bf5ea4 Author: heather Date: Thu Aug 24 20:49:23 2006 +0000 tweaks commit 4f9b105204f9fd323e62c3270ecdd5d8a080fa26 Author: heather Date: Thu Aug 24 20:05:28 2006 +0000 tweaks commit 47ccc8f860dfb55894d63e05df7ef270800c92a7 Author: kate Date: Thu Aug 24 18:53:51 2006 +0000 Retain metadata about custom tracks for hgCustom when tracks are loaded in database commit c39f72d42ab08767ca023b1253e5a252ad5a0415 Author: hartera Date: Thu Aug 24 18:04:38 2006 +0000 Added explanation of gaps at ends of scaffolds. commit 8d68eda998fa66eca2089e6a58a55d31c52bf9e4 Author: angie Date: Thu Aug 24 16:21:11 2006 +0000 Resolved -Wall warning: cast to int for char used as array subscript. commit 6bb10198ac1b48a2e041d301c2ab069513f828a9 Author: galt Date: Thu Aug 24 15:00:27 2006 +0000 "Encode release log update" commit e76d5c4fec94c12e0026aeda9eb2798337e52755 Author: galt Date: Thu Aug 24 15:00:26 2006 +0000 "Release log update" commit da7d63c5ac9b8c4131ca92b47e6780c8343148ff Author: heather Date: Thu Aug 24 06:42:33 2006 +0000 combine base SNP data with ortho table commit d9c148363394ff98e7cbfd8e4a3d78e9ee71cfff Author: heather Date: Thu Aug 24 06:42:12 2006 +0000 add snpOrthoLookup commit 1afa9a4c9e54067ad7d994962f24e8f2b63c76de Author: markd Date: Thu Aug 24 05:41:02 2006 +0000 make bcgsc clone tracks separate commit 492af3ccf9f1c0f7f64f461019fbc32107e08d78 Author: heather Date: Thu Aug 24 01:33:00 2006 +0000 add createTable() and loadDatabase() commit 045ed418b37cc8d8a7c0f6c66f4258008fd16668 Author: kayla Date: Thu Aug 24 00:55:14 2006 +0000 Added a line to the snp125 block so that chroms with no data wont have track controls. commit fee58d664b3545cef6e7e3770f705783d3b63ab3 Author: kayla Date: Thu Aug 24 00:23:20 2006 +0000 Removed spaces between the chromosomes in the snp125 block commit ae3c70f2f7daa118417052bc465b01d1ba7c12be Author: kate Date: Thu Aug 24 00:18:26 2006 +0000 Be more selective when determining if there's a file error commit 37250df9b70dbdd743c900daad31553d378fffea Author: kate Date: Thu Aug 24 00:13:16 2006 +0000 Fix scope commit f643d78ea97d7a20a1ec93295a872cd39f3cc621 Author: kate Date: Thu Aug 24 00:12:40 2006 +0000 User interface suggestions from B0b commit d1d748a74cf33d63ca9771dab5ebbf671a91fc43 Author: kent Date: Thu Aug 24 00:10:30 2006 +0000 Putting up error message rather than err 500. commit f05e2e300aba2b794c432924aa5587d696bb3d27 Author: markd Date: Wed Aug 23 23:53:11 2006 +0000 added warning message about not using cross organism commit 202a791c85fa4729dac359bc0b06255a90e0aff8 Author: markd Date: Wed Aug 23 23:44:39 2006 +0000 correct info about tables to push commit 996562bacd02cc4d825057e3898489d93674a9d5 Author: angie Date: Wed Aug 23 23:41:22 2006 +0000 Added a few basic test cases. commit b16de7a202a9f8f09393f40638732496dcb28ecb Author: angie Date: Wed Aug 23 23:41:04 2006 +0000 Added -exclude and support for .2bit, for automation work. commit 4a4f131901ef334693af85413c8462b9ef3ec969 Author: kate Date: Wed Aug 23 23:36:02 2006 +0000 Add button for hgCustom if custom track commit 76b7289e92a34c075c7f294c9e98fa6ddb3f3d23 Author: kuhn Date: Wed Aug 23 23:10:32 2006 +0000 added maxHeightPixels setting to tajima's D track. It was displaying way too big by default commit a0a7b025fee7f2249f748ba08a30b23b0a12ad88 Author: kate Date: Wed Aug 23 22:55:54 2006 +0000 Cleanup javascript commit d6305ed1b4f3a5cc66f8c19b0cf875c5681e8453 Author: kayla Date: Wed Aug 23 22:47:12 2006 +0000 Added a " so the NCBI link will work. commit 9a8670f8fdc6d12281381c80ac457bd753e05ea6 Author: kayla Date: Wed Aug 23 22:42:13 2006 +0000 Added a " so that the NCBI link will work commit bcbf8b326807d6dc6c5a41a2b3acd8911f0808ee Author: hartera Date: Wed Aug 23 22:01:35 2006 +0000 Changed printEnsemblCustomUrl function so that the outside link for Ensembl is constructed using the url in trackDb else it constructs a link to the current version of Ensembl. commit c9cbc7bda43999a8bcee3ac5cd811b9979cdb2e5 Author: genbank Date: Wed Aug 23 20:07:47 2006 +0000 added mgcGenes for bosTau2 commit 9244872ad5f3406ab928094c800996de05f6c5f8 Author: genbank Date: Wed Aug 23 20:07:06 2006 +0000 added bosTau2 to MGC_DBS commit 5216ee524409624de005c05156375610550cd52f Author: genbank Date: Wed Aug 23 19:45:32 2006 +0000 enabled bosTau2 mgc-specific tables commit ef41af245fc66c857dbfbbc2301cd2a0f9eae351 Author: markd Date: Wed Aug 23 18:32:48 2006 +0000 ccds bug fix commit 0f798de8ee422a6814614f425fe22af9913c83a5 Author: markd Date: Wed Aug 23 18:23:47 2006 +0000 Added sanity check for ccdsInfo having genes in for both hinxton and ncbi. Fixed bug that omitted some source genes from ccdsInfo when these entries are under review. commit cea3dcdc0d951563ffe7d8b009dbb1d6a7eaf4ab Author: ann Date: Wed Aug 23 18:18:48 2006 +0000 fixed logic error when looking for table names that aren't track names commit aa8fef2784ec8c443e2cc7683064bf3471ee399f Author: kuhn Date: Wed Aug 23 17:20:26 2006 +0000 made reference jump to new window on click commit f7b6db228db29fb44c1a36e92dd3578d225a8df6 Author: ann Date: Wed Aug 23 17:13:08 2006 +0000 added mgc to usage statement commit e03a500598ddb0dec39297707b16471793750b89 Author: kuhn Date: Wed Aug 23 17:11:12 2006 +0000 reworded slightly in two places commit 750b0aae78d4e26b7803caedc520c9f8f3f25c1c Author: kuhn Date: Wed Aug 23 16:53:27 2006 +0000 rephrased to clairfy - with help from daryl commit b86ef63d7342026fb678c5c2d4c40adf8c347874 Author: kuhn Date: Wed Aug 23 16:47:46 2006 +0000 trivial tweak for alpha order commit 9cce87de9e9090effbd5b5b8ee1d25fac495b43b Author: galt Date: Wed Aug 23 15:00:26 2006 +0000 "Encode release log update" commit 1da359f4e2371150fa5daef8e569a3fb735fea58 Author: galt Date: Wed Aug 23 15:00:25 2006 +0000 "Release log update" commit c54c2f22dda21ff63e67f3bd201d5b04b10587d7 Author: kate Date: Wed Aug 23 00:09:06 2006 +0000 Guard against missing terminal newline that upsets custom preprocessor commit d36fc39a344cefa207e6fa50d2c7dffc21c21ada Author: heather Date: Wed Aug 23 00:05:08 2006 +0000 first draft without human SNP data commit ce4478ce6691cb3bb6424fae808366a7b5da103d Author: heather Date: Wed Aug 23 00:04:45 2006 +0000 add snpOrthoStats commit 1bcd476396ed32d7eaa30db7d32a601ab23bfc3b Author: angie Date: Tue Aug 22 23:12:15 2006 +0000 Use verbose instead of printf for info messages so that output can go to stdout. commit 2dca7192e149cf611a71868c158ea9889afea444 Author: kate Date: Tue Aug 22 22:49:15 2006 +0000 Spruce up error reporting. Avoid parsing new tracks if we're doing a delete or update commit 70cb5ceb109fcb53390b80f0b18663bd9221c498 Author: kate Date: Tue Aug 22 22:22:34 2006 +0000 input type not overriden commit e410fdd468705d12157c4c1ede543eb44f2633dc Author: kate Date: Tue Aug 22 22:09:23 2006 +0000 Fix up file error reporting commit c6dc942e9479dbd376e0424e209e7cc2779c835c Author: hiram Date: Tue Aug 22 21:06:27 2006 +0000 No longer dbRIP_ but now dbRIP commit 50262aee8c08b10d0ba60b7d53cc5acbfd1a18c8 Author: hiram Date: Tue Aug 22 21:05:34 2006 +0000 No longer dbRIP_ just dbRIP commit 80e8e30b79f2930777e6ac01ea3508048f1d3540 Author: kuhn Date: Tue Aug 22 20:42:07 2006 +0000 added mgc commit 28e9a8e946254782c1bfd9631d75c8f49e6a696d Author: hartera Date: Tue Aug 22 20:21:43 2006 +0000 First draft of description for zebrafish Vega Genes. commit b994b51a231e2b7d3b611c8039afc1e562ce4b58 Author: hiram Date: Tue Aug 22 19:35:33 2006 +0000 No message about missing bed item names for bed 3 commit 3e0f4300ff27372f20906a3ef95b615214272d9f Author: kayla Date: Tue Aug 22 18:33:54 2006 +0000 Added a line which disables track controls from chrM and chrUn commit ad361fb7aa5dfc50e5100ba0703d706bd2398586 Author: kate Date: Tue Aug 22 17:19:26 2006 +0000 UI cosmetics: 1. Set button inserts header line. 2. Move submit button and error msgs to top of page 3. Avoid showing empty columns in management table commit 8704c1c0474bef1865738ed6f58e713ce02b6b07 Author: angie Date: Tue Aug 22 16:14:18 2006 +0000 Resolved -Wall warning: extra comma in multi-line format string passed to errAbort. commit 9d816c60df4643ccd46dfb969a17ccd96c29fef2 Author: kate Date: Tue Aug 22 16:13:38 2006 +0000 1. Clean up trash filenames (remove extra underscore. 2. Resuscitate auto-increment of default (unnamed) track names commit 5d1699e500f46e20ee044c2041dff496357f4e6b Author: kate Date: Tue Aug 22 16:12:11 2006 +0000 Expand initialPos setting so that first item is used if no browser position line commit 2c5c31a256f231eb33827d4d72bbde46c389ae76 Author: galt Date: Tue Aug 22 15:00:23 2006 +0000 "Encode release log update" commit 48fb1e3679219abe04aff9c2dc8ade3a5e34c0d9 Author: galt Date: Tue Aug 22 15:00:22 2006 +0000 "Release log update" commit 39fa2be5ff472a5cc2b099b6780a5b866a9b4c47 Author: hartera Date: Tue Aug 22 01:22:22 2006 +0000 Added doVegaGeneZfish function to handle click on zebrafish VEGA genes track. commit 7c86e9e56ab36cda7575ed2ac40d3c35d0210e43 Author: hartera Date: Tue Aug 22 01:15:10 2006 +0000 Update of ChIPOTle Peaks subtrack for UNC FAIRE. Updated track downloads. Changed the Peaks and Signal subtracks to bedGraph format. commit 3e99beb50fdaa841c54077aa0d3c80879fda23a8 Author: hartera Date: Tue Aug 22 01:02:53 2006 +0000 Creating VEGA genes track. BAC ends track in progress. commit 775c7cdf0ef7fbe1c17ba8bbaa7f6e690ae71325 Author: aamp Date: Tue Aug 22 00:35:27 2006 +0000 Adding new microarray config stuff. commit 70b0d12380fa0b2fc5ef39724bc089de55fed5f4 Author: angie Date: Tue Aug 22 00:35:17 2006 +0000 Added bacEndPairs, gc5Base, liftOver'd FlyBase Genes, several chain/net's; GenBank in progress with one alignment job taking a long, long time. commit 67e6ed3af3fcd447e047059432704e5c970bfba8 Author: galt Date: Tue Aug 22 00:33:43 2006 +0000 "Encode release log update" commit e8448119242e20dadf9c905c0f3e6e7c06e236f7 Author: galt Date: Tue Aug 22 00:33:42 2006 +0000 "Release log update" commit e6274e4401379b36cff72f6ccd2149b46dd724a6 Author: markd Date: Tue Aug 22 00:05:25 2006 +0000 support creating single exon genePreds for BEDs with 4 columns commit a15728caa7a0cb2719412b803beb19d6c840c515 Author: heather Date: Tue Aug 22 00:00:40 2006 +0000 don't skip random and hap here commit 781a1a8e1fcbb557bcbc946d844217cf1de2655a Author: heather Date: Mon Aug 21 22:44:42 2006 +0000 tweaks to output format commit 819dea9da3325ebc7ee9075819450254b9e7c034 Author: fanhsu Date: Mon Aug 21 22:09:08 2006 +0000 Created makefile. commit 831f18167a7dbc3dcbf183e3344f610fefc1a8ee Author: fanhsu Date: Mon Aug 21 22:07:41 2006 +0000 Crated section.ra. commit 4c9c1610847d250ee7245645535bcf956d0a7039 Author: fanhsu Date: Mon Aug 21 22:06:40 2006 +0000 Created sequences.c for the Sequence section of GSID project. commit 7ba20e11b14885522cdcfa2f7a20ea3f62f81e68 Author: fanhsu Date: Mon Aug 21 22:06:12 2006 +0000 Created clinical.c for the Clinical section of GSID project. commit 67499e385234bc5fdb3cba2761afe7408eb50a62 Author: fanhsu Date: Mon Aug 21 22:05:48 2006 +0000 Created vaccine.c for Vaccine section of GSID project. commit 4d84be4ad2097d211476e46c4d4efaa4d3745f92 Author: fanhsu Date: Mon Aug 21 22:05:16 2006 +0000 Created hgSubj.h. commit 1b6d9bdcea0a7f04ddcec4dc7bdba7c605a29132 Author: fanhsu Date: Mon Aug 21 22:04:56 2006 +0000 Created demog.c for Demographic section of hgSubj. commit 632d528c7623c6a85019f1860efa35687efa6a04 Author: fanhsu Date: Mon Aug 21 22:04:27 2006 +0000 Created hgSubj.c for Subject View of GSID project. commit 76c52b8c25b5da87e80894074ae075050dfecf8b Author: archanat Date: Mon Aug 21 21:54:05 2006 +0000 Added warning about genePred tables needing bin columns commit 55466cd4a6d525c179b77cb051ed0663883ebf1e Author: archanat Date: Mon Aug 21 21:29:25 2006 +0000 Added warning about genePred tables needing bin columns commit 44fdaf63d430bf3aa7d06d1d7a394947a4385b41 Author: archanat Date: Mon Aug 21 21:08:37 2006 +0000 Added warning about genePred tables needing bin columns commit d742c2e4fd20c254c94cd69f7055f5186dab6156 Author: galt Date: Mon Aug 21 20:51:13 2006 +0000 "Release log update" commit 581fa39127a5a1eef328eba044aea91f4b1f1de9 Author: archanat Date: Mon Aug 21 20:42:47 2006 +0000 Added warning about genePred tables needing bin columns commit cfbe4d04b893a51083d0aee8f691209e1095320e Author: archanat Date: Mon Aug 21 20:14:18 2006 +0000 Added warning about genePred tables needing bin columns commit 0deb0125158944e91c7e5d8a2ac99a3895a598ff Author: archanat Date: Mon Aug 21 18:43:25 2006 +0000 Added warning about genePred tables needing bin columns commit 89dced4d89e6b9c8d95f594c18dc8d82e34cc213 Author: hiram Date: Mon Aug 21 18:35:45 2006 +0000 Should remove items from settings hash even if they aren't being saved on the track line since they are defaults commit 02b12426e7f3d36b980fc2270c7423f437ee4a4c Author: archanat Date: Mon Aug 21 18:31:59 2006 +0000 Added warning about genePred tables needing bin columns commit 27fd95d0836432bdd7513f96d483331d71290bc0 Author: kate Date: Mon Aug 21 18:10:56 2006 +0000 protect color setting from parse destruction commit 6b4506da21bd1b616382e24edc6f68d5d1a6ff90 Author: archanat Date: Mon Aug 21 18:09:45 2006 +0000 Added warning about genePred tables needing bin columns commit 3932a07227b2c5cc492183c0c32b6e8a9d3a64c4 Author: archanat Date: Mon Aug 21 18:03:19 2006 +0000 Added warning about genePred tables needing bin columns commit f0089962428e00d029e1c34083022920b1d84c1d Author: kuhn Date: Mon Aug 21 17:43:13 2006 +0000 added warning about genePred tables needing bin columns commit 9edc0ebf36d07959effd6456b625f2abd12688d0 Author: angie Date: Mon Aug 21 15:45:23 2006 +0000 Resolved -Wall warning: unused variable. commit f35aa9770568f6f2c170b5217e9f668762359770 Author: galt Date: Mon Aug 21 15:00:17 2006 +0000 "Encode release log update" commit 1b2687571a4a06080437618515063d458df85fa2 Author: galt Date: Mon Aug 21 15:00:16 2006 +0000 "Release log update" commit 21b54f646b6dcace7a816048abef8e7afafb0f84 Author: hartera Date: Mon Aug 21 00:31:05 2006 +0000 Added vegaInfoZfish for additional information for zebrafish Vega Genes. commit 1ab39cebc61f44c8375afd3a98ba21d1a78b590c Author: kate Date: Sun Aug 20 17:50:51 2006 +0000 chromGraph type fields are set differently -- accomodate this commit e7f8f52719527baf38a609a7765ed7d05882e559 Author: kate Date: Sun Aug 20 16:59:31 2006 +0000 Restore error message when using old custom track page commit 8ca1dcdf27d861f9878529b59d6d99d060e7eac0 Author: kate Date: Sun Aug 20 16:33:35 2006 +0000 Add second custom tracks button for hgCustom. There are two buttons temporarily during review commit 18ea89b052bfc5edc96004589bd515bd58614017 Author: baertsch Date: Sun Aug 20 16:31:41 2006 +0000 struct psl *pslTrimToQueryRange(struct psl *oldPsl, int qMin, int qMax); /* Return psl trimmed to fit inside qMin/qMax. Note this does not * update the match/misMatch and related fields. */ commit 5f781903112c411829b0230be14ccaa5ca4fa70e Author: baertsch Date: Sun Aug 20 16:31:36 2006 +0000 > struct psl *pslTrimToQueryRange(struct psl *oldPsl, int qMin, int qMax); > /* Return psl trimmed to fit inside qMin/qMax. Note this does not > * update the match/misMatch and related fields. */ commit 0cdc92d75ef1d8cd6efb044e9ca616af9c11c300 Author: galt Date: Sun Aug 20 15:00:18 2006 +0000 "Encode release log update" commit 7e38609add9f14570e079eabfaa0a0c6e875056a Author: galt Date: Sun Aug 20 15:00:17 2006 +0000 "Release log update" commit 55844aa37e53a100adad018d8eb757338ad62de3 Author: markd Date: Sat Aug 19 17:25:51 2006 +0000 added ignore entry commit bc6c1ee04e954dbb386daa8b2a7bd26aa2d1a9f1 Author: galt Date: Sat Aug 19 15:00:22 2006 +0000 "Encode release log update" commit d713a7bdfc6cd850ce38ddb5ea7c417030f1841c Author: galt Date: Sat Aug 19 15:00:21 2006 +0000 "Release log update" commit ffd10f55eafdd88e304d17edd4e3fe18083aa66d Author: donnak Date: Sat Aug 19 05:15:39 2006 +0000 Added news announcement abt archiving indexNews.html. commit 823f90c4727082038fb5bafefdf05600eb32fb6d Author: kate Date: Sat Aug 19 04:52:55 2006 +0000 Add checkbox and buttons with mouseover commit 26ee4bc2fde20c24a7855b3eb572127bb46278c7 Author: kate Date: Sat Aug 19 02:55:14 2006 +0000 Revamped hgCustom and support in libs and other CGIs. Changes based on code review (Mark D.) and preliminary Q/A review (Archana). This version provides dual usage of hgCustom and previous custom track page, with two buttons on invoking CGIs, to allow comparison during review commit 755f5b9b14549901f7cf4266c48aaede310be1aa Author: hartera Date: Sat Aug 19 02:10:50 2006 +0000 Autosql file Vega Gene additional information specific for zebrafish. commit bcb21c1902d943eeec744e16905d306f47f26e1b Author: hartera Date: Sat Aug 19 02:10:18 2006 +0000 Vega Gene additional information specific for zebrafish. commit f975472f76463449d887ea88fb03e7ebc853a21f Author: kate Date: Sat Aug 19 01:32:03 2006 +0000 Revamped hgCustom and support in libs and other CGIs. Changes based on code review (Mark D.) and preliminary Q/A review (Archana). This version provides dual usage of hgCustom and previous custom track page, with two buttons on invoking CGIs, to allow comparison during review commit 2ecad84f0591fffa2363b740f2c8aa11e783db98 Author: braney Date: Sat Aug 19 01:05:41 2006 +0000 some little instructions for something I did long ago commit eeb1f1b9868336ba5aa4c6ec1d712e780636c020 Author: braney Date: Sat Aug 19 01:05:08 2006 +0000 the DM2 proteins track commit 2fdda296d95665362b429355ccb4a332b890edc9 Author: braney Date: Sat Aug 19 01:04:36 2006 +0000 the right sort command. forgot to check this in from long ago commit 17d643e11a60b40a0140c09102710dc9f3d50916 Author: kate Date: Fri Aug 18 23:49:52 2006 +0000 Add description of new custom track setting for HTML track description commit 6b87228bf0a715340f2b513f97721ada93d5ffdc Author: kuhn Date: Fri Aug 18 23:42:14 2006 +0000 background for archive server commit c37f069809ee372882ef144fb7068fac3485ef20 Author: angie Date: Fri Aug 18 23:35:01 2006 +0000 Added dm3. commit 6af5b7f5ea7a9c75cc326bb60ccd846034481fea Author: angie Date: Fri Aug 18 23:33:49 2006 +0000 typo fix commit 7de967cefd6b045aeb055e1f8442a157e92f9162 Author: angie Date: Fri Aug 18 23:30:00 2006 +0000 BAC end pairs from CHORI, not NCBI (same as used for dm2). commit 9e37166ddd92c393457c99d6b8ef87abb9ee12e9 Author: angie Date: Fri Aug 18 23:28:49 2006 +0000 Initial dm3-specific track defs. commit 86b1d021a73d8cfe4d6795db064debf60c741902 Author: angie Date: Fri Aug 18 23:17:43 2006 +0000 Initial descriptions for dm3. commit b76d94c4afdbfbdb714fa79a10cbe7ebbd952582 Author: angie Date: Fri Aug 18 22:15:17 2006 +0000 Added support for naming a single .2bit file as the "nibDir" argument. commit 9e76be1f0942eaced2e69ff7bf15c5f39c27f02b Author: angie Date: Fri Aug 18 22:14:33 2006 +0000 Use verbose instead of printf for info message, so that stdout output doesn't include it. commit 057b0fb6fe8949e15e5e1a275d9d97508347ae87 Author: hiram Date: Fri Aug 18 21:44:58 2006 +0000 A copy from the Wiki page commit 363f24d47fb0b1e8fbc2f31da8c812f491d88c87 Author: braney Date: Fri Aug 18 21:16:43 2006 +0000 sort -u is different than sort | uniq which is what I want commit d061c6a3c6c7e5628e8bbf2ce2944ebecdb0c034 Author: heather Date: Fri Aug 18 20:42:48 2006 +0000 fix typo commit ec2e5bc18bc466fdbf9e0ae6917eb3a94b8957a8 Author: hiram Date: Fri Aug 18 19:12:42 2006 +0000 Correct typo in href link commit e8a62d966b976ed01446915faea8c1f33fca4f35 Author: kate Date: Fri Aug 18 19:01:22 2006 +0000 Update for July and August commit 39ecd3ea68abb8db334917affffc6e0202d5fb73 Author: angie Date: Fri Aug 18 18:40:34 2006 +0000 Tolerate absence of chrM.fa.out -- RepeatMasker may not find anything to annotate there. commit 1eb17c22304dc9596c7ada0bbe809b40cd8b89a6 Author: angie Date: Fri Aug 18 18:39:42 2006 +0000 Added quality and gc5Base track generation. Fixed up the agpToFa usage and various other bits while getting it to run on gasAcu1. commit 25e8d24e49d1fd1a3799212ddc657f472cbf26ba Author: angie Date: Fri Aug 18 18:34:17 2006 +0000 Added -species for when a closely related species has a much better lib. commit 99d243ce6498a2d3038c77265e8402238e89ab26 Author: kate Date: Fri Aug 18 18:21:32 2006 +0000 Add data versions to some ENCODE tracks commit 14c240fb6c08ceecb73836b7a5d1ef8b609f28ba Author: angie Date: Fri Aug 18 18:11:19 2006 +0000 Updated dm3.ooc. commit 686a07fa219c8c2bb99bb7b590a84d5905442eab Author: hiram Date: Fri Aug 18 18:10:48 2006 +0000 Brought the hg.conf example up to date with the latest options commit f8a8c1e2cd44b5520d7a8446eaab756a63094695 Author: hiram Date: Fri Aug 18 18:06:08 2006 +0000 Updated with the latest options commit 3b3fd86e950a6e57a528770547023fb88ac37290 Author: markd Date: Fri Aug 18 17:17:26 2006 +0000 fixed documentation of informat organism commit 68a2147fb9a443ad0bfbd8f9b8bb9f77584e44a2 Author: fanhsu Date: Fri Aug 18 17:13:52 2006 +0000 Minor edit of Reactome event heading per Reactome's feedback. commit 3ff83642200238b18a7c06da22dd5998310243e5 Author: fanhsu Date: Fri Aug 18 15:29:03 2006 +0000 Updated Reactome tables. commit 99cbcd72158beec3beb4d2f7df34f102b9eb34c2 Author: angie Date: Fri Aug 18 15:17:50 2006 +0000 Resolved -Wall warning: unused variable. commit 027237f7b1f51c916ed990d6a092bf962409a547 Author: galt Date: Fri Aug 18 15:00:26 2006 +0000 "Encode release log update" commit 96e026ac9d3e10b914299ea66dc2a6ad97a447f9 Author: galt Date: Fri Aug 18 15:00:24 2006 +0000 "Release log update" commit bfae9075a8ce232a51d69475359233d4b44c0971 Author: heather Date: Fri Aug 18 00:01:07 2006 +0000 exclude SNPs that align multiple places commit a4e09bc830ec4b6366ac0775099558ceb46592c7 Author: heather Date: Thu Aug 17 23:33:04 2006 +0000 yes, okay to use 3 args, I think commit 97c78e6ef2c68d0b4eaa6b58c99dd4dbcbd1aae0 Author: heather Date: Thu Aug 17 22:35:48 2006 +0000 change output order commit 1e34556a4e321390da325bd9a59b57bc034e690d Author: heather Date: Thu Aug 17 22:30:19 2006 +0000 include database name in output commit ce8609f300bbe7e4bb89209216db81827d5c3ffe Author: heather Date: Thu Aug 17 22:19:54 2006 +0000 for ortho pipeline commit 795323579d65f7fb746294380524969f6a589129 Author: heather Date: Thu Aug 17 22:18:00 2006 +0000 add fetchSeq commit 5f63aed111997caf34ee2b16d67de0d144f8b7fc Author: heather Date: Thu Aug 17 21:11:05 2006 +0000 add comment commit 1b515d666d8726686103a8ca9ffa31e16dce7367 Author: heather Date: Thu Aug 17 21:03:31 2006 +0000 add createTable() and loadDatabase(), change table name commit 961d837f667fc51b08d08977dfaa1c9361be12df Author: archanat Date: Thu Aug 17 20:58:06 2006 +0000 Changed the short label and priority of Human (Hg17) Proteins commit 54b14f5c310e235456053d36484283d05cee514d Author: archanat Date: Thu Aug 17 20:45:15 2006 +0000 Added canFam2 to blastHg18KGPep04Id commit 72f51ed190fc38a75be525ec2c491faa2412245d Author: angie Date: Thu Aug 17 20:12:16 2006 +0000 Added dm3.lift definition. commit 2e96b486a76b864416629a8d43944ddc70bb06ae Author: ann Date: Thu Aug 17 19:27:55 2006 +0000 removing release alpha/beta blocks for encodeSangerChip blocks and subtracks commit be912049e7dd915ac77a2ec04b9e2095b6a2a87b Author: angie Date: Thu Aug 17 19:01:02 2006 +0000 Added dm3. commit 5baedd54ff9150d92dba2051a41ca32d9510afca Author: donnak Date: Thu Aug 17 17:48:03 2006 +0000 Slightly reworded one sentence. commit 5aa072f0f1b24c74f36633ff992baa72e92b20b9 Author: angie Date: Thu Aug 17 16:22:25 2006 +0000 Initial descriptions for stickleback (gasAcu1). commit a543fd72434712c847b910cab469b284a449cc50 Author: angie Date: Thu Aug 17 16:21:50 2006 +0000 Added gasAcu1 to DBS. commit 1992bad5b51a2765eea8f2069de09a94f5548d80 Author: angie Date: Thu Aug 17 15:45:51 2006 +0000 Resolved -Wall warning: unused variable. commit 3017c5b6e179089cb0ffddb02ff2fd655f4cdc21 Author: braney Date: Thu Aug 17 15:42:36 2006 +0000 update human proteins track to hg18 proteins commit f727f4a54c6d28659d6b987806339bc0f0d1219b Author: galt Date: Thu Aug 17 15:00:27 2006 +0000 "Encode release log update" commit b21fd11a49b10bd7931384d683dda47c69cfb19f Author: galt Date: Thu Aug 17 15:00:25 2006 +0000 "Release log update" commit 50d7f0761bf59c318e26d5f2c03a7f6062d4fd7a Author: heather Date: Thu Aug 17 03:20:22 2006 +0000 for ortho pipeline commit 8e4d3dd08f219771c11238951a000c76e41765bd Author: heather Date: Thu Aug 17 03:20:05 2006 +0000 add snpSplitByChrom2 for ortho pipeline commit ea0b3e567ee5ae46781d6ef4f98e1198a3f17579 Author: hartera Date: Thu Aug 17 01:51:34 2006 +0000 Changed wording. commit 30d0cdafa1527f219364958aca94d3b3f64572d3 Author: hartera Date: Thu Aug 17 01:50:02 2006 +0000 Noted that the signal averages and their peaks can be downloaded. commit dcb1ce0c60faea0471d05b2059e8b97d1a1f638d Author: donnak Date: Thu Aug 17 00:21:59 2006 +0000 Made a minor change, per Brooke. commit 3101a7858012420ac4d075903c3b76422dccff9d Author: donnak Date: Thu Aug 17 00:00:45 2006 +0000 Made some edits, fixed a typo. commit 0beb1d3fd145b4ac7483d0356cca5f038f6f7c5c Author: heather Date: Wed Aug 16 23:49:45 2006 +0000 simple wrapper to generate ortho files commit 6859e86a799585440c94d30252647be26eb6cde0 Author: heather Date: Wed Aug 16 23:49:20 2006 +0000 add snpGetSimple commit a0c46579f1c6cdff9043a500d60cf7f99024395f Author: markd Date: Wed Aug 16 23:09:38 2006 +0000 include gss sequences commit eb03de16229c86306de0749b1566810465fa34be Author: hiram Date: Wed Aug 16 23:07:10 2006 +0000 Changing dbRIP table names to eliminate the underscore commit f7a26b8069c5e51de1e2198caad0af623a209b2e Author: angie Date: Wed Aug 16 22:42:30 2006 +0000 Resolved -Wall warning: unused variable. commit 7eb85cbb7cba52259255eabda3a497918dda7f1f Author: ann Date: Wed Aug 16 22:14:34 2006 +0000 added encodeSangerChip to 'ignore' list commit fdaebaaa5a9a3db0bc97f4d0f7cae3e653bb6e9d Author: ann Date: Wed Aug 16 21:59:49 2006 +0000 fixed some small errors in encodeSangerChip track commit 3657cc86fbd2ba46aef3ccdbad91bc63c6a4612f Author: kuhn Date: Wed Aug 16 21:48:11 2006 +0000 added some error checking and simplified some of the if-then sequences commit b666a38862af529a0c46ab0ea252d15848dd1cfc Author: hartera Date: Wed Aug 16 20:55:48 2006 +0000 Added text to state that the graphical configuration only works for the Signal subtrack. commit 14a2fd643ee327fe9e1d6a82b93b55abdcc29098 Author: hartera Date: Wed Aug 16 20:46:35 2006 +0000 Changed default pixel height for subtracks. Added min and max limits for the Signal subtrack which is the only one that is configurable. commit 60deaa4f714fb6caf0a6b05d7c41ff01924ba203 Author: fanhsu Date: Wed Aug 16 19:02:47 2006 +0000 Changed hgFaToTab to faToTab. commit c3671355d8cb5a4b74731572a1624d1256af07bd Author: angie Date: Wed Aug 16 18:46:19 2006 +0000 Don't warn about lack of block support unless the input has at least 12 fields. commit 696d95d16e29c06b765ff22814dec96996cfb988 Author: donnak Date: Wed Aug 16 18:39:57 2006 +0000 Fixed tiny typo. commit c01e70becb5703e4c9cd907a849304192545384b Author: galt Date: Wed Aug 16 15:00:29 2006 +0000 "Encode release log update" commit 02d81ec78f99750aa17f2d2269da03f291007452 Author: galt Date: Wed Aug 16 15:00:28 2006 +0000 "Release log update" commit 61c0f68abd32f7ba5be8239b76a4f801cfb2bbb4 Author: galt Date: Wed Aug 16 02:44:01 2006 +0000 "New version number v140" commit d9c0f6ba258325a6ce1f1d52cebb735d9261350f Author: hartera Date: Wed Aug 16 00:18:36 2006 +0000 Shortened labels. Added noInherit for Peaks subtracks and added defaults for Peaks subtracks. commit 1040100e9ea7e5925413ec4063de1c949b3f263c Author: donnak Date: Tue Aug 15 22:47:36 2006 +0000 Removed comment -- feature is now in release. commit 4e349b8d77384b9d4ca1801a58dd6c0bdc55ca85 Author: baertsch Date: Tue Aug 15 22:05:50 2006 +0000 remove warnings from netSkipHttpHeaderLinesCatch() commit 859afa0687bf4a211369db818f070ef673c86d8f Author: baertsch Date: Tue Aug 15 22:01:25 2006 +0000 add netSkipHttpHeaderLinesCatch(int sd, char *url) /* Skip http header lines. Return non zero error if there's a problem. The input is a standard sd or fd descriptor. This is meant to be able work even with a re-passable stream handle, e.g. can pass it to the pipes routines, which means we can't attach a linefile since filling its buffer reads in more than just the http header. positive return code is http error, -1 = http header too long, -2 is a strange http header, -3 is error reading descriptor. add netLineFileMayOpenCatchError(char *url) /* Return a lineFile attached to url. http skips header. * Supports some compression formats. * Return NULL if there's a problem without printing error. */ commit ccacaca5d9c781b12c1a0c7da22c5948c1fc5297 Author: markd Date: Tue Aug 15 21:46:05 2006 +0000 use bin column in ccdsGene commit 4b56db845837e66191f6a5a9f05184c9506fc1ae Author: donnak Date: Tue Aug 15 21:38:28 2006 +0000 Archived rheMac1. commit 8d0573d76a60d2ed99831d2c7c24c4bff39b6c72 Author: markd Date: Tue Aug 15 21:28:11 2006 +0000 updated CCDS commit bdefd9b714a336e7cb644cc44e1184a55669ad0d Author: markd Date: Tue Aug 15 21:03:02 2006 +0000 change to code to build CCDS tables to make them more general commit e96f0ee3bc11524d9a7a4b92e7f38dc78b302f0c Author: kate Date: Tue Aug 15 20:29:30 2006 +0000 Fix typo commit 0fa08e8d52010d8e4d35b61b90f5c7c42d582803 Author: heather Date: Tue Aug 15 20:24:56 2006 +0000 check chain file for duplicate ids commit c700468e41d6a4cec3f55f2180c97acba2982983 Author: heather Date: Tue Aug 15 20:24:29 2006 +0000 add checkChain commit bbed1467dac07395a177d2ec00868abe8fe94eff Author: hiram Date: Tue Aug 15 19:02:02 2006 +0000 The dbRIP coordinates need to be loaded chromStart-1 to be correct commit e203a202efef4dc4c51d300716afd73a4467c04a Author: angie Date: Tue Aug 15 17:45:57 2006 +0000 Resolved -Wall warning: unused variable. commit 006134d6937bd312016671ece85ebcc5675bc380 Author: heather Date: Tue Aug 15 17:45:19 2006 +0000 only set showDiffCodonsAllScales if tg not NULL commit 9186ed79383c79458580355fa37e815ab01bcd1a Author: kuhn Date: Tue Aug 15 17:34:10 2006 +0000 removing rheMac1 from the dailies commit f0447ddcd6c23cbf835f34810268a2b59c0b21d1 Author: kate Date: Tue Aug 15 17:30:51 2006 +0000 Need to handle empty html string assigned by trackDbPolish() commit 563947c34417939cdc04cc1d0f2c382bf2698e30 Author: kate Date: Tue Aug 15 16:58:59 2006 +0000 Add pvalue data to DnaseI Raw track commit 81509db35cce83f5327ab42de88c13e4900f0993 Author: galt Date: Tue Aug 15 15:00:26 2006 +0000 "Encode release log update" commit b35a3b6fc3350f20abfc5efa1990beea6ae55737 Author: galt Date: Tue Aug 15 15:00:25 2006 +0000 "Release log update" commit f55e1910b15e7344152e093205539ff5a9d8ec0f Author: markd Date: Tue Aug 15 03:10:25 2006 +0000 modified CCDS import to handle changes in dump file format commit da1f98bf2e9b99a95370bf0f046c2f6b97a1b135 Author: angie Date: Mon Aug 14 23:50:36 2006 +0000 When making liftOver chains, run chainStitchId after netChainSubset so that fragments of each chain are stitched back together. This prevents duplicate-ID errors in downstream programs that read liftOver chains (liftOver happens to be immune to duplicate-ID problems, but other programs are not). commit b098566e4f98816b4626aacde04ed9b810ad6b87 Author: angie Date: Mon Aug 14 23:17:22 2006 +0000 In unsplitTableName, look for the last _ as the end of chrom name instead of looking for first _ and working forwards to catch oddities like _random_ or *hap*_. The list of oddities only grows as we get new assemblies, and we don't accept table names with underscores (mustUseInitialCaps convention). commit 313c43893073567eab956a4bedaf1b26e170f699 Author: galt Date: Mon Aug 14 22:18:49 2006 +0000 typo fix commit a84b72018e5e5460186209dd007fa8ba878c0bb8 Author: kate Date: Mon Aug 14 21:31:21 2006 +0000 Expand Crawford DNaseI-HS tracks commit 328b8861051874d280d88531251a8133fbaa9e3c Author: angie Date: Mon Aug 14 20:44:31 2006 +0000 oops, typo in previous rev. commit 669a401fe8891716612f475ff46f9c2e862ae71c Author: daryl Date: Mon Aug 14 20:18:03 2006 +0000 fixing population names for HapMap SNPs track commit 8a706f454b5b327382361fa03d7aa10f3f6e6dfe Author: hiram Date: Mon Aug 14 19:23:14 2006 +0000 Honor variables from old-style tracks to avoid glitch during upgrade to new system with existing tracks in place. commit db154c782bc4b306e6c77dc89ceb4244ddcf3f95 Author: hiram Date: Mon Aug 14 18:58:17 2006 +0000 Remove offset from the settings hash so it won't get saved commit a557d564931328f7c9f77712377cb5e9f982d0cf Author: hiram Date: Mon Aug 14 18:57:38 2006 +0000 Not for db type tracks commit 8976740ee11502e1d0bc7d2a424fb8486049e8a4 Author: hiram Date: Mon Aug 14 18:56:19 2006 +0000 Can never the less print out position information for bed 3 type items commit 0204c6a0a79088ad11e24c44cfbb09c6b0b13afb Author: angie Date: Mon Aug 14 18:36:04 2006 +0000 Added cds.h dependencies. commit 27f9201ab7c3c891315d7a6fb285822033dfd7fc Author: markd Date: Mon Aug 14 16:58:03 2006 +0000 sort stderr from two test process before comparing, since order depends on process scheduling commit 23df8222a378d48c3b454282d246dcaefb6fe896 Author: kate Date: Mon Aug 14 16:55:28 2006 +0000 Tweak display to accomodate polished trackDb's commit e21e531e9ef888d0e44768856f0a850f50e56018 Author: ann Date: Mon Aug 14 16:15:03 2006 +0000 added link to sequencing center from chimp image commit dcc25bd8bebe6d6765ef95066131fcf3d4c1a440 Author: angie Date: Mon Aug 14 15:42:14 2006 +0000 Resolved -Wall warning: unused variable. commit dd6182ffb8aaac0160edba0c9daba17dc92a7353 Author: angie Date: Mon Aug 14 15:41:20 2006 +0000 Resolved -Wall warning: unused variable; added parens around assignment used as truth value. commit 1a679287f8462d4b4e70c5870676c4239f64d853 Author: angie Date: Mon Aug 14 15:39:44 2006 +0000 Resolved -Wall warning: added parens around assignment used as truth value. commit 6b4937e48a49c7d23696b719f91c6f75def9d9b3 Author: galt Date: Mon Aug 14 15:00:19 2006 +0000 "Encode release log update" commit a9ba464a1adae69088b84c0f14aa78bf6716b6e8 Author: galt Date: Mon Aug 14 15:00:18 2006 +0000 "Release log update" commit 483ad75d83ca04cb69198566870de0964b76e4de Author: galt Date: Sun Aug 13 15:00:19 2006 +0000 "Encode release log update" commit e9996dd9fd7b8333d5aff70aa3e15e2e0a55a26f Author: galt Date: Sun Aug 13 15:00:18 2006 +0000 "Release log update" commit 163f6334f1f8ed761d21f7d103064d5e4a60312e Author: hiram Date: Sat Aug 12 23:04:23 2006 +0000 Update to current assemblies (well, most of them) commit 42e1478f0a44c3722bc70906e8657f78079b7b47 Author: hiram Date: Sat Aug 12 22:18:06 2006 +0000 Up to date with current source commit 23970edfd50dd9ddf86ff7985a8edfde4cc0f04e Author: hiram Date: Sat Aug 12 22:15:43 2006 +0000 Up to date for current hgcentral.sql file commit b8b7460b5c307908273ef1c179fd8368c794143e Author: hiram Date: Sat Aug 12 22:11:30 2006 +0000 Initial description of a minimal browser commit c275794ce66699e3fbec63db2aedb9c79dd0adbe Author: heather Date: Sat Aug 12 04:52:03 2006 +0000 add bin commit e8579494f24842f5029e7a8454a1f2dc32846f58 Author: heather Date: Sat Aug 12 04:41:53 2006 +0000 add hapmapSNPs 2; remove illumina (moved to hg17 SNP Arrays track) commit d6e03e4aa52e71f4bf6e3111d22df6a10aa77d8b Author: heather Date: Sat Aug 12 03:27:43 2006 +0000 fix typo commit c8e273923a42e2bc804bcf9b14869f4d090c3b03 Author: heather Date: Sat Aug 12 03:22:20 2006 +0000 new format for orthologous alleles commit 3a0153bb69da157e3164802525b8caa0a11002f4 Author: kate Date: Sat Aug 12 01:34:21 2006 +0000 Fix visibility options displayed in menu for track configuration of custom tracks commit d24434150bbdab12af3da449bdeb99b42fd511b5 Author: hartera Date: Sat Aug 12 01:20:55 2006 +0000 Added further explanation of Experiment Display options. commit 28b1d43219c698a237e00d8dd968987bac130b23 Author: hartera Date: Sat Aug 12 01:10:56 2006 +0000 Update zebrafishZonWTAllExps and zebafishZonWTMedian Exps tables. commit 2b3b71e75e0074b5c27a9ec9854df537147b0962 Author: kate Date: Sat Aug 12 00:30:59 2006 +0000 Additional work on Crawford data commit 24dbd2645f3e413ffa052ec663b44dfa98634565 Author: hiram Date: Sat Aug 12 00:17:40 2006 +0000 Also need maxChromName for loader on tracks coming from table browser commit 881a4fec18a2513a52109dccf384895dd2a41261 Author: hiram Date: Fri Aug 11 23:45:39 2006 +0000 Same change here as was in bedList.c - now cooperating with the customFactory business commit f10c5ea615b63fc5dcb8d8ec72a0b1b53fb7bad5 Author: hiram Date: Fri Aug 11 23:42:51 2006 +0000 Now processing incoming wiggle data from the table browser. HACK ALERT - using a private method of customFactory from customTrack. commit 0c1ee862b71e413e0743bcf1013e902ec647bb47 Author: hiram Date: Fri Aug 11 23:41:54 2006 +0000 HACK ALERT - add wigLoaderEncoding() public function in violation of this object's private methods. Used from customTrack.c to handle custom wiggle data coming in from the table browser commit 2435a74fd64fc91a3cd9d9dc08aedb23e3eeb108 Author: hiram Date: Fri Aug 11 23:29:38 2006 +0000 Making this business work with the new custom factory. commit a4406e78af750a21754530922a58476779c9b558 Author: kuhn Date: Fri Aug 11 23:05:57 2006 +0000 taking rheMac1 out commit af1fe1f9c362dc516e67d1975791c15edead7048 Author: heather Date: Fri Aug 11 21:36:44 2006 +0000 add snp125 commit 45d37ea24525839351e8ea0eb9ffbbf63eb9a789 Author: markd Date: Fri Aug 11 21:32:23 2006 +0000 reloaded N-SCAN genes to require CDS commit c9dd1359ad131e749cf2604f5271affc8f7425c3 Author: heather Date: Fri Aug 11 21:11:28 2006 +0000 add snp125 commit 5d69dbd1bc919e00ff3c010aa55e07df40405b43 Author: heather Date: Fri Aug 11 21:11:17 2006 +0000 includes dbSNP/UCSC chrom translation commit fc8762cb8c98377b74b2734a790e7ce016bd47f6 Author: hiram Date: Fri Aug 11 20:59:36 2006 +0000 No = signs on a ra style string setting commit 25167f5e2074323000965008ba44f3b0c7df5765 Author: hiram Date: Fri Aug 11 20:58:14 2006 +0000 Fix the first bit of the problem of loading wiggles into the new custom system commit 8b99e40cb385eb64db08e18009c37821fd75fbe0 Author: hartera Date: Fri Aug 11 20:45:22 2006 +0000 Changed the MedianExps table so that when Tissue Averages is selected, the average across all strains for each stage is displayed for the zebrafish Zon lab WT data. commit 4e6af8acdf10dbd7213cce0e9af2d4404b2d7383 Author: donnak Date: Fri Aug 11 19:26:20 2006 +0000 Added note/workaround abt larger fonts garbling PDF/PS output. commit 73ae4fe4f22c1222ae634ec80173799c54f4ca4a Author: hartera Date: Fri Aug 11 19:11:26 2006 +0000 Changed all subtracks for encodeUncFaire to bedGraph type and removed extra lines. commit 9a1afc6398b23be64b6002ca0422c467a84d24e6 Author: hartera Date: Fri Aug 11 18:54:08 2006 +0000 Clean up for liftOver to danRer2. commit a2ed712db77bc9a950f7802efc5e68dcc0c4837d Author: donnak Date: Fri Aug 11 18:46:33 2006 +0000 Added line mentioning that display modes can be specified by either numbers or words. commit cb6645f0c370407f4fc1a3dd4b385fbc016841fc Author: donnak Date: Fri Aug 11 18:26:22 2006 +0000 Added a link to the Blat FAQ. commit 71a4b86225cea857ffed1ffa08a65008170c4ae3 Author: kate Date: Fri Aug 11 18:14:31 2006 +0000 New data from Crawford lab at Duke commit ceceae04d31441c9cf4783bd1321ce24f0f71214 Author: markd Date: Fri Aug 11 17:46:30 2006 +0000 reloaded nscan proteins commit c0914f3f4c40ae40721be0bedc17be14d804c9c7 Author: ann Date: Fri Aug 11 17:25:17 2006 +0000 added credits for phylogenetic tree commit b3569ea2a1b16c93191339d8b689586bf06debf5 Author: kent Date: Fri Aug 11 17:06:48 2006 +0000 Adding customFactorySetupDbTrack commit 56108fa9c861db9deba523a7a9cd1d38c77eebce Author: ann Date: Fri Aug 11 16:06:21 2006 +0000 added archana to email list commit de0e15e59a1c596a60915cb21fd54b09eb3cb7aa Author: donnak Date: Fri Aug 11 15:34:56 2006 +0000 Changed "Zoom in" to "Zoom factor" on ruler description page (one of the config options). RT #1010 commit e1ce6ac2caba842b671f5b424cdcb58024c4c045 Author: hartera Date: Fri Aug 11 15:18:29 2006 +0000 Added encodeUncFairePeaksChipotle to list of tables to ignore. commit 1c8f4337038b35708e0f136b3c07064e2020932c Author: galt Date: Fri Aug 11 15:16:17 2006 +0000 "Encode release log update" commit 29e8dcfe7083ab6d85885e73911f3e2eb58f13f4 Author: galt Date: Fri Aug 11 15:16:15 2006 +0000 "Release log update" commit 102fde5ae4d39d65007504e8bb66d1dddb1dbfe6 Author: donnak Date: Thu Aug 10 23:27:38 2006 +0000 Temporarily commented out a phrase until Angie's patch goes out the door w/next release (mid-Aug 2006). commit d420cf1bc1e31865fce02daf36ee3520d0e61c96 Author: heather Date: Thu Aug 10 23:15:18 2006 +0000 add snp125 commit 13358210df698a0c7744d5b73f0ade6f9841c28e Author: heather Date: Thu Aug 10 23:15:07 2006 +0000 small change to data source from top level commit e310fbc38bc6371d2992722b0e5cda46df3c6c0e Author: heather Date: Thu Aug 10 23:04:15 2006 +0000 add snp125 commit 19bca1ff3891d4382b858923027d0cecd82aa8ce Author: ann Date: Thu Aug 10 22:47:20 2006 +0000 added credits for phylogenetic tree commit 5e785d5f4bea44422f3adecc77b9c0a1cdecaa82 Author: markd Date: Thu Aug 10 22:15:50 2006 +0000 added FIXME note about problems on mgc commit 5e137191b38d421069ca55051cbfa9274d6297b4 Author: kuhn Date: Thu Aug 10 22:13:53 2006 +0000 corrected parsing of output stream so it counts number of diffs better and adjusted parsing of getAssemblies return to account for change in output commit 34c793f7a8ea4354fc4abb4e654b5db7dd428d38 Author: heather Date: Thu Aug 10 18:38:10 2006 +0000 customized to use with snpContigLocFilter125 commit f9c84696a9be930c98971e5e73751bcbeb7411c1 Author: heather Date: Thu Aug 10 18:29:25 2006 +0000 a clone of snpContigLocusIdFilter that uses contig_acc instead of ctg_id commit 3ac8e2e364302b663d9c8a47762fea3b63bf3a62 Author: heather Date: Thu Aug 10 18:21:55 2006 +0000 fix coords for range locType commit 7047bf2425a9dbdd5e72b7ad88c370b5b212d42a Author: heather Date: Thu Aug 10 18:16:09 2006 +0000 add snpContigLocusIdFilter125 and snpLocType125 commit 85874682689300222d17d5195ceaf79006d48435 Author: kent Date: Thu Aug 10 18:05:19 2006 +0000 Adding comma to message. commit 30539bbc681b5bba9b01d72f717f0e97737a3112 Author: hiram Date: Thu Aug 10 18:03:16 2006 +0000 Was missing the maxChromName from the db in the case of no track line commit b76e7020850a70414c004aec34f9597d31a7c702 Author: kent Date: Thu Aug 10 17:34:13 2006 +0000 Adding some test cases. commit f5af851c52f3fc909d19d63a4b49de9655e5c23b Author: ann Date: Thu Aug 10 17:17:28 2006 +0000 italicising journal names commit 80aa61a9f7a84bbc416f72f9a879684f3ca1ff82 Author: hiram Date: Thu Aug 10 17:14:41 2006 +0000 Change CGIBIN to CGI_BIN to match the source tree usage of this variable commit e6e1e97e341590f5a3f2ae2b15dda9b86785fe72 Author: fanhsu Date: Thu Aug 10 16:43:01 2006 +0000 Added Exon Primer link. commit 47e9c1bf89bfe773e9e4a3e68bb96cecd0707a32 Author: angie Date: Thu Aug 10 16:15:16 2006 +0000 Resolved -Wall warning: unused variable; parens around assignment in if. commit d2d43323c517d58c2b35a3f0bf662fe01213be41 Author: galt Date: Thu Aug 10 15:00:27 2006 +0000 "Encode release log update" commit bfa238e40f6ae4665d0cef4042ecdf9d2b926340 Author: galt Date: Thu Aug 10 15:00:26 2006 +0000 "Release log update" commit 71c43f7fb336c22223290a2f05698c569aee9f09 Author: kent Date: Thu Aug 10 08:28:29 2006 +0000 Making it so that some track types (like chromGraph) can more safely ignore the database request. commit d302abfab0ca0e743a8a60929a02891a6cd05c9d Author: genbank Date: Thu Aug 10 07:02:31 2006 +0000 added mRNA bases option for MGC commit d19a9f1ab877495fbd0b8b6ded528e83c455def5 Author: kent Date: Thu Aug 10 06:51:36 2006 +0000 Making hgTrackUi work for chromGraph custom tracks. commit 012d2a50973d62611cdc71a8bda85bc9ae30f393 Author: kent Date: Thu Aug 10 06:40:33 2006 +0000 Adding support for use-uploaded chromosome graph tracks. commit 15ed9f7b10fc9a353ef974388ea3783644a76eaa Author: kent Date: Thu Aug 10 05:46:58 2006 +0000 Handling missing chromosome data in chromGraphDraw custom track case. commit e2bb0c2f06471ccbdea2f5563a330573ccb34332 Author: kent Date: Thu Aug 10 05:04:42 2006 +0000 Fixing off-by-one problem in drawing. commit 3fe5e67488a2e7a930f84cf2ded091083d8376a5 Author: kent Date: Thu Aug 10 04:28:46 2006 +0000 Starting to hack in chromGraph type custom tracks in to hgTracks. commit adc00c294a5684fb760d470182197ad585b3f35d Author: kent Date: Thu Aug 10 01:27:25 2006 +0000 Moving from using .ra file to using a customTrack file to keep track up uploaded data. commit 77f86ce78b77efd079bc7a3d445db138ab28d4de Author: kent Date: Thu Aug 10 01:10:55 2006 +0000 Adding chromGraphFactory to factoryList. Fixing a little bug that would only happen in db case. commit 4a59dfa4fc4f0adc88cf91e797639aad3d69b844 Author: kent Date: Thu Aug 10 01:09:46 2006 +0000 Shortening code by replacing some in-line stuff with calls to library routines that do same thing. commit 7b75a7ff52657a66647270aa224ff9f2f9a231f5 Author: kent Date: Thu Aug 10 01:07:46 2006 +0000 Include jksql.h since this uses a sqlConnection. commit 70159979229a3efbb260ae598e883df86483b84f Author: kent Date: Thu Aug 10 01:06:49 2006 +0000 Adding chromGraphToBinGetMinMax to return min/max as well as make the binary file, since the min/max is right there, and we often need it for default settings. commit b4154f154957433d820207cf51b6129e14a1e967 Author: kent Date: Thu Aug 10 01:05:24 2006 +0000 Adding chromGraphFactory module - an instance of a customFactory. commit 6da47b43ab384a458d10d4929eda5f87d60897e1 Author: kent Date: Thu Aug 10 01:04:05 2006 +0000 Freen helps test custom tracks some more. commit 011a18f9cf1957c5cde50960dfbfb3c7dbe14042 Author: kent Date: Thu Aug 10 01:03:14 2006 +0000 Adding nullIfAllSpace commit 2954d3c3eeff3848258d4516f4eaf2724c1ea9e4 Author: kent Date: Thu Aug 10 01:02:47 2006 +0000 Adding errCatchFinish. commit 4565f73c35b8f6d09475338e6f17f477bec5b618 Author: kent Date: Thu Aug 10 01:02:16 2006 +0000 Adding hashOptionalVal commit 870108162feea21e238a91283a85d58961fc0bb8 Author: hiram Date: Wed Aug 9 23:25:30 2006 +0000 Begin sql performance test commit 501e6bf7a76dbb00388208135ad6a92cee14260e Author: angie Date: Wed Aug 9 23:14:03 2006 +0000 Updated to match recent improvements to code. commit dd7915e13901ed6980f18b52b6cb1a7b2658590a Author: rhead Date: Wed Aug 9 23:04:11 2006 +0000 Added note to make category descriptions generic to all assemblies commit 8443b5b47e370962c32b4a8ce1491ce11c363fd0 Author: heather Date: Wed Aug 9 23:03:23 2006 +0000 add text commit f8780d6959ff25e4506ac12d62c28e9bee61dede Author: rhead Date: Wed Aug 9 22:56:52 2006 +0000 Nevermind. Decided not to keep a mouse-specific copy. commit 691464a5389255dea56907e630a462ee1a466746 Author: hiram Date: Wed Aug 9 22:23:33 2006 +0000 Fixup query construction statement for dbRIP loader. Need to use winStart and winEnd, the bins are good enough to eliminate items commit fe5ef9b7213de5c0169b820d4ac3b0a45ef92ac4 Author: galt Date: Wed Aug 9 22:08:15 2006 +0000 fixing problem created by somebody elses web.c changes - cannot pass NULL var args now commit a278cf3214a04449998ac9fa8ae9d65e04c82120 Author: rhead Date: Wed Aug 9 21:59:22 2006 +0000 Put a copy of snp126 description in mouse in order to take out unused 'class' and 'validation' categories. commit 964d66e28f5926bb6951014111e3ba52d95f448b Author: kate Date: Wed Aug 9 21:44:17 2006 +0000 Add ident string commit 63d631c794997feed0eab0398468b1187851b700 Author: hiram Date: Wed Aug 9 21:38:06 2006 +0000 Eliminate unused argument passed unneeded to web start internal commit 6c25b5a1804da82dd0aab4ecf36628154417d32e Author: hiram Date: Wed Aug 9 21:27:49 2006 +0000 Lets see what RIPs look like instead of Retrotransposon Polymorphisms commit f9f9df3258958cb66896128b2c8c72f46cadd90a Author: rhead Date: Wed Aug 9 21:24:20 2006 +0000 Moved 'average heterozygosity' description above 'weight' description to match the order of the links on the hgTrackUi and hgc pages commit f229f74482c2180540b96bab6d33cc1c87728e25 Author: hiram Date: Wed Aug 9 21:19:19 2006 +0000 Better indication of what polySource means to a reader commit d640464e4ba86e4769e5aa5257baca54e29014d0 Author: hiram Date: Wed Aug 9 21:12:34 2006 +0000 The frequency filter on dbRIP tracks doesn't actually work due to the way the tables are interlinked to their allele data. commit 76b55b17a4423f00a3c3daeb8fce6132e122d613 Author: kent Date: Wed Aug 9 20:41:07 2006 +0000 Renaming some things in preparation for switching from .ra file to custom track representation of uploaded graphs. commit fc6ea2ed4eaacbc8c9c25384d476697cb620bd4b Author: kent Date: Wed Aug 9 20:40:13 2006 +0000 Fixed scale for uploaded graphs with no explicit scale. commit c4332d0c100803a07a30f56ab0e7fbc04fdf8d88 Author: fanhsu Date: Wed Aug 9 20:29:47 2006 +0000 Added Gene Bound track. commit e4f9494e70f5082e7a9a9ebc4124f9572e95d245 Author: ann Date: Wed Aug 9 19:59:22 2006 +0000 adding initial to shortLabel of Wanker and Vidal columns commit 768608830f448c1a4225ff3516586e8d87dae98b Author: kate Date: Wed Aug 9 19:39:13 2006 +0000 Remove extra save to file commit 724826979b1299dab35291752c92e900be4558f8 Author: hartera Date: Wed Aug 9 19:07:40 2006 +0000 Changed check for number of inputs since there is an optional input. commit 7656879ada7df4aee372b2bf3a3e29bbf2aad308 Author: hartera Date: Wed Aug 9 19:01:09 2006 +0000 Changed sprintf to safef in printBacStsXRef function. commit 2db601f5f71accfaff2ad7fc1122df3d77bf40d1 Author: kent Date: Wed Aug 9 18:56:29 2006 +0000 Fixing two bugs: missing fileClose in customTrackSave, and uninitialized settings hash in saveTdbLine. commit c53c5f7517645755c6895d99866a60c5b2e82c74 Author: hartera Date: Wed Aug 9 18:55:08 2006 +0000 Minor changes. commit db28cf81e29b2629dcd9168955e77b8de8260b4d Author: ann Date: Wed Aug 9 18:51:00 2006 +0000 typo commit b60ef1cdb7c774972bf6c9c947fad09538ec2dc8 Author: kuhn Date: Wed Aug 9 17:54:23 2006 +0000 added quiet mode to suppress all the database names commit 6b1c0b16f5ac12d04c48326fe88eb8c203c13618 Author: angie Date: Wed Aug 9 17:47:19 2006 +0000 Removed zooming constraint from display of nonsynonymous mRNA codons, when trackDb setting showDiffBasesAllScales is present. In pslTrack.c::lfFromPslX, split into codons even when zoomed out if enabled. Refactored cds.c::drawDiffTextBox to pull out some shared code into getMrnaBases. Added drawCdsDiffCodonsOnly to cds.c and call it in hgTracks.c::linkedFeaturesDrawAt if enabled. When zoomed out beyond zoomedToCdsColorLevel, this is done in a separate pass instead of inside drawDiffTextBox because if each codon were drawn separately, matching codons could occlude nonsyn codons. So when zoomed way out, the whole feature is drawn without coloring and then nonsyn codons are marked by drawCdsDiffCodonsOnly. commit 0ef06c9733a540332d69c779ccbf26c0381bcba8 Author: ann Date: Wed Aug 9 17:42:46 2006 +0000 major revisions to put into standard format commit 62c51c176199922fd7106f12cf6b1f603e5e4eb4 Author: ann Date: Wed Aug 9 17:41:55 2006 +0000 added more detail commit 96e770190cef010ffe8e3365d57518351cc3372f Author: ann Date: Wed Aug 9 16:59:35 2006 +0000 major revisions to put into standard format commit b8e0cdd879f9d1fba051cfec62a61f2a6759a53a Author: archanat Date: Wed Aug 9 16:49:33 2006 +0000 Moved Rat Chain/Net to mouse level and changed the priority commit 155cb96b491741827475d71036ada94174ecebf8 Author: galt Date: Wed Aug 9 15:00:26 2006 +0000 "Encode release log update" commit 4889722ed0b80a16b2f4f5b0226909b70f50a68a Author: galt Date: Wed Aug 9 15:00:25 2006 +0000 "Release log update" commit ebcd671135adc0046584586c27108e31f22e4356 Author: heather Date: Wed Aug 9 02:03:06 2006 +0000 off by one in row index commit 7f97ff17a12f243c096ddb30d6204cd69c507201 Author: heather Date: Wed Aug 9 01:58:37 2006 +0000 don't need chr for chrom commit 986d5beb1962f13e4dcdbbddab092f7fdff45a60 Author: heather Date: Wed Aug 9 01:06:04 2006 +0000 get rid of where clause commit 7e0b78679ed953772d3a0339168128cb61bdb2d8 Author: heather Date: Wed Aug 9 01:01:32 2006 +0000 fix typo in usage message commit 5cf06a225b3a1231510f5e0746a8398deaf6f972 Author: heather Date: Wed Aug 9 00:59:29 2006 +0000 for cases with phys_pos (but no ctgPos) commit 1c85fe1b677decffdff454b6f0acfb1504f8511d Author: heather Date: Wed Aug 9 00:58:25 2006 +0000 add snpContigLocFilter125, delete snpExceptionCheck commit eef2abb7673f90b78b16c280002d02543dac0386 Author: kate Date: Tue Aug 8 23:03:26 2006 +0000 Rework trackDb settings handling in customtracks to assure consistency and prevent repetitive settings commit bbeba1f979217ad6c21b07d2cbf98c873e709457 Author: ann Date: Tue Aug 8 22:58:51 2006 +0000 updated date commit 894529a24d570aaeef45ba23c8513436b1a72d40 Author: hiram Date: Tue Aug 8 22:27:03 2006 +0000 Fixed up padding for results to dbRIP tables commit 3a1232d5f2c1628ee96c3227c2d0cee7b5ade0dd Author: hiram Date: Tue Aug 8 22:09:58 2006 +0000 Fuzzy business in the dbRIPName identifiers commit 5c7cdf96bab42d8ef80c0c4071747805cd4589d3 Author: angie Date: Tue Aug 8 21:52:00 2006 +0000 Fixed cds.c::splitByCodon to recognize UTR at end of coding exon (not just at beginning). Fixed cds.c::drawDiffTextBox partial-codon completion coord bug (newIdx). Fixed pslTrack.c::lfFromPslx to use lfCalcGrayIx instead of linkedFeaturesBoundsAndGrays when coloring codons because BoundsAndGrays clobbers tallStart and tallEnd. commit b5637ffba366eb4e6c70e974b5aacfc253a7f11e Author: heather Date: Tue Aug 8 21:33:19 2006 +0000 support highlighting in snpDrawItem for pack and squish modes commit 2c8e334d39090a9dda5df2e1e92b8b2be2c01fa9 Author: rhead Date: Tue Aug 8 20:03:39 2006 +0000 Changed wording in several places to passive voice (rather than we), and changed some puntuation. commit 8abaa12af5dcfb80210929c16723a3ebe101f8f8 Author: rhead Date: Tue Aug 8 19:55:15 2006 +0000 Changed wording so it would match snp125.html commit b75f1d591dc641a8eb8c10d8464f1638293a05ef Author: kayla Date: Tue Aug 8 19:35:43 2006 +0000 added monDom4 commit 00f7b852f16aa4e97159325f14fc463efc02d13c Author: rhead Date: Tue Aug 8 19:10:42 2006 +0000 changed 'our reference allele' to 'UCSC reference allele' and added a comma commit 853ed6f8875a9bf780e241ca0a15377561efbbaf Author: donnak Date: Tue Aug 8 18:12:22 2006 +0000 Made a few more mods to monDom4 news item. commit 8fe8765e07b98b70122b9dd4a51e223bddd965b3 Author: archanat Date: Tue Aug 8 18:06:15 2006 +0000 Changed the link to image commit ff8dd0f9a75be797c227ea9a335bde0e98abe9ac Author: kate Date: Tue Aug 8 17:46:41 2006 +0000 Add 8 tracks of Sanger chip/chip data (2 new cell lines) commit e801e758027e0569927c56ee73a5af90e311475f Author: baertsch Date: Tue Aug 8 17:18:38 2006 +0000 don't show "track order" if option is disabled commit e1081a5e706ba632ed55e793062aa46d7dcc05a6 Author: donnak Date: Tue Aug 8 17:17:14 2006 +0000 Changed date on monDom4 news item. commit 63134e19a712b524aa0bc289964751c07d327168 Author: angie Date: Tue Aug 8 17:12:57 2006 +0000 Resolved -Wall warning: unused variable. commit 078817ff6d8b49a7298c2079dda2f4ca08c0bc38 Author: angie Date: Tue Aug 8 17:11:33 2006 +0000 Resolved -Wall warning: unused variable, too few args for format. commit 989ba85ec440ce360ab8ee2fd091edc54ee98628 Author: kuhn Date: Tue Aug 8 16:52:27 2006 +0000 modified usage statement commit c434715b81af6efe0037e414dfe73ec2bcaad6c8 Author: donnak Date: Tue Aug 8 15:40:37 2006 +0000 First edit pass at this description. commit e7d9bcd2a280f509f862ba7d0c520456cc9140e5 Author: galt Date: Tue Aug 8 15:00:23 2006 +0000 "Encode release log update" commit 961041a56dc91f4bef813b944ac73f0cff4b5e99 Author: galt Date: Tue Aug 8 15:00:22 2006 +0000 "Release log update" commit 0f9f8593b9fabcfc8abc6ab9659fcb0f4445ea04 Author: kate Date: Tue Aug 8 05:53:48 2006 +0000 Add custom tracks manager commit 1e423c7841d3762b5703067bd7773e72c7a38037 Author: kate Date: Tue Aug 8 05:49:39 2006 +0000 Keep settings hash and string in sync -- it's problematic that this is required commit 26dd351a3cfffb4519d53cb792edfe2d9c6d85c8 Author: kent Date: Tue Aug 8 04:15:36 2006 +0000 Making it so that customPpReuse can be called repeatedly. commit 4413347243700e890e60cf6d977f70b032e32707 Author: galt Date: Tue Aug 8 01:34:03 2006 +0000 "New version number v139" commit f92bb9d627f02a01b2404972460d42a7762b6056 Author: markd Date: Tue Aug 8 00:34:31 2006 +0000 changed title to MGC/ORFeome in MGC browser commit b4a303c4ba2a4431664bdfcc867d8264112f5aea Author: angie Date: Tue Aug 8 00:20:50 2006 +0000 The beginnings of a browser, made mostly by new automation scripts. It has been slow going since most of the time has been spent working on automation and other things. Still needs lots of tracks... commit b5d8bd58255da6654b3467264ea15c8b9b7c03f9 Author: angie Date: Tue Aug 8 00:15:41 2006 +0000 Added splitFileByColumn to USE_DIRS. commit e723a8e214bccc4a87d63a2c372d07155e9b496d Author: angie Date: Tue Aug 8 00:15:19 2006 +0000 For chrom-based assemblies, split $db.fa.out into per-chrom files for bigZips downloadable file generation (makeDownloads.pl). commit 043930102d21f39737f77581ce703f5c09ea16b1 Author: kate Date: Tue Aug 8 00:08:24 2006 +0000 Custom track config's are working now, so remove this disabling code commit 08ad4f3888442fe31cbd024a81e54cb82105504c Author: kate Date: Tue Aug 8 00:06:43 2006 +0000 Allow some vis settings from cart, for new custom tracks CGI commit 386ef0d0425e9e60bcdf3bc99d43d93b21ad72ff Author: kate Date: Tue Aug 8 00:04:48 2006 +0000 Move useful function out to library (hash.c) commit e06ca9f46e170244573b1fd1955b266fcaf55f0f Author: kate Date: Tue Aug 8 00:04:11 2006 +0000 Fix a problem with new tdb save turned up by wiggle testing commit bf2d216caee20ea2cda847ecf8f71b4facfe6fe8 Author: kate Date: Tue Aug 8 00:03:05 2006 +0000 Fix a wiggle problem commit dceeecab2e7f8d2e35150a848ea23a61b2e8840e Author: ann Date: Mon Aug 7 23:55:39 2006 +0000 updated date commit 77ed1541dd6c35d7e4176875661b3dd134d82876 Author: angie Date: Mon Aug 7 23:48:55 2006 +0000 David's request: when coloring nonsynonymous mRNA codons, do not color start and stop codons as usual -- color only different codons and make them red. commit 3c74d517b4ca02c9b79bb1fcd0aca8deefa397ac Author: markd Date: Mon Aug 7 23:43:02 2006 +0000 fixed bug when querying from table commit 52e02e43d9406449f5065e1426811bea4b5a73cf Author: angie Date: Mon Aug 7 23:41:49 2006 +0000 David's request: change option label "different mRNA codons" to "nonsynonymous mRNA codons" but accept the old label value if it is still in user's cart. commit 8fff9dd28c89ffb60c3091fce270e8d799259051 Author: kate Date: Mon Aug 7 23:13:59 2006 +0000 1. Add Refresh from URL feature 2. More tweaking layout aesthetics 3. Add mouseovers commit 9d63459a0918a4afc93eb6ba554e6160f1a66533 Author: kate Date: Mon Aug 7 23:09:29 2006 +0000 Suppress duplicate track settings during file save commit bc913764c395b315d6648d04f57ccd13364b1224 Author: kate Date: Mon Aug 7 23:08:31 2006 +0000 Add routines to replace and leniently remove, and a handy string generator moved here from customFactory commit 09edbfdf7e61f3e42b38a98dae392e4a42940367 Author: rhead Date: Mon Aug 7 23:05:00 2006 +0000 changed several uses of 'we' to the passive voice; made minor grammar changes. commit d71775fe9e73e044d7f6638487ffe6cb1a7056a1 Author: donnak Date: Mon Aug 7 22:44:47 2006 +0000 Edited opossum credits. commit e7a133070a8265bbc0b699a84308ae7e172f9603 Author: donnak Date: Mon Aug 7 22:43:59 2006 +0000 First draft of monDom4 news item. commit be341a92730ae584ce3a07f4812a221df6246130 Author: kuhn Date: Mon Aug 7 21:00:35 2006 +0000 removed some uses of 'we' and added a 0 in front of a '.5' commit 16f7a04ec71c3a2ac62c6b66c79070cac2e1a4b5 Author: angie Date: Mon Aug 7 20:36:45 2006 +0000 Added new setting showDiffBasesAllScales to mrna. commit 953419bc4e6a7767b0443d0d9e1fd60fa2feebe4 Author: angie Date: Mon Aug 7 20:21:55 2006 +0000 Added support for trackDb setting showDiffBasesAllScales which removes the zooming requirement for highlighting of different mRNA bases. commit 31a8da72f195c9039135ac7bb0005adf52f0d7c9 Author: donnak Date: Mon Aug 7 19:37:20 2006 +0000 Archived 1 item. commit 21c7f1dd7a473b5b25a9737dcba9e1ad78172bf1 Author: kuhn Date: Mon Aug 7 19:20:49 2006 +0000 changed so it will accept MySQL wildcard commit 1066f4597a13e0e8137ac74d2dd8b0badad62686 Author: kayla Date: Mon Aug 7 18:39:28 2006 +0000 added galGal3 commit 075673d1353d91de4484af8ec13f024eb2d66829 Author: donnak Date: Mon Aug 7 18:08:41 2006 +0000 Added monDom4. commit a13abddf40f2af51d1a0ff001f1789b2e53e46a8 Author: donnak Date: Mon Aug 7 18:03:26 2006 +0000 Added monDom4. commit 0974664d05e9cbd666ccfbeae51036a0d27286ed Author: angie Date: Mon Aug 7 17:44:27 2006 +0000 Make tickmarks for differing bases/codons red instead of white. commit f00558d6cf090add443c616a6b3ec28f421f9ac2 Author: angie Date: Mon Aug 7 17:13:19 2006 +0000 Split text input into files named by column value (e.g. by chrom). commit 172029b381c1fa496d9c9c5864a5e25f234ea29e Author: angie Date: Mon Aug 7 17:08:30 2006 +0000 Fixed filenames passed to tar cvzf for per-chrom downloads: was passing full pathnames which is a bad idea (tar keeps all of the path except for initial / or ../) --> pass relative filenames. commit c2904bef79123e9039cd035167bd97efd022172a Author: angie Date: Mon Aug 7 17:04:56 2006 +0000 Resolved -Wall warning: unused variable. commit abf7f7a34cb731b51fcf79265768f6bd243c6427 Author: kent Date: Mon Aug 7 16:40:32 2006 +0000 Making it so loader can return multiple tracks. commit c117fcdd18565d9999ea7b07dffa32546d179478 Author: kent Date: Mon Aug 7 16:21:31 2006 +0000 A little rearranging of customFactory code for better modularization. commit 18c663e64c23d61f036fe339049b8a76924818f9 Author: kent Date: Mon Aug 7 15:57:47 2006 +0000 Shortening lineFileErrAbort to lineFileAbort. commit d660d0ab5811745e311b9c895ddffb99dd93b294 Author: kent Date: Mon Aug 7 15:55:04 2006 +0000 Adding printf parameter check to lineFileErrAbort. commit de97fc85bc18ac0689ca5efb283fd02602ab8097 Author: kent Date: Mon Aug 7 15:48:05 2006 +0000 Adding lineFileErrAbort commit 407db29e0dee4164bfcd989877451c3b0e095f2f Author: kent Date: Mon Aug 7 15:47:45 2006 +0000 Testing lineFileErrAbort. commit 55bcbf1127cd543a49d5aeec7a97dc4393a0911d Author: kent Date: Mon Aug 7 15:00:30 2006 +0000 Adding some test sets for chromGraph. commit e3b00a35ef20616c91ac6103867a1be3074fa52d Author: galt Date: Mon Aug 7 15:00:19 2006 +0000 "Encode release log update" commit b2beee7f2b00e66ca62f8f1ac746aa1f38635e61 Author: galt Date: Mon Aug 7 15:00:18 2006 +0000 "Release log update" commit 2b6bd13d2bca0ebec8841324a0d86441f8ea2fc2 Author: aamp Date: Mon Aug 7 10:21:03 2006 +0000 Added some download options for restriction enzyme track. commit 3f96f84336a67deba85532e8b10f692b64e4ff2b Author: galt Date: Sun Aug 6 15:00:18 2006 +0000 "Encode release log update" commit f397e75727b62cd291653de386b6f499678e9944 Author: galt Date: Sun Aug 6 15:00:16 2006 +0000 "Release log update" commit 9d6a6ab61ccd42b65f550fd46fd323d4fa7d71e0 Author: kent Date: Sat Aug 5 16:46:16 2006 +0000 Rearranging code to separate factory helpers from framework functions better. commit fd0731ea9ce33f039f0d09ffe53c86fc452995c0 Author: kate Date: Sat Aug 5 16:27:13 2006 +0000 Defining some string constants, adding netUi. commit bc6d93bc6ee6833f5219fe679bc1151497287e14 Author: galt Date: Sat Aug 5 15:00:22 2006 +0000 "Encode release log update" commit 16d98dc0bfd601d66647fafbcc21a2ef5d75aa91 Author: galt Date: Sat Aug 5 15:00:21 2006 +0000 "Release log update" commit 8de8d4a60141654c14d347bbbfc3aa17608517b0 Author: kate Date: Sat Aug 5 07:33:41 2006 +0000 Clean up HTML file parsing commit f54a5f47c870c8c8cdd52239e36e576b256396a7 Author: kate Date: Sat Aug 5 05:23:00 2006 +0000 1. Integrate with new customFactory 2.Save browser lines initial position 3.Try some new buttons commit f14767df4ffcc4336e729100ddd935f304f33738 Author: kate Date: Sat Aug 5 04:06:24 2006 +0000 Fix unused variable commit e2e3360995456314fcfc14c792a1a23ca313b57a Author: kate Date: Sat Aug 5 03:44:17 2006 +0000 Name unnamed tracks with unique sequence number. Partial fixes to defunct test function commit 1b4766e95a06d9d573a560a1673ff0e1edd31db5 Author: kent Date: Sat Aug 5 02:52:44 2006 +0000 Improving error messages, and handling of tracks with no type= and no data lines. commit fc93dcecf816fa77cd609acd3e1e3df08562d69c Author: kate Date: Sat Aug 5 00:25:57 2006 +0000 Fix handling of input lacking track lines. Defers processing of default track so that recognizers handle it commit 8fcb0a1b1b86fed09128c11a27896d24148c87bc Author: heather Date: Fri Aug 4 23:38:29 2006 +0000 proper option for snpContigLocFilter commit d645422bd488da9ae6c7a8eccc038b5f3b996edd Author: angie Date: Fri Aug 4 23:37:50 2006 +0000 Corrected the recorded version of RepeatMasker (looks like a copy-paste- forget-to-modify error). Re-ran downloadable file generation to correct the too-long paths given in the .tar.gz files. commit 68ce2ee7f20533d0e0e8c550a8ee940c646f80bc Author: heather Date: Fri Aug 4 23:37:45 2006 +0000 add option for filtering MapInfo commit 17b2b524e8931ef35e77cb2e49df14fd28b91936 Author: hartera Date: Fri Aug 4 23:26:44 2006 +0000 Removed danRerBacEndNames rule for split allBacends tables on danRer3. Allow danRer3 to be used for bacEndNames rule. commit 726e42d3082d728bbea91aaad9a897dd0288d17c Author: baertsch Date: Fri Aug 4 23:17:07 2006 +0000 added for group reordering commit d7d3a79dc45ceeff50be82f7669f30aefb625ad1 Author: hartera Date: Fri Aug 4 22:54:45 2006 +0000 Program for extracting PSL alignments from a file for each item in an lfs file. commit 7a7e4a4e375fde2a78a699065ad08c2dd21eabc0 Author: heather Date: Fri Aug 4 22:46:58 2006 +0000 snp126 commit 08da59a66a3559004e0a460afd5b020d9fdc486d Author: hartera Date: Fri Aug 4 22:45:59 2006 +0000 makefile for extractPslForLfs. commit e7c55fb44ef29584ee01cf2b51a914d38fdbcd34 Author: hartera Date: Fri Aug 4 22:43:46 2006 +0000 Check if bacCloneAlias and bacCloneXRef tables exist before trying to query them. commit 549c0113c5a114e2bcdbcc1078832a6e893909c4 Author: hartera Date: Fri Aug 4 22:34:32 2006 +0000 Updated all_bacends PSL table. Only extracted the relevant alignments from the BAC ends PSL to create this table. Removed replicate rows from bacCloneXRef and bacCloneAlias tables and tested. commit 850bf5b7e1f516b456b0c2c735e8110c2cd40ef2 Author: archanat Date: Fri Aug 4 22:13:37 2006 +0000 Edited the description page commit 5fcf6ce37c6c5edeab9467adb9a870b963535755 Author: hiram Date: Fri Aug 4 21:50:05 2006 +0000 Mistakenly used danRer4 in the frames annotation, instead use danRer3 commit 561ea34af1a3d5272fbc2d94badc30f74637304e Author: baertsch Date: Fri Aug 4 21:20:17 2006 +0000 implemnt default group reordering commit 53e0561f7bd38af8544f4d0e2bc7ecf8440e436a Author: baertsch Date: Fri Aug 4 21:19:22 2006 +0000 cosmetic changes to track group commit cd7488495d34aea19c3b7ea455dca1b5b74d23a4 Author: baertsch Date: Fri Aug 4 19:46:58 2006 +0000 fix to support track reordering with short match track commit 52b1f715bb15d1350579811b4ec224977f1bc8c8 Author: baertsch Date: Fri Aug 4 19:45:51 2006 +0000 fix to support track reordering commit 718f71d316950ecaa147e7803a24f5bb76effded Author: rhead Date: Fri Aug 4 18:58:15 2006 +0000 Shortened Structural Variation track shortLables. Thanks, Daryl. commit bc5971dad1764918b97c592233c77e57af6fb1d6 Author: fanhsu Date: Fri Aug 4 18:46:18 2006 +0000 Removed "Submitter" info from GAD section per request from Kevin Becker. commit 4fe60f26b42d38e0d72f3f443e2835528ba4f103 Author: ann Date: Fri Aug 4 18:24:02 2006 +0000 adding new script - findLevel commit dbd20e8675bcb510b9cd6f52e47298a79c22e645 Author: ann Date: Fri Aug 4 18:23:36 2006 +0000 typo commit 90dcb1fdce57c1e9a2bcad38b437abbfdba68a11 Author: ann Date: Fri Aug 4 18:22:47 2006 +0000 new script to find where a track and its html is in the trackDb hierarchy commit a8afc7d952f3f7d83012ebbd7785b88826733d4f Author: galt Date: Fri Aug 4 18:20:33 2006 +0000 fixed help bug, improved usage messages commit a214304dc600a84dafdd75cc1e312de8c4515d95 Author: markd Date: Fri Aug 4 18:13:30 2006 +0000 added rheMac2 N-SCAN commit 91611237348424cbf252e911c8ac02664707e3ff Author: markd Date: Fri Aug 4 17:50:10 2006 +0000 deal with new argument to pipeLineOpen commit c80d7bc203bba0dfe54c2691f13e4a2183806523 Author: heather Date: Fri Aug 4 17:13:00 2006 +0000 handle chrUn commit 59fa9e9286a06f76bc481cb0bb5dfe665916a533 Author: heather Date: Fri Aug 4 17:04:31 2006 +0000 allow for loc_type == 2 for deletions commit d9c69d8b9a83ad066d92a5c034526b44f3d6216d Author: markd Date: Fri Aug 4 06:11:08 2006 +0000 imporved pipeline stderr redirect commit d60ed4d2ea2c3b119e84da359cdcece9995c2bcd Author: markd Date: Fri Aug 4 06:00:20 2006 +0000 added parameter to pipelineOpen to redirect stderr commit 0a3967f64e404eeb84df86c30432ece7c592406e Author: aamp Date: Thu Aug 3 23:21:51 2006 +0000 Extended some custom functions to allow multiple hgFindSpec tables to be used when multiple trackDb tables are used. Mark already reviewed the code and it's been tested somewhat. commit 1d4438a1fc9f3df837197e7c0624922ca89ec7c6 Author: hiram Date: Thu Aug 3 18:51:43 2006 +0000 Everyone needs the isCustomTrack() definition, include customTrack.h commit df025e25b42a09f9074c3a52bc936655fd5462a5 Author: hiram Date: Thu Aug 3 18:46:00 2006 +0000 Now getting definition of isCustomTrack() from customTrack.h commit c5e2fa5ff98fd81029e4c6c79f520f8feb3652a0 Author: hiram Date: Thu Aug 3 18:41:33 2006 +0000 Rework the webStartWrapperGatewayHeader business commit 82595662721296df846d8651bab998a6ecf7ae93 Author: kate Date: Thu Aug 3 18:29:38 2006 +0000 Remove prototype for subroutine moved to lib commit 354f68a7cd508c9ac3addb967739dfe567398800 Author: kate Date: Thu Aug 3 18:29:01 2006 +0000 Add a note for future work commit 5c0721d644c8488608cab0aa26813ada68d143aa Author: hiram Date: Thu Aug 3 18:18:40 2006 +0000 Properly use a define for the memory limit based on machine type commit 96d95acfe1008690234d2218f9138ef3db4ef4ae Author: hiram Date: Thu Aug 3 18:17:35 2006 +0000 Properly use a define for the memory limit of 2 or 8 GB based on machine type commit 75b37486b46f5b82166c2f328e547546c52ab919 Author: hiram Date: Thu Aug 3 18:16:45 2006 +0000 Defining a MEM limit to use which will be appropriate for machine type commit 8c9b3a57bb07538f086cf4fe6db83e4d4af4892a Author: kent Date: Thu Aug 3 18:08:47 2006 +0000 Refactoring custom track parsing system to use customFactories, which are more modular. commit fb7201aa4e7b03f73c4d0ca7b5f80f9b5701700d Author: kent Date: Thu Aug 3 18:07:16 2006 +0000 Adding semiUniqName, which is a part shared by the makeTempName and sqlTempTableName. commit 49ebc1687d95ed90de3308c813c8ecbe20306491 Author: kent Date: Thu Aug 3 18:06:03 2006 +0000 Freen tests some custom track stuff. commit 62090b23738ea9fb326bf775b0596ecdd246c1db Author: kent Date: Thu Aug 3 18:05:26 2006 +0000 Adding fake chrom graphs for testing. I've mixed feelings about this, but I think they are needed for hgGenome testing on genome-test. commit 88f811b7b89437c5eaaf72ee81df90ae7836ff0c Author: kent Date: Thu Aug 3 18:03:34 2006 +0000 Added sqlTempTableName. commit dc07201c3b43805e76b62edeb0ecbac199870ff4 Author: kent Date: Thu Aug 3 18:02:55 2006 +0000 Adding a little bit to some error messages. commit 419cfe403b85a5ee6817c0ed58346fba171b4248 Author: kent Date: Thu Aug 3 17:07:03 2006 +0000 Adding pipelineDumpCmds commit b221231e70c405b35dbe7334d229a3bd4c83bba1 Author: kate Date: Thu Aug 3 16:44:23 2006 +0000 Add 'Type' to display of cts commit 4e980f6b883f41f94cefd7cf716ac223fc8e7d83 Author: galt Date: Thu Aug 3 15:00:26 2006 +0000 "Encode release log update" commit 9a15a6a5c79467c078d05bf7d5a7daffac008741 Author: galt Date: Thu Aug 3 15:00:25 2006 +0000 "Release log update" commit 01d6ff6e4ec28351362c9407760ac7e3b3ba5a21 Author: angie Date: Thu Aug 3 00:52:55 2006 +0000 Fixed mrna base (or diff-base) coloring bug: filter color was ignored. The problem was that codon coloring was applied even when base coloring was selected. Added white tickmarks to mark differences when zoomed out too far for text, but close enough for codon coloring. commit 1bd53725bb3a5f27d6e0a6f2de8a0c81e73f6c3d Author: kate Date: Wed Aug 2 23:59:42 2006 +0000 Expand reporting of rejected blocks commit dce032f40fd8d8b359ec02919d3197adf2869319 Author: fanhsu Date: Wed Aug 2 22:08:28 2006 +0000 Created description.html. Initially just copied from SARS. commit bea3c65f1e43fb64e268c9d0126c28deb892bedd Author: genbank Date: Wed Aug 2 20:53:35 2006 +0000 renamed mgc trackDb table to trackDbMgc (doh!) commit 508854bbe6648e6f2f6ab8b2f49122126e2781a7 Author: genbank Date: Wed Aug 2 20:50:58 2006 +0000 updated to new A/B list tracks commit 81d772400ac4fbb740fdf07f8ced12c49271e71b Author: genbank Date: Wed Aug 2 20:39:56 2006 +0000 need eval in shell code to run on mgc server commit cfb22af188fc60136f78420e01b667c93d258eb1 Author: markd Date: Wed Aug 2 20:11:18 2006 +0000 added protein_id to info file commit ffb322ce74f4428aac0a515175bc928c775372fd Author: markd Date: Wed Aug 2 20:10:58 2006 +0000 support retieving gtf protein_id files commit dfbe05f7d0498047c1308b079e2fbd8fc93dd476 Author: markd Date: Wed Aug 2 20:10:11 2006 +0000 fixed long-standing bug in slDoubleCmp commit b337e1fff3979ddd1e38c43e95274d37059ca9ee Author: kent Date: Wed Aug 2 19:57:27 2006 +0000 Fixing indentation. commit 00c8ee330cde4f93c5ef943c2ffd42e123c24169 Author: fanhsu Date: Wed Aug 2 17:30:48 2006 +0000 Added exonPrimer link. commit 1403f07883410e7cbecde74ec08d1bbadbb2753f Author: angie Date: Wed Aug 2 16:46:58 2006 +0000 Made dm2 to dm3 liftOver chains using doSameSpeciesLiftOver.pl. commit e3b9e29d6887653f407373a0eb4f3856508a4c54 Author: angie Date: Wed Aug 2 16:44:26 2006 +0000 Resolved -Wall warning: unused variable. commit a97e76702a6a45fd94a2f485feec642be247f0f8 Author: baertsch Date: Wed Aug 2 16:18:04 2006 +0000 ensembl gene commit c12de03467392aae6fce4d63744d6f87c964a9be Author: fanhsu Date: Wed Aug 2 16:00:54 2006 +0000 Replaced gadExpand() with replaceChars(). commit e7da8475a5f824b4de854be804f0f94a8ae7f120 Author: giardine Date: Wed Aug 2 15:24:54 2006 +0000 removed DV track commit ccad52fca6a24e3c9f918ecebd97c94e4b0b0eb7 Author: galt Date: Wed Aug 2 15:00:26 2006 +0000 "Encode release log update" commit f282bf1c122e52df38c95771154f56833a9ae951 Author: galt Date: Wed Aug 2 15:00:25 2006 +0000 "Release log update" commit 00ace7d251d7e3973bc920438681a2914bc9cfe4 Author: donnak Date: Wed Aug 2 04:57:43 2006 +0000 Fixed typo. commit 91ffb907fa284b84348438c4e7a54e655dae4b1d Author: donnak Date: Wed Aug 2 04:26:36 2006 +0000 Updated date on galGal3 announcement. commit 803e2cd452760f51610d43ab75593fbf0a42bd14 Author: angie Date: Wed Aug 2 03:58:10 2006 +0000 swapped -> {chain,net}DroSim1. commit 0ddb35eba8d5646be4ea3bef453b44dd521a8bc0 Author: baertsch Date: Wed Aug 2 00:05:53 2006 +0000 implement default group track ordering when pressing default on config page commit ace4f7836b856f4027cd76fa14df868f77db0559 Author: kate Date: Tue Aug 1 23:40:14 2006 +0000 Mods to UI based on feedback from Mark D. and Bob K. commit 2e5d1e1cbc08d208991d3ebbb1912dc13a83b0d3 Author: hiram Date: Tue Aug 1 23:37:01 2006 +0000 Updated the dbRIP track with latest data, now ready to go commit 4387abe18d3f9022f2e9c6f62f1fd665f1369287 Author: hiram Date: Tue Aug 1 23:29:29 2006 +0000 Ping Liang requested a change to the short label for the Retrotransposon Polymorphisms commit 3e0698cb2b76338d60f24a603a151cfdf8981448 Author: angie Date: Tue Aug 1 23:16:47 2006 +0000 Swapped {chain,net} from droSim1. commit 88de7126d52bdd57f5cdf41b3c48001b2e192947 Author: angie Date: Tue Aug 1 23:11:38 2006 +0000 Re-ran doBlastz vs. droYak1 with better params. Ran doBlastz vs. droYak2 and added reciprocal best chains/nets for UChicago guys. commit 636e93b6707a503fdc294ed9a3e4fbb737f00702 Author: hiram Date: Tue Aug 1 22:16:40 2006 +0000 Added annotated frames to the multiz7way conservation track commit 32b2090786cc9922b3d1831175c0364e453e00fd Author: hiram Date: Tue Aug 1 22:14:38 2006 +0000 Proper month for release of Hg18, and now using annotated frames on the conservation track commit ae48dec44e889d4b3e616d4cc9701b4a87026a31 Author: fanhsu Date: Tue Aug 1 19:14:47 2006 +0000 Updated according to GAD's suggestions. commit 5c17995fa772cce3aba69d8ddc01c313d60bc824 Author: angie Date: Tue Aug 1 19:02:56 2006 +0000 Resolved -Wall warning: unused variable. commit 537a95f975519c215abbfd00085e93a713cfe4e8 Author: angie Date: Tue Aug 1 18:48:25 2006 +0000 Added -q (quiet) flag to cvs up commands. commit 107dbfae74952ba620a2be6ebb069d70da3ea457 Author: archanat Date: Tue Aug 1 18:43:11 2006 +0000 Added QA NOTE commit 3ac5602aa8781dc3987236c684343feff2ea21af Author: angie Date: Tue Aug 1 18:41:41 2006 +0000 Added noScoreFilter setting (requires hgTrackUi.c 1.295) to genomicSuperDups. commit 36befff0040338280d78024f34fde1b44cc554e8 Author: angie Date: Tue Aug 1 18:40:53 2006 +0000 Added support for new trackDb setting noScoreFilter to generic bed handler in specificUi. commit 33219834767191f495bfbd7c5e80b467c4b772ed Author: fanhsu Date: Tue Aug 1 18:37:31 2006 +0000 Updated hgc.c GAD section per modification suggested by GAD. commit 5a839a81c3087ddaf4055c0a1964d0e00845396a Author: fanhsu Date: Tue Aug 1 18:33:06 2006 +0000 Updated gad.c per modification suggested by GAD. commit 1270ae4b2c76ddb640e61de139b6fd49b14a7cc8 Author: kent Date: Tue Aug 1 16:59:29 2006 +0000 Adding microsat track build info. commit eb1ba10683c4b66cdb0092a330d44d7e19437132 Author: galt Date: Tue Aug 1 15:00:22 2006 +0000 "Encode release log update" commit fceb4bd1ef79c22424edca4931ab2741df38aaf0 Author: galt Date: Tue Aug 1 15:00:21 2006 +0000 "Release log update" commit 613748df8baadd9384fc3ae3eabce494647c1c66 Author: hartera Date: Tue Aug 1 03:23:09 2006 +0000 Updated the ChiPOTle peaks data to May 2006 update and renamed table. commit be6aff85303cd4f9b35884af9064b8a660369ed0 Author: angie Date: Tue Aug 1 01:36:39 2006 +0000 Added doRepeatMasker.pl to SCRIPT_FILES. commit 1233c9581c00738693abd4a41eb27d997987affb Author: angie Date: Tue Aug 1 01:35:36 2006 +0000 Fixed quoting bug and cleanup file name misspelling. commit 354b605114ce98936f2299dbc86a57f44500fe71 Author: kate Date: Tue Aug 1 00:19:55 2006 +0000 Restore file input functionality commit a5378abde547a01e6f47632a09022cad4e2e3558 Author: angie Date: Tue Aug 1 00:18:48 2006 +0000 Automation script for RepeatMasker (currently with its built-in species lib only). Results are loaded into the (possibly split) rmsk table and used to make masked twoBit /cluster/data/$db/$db.rmsk.2bit. commit ed00bb55a4891b4b8f4a70b9f93f035aadf2e8d0 Author: angie Date: Tue Aug 1 00:14:43 2006 +0000 Added -split (for loading split tables from one or more files). commit 4a47e7470e267f13f1b541f1c0bbc96e0b3ab3eb Author: kate Date: Tue Aug 1 00:13:35 2006 +0000 Improve HTML file naming -- instead of basing on track name, create a trash filename and save this as htmlFile= in the track line commit 3461e5f45c892560751a3219d2fd8009cce1654e Author: galt Date: Mon Jul 31 23:40:56 2006 +0000 Vidal and Wanker Human P2P interaction GS columns commit bab19d2f06f5ed60250b07c8c981f9c785c0eecf Author: galt Date: Mon Jul 31 23:09:40 2006 +0000 Marc Vidal and Erich Wanker - human P2P data columns for GeneSorter commit e23114c743d39fe2e5898603db252a478736f28e Author: angie Date: Mon Jul 31 22:37:02 2006 +0000 Added warning if BED file seems to have block coordinates (not supported). commit cbc39073c85590160dc4184adc75de7d384e0bc8 Author: angie Date: Mon Jul 31 22:28:43 2006 +0000 Added twoBitMask target. commit 147ee0b7dc81a0b036a84dc71010f518644abe2b Author: angie Date: Mon Jul 31 22:22:25 2006 +0000 Utility to apply masking to twoBit directly at the coordinate level instead of through fasta/lower-casing. commit 8f8125715ded47e8a697a8c2a8e02884a96877b6 Author: angie Date: Mon Jul 31 22:18:22 2006 +0000 Added twoBitFromFile for direct manipulation of twoBit data structures. commit 552cb536931cb826085adad6a5c3934451e3d75b Author: markd Date: Mon Jul 31 21:38:07 2006 +0000 fixed bug where last codon was being truncated because of not allowing for zero byte in protein string buffer commit 19698714a5fb05969c1eb16730a263121ff6f030 Author: kate Date: Mon Jul 31 21:14:07 2006 +0000 Was displaying trackUi for custom tracks with none -- this fixes commit d2b38f6d3a886665e2fb0a6ed8cc0d0d20c7efe8 Author: markd Date: Mon Jul 31 20:47:42 2006 +0000 added option to keep accession suffix commit a677a8b50e93fb92ae910ccc7d55e8d0d094aad2 Author: markd Date: Mon Jul 31 20:40:19 2006 +0000 do not corrupt stdout commit e798e78159069a5275ae98a67e4e6bdcedfd5815 Author: markd Date: Mon Jul 31 20:38:10 2006 +0000 added missing terminator in optionSpecs commit 85eafed86fa6ed59eccade03c9c0a6c9d4be032a Author: giardine Date: Mon Jul 31 20:10:27 2006 +0000 Changed default method of coloring Human Mutation track. commit 8784dfbf6a2f32ec957498bac1b8392b23e3d0ab Author: ann Date: Mon Jul 31 19:36:51 2006 +0000 reverting back to the v1.1 text (the v1.2 data is not ready yet). commit ac5a341c1c481c3d7e2a1b7eb2374e1eaf222746 Author: hiram Date: Mon Jul 31 18:47:49 2006 +0000 Adding upstream 1000, 2000, 5000 maf files for downloads commit 239395b6cbac7147ace56e897cc4069c97fdd86e Author: hiram Date: Mon Jul 31 18:47:23 2006 +0000 Adding ensGtp and ensPep tables commit 7ba37c91879e83df08d2e0b8b30388ee7a6dd14f Author: fanhsu Date: Mon Jul 31 17:15:38 2006 +0000 Updated H-Inv link. commit fc8501da94f9eb704461ed608ff6710fcd6e56c5 Author: ann Date: Mon Jul 31 17:07:12 2006 +0000 cleaned up reference link. commit 24caa02abeca473c98ceffaef7f7a2969d13d7f1 Author: angie Date: Mon Jul 31 16:49:35 2006 +0000 Re-ran annotation of MAF and subsequent steps (downloads, frames) after Kayla found overlaps and Brian fixed mafAddIRows. commit c0f499a22a9c865f60690c590a18c23b5f9fbe92 Author: angie Date: Mon Jul 31 16:25:32 2006 +0000 Resolved -Wall warning: unused variable. commit 74f32cc6458e3ab17293c71c990af1a11fc96893 Author: markd Date: Mon Jul 31 16:23:15 2006 +0000 added N-SCAN track commit b55a7753b41f4277b264c3dc852d104ce714d228 Author: giardine Date: Mon Jul 31 16:04:17 2006 +0000 Added perl scripts and other code that helps in parsing LSDB data for the Human Mutation track. READMEs give details for each LSDB. commit db4af17fbb533f007c5a6193c62c10fd257f8c19 Author: fanhsu Date: Mon Jul 31 15:56:51 2006 +0000 Updated links to H-Inv. commit 99a5f27b9e7bd8a01ec75cd01184dfb8a7edb19f Author: giardine Date: Mon Jul 31 15:49:24 2006 +0000 Updated how Swiss-Prot entries are computed, and documented most recent reload with new sources and improved Swiss-Prot variants. commit 6d1a3e1236b95aeceee60be3fab35f7346a68369 Author: galt Date: Mon Jul 31 15:00:17 2006 +0000 "Encode release log update" commit 2f9562473f245024ae6540a99731e5ace449934c Author: galt Date: Mon Jul 31 15:00:16 2006 +0000 "Release log update" commit 6cc395e4af7f48b5aabe0cbe9b3ac1c3404c4e7d Author: galt Date: Mon Jul 31 05:38:08 2006 +0000 fix mem leaks commit 17a37dfab627d3c28e262eebc4b62ccdc975f5c1 Author: galt Date: Mon Jul 31 04:56:34 2006 +0000 fix mem leak commit fca6fa24b0b2dbffc8be4c6575e853af44262003 Author: hartera Date: Mon Jul 31 03:07:09 2006 +0000 Added affyUi for affyZonWildType track. commit 65e4d62c319f51086029fd710d0ff619566dee1e Author: hartera Date: Mon Jul 31 03:06:29 2006 +0000 Added track handler for affyZonWildType track. commit dbe5d30af08f72cb302d48693a15f4f0f093221f Author: hartera Date: Mon Jul 31 03:04:40 2006 +0000 Changed extras for MedianExps table and reloaded Median tables for Zon Lab data. commit b0ec596d069035c876809150a2daf448c84a12a3 Author: hartera Date: Mon Jul 31 01:37:58 2006 +0000 Added more information about Zon lab microarry data and noted that two of the data tables were renamed in hgFixed. commit c3a0e8c9e6479a253c00b63a2cc6c35c13616041 Author: hartera Date: Mon Jul 31 01:35:40 2006 +0000 Documented that Affy Zon WT data tables in hgFixed were renamed. commit 9ce958879602f812b6fcdde242cca638294822a3 Author: hartera Date: Mon Jul 31 01:25:39 2006 +0000 Changed names for zebrafish Zon WT array data tables. commit 1bb8d85212d7809eb25c0a87ce0e98cdab5a24b4 Author: galt Date: Sun Jul 30 15:00:18 2006 +0000 "Encode release log update" commit fd045057599047f2c69ac63b582494f104df5bb2 Author: galt Date: Sun Jul 30 15:00:17 2006 +0000 "Release log update" commit 47b2945c2e9a1a877f05cfe166890ec5e39d7a7f Author: galt Date: Sat Jul 29 15:00:23 2006 +0000 "Encode release log update" commit 6fa7b39b6c06009bc2122749c197c27986794040 Author: galt Date: Sat Jul 29 15:00:22 2006 +0000 "Release log update" commit 30cbedf8e1a17dceaac62f7eed9d7b8ac5b44a9d Author: markd Date: Sat Jul 29 05:51:58 2006 +0000 added hgSelect cmd to make it easier to get data from split or binned tables commit f15d322af5ee8b520c5da8909263a7937bd92838 Author: galt Date: Sat Jul 29 00:17:28 2006 +0000 fixed memleak in htmlPageFromForm() commit f490f47a8209335a52c98dbfa60a1ac8fba01ad5 Author: hiram Date: Sat Jul 29 00:02:02 2006 +0000 Incorrectly moved the printout of the details page into the incorrect location commit ae447468e6f89ed222014bbfd7f1dc532831f375 Author: hiram Date: Fri Jul 28 23:56:17 2006 +0000 Incorrectly moved details page printout to the wrong place commit d579aaeeca4d3218cae4e8e0a1aee917f5117c34 Author: donnak Date: Fri Jul 28 23:42:21 2006 +0000 Edited this description. commit 537dbf58c6543f0bb22061fd073b830b5327604e Author: galt Date: Fri Jul 28 23:41:41 2006 +0000 fixed memleak in formParseVars() commit 49e6b542a690976f6f4e0095b929a214b5e8c0d0 Author: kayla Date: Fri Jul 28 23:40:04 2006 +0000 added monDom4 commit 7e9650b8a56040cef1f9f13d6a65bc2871d8e590 Author: hiram Date: Fri Jul 28 23:34:18 2006 +0000 A free() call was causing a seg fault, change to freeMem and it is OK commit a5626dc04ed0a0823cc1c5d5ec3d44c07af0a269 Author: donnak Date: Fri Jul 28 23:29:26 2006 +0000 Archived an item. commit a10e8eff84db269674102a32718c49cba1d60802 Author: donnak Date: Fri Jul 28 23:28:29 2006 +0000 Added announcement for galGal3. commit 9077b36f591db42f1e3e1184643da1a35b4030cf Author: galt Date: Fri Jul 28 22:42:47 2006 +0000 oops, that was not the memory leak commit 748b8a00050e81ddb0468dea36ab3bba52d20ff5 Author: galt Date: Fri Jul 28 22:38:46 2006 +0000 fixing memory leak commit 1ab241257043fa9d70d47ce689f22c552a4e4fdc Author: hiram Date: Fri Jul 28 21:35:53 2006 +0000 Raise correlation point limit to 300,000,000 the 64 bit 8 Gb machines can handle it easily. And some more extensive debug options available with the correlation. commit 7e764a0f409aaff38d136e26465696423dae1c53 Author: ann Date: Fri Jul 28 21:23:26 2006 +0000 changed priority of panTro2 chain/net commit 042ba991eef47ec1cc90170539d6f5c40725b52f Author: ann Date: Fri Jul 28 21:22:52 2006 +0000 copied from top level commit f2c4bfef94fce93c787bf2242504a7da188c0929 Author: ann Date: Fri Jul 28 21:09:49 2006 +0000 added blocks for chain/net to panTro2 including matrix commit b8ed717f20c06a720d8ea5b197b0ef2c7ea75a6b Author: ann Date: Fri Jul 28 21:09:29 2006 +0000 copied from top level commit 7b435375afb4ee1396d8af7b9cb8fa6c9c6ad98f Author: kent Date: Fri Jul 28 21:06:40 2006 +0000 Changing case insensitive firstWordSame to case sensitive startsWithWord. commit 232832b2f09d9cd31e06f7ce2be34cc1ca374f7a Author: kent Date: Fri Jul 28 21:05:51 2006 +0000 Testing startsWithWord. commit c6fbd3d13e7f5f353bae4efae77882dad5c3be34 Author: kent Date: Fri Jul 28 21:00:56 2006 +0000 Adding bedKnownFields define commit 10520e7577d51cf3490f2c7c87b36489232370d5 Author: kent Date: Fri Jul 28 21:00:10 2006 +0000 Adding firstWordSame commit fc71e66544e2ee9162a6fbf1f2dad217c420424c Author: kent Date: Fri Jul 28 20:59:34 2006 +0000 Testing firstWordSame commit 313d51be41a65c9d6517c4f5cc642c41712bb7c3 Author: hiram Date: Fri Jul 28 19:51:49 2006 +0000 One more encoded name in the custom track visibility pull down menu label commit 292b4c33fd717707b9bd46a070392d2d68f97434 Author: ann Date: Fri Jul 28 19:40:07 2006 +0000 added blocks for panTro2 chain/net with matrix commit ed9b70a8bcc584ad731a252f2bbb2d9d975eb149 Author: ann Date: Fri Jul 28 19:39:31 2006 +0000 copied from top level commit 9bb3c0fbe0c574dddfa3753416f507ae3249fd8d Author: ann Date: Fri Jul 28 19:23:08 2006 +0000 fixed error in chainGalGal2 block commit 44434c7df6fb1d85a0ae45cceef2e78a7201e626 Author: ann Date: Fri Jul 28 19:20:46 2006 +0000 copied from top level commit 85b10e93a006eb5949cefb279f9bd24aca8a62eb Author: ann Date: Fri Jul 28 19:18:34 2006 +0000 added chain/net to galGal2 with matrix commit d3217ed721f9de51c2bb2917b0eedebbe6443567 Author: hiram Date: Fri Jul 28 19:18:20 2006 +0000 Beware of custom track clicks on items, don't try to go to any database to get schema and so forth. Just print out the html description if there is one. commit fb4559c877cfce4c9ced9c9ffa7acf4db7086652 Author: hiram Date: Fri Jul 28 19:14:40 2006 +0000 For custom tracks, don't try to go to a database to get the description page commit 9562898da3f34629cb0b65a0db2a39c7064a0874 Author: lowe Date: Fri Jul 28 19:12:49 2006 +0000 Added fourth parameter to specify the "KEGG" genome id -- allows "make-browser" program to figure out correct KEGG id on the fly and pass into program (instead of static case statements) commit 1d829c532ebe806c5f91ddc18f1e8b0bb3f7bcf5 Author: angie Date: Fri Jul 28 18:50:29 2006 +0000 Resolved -Wall warning: unused variable; format %d -> %ld.w commit f1bf0220235e33aa2afc896182823361a508d600 Author: hiram Date: Fri Jul 28 18:45:49 2006 +0000 A couple more cgiEncodings of track names on hgc, hgTrackUi and map box URLs commit 371eef042ab8af717fc4523f0c5f61cab5579d4d Author: hiram Date: Fri Jul 28 18:18:30 2006 +0000 no quotes allowed in custom track names or descriptions commit b93c05cd55cc445b29c14ba21ae3e643374241b1 Author: giardine Date: Fri Jul 28 17:46:48 2006 +0000 Moved gv tables to hgFixed database commit c4af0e3b56c5636d61040298509496a4019def81 Author: giardine Date: Fri Jul 28 17:28:08 2006 +0000 updated schema for omimTitle table commit 3effd313fe5b505e0351d86568eb9a407d787ed1 Author: baertsch Date: Fri Jul 28 17:27:01 2006 +0000 rename rmskNew to rmskCensor for repeatMasker annotation by CENSOR (giri insitute) commit 1e43826e86fb7ecc00e134b6e5db588caef20485 Author: baertsch Date: Fri Jul 28 17:23:06 2006 +0000 register rmskCensor repeatMasker generated by CENSOR (giri) requsted by Brian commit c86f9b3f94a7d68e0e4cb435c953b94cc6ed836e Author: giardine Date: Fri Jul 28 17:19:13 2006 +0000 moved gv tables that are not build specific to hgFixed commit 4687975b9142cf53b7a3ea0a84decb746e41efa0 Author: baertsch Date: Fri Jul 28 16:58:49 2006 +0000 fix description commit 7027667df7f73a2867a060582e77d341b4843521 Author: braney Date: Fri Jul 28 16:56:04 2006 +0000 make a fix to a bug the resulted in the spurious generation of annotation blocks commit e10856cf232648de24a7ad24d0c74089fcc37449 Author: baertsch Date: Fri Jul 28 16:05:42 2006 +0000 add nucleasome best and stable be commit a526d37cf261fd5cf72fb1f01dab1546791692b2 Author: giardine Date: Fri Jul 28 15:42:43 2006 +0000 Added new attributes under protein effect. commit 3ef6b871a066380f1bf06107887f4b8a122fc819 Author: giardine Date: Fri Jul 28 15:25:51 2006 +0000 Add free connection when leave subroutines early. commit 2cc4835d5decaf67fe70e70598a8ee2457512ce6 Author: fanhsu Date: Fri Jul 28 15:19:15 2006 +0000 Added gadExpand() to accomodate GAD processing of "'" in disease names. commit d17c71b2e72e004ebf192f16b0269588cd940819 Author: fanhsu Date: Fri Jul 28 15:05:38 2006 +0000 Added hg17 -> hg15 liftOver. commit 4c5f5c4c9948ba36cf0c2d96d0f14a0e6c4d8944 Author: galt Date: Fri Jul 28 15:00:25 2006 +0000 "Encode release log update" commit 3d6e11f439f6757aecca8a6250bd17dbd5b2e8e5 Author: galt Date: Fri Jul 28 15:00:24 2006 +0000 "Release log update" commit 26deeb6f8a3923ed2c2bd41cdd70410b6bef559b Author: baertsch Date: Fri Jul 28 06:23:12 2006 +0000 remove old header files commit b49495d0bde6b6803eb378b88897962f3445c95b Author: lowe Date: Fri Jul 28 06:16:41 2006 +0000 add lowelab.o commit 272749c2d4deb6a21c7ddd2241c3405eb3bb108b Author: lowe Date: Fri Jul 28 06:14:21 2006 +0000 move lowelab click code from hgc.c to lowelab.c commit 5f36c635e269f54114477b475f00f29a772ac0a2 Author: lowe Date: Fri Jul 28 04:23:34 2006 +0000 changes for archaea gene detail page cVS: ---------------------------------------------------------------------- commit 8b6a3fc4185a7f12cbfe2989b34d4e3aa549aca6 Author: lowe Date: Fri Jul 28 03:42:33 2006 +0000 kegg code mapping commit e2f8c289ab7553d99bfa1f36ef5cd75a3939766f Author: baertsch Date: Fri Jul 28 02:38:18 2006 +0000 fix pfam description for archae gene details page commit 69f6fb1ba2f5f8ce9a022c0f06a703da99ec5dc1 Author: baertsch Date: Fri Jul 28 01:49:32 2006 +0000 make grep case insensitive for kegg download commit 5ad5d29d813204105c06d969979928acd8530b1d Author: baertsch Date: Fri Jul 28 01:48:53 2006 +0000 case sensitve bug commit 7c9774fc9a23b69fdb1a8aca47e7870c54abd1e6 Author: rhead Date: Fri Jul 28 01:08:12 2006 +0000 Added note about renaming BAC End Pairs tables. commit 833d530325037436b8759d96a15ed0d6a3090c45 Author: kayla Date: Fri Jul 28 00:49:21 2006 +0000 Added three searching blocks to enable searching for affyMOE430 commit c99a0435654b2ef740ca7ba034b7d3fb2ef999b5 Author: hiram Date: Thu Jul 27 23:25:04 2006 +0000 Avoid installing the test scripts on an ordinary install. commit e0b6794e0282aff68312c5aa175d22a621b153cf Author: archanat Date: Thu Jul 27 23:18:38 2006 +0000 Changed the order of organisms commit 14907596b921c86b2b1a9c80124b59259cf23cc8 Author: hiram Date: Thu Jul 27 23:13:32 2006 +0000 The disease search didn't work commit 658c87b9df6a46321557f984cd7f3259eb34d10a Author: donnak Date: Thu Jul 27 23:13:27 2006 +0000 Edited chicken credits for galGal3. commit 11b7beb4a482781ce4c1e739cda63b1cd20d1bf1 Author: hiram Date: Thu Jul 27 22:53:48 2006 +0000 Add a clean target commit f7c579d96ad4ef8e30ed26ae7ea68e67b36ff78c Author: kuhn Date: Thu Jul 27 22:45:59 2006 +0000 added image commit ff4a744fab973a0dbe2946a4f77aa4f37257eb9f Author: kuhn Date: Thu Jul 27 22:42:05 2006 +0000 new image commit 1ec489d155db68656021cc902d225628123795e6 Author: hiram Date: Thu Jul 27 22:39:28 2006 +0000 Better malloc limits for machine types, and some extra information about gaps on verbose output commit ba6fde9901c2f08a334dc5ffcb3e2e8bfd7c4e4a Author: hiram Date: Thu Jul 27 22:36:11 2006 +0000 Add a compile target for debugging commit 06551b013ff19f9dc19b3fe9dc78d8dce9195a96 Author: hiram Date: Thu Jul 27 22:35:32 2006 +0000 No limit applied to kolossus only. Can now work on hgwdev commit 572ddae0d8d93b46fd6b48ca6808fc7c153d9ca7 Author: hiram Date: Thu Jul 27 22:33:45 2006 +0000 The doTest should be ./doTest for security conscious shells that do not have . in PATH commit 5a9c4dc3533c61d0723195559f5b895d9d9b25fc Author: kuhn Date: Thu Jul 27 22:33:14 2006 +0000 changed a name back to xenopus to match others commit 6810a2fe69793264fec3f6859d9acad5b87db919 Author: hiram Date: Thu Jul 27 22:32:47 2006 +0000 Raise MAX_ID_LIST limit to handle much more in Mm8 commit a9ac0e775f2acd72f4500da8a81b97c0d36a412d Author: kuhn Date: Thu Jul 27 22:20:21 2006 +0000 added image to Conservation track for monDom1 only commit 3dcaf818028fadd69d7b0cd77fea9a0873896aef Author: hiram Date: Thu Jul 27 22:15:15 2006 +0000 Add compile target for debugging business commit ea73e0b6bed88ca63395beddf8bc33b8d85191f4 Author: hiram Date: Thu Jul 27 22:14:26 2006 +0000 Add more output on verbose=2 for waba lift debugging commit ea7511535418780b2a8fb9e0df3d18e69e82fbfc Author: hiram Date: Thu Jul 27 22:12:42 2006 +0000 Better warning message on custom track size limit reached commit e2a66b0336b736e5461244e285b9af851376dbed Author: ann Date: Thu Jul 27 22:11:35 2006 +0000 resetting order of species in Conservation track commit fd3813f82adafb1eb2d68a9eae874e93e5c3c3a4 Author: rhead Date: Thu Jul 27 21:49:58 2006 +0000 Changed number of Tuzun sites after editing cnpFosmid table to delete name='Gap'. Also minor grammar/punctuation changes. commit 335e6b2fd3114c223d4b38206057190b24d39b83 Author: rhead Date: Thu Jul 27 21:45:29 2006 +0000 Minor changes: single to double quotes; are-->were. commit 7c2e21aab7f9c426d258a5dcc4c183f638e17108 Author: hiram Date: Thu Jul 27 21:36:59 2006 +0000 Must decode incoming FORM NAME variables too, not just their values commit 592d36326db08b1a41b6bc70a16d2deb62db886f Author: ann Date: Thu Jul 27 21:31:00 2006 +0000 changed order of species in Conservation track commit 9f37ecc89516df2cdadf8bfa12945bb257f81ea9 Author: rhead Date: Thu Jul 27 21:28:30 2006 +0000 Added note about editing the cnpFosmid table commit 3c960582951ac6457276f0c92930f7bad4531ec6 Author: kate Date: Thu Jul 27 21:16:13 2006 +0000 New screen layout. Initial checkin -- file upload needs resuscitating commit 1b51e62cd914984103cc2a425071d941b45453cb Author: kate Date: Thu Jul 27 21:15:08 2006 +0000 Support for HTML docs for custom tracks commit c3bc8e11b192856aca8d91b4790dab0b20dcf5af Author: kuhn Date: Thu Jul 27 21:10:29 2006 +0000 changed the other usage of 23way image to gif version commit 096bb3e2b2eb474ff2eeead1a7d7bd0d3a50759a Author: kate Date: Thu Jul 27 21:02:14 2006 +0000 Libarified a custom track routine commit 99e83ad283d7381c12ea1da059f87b40238b1ce9 Author: kate Date: Thu Jul 27 20:58:41 2006 +0000 Library changes for hgCustom; support for HTML doc files, add defined constant for filename convention commit 44139852b8540fc4163f60bb3fb09044e915c0cf Author: kate Date: Thu Jul 27 20:41:58 2006 +0000 Redo reciprocal best with hg18. Additional work on conservation track commit f4aa283f3c0d6ac640c7b4a8b850ac9ee13f071b Author: baertsch Date: Thu Jul 27 20:34:04 2006 +0000 add comment commit 73708dea28ea4abb04ac67860794c2029a543e0d Author: archanat Date: Thu Jul 27 19:05:36 2006 +0000 Added matrix value to chainMonDom4 commit 1f3eaacc8686c9f092ad84ef007b04501ee8dade Author: archanat Date: Thu Jul 27 18:59:57 2006 +0000 Copied mm8 chain/net to the organism level and added matrix value commit 39ad6738b6b6c1ca6b7419d24f07c35a63efcfaa Author: kuhn Date: Thu Jul 27 18:56:31 2006 +0000 changed some wording to conform to convention used in other images commit d954b35beb297f6f086d7666d082086d2c939aa9 Author: donnak Date: Thu Jul 27 18:29:46 2006 +0000 Fixed some typos & made a few minor edits. References to the Experiment Display configuration menu are erroneous at the moment -- am checking on why these don't display. commit d9c6e3a8a823f51d5439e64c7803eb3c3fbc2bd0 Author: hiram Date: Thu Jul 27 18:08:38 2006 +0000 Better error printout for problems with a variable name commit 630d778e2939f92601e46333679652cdbff823b3 Author: giardine Date: Thu Jul 27 17:49:19 2006 +0000 added coloring and exclusion based on disease-association and explainations to html commit 96b84bf144d102cee9eedf2143efccc9f4fb44a6 Author: galt Date: Thu Jul 27 15:00:03 2006 +0000 "Encode release log update" commit e09be67f812a9866b32ea336372ae9e09ba48e14 Author: galt Date: Thu Jul 27 15:00:02 2006 +0000 "Release log update" commit fac2898d6aaeb241a20126431d7b84f65b5b6a93 Author: genbank Date: Thu Jul 27 07:15:38 2006 +0000 fixed problem in BCGSC tracks commit acf8ecce343ed46d64b60bd9a9fa130e564920d0 Author: baertsch Date: Thu Jul 27 07:05:46 2006 +0000 E Segal nucleasome track - Nature July 2006 commit 76ee0353c7dda379bd7d8cea458f7fedb8d6d2d3 Author: genbank Date: Thu Jul 27 06:52:15 2006 +0000 added new BCGSC clones commit af1b8fa7f189b5c973298ce67b442c65dbba5078 Author: baertsch Date: Thu Jul 27 01:40:43 2006 +0000 do not default priority when pressing hide all or show all commit 9c396f2c855600512d5fd5ab4de1ecc65ea86a0a Author: baertsch Date: Thu Jul 27 01:35:01 2006 +0000 fix default bug on track reordering reported by Brooke commit c90b88a15e76adcc1d43594726ae6c672c20bb8c Author: hiram Date: Wed Jul 26 23:29:19 2006 +0000 Fixup menu items that have unusual characters commit aeb461ba5ff4ed05af2a9eee21140688dab813e6 Author: kayla Date: Wed Jul 26 23:26:56 2006 +0000 added galGal3 commit 2a60e4c4b4df510be0ff45b196c879e20be57ecb Author: kuhn Date: Wed Jul 26 23:22:34 2006 +0000 changed consservation image to a gif commit 66537e549f1369d17bdef898f07d7608fcc86fad Author: kuhn Date: Wed Jul 26 23:21:10 2006 +0000 hg16_23way.gif commit 44bf4b3667acb0564c8f8473ada99d841e8f1f9d Author: kate Date: Wed Jul 26 23:19:06 2006 +0000 Pretty up table browser error message for missing chimp chroms in position query commit f1e695f2a9b4bd3424b8d5a63b970e0270e51df6 Author: baertsch Date: Wed Jul 26 23:07:52 2006 +0000 allow user to move tracks between groups, remove cart variables if they match trackDb settings. commit 569066e8b418cd6f157c245f9d270cf29c5778ee Author: kate Date: Wed Jul 26 22:59:56 2006 +0000 Add conservation wiggle, codon framing, and tree drawing to Conservation track commit 4de1dcfcdee27ee440979df149faada545eb3d3e Author: archanat Date: Wed Jul 26 22:41:06 2006 +0000 Added monDom to xrg commit 327d5ddf2fb7c219db060120947c7c048e3d2e32 Author: angie Date: Wed Jul 26 22:14:57 2006 +0000 Several old changes: Reloaded flyBaseNoncoding, flyBase2004Xref; reloaded flyBaseGene; recip-best alignments for UChicago guys with new process. commit ae3a9bdbe9f500cf61dbbacefdb4f8847c50dff2 Author: galt Date: Wed Jul 26 21:44:39 2006 +0000 minor fixes commit f433a0832b0227a65ea88d9dea60e244f0b7b259 Author: hartera Date: Wed Jul 26 18:57:36 2006 +0000 Changed log scale for affyZonWildType track. commit 4363767a5461f90952cbc10668c86263d377d230 Author: hiram Date: Wed Jul 26 18:38:59 2006 +0000 Remove ancient garbage debug fprintf() statements commit 8d08731ee6e07b2e38dd719ead3b04f2611c9499 Author: hartera Date: Wed Jul 26 18:38:29 2006 +0000 Updated to latest Ensembl predictions for Zv5. Ensembl 38 is same as v32 for protein coding genes. commit d670b22df6fbb87051df4385e226a436cea1d5b8 Author: baertsch Date: Wed Jul 26 17:45:28 2006 +0000 remove redundant meta data code from lineFileNextReal commit 19be8eaceabafd1d9ec2fe9230e1d8bae70c6965 Author: kent Date: Wed Jul 26 17:36:08 2006 +0000 Adding customPpNextReal. commit 701adb0d9a11cf24dde96b69ca8e5200efb28cf3 Author: baertsch Date: Wed Jul 26 17:01:50 2006 +0000 meta data optimization requested by Jim commit dab3a47e0121ac7d96033f917af4282f1e7a35e1 Author: angie Date: Wed Jul 26 17:00:00 2006 +0000 Replaced kludgey exiting-shell-script method of setting emacs mode with proper mode line. commit 5c86fb79d4d05cc6846b61a6ae6709383f2ad79a Author: archanat Date: Wed Jul 26 16:58:48 2006 +0000 Moved panTro2 chain/net to organism level and added matrix commit 663b4e11e8da93bfc6390eadaf44ef5a2748d649 Author: fanhsu Date: Wed Jul 26 15:32:05 2006 +0000 Minor edit. commit a74be25b7f3de7ff0e7004f7abc83724b525ebda Author: fanhsu Date: Wed Jul 26 15:29:24 2006 +0000 Minor edit. commit b62478b08f00c12846f3c0f123a93eca0378e1cc Author: angie Date: Wed Jul 26 15:25:20 2006 +0000 Resolved -Wall warning: unused variable. commit 81968a25519b425fd192c0a382baae713142fb75 Author: fanhsu Date: Wed Jul 26 15:20:42 2006 +0000 Changed sprintf to safef and strdup to cloneString. commit f716aced2936222dde45e712a914af8031dcb290 Author: galt Date: Wed Jul 26 15:00:03 2006 +0000 "Encode release log update" commit ffab8cded9176031c99e39005cc8e81485dabda3 Author: galt Date: Wed Jul 26 15:00:02 2006 +0000 "Release log update" commit 47cf06fb5bf136e28fd983bf21103b1e6bf12aa2 Author: markd Date: Wed Jul 26 06:12:28 2006 +0000 fixed warnings commit 67c1c87a313f007896dc15c0e31affe6056f4f9b Author: kent Date: Wed Jul 26 06:10:37 2006 +0000 Seems to work commit ca83bce8391e022ef94c3a661a76bcbd47f8de13 Author: kent Date: Wed Jul 26 06:10:21 2006 +0000 Testing customPp.c commit 31ad0dd6d817653f488ee0ff3f1bf4b01854a2cc Author: kent Date: Wed Jul 26 06:03:00 2006 +0000 Added lineFileCloseList. commit 5af93cbc4d54160c04aa5cd76ee5ab4e0f289595 Author: markd Date: Wed Jul 26 05:54:27 2006 +0000 move src/hg/makeDb/tailLines to src/utils/tailLines commit 009276f4a900d23d835d157f884c78b99c4b01b2 Author: markd Date: Wed Jul 26 05:53:20 2006 +0000 move tailLines src/utils/tailLines commit 21ac5bc2901c9ce7f5cf077f3da7e839d2563073 Author: markd Date: Wed Jul 26 05:52:40 2006 +0000 renameTo: src/utils/tailLines/tailLines.c commit 41a6002df27969de7d5fac10dbf23607c0131dc5 Author: markd Date: Wed Jul 26 05:52:32 2006 +0000 renameTo: src/utils/tailLines/makefile commit a019cf6f4ba267606739b529da62d82f2d99be67 Author: markd Date: Wed Jul 26 05:51:51 2006 +0000 renameFrom: src/hg/makeDb/tailLines/tailLines.c commit 12d6109e38952dabdebb0570a4e29eb823552139 Author: markd Date: Wed Jul 26 05:51:42 2006 +0000 renameFrom: src/hg/makeDb/tailLines/makefile commit 45b8438844165d3b1144a52c9e862bee81606cc4 Author: markd Date: Wed Jul 26 05:43:33 2006 +0000 added options for skip certain steps commit f52de2295c63c4e8680926646142df96158354b4 Author: markd Date: Wed Jul 26 05:38:55 2006 +0000 fixed compile issues with outside directory commit 0d28aaf1d994baf439225478dd554702321e9bfb Author: baertsch Date: Wed Jul 26 05:32:55 2006 +0000 add hg.conf option to enable track reordering commit bb2931bb743ec52367ca344769d3f89ef0e37198 Author: markd Date: Wed Jul 26 05:10:02 2006 +0000 added build of outside directory commit 1a435a617c0a1690ddd487a3235be5338f343aca Author: markd Date: Wed Jul 26 04:59:20 2006 +0000 moved many modules to outside directory, fixed some compile warns and DOS format file commit c71b10f4c9ac58cf636f24e758395945913c2915 Author: markd Date: Wed Jul 26 04:55:36 2006 +0000 added one more level to includes to handle outside directory commit 2a91c5ff06633e8d23775c0860a3e551595557f0 Author: baertsch Date: Wed Jul 26 04:18:03 2006 +0000 add -chromSize=sizefile read chrom sizes from file instead of database. commit a7764858385ee756b31dd27771f7f871f19c1b01 Author: baertsch Date: Wed Jul 26 04:16:42 2006 +0000 rerun autoSql to get latest code commit aa15e6b0957b47fbfc61f17596b9efdc76671f56 Author: markd Date: Wed Jul 26 04:01:36 2006 +0000 renameTo: src/hg/makeDb/outside/yeast/hgYeastRegCode/makefile commit a334039b3e8c3f5575d134c89386928a1bc2786b Author: markd Date: Wed Jul 26 04:01:35 2006 +0000 renameTo: src/hg/makeDb/outside/yeast/hgYeastRegCode/hgYeastRegCode.c commit cc2ebdb0e7532844767c626dfd21545de409e238 Author: markd Date: Wed Jul 26 04:01:34 2006 +0000 renameFrom: src/hg/makeDb/yeast/hgYeastRegCode/makefile commit b2a488f39ed2a5d949c93faf2dff39ccbceda529 Author: markd Date: Wed Jul 26 04:01:33 2006 +0000 renameTo: src/hg/makeDb/outside/yeast/hgSgdPep/makefile commit 47375aad358c98e5981a366e03ff5bb9973f2aaa Author: markd Date: Wed Jul 26 04:01:32 2006 +0000 renameFrom: src/hg/makeDb/yeast/hgYeastRegCode/hgYeastRegCode.c commit 27d2bdf818abcaabfb2ba439b4703e1cf48fcf0d Author: markd Date: Wed Jul 26 04:01:31 2006 +0000 renameTo: src/hg/makeDb/outside/yeast/hgSgdPep/hgSgdPep.c commit 5f54747c4d7344e7f69e95c40374df4d733f94b9 Author: markd Date: Wed Jul 26 04:01:30 2006 +0000 renameFrom: src/hg/makeDb/yeast/hgSgdPep/makefile commit f8cd798b9added441c5e1ebb186b5ebe384a914f Author: markd Date: Wed Jul 26 04:01:29 2006 +0000 renameTo: src/hg/makeDb/outside/yeast/hgSgdGfp/makefile commit 00c9ca16711dd1a853d209e0eb040210460f56ec Author: markd Date: Wed Jul 26 04:01:28 2006 +0000 renameFrom: src/hg/makeDb/yeast/hgSgdPep/hgSgdPep.c commit 1f192387e791d417bff8f082f0a0832a1749fc6d Author: markd Date: Wed Jul 26 04:01:27 2006 +0000 renameTo: src/hg/makeDb/outside/yeast/hgSgdGfp/hgSgdGfp.c commit 72592a70a8458286e1b075a74e313ec0f94a4fe0 Author: markd Date: Wed Jul 26 04:01:26 2006 +0000 renameFrom: src/hg/makeDb/yeast/hgSgdGfp/makefile commit ab7a3895f0fc0b11ce5eb6f33cb66cc23e718596 Author: markd Date: Wed Jul 26 04:01:25 2006 +0000 renameTo: src/hg/makeDb/outside/yeast/hgSgdGff3/makefile commit 34d199e2ceeb809455c11e97ae6c3e96d39e94ff Author: markd Date: Wed Jul 26 04:01:24 2006 +0000 renameFrom: src/hg/makeDb/yeast/hgSgdGfp/hgSgdGfp.c commit 2ea74522db51577d5d7aeae3ea89b7253b014e19 Author: markd Date: Wed Jul 26 04:01:23 2006 +0000 renameTo: src/hg/makeDb/outside/yeast/hgSgdGff3/hgSgdGff3.c commit e05273e2c24b5b02f275f65bf919a5bb74be8b67 Author: markd Date: Wed Jul 26 04:01:22 2006 +0000 renameFrom: src/hg/makeDb/yeast/hgSgdGff3/makefile commit 7d6adad895d21dbd3c49ef5df32fa8e2552a47c7 Author: markd Date: Wed Jul 26 04:01:21 2006 +0000 renameTo: src/hg/makeDb/outside/yeast/fixHarbisonMotifs/makefile commit d68e6fac83d0441eee2e2b77783fbab23bf7e3aa Author: markd Date: Wed Jul 26 04:01:20 2006 +0000 renameFrom: src/hg/makeDb/yeast/hgSgdGff3/hgSgdGff3.c commit 970ddd9385e66b356561d633bb317d9766e9d137 Author: markd Date: Wed Jul 26 04:01:19 2006 +0000 renameTo: src/hg/makeDb/outside/yeast/fixHarbisonMotifs/fixHarbisonMotifs.c commit 65686427b3d620f6b1ff12ad330ca07e8b4b8ff7 Author: markd Date: Wed Jul 26 04:01:18 2006 +0000 renameFrom: src/hg/makeDb/yeast/fixHarbisonMotifs/makefile commit 2882ec4c5f8ab8764a6d0612cc9ca3ec9570dec2 Author: markd Date: Wed Jul 26 04:01:17 2006 +0000 renameTo: src/hg/makeDb/outside/yeast/checkSgdSync/makefile commit 04738f1ec6ab6dc86af6e4b744e8c9eb7f55ccdd Author: markd Date: Wed Jul 26 04:01:16 2006 +0000 renameFrom: src/hg/makeDb/yeast/fixHarbisonMotifs/fixHarbisonMotifs.c commit 0bddb3864d7b9c595027da73f7575fdf840fac0b Author: markd Date: Wed Jul 26 04:01:15 2006 +0000 renameTo: src/hg/makeDb/outside/yeast/checkSgdSync/checkSgdSync.c commit 313ab91062acb59a9e89ab3471d181cf7c6e9b75 Author: markd Date: Wed Jul 26 04:01:14 2006 +0000 renameFrom: src/hg/makeDb/yeast/checkSgdSync/makefile commit e5a0dc5f3e6f07b5126a517a35dfae60fcb74867 Author: markd Date: Wed Jul 26 04:01:13 2006 +0000 renameTo: src/hg/makeDb/outside/vegaBuildInfo/vegaBuildInfo.c commit 1e6178686cbb2e086e33c8641d572fc68d8cf0f5 Author: markd Date: Wed Jul 26 04:01:12 2006 +0000 renameFrom: src/hg/makeDb/yeast/checkSgdSync/checkSgdSync.c commit 4ac36e8d35961fecdc4a0b347f2ff8b716933f22 Author: markd Date: Wed Jul 26 04:01:11 2006 +0000 renameTo: src/hg/makeDb/outside/vegaBuildInfo/makefile commit effef4d51ec090c711b2b6be7e655b5fc78da569 Author: markd Date: Wed Jul 26 04:01:10 2006 +0000 renameFrom: src/hg/makeDb/vegaBuildInfo/vegaBuildInfo.c commit f8088467475809908eaff8723c0c5005f1377cbd Author: markd Date: Wed Jul 26 04:01:09 2006 +0000 renameTo: src/hg/makeDb/outside/samHit/samHit.c commit 364cd5970218c585e21726ddf813004d821e6b9e Author: markd Date: Wed Jul 26 04:01:08 2006 +0000 renameFrom: src/hg/makeDb/vegaBuildInfo/makefile commit 50e4ccdc6f780869cbe4fa7457c4ce9d5e669380 Author: markd Date: Wed Jul 26 04:01:07 2006 +0000 renameTo: src/hg/makeDb/outside/samHit/makefile commit c8cc2b80915148dba99c42e129239cd191d9ed97 Author: markd Date: Wed Jul 26 04:01:06 2006 +0000 renameFrom: src/hg/makeDb/samHit/samHit.c commit 4036c570e26ba38527ebd6827c01ad716f1d5058 Author: markd Date: Wed Jul 26 04:01:05 2006 +0000 renameTo: src/hg/makeDb/outside/sanger22gtf/sanger22gtf.c commit 407cae425c9b1395ba5ceffde9894c21276e6676 Author: markd Date: Wed Jul 26 04:01:04 2006 +0000 renameFrom: src/hg/makeDb/samHit/makefile commit b1b3f89abef425c6b0dd6b34c3f621206a022399 Author: markd Date: Wed Jul 26 04:01:03 2006 +0000 renameTo: src/hg/makeDb/outside/sanger22gtf/makefile commit 222306ac697cc4b24dac36424d3d8e2f56e7eb31 Author: markd Date: Wed Jul 26 04:01:02 2006 +0000 renameFrom: src/hg/makeDb/sanger22gtf/sanger22gtf.c commit cf0a6c9cc0e1dcf1bbaa44cc7f989d66c9f68e88 Author: markd Date: Wed Jul 26 04:01:01 2006 +0000 renameFrom: src/hg/makeDb/sanger22gtf/makefile commit 1568bc914bd8ddc0762e3b9298311ad7dd1745bb Author: markd Date: Wed Jul 26 04:01:00 2006 +0000 renameTo: src/hg/makeDb/outside/nibb/nibbPrepImages/nibbPrepImages.c commit ed9da5e1c7e6ecd0cbb0498ae5da8b8266d0e609 Author: markd Date: Wed Jul 26 04:00:59 2006 +0000 renameFrom: src/hg/makeDb/nibb/nibbPrepImages/nibbPrepImages.c commit 5da253a177323b4759b3623a2190093fc2769bd2 Author: markd Date: Wed Jul 26 04:00:58 2006 +0000 renameTo: src/hg/makeDb/outside/nibb/nibbPrepImages/makefile commit 3ba1ad56114c406383acdf9935ae536a6ad4ab5a Author: markd Date: Wed Jul 26 04:00:57 2006 +0000 renameFrom: src/hg/makeDb/nibb/nibbPrepImages/makefile commit 9332d4f79e48a32cc0809757ad07d2b62ddf8400 Author: markd Date: Wed Jul 26 04:00:56 2006 +0000 renameTo: src/hg/makeDb/outside/nibb/nibbParseImageDir/nibbParseImageDir.c commit ea0857beab4df041bdb3d15f239580ddabb6e7e4 Author: markd Date: Wed Jul 26 04:00:55 2006 +0000 renameFrom: src/hg/makeDb/nibb/nibbParseImageDir/nibbParseImageDir.c commit 60ed092b7311f8d9f08fb33598e55efe97f7c796 Author: markd Date: Wed Jul 26 04:00:54 2006 +0000 renameTo: src/hg/makeDb/outside/nibb/nibbParseImageDir/makefile commit 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+0000 renameFrom: ../makeBME230.doc commit 1ddc30dfeb57f9c173d270bf7cf14538143c1510 Author: markd Date: Tue Jul 25 20:12:57 2006 +0000 renameFrom: ../makeArchFulg1.doc commit 979ee76466d80fd51003a90a4c23c7d48c6fee7f Author: markd Date: Tue Jul 25 20:12:56 2006 +0000 renameFrom: ../makeApiMel3.doc commit dc8b60fb2bd329c13eb1412c2612621a8486a372 Author: markd Date: Tue Jul 25 20:12:55 2006 +0000 renameFrom: ../makeApiMel2.doc commit 8954efd844594888a8e534d7c5f8a4b25d12e9e1 Author: markd Date: Tue Jul 25 20:12:54 2006 +0000 renameFrom: ../makeApiMel1.doc commit aabae12765a119219aaa3f1f19497ca65d1632dc Author: markd Date: Tue Jul 25 20:12:53 2006 +0000 renameFrom: ../makeAnoGam1.doc commit c13c748adf2201ec00685d0d834c3ad20965f360 Author: markd Date: Tue Jul 25 20:12:52 2006 +0000 renameFrom: ../liftOver.doc commit 1109b931bdda94428657140d7bf3be546ce53037 Author: markd Date: Tue Jul 25 20:12:51 2006 +0000 renameFrom: ../bashVsCsh.doc commit 2d6e0ccca2de2ef53548d0c0a4b21afe148927ed Author: markd Date: Tue Jul 25 20:12:50 2006 +0000 renameFrom: ../addTrack.doc commit 184b9c07f39e1e411ead08b10ebb4c394f6ddbe6 Author: hartera Date: Tue Jul 25 18:48:47 2006 +0000 Added Zon lab Affy wild type expression data. commit e136957d9a889624d97a751600dc1fafa8428280 Author: hartera Date: Tue Jul 25 18:47:30 2006 +0000 BAC ends track in progress. commit 9f6fdd05ece95010c7afd3fb243486f33d6f433f Author: hartera Date: Tue Jul 25 18:46:31 2006 +0000 Wrote a program to extract PSL alignments from the BAC ends PSL file that correspond to those alignments in the bacEndPairs, bacEndSingles and bacEndPairsBad tables. commit 3883e110e875d74fe922e26eb6b1807192fd7771 Author: hiram Date: Tue Jul 25 18:35:42 2006 +0000 Preliminary unfinished Ce4 build commit a3317715c6f725623223e0bed3e4717e3cefb2ae Author: hiram Date: Tue Jul 25 18:35:20 2006 +0000 Adding a download directory commit 58523453ba632cec07f6e3904029c5bc6953e8ff Author: kate Date: Tue Jul 25 18:35:06 2006 +0000 Working on conservation commit 7c6f1a39d2c86576b3c14dafa42cac1f457e5178 Author: kate Date: Tue Jul 25 18:34:48 2006 +0000 Late appearance of a 2bit file commit 84f4d77bcf9e1e2e59d0548b6988525178c10b08 Author: kate Date: Tue Jul 25 18:34:27 2006 +0000 Chimp panTro2 alignments commit dde29c690ff19e2986e28b21d6a9389ace241eca Author: kent Date: Tue Jul 25 18:03:43 2006 +0000 Seems to work - better than straight SQL query anyway. commit 2e817dbf6230a4647dba398ccf8bc13686d5c738 Author: angie Date: Tue Jul 25 17:39:18 2006 +0000 Fixed used of wrong regex result variable in parseFileSpec -- thanks to Robert for uncovering the problem. commit 9f373418ae7e99f7864879dc1d174de0827ce203 Author: angie Date: Tue Jul 25 16:44:48 2006 +0000 Resolved -Wall warning: unused variable; cast to int for char used as array subscript. commit d285ea44c92e380f60f857e5fe14bcb83a697c60 Author: galt Date: Tue Jul 25 15:00:03 2006 +0000 "Encode release log update" commit bfd3c15f6ad220742f3560d3016255edc2743f6b Author: galt Date: Tue Jul 25 15:00:02 2006 +0000 "Release log update" commit 84ccfe566f6a87881a7e98782358041a91983aea Author: donnak Date: Tue Jul 25 01:39:35 2006 +0000 Fixed extraneous paren that caused Firefox browser to barf. commit a3209db48722e50d5482fc2b6ea4fdce66e5f7ac Author: rhead Date: Tue Jul 25 01:34:45 2006 +0000 Changed numbers of items in subtracks to reflect hg17 tables (the changes were due to lifting from hg16). commit d4b54dffc01cd351694a48b0b888ebfdb6655396 Author: angie Date: Tue Jul 25 01:13:29 2006 +0000 Quoting typo in previous revision. commit 8f9fbe77e961128dc501cdf078d7bf586f3f21e6 Author: ann Date: Tue Jul 25 01:01:43 2006 +0000 added blocks for panTro2 chain/net commit f1958104832500d09e819eaba6603bf810f7c67a Author: ann Date: Tue Jul 25 00:11:01 2006 +0000 "New version number v138" commit d5cb00a1b91d038aca4c18d4bbcbdb2128216136 Author: angie Date: Tue Jul 25 00:07:31 2006 +0000 Compute a partition of a .2bit, creating as many directory levels as needed in order to guarantee <= 1000 directory size. Uniform usage of .lst, sequential naming, generation of .lft files, and leaf directories for partitions are intended to make cluster batch generation and ordered concatenation of results as easy as possible. commit 68437c5153463c9b456f170a28cb05863de211a8 Author: fanhsu Date: Mon Jul 24 23:58:59 2006 +0000 Added GAD section. commit 65bd1e08afcc829715d7c5c0da2481fc18f66a48 Author: fanhsu Date: Mon Jul 24 23:31:23 2006 +0000 Added "Possibly Not Associated" diseases for GAD. commit 9e39faa52b29908e09a8d5efb985ec21c197adac Author: braney Date: Mon Jul 24 23:12:59 2006 +0000 a bug fix to a bug that caused the browser to crash on some 3 base alignments commit ccd978d16263294cf454c2943c5d1361b6a0f2e9 Author: fanhsu Date: Mon Jul 24 23:04:56 2006 +0000 Addec GAD section. commit 2b732ff532e4c746eec39feb64070c162de548e0 Author: hiram Date: Mon Jul 24 23:03:01 2006 +0000 Allow specification for maxItemsToOverflow to come from a trackDb entry commit 7eabf4dfe5840a23773122a9c8a03158dda6c792 Author: fanhsu Date: Mon Jul 24 23:02:31 2006 +0000 Added gad.o. commit 399561fe444cfbc3064a248f8477a48bc4abe6e1 Author: fanhsu Date: Mon Jul 24 23:02:11 2006 +0000 Added GAD. commit 6d52145ee82aa47ac14bc2f4c9f521830d3fac22 Author: fanhsu Date: Mon Jul 24 22:51:33 2006 +0000 Created gad.c for GAD section. commit 3661507cfd3202503e7039421d526db76c54daea Author: rhead Date: Mon Jul 24 22:22:35 2006 +0000 Fixed some typos. commit 9be5f18e095d853f4469727e655b4dff4ce092f7 Author: ann Date: Mon Jul 24 22:16:26 2006 +0000 added nscanPep table to nscan track entry commit 548af805ed84c051341b5a717ac3270ae38bbfbf Author: archanat Date: Mon Jul 24 21:49:21 2006 +0000 Added matrix for monDom4 chain commit 95978a2e99c224f16e3c513917a0e36c30369004 Author: kate Date: Mon Jul 24 21:44:51 2006 +0000 Swap alignments for zfish, dog, chicken. Conservation track. commit f47b4c253634e0d2e5afbb43dfcffeb753d418a8 Author: markd Date: Mon Jul 24 21:38:07 2006 +0000 reloaded nscanPep to fix naming bug commit 24b2d5457e072033363a6e2326e180725ff1133c Author: ann Date: Mon Jul 24 21:37:54 2006 +0000 removed 'chopAfter' from nscan rule commit 2ad9c1654f756ea284b37abbcc92ff8f2c10fe73 Author: archanat Date: Mon Jul 24 20:37:33 2006 +0000 Added matrix for Hg18 chain commit 3e0bc463a75d1f6b15abd33b4e937d90f44d1191 Author: markd Date: Mon Jul 24 19:36:08 2006 +0000 refactored in preperation for being able to read directiy from databases tables commit 4fcda3fa05ae459e5f0fa1cf19829d39f0617fe6 Author: donnak Date: Mon Jul 24 19:11:44 2006 +0000 Added new pub from Hiram. commit 70d82bb43b3bddc211c3e010a62470099f38d654 Author: donnak Date: Mon Jul 24 19:11:16 2006 +0000 Added some additional text to panTro2 announcement re: chrom numbering. commit 91f8e2905b271c7283abb9fb4dc8eb81fd00c891 Author: ann Date: Mon Jul 24 18:44:08 2006 +0000 added rule for nscanName commit 754dbe3004ff6cb248c9bd84051a88124b713c9f Author: donnak Date: Mon Jul 24 18:05:22 2006 +0000 Added more text to chrom numbering section. commit 27fb1c93d0fa4b8f659afda5edbb1aed9216dae7 Author: rhead Date: Mon Jul 24 17:47:32 2006 +0000 Somehow got two McCarroll subtracks and no Hinds subtrack on hg17. Replacing Hinds subtrack. commit 0bd75abb7b0454fe71f32c13c573b3e074014c3c Author: angie Date: Mon Jul 24 17:40:50 2006 +0000 Resolved -Wall warning: unused variable. commit 3785f40715449d2d6ca9bbefec63e51dfc4418f9 Author: rhead Date: Mon Jul 24 17:04:51 2006 +0000 Accidentally left off two subtracks (mcCarroll and Conrad) when moving the cnp track down from human level. Replacing them. commit 725b812c0b259842fc8f4841f30bddce5a08f4b2 Author: ann Date: Mon Jul 24 16:59:20 2006 +0000 Added geneidPep to geneid block (to force it to use peptide table). commit e583e92434c72331e989cc0bc4bbdc5746ee0cb0 Author: ann Date: Mon Jul 24 16:58:32 2006 +0000 added nscanPep table to nscan block commit eaaa122accec57c75ef5406c26ab0a77d1e4a682 Author: kent Date: Mon Jul 24 16:19:06 2006 +0000 Fixing an offset. commit ce6c738eb0131ebedd379c6a92f285e1b66a2d95 Author: galt Date: Mon Jul 24 15:00:03 2006 +0000 "Encode release log update" commit fee3e74bf2fb483329a2ea507756774c60b9725c Author: galt Date: Mon Jul 24 15:00:01 2006 +0000 "Release log update" commit 16a8b7dca1d78505ac0488d8a7aa996a283c30d6 Author: baertsch Date: Mon Jul 24 13:17:15 2006 +0000 snp usage commit 4fefffaea821bce99d3155f85cd8e3550281f301 Author: baertsch Date: Mon Jul 24 13:13:22 2006 +0000 upgrade to snp126 format commit 2610e43309540b503dffb729df03e8ee5be90625 Author: markd Date: Sun Jul 23 16:55:45 2006 +0000 remove hack of saving default db connection and just open connection as needed for transMap commit 3fd353896091ea1a85fb3b876b2afe83bec896f1 Author: galt Date: Sun Jul 23 15:00:17 2006 +0000 "Encode release log update" commit ce47c694456ceedf3bea828b74f087f7b11b6909 Author: galt Date: Sun Jul 23 15:00:15 2006 +0000 "Release log update" commit 5a83029029c1ad17b59c94e2355124c9390e4f72 Author: markd Date: Sun Jul 23 01:12:42 2006 +0000 modified MGC details page wording. Link CCDS to MGC details page commit 2fe4ad208baee403687c7bbd26c87be56f3f6806 Author: markd Date: Sat Jul 22 19:21:19 2006 +0000 removed obsolete files commit c80bf22985424153deaf5c3bac47d184ef4949b5 Author: galt Date: Sat Jul 22 15:00:03 2006 +0000 "Encode release log update" commit 7c649c3052512350cf00f7651127f69d9e22e715 Author: galt Date: Sat Jul 22 15:00:02 2006 +0000 "Release log update" commit a07e928877416e627af9c66e3d73217b397d8b51 Author: genbank Date: Sat Jul 22 08:24:13 2006 +0000 fixed log parsin problems commit d2db3830393436f00bfbc78294c14122c67f6bb3 Author: markd Date: Sat Jul 22 06:26:21 2006 +0000 added -overlapBases option commit 8f6e6f39df6b0bc17689eca9c33fec73a6213203 Author: markd Date: Sat Jul 22 03:20:45 2006 +0000 Redid MGC details page to make it more useful and add link to NCBI clone order CGI. Refactor the MGC and CCDS modules to simpilify this implementation. commit 9cc3fe95c81bcc4bbfa3cb920ba53828f1c05c62 Author: markd Date: Sat Jul 22 03:15:09 2006 +0000 added addition table building functions commit b7b58edf21359ec43d8db483d620006dba2fa2d1 Author: markd Date: Sat Jul 22 00:20:34 2006 +0000 added warning about not changing mgcGenes commit fc733d42395a848020ebb63c998f7c3fc5e8e9dc Author: ann Date: Sat Jul 22 00:16:32 2006 +0000 removed MGC block commit e1813ffcc1c242ddaa8147cb20f6bb7f62ff4cad Author: hiram Date: Fri Jul 21 23:54:50 2006 +0000 Pretty up the sample row output on schema display when text columns are really long or contain HTML markup. Turns spaces into   so there are no line breaks in the resulting rendered output in the WEB browser, makes the rows stay as single lines displayed. Limits string display to 128 characters max. commit 70cda72169471b89e413bc42d762f64727188ff9 Author: markd Date: Fri Jul 21 23:45:54 2006 +0000 fixed error coloring and codon annotation problems created by removing noInherit commit 93c152f2566a8a4c344ce48757b52742738c10ff Author: rhead Date: Fri Jul 21 23:41:37 2006 +0000 Moved cnp track (structural variation) down one level to hg16 and hg17 commit 6dcf347cce3cccf7ab6ca9633f8ae9a07265c408 Author: aamp Date: Fri Jul 21 23:12:55 2006 +0000 Moved track entry from hg18 to human (to accommodate hg17 as well). commit a7f445e475e21b0d422ace42756f6a94d5c67fbf Author: aamp Date: Fri Jul 21 23:10:54 2006 +0000 Added details for affy all human exon track. commit e3c2f3136cc55179a0df5db86767339c521540a8 Author: aamp Date: Fri Jul 21 23:09:18 2006 +0000 Changed settings on affy all human exon track. commit dc79e447fb4457645985b358f95981d6a62fb313 Author: rhead Date: Fri Jul 21 22:57:41 2006 +0000 Moved cnp.html to hg16 and hg17. Used -r1.17 for hg16 and -r1.19 for hg17. commit acc78d687efab8f078e208601bf20e448b08c685 Author: rhead Date: Fri Jul 21 22:55:05 2006 +0000 Moved cnp.html back down to the assembly level. Used human/cnp.html -r1.19 (latest, including Heather's changes specific to hg17) for human/hg17/cnp.html. Also added a comma. commit 80236121b468c37fbfd701c09c9c885d7b9015e6 Author: aamp Date: Fri Jul 21 22:55:04 2006 +0000 A few commands building the affy human all-exon track. commit 776c228852816a5adf22ee20c74130b481989e17 Author: rhead Date: Fri Jul 21 22:53:49 2006 +0000 Moved cnp.html back down to assembly level. Used human/cnp.html -r1.17 (before Heather's changes specific to hg17) for human/hg16/cnp.html. Also added a space and a comma. commit 3a2a0f01a8c9f19bb4087c83c7f5333ac9d284da Author: aamp Date: Fri Jul 21 22:47:36 2006 +0000 Added all.joiner stuff for the human all exon arrays. Currently hg17 and hg18. commit 4bf4634a0ff3b846c12f22147d816e68b288638e Author: aamp Date: Fri Jul 21 22:14:22 2006 +0000 Oops I meant to commit this along with kent/src/hg/inc/expRecord.h commit cfe196214403f1b2603f906a0d967b5044530314 Author: aamp Date: Fri Jul 21 22:10:41 2006 +0000 For the Affy Human exon arrays. commit a76cb283c684fdf772c8140b6c7e6c567bcd214c Author: aamp Date: Fri Jul 21 22:06:48 2006 +0000 Changed the default expRecord creation to have 3 extras things by default, with the first two being n/a. commit dd9dc7fc5c40d0053711254e9793a5fe79756f04 Author: aamp Date: Fri Jul 21 22:01:22 2006 +0000 Added functionality that a minimum number of measurements must be used for a mean or median when combining arrays. commit cd6b542fafab0e71da19f6a6b87ba483ce5b750b Author: aamp Date: Fri Jul 21 21:58:00 2006 +0000 Updated to use the new microarray.c lib. commit 2c1a64b8c9ec5362b207787e4192a4dc58d055dc Author: aamp Date: Fri Jul 21 21:57:10 2006 +0000 Fixed a bug that would treat missing data in microarrays (designated -10000) as real. Along with all this, the new microarray.c is used instead of the ratio/median business that used to be here (which is duplicated often throughout microarray CGIs and utilities). One thing to note is that this version doesn't discard probes with minimal expression, rather it'll set them all as missing data. commit dbf6efbbd4c99e37725d8bfd420555ecc35e8a00 Author: giardine Date: Fri Jul 21 21:54:07 2006 +0000 Added some more types to the attributes. commit fa75a7323e47dae1ab57e4439adcac33a2aaf973 Author: aamp Date: Fri Jul 21 21:52:12 2006 +0000 Convenience functions autoSql doesn't include. I added similar ones to these in expData.c/h. commit 385601db362eff9dfa005cd2106e43f51a97ae44 Author: donnak Date: Fri Jul 21 21:26:22 2006 +0000 Changed Jan. 2006 release date to Mar. 2006. commit e7cb1af644a596dfe33bd6e8a5df6a01c28c13da Author: donnak Date: Fri Jul 21 21:22:43 2006 +0000 Changed panTro2 release date from Jan. 2006 to Mar. 2006. commit 78e7442f05a102de9c86140d134b1785cc3b69de Author: donnak Date: Fri Jul 21 21:17:59 2006 +0000 Changed chimp release date from Jan. 2006 to Mar. 2006. commit c775dce35deeffb758e854f172f2c28b97058101 Author: baertsch Date: Fri Jul 21 20:35:47 2006 +0000 *** empty log message *** commit f577978bcc8d636d9e5294b1b1a82d1f8968f530 Author: baertsch Date: Fri Jul 21 19:42:39 2006 +0000 remove call to printSwissProtProteinUrl() in doRefSeq() commit e276f6f1d15cb612698e8ad4ecdcb38144cd48dc Author: rhead Date: Fri Jul 21 19:24:12 2006 +0000 added a space commit 83fe66272a543fa6d5f6d4828b89bc32d36c4800 Author: aamp Date: Fri Jul 21 17:45:52 2006 +0000 Added a way to limit the number of rows loaded. commit 5442fdc9ebd6701a84d7321ad70e96fd8c25dd62 Author: angie Date: Fri Jul 21 17:19:56 2006 +0000 Resolved -Wall warning: unused variable. commit 73afe726af5ec20034b24ed40c5b65d2d3dfd8d3 Author: fanhsu Date: Fri Jul 21 16:42:44 2006 +0000 Changed long label of wgRna track per authors' request. commit f5eb6fd54d6bee590ee0dbd446efe4e1237dfe7a Author: markd Date: Fri Jul 21 16:17:38 2006 +0000 hide transMap by default trackDb commit 0a44a31270de5e3cd0057fafefe12568f4598d42 Author: aamp Date: Fri Jul 21 16:14:10 2006 +0000 Stopped using the enum and started using an actual 2 there because the enum only has two things, but the table has three. This will need to be fixed eventually. commit 4785b8603b5e1533e797c869aadd14c19f34faa5 Author: galt Date: Fri Jul 21 15:00:28 2006 +0000 "Encode release log update" commit 52daa4c206b5aab031ea92e695d1be0ab715a01d Author: galt Date: Fri Jul 21 15:00:27 2006 +0000 "Release log update" commit 3ff6ba6e50a5b2089f5100dca672f84e29c93afd Author: baertsch Date: Fri Jul 21 00:59:54 2006 +0000 set hanging pointer to NULL commit 0b38a6cd572cc5c71e83373535034e92082217b7 Author: angie Date: Fri Jul 21 00:19:03 2006 +0000 Swapped -> {chain,net}GalGal3. commit 13322abe79d40fab86df7a9ab5bd3b2494c0e883 Author: angie Date: Fri Jul 21 00:14:18 2006 +0000 Typo fix in comment. commit b2c8925bd4add3c2f097f9132c67b21aa6f8d0b9 Author: angie Date: Fri Jul 21 00:13:57 2006 +0000 Updated the multiz7way entry with recently added settings for summary, frames, treeImage etc. commit 717ee158c429862dd8e06775360cc9eb23c2a101 Author: angie Date: Fri Jul 21 00:05:38 2006 +0000 Conservation, Most Conserved. commit 2cc5beac329d6c327f02068b6111a15df654cce7 Author: angie Date: Thu Jul 20 23:58:01 2006 +0000 phyloGif-generated galGal3 7way tree image. commit 65586f3408a62591d06ff9df9abb71b6959851dc Author: donnak Date: Thu Jul 20 23:57:17 2006 +0000 Updated sample query section, did some initial work on narrative (needs more work before release). commit 991f1278b8f8ec39e28bccb97f5b33c2d6bc64b9 Author: hiram Date: Thu Jul 20 23:39:06 2006 +0000 Implement the exclude noKg properly on the pseudoGeneLink commit 39b9c619c7177de8f41639439c5dac7ef25160fa Author: kayla Date: Thu Jul 20 23:03:00 2006 +0000 added panTro2 commit b1fb5fe2f888c147bf480f417928e2f4a002c222 Author: donnak Date: Thu Jul 20 23:01:51 2006 +0000 Added galGal3. commit e2996bb769bf2b9cd25775fb55cf586d493884e6 Author: donnak Date: Thu Jul 20 22:52:26 2006 +0000 Updated chicken section to include galGal3. commit 1dc6614e46fbe853e2a7e7f829a530f523bd2158 Author: angie Date: Thu Jul 20 22:42:20 2006 +0000 Added descriptions of Conservation and Most Conserved. commit 2fcc030f407efad46921580f95834b9e194f8ebe Author: donnak Date: Thu Jul 20 22:41:22 2006 +0000 Updated LocusLink reference to Entrez Gene. commit 65cc08191c7be2a30dd2cb02a9ed72bf6e356b5e Author: donnak Date: Thu Jul 20 22:37:55 2006 +0000 Changed LocusLink -> Entrez Gene, removed duplicate sample query. commit 44955efce437932d409197895fae50b8dde3ff85 Author: ann Date: Thu Jul 20 22:01:10 2006 +0000 added "toDb" to liftOverChain table check (it was only looking for the db in the "fromDb" field) commit 93e8182bf5a4f193e74a00cf3dfe502f5ab2539b Author: ann Date: Thu Jul 20 20:53:50 2006 +0000 switched short & long labels for chains/nets panTro1 and panTro2 commit 4b6cfcf90077ea23e4ba65cf3559723d650075e8 Author: donnak Date: Thu Jul 20 18:01:20 2006 +0000 Changed date on panTro2 announcement. commit 5fd5440fe3746516cb365755e10481c915dee46f Author: hiram Date: Thu Jul 20 16:55:48 2006 +0000 adding galGal3, xenTro2 and danRer4 definitions to blastHg18KGPep04Id commit 3c994fa9c716789d2830fe01db867c806ee61f24 Author: angie Date: Thu Jul 20 15:10:51 2006 +0000 Resolved -Wall warning: unused variable. commit 80a405da2442f2d062c57251a26f2e1ccd6531d6 Author: galt Date: Thu Jul 20 15:00:22 2006 +0000 "Encode release log update" commit cad9f9e94d3ee90ba59c95c2a030cdd87312f8c9 Author: galt Date: Thu Jul 20 15:00:20 2006 +0000 "Release log update" commit c9952ee9894ac638a7804b3e2cd5268c7b308863 Author: kate Date: Thu Jul 20 01:47:33 2006 +0000 image for chimp conservation track commit 725ef7b13ba901fe3cfccda390e0d4f4ed2c720d Author: kate Date: Thu Jul 20 00:54:22 2006 +0000 1. Downloads for quality scores 2. Genscan 3. Conservation track commit 76822bdb927bd06184248ae582f7acc4884d4370 Author: hiram Date: Wed Jul 19 22:56:27 2006 +0000 Add the blastKGPep04, blastKGRef04 and blastHg18KG relationships commit 0f357bca9da6a3f87c8259b877c51fc2d6f36c1a Author: markd Date: Wed Jul 19 22:38:37 2006 +0000 removed bogus mgc genes config for monDom4 commit ce58566162e584e567b788ede6414a9b5b8e7aec Author: hiram Date: Wed Jul 19 22:33:01 2006 +0000 Now allowing filter on known or not known disease state commit e0c3e2fdce05c40b6756c8d3b56ccdd0980bf6b3 Author: rhead Date: Wed Jul 19 22:22:39 2006 +0000 Split ensGene into release alpha and release beta to keep hgGene from going to RR prematurely. Used Rachel's previous URL (from -r1.30) for release beta. commit 57695cf1e8ccd5a7cecc9cd507b313c186f814ea Author: hiram Date: Wed Jul 19 22:22:07 2006 +0000 Now filtering for known or not-known disease state commit 0bc2c7e39b901ca7f6472d52d105a5ff03873ab7 Author: hiram Date: Wed Jul 19 22:01:47 2006 +0000 Now allowing filtering on allele frequency commit 7ba6f7854104c4c3ed1d1e3a8ae966325880071b Author: hiram Date: Wed Jul 19 22:00:02 2006 +0000 Now allowing allele frequency filtering for the dbRIP tracks commit 2774815d6f285453e1525311a3b6b3b19b26af71 Author: hiram Date: Wed Jul 19 21:57:42 2006 +0000 Better descriptive comments on the fields commit 88640616ceaf6dcb96cd5a0e9661e8cf96a05d56 Author: hiram Date: Wed Jul 19 21:56:50 2006 +0000 Adding allele frequency filters, and better labels on the polyGenotype fields commit 3f1f75b2a3e6daf49ecfd0f4b4fca18da7a2fa68 Author: hiram Date: Wed Jul 19 21:55:36 2006 +0000 Adding dbRIP relation to polyGenotype commit f02fb5baf6d7f56a6402698a6f4a5c82fa974d0f Author: donnak Date: Wed Jul 19 21:22:27 2006 +0000 Added even more stuff per Kate. commit 57f17866ec8342420889f2e898c33cbbff1c2635 Author: markd Date: Wed Jul 19 20:55:58 2006 +0000 add organism label to transMap alignment tracks commit dff76471ff40aecc4068b1e13ba71f9039d0cc58 Author: markd Date: Wed Jul 19 20:45:45 2006 +0000 added support for transMap indirect mappings using reconstruction commit 4975f79ae8f72070405dfef891c2ef123c6dbb51 Author: fanhsu Date: Wed Jul 19 20:29:59 2006 +0000 Temporarily disable microarray section for Zebrafish, until a bug is fixed. commit e5f36351384ffd97d8a14e07b956a240212f1d25 Author: donnak Date: Wed Jul 19 20:18:37 2006 +0000 More changes requested by Kate. commit 42d60f3ea73a8ed765246fbefdd1244250e7b379 Author: hiram Date: Wed Jul 19 19:43:42 2006 +0000 Adding monDom4 to the list for monDom commit 85b008b963e2db7e008953650dde922d7904cf83 Author: kate Date: Wed Jul 19 19:07:01 2006 +0000 Add check for chimp chromosomes that no longer exist with new numbering scheme (panTro2 and later) commit ea4bd64e34981b93e8f1deced148fc169aee9210 Author: hiram Date: Wed Jul 19 18:23:01 2006 +0000 Proper target of _blank for all outside references commit 1159a5f0d2df0af4771feeb6f7a830100387dc3b Author: donnak Date: Wed Jul 19 18:13:05 2006 +0000 Fixed typo, minor edit to chimp chrom section. commit 594fec208d95ca2a6aacdf2c9f38974943cab478 Author: markd Date: Wed Jul 19 18:06:03 2006 +0000 added gi column to gbCdnaInfo commit cf4bb115fcc3687bab144aa85373dbeecf3e747f Author: donnak Date: Wed Jul 19 17:58:32 2006 +0000 Added info abt panTro2 chromosome renumbering scheme. commit 53d16af34d4d5ff5f1c46761d17789ece13b4c4e Author: donnak Date: Wed Jul 19 17:42:21 2006 +0000 Fixed 2 typos. commit 369c40b45d79aa49d6e9a1b0e499936e3755fb81 Author: giardine Date: Wed Jul 19 17:31:10 2006 +0000 Added not to Swiss-Prot noteing which are included. commit 2678dd7ca8375c93e66e366f7fe82db03b5a0d83 Author: donnak Date: Wed Jul 19 16:59:59 2006 +0000 Made a minor edit. commit 231250723e203e5eb744ffbe13f35cd2904bd302 Author: ann Date: Wed Jul 19 16:45:50 2006 +0000 changed visibilities at Jims request commit b5d42044c422109e0b2fbb1e91543a17c249e6a0 Author: archanat Date: Wed Jul 19 16:41:12 2006 +0000 Changed the priority of Human Proteins track commit df1fcc1cc4fc1f9564c22597f80f0a58acd55974 Author: kent Date: Wed Jul 19 16:27:23 2006 +0000 Adding microsat html to source tree. commit c303cb0ff7916d87633e3acdc04b807c9bfcb1f7 Author: giardine Date: Wed Jul 19 16:01:38 2006 +0000 Added new source. commit 0c98e10fa0921635c6f2f051018d6f90ea5c6a07 Author: ann Date: Wed Jul 19 15:48:43 2006 +0000 added link from chimp picture to sequencing center commit 4be8dc1b80a78a7855f6e725c09bc08b90350543 Author: markd Date: Wed Jul 19 15:19:54 2006 +0000 fix warnings and correctly enabled them commit 8fe3178fa2bdb9af0686494437b282e3dde802a9 Author: galt Date: Wed Jul 19 15:00:22 2006 +0000 "Encode release log update" commit ce0ec7a32333d9b656480097c77f9933b29fa75d Author: galt Date: Wed Jul 19 15:00:21 2006 +0000 "Release log update" commit 7e82cd11aec91e8ce79d32ce6c289834f671218a Author: markd Date: Wed Jul 19 07:43:59 2006 +0000 deal with new parameter to genePredFromGroupedGff commit 5b9d20b95b0b6d8681cd268b3554e6652f5e8808 Author: markd Date: Wed Jul 19 07:30:08 2006 +0000 added -impliedStopAfterCds option commit fae6cb2dd3536a37130adf15276a22a383da7d81 Author: markd Date: Wed Jul 19 06:51:45 2006 +0000 added option to handle implied stop codon outside of CDS commit 01dbf51d2c636b0e58ae01abb67ebac6c19f60a8 Author: donnak Date: Wed Jul 19 01:13:35 2006 +0000 Minor grammar fix. commit c253a80c8370af3f239002ff571fd057ed0c464c Author: donnak Date: Wed Jul 19 01:13:14 2006 +0000 Added chimp pic. commit 1bc704446a84716b7c71f7ee73a6680b368e7d41 Author: baertsch Date: Wed Jul 19 01:09:35 2006 +0000 add censor repeat mask commit ec751ef01f4e38a495b5fb25e1eebf00b2ecaac3 Author: baertsch Date: Wed Jul 19 01:04:22 2006 +0000 details page for censor repeatmasker commit e1bd86767d5027a58f0a6e1b353973ff734d0bb0 Author: donnak Date: Wed Jul 19 01:03:25 2006 +0000 Added note abt new chr2 numbering scheme in panTro2. commit 645f585fa02d28ad1e6456a4652bd10efa67d627 Author: donnak Date: Wed Jul 19 00:18:44 2006 +0000 Made a few edits, fixed typo. commit 47d0f90cce23f68a19874247519d5bd37715a97d Author: donnak Date: Wed Jul 19 00:13:32 2006 +0000 Archived a news item. commit 7e44f89c69537c4314ad6c25c2f6287067364d73 Author: donnak Date: Wed Jul 19 00:13:14 2006 +0000 Added panTro2 release announcement. commit 1ccad32698668b7fe85c61718090be639de2cff7 Author: rhead Date: Tue Jul 18 23:52:50 2006 +0000 Changed rn3 to rn4. commit 8499478b9f19b3b70bfcfff48c8816a58363c3f0 Author: hiram Date: Tue Jul 18 23:48:15 2006 +0000 Change dbRIP track primary color to black so the labels will be black commit 8910b8b7364d6b8f9a4ee3e1d56ce2b7d857437d Author: hiram Date: Tue Jul 18 23:44:52 2006 +0000 Need to group by name to get unique results for the ethnic name match commit 9408183373d1e51374a7f7b5b6b0b70005d27418 Author: donnak Date: Tue Jul 18 23:34:41 2006 +0000 Rearranged & edited the initial draft of this page. commit 5cb1f093d0da6dd0b2838be49c0ef22bc6d2dbe8 Author: rhead Date: Tue Jul 18 23:11:53 2006 +0000 Added section for rat (rn4). commit fdc79b220ae81f592b4c2ccf8854cc26bd65c691 Author: hiram Date: Tue Jul 18 22:55:07 2006 +0000 geneContext is actually geneRegion commit ebc045409524ec68a9dc537af83a94b6f5e88fed Author: hiram Date: Tue Jul 18 22:54:22 2006 +0000 removing a useless blank line ... commit 6d2b89dbd7d4b8016df07709fded479a95066fea Author: hiram Date: Tue Jul 18 22:52:49 2006 +0000 Now doing the join select between the dbRIP tables and the polyGenotype commit 5353f35c22f6eb8759f6f55636f94be9f8b768ba Author: rhead Date: Tue Jul 18 22:37:25 2006 +0000 Changed rn3 to rn4. commit ac14d6b7a9844d0c66df5d72baafd5fd22b06e0e Author: baertsch Date: Tue Jul 18 22:29:35 2006 +0000 *** empty log message *** commit 267f3e38639bb570fef43d0777bf716a6b634c46 Author: ann Date: Tue Jul 18 22:19:56 2006 +0000 correct range of scores commit 61c3e0573f4680ef2c9337e8cba89e55db8a7880 Author: donnak Date: Tue Jul 18 22:14:33 2006 +0000 Made a few edits, updated the reference to conform to our style. commit c4747a047968e3f109b791496362d2e9649b1cbe Author: donnak Date: Tue Jul 18 22:11:04 2006 +0000 Few minor edits. commit b79a947954faaa97207568355a4c7b32cd3410d2 Author: hiram Date: Tue Jul 18 20:07:31 2006 +0000 Eliminate dbRIP debug printout commit 74a0fa355ef11cb61b5b5fc27c683552669098d5 Author: hiram Date: Tue Jul 18 20:06:52 2006 +0000 fixup potential divide by zero situation commit 893e35d8c9a50b9a86ee288162c15ad8c6dc5c91 Author: hiram Date: Tue Jul 18 19:21:33 2006 +0000 track polyAluL1SVA become retroposons and now honoring some of the trackUi settings commit b941778500aa2154feda6be994c79045ba6407e4 Author: hiram Date: Tue Jul 18 19:17:47 2006 +0000 geneContext is actually the column geneRegion - use the correct name commit d2a0388d47c39da6a3c989b72cd94203d9530b5b Author: kate Date: Tue Jul 18 19:16:57 2006 +0000 Adjust chroms for quality track. Add conservation track and elements as alpha commit 3f442db7cb14cd7f54070945fb4865c4860e392b Author: hiram Date: Tue Jul 18 19:16:39 2006 +0000 Changed column name in polyGenotype from databaseId to 'name' so it will match the dbRIP table column of the same name commit 0a0f8182a492c532ad88f423977ac262a0203ea9 Author: hiram Date: Tue Jul 18 19:15:05 2006 +0000 Add the allele homozygosity and heterozygosity calculated frequencies commit d361507253715e2455368358cb001dffaedb876d Author: hiram Date: Tue Jul 18 18:52:03 2006 +0000 Reloaded the MonDom4 chains and nets on Mm8 commit 979e11fe6bbb9f728c8a6baabe683f30f7a928a4 Author: ann Date: Tue Jul 18 18:41:19 2006 +0000 cleaned up commit 15f96cd4fa977df82ff0d1d876f9a07117bda413 Author: kate Date: Tue Jul 18 18:33:31 2006 +0000 Conservation track commit c98d83450e9e4e98f99a0c56f6d4d4e8e2d7d33f Author: galt Date: Tue Jul 18 15:00:18 2006 +0000 "Encode release log update" commit 1cf2a7b27ff396902b5c6527baca6a5804fa6aa3 Author: galt Date: Tue Jul 18 15:00:17 2006 +0000 "Release log update" commit f897ea8bb32de97585444bfbab0cdfcfe98c6a69 Author: angie Date: Tue Jul 18 14:49:23 2006 +0000 When reporting a single match, list the name, browserName and description if given. commit 63c2f465c098d37a25f7eda596d5165b6f4ad80e Author: angie Date: Tue Jul 18 14:47:01 2006 +0000 Resolved -Wall warning: unused variable. commit e3b150667039ea9159c1b85328f52e9ec3cd9d5d Author: markd Date: Tue Jul 18 06:08:10 2006 +0000 removed doa program commit 96b947edcb5484c22f76773dce4f6526130c220b Author: markd Date: Tue Jul 18 06:03:32 2006 +0000 removed some code now in psl module commit f8d257f2039174ba91b3a84f50266446b1d13b9f Author: angie Date: Mon Jul 17 23:59:00 2006 +0000 Added new Initial Release entry in Main Push Queue to refer to the new push queue. Thanks to Ann for suggesting this! commit fcf6c0275f1eb4465a3fc7d4c988a0d52bfa693e Author: ann Date: Mon Jul 17 23:28:06 2006 +0000 clean up commit a9bdc8440f464f3ffd14d530ae063fb804514366 Author: angie Date: Mon Jul 17 21:51:59 2006 +0000 Added some more directories required for "make update" to the cvs checkout command and added a call to HgAutomate::closeStdin. commit f08595c6cac970c7ba5ae59f5bb13aca2d1b986c Author: angie Date: Mon Jul 17 21:51:11 2006 +0000 Automate the generation of assembly download files and partially automate the generation of README.txt files that explain what we offer. Some editing of the README.txt files is still required, but weak spots are highlighted with '*** ALL CAPS ***' notes. commit 02a448d21ce10381f5aea9aa7e6d3d6604aa2793 Author: donnak Date: Mon Jul 17 21:34:48 2006 +0000 Added Brian to panTro2 credits. commit 4432edf8c09d85764da3d6c1e170a427b6b7c1db Author: angie Date: Mon Jul 17 21:01:10 2006 +0000 Updated the link to humanparalogy.gs.washington.edu for hg18 genomicSuperDups. commit f87d51a3b13dc066032cc1e89462315c449fcbfa Author: donnak Date: Mon Jul 17 20:44:21 2006 +0000 Added panTro2 to DB list. commit 44bc67c90845b0125544ce1cd0319f0ad511990f Author: donnak Date: Mon Jul 17 20:39:51 2006 +0000 Reorganized panTro credits & added panTro2 info. commit c527f1e5121cabc240423ff042411f2b019ced86 Author: angie Date: Mon Jul 17 19:44:56 2006 +0000 Finished bacEndPairs, added downloads, in prep. for QA. Still need to add Conservation. commit 454bc799d0ea360b47b7954c33b6b609501def63 Author: markd Date: Mon Jul 17 19:35:38 2006 +0000 added support for enum and set columns commit 2631267a0a5cf6730dc0bad6683399268d01ec11 Author: markd Date: Mon Jul 17 19:34:41 2006 +0000 improved documentation commit 93d896ebd0fbcc59111634bd5e998e10c919fb0a Author: markd Date: Mon Jul 17 19:34:18 2006 +0000 change .c.o rule to pattern rule, which is more flexable commit 00b927dcda9e1fb7c962a035855814a71f5f00a2 Author: donnak Date: Mon Jul 17 19:19:27 2006 +0000 Slight edit. commit 16746673f6cc817b319262f3d3bfaa3ed2e418fd Author: hiram Date: Mon Jul 17 19:16:49 2006 +0000 Adding options for dbRIP retroposon track commit 80581ed5a5e97f5edcb1adacb775bdb510f42958 Author: hiram Date: Mon Jul 17 19:15:35 2006 +0000 Adding trackUi option defines commit 36f00167519f82183aefdc91047ea57f83d3e734 Author: donnak Date: Mon Jul 17 18:57:50 2006 +0000 Added panTro2. commit a3943a108dfe09eb3c93d28b18ec5eccf7e924a0 Author: hiram Date: Mon Jul 17 18:32:10 2006 +0000 Add slNameSortCase - ignore case commit a4fddc153bdc83b79d8c826574a42224afbe401c Author: hiram Date: Mon Jul 17 18:31:40 2006 +0000 add slNameSortCase - ignore case commit 5646cfead94c711d93e0859c52b694b5260656a8 Author: hiram Date: Mon Jul 17 16:44:51 2006 +0000 Change genomic region to gene context commit ddd00ff4d5ba61caebcdca4a0b3fb06e9901ab0a Author: hiram Date: Mon Jul 17 16:41:50 2006 +0000 Changing name for Retrotransposon Insertion Polymorphisms commit 1c5e29663db560db8464c35366a0a66570c9af01 Author: fanhsu Date: Mon Jul 17 16:37:31 2006 +0000 Turn disease string to upper case and apply cgiEncode on it. commit df65960f5b3376cf728fc8f996e75de24b671035 Author: fanhsu Date: Mon Jul 17 15:38:20 2006 +0000 Minor edits. commit 538e283a46e622e594ee5511ec48afb29382b889 Author: galt Date: Mon Jul 17 15:00:14 2006 +0000 "Encode release log update" commit 7f96f91d0054458bc195830eb0e5a72f9f3512f6 Author: galt Date: Mon Jul 17 15:00:13 2006 +0000 "Release log update" commit 5aa10c45c981f9f8681d57750f053216ecb74fe6 Author: aamp Date: Mon Jul 17 10:05:48 2006 +0000 Changes suggested from Angie's review. commit 03b15a625dadfe2a321bcf0451269cbaea229ef5 Author: braney Date: Mon Jul 17 00:13:12 2006 +0000 load native ests on rabbit commit d6d75fe6e6f0821f2fc657ce2a115c1583bdf066 Author: markd Date: Sun Jul 16 16:35:04 2006 +0000 fixed expected output due to mafFlipStrand bug fix commit d8e3939e383c21741912c7d2b8c714d787dcf6bb Author: galt Date: Sun Jul 16 15:00:17 2006 +0000 "Encode release log update" commit 0592f582e3772d5d5a098bd6577097090614a479 Author: galt Date: Sun Jul 16 15:00:16 2006 +0000 "Release log update" commit c63c250549375dc35d953be2d157a750ef6211c9 Author: angie Date: Sun Jul 16 06:06:11 2006 +0000 Fix to wc -l usage -- use "<" on input so that output is only a number (no filename). commit 9a59e8ff29e73a7f2764cc1ca4da30d8fc52fcad Author: angie Date: Sun Jul 16 06:05:34 2006 +0000 Fix to sh stderr-redirect syntax (thanks to Kate for reporting!). commit 0bda7a4a7c75d622932d69bbf55b00c8fb890c35 Author: kate Date: Sat Jul 15 21:50:22 2006 +0000 Continuue genscan and liftUnder commit 188aa54a646189dffa069e5ea4c122682197718b Author: galt Date: Sat Jul 15 15:00:22 2006 +0000 "Encode release log update" commit 37b38a017e6ea0d5e3ebb0a8c10ad78d937ca204 Author: galt Date: Sat Jul 15 15:00:21 2006 +0000 "Release log update" commit 70d243dc71037fefd6f61f52b946babeb3201c9e Author: markd Date: Sat Jul 15 06:20:42 2006 +0000 fixed mafFlipStand getting start wrong commit 4c54aab6e4fa2eabd7b0613454cf9bb94434fdb5 Author: fanhsu Date: Sat Jul 15 03:21:00 2006 +0000 Changed "NIA GAD" into "GAD". commit 6cd9506f1dea0feb4939437df5b4268fe6d835a4 Author: markd Date: Sat Jul 15 00:55:23 2006 +0000 improve error message when sequence sizes do not match commit 1fc8b54e8131f1d52a4adbe0efe269d67afe8824 Author: angie Date: Sat Jul 15 00:09:33 2006 +0000 In doGetBedOrCt, if a bed->name has space(s), replace with '_' instead of truncating at first space. commit 649baac19ab5d846a2adb1a85092ff41bdeaacbd Author: hiram Date: Fri Jul 14 23:58:56 2006 +0000 Add search reference column of dbRIP_L1 and dbRIP_SVA tables commit c3ce03f66109e1689c6595b5ed089dd29c079af1 Author: hiram Date: Fri Jul 14 23:51:52 2006 +0000 Add search specification for the references column of the dbRIP_Alu table commit 47f97c47b5856c99f6403220e392bc7d7a266616 Author: hiram Date: Fri Jul 14 23:23:00 2006 +0000 Add description of dbRIP data track additions commit b6070ea2296c3712b6652cbcba2d494b8678d724 Author: hiram Date: Fri Jul 14 22:24:38 2006 +0000 Add note about item coloring meaning commit e892269f6557c477144ab48a42de08b399b60f56 Author: hiram Date: Fri Jul 14 22:04:49 2006 +0000 Remove dbRIP debugging printf commit ad9fbc930ed440d274f1f134b590d47f6cf3fa3c Author: hiram Date: Fri Jul 14 22:02:14 2006 +0000 Turn on coloring for the dbRIP tracks, and a new thickDrawItem option commit 10830afc7b479dd65ae5702adb40d444736f3cf3 Author: hiram Date: Fri Jul 14 22:00:49 2006 +0000 Allow tiny items to stay at least 4 pixels wide when they are smaller than that commit 24c6030b8e2382a173641792188f6452f09029ba Author: hiram Date: Fri Jul 14 21:34:52 2006 +0000 Add specific business for drawing dbRIP tracks in the blue and red color scheme commit 0a26e5d8b0ea2cc98bf541373f03ecce341c9bc0 Author: angie Date: Fri Jul 14 20:54:47 2006 +0000 Fix to how $opt_verbose is forced for debugging. commit 16407246c5bedcd8171a1a8e45a9eef89ec5530c Author: angie Date: Fri Jul 14 20:49:31 2006 +0000 Use $Bin for path of other scripts instead of hardcoding to /cluster/bin/scripts -- that enables development/testing of simultaneous changes to multiple scripts when this is run from a checkout tree. Moved the stdin-closing but to HgAutomate::closeStdin. commit 96916b6da9da0833428110b12dd1eec8934bb930 Author: angie Date: Fri Jul 14 20:14:05 2006 +0000 Added detection of chain/net download files. commit af73bea65609bb4efc924d81fed90c61d7c5348d Author: hartera Date: Fri Jul 14 19:33:06 2006 +0000 Added a note that Known genes is not an option in later BioMart versions. commit c232acdfd84cd438611384e9a526c5aa1317fb43 Author: hiram Date: Fri Jul 14 19:07:33 2006 +0000 Now properly calculating the Unbiased Heterozygosity commit 0ec08263c36f0391da810b15b4674ce5befdaba9 Author: fanhsu Date: Fri Jul 14 19:01:39 2006 +0000 Added gad.html commit 399bee7227199468affb5a8c81745a2b7957eb4b Author: angie Date: Fri Jul 14 18:49:40 2006 +0000 Added makePushQSql.pl to SCRIPT_FILES. commit 1f31e9077c9346d25ce5dbb4097333428b6c4ec8 Author: angie Date: Fri Jul 14 18:49:28 2006 +0000 Utility to print SQL commands for adding a new-genome-database table to the qapushq database. Some editing will most likely be required before actually executing the SQL on hgwbeta, but hints about what probably needs to be edited are printed to stderr. commit 305c88e3cdd0e417be3b2ba14057971d149a160a Author: angie Date: Fri Jul 14 18:44:39 2006 +0000 Added a call to HgAutomate::closeStdin at the beginning, just to be safe. commit 038cdbc68b99bb6c047e176c25cf704958823de4 Author: angie Date: Fri Jul 14 18:43:14 2006 +0000 Added closeStdin and added a newer, more stringent (<= 0.1) round of load-checking in chooseWorkhorse. commit 752d8498a0b4659442d598afdc77b95e817ec0fd Author: fanhsu Date: Fri Jul 14 18:40:27 2006 +0000 Added GAD details page. commit 420c5dcf4a6eb9c5abe4e54eb58612337531170e Author: fanhsu Date: Fri Jul 14 18:39:52 2006 +0000 Added GAD track section. commit 8a60d78a54d846b289fe891addb4738058f6941e Author: fanhsu Date: Fri Jul 14 18:39:15 2006 +0000 Added GAD track processing. commit 5d4c3cb0ef1cce4c207a749d8c91193c304c8474 Author: hiram Date: Fri Jul 14 18:33:57 2006 +0000 Add name searching on the dbRIP tracks commit eb72b40cba9ba50783842d85f0c20aeea62a3320 Author: hiram Date: Fri Jul 14 18:14:34 2006 +0000 Adding polyGenotype to the build commit 28c7d72c316317314651348eacc281a0af389d5a Author: hiram Date: Fri Jul 14 18:06:51 2006 +0000 Now doing the allele frequency table, still need to know how to do Unbiased Heterozygosity commit e2488e4d3ef2e39ceb3e1cd095d210741c999e60 Author: hartera Date: Fri Jul 14 17:54:50 2006 +0000 Added mm7-specific columnDb.ra with url for Ensembl genes with stable archive link for Ensembl v38 for mouse NCBI Build 35. commit dde890dca20d30ec13e8aab1c3bec3f8793145e1 Author: hartera Date: Fri Jul 14 17:51:10 2006 +0000 Added link to archive for Ensembl v38 for mouse build 35. commit 03610ca5941564e9919181f53694e98f902f60e0 Author: kuhn Date: Fri Jul 14 16:47:37 2006 +0000 added tool for getting stats on a user commit e1b1193bdee13c0f10e5ba1e49ffd6ae8106da4e Author: angie Date: Fri Jul 14 16:37:27 2006 +0000 Include our common.mk and use HG_WARN_ERR to maintain -Wall cleanliness. commit 914bf9f2736b4e102792b90971afae20b5e72f9b Author: angie Date: Fri Jul 14 16:35:04 2006 +0000 Use STRIP and EXE from common.mk. commit cdd0b9956410f6e9bdbd8bfb72f4d02b382aff05 Author: angie Date: Fri Jul 14 16:32:19 2006 +0000 Resolved -Wall warning: unused variable. commit 67494dfcf670ace8fada160a7ee12aeb59059c8e Author: kate Date: Fri Jul 14 16:15:48 2006 +0000 Add some specifics for panTro2 commit a5eb4cd1b0498714fe6be7f82071edd93cc5317b Author: galt Date: Fri Jul 14 15:00:23 2006 +0000 "Encode release log update" commit a7883b21ea8171a59e94e9aa8cdebaf8d1ed5544 Author: galt Date: Fri Jul 14 15:00:22 2006 +0000 "Release log update" commit 3c4a1bde2c695f693ed0c802e8f2ff4d85f0eedd Author: angie Date: Fri Jul 14 14:33:55 2006 +0000 Added genomicSuperDups (Segmental Dups) from Xinwei She, Eichler lab. commit 4e7e1e03c6eda0fcdbed20cc79b17bd18802e582 Author: baertsch Date: Thu Jul 13 23:39:42 2006 +0000 move extern to hgTracks.h (withPriorityOverride) commit a82432c345e8d1cf27c783fc04302b2413b5158d Author: hiram Date: Thu Jul 13 23:18:59 2006 +0000 New database table type for Retrotransposon Insertion Polymorphisms in Humans commit 63f65e524a108ea10f376284d257c7303524beca Author: hiram Date: Thu Jul 13 23:17:14 2006 +0000 Should be in ../inc/ not here commit 04f07d38e92878b51ea3934138ea5d7ec75a5306 Author: ann Date: Thu Jul 13 23:15:46 2006 +0000 prettied-up again commit 1b1c375dcbf0b2dae8dc18a8f7ac2566b5f1861f Author: ann Date: Thu Jul 13 23:03:52 2006 +0000 added block for gold track commit 9453313a8b5e6aac680018e2b4e30ee4ab244cf1 Author: ann Date: Thu Jul 13 23:03:35 2006 +0000 prettied-up commit 67cb3b5ff378a4ed41474abceaa571fbe6fc2342 Author: ann Date: Thu Jul 13 22:57:02 2006 +0000 initial file - editied for contig types commit f620d5b8a1d2a9e1e7e0b16f38cf4a68d1cfc960 Author: baertsch Date: Thu Jul 13 22:32:40 2006 +0000 cosmetic change commit f78e57d965a7dbbf57a576c3457ae4a85f373fd2 Author: baertsch Date: Thu Jul 13 22:30:52 2006 +0000 remove debug commit b4862fe89bce1f5b9aeecd9758633ec7f2bf7e40 Author: baertsch Date: Thu Jul 13 22:29:18 2006 +0000 sort track control groups based on group priority commit 403b37960accef4d620a45e8d23aed9906010420 Author: hiram Date: Thu Jul 13 22:13:40 2006 +0000 Properly declare dbRIP() so everyone can see it here commit 05a6262aaf9f276cb574c36b5d9a0543242df960 Author: baertsch Date: Thu Jul 13 22:00:16 2006 +0000 allow user to reorder tracks commit c9c3dcf41fbbeb7f4f28fc80737d815abcd888bf Author: hiram Date: Thu Jul 13 19:22:45 2006 +0000 Add genotype table for dbRIP correspondence commit 3517f39ad798688c82bd30d2fe7a95ac71503178 Author: hiram Date: Thu Jul 13 19:07:35 2006 +0000 Adding sql definitions for data type Retrotransposon Insertion Polymorphisms in Humans commit 58590ee2be0732bbb7832d2015de61aac0035b3b Author: hiram Date: Thu Jul 13 19:03:50 2006 +0000 Move dbRIP stuff to disease phenotype group commit 49fc1e6e2f5302166b5492233d2564a10f8ddf7c Author: hiram Date: Thu Jul 13 18:23:12 2006 +0000 Adding new track for Retrotransposon Insertion Polymorphisms in Humans commit 5616d88db69d35db38cca3de0f67e416f8da67da Author: hiram Date: Thu Jul 13 18:16:07 2006 +0000 Adding support for new track type Retrotransposon Insertion Polymorphisms in Humans commit 2e104e83418977e47377dca372ce3f9169f547dc Author: kuhn Date: Thu Jul 13 18:14:00 2006 +0000 format tweak commit 3c03078eebab2c48e857200828f84985dbc479cd Author: hiram Date: Thu Jul 13 18:05:11 2006 +0000 Adding new click handler for Retrotransposon Insertion Polymorphisms in Humans commit 116bc6ffecedee97e3b238d2972b6c0978f78819 Author: hiram Date: Thu Jul 13 18:04:06 2006 +0000 Adding new click type for Retrotransposon Insertion Polymorphisms in Humans commit e2a08a4dc364b87c64f64807faf1fd191b8983a5 Author: hiram Date: Thu Jul 13 16:42:51 2006 +0000 Incorrect use of type cast on left hand side of = sign, should be to the right commit ccff2bd889c079cfc14973a1ed4297e055322a5d Author: archanat Date: Thu Jul 13 15:58:02 2006 +0000 Changed the short label for Rn4 nets/chains commit 7ddd7d5b0b3a49b0fb237de951400790b7e91fc8 Author: galt Date: Thu Jul 13 15:00:21 2006 +0000 "Encode release log update" commit f9b7709d44c0cb758590caafde957186630ac376 Author: galt Date: Thu Jul 13 15:00:20 2006 +0000 "Release log update" commit 6eaa6f8dabd0b78ce7b4a54d931333b2aff6e6ca Author: baertsch Date: Thu Jul 13 00:50:35 2006 +0000 add -noMask option commit 3de3ee4c472856ebcee623f35493b3fe009adb8d Author: markd Date: Wed Jul 12 23:54:59 2006 +0000 added snp126.o to makefile commit 32b707808856c898dfd0207974dae75d7118b9b7 Author: ann Date: Wed Jul 12 23:25:23 2006 +0000 small edit to matrix variable commit e9c23343c5279eaa62d81c5af95a508c22699167 Author: archanat Date: Wed Jul 12 22:40:21 2006 +0000 Added matrix for Rn4 chains commit abdfbe31bb32db5514e6f66db0e5fa69f6cb5611 Author: angie Date: Wed Jul 12 21:30:49 2006 +0000 A script that illustrates basic use of automation infrastructure in HgAutomate, HgRemoteScript and HgStepManager. To be used as a template for scripts that actually do something useful. commit 382bb558e02293dc3926148233bf8f6abfff3b87 Author: hiram Date: Wed Jul 12 21:13:09 2006 +0000 Properly get the ignoreEmpty option in commit e99267110c2bee85e5b6090efa2a259a2dca572d Author: hartera Date: Wed Jul 12 21:08:00 2006 +0000 Added to geneId track method. commit 24bc1fbffd29854fbb8a833fb6a9553632309a64 Author: hiram Date: Wed Jul 12 20:38:31 2006 +0000 Now using -ignoreEmpty on the hgLoadBed to allow empty custom tracks. Because it used to work on the file entry situation, should also work for database. commit 842ce2b5172c049cd310c64e013786e6116101d4 Author: hiram Date: Wed Jul 12 20:35:17 2006 +0000 Allow empty input files with -ignoreEmpty option (for custom tracks) commit ac96767a5e22ed42053fa16626a0a573f9bc0b8d Author: galt Date: Wed Jul 12 15:00:23 2006 +0000 "Encode release log update" commit 319898b8d2b12c469e2df461e1bfaa41482263cf Author: galt Date: Wed Jul 12 15:00:22 2006 +0000 "Release log update" commit ca6f3dc6ea4ebb9e8e417c4d3841a6f8f26b28ab Author: kate Date: Wed Jul 12 05:19:14 2006 +0000 Finish danRer4 alignments. Start liftUnder commit 60d36899823995f167a9103d0b0f904cfa903e64 Author: donnak Date: Wed Jul 12 05:02:58 2006 +0000 Fixed typo that broke google search for mailing list archives. commit 2f08039bca7ec3ab799dc4204eaaf807313d5b49 Author: hartera Date: Wed Jul 12 01:24:43 2006 +0000 Reloaded geneidPep table. commit 5aeae557fe1f4ea10da6334480ba17817479be2c Author: hartera Date: Wed Jul 12 00:41:47 2006 +0000 Reloaded genscanPep table. commit 164226fe48634e5a6dbb1092fca7c6348816c41c Author: hartera Date: Wed Jul 12 00:32:46 2006 +0000 Added ensPep table. commit f0daed5497f76c8a9a13c1ce6673f37318e23533 Author: kate Date: Tue Jul 11 23:14:08 2006 +0000 Additional material about chimps and the assembly, plus links commit a5ef97e02750c948f609e70543ebc458be741c1f Author: hartera Date: Tue Jul 11 22:58:03 2006 +0000 Added zonWildType array data track. Added to doAffy function to support display of orthologs for zebrafish. commit c9ca580ff47aee1d09f3eda1d44ed2d0dd04f093 Author: hartera Date: Tue Jul 11 22:41:23 2006 +0000 Added Affy wild type expression data. Added human orthologs table for affyZebrafish track. Added search for human orthologs on Affy zebrafish track. commit cf2651d147df25862cc51036e55ac972afc752aa Author: hartera Date: Tue Jul 11 22:38:49 2006 +0000 Added description and methods for human hg16 orthologs for Affy chip probesets. commit 35aad38a0fe4432e5a959fac8147b6e7760d701a Author: hartera Date: Tue Jul 11 22:37:15 2006 +0000 Description for affyZebrafish track for danRer2. commit daa7fad13056336417d9154d394d94f4aa1dc599 Author: hartera Date: Tue Jul 11 22:36:52 2006 +0000 Added affyZebrafish track. commit a0e718aa1618a0e639ec779400814db48fdc52cc Author: hartera Date: Tue Jul 11 22:35:52 2006 +0000 Description for affyZebrafish track for danRer1. commit a05aafc15fd4c471df6ab5b08d250c36db32962a Author: hartera Date: Tue Jul 11 22:35:07 2006 +0000 Added affyZebrafish. commit 58a44dc1e5b31c210ad187735ce830047a70d42b Author: fanhsu Date: Tue Jul 11 22:25:07 2006 +0000 Added logic to show "None" if no "Other Organism" entries in search result. commit 3f07cf0b792f504e20e86f1e238da77489e62152 Author: hartera Date: Tue Jul 11 21:34:23 2006 +0000 Added more information about the method. Minor edits. commit 5c06e1357b2b87b58f9c0361c470b628a84de05e Author: kate Date: Tue Jul 11 21:05:42 2006 +0000 Update chrY agp (centromere should be unbridged). Redo hg18 alignments with better params. Start danRer4 alignments commit b23eeb3ad3e4cdd2e1c8c4c9a190071e8bd7e7a8 Author: fanhsu Date: Tue Jul 11 20:53:02 2006 +0000 Changed doSuperfamily() logic to avoid duplicating domains displayed. commit ce427b10158e83ff0cdef47830daff6797ebbe73 Author: fanhsu Date: Tue Jul 11 20:35:59 2006 +0000 Added mouse over showing domain names for SF. Per request by Kayla. commit 406a7cf8c4c79bcb349446bfad5a31b86a57c32d Author: ann Date: Tue Jul 11 19:46:22 2006 +0000 added block for rheMac2 chain commit c89a6f5ef298e73fd140f12c37a63172568c8885 Author: ann Date: Tue Jul 11 19:40:32 2006 +0000 priority tweak commit b9b2ba45544797b825304502ea29414facb6e4bf Author: kate Date: Tue Jul 11 19:32:55 2006 +0000 Fix args commit dcafad045ae116ccaa16668d5a5e686def9379db Author: ann Date: Tue Jul 11 19:31:22 2006 +0000 added matrix variable to panTro2 chain blocks commit 8f32cd4ed7dad92b13eab721275dcd64de988af5 Author: ann Date: Tue Jul 11 19:30:58 2006 +0000 added blocks for chains to mm8 and hg18 commit e55e3f3f66916d040a893ee548878b5231c7cb08 Author: kate Date: Tue Jul 11 19:28:33 2006 +0000 Add utility to drop split tables from the database commit 2075ed6a608e60471dc9270ea60bcdbc14e4925f Author: kate Date: Tue Jul 11 18:37:01 2006 +0000 Fixes to PECAN in-progress section commit 83f42fb4fff1dbd0826573bbac4637d3e7fedb4c Author: kuhn Date: Tue Jul 11 18:10:07 2006 +0000 added image - pending approval to release commit 4590ad18f5fa70ea62fbe926761d8165ef287a09 Author: kuhn Date: Tue Jul 11 18:09:26 2006 +0000 new image for chimp browsers commit 4aa68585e76412a9b540721e7103d1bfcb364e76 Author: ann Date: Tue Jul 11 16:57:25 2006 +0000 added QA comment about gap table commit 961ea0b14f615957a0a3b941495f5a9606ba51ed Author: giardine Date: Tue Jul 11 16:45:06 2006 +0000 changed Swiss-Prot entries in Human Mutation tracks to be hidden by default. Also changed types on array to match what is used in the C structure gv. commit 6da3ab05a3db4c27827045043ccaa9824aa0c4a9 Author: ann Date: Tue Jul 11 16:34:10 2006 +0000 change panTro2 chain/net to o_db because it's not on the RR yet commit 310482a15480ef188f23b0ecd79cb00f106ae061 Author: ann Date: Tue Jul 11 16:32:14 2006 +0000 changed priority of mm8 chain/net - it was in the wrong place commit 4982b7cbbd0323690f0b26c6389d26caa9c96086 Author: markd Date: Tue Jul 11 16:11:24 2006 +0000 removed functions now in psl.h commit bf60a12053d9db65854b56572af2565d8ea60086 Author: markd Date: Tue Jul 11 16:06:00 2006 +0000 added macros to return strands commit 7f31a685fd8784036061894a0c4aed0a249071a5 Author: galt Date: Tue Jul 11 15:00:21 2006 +0000 "Encode release log update" commit 4252fbb16b76494730c85276053aa3522f205094 Author: galt Date: Tue Jul 11 15:00:20 2006 +0000 "Release log update" commit 15677342c90f278692fe59537c9bd4c440349dd8 Author: kate Date: Tue Jul 11 05:51:39 2006 +0000 Avoid duplicate entries in liftOverChain table commit a3c9306a21f9e329d8297bc64cc122386c6e2300 Author: angie Date: Tue Jul 11 05:40:09 2006 +0000 Fixed a couple bugs in the reallocation -- first, don't just assume that doubling once will always be sufficient, and second, use sizeof to determine the byte size of array elements. commit aa8ef764449e4ab2a8846bb7ac11e782f9763dcb Author: heather Date: Tue Jul 11 02:01:10 2006 +0000 add notes about hg17 lifts commit 8b99e9f184a53137ff35a33a8b598e695f45dad1 Author: heather Date: Tue Jul 11 01:48:20 2006 +0000 lift SV from hg16 commit 875c81fe70d8931315552ecb05fc019f95b50c3f Author: heather Date: Tue Jul 11 01:32:59 2006 +0000 don't generate bin commit 3b7e07a3a641ffb4b00d79799933e7e298e68938 Author: hiram Date: Tue Jul 11 01:26:47 2006 +0000 Proper description of gaps for this assembly commit 9ba9963290e1bf230a5975bf11d470bdaee7136b Author: ann Date: Tue Jul 11 00:38:48 2006 +0000 "New version number v137" commit a1a50c82d7fc97f928d107b080e006b6370d18a8 Author: aamp Date: Tue Jul 11 00:35:31 2006 +0000 A start on a microarray library designed to unify code in hgTracks, hgc, the gene sorter, hgGene, and the various command-line loaders and manipulators of microarray data. So far there's just code targeting the command-line stuff. commit 38629801b798f1b99863b3267a1f4b72c4c4deef Author: heather Date: Tue Jul 11 00:34:30 2006 +0000 add -Wall for consistency with other CGIs commit 05ad929d38e39db38e4fd2c557dd09ea433683ab Author: heather Date: Tue Jul 11 00:33:56 2006 +0000 add phyloGif to BROWSER_BINS commit 677407d96e64f2a7151d362eef07465af8d8d026 Author: angie Date: Tue Jul 11 00:15:33 2006 +0000 Some very old changes, removal of an unused section, and (finally!) canFam1 -> canFam2 liftOver chains using new script doSameSpeciesLiftOver.pl. commit b1f7b6c6cced02090d60c8ec10ee5de4fdee71d6 Author: angie Date: Tue Jul 11 00:11:53 2006 +0000 Added Andy's required arg seqLimit to usage message. commit da692e6da4e839d4e2b351aa92351074e073147b Author: angie Date: Tue Jul 11 00:11:13 2006 +0000 Moved several common hardcoded paths, commands and constants into HgAutomate. commit 4fa3d5d83ab6139e66c4784fffdb3bef39b9068c Author: angie Date: Tue Jul 11 00:10:00 2006 +0000 Added doSameSpeciesLiftOver.pl and makeGenomeDb.pl to SCRIPT_FILES. commit bc463ea7dfe322425bb9cdeba5f7656411102832 Author: angie Date: Tue Jul 11 00:08:38 2006 +0000 Automation script for the first few steps of building a new genome browser database: unpacking sequence and AGP, creating the database and loading basic tables (chromInfo, grp, gold, gap). Also creates template trackDb.ra and .html files, but they need a lot of editing. commit 8ed05941ac34ddc647862074dba0a83089a44e33 Author: angie Date: Tue Jul 11 00:07:17 2006 +0000 Automation script for same-species liftOver chain generation (blat -fastMap, chain, net, netChainSubset), based on Kate's makeLoChain-* scripts. commit c27f489c144532f142d56cb29fd4535da16635dd Author: angie Date: Mon Jul 10 20:41:14 2006 +0000 Added variables for common hardcoded paths, commands and constants. Added checkCleanSlate and checkExistsUnlessDebug for testing state at the beginning of a step. Added machineHasFile (for testing existence of cluster-scratch files). commit c42a798cfdd2ac9fd952c3fbf128b439b9d2c1a4 Author: angie Date: Mon Jul 10 19:43:53 2006 +0000 Improved arg-checking. commit 11b01643610ec8f25a61b629c7d374ba0d001547 Author: heather Date: Mon Jul 10 18:00:27 2006 +0000 handle variant chars commit 2a634835a9726bf866014612dfdbe4e32d2ec44f Author: heather Date: Mon Jul 10 17:46:13 2006 +0000 tweak for cnpSharp names commit 35918cc3432aa549dbc0b85b9137f82fd5189c66 Author: heather Date: Mon Jul 10 17:38:26 2006 +0000 use bacEndPairs for CNP lift commit 783003c8c19c60f9096d396c4a79db1879b6bf7b Author: heather Date: Mon Jul 10 17:38:04 2006 +0000 add cnpLookup commit 7889ee062243d89e86606ced94546e435bbc2224 Author: kate Date: Mon Jul 10 17:32:18 2006 +0000 Start loading PECAN alignments. Update needed from submitter commit 1424a5f2079a65aa1efa184645063080588c8093 Author: kayla Date: Mon Jul 10 17:26:02 2006 +0000 Added panTro2 commit 87d934dfaf4dacf2f17ed7fadf77165446335575 Author: angie Date: Mon Jul 10 16:31:55 2006 +0000 Oops, forgot a twoBitClose() in previous rev. commit 2f2461b46a84757d9085a46fc29b485b9707393d Author: galt Date: Mon Jul 10 15:00:15 2006 +0000 "Encode release log update" commit 403c218df7921c01a664e8dae6e81b7711a9898f Author: galt Date: Mon Jul 10 15:00:13 2006 +0000 "Release log update" commit 33b641175c145b4814afde348931ca4f4f9106c4 Author: daryl Date: Mon Jul 10 04:18:52 2006 +0000 removed old code; changed error message commit 1bb2ffdee3a73cdfa6f39972fc914f1630179d98 Author: galt Date: Sun Jul 9 15:00:16 2006 +0000 "Encode release log update" commit ab372503c9460ffd2ca3dca9a3906421b624cc97 Author: galt Date: Sun Jul 9 15:00:15 2006 +0000 "Release log update" commit 25e4f8ab5ce80694ecfebef8ee3177eea01e2b65 Author: daryl Date: Sat Jul 8 18:35:46 2006 +0000 Changes from March 1 that I forgot to commit commit 4ed3a593fea9596a19c4c81345d2f921c68b99ac Author: daryl Date: Sat Jul 8 18:30:00 2006 +0000 Changed the color description slightly commit 2f9d8d1917cfc4332295225834de7a5d3c425327 Author: daryl Date: Sat Jul 8 18:27:59 2006 +0000 Added more error messages commit 03712b5f9c95f1eabe0bcd7bef935c36caa3689f Author: daryl Date: Sat Jul 8 18:14:52 2006 +0000 chimpSimpleDiff commit 07dcd8bc118227e8d870d80c476dd317a02a0c16 Author: daryl Date: Sat Jul 8 18:14:30 2006 +0000 small cleanup commit 8741804935344ea6df1ac571c0ce20d5123debdd Author: galt Date: Sat Jul 8 15:00:21 2006 +0000 "Encode release log update" commit 946e3185552143f44bb5ddef39fa7543cace7294 Author: galt Date: Sat Jul 8 15:00:20 2006 +0000 "Release log update" commit 6c97a378fd27e84dd9d5193ac27f9e33109c94c0 Author: heather Date: Sat Jul 8 03:45:17 2006 +0000 remove shortCircuit for illumina commit cdc6aa01f367719055380a9fab88514fd27caca5 Author: heather Date: Sat Jul 8 03:44:46 2006 +0000 remove shortCircuit for snp125 because now we also have snpArray track commit 0462b94fdd067ef6ab470ada1d072371f2be2839 Author: heather Date: Sat Jul 8 03:37:45 2006 +0000 add search for snpArrays commit a3fbedcf0c20bd242ff1dcb7b247bc57636f6827 Author: heather Date: Sat Jul 8 03:28:55 2006 +0000 update for affy 500K (lookup dbSNP rsID) commit 83b2674fdd2266f504f57ef50970b4ce796bcda5 Author: heather Date: Sat Jul 8 03:24:10 2006 +0000 fix typo in cross-link commit 8af9bce8c2b38c021253816b0279806530ac7a9f Author: heather Date: Sat Jul 8 03:17:15 2006 +0000 illumina edits commit 40296b2b51d8afe7aa4d3b25d9f56d3fe3e449af Author: heather Date: Sat Jul 8 03:13:55 2006 +0000 doAffy500K commit c533dd218088940d5ed4f5a04642fd57dd34edd6 Author: heather Date: Sat Jul 8 01:04:55 2006 +0000 tweaks commit bc5ceb97833a62cb3fa917efec78e4cf3c61884c Author: heather Date: Sat Jul 8 00:25:55 2006 +0000 add affyLookup commit 869704e6a6f63cf23a54bfa50ffc293534a79b9b Author: heather Date: Sat Jul 8 00:25:43 2006 +0000 get rsIds for Affy SNPs commit 345cc8399a1ee6a00bc36af0e99d7b2d3ec7f14d Author: angie Date: Fri Jul 7 23:12:26 2006 +0000 Fixed syntax error/typo. commit 9eeb90825f9b049253c4ebb8a33a21e624224190 Author: heather Date: Fri Jul 7 21:10:20 2006 +0000 Affy 500K commit f801d7e8f10046b290d692c3c068134d4323bd57 Author: donnak Date: Fri Jul 7 20:53:11 2006 +0000 Made a slight grammar change in narrative about assembly. commit 54b1403f03ea733830f576449fe54a6cb7d48f64 Author: ann Date: Fri Jul 7 19:45:57 2006 +0000 initial files (copied from hg18) commit a08ffd7300ab7e058666600e646d2ed250dedbee Author: ann Date: Fri Jul 7 19:45:25 2006 +0000 added chain and net blocks for panTro2 commit b38b940b919641ba810ab1f65bf399f977f904ae Author: ann Date: Fri Jul 7 19:40:45 2006 +0000 added matrix values to panTro2 chain commit bad284b26487018f72a6873c9b92090487af93a4 Author: heather Date: Fri Jul 7 19:09:55 2006 +0000 add snpArray commit 9018baec3b7e3d5925ddb3e20f0a90addfced09e Author: heather Date: Fri Jul 7 19:09:41 2006 +0000 initial revision commit 56f860e9feb52260dec0340cff43cd0f28c38f6c Author: ann Date: Fri Jul 7 18:14:49 2006 +0000 added chain/net blocks to panTro2 commit c45973f4be74ec457b58bb4d9ef66ab2fedfb4eb Author: ann Date: Fri Jul 7 18:04:17 2006 +0000 deleted extra o_Organism commit 91c8485492fe0918776775e2869223f36169c817 Author: ann Date: Fri Jul 7 17:52:36 2006 +0000 added panTro2 as otherDb commit 603f1666ca1c5e716d1e12c181f7de7c8cc55735 Author: ann Date: Fri Jul 7 17:46:58 2006 +0000 changed panTro2 to o_Organism commit ddcca30fb806bfeaaa5657e323774a65eef343c3 Author: ann Date: Fri Jul 7 17:43:46 2006 +0000 added blocks for panTro2 chain/net commit db7f02b2e31543b16d504f71be78da4909624eda Author: kent Date: Fri Jul 7 16:53:37 2006 +0000 Plotting threshold and adding some explanatory text to uploads. commit 0d56d7e922ce1b96fd34da916f21101324447002 Author: heather Date: Fri Jul 7 16:42:06 2006 +0000 tweaks for illumina commit 5e0ea67aafeef93c8697037187217cfbba251b18 Author: kuhn Date: Fri Jul 7 16:34:27 2006 +0000 more images to replace fuxxy jpgs commit e6287b89ada0753a69f42b26be2dd68bfce6de7f Author: heather Date: Fri Jul 7 16:00:16 2006 +0000 snp126 edit: condense UTR/intron func into just intron commit 2a344b5abe372be347b1361ee8ee0c4c36baadb6 Author: acs Date: Fri Jul 7 15:11:13 2006 +0000 added DLESS info, belatedly commit c5ffb33058c48236903dddc064b5400738a43178 Author: galt Date: Fri Jul 7 15:00:22 2006 +0000 "Encode release log update" commit 800a1174557649d939a26917e9333522944467c3 Author: galt Date: Fri Jul 7 15:00:21 2006 +0000 "Release log update" commit 618020bf236f6351ec9259816916680d904f7d39 Author: kent Date: Fri Jul 7 06:01:10 2006 +0000 Reworking upload page so that you can use multiple-column spreadsheets. Also can have labels in first line. commit 5770b72c9e2d403461f07e7cada080337c7fe2f7 Author: angie Date: Fri Jul 7 00:18:15 2006 +0000 Minor bug fix for .nib query (carefulClose of unused, uninitialized FILE *). Added support for .2bit:seq[:start-end] query (complete .2bit file was already supported, but not fancy specs). Refactored a common sequence of commands from stanzas of searchOneIndex into searchOneMaskTrim. commit 11c63527357ec26fa9519171de61821f95062407 Author: heather Date: Thu Jul 6 23:00:56 2006 +0000 illumina name is actually position commit 296ec89213499e3520c67ba7362c1f4911060b6b Author: kuhn Date: Thu Jul 6 21:57:58 2006 +0000 corrected the image name commit ccbb50221a5f228be1d2333f598a79c00ae28fbd Author: kuhn Date: Thu Jul 6 21:50:54 2006 +0000 changed images commit 8faf1f3ceb13cc6f8c33f19ed5a174ddc60071e7 Author: kuhn Date: Thu Jul 6 21:48:18 2006 +0000 created the image commit dced00fa9f9e41cf78f056fa93aa763f6ba2a32e Author: kuhn Date: Thu Jul 6 21:24:22 2006 +0000 more images commit 7b54aea50d8293bb2cf2cd9671ef54f1a8e105b9 Author: fanhsu Date: Thu Jul 6 21:09:27 2006 +0000 Added ID line. commit 00b60d700d09fc4cec01b5050c0b1eb4d3d02ae2 Author: hartera Date: Thu Jul 6 20:59:10 2006 +0000 Added strains and stages table and other edits. commit bb008fe3eb789bfe621e686ab70364e546fa92a4 Author: kuhn Date: Thu Jul 6 20:41:14 2006 +0000 shortned the branch values displayed in the textbox to display fewer sigfigs and made the box less wide commit ff0bfeee408b968005f408911a53e5f63aa40322 Author: markd Date: Thu Jul 6 19:24:44 2006 +0000 added MGC synthetic entries commit 69281f2625d3b5555a5870f7d63b706b10509e69 Author: hartera Date: Thu Jul 6 19:21:00 2006 +0000 First draft of description for Wild Type Array data from the Zon lab. commit a14e420e77ed34eb30a6056b89557099a4a85e67 Author: markd Date: Thu Jul 6 19:20:00 2006 +0000 don't include NC and NR refseqs commit 80a7e834beebfaf8306f3c5e7ec1cb0eebab3db1 Author: fanhsu Date: Thu Jul 6 18:26:03 2006 +0000 Added ID line. commit 7a8d681de1d9fdecd1be324a8460b262a60ccacf Author: hartera Date: Thu Jul 6 18:16:30 2006 +0000 Deleted record from rgdQtlLink that was not in rgdQtl. commit cee2ff51c996b3d2110418f27d4e6f1c08d9b933 Author: heather Date: Thu Jul 6 17:34:25 2006 +0000 add special case for UTR/intron commit e76b2976534a5249fbc2d929c62e83f49dd691f3 Author: galt Date: Thu Jul 6 15:00:19 2006 +0000 "Encode release log update" commit de33519e6c9e92feabaf49210014c6640f50ba5e Author: galt Date: Thu Jul 6 15:00:18 2006 +0000 "Release log update" commit 55f300463da35a1c7c37c40a2ec36ad57c8f5274 Author: kuhn Date: Thu Jul 6 00:26:17 2006 +0000 better image than the jog commit 0d24b55552384868a08e894d22ce000dd07fb9d8 Author: kuhn Date: Thu Jul 6 00:20:12 2006 +0000 new images commit b4f53a2c488eb8f81d201050bb52873c6de43082 Author: hiram Date: Thu Jul 6 00:06:26 2006 +0000 New data set for UW/Regulome commit 297f34225a437414092b543dc1f52850eaa1743a Author: aamp Date: Thu Jul 6 00:06:07 2006 +0000 Don't pay attention to this one. I'm testing a cvs thing. commit d382bec7e4051613006780b8d5e7d4a420b5f7ec Author: kuhn Date: Wed Jul 5 22:38:52 2006 +0000 better image than the jpg commit e7f87f77ace528b77e108c2c9146412e042e52da Author: hartera Date: Wed Jul 5 22:10:43 2006 +0000 Added more searches for affyU133. commit 93d70b0a5ab922fca527591f0f21d5bdd6a6c4a8 Author: hiram Date: Wed Jul 5 19:42:47 2006 +0000 Add information about mysql_config commit 445fe874a5e316bf45fdf2943f7d76753bdd5406 Author: hiram Date: Wed Jul 5 18:49:26 2006 +0000 Add information about mysql_config commands commit 1c2005ae38e6d8c016952986263d6bd59ba8ba06 Author: hiram Date: Wed Jul 5 18:48:40 2006 +0000 Add information about mysql_config commit 3d1cd0d0f5062d7b6bf2e57c4c504ba6571bb122 Author: heather Date: Wed Jul 5 18:31:23 2006 +0000 try using scratch, tmp seems to get cleaned over the weekend commit b62de342bc43e126e366d71e34f0b7f31797b3a8 Author: kent Date: Wed Jul 5 18:13:17 2006 +0000 Adding microsatellite track commit 964d21495d429ebedd475f1b901d5076bd6658ac Author: hiram Date: Wed Jul 5 18:03:39 2006 +0000 some reg potential updates commit 103568ac36516abf0d1c109e64c0e79e75c372f6 Author: kent Date: Wed Jul 5 17:37:46 2006 +0000 Decided didn't need a separate file for this after all. commit d0ad43b6f276d08157dd83df11d93043e9ae6109 Author: fanhsu Date: Wed Jul 5 17:34:54 2006 +0000 Added a hFreeConn(&conn); for rgdQtl processing. commit c6f5b427aaeeadefe39fbcbdaa05e25ee9d99def Author: kent Date: Wed Jul 5 17:27:06 2006 +0000 Adding microsat table - same format as simpleRepeat. commit b9c461bb02f7728e0ec4b4c8a730de5db7f67d02 Author: ann Date: Wed Jul 5 17:25:44 2006 +0000 changed to more closely describe real data values commit d86238fc7391abef51202e4b4a0ad3d5882588cf Author: fanhsu Date: Wed Jul 5 17:20:45 2006 +0000 Updated select statement to get unique protein IDs to avoid duplicate display. commit 7a732b201062595a99dc041e3d5cc7fc640d12eb Author: jill Date: Wed Jul 5 06:50:34 2006 +0000 added -noHap filtering option commit 5f441ecc56c67cefbbd8e4db43f012f42b9e4510 Author: hartera Date: Wed Jul 5 01:35:54 2006 +0000 Minor edits in hgNear section. commit dea7df0bebd99de1af167cdeb6a0b83f80964ba0 Author: kent Date: Tue Jul 4 23:26:03 2006 +0000 Getting rid of case dependence. commit 716a1910d846b56752430dcc2d7b3395b25cebbb Author: hartera Date: Tue Jul 4 19:22:46 2006 +0000 Zebrafish-specific ordering information. commit 91d87f1e8ea0642cd0b21cbef38dc039a5e6b6f5 Author: hartera Date: Tue Jul 4 19:22:07 2006 +0000 Columns for zebrafish Gene Sorter. commit daae554ae4afa99aca958e82150723d86d605845 Author: hartera Date: Tue Jul 4 19:21:13 2006 +0000 Edited example searches. commit 4e93f7226222894a6c4eeeb17096ddb20bbd3f33 Author: hartera Date: Tue Jul 4 19:20:28 2006 +0000 Added zebrafish assembly-specific URL for orthologs using transcript ID instead of protein ID. commit c851b46cfb062be4831d53a1e8a75e7d1a60e7ec Author: hartera Date: Tue Jul 4 19:15:47 2006 +0000 Added zebrafish orthologs URL for transcript ID instead of protein ID. Zebrafish drBlastTab now uses trancsript ID. commit 7d347f659b17b18adb50ef6b0399d31d937dd157 Author: hartera Date: Tue Jul 4 19:12:23 2006 +0000 Added new URL for zebrafish and removed mySQL statement to get transcript ID since BlastTab zebrafish tables are now using transcript ID instead of peptide ID. commit 65f26669e5cd850b2d5830f5121e06d45e4e571d Author: hartera Date: Tue Jul 4 19:09:36 2006 +0000 Removed mySQL commands to obtain transcript ID. Now using transcript ID in BlastTab tables instead of peptide ID for zebrafish. commit 65f3e9bd1dcd2f4011c2711a0935b9b18ba3c208 Author: hartera Date: Tue Jul 4 19:06:52 2006 +0000 Added assembly-specific URL for zebrafish Ensembl genes. Updated from danRer1 to danRer3. commit 2f24bf00a378dc73df04e23b96cff3aa1119a0ee Author: hartera Date: Tue Jul 4 19:06:24 2006 +0000 Added assembly-specific URL for zebrafish Ensembl genes. commit bfaf43d03af728b14aa5765d6cfb86e09929600f Author: hartera Date: Tue Jul 4 19:05:06 2006 +0000 Added assembly-specific URL for zebrafish Ensembl genes. Updated from danRer2 to danRer3. commit 6f7f25dd0d4d3a0ba1e54e707ed175277617c677 Author: hartera Date: Tue Jul 4 19:01:09 2006 +0000 Added assembly-specific URL for zebrafish Ensembl genes. Updated from danRer1 to danRer3 commit 960902c96ecd55e0129326ed669ab49b83593553 Author: hartera Date: Tue Jul 4 19:00:20 2006 +0000 Added assembly-specific URL for Ensembl genes. commit 659797402d9de8846b772fb8d8b9f3cc5deb2a94 Author: hartera Date: Tue Jul 4 17:34:57 2006 +0000 Changed Blastp tables to use Ensembl transcript ID rather than peptide ID and updated some older assemblies to use the Ensembl 38 for Zv5 (danRer3) for blastp (drBlastTab) homologs. commit 2c01a8fcce47b589c3ba8548bbb1d55c44c3d15e Author: angie Date: Tue Jul 4 16:13:59 2006 +0000 Resolved -Wall warning: unused variable. commit 75e9ed20402ab7992a168ef328fa30f780f70091 Author: galt Date: Tue Jul 4 15:00:23 2006 +0000 "Encode release log update" commit 823b81fa80cc1776def475fb2368623570d553d9 Author: galt Date: Tue Jul 4 15:00:22 2006 +0000 "Release log update" commit 0725286f1f1fff544871619833457cb612f4cd51 Author: heather Date: Tue Jul 4 03:19:23 2006 +0000 handle func value that contains more than one value commit 7570d5abaa68764de8f444d0561eba5f85b9c3ec Author: kate Date: Tue Jul 4 01:11:48 2006 +0000 Fix up Regulome Oct. freeze track configs (tho soon to be replaced with QCP track) commit 6baaba1cf73da07cb5f15529bc6d741046c95e6a Author: kuhn Date: Tue Jul 4 00:43:05 2006 +0000 had to add track-type info in each subtrack to get it to work on both dev and beta commit 78a350de4aa098f77d4169b341873553452e1038 Author: angie Date: Tue Jul 4 00:32:07 2006 +0000 Moved $dbHost, $centralDbSql and &getAssemblyInfo out to HgAutomate.pm. commit c5a8034baefc719d30fa397f750520e9db055dbb Author: angie Date: Tue Jul 4 00:28:46 2006 +0000 Added some basic knowledge of our local clusters and filesystems so that automation scripts can ask for suggestions of which cluster, fileserver, or "workhorse" machine to use, or can have a cluster+path combo checked. Also added getAssemblyInfo and $dbHost from doBlastzChainNet.pl. commit 4355e5881e542c4ead62623072adcdaa9c122502 Author: galt Date: Mon Jul 3 23:21:55 2006 +0000 making better examples commit 76b80a1e04aef0670ecaa159f30bed0b459d25ee Author: galt Date: Mon Jul 3 23:10:30 2006 +0000 fixing permissions on jksrc.zip file commit 71e392a3fbdfc356fa4ed1a0a3819ee16f0ae157 Author: angie Date: Mon Jul 3 23:00:05 2006 +0000 Ran doHgNearBlastp -queryOnly to update other databases' rnBlastTab tables. commit 99051c78fdd649c25f1ba6c39c00b57f08a0735a Author: ann Date: Mon Jul 3 20:59:25 2006 +0000 added block for gap track commit 2002e25bff14582858bd8fec4eab132b6d6ad63f Author: galt Date: Mon Jul 3 19:59:35 2006 +0000 added exclude clause commit 0557cc5452fd47df8ba4db14933561ba51e56971 Author: galt Date: Mon Jul 3 19:31:25 2006 +0000 fixed typo commit 8a3d4347d7e5637668d6cbc286571dd8e7fd05bb Author: galt Date: Mon Jul 3 19:21:07 2006 +0000 addendum to clean out antibodySource table commit fd571f39dade5b28b6619120e8168b90e2acc43d Author: kuhn Date: Mon Jul 3 18:56:57 2006 +0000 changed Conservation image to a gif commit 1c007b92faa42e6976c77c984abc57ba3ff5a422 Author: kuhn Date: Mon Jul 3 18:55:02 2006 +0000 changed the size commit 71e870a9d318b289a732f2924be17152a2cc5282 Author: kuhn Date: Mon Jul 3 18:21:18 2006 +0000 new image for mm6 Conservation track commit db646e0dd4f13d7828841726ed240e99ffdb4611 Author: donnak Date: Mon Jul 3 17:30:30 2006 +0000 Fixed typo. commit 4a419ef16e11ec513f62e0856e4bfd798a4501dc Author: donnak Date: Mon Jul 3 17:12:31 2006 +0000 Updated Kent Informatics website URL. commit 23b53a3905e2b4e465501f75bdbf24e55ae4352b Author: donnak Date: Mon Jul 3 17:07:20 2006 +0000 Added Kent Informatics website link. commit 44c45ced5cf2291da771eb4242fc26a3d1de135a Author: kate Date: Mon Jul 3 15:18:50 2006 +0000 Add include file routine commit eee51396cece8ee803a23fc59df322f2b62ebda6 Author: galt Date: Mon Jul 3 15:00:33 2006 +0000 "Encode release log update" commit 812d65558711512143938a6c0c0ddc866eb07263 Author: galt Date: Mon Jul 3 15:00:32 2006 +0000 "Release log update" commit 085537663d75f98b2ddd774e4f8b33a465387b1e Author: kent Date: Sun Jul 2 23:04:12 2006 +0000 Integrating in common.h bool ifdef changes for mac. commit 83eaca318d6e06f1eedcfa027197bb4b004db192 Author: kent Date: Sun Jul 2 19:04:33 2006 +0000 Polishing up main page a little. commit 3b663d22519e26ba4b8f59d3ad5ea78384615fc5 Author: kent Date: Sun Jul 2 18:58:08 2006 +0000 Getting click on image to work. commit d33ce69d599d414c5b748cd49e6ccb8d327fa851 Author: kent Date: Sun Jul 2 18:56:34 2006 +0000 Adding cartWriteCookie and cartForSession for things that need very fine grained control over what HTTP lines are written. commit 3a85b99cf532f3ee6c18af469e4f08492e8c5cb6 Author: markd Date: Sun Jul 2 18:07:31 2006 +0000 support genbank format CDS input commit ef6595078b54b8f127a1a5c4722892484d143e07 Author: galt Date: Sun Jul 2 15:00:17 2006 +0000 "Encode release log update" commit d2846d289cfe00550603b7834f51894255302b10 Author: galt Date: Sun Jul 2 15:00:15 2006 +0000 "Release log update" commit 200ecc7df19692f453d2cabd57486eb6220da53a Author: markd Date: Sun Jul 2 07:47:32 2006 +0000 make include files C++ friendly commit 67016b5502c017dfaf55bfd2476dec4bc91a5dc2 Author: kent Date: Sat Jul 1 20:10:32 2006 +0000 Some more work on click in image. commit d2bdbb1bcc5925087ca87d7909f1c34098c904c0 Author: kent Date: Sat Jul 1 19:50:20 2006 +0000 Starting on clickOnImage. commit 2f0d25e1c66f96f90b79a961a6041ee4399d1fa7 Author: kent Date: Sat Jul 1 19:49:46 2006 +0000 Adding one to margin commit 80b8f80d8b6653ddad896ff171d7c2232ca7059f Author: kent Date: Sat Jul 1 09:24:37 2006 +0000 Adding configuration option to turn off numerical labels. commit 15260610142a28da31ac1da53e1cc9e8436e3fa4 Author: kent Date: Sat Jul 1 09:14:52 2006 +0000 Fixed crash when there are ore than 2 columns commit a0fea3ec32639670b161aca2290a82160dd28abb Author: kent Date: Sat Jul 1 08:53:07 2006 +0000 Adding a button to get back to the main page from the correlation page. commit e8da7c20ddb7b0c908c8a3000a7460421b986503 Author: kent Date: Sat Jul 1 08:46:51 2006 +0000 Polishing up correlation page. commit 5fcba04592b05fa97605f6b6673183c08bd03c9d Author: kent Date: Sat Jul 1 08:32:34 2006 +0000 Moving some table routines from hgGene to hg/lib/web.c commit 0b068198709ffab6e8d2015288cfd3b38769ff5d Author: kent Date: Sat Jul 1 08:20:21 2006 +0000 Adding correlate module commit a48c61c67a4118b65d18f7c2d8f055522917da59 Author: kent Date: Sat Jul 1 08:20:01 2006 +0000 Doing first cut of correlation button. Still some debugging info left in. commit f0830610bc6af41a61e43cacd942cde3b8c96eca Author: kent Date: Sat Jul 1 07:09:40 2006 +0000 Adding correlate module. commit ef0e642e006acf8bb9b04665c05b7207aabd590a Author: kent Date: Sat Jul 1 07:09:14 2006 +0000 Testing correlate. commit 207a6e3288bf5ee29652df0818c3be2b9720e46d Author: kent Date: Sat Jul 1 05:02:35 2006 +0000 Implementing Sort Genes button. commit ea54fbf14ef619756959e7d3b95cac57907a104e Author: kent Date: Sat Jul 1 05:02:05 2006 +0000 Adding sqlQuickHash commit 797c14a02778f3d30fb90454d5e8385e63a27d8e Author: kent Date: Sat Jul 1 05:01:25 2006 +0000 Adding binKeeperAnyOverlap commit f0a7abead9da39731d5d8d1da207e4a281b2a212 Author: hartera Date: Sat Jul 1 01:22:40 2006 +0000 Added hg17 to rgdQtlId rule. commit 2ca4553c6963999aaec04eb94d6fbb6a8a4da4b7 Author: jill Date: Sat Jul 1 00:08:09 2006 +0000 turned off default stderr output. it stalls long jobs when spawning window is closed. commit 477b356dec57b9b1cc8630b97ae541303e3e3a03 Author: kuhn Date: Fri Jun 30 23:47:06 2006 +0000 added new gif image for Conservation commit 5516d93453c2b5ad464da60212c9481ca376475b Author: kuhn Date: Fri Jun 30 23:38:09 2006 +0000 checking it in aqain as a bineray commit 39b3ec653f52f50f1dac425c553e4351609e120e Author: kuhn Date: Fri Jun 30 23:37:26 2006 +0000 removed because not checked in as binary commit 00f192dd90a8951747a4adba08a0f182731325be Author: ann Date: Fri Jun 30 23:31:31 2006 +0000 copied from top level and edited to inlcude all types of gaps in this assembly commit 78aab55bd203e42960249d578390b39db67360c7 Author: kuhn Date: Fri Jun 30 23:31:10 2006 +0000 new image for Conservation tracks commit 934cd21f9d37a604b2306716c5d38c2a6ef3d5cc Author: kuhn Date: Fri Jun 30 23:26:59 2006 +0000 changed to new gif image for phylo tree commit b56bc0e017893a1ca38448ed442d585658f0f2c1 Author: markd Date: Fri Jun 30 23:24:39 2006 +0000 split main index page into included subpages to make maintaining MGC page easier. Added ORFeome to MGC browser title commit 5cadfae4b32d456397d272361b78c20dd2f0cf47 Author: galt Date: Fri Jun 30 23:13:37 2006 +0000 better error handling and messages to user commit 121a16890af0b876a1720706f033c4776fff3ea8 Author: galt Date: Fri Jun 30 22:44:12 2006 +0000 remove unneeded genomeVar* - Belinda requested commit 199424a5bd9d1e35148bcbb1c45460ed73613d6a Author: ann Date: Fri Jun 30 22:38:55 2006 +0000 some clean-up and typos commit bc09db9ff41714f6a57d97b99f5e913d6f258595 Author: kent Date: Fri Jun 30 21:10:59 2006 +0000 Polishing Browse Regions a little. commit 96342654171f3660ab897c62742b0e2b3b2f20f7 Author: kent Date: Fri Jun 30 21:10:43 2006 +0000 Adding bedTotalSize commit 2155110e4edab171ddee06696da8fbb726e453a7 Author: kent Date: Fri Jun 30 20:38:13 2006 +0000 Implementing Browse Regions commit 52233e139af1da55ada7c2253ece4f88c9e0aac9 Author: kent Date: Fri Jun 30 20:35:27 2006 +0000 Adding chromGraphBinToBed3 commit f6bdf11dc3392b362b4d1db942cf00c91958f91b Author: kent Date: Fri Jun 30 20:35:07 2006 +0000 Adding bed3New commit b4b1b211f75b042028b49194e0a2009848c4bfec Author: kuhn Date: Fri Jun 30 20:20:53 2006 +0000 new images for Conservation. thanks to galt's new tree-draw utility commit cce1b8bce698ba708bad8340dd1495e1cbaed20a Author: galt Date: Fri Jun 30 20:03:22 2006 +0000 redundant bit removed commit ac36efeb6ff0d4ac8f184e3592674cebc2ae00df Author: giardine Date: Fri Jun 30 19:57:03 2006 +0000 Added table for long attributes, the reason is that several official names were too long to fit in varchar, but not enough to warrant changing the gv table or the gvAttr table. Added to cgis to handle abreviated and full names of mutations. commit 7e2b7a1d358a9c664798dea3ae7e06277ac633b7 Author: braney Date: Fri Jun 30 19:41:06 2006 +0000 make sure we're not getting one species instead of one that just has the same prefix commit 34312f3fe0954d0129a9182aac5251b13e5a218c Author: braney Date: Fri Jun 30 19:40:03 2006 +0000 fixed problem where wrong sequence was used when one species name was a prefix to another in mafs commit 7b7a2b734e3b5ffbed7f7c04d73809a28f9a5478 Author: braney Date: Fri Jun 30 19:38:59 2006 +0000 fix problem causing hang when one species was a prefix to another in maf file commit c2c0223dc1dc2033bf3eccafdb5384ef53626b3d Author: braney Date: Fri Jun 30 19:37:42 2006 +0000 added a couple of routines to better deal with sequence lines in mafs that may or may not have '.''s in them commit fd198e504765a8d3fefbd2ec337dd63be78f06a3 Author: braney Date: Fri Jun 30 19:36:44 2006 +0000 added a couple of routines to better deal with sequence lines in mafs that may or may not have '.'s in them. commit 65cefceecd0454f7d53e5ef8aae4aa161c41bf35 Author: angie Date: Fri Jun 30 19:19:03 2006 +0000 Fix from Bernard Suh: when making self chains, in loadUp(), $successDir is actually a file so use -e instead of -d to test existence. commit 8023ab61926824365338c59ecf0b1cd86b38ecca Author: galt Date: Fri Jun 30 18:02:59 2006 +0000 adding link for phyloGif utility commit 42f2aeec8e98e93414f62b010c78a0b07de58ebe Author: galt Date: Fri Jun 30 17:47:19 2006 +0000 making notes better commit d1405aa023177025ef8ecb5b4b23b341a641d759 Author: angie Date: Fri Jun 30 16:15:39 2006 +0000 Adding local description of genomicSuperDups, with fr1-specific thresholds. commit 8fe28c6a2125ed600d44455b0182ba55c90261a9 Author: angie Date: Fri Jun 30 16:12:02 2006 +0000 One more fix for genomicSuperDups: Kayla found some items below the length threshold and Xinwei asked to filter them out. commit 98e7ce72445ea5e1e57a38d89d473c2f04c61710 Author: braney Date: Fri Jun 30 15:43:24 2006 +0000 take out definition for bed3, it seems to be in bed.h commit 782b8d5205a4067982097237efb2b744b26dda27 Author: angie Date: Fri Jun 30 15:29:28 2006 +0000 Resolved -Wall warning: cast to int for char used as array subscript. commit 8b221f79d19c107c9cb4d4ffb96066fd8022633f Author: galt Date: Fri Jun 30 15:00:24 2006 +0000 "Encode release log update" commit d244d1fb48af2f969acd4a11983bfca48a4aa58f Author: galt Date: Fri Jun 30 15:00:23 2006 +0000 "Release log update" commit 102b990301ab21a0a4bba446f75ce396ad57a539 Author: galt Date: Fri Jun 30 08:22:39 2006 +0000 trivial changes commit a3b198f97450d4be703d2dce3ce63ad313bfed89 Author: galt Date: Fri Jun 30 08:08:18 2006 +0000 integrating with cart and general browser cgi behavior and look and feel commit 24c192c9c2ff387fe2a43a8eb97363af6677c0e8 Author: galt Date: Fri Jun 30 05:49:10 2006 +0000 uninitialized pixel mem by design, at least I added a comment warning users commit f8e283a42ef2575853773fda675add2c98858230 Author: kent Date: Fri Jun 30 05:30:37 2006 +0000 Adding chromGraphBinRewind, so that can have the same graph appear multiple times. commit 5e3e8287d32b06533ef783731733b135c115bbc1 Author: kent Date: Fri Jun 30 05:27:44 2006 +0000 Unreversing chromList in chromGraphBin. commit 156a8b30694a444b0001e61421bab6a4670721cd Author: kent Date: Fri Jun 30 05:25:17 2006 +0000 Adding chromGraphBinRewind. commit 5bffb9410d3158e479ed2d3701df84139f2d1299 Author: galt Date: Fri Jun 30 00:56:06 2006 +0000 clearing pixels so you dont get trash off mem heap commit d8b0e206ed4156c2cce8e1f5688f8ac85cf5fb35 Author: kate Date: Fri Jun 30 00:23:47 2006 +0000 Exclude composite tracks from gene pulldowns (just use their subtracks commit f65e9f51463ffa9941f283ff180479f818ef1a93 Author: donnak Date: Fri Jun 30 00:10:42 2006 +0000 Added sample query for position+N. commit 3174d0d44f5bb5ded78cdb33fe89f9f922eec34b Author: donnak Date: Thu Jun 29 23:16:59 2006 +0000 Added PAR info for X chrom. commit 91c78da122d9db5ce13b70f634da556a9ec6dd64 Author: braney Date: Thu Jun 29 21:41:14 2006 +0000 take out some comments, add in some bug fixes commit f33413f3dfc1230074a767ca3d1c33db64f6f2ac Author: kent Date: Thu Jun 29 18:50:40 2006 +0000 Starting on browse regions page. commit e2cdbb6845582b1b14b7d8d99f0e2745ce809056 Author: kent Date: Thu Jun 29 18:50:09 2006 +0000 Adding bed3 and bed4 structures. commit c9c6915ecaa8df4a270181231546a802f9ad3b87 Author: kent Date: Thu Jun 29 17:43:45 2006 +0000 Adding linesAt labels to upload page. commit 43f669c9bdc839620214fb3dfc543cc594c8b041 Author: markd Date: Thu Jun 29 17:06:54 2006 +0000 added option flag for skipping gbLoaded optimization commit f857871a0e3a40719ef26ed674dd14460e3fa5ae Author: donnak Date: Thu Jun 29 17:00:49 2006 +0000 Made a few minor edits. commit 45f74fb9f37cb0aa208ff41246ad50d77204fb78 Author: angie Date: Thu Jun 29 16:43:11 2006 +0000 Resolved -Wall warning: added parens around assignment in if. Really, jksql functions should be used instead of system-ing hgsql commands which ignore warnings. commit 05c14c71050ff9ff760eeb131a7d384db510701e Author: donnak Date: Thu Jun 29 16:41:18 2006 +0000 Made some minor edits. commit d3ca49787189c5a4107cf6b8da60baa03b66a196 Author: angie Date: Thu Jun 29 16:37:08 2006 +0000 Resolved -Wall warning: unused variable; errAbort format in usage(). commit 531f6b6e14189d0402b136605c64aa3bf17e0986 Author: ann Date: Thu Jun 29 15:54:39 2006 +0000 fixed references commit 9c9cfa5bfef4ea637844952ee49aed534486b7c0 Author: donnak Date: Thu Jun 29 15:31:42 2006 +0000 Made a few minor edits. commit 90583d325714a69480a73029d11cecbd58146730 Author: galt Date: Thu Jun 29 15:00:25 2006 +0000 "Encode release log update" commit 1a681058de07d72a5d8454a59f6ee780692f8d76 Author: galt Date: Thu Jun 29 15:00:24 2006 +0000 "Release log update" commit 3974d4cb5397afbb77ce146e8ee95531a6d978a4 Author: kent Date: Thu Jun 29 14:55:14 2006 +0000 Adding numerical labels. commit 1ea09ef5319062fcc09480ad25478fc390918f7c Author: giardine Date: Thu Jun 29 14:11:12 2006 +0000 Updated data in omimTitle table, and added to make doc. commit 1877c11a869f52b76842ed240b39bea696550a01 Author: markd Date: Thu Jun 29 05:44:44 2006 +0000 added file for orfeome IMAGE ids commit 8f5cd7669e9d9df8e1358f913fd735a61e704870 Author: markd Date: Thu Jun 29 05:42:23 2006 +0000 treat ORFeome synthetic clones as native for alignment commit db866901c632aba02aeae5f6da0abed1375beec2 Author: kent Date: Thu Jun 29 03:00:18 2006 +0000 Adding in sts alias processing. commit bf4d7fc09443b4b45be2c34310b8892921fd4707 Author: kent Date: Thu Jun 29 01:27:45 2006 +0000 Freen tests read/writeBits64 commit b873861469da59fe9a996557808e015df6425d14 Author: kent Date: Thu Jun 29 01:27:08 2006 +0000 Adding trackDbHashSettings commit f7fa6ccf35e5b76e73db22878846f6bcb9797e35 Author: kent Date: Thu Jun 29 01:26:20 2006 +0000 Adding chromGraphSettingsFillFromHash and some misc. commit 3d71354444aa20cea2aa612f7ac6ad2ab66d65a1 Author: kent Date: Thu Jun 29 01:24:52 2006 +0000 Starting to make uploads relative to sts maps or snps work. commit 946ae25ab2248de5b3b15eb4ce916bc979b50ea9 Author: kent Date: Wed Jun 28 22:29:28 2006 +0000 Starting to display uploaded values. commit 5fda7b8e785160a5e4ea0cc08b5f83358d6bfc11 Author: kent Date: Wed Jun 28 22:26:20 2006 +0000 Adding cgiMakeDropListWithVals, because cgiMakeDropListFull is pretty much broken as far as keeping your selection goes. commit 5a1aa047690fc4ba62d069bcf5a2f2373ba6bf1a Author: heather Date: Wed Jun 28 22:17:16 2006 +0000 add rcsid commit 6b3a2ea8af39a584d14e25ab598169da4cbd80ec Author: heather Date: Wed Jun 28 21:44:40 2006 +0000 avoid bad indices commit ef0634b2a922b6f351ef82202cdee5b7e205f337 Author: heather Date: Wed Jun 28 21:34:52 2006 +0000 fix locType data name commit 6cb8f65e77af44cf9b24800eb45e4ee042a23bfb Author: heather Date: Wed Jun 28 21:16:45 2006 +0000 swap order of molType and locType color source commit 533248612e108232db882de5a6cb4c3409b4c111 Author: heather Date: Wed Jun 28 21:13:34 2006 +0000 adjust for rangeInsertion/Deletion commit 96f70c01fa2e9c5a9d831d2eb3cd636a06107b8d Author: kent Date: Wed Jun 28 20:56:28 2006 +0000 Working on uploads. commit f2c2ff6c47227bf24f38ed44461860d6e87d1a00 Author: kent Date: Wed Jun 28 20:25:55 2006 +0000 Adding raReadAll commit 736b8cc03dfc805aee855e246dbafd983ba84db2 Author: kent Date: Wed Jun 28 19:57:54 2006 +0000 Tweaking chromGraph binary format one more time. Adding min/max values to header, along with 16 bytes of zeroes. Tweaking signature. commit d554e222452c1c1bfb90bde6aefe23205b588230 Author: kent Date: Wed Jun 28 19:35:01 2006 +0000 Changing chromGraph binary suffix to .cgb. commit 9044cc9162fe60fce8dbb7cbf5bd23ea466e89ee Author: kent Date: Wed Jun 28 19:27:00 2006 +0000 Adding -chrom option commit b267993ca908058b0eb06c219a0cee4db14ad5ae Author: kent Date: Wed Jun 28 19:25:32 2006 +0000 Added chromGraphBinSeekToChrom and adding index to binary chromGraph file format. commit 007af44ad2f59f9b042fe44bdbc7a28597ed9ce7 Author: heather Date: Wed Jun 28 19:09:27 2006 +0000 add comments commit 015f21a776812963365a0236e075d321802b5e86 Author: galt Date: Wed Jun 28 18:51:10 2006 +0000 giving user control over how many decimal places to show on branch length labels commit e1bd54438e6e2a5a7b9509feeaab99e13f024403 Author: galt Date: Wed Jun 28 18:22:54 2006 +0000 describing phastCons branchlengths commit d08f1d3216e19e485b65259c902c7db51c867d96 Author: kent Date: Wed Jun 28 17:59:35 2006 +0000 Adding readBits64/writeBits64 commit 25e8d4261b2022044498b55e5db734f06c01e7e5 Author: ann Date: Wed Jun 28 16:20:34 2006 +0000 reordered species in alignment list. fixed author typo. commit 02a3b6076e84ac3013596e6ca6f1d279526eb119 Author: angie Date: Wed Jun 28 16:19:01 2006 +0000 Resolved -Wall warning: unused variable. commit c0a7c994c1d91ca67d3469c6c8c6d697a855930a Author: galt Date: Wed Jun 28 15:00:25 2006 +0000 "Encode release log update" commit 244066c274e3926008e10ec5058c3090f5da8de7 Author: galt Date: Wed Jun 28 15:00:24 2006 +0000 "Release log update" commit bd511ff6f781e12e080225a99f1a2983d7633238 Author: kent Date: Wed Jun 28 05:44:02 2006 +0000 Starting on upload page. commit 0509b379c71282c71480dbbe4a5988be46ee81c5 Author: kate Date: Wed Jun 28 03:04:54 2006 +0000 Add Fill button for description commit c732afa59b8dd9a8c945cd1c10d9e87930666ada Author: aamp Date: Wed Jun 28 00:50:47 2006 +0000 Stuck a function previously in a bed-related utility into the bed library code. It fills in fields out to bed 12 if the bed doesn't have those defined. commit 0df6a3800a06e38b1668f14c1db90ab7ba92f4b5 Author: donnak Date: Tue Jun 27 23:55:41 2006 +0000 Slight wording change to Cornell mirror blurb, per Adam. commit 66728219beed642739aef32104b5aa687677afeb Author: kent Date: Tue Jun 27 23:46:28 2006 +0000 Making system use graph controls. Starting on upload page. commit 9430cf5bc6128237d9c8673779b2c62d70acaf07 Author: angie Date: Tue Jun 27 23:25:15 2006 +0000 Use HgStepManager to specify and execute steps and to handle -continue and -stop. Use HgAutomate's common command line option support. commit 3d3a3f198bb72f4ebe7c9211479fff1259e13e29 Author: donnak Date: Tue Jun 27 23:15:38 2006 +0000 Added more visibility for genome-announce & genome-mirror mailing lists. It's a little cluttered now, but I don't have time to reorganize it -- just want to get the information out there at this point. commit 05e4ec0ad5ed836359b6694dc08a241cb43fd531 Author: angie Date: Tue Jun 27 23:04:23 2006 +0000 Added HgStepManager.pm to SCRIPT_FILES. commit 3cbb766346d41c8f5335e777bdc593cfdacb10b4 Author: angie Date: Tue Jun 27 23:03:26 2006 +0000 Perl object for specifying and executing distinct sequential steps of a process, with support for -continue and -stop options. commit 107cb0b789f84a0b775ade59396c28c7632c8654 Author: donnak Date: Tue Jun 27 22:48:19 2006 +0000 Added capability to search genome-mirror mailng list archives. commit 7c9d9c59201f07a64be81fd3dbd08420ff339d31 Author: angie Date: Tue Jun 27 22:47:22 2006 +0000 Added support for command line options that are expected to be common to many automation scripts: options for specifying which machines to use and -debug, -verbose, -help. commit c694221ba731a6d47b22c6491d5830df41d17cd6 Author: donnak Date: Tue Jun 27 22:44:19 2006 +0000 Added Adam's mirror site to the list. Added ability to search genome-mirror archives. commit d7a5ce6a7b8af6213e5870fe4aac09ec129226f0 Author: ann Date: Tue Jun 27 22:14:57 2006 +0000 removed binCons subtracks from three Conservation tracks commit 6b3894410ebe8b82a4456cd1bd19637cb423971e Author: donnak Date: Tue Jun 27 21:29:32 2006 +0000 Minor grammar change suggested by Brooke. commit 33d0017e921ae99977a0ca1fe614d4dbffb55b55 Author: kate Date: Tue Jun 27 20:18:44 2006 +0000 Display density plot (dense vis) or graph (squish mode) at base-level when wiggle is missing (e.g. ENCODE alignments) commit 9ef285026f522adee93b71e28f74f3440f126d86 Author: galt Date: Tue Jun 27 19:56:27 2006 +0000 fixed pedantic warnding mixed decl and code commit 818e4312db89750d0b033c093871e40c4bb6d25a Author: galt Date: Tue Jun 27 19:45:01 2006 +0000 fix tableDescriptions.pl error checking commit a2648a683106050f5940c023b8b8ec95889d2abe Author: kate Date: Tue Jun 27 19:09:03 2006 +0000 Remove obsolete references to union and intersection subtracks commit 1c3e457ec1478cdf89ef4140da383336c5e153d1 Author: kayla Date: Tue Jun 27 18:45:04 2006 +0000 swapped mention of binCons and phastCons subtracks in the description to reflect how they're displayed commit a9873a315d8c8b947b9797dcede5ec51d3ef0f5c Author: fanhsu Date: Tue Jun 27 18:26:12 2006 +0000 Updated doTracks.c to prevent SF painting into negative space. commit 31fd156efaad4a6724ef1fe0ac8117262f199b7b Author: hiram Date: Tue Jun 27 18:15:20 2006 +0000 Add option noNameIx to eliminate the name column index upon request. Right now this is just for the custom track db loader, but may be useful elsewhere. It does indeed same some time on a table creation and load. commit e6a0e689a0b023361de01f7ff9e645e7b174388f Author: fanhsu Date: Tue Jun 27 17:51:32 2006 +0000 Added delete mySQL statements before loading new data for sfDes and sfAssign table of proteome. commit 3068666f1a89e73958e66f475f32aef2db09b1e3 Author: angie Date: Tue Jun 27 17:42:04 2006 +0000 Resolved -Wall warning: unused variable. commit fcd0e0e2960cff94d51c2385a75ae71371278ee8 Author: kent Date: Tue Jun 27 17:29:44 2006 +0000 Adding configuration page and tweaking controls some. commit 331b9eb7a00505c1957a3a2b287a0bebe7062c77 Author: heather Date: Tue Jun 27 16:21:44 2006 +0000 put measureTiming back to FALSE commit 9ba531513b3ed8b61a51a03738abcb5ad2bae32e Author: ann Date: Tue Jun 27 15:45:43 2006 +0000 set kgProtMap to release alpha commit 39927fa5035c54fb285a97f024d8860c475a83a1 Author: galt Date: Tue Jun 27 15:00:21 2006 +0000 "Encode release log update" commit 0f5787dbd19f1daf1a973f3c86afd5e0c081ce93 Author: galt Date: Tue Jun 27 15:00:20 2006 +0000 "Release log update" commit e212efba533ca97790ffcbdce1a4257b32cefbbc Author: giardine Date: Tue Jun 27 13:57:01 2006 +0000 Reworked the Human Mutation tables again (now gv*). Simplified attributes and links, moved aliases to attributes. commit b4a88771e4a5dd2bccf4dae88b7e1cc49d4a0345 Author: galt Date: Tue Jun 27 04:20:44 2006 +0000 fix for multiple occurrences of warnings flags - Hiram produced one with his new hgCountAlign makefile that broke utils build commit df4cf7d35801cca7948392e94377e9f47aeaec17 Author: galt Date: Tue Jun 27 02:43:40 2006 +0000 "New version number v136" commit 6b3f6deb175d00ebe0276732431dd697089bc4c7 Author: markd Date: Tue Jun 27 01:17:28 2006 +0000 store character width of left labels in variable to make it easier to patch for making publication pictures commit 53a61ff0ed705536851a5f240024cff024e46c7b Author: galt Date: Tue Jun 27 00:47:25 2006 +0000 adding features to phyloGif - ability to preserve underscores, a length-legend ruler option, ability to automatically return a form for interactive input commit daf4d1a1fb384e2ff928178bc131ee4df21d62af Author: kayla Date: Tue Jun 27 00:36:09 2006 +0000 added TARGET=_blank so an off-site link would open in a new browser window. commit 2d09e9aa20772f6a2f55c94b8cc87e3628f49863 Author: aamp Date: Tue Jun 27 00:29:01 2006 +0000 Just a couple convenient functions. These are added after the autoSql though. commit cf85691ce110fb0642c72b982613be72c4047304 Author: kate Date: Tue Jun 27 00:11:35 2006 +0000 Fix problem with tree image in Conservation track overlapping pairwise species checkboxes commit 72ab3cecdd4e59f1c6eb04a6708acd36500405fa Author: heather Date: Tue Jun 27 00:07:56 2006 +0000 handle variant BAC names commit 75e25f4824d8334863d4042f62b920f5e4608413 Author: angie Date: Mon Jun 26 23:17:08 2006 +0000 Fixed the strand for genomicSuperDups (contrib file had _ instead of -, thx Kayla). commit f9a473002c45a9ac5087afd4bdc1ed5d9a35c4e5 Author: heather Date: Mon Jun 26 22:53:03 2006 +0000 minor changes, mostly noting the new source for class and observed commit a122a5482a025d206d426586383ef669ef089af1 Author: heather Date: Mon Jun 26 22:50:22 2006 +0000 tweak comments commit a15edf2fe9eec1d71e63f0393481b1d8330cb1ad Author: heather Date: Mon Jun 26 22:16:38 2006 +0000 change in process for getting class and observed commit 711b41a21cc0d67cbe5cd72fe1536dd5c6603d2f Author: archanat Date: Mon Jun 26 22:11:58 2006 +0000 Fixed a typo commit d3491939c037ca041ff46f09a5331ee1de1029de Author: donnak Date: Mon Jun 26 20:49:23 2006 +0000 Made a few minor formatting changes, fixed a few typos. commit 96d09adb58ffc727505a58a27029d228c34fcb5c Author: fanhsu Date: Mon Jun 26 20:46:12 2006 +0000 Enable DNA print for superfamily. commit 9c8e377c5953b6d62c2d8395a65ed29700044318 Author: fanhsu Date: Mon Jun 26 20:39:59 2006 +0000 Added GB link for superfamily details page. commit a0933e491da8f207367ef8a516f8165b10c197fb Author: angie Date: Mon Jun 26 19:18:10 2006 +0000 Added HgRemoteScript.pm to SCRIPT_FILES. commit c752ca8bb8539391436521dc7f2c8d022ed2f91b Author: angie Date: Mon Jun 26 19:17:11 2006 +0000 Use HgRemoteScript to handle the templated "bossScript" in each step. Use mustOpen and makeGsub from HgAutomate. commit 34edd7a562f0de6b1fb3caa01ad39624772a9b7e Author: kate Date: Mon Jun 26 19:07:55 2006 +0000 Fix truncated species names commit fb14cd95983adae999dc7b7813e6ebbbf1194da1 Author: angie Date: Mon Jun 26 19:04:01 2006 +0000 Use mustOpen and makeGsub from HgAutomate. commit 34b513e1ecafa1ad819a1bb1a0d48eb854d785a4 Author: angie Date: Mon Jun 26 19:02:55 2006 +0000 Added mustOpen and makeGsub. Made nfsNoodge exit immediately if -debug -- the file won't exist anyway, so no point wasting all the delays. commit d1af08e9df085d2393ef005550648a5354e163b9 Author: angie Date: Mon Jun 26 19:01:03 2006 +0000 Perl object for creation and execution of a script (with templated header) on a specified machine. commit 916e1e6fba966b5b540e3c347ab0ee0f9f8d7385 Author: ann Date: Mon Jun 26 18:21:12 2006 +0000 added line in Conservation block for speciesCodonDefault commit 52ddb11ff434cfd5cd4176f27b8a287df4f3c726 Author: heather Date: Mon Jun 26 18:08:53 2006 +0000 change suggested by Kayla commit ddf15eee42efb66276d0566e7e58d99e52da1a10 Author: fanhsu Date: Mon Jun 26 17:21:38 2006 +0000 Minor edit. commit 450fc8295c978ea53abcb143577e3f6fab899706 Author: hiram Date: Mon Jun 26 16:00:59 2006 +0000 Incorrect comparison of strand with < 0, should be == '-' commit d6fc5c7ce9ef33fdb48a5b7cc1be89936979279a Author: angie Date: Mon Jun 26 15:00:56 2006 +0000 Resolved -Wall warning: unused variable. commit d76fd3ce235e689c1aac8f8cf6eec5ec41d62867 Author: galt Date: Mon Jun 26 15:00:14 2006 +0000 "Encode release log update" commit 92e6cca1e6020a6ca8370ecf43642091a097e077 Author: galt Date: Mon Jun 26 15:00:13 2006 +0000 "Release log update" commit 1d2f065abd4df81fbff4eb4c953cc788ea1bd6d1 Author: kate Date: Mon Jun 26 04:35:31 2006 +0000 Update species tree image in MSA tracks commit b89af2be9409bffef39a158e598115e11746d85e Author: kate Date: Mon Jun 26 00:35:25 2006 +0000 28-way tree for ENCODE commit f9a8de27c1d9d1646b83a7cd64a73ab04ad2d823 Author: kent Date: Sun Jun 25 18:08:33 2006 +0000 Making chromGraph return empty list rather than abort with an error, when no metaChromGraph table present. commit 2290db871024734995a0139d436bbf4cbe696109 Author: galt Date: Sun Jun 25 15:00:16 2006 +0000 "Encode release log update" commit 2d5bde4e55b27d31ed0c2a8e7f866feb46d64adf Author: galt Date: Sun Jun 25 15:00:14 2006 +0000 "Release log update" commit 009cbb9579a3dcd843acb21caa26d312a4c60b5f Author: galt Date: Sun Jun 25 01:38:40 2006 +0000 changing vgGetText to be a utility and run only automatically for the branch build on hgwbeta commit 9a8f2bcb707ea731630e5b05233d755d77454dac Author: galt Date: Sun Jun 25 01:11:45 2006 +0000 making visiSearch tolerate missing vgGetText files in visiGeneData, but to put message on title bar and in stderr apache error_log commit 9f37b9dbc8de66f44493e6913ea8d9b680d13712 Author: galt Date: Sun Jun 25 01:10:19 2006 +0000 changing vgGetText to be a utility and run only automatically for the branch build on hgwbeta commit 7ebf3999ecb804ec2b4ebd6c3dd5cca91e9f8139 Author: galt Date: Sun Jun 25 01:04:44 2006 +0000 changing vgGetText to be a utility and build only automatically for the branch build on hgwbeta commit f71fe334e5660206a27650f813aaa01d657164e9 Author: galt Date: Sat Jun 24 23:10:55 2006 +0000 fix warnings commit c68420604179068255725d584266cd442ac03956 Author: kent Date: Sat Jun 24 22:00:45 2006 +0000 Added cartUsualIntClipped commit dd77c467e68e9fff478c1093cca86bb3c49ac134 Author: kent Date: Sat Jun 24 16:41:20 2006 +0000 Adding a little stub logic for config/browse/sort. commit 9a6453e0503cac2ab98e65f7e22318652d24bb1f Author: kent Date: Sat Jun 24 16:34:24 2006 +0000 Putting in some dummy controls. commit 9f914984e8bf606082e8da1ab19e27fb01d400da Author: braney Date: Sat Jun 24 16:31:08 2006 +0000 added speciesCodonDefault lines to multiz17way and multiz6waySyn commit 64990b8bc3c01a64039fdfd13bd2fe855340228e Author: kent Date: Sat Jun 24 15:42:29 2006 +0000 Refining interface to genoLay a little. commit 59df789160fb9cafae7d12aacb2a1df3708b7959 Author: kent Date: Sat Jun 24 15:12:11 2006 +0000 Removing duplicate vgFindRgb. commit afb07c1073bff57c091aeca1853cc2308ca0ff7c Author: galt Date: Sat Jun 24 15:00:21 2006 +0000 "Encode release log update" commit 52fbb5686db2b2d9d45407670b210fdcfe779ebb Author: galt Date: Sat Jun 24 15:00:20 2006 +0000 "Release log update" commit 51379fb0da0346ff5a70c5d9db690e3d493183a6 Author: kent Date: Sat Jun 24 01:33:57 2006 +0000 First attempt to draw chromGraph in hgGenome. commit 3e484b7091b376ce678f888361c6f080cd36c0b0 Author: kent Date: Sat Jun 24 01:33:26 2006 +0000 Moving dump routine to genoLay library. Saving lineHeight in genoLay. commit 8be304246c2cdfaca3654029626bb4c8c053982f Author: kent Date: Sat Jun 24 00:56:40 2006 +0000 Moving genoLay routines to library. commit 9d4b911854cc1db01b4db8332266bf22bee6abd4 Author: heather Date: Sat Jun 24 00:46:13 2006 +0000 tweak commit 3a457600669c367f894d3e244bc1cd792cafa626 Author: kent Date: Sat Jun 24 00:44:34 2006 +0000 Cleaning up visuals and code a little. commit b9a8a04e13a0f2d78be49b6b1d633a6e3fa93735 Author: galt Date: Sat Jun 24 00:34:04 2006 +0000 trying to solve FF shrinkblt problem by adding option to wrap in html page commit d6a535083534e09d3a097e8e77fc2b85b10377d2 Author: heather Date: Sat Jun 24 00:21:20 2006 +0000 add log message commit 843eab704505ad675926364a916dda545a735b13 Author: heather Date: Sat Jun 24 00:09:59 2006 +0000 snp edits commit 18b87cdba5bc0965b111c8c24945900e5b5065b9 Author: heather Date: Fri Jun 23 23:48:00 2006 +0000 delConrad commit 4b7e09e0c29c563d19c21b8538a4f88e7772369c Author: kent Date: Fri Jun 23 23:45:05 2006 +0000 Factoring out some code, particularly from the cyto-band track, for reuse in hgGenome. commit 28973fe51de2be3f6dfb640ff7ad0fd69e5ff797 Author: rhead Date: Fri Jun 23 23:15:35 2006 +0000 changed danRer3 chain/net to o_db shortlabel commit f7bf0251d5f149f8ccc86ddc0cf149db11262717 Author: rhead Date: Fri Jun 23 23:08:32 2006 +0000 changed xenTro priorities commit 0e1b1a9a99d79448dbbbb195bf83bcd0fabf0bfe Author: heather Date: Fri Jun 23 23:02:32 2006 +0000 don't want primary key commit 3693d07d6c0d6b98233bf77dac8dc49078ed5940 Author: rhead Date: Fri Jun 23 23:01:34 2006 +0000 added netXenTro1, chainXenTro2 and netXenTro2 blocks. Gave xenTro2 o_Organism shortlabels. commit 4b66a1bde35aed76399e00490b12cbb5711d2b55 Author: heather Date: Fri Jun 23 22:51:57 2006 +0000 delHinds commit 6d138e5c6e3bb5e0bfc5e99cc8e037b5b7470894 Author: heather Date: Fri Jun 23 22:10:23 2006 +0000 morph snpReadFasta into snpClassAndObserved and snpMoltype commit 36d7a03f5ffbaa56da349464e40c01b3dd690406 Author: rhead Date: Fri Jun 23 21:58:22 2006 +0000 added blocks for rn4 nets and chains commit 27c495c3ac5bf4199bdfa4579fcaeeee781af433 Author: heather Date: Fri Jun 23 21:58:07 2006 +0000 enable commit a49651db7b29041f88ef570e829a98e0b543b7f6 Author: heather Date: Fri Jun 23 21:53:07 2006 +0000 add snpMoltype commit fab5185660c63ef634ea92e3c8e28498e8b3d9e8 Author: heather Date: Fri Jun 23 21:52:54 2006 +0000 remove molType commit 69f44f8891881e6775871569a8cf08854a13ffcd Author: heather Date: Fri Jun 23 21:52:04 2006 +0000 get moltype from fasta files (cloned from snpReadFasta); last step commit 17c96c2de4fc30ee2e32c0f9002cb71ca9ef1741 Author: hiram Date: Fri Jun 23 21:44:04 2006 +0000 Now doing mkdirTrashDirectory() with stat() instead of opendir() - slightly faster commit 27af2a94c79ff61c4c5f5ef48d64db37d94c6c9d Author: hiram Date: Fri Jun 23 21:43:24 2006 +0000 Now sending post script images to trash subdirectories commit 17b6618e0b1ff20a5589707b07e4126f460b0673 Author: heather Date: Fri Jun 23 21:15:13 2006 +0000 remove molType commit 8ca876ba6d29f8d6938e6207236c78bc3dea6edf Author: hiram Date: Fri Jun 23 21:14:43 2006 +0000 Indicate which chroms have chainSelf data commit 02f43671ab27f45b26815589454e21d15a789654 Author: rhead Date: Fri Jun 23 20:59:36 2006 +0000 took out rn4 'release alpha' and 'release beta' for nets and chains commit dd28a2b72a37991bcf380c3d90ebf633096cf8a5 Author: kuhn Date: Fri Jun 23 20:52:55 2006 +0000 dropped links info at assembly levels to allow organism-level block to run the show commit 845dd6e03065aa542d707dbaa43030de1674fd4d Author: heather Date: Fri Jun 23 20:52:01 2006 +0000 fix hard-coded constant commit 124b60ebcb3c8ac60167f25272be7e5bf1a0293d Author: heather Date: Fri Jun 23 20:49:42 2006 +0000 include loadDatabase commit d8935cb78ff63884da4d9fce16d81d7ea7c93a1e Author: heather Date: Fri Jun 23 20:46:48 2006 +0000 add snpClassAndObserved commit 824cad53fda5a3bf70e1e21012fdc8c67292b31c Author: heather Date: Fri Jun 23 20:44:49 2006 +0000 use SNP.univar_id and UniVariation table for class and observed; replaces snpReadFasta commit 3901b0d17f556f2724503dc42133b5a1a92b6987 Author: angie Date: Fri Jun 23 20:31:07 2006 +0000 Resolved -Wall warning: unused variable. commit aca7a4cade2230518a6cdd4874a70af5679b225f Author: heather Date: Fri Jun 23 20:15:52 2006 +0000 use blob commit 347c6a898f4fb38364a00e4d340e6b328e61a721 Author: angie Date: Fri Jun 23 19:46:50 2006 +0000 Added missing bigZips/upstream*.fa.gz files. commit 74d0cf4a11d7b7adf28a1a0c0c8329e2c94045aa Author: giardine Date: Fri Jun 23 19:37:47 2006 +0000 Added user choice of colors for types of mutations, in the Human Mutation track. commit 65fa880a554f617717d2001efa9292e6fbfe3265 Author: hiram Date: Fri Jun 23 18:55:55 2006 +0000 Initial source commit c6645c890f6bd7c365fee418beb722785d841f90 Author: kuhn Date: Fri Jun 23 17:33:25 2006 +0000 added protBrowser block to organism level so we won't miss it when making a new assembly commit 4101d6b5599f6a505fd042d92f897add2a367ae0 Author: kuhn Date: Fri Jun 23 17:29:21 2006 +0000 moved protBrowser block up to Rat level commit aae15c209acb4af2b5633dbb8648bf6f6b92a4a0 Author: heather Date: Fri Jun 23 16:52:08 2006 +0000 remove limit used for testing commit 4cc5d30b119cb3b945ff35202f24066af32acc5a Author: heather Date: Fri Jun 23 16:51:45 2006 +0000 add firstBuild/lastBuild commit 8a4cd3cecd671673a0c39b9a3d908083485414f3 Author: braney Date: Fri Jun 23 16:37:04 2006 +0000 boreoeutherian ancestor browser commit 0e8b91b5830ac07a043b3656e2f6ed42792d7285 Author: giardine Date: Fri Jun 23 16:00:35 2006 +0000 Added filtering to genomeVar. Exclude mutations with estimated coordinates. commit a36c2b1ee538fdd8a576137aa460807faf353579 Author: galt Date: Fri Jun 23 15:00:25 2006 +0000 "Encode release log update" commit 44bc8740e08e665c7182cd95323d408eeddbcec2 Author: galt Date: Fri Jun 23 15:00:24 2006 +0000 "Release log update" commit a10a7b62e98f96c71a2c99567be80c6a9c6422f9 Author: heather Date: Fri Jun 23 07:04:21 2006 +0000 condense SNPSubSNPLink table commit 198609572c41aa530bcef18995a3d87382aebd1f Author: heather Date: Fri Jun 23 07:03:59 2006 +0000 add subSnpCondense commit 5f9d959b75158f84100a032503b3c3a2282512cb Author: kate Date: Fri Jun 23 03:03:52 2006 +0000 Fix bug adding tracsk commit 0ea40901b51a1acfd6b53ea6b14dff5a84d31f02 Author: kate Date: Fri Jun 23 02:31:39 2006 +0000 Update elements as per Elliot M., to fix off-by-one error commit 809c85db47de4b9bca43bdbeea8d7a54a951b4df Author: galt Date: Fri Jun 23 01:36:08 2006 +0000 adding branch-lengths and their labels as options commit 6cfcdf7977bdb7565c2c22563d613eba787402ea Author: braney Date: Fri Jun 23 00:50:03 2006 +0000 changed species names to match non-annotated versions commit d30d03991221cfb255e3c48b68a051624a27005e Author: rhead Date: Thu Jun 22 23:49:10 2006 +0000 fixed an html typo commit 9959192772715301a3c2a3f597f1b2b94e2d11e7 Author: fanhsu Date: Thu Jun 22 23:47:19 2006 +0000 Added PB link. commit 680df45ef7897a7dab2164873fa560947036bd00 Author: angie Date: Thu Jun 22 23:25:04 2006 +0000 Tweak to optimal alignment url for Segmental Dups (genomicSuperDups). commit c62aca374ceefd43c3f4d692b1d207c79bccc905 Author: donnak Date: Thu Jun 22 23:07:41 2006 +0000 Minor wording change. commit da3ff68fd15b50007861f9963981ee84668af058 Author: hiram Date: Thu Jun 22 23:00:24 2006 +0000 Run experiment to determine if Ensembl peptides differ much from peptides produced directly from genome sequence as specified by the ensGene table commit 815b9ede92907b85bee51b8fc15bc1e8a306a241 Author: donnak Date: Thu Jun 22 22:47:18 2006 +0000 Fixed a minor formatting error. commit 9fea8d74782cda6dbf0f9d263f5a741d971e694a Author: hiram Date: Thu Jun 22 22:44:39 2006 +0000 An alternative to the C version - to allow an exclude list commit 39b4a0cc6c442f45512310644f4bc68b8ebcf7d8 Author: giardine Date: Thu Jun 22 22:07:07 2006 +0000 I have changed the hgMut tables by removing attribute and type from the tables to the code, removed unused field hasPhenData. Tweaked attribute links display. Since the changes were major, I changed the name of the tables to genomeVar, and wrote separate code. commit 2160c43f8a320b163c72e369e085fca9da2b7dca Author: giardine Date: Thu Jun 22 22:00:35 2006 +0000 The sql file to go with the landmark.as file, missed on earlier commit. commit 792b4e54393e04d7aaf87620b2535b02f084bdd4 Author: kate Date: Thu Jun 22 21:50:19 2006 +0000 Backdate the news, as it's old commit f69db76991f93c2ddc650470116087ea4c2376c6 Author: kate Date: Thu Jun 22 21:39:57 2006 +0000 Swap button positions for consistency with subtack ordering commit 1ba1781459cfb2038b6d80b381f9c659498d3533 Author: rhead Date: Thu Jun 22 19:43:10 2006 +0000 added sections for rn4 chain and net commit a908a23e64a3a0f27efd59cd064a695d52365740 Author: galt Date: Thu Jun 22 19:13:42 2006 +0000 phyloGif cgi and utility makes gif from standard .nh tree input commit b2e2cfcea7ed77dc55dbaa6329371170670c04cc Author: kate Date: Thu Jun 22 19:11:23 2006 +0000 Edits based on review by Elliott commit 64123d78fea931aebcf3c9b292092de61d9e4f4c Author: hartera Date: Thu Jun 22 18:53:52 2006 +0000 Added further clarification to Methods and also e-mail address for contact in lab providing data. commit b90480c89ba514bb23c203f988ac6c81b57a2385 Author: rhead Date: Thu Jun 22 18:53:50 2006 +0000 changed priority of cow to be higher than rat commit b0df44ac20a2da4862404dbb5e62867a7dc18a55 Author: rhead Date: Thu Jun 22 18:48:51 2006 +0000 added rn4 net and chain sections and changed prioirities commit 2b1039d7c10db2b26ee8ec6036bf706328f7f016 Author: rhead Date: Thu Jun 22 18:39:20 2006 +0000 added sections for rn3 nets and chains commit 263b4633c35808c80480f5310c7e3bec0704c19c Author: fanhsu Date: Thu Jun 22 17:42:55 2006 +0000 Added Superfamily track for mm8. commit fa36bdd3fc3ef3d794e9b26e796d27e872f171a0 Author: donnak Date: Thu Jun 22 17:19:13 2006 +0000 Added another news item & archived an item. commit 423c66e7e447f0e370d3c357d96bdccfe3acbe03 Author: hiram Date: Thu Jun 22 17:07:55 2006 +0000 Add ensGtp table commit 2238a5a58592f935aec1d5aae25f00744a788c39 Author: donnak Date: Thu Jun 22 16:50:30 2006 +0000 Added 2 news items for Kate, archived some old items. commit cb66a0f98b60b64d9882f750ac51aba835d96e06 Author: kent Date: Thu Jun 22 16:24:44 2006 +0000 Fixing bug Ian Gibbons found with dynein protein in sea urchin. Was an end condition in loading section of genome/translation logic that came into play when the protein aligns with the very end of a contig. commit c63fcdb6bbf0215db890151ede06178c251c385f Author: kent Date: Thu Jun 22 16:22:35 2006 +0000 Documenting sea urchin protein fix. commit 4c2cab0e2104f1071c285e79c2cf51c06a8ab2e7 Author: kent Date: Thu Jun 22 16:22:07 2006 +0000 Bumping blat version number. commit 0660863e9ee92d40787ab236fb7b45d0c5e5f062 Author: angie Date: Thu Jun 22 15:20:27 2006 +0000 Added probe sequence fasta for IGTC Gene Trap. commit 2c5ba07eeccf705e5f2a8a228805b2ebeb861564 Author: galt Date: Thu Jun 22 15:00:23 2006 +0000 "Encode release log update" commit 887c95e92ec49492639478a858e8980b9b7ec83c Author: galt Date: Thu Jun 22 15:00:22 2006 +0000 "Release log update" commit d0d26844a03e494d730bacf6417289efe017f5f9 Author: jill Date: Thu Jun 22 08:27:02 2006 +0000 taught -noRandom to recorgnize the non-canonical chrUN*|NA|U maybe someday they'll all be canonical _random... commit 22f9f5be3ac3829ad9d41c53f1950073284a538b Author: kate Date: Thu Jun 22 05:37:29 2006 +0000 comment out debug statements commit a66ec7703a38115d8ef9afbd3df020fd0afbcde2 Author: kate Date: Thu Jun 22 05:23:27 2006 +0000 Prettify Remove CT table commit c578b228277e0fd6bc04d110f5e3b5e64b9380cc Author: kate Date: Thu Jun 22 05:06:12 2006 +0000 Prettify UI commit a92dc923bc9ad6ca9746a4357c7d6954885a9590 Author: kate Date: Thu Jun 22 01:03:55 2006 +0000 Adjust pairwise height for MSA alignments commit cff87cea70d3872c7b8dfa1875ef9fdf3470f583 Author: kate Date: Thu Jun 22 00:57:18 2006 +0000 Add missing variable for wigMaf commit 160faea772ec238cd65a7cc6f0239da329473a26 Author: kate Date: Thu Jun 22 00:52:09 2006 +0000 Adjust settings for MSA alignment display commit 230ffbb69cec19fcfca94b351b19409fc1af59ea Author: kate Date: Thu Jun 22 00:32:37 2006 +0000 Redesign Add UI commit 8fe69e2182f61d2288af561dc145c1ebc830d84f Author: hiram Date: Wed Jun 21 23:03:14 2006 +0000 Adding Ensembl ensGene track commit e7e1d2b4c170b4d78d8be882f66b405f0fc7edd7 Author: angie Date: Wed Jun 21 22:20:03 2006 +0000 In doIgtc, if we have the probe sequence, show link to detailed alignment. commit 5bc272828f96802f49f58aa73f1abaee7f3ef926 Author: fanhsu Date: Wed Jun 21 22:15:59 2006 +0000 Updated RGD QTL track. commit 79911b2f2e9a92cc347a188d7d5b7356e01490a9 Author: heather Date: Wed Jun 21 22:01:05 2006 +0000 add snp126 commit a3105d1a3ebc4e5c0347ac8c0cd58ee38fa69304 Author: hiram Date: Wed Jun 21 21:58:53 2006 +0000 Adding regPotential7X instructions commit a850a6be46a04772e09d81ed7fd26ca8bc97f1c3 Author: hiram Date: Wed Jun 21 21:42:09 2006 +0000 Incorrect comment in the Ensembl gene instructions commit 01b6537aed65e353f84b06e81c80f52e86adb0ef Author: hiram Date: Wed Jun 21 21:34:19 2006 +0000 ensGene ensemble genes loaded commit 280ba2998732127dfe8511fe423ccb828a2f9d20 Author: heather Date: Wed Jun 21 21:23:59 2006 +0000 simple table commit 71f80a3a08dd91a80388d38899c78f95b2ab4a9c Author: kayla Date: Wed Jun 21 21:13:00 2006 +0000 added rn4 commit 563d1bf9af327e0bf5ca1e5ac8008de568e403be Author: heather Date: Wed Jun 21 21:09:43 2006 +0000 replace stub with full text commit 3269af45973a94c034a432a1503c91009d868f96 Author: archanat Date: Wed Jun 21 21:02:21 2006 +0000 minor edit commit de7520497afeab23da49d9fbd2660addd11a2784 Author: galt Date: Wed Jun 21 20:52:25 2006 +0000 "Release log update" commit 08396a3e43d0cd2396e1a1ef313acf89af8c7408 Author: kate Date: Wed Jun 21 20:35:45 2006 +0000 Update commit 181fc205d3c9468562df7202361c9ed8a670008d Author: heather Date: Wed Jun 21 20:07:03 2006 +0000 add writeSnpExceptionWithVersion and doSnpWithVersion commit 04b92e8f5a7411704f189e410f270039ef98fbc5 Author: rhead Date: Wed Jun 21 19:47:34 2006 +0000 added blocks for rn4 nets and chains commit eaf7da6d5919f4a38ca26c73f0bbee822a8ac421 Author: kuhn Date: Wed Jun 21 19:17:18 2006 +0000 added some more keywords commit e4757918df52c7477c760265c6adf0c60c528840 Author: kuhn Date: Wed Jun 21 19:14:33 2006 +0000 added some more keywords commit 0f59f4e43ef4f3765d5e060d6e80e844a8f26374 Author: galt Date: Wed Jun 21 19:03:55 2006 +0000 fixing includes and defines commit 300e0efec92f2cbd48935b15690a7d5e8d784a94 Author: heather Date: Wed Jun 21 18:48:51 2006 +0000 add search specs for snp126 commit d4be86a94bafe2c06fb72b7493abbecc66cbaed8 Author: heather Date: Wed Jun 21 18:44:02 2006 +0000 tweaks to exception desc table commit 4d8f2eb9a89520c0fb8849c3970e811c739302ef Author: heather Date: Wed Jun 21 18:02:33 2006 +0000 add snpCompareWeight commit dad8b63415a012d56f106bbff8cef68e116b6f7c Author: heather Date: Wed Jun 21 17:50:58 2006 +0000 fix typo commit a1746a7723b7c0b83fc7626a62bfb61307324ab0 Author: heather Date: Wed Jun 21 17:21:55 2006 +0000 compare weights commit 17fab747006a3a2e00633b010ff1c784342e3215 Author: heather Date: Wed Jun 21 17:21:34 2006 +0000 add snpCompareWeight commit 140f0e33a2905fba719b7c9e5f3839b6e12fdfa7 Author: hiram Date: Wed Jun 21 17:12:50 2006 +0000 Incorrect comparison for wibSize limit commit d41ffb16a188a9abfa3424fee7584c6f4f4af8b8 Author: heather Date: Wed Jun 21 16:51:39 2006 +0000 use snp125 methods for snp126 commit 42f6d918bd22fd35c59a774ef5fb4eeed9dae5ed Author: fanhsu Date: Wed Jun 21 16:00:16 2006 +0000 Built Superfamily track. commit 50f6654e799f8955a00d4e414539cdee3fb82f23 Author: kuhn Date: Wed Jun 21 15:55:23 2006 +0000 removed errant repeat of a header commit 48423362776ec0136e7789c4cefbd2bf466b97e6 Author: fanhsu Date: Wed Jun 21 15:34:16 2006 +0000 Built Proteome Browser tables for rn4. commit 29a251a3e0df3515016b3d2bfb4fa6fa8a0364ed Author: fanhsu Date: Wed Jun 21 15:32:35 2006 +0000 Rebuilt kgProtMap. commit 1e55a49ef348d5d4cf91f03fceb37ae9ccb7d44b Author: galt Date: Wed Jun 21 15:00:22 2006 +0000 "Encode release log update" commit 204bb912a09aa9ee1826e38281c40d88655bf321 Author: galt Date: Wed Jun 21 15:00:21 2006 +0000 "Release log update" commit 5568235bbf1b4c379a8a2c690362ec6a5c5e629f Author: angie Date: Wed Jun 21 14:38:30 2006 +0000 Resolved -Wall warning: unused variable. commit f88f697e6f540128b206248efccb16684083e7dc Author: angie Date: Wed Jun 21 14:31:35 2006 +0000 Resolved -Wall warning: unused variable. commit daf827ec71299e4132c7178dc57aa7ae19c7659e Author: hartera Date: Wed Jun 21 02:56:21 2006 +0000 Added danRer4 chains, net, liftOver, mafNet, axtNet and downloads and did swap to create these alignments for rn4 on danRer4. commit 32fc6a83f2bd6d4192e46fbb887ad534910985b7 Author: hartera Date: Wed Jun 21 02:54:50 2006 +0000 Did swap of danRer4 chains on rn4 and created net, liftOver, mafNet, axtNet and downloads. commit 91d352a3146d2df21909ea528a2c5281e6072443 Author: angie Date: Wed Jun 21 00:30:48 2006 +0000 Added chainStitchId target. commit 1edde026a37da676e85e6505fe0190d57d9730f3 Author: angie Date: Wed Jun 21 00:29:17 2006 +0000 Util to stitch back together fragments of the same chains, using chain id. This is intended for use after netChainSubset and before other programs that expect unique chain IDs. commit 6552e240e7a82eb4d10d4e87b3189729a40ffdd8 Author: heather Date: Wed Jun 21 00:22:15 2006 +0000 edits for snp126 commit 53de816d3935fbc7e6c46931ae2707a0801b626a Author: fanhsu Date: Wed Jun 21 00:13:02 2006 +0000 Added Superfamily Track. commit f8c7d2bc423082b92654408c86196f0c1377d03e Author: heather Date: Wed Jun 21 00:10:25 2006 +0000 dbSNP build 126 commit 1ee69f473582b38f7b2274545110a70e6decc90d Author: heather Date: Tue Jun 20 23:35:35 2006 +0000 tweak for snp126 commit 5effbcc4481975f82560da473ffe6628db5fdcbe Author: heather Date: Tue Jun 20 23:26:48 2006 +0000 simplify commit 0c987ede6724d0deabe58ad09b87fc8f4511b2f1 Author: donnak Date: Tue Jun 20 22:39:05 2006 +0000 Changed date on rn4 announcement. commit 50b2b03964421f98addbbd8c48c96df65ec6cf4d Author: donnak Date: Tue Jun 20 21:51:18 2006 +0000 Fixed google search box & added additional one. commit ed6dd8984aec2eebfb5833e669dcd9b7168fb58e Author: donnak Date: Tue Jun 20 21:51:02 2006 +0000 Fixed google search box & added 2 additional ones. commit 5d2216a852fe98f15abb5b111b1da0e1395e7b17 Author: donnak Date: Tue Jun 20 21:49:39 2006 +0000 Added Fan to credits for rn4. commit b8317c266eb747a32c94968dfbcc4502b950f5de Author: donnak Date: Tue Jun 20 21:12:06 2006 +0000 Added Fan to rn4 credits. commit 72c825ee5a13cdd36b2ae37639ba11521971e1b9 Author: heather Date: Tue Jun 20 20:27:48 2006 +0000 open input file commit a8929a7d0aa25d718b93f4587c73b831ee356590 Author: donnak Date: Tue Jun 20 20:01:44 2006 +0000 Fixed minor formatting issue, per Bob. commit f354f65a9e272d36dc41f56ba5f6572f29a2384a Author: kate Date: Tue Jun 20 19:28:45 2006 +0000 Create and update ENCODE MSA description pages commit f93fe81835d152859456b383aef68897758c346e Author: hiram Date: Tue Jun 20 19:21:28 2006 +0000 Actually it should be an int, not a signed char commit 13a70070cd9fe82d23535521a868d6e621f19196 Author: hiram Date: Tue Jun 20 19:15:50 2006 +0000 Fixup signed char usage when compiler thinks everything is unsigned commit eb6937ed6a5bff86f7d0cc4063e0318ae67c58e9 Author: hiram Date: Tue Jun 20 19:14:13 2006 +0000 Fixup signed char warnings when compiler thinks everything is unsigned commit cdf9bbe590ed50ad60e1b7591e817f18d35fe515 Author: galt Date: Tue Jun 20 19:13:33 2006 +0000 added hgcData commit 7420237f79207d640ef163c13345abafb9ceadde Author: kuhn Date: Tue Jun 20 18:53:07 2006 +0000 cleaned up the type and changed the size commit 007cd1f82eaf60f1fc2e35a9f8ea93dd488c1e32 Author: heather Date: Tue Jun 20 18:49:50 2006 +0000 add notes on snpPAR commit d97e6314a182a995a4aac8e0ad6f00b987a9325c Author: donnak Date: Tue Jun 20 18:48:33 2006 +0000 Updated the rat credits to include rn4, revised the data use section. commit be4ca2f69510ad1c59897341351618dce9be5100 Author: donnak Date: Tue Jun 20 18:48:08 2006 +0000 Archived a news item. commit 5f5e9cdd0c35a8558f80ab00fc4c299c7e458838 Author: donnak Date: Tue Jun 20 18:47:32 2006 +0000 Added news item about rn4 release. commit 59b34d0df5c497a0baa59511d88c3749fb18ee59 Author: hiram Date: Tue Jun 20 18:43:40 2006 +0000 Eliminate warnings commit 44c16376c8660d823e2838491aee10944e0ce94b Author: hiram Date: Tue Jun 20 18:39:52 2006 +0000 Restore full warnings commit 197d9618bcbbfb19a9244a37a71476438b5ad412 Author: heather Date: Tue Jun 20 18:36:27 2006 +0000 edit to be specific for hg18/snp126 commit e291fd6bd95bbc4d4935af4221f51199ac38fd29 Author: galt Date: Tue Jun 20 18:31:24 2006 +0000 adding back #ifdef DEBUG lines commit 772ad4f729c88aba78ca153d57ee798cea99271b Author: heather Date: Tue Jun 20 18:24:08 2006 +0000 add version argument commit 7e2f984082b4426e5f06e661bae0b18949348e6b Author: hiram Date: Tue Jun 20 18:17:38 2006 +0000 Properly declare gem offsets to be signed chars to avoid differences in compilers commit fbd9833852ea0c2792c446862dacd5600e441f3b Author: hiram Date: Tue Jun 20 18:13:32 2006 +0000 Eliminate unused variable in fileExists() commit c1d14b42e500c31c87d0841e71266a9bc66de963 Author: heather Date: Tue Jun 20 18:13:21 2006 +0000 fix typo commit 6c26e457acdd799fffbfa237e8f3d14c31397a48 Author: heather Date: Tue Jun 20 17:46:55 2006 +0000 fix typo commit 5b1e20c8ea9846b6d8ff80f1a5357d0851aad523 Author: giardine Date: Tue Jun 20 17:31:55 2006 +0000 File for new Human Mutation track where class and name of attributes are moved to here. commit ff9e3b77676c2c0b3cd01169f9203a82e3d9fcb3 Author: hiram Date: Tue Jun 20 17:07:29 2006 +0000 Should be ESPERR not SPERR on the regPotential7X tracks commit f75d7c50f88679bd4062974a1c0b0db306178e40 Author: hiram Date: Tue Jun 20 17:03:59 2006 +0000 Creating temp files in sub-directories of trash commit e51e3553def63cddb11c9208417a3c19dc02e01f Author: angie Date: Tue Jun 20 16:57:36 2006 +0000 Include our common.mk and use HG_WARN_ERR to maintain -Wall cleanliness. commit 85fcff1aa3c1890818caa3a0151f703367960913 Author: angie Date: Tue Jun 20 16:52:27 2006 +0000 Include our common.mk and use HG_WARN_ERR to maintain -Wall cleanliness. commit c51681d762bda69959acb7381021b2117925eb3d Author: angie Date: Tue Jun 20 16:45:13 2006 +0000 Added chainToAxt (and removed duplicate chainToPsl) target. commit 3cfa1ea78ae764e304f30ceaaee85fa2172a2462 Author: angie Date: Tue Jun 20 16:44:18 2006 +0000 Resolved -Wall warning: unused variable. commit 71d34854bbf2ffc0f25611ef423ada8acb7c6b82 Author: angie Date: Tue Jun 20 16:37:58 2006 +0000 Resolved -Wall warning: added (int) before char used as array index. commit 78345991d960331895e0fa3950cde1e577be2640 Author: angie Date: Tue Jun 20 16:37:00 2006 +0000 Resolved -Wall warning: unused variabl; added (int) before char used as array index; removed no-op "f, " before statement. commit fae20976a9e7ccfc984ccf8dc2e540baa9d1e776 Author: angie Date: Tue Jun 20 16:32:01 2006 +0000 Resolved -Wall warning: unused variable; added braces to avoid ambiguous else; added parens around && within ||. commit 2092179dcbea7028a84744976618bd7ff450d001 Author: hiram Date: Tue Jun 20 16:14:52 2006 +0000 Temporary files now going to trash/hgSs/ directory commit 98cfaf19a7263eb71be8d640b9ebadd87a7a636d Author: angie Date: Tue Jun 20 16:11:36 2006 +0000 Resolved -Wall warning: unused variable; errAbort format; added braces to avoid ambiguous else; added parens around assignment used as truth value. commit 5e5d552cf06b7e0d099f28db45f5676a6b0a6f6a Author: angie Date: Tue Jun 20 15:55:18 2006 +0000 Resolved -Wall warning: added (int) before char used as array index. commit 55bbc2036531c08e7934cc6b538aff9e0c569b66 Author: angie Date: Tue Jun 20 15:52:48 2006 +0000 Resolved -Wall warning: unused variable; added parens around && within ||. commit 3031af4daf82bccbe64930c5289f9d1cbc8306df Author: angie Date: Tue Jun 20 15:47:11 2006 +0000 Resolved -Wall warning: unused variable; errAbort args. commit 159f8ef097cd8b85bdf88d83104a6762a7f51a89 Author: angie Date: Tue Jun 20 15:41:54 2006 +0000 Resolved -Wall warning: added parens around assignment used as truth value. commit e98d88083bb9f96f8d390b206b0e0e38708181fa Author: angie Date: Tue Jun 20 15:30:07 2006 +0000 Resolved -Wall warning: unused variable. commit d762a2cc548d56690cfa4bfe22dddd3355ab656b Author: galt Date: Tue Jun 20 15:00:20 2006 +0000 "Encode release log update" commit 58c86bdc1d4bed4ba4da47ad55c585333453be76 Author: galt Date: Tue Jun 20 15:00:18 2006 +0000 "Release log update" commit 370221ec118453c871f7b72ac2758a4b7747381d Author: giardine Date: Tue Jun 20 14:59:37 2006 +0000 Updated landmarks to include attributes and links. also moved landmarks back to expression and regulation section. commit c8de1639db4f31bf0a54091004d574eaddda815e Author: giardine Date: Tue Jun 20 14:58:53 2006 +0000 Updated landmarks to include attributes and links. commit 82c7b4505c2860962125e513b9a675dfbf89e8cf Author: angie Date: Tue Jun 20 01:27:33 2006 +0000 Added xref searches (with different xrefTable than top-level trackDb.ra) for blastHg17KG. commit a9ac4a9a50674a7587f76f296c0a988cb21947ab Author: hiram Date: Mon Jun 19 23:32:19 2006 +0000 No need for the extra _ sign commit d9f0a17a98631a3569985de7f3a42b783beb630f Author: hiram Date: Mon Jun 19 23:23:44 2006 +0000 Need larger name for ideogram commit 59c7f9741a852ce58c1b7498bcdd05182d1078c1 Author: hiram Date: Mon Jun 19 23:16:44 2006 +0000 Take that mkdirTrashDirectory() up to the portable layer commit 17404cfa5ca3270dcb21c4a81f53db3f59bc811e Author: hiram Date: Mon Jun 19 23:16:05 2006 +0000 Now creating trash files in sub-directories of trash commit 9e140363b6499be56c29e38232d0f666718de279 Author: hiram Date: Mon Jun 19 23:15:09 2006 +0000 Adding mkdirTrashDirectory() function commit 320ded98eaa8bab955f667c2fcad4350371b98d3 Author: hiram Date: Mon Jun 19 23:14:48 2006 +0000 We need mkdirTrashDirectory up here so everyone can use it commit b7266ac4b2c9d3ed086c64c764994b2fb7541f19 Author: hiram Date: Mon Jun 19 22:43:25 2006 +0000 Make sure struct tempName is defined before it is used commit 89a60a89df8984dedc413ad0a05b8ceeb8d5220d Author: hiram Date: Mon Jun 19 22:37:35 2006 +0000 Make sure struct tempName is defined before using it commit 0a1fdef408021a6b28bf5a70385b32cc32eb0f70 Author: hiram Date: Mon Jun 19 22:27:37 2006 +0000 Custom track files now going to trash/ct/ directory commit ce3ed3acafc786eb2d3fdc0ca881cc6d261ed7d0 Author: heather Date: Mon Jun 19 22:14:44 2006 +0000 fix typo commit 1d1ace83818c6107cd697e8992c8cff7457a7e4a Author: hiram Date: Mon Jun 19 22:02:57 2006 +0000 Providing a handle to obtain trash directory location commit fe92ad4bb0187c7b2180ee89545c578f78e7e836 Author: hiram Date: Mon Jun 19 22:01:50 2006 +0000 Adding trashDir() function commit aab1891eca4353cd99f7027e2398ced257c61e37 Author: hiram Date: Mon Jun 19 21:34:08 2006 +0000 Get the creation of the custom track trash file in one place to better control it commit 37111c2f5d18c8fa1af258a3b8e14977dd27ca38 Author: hiram Date: Mon Jun 19 21:33:39 2006 +0000 Get the creation of the trash file in one place so it can be better controlled commit 48f6b29d1309be25ea7b016e0752118d5a2d3ef8 Author: hiram Date: Mon Jun 19 21:31:04 2006 +0000 Getting trash file creation all in one place to better control it commit 619dc860e6ff63cced79a7edfdede8598db6cf60 Author: donnak Date: Mon Jun 19 20:23:41 2006 +0000 Made a few edits to Rachel's edits. commit 819a3bec4abb30a3dd10656037b3dbdd1fe80a9f Author: hiram Date: Mon Jun 19 19:52:57 2006 +0000 Properly use envUpdate() instead of putenv() commit 14fe7d7ae829c5fc24bfd013330a4912e36b0ad6 Author: hiram Date: Mon Jun 19 19:52:05 2006 +0000 No need to be issuing warnings from here, just send back the indicator, let the caller decide on the error message commit 6fd70221964fa06b7f0755477a4bf6ee4a53e25f Author: archanat Date: Mon Jun 19 19:49:49 2006 +0000 removed the line 'release alpha' commit 6d522c3623fd24b49f19e5fc9a3698e718168316 Author: hiram Date: Mon Jun 19 19:48:20 2006 +0000 Can't get a message back to the browser because we are first in a pipeline ... commit 2230219ae81b177efa2b2d1cd3529c28c8251ca4 Author: hiram Date: Mon Jun 19 19:12:38 2006 +0000 Add a wibSizeLimit check to 300,000,000 bytes when loading custom wiggles commit cac644a6ddd729115a361883710841551bc092a7 Author: hiram Date: Mon Jun 19 19:11:25 2006 +0000 Forgot to remove the temp file while loading wiggles, and then add a wibSizeLimit argument to wigEncode commit c20936facea324413e794c1a50faad7142643a34 Author: hiram Date: Mon Jun 19 19:08:40 2006 +0000 Get the custom track loaders built at the correct times commit dd5fb8a2e17ffb108dedc6f777083a9811d0618c Author: kayla Date: Mon Jun 19 18:42:22 2006 +0000 Changed priority so that chainDanRer3 comes before netDanRer3 commit 7afee2b225867be277517c02c3d083b41c4deaa5 Author: kayla Date: Mon Jun 19 18:38:59 2006 +0000 Changed $o_db to $o_Organism for chainDanRer3 commit d8f14051b64ba172cb606619193ff54af24e79be Author: hiram Date: Mon Jun 19 17:58:33 2006 +0000 There isn't any unsigned option, so use long long instead commit c4534af27e64d97317b3ee52673bae3bde5449b9 Author: hiram Date: Mon Jun 19 17:40:47 2006 +0000 Adding wibSizeLimit to options for encoding to avoid trash NFS overload commit 93f6b83761d1e11366078cb976a14f39f905c23f Author: fanhsu Date: Mon Jun 19 17:12:57 2006 +0000 set blastDir=/iscratch/blast. commit 34e8c6ee9c54064043596e4b8bcbd5424878caee Author: fanhsu Date: Mon Jun 19 17:12:11 2006 +0000 Updated to replace i386 with $MACHTYPE commit 628c042442316aa523420103811dc989bbabfe99 Author: heather Date: Mon Jun 19 17:02:57 2006 +0000 remove debug statements commit 43b3c0fe46a3cace7f44a8502a2cfa8400aa636d Author: angie Date: Mon Jun 19 16:52:43 2006 +0000 Moving protein blast track(s) from group compGeno to group genes. commit b3b775fd7b2f3a52fc59423fb3a0fe49d5189c58 Author: braney Date: Mon Jun 19 16:30:31 2006 +0000 add buildMafFrames commit bb9dfd344a4ff98c2d2a5e2d0d1c331382c2d326 Author: galt Date: Mon Jun 19 15:00:14 2006 +0000 "Encode release log update" commit a10b07c56c3045ab75a8699a5d974dde4eec2892 Author: galt Date: Mon Jun 19 15:00:13 2006 +0000 "Release log update" commit eab112e01f055b4a3a75bf5fdbe3e7c8d0f34277 Author: donnak Date: Mon Jun 19 14:58:01 2006 +0000 Added rn4. commit 52f8a10fcaf52b4e1b337a05a4ac491b9aacd402 Author: angie Date: Mon Jun 19 14:50:29 2006 +0000 Resolved -Wall warning: unused variable. commit eaa1474939b7c7425d794dff04db6ef2992054d9 Author: kate Date: Mon Jun 19 05:32:00 2006 +0000 Update for hg17 commit 1f1b6eb3f4d12800bce53b9cf20d64b1e8dbf6ab Author: kate Date: Mon Jun 19 05:02:07 2006 +0000 Update TBA Alignment track for hg17 commit 0d887728585e052e4417e98b19a48fc7e7606ed9 Author: kate Date: Mon Jun 19 04:31:12 2006 +0000 Tree image for ENCODE alignments commit 69af1411709281c8ae95fe37f60713e0d7dd4fce Author: kate Date: Mon Jun 19 04:28:01 2006 +0000 Add tree images for ENCODE alignments commit 4b2a386038aa2fc10a655aa9ff600429573c6ed8 Author: kate Date: Mon Jun 19 04:23:54 2006 +0000 Redo hg17 alignments with better scoring matrix commit 43ccf4b579453a09800bfdd2ca04ab6be803fa2f Author: kate Date: Sun Jun 18 23:14:31 2006 +0000 Streamline header comments (metadata) produced by the chainer, using the linefile metadata uniquifyer commit b089a525603e61095f6efdeb41f4c2e403c97ca6 Author: kate Date: Sun Jun 18 23:11:58 2006 +0000 Expand metadata (comment) output for scoring scheme to include gap penalties (default or from the matrix file) commit 44a6cc161b0216636966ae483d2bbb8b7d7db5a2 Author: kate Date: Sun Jun 18 23:09:36 2006 +0000 Clarify comment: distinguish simple gap penalties from the linear gap costs commit 8fc35c67917d4fdd37a52b84b379f9f26e3896b6 Author: kate Date: Sun Jun 18 23:07:43 2006 +0000 Add config option to linefile metadata so thatduplicate comments can be suppressed (useful in alignment pipelines where file merges cause comment explosions) commit 1d735bbc12dd4ac13c993284077d98acb9c68156 Author: kuhn Date: Sun Jun 18 19:47:20 2006 +0000 removed some background that looked dark in some browsers commit 4d48eb1ddbcf9b99250ec4a8dd5f3fd8ff47c364 Author: galt Date: Sun Jun 18 15:00:15 2006 +0000 "Encode release log update" commit a4b84646bfb411b78bb85b9668cb8a22175e6ea6 Author: galt Date: Sun Jun 18 15:00:14 2006 +0000 "Release log update" commit ddb0088d38cb84281a5135a6170410ecac73aa71 Author: kate Date: Sun Jun 18 05:46:03 2006 +0000 Utility to rename split or non-split tables commit c8536c9b7720f28a94f079f4443bf7f815f9e1d8 Author: markd Date: Sat Jun 17 16:27:30 2006 +0000 fixed item color table table for transMapAnc tracks commit 410049015f86c2ffd0e9c3455c18a9a810b37db8 Author: galt Date: Sat Jun 17 15:00:20 2006 +0000 "Encode release log update" commit d1db1e45b6df738bcbff7e033102822e30d8f3db Author: galt Date: Sat Jun 17 15:00:19 2006 +0000 "Release log update" commit e3753f819d211ab2dc3c85e953700cc728e89ed9 Author: markd Date: Sat Jun 17 08:32:18 2006 +0000 added itemAttr tables to transMap tables commit d7bb89673dcc45044d0b1bd3bf2df5ecbca46238 Author: markd Date: Sat Jun 17 08:15:22 2006 +0000 added display of gene check results associated with transMap commit 6f2d93ff60a2f241106536b213f09dc871924643 Author: markd Date: Sat Jun 17 08:14:21 2006 +0000 added gene-check related objects commit 7ab699dfd0e0954f717cc30cebce9800f85a45ab Author: markd Date: Sat Jun 17 08:12:43 2006 +0000 added classes for transMap commit 3b9ca4023c34ca540bfda24f6fc399f2b6b87802 Author: galt Date: Sat Jun 17 03:00:12 2006 +0000 fixing bug: " and src in () order by " fails when all the pairwise of maf summary are deselected commit 75843b25a8c26f4d8841de11b4c61b788684ed4d Author: donnak Date: Sat Jun 17 01:04:14 2006 +0000 Removed reference to hgText. commit acd75fed3febc28d760ae5015a694ef399fe0c6f Author: galt Date: Fri Jun 16 23:09:32 2006 +0000 upgrade hgText usage to use new hgTables commit 075a4b15a8e7461c26924f2a05abab3fd48acc12 Author: heather Date: Fri Jun 16 22:50:38 2006 +0000 check for coords larger than chromSize; log as errors commit 172e976d0b959044bbcaf977ad660f694f9106b7 Author: galt Date: Fri Jun 16 22:50:37 2006 +0000 old test not needed commit 216ae5e29ff03932cbbbcb8f26bf24c72d791699 Author: kuhn Date: Fri Jun 16 22:44:02 2006 +0000 made image a bit larger and made text sharper commit 6b78d0a2bdce7738d21d2d8f5cd33a3ef7816bf3 Author: galt Date: Fri Jun 16 22:30:59 2006 +0000 remove old faToNib that is already in kent/src/utils commit 0bfa44f103730c0d3d95ba279dad2a4c23b80727 Author: hiram Date: Fri Jun 16 22:20:54 2006 +0000 Add the google meta verify tag for sitemaps operations commit 80f15df452c928f4008a759faba6cc86be4a933e Author: hiram Date: Fri Jun 16 22:13:25 2006 +0000 Updating the bacends processing to get more of them included commit d3dfddfe2411a15f39cb9b342f4f81013e0a92ed Author: heather Date: Fri Jun 16 22:00:03 2006 +0000 fix typo in previous commit commit c288a06f81c2b60e78d741ede07753470614bf9a Author: heather Date: Fri Jun 16 21:59:32 2006 +0000 clean up commit 608a9a30a8e965f6912d5849f5f5437f3a3fa779 Author: hiram Date: Fri Jun 16 21:08:16 2006 +0000 Now recognizing all the types of clone ends in the hg18 set commit 591e6c93e2d20155718890e790279eae374822ad Author: kate Date: Fri Jun 16 20:57:37 2006 +0000 MAVID alignments from UCB commit 22ab9bf0bafbb51c26d1b7ed16e972ed72dd91ce Author: heather Date: Fri Jun 16 20:54:22 2006 +0000 edit comments commit 23ca519fdf555a59a3cc453bc7b5df6bd510c7db Author: kate Date: Fri Jun 16 20:23:46 2006 +0000 Minor changes based on feedback commit 5a5a2a2966e016ca92e4bf3263b4afb495ec5d7d Author: heather Date: Fri Jun 16 20:10:49 2006 +0000 no special handling for randoms commit 262ac6baa6300c6b5ea58f9bcdf0486223302aaa Author: heather Date: Fri Jun 16 19:43:44 2006 +0000 addition to previous commit commit fa83e5f00f0463b1ce0470912b2fc14be17cb60b Author: kate Date: Fri Jun 16 18:40:42 2006 +0000 Update for new freeze and methods commit e6a96ab61069b2636071b7d411a65118cb1ade8c Author: heather Date: Fri Jun 16 18:39:08 2006 +0000 fix typo commit f7c92bab51298b569c04e091d981b64fc348e47f Author: heather Date: Fri Jun 16 18:33:58 2006 +0000 handle weight = 0 commit 8d39b8e77353903e2bbf2e816b722ff02cdf2900 Author: heather Date: Fri Jun 16 18:12:57 2006 +0000 dbSNP no longer provides phys_pos; adjust to use lifted contig coords commit be2250afad5c49a905770d46043172b88070dc0b Author: kayla Date: Fri Jun 16 17:42:36 2006 +0000 added xenTro2 commit b4c284c284a0856d8801ddeac2222efb0eeab561 Author: braney Date: Fri Jun 16 17:28:32 2006 +0000 finished human proteins track commit 3c4f1eb45441414da3a73e639ed6f4c6e1f02cd8 Author: braney Date: Fri Jun 16 17:25:59 2006 +0000 add human proteins track commit 6e3f257911b6f4083ecf3ab38204a5cdfed60195 Author: angie Date: Fri Jun 16 16:33:22 2006 +0000 Resolved -Wall warning: unused variable, array subscript has type char (cast to int). commit e058d0b668325e1bf81a2b594c16c9137c30e11d Author: galt Date: Fri Jun 16 15:00:22 2006 +0000 "Encode release log update" commit fc7246878a94948c0c2bb32dd9221f528d920eb2 Author: galt Date: Fri Jun 16 15:00:21 2006 +0000 "Release log update" commit b4236f0dcf99aa10461615512cd41c14d8e2c1ca Author: hartera Date: Fri Jun 16 07:03:53 2006 +0000 Edited description of assembly. commit b57ec407de20296795cde4aa968ce56256f93e7f Author: hartera Date: Fri Jun 16 06:43:15 2006 +0000 Corrected description. commit 2d97ce4b7078ed28ef5e31e5d7426f133e8c0ffc Author: hartera Date: Fri Jun 16 06:18:55 2006 +0000 Corrected typo. commit 32ad36ab7e5a36fc0b411c398eb58a46026879f4 Author: rhead Date: Fri Jun 16 02:08:35 2006 +0000 Took out Gene Sorter link -- it was causing confusion with the cart. commit eb2c18243cda725b6377fd33efb714598afa9eec Author: rhead Date: Fri Jun 16 02:03:33 2006 +0000 Took out Gene Sorter link -- it was causing confusion with the cart. commit c70862b2571faf9fd7f82f4b4bdc5d018560ba58 Author: rhead Date: Fri Jun 16 01:32:04 2006 +0000 changed RAE230 to U34A. Angie confirmed that the track was built from U34A chip data. commit 9b88b6bd8fa5c85a960994a5dbc0b0c618c61d67 Author: rhead Date: Fri Jun 16 01:18:01 2006 +0000 changed RAE230 to U34A. Angie confirmed that the track was built from U34A chip data. commit 0437a62acf46cd383a8f184c60d52de7cf0f525d Author: rhead Date: Fri Jun 16 00:27:20 2006 +0000 Took out Gene Sorter link -- it was causing confusion with the cart commit cfe25fede50bb88488c8c21832eb08b1149c9fc0 Author: hiram Date: Fri Jun 16 00:14:35 2006 +0000 Reset the ctgPos build situation commit 3c2cff8cf02c3ac3f5fc76e25d4de7f89c98934c Author: hiram Date: Thu Jun 15 23:30:54 2006 +0000 Generated sitemap.xml.gz file commit 6d06e429589f98a5871ab264061a84715959484b Author: archanat Date: Thu Jun 15 23:23:47 2006 +0000 Added details about sts marker colors and how to use the filter options. commit d7e4117767719b7a3a68226f649e77d9560548a4 Author: archanat Date: Thu Jun 15 22:21:38 2006 +0000 edited the short label for unc faire subtracks commit 932fe18efad49cefc7103c730431b16b5c7c2164 Author: hiram Date: Thu Jun 15 22:18:01 2006 +0000 Add google sitemaps verify link and bgcolor commit 0948fb4511909469c6f412d91b2f2651093fd5ad Author: angie Date: Thu Jun 15 20:45:32 2006 +0000 Fix: hgTracks expects unspecified chroms to be "" not "0". commit 9a6f2237e32ac81b62fa7ed72b4e13ba04c90122 Author: angie Date: Thu Jun 15 20:44:46 2006 +0000 Reloaded stsMapRat after fixing createStsMapRat script -- hgTracks expects unspecified chroms to be "", not "0". commit 50fc2dbb0472029e049b91c2b1f793dc691814b7 Author: donnak Date: Thu Jun 15 20:39:32 2006 +0000 Slightly edited this description. commit 4a9e0d9084654b05916c77275abc6be22d0fa07f Author: angie Date: Thu Jun 15 19:22:42 2006 +0000 Fixed typo (missing newlines). commit ae71e6740c7f583e1b3d802a15f5b84e1c2d64b4 Author: angie Date: Thu Jun 15 19:15:14 2006 +0000 Fixed typo (missing newlines). commit 97859bda328a73efff5c8df84e8e2568dee51355 Author: hiram Date: Thu Jun 15 18:23:21 2006 +0000 Added ctgPos Map Contigs track commit ef9963a44002f347b5de078cea5520e4ecb76867 Author: angie Date: Thu Jun 15 16:57:36 2006 +0000 Added for documentation purposes. commit 2968a9f254baa59332d5dff2f528401b0ce659c3 Author: angie Date: Thu Jun 15 16:45:33 2006 +0000 Updated to match the createSql in mafFrames.c. commit 18f1de9bbb3bfd31081adae1a6ef7ff898c0e45e Author: kent Date: Thu Jun 15 15:27:00 2006 +0000 Seems to work. commit d678e09309d9038d4308ba4fb54c2d00b5f84de1 Author: galt Date: Thu Jun 15 15:00:24 2006 +0000 "Encode release log update" commit b226a913d3b168bb8270f3844cf7eb2bff219104 Author: galt Date: Thu Jun 15 15:00:23 2006 +0000 "Release log update" commit 403ad9eda81091fd6107378f180849a6a323870e Author: angie Date: Thu Jun 15 14:33:55 2006 +0000 Resolved -Wall warning: unused variable, array subscript has type char (cast to int). commit f7a5f17fe47e3acc7248bc51d095b2cd11bf58c8 Author: galt Date: Thu Jun 15 03:58:44 2006 +0000 fixed handling of multiple checkbox. 1st it is now remembered, and 2nd, when used with position, it is ignored with a note to the user explaining why commit 44dd203bd8fd40248f2991888c72c2eb2c894bc0 Author: hiram Date: Thu Jun 15 00:09:35 2006 +0000 Added regPotential7X to Hg18, hg17, mm8 and mm7. UW Regulome track to hg17 encode commit 9c0229e1112587d55ece4b7fff835125e3e4ff6b Author: angie Date: Thu Jun 15 00:07:17 2006 +0000 Added a missing hgLoadSeq command to stsMarkers. commit 1444a93d50b0a649034fb3b5468ea70a29199f92 Author: hiram Date: Wed Jun 14 23:39:11 2006 +0000 Moved regPotential7X up one so it can apply to both hg17 and hg18 commit a5703560eb1689a767b881de195a21a1c7e989a8 Author: hiram Date: Wed Jun 14 23:38:29 2006 +0000 regPotential7X applies to both hg17 and hg18 commit 2cd24a218de8ef7ab7e6a695de859c3db7b6d3ee Author: hiram Date: Wed Jun 14 23:35:19 2006 +0000 No need to make it specific to mm8, it works for both commit fbdc74efdc88bd0fd1e8d510d840bcb1021f7473 Author: hiram Date: Wed Jun 14 23:30:50 2006 +0000 Adding encodeUWRegulomeBase track commit bc57bb05d565e0a40317ee37bc247358f489617b Author: galt Date: Wed Jun 14 23:25:44 2006 +0000 fixe typos commit 5192ba76f6afa123b9c762d3d20edf5fb4a6e2b0 Author: heather Date: Wed Jun 14 23:12:41 2006 +0000 cleanup per Angie commit f7a1dbfbbfd212081cb47c98ee5c8efc7579fa2b Author: angie Date: Wed Jun 14 22:17:14 2006 +0000 In intersectDataVector, when looking up the trackDb for the secondary track, instead of hTrackDbForTrack which ignores custom tracks, use findTrack. There are still several other uses of hTrackDbForTrack where findTrack might be a better choice, but I think the handling of composite/subtracks might be a little beefier in hTrackDbForTrack than in hTrackDb which our getFullTrackList uses. So in order to avoid breaking anything else, I'll leave the other hTrackDbForTrack's in place for now, but will ask for testing with wiggle custom tracks. commit 43ed8b8f516523b34056b14a2bf7befdfd90dc32 Author: donnak Date: Wed Jun 14 21:50:32 2006 +0000 Updated link to liftOver executable. commit 10d9d7925846da4d767e57a10e84e3c6c3f527a2 Author: donnak Date: Wed Jun 14 21:48:30 2006 +0000 Updated liftOver link. commit 9a6b131adc08baeca89f9d2a3e1f4ec0334ac399 Author: angie Date: Wed Jun 14 21:34:56 2006 +0000 Reran phastCons with elliotsEncode model, which was a better choice than phyloFit after all. Regenerated the tree jpg and added instructions for properly checking it into brower CVS. Regenerated phastCons download. commit 68d6352de6dd78d668dbd99122fdaae48d2298c2 Author: galt Date: Wed Jun 14 21:16:26 2006 +0000 just wanted to put this in cvs commit 992db4a060c3e09e7b33f8070fc0bdb5ffa81021 Author: donnak Date: Wed Jun 14 21:14:12 2006 +0000 Fixed typo. commit bc6c9ba277f7a1d83a62f03e6265afbce7931149 Author: galt Date: Wed Jun 14 21:12:43 2006 +0000 more updates commit d539f5e6b33dafa357b1b97b47cf042c44cd20a5 Author: galt Date: Wed Jun 14 20:53:17 2006 +0000 more updates - fixing robots and pushes to hgdownload commit b83412e76a4e7728a0faff47028edfcded2bb4b6 Author: angie Date: Wed Jun 14 20:44:35 2006 +0000 Updated to use pruned version of Elliot's ENCODE model instead of phyloFit model. commit 7ec961f45aeeb01b887b4b6054a60611ea8a0f23 Author: braney Date: Wed Jun 14 19:58:32 2006 +0000 add catarrhini ancestor commit 3340d79e8c71adfbd98f75817647fba945dbb8b9 Author: braney Date: Wed Jun 14 19:16:36 2006 +0000 new species order for maf commit 2a955e292660bca8e4086b756ea3daeb3f3db29a Author: hiram Date: Wed Jun 14 19:14:14 2006 +0000 Working on regPotential7X commit b6df4366f758e657b7f3db03f8a2e188edc0418a Author: galt Date: Wed Jun 14 18:41:40 2006 +0000 fixed - chains have .gz now, and mysql only allows hgcat when connecting to hgwdev.cse.ucsc.edu -- localhost is not specifically allowed commit f6487d27a2f61bd05c203c5b640a19bdba02c557 Author: jsp Date: Wed Jun 14 18:40:43 2006 +0000 Removed hg17-specific evofold.html in order to use the human generic version instead commit c756b3a76eb17d3aabd0348975ce9c8793849adf Author: braney Date: Wed Jun 14 18:20:35 2006 +0000 starting human protein track commit 00e8aba5da3679571e278eb9eafc0e3791d80596 Author: fanhsu Date: Wed Jun 14 17:51:24 2006 +0000 Updated again. commit 6e4545ed5c43f4cea1816c50225d54df0ece3f0b Author: donnak Date: Wed Jun 14 17:49:23 2006 +0000 Fixed missing links. commit cdd29f593bd72f80f9e745d26a11c1847dca67d0 Author: kate Date: Wed Jun 14 17:47:12 2006 +0000 Deposit UW/Regulome QCP data commit 372777828f55777084a878e987ffd5d51d869af8 Author: fanhsu Date: Wed Jun 14 17:44:30 2006 +0000 Updated makefile. commit 017f944a7412e88de0d1871c09d54c51cc109420 Author: donnak Date: Wed Jun 14 17:40:43 2006 +0000 Fixed typo. commit cec591d9c283b3ec507a4c550ee902cbd6ee21bd Author: hiram Date: Wed Jun 14 17:22:29 2006 +0000 Illegal use of cluster/home and i386 in destination commit f73b16ad05d7f50f4cf4597e8e254ddc2c0cd60e Author: hiram Date: Wed Jun 14 17:20:54 2006 +0000 Illegal use of cluster/home in destination commit 22cc39eef65eb0982d530cc048d377acd7b122b2 Author: hiram Date: Wed Jun 14 17:19:35 2006 +0000 Illegal use of cluster/home target commit 2e72c0fe8c3a069f47806c2f2d70ab5cc10ad576 Author: hiram Date: Wed Jun 14 17:18:05 2006 +0000 Illegal use of cluster/home destination commit c80d2bb23584a861654e7bf1bade8b5a13513670 Author: hiram Date: Wed Jun 14 17:11:12 2006 +0000 Illegal use of cluster/home in makefile commit 63151c8201a4620ae346d232b8d1f652840479c4 Author: hiram Date: Wed Jun 14 17:05:25 2006 +0000 Illegal use of cluster/home directory commit ecda85639401e92e41c574981ea93764004f9c03 Author: kent Date: Wed Jun 14 16:58:10 2006 +0000 Putting in an error check. commit 21a8f64f534558a9e427a8836c10ffced0390dab Author: hiram Date: Wed Jun 14 16:54:46 2006 +0000 Incorrect usage of cluster/home in a build target commit 1f1690b8d49635e79b9b0cea521097991c111cf7 Author: angie Date: Wed Jun 14 16:31:30 2006 +0000 Resolved -Wall warning: unused variable. commit 4de49aa92d4767387a07ad7209c2896e8f61cd96 Author: galt Date: Wed Jun 14 15:00:24 2006 +0000 "Encode release log update" commit 2c3d44378eb45d5b5122be00e01e73c62f23cf96 Author: galt Date: Wed Jun 14 15:00:23 2006 +0000 "Release log update" commit eda4526e8d00c0648e4da26bfe2cf7afa9ee225f Author: galt Date: Wed Jun 14 08:42:17 2006 +0000 fixed cookie header line. semi-colon is a separator, not a terminator. Caused "malformed header from script" error in cheap.cgi commit 179951bb295c2664293d42c9f8626caf53ca2a53 Author: heather Date: Wed Jun 14 05:54:41 2006 +0000 tweak commit ca47bb8dc5eab77a5abd3d660d85034ac10a775a Author: kate Date: Wed Jun 14 05:01:45 2006 +0000 Fixes commit 466cb2d16c082bdcc068ee39c031957b9c73b5ca Author: kate Date: Wed Jun 14 04:55:32 2006 +0000 Update commit a386f9236557291d63e9d4ff94fd411b4cc1660a Author: heather Date: Wed Jun 14 04:49:33 2006 +0000 another typo commit 35aa6ffd5ae81365dcb7b7aafde14132d6d247c7 Author: heather Date: Wed Jun 14 03:50:41 2006 +0000 fix typo commit 5cadcfb66ac74af1044c8d9af0a5464ce809f1ee Author: donnak Date: Tue Jun 13 23:10:02 2006 +0000 Changed Swiss-Prot to UniProt, per Fan. commit f4da4d3c27130cb8831b0c5b120eb4f46339e055 Author: hiram Date: Tue Jun 13 23:08:49 2006 +0000 Complete Uppsala data submission commit e8017d39910d36b294419f6cc32ccc280a867662 Author: hiram Date: Tue Jun 13 23:06:05 2006 +0000 More Uppsala chip chip tracks commit e31de2fa07b9c2f67c37d24ecb5db5e550be2c91 Author: braney Date: Tue Jun 13 22:39:55 2006 +0000 a trackDb for another monkey ancestor commit c1cefa55491e6fbc23cdb8759bd08c76b340186f Author: ann Date: Tue Jun 13 22:11:19 2006 +0000 fixed typo commit 2f3eaa34c63d1f57198b28ed4dc9b18ebe2a55cd Author: donnak Date: Tue Jun 13 21:57:12 2006 +0000 Edited pages to make consistent with other GB description pages. commit 9f9073f904e627a419aa5111404bb9e160a2039e Author: kent Date: Tue Jun 13 21:33:57 2006 +0000 Tweaking fake chromEnd on chromGraph (adding 1) commit 12d77e661cd98cf95d159345c2776464f84ea014 Author: kate Date: Tue Jun 13 20:44:05 2006 +0000 Correct some dates commit 94c49f01761c9847572218203c050f71b7db06f6 Author: kent Date: Tue Jun 13 20:21:04 2006 +0000 Adding a couple of new utils. commit d1bf796fc387a9e506bcec0d02045b6cf4bfe6f8 Author: kent Date: Tue Jun 13 20:20:50 2006 +0000 Fixing warning. commit e31373c522c82a84a6404fa1ece63ad1dfb8eb45 Author: hartera Date: Tue Jun 13 19:58:55 2006 +0000 Documented adding description for data update to UNC FAIRE track description. commit 5578aa7860e5e8949312e4a340564a11c69cea5f Author: giardine Date: Tue Jun 13 19:32:11 2006 +0000 Removed omimTitle entry as table hasn't been pushed commit 9aa749054894f756be2b93a5e77710ce3bab68da Author: galt Date: Tue Jun 13 18:32:22 2006 +0000 oops, fixed - removed -g debugging symbols, accidentally checked in commit a5b070add12bcdbd8ba31aaefa175e7c68ae9dd4 Author: heather Date: Tue Jun 13 18:20:14 2006 +0000 add getChroms commit bedac46e2c0049a06500cf30617b5b780cb28e3f Author: heather Date: Tue Jun 13 18:17:29 2006 +0000 sample code commit 0e2e843cbb3602642b7875d490c32f7824d11441 Author: kent Date: Tue Jun 13 18:09:17 2006 +0000 Moving refListFromSlList to lib/common.c commit 87b4c8311e13ac2c971084d4e9ffcc5c3c569a91 Author: kent Date: Tue Jun 13 18:05:17 2006 +0000 Adding refListFromSlList commit b89e5ed9e47aac40ee00721db2cc8f0547f6a67b Author: hiram Date: Tue Jun 13 17:55:23 2006 +0000 No need to make cgi during ordinary build commit dfb9f99b43bd20109ab4d80b3956a124e8b5c039 Author: hiram Date: Tue Jun 13 17:51:06 2006 +0000 No need to make cgi on top level build commit f75c95f98cd05595dd1624e8144e87508f53969e Author: hartera Date: Tue Jun 13 17:49:33 2006 +0000 Added new Peaks subtrack for UNC FAIRE. Changed labels on original Peaks subtrack. commit 49053aa0f1f9467193a34facac6718277a9b2936 Author: giardine Date: Tue Jun 13 17:32:59 2006 +0000 Updated description, added methods. commit 314af2a723b6ff7610d4efd1cb973892223a68fa Author: kent Date: Tue Jun 13 17:25:51 2006 +0000 Making right/left/bottom lists just references to main chromosome list. Separating out label drawing from chromosome drawing. Letting overall label space be larger than chromosome labels. Renaming to 'genoLay' commit dd4c1044dfaeaeefb33db0a7323752be58b96f5d Author: hartera Date: Tue Jun 13 17:24:32 2006 +0000 Updated description with analysis method for new peaks subtrack - Apr. 2006 update. commit a52d9f936600d2ccb2c65547464ad1f74e2dfa21 Author: angie Date: Tue Jun 13 17:18:56 2006 +0000 Added upper-casing of key to doGrepQuery so that its call to allKeysPrefix would work, even if the caller of doGrepQuery had not upper-cased the key. The findRefGenes call to doGrepQuery did not do the upper-casing, and I doubt that future callers of doGrepQuery would anticipate this either, since the requirement for upcasing is a couple levels down. Added a note to allKeysPrefix that it expects caller to force case. commit 38b92d71956e7e1b794c466bca6f5572afb3c9cb Author: jsp Date: Tue Jun 13 17:17:19 2006 +0000 Added additional doc on the generation of EvoFold track commit 362ca99926147da623e10ca7b466c311472c2396 Author: jsp Date: Tue Jun 13 17:06:20 2006 +0000 Added EvoFold sql table definition commit 7a7b9774671cb71f5b9af5c0f445ff78ecd8383c Author: heather Date: Tue Jun 13 16:56:24 2006 +0000 remove unused var commit 8e97c29f8cf4b73d71ffaddd1731074fa2a210e1 Author: kent Date: Tue Jun 13 16:42:26 2006 +0000 Some symbol renaming. Improving sort. commit f26504531ceed8bb96f91c1974d6284585e429c4 Author: ann Date: Tue Jun 13 16:37:30 2006 +0000 set default visibility to hide for Human Mutation track commit a47885bccc7f9459bb9108767c85560a1d3878df Author: angie Date: Tue Jun 13 16:24:26 2006 +0000 Tweak to ensGene: MT --> chrM. Reloaded other Ensembl tables for timestamps. commit e3b43159c839d4f0b6089de685ce3e19c7ed402c Author: kent Date: Tue Jun 13 16:15:50 2006 +0000 Adding binary file. commit 569fb08f42fc1301d95197316df4e1729b051ce7 Author: kent Date: Tue Jun 13 16:15:18 2006 +0000 Adding missing include. commit e24a2a3b1583cb6d7bf1eb978e5c1c50c5a83333 Author: kent Date: Tue Jun 13 16:14:26 2006 +0000 Adding binaryFile field. commit 7673ae3744ad8983bc4aa72276c8ebee05e7e17f Author: angie Date: Tue Jun 13 15:52:56 2006 +0000 Resolved -Wall warning: unused variable. commit 3fab981affb2e4c4dddc2903783d029712f8f66e Author: giardine Date: Tue Jun 13 15:11:37 2006 +0000 Updated location of .ra file for hgMutAttrs, from test to real location. commit 48c91c57bec4f3fe28bffafd5db3e922497c7242 Author: galt Date: Tue Jun 13 15:00:20 2006 +0000 "Encode release log update" commit 67c3946c313905d129651b951c5897392fd104d0 Author: galt Date: Tue Jun 13 15:00:18 2006 +0000 "Release log update" commit b8ff2c55928d354ff1cb611c15ee5bd246da3fce Author: kent Date: Tue Jun 13 14:17:47 2006 +0000 Adding chromGraphBin stuff. commit ae6fabe630a20f99f0b0a631ced1a212faaec55f Author: kent Date: Tue Jun 13 14:11:37 2006 +0000 Seems to work. commit 9acae34dce855cebcae8fa541675eff0cb3bb612 Author: kent Date: Tue Jun 13 13:01:49 2006 +0000 Adding chromGraphSig commit 63c224ed10e800b3842d5e8865760d81a13902f1 Author: kent Date: Tue Jun 13 12:40:51 2006 +0000 Updating version doc. commit 26d8e4531325d8b485032b0d324d791ce1752c3c Author: kent Date: Tue Jun 13 12:39:12 2006 +0000 Adding hgLoadChromGraph. commit 5f454a76cd3db2c00735c8eb5b2b65017a21e918 Author: kent Date: Tue Jun 13 12:30:30 2006 +0000 Seems to work. commit 025db03985fa2e038345e988ec4a98df815d34ad Author: kent Date: Tue Jun 13 06:45:34 2006 +0000 Describing chromGraph. commit fd346098413b1693fe702566437b277c8d9bcf7e Author: kent Date: Tue Jun 13 06:04:59 2006 +0000 Supporting chromGraph in field-finder. commit 2e74699ee567ceb616e1e5c5df52adf3d5ff2ab6 Author: markd Date: Tue Jun 13 05:50:26 2006 +0000 increased make binkeeper size commit 0b85893dffa89acc18fa52687c5b74bded54de84 Author: kent Date: Tue Jun 13 05:32:37 2006 +0000 Making map box work for chromGraph tracks. commit 4f7cb81023f60a47798fed830181e2c359320777 Author: kent Date: Tue Jun 13 05:24:54 2006 +0000 Doing map box for chromGraphTrack.c commit 7396c0e2e241b193fa3904578cfee9333effb2ba Author: ann Date: Tue Jun 13 03:25:52 2006 +0000 "New version number v135" commit e45567c9fe1be1a11292185c27eed5f53c3a5bce Author: kent Date: Tue Jun 13 03:16:25 2006 +0000 Flipping off track timing. commit 9583b9d9e6bb31c426de3e845dd44fcbdbc0274d Author: kent Date: Tue Jun 13 03:15:59 2006 +0000 Drawing numerical labels from bottom to top rather than vice versa commit 6e1e9d8a7a9bf164ce8456a5dbff6506ed210b3b Author: hartera Date: Tue Jun 13 03:10:37 2006 +0000 Added dbDb entry for Gene Sorter. Remade bacCloneAlias and bacCloneXRef tables. Tested the tables. Added a proteinID column to the ensGene table and added UniProt IDs. Created microarray data track of wild type strains. Build Gene Sorter tables. commit 4e5e92fe5f6ac9bd4fbb11165b712af9e79eb4c7 Author: kent Date: Tue Jun 13 03:03:50 2006 +0000 Adding left label to chromGraph. commit ad0a9b74c0156d79da0ad52ff5acd6d16bd6b6af Author: kent Date: Tue Jun 13 03:03:17 2006 +0000 Renaming some functions. commit 840910e96cb09dbad84169efc9ff9acef3232bee Author: kent Date: Tue Jun 13 01:58:08 2006 +0000 Took out double read. commit 9e5b6aee95721aa29f33f08b87da019cb2f4b758 Author: kent Date: Tue Jun 13 01:54:25 2006 +0000 Avoiding redraw of vgLines. commit 78c2bfa4af820e7185201d3ded0b908475f2345e Author: hartera Date: Tue Jun 13 01:03:31 2006 +0000 Remade some of the bigZips downloads so that they are in the same format as for other assemblies. commit 451a2a09c3f47b99a882da4b7997ca5e03df7487 Author: hartera Date: Tue Jun 13 00:58:06 2006 +0000 Added wild type microarray data track. Added human orthologs for Affy Zebrafish details page. commit 970d12b4debc678d428ec3701d62325a0b6c779d Author: kent Date: Tue Jun 13 00:53:12 2006 +0000 Oops, forgot to commit this. commit 70b141963d33c471cff6f5f07ac661468007f243 Author: angie Date: Tue Jun 13 00:11:10 2006 +0000 Some item names may contain single-quotes, so use dyStringAppendEscapeQuotes when building a filter query. commit bfda803f345f7b8d578a19b59f22bc717d0ae42b Author: donnak Date: Tue Jun 13 00:10:43 2006 +0000 Fixed capitalization for long labels on Landmarks and Human Mutation tracks. commit e179b2bd0405fab78b4c27e52abe08e5f8180152 Author: markd Date: Tue Jun 13 00:03:35 2006 +0000 fixed typo in augustus track description commit 969b3375cec7e5a410450e33d927e51b84bb5478 Author: angie Date: Mon Jun 12 23:59:21 2006 +0000 Use makeQuotedString to escape single-quotes contained in item names (e.g. myFeature_5') when building a name-matching clause to pass to hgSeqItemsInRange. There are probably still other spots in the code where we need to watch out for quotes. commit 46dd7e40cbba2c48b8a80dd3efee1473001e3d2a Author: hiram Date: Mon Jun 12 23:41:45 2006 +0000 Adding regPotential7X to mouse commit 008915217dfe0afa5b0795135d582b6adaad39f6 Author: hiram Date: Mon Jun 12 23:41:26 2006 +0000 Adding regPotential track to mouse commit 6086cbf74573c231791cc92e3da560b830b0d852 Author: fanhsu Date: Mon Jun 12 23:23:39 2006 +0000 Built some knownTo... tables. commit 4dd1280ed0ea01acdceb4dcbe6d5190b1a3751fb Author: braney Date: Mon Jun 12 23:11:49 2006 +0000 add frames to the buildMaf commit ae0d8e1960a58ee196a06eed1fd2d5dc8f8ed6c6 Author: angie Date: Mon Jun 12 23:06:11 2006 +0000 In bedToGffLines, watch out for (thickStart==thickEnd==0) which is one way to signify no CDS for that particular item. When found, tweak to thickStart=thickEnd=chromStart so that we simply pass over the clauses that handle CDS, and only do the exon bits. commit a6a9d4d991f8f89021c2253e0a1a6c527f48b8fc Author: hartera Date: Mon Jun 12 22:44:49 2006 +0000 Added information on renaming of the UW/Regulome CAP track. commit ba53366469ea5244a93032f629d1e75ca2de98a9 Author: ann Date: Mon Jun 12 22:25:33 2006 +0000 changed order of types to match order on details page commit 48736ff603abe55e87cdff9d431cd4d467230945 Author: markd Date: Mon Jun 12 22:16:00 2006 +0000 converted to work with new snp commit 491a6463a703e86cd0a9a2d0f711a40138ae4cb5 Author: angie Date: Mon Jun 12 22:13:28 2006 +0000 Updated Ensembl Genes and knownToEnsembl. commit e782cfd1dcc1b46ae0fd6d739a1d699a87d6722d Author: galt Date: Mon Jun 12 21:52:15 2006 +0000 improve gateway/transfer to-Queue choices page commit b5b3d2f5853945f8dd49581f634d87f5299c0eff Author: hartera Date: Mon Jun 12 21:41:51 2006 +0000 Made liftOver chains from mm7 to mm6. commit 77b2873584153133e297f0bfdd8049a01ec3bf5e Author: hartera Date: Mon Jun 12 21:41:06 2006 +0000 Split mm6 sequences for making liftOver chains from other assemblies. commit e6ea44d7d07bdf29f205be19073ebb0078a6226e Author: galt Date: Mon Jun 12 21:34:35 2006 +0000 bug fix initializing q commit c2ce528f2a9977656afcf7acdb29528b6bb5554e Author: braney Date: Mon Jun 12 21:21:50 2006 +0000 a mapping track to the chimp/human ancestor commit 46f0d54b05526450369d2ea6f0620f4b46ac816d Author: fanhsu Date: Mon Jun 12 21:05:23 2006 +0000 Built KEGG related tables. commit 927659b984ec10df73d9842c6dd9b4c192749a81 Author: angie Date: Mon Jun 12 21:03:15 2006 +0000 Added a dump of $HTTP_COOKIE, to help diagnose clashing-cookie problems which can be caused by incorrect hg.conf central.domain or central.cookie settings. commit caee5e6a08fdf3d80ec4bfe9e013ceb09fc4c79e Author: angie Date: Mon Jun 12 21:00:12 2006 +0000 In parseCookies, chop up a clone of the the $HTTP_COOKIE string so that other parts of the code can examine it later (for debugging). commit b93b9702fed5c6aef65235754bc9178dad6dd44b Author: angie Date: Mon Jun 12 20:51:56 2006 +0000 Added GenBank tracks. Tweaked defaultPos. commit 3c461e6f2be7d10a84676fd836625e9f77449a23 Author: braney Date: Mon Jun 12 20:47:58 2006 +0000 a chimp/human ancestor track commit d16fe8ef6a0f7508b93e66d29a976ea6c9b5a695 Author: donnak Date: Mon Jun 12 20:14:56 2006 +0000 Fixed spacing in UniProt column labels. commit f1320ddfbd4e3af2f3629aaccba773c2f0f0bf94 Author: donnak Date: Mon Jun 12 20:14:37 2006 +0000 Updated UniProt data use blurb. commit 87e525f9d653bea5924b5547ba653e68c918a565 Author: braney Date: Mon Jun 12 20:13:01 2006 +0000 a trackDb entry for the rodent ancestor commit 1ac83ba52ece19cdf2283e035544061a41491bcf Author: donnak Date: Mon Jun 12 19:59:59 2006 +0000 Updated xenTro entry. commit c573493713415582086ea9fcd2885b7f363e453e Author: donnak Date: Mon Jun 12 19:59:27 2006 +0000 Archived an item. commit 8c92acb8f79fc51efd065af103e622afa165e276 Author: donnak Date: Mon Jun 12 19:59:12 2006 +0000 Added announcement for xenTro2 release. commit b7091f157168e9763d218270643d6efec43214a6 Author: donnak Date: Mon Jun 12 19:58:54 2006 +0000 Updated the examples & narrative for this assembly. commit d8294cc77e1c28613ba28b805344a78100a72a12 Author: braney Date: Mon Jun 12 19:57:41 2006 +0000 a trackDb for the glires ancestor commit 750a96e91040de80e8b4e7d7a5b4dab2237798eb Author: hartera Date: Mon Jun 12 19:30:23 2006 +0000 Corrected rule for danRerBacEndNames. commit fbcc8204dad0f98fce305e9cab1ebd76af70cf43 Author: braney Date: Mon Jun 12 19:19:19 2006 +0000 a trackDb for euarchontoglires commit d6e5aff55835fab3e4af7754880160dd5f742fc3 Author: kent Date: Mon Jun 12 19:06:02 2006 +0000 Adding chromGraph support. commit 1f4b8e0edfa2f59f6813e9fc44bfcc098a598b70 Author: braney Date: Mon Jun 12 19:02:44 2006 +0000 add mapping chains to rheMac2, homIni13, and euaGli13 commit f6af6fbbb4bda7288454596d4a31c145d9ad59b3 Author: hiram Date: Mon Jun 12 18:51:16 2006 +0000 Broke the rsync command commit 29d68ea4bea632af4d02024141afba976362639a Author: hiram Date: Mon Jun 12 18:50:26 2006 +0000 Add hgcData for .ra files commit fd7072da6e580c401ec15b7a9e1448bf57b997a4 Author: giardine Date: Mon Jun 12 18:37:07 2006 +0000 This contains internal and external links for the hgMutAttr table. commit ca133a144f4121a7796ae54aabc4774ff44889ae Author: donnak Date: Mon Jun 12 18:36:10 2006 +0000 Added xenTro2, fixed some chicken formatting. commit bbb4dd386ea7bffd56675cb0a7c89354c6732552 Author: hiram Date: Mon Jun 12 18:28:20 2006 +0000 Use the rsync exclude instead of the find and rm commit 3a54ffc9efc8bf21e39e479143d2345bb8fdd880 Author: hiram Date: Mon Jun 12 18:27:52 2006 +0000 Use the rsync exclude instead of find a rm commit 50a5e6f49d130ed9cfb0d40f040f347ec60b61ae Author: kent Date: Mon Jun 12 18:23:49 2006 +0000 Adding in chromGraph stuff. commit 061553782d4541ace72285cc406fb222f65979bb Author: kent Date: Mon Jun 12 18:23:00 2006 +0000 Adding routine to read in chromGraph settings from various sources. commit b8f65e31fc1f9ac739c629c7ce77bfe1c9d2b930 Author: braney Date: Mon Jun 12 18:19:45 2006 +0000 add mapping chains commit a6b715bcf8cdab4febfd2df0182adeffffc17c12 Author: donnak Date: Mon Jun 12 18:09:57 2006 +0000 Added xenTro2. commit 4b3dc0a5e7edb33d6fba98e65ae1a3c8c76a4b55 Author: braney Date: Mon Jun 12 17:53:53 2006 +0000 add some more ancestors commit cd58b9d3452df99639b9796dcceeff23ca917d4f Author: kayla Date: Mon Jun 12 17:06:11 2006 +0000 added xenTro2 commit ff40d515968204ba39607df8aad6f65e7e34b3ca Author: hiram Date: Mon Jun 12 16:54:16 2006 +0000 Added SGP Genes commit 7f5cc4cfd7356fda6ecce7b8f0297f936d450c07 Author: kent Date: Mon Jun 12 16:21:30 2006 +0000 Removing tab file when done. commit ee46af4114877761575555f03a50bda0f8e85241 Author: kent Date: Mon Jun 12 16:13:16 2006 +0000 Checking in chromGraph data structure - similar to wiggle, but draws lines between elements, and much simpler. commit 80f282bab9cfbb4c1f8888f0efc9dce7a7fa627d Author: kent Date: Mon Jun 12 16:12:02 2006 +0000 Seems to work. commit f6729e1d568231aef5302128d5acce4e02c9b8c6 Author: angie Date: Mon Jun 12 15:57:11 2006 +0000 Resolved -Wall warning: unused variable. commit 4bfd8c201fafc2f96952f9301e02bb15c0413bfc Author: angie Date: Mon Jun 12 15:55:20 2006 +0000 Added IGTC Gene Trap. commit eb44b0ae49dd01309d150f83962d2efd8434306c Author: archanat Date: Mon Jun 12 15:45:31 2006 +0000 Changed the short label for danRer4 nets/chains commit 0c9407b9141f3b8925d243185535d93fa871b8f8 Author: galt Date: Mon Jun 12 15:00:14 2006 +0000 "Encode release log update" commit 0186f7cfd7e9e5b2a0777042afc61956a163b76c Author: galt Date: Mon Jun 12 15:00:13 2006 +0000 "Release log update" commit 9416d75ce772a14368d314017c142df1c6158ce1 Author: galt Date: Mon Jun 12 04:38:11 2006 +0000 Adding ability to transfer a record from one push Q table to another commit ad04eb600659464473ba4f00baec1b75fe011eab Author: hartera Date: Mon Jun 12 03:09:17 2006 +0000 Corrected links to rabbit bigZips files. commit 1d7bd6fcc48758e59f5717eb193b1776fb9812fa Author: kent Date: Sun Jun 11 23:56:11 2006 +0000 Sped up wiggle track a little. It's really complicated code, and doesn't do what I want. I think I'm going to just make a 'jiggle' track that does do what I want rather than bend the 8000 or 9000 lines of wiggle into shape. commit 006eb983f2fe1176bcec17506f0c9ba91c957493 Author: galt Date: Sun Jun 11 20:22:54 2006 +0000 improved handling more types of MIME data commit 0e23365528b90aab5d44008b912defef7c6c364e Author: markd Date: Sun Jun 11 19:40:56 2006 +0000 handle mappings from a reconstructed ancestor to its parent commit f3e07a88a5d8446cdf526906cd0838a20fabdabf Author: markd Date: Sun Jun 11 18:53:24 2006 +0000 default to aborting on errors, added -warn flag to only warn commit bd7ca061480d0fc057b814bb1dc498927aed8bbd Author: markd Date: Sun Jun 11 15:45:22 2006 +0000 include COPT in debug target commit b0694702c0dfe5afdaa8c7a857ec0d28d1869592 Author: galt Date: Sun Jun 11 15:00:16 2006 +0000 "Encode release log update" commit 5fd9674a351785e85c0664e0a29556b4858cc484 Author: galt Date: Sun Jun 11 15:00:14 2006 +0000 "Release log update" commit 80f0179cdd0189373555cadeadfafda8e3e2d749 Author: jill Date: Sun Jun 11 07:26:50 2006 +0000 initializing dash to NULL, to make away with compiler warning commit 4f98dfa6dc8680ca63970d6622f6805f010c0fc2 Author: galt Date: Sat Jun 10 23:12:59 2006 +0000 prevent mixing decl and code commit 39c3224ed3b19db2f3998e0ea04b946b750b8137 Author: markd Date: Sat Jun 10 21:48:25 2006 +0000 added support for transmap details page and mappings done using ancestor tree commit 1b81a61f500363eb47e356129cfa9892a0339daf Author: markd Date: Sat Jun 10 21:36:05 2006 +0000 added tracks for transMap via the ancestor tree commit 2e7e630c4e7ce191698f59960882849286a1a130 Author: markd Date: Sat Jun 10 21:35:29 2006 +0000 fixed help typos commit d1b8cb48d7b4643bbdd175721feebe06688218c0 Author: galt Date: Sat Jun 10 19:19:28 2006 +0000 fixed handline of multi-line header defs commit 04a0b7b6c11394ebed9421a6bd8dadf77ba693f7 Author: galt Date: Sat Jun 10 15:00:03 2006 +0000 "Encode release log update" commit e85561029c4690231e37e6a6287819663eb1fdf4 Author: galt Date: Sat Jun 10 15:00:02 2006 +0000 "Release log update" commit 50d172cfc9a8c322bb1e20c045b84e4454d80dbd Author: galt Date: Sat Jun 10 08:46:03 2006 +0000 added mime decoder test commit 0ebea4dfbe2aa291ffec1ab01e02b489b342d5e5 Author: galt Date: Sat Jun 10 08:18:34 2006 +0000 added tests for quoted-printable encode and decode commit d654ee90fe5c6f849805c527494c28ac78aeb990 Author: galt Date: Sat Jun 10 07:51:15 2006 +0000 minor bugfix to remove unwanted trailing newline commit 032f491ed9d179b55dcd5b4d212f4037825a12ac Author: galt Date: Sat Jun 10 07:42:23 2006 +0000 added quoted-printable encoder/decoder commit 0b474b699303eca1fd02d4cb4271ee037dbab679 Author: markd Date: Sat Jun 10 05:28:24 2006 +0000 updated frame annotation to fix bug with spliced codons commit dd28827d347de7c0fbadf97a38981596e17e9abb Author: markd Date: Sat Jun 10 05:19:27 2006 +0000 updated frame annotation to fix bug with spliced codons commit 697c23275a13a56de28a2728a2f0e2f2679e428e Author: markd Date: Sat Jun 10 05:03:20 2006 +0000 updated frame annotation to fix bug with spliced codons commit 32c670253f3a3dc72b4c031705e2a060910e55dc Author: markd Date: Sat Jun 10 04:30:50 2006 +0000 updated frame annotation to fix bug with spliced codons commit 45392287eb565b641b80292d0bab56ae9996bb64 Author: markd Date: Sat Jun 10 03:56:46 2006 +0000 updated frame annotation to fix bug with spliced codons commit 440c413682617fb607a48fdd3100596b1545fade Author: markd Date: Sat Jun 10 00:21:52 2006 +0000 updated frame annotation to fix bug with spliced codons commit 4f3e105dbb60edec8fac1de11eaa0eb1290f641f Author: markd Date: Fri Jun 9 23:54:59 2006 +0000 updated frame annotation to fix bug with spliced codons commit 8b674c01c58227c2536a910137de2f68e57d76c4 Author: angie Date: Fri Jun 9 23:51:03 2006 +0000 Used mafFilter to remove two single-row (xenTro2-only) alignments from the annotated maf. Reloaded multiz tables, regenerated maf download file. commit f86b628ca842638dcc6c1473bd497c4aa173a0d3 Author: markd Date: Fri Jun 9 23:21:47 2006 +0000 updated frame annotation to fix bug with spliced codons commit c4c8071bdbd88217f7a42af80b2a2a2651c3cfad Author: hiram Date: Fri Jun 9 22:55:58 2006 +0000 Indicate spanList option for trackDb entries on wiggles commit 7018a7655434748eb42fbdcf134cde3b90337033 Author: galt Date: Fri Jun 9 22:53:38 2006 +0000 added base64 input validator commit ac0335d12d179edbf97bff890a4e25f5b07797fa Author: kate Date: Fri Jun 9 22:18:09 2006 +0000 New Uppsala chip/chip commit d46b386f0394d06ab636fd737972860594afa999 Author: galt Date: Fri Jun 9 22:10:48 2006 +0000 extending to handle binary data with base64 commit 5ba04ce8f23019fae6ea5f41ce441ca9360712c7 Author: galt Date: Fri Jun 9 22:08:27 2006 +0000 tests for base64 commit 565d648145a64991e5c76b0fc2ce3b141d76535f Author: hiram Date: Fri Jun 9 22:05:58 2006 +0000 Loaded reg potential 7X commit 0fd35f5c47c95cbb14539f44d423dacde0872678 Author: hiram Date: Fri Jun 9 22:03:21 2006 +0000 Adding regulator potentisl 7X commit 3d95a7efb69e8b4e2aef72a3f4efee6b214ce268 Author: angie Date: Fri Jun 9 21:45:37 2006 +0000 Overlap detection was not taking the src (target sequence) into account, so in .maf files with multiple targets (e.g. scaffold-based), overlap was sometimes reported incorrectly (overlapping ranges but on different targets). Added test for same src. commit 7d420e5b22a71bdc6c5ac7aff2d0810ada586e5c Author: hiram Date: Fri Jun 9 21:45:15 2006 +0000 I can't believe this has been in there all this time. There is no need to read all of the wiggle binary data if it isn't going to be used. Only read it when you need it. commit 6e21b1bf5e731f244ad149c2b10a765c870f891b Author: galt Date: Fri Jun 9 21:40:55 2006 +0000 fix refreshOnly type commit 661afbd784807ee8ee157283552a120484ca11f3 Author: kent Date: Fri Jun 9 21:36:24 2006 +0000 Seems to work. commit 075f288439af76abe51fc6a0923cfc9ee766bcf8 Author: galt Date: Fri Jun 9 21:25:35 2006 +0000 extending to handle binary data with base64 commit 61f5196f5c4599c7e83a49bdc674d79f30d49ab9 Author: markd Date: Fri Jun 9 21:03:57 2006 +0000 rebuild multiz17wayFrames commit 7379ec7a044dd2398d1c958af27455fca928c343 Author: galt Date: Fri Jun 9 20:25:26 2006 +0000 fixing expected now that content-transfer-encoding is output commit 29dda826c1915c178aae47d2a5f4b6f7bed35f93 Author: angie Date: Fri Jun 9 20:17:07 2006 +0000 Added galGal3. commit f97cd38f318f08d4ac5b6ebfe22726cf0a877cd9 Author: galt Date: Fri Jun 9 20:03:52 2006 +0000 added ability to detect newline type, and support for simple autoBoundary detection commit caff0d00bb216388ffa8152c412107b1dde27d0b Author: galt Date: Fri Jun 9 20:02:57 2006 +0000 added autoBoundary commit d56c70a7f8e05a5ef014a0f147624ce2685cfc86 Author: galt Date: Fri Jun 9 18:22:21 2006 +0000 changed fsize to new enhanced fileSize commit ba52c01f73cb1839acbff1deeb44abfa87cbc32c Author: angie Date: Fri Jun 9 17:44:09 2006 +0000 Rebuilt mafDownloads with annotated maf. commit 4cd35319ecbf2904522dc0fcaa897ee283ba3ed6 Author: heather Date: Fri Jun 9 17:39:08 2006 +0000 new case for ObservedWrongSize in snp125 commit 3e315febcd11259b52119f584167ba129abc0f0d Author: archanat Date: Fri Jun 9 17:00:04 2006 +0000 Added $matrix to rn3 chain description page commit 6915cd22298cdbb6e78db49900736ab1ac48e98f Author: hiram Date: Fri Jun 9 16:39:18 2006 +0000 Fixup display of GFF example from our help pages. commit 0f3b52ecdc0c327640bee6623c70cb03322a982d Author: angie Date: Fri Jun 9 16:32:49 2006 +0000 Updated IGTC Gene Trap. commit 0d9a5609496f534f3247a2ada33149a00d06381b Author: angie Date: Fri Jun 9 16:32:03 2006 +0000 Loaded IGTC Gene Trap. commit c89e024b0a68e15da1639e4c2a1290096cf6b248 Author: genbank Date: Fri Jun 9 16:31:32 2006 +0000 added novel SEG track for MGC commit dd03a8e7b5178ee0f7aac3b8534c71cae48b8715 Author: angie Date: Fri Jun 9 16:30:33 2006 +0000 Resolved -Wall warning: unused variable. commit 4a4789c61a930dc69b1f57d6228aaa1f4691f0fc Author: heather Date: Fri Jun 9 15:59:14 2006 +0000 add credit commit db2160da3b289c71494c57a2fbe26f0d08aa8845 Author: heather Date: Fri Jun 9 15:58:14 2006 +0000 tweak commit 6bf4dbc91526a7f2f8948587fdc3e57ea4bc4ea5 Author: hiram Date: Fri Jun 9 15:54:16 2006 +0000 These links can't be relative, go straight down commit 98df3759ff0f76d2702e747c45962f6ed235e029 Author: braney Date: Fri Jun 9 15:29:31 2006 +0000 add net track to homIni13 commit 0a4001b17c1349c47637b0380399e53927d4a0e4 Author: galt Date: Fri Jun 9 15:00:24 2006 +0000 "Encode release log update" commit e6e81a69830eef3dcbbbe9d8338849a2191fb124 Author: galt Date: Fri Jun 9 15:00:23 2006 +0000 "Release log update" commit 2c53c28060b6142c60cfb0ba6fa8883138d62f92 Author: donnak Date: Fri Jun 9 13:39:47 2006 +0000 Changed Gill's Nature paper to point to abstract. commit bce1af2c6f3e0b4918055bd8bda279f609ed97f3 Author: daryl Date: Fri Jun 9 06:10:29 2006 +0000 February 18, 2004 version of ENCODE regions commit 507bd678fd11230d6b8dd605f3e7649abf0b43bf Author: kate Date: Fri Jun 9 05:24:32 2006 +0000 Update commit a1d15945868c177f1a177f240e90e1fdb55bef37 Author: galt Date: Fri Jun 9 05:17:53 2006 +0000 changed float to double commit 3962ae3ed33fae53a57f6b313480bf4268ac4efd Author: markd Date: Fri Jun 9 04:35:34 2006 +0000 made easier to user valgrind commit 07cceecc9e15854762f162290a6e93d983283154 Author: markd Date: Fri Jun 9 04:34:59 2006 +0000 fixed problem with going outside of psl arrays commit ed72c7069776cc8943d20c8e461096ea20748c2b Author: markd Date: Fri Jun 9 04:13:44 2006 +0000 fixed memory corruption with pslRc and pslx format commit 1be675f87a93634e62388791224106b8af709051 Author: fanhsu Date: Fri Jun 9 03:21:10 2006 +0000 Updated to make it work with hgGene. commit daed5ba6af4b5beed214367434d44b706763acfb Author: acs Date: Fri Jun 9 01:15:19 2006 +0000 tweaked priority of SEG track commit 8f58c02b03ac7098c9019e1839f2b39620961054 Author: acs Date: Fri Jun 9 01:15:00 2006 +0000 Details page for SEG track commit 70f7e6a6f8408466a580b02fb747c521cd92db5b Author: galt Date: Fri Jun 9 01:10:03 2006 +0000 cleanup unneeded hidden form commit 5b38bb735fd23ab5d6468f4728c040363bde5e40 Author: kayla Date: Fri Jun 9 00:26:09 2006 +0000 changed an S to an s commit 2d5190710091d010bdd151ae1cc2a2f154617477 Author: galt Date: Fri Jun 9 00:08:11 2006 +0000 fixing fsize to fileSize commit 25ba9efe2415a845772861c2ba5e1fab5d25403d Author: kayla Date: Fri Jun 9 00:02:30 2006 +0000 turned off rn4 from the default view commit 01f41b74e249e652ff6152e61074810f7b4c2438 Author: galt Date: Thu Jun 8 23:55:59 2006 +0000 improved fileSize instead of opening the file commit 05145a7c2aab9c9b4a188b54522a7ea5db1e7e2a Author: galt Date: Thu Jun 8 23:42:20 2006 +0000 rolled fsize and fileSize into one, dont need fsize now commit 5e4042d41c7122fbca725d47f7a9697ffa760850 Author: galt Date: Thu Jun 8 23:40:57 2006 +0000 improved fileExists to use fstat instead of opening commit 30bbd21982fc45d51aec00064d95e77dd0946a3c Author: heather Date: Thu Jun 8 23:37:18 2006 +0000 tweak commit 98e9bf0e97ba76a908e9d3dca4722cfbd9aed148 Author: galt Date: Thu Jun 8 23:33:28 2006 +0000 improved function scanning for digits commit 8ffbd99862b374733aa3b9497b56d691c743e3c7 Author: galt Date: Thu Jun 8 23:32:39 2006 +0000 added macro for testing same strings tolerating NULL commit b4ec5f7810f322f16cdd81636950f2e277b49f77 Author: galt Date: Thu Jun 8 23:31:57 2006 +0000 improved score with float, removed unnecessary stuff commit d7dc85397d28f0082ebb1a4864ecd6ccea084523 Author: heather Date: Thu Jun 8 23:24:39 2006 +0000 illumina hap300 commit decbdd320779f2fbcbbdf0ea6d33182385720b18 Author: heather Date: Thu Jun 8 23:22:07 2006 +0000 add doIllumina commit b941d0e91183e476b35d3ed8cf5e634077c8fb8b Author: heather Date: Thu Jun 8 23:21:33 2006 +0000 add illumina Hap300 commit 2ae1319526a5be58e73db03155918520dbf1573d Author: heather Date: Thu Jun 8 23:21:21 2006 +0000 initial revision commit 7e6c8e5b2480f80c1789fdb40907a0de000c0d76 Author: kayla Date: Thu Jun 8 23:13:51 2006 +0000 changed the priority of the net/chain tracks to conform with being the mirror image of the organisms in the conservation track. commit 0a27aadf64c82eeda3f5c37b5e5cfc01629c8859 Author: kayla Date: Thu Jun 8 23:07:19 2006 +0000 added blocks for rn4 nets and chains commit 5b724def106e307d8dd4ac64ea56278d3f14a763 Author: kayla Date: Thu Jun 8 23:05:59 2006 +0000 Changed mouse and opossum to say $o_Organism commit 2881ca94bf80080ce9a2e6cc25108bf40b23f71f Author: angie Date: Thu Jun 8 23:02:06 2006 +0000 Rebuild Conservation maf downloads with annotated maf. commit aac76fcbb3309935155ed63367cbfa8e569633ba Author: galt Date: Thu Jun 8 22:39:20 2006 +0000 fix expressionPattern join commit 11da6442c868b7bf534cfc879a9fb076673a144c Author: hiram Date: Thu Jun 8 22:35:43 2006 +0000 Remove the encode link commit 66665ff72cf1c08c675440652ea0a88257d7237b Author: hiram Date: Thu Jun 8 22:23:08 2006 +0000 Initial source commit 2cf08d0a6511e64ab1d5a4fa8200bda3890b574d Author: heather Date: Thu Jun 8 21:18:47 2006 +0000 don't save chrom mismatches; tweak output format commit cfbd40a70247a860e06dfabff0cb26cad0b9a9a0 Author: giardine Date: Thu Jun 8 20:42:04 2006 +0000 Changed the Human Mutation display to put the Variation and Disease info under the attributes in a more general fashion. A variant from any source can link to the gene level data using this system. Unrelated also fixed queries to escape the item name before putting into the sql, more secure and quote proof. This is for landmarks and Human Mutation. commit 338d8b4666cb09f55846234e6b7692f5a4f5b987 Author: fanhsu Date: Thu Jun 8 20:39:09 2006 +0000 Fixed a bug. commit 404e2edb0c1f02eee15e2ac2b926c08955bef024 Author: fanhsu Date: Thu Jun 8 20:38:45 2006 +0000 Updated makefile. commit 9336aa43468f0c7fdbd907329a09f9bef7015484 Author: donnak Date: Thu Jun 8 20:28:54 2006 +0000 Changed this file into a redirect that points to FAQ/FAQformat.html#format5. commit 83b6dca2f965334887c399c6050f8bee7da20062 Author: heather Date: Thu Jun 8 20:22:49 2006 +0000 handle multiple alignments (also changes to error handling) commit 58d4ebd849218708bbc557dc7729c31aa6818008 Author: donnak Date: Thu Jun 8 20:16:29 2006 +0000 Updated link for MAF format. commit 10d58558656211582fcf0239f27395c546aea34f Author: donnak Date: Thu Jun 8 20:14:29 2006 +0000 Updated MAF link. commit f13c99273591fd29a83bc94585c11055996f6f63 Author: acs Date: Thu Jun 8 19:54:44 2006 +0000 added novel SEG track for MGC commit b2a9eea05a63da5930669e41ffb15e0875193734 Author: markd Date: Thu Jun 8 18:32:02 2006 +0000 fixed typo commit 1b2e7d5c7b6fba69959b44617d23404c0a3b43c3 Author: heather Date: Thu Jun 8 18:23:16 2006 +0000 add illuminaLookup commit b5c9c83431e8e8b4fbf86b933ccfb97b1d6f2fd8 Author: heather Date: Thu Jun 8 18:23:01 2006 +0000 initial revision, doesn't handle multiplying aligning SNPs commit b88d1f30cd2e1c9945adeb1c1c6e5622c2f37af2 Author: hartera Date: Thu Jun 8 17:33:31 2006 +0000 Shortened short label for UW DNase Array track. commit 5dadd51dc7d5bbf8d300da9e66308a556da5dc5c Author: heather Date: Thu Jun 8 17:30:51 2006 +0000 fix typo commit 94fdfcf80f9d63cda02d004e30633a23c9e26a3f Author: ann Date: Thu Jun 8 17:16:14 2006 +0000 minor updates based on hg18's copy commit bc682ad9094a295bd9199f20377a2ce1d13e62f6 Author: ann Date: Thu Jun 8 17:13:22 2006 +0000 cleaned up a bit, based on hg18 copy of this page commit d29d1b30c6e3c14d5fa5156d9f94f68f56a5ed4f Author: ann Date: Thu Jun 8 16:51:28 2006 +0000 turn off visibility of SynConservation track commit dc5fc95b2491cf40ae79f5dbf1f08e3fd11fbd29 Author: hartera Date: Thu Jun 8 16:06:53 2006 +0000 Minor edits. Recreated chrN_allBacends tables. commit 13639fb5622d21e13a40a96ed4d45a2df15dd7a7 Author: angie Date: Thu Jun 8 15:12:03 2006 +0000 Resolved -Wall warning: unused variable. commit dbaa33911ae14a88d4f320ed34dc4485529ad248 Author: galt Date: Thu Jun 8 15:00:25 2006 +0000 "Encode release log update" commit f3bec42558f3baf787e00873478826a22e89d3e0 Author: galt Date: Thu Jun 8 15:00:24 2006 +0000 "Release log update" commit 75f0ed5c1f2473d6bfceb5b671e2e80eb65b03ac Author: giardine Date: Thu Jun 8 13:10:57 2006 +0000 Moved Landmarks to new phenDis group and put under Human Mutation (priority). commit 8805adbf53d0be7fb05f31315343c3dbf75d4401 Author: markd Date: Thu Jun 8 06:28:08 2006 +0000 added transMap style element commit ec7a0574de19b52599ee171018444d34c2fbd7bd Author: galt Date: Thu Jun 8 03:42:57 2006 +0000 needed to add assayKey to make it specific enough commit 19fe3d3d46a35cba7166f2baea2bdb92c6146427 Author: markd Date: Thu Jun 8 01:26:39 2006 +0000 for genes from files, read entire gene set into memory to improve performance on genemes with a large number of scafolds. Reading from tables on such assemblies still needs to be optimized commit 201b2d7df15533cb9e9ea503fdf36d6db4253a07 Author: braney Date: Thu Jun 8 01:11:18 2006 +0000 fixup speciesOrder commit 1008415c364b9e7cb797aaec66b3b601adf752b5 Author: aamp Date: Thu Jun 8 00:50:17 2006 +0000 Added e.g. "Next Feature (9/10)" to the next-exon button's mouse-over message so you'll know how many exons are left and how many there are total. commit d491e7a5c057779b7a1eacbe350ba2a8b534eeab Author: fanhsu Date: Thu Jun 8 00:22:18 2006 +0000 Added logic to squeez in shorter QTL display entries. commit 17e6b603fae4843c61e38d583a582fe4cbfa2d44 Author: archanat Date: Thu Jun 8 00:12:43 2006 +0000 changed short label for rn3 net/chain back to $o_Organism commit c49ace59a7cd479af90e1cc6d52d9c68eb65a9b4 Author: heather Date: Wed Jun 7 23:54:02 2006 +0000 addition to previous commit commit 3c4a2b90826d07ef87b89c4f952519b679fd360d Author: kate Date: Wed Jun 7 23:44:32 2006 +0000 Fix celltype HLF-1 setting for Sanger Chip/chip commit 885706502a9ef7e16ce6e27287450c789dca18da Author: fanhsu Date: Wed Jun 7 23:39:40 2006 +0000 Added logic to display exon count(s). commit 7551e020fc4525bd173c364cde13ca7d35411b5e Author: braney Date: Wed Jun 7 23:36:56 2006 +0000 add a Hominidae track commit 5d253bdc7510c8fde504b4c659d33878c5376fe8 Author: archanat Date: Wed Jun 7 23:35:31 2006 +0000 changed the short label for rn3 chain/net to $o_db commit 394bcfad7e4c4bc98fc87c3b4ab3819cb2e13a82 Author: fanhsu Date: Wed Jun 7 23:33:27 2006 +0000 Moved hgMut to phenDis group. commit 749d20efccc1a9d01b1a67d558ca12e14857897c Author: braney Date: Wed Jun 7 23:33:09 2006 +0000 add chain to Hominidae browser commit 97a5dde25a3ee28e97372b22fc1edd5e3eac2923 Author: braney Date: Wed Jun 7 23:24:44 2006 +0000 an initial trackDb for priMat13 commit 1bacd472331d80cd36a2f9da8bf92d8a51ca2ebe Author: braney Date: Wed Jun 7 23:24:15 2006 +0000 an initial trackDb for homIni13 commit 344ce5f1ffc99626bdec8096eb58d77069576b1b Author: heather Date: Wed Jun 7 22:28:18 2006 +0000 check observed size for deletions with loc_type exact commit e74b500fd6abd36396166a5c85be23339cf93ca6 Author: rhead Date: Wed Jun 7 22:28:12 2006 +0000 turning on rn4 updates after syncing dev and beta commit 24c4fa19e0ca2d4531e421b91dbc62fb98529ff2 Author: giardine Date: Wed Jun 7 22:21:47 2006 +0000 Added another "author" to BGMUT database. commit ca01ed1c9462a5fbdcddd04b7ef13b04e74b1e56 Author: kuhn Date: Wed Jun 7 21:52:17 2006 +0000 made it a little bigger commit 7a4e13f91f288d55ac80a3cf2b0f2aa63f112339 Author: fanhsu Date: Wed Jun 7 21:35:42 2006 +0000 Separate a variable, w, in rgdQtlDrawAt() to make the logic cleaner. commit 1a5ae45cde86a5bb4a506b52192a5143e9400d1f Author: fanhsu Date: Wed Jun 7 21:31:37 2006 +0000 Updated rgdQtl draw logic to display text when the QTL is zoom in a lot. commit eb6d1e9e7fc55cbd89e96928bedcbaf11b09e6ac Author: angie Date: Wed Jun 7 19:25:57 2006 +0000 Resolved -Wall warning: unused variable; incorrect format in usage caused incorrect reporting of default minScore. commit 786562356c0b541e08c1fbc9238e52ac6a2fb920 Author: giardine Date: Wed Jun 7 18:36:19 2006 +0000 Added summary of Human Mutation track commit 1122a1467be62a0e31a088fc3c0cc40f2a575d56 Author: acs Date: Wed Jun 7 17:06:57 2006 +0000 whoops -- repairing Mark's fix of this morning. Strand needs to be between frame and score. commit a61bacf950b089fb968cbb148f9b67261dea57fb Author: angie Date: Wed Jun 7 16:45:32 2006 +0000 Updated IGTC (genetrap.org) link to include the _SOURCE suffix. commit 35df08ad534a103992abaed2d8d22e0b9f2f9c0f Author: markd Date: Wed Jun 7 15:28:49 2006 +0000 score and frame columns were reversed commit 5729a0ec8b55a72987b047efde0dbf044c9a4443 Author: angie Date: Wed Jun 7 15:17:03 2006 +0000 Resolved -Wall warning: unused variable. commit 6e3288967752a9ea4b0ca6891e0dc89e82def6f9 Author: fanhsu Date: Wed Jun 7 15:15:08 2006 +0000 Created md5sum.txt under BigZips. commit 46ecaf2b4f90b8cb26830920ff5cc40d7e098f55 Author: galt Date: Wed Jun 7 15:00:26 2006 +0000 "Encode release log update" commit 3ef0efce170766f6e8e1000d989a425f33af9eb4 Author: galt Date: Wed Jun 7 15:00:25 2006 +0000 "Release log update" commit 5ef851175de9f7458293396fc80cb824d33e4351 Author: galt Date: Wed Jun 7 06:41:49 2006 +0000 jax update to fix expression commit b0eedac360f7a912422cec7e4b34ebc3f49af7e7 Author: aamp Date: Tue Jun 6 23:47:32 2006 +0000 Because of a change in CDS drawing logic that instead puts split codon simpleFeatures in a new stucture member called lf->codons instead of lf->components, this change was needed here. commit 7c5e87fddba46fc421db0fe88b824089e5769ede Author: hartera Date: Tue Jun 6 23:09:34 2006 +0000 Minor modifications. Also, updated mouse and rat Best Blastp for hgNear and hgGene. Ensembl Genes track in progress. Added split sequence to san for making liftOver chains. Re-created bacEnPairs, bacEndPairsBad and bacEndSingles tables and made all_bacends into split tables. Created liftOver chains and downloads for danRer3 to danRer4. commit 726ba12b7e4a192d9d387b2fa4d7cac0c1485cbc Author: angie Date: Tue Jun 6 21:49:56 2006 +0000 Fixed incorrectly formatted errAbort. commit bef3e36973e8f9ab3ed6c1cc074efa217ce71015 Author: angie Date: Tue Jun 6 21:19:28 2006 +0000 Adjusted priority of {chain,net}Mm7. commit a1b3e20286f7775c31296ba28ad862032ca5ca8b Author: angie Date: Tue Jun 6 21:12:23 2006 +0000 Adjusted priority of {chain,net}Mm8. commit e5662f60c0ffcbf02e96f8e3cd9c3e7b086268f9 Author: angie Date: Tue Jun 6 21:10:07 2006 +0000 Added $matrix. commit ead509898c143988e105455574a4d39b3f16d69d Author: angie Date: Tue Jun 6 21:09:28 2006 +0000 Moved {chain,net}RheMac2 up to top level. commit c6e8b0484dfa904f1184d888efd136abe64f96b6 Author: hartera Date: Tue Jun 6 19:55:18 2006 +0000 Added tab to comment line. commit d8c46919e159af60b97cac9199d80e0b1694049c Author: kuhn Date: Tue Jun 6 18:23:00 2006 +0000 turned off rn4 so we can sunc to beta commit de3bd97e592697f679fffc6dc6d8cd267aca9894 Author: hiram Date: Tue Jun 6 18:21:33 2006 +0000 Add careful mem handler to limit amount of memory used commit 2675b27d939cabf113501eb32f95022b0a2fe9ce Author: kuhn Date: Tue Jun 6 18:00:33 2006 +0000 removed some old KGI knownGeneLink stuff commit b5e1acbd644d4066d952f6a3280eb2afbb1f7f23 Author: fanhsu Date: Tue Jun 6 17:40:46 2006 +0000 Removed 1 line of comment. commit 10bc730f01eccb18e6fdd33fe52ad8ff4e3a7c17 Author: fanhsu Date: Tue Jun 6 17:35:59 2006 +0000 Added KG lists. commit f0aa6393f5c2b02d42279db654917784dd3637f3 Author: hartera Date: Tue Jun 6 17:32:47 2006 +0000 Set default viewing range to start at 0 for UW DNase Array Sensitivity subtrack. commit 06c83af45bb76de94c8323ede1987feef002cb83 Author: hartera Date: Tue Jun 6 17:17:22 2006 +0000 Added new identifier for danRer BAC ends with split tables - danRerBacEndNames. Added a rule for bacEndNames to state that it should not be used for danRer3 due to split tables. commit ad18af9633030da45d211f4ef1873b28c31e6790 Author: angie Date: Tue Jun 6 16:27:35 2006 +0000 Added galGal3. commit a11cd42d941d6b21c71b5d4a72ae7e202d66d894 Author: hartera Date: Tue Jun 6 16:17:32 2006 +0000 Changed viewing limits for UW Dnase Array track. commit 2892ee648a5b3957e7bbdeb14c116c9f25a8d78f Author: hartera Date: Tue Jun 6 16:03:48 2006 +0000 Added encodeRegulomeDnaseArray track tables to the list of tables to ignore. commit f0701ad2fac96c6c887244fea4fdc12d8ff746a5 Author: angie Date: Tue Jun 6 15:52:46 2006 +0000 Resolved -Wall warning: unused variable. commit 6399196efae2c4f81035b4caf3b8a15e3ea41121 Author: angie Date: Tue Jun 6 15:46:53 2006 +0000 Added check for NULL curTrack (can happen when positional non-track table was selected from All Tables, e.g. a chainLink) to showTableField. commit f1f942d7aae3919a36337234b3f1f612b288baa6 Author: galt Date: Tue Jun 6 15:01:02 2006 +0000 "Encode release log update" commit ed7fee1c2cb94dd719ad879183b6814de3e95ed9 Author: galt Date: Tue Jun 6 15:00:44 2006 +0000 "Release log update" commit c25444f0001c133829c345d0604ae5e56d4b2cdb Author: markd Date: Tue Jun 6 14:56:43 2006 +0000 enabled updates on dasNov1 and loxAfr1 commit d30d320b13aed9e05e4aa5f29a6a559cd742f9b0 Author: galt Date: Tue Jun 6 01:21:13 2006 +0000 making better default chain choices commit 0e400d5b0844d1ce183f3691fa398a98f2ca64a8 Author: galt Date: Tue Jun 6 00:57:45 2006 +0000 removing unneeded bits commit 98fe307c268fb2adb96a6d1d37e145018b18b4f3 Author: galt Date: Tue Jun 6 00:50:37 2006 +0000 filtering for chains that exist commit a118791e9dc1da4b3c9fe0051d0bc0da4338e714 Author: galt Date: Tue Jun 6 00:46:34 2006 +0000 making better default chain choices commit 5257543c228ada8b211e8b70f594380d48601e19 Author: galt Date: Tue Jun 6 00:39:10 2006 +0000 added functions to filter out missing chains commit acf667146e49b54a5fde428615b3644cb778951d Author: kayla Date: Tue Jun 6 00:09:16 2006 +0000 changed hg18 Chain to Human Chain commit 1ec280978f90328ca9d7b64fc9f7fe0c5ff78fc5 Author: hiram Date: Mon Jun 5 23:48:58 2006 +0000 Finished liftOver to Mm8 commit 04295b7c3f4be04222d91d16a33d9310d779db2b Author: galt Date: Mon Jun 5 23:37:44 2006 +0000 dealing with hgwdev becoming 64-bit now commit f1245a71e65d9d46328a17ef125eca4df35f1bd0 Author: donnak Date: Mon Jun 5 23:05:39 2006 +0000 Added Gil's latest pub. commit 8c827977b54e8d8cd221c75ff858de1a08bafbfc Author: heather Date: Mon Jun 5 20:37:18 2006 +0000 describe display convention for delConrad commit 1e81d0cbd484aa4dffcc4c8192b089e251506b06 Author: heather Date: Mon Jun 5 20:14:42 2006 +0000 use red for delHinds commit d6338cc3e8475c36f20ec81eb2d094eb2099f2a9 Author: archanat Date: Mon Jun 5 19:45:00 2006 +0000 copied the blocks for fr1 & tetNig1 net/chain, mm8 & hg18 net from zebrafish/trackDb.ra and changed the priorities commit bc88e599ba94daca31702a7abf4d1b63c2ace563 Author: archanat Date: Mon Jun 5 19:34:38 2006 +0000 copied the block for xenTro2 and monDom4 nets/chains track from top level and changed the priorities commit 1abbdf611aa531e08a5f3282964dbe4fc1cb8c0e Author: heather Date: Mon Jun 5 19:25:15 2006 +0000 add Hinds reference commit 55941c1c821532ab67d43297db942f05b4a4e3ee Author: angie Date: Mon Jun 5 18:29:47 2006 +0000 Use ${STRIP} and ${EXE} from common.mk. commit b0ecce1c620ccdcfa9f2619e8431655c6ea43ead Author: angie Date: Mon Jun 5 18:27:48 2006 +0000 Added galGal3. commit 4baa9c42875ddddfe83f64f4efc7673e05830e7f Author: galt Date: Mon Jun 5 18:27:35 2006 +0000 fixing warning commit 719052e7fd21577de3daaa7d4ab5fd19589f9f06 Author: angie Date: Mon Jun 5 18:26:03 2006 +0000 Template description for {chain,net}GalGal3. commit 0417eaffb6c098d07d468e608aa5bb0431dd1eaa Author: angie Date: Mon Jun 5 18:24:05 2006 +0000 Loaded genomicSuperDups (from Xinwei She in Eichler's group). commit 88324e34a7743baedf5666b29f59f4857299adf0 Author: angie Date: Mon Jun 5 18:16:33 2006 +0000 Added {chain,net}GalGal3. commit 71c939cf44dd8e9c2d5a6779edcb675c4a537301 Author: angie Date: Mon Jun 5 18:06:54 2006 +0000 Most basic & comparative tracks -- still needs GenBank, Conservation and BAC ends. commit 8ef893277a7b2d1cd7618e2207f051710e1554d4 Author: galt Date: Mon Jun 5 16:43:00 2006 +0000 updated appearance of level, added pattern (for expression info) commit e4f401d94c876299a5d7cf6d680df0772064c9b3 Author: galt Date: Mon Jun 5 16:41:23 2006 +0000 new treatment of level, added pattern commit 7c78127e5b3e12c55dc57d249c31ac35ac2442b5 Author: angie Date: Mon Jun 5 15:38:29 2006 +0000 Resolved -Wall warning: unused variable; parens around assignment used as test. commit 8f7a0987350ed26abebaa29a0e74669652192995 Author: galt Date: Mon Jun 5 15:00:02 2006 +0000 "Encode release log update" commit d2e2f945b376f48e7d988047dc018d150758b341 Author: galt Date: Mon Jun 5 15:00:01 2006 +0000 "Release log update" commit 70bd2eadc84c973889ce02c94e71b4352da3444a Author: kate Date: Mon Jun 5 05:35:13 2006 +0000 Implement visibility specs from browser lines in new custom tracks CGI commit 84d0480f5104dbd53334584a2cc7a5bb0ec06f7e Author: kate Date: Mon Jun 5 04:14:58 2006 +0000 Rework layout commit 0949a72a525188d8047257ebb6ff81d09666ce78 Author: markd Date: Mon Jun 5 03:58:48 2006 +0000 simplified command line for multiple genePred operations; dropped support for old command line commit e7f85d0645d9d60ebf0c3abbdeb40ccf238e402d Author: jsp Date: Mon Jun 5 00:40:55 2006 +0000 Corrected typo. commit f627d9174245b883d63209e4e9c5642ea6c2c12a Author: fanhsu Date: Sun Jun 4 00:47:06 2006 +0000 Added logic to doHgMut() to process DV entries. Needs to be polished later. commit 657af61a2a4b2a42a1ae06aafe6855696b417808 Author: markd Date: Sat Jun 3 23:18:27 2006 +0000 added option to process multiple organism with one pass through the MAF commit ba42846aece277cb1c985c263deb1c827f52e49f Author: fanhsu Date: Sat Jun 3 18:29:09 2006 +0000 Added methods for rgdQtl. commit 1409a8d00ea6368af3a532918452f0f51e28fe54 Author: fanhsu Date: Sat Jun 3 18:24:57 2006 +0000 Created a new track group, phenDis. commit 4e999f852cb773f716264f0a969518e582c5905c Author: galt Date: Sat Jun 3 15:00:03 2006 +0000 "Encode release log update" commit a59bb2bbab1fae46599d4f79e192c6bb7ef645d2 Author: galt Date: Sat Jun 3 15:00:02 2006 +0000 "Release log update" commit a1bf52baa1a2879daa1e33c5419cf1c5fdcac011 Author: markd Date: Sat Jun 3 07:34:25 2006 +0000 fixed bug with unitialized variable and forced reload commit 23bfdce8c4e26fbfc10617c074235ffa547c6dc3 Author: markd Date: Sat Jun 3 06:14:12 2006 +0000 change transMap alignment track to genePred to chow cds commit 1316dcf1c958dac356b818c8bafe34c9ba58dfa2 Author: hiram Date: Sat Jun 3 04:03:39 2006 +0000 Better to remove cgi bin targets before moving there commit b19dfe975f3146371882ad5034714648ea8e3841 Author: hiram Date: Sat Jun 3 04:02:12 2006 +0000 Better to remove cgi bin binaries before moving new one there commit 473cd8900a361ad6c07e604c241411326ec20fb8 Author: hiram Date: Sat Jun 3 00:20:09 2006 +0000 Correct comment on loader command commit bb54f64e29ea935d4c68242018ff23d6b7b0391c Author: kuhn Date: Fri Jun 2 22:08:00 2006 +0000 added some error checking for presense of db on beta commit 889c5d4e904178bc57f74aa801aacd82097564ed Author: kuhn Date: Fri Jun 2 21:45:03 2006 +0000 fixed indentation commit 09e367389165629edc4ea2f4c3a58e8d87a1ff92 Author: kuhn Date: Fri Jun 2 21:41:00 2006 +0000 added more comments to de-abscurify output commit 45fbd7877ac36296f6455909230af915f8dba61e Author: fanhsu Date: Fri Jun 2 21:31:45 2006 +0000 Fixed the spMrna table. commit 439245bb68b89e9997718ab6e4aea02b964502e5 Author: kuhn Date: Fri Jun 2 21:29:36 2006 +0000 added a little more explanation to some output commit 52689f4c93fa1ee75127ca37f635afb527450096 Author: angie Date: Fri Jun 2 20:11:47 2006 +0000 name index is no longer unique because the contributors no longer include a unique ID in the name (or in the uid column). Removed the unused chromEnd index. commit 5f79051f2afa8f477ea0355e032e3845307c8ae9 Author: angie Date: Fri Jun 2 20:10:46 2006 +0000 Updated the name-parsing for genomicSuperDups: the contributors no longer include unique IDs in names (and uid column is now all 0). commit 2743c7e63d14f1fd60d96a9f76ac67bf4eac560d Author: ann Date: Fri Jun 2 19:30:24 2006 +0000 turned fr1 off by default in Conservation track commit 98738b96ebd2de9d61722baee9b5abf32d92a984 Author: heather Date: Fri Jun 2 19:12:24 2006 +0000 fix typo commit 148dd8d686b1c15f9d57f2d89b277de5a88fbbdc Author: hartera Date: Fri Jun 2 18:57:03 2006 +0000 Added upstream files to maf downloads. commit 095c3408706ee69a3ed403c7906dc04f9456767e Author: ann Date: Fri Jun 2 18:53:27 2006 +0000 added danRer4 to blastHg17KG commit b78984b982c3a26561c71092e05619739fc37ac0 Author: kuhn Date: Fri Jun 2 18:49:29 2006 +0000 cleaned up previous commit using an option I just found commit f0e71edd65486028714590c009fbbd4c412ed1ff Author: kuhn Date: Fri Jun 2 18:39:28 2006 +0000 added gene occurance histogram commit 33c2f145a6f3b8adbfc1b18a9d42c1f0daca69ec Author: fanhsu Date: Fri Jun 2 18:38:51 2006 +0000 Created knownToEnsembl table. commit 896e683f9df61b8172492a6861a30ee41b4eb956 Author: kuhn Date: Fri Jun 2 18:31:06 2006 +0000 a uniq count was not working properly. removed some kruft commit 31f2e282f790c8f98ee9d7c6d5aa0d569ec5578c Author: hiram Date: Fri Jun 2 18:18:15 2006 +0000 Included the Dropped stats message in the verbose 2 output commit cdc0b3518973609e6cb8f969d5438d26abdccd6f Author: hiram Date: Fri Jun 2 18:07:56 2006 +0000 Remove superfluous ../trash from the path prefix to the wib file commit 7077b7751d1583292a5014e0764a22b072ef05e7 Author: hiram Date: Fri Jun 2 17:45:09 2006 +0000 Do not attempt to convert existing wiggle file based tracks when the useAll signal is turned on commit 89360a0a0125d1f50411a50dfe3ce94b945e935d Author: braney Date: Fri Jun 2 17:17:28 2006 +0000 fix a bug where initial columns with '-'s in the reference sequence were being removed. commit 92dfd65f1284dceca2763a78e3d04ecedc8a56d3 Author: hiram Date: Fri Jun 2 17:15:37 2006 +0000 Add hgLoadBed and hgLoadWiggle,wigEncode to cgi-bin binaries builds for the customTrash loaders, and making dbTrash for customTrash cleaning commit c5473fd660a29c9fec0e23698963bf0d5c209621 Author: hiram Date: Fri Jun 2 17:13:43 2006 +0000 my:: is actually cgi:: commit 42c48ea09631228f4895823290e8f88687407450 Author: hiram Date: Fri Jun 2 17:12:49 2006 +0000 Adding rules to make the cgi-bin loader binaries installed properly commit 1eea220a5081929c380b884669a226f53abb9e77 Author: hiram Date: Fri Jun 2 17:05:45 2006 +0000 Properly done to make cgi-bin loader binary commit 7a4eeb9d3763d14e7d49064a4bdb770724ae7404 Author: braney Date: Fri Jun 2 17:03:54 2006 +0000 fix two bugs: disappearing -'s at the beginning of maf blocks, and weird orange text when zoomed into a single base commit f9235bc80be2d5b46d485738990a7a5d77c356a6 Author: hiram Date: Fri Jun 2 16:53:07 2006 +0000 Add this binary into the cgi builds commit 3fa74772728efc7c86caf064f641a6fc09bd2b32 Author: kuhn Date: Fri Jun 2 16:35:36 2006 +0000 adding Conservation track images commit 3c8d877c12da0ba8477d66e64b48f9ad2c217616 Author: braney Date: Fri Jun 2 16:28:17 2006 +0000 add a function to get a mafSubset without removing initial dashes commit bf0eca6571ebba1fc4e59d165982c226c3a08ff4 Author: braney Date: Fri Jun 2 16:23:57 2006 +0000 add a mafSubset function that doesn't remove initial dashes commit 4d6c84f09dc0e39250dfc8068aa5110a49fd0501 Author: fanhsu Date: Fri Jun 2 16:20:59 2006 +0000 Polished error message. commit 11568d6f6b776d8e9fd718d192f3c36f38baf6a5 Author: kuhn Date: Fri Jun 2 15:53:40 2006 +0000 adding Conservation track images commit 219f10fa8868767a086889a0ac862638be47d725 Author: markd Date: Fri Jun 2 05:46:01 2006 +0000 Fixed bug deleting intronEst entries based on etc/ignore.idx entries for genomes without per-chrom est tables. Added -forceIgnoreDelete option for hard-core cleanup commit 2c0fb927a07c7575d61d83414120faf693dd71de Author: markd Date: Fri Jun 2 05:15:51 2006 +0000 removed redundant comments to reduce size of file commit 3381f76b176732a516b65d2b97b59e08b502b259 Author: heather Date: Fri Jun 2 01:13:46 2006 +0000 fix typo commit 7d25b3d7822b2738f4f4be781c61319f9e1ca7f3 Author: heather Date: Fri Jun 2 01:12:16 2006 +0000 tweak longLabel commit 3693b623dca3cfcb165859d205c3c1db9b27cca4 Author: heather Date: Fri Jun 2 01:12:01 2006 +0000 edits for Hinds dels commit ccba9b8de6dcadee73d4dea57fb20a144b8ea35a Author: ann Date: Fri Jun 2 00:25:13 2006 +0000 typo commit b66bfa3a11bbf0099a273c3d23225a77896771b3 Author: kate Date: Thu Jun 1 23:59:48 2006 +0000 Add support for browser lines. Initial implementation (ifdefed out) for HTML support commit 4dd5351083f4e78aea2ac5d95710f27417791044 Author: heather Date: Thu Jun 1 23:58:22 2006 +0000 fix typo commit eb992f3a9bb4c5f5b205396bc89106650b096a75 Author: heather Date: Thu Jun 1 23:56:53 2006 +0000 starting on Hinds edits commit 050d1800f79ee4e3a17f6bd5e3921fc7de112a49 Author: heather Date: Thu Jun 1 23:56:39 2006 +0000 add delHinds commit ff89b5e508288023a740892e6e2b506a029167b9 Author: ann Date: Thu Jun 1 23:49:20 2006 +0000 massive changes to bring it up to the new standard (based on hg18) commit 2e8dbc9bd38af7fc5e58f3e70aef1ca017a19c02 Author: hiram Date: Thu Jun 1 23:44:29 2006 +0000 Add Genome Browser link into blue bar for hgSession commit 2208878137e33b59a13ecc013392d6db43eb5fbc Author: heather Date: Thu Jun 1 23:25:41 2006 +0000 update for new hgwdev commit cc2ce799d7b8db898c134614998b7f17dc2f3e37 Author: hiram Date: Thu Jun 1 22:41:04 2006 +0000 Now handling wiggle custom track creation from the table browser commit 96d009ad73bd42c3fa855eb955799178999854b2 Author: fanhsu Date: Thu Jun 1 22:40:23 2006 +0000 Added rgdQtl.h. commit 96b7d6d9fb1074a03b5eb1277f5f476dcacf92e5 Author: fanhsu Date: Thu Jun 1 22:38:50 2006 +0000 Added rgdQtl.o commit 63b3c9addfce7503ee181a51eb883761a465bd2a Author: fanhsu Date: Thu Jun 1 22:37:50 2006 +0000 Created (by autoSql) rgdQtl.c. commit c3a92dbed4605d8a15bc343f76ec5dcdd26ee26e Author: archanat Date: Thu Jun 1 22:32:32 2006 +0000 Changed the priority for Human Proteins track in danRer4 commit 794878515086a0857edf739dea59cdb04b5cfdee Author: markd Date: Thu Jun 1 21:59:01 2006 +0000 added canFam2 NSCAN gene predictions commit f2af41c41bcde7d69e074acf1b42e0d24e2b8735 Author: heather Date: Thu Jun 1 21:47:32 2006 +0000 show 2 HREFs commit 7af675e9b669804541330d49c2249a823b5353dc Author: hiram Date: Thu Jun 1 21:31:45 2006 +0000 Now sending wiggles to database when at all possible commit 2d4d48b2cf6c6946f25e97486a7576736d5004b2 Author: heather Date: Thu Jun 1 21:25:18 2006 +0000 template commit 4ae377c9bcf2c4a1daf947c1fb0eb512207602f5 Author: fanhsu Date: Thu Jun 1 21:12:41 2006 +0000 Added gdbPdb entry for rn4 in the central DB. commit bfde26a60a1ede63015ca277a70226bf92cbbf01 Author: kayla Date: Thu Jun 1 20:00:44 2006 +0000 added danRer4 commit 7eb1ae153ee434d45d09c681ce857436a5dbcb93 Author: kayla Date: Thu Jun 1 20:00:12 2006 +0000 enabled danRer4 commit b6cc2b6ae1ef8243589ed128f83d556c743d1962 Author: heather Date: Thu Jun 1 19:00:49 2006 +0000 add snp126 commit d757da730b1e122140165042234171321eceed41 Author: heather Date: Thu Jun 1 19:00:25 2006 +0000 use mapName to enable snp126 to use snp125methods commit d431ee7e1c874f647d22e7685c33bb8cc4eb9b1a Author: heather Date: Thu Jun 1 18:58:50 2006 +0000 add snp125 commit eda93035b7c0e45fd462e363c9abce73dded822f Author: angie Date: Thu Jun 1 18:54:19 2006 +0000 Removed extraneous --not-informative from phastCons (of species that weren't aligned anyway). Added {chain,net}GalGal3. commit 63223f44cfe392f177032bb0884f62b9cb8f00eb Author: hiram Date: Thu Jun 1 18:53:53 2006 +0000 Remove unused variables commit 542689c1e2a2764d670dd3d56ffc1cc7184669ca Author: angie Date: Thu Jun 1 18:52:56 2006 +0000 {chain,net}GalGal3. commit c8e5d44d6d99433aae24ef0670747c9874b0f0e9 Author: angie Date: Thu Jun 1 18:51:19 2006 +0000 Reloaded flyBaseNoncoding and flyBase2004Xref after changing extractGenes to catch some new RNA keywords after user reported loss of many mir's. commit c39ee8382aa69b60a4112c5068491825c2730401 Author: angie Date: Thu Jun 1 18:28:44 2006 +0000 Description for IGTC Gene Trap. commit 3e74a407b6eee94c5ba1dea97e1c06190ba3b3d1 Author: angie Date: Thu Jun 1 18:27:49 2006 +0000 Updated link to IGTC (genetrap.org). commit 35efd7d7a1dc494bd8dd01d9a001c47cc9a79aff Author: hiram Date: Thu Jun 1 17:12:10 2006 +0000 Add history comment for stats on dropped tables commit 8ef14c83012b4f5b673a6c0cfb9a1ff40988acda Author: heather Date: Thu Jun 1 17:06:46 2006 +0000 tweak priority syntax for SV commit 2ae4df4740d3ef5416a2af4e4abf307fdc8f23c9 Author: heather Date: Thu Jun 1 16:51:08 2006 +0000 use snp125Methods for new snp126 tables commit d219585b1ad40eabd670fcebe963e5dbfcb6e0b2 Author: heather Date: Thu Jun 1 16:27:15 2006 +0000 use red for new deletions commit 58dd61a77968a2ab3dcb2c2b221a64e049e91dc1 Author: ann Date: Thu Jun 1 16:05:58 2006 +0000 added list of species to default off in the Conservation track commit d36c824949bbb823789dcb523618612d82d9e2ea Author: galt Date: Thu Jun 1 15:00:03 2006 +0000 "Encode release log update" commit 86adc3270f9f8a75bf0a17ed0bbfe79dc15d617d Author: galt Date: Thu Jun 1 15:00:02 2006 +0000 "Release log update" commit 6068e97535c076a814a3177550d04357500e67f3 Author: galt Date: Thu Jun 1 04:44:41 2006 +0000 adding ability to find the newest chain available for an org commit f682fef5da43ab2285746fbdbd2e8658631d9662 Author: galt Date: Thu Jun 1 04:42:40 2006 +0000 adding function for comparing dbs, e.g. mm9 vs mm19 or mm9 vs hg17 commit 41eb8d035e5081f3ef7ff024b5ac31ae9279b11c Author: galt Date: Thu Jun 1 04:41:46 2006 +0000 adding functions for splitting alpha999 strings commit c98bc86d695c97181e6822e66269e07f9b2ac9eb Author: markd Date: Thu Jun 1 01:15:09 2006 +0000 fixed really stupid bug reading config variables commit 828bdf3856f16e4f46696e3ac3b316175f0c9bfb Author: heather Date: Thu Jun 1 00:20:11 2006 +0000 delMccarroll commit b321457d0366d958af24116907c166e978f40548 Author: heather Date: Thu Jun 1 00:00:24 2006 +0000 tweaks to SV track commit e9d81d1caddb8f89cb0f3a37df559368d07732ab Author: markd Date: Wed May 31 23:56:50 2006 +0000 moved loxAfr1 and dasNov1 oocs to iscratch commit 1911839cffebc862e8f1116fc5c40e5b0fd27baa Author: hiram Date: Wed May 31 23:51:46 2006 +0000 Beware empty lines in the tdb settings ... commit bdb07521d156bb6e73b3164212c5af14ebb899be Author: kate Date: Wed May 31 23:49:45 2006 +0000 Template description file for custom track commit 86431d185d1920f397a0314e63064c54f4337f79 Author: braney Date: Wed May 31 23:47:24 2006 +0000 ooc files for dasNov1 and loxAfr1 commit 75dc72fb41d43fc1e83d16c67b2e968d17884619 Author: hiram Date: Wed May 31 23:32:02 2006 +0000 Beginning to allow all tracks to go into the DB regardless of source commit 024f5f6e66331f8d5bd482773ecb694e32f19195 Author: heather Date: Wed May 31 23:31:26 2006 +0000 mysql doesn't like trailing comma commit 348d79cbf30fe79e11f4765e95f64a8f095ff7be Author: hiram Date: Wed May 31 22:18:48 2006 +0000 dbTrackName is actually dbTableName and beginning to allow all custom tracks to go into the DB commit 521755d278c3ed9d4fadf52f95668788d61bb185 Author: hiram Date: Wed May 31 22:18:00 2006 +0000 dbTrackName is actually dbTableName commit 9908d82e78bd9e1ebe385de03dbc42d91387c2dc Author: hiram Date: Wed May 31 22:16:38 2006 +0000 dbTrackName is actually dbTableName, and make the db check also be able to verify a table exists commit d4903fef0690fde9c577744a0f0852151881be38 Author: hiram Date: Wed May 31 21:48:28 2006 +0000 Now properly ignoring tracks whose files or DB tables have expired commit e914ad46681c1644f072293b523447c34a45b30b Author: kuhn Date: Wed May 31 21:30:54 2006 +0000 changed label on hg18 Huamn Proteins track commit 9796fa1cefa8c5d8726203dc8a1c9d5efaa45bc8 Author: fanhsu Date: Wed May 31 21:18:32 2006 +0000 Added links to GeneNetwork. commit e71e6382b7ed95090a247255197b0627b835c8a7 Author: markd Date: Wed May 31 20:48:32 2006 +0000 fixed bug with linking mafFrames on reverse strand of source genome commit 9da9a4e89859583d474c4f11aba455bcc7f05df1 Author: hiram Date: Wed May 31 20:39:51 2006 +0000 Recognize types gff and gtf commit ec79892423f5187e0c576d38b6b90397737a0964 Author: hartera Date: Wed May 31 20:27:51 2006 +0000 Added searches for hg18 human proteins track. commit 3c1acee354ead8192d7baa3c3019024f4ab8d14c Author: hartera Date: Wed May 31 20:17:50 2006 +0000 Updated rat to rn4. commit f3ce8d13b6227ec2baf2b0b80adbb9a45b912b85 Author: angie Date: Wed May 31 19:52:57 2006 +0000 Added local description of gap.html to reflect hgFakeAgp usage. commit 7d7ae1a67c473a9f4c6d202f3e4a7264bbc8d5e3 Author: heather Date: Wed May 31 19:25:16 2006 +0000 use subTrack specific methods commit 4e7a7aeccc34821da10704823b63f85e21af02b9 Author: angie Date: Wed May 31 19:12:18 2006 +0000 Resolved -Wall warning: unused variable. commit 01b17c467e6066868a262821c220080368876c68 Author: galt Date: Wed May 31 18:33:30 2006 +0000 oops, just wanted to remove the view link, not the download link commit 7f353d69547079298f968a478ad893e52bf4b3ea Author: hartera Date: Wed May 31 17:46:38 2006 +0000 Repeatmasked pseudo-contigs and added to iServers and san for cluster runs. Checked AffyZebrafish alignments still the same using masked contigs. Re-did blastz chain swap to make chains, nets, liftOver, mafNet, axtNet and downloads for mm8 alignments now including the danRer4 random chroms in alignment. Re-did multiz7way and phastCons using new mm8 alignments. Created downloads of phastCons scores. Split sequence for making liftOver chains from other assemblies. Created danRer4 to danRer3 liftOver chains. Created genscan predictions track. commit 44263ec506f0520678d898fe1798642f70f527a4 Author: kuhn Date: Wed May 31 17:26:57 2006 +0000 changed some priority numbers for danRer chains and nets commit 9cc48a4348021685309956075e7c13ec4083f18b Author: kuhn Date: Wed May 31 17:00:12 2006 +0000 changed some danRer3/4 shortLabels and priorities commit aa7a5cf40a1876431a1236ce78bb71c5d607e5a8 Author: hartera Date: Wed May 31 16:20:16 2006 +0000 Changed url for Ensembl genes. commit 3c6eee2ab1512ca2b05536ed85387727cbb7babb Author: galt Date: Wed May 31 15:00:03 2006 +0000 "Encode release log update" commit 6dfa0ec4603e8cdab2bd124d237012c82a6bbf3c Author: galt Date: Wed May 31 15:00:02 2006 +0000 "Release log update" commit a1357b84a3d2485c9aa6a65513e195dc5d041882 Author: markd Date: Wed May 31 05:40:05 2006 +0000 replace rn3 twinscan with nscan commit 9677f50fe0a6fef1df1a0a1e06725d00103814a9 Author: galt Date: Wed May 31 03:03:41 2006 +0000 "New version number v134" commit 4d1f5dd83d46b3b807f2087a8d3705f6dfab78c8 Author: angie Date: Wed May 31 00:56:01 2006 +0000 Resolved -Wall warning: unused variable. commit d5a1f242344cdba28138940ed55dee96b547e8d4 Author: hartera Date: Wed May 31 00:03:28 2006 +0000 Changed color for UW DNase Array sensitivity subtrack and updated subtrack names for this track. commit bcd79eabd2eba854607f181086c10c372720eda0 Author: hiram Date: Tue May 30 23:52:04 2006 +0000 Correct comment about sqlConn to ct tracks when database commit bdf94105c624f47f6920f2bdbb9aeaf3f6052d72 Author: hiram Date: Tue May 30 23:51:25 2006 +0000 Add overall timing indicator from beginning to end commit c23f478182ff9ac6f543c604515968cbd4be90f4 Author: hiram Date: Tue May 30 23:49:42 2006 +0000 Also need to list thickStart and thickEnd when offset specified commit 64c2d41b2953a064f62a02d74422f889ef1e3b00 Author: hartera Date: Tue May 30 20:16:15 2006 +0000 Changed track titles for UW DNase Array track as suggested by data providers. commit f80a82769574521dd4c2726d75c38418ec5f081a Author: aamp Date: Tue May 30 20:13:42 2006 +0000 A new function to make a hash out of a simple named linked list. commit 69e25f57282b32704798d2c384d281d95285be2a Author: hiram Date: Tue May 30 19:59:26 2006 +0000 Error in compare function when range in a bin is zero. commit 77c5723ff0d6d22d4f357ae06d5f7b246fb714c1 Author: hiram Date: Tue May 30 19:58:47 2006 +0000 Now working with custom database tracks commit 1566afc4adab6f14ad37779bb39a5fbfff3744db Author: kent Date: Tue May 30 16:56:10 2006 +0000 Making it so that you don't have to specify database (just organism) if doing deep blat links into us per request of rwilliam@nb.utmem.edu. commit b091b104978a7d286ddb3f772beb81ab871c0866 Author: galt Date: Tue May 30 15:00:02 2006 +0000 "Encode release log update" commit ed2a366aa1daa511003538674200859d52f9bec5 Author: galt Date: Tue May 30 15:00:01 2006 +0000 "Release log update" commit 5fbd8cd20edd21da81d9493d2ee4d415740ed559 Author: giardine Date: Tue May 30 14:45:45 2006 +0000 Fixed typo in address. commit 5b556cb5e8117f37afe4af3f3e0c65df7f77dfb3 Author: kate Date: Tue May 30 04:19:28 2006 +0000 Add html file support, collapse duplicated code commit 0a92d2d622850cbe955584f8d8f8e7b71264d75e Author: markd Date: Tue May 30 03:37:27 2006 +0000 added itemAttr table to ancestor transMap refgene commit dba73a67b45d87e01efaa8f7010bbc4438a79043 Author: markd Date: Tue May 30 03:36:39 2006 +0000 changed color of transMpaRefGene track commit 1e9c3a52bbbe39d39930fde961e5096dfcdb377d Author: hartera Date: Tue May 30 01:48:26 2006 +0000 Update of UW/Regulome CAP track. Renamed as UW/Regulome DNase I Array. commit 23d6d612529a88fc9cc56e502d3f3b4f2b8e7436 Author: hartera Date: Tue May 30 01:18:21 2006 +0000 Updated trackDb entry for encodeRegulomeCap. Track is now renamed as encodeRegulomeDnaseArray and contains a data update. commit fc9ba5f3fad11accb2cb5e8370927cce85eaa914 Author: hartera Date: Mon May 29 23:33:25 2006 +0000 Documented adding stable archive URL to trackDb for ensGene track. commit 44cf483bb1c7c1cac5100111b3850f461a3c6c5c Author: hartera Date: Mon May 29 22:22:59 2006 +0000 Added entries for danRer4 chain and net tracks. Added stable URL link for Ensembl Genes. commit 3262436d096ab1344ab5bf4d292d0ac923e105a9 Author: hartera Date: Mon May 29 20:50:44 2006 +0000 Description for 7-way multiz and conservation track. commit c927f8b0e9008cfb422c27da47d69e557f6539f5 Author: hartera Date: Mon May 29 20:29:27 2006 +0000 Added wiggle track and frames for multiz7way. commit 17603f26a90c9dbb5fc204abd3074ac6331fc466 Author: galt Date: Mon May 29 15:00:03 2006 +0000 "Encode release log update" commit f43d8452db374fc6665f2a5fc91c37f1238af565 Author: galt Date: Mon May 29 15:00:02 2006 +0000 "Release log update" commit 4f30cc830e5e0db556938191dfc4dfc4cb404712 Author: kate Date: Mon May 29 05:16:16 2006 +0000 Allow subtrack type to override composite type (e.g. for net tracks) commit 2699d2ca7a2fd51de1128b15e1c99b2ca0d71ddf Author: kate Date: Mon May 29 04:49:14 2006 +0000 Fill in substitution variabiles in subtracks commit 3cb90d1874e8ced34909b922db8dd10e9cffb90b Author: baertsch Date: Sun May 28 23:32:26 2006 +0000 change default on spliced overlap commit 4d4e6caa082db2939cdf6b0f103eba9ed764d005 Author: baertsch Date: Sun May 28 23:16:08 2006 +0000 allow suffixes on mrna's for references, tweak expressed coverage threshold add score bump to get prioritize parent, 1st mgc, 2nd refseq, kg fix off by 1 error in axt output file, clean up debug message commit 90314eac4f0bcb202f208e029901c41197056354 Author: baertsch Date: Sun May 28 22:49:33 2006 +0000 add -componentFilter=filename - Filter out blocks without a component listed in filename commit 1a16483ddc35190b1f1bfbd3725dd5b41cd6273c Author: baertsch Date: Sun May 28 22:48:45 2006 +0000 add struct mafComp *mafMayFindComponentInHash(struct mafAli *maf, struct hash *cHash) /* Find component of given source that starts matches any string in the cHash. Return NULL if not found. */ commit 3b2174a7a2c367e7a420b6982bb541c3d0e32cf5 Author: kent Date: Sun May 28 16:50:04 2006 +0000 Starting to draw picture. commit 9d51796e198d3246eb15c69b3836b9ff070c4385 Author: galt Date: Sun May 28 15:00:02 2006 +0000 "Encode release log update" commit 0770424185ae25e1038ffe708b26af69eaa71760 Author: galt Date: Sun May 28 15:00:01 2006 +0000 "Release log update" commit 41d1c0e492c2b4ec1291b81fb68ba4834ae0b4fc Author: angie Date: Sat May 27 19:11:48 2006 +0000 Added IGTC Gene Trap track. commit 5792d740c4bcf022ca65192aec7c309f71383284 Author: galt Date: Sat May 27 15:00:03 2006 +0000 "Encode release log update" commit 13b41ac849082512e8888aee2c3cbd12f85b204d Author: galt Date: Sat May 27 15:00:02 2006 +0000 "Release log update" commit dd25167a4447b139c1885b4f66a7d10c63b69111 Author: rhead Date: Sat May 27 01:04:24 2006 +0000 minor wording change commit 687131ce891ec331528553f1d28962ae3429c17b Author: rhead Date: Sat May 27 00:55:28 2006 +0000 minor wording change commit 12991545a8f2eaae1816db6193d8d396ae29e5cf Author: heather Date: Sat May 27 00:49:48 2006 +0000 fix typo commit 5447514e3f3689d2018ed4962af819c05f92eb54 Author: heather Date: Sat May 27 00:47:42 2006 +0000 edit refs commit c771db909341c7b09c9442afd7b3aaa90515ce5a Author: heather Date: Sat May 27 00:23:01 2006 +0000 additions for Conrad commit 2c4db3be3a5e89f0f35df637f0081e5d716a62fc Author: heather Date: Fri May 26 23:24:39 2006 +0000 fix typo commit 8d20543d4faf733362496bb982dd6bb348d9390f Author: heather Date: Fri May 26 22:37:20 2006 +0000 a few updates commit 6d439c94221ef929bade3c4886aae362a18f02ce Author: angie Date: Fri May 26 22:36:36 2006 +0000 Add 1 to chromStart when printing out position range. commit 937eed9871e6718c110d6b9a606b577a3328e045 Author: heather Date: Fri May 26 22:25:52 2006 +0000 another longLabel change commit 6b5c6fceff29db0cc5a5708367831e95dd5f9d6b Author: hiram Date: Fri May 26 22:24:40 2006 +0000 Now calling wigLoadItems for wiggle custom track database items commit 389a31e88ce0faf0626520d4aac168971ae7c97e Author: hiram Date: Fri May 26 22:24:07 2006 +0000 Now doing wiggle custom tracks from database correctly commit b82f197f60123aa0a77bcbdae53826fd77709dcf Author: hiram Date: Fri May 26 22:23:30 2006 +0000 wigLoadItems has become global, now used with wiggle custom track database commit 8cf072fe0cf9c6fa6aed8f635ec988f6b4da14b7 Author: hiram Date: Fri May 26 22:22:28 2006 +0000 Now doing wiggle custom tracks click properly commit beebb4ce574f5dce4b8b2d1ee3f41d84b4b67eb6 Author: hiram Date: Fri May 26 22:21:34 2006 +0000 Now properly doing wiggle custom track database clicks commit 0c9855dc23b0400d186dadf2c88fb2b99355bb40 Author: angie Date: Fri May 26 22:13:06 2006 +0000 Added support for IGTC Gene Trap track: cell line source is encoded in the name, and we use it to color items. commit 8a96532bbddd92f9516cb4972078951b7936c8f9 Author: angie Date: Fri May 26 22:07:11 2006 +0000 Added IGTC Gene Trap track. Removed duplicate entry for xenoRefGene (there were two in this file). Moved bacEndPairs track def up to the "group map" track section (it was in the search section). commit 22d26c1d80ea8baaf468e66218959fea83fc50ca Author: hiram Date: Fri May 26 21:53:06 2006 +0000 Add spanList to the wiggle track settings commit a2a200d5242bfaaa4d38d09f0572ea1e8b324549 Author: hiram Date: Fri May 26 21:52:28 2006 +0000 Fixup for custom track database operation commit 4c3ea810b2d1f680e85655f9e7018e58f984bf6e Author: kent Date: Fri May 26 21:49:32 2006 +0000 Looks like layout routine is working. commit 45d4e73bbab18dd44ad82eb2ec8b6c0b7d10d375 Author: angie Date: Fri May 26 21:04:39 2006 +0000 Enlarged a char buf to handle very long table names (for Merck) when making subtrack cart variables. commit 6e51e12d18a96f5c5bcb339f07914c0cf4ab7e90 Author: hiram Date: Fri May 26 18:57:19 2006 +0000 Add spanList to trackDb entry for these database wiggle tracks commit b942291d8e5c342398562aa52c00432020fea612 Author: hiram Date: Fri May 26 18:34:25 2006 +0000 The pipeline commands to wigEncode are now all in here, and do the wigSettings and dbSettings properly. commit 1d44d2377c5b728060d551b59d7b5efd0b407afc Author: angie Date: Fri May 26 18:28:16 2006 +0000 Updated knownGene-related IDs to handle rn4 as KG II (not original KG). commit c0a031a931f68686b9284e9116fccb63cecd6e62 Author: hiram Date: Fri May 26 18:12:19 2006 +0000 Do not mess with the input until it is being read. Doesn't work for stdin. And make routines here private, they are not globals commit 776bf4c7d868dfbbff8a87dd6f95f79702030757 Author: hiram Date: Fri May 26 16:50:05 2006 +0000 Add the arguments chromInfoDb, maxChromNameLength, and tmpDir to allow use as a cgi-bin loader command commit 1542d791fb5ad6d54c9afba131b68298111a011b Author: hiram Date: Fri May 26 16:27:50 2006 +0000 Add timing functions commit d150c8758ed927f064939018ad33f3d0fdd73bdc Author: hiram Date: Fri May 26 16:23:20 2006 +0000 Now properly setting is_dst commit 1e548d6e4b089d7a081d2d1573158a1f2a492439 Author: angie Date: Fri May 26 16:14:35 2006 +0000 Resolved -Wall warning: unused variable. commit 812b6850aac2578f25ce734061bdba942ff785bb Author: galt Date: Fri May 26 15:00:03 2006 +0000 "Encode release log update" commit 66837f366908c7adac9b61cfb4300df62acf8575 Author: galt Date: Fri May 26 15:00:02 2006 +0000 "Release log update" commit e79ca2a9f9be7361cfd0d3b10b21aeda46bc952f Author: giardine Date: Fri May 26 14:56:16 2006 +0000 Fixed address. commit fc6f6f5e5ea684b0a139915049a6e87bf30e9b06 Author: giardine Date: Fri May 26 14:31:39 2006 +0000 Updated sources to reflect adding of CFTR data. commit 8fc48feb6aad176af6a2ec7b2fbb6cbd7ceba81d Author: kent Date: Fri May 26 02:08:12 2006 +0000 Starting to figure out chromosome layout. commit 867d5225de6ac759ca5869731ce753a6a2b53b1a Author: heather Date: Fri May 26 00:12:15 2006 +0000 change longLabel commit 3711290c966ca84c34eb698233a61d933cb6948c Author: hiram Date: Thu May 25 23:55:51 2006 +0000 Now working with wiggle data types commit a221aaa272a84dde6628789a7ef2f00c23833543 Author: kuhn Date: Thu May 25 23:25:14 2006 +0000 changed labels for danRer3 to danRer4 update commit e75f4a4eb808e3a987905a0efed1daf23ca35d4a Author: kuhn Date: Thu May 25 22:53:24 2006 +0000 changed danRer3 to o_db and danRer4 to Zebrafish for chaina and nets commit 63f4d8e05653f4d10f4a39408f049cb42ca4c51e Author: donnak Date: Thu May 25 20:17:01 2006 +0000 Added danRer4 announcement, archived 1 item. commit c4d437747447875cae1c2f203b795db006f41dc4 Author: donnak Date: Thu May 25 20:16:37 2006 +0000 Archived an item. commit 4fee1e68c776b61502a2dcffd81532abd84fa16f Author: donnak Date: Thu May 25 20:00:38 2006 +0000 Fixed typos. commit ffacdfcd50acf4c745b7cc6d27fbb827761515b2 Author: donnak Date: Thu May 25 19:48:24 2006 +0000 Added danRer4 browser. commit ccdb0fea03ab71d2efad0df09a6ba663cb78c360 Author: donnak Date: Thu May 25 18:54:43 2006 +0000 Added danRer4. commit 4b6e9b34d5437b6896e15ffcfc74b2a4124c8f1a Author: hiram Date: Thu May 25 18:30:41 2006 +0000 static addToSettings() becomes global ctAddToSettings() commit 7ef3659dad8c707dbb052cb12bb97f07d7e8c8d8 Author: hiram Date: Thu May 25 18:29:30 2006 +0000 added ctAddToSettings() function commit 161f31dda7156fe9012a21dc15a265348c3d60c1 Author: hiram Date: Thu May 25 17:53:56 2006 +0000 Remove unused variables commit 2e8c0f170d0a3f4e2d3db79ba6350a33c85f977d Author: angie Date: Thu May 25 17:53:23 2006 +0000 {chain,net}GalGal3. commit 14bd40736a53c2ca7b5c24157b9a52ffa63a95fb Author: angie Date: Thu May 25 17:53:01 2006 +0000 {chain,Net}GalGal3. commit 725a9d43fbc855b93695706ca432542de7fb62fa Author: angie Date: Thu May 25 17:51:31 2006 +0000 Resolved -Wall warning: unused variable. commit 4c5c9209b37aa4ebf0f1bce3d47b7c0a9bfd3305 Author: hartera Date: Thu May 25 17:42:31 2006 +0000 Removed nib dir in gbdb and added 2bit file to chromInfo table. Run phastCons for multiz7way. Created multiz using recriprocal best nets and then ran phastCons for this. BAC ends track in progress. commit f784bcd57b80bd659bbeade5479fd76313bb9716 Author: hiram Date: Thu May 25 17:17:43 2006 +0000 Now working with gff, gtf and psl file types commit bbd8978bd560b09caceb68898135ea4deb164d72 Author: hiram Date: Thu May 25 17:15:33 2006 +0000 Add ctDbAvailable() test commit 70d862c8dd2596bc69c6e8fb62f542abf848cccd Author: hiram Date: Thu May 25 17:15:01 2006 +0000 Was too early on the bail out for bed 3 no information commit 0254d92b29c4bf5fd873d96bbbbb16648715142d Author: kent Date: Thu May 25 15:38:45 2006 +0000 Factoring out some hgTracks.c code into src/hg/lib/trackLayout.c for reuse in hgGenome. commit 82939aefc0be7a9fd8849c2326a52063893eb0d9 Author: galt Date: Thu May 25 15:00:02 2006 +0000 "Encode release log update" commit 240d4d3099a6176dd7bea89330281b0a5be0c359 Author: galt Date: Thu May 25 15:00:01 2006 +0000 "Release log update" commit 42f6006b339429a643dad7c8d9fd9c0ae709fd50 Author: kent Date: Thu May 25 14:55:50 2006 +0000 Got shell of new cgi up. commit 76780c058eafcce93ade72c6dbf77923d54142f2 Author: galt Date: Thu May 25 06:28:09 2006 +0000 fixed jax expression level processing, turns out that GXD_Expression was not needed and only messed things up - probably jax is phasing that table out. commit 07c698fb119f6b4bd05c6f57869c3ac3b16ecbad Author: markd Date: Thu May 25 05:18:10 2006 +0000 added option to still get mRNA even if cds can't be obtained commit c5146db20d26654e9b5f50fa75bb941c7d57a502 Author: baertsch Date: Thu May 25 00:08:51 2006 +0000 move syntenic nets up a level commit 5accaeafe3fe1585add15d6e12eedc5530bc9af7 Author: baertsch Date: Thu May 25 00:03:20 2006 +0000 fix names to due to subtrack $organism bug commit 83b24e63183bb5eb57f029e3bf7fa79cf2b3e61e Author: kate Date: Wed May 24 23:55:05 2006 +0000 Submit File is working. Dup tracks are replaced. commit 31598140ac6577383264fad8c4078e8ef6a44d92 Author: angie Date: Wed May 24 23:24:55 2006 +0000 Resolved -Wall warning: unused variable. commit c599eb43b92d3c5e2633d79c3a8553a81313b2e1 Author: aamp Date: Wed May 24 22:51:26 2006 +0000 Fixed a bug in logic whic prevented item clicks to hgc in full-mode unless next-item navigation was set. commit a2be9128ef04083f7d27a2bf5283f4e4532af662 Author: hiram Date: Wed May 24 22:31:01 2006 +0000 Adding search for picTar data tracks commit 531fd6e51053fca7562805d6d457da2bb3e81f89 Author: kate Date: Wed May 24 21:05:36 2006 +0000 Remove value attribute from file widget, as it doesnt seem to be used in any browser commit 5739781a602a23261ad5f5c7d0987aee4d5a0446 Author: hiram Date: Wed May 24 18:36:23 2006 +0000 No SQL connection needed in mapBoxHgcOrHgGene, and indicate no item name in bed 3 type custom track data commit fa098011fbdfbcebe78c3bc3211c254054fc3112 Author: hiram Date: Wed May 24 18:35:09 2006 +0000 No information available for bed 3 type custom track items commit a84e6b3b4a6778ecabca1e7cc97208fec7145c39 Author: ann Date: Wed May 24 18:10:43 2006 +0000 removing nextItemButton line from knownGene section (no longer needed to cause the double-arrows to display) commit 88c5543c0e8222b0baa93f9fe1aeb02abd4d3970 Author: rhead Date: Wed May 24 18:10:09 2006 +0000 Changed pointers from hg16 to hg18 and from mm7 to mm8 because Angie rebuilt sacCer1 hgBlastTab and mmBlastTab on 5/22/06 using the newer assemblies commit 311486f79630f1b47c3b22c7ab9a0562f43b6497 Author: hiram Date: Wed May 24 17:45:03 2006 +0000 Was incorrectly passing up on all wiggle data track saves commit e3bda4919a6473a47f716a47a2d7e81b0903c937 Author: hartera Date: Wed May 24 16:59:19 2006 +0000 Moved liftOver files for download and corrected md5sum.txt for vsMm7 and vsHg18. commit 3e9f0baee34b746f4db3377bce275ba232b80c1f Author: hartera Date: Wed May 24 16:58:52 2006 +0000 Moved liftOver files for download and corrected md5sum.txt for vsMm7. commit 1790b56d7ae6b27fc4c6b050359ffe97e84fcec5 Author: hartera Date: Wed May 24 16:56:59 2006 +0000 Edits to downloads section. commit 9664b420809f6eee4ecd5c657387389c1cf17e37 Author: hartera Date: Wed May 24 16:17:14 2006 +0000 Moved liftOver files for download. commit 6d9fd07c37ddd4ac99150c0c1e3df15eda454826 Author: hiram Date: Wed May 24 15:52:58 2006 +0000 Updated description from Nikolaus Rajewsky commit 99168a1c8e57308358bc5f3746927eee4efdff17 Author: giardine Date: Wed May 24 15:26:59 2006 +0000 Added link table for attributes. Checked in other files previously, just forgot this one. commit 8adb2e18bde3245478920162196b40c9ebf159fd Author: fanhsu Date: Wed May 24 15:13:06 2006 +0000 Rebuilt ensGene. This time, simply remove all hap chrom entries. commit 4ee4ea029681ae405a4e3cbb4b729f276f12390e Author: galt Date: Wed May 24 15:00:03 2006 +0000 "Encode release log update" commit 405b313210934ede8553821e2ea268e31e1872ac Author: galt Date: Wed May 24 15:00:02 2006 +0000 "Release log update" commit f86d635d4539918d78b9788689864f7a7dc7742b Author: angie Date: Wed May 24 14:58:45 2006 +0000 Removed dp1 and triCas1 from active targets. Added BACT_DBS target (for databases used by Jenny Draper and Josue Samayoa). commit bf328b79c3b904917ea1b86b8ca3f0dd6c7e3c95 Author: daryl Date: Wed May 24 11:23:40 2006 +0000 added options to include chimp position and to ignore quality scores of 98 commit 82f2e60e5ac92c3697af00f29985231fea39f32c Author: aamp Date: Wed May 24 02:03:14 2006 +0000 Moved some code out of genericDrawItems, and added full-mode compatibility to the next-item button. commit 5facbcb9f2047419498a7a1bdac35a2326064648 Author: hiram Date: Wed May 24 00:10:16 2006 +0000 Properly free connection to customTrash DB commit 899e634cf737f055d239ebcaaaa1c3c97590eeb6 Author: hiram Date: Wed May 24 00:09:49 2006 +0000 Beginning to work with gff format, almost there commit 8a5a295dd537a57a53609649c67615f7364284e2 Author: hiram Date: Tue May 23 23:11:53 2006 +0000 Add hgCustom to the blue bar genome browser enabled link commit e72ce5ff4b06056ea67e35ddddd3dfb048e4f25e Author: hiram Date: Tue May 23 23:10:45 2006 +0000 Add webEndSection() definition commit 7c598ee2a97ba6f6cf42a98c57809d14fb566594 Author: donnak Date: Tue May 23 22:16:19 2006 +0000 Re-added Milwaukee mirror to list. commit ba6ce72cee6eb9db89f0f63329382e7752b4d11b Author: angie Date: Tue May 23 21:15:41 2006 +0000 Add -minMatch=0.1 to hgAddLiftOverChain since this is for cross-species alignments (thanks Ann!). commit 7dce4c370aa94b754a89bf72c6855cc09726d250 Author: donnak Date: Tue May 23 20:47:56 2006 +0000 Created this special version of top menubar for downloads.html, but apparently never checked it in. commit 5fad391c249a8b3140b37cbd1af5f2355128e374 Author: jsp Date: Tue May 23 19:07:18 2006 +0000 Added documentation of EvoFold lift and filtering. commit d9caf7dd22da05c95981f8a28dc43594f0e53701 Author: donnak Date: Tue May 23 19:01:13 2006 +0000 Edited the Havana methods & reference sections. commit c1e5bbbb983a5b642c81585b53c7122680a1adac Author: kate Date: Tue May 23 18:29:49 2006 +0000 Drop unused indexes in maf summary table commit 2a89e57aea38ae1586dbb9cbb8687e3079e93f28 Author: aamp Date: Tue May 23 17:28:28 2006 +0000 Turned next-item button off for PS/PDF output. commit f7efb9e8109e4c69071648b284cc829982d72950 Author: angie Date: Tue May 23 17:24:51 2006 +0000 Resolved -Wall warning: unused variable; missing arg in errAbort message. commit aa8cf8e2f379e76790c20ea35f47d8e3f23479ab Author: angie Date: Tue May 23 17:13:27 2006 +0000 Regenerated dmBlastTab, hgBlastTab, mmBlastTab with proteins from current sgdGene and latest fly/human/mouse proteins. commit bf88ca1dfaffcfea364ec9486b8628289db32e62 Author: galt Date: Tue May 23 15:00:03 2006 +0000 "Encode release log update" commit ca70893c70cb37189dac2f57fcdd1826fbe758a9 Author: galt Date: Tue May 23 15:00:02 2006 +0000 "Release log update" commit adae8cdeae0a89395248641eab119ba1ddcf4d5c Author: hartera Date: Tue May 23 03:39:19 2006 +0000 Added clarification of the Data Freeze for consensus pseudogenes. Added description for the Havana-Gencode subtrack. commit 7567571f6f19f523a11d7d89f730492bd1fc51e8 Author: hiram Date: Tue May 23 02:47:05 2006 +0000 Adding CUSTOM_TRASH name commit ce5fa224926f6361c8421b3d7e0a10407cebc5ff Author: angie Date: Tue May 23 00:27:48 2006 +0000 Fix for dmBlastTab.target (otherDbs being updated to dm2 from dm1). commit 3623839d7cedf8f10d24ce91813b39ccef1fc1b6 Author: kate Date: Tue May 23 00:14:22 2006 +0000 Add util to create file input widget commit e2afb9be39c9d5eebfef27dfd10958760992d0a3 Author: kate Date: Tue May 23 00:13:02 2006 +0000 Add functions to include HTML files in a page commit b9641dbec7beaadca03fc00d223db6887c0ac386 Author: kate Date: Tue May 23 00:11:43 2006 +0000 More features working commit cc17e0690c33661e4c12709158c546c1c47b5db8 Author: hiram Date: Mon May 22 23:46:58 2006 +0000 Add genome browser link in blue bar when on table browser commit 94153f4dcdef2882234974b4557946fdb6cf7a32 Author: baertsch Date: Mon May 22 23:01:28 2006 +0000 fix name on refGeneBlatz commit a79f41f7223a31ad9b187955c8c9e49dcd8ebcf1 Author: markd Date: Mon May 22 23:00:20 2006 +0000 hide transmap alignment subtracks by default commit 89f687a6ad54d86aa6f9dcfea8c5f5865ed0c884 Author: hiram Date: Mon May 22 22:59:57 2006 +0000 Correct usage message. commit a853b75b861b161c9d51c0e40a1909f3d8c45a9a Author: hiram Date: Mon May 22 22:55:37 2006 +0000 Properly handle daylight savings, and makefile with compile target commit 02b3cccff106b291e1bf15ebf07d5ae2b1118098 Author: markd Date: Mon May 22 22:53:32 2006 +0000 turn off find match highlighting when making postscript output commit 8afca34b66b0e978847d54a044f32fe91bb1dd3a Author: baertsch Date: Mon May 22 22:53:13 2006 +0000 add refGeneBlatz commit 8c08c440d12817a153cf47cd53ec3c70bf95e4d8 Author: hiram Date: Mon May 22 22:41:47 2006 +0000 Can now drop tables, seemingly properly ... commit 75ed7bf4f8a5ac1b63e3db5f208c7ccc2e3c04e8 Author: donnak Date: Mon May 22 22:39:33 2006 +0000 Italicized X. tropicalis. commit e3bb05a120f6ec5423a0bff5c1b16e8e62e65fd6 Author: donnak Date: Mon May 22 22:39:07 2006 +0000 Capitalized Tetraodon. commit db9f89c8b5cae94c47a21cd934111cf2bdbabbcd Author: donnak Date: Mon May 22 22:38:37 2006 +0000 Capitalizied Fugu. commit 30d1991c303734d96d168876ea71567480ece6da Author: ann Date: Mon May 22 22:28:00 2006 +0000 two small typos commit e9e226d8f331d0d0207f813abde5731cf7da7c9f Author: ann Date: Mon May 22 22:24:58 2006 +0000 edited to update Ensembl name (more closely aligned with hg17 ensGene.html commit 973a1a043e7187c6a424f7d75ca74ac6f876c000 Author: ann Date: Mon May 22 22:20:32 2006 +0000 added block for ensGene commit 5605b237bda3e41c5e88090411ee848e4d45e63f Author: hartera Date: Mon May 22 21:36:56 2006 +0000 Removed hgGene on as the tables not present to support this. Added stable archive URL for Ensembl Genes and added correct version. commit a69fed4fe8eba9c735e0e37d58af20db19e5142a Author: acs Date: Mon May 22 20:51:02 2006 +0000 lifted vega tracks from hg17 and add syntenic net composite track commit f3b1a7fc70641f9833b3622ef06ff8a1d0612c76 Author: acs Date: Mon May 22 20:47:24 2006 +0000 added syntenic net composite track commit a965cf184f714f86f508a00e3b86879ed8a7101c Author: aamp Date: Mon May 22 20:00:13 2006 +0000 I forgot this bit of logic. The nextItem buttons were being displayed all the time. Now that checkbox shouuld matter. commit 7177e5ecfca78f6a2745607ea8dd91873cbc5348 Author: hiram Date: Mon May 22 19:14:59 2006 +0000 Processing input arguments, have times established commit e834c0a908bd0dd3b85a985dcae290889234a9ad Author: angie Date: Mon May 22 19:08:48 2006 +0000 More joinerCheck fixes: regenerate BlastTab vs. hg18, update flyBaseToRefSeq. commit f52e7dbc58c0e91a8ddbc95a1c96c75c9d870668 Author: hiram Date: Mon May 22 18:43:07 2006 +0000 Initial do-nothing source commit 72cb1d261c298eaaeb32ddcd67d4723ef939b0bb Author: hiram Date: Mon May 22 18:35:20 2006 +0000 Removed monDom2 from the active list commit 5b6d83b39c542679fe6bbe5b44486d2422fd0259 Author: markd Date: Mon May 22 18:32:43 2006 +0000 disabled errAbort for converting protein psl to a genePred, as the browser uses this for AA coloring commit d7fb14e8c3659ed13583e06f6a37ad9a4a8eea4c Author: fanhsu Date: Mon May 22 18:29:21 2006 +0000 Added miRNA.html. commit ad8b34404ef0c3594f487e83b93546ca428386dd Author: fanhsu Date: Mon May 22 18:13:08 2006 +0000 Added miRNA track. commit fae876c99c72d8f3d6d9526ed0c17355bb739f0e Author: fanhsu Date: Mon May 22 18:09:21 2006 +0000 Changed long label of wgRna. commit a1f566707ae920fe7f70bb472e031d089add8d07 Author: angie Date: Mon May 22 17:34:58 2006 +0000 Resolved -Wall warning: unused variable; fixed small bug (== used instead of =) caught by "statement with no effect" warning. commit a61c95e53541678ca466c41197357100dc8b5d99 Author: ann Date: Mon May 22 17:03:52 2006 +0000 Changed date for ENCODE MSA sequence freeze commit 7f510d5f1f93be782e9c7a4b6e695704309bca22 Author: braney Date: Mon May 22 16:50:55 2006 +0000 more hacks to work with modern knownGene commit b7d12f6ffdc84007cd8fe1ccf269cc702006c4b4 Author: fanhsu Date: Mon May 22 15:49:42 2006 +0000 Updated wgRna. commit fc144e732e48450e4d694d81e3fd04ea296e97ce Author: galt Date: Mon May 22 15:00:03 2006 +0000 "Encode release log update" commit 9aba9750cbcf854bab53495e606a0c7a211035ba Author: galt Date: Mon May 22 15:00:02 2006 +0000 "Release log update" commit ac86cbe004470c41500094c78a20430695bd7857 Author: braney Date: Mon May 22 14:04:33 2006 +0000 take out old ancestorS commit 9e029496327b4d41da850167603918abc7696c4e Author: galt Date: Mon May 22 10:03:17 2006 +0000 bugfix: was trying to re-use a conn before the result set from the previous query had been freed commit 5e52f33bda42b4f9243ad8a4450c766a4a3fc170 Author: galt Date: Mon May 22 09:18:58 2006 +0000 fixing expression data - tying pane to specific expression structure commit 1dea62038908c04c98627e7ca7d2608cf5bc33b4 Author: galt Date: Sun May 21 21:42:55 2006 +0000 "Encode release log update" commit a3da60e1be4a8ef4b15437fdac814ac62e40566e Author: galt Date: Sun May 21 21:42:54 2006 +0000 "Release log update" commit 24d4721a21e04c1889b0869baa7b1c9080fda1d3 Author: baertsch Date: Sun May 21 19:51:41 2006 +0000 add frames to 6way commit a4edbf00ec8af7f48c5aa82060d949946f682971 Author: baertsch Date: Sun May 21 18:07:09 2006 +0000 add 6way multiz syntenic commit e121e0ad5f0c923c60d9b8fdc1e931746465f914 Author: kent Date: Sun May 21 15:39:18 2006 +0000 Fixed a warning message and trimmed some unused code. commit ca99ae8d04f8588cce01ed7228f0177db2696569 Author: markd Date: Sun May 21 08:12:41 2006 +0000 fixed build with new config align option commit 356deb7348dc174477f6890948a4b274c76fb326 Author: markd Date: Sun May 21 07:24:29 2006 +0000 added ignore entries commit 74d26bab67994c524faa5a0c5efa9d70f1e8f0cf Author: kent Date: Sun May 21 02:49:24 2006 +0000 Improved usage message. Clipped out some unused code. commit 5bfcfa1f89b9438587781ada87fb02690b6ffec8 Author: kent Date: Sun May 21 02:36:06 2006 +0000 Adding additional error checking commit bebc954bbf428114522cf479c272d5576c2a94d1 Author: markd Date: Sat May 20 23:59:45 2006 +0000 fixed bug where negative query chain would be missed commit f2554cef524aecf62612821170b3455e700f5e74 Author: hiram Date: Sat May 20 14:56:35 2006 +0000 Add subdir utils to the utils build commit a3198a1d8b1e88963ba4e827a7c2db31bdb7fd3c Author: hiram Date: Sat May 20 14:42:23 2006 +0000 Initial makefile commit 9ffc35f8200eb2a2c54f04d0cfe3a5aca38835bd Author: baertsch Date: Sat May 20 05:16:10 2006 +0000 add 6way commit 37a76c43baebbe37a56fff0b60524ce892af53ab Author: hartera Date: Sat May 20 01:45:28 2006 +0000 Description for UW Regulome DNase Array track. commit 6b339e3398a3d32a083f5acc4629f44e3a601dae Author: kent Date: Sat May 20 00:59:31 2006 +0000 Fixed it to work with mySQL 5. commit 52a87c6bc2c6fea3283199e0603774446041db71 Author: kent Date: Sat May 20 00:55:14 2006 +0000 Made it work with mysql 5.0 commit 40cfce3809fc1adc207e5e88c14d0c031253877f Author: kent Date: Sat May 20 00:54:56 2006 +0000 Adding functions to test mySQL version. commit 7ae034aa314c2c669985a41e5525deff648e46f4 Author: kent Date: Sat May 20 00:28:17 2006 +0000 Fixed rare bug. commit 315370b998e512a4d0bb63e802764fe4f1fcb7d2 Author: hiram Date: Fri May 19 23:53:25 2006 +0000 Would be nice if it would work commit 6758974ac65041d27981bd4d0d91f7cd5de145c5 Author: hiram Date: Fri May 19 23:49:20 2006 +0000 Initial source commit 0ff2764f7847d4281eced0aacf565b436a028207 Author: hiram Date: Fri May 19 23:26:19 2006 +0000 Eliminate some useless query constructs commit 3b7db2fe2d57f58f6b482935113ec8e2293e9fe9 Author: hiram Date: Fri May 19 23:23:45 2006 +0000 Now handling item clicks for database custom track items commit 11d5474c831bcdf4b19f70f7be7d270de9c3fb18 Author: hiram Date: Fri May 19 22:58:35 2006 +0000 Fix comment text commit dcbcac7a427308f9f0b376c8921921ed94c36970 Author: aamp Date: Fri May 19 22:06:21 2006 +0000 Turning nextItemButton to "on" by default. Can be turned off in trackDb. commit 48d02dfcf795d912c5163cf2054189304726cfac Author: kayla Date: Fri May 19 21:56:25 2006 +0000 took out the "release alpha" commit 940df0ce87ee091851312e8c728854e3b1ecdcd7 Author: donnak Date: Fri May 19 20:08:50 2006 +0000 This version removes explicit reference to # of src code lines. commit b4d8295d727696f807cdacc0737bff2f16a3c713 Author: hartera Date: Fri May 19 19:58:22 2006 +0000 Minor edit. commit e59e3c5b7933264f1adcb44dc52edc19787d212d Author: hartera Date: Fri May 19 19:55:05 2006 +0000 Added that dynamic masking was used for Blastz alignments. commit fbc0553cea999e400c3876f1b9ad5733c636ca25 Author: hartera Date: Fri May 19 19:52:36 2006 +0000 Description for danRer4 chain track on fugu. commit f3c9182fd822cbec3ae1faf27b967b3f508ecf66 Author: hartera Date: Fri May 19 19:45:55 2006 +0000 Description for danRer4 chains on tetraodon. commit 4d29529fe019268224acfae091765838ea89b50c Author: hartera Date: Fri May 19 19:37:24 2006 +0000 Description for danRer4 chain tracks. commit e5b4783357d630f0f27c8fb46251bdf337c3eede Author: hartera Date: Fri May 19 19:12:28 2006 +0000 Added description for danRer4 chain track on xenTro. commit fb63305cc6d51436e95253b674985b2cc76a4b87 Author: hartera Date: Fri May 19 18:56:24 2006 +0000 Edits to correct description for danRer4 net. commit 41be3e1a75bc1a5f2760b93734e48620b101b6e2 Author: hartera Date: Fri May 19 18:54:12 2006 +0000 Edits to correct description for danRer4 chains. commit 395fee9fca1d9f66c8eba36235d3bf6ef7bfca46 Author: kent Date: Fri May 19 15:58:58 2006 +0000 Added some debugging, and tested times. commit 2d76c743795f1d6575a82cdfccf32734ca63b54e Author: galt Date: Fri May 19 15:00:03 2006 +0000 "Encode release log update" commit 3dc9e9c5db00d24fc30730083c9dca6ffcbcda13 Author: galt Date: Fri May 19 15:00:02 2006 +0000 "Release log update" commit 65e86798110c8e6535f2ab9b6046e4d0211ce5e4 Author: kent Date: Fri May 19 06:29:25 2006 +0000 Polishing usage message commit ffce84c876793d31c2cbdfb8568c88dd9cbb6fbc Author: kent Date: Fri May 19 06:18:19 2006 +0000 Seems to work. commit 2e1b44c47f570af8bbf300842f465b1a88507b8a Author: kent Date: Fri May 19 06:10:50 2006 +0000 Seems to work, at least after a fashion commit 1b62746f80c3f08eb5fc913b66f1d22d28601c5f Author: galt Date: Fri May 19 04:57:58 2006 +0000 worried about machines under 1GB thrashing on the view link, so suppress it for now commit ed030eff17cd7b679b82f16395512dbf04d389af Author: kent Date: Fri May 19 01:58:08 2006 +0000 Making this go by default, no 'really' needed. commit 892528028be783e6f0108aada1bb83f931967a09 Author: kent Date: Fri May 19 01:44:01 2006 +0000 Seems to work better now. commit 835578ec320d872ed6dce385a2f9c5292beb8774 Author: kent Date: Fri May 19 01:18:10 2006 +0000 Seems like it might work. commit 96487d9a224bca96d6de1dbd411c33e9bfa009cd Author: hartera Date: Thu May 18 22:49:55 2006 +0000 Corrected fragment type. commit 44d1c971c0ddbc7b237241ac2a00f2d5f0135ace Author: hiram Date: Thu May 18 22:12:18 2006 +0000 Update picTar long labels to indicate correct species commit d8da159cdb6a8208d6d45dee0bbaec8d8675cfc3 Author: kate Date: Thu May 18 22:06:08 2006 +0000 Additions MSA group commit a067b60506941466605143e9bbfd359ee999bfe0 Author: hiram Date: Thu May 18 21:24:33 2006 +0000 tm_mday is 1 to 31, *not* 0 to 30, do not add one to it ... commit cbfc9d4d34baa341406f37d52041cafa2a9dec22 Author: daryl Date: Thu May 18 18:53:25 2006 +0000 fix typo commit ba6c0826d0fe720eec205912c1e36b192bc96c6e Author: angie Date: Thu May 18 18:03:12 2006 +0000 hgPosBrowserRange was neglecting to add 1 to chromStart for display -- thanks to Rachel for catching this. commit 9b7ccbd1b6893711c9505c6be96f922d90f0457e Author: angie Date: Thu May 18 17:56:32 2006 +0000 There are multiple types of tracks/subtracks whose names begin with "encodeGencodeIntron" so take type into account when dispatching. commit ef9ff938f4be740b5784ac2baa499acbdd0574c7 Author: angie Date: Thu May 18 17:37:21 2006 +0000 Added rowOffset to gencodeIntronLoadByQuery to support bin field in table. commit 4b26397c01de03376db382bfa8bcd10677abdb65 Author: daryl Date: Thu May 18 17:16:17 2006 +0000 fixed bug in snp125WeightFilterItem commit 2a0faf2c405d036eea29e5ea5e038955813f8c2a Author: angie Date: Thu May 18 16:33:14 2006 +0000 Fixing typo in previous rev that caused the value given for -sqlTable to be used for -tmpDir. commit ae686392861e46a44d525a2618cff57e7b34e76c Author: angie Date: Thu May 18 15:27:22 2006 +0000 Resolved -Wall warning: unused variable. commit b2f9202f21fddff3a085eaf432a5a9e1754d3e4c Author: galt Date: Thu May 18 15:00:03 2006 +0000 "Encode release log update" commit 39c2a926e54d82d3d195a6d3cc71fb677ed1fde4 Author: galt Date: Thu May 18 15:00:02 2006 +0000 "Release log update" commit e81139a62c8c8506a81613daddae3079893cff6a Author: baertsch Date: Thu May 18 04:53:05 2006 +0000 remove cgi/clustalw commit 5fee28fde59d8a63b884617ece09296815d434b3 Author: hiram Date: Thu May 18 02:12:08 2006 +0000 Fixup galaAvail.tab chmod commands and get them in the correct location commit 3886e8900910e9375dfce137a1fe973f521b3256 Author: braney Date: Wed May 17 15:17:53 2006 +0000 add historyFile. Fix some bugs. commit e94e27f68fd393e685fbfc3d99d67f851fa1e5e4 Author: braney Date: Wed May 17 15:17:09 2006 +0000 almost works perfectly. commit 5c1735e7315c94279755f2b6aef36d8a14c37a0c Author: braney Date: Wed May 17 15:16:24 2006 +0000 fix up some error messages, add removeXs() function for generic removal of char's from node names commit 1e6da78140d2391071647ce8cc2fceed0017dd0a Author: braney Date: Wed May 17 15:15:43 2006 +0000 add generic function removeXs() commit efad70d37bf9b99cb29726030fdb3077f968e14e Author: braney Date: Wed May 17 15:14:58 2006 +0000 make removeX() generic commit 7df7fa787f0dda99dbfe2dede146d1ce19b7a009 Author: braney Date: Wed May 17 15:13:49 2006 +0000 add options to compare only speciation nodes commit e2eb7648b77b2e5910d4352bbea97b16cd89cf3e Author: braney Date: Wed May 17 15:13:02 2006 +0000 make removeX's generic commit dbb491d7afa0afc766c825fc7daf234f7222646e Author: braney Date: Wed May 17 15:12:32 2006 +0000 comment some stuff out, make version strings inheritable commit 934e05433c3ec6fe0271477922b8867554965064 Author: hiram Date: Tue May 16 18:16:17 2006 +0000 Properly display itemRgb column data on BED output commit d852c7ec06f2e8ee2937056f74691a3f36306b31 Author: hiram Date: Tue May 16 18:15:42 2006 +0000 Properly display schema and sample rows for DB custom tracks commit ce43bd5f4c8568ac6c0046167e79afd3a62ce3c3 Author: hiram Date: Tue May 16 18:14:57 2006 +0000 Missing a cloneName argument in a warning printf commit cb82e7bcefb4185f26141780afa850c52d1c18c5 Author: angie Date: Tue May 16 18:13:50 2006 +0000 Resolved -Wall warning: unused variable. commit dd6c7068cfffd291ddb9614af376086a34469bb7 Author: hiram Date: Tue May 16 18:13:39 2006 +0000 Now loading directly from Internet through pipe to hgLoadBed, no trash intermediate file commit 9290f3eeb71f13ce6c92e870347aaa1cb1716acc Author: hiram Date: Tue May 16 18:12:10 2006 +0000 No longer any need for the data file in trash, straight through a pipe to the DB now commit 8e746dfe0ccc693bcd6b1b50d0b442f31fa6c843 Author: fanhsu Date: Tue May 16 17:44:22 2006 +0000 Updated ensGene table to change hap chroms into ref chroms. commit 9d0b4eafe674ade70146b627cb4c0613ccc14cc4 Author: ann Date: Tue May 16 17:21:12 2006 +0000 added block for chain to Hg18 (including matrix variable) commit c79dba10a7afdd2baf29fe73df3d2fa659f8c70d Author: hiram Date: Tue May 16 16:48:20 2006 +0000 Updating picTar track status and adding one to Mm7 commit f526c86598acf9fdb7462a8016fe4d35c98eae7f Author: hiram Date: Tue May 16 16:36:03 2006 +0000 Adding picTar miRNA tracks commit f9adb9e6b7427d7534301965239fdcc92f85bab6 Author: galt Date: Tue May 16 15:00:18 2006 +0000 "Encode release log update" commit a1c7caa36dae9962640d3b8573fa802bb08f3485 Author: galt Date: Tue May 16 15:00:17 2006 +0000 "Release log update" commit 160b485e671599f5b87d03daa8ef994ea293488d Author: giardine Date: Tue May 16 14:45:10 2006 +0000 Updated tables to allow attributes to link internally and externally. commit f532a3fc1bcdb47304f191de9cdeee2a32e027a8 Author: baertsch Date: Tue May 16 05:48:14 2006 +0000 remove cgiClustalw commit 19796f57c9530597542613bb9b141f087a68e124 Author: galt Date: Tue May 16 04:35:11 2006 +0000 lastest script version various changes commit 05fc6ca30fa1afb8141d7c013bdd41279adbadcc Author: genbank Date: Tue May 16 00:46:59 2006 +0000 removed special settings for refgene and est tracks on MGC commit cfb47a3eb5d344e3037670db384f6401258b1fa1 Author: hiram Date: Tue May 16 00:01:31 2006 +0000 Add tmpDir argument to get temp file creation over in trash and unlink it when done commit e2dad7289e71ea11f775c4d5cefa9c2630f633be Author: hartera Date: Mon May 15 23:34:45 2006 +0000 Loaded human hg18 Blastz psls into database and checked for human contamination in danRer4 genome sequence. Documented adding trackDb entry and description html for Human Proteins track. Finished multiz 7-way alignments. Started phastCons run to make most conserved track. Made mafs from reciprocal best net. Downloaded BAC end sequences for BAC end tracks. commit 68490618ae7613e416de79423e7451b2ff8576db Author: rhead Date: Mon May 15 23:18:44 2006 +0000 moved dm2 pointer to hg18, mm8 and danRer3. commit 4ce3442f0d9f0aa9bece8df0e270062d6f608f67 Author: angie Date: Mon May 15 23:17:34 2006 +0000 Added galGal3. commit f67bef61e157111c290f77553dbc9d9b5567984b Author: angie Date: Mon May 15 23:09:23 2006 +0000 Initial description for galGal3. commit 8d0369c990c776757109c813510fa22c9ce87be6 Author: hartera Date: Mon May 15 23:08:43 2006 +0000 Finished Pseudogenes track. Update of UNC FAIRE peaks subtrack data. commit c6e9eecde0ef5fa4972675c2a8ee540f18133fac Author: aamp Date: Mon May 15 23:03:52 2006 +0000 Turned next-item button on for known genes. commit f957facaff774ba76f3481f8a41e8305f4d04dfc Author: genbank Date: Mon May 15 22:58:34 2006 +0000 added mgc tracks and database commit e3dcb5741548c51ea6679bdfd94604a7d51eff9c Author: aamp Date: Mon May 15 22:49:43 2006 +0000 Merging Andys_button branch with trunk. commit 5f00d83b83c5eedb76c84c4c0d4b5b692ab93bd5 Author: markd Date: Mon May 15 22:31:00 2006 +0000 enabled alignments of monDom4 commit 1de737ec2f4c936c28ad2aef39699e4bca709eb2 Author: hiram Date: Mon May 15 21:12:43 2006 +0000 Starting liftOver creation to Mm8 commit 648bc0541b234ebcbe9d91f23b5b9b1de5ceef55 Author: hiram Date: Mon May 15 20:45:30 2006 +0000 Indicate that appropriate disk space should be verified commit 47be21dcda01fac7c49640ec171a0f23aa4a65ad Author: hiram Date: Mon May 15 20:42:19 2006 +0000 Better filenames on the gensub2 operation commit 17d9b71ec357292270e11e92878d9bec5b3e445d Author: hiram Date: Mon May 15 20:41:36 2006 +0000 Better file names on the gensub2 operation commit b4f5250317edf82a5e8fc9e95d94ce5e88e89b6c Author: baertsch Date: Mon May 15 20:37:37 2006 +0000 minor edits commit dab6219e0d96e144c327eab5e244069280f63563 Author: baertsch Date: Mon May 15 20:35:48 2006 +0000 multiz and conservation commit 4264c084caaa480af8fdef3636ab43f8517e12b4 Author: hiram Date: Mon May 15 20:27:09 2006 +0000 A correction to bigZips procedure commit fdc46f402ee75b5af485e66304dd16fa4fd93da7 Author: hiram Date: Mon May 15 20:26:26 2006 +0000 Added bigZips and chromosomes downloads files commit 1ebdc5e55fee979bce1748b408d7cd7d8a59c6af Author: ann Date: Mon May 15 18:44:41 2006 +0000 fixed canonical typo commit 052e8a7de57cdaba7b5defc8a9febb369293917a Author: hiram Date: Mon May 15 18:35:12 2006 +0000 This should have been checked in long ago to correct the compile target commit c04fe6048f4381411e3a69adbeab991de1f2588a Author: kuhn Date: Mon May 15 17:45:24 2006 +0000 added date to affyMOE430 track commit 91a57f6f0acfd0c47aa18560e8756cd102e286cc Author: galt Date: Mon May 15 15:00:02 2006 +0000 "Encode release log update" commit d51895c833271c8678d156105096477d84dcba85 Author: galt Date: Mon May 15 15:00:01 2006 +0000 "Release log update" commit 8e6ffaba61b84f5cc06ae04bfe1b2f1c477861e2 Author: galt Date: Sun May 14 21:05:32 2006 +0000 fixed bug - suppress expansion of search terms by passing FALSE. This bug has been there for more than a month. Jim found the fix commit b1f16b17fa99cc89a9ae611d3ef665a1503e5e23 Author: genbank Date: Sun May 14 15:56:11 2006 +0000 ops, rename droEre2 -> droEre1 commit 2b1b044154b30d56d0540b3118f19446873ebefd Author: genbank Date: Sun May 14 15:54:51 2006 +0000 disabled droEre2 on hgwbeta commit a3bad3b1f231ce73805d08842e7668ff06445bdb Author: galt Date: Sun May 14 15:00:12 2006 +0000 "Encode release log update" commit 73705a2fea0358d1205424d21efa7de554d7a9b2 Author: galt Date: Sun May 14 15:00:11 2006 +0000 "Release log update" commit caff1a6bd9e8b8114fd400dc10b3a2097e8eb8f9 Author: kuhn Date: Sat May 13 19:20:41 2006 +0000 turning on some assemblies now synced up commit 1c89e509aaa1054c2a6ea4ef1b0cddac08b39548 Author: galt Date: Sat May 13 15:00:17 2006 +0000 "Encode release log update" commit 436b04e330b18d0313a57f2b58fab57f89f165d1 Author: galt Date: Sat May 13 15:00:16 2006 +0000 "Release log update" commit 796a3927d3fcb53c90a10e7f122baa3cebaddca6 Author: markd Date: Sat May 13 06:45:35 2006 +0000 created missing nets commit 93e85ecac941ea558443b17a41908aeaa74b8725 Author: markd Date: Sat May 13 05:39:56 2006 +0000 prevent SIGPIPE, consume remain stdin in input is on a pipe commit db880785d8213a9cbcb572fa961321c99a1b3a37 Author: markd Date: Sat May 13 05:39:09 2006 +0000 added function to test if an open file is a pipe commit 3414bcf8bd11314f296ea261cfe03a72a70a5bd7 Author: jsp Date: Sat May 13 00:32:21 2006 +0000 Added EvoFold track. commit a83af44229e1718791e3e93a117000584f340f20 Author: jsp Date: Sat May 13 00:31:02 2006 +0000 Updated references and alignment info. commit f18c14733473863ff0ecc32a138b753bf64bd891 Author: kate Date: Fri May 12 23:55:01 2006 +0000 First cut of custom track manager. Partly works commit b8bc6bac9819c03dcbb3810816691a9395dafa8b Author: hartera Date: Fri May 12 23:12:59 2006 +0000 Extended termRegex for sgpGene search. commit 193028b483516452cdee6871356fb167c28bc9fb Author: hiram Date: Fri May 12 23:08:10 2006 +0000 This appears to fetch data from a database custom track commit 2f7cfd19bf8f48e4bc76f521c13e9c3f72dc1185 Author: hiram Date: Fri May 12 22:27:49 2006 +0000 Now doing custom tracks from database for bed types 3 through 12 commit 89bb5df505dbc846a35f3e32f350c1e5b4871b97 Author: hiram Date: Fri May 12 22:26:14 2006 +0000 Cleaned up debug printfs, now working for bed types 3 through 12 commit 93ca99bf637b9ca942c800df600eeb29ac06793c Author: angie Date: Fri May 12 20:50:18 2006 +0000 Oops, needed to check for NULL ctNew in previous fix (ctNew is not created until we get results). commit 575b9fb67f0d52d7b86d30a749b033ecdae2b843 Author: hiram Date: Fri May 12 19:34:59 2006 +0000 Better error message on bad coordinates commit b2a45d6c0e1f2f326249b2f403da563afd22fe36 Author: hiram Date: Fri May 12 17:50:19 2006 +0000 Add customTrash database connection function commit 2f68339f20b8a145615815148d9876023e6ca2e5 Author: hiram Date: Fri May 12 17:49:50 2006 +0000 Now reading custom track data from customTrash database commit c611d40fbac8d47b5728d399701112ce431df8c8 Author: fanhsu Date: Fri May 12 17:46:20 2006 +0000 Added ensGene. commit 3ac1ebb55a7d42b8f77a5fb22f94c658a027e2bf Author: galt Date: Fri May 12 17:26:54 2006 +0000 jim wants to include more in case mm8 and hg18 were not having as complete coverage? commit 57dc138481ed2d7b6cc47ffb9c7be456a9b78e22 Author: kuhn Date: Fri May 12 17:10:44 2006 +0000 changed name of chainMm8 track to Mouse (was Zfish) commit c611b94767637ff6702cb03725a2cd0575df556e Author: galt Date: Fri May 12 15:00:11 2006 +0000 "Encode release log update" commit 3217276cbc36e8f6fed9397f5c69269982a64c10 Author: galt Date: Fri May 12 15:00:10 2006 +0000 "Release log update" commit 65ce74d29edb1ea0851d3b420091700b566c83af Author: markd Date: Fri May 12 06:35:15 2006 +0000 added support for align but don\'t load commit 6baf1d58694b5ab8e4e37fe7f1345c890eeb40e2 Author: kuhn Date: Fri May 12 01:12:53 2006 +0000 added some assemblies for turning on tomorrow after a database sync commit b00f6d5536f43b3c211bf97bd3da5dc3ac9ff28d Author: kuhn Date: Fri May 12 01:06:51 2006 +0000 turned off several updates on dev and beta so the tables can be pushed en masse as needed. several have been running for 2 or more months. commit 0c4c35ef66f83cd564e0995eb72952fb107f4133 Author: kuhn Date: Fri May 12 01:02:29 2006 +0000 turned off several updates on dev and beta so the tables can be pushed en masse as needed. several have been running for 2 or more months. commit 02ae5e5c401c7ca376c25c371e01741e7ca51e55 Author: hiram Date: Thu May 11 22:31:52 2006 +0000 Need to keep track of maxChromName for loader commit 490513458e6bf85042eb98f2e052b30b2688f1a5 Author: hiram Date: Thu May 11 22:31:24 2006 +0000 Now running loader directly, proper error messages on errors commit bc46a78a0e8f9e8c8e79435eac6412d87cf1e279 Author: kuhn Date: Thu May 11 21:53:08 2006 +0000 moved mouse pointer to mm8 commit 3190680aae3f96d53bf27881bac1c7bce5d56e8a Author: markd Date: Thu May 11 20:35:57 2006 +0000 added native refseqs commit ddfa19899e09eb3f9c3b096848e46fbd4fb7335a Author: markd Date: Thu May 11 20:12:09 2006 +0000 enabled refSeq for bosTau2 and xenTro2 commit b9a1c08c130e0f24d4b7e550b4cb02afb3f96779 Author: ann Date: Thu May 11 19:36:10 2006 +0000 copied from /human then edited commit 23cff3102e57be7e9eb6a48ab64819c513624683 Author: baertsch Date: Thu May 11 19:07:43 2006 +0000 fix spelling dog syn net commit ee3a816e72f2bdfb0eaaf9f28a00b778a6332f48 Author: ann Date: Thu May 11 19:05:31 2006 +0000 set Softberry link to open new browser commit 09788a91afea8de3824eca1da29e0b8df5a68eb4 Author: hiram Date: Thu May 11 19:05:21 2006 +0000 Remove warnings about unused variables commit 3787782a9fae12980f27d3404d32e8ccf6ee5de2 Author: baertsch Date: Thu May 11 19:05:00 2006 +0000 added dog syntenic net commit 6042ec6f2210d9bedfcc7172b0d34e531047ee6e Author: hiram Date: Thu May 11 19:04:10 2006 +0000 Added option to specify the maxChromNameLength to avoid chromInfo references commit 019266df8c5603d2f59331f8c52013ecd561825e Author: hiram Date: Thu May 11 19:03:27 2006 +0000 Now loading custom track data into database commit 708ba5eef0f2f1caa82fb9229cffcaf94dcaaaaa Author: hiram Date: Thu May 11 19:02:44 2006 +0000 dbDataFile and dbDataType commit 1f5c4f377fc1ffe3139a3b75d41d246a17d81f00 Author: ann Date: Thu May 11 19:00:59 2006 +0000 moved down from the top level. commit 1f4e3f68b327105fedc018f4188316f740acee60 Author: ann Date: Thu May 11 18:57:23 2006 +0000 removed link to Exoniphy commit 8bf6c5d3cd16639e6d1b04085fa07170f294f778 Author: ann Date: Thu May 11 18:51:00 2006 +0000 added separate rules for identifier estOrMrnaAccession for hg18 and mm7 commit 1395dc8934c45fd66c4eef995b22302f3456599f Author: kuhn Date: Thu May 11 18:33:22 2006 +0000 added '_random' to two chrom names commit c0491b09f508bfafb31623d71f700094d14b1a1b Author: ann Date: Thu May 11 18:08:18 2006 +0000 switched the multiz17wayAnno track to point to phastCons17 wiggle (the other table is missing) commit aecc8154ac5583bc96d3ba43358750a1c310a79e Author: baertsch Date: Thu May 11 17:55:43 2006 +0000 rename human net to hg17 net commit e7b5f9418c4dcf08debf15e63c0483905d873450 Author: ann Date: Thu May 11 17:47:09 2006 +0000 added sort to liftOverChain check commit bb701a5f7b843403435f4892f8d77666d906d97c Author: galt Date: Thu May 11 17:14:27 2006 +0000 setting to latest mouse and human commit 53e01c0d9d0d6c74bd7747f93f3378effaf37e05 Author: ann Date: Thu May 11 16:55:16 2006 +0000 added note about dropping geneidPep table commit 0c37f5ae1925424673109f8cb9adb3b483917122 Author: ann Date: Thu May 11 16:42:26 2006 +0000 put Kayla's name first for mm8 credits commit 86d593cfb37939c83b42f985b767f465e0f7da8e Author: markd Date: Thu May 11 15:32:05 2006 +0000 added extected results for new test commit cba56489a6528f9a669f31a4b8076c591eab1d3a Author: galt Date: Thu May 11 15:00:21 2006 +0000 "Encode release log update" commit 413fa3f5f71750fb9e19cf61815ba01fd6b5f950 Author: galt Date: Thu May 11 15:00:20 2006 +0000 "Release log update" commit b44a2fbcb67bc9d168d00eed0cfcc4bd414367ab Author: markd Date: Thu May 11 05:57:51 2006 +0000 handle ancestor browser with no gbCdnaInfo table, also allow for accessions in transMap track where the genbank entry has been deleted commit 869435d7615bf7d5b6b881ddb62a75db0e7380dd Author: markd Date: Thu May 11 00:59:08 2006 +0000 fixed difference in expected results causes by something I don't remember (how lame) commit 2087c4068b5fb82b509fc8c4cf4714c483d796b6 Author: markd Date: Thu May 11 00:57:18 2006 +0000 added test case commit 8bc8a876a72a1d966ba0c6d1b23e4b7742512607 Author: markd Date: Thu May 11 00:56:53 2006 +0000 clean up usage message commit df06630dcd5deedfeeec7f04988f6c596d9299e3 Author: markd Date: Thu May 11 00:55:50 2006 +0000 fixed a typo commit 7251e613e7fd067c5885876786ee5b4b7a99d257 Author: markd Date: Thu May 11 00:55:22 2006 +0000 allow loading multiple genePreds commit c32121fb77d18ba4bf89386c827010cb942f59a7 Author: markd Date: Thu May 11 00:54:51 2006 +0000 improved error message commit 58c4d8e5a9dc6c23dbaffded8e55791111aef1ff Author: markd Date: Thu May 11 00:54:12 2006 +0000 create panTro2 swapped alignments commit c3eb418201f9aaffc4aa8581dc9db06884271dda Author: markd Date: Thu May 11 00:53:25 2006 +0000 fixedfix problem enabling codon coloring on genePred tracks commit 9cd6bbd0d15e8ca7d0fd4082fb6d560491a3143f Author: markd Date: Thu May 11 00:47:36 2006 +0000 allow compressed files as input commit 80f87c08010cf99dcfbe63116286169f71457b29 Author: hartera Date: Thu May 11 00:13:57 2006 +0000 Changed name of MGC track to ZGC (Zebrafish Gene Collection) for zebrafish browsers. commit 319e9eaa5f73282d2d2388ed8e834e85e483eca4 Author: hartera Date: Thu May 11 00:13:07 2006 +0000 Description for Zebrafish Gene Collection (ZGC) track. commit 4ace19c1f5af0b95062bb4b035b8d46e6a329fe3 Author: hartera Date: Thu May 11 00:12:36 2006 +0000 Removed duplicate lines. Added Alignment and Conservation track entry. commit 845f09540a0a674e14763a5e31aa43fa845bbb5f Author: hartera Date: Thu May 11 00:11:26 2006 +0000 Removed duplicate lines. commit fbf6df480bf6aa6401a82259530b4050909307e9 Author: hartera Date: Thu May 11 00:09:13 2006 +0000 Corrected typo for track labels. commit a9d7f7018e514736b99e2dd0d1f9b2a1527012b5 Author: donnak Date: Thu May 11 00:08:38 2006 +0000 Fixed a typo. commit c4b3d1566a5614b22556679c0943ae4c6ec6421f Author: markd Date: Thu May 11 00:06:20 2006 +0000 enabled danRer4 auto alignments commit 211f97061665d3fbe710d75e5c50661edad03585 Author: galt Date: Wed May 10 22:36:04 2006 +0000 added visiGene new tables/structure commit 14c0ef9039953192af7228a4422effac65ad4cdd Author: mario Date: Wed May 10 21:30:02 2006 +0000 added augustus abinito track commit 81a6a8c8b7d83c02e69ef3209892ad24253e69ca Author: braney Date: Wed May 10 16:36:53 2006 +0000 add cat and platypus commit 4eac20433a8e32a79964ec59f8cb635abaa17194 Author: braney Date: Wed May 10 16:35:21 2006 +0000 fix up species names in buildMaf commit bbcc3308816b655d4eefa25ec5dc6306b4898826 Author: braney Date: Wed May 10 16:34:33 2006 +0000 change borEut13X to borEut13 commit 0060bdec6710b91a0280bd58e28126099154609c Author: galt Date: Wed May 10 15:00:22 2006 +0000 "Encode release log update" commit 5c8beb1a091ad3e730255185e97d7d4756ae8515 Author: galt Date: Wed May 10 15:00:21 2006 +0000 "Release log update" commit 1895e6770393400e6588820b418cd5ba01b105dc Author: angie Date: Wed May 10 14:28:00 2006 +0000 Resolved -Wall warning: unused variable. commit 3e0114338c642565c256430b9e7001ad7708a322 Author: donnak Date: Wed May 10 08:10:37 2006 +0000 Edited/updated the gateway text. commit 2638088c9aeb11d60de6d6be6ec7aa7014c37c77 Author: donnak Date: Wed May 10 08:10:14 2006 +0000 Archived a news item. commit 42d1eac9a3c5a717fc71ef4af90a44fd1fd481b7 Author: donnak Date: Wed May 10 08:09:57 2006 +0000 Added news item about mm8. commit a8b9a9173cbd9fb4dd937047e0ef8c360b912d0b Author: donnak Date: Wed May 10 07:37:39 2006 +0000 Added mouse information from Deanna Church. commit 44c7c23f88c072a817c7706794fc5d9fdeb59c92 Author: kate Date: Wed May 10 00:30:24 2006 +0000 Remove useless indexes commit 5754d7e6ce21e84a8e3fde67bc776995b09ff0ca Author: hiram Date: Tue May 9 23:38:58 2006 +0000 Correct usage of cd ...; make commit bab74fc1886b9655cbd4127d6d33f26c684c514d Author: hiram Date: Tue May 9 23:37:51 2006 +0000 Correct incorrect usage of cd ....; make commit 3608e1dbfd7ee13c537b634e770aaad8f18e9698 Author: hiram Date: Tue May 9 23:30:29 2006 +0000 Corresponding definitions for database custom track type commit ec60b25d015804736737e95105b012eb939b19cb Author: ann Date: Tue May 9 23:25:17 2006 +0000 added block for geneid commit 36f8c9e23484e4923d6a6cd1e91319b8e4e052a6 Author: hiram Date: Tue May 9 23:21:23 2006 +0000 Beginning to recognize a custom track asking for a database commit 9512f34180ce7aeb8df8fb8a61e7df2adc11878a Author: kayla Date: Tue May 9 23:07:05 2006 +0000 added mm8 commit 61fc49fac30bbc16e401e6a97208350d5e42e8d1 Author: angie Date: Tue May 9 22:34:44 2006 +0000 In redirect to Genome Browser after making a custom track, use hgsid in case cookies aren't enabled, so that the custom track is not lost. commit 83d9769bd12314542527ff29a145980c3598be29 Author: hiram Date: Tue May 9 22:25:34 2006 +0000 Improved searching for geneid track commit b9e484102fa4878df8e30ac5624b46ffba1e2132 Author: kate Date: Tue May 9 22:12:28 2006 +0000 Fix tables dropdown for conservation track in TB commit 424ba775fe4757838ab5aa0d41a5607590f5de8e Author: hiram Date: Tue May 9 22:11:17 2006 +0000 Fixed geneid protein business commit f54724b64963ae6ea0a32c44288d131595b3ad8f Author: kate Date: Tue May 9 21:08:23 2006 +0000 Move conservation wiggle dropdown to top of config page commit 2d645fd473bf880c2b9f0829329cd3ba3048b15e Author: hartera Date: Tue May 9 20:47:24 2006 +0000 Removed ambiguous reference to data freeze. commit e81e7a9febc3fb5ed5ddd2ddd759f2bb7b2cd657 Author: donnak Date: Tue May 9 20:27:57 2006 +0000 Fixed date on mm8 release. commit 67c0cfe5b36a77817b34193f09187acb5915ce6a Author: donnak Date: Tue May 9 20:22:05 2006 +0000 Added mm8. commit d21b88d47cb49196ef6891ace8a9918c9da9007b Author: donnak Date: Tue May 9 18:38:59 2006 +0000 Created this new file to describe the newer KG II process. commit 3bf203d690c255f0b854ac998a779f095dd6ec23 Author: angie Date: Tue May 9 17:24:13 2006 +0000 Relax minCheck on $gbd.ceBlastTab.target. commit 89d15081808c238e3436ede5d87449e935e4aefb Author: ann Date: Tue May 9 16:58:12 2006 +0000 added windowingFunction line to Conservation block. This sets the default to 'mean' for the wiggle. commit 702f2b29d5e7afa532514b419823ae58d314b89a Author: ann Date: Tue May 9 16:40:22 2006 +0000 added windowingFunction line to Conservation block. commit e5f587887157f116fb651a7bef1c3f87b8405a77 Author: galt Date: Tue May 9 15:00:18 2006 +0000 "Encode release log update" commit 7426580b76ebcfb1ee325d349ca24532942e174f Author: galt Date: Tue May 9 15:00:17 2006 +0000 "Release log update" commit 2b27ae50fe06bdfbffb15f7f0ab5309a114426db Author: angie Date: Tue May 9 14:36:05 2006 +0000 Resolved -Wall warning: unused variable. commit b468641be1ca99e9340777429de5f48ae36f73f1 Author: galt Date: Tue May 9 07:40:26 2006 +0000 new build system with separate local disk sandboxes for hgwbeta and hgwdev commit 8e39f11fcb2dfa569d0b4461e29695e9223377be Author: braney Date: Tue May 9 04:43:15 2006 +0000 add some stuff commit b3f588ab9ad4105208f34205160b9977b1a20252 Author: braney Date: Tue May 9 04:42:49 2006 +0000 add some chains commit 49d45d61dbbae749040a87acbae0831ae68c5fbe Author: braney Date: Tue May 9 04:41:35 2006 +0000 add borEut13 commit 4ca4e6fd241ac53b368e3d43317b99c6fef60299 Author: galt Date: Tue May 9 03:01:31 2006 +0000 making 32/64 bit happy commit 7de66131857f882fdddc139122859fef9791edf9 Author: galt Date: Tue May 9 02:43:48 2006 +0000 fixed so compiles with lib/liftOver.c commit cf95612e263c8ee94adcd7a1ba24747506d7f7bc Author: galt Date: Tue May 9 01:49:42 2006 +0000 fixed warning about type commit f197334735b0761267fe33fa8c4766fc47ec36b6 Author: galt Date: Tue May 9 01:08:21 2006 +0000 "New version number v133" commit cdf0c927bfba189840cadd7cd7503c0c00494545 Author: markd Date: Tue May 9 01:05:55 2006 +0000 fixed warning with -O3 on x86_64 commit 232db95dcf905b500ec32af20cfd2157b1c328cf Author: kayla Date: Tue May 9 00:33:31 2006 +0000 changed to nets/chains with mm7 say "$o_db" and mm8 say "$o_Organism" commit 3b0379eb33cb68b726ded6818162beb5771aed1b Author: markd Date: Tue May 9 00:18:31 2006 +0000 added organism labels to transMap mRNAs commit f5dbdc6bdfbc070990586415a761f01fde7bf885 Author: markd Date: Tue May 9 00:16:54 2006 +0000 added transMap aligment tracks commit e839847734a60f981cb5c939ac88362a45ace0b1 Author: kayla Date: Mon May 8 23:50:52 2006 +0000 changed net/chain mm8 to $o_Organism commit 13cb0c253574c6cff36f0e08de7fd20587d9e5e6 Author: kate Date: Mon May 8 23:37:31 2006 +0000 Add support for alternate conservation wiggles to wigMaf type (Conservation) tracks commit b9a17c18b0c856262cfbb630ff872d633492cfd5 Author: kayla Date: Mon May 8 22:37:15 2006 +0000 Changed nets/chains with mm7 to say Mm7 instead of mouse commit 19d6cf8f64a74ad8223189c8c305de68b7fc5740 Author: angie Date: Mon May 8 22:36:03 2006 +0000 Added bdgpExprLink (in situ images for hgGene). commit edd5ddc45de48c81d26f3c1db8032ff7521c98c9 Author: aamp Date: Mon May 8 21:23:34 2006 +0000 Forgot to commit this. commit 361fa1644e57fb80e7737f85ce1350cd790bdef7 Author: aamp Date: Mon May 8 21:18:01 2006 +0000 Made liftOverPositions more flexible. commit 124af0b731df8b29cb288951b2098c3387665a14 Author: fanhsu Date: Mon May 8 20:25:16 2006 +0000 Added KG section. commit 3179fa47187f739d14aad8ab3dfc95fcee3200db Author: fanhsu Date: Mon May 8 20:22:59 2006 +0000 Added knownGene.html. commit 6315674e2c05add584ea4e14d8fe66b9a56cf712 Author: fanhsu Date: Mon May 8 20:21:38 2006 +0000 Added reference to the KG paper. commit 5951918c5d8f6cdf4d69abaedc4cca0ba99b7961 Author: fanhsu Date: Mon May 8 20:11:00 2006 +0000 Added reference to the KG paper. commit e8bdffc3667922d3333ae5a3dd1959c4abd7d6c5 Author: fanhsu Date: Mon May 8 20:08:15 2006 +0000 Added reference to KG paper. commit 94fce2d500204bcb5ea1847cc2402acb25f5bd07 Author: fanhsu Date: Mon May 8 20:07:21 2006 +0000 Added reference to "The UCSC Known Genes" paper. commit 43ce6778a604b94d91fd51274170e776aeed5ab3 Author: markd Date: Mon May 8 19:51:02 2006 +0000 store mapping alignments in a range indexed object. 5x speedup when using chains commit 19e34ae74da8b28c1c1647797efab90b50ff8792 Author: angie Date: Mon May 8 19:39:56 2006 +0000 Added stsMapAliasMrnaAcc: semiShortCircuit on only those STSs that might also have mrnaAcc matches. Original additive STS search is now named stsMapAliasComprehensive. commit 1c67640dbcc797839627980297decb1a96179545 Author: hartera Date: Mon May 8 19:00:41 2006 +0000 Added missing comma. commit 451fc4ad6561223458d75c45263cc25a85228b09 Author: ann Date: Mon May 8 18:57:05 2006 +0000 changed list of species which are on by default in Conservation track commit 14ac6aa03e4678751e8ca08a7e5f209762c1ebac Author: hartera Date: Mon May 8 18:56:15 2006 +0000 Added name index as for bacEndPairs table. commit dd91bfa981e45af32effc22d23dd279303f68a3b Author: ann Date: Mon May 8 18:49:56 2006 +0000 edited list of species that show by default in Conservation track. commit a0b24c8fed41b6313329f5f2efe3451dfcc8d9cb Author: kate Date: Mon May 8 18:34:38 2006 +0000 Added new chimp assembly commit e648419592d2a360aca037979b14ccc08a6bf42a Author: donnak Date: Mon May 8 18:18:25 2006 +0000 Added links to chain & net formats, added html-ized draft of Brian's new MAF parameters -- the MAF example needs an update to incorporate these. commit 9084843068fb1d26702718d4b034ea0859483acc Author: kayla Date: Mon May 8 18:17:54 2006 +0000 reenabled mm8 updates on hgwbeta commit 9ad56d68bbcf5be7c34986d1e7a08d03cab42760 Author: galt Date: Mon May 8 17:14:55 2006 +0000 added contributors patch to allow search for "mahoney" commit a34681c5758359eb00d6f482e028f23d4f20bf00 Author: fanhsu Date: Mon May 8 16:34:01 2006 +0000 Added comments on blastz run of hg18/loxFr1. The swap was not successful. commit 74315ddfc8886e4ee71abce44eb033c98e77921b Author: angie Date: Mon May 8 15:35:20 2006 +0000 Resolved -Wall warning: unused variable. commit 92add915341fe3dc096eeed078ddcb39f7f84db3 Author: galt Date: Mon May 8 15:00:12 2006 +0000 "Encode release log update" commit 1dd3fed5ea42f2ad6148af1379356ecd3c40cdf5 Author: galt Date: Mon May 8 15:00:11 2006 +0000 "Release log update" commit 38fbf3f923028073cd94d33fa23fa16d5dbcade3 Author: markd Date: Mon May 8 14:50:42 2006 +0000 3x speedup by RCing input instead of mapping psl that can be build from chains commit 06e86e0be7dc8b61701beaa017b9dbbcfc68d3a9 Author: aamp Date: Mon May 8 09:43:36 2006 +0000 Added a button for use later with the next-item stuff. commit f15caf9797cfeb2003161999c64894d751303721 Author: kent Date: Sun May 7 18:21:55 2006 +0000 Testing binKeeper. commit f22afac482e4bfcf97e90baffdb7df1e8c8e6004 Author: kent Date: Sun May 7 18:20:58 2006 +0000 Changing some atof to sqlDouble (better error checking). commit 4c354d62fca8b094d7ed5a07407c07a741926027 Author: baertsch Date: Sun May 7 17:40:52 2006 +0000 fix wiggle name in conservation track commit 3fa4e32dcfd6fb482dd002a23062c997e3aa982d Author: baertsch Date: Sun May 7 17:06:48 2006 +0000 add refGene and phastConsElements commit 2e2e9e206ae56d9c0f2595f55c662861c9e23714 Author: galt Date: Sun May 7 15:00:13 2006 +0000 "Encode release log update" commit 5fc6ceb55e51456a8cb5a024a965abd440907136 Author: galt Date: Sun May 7 15:00:12 2006 +0000 "Release log update" commit 004677be09c379f7948d7bdb5086e42b9c503c97 Author: baertsch Date: Sun May 7 04:03:54 2006 +0000 description for multiz 5way commit 25253bad0394386a517722bf5ad1edf2b16e2997 Author: baertsch Date: Sun May 7 03:57:19 2006 +0000 add conservation track for rheMac2 commit 90cbefed129a0975a35df3bfa405f984af86d9df Author: baertsch Date: Sun May 7 03:49:56 2006 +0000 added multi5waySyn and downloads commit 58cf504595ab95c515124fa1ca1dd5c4ff0a9bab Author: markd Date: Sat May 6 22:39:32 2006 +0000 created missing net files commit 2a7b7fab15d0cf8e07398cd8712b16ba84f2aee4 Author: kent Date: Sat May 6 19:09:52 2006 +0000 Starting to implement a two sample T test based on Student's T distribution. commit 6c48e8a5d3fa95c93964ddf503cdfe253d5dadfc Author: galt Date: Sat May 6 15:00:18 2006 +0000 "Encode release log update" commit d3353b08f2514a668042e3c82299c8fefe8009ca Author: galt Date: Sat May 6 15:00:17 2006 +0000 "Release log update" commit f6ae481c176c9257897a3e150b2191390c51e532 Author: hartera Date: Sat May 6 00:18:12 2006 +0000 Added matrix for tetraodon tetNig1 chain track. commit 53a8f26a6afbe297ffc02bd815f78883bdc997bf Author: hartera Date: Sat May 6 00:11:10 2006 +0000 Added matrix. commit c4d630fe8ce52ea23996c4dbe98bbc6d5179077d Author: hartera Date: Sat May 6 00:08:57 2006 +0000 Added fugu fr1 chain track. commit ad052412bc6420ead95ccfbc9d815a5365d70570 Author: hiram Date: Sat May 6 00:05:45 2006 +0000 Beginning to parse more clones commit 45409bccfcba731f8741591821d204f232d09425 Author: hartera Date: Sat May 6 00:03:01 2006 +0000 Added HoxD55.q matrix for tetNig1 chains and added mouse mm8 chain track. commit f4104430f50449d48edcecf1ff6e4a3c00d86703 Author: angie Date: Sat May 6 00:01:26 2006 +0000 wikiLinkUserLoginUrl and wikiLinkUserLogoutUrl now use hgsid to formulate links to our wiki extension pages that return the user to hgSession automatically. hgSession links to wiki in same window instead of in new window so user doesn't have to manually return to the original window. commit 540db71672a5647cc58de75d3ea64ba4e7a8b658 Author: hartera Date: Fri May 5 23:54:45 2006 +0000 Mouse mm8 chain track description. commit 6630a0a5a1e7c38fc5f98d4dc6b1aa3fce855417 Author: hartera Date: Fri May 5 23:51:47 2006 +0000 Added matrix. commit 6472cb99ea484694abbe43a75b2aed12e669465a Author: hartera Date: Fri May 5 23:39:46 2006 +0000 Added that no lineage-specific repeats were used for the Blastz alignments. commit d5a4bf9a091c626fb538e25426d4f157388884c4 Author: hartera Date: Fri May 5 23:37:34 2006 +0000 Minor edits and added that no lineage-specific repeats were used. commit 1e3bfb06f7c2acd88e36d3b5f88a125b50017ffc Author: hartera Date: Fri May 5 23:33:51 2006 +0000 Description for fugu fr1 chain track on zebrafish danRer4. commit 4dba255a208478e21e8236e0e6546e1336b4993d Author: hartera Date: Fri May 5 23:24:57 2006 +0000 Description for tetraodon (tetNig1) chain track on zebrafish. commit 3306365b5778351237affec3d3a8c6c01b70951c Author: hiram Date: Fri May 5 22:58:25 2006 +0000 Initial copy of Heather's original script commit 1a54e2e2690ca8c3608aa1ede0666c48cd940f53 Author: ann Date: Fri May 5 21:38:07 2006 +0000 changed Conservation track back to visiblitiy of pack commit 880264da52635e377a1b41cc8061a701aaffab9a Author: fanhsu Date: Fri May 5 21:26:30 2006 +0000 Added comment that the sgpPep table was dropped. commit a18d4c615a3e5b058fcca1abd64ba1dc06d97b43 Author: fanhsu Date: Fri May 5 21:24:23 2006 +0000 Updated sgpGene track. commit cbfcd006fee0f077922d480b5be05caea06cc97d Author: angie Date: Fri May 5 21:15:28 2006 +0000 UI improvements suggested by Kate in code review: group saving options and loading options (not by database vs. file); present options in order of how frequently we expect them to be used; use HTML tables to make inputs line up a bit better. commit 482ce76eed8a93cd99a799ca0b5862a69ddfb893 Author: hiram Date: Fri May 5 19:26:14 2006 +0000 Tuning up the multiz display commit b4ef6dfc5e88b44ff44d8db0428b9f8d157bbf84 Author: hiram Date: Fri May 5 19:25:54 2006 +0000 Order the chain and net tracks in reverse order by featureBits coverage of their chainLink table on Opossum commit 71db00c0ba3c0ba308ee3614e4663abbd4f4f336 Author: kent Date: Fri May 5 18:45:30 2006 +0000 doing some testing on chains for Wes Barris commit 3d4b7e27e2f5687142fb45bc76873c0913982d5e Author: hiram Date: Fri May 5 18:07:37 2006 +0000 Document the error in the genscan command commit ecac5917b27c6e6fd1fd4b5ef852cdc1a07385c3 Author: ann Date: Fri May 5 18:06:53 2006 +0000 changed name of wiggle table in conservation track. commit 3f15a60cc955a501ebf2b90a3de978a79f21e2e5 Author: ann Date: Fri May 5 18:06:19 2006 +0000 added Siepel note. commit 02167fe3a47249d8beb64d682be7567990719eaf Author: hiram Date: Fri May 5 16:49:21 2006 +0000 An enhanced genscan search method to allow just the contig name as well as a full genscan gene name commit 2e9fe33beb11e9d337e0803b2273c498252ae98c Author: hiram Date: Fri May 5 16:31:11 2006 +0000 Done with genscan with better gene names commit 499295091293bcb7179d2b957bbebb7604028e6d Author: angie Date: Fri May 5 16:03:48 2006 +0000 Corrected the allTranscriptQuery and oneGeneQuery to dig up the uniProt ID from flyBaseToUniProt instead of expecting to find it in flyBaseGene. commit 941975c97974b0258ee19a2330340ea3b920a006 Author: angie Date: Fri May 5 15:43:14 2006 +0000 Resolved -Wall warning: unused variable. commit 78293b98bf3f8b7ad751dadc20e02d92d89db956 Author: angie Date: Fri May 5 15:39:35 2006 +0000 Minor bug caught by -Wall: optionSpecs was defined but not used (optionHash was called instead of optionInit), so invalid arguments used to be ignored instead of caught. commit ff1828fa836f1168791b113943e64091e636eb2e Author: galt Date: Fri May 5 15:00:03 2006 +0000 "Encode release log update" commit 84cbb0219e01cbe111134cba8badedfd7e4c405d Author: galt Date: Fri May 5 15:00:02 2006 +0000 "Release log update" commit 5c4a0ac4515b60c0fdd1b1f37beb4d0457d1b6e2 Author: hartera Date: Thu May 4 23:59:14 2006 +0000 Added danRer4 to list of danRer databases. commit 41b5bcdf9f816fac811f5783e9f45bc89b681e2e Author: ann Date: Thu May 4 23:12:43 2006 +0000 changed Methods section to be similar to other chain*.html pages. commit 9fd6ea5e8b5f0ffaa19b3e155039aeb81b00cb09 Author: ann Date: Thu May 4 23:08:12 2006 +0000 added $matrix variable. commit 2cbdcebd7e6718d08f4e4603deb32490607f3a6d Author: hiram Date: Thu May 4 22:53:14 2006 +0000 Clean up some WORKING tags to be DONE, and now adding genscan commit a1581150e261814dc1fe5e7e762c3447c5ff71b5 Author: hiram Date: Thu May 4 22:52:33 2006 +0000 Reworking genscan to get better gene names out of the process commit b8ae0987f1c717ea5b5f19f09500af77c9611c22 Author: hiram Date: Thu May 4 22:51:34 2006 +0000 clean up monDom2 instructions commit 36b9f9c9a3a5398ef63ba62c154376f3f596cbcf Author: ann Date: Thu May 4 22:51:02 2006 +0000 moved chain*.html files around so that they are more generic. most moved from an assembly up to /mouse level. commit 361514720f747c2b879bfa88f259380d6585328f Author: hiram Date: Thu May 4 22:50:41 2006 +0000 Add featureBits result for chainMonDom4Link commit 2822ffe9b9a22eeb00ed1a84a6e2066e25e895b4 Author: galt Date: Thu May 4 22:40:48 2006 +0000 adding definitions for filling new tables commit 74cdcd160a47973b67ec82c22da725eed9a486b9 Author: donnak Date: Thu May 4 21:41:39 2006 +0000 Fixed typo. commit e2fd34d0d1329c63720edd0fc1b8d6ba0202892d Author: ann Date: Thu May 4 21:18:42 2006 +0000 added matrix lines for chainDanRer3 commit 288430b4d5017d7158c908ddb3ff0996217138e3 Author: ann Date: Thu May 4 21:08:27 2006 +0000 removed block for chainDanRer3. this has been moved to the mouse level. commit fe11abd6303e858ab42670d27416c66e2fba93a7 Author: ann Date: Thu May 4 21:07:45 2006 +0000 removed all chain blocks. these have all been moved up to mouse level. commit 422b2c62add2fb5705671083895d8491c8b0e1b2 Author: ann Date: Thu May 4 21:06:56 2006 +0000 added block for chainGalGal2. it was run with different params than any other assembly. commit 20af38bf9e7d213680d2b27162aa80371538510d Author: hiram Date: Thu May 4 18:41:27 2006 +0000 Can also remove the scaffold prefix which is simply scaffold with nothing else commit 5a83761be7a1871fe6f7ab785f0f2459af2495f5 Author: hiram Date: Thu May 4 18:40:30 2006 +0000 Do not allow nets to display in white commit 7ee749c7447cada3fbc9f356b7ef126e33b0bc4e Author: kate Date: Thu May 4 18:40:07 2006 +0000 Initialize subtrack visiblities from trackDb setting commit 0d53b0083ad58f1699530a57ce0c93f7282e0bcb Author: archanat Date: Thu May 4 17:50:33 2006 +0000 Updated RNA catagories commit 912c75fb5818a725bccb50f532f081fff9c22612 Author: ann Date: Thu May 4 17:18:49 2006 +0000 made huge changes to more closely refelct the changes made to this track for hg18 -- explaining the new maf display. commit f8b77cdeddec407ba040e3118fd76c1bef678d34 Author: hiram Date: Thu May 4 16:18:58 2006 +0000 Adding to source tree from mm7 build process commit f9aa66cb505c8eff5e8aa9af18448c2565bec176 Author: hiram Date: Thu May 4 16:13:26 2006 +0000 Moved to proper source tree location hg/utils commit 7b453db57546dfd31ae64e3f59e59517f62bc639 Author: hiram Date: Thu May 4 16:13:05 2006 +0000 Proper source tree location is here, not in src/utils commit 5eb5f071438739f0a32b30ab7d48dcaca0d49bdb Author: galt Date: Thu May 4 15:00:19 2006 +0000 "Encode release log update" commit eed4153a165b17572f15f56b4701667f0d4d7c10 Author: galt Date: Thu May 4 15:00:18 2006 +0000 "Release log update" commit c25c86529a53f2f206862cef23bcd6f6f57bbe13 Author: hartera Date: Thu May 4 04:03:32 2006 +0000 Description for Hg18 Proteins (blastHg18KG) track. commit d48ccf67bb529e896d2da211e7b5f109c715aac2 Author: hartera Date: Thu May 4 04:02:44 2006 +0000 Changed some priorities. Added blastHg18KG track. commit 036f6a50b8208b54a0c00290087dbc7ce13de900 Author: hiram Date: Thu May 4 03:52:37 2006 +0000 genscan track done commit eb115002c9eb1738db3c8e0f5a2c190294c00043 Author: braney Date: Thu May 4 02:35:47 2006 +0000 initial build stuff commit ede0fc5a468c4d652a88d892ce64dd571edcb6f9 Author: braney Date: Thu May 4 01:56:39 2006 +0000 add balstHg18KG commit 9815e6b8ab07818ec9cadd21f3a9d0a718430503 Author: angie Date: Thu May 4 00:30:28 2006 +0000 When creating a custom track with a featureBits region qualifier, be sure to adjust the custom track's fieldCount -- it starts out being whatever the parent track's fieldCount is, but featureBits may knock it down. commit cdd7c1c50a82751f3d7475dbbb601aa89fe25231 Author: hartera Date: Thu May 4 00:23:23 2006 +0000 Added search for scaffolds (gold) track. commit 5657e8ffb769c5eae4ee92e207053875429dec7d Author: galt Date: Wed May 3 22:37:37 2006 +0000 typo fix commit c0c666e483607b01617894c0bc358446ea470d2b Author: hartera Date: Wed May 3 22:28:01 2006 +0000 Added that chrM has fragment type, Finished. commit dc28dd0b313b3af5925fcbb0028934c9ef25002c Author: braney Date: Wed May 3 22:14:14 2006 +0000 add support for blastHg18KG commit 429772fd3640798b42efde67b16a80b22e12375c Author: kayla Date: Wed May 3 22:07:31 2006 +0000 changed to mm8 net/chain now says $o_Organism and mm7 net/chain says $o_db commit 3a94bcb1b7c2ef4f32535be68db083b8cf3ea82c Author: kate Date: Wed May 3 22:03:16 2006 +0000 Alternate conservation wiggles for testing (chr7 only) commit 0e4fa754a3c888fd32515a99f31c99e5f5c882e6 Author: hartera Date: Wed May 3 21:46:02 2006 +0000 Added quotation marks for type F. commit 9dc7b35c4327b6ae99f9a4696fe377d2d6a4f21b Author: hartera Date: Wed May 3 21:44:28 2006 +0000 Added type for chrM. commit 6f1bbb6cb7d543a6f2f94e101707650b65d05968 Author: hartera Date: Wed May 3 21:41:44 2006 +0000 Capitalized first letter of type. commit b4e91fe389451fa63d06f356f5dc888ee528fba4 Author: hartera Date: Wed May 3 21:37:04 2006 +0000 Corrected contig types in this track. commit 1ab439a1bb3813b64b2c07a3be09ec10592b7844 Author: hiram Date: Wed May 3 21:36:50 2006 +0000 Rerun multiz17way, annotations, and phastCons to use danRer4 in place of danRer3 commit 9722cd97c473a43275b2a67dd69e20903425862b Author: hartera Date: Wed May 3 21:04:00 2006 +0000 Added test section for Blastz of monDom4. Started BAC ends track. commit 0fc3c562d99ac9a81f69037b06ad7ff56724678f Author: kate Date: Wed May 3 20:34:40 2006 +0000 Fix phastCons tracks commit cb657cdae37accf5476a4a0b00058a41b9f2f16f Author: angie Date: Wed May 3 19:42:55 2006 +0000 Added "GenBank" to longLabel of mrnaDescriptions for clarification. commit cd1d230224de50e1b6338a68c05d9b0e4997a035 Author: hartera Date: Wed May 3 19:29:21 2006 +0000 Added lfsOverlap. commit 665656f29f7bc82f7e53ee651efe695a760918a1 Author: hartera Date: Wed May 3 18:41:00 2006 +0000 Created liftOver chains from danRer3 to danRer2. commit 6b8c221b87b676dd075c1d61e2b1efdff653ba27 Author: hartera Date: Wed May 3 18:28:42 2006 +0000 Split sequence for making danRer3 to danRer2 liftOver chains. Corrected error. commit 775fa2abcb75c2a738be12b0959b4d154264ea6f Author: angie Date: Wed May 3 18:11:06 2006 +0000 Label fix for methods: BDGP --> FlyBase (thanks Brooke). commit 03741a610261aee4ef02919dfd4757d19387c42f Author: kate Date: Wed May 3 17:48:55 2006 +0000 Remove unfinished liftOver chain run commit c5c776fb5305f332a569410c4881c057bedc8f06 Author: hiram Date: Wed May 3 17:48:38 2006 +0000 change danRer3 to danRer4 in the multiz17way commit cd9cb6323069fd45fc711e2731e7c47436c50001 Author: ann Date: Wed May 3 17:26:25 2006 +0000 moved up from mm7. now shared by mm6, mm7, mm8. commit 87eeef1ff0bf593e456d1c8911de2eb20027cce3 Author: ann Date: Wed May 3 17:14:21 2006 +0000 moved up to mouse level commit 13b4741a0f753fe413691eeb93aaa9118a8f1c28 Author: ann Date: Wed May 3 16:39:11 2006 +0000 changed danRer3 to danRer4 commit adac0e69dceaacc10b0f0fd97460e8a8005ccee7 Author: hartera Date: Wed May 3 16:24:45 2006 +0000 Started to archive danRer1. commit 2b246029a5626a5628b93901defd1b5900ce9fcb Author: fanhsu Date: Wed May 3 15:41:52 2006 +0000 Added sgpGene track. commit 76ba3a37aca7b39b82f3bc20a9081ffda614e032 Author: angie Date: Wed May 3 15:41:18 2006 +0000 Resolved -Wall warning: unused variable. commit 7a77f41d7a4e373efd4648f845c3522c668ab68b Author: galt Date: Wed May 3 15:00:03 2006 +0000 "Encode release log update" commit 805dab105460cc731d3bd37802ad26cb9b35e65c Author: galt Date: Wed May 3 15:00:02 2006 +0000 "Release log update" commit c46845afe9dec580e1306032c41f58f7df82a13f Author: galt Date: Wed May 3 03:20:54 2006 +0000 typo fix in usage commit 4323672c92df6cc450549926bf7b1a1ae5d0166a Author: kate Date: Wed May 3 00:50:02 2006 +0000 Fix track label for ENCODE track commit 2f18952bf738f9e8e36b1ab9ca674110a0d35d4c Author: kayla Date: Wed May 3 00:31:22 2006 +0000 changed "Mm8" to "$o_Ogranism" for nets/chains commit 17156b5cf15c2ee719f7741e89483d2876bbf56c Author: kayla Date: Wed May 3 00:29:41 2006 +0000 changed $o_Organism to $o_db for net/chain for mm7 commit 54be86dde84d149d32d120495f523088e6e55b32 Author: rhead Date: Wed May 3 00:27:50 2006 +0000 added a block for snpMap, and changed the shortLabel to SNP Map commit 283f57b96a6bac4f33d3230f262a949b03a17bc1 Author: kayla Date: Wed May 3 00:03:53 2006 +0000 made net/chain mm8 use $o_Organism and made net/chain mm7 use %o_db commit 936c866dc376c642c3e6cd07ff6f8d5403a526bb Author: hiram Date: Tue May 2 22:26:48 2006 +0000 html descriptions for 7-way conservation commit c45774b6db2c85e61a43fdb309ca865ae7fc2fb8 Author: hiram Date: Tue May 2 22:26:23 2006 +0000 Adding 7-way conservation commit 55c5087b1e6b90e050ef6c47c4fc239f159626c3 Author: ann Date: Tue May 2 22:21:32 2006 +0000 temp change to Conservation track visibility = hide commit 74654201c01f34c79a2e343b3a3b1102a4e4288e Author: kate Date: Tue May 2 21:46:44 2006 +0000 Tweak label on Refseq track for consistency commit 14cc3e87fbc6494961451420a481822a6d5f73e2 Author: donnak Date: Tue May 2 21:46:29 2006 +0000 Updated Known Genes pub entry. commit d7c872e16579b85c4bee844d7517ede84792a8c1 Author: angie Date: Tue May 2 20:56:21 2006 +0000 Added xenTro2. Added several other recent assemblies to chainDest. commit 30b1e889b00094aeb13256e33714e2218605fa76 Author: kate Date: Tue May 2 20:54:32 2006 +0000 Change Ren Chip/chip track vis commit 6846db8812dea9ce270178bc4b89e4315a3c947e Author: angie Date: Tue May 2 20:53:22 2006 +0000 Descriptions for 7way Conservation, Most Conserved. commit 14e56ff54dc9facf6873ca7b4eeff4e2306e153a Author: angie Date: Tue May 2 20:52:28 2006 +0000 Tweak to order of mammals in Conservation track. commit e1a29e0a91caad0bb136bf7f659c4018689fd87c Author: hiram Date: Tue May 2 20:47:31 2006 +0000 Creating 7-way multiz conservation track commit fd38692400f6509df35e3d761c88f7e733cf8b3f Author: angie Date: Tue May 2 20:47:06 2006 +0000 Finished up phastCons, using phyloFit model instead of pruned elliotsEncode model, because the postProbs were pretty much clipped to 1 ( almost anything that aligned was called conserved) while the phyloFit-generated wiggle showed a lot more dynamics (even though the elements' coverage is quite low -- xenTro1 also had that problem). commit fab53303ae65cb777d0794b4a64b12ffd6de7d01 Author: fanhsu Date: Tue May 2 20:37:56 2006 +0000 Added ensGene track. commit 36ae66fa293d2fa5b5172fa2d402e024da5df5b6 Author: donnak Date: Tue May 2 20:35:15 2006 +0000 Clarified Jan 2006 freeze. commit 530a07a59a9587a59d782d534ab2102debab08dd Author: donnak Date: Tue May 2 19:47:15 2006 +0000 Fixed typo. commit 911f772f814cf84ee58085bdbd15c891cb7a3dfa Author: galt Date: Tue May 2 19:07:58 2006 +0000 probably not going to need this anymore commit 4da3eac0043629cb7f4c79235a06bbbf5bb7164f Author: kate Date: Tue May 2 18:01:41 2006 +0000 Fix ENCODE track default vis (reversed alpha and beta) commit 1744e6a2db1758d8ad7b0b132bc757b0d6e28f4b Author: fanhsu Date: Tue May 2 17:44:42 2006 +0000 Added ensGene track. commit 6bcbaf20b9393a247d48ba03dccadc56a06e9d21 Author: rhead Date: Tue May 2 17:25:53 2006 +0000 added block for snp124 commit 6d0f0ef463fd3320328650e5a6793a847cfd711b Author: kate Date: Tue May 2 17:00:28 2006 +0000 Make UCSD/LI (Bing Ren) Chip/chip the default transcription track in hg17 commit 7772e2efe3286b0e96de55ffa44590ac3b107aa5 Author: archanat Date: Tue May 2 16:57:39 2006 +0000 Added track gold commit 02d3fd3f11cad60928029b084bcc890210c246a7 Author: archanat Date: Tue May 2 16:52:40 2006 +0000 Listed clone types for rn4 commit 3e1f5e630f9b52735ebde0c70a3379112a342c84 Author: kent Date: Tue May 2 16:38:30 2006 +0000 Adding a bit to usage info. commit b54a31bb5981022544ded20e2fc79c2e96c2b018 Author: heather Date: Tue May 2 16:10:41 2006 +0000 arrayCheck not committed commit 73b80e9aa7a4f00d9ac16293345f6090ba5a92fb Author: angie Date: Tue May 2 15:51:28 2006 +0000 Resolved -Wall warning: unused variable; added {} to make an else extra-unambiguous. commit 11736ffc0adf76fe7a8798e6c46d3311fdc33873 Author: galt Date: Tue May 2 15:00:16 2006 +0000 "Encode release log update" commit 6f68701ef157e2314c460dc3da824cd1dac7d34d Author: galt Date: Tue May 2 15:00:15 2006 +0000 "Release log update" commit c0bf93d83fa816cfa715b7ac8c9ca7378a59843e Author: heather Date: Tue May 2 10:39:46 2006 +0000 add an assert commit 96f6d969ac299b41a48f71bf5817c8be94b0bc30 Author: heather Date: Tue May 2 10:24:21 2006 +0000 increase MAX_EXONS commit 6699eb3c448a1eaa20853e81bfb3017af3f2ecc9 Author: heather Date: Tue May 2 09:41:36 2006 +0000 proper makefile commit 2830afd6e8b0a7fec9478c77f1110dd8dcd57199 Author: galt Date: Tue May 2 05:54:58 2006 +0000 latest version commit 5781c83e1873118c554d43d40b47639633765a54 Author: galt Date: Tue May 2 05:37:52 2006 +0000 added changes covering mapping from mahoney to jax commit 33b6d534361a90d84e23276a1d119dee823bc36f Author: kate Date: Tue May 2 04:50:30 2006 +0000 Finish quality files and track commit 14040373086cdf20f69b88cbc4127c8b2a52be81 Author: hartera Date: Tue May 2 03:27:10 2006 +0000 Changed Retrogenes short label. Added searches for Consensus, Havana, Yale and GIS pseudogenes subtracks of Pseudogenes track. commit 4ff06a8e45cf34f3da033359bae50dea4306ae3c Author: kent Date: Tue May 2 03:17:39 2006 +0000 Seems to mostly work. commit b4c4557dba6ec2bea70a4f6aff6f5816771dd547 Author: acs Date: Tue May 2 01:34:13 2006 +0000 added chromosomes line to encodeDless commit 3d9b09458e4902f60f57ff95b73bfae36521d233 Author: angie Date: Tue May 2 00:57:50 2006 +0000 Added rn4-specific gold search. commit 770590af9fe7915bfb79e9dc429d24a26ff0e358 Author: hartera Date: Tue May 2 00:11:30 2006 +0000 Added all repeats as lineage-specific repeats and nibs to the san for Blastz cluster runs. Blastz alignment swap of monDom4 vs danRer4 alignments to create alignments of zebrafish danRer4 on monDom4. commit 6a603bb5e34fba3a9db4dedb641d623f37b3d461 Author: hartera Date: Mon May 1 23:52:31 2006 +0000 Create sequence download files. commit 57ebd628af479af16effbd53fa59a76e1bf305ab Author: ann Date: Mon May 1 23:50:44 2006 +0000 added notes about table name changes commit 8146a9ed8e86aa438e5273ba43438475efcd1f08 Author: angie Date: Mon May 1 23:47:37 2006 +0000 Swapped chains/nets from other species; multiz; phastCons in progress. commit c44434b77d0da35fb36d8f28b8274366659b741c Author: kent Date: Mon May 1 23:21:53 2006 +0000 Adding a few new utils commit 1b77fd56eb2a9544021d65391a5edb5d614f4fea Author: kent Date: Mon May 1 23:20:03 2006 +0000 Seems to work. commit 829a471738df5f74281f293238f20b66f4ce3c8f Author: markd Date: Mon May 1 22:40:29 2006 +0000 fixed crash bug display transMap track if genbank has not been loaded commit f90755fd9457f6ac8c37448c6eb269b426b53411 Author: hartera Date: Mon May 1 22:27:17 2006 +0000 Added code to handle split tables for BAC ends psl table. commit 77b8f01352e96aa8a232d109f47a0c6fc93884e8 Author: kate Date: Mon May 1 22:27:11 2006 +0000 New peaks data for UNC FAIRE track commit 97a94c484cfb5b4064c8b66b9a7f6c07967ca688 Author: hiram Date: Mon May 1 22:26:05 2006 +0000 Statements made less specific to account for differences from reality ... commit 830f73cb9d3de84e8eb5346d13808e3db8789536 Author: markd Date: Mon May 1 22:02:49 2006 +0000 added transMap tracks commit f98cd13d85adc7178a25dfd37d5a3e891fd45b2f Author: markd Date: Mon May 1 22:02:11 2006 +0000 added initial version of tracks for transMap commit d98bf54c959331802372358fedcfd1a29c14e1c9 Author: kent Date: Mon May 1 21:09:48 2006 +0000 Seems to work on all test cases. commit a6991da3662cd4e08ce609334407ac9ef0c20314 Author: kent Date: Mon May 1 21:09:01 2006 +0000 Adding tabRow parser to convert lines of text to arrays of strings a variety of ways. commit 001c9ac7b5b21490e25d3d739ad6bfb133c71b17 Author: hartera Date: Mon May 1 19:48:24 2006 +0000 Added Blat servers. Created alignments for human hg18, opossum monDom4, Fugu fr1 and tetraodon tetNig1. Created lift file for random scaffolds. Auto update of Genbank mRNA and EST and also MGC runs set up. Split chrUn and chrNA masked sequence into scaffolds and put on Iservers and san for cluster runs. Started creating Human Proteins track for hg18 Known Genes Proteins. commit 507b2923748bcb8c73994a68f0acbf738a6c2d10 Author: hiram Date: Mon May 1 19:46:26 2006 +0000 Change phastConsElements to name phastConsElements17way commit a677e9e778f77e22b246d91a2b6cbbc48a083c03 Author: hartera Date: Mon May 1 19:30:18 2006 +0000 Added alignment directory for danRer4 swap. commit ec4ceb571d3be21ac5f2e1deb2b6b5b0fc94fb48 Author: hartera Date: Mon May 1 19:26:48 2006 +0000 Blastz alignment swap for tetNig1 vs danRer4 to create zebrafish danRer4 alignments for tetNig1. commit 765a11408de6eea43e31b91e2db37fd3fdd859c2 Author: angie Date: Mon May 1 18:59:42 2006 +0000 Corrected the nibPath in hgcentraltest (needs to be dir, not complete path, for hgBlat). commit 01538ef0c9abb931b1454997b3416b184a158611 Author: angie Date: Mon May 1 18:59:14 2006 +0000 Regenerated mmBlastTab (and mm8.dmBlastTab) -- the mm8 run used 4.1 genes instead of 4.2. commit bb00234d536df833ed2e55059f8622768af7ee85 Author: kent Date: Mon May 1 18:30:44 2006 +0000 First cut. Seems to work on space-separated constant # of row case. commit afb8c66fa5163a45f9273e0f7b602251cbb03d46 Author: ann Date: Mon May 1 18:01:39 2006 +0000 corrected typo in panTro2 net commit d756db9be39137b56dbe407113d306cded598e5a Author: angie Date: Mon May 1 17:52:11 2006 +0000 Added semiShortCircuit setting to knownGeneAcc and mrnaAcc searches. When the hgFind.c code that supports semiShortCircuit has been released on the RR, the shortCircuit settings can be removed (semiShortCircuit can replace shortCircuit). commit 6680c2168195c7ff8a879ed0c792d0c201238692 Author: angie Date: Mon May 1 17:49:28 2006 +0000 Added support for semiShortCircuit setting: if a match is found, allow other shortCircuit (or semiShortCircuit) searches, but not the additive searches. commit df7cfc405f232af02691f5715c812c80373e66e9 Author: rhead Date: Mon May 1 17:34:27 2006 +0000 changed snp125 section for release to RR commit 0e0bca7dee50722b207999ef34aaf91259d546b6 Author: angie Date: Mon May 1 16:34:29 2006 +0000 Resolved -Wall warning: unused variable; use long instead of int to match %ld format (and for consistency with other longs). commit db21f95ae78ffd849c13da5251d2958c6ed52417 Author: hartera Date: Mon May 1 16:33:42 2006 +0000 Added scaffolds 2 bit file and lift file and chrUn 2bit file to the san for pk cluster runs. Blastz swap of fr1 alignments on danRer4 to create alignments of zebrafish danRer4 on Fugu fr1. commit 75a205a3b1c5613458be58b1af6827c99b0f0188 Author: angie Date: Mon May 1 16:33:35 2006 +0000 Resolved -Wall warning: unused variable. commit 10a286b58e84771410f13593dcbcad1514bbe25b Author: hartera Date: Mon May 1 15:48:30 2006 +0000 Blastz swap for hg18 chains on danRer4 to create alignments for danRer4 on hg18. commit da3da9272c3aa268b820667495117a4668aa95ba Author: fanhsu Date: Mon May 1 15:09:08 2006 +0000 Updated FirstEF track. commit 0df818194225dfcaef946cdc9dd484bf03586f84 Author: galt Date: Mon May 1 15:00:11 2006 +0000 "Encode release log update" commit fefce6c19824f4cc1970cb50446dafb39c00a48e Author: galt Date: Mon May 1 15:00:10 2006 +0000 "Release log update" commit 714f7042d5dad1016086dd150bf6b75fd664e38d Author: angie Date: Sun Apr 30 16:20:05 2006 +0000 Resolved -Wall warning: unused variable. commit 367d99afa233a5117e637cf78b81d0c8debdaee8 Author: kent Date: Sun Apr 30 16:05:57 2006 +0000 Seems to work. commit 4030c1aee5031deaec51d3ec3ebcdc8c57258a0b Author: galt Date: Sun Apr 30 15:00:10 2006 +0000 "Encode release log update" commit 823f5bdc8b38cfa7eb3d652c8c4d11c0b25e4946 Author: galt Date: Sun Apr 30 15:00:09 2006 +0000 "Release log update" commit b7d410e466660f7da5bcd80ee986b838c876b46d Author: angie Date: Sat Apr 29 16:45:46 2006 +0000 Resolved -Wall warning: unused variable. commit ccd964bcd4ee9834f15259f4e828d3bfb150f525 Author: galt Date: Sat Apr 29 15:00:14 2006 +0000 "Encode release log update" commit d2dde09479bcf5847b277f376bd94d386a3055f1 Author: galt Date: Sat Apr 29 15:00:13 2006 +0000 "Release log update" commit 84d58780f0bc1997dccc4ff9cd7b068af35a9a9b Author: kent Date: Sat Apr 29 07:28:28 2006 +0000 A small fake data test case that mimics what you might see on a trial with a reasonable number of patients, reasonable phenotype info, but not a whole lot of genotype info. commit 4dab9efaca3505bdb5b8fc6c2d1b74de21cebe54 Author: kent Date: Sat Apr 29 07:26:58 2006 +0000 Seems to work, but I'll never tell. commit 2be8f946fc001dd2a799e4bc583e46aeaf1102ab Author: kent Date: Sat Apr 29 07:26:19 2006 +0000 Seems to work, but I'll never tell. commit a7c178845d7deddd54a1ff658a59c301ea177f09 Author: angie Date: Sat Apr 29 05:13:45 2006 +0000 Updated comparative tracks for xenTro2. commit eba06442f86589f7b886e66d4e28fe9b3c52c0ff Author: hartera Date: Sat Apr 29 02:07:20 2006 +0000 Minor edit to Methods for UCSC Retrogenes subtrack. commit 77cb1e7f4966a0181447ff75239e078c30fc6775 Author: hartera Date: Sat Apr 29 02:06:34 2006 +0000 Minor edit to Methods. commit a951d45fb64407447b526ace81ab5cc687e583d0 Author: hiram Date: Sat Apr 29 00:03:16 2006 +0000 Swapped Hg18 blastz and started 7-Way conservation commit 35cfef5c80ec71c89c89b5c61884e180d3147614 Author: hiram Date: Fri Apr 28 22:20:44 2006 +0000 danRer4 blastz and cytoBand tracks done commit 5b2783d7867fd5afecf01ed7a9dbf3ef106750a2 Author: hiram Date: Fri Apr 28 22:16:46 2006 +0000 From Terry's script that produces the cytoBand track for mouse from the NCBI ideogram file commit 2bf4325ffd61eef5543cfe127ac0bd217a7f826f Author: braney Date: Fri Apr 28 22:09:43 2006 +0000 add pslxToFa commit cbfb2a84509fcad1ae7ec54ab6cbaf1c3becd134 Author: hiram Date: Fri Apr 28 22:01:46 2006 +0000 Adding swap of mm8 blastz to danRer4 commit ed45ee632052f5525e1e2c6916a495defa6a1d7b Author: hartera Date: Fri Apr 28 19:51:00 2006 +0000 Description page for danRer4 net track. commit 349684a7dc8b3653fae3cd46cb8ac7de1c55e5d3 Author: hartera Date: Fri Apr 28 19:50:48 2006 +0000 Description page for danRer4 chains track. commit a1fbc570de29b0c89db1879d5ae4392d3a35313e Author: hartera Date: Fri Apr 28 19:50:01 2006 +0000 Added chain and net tracks for danRer4. commit c2a528f05de8f2e3898ad412eb8de7e90367c28c Author: angie Date: Fri Apr 28 19:22:56 2006 +0000 Resolved -Wall warning: unused variable. commit 1c91c41aab1edf3b12fe90f599bb1c40bf5504e4 Author: angie Date: Fri Apr 28 19:20:30 2006 +0000 Added -byTarget, -outDirDepth and -useSequenceName options (for splitting a monolithic maf file with many thousands of numeric target sequence names e.g. scaffold_12376 into a multi-level directory structure with one file per target sequence at the leaves). commit e0b19fcf8bfeb354bf84df314555d4fb5e612e32 Author: rhead Date: Fri Apr 28 18:07:23 2006 +0000 removed release alpha/beta to enable hgGene commit f473f6e84355635313dd660d64e2da303b423d17 Author: hiram Date: Fri Apr 28 17:58:35 2006 +0000 quality track done commit 95a16c16da775d67c961d698f6a208efe37879b5 Author: acs Date: Fri Apr 28 17:40:48 2006 +0000 details page for DLESS commit e720014c0c1d5c27ec1b8ca813c7c310234013f5 Author: kent Date: Fri Apr 28 16:32:10 2006 +0000 Seems to work. Still some hard coded stuff that might be best as command line options. commit 78ec9aba84c248ffa743ef6b9734ea9aa90bf2c3 Author: galt Date: Fri Apr 28 15:00:09 2006 +0000 "Encode release log update" commit 9ef3bddacbbca393d782f6a75ffa516a2192d569 Author: galt Date: Fri Apr 28 15:00:07 2006 +0000 "Release log update" commit 64a62d185f2d463ab74d2c48cc8b3af4900e64e4 Author: rhead Date: Fri Apr 28 00:32:48 2006 +0000 took an accidental caret out of the link commit cf2d6d72467ddb97eb00a952a83a2e444a19bf56 Author: rhead Date: Fri Apr 28 00:08:31 2006 +0000 forgot to change text to say version 4.2 commit de97bb48e077f27d3fbeeb6d4645f479028f0647 Author: rhead Date: Fri Apr 28 00:01:09 2006 +0000 updated 4.1 --> 4.2 after pushing the 4.1 version of trackDb to RR commit 0356533aa7ff822f0e792a7c23b55f4b1805fe95 Author: hiram Date: Thu Apr 27 23:28:31 2006 +0000 Might get a fixedStep section that is empty ... commit 03e42c45d75283eeb46c73c56824e4184102f39a Author: kate Date: Thu Apr 27 23:26:22 2006 +0000 Quality track for chimp commit a288f10f42e7477f6e6a3be27c1e937f13688649 Author: rhead Date: Thu Apr 27 23:26:03 2006 +0000 old version 4.1 flybase link was broken; fixed link commit 47c33fe5f5a9737cde5cefcafaf61f3616e299e5 Author: rhead Date: Thu Apr 27 22:25:12 2006 +0000 rolled back to flyBase version 4.1 because of html leak to RR commit 0cd4eb554360f8afe9253fbe9d6e33139ee9d649 Author: heather Date: Thu Apr 27 22:12:23 2006 +0000 use snpTable arg commit 73ef62249d0a246519bd1f722820afd90ea1d309 Author: galt Date: Thu Apr 27 21:14:06 2006 +0000 fixed bug - used id before it had been swapped with the forwarding id commit 07b97bf4de30588474fd34f0e0c585d716766aba Author: angie Date: Thu Apr 27 17:52:20 2006 +0000 hgLoadChain cleans up its .tab files now, so don't try to remove them (expansion of *.tab causes failure, doh). commit 05c05bb62bcc56b974f92191134da9b26f8bda0f Author: angie Date: Thu Apr 27 17:42:44 2006 +0000 Resolved -Wall warning: unused variable. commit d7e37730effc1cc632ec6b6a41435899191b7ccc Author: kent Date: Thu Apr 27 16:23:29 2006 +0000 Add class field test cases. commit 8f4485ff94f625026d2e4b7c55d4470f3ab95ce1 Author: archanat Date: Thu Apr 27 16:19:07 2006 +0000 Fixed a typo commit cea303bcc55b7940e9b66901de3e2c37411eba4c Author: kent Date: Thu Apr 27 16:13:22 2006 +0000 Made alignment of longs and doubles agree between back end and runtime. commit c9eefcec653ad35d9c5715f660862839249ef8a5 Author: kent Date: Thu Apr 27 15:58:15 2006 +0000 Removing some debugging. commit c6cfa66e3745ec215dc3da4c34cda616d877acca Author: kent Date: Thu Apr 27 15:35:17 2006 +0000 Improving code generation for isxIndirect. commit 447b1b25fe2c1fedce6ce92fab03db673ca7fa26 Author: galt Date: Thu Apr 27 15:00:09 2006 +0000 "Encode release log update" commit 9378992f2eb36b7d46ad36898b87a2a769076454 Author: galt Date: Thu Apr 27 15:00:08 2006 +0000 "Release log update" commit 30c28c9d3ff9cfacd7d53c8e743f27c45052225f Author: galt Date: Thu Apr 27 07:14:38 2006 +0000 oops commit f606bef402d702a9aca11f7773966b987d85c01f Author: galt Date: Thu Apr 27 06:59:52 2006 +0000 making bodyPart a command-line parameter commit 6d7eeaec7292851a02f331465a3d3c5ebc19ccf6 Author: galt Date: Thu Apr 27 06:33:58 2006 +0000 added imageFileFwd table commit 455c0f10a8bbf91510f545af179b6b78c6b219e1 Author: galt Date: Thu Apr 27 05:52:06 2006 +0000 better target name and helpful comment commit e44ea2a589754d6df14cd038ad57e092defaca9d Author: galt Date: Thu Apr 27 05:51:09 2006 +0000 removed special handling of mahoney submissionSet, added ability to specify a single submissionSet to process commit da7466f1eeb2735a00df701c98f6df1137776abc Author: heather Date: Thu Apr 27 01:42:41 2006 +0000 grammar tweak commit 18d31443dfc4be308ca966f6fcc7e378b480524b Author: kate Date: Thu Apr 27 01:04:22 2006 +0000 Fake up quality scores for regions missing it, for use by downstream analyses (e.g. chimpHiQualDiffs, Daryl T.) commit deef4dba3ec1c595b33dab95236a39f5fa7651cf Author: kate Date: Thu Apr 27 00:49:51 2006 +0000 Add message to indicate size of qa commit 2a0bacc06dcebe37824ddaf05f696c7691f0a2bb Author: ann Date: Thu Apr 27 00:38:15 2006 +0000 added definition of 'phast' commit daca168e30ed00618f7b9eb98299a1e7a5a3673d Author: kate Date: Thu Apr 27 00:30:37 2006 +0000 Add option (-mScore) to assign a score to regions with missing data -- e.g. clone referenced in AGP doesn't have quality info commit ab9b68d2fba79477e8fb8d8b397060515a20b6cc Author: donnak Date: Wed Apr 26 23:52:06 2006 +0000 Made several edits to this file pre-release. commit 307943b9057c98f8e176aa3430aa0be4c3e8207d Author: hiram Date: Wed Apr 26 23:19:17 2006 +0000 xenTro2 measured, phastCons verified OK commit 6df435fd2460de29847800f53209021b111adbf9 Author: acs Date: Wed Apr 26 21:49:24 2006 +0000 added encodeDless commit a10766f32a6ba22c34ffea55a126d097c8b4fc33 Author: acs Date: Wed Apr 26 21:48:01 2006 +0000 allow dless track to be named either 'dless' or 'encodeDless' commit 425b6e7ce2bf87748ac2dd76436cf521e3a6c26f Author: acs Date: Wed Apr 26 21:47:15 2006 +0000 changed name of dless track to "encodeDless" commit 8117f5fe385c0db718c14d54a8e647b99722de91 Author: sugnet Date: Wed Apr 26 21:08:13 2006 +0000 Adding docs for altGraphX and exonWalk tracks. commit b1fe172cc746f65d722ac67344a26e7bf71ee3cb Author: aamp Date: Wed Apr 26 21:05:35 2006 +0000 Added a silly option to allow a file of browser positions, e.g. chr1:1-20, etc. commit 29e9293389cfc4d6dbef3af3170e6e3f369b23d2 Author: sugnet Date: Wed Apr 26 21:00:25 2006 +0000 Adding docs for altGraphX and exonWalk tracks. commit 7bdd5d21fe3bf8bebd6ad3088aa8c5268272224d Author: sugnet Date: Wed Apr 26 20:33:30 2006 +0000 Making number of exon threshold dynamic. commit 4899d08d7d342ee64b9c08ae57095bf3c9583cef Author: hiram Date: Wed Apr 26 18:57:53 2006 +0000 Now properly detecting overlaps in fixedStart records commit 12209dd4fa62deec5fcae468040c1b17e42c292a Author: angie Date: Wed Apr 26 18:53:38 2006 +0000 Added -noSort option for cases where sorting runs us out of memory. In these cases, chainSort -target should be run first on a machine with enough memory to handle the sort. Also added a history table comment. commit a3ba6fa6d7d0ee3f1960b6b2dee4c28b47d0d6c5 Author: angie Date: Wed Apr 26 18:12:47 2006 +0000 Adding hgSession - Interface with wiki login and do session saving/loading. commit 1f1186a094acc33db74e75abb8bedd29423e753c Author: angie Date: Wed Apr 26 18:09:03 2006 +0000 Added webPushErrHandlersCart so that on error page, hotlinks are correctly constructed (cart is required for that). commit a7544273c3446808c96b5b42963d38f5c68c307a Author: angie Date: Wed Apr 26 18:04:49 2006 +0000 Made cartParseOverHash public (with cart as a parameter instead of cart's hash) and added cartEncodeState so that hgSession can do wholesale import and export of cart state. commit 188adbec7c0fe6e32720b3ce98da80bb9af98a0a Author: angie Date: Wed Apr 26 17:57:42 2006 +0000 Adding wikiLink: interoperate with a wiki site (share user identities). commit f0075bcc952c710a7d7d6c7be954d89c959c4822 Author: archanat Date: Wed Apr 26 17:56:03 2006 +0000 Reworded the definition on pseudogenes under consensus pseudogenes commit 4a577fbc9aeb716bfcb7b8b4ac34c09f80a3b4eb Author: angie Date: Wed Apr 26 17:55:45 2006 +0000 Storage for named user sessions in central database. commit dbb39138b64a64e59077cb56291c039b8f942bd2 Author: ann Date: Wed Apr 26 17:27:23 2006 +0000 removed 10way conservation blocks, changed priotiry of 8way Conservation track commit ead0632f87c12542f6f636272d291da0fe8644fc Author: heather Date: Wed Apr 26 17:17:23 2006 +0000 edits to class commit c688f944944cdb3ae2401ab89ea2867fdb41c6ce Author: angie Date: Wed Apr 26 17:05:25 2006 +0000 {chain,net}XenTro2. commit 4c47f587819281998ff13d582eb58c650c3351a7 Author: galt Date: Wed Apr 26 17:04:58 2006 +0000 improving dependency check commit 72871cbf2840e2f277db0719b7f26f7cb2d710c8 Author: kent Date: Wed Apr 26 17:03:10 2006 +0000 Fixed bug where minMatch ignored in GFF case commit e28c02b5381b9f4991cf24b37864d4a43321906b Author: kuhn Date: Wed Apr 26 16:48:53 2006 +0000 uncommented an rm statement to get rid of a temp file commit 4d31e640142852a224b27101bee41277b31fbe52 Author: angie Date: Wed Apr 26 16:23:16 2006 +0000 Resolved -Wall warning: unused variable; needed parentheses around || within && (minor bug!). commit 2907e2e6629b8f2d1df25fbcff0b8e16f6fdde0d Author: galt Date: Wed Apr 26 15:00:09 2006 +0000 "Encode release log update" commit 5212ea574e7beaff01915a55dff35021fe1b5312 Author: galt Date: Wed Apr 26 15:00:08 2006 +0000 "Release log update" commit f73f45cf9e29b0fcb17ea0a4958c7c8a88633fb0 Author: heather Date: Wed Apr 26 04:10:45 2006 +0000 change to using binKeeper for big speed-up commit 0e2c5ed93dfa9ea65b4c6a5b882141df448fad46 Author: kate Date: Wed Apr 26 03:56:56 2006 +0000 Add blastz of hg17, danRer3 commit 8e6790eb0cd512a38e04a6ef3eda0f882ee1b25b Author: heather Date: Wed Apr 26 03:52:13 2006 +0000 fix typo commit 20e932d3a88ba3052ad8cff677975b7f76ac5d77 Author: heather Date: Wed Apr 26 03:50:13 2006 +0000 add HREF for snp weight commit 24ed63b676a439706e5769721ea18b168516a197 Author: heather Date: Wed Apr 26 03:18:10 2006 +0000 tweaks for weight and avHet commit 8778cd293c55e8747b029dd332b2775f73985620 Author: heather Date: Wed Apr 26 03:02:55 2006 +0000 fix order for PAR and multiples commit dfc87a2d7dad5f0a21b67afce492294fb3181ad6 Author: heather Date: Wed Apr 26 02:52:06 2006 +0000 fix some labels commit 18231fbf813d0363e5f7b75a6c7796f7cf1e1901 Author: heather Date: Wed Apr 26 02:45:04 2006 +0000 ignore hg snp tables for now commit c939c395151169d8b8767b20633c807ace88952b Author: kate Date: Wed Apr 26 01:27:34 2006 +0000 Correct symlink commit 933602f05f538fabfb1c99a7eef5eba6db901643 Author: hiram Date: Tue Apr 25 23:12:06 2006 +0000 Adding noOverlap to wigAsciiToBinary function commit b63d30f2eaa5f5f5ff01585f98f321c5c62a8e60 Author: hiram Date: Tue Apr 25 23:11:27 2006 +0000 Adding noOverlap option to wigAsciiToBinary function commit 3b4b519090df9a1003316965b03355bc5be3b2fd Author: braney Date: Tue Apr 25 22:55:48 2006 +0000 a chain track to borEut13X commit ea0d9fd2ee714f3383d1bcad0d2eeffd735f4497 Author: braney Date: Tue Apr 25 22:29:04 2006 +0000 a trackDb for borEut13 commit e994de26cb82c729cdb9afc25e355d2639588316 Author: kent Date: Tue Apr 25 22:28:09 2006 +0000 Restoring regular database. commit b47d2ff16f0b5d41b0b49951c8b057bffa5e00be Author: kent Date: Tue Apr 25 22:24:19 2006 +0000 Simplified the forwarding logic and display a little. commit 9d1140331192099941c7b4ea35a524783500ec50 Author: rhead Date: Tue Apr 25 22:13:47 2006 +0000 typo fixes commit 0b11b3eba3c2e8298c32cce9a03e553b0a04e72f Author: heather Date: Tue Apr 25 21:58:04 2006 +0000 add weight commit 3c9846023f2ec8d6d6c18ef34a22528ecd2fc375 Author: ann Date: Tue Apr 25 20:34:34 2006 +0000 updated instructions for the TB commit 4faf2d0f7bf785cb115389edf202feae5174a52f Author: hartera Date: Tue Apr 25 19:50:32 2006 +0000 Added danRer4. commit 30c17251b470f286b709146621f0e9357dae5247 Author: galt Date: Tue Apr 25 19:25:49 2006 +0000 makefile cleanup commit 97eb285abb0318cfc7fbc92f6c720110408232a0 Author: galt Date: Tue Apr 25 19:17:09 2006 +0000 fixed handling dependency on vgGetText commit 3e9ab4902fdc5dac3b03f52011b829b1794a3e7f Author: fanhsu Date: Tue Apr 25 18:26:47 2006 +0000 Added firstEF track. commit 01c5dc1c9e541731e32690e33db014abcd1b31e5 Author: ann Date: Tue Apr 25 18:21:19 2006 +0000 correct fugu capitalization commit 13a742e3b640312d877f7daa66a6ba145b9fd1d4 Author: angie Date: Tue Apr 25 18:19:35 2006 +0000 Don't try to getHti (and don't assume it's non-null) if curTable has a . in it, i.e. if the current table is not in current database. commit c8f49150064663503cd56e52977223dbd7a2e8c3 Author: archanat Date: Tue Apr 25 18:16:50 2006 +0000 Fixed a typo commit 8a19e864abbf1f09b23a8c0eb8b0cc94a8df7ca0 Author: kate Date: Tue Apr 25 17:58:15 2006 +0000 Create data download from multiz8way table commit 9ca81b2a89a3bd3836241e92f4c03891bea6a189 Author: hiram Date: Tue Apr 25 17:37:41 2006 +0000 Add mafFrames to 17way commit 3857f3ecb5a4ebcad367754a23bcb2ddb767efef Author: hiram Date: Tue Apr 25 17:33:47 2006 +0000 Finished with mafFrames for multiz17way commit 2536610345bc83d576771b122947c502211ac82b Author: angie Date: Tue Apr 25 17:01:48 2006 +0000 Added removal of temporary/trash files to clean target. commit ae45e122ccc39bdee4eca3f53ddf555216cb511c Author: giardine Date: Tue Apr 25 15:41:33 2006 +0000 Took out comment about SwissProt data being redone. commit aa63219cde5e22a9de56dead5ba681335cf56086 Author: galt Date: Tue Apr 25 15:00:04 2006 +0000 "Encode release log update" commit c8cdd8792b604948502d3f2d624e7098eb97a6c1 Author: galt Date: Tue Apr 25 15:00:02 2006 +0000 "Release log update" commit d5a8513140ba94c08e395d8d157fe6439253feb1 Author: angie Date: Tue Apr 25 14:38:38 2006 +0000 Resolved -Wall warning: unused variable. commit 8cfb3f5f7d7950f9e3397bb5e0cde4d000ed1bf9 Author: angie Date: Tue Apr 25 14:36:36 2006 +0000 Oops, had to move a variable declaration up to beginning of block to avoid compile error on some platforms. commit abdc752c8ba4182516c2c3ca66ff854df3cb8b9b Author: fanhsu Date: Tue Apr 25 01:18:22 2006 +0000 Created dv2.c. commit d28034d07e130b508a6a05890cd4bcb731b48b9d Author: fanhsu Date: Tue Apr 25 01:18:08 2006 +0000 Created makefile. commit a811da51c859fac663ee22719eb81f04cb14f452 Author: markd Date: Tue Apr 25 01:05:59 2006 +0000 allow use of other than the MAF target component as the target database commit 5bdccfb0d01e7d1c89a4f5f441bb5719a7dfdd6e Author: heather Date: Tue Apr 25 00:25:40 2006 +0000 "New version number v132" commit be004eff25aa9f9a523a0d987bcdc1daa29d21ba Author: baertsch Date: Tue Apr 25 00:07:34 2006 +0000 remove comparative seq feature commit 61abf86aa2a4e473abcd9b5ecac44c169a748d0d Author: angie Date: Tue Apr 25 00:00:25 2006 +0000 Libified textOutClose. commit 041bcdd0cbb156c746cdf679e476ce767b1c095a Author: angie Date: Tue Apr 25 00:00:04 2006 +0000 Added textOutClose. Corrected exec paths. Added cgi menu #defines. commit 13b7b598f45dbe207e4a79bc71a5eae62402a649 Author: heather Date: Mon Apr 24 23:12:59 2006 +0000 fix typo commit b3e8b03bcf4f1b1d5e7a98284abc55fe110730de Author: hiram Date: Mon Apr 24 23:12:00 2006 +0000 Working on the mafFrames for the multiz17way commit afb2eef7bddf961cfb397c948c9781bb3a996664 Author: hartera Date: Mon Apr 24 23:08:41 2006 +0000 Create ooc files for Blat. Create Affy Zebrafish track. Add lineage-specific repeats to the san for Blastz runs with other species and also the chrom sizes file. commit ed1015cb255ac0969b0c41c6182dd7a6001b5878 Author: angie Date: Mon Apr 24 23:03:13 2006 +0000 Added $db to a couple warning messages; broadened split table regex to handle new chr*_hla_ etc., not just chr*_random_. commit a91b5c5406dcdee8275894a68b0599f81d1eaf06 Author: angie Date: Mon Apr 24 23:01:30 2006 +0000 {chain,net}XenTro2. commit 3db182e12b2ce6b4a0deb437c537726d09ed9648 Author: angie Date: Mon Apr 24 22:59:21 2006 +0000 Added another nfsNoodge delay. commit 8fc6cac2bcc3d15466ec91354d39c1d314076176 Author: hiram Date: Mon Apr 24 22:39:20 2006 +0000 liftOver to Mm7 done. Continuing with annotated frames for multiz17way track commit e5670fd08c33b44ddef6b4d388834f8f211129f9 Author: hiram Date: Mon Apr 24 22:38:46 2006 +0000 liftover to Mm8 done commit 8ff4c21df2615baa4921c98fa04c7c43ce17ffa3 Author: hiram Date: Mon Apr 24 22:37:16 2006 +0000 Add empty table for rheMac2.chrUr_chainMm to satisify all chain tables commit cec587ebb993cb8a8c8a9fe7472eed21fe5c8012 Author: hartera Date: Mon Apr 24 21:58:37 2006 +0000 Minor edits and corrections. commit a700d127bc2abc8b7394e0e0247dbb88336add45 Author: hiram Date: Mon Apr 24 21:53:57 2006 +0000 Update panTro1 to panTro2 and xenTro1 to xenTro2 in the multiz17way business commit 49902ec44437946f362d3a7feff9eef78ccc38d1 Author: hiram Date: Mon Apr 24 18:00:58 2006 +0000 Working on the blat of Hg18 proteins to monDom4 commit ea828d3f83070a61111aced945a25562dd2d75fb Author: hiram Date: Mon Apr 24 18:00:14 2006 +0000 Reworking the multiz17way, and Mm7 liftOver started commit e76e00edf263a3cc9141b35b8b46aa5c6908f0d2 Author: hiram Date: Mon Apr 24 17:59:43 2006 +0000 working on Mm8 liftOver commit 26a6c5c67c8510c784741c47b5d4e58adaef6031 Author: hiram Date: Mon Apr 24 17:58:52 2006 +0000 Add GENEID build commit 7264eff5e32eea3a06e44b16746811deb1cdad63 Author: kent Date: Mon Apr 24 17:54:44 2006 +0000 More progress in coding field access in assembler. commit b0589d71a0c396c0d62ec09c59a04ff1fc78c23f Author: angie Date: Mon Apr 24 17:18:32 2006 +0000 In cartDumpItem(), substitute newline (and \r\n) with encoded \n to avoid making stuff after newline appear as a new cart variable. commit aa4d97ebfcf88273c1a4ede0a5b60e67638b74e1 Author: hartera Date: Mon Apr 24 15:34:48 2006 +0000 Names of unordered chroms changed to NA_random and Un_random. Recreate agps for these chroms. Documented script to check scaffold and contig sizes in agps. Create FASTA file again for random chroms and check sequence file sizes. Change date format in hgcentraltest entry. Split sequence for random chroms to 5 Mb chunks and remake lift file. Finished description page for assembly. Re-run trf just for randoms and reload simpleRepeat table. Split sequence to 500 kb chunks again just for random chroms and finish RepeatMasker run and load these repeats into database. Mask sequence. Create chromInfo table and gap and gold tracks and store sequence in gbdb. Put masked sequence out on iServers and the san for cluster runs. Create contigs track and gc5Base wiggle track. commit 24134dcf5c5a704d07d8ad152ddcd3d306a3e49d Author: braney Date: Mon Apr 24 15:18:09 2006 +0000 add mafOrder commit 0cb1bc9612681d76abe25f19e290ff2540aa046e Author: angie Date: Mon Apr 24 15:11:37 2006 +0000 Moved text output code (with support for output to file or compressed file) to src/lib/textOut.c. commit 7a93bd61c1dab5f0ce7756530313fc3b0686867e Author: angie Date: Mon Apr 24 15:09:07 2006 +0000 textOut - set up stdout to be HTTP text, file or compressed file. Libified from code in hgTables.c. commit 41d39422943c613e3868b3e25ae05d0765d39046 Author: galt Date: Mon Apr 24 15:00:04 2006 +0000 "Encode release log update" commit da89676a8178d0b3b4bee58f6eb9555f86a8fa17 Author: galt Date: Mon Apr 24 15:00:03 2006 +0000 "Release log update" commit 4ad1bc13bfb7d44a52a3256c293ba6e35c1ac9dd Author: angie Date: Mon Apr 24 14:51:21 2006 +0000 {chain,net}XenTro2. commit 68195c09079c59d7ab28a0fb6ebc9f463165468f Author: angie Date: Mon Apr 24 14:47:36 2006 +0000 Resolved -Wall warning: unused variable. commit 770cbca24282e9719142704661274923e5942153 Author: kate Date: Mon Apr 24 05:36:03 2006 +0000 Fix maf links commit 8af17159b7cb94e32cbb06ac9388cb31068fd6ad Author: heather Date: Mon Apr 24 04:16:41 2006 +0000 tweaks to snp125 weight display commit 7b0a78dce5ef73db74696e164a7551b86210600d Author: hartera Date: Mon Apr 24 03:29:30 2006 +0000 First draft of description page for contigs track. commit e6d727ae5eb78ea3441f6dfff0e080d1f7ea2e24 Author: hartera Date: Mon Apr 24 03:24:45 2006 +0000 First draft of description for assembly (gold) track. commit d662608c460c20d39111b4d24f987c7279c686c9 Author: hartera Date: Mon Apr 24 03:22:10 2006 +0000 Added ctgPos2 track and search for this track. commit de2905e03f73eba6b2f6a786c576c0b3e5ac5f6e Author: heather Date: Mon Apr 24 01:27:11 2006 +0000 utilize binKeeper to lookup snps in exons commit 79ad029248f3b8a737c471c40e5e8b0977d9b80f Author: galt Date: Sun Apr 23 23:00:56 2006 +0000 added utility to help fill imageFileFwd table for Mahoney slices, matching to jax version for additional annotations commit 465b511ae594a52860b53809ef160738753f5a8d Author: hartera Date: Sun Apr 23 21:10:23 2006 +0000 First draft of description for danRer4 gap track. commit 293b523133a2bb9286e65a6410814ff7299a9d2a Author: hartera Date: Sun Apr 23 21:08:05 2006 +0000 trackDb.ra for danRer4. Added gold and gap tracks. commit c6e7ff443c85dcecf190d5fcfd17cc63faa4f6b1 Author: hartera Date: Sun Apr 23 21:07:33 2006 +0000 Added more information about the assemly. commit 578a9cd0a745467c2f581f3d612315067c4cd727 Author: donnak Date: Sun Apr 23 18:19:57 2006 +0000 Updated info for Jakob's latest pub. commit 96c3bd097132eba302f86411aea957a39ed318df Author: kent Date: Sun Apr 23 17:27:53 2006 +0000 Some work towards generating code for class members. commit 00994bb42ae9c9fd928cb6c6d6e2425c3aa2667e Author: galt Date: Sun Apr 23 15:00:05 2006 +0000 "Encode release log update" commit 39a0268e9de9c655543ef60c4b134293d7c63e50 Author: galt Date: Sun Apr 23 15:00:04 2006 +0000 "Release log update" commit 06efc79f372ae4ec29c613155d0d937dfe0e9da2 Author: galt Date: Sun Apr 23 03:25:11 2006 +0000 added code for handling forwarded images i.e. tracking imageFile equivalence between mahoney and mahoney-in-jax commit da19ba5839e8e9d4420f229f66792de07c8a7086 Author: galt Date: Sat Apr 22 15:00:02 2006 +0000 "Encode release log update" commit e9bfca98fc6bc5ecb49f94f43b2758d78ae7a08a Author: galt Date: Sat Apr 22 15:00:01 2006 +0000 "Release log update" commit 9d2484eafeed3355c166eb578d28a20daf8dd38b Author: heather Date: Sat Apr 22 05:10:41 2006 +0000 show weight for snp125 commit 084ce3bbcb1e62cfc429b77c971c50c122569bbc Author: heather Date: Sat Apr 22 00:34:49 2006 +0000 add het and weight filters for snp125 commit 612176dbe1208df94c888f3be109616b497482d2 Author: heather Date: Sat Apr 22 00:33:20 2006 +0000 add weight commit db77447c910ec72f5f083fae7a908fd794f71225 Author: heather Date: Sat Apr 22 00:30:15 2006 +0000 don't save cds-reference commit 7d9c0d7a71ec252c0d9d72cb1035686d2dd9c7a5 Author: heather Date: Sat Apr 22 00:29:25 2006 +0000 save weight commit 43db4e08e18e3d865e605637da44cb65d5cec9c0 Author: ann Date: Sat Apr 22 00:14:24 2006 +0000 added mm8 to list of destination chains commit b85f650f2713924c5fa8836f1e9d3e6303717fa9 Author: hiram Date: Fri Apr 21 23:28:58 2006 +0000 Take out broken NCBI links. And remove wording about specific chroms being finished. At this point, they are all considered finished. commit 7eec3df82f0e456b6d5ba9e194d0239b3d18a4e5 Author: kayla Date: Fri Apr 21 22:08:10 2006 +0000 added mm8 commit 259d90612ee5cc654976a04ffeab0b3d9c512f2e Author: angie Date: Fri Apr 21 21:59:22 2006 +0000 Don't assign hti until after curTable has been assigned. commit 879c8f1bf8ff2eff978fcd17f610c65fbf817547 Author: hiram Date: Fri Apr 21 21:58:12 2006 +0000 More efficient use of rsync instead of the takes-forever iSync commit 37237985eccd05424117ea054e7628012135764e Author: hiram Date: Fri Apr 21 19:38:04 2006 +0000 chain and net Mm8 moved up one level commit 4d2421580ce9c28480e5ecc0de99391d9b232b6e Author: hiram Date: Fri Apr 21 19:37:41 2006 +0000 Move Mm8 chain and net to the top to run on both versions of assembly commit edb8ba37a54b1e9a756a33af9649037ec2478a51 Author: angie Date: Fri Apr 21 19:31:21 2006 +0000 Added check for NULL update time -- happens every once in a while and used to cause errAbort in sqlDateToUnixTime(). commit bfb48dbe793bbac001ec73c45bcdff92e93886b1 Author: giardine Date: Fri Apr 21 19:02:46 2006 +0000 Added new variant sources, corrected David Chui's location. commit 4ce3598a3fe92c706bac009379193bda7710d00c Author: giardine Date: Fri Apr 21 19:01:42 2006 +0000 Added field to hgMut to indicate accuracy of coordinates. commit 49b02df89c1b51dd38374df9c5922ca378419175 Author: kent Date: Fri Apr 21 18:58:55 2006 +0000 Nulling out cleanup method on assembler-derived objects for now. commit aa0729a95823b98a64e36dfb99817316b4ce8aec Author: giardine Date: Fri Apr 21 18:51:17 2006 +0000 Add connections from hgMut to attribute tables, so that attributes can be queried via the table browser. commit c1ad281e110774350e394bb6e9229b7a0387a46c Author: kent Date: Fri Apr 21 18:22:00 2006 +0000 Working on generating objects in assembler. commit ed646f13be5113e2d75c4ccee32b4bd9675626d7 Author: angie Date: Fri Apr 21 17:56:52 2006 +0000 Resolved -Wall warning: unused variable. commit f61e93dde9ba2c2f5d73592b1401493bcb57df6a Author: angie Date: Fri Apr 21 17:26:54 2006 +0000 {chain,net}XenTro2. commit f770f57ec2aba3f94f1e3877c6c65d0f086acc9c Author: heather Date: Fri Apr 21 16:36:08 2006 +0000 go with just filtering weight = 10 for now commit 92e8b59308201306ca32cb84c05e1c95efa43068 Author: kuhn Date: Fri Apr 21 16:34:57 2006 +0000 added search for nscan commit 69743e5b1b81ffedb347ed71ebfb7cc5f73fd63a Author: galt Date: Fri Apr 21 15:00:08 2006 +0000 "Encode release log update" commit 7ba7402db22050e8880bb7305bd521dbdcd6f665 Author: galt Date: Fri Apr 21 15:00:06 2006 +0000 "Release log update" commit ce011f8be30b3244e5372e58e6df652f10991bd2 Author: angie Date: Fri Apr 21 04:55:19 2006 +0000 Don't offer the paste/upload list option if we have a positional table with no (recognized) name field. commit 02d065d60a37a07a44bc944203e37e57c722e193 Author: angie Date: Fri Apr 21 04:53:42 2006 +0000 Added ctgPos to the list of oddball tables recognized by hFindBed12FieldsAndBinDb -- it uses "contig" instead of "name". commit 8e0b6005bc72510fc266ca6f93749f46ccfb25da Author: ann Date: Fri Apr 21 00:09:53 2006 +0000 added description for shotgun source commit 23ae82d0d87df669d5b2eeddffb792b2eaeb76d1 Author: hiram Date: Fri Apr 21 00:08:14 2006 +0000 Done with first part of mafFrames commit 2dd6bfbf67cab9cd1551ea14cfa38ed31b4ca6a3 Author: kuhn Date: Thu Apr 20 23:04:14 2006 +0000 moved protBlat away from the irst position in the Gens section commit 273496cb562ea4305c158f15721790f7af44bd84 Author: archanat Date: Thu Apr 20 23:00:07 2006 +0000 Reworded the text on spliced EST commit 4ef16df401d0e166cf3b5a3b250040399e7d411c Author: kayla Date: Thu Apr 20 19:23:44 2006 +0000 removed mm8 commit 07dbf2ac3f823a1dc9056b51ac8241b25be4f895 Author: angie Date: Thu Apr 20 18:44:01 2006 +0000 Added dontCheck for goldPrefix search, for checkHgFindSpec -checkTermRegex. commit 67b7e2980150c51b760edc9d633ef34ce16c86c3 Author: angie Date: Thu Apr 20 18:39:47 2006 +0000 priority tweak. commit 5585c20f77329ff19962f10e20586c7929377cfa Author: angie Date: Thu Apr 20 18:11:03 2006 +0000 Added {chain,net} xenTro2. commit fca9932c88c8127c7207be56e0973d518088c92d Author: hiram Date: Thu Apr 20 17:50:43 2006 +0000 Started xenTro2 blastz commit a51aeb03d4b529612945aafdd8046ef1c3709d4b Author: angie Date: Thu Apr 20 17:30:38 2006 +0000 Resolved -Wall warning: unused variable. commit a8431ae2a3065eced6076b20cc3b9e5e89b4d590 Author: galt Date: Thu Apr 20 16:00:17 2006 +0000 "Encode release log update" commit 61ce207f3da24ab3a8c1ce85cf94bec03c38e864 Author: galt Date: Thu Apr 20 16:00:16 2006 +0000 "Release log update" commit 1784752c26f41647e088c00b3f7759fa5f6f5ae8 Author: galt Date: Thu Apr 20 06:03:32 2006 +0000 added code to parse probeNotes to look for forward and reverse primer sequences commit 93dd76670a111ee04f65c01c24771e96652b4c4f Author: heather Date: Wed Apr 19 23:54:06 2006 +0000 fix typo commit 290a09a60ef8d5a5a9b3f06a9551e9dac586fbe4 Author: hartera Date: Wed Apr 19 22:12:03 2006 +0000 Mouse Blast Tab updated to mm8. Drosophila BlastTab is dm2. commit 89a88372e12d1f6720bcb5f9270b208880c647a9 Author: heather Date: Wed Apr 19 22:09:19 2006 +0000 recalculate bin commit 66cd832c4c283529614409aa0d8b865112fc63f5 Author: angie Date: Wed Apr 19 22:04:20 2006 +0000 GenBank, GenScan, CpGs; still need comparatives. commit a31be691aa68f771722e464d86e352e544ee988d Author: hiram Date: Wed Apr 19 21:34:02 2006 +0000 Move TargetScanS miRNA Regulatory Sites into the regulation group to go with picTar commit 3d196d55c7e2212b0df974d35799626c7fab8545 Author: hiram Date: Wed Apr 19 21:23:19 2006 +0000 Correct spelling on Rajewsky commit 76968b3be2fe9e60b388a77624b206bff6bd3297 Author: hartera Date: Wed Apr 19 20:23:30 2006 +0000 Removed an erroneous row from the bacCloneXRef table for BAC ends. Documented fixed regular expressions for searches for BAC ends. commit ddfdc0f3c6191d120c2c18cee6099a062d395578 Author: fanhsu Date: Wed Apr 19 20:22:27 2006 +0000 Added mm8 to pbDb. commit 212497a5c742697919b56aee874f29b26ae11194 Author: hartera Date: Wed Apr 19 20:19:47 2006 +0000 Fixed termRegex for some searches that were not working. commit 74a11ee6b0d73ee96f7b1eca57fd792d38eeda24 Author: fanhsu Date: Wed Apr 19 19:45:27 2006 +0000 Added mm6 and mm7 to pbDb. commit 2c2fb6b02bb7f0136d4b4705644d6c4baca45323 Author: hiram Date: Wed Apr 19 19:30:45 2006 +0000 blastz panTro2 completed commit f9e47aab83e0092ecf90096879ffa98a442d3fc9 Author: hiram Date: Wed Apr 19 18:49:17 2006 +0000 Completed Hg17 blastz commit 5d8b72e7b329ac041fd1f330dfed06a8b39ec026 Author: hiram Date: Wed Apr 19 18:42:33 2006 +0000 Bring Hg17 chain and net down here so it can have a specific short label commit 5fe80b2c9ae4984623580adaa665c061dff5b48d Author: hiram Date: Wed Apr 19 18:14:49 2006 +0000 Adding Mm8 alignments for Krish commit 8797f7886c2aeffb1eb51a64454462ac1fe62b41 Author: hartera Date: Wed Apr 19 18:08:36 2006 +0000 Added back tab that was removed. commit 70952ff364a075f176c75dcd6babd72e2797aebe Author: kayla Date: Wed Apr 19 17:58:07 2006 +0000 took out "hg18" from the shortlabel so it just says "human" commit 3549f00a3fae4db455310b398f58a9e4c28fa832 Author: galt Date: Wed Apr 19 17:54:58 2006 +0000 fixed genotypes list commit d78af3aa16171a4422042e7f95cf49d17fe44283 Author: hartera Date: Wed Apr 19 17:43:28 2006 +0000 Uncommented out line used for make strict. commit 871269984f4981f0eb43297cbfd031b30941b2b5 Author: ann Date: Wed Apr 19 17:13:18 2006 +0000 added gene table for codon translation commit 39294ebc97484e053454fda8777a17b0bc05c066 Author: ann Date: Wed Apr 19 17:01:24 2006 +0000 added list of gene tables used in codon translation commit 46dba146193cc10a40388fff9a9383e7fdc3e849 Author: ann Date: Wed Apr 19 16:50:50 2006 +0000 added line for species which are not translated in the frames commit 76ec7318d79de8bf54937b6ef99b94602bb19cad Author: ann Date: Wed Apr 19 16:45:14 2006 +0000 added list of gene tables that frames are based on commit 51df09e2e300e4f7e79e9cd691ec760e5724e918 Author: galt Date: Wed Apr 19 15:00:09 2006 +0000 "Encode release log update" commit 51a37ed8b3efa5a14f4f8185b84e722a58ded574 Author: galt Date: Wed Apr 19 15:00:08 2006 +0000 "Release log update" commit 3e89700b2c013c4bbd5a067c5c16af1f9807a638 Author: angie Date: Wed Apr 19 14:54:26 2006 +0000 Resolved -Wall warning: added parentheses around assignment used as truth value. commit 999880ab86b55233033600f009817d9f2672aab2 Author: heather Date: Wed Apr 19 04:58:08 2006 +0000 compare ContigLocusIdFilter.mrna_acc to refGene commit a81b9244a07431f665778ed32ef61fa5851db81b Author: hartera Date: Wed Apr 19 00:44:04 2006 +0000 Finished making liftOver chains from danRer2 to danRer3. commit 53fcf220e100fe90732c64580751ee651dabec76 Author: kuhn Date: Tue Apr 18 23:00:32 2006 +0000 decided to enable mm8 commit 307d5d69dec1dd91f2dfa71b4719572364c56109 Author: kuhn Date: Tue Apr 18 22:58:09 2006 +0000 adding mm8 to updates. running alignments now commit 417c90a0a9eb2efca3cfd6ad70ff70fbfdb42570 Author: galt Date: Tue Apr 18 22:24:33 2006 +0000 moving abSubmitId into separate table antibodySource commit 84c6d4ce9cfc7f47ad6f15664833de0dfe9a985c Author: markd Date: Tue Apr 18 21:55:25 2006 +0000 added ignore entry commit 74689f026c29b12511da7e4b8b04495fbf7b7aab Author: galt Date: Tue Apr 18 21:43:10 2006 +0000 trivial bugfix commit 1fc7747ea6b66746632e5a1376f97b3a4078f989 Author: kent Date: Tue Apr 18 21:43:04 2006 +0000 Improving docs on trackDb a little. commit daa97e70c8fcc060675581c85e9c6fc698764afd Author: galt Date: Tue Apr 18 21:39:35 2006 +0000 changing verbose to just printf so that make cgi calls this and does not think it is an error commit a604aa9ca7f50b061d75bddc0d59cf31669c7f84 Author: galt Date: Tue Apr 18 21:03:44 2006 +0000 moving abSubmitId into separate table antibodySource commit fd392e880cacea8265ce755b7b6e7537e0b50700 Author: heather Date: Tue Apr 18 20:37:53 2006 +0000 speed up commit a9d38a5ec17ff2b8a6d538fb13725e30d8a38042 Author: galt Date: Tue Apr 18 20:04:58 2006 +0000 activating faster method to try for beta tag maintenance commit 981d12369f6304641d0bcff1e2033ff6fe367d40 Author: galt Date: Tue Apr 18 19:44:58 2006 +0000 changing verbose to just printf so that make cgi calls this and does not think it is an error commit f95c789be735f380856e4737112faa83e25c3068 Author: hiram Date: Tue Apr 18 19:38:53 2006 +0000 Add dumpDb.pl to the installed scripts commit 093bc01b873d5098666f8670f498fefe28065185 Author: kate Date: Tue Apr 18 19:35:56 2006 +0000 Fix overlaps in net axt's (and maf's) commit 4cecdbf8bac6bb68e43139c46fa38157e3b8d121 Author: hiram Date: Tue Apr 18 19:35:14 2006 +0000 Take care of the MySQL 5 difference commit 434c4fcf44c1e9c1843f4e2b954fac38536dc50d Author: hiram Date: Tue Apr 18 19:02:22 2006 +0000 And check for missing files to ensure it is working OK commit 32d4175170c0bea9021028bff261fb5e210dbf89 Author: hiram Date: Tue Apr 18 18:58:28 2006 +0000 Take care of the mysql ownership situation commit e2cb0da1a78e145d9a6aa4842180f95443b920dd Author: hiram Date: Tue Apr 18 18:48:36 2006 +0000 Initial source commit 39eb9e8cf08607614b1d59fade11821b34a57674 Author: angie Date: Tue Apr 18 15:56:39 2006 +0000 Adding all_mrna and all_est entries (scaffold-based). commit 7a8c3eed0fb7e8385dfb5e8855080e39ee766e7b Author: galt Date: Tue Apr 18 15:00:05 2006 +0000 "Encode release log update" commit 38c27166c4d7540a27f43889175eb4ff61fff885 Author: galt Date: Tue Apr 18 15:00:04 2006 +0000 "Release log update" commit 7275ee481a0a038812f6048b07fc4ebd074c6aa2 Author: angie Date: Tue Apr 18 14:53:40 2006 +0000 Added xenTro2. commit 9ec5aed3bcef134335b2feaa3e9913de0e892bad Author: angie Date: Tue Apr 18 14:35:41 2006 +0000 Resolved -Wall warning: unused variable. commit 4c328150861c8ecb7dfd5d569486300abdd64d72 Author: galt Date: Tue Apr 18 09:14:47 2006 +0000 adding support to link jax antibody page commit 07c640900d310135dbb03da6ec897f95d9a57ccd Author: galt Date: Tue Apr 18 08:53:17 2006 +0000 adding support to link jax antibody page commit d4a49cfc402727a06b8c9dd9503a22350546d540 Author: galt Date: Tue Apr 18 07:26:22 2006 +0000 adding support to link jax antibody page commit d0fa94820ca4c050ded625d0fb983b92af6f3a3a Author: galt Date: Tue Apr 18 06:54:10 2006 +0000 fix null abSubmitId commit 2ad7556e03b70f392a871310be4bfbebb4412977 Author: galt Date: Tue Apr 18 06:34:13 2006 +0000 adding support to link jax antibody page commit b8d72a68b347da764d35e00035b9e127f716f359 Author: galt Date: Tue Apr 18 06:21:48 2006 +0000 adding support to link jax antibody page commit 69b9916e79c85e978548c944d60f4f83db0bb31f Author: galt Date: Tue Apr 18 06:03:50 2006 +0000 adding support to link jax antibody page commit 7c604f8378f1943ba26a973189a7f228ce33cdcc Author: angie Date: Tue Apr 18 05:47:34 2006 +0000 Added xenTro2. commit 9a66df8ed11db26fc2f9b9d042a8b9a7c7b7f8cc Author: hartera Date: Tue Apr 18 03:05:12 2006 +0000 Started a description for the Havana-Gencode subtrack. commit 6951f2df647e7d797c5dccfbf7870dd4ffd05d2b Author: angie Date: Tue Apr 18 01:03:01 2006 +0000 Skeleton browser for xenTro2 (Aug. 2005, JGI v4.1). Needs gene tracks, CpGs and comparatives. commit d95800bc73cd0c4e838450e0d8e7bab8e8ce5b94 Author: galt Date: Tue Apr 18 00:40:13 2006 +0000 adding itemUrl commit 79bfbec93ae4155e488789fb2febb37915ca53b8 Author: angie Date: Tue Apr 18 00:29:56 2006 +0000 Added xenTro2. commit 3ba04ea4024540c49eb7d1a967c25b89cfc87526 Author: angie Date: Tue Apr 18 00:29:34 2006 +0000 New description for xenTro2. Still needs several ?? statistics filled in. commit 923ffd78a6f4d9f48c367b84a0419a1fa156dd1f Author: hartera Date: Mon Apr 17 23:24:58 2006 +0000 Creation of liftOver chains from danRer2 to danRer3 are in progress. commit 9680ea2cb91c76f10cb8e0bfc96be9da57d01ca2 Author: hartera Date: Mon Apr 17 23:17:00 2006 +0000 Minor edits and corrections. Split sequence for making liftOver chains from danRer2. commit 0f50767296e33a9e713ed019474609974b865646 Author: angie Date: Mon Apr 17 23:08:38 2006 +0000 Added local definition of {chain,net}Rn4 to correct the matrix values and priority. commit ccfdaa776b51fd7c6703ec9077eab06a378b5c1e Author: angie Date: Mon Apr 17 23:02:32 2006 +0000 Added local definition of {chain,net}Rn4 to correct the matrix values and priority. commit 357b47d6d080676fc4fc41b7c1b0f440483391d2 Author: angie Date: Mon Apr 17 22:56:59 2006 +0000 Added local definition of {chain,net}Rn4 to correct the matrix values and priority. commit 1558ff125633762bae07dc0203b61523801dd9c2 Author: angie Date: Mon Apr 17 22:42:17 2006 +0000 Moved {chain,net}Rn4 descriptions up from hg18 and mouse to top-level, with default blastz matrix settings. commit 53880e7b307b9c61e1d3d42ebe5cdfe2e02ca324 Author: hartera Date: Mon Apr 17 22:29:08 2006 +0000 Check chromosome sequences. Create danRer4 database and grp table. Make hgcentraltest entry for danRer4. Break up sequence into 5 Mb chunks and make liftAll.lft file and trackDb entry. Create Simple Repeats track and process repeats into a mask. Additional zebrafish repeats library were obtained and added to RepeatMasker library. Sequence was split into 500 kb chunks and RepeatMasker was run on the genome sequence. Description html is in progress. commit 328aa43f1e7d0a3f8722d99741a4645b705e52f0 Author: hartera Date: Mon Apr 17 22:17:10 2006 +0000 Added a note to improve Affy Blat alignments in future. commit 45aac615f926987caaac502c679f0b96108be4d6 Author: kuhn Date: Mon Apr 17 22:06:34 2006 +0000 added some ### commit 57bbb7a9cdce810fb1a5d3e0abcde1b96d227a04 Author: angie Date: Mon Apr 17 21:43:14 2006 +0000 Updated all databases to latest, to match *BlastTab contents. commit 1b337baa428fa0375e29e0d608e55f2de2c90f24 Author: angie Date: Mon Apr 17 21:42:49 2006 +0000 Changed top-level otherOrgs.ra default settings to match dm2 instead of dm1. Added dm1-specific settings to otherOrgs.ra of databases that still have dmBlastTab built with dm1. Updated hg17, mm7, rn3 and sacCer1 otherOrgs.ra to use dm2 instead of dm1 because their dmBlastTab tables have been updated. commit 05c764f07236eeb1a9967867bf28f8f16e94a3f3 Author: angie Date: Mon Apr 17 21:35:47 2006 +0000 Added a few tests for NULL to avoid safef of NULL, which is not a problem for us (linux) but can cause SEGV on other platforms. commit 7339d5ce3a0b140980f2a4c34ccfb9f560efa274 Author: kate Date: Mon Apr 17 20:52:37 2006 +0000 Update Conservation track to fix overlaps commit e2415571c06edcb0bb7eb2fee4de2900e1f13ac5 Author: angie Date: Mon Apr 17 19:09:47 2006 +0000 Added who & when to a couple DONE lines. commit d0ffd6147e3f6f8403c1c10a2338ec3da4f26ddb Author: angie Date: Mon Apr 17 19:07:32 2006 +0000 emacs-motivated formatting tweaks. commit 8593e9f4e45c6d5a5e75f8bdcc73aa20fb3be27e Author: angie Date: Mon Apr 17 18:59:46 2006 +0000 Adding columnDb.ra for rn4 (same as for rn3). commit 3052d89299680404f1c8074e564c60f48a299955 Author: angie Date: Mon Apr 17 18:58:33 2006 +0000 Adding rn4-specific otherOrgs.ra. commit 229ae16f3d4eb85eee2e697800fecca0c1981953 Author: galt Date: Mon Apr 17 18:35:48 2006 +0000 people tired of needing manual reminder to make vgGetText, so I am adding it commit 2b93c99c6ce8c0d866ee2d9262b92b70c5607565 Author: kate Date: Mon Apr 17 17:37:19 2006 +0000 Update description for new cell line. Remove info redundant to their web page and add reference to it commit d4c93ab5e1f2ef915486c24ad8a632e5cdc2e876 Author: angie Date: Mon Apr 17 17:32:49 2006 +0000 Removed indices on chromEnd. commit 3a2f1a983df6770ef8f9cf880c752fdff885c1b1 Author: angie Date: Mon Apr 17 15:55:41 2006 +0000 Corrected usage description of -outDirDepth. commit d094aec3b1d3d99c0eb18d2b998beebeb72979ce Author: galt Date: Mon Apr 17 15:00:04 2006 +0000 "Encode release log update" commit 852bef4302df247baab4651233c50c90430e9daf Author: galt Date: Mon Apr 17 15:00:03 2006 +0000 "Release log update" commit 5d3ffae17e1c1ec3bba582a944ef65cde6d7f1c0 Author: donnak Date: Mon Apr 17 14:58:31 2006 +0000 Updated GenBank update info, per Mark. commit d28e59e29e4ce04141849e45b9a0fa0c13af23a9 Author: angie Date: Mon Apr 17 14:16:08 2006 +0000 Resolved -Wall warning: unused variable. commit 1693f85996a63f5ee515dd5b4d39fe3d785ccf7f Author: genbank Date: Mon Apr 17 06:44:53 2006 +0000 added GSC clone track commit 439e9776a0841f3315ed001bec64e2caa0ecd4b6 Author: markd Date: Mon Apr 17 06:44:14 2006 +0000 added not on mgc commit 97e425836d05d5f6b81bc65577a13ec4d90942fa Author: angie Date: Sun Apr 16 23:34:14 2006 +0000 Resolved -Wall warning: unused variable. commit 81e6beb9899f33b0616438ff23a9e07cc832b48a Author: markd Date: Sun Apr 16 19:11:28 2006 +0000 converted RT-PRC confirmed to PSL commit 8d4e564f9921d25a76f5fc5abbd56a527c66de76 Author: donnak Date: Sun Apr 16 19:02:53 2006 +0000 Added link to NCBI build statistics. commit 6122a227d935b90643a3da3830582a121c82300b Author: donnak Date: Sun Apr 16 18:38:09 2006 +0000 Added link to Build 35 release notes, other minor edits. commit dfed7bb0dd63fc8b20b1556fb8fd975d79481eb9 Author: donnak Date: Sun Apr 16 18:38:03 2006 +0000 Added link to Build 34 release notes, other minor edits. commit 57ea08eeaa8cd09ed137b55549c9ca0c659e0582 Author: donnak Date: Sun Apr 16 18:11:59 2006 +0000 Changed starting chrom position for first PAR to "1". commit 4d9acfcc31ad0c6d4a4762b234291ef957ac5fa7 Author: donnak Date: Sun Apr 16 17:57:33 2006 +0000 Added link to NCBI Build 36.1 release notes in hg18 announcement. commit 29393e073d577073afa512e61b817c58f5cdcd7f Author: donnak Date: Sun Apr 16 17:56:50 2006 +0000 Edited a few things in the gateway text, including changing the chrom start of the first PAR to be one-based. commit 3827daea61a02bd2ce0d062f7a03ae8fb61a9516 Author: donnak Date: Sun Apr 16 17:38:59 2006 +0000 Edited the hg18 news announcement. commit 07dc19b5b24932ca03430bda5a74ddd53f66b05e Author: donnak Date: Sun Apr 16 16:19:39 2006 +0000 Commented out Milwaukee mirror until it's fixed. commit b5647afaeb8ca449fb939aec8d6176ba79374fae Author: galt Date: Sun Apr 16 15:00:05 2006 +0000 "Encode release log update" commit f563db21319a49d6136e366b54badd73056303b3 Author: galt Date: Sun Apr 16 15:00:03 2006 +0000 "Release log update" commit 2ad61b33e96cacf7e1bf213756a652c501669e0c Author: fanhsu Date: Sun Apr 16 12:34:27 2006 +0000 Call PB using UniProt accession instead of display ID. commit 15bb9bc9fb5ee61e4e52b713d3afaa91159db576 Author: markd Date: Sun Apr 16 02:12:54 2006 +0000 switch to bluearc commit 4f0b057c7e74e07694cd471ee0c43a3a18bb3883 Author: heather Date: Sun Apr 16 00:29:13 2006 +0000 another flavor; this one reads a SNP list commit 694f5f16bcb9443941af8eec4e2bcc86445111f0 Author: kent Date: Sat Apr 15 17:35:40 2006 +0000 Fixing nested function calls of more than one parameter. commit 7c461cc1203832cf3ca3662e5ba2a21dc61a2bac Author: galt Date: Sat Apr 15 15:00:02 2006 +0000 "Encode release log update" commit 8df20f730a7c238622a0b599690519aecaa803c2 Author: galt Date: Sat Apr 15 15:00:01 2006 +0000 "Release log update" commit 27453136e7b92f731138625834cb81ab113e9683 Author: heather Date: Sat Apr 15 03:43:59 2006 +0000 add snpPAR and snpExceptionCheck commit 5491c795d351ddf282c1237b25314338d730a693 Author: heather Date: Sat Apr 15 03:43:33 2006 +0000 check that coords of exceptions match main table commit be8b34e5aa79c6d0db8090482f9c816524aa4bf0 Author: markd Date: Fri Apr 14 23:40:09 2006 +0000 started work on auto CCDS update commit cbfaad22534a038d01d16388b3379dd98a5b82c2 Author: markd Date: Fri Apr 14 23:38:14 2006 +0000 fixed bug running gbMkOrganismList commit 155d5ed4811a12d5ba604e632d044467a6e7d77a Author: heather Date: Fri Apr 14 21:45:29 2006 +0000 make sure exceptions have matching coords commit 07690f6fb55a04d486b257fab7133c6c4332958e Author: heather Date: Fri Apr 14 20:23:22 2006 +0000 definition of heavy hitter based on minutes value commit 6571f24fa0897e65a602f196b336aefb7f6303ea Author: sugnet Date: Fri Apr 14 20:14:34 2006 +0000 Adding check for borf prediction. commit 2a4634765834bc35a6f94679f2cc374c57f88216 Author: heather Date: Fri Apr 14 20:04:49 2006 +0000 report remote_host with more than 1000 hits commit 2f3141a383ccef93f65cdb4b0fd01b0952bc7a0d Author: giardine Date: Fri Apr 14 19:27:31 2006 +0000 Changed parameter names for the omim labels to include db. This avoids confusion when switching between genomes which have OMIM IDs and those that don't. Also changed OMIM available check for RefGene to check specifically for refLink entries linked to RefGene and have OMIM IDs. commit 3726cc43ecf9c2fed921dbd371cf6f285766ec02 Author: giardine Date: Fri Apr 14 19:21:56 2006 +0000 Removed db queries that checked on OMIM availability. Changed parameter names to include the db to prevent funny behavior when switching genomes, making the availability check unnecessary here. commit f79a7d7b2d9a2b834f38237498f6d95293d9a31e Author: kayla Date: Fri Apr 14 18:43:05 2006 +0000 Changed $o_Organism to $o_db for hg17 nets/chains commit d2338fb4a0d58117c0284c9d2edeba62f2cac590 Author: kayla Date: Fri Apr 14 18:25:10 2006 +0000 added hg18 commit e02e7cb686ca1e4606666c077faa4da9b196377e Author: kayla Date: Fri Apr 14 18:20:20 2006 +0000 for the hg17 nets/chains changed $o_Organism to $o_db commit dc563198687d5244dfe75e6cacd9c26a0b893a9f Author: heather Date: Fri Apr 14 17:18:15 2006 +0000 grammer improvement commit 6ce339179aaf775a8c88e4f991616d1afba30fd5 Author: ann Date: Fri Apr 14 16:55:26 2006 +0000 edited release date and name for hg18 commit 9aafb6d5101a373eae89600b4050a9399711de24 Author: hartera Date: Fri Apr 14 16:14:01 2006 +0000 First draft of description page for danRer4. commit 745f61646119fad8b2c385bff90e1300f59417bf Author: archanat Date: Fri Apr 14 15:54:09 2006 +0000 Added details about marker colors, using the filter, changed credits commit 83f09fd6f0eb6fa6ed20bb4ce9f56e96e18f47b6 Author: angie Date: Fri Apr 14 15:52:02 2006 +0000 Added more hgNear tables: *BlastTab, several knownTo*, expression distance for GNF Atlas 2. commit 2211d0aa0bd6a7b70c082fc3128a2b7cb9c76a8c Author: hartera Date: Fri Apr 14 15:45:20 2006 +0000 Added danRer4. commit 3e2c4f2a85ab15a703446ad4788896e8f0b6ed38 Author: angie Date: Fri Apr 14 15:36:18 2006 +0000 Added -targetOnly and -queryOnly options, so that a brand new database can have its *BlastTab tables built (-targetOnly) without overloading other databases' *BlastTab until it is released, at which point the other db's *BlastTab can be updated (-queryOnly). commit 39e0017496c2165dc5cef00a1b6a8955074b604c Author: hartera Date: Fri Apr 14 15:07:33 2006 +0000 Changed name of scaffolds agp file. Added chrM chunks agp file. Created lists of chromsomes. Made jkStuff and Bed directories. Checked agp files and FASTA sequence sizes. Split agp files by chromsome. Created agp files for chrNA and chrUn. Built chrom-level sequence. commit 851c7996f54d339619d01d2188152fd5522a36b2 Author: galt Date: Fri Apr 14 15:00:05 2006 +0000 "Encode release log update" commit 9bf2b18297bf598ae45d68c9c1fc2ef85263f818 Author: galt Date: Fri Apr 14 15:00:04 2006 +0000 "Release log update" commit 0a5d9d2da859bba12955e2d9523edd078dc79dc3 Author: angie Date: Fri Apr 14 14:53:33 2006 +0000 Resolved -Wall warning: too few arguments to errAbort. commit 3ed2c27630d34afac8cb1c5d66b1acd4182c92d2 Author: heather Date: Fri Apr 14 12:34:59 2006 +0000 fix order commit ab77a89c942fd41c5ebf311ae595f7fdb8d89eb2 Author: heather Date: Fri Apr 14 04:21:07 2006 +0000 more Brooke comments commit fc77485bb0856dd16a4c672883facc2ba34c11e7 Author: heather Date: Fri Apr 14 04:02:34 2006 +0000 change order of locType and molType commit d272433d7fbffcc8eb77821e1ba97869427b5831 Author: heather Date: Fri Apr 14 03:57:09 2006 +0000 implement function colors recommended by Jim; RT #1143 commit 4582b9f7d42fff9e2fc09a7da91b73c382ad51f9 Author: heather Date: Fri Apr 14 03:48:01 2006 +0000 add gray commit 351b684bef14d05981e8584d8f5122bd01bf372f Author: heather Date: Fri Apr 14 03:46:10 2006 +0000 add MG_GRAY for snp125; use standard green commit ac7ea75e0e06b55098de9845558e14d24d8a04a8 Author: heather Date: Fri Apr 14 03:34:19 2006 +0000 change another locType to location type commit 8761b3c362d6ab5b96184f5da078a72f1a490e78 Author: heather Date: Fri Apr 14 03:32:42 2006 +0000 fix to match snp125Ui commit e0b69f160c37f30d3ea5ef9bd1f2e3418270a8e3 Author: hartera Date: Fri Apr 14 03:17:47 2006 +0000 Added option to specify the number of Ns inserted between scaffolds. commit 394b2f46a378cf07f7f23e994a42c93ba2bbcea1 Author: heather Date: Fri Apr 14 03:05:10 2006 +0000 remove coding (not used by dbSNP) commit 2ebe61fbb4734aa9e86a1e5440c20478ce4af3d9 Author: heather Date: Fri Apr 14 03:02:10 2006 +0000 change order of locType and molType in color specification commit eea7b4a196749233bfbc19dca84987abd1d5f65a Author: heather Date: Fri Apr 14 02:53:56 2006 +0000 changing order of excludes commit 9cc73bb5b5c8e43ffb7e167fdbeff3cf1f370f65 Author: heather Date: Fri Apr 14 02:48:55 2006 +0000 feedback from Brooke commit fb1a7ef423cda130dd93601a7fac34ed9d495a08 Author: heather Date: Fri Apr 14 02:42:32 2006 +0000 change to match hgTrackUi commit 16d3c340a4b6e5a3c0ae90ae655484817308a871 Author: heather Date: Fri Apr 14 02:39:21 2006 +0000 further feedback from Brooke commit 5e3793b0491d7ac1e4ddbf24a6815561d5ad14e6 Author: galt Date: Fri Apr 14 02:38:00 2006 +0000 fixing handling of thumb caption for Mutants and Organism when the imageFile has multiple panes commit 673c6198ce3cc7c110abe9aa37572f740f264026 Author: kayla Date: Thu Apr 13 23:50:55 2006 +0000 Added hg18 net/chain blocks in order to change the priority number. commit 31257d0672bccf0602d99a4b1311d3e4200a2357 Author: hiram Date: Thu Apr 13 23:24:11 2006 +0000 Nearing the completion of the Hg18 protein mapping situation commit 45cfcb22924d3c24e4bf75b302ca61b6dbfceaff Author: hiram Date: Thu Apr 13 23:23:48 2006 +0000 Started blastz on Hg17 for Krish commit 11043f848ce353b7b50654b9584038c9101622b0 Author: kuhn Date: Thu Apr 13 23:13:22 2006 +0000 typo commit 7f0c1312d0cd8f9169c6bdccf746e0c85cd125e4 Author: baertsch Date: Thu Apr 13 23:01:49 2006 +0000 missing ; commit b3cecf6799271b3698fe35432e904d57dbdec492 Author: baertsch Date: Thu Apr 13 23:00:59 2006 +0000 add struct dnaSeq *hChromSeqMixed2(char *chrom, int start, int end) /* Return mixed case (repeats in lower case) DNA from chromosome. */ struct dnaSeq *hDnaFromSeq2(char *seqName, int start, int end, enum dnaCase dnaCase) /* Fetch DNA */ commit 8d1ff306d9f8566568da40633a972c1e1bb652a5 Author: baertsch Date: Thu Apr 13 22:57:14 2006 +0000 add two routines: struct dnaSeq *hChromSeqMixed2(char *chrom, int start, int end) /* Return mixed case (repeats in lower case) DNA from chromosome on second connection */ struct dnaSeq *hDnaFromSeq2(char *seqName, int start, int end, enum dnaCase dnaCase) /* Fetch DNA from second connection*/ commit c60b8bdba8c0623870a0e644f9caa563698afa30 Author: hiram Date: Thu Apr 13 22:39:32 2006 +0000 Adding chainSelf and blastHg18KG tracks commit 8f93ef528ec143854d33b7ea7647cab866e85aee Author: krish Date: Thu Apr 13 22:08:39 2006 +0000 added -noPrefix option to not output "chr" prefix commit b7d396f46e1b16f0b4048bbf31d20d7085eb1c0b Author: kent Date: Thu Apr 13 21:49:27 2006 +0000 Removing mysql dependency. commit 63782d48d2eeb113cd6292f8f77c60ffaa5938d0 Author: ytlu Date: Thu Apr 13 21:42:59 2006 +0000 modified the stsMapMouseNew color commit 503d19dba4d85c1a9db35135e89f76a3fd71b710 Author: kayla Date: Thu Apr 13 19:50:58 2006 +0000 Changed net/chain hg17 short labels from $o_organism to $o_db commit eb27b709a17d9968041b5fdc1125dbbc3780dab1 Author: ann Date: Thu Apr 13 18:49:00 2006 +0000 changed hg18's Release Name to NCBI 36.1 commit fbc2c863bf274a474948ee4b7756388781edec25 Author: kent Date: Thu Apr 13 17:57:23 2006 +0000 Adding maxItem setting commit fb3a04ab6f2f0127abaa902d4db31d2c0bac67e1 Author: kent Date: Thu Apr 13 17:57:03 2006 +0000 Adding maxItems setting. commit 427b80ff54b4d1caf028a2015fe5d919d2c0798a Author: kate Date: Thu Apr 13 17:44:08 2006 +0000 Suppress selection checkbox for subtracks in trackDb that lack tables commit c32bad8544a38ba088ce64cb14f443c3a1f20bdc Author: kent Date: Thu Apr 13 17:00:06 2006 +0000 Starting to work on object creation in assembler. commit c8881f815bef30b4f0d17b31e192fd68ec49c6a0 Author: angie Date: Thu Apr 13 16:59:56 2006 +0000 Resolved -Wall warning: unused variable. commit 83048a8931099e16d2a93e83e69648fbb6fc387a Author: kent Date: Thu Apr 13 16:56:46 2006 +0000 Making stub for object creation from tuple function from assembler. commit 7c077db72d4047035010afee874720ff3f56e265 Author: kate Date: Thu Apr 13 16:55:34 2006 +0000 Remove obsolete file commit d04ae59bf080fd27eae748521cabb0c5842d5d33 Author: hiram Date: Thu Apr 13 16:54:42 2006 +0000 Reloaded picTar data tracks commit 900f79e77d9401ed2c2cf4c15ef73c8732e0df01 Author: hiram Date: Thu Apr 13 16:54:14 2006 +0000 clean up garbage commit 4dca9200004960dea80245d6d959e9e4c680eeb4 Author: fanhsu Date: Thu Apr 13 16:43:36 2006 +0000 Added knownToHInv table to enable H-Inv link in KG details page. commit 5cb8b0dfb270110cc17ad59b55aa3d259f90a2b8 Author: hiram Date: Thu Apr 13 16:29:26 2006 +0000 Updated picTar data tables commit 88474a82d7b190e585ea4c53cc0c317e140dc213 Author: hiram Date: Thu Apr 13 16:28:52 2006 +0000 change picTar table name commit 4583ae756988350ba5c7cdb922217e15882cc91e Author: hiram Date: Thu Apr 13 16:16:57 2006 +0000 Updated credits for picTar track and renamed the track table commit 8a71da84d5c861abb3a2968e813e5f1ebd8be50d Author: hiram Date: Thu Apr 13 16:15:34 2006 +0000 Updated picTar credits links commit 38f50fba6a73dcefd802e358089d59eeb8bafff3 Author: hiram Date: Thu Apr 13 16:10:06 2006 +0000 updated picTar comments commit 23b450d0a7dbb0bf49cae66612c7a3d14cbf3bf2 Author: galt Date: Thu Apr 13 15:00:07 2006 +0000 "Encode release log update" commit 2c11f513791f35947394d74a70ad45eb33ece681 Author: galt Date: Thu Apr 13 15:00:06 2006 +0000 "Release log update" commit 5c6513be7d4066a11ee548d078b52eb7387afe63 Author: fanhsu Date: Thu Apr 13 12:33:46 2006 +0000 Removed the link to ExonPrimer. They are not ready yet. commit e4b46270da1312db40abc929e93246d1fd783349 Author: donnak Date: Thu Apr 13 06:55:45 2006 +0000 Updated hg18 credits. commit e6fe36f82fe272e2b16774d36022901849429ed0 Author: kent Date: Thu Apr 13 06:55:08 2006 +0000 Getting rid of some debugging. commit cfc5c35cd6abf8c11e0e28ef42b31902d4d03037 Author: donnak Date: Thu Apr 13 06:54:26 2006 +0000 Added news item abt hg18. commit 82b6511159c8593d4447bd4ba29acb783cb3db9a Author: donnak Date: Thu Apr 13 06:53:59 2006 +0000 Archived a news item. commit ec000fe7ec7a7dc4e71665eccecbc90ceac2c421 Author: kent Date: Thu Apr 13 06:53:05 2006 +0000 Making print forgive missing pf_cleanup routine. commit 416fd7537a6a25f814b288a0a3b43444cec5212a Author: kent Date: Thu Apr 13 06:52:44 2006 +0000 Putting in print. commit 1566537a77ef76d984b01bae904ff2a3f42fc6d6 Author: donnak Date: Thu Apr 13 06:27:31 2006 +0000 Added info about the haplotype regions, updated PAR info. commit 3be9122529882ca5c92a8531f39e5dc069d0b785 Author: markd Date: Thu Apr 13 03:44:53 2006 +0000 reloaded genbank commit 759fcd85640f89cd7a41016fe86628ae4da8dd78 Author: markd Date: Thu Apr 13 03:42:18 2006 +0000 enabled oryCun1 alignments commit 99b258929a61dbc0202d4da1b0053c8c126af646 Author: ytlu Date: Thu Apr 13 03:28:34 2006 +0000 change color for stsMapMouseNew. commit cf390b5233e02b07740e0000eb26910827114a50 Author: kate Date: Thu Apr 13 00:44:48 2006 +0000 Add panTro2 commit 47cba0a03f728a0854b296aae15ee9ca9966ce89 Author: kate Date: Thu Apr 13 00:36:52 2006 +0000 Add panTro2 tracks commit dcae45fb8a50c5f314fbdb5f5aecafee15f5da80 Author: kate Date: Thu Apr 13 00:11:19 2006 +0000 Customize for chimp special Genbank procedures commit a76f067ea0948316b343ed2b8bda032e8c0885a6 Author: markd Date: Thu Apr 13 00:04:06 2006 +0000 created nets for hg17 commit c5ccb16cd499e2b3621f719dfc34acea6c9aa5a0 Author: kate Date: Wed Apr 12 23:33:20 2006 +0000 Fix new Sanger ENCODE subtrack label, and remove from public site pre-Q/A commit 91516e73670fdc384c4adceca7aa0475817dbe94 Author: ann Date: Wed Apr 12 23:30:53 2006 +0000 added block for mgcGenes commit ca660c914723818a958fdcddc3728d7cae8fc482 Author: hiram Date: Wed Apr 12 23:21:19 2006 +0000 broken cut and paste lines fixed commit f796140e3e44e76e9090d1c615dbaa2b004f9e65 Author: galt Date: Wed Apr 12 23:04:30 2006 +0000 made allen brain probe alignments to mm8 and KG-url-to-ABI to mm8 commit 3eafe150cac4691caf6772459b94b47afb15e8a3 Author: ann Date: Wed Apr 12 22:31:52 2006 +0000 edited short and long labels for some chains/nets commit 05a82c522787014de2008a82d2423dfe147746a7 Author: fanhsu Date: Wed Apr 12 22:23:52 2006 +0000 Re-built go DB. commit 3b018a2fb5897783bab7b12be3f43dad686142c9 Author: ytlu Date: Wed Apr 12 22:05:16 2006 +0000 update the color for stsMapMouseNew marker commit 9ae5e5e8c7a1fd2798bf0b3d0cadd538ba874b33 Author: hiram Date: Wed Apr 12 22:02:33 2006 +0000 Reloaded stsMapMouseNew to remove blanks commit 4a2613a321255a19b4fe84bbca65558718d8c1f7 Author: galt Date: Wed Apr 12 21:44:16 2006 +0000 handle attachments > 100MB commit 7649398b42d039b5fceba9839c2fb3548bfd9430 Author: ann Date: Wed Apr 12 21:06:31 2006 +0000 fixed typo commit c5f78a6728c6ac341001a01b910fe33adec0ff95 Author: fanhsu Date: Wed Apr 12 20:39:39 2006 +0000 Switched Exon Primer to hg18. commit a059b347ea9d26f1e4af751b6dbb776da4bba71c Author: kent Date: Wed Apr 12 20:29:48 2006 +0000 Getting integer 'print' to work in code generator. commit 5b532f23266950b1843a8162c8621c5d12252429 Author: hiram Date: Wed Apr 12 20:27:21 2006 +0000 Better error messages on out of memory limits, asserts become errAbort() commit b8d21c34aa5ae18f9fe0ab2ba1a0ebe0fc08edf8 Author: heather Date: Wed Apr 12 20:19:23 2006 +0000 note when more than 5 seconds commit a21d7b1167bd3df492a94eb29a920bcd86224001 Author: heather Date: Wed Apr 12 20:11:21 2006 +0000 check for no rows commit 853d30164e6e6b068ae8da04bbc284b510d52f63 Author: kent Date: Wed Apr 12 20:08:02 2006 +0000 Starting to handle var types in code generator. commit 5fd1c2ca3da8137f0b043f95bd65c1efef894017 Author: kuhn Date: Wed Apr 12 19:32:34 2006 +0000 added some ### to make searching easier commit f867be8f94a4d8151e9d6e785bf06214707a99e5 Author: heather Date: Wed Apr 12 19:12:21 2006 +0000 add desc500 commit 33e350a39d279fd13f3b1c05db603282c8ec1c38 Author: ann Date: Wed Apr 12 18:46:12 2006 +0000 one more edit to the liftOverChain check commit 96aeee3e22eeaec0996d43edc24fc1cec911ca04 Author: ann Date: Wed Apr 12 18:42:41 2006 +0000 fixed error for checking the liftOverChain table commit eeafe28a92cdc2f32454679873b12444df0734c8 Author: kent Date: Wed Apr 12 16:36:08 2006 +0000 Making isxAddress use a simplified token. commit f4e72bb2c84f048f59d1474b18c26c107082bff1 Author: kent Date: Wed Apr 12 16:06:46 2006 +0000 Putting back in hgGene on for transition period. commit 0e10e333c2eb94236d68f39a79b908a3a52de673 Author: galt Date: Wed Apr 12 15:00:05 2006 +0000 "Encode release log update" commit 10af0e1fd0ecba8c5ea9f52528509147b981c028 Author: galt Date: Wed Apr 12 15:00:03 2006 +0000 "Release log update" commit 8ee45620102725d006a5a9c44fbf46322da9fb12 Author: angie Date: Wed Apr 12 14:17:35 2006 +0000 Resolved -Wall warning: unused variable. commit d07be65834d1cf03478f64ff9760c09e47a32efd Author: galt Date: Wed Apr 12 07:15:04 2006 +0000 added JAX,MGI searches by patching contributors commit 982b052a899fc3e12611b7728d37ca0d98bcb758 Author: galt Date: Wed Apr 12 06:37:30 2006 +0000 added "Mutant " in front of those those thumb captions needing it commit f65c619e0c88ea745cf9732fcdf4d0c20844076e Author: donnak Date: Wed Apr 12 06:23:47 2006 +0000 Added credits for hg18. commit 15357b81ff77713277fb80ba80021a27446c6c72 Author: kuhn Date: Wed Apr 12 06:13:21 2006 +0000 tweaks commit ba5f900de76f44cace0304dc622dcd03a7fe1e06 Author: kuhn Date: Wed Apr 12 06:09:12 2006 +0000 fixed format and typos and English commit ee8680c0fead2e23d854c6023e14d4c0ecdba768 Author: kuhn Date: Wed Apr 12 05:44:07 2006 +0000 put back original first sentence commit 659b434f810f136f6ca7147a3e34dd5785fe3a1f Author: markd Date: Wed Apr 12 05:30:06 2006 +0000 fixed flag for organism list build commit 939a1597a515b4177a368e5867c26e311a21966e Author: kuhn Date: Wed Apr 12 05:24:16 2006 +0000 tweaks commit b05e45e270371d2170ea27dd7358b3c95211bcb7 Author: kuhn Date: Wed Apr 12 05:04:51 2006 +0000 keep finding little tweaks commit b6eac3dea399a8ea1983e7c1935e3d323c2b4909 Author: kuhn Date: Wed Apr 12 05:02:09 2006 +0000 typo commit 09d1dc561651d5df73dbc3e92b9f0634d884db0d Author: kuhn Date: Wed Apr 12 04:59:54 2006 +0000 grammar tweak commit 969071919a1d34ab1c1a274611e271192510aaaa Author: kuhn Date: Wed Apr 12 04:52:22 2006 +0000 mostly format tweaks, typos and a littlerewording commit 4b3970f30f51ac556042c318b531646a4bcc0414 Author: kent Date: Wed Apr 12 03:27:29 2006 +0000 Implementing directUrl setting. Getting rid of some old unused code. commit c2c2e570648764d18ba3973b3e60c1d6bf89cf8a Author: baertsch Date: Wed Apr 12 02:44:42 2006 +0000 revert really commit 260aa77772e4f66d0ce19e377a501726a9ac5c6c Author: baertsch Date: Wed Apr 12 02:43:56 2006 +0000 revert to last version commit b141ac2a6a04d8921974a2cff79e008e472066b3 Author: baertsch Date: Wed Apr 12 02:24:38 2006 +0000 taxonomy records commit d46496a9ad44fcf109fc8cb5db4e658f363f019d Author: baertsch Date: Wed Apr 12 01:18:55 2006 +0000 back out debug change commit 653279a3158673c4928637ce18f9a2bcdc753d30 Author: angie Date: Tue Apr 11 23:38:45 2006 +0000 Added Affy tracks: affyRAE230, affyU34A, gnfAtlas2. Also knownToRAE230, knownToU34A tables for hgGene, hgNear. commit 51b87796700ead0887db170a41791275993face3 Author: baertsch Date: Tue Apr 11 22:41:59 2006 +0000 add missing sql to taxon table load commit d1c4298ab3f45fc02a901f74c3466886dff728f4 Author: baertsch Date: Tue Apr 11 22:40:26 2006 +0000 added 5 taxon* tables commit e421b074a62e2890d8927842c211cab78b51d35e Author: hiram Date: Tue Apr 11 22:21:39 2006 +0000 Correct paragraph breaks commit cbd7cfdb168df38b82e0a7aac18c4362429d3898 Author: baertsch Date: Tue Apr 11 22:15:50 2006 +0000 add comma commit 37e7cc5dd78a200e7f81eab383ae5ede00d9ec5a Author: baertsch Date: Tue Apr 11 22:15:09 2006 +0000 make name primary key commit 08b7492bca8584f8e05f181b804ca596dba3f7d6 Author: markd Date: Tue Apr 11 22:02:31 2006 +0000 get chimp subspecies commit 6fcf17c2c1784bcc4709d85408e2e64960326319 Author: hiram Date: Tue Apr 11 22:00:43 2006 +0000 Corrections to picTar references commit 49fdee6d5f01061242c36ce9b944a3cbc9c0cb7b Author: hiram Date: Tue Apr 11 22:00:18 2006 +0000 Updated descriptions for picTar data from Nikolaus email of 2006-04-09 10:45 commit 80231b8c014b87a1ddb1eb18df95e0c3ba8bfb29 Author: hiram Date: Tue Apr 11 21:49:39 2006 +0000 Updated picTar descriptions from Nikolaus email of 2006-04-09 10:45 commit 49b4a6eba3bf50a2bf1bb28a7c7964f31dc612ad Author: baertsch Date: Tue Apr 11 21:44:07 2006 +0000 remove .o files commit d9a289ed691f90d0c238bedd2e3b9727f651695c Author: baertsch Date: Tue Apr 11 21:43:11 2006 +0000 add taxonomy tables commit b70bec2fc775d9fdc51a77098a68d923d3a56e00 Author: hiram Date: Tue Apr 11 20:35:21 2006 +0000 picTar proper long label commit 360ac47ae99c5bfe54cb26df0ce161e10aeeef79 Author: hiram Date: Tue Apr 11 20:33:35 2006 +0000 Move the picTar track to the regulation group commit 8688392432f7e93d381abe9942494234ca41292a Author: hiram Date: Tue Apr 11 20:31:54 2006 +0000 Added full description from Nikolaus commit 013f6cd93983da5283a120009ed5cab9344f1c49 Author: ann Date: Tue Apr 11 19:08:41 2006 +0000 removed 'release alpha' blocks for old 8way Conservation track, bosTau2 chain track, and bosTau2 net. Also removed 'release beta' line from the corresponding blocks. commit bf2a80cce71cbbb66cf131b25c47b61a1a926ac9 Author: heather Date: Tue Apr 11 17:34:11 2006 +0000 add note about underscore commit 8e6cd167d16019ed0cc49f7cab8eb73a068c1645 Author: markd Date: Tue Apr 11 16:33:44 2006 +0000 only count refseq NM_ commit 8761ec1b343e914a3cbbe7499512f93171e88e8f Author: angie Date: Tue Apr 11 16:26:27 2006 +0000 Resolved -Wall warning: unused variable, too few args to errAbort. commit f6739885d529653a95e4b2ec72f98fb93532c62a Author: galt Date: Tue Apr 11 15:00:03 2006 +0000 "Encode release log update" commit 6a005898efae7ce7da30ab3ec45aa8a93a305b58 Author: galt Date: Tue Apr 11 15:00:02 2006 +0000 "Release log update" commit 5c104e9eaf4907573654bd9de21844f4cc487a65 Author: kent Date: Tue Apr 11 06:23:38 2006 +0000 Putting wrapper around module entry point to make sure not called twice.\n commit 5136d72d8a324c2ca3c57f645e1e716fd1007eeb Author: kent Date: Tue Apr 11 05:49:41 2006 +0000 Linking in cMain with assembler output. commit 108fdaa6b3bc24e7dfc5f6a15d7e5b9378b12f10 Author: donnak Date: Tue Apr 11 05:43:43 2006 +0000 Uncommented hg18 from release table. commit 6fae7b2c1cb6c78a30e8b5a019a9998689888443 Author: kent Date: Tue Apr 11 03:22:41 2006 +0000 Realized can keep main module and main type table in C even when doing assembly coding of rest of things. This simplifies a lot of things. commit 991bceba9528784b5ae5bccd1df40259547faf22 Author: kent Date: Tue Apr 11 02:34:15 2006 +0000 Printing out module table in main module, and poly_info table in other modules when generating assembler. commit 03ba620ee54ea36d320c781c7b90658457c3991a Author: heather Date: Tue Apr 11 01:41:32 2006 +0000 include exceptions commit e98dd41ef8f75cba57f48af6379a3a85d44bf0e2 Author: heather Date: Tue Apr 11 00:51:07 2006 +0000 report contents of genelist commit 40f41ecacba9e5369286665f75104cb20493126a Author: angie Date: Tue Apr 11 00:42:31 2006 +0000 Added miRNA. commit 6ede6489f890577f073166f6ef1c15141e65bc82 Author: heather Date: Tue Apr 11 00:25:11 2006 +0000 "New version number v131" commit d800af88f4580328633ba31c3e9022d7e8f94c84 Author: ann Date: Tue Apr 11 00:09:00 2006 +0000 initial doc. copied from mm7. added $matrix variable. commit 60a49f8c0636a1d1f548fb5d029358426ca77837 Author: angie Date: Tue Apr 11 00:04:23 2006 +0000 Added latest reference (the miRBase site requests that users cite both the 2006 and 2004 NAR DB issue papers). commit 09f3f70d9ebbeba9b0fae238db54e9c31d94cb25 Author: heather Date: Tue Apr 11 00:01:00 2006 +0000 initial revision; generate chrY PAR SNPs from chrX commit 313f0576b38f0f45f0c24a2fafdf2f3150053057 Author: heather Date: Tue Apr 11 00:00:45 2006 +0000 add snpPAR commit de49e96ede0af0e1f782f2c2d34f5528493459a1 Author: kent Date: Mon Apr 10 23:58:39 2006 +0000 Looks like am saving type info in assembler. Still need to connect it up. commit 866868394730a46ed5d5a1608fed0139cf31b1b2 Author: donnak Date: Mon Apr 10 23:53:15 2006 +0000 Updated UniProt data use restrictions section. commit ad195527faef9f871018d0404de4379b89eb99a7 Author: ann Date: Mon Apr 10 23:40:57 2006 +0000 copied from mm7. needed to add at this level because the default matrix was incorrect commit 0a58c48ef12c918db2fb3372b833d8bb20eacf3d Author: heather Date: Mon Apr 10 22:53:21 2006 +0000 add checks of page returned commit 65be0dd22f67e0e214067badcaf0116a8c449d10 Author: ann Date: Mon Apr 10 22:17:23 2006 +0000 added matrixHeader row for chainDanRer3 commit 4e5956f3c75599204fb3e31d1844fa48739adc64 Author: heather Date: Mon Apr 10 21:34:11 2006 +0000 fix typo commit a680189ffd147009eda7f98c625f33819fee1f21 Author: ann Date: Mon Apr 10 21:29:12 2006 +0000 made description more generic since it is used by several assemblies commit aece2173cf254c6cf27594a123d57600ff25aff0 Author: kent Date: Mon Apr 10 20:35:13 2006 +0000 A little more work in emitting types in assembler. commit 6835d5065f0beaaa148399ee51175621d6d2ce95 Author: heather Date: Mon Apr 10 20:32:59 2006 +0000 change comment commit 1bc67b9bf6d4b77fc23ef6c1fb0ea4ff12df73a9 Author: heather Date: Mon Apr 10 20:27:15 2006 +0000 change comment commit e73ac7f623311d719141b88b31ef88c4e3550d6c Author: kent Date: Mon Apr 10 19:47:38 2006 +0000 Starting to build up a backEnd interface structure. In theory at least saving local type info via backEnd. commit dd43f67ba5586c8f7abffbe13aae87aa56e0efd2 Author: angie Date: Mon Apr 10 17:37:07 2006 +0000 Clarified the message about when blocks are merged for display. commit 4f3812f23636658a3e90dc259c00c090653ba698 Author: angie Date: Mon Apr 10 16:55:17 2006 +0000 Replace the tRNA category with RNA which is a catch-all for *RNA classes (tRNA, rRNA, scRNA, snRNA, srpRNA). commit 23d72bb84a59bdfa6c0112940504553dca72a313 Author: angie Date: Mon Apr 10 16:27:18 2006 +0000 Added maf annotations and removed the part about loading unannotated maf. Reloaded cpg* tables with bin field. Reloaded bacEndPairs without chromEnd index. commit 9e8135d36f3d49dbbb7e7602e9d0ba4dc3f67cd4 Author: angie Date: Mon Apr 10 16:24:26 2006 +0000 Adding mkMafFrames.pl: perlified version of MarkD's script to run genePredToMafFrames on a cluster node. commit 10f7919061029461c46bf400b9b2cc657cdde240 Author: angie Date: Mon Apr 10 16:19:30 2006 +0000 Typo fix in matrixHeader (A, C, G, T not A, C, T, G!). commit e1b7806108e789de87fb7e2e21ae5eddd1117c21 Author: angie Date: Mon Apr 10 16:14:41 2006 +0000 Added local chainXenTro1 def in order to pick up local chainXenTro1.html. Typo fix in chainDanRer3 matrixHeader setting. commit c762cca63d13db1d4c3022132a4073da45f612ef Author: angie Date: Mon Apr 10 16:14:20 2006 +0000 Moved {chain,net}MonDom4 up to top-level. commit 089ef71b2156cfafba98ea82c8718f35628b522e Author: angie Date: Mon Apr 10 16:14:03 2006 +0000 Moved up {chain,net}MonDom4 from rat/trackDb.ra. Added matrix setting to chain{XenTro1,GalGal2,MonDom4,BosTau2,CanFam2}. commit 3acad8f506a659c9e50040da467a003d3a8abfbb Author: angie Date: Mon Apr 10 16:12:13 2006 +0000 Added $matrix. Updated axt-->psl. commit 863f8acc5acc9d9287607100ee5b3f8c0736d30b Author: angie Date: Mon Apr 10 16:11:20 2006 +0000 Updated axt-->psl. commit e811e061f1cc2251e0fd1174d45e54c35831f5f6 Author: angie Date: Mon Apr 10 16:09:21 2006 +0000 Removed description of abridging of lineage-specific repeats. Added $matrix and updated axt-->psl. commit ba01fba5545e5a1e0f765040e90578ad61481225 Author: angie Date: Mon Apr 10 16:05:29 2006 +0000 Chain description -- no abridging of lineage-specific repeats. commit 46ab1c49d959084a7268827d1d6717532f5f80f2 Author: angie Date: Mon Apr 10 16:04:29 2006 +0000 Nets for monDom4. commit 162aab2e3f310f1d1c3f1e7b29c52b29c1dbde92 Author: angie Date: Mon Apr 10 16:03:33 2006 +0000 Chains for monDom4 -- no abridging of lineage specific repeats. commit 4cc8e57f8a447b57e838b35a0f48603a14d4baa9 Author: angie Date: Mon Apr 10 15:22:35 2006 +0000 Resolved -Wall warning: unused variable. commit 5ff9cbf94785e4244a0cc6499c195849bb4a5750 Author: galt Date: Mon Apr 10 15:00:03 2006 +0000 "Encode release log update" commit 93d8ed8fcb7c82dd9e5bcb3f8cd380ea6dae5395 Author: galt Date: Mon Apr 10 15:00:01 2006 +0000 "Release log update" commit 20de4678da7abc5a7eca60d3610315686de4df76 Author: fanhsu Date: Mon Apr 10 13:42:23 2006 +0000 Added defensive logic to guard against curProtId being NULL. commit 65cedd2616f92d3e6746077a07175d19d6f96e7b Author: aamp Date: Mon Apr 10 09:43:51 2006 +0000 Oh that was dumb. commit bbfbfb31021ab15ca03fff582209f1a6fcfa4d02 Author: aamp Date: Mon Apr 10 09:42:45 2006 +0000 Utility to convert windowmasker output to bed. commit 5da30d76f515f24705d4b55397264da31b5844d1 Author: markd Date: Sun Apr 9 20:54:04 2006 +0000 created hg17 swap chains/nets commit 379683d928a153a29f955bb0322927b67a93afd8 Author: angie Date: Sun Apr 9 20:09:01 2006 +0000 Resolved -Wall warning: unused variable. commit 96b0d5d76243589ebb2a3b4015e257d264ed5800 Author: galt Date: Sun Apr 9 15:00:03 2006 +0000 "Encode release log update" commit 8e28185457b2d5eb4d7d50e09ed8632dc965db57 Author: galt Date: Sun Apr 9 15:00:02 2006 +0000 "Release log update" commit 864eae1e779ed3177d3e440e52dbce4043efa40f Author: markd Date: Sat Apr 8 23:49:31 2006 +0000 added estOrient to build commit df1bb2ad7bbe567dd69f24c432e60466edf0b626 Author: angie Date: Sat Apr 8 16:32:45 2006 +0000 Resolved -Wall warning: unused variable. commit 2a02b420f22337509c7c89e57eb19c7b3e1f2bf1 Author: galt Date: Sat Apr 8 15:00:02 2006 +0000 "Encode release log update" commit 8464b84516c59430629ffdee1dd47049df76e9ea Author: galt Date: Sat Apr 8 15:00:01 2006 +0000 "Release log update" commit 59cd87a1b9cb25cc7b39705ac674b88a036807b8 Author: fanhsu Date: Sat Apr 8 02:12:02 2006 +0000 Created knownGene.html. commit 8a28e4a0165f2a85ee01b20c51b042f61b71bb8f Author: fanhsu Date: Sat Apr 8 00:12:59 2006 +0000 Updated the phaseCons section to reflect the rebuilt. commit 2fe7ac6cb4dd4ef31e4c12e6c8a7bda1be5d37d3 Author: heather Date: Sat Apr 8 00:08:15 2006 +0000 note off-by-one for between commit 5384f72c4f32e888c3f821699d41e654cc00b704 Author: heather Date: Sat Apr 8 00:07:30 2006 +0000 also exclude weight = 3 commit c7aa66341ca9fbdb33476275bddf14a52016adc3 Author: fanhsu Date: Fri Apr 7 23:19:33 2006 +0000 Updated the PDB image URL. commit ade0e5f3862e24ae4784c40b284965c31c67f4d3 Author: kuhn Date: Fri Apr 7 22:44:07 2006 +0000 undoing Fan :-) don't want mm8-pointing tables to go out prematurely commit 732a3be1282c893f964260fbe7eb16b745473aee Author: markd Date: Fri Apr 7 22:29:08 2006 +0000 made column names reflect std convention commit ae050ae31a891d8410814ac1f29fea08b60dab83 Author: angie Date: Fri Apr 7 20:30:54 2006 +0000 Corrected the description of score. commit d306a6d866b01e9e22a64ee91588f72a6f008d2a Author: angie Date: Fri Apr 7 18:55:05 2006 +0000 Added history table comment. commit 2700b178a15b2c5f22594e934dfbb7bb7449bc48 Author: heather Date: Fri Apr 7 18:20:27 2006 +0000 124/125 coord changes commit 3b6c3215ab85fda94315efc3cdac4a83463aff26 Author: angie Date: Fri Apr 7 18:15:07 2006 +0000 Removed chromEnd index. commit de128801282d87bdfb2a6b9e4f1e43da2b46c0ae Author: angie Date: Fri Apr 7 18:13:27 2006 +0000 Added bin and removed chromEnd index. commit 4b36f55a34d6fe597c7b63462d53e4fd014e4b96 Author: fanhsu Date: Fri Apr 7 18:03:22 2006 +0000 Changed mm7 to mm8. commit 3a4c72629c0056e66c9bfc99b1fbb672a859ac35 Author: heather Date: Fri Apr 7 17:57:04 2006 +0000 add snpCompareLoctypeCounts.out commit 4df7a9c67b78c26b8b96bfb8214ee2cd17a362ac Author: heather Date: Fri Apr 7 17:48:25 2006 +0000 updates for snp125 commit 3c93779803b15ac388ca0ce062bd08c0b5031f4c Author: angie Date: Fri Apr 7 17:29:35 2006 +0000 Removed index on chromEnd -- not used. commit b1e11208e6bd543fc0fc06a674c475eb831ea865 Author: ann Date: Fri Apr 7 15:50:01 2006 +0000 added QA note about pushing new cutters data commit 14f8142ef669f17267545d2196b1f2e38224d9a6 Author: heather Date: Fri Apr 7 15:25:48 2006 +0000 automate processing after snpContigLocFilter, snpContigLocusIdFilter, snpContigLocusIdCondense and snpLoadFasta commit 0b3bbc78d4401bb4481d9e6436e3ae2c2a082bfd Author: angie Date: Fri Apr 7 15:25:26 2006 +0000 Resolved -Wall warning: unused variable, char used as array index (cast to int). commit 954b086421dd9ad9f8350e3d4f18ea30117a2229 Author: angie Date: Fri Apr 7 15:25:18 2006 +0000 Resolved -Wall warning: unused variable. commit 7004dbad9ac14c9ddb591ece80a55981acfbef49 Author: angie Date: Fri Apr 7 15:18:29 2006 +0000 Resolved -Wall warning: char used as array index (cast to int). commit c76fd3726126edbdd91b2a3e7730d730b2862011 Author: heather Date: Fri Apr 7 15:17:30 2006 +0000 simplify commit 88be8526bb7b21212e383bd3fac201a5ade6cf32 Author: angie Date: Fri Apr 7 15:11:38 2006 +0000 Resolved -Wall warning: unused variable, char used as array index (cast to int), multi-line // comment (with \). commit 1dbc9a765c8836643dae907521dcf23a2ec064aa Author: galt Date: Fri Apr 7 15:00:02 2006 +0000 "Encode release log update" commit 7019be85b914df3fe9e7cdd0b52c889c5c3991fe Author: galt Date: Fri Apr 7 15:00:01 2006 +0000 "Release log update" commit 4b1de55699b35065de7b1cfda517a4a2d65a58f1 Author: angie Date: Fri Apr 7 14:35:43 2006 +0000 Resolved -Wall warning: unused variable. commit 5238ccb3e5a58ea5d7cd549a017322f4cf1efee9 Author: angie Date: Fri Apr 7 14:29:10 2006 +0000 Resolved -Wall warning: unused variable, char used as array index (cast to int). commit ba11796975ebec511c3380fdda4478f5bb6e2860 Author: angie Date: Fri Apr 7 14:21:24 2006 +0000 Resolved -Wall warning: unused variable. commit e585f5e7f4c2576cf64adbe97471f1f95234cdbd Author: markd Date: Fri Apr 7 14:10:27 2006 +0000 added program to build species list with count of cDNAs commit 417d122cdcd7d09660e7f855d077dc804e3fafc0 Author: markd Date: Fri Apr 7 14:00:28 2006 +0000 fixed passing of verbose option commit f2c0f10f22a0f0009092a3fa0fa967f33f3fc855 Author: kate Date: Fri Apr 7 05:27:40 2006 +0000 Customize genbank tracks for chimp commit 0da9fb1834d6e7f00db35ce364671918628ee6fc Author: kate Date: Fri Apr 7 05:26:23 2006 +0000 Special handling of chimp in mRNA search results commit f3fa4c4764403c6b31f148521d95834088b677bc Author: kate Date: Fri Apr 7 05:06:36 2006 +0000 Adjust item labels for chimp mRNA tracks commit 54b88b6c67b9433cd1bda987eb28a35ee3f6243b Author: kate Date: Fri Apr 7 04:15:45 2006 +0000 Restore from debug code commit d51331bf7104301ef8d26319626c93846989544b Author: kate Date: Fri Apr 7 04:13:56 2006 +0000 Special handling for chimp: label organism in refSeq, mrna, and est tracks, as human or included with chimp in the 'native' tables commit d5ae27188b2205035861878e4d1bca73bcabb514 Author: markd Date: Thu Apr 6 23:59:37 2006 +0000 build download sequences when updates are enabled on hgwbeta commit 0fed84aeee37864e6d4e36259ebd2681e8ce73ce Author: heather Date: Thu Apr 6 23:43:29 2006 +0000 correct iupac, correct RangeSub commit dfb84119619ee41297489747cf8e7050c94717c3 Author: aamp Date: Thu Apr 6 23:21:54 2006 +0000 Some rebase stuff. The affy all exon stuff is ongoing work.` commit dc6d127c456b690e175ad4b5e3bc9df283f9a719 Author: fanhsu Date: Thu Apr 6 23:12:46 2006 +0000 Added phaseCon downloads. commit 36495a74fe2ec48e608123dd8adaf5fbac98cd09 Author: fanhsu Date: Thu Apr 6 22:49:13 2006 +0000 Added 2 lines about blastz runs between other organisms. commit 27d05b5fb18316b7e1fcdf8c2b609c0fc748a89a Author: heather Date: Thu Apr 6 22:30:59 2006 +0000 adjust to updated annotations; more comments from Brooke commit 0b644848fab72dfd2aecd794247bdbfc8d738730 Author: fanhsu Date: Thu Apr 6 22:26:26 2006 +0000 Added several more blastz runs for various organisms. commit 3e21557bf42e0d6b181ebb5dbb37fbe5c70d2b1d Author: heather Date: Thu Apr 6 21:44:50 2006 +0000 rewrite commit 1b4a66ae95b4861dd2cbcf6139e83ef4204f23ce Author: hiram Date: Thu Apr 6 21:28:55 2006 +0000 Working on panTro2 alignments commit 169f3cc0b0c7054f03de3b5557c8e57f1f91cf9b Author: fanhsu Date: Thu Apr 6 20:36:52 2006 +0000 Added blastz for panTro1. commit f3292f42b5684aeaedf92e110710d63570499af4 Author: kate Date: Thu Apr 6 19:12:28 2006 +0000 Fix syntax error commit 75f0bdf8ead8e053ef45b23360ec07cbc0537e4f Author: heather Date: Thu Apr 6 18:34:28 2006 +0000 only adjust range coords for non-random commit cd33d212d7c9429eeff61897887704c4c6cb31a7 Author: heather Date: Thu Apr 6 18:19:37 2006 +0000 change comments commit b2b82fb22d41b8ac0618f1d8ae6655b91282135c Author: ann Date: Thu Apr 6 18:14:48 2006 +0000 removed Fan's addition of blocks for Conservation and Most Conserved. I had already added them! commit 894d1d916b7e87f92e9058dbd15bc8e6fd0b5bc0 Author: heather Date: Thu Apr 6 17:42:25 2006 +0000 fix typo commit f5233aa280ec40f1f9cb33e17795c1232283280b Author: fanhsu Date: Thu Apr 6 16:02:36 2006 +0000 Updated .agp files of the 4 haplotype chroms and regenerated gold and gap tables. commit 0a384a4efd1fd84d7baf042bbe4b0a7580cc82e5 Author: angie Date: Thu Apr 6 15:59:47 2006 +0000 Resolved -Wall warning: errAbort format, unused variable. commit f4af1f36823b5284f9fa6b9d4cb5ee6a367a6356 Author: galt Date: Thu Apr 6 15:00:02 2006 +0000 "Encode release log update" commit 1da0741228e7c100672018d4cafebcfdee2effa8 Author: galt Date: Thu Apr 6 15:00:01 2006 +0000 "Release log update" commit 1f941c724a1ccb36bf13a3bbadb510576cda6dbc Author: fanhsu Date: Thu Apr 6 13:35:18 2006 +0000 Added "autoTranslate 0" to ecoresTetNig1 to disable protein sequence link. commit a888f2db96827b8f89d2bb54cb28b7160bdc2d72 Author: angie Date: Thu Apr 6 01:03:00 2006 +0000 Added missing fields (leftSummary and rightSummary). commit 3cce55e47c8761b39f78407422b0abac24f43aa2 Author: galt Date: Thu Apr 6 00:41:44 2006 +0000 visiGene : updated JAX and probeTrack and *.knownToVisiGene commit 7c7f544f3f1187f58ea11eede7ee5443d4c82298 Author: heather Date: Wed Apr 5 23:12:38 2006 +0000 rename exception; don't double count RefAlleleWrongSize commit f1253fc95594247625006dba9bde55664cfd34e9 Author: heather Date: Wed Apr 5 23:02:59 2006 +0000 change exception name to RefAlleleWrongSize commit f7660a15cff942c75dab7b2880688ed3de71acf3 Author: heather Date: Wed Apr 5 22:46:01 2006 +0000 change exception name to RefAlleleWrongSize commit a568dabdaf57a51b96f5afb15a4d3a456b4ce6d1 Author: angie Date: Wed Apr 5 22:38:44 2006 +0000 Moved cytoBandIdeo up from rat/rn3/ to rat/trackDb.ra . commit 557a31c88615d12349868c92c09cb213c9d3b8c6 Author: kate Date: Wed Apr 5 19:25:44 2006 +0000 Reciprocal bests commit 3f034c5bdbc75a526e2561e1583b93c723c9bcd6 Author: kate Date: Wed Apr 5 19:25:26 2006 +0000 Liftover chain to panTro2 commit c25c720fadc8cab74ee7b31499a7742c0efc145b Author: angie Date: Wed Apr 5 19:20:47 2006 +0000 Local {chain,net} shortLabel tweaks: $o_Organism for DanRer3, $o_db for Mm7. commit 117c6e85a9430c5146d183cd4a43fe486d560230 Author: angie Date: Wed Apr 5 19:19:51 2006 +0000 Added {chain,net}MonDom4. Added local release alpha vs. beta for {chain,net}Hg{17,18}: shortLabel uses $o_db if alpha and $o_Organism if beta. commit 7270f3bee2cc2f4808948cec03d77b4951e930b9 Author: kate Date: Wed Apr 5 19:15:31 2006 +0000 Update to match recent script changes commit e3541a99ef474280890ff830158777017aa7af1b Author: kate Date: Wed Apr 5 19:06:11 2006 +0000 Update for new cluster configurations. Make more flexible regarding directory usage. Adapt to Angie's convention from blastz automation commit 992944502e7aa2f112fdaf5c80dfcca9dfea8baa Author: angie Date: Wed Apr 5 18:46:51 2006 +0000 Added multiz9way and phastConsElements9way. commit ecf4a4ce4a3163dfdd140aabb5aa7307c00e1cf0 Author: galt Date: Wed Apr 5 15:00:03 2006 +0000 "Encode release log update" commit 61a5bca42116d08cb0907bb4c03ab987115a78d1 Author: galt Date: Wed Apr 5 15:00:01 2006 +0000 "Release log update" commit 6edf2e2064a5fffb3aac538c4bdaf4cc44f5ae11 Author: angie Date: Wed Apr 5 14:19:55 2006 +0000 Resolved -Wall warning: unused variable. commit a3e5a1b2de668a5429c8b554cd3f8428c09c1231 Author: angie Date: Wed Apr 5 14:17:42 2006 +0000 Removed car46 (database no longer exists). commit 47c4a2e1797dc8a17418426c43b49089e94bc36d Author: galt Date: Wed Apr 5 08:59:57 2006 +0000 upated jax and redid probetracks commit 5ff584243fdf08f6ec90a3262c2a4bd50da7319f Author: galt Date: Wed Apr 5 07:40:38 2006 +0000 fixed minor problem, was creating file with one newline when I wanted an empty file commit 98b963232c762dc6d115f519723a4b34ee58575e Author: kent Date: Wed Apr 5 00:10:41 2006 +0000 Added submit button next to reset of custom track. commit 3c6258eb3e6ee8c73f0af39614bd9fa67dffff9c Author: fanhsu Date: Wed Apr 5 00:08:00 2006 +0000 Rebuilt GENOSCOPE TETRAODON (tetNig1) ECORES. commit f36a84a88146fbd8781cc5f2c704002c2a13a654 Author: angie Date: Tue Apr 4 23:57:26 2006 +0000 Don't do chromField checks on those rare tables (i.e. chr*_gl) that don't have a chromField. commit e3613cd861355e050b1afe738d2227dc421705e4 Author: fanhsu Date: Tue Apr 4 23:36:22 2006 +0000 Put back multiz17way and conservation tracks. commit c23b8a1fbced3ec51ba96442d2eba9cfe5879d46 Author: hiram Date: Tue Apr 4 23:33:59 2006 +0000 Coverage track done commit d86d4eb0f3063f566854a3a4a6c387e2ec83055e Author: galt Date: Tue Apr 4 23:09:13 2006 +0000 made visiGeneXml as permanent test db for this commit c09e4047790980ea255344e96a43c2fbcb045032 Author: heather Date: Tue Apr 4 22:51:02 2006 +0000 watch out for unknown observed commit 79b7db8650e7c4ad83cb3d6dde5f983311d71e79 Author: heather Date: Tue Apr 4 22:19:49 2006 +0000 add RangeSubstitutionLocTypeExactMatch commit 61ef750c9ee219f0dfbaad965906021172d8723e Author: galt Date: Tue Apr 4 22:18:19 2006 +0000 renaming visiGene to visiGeneXml for test commit da847d1af7db768a731561cc794bf14e1592333a Author: ann Date: Tue Apr 4 21:38:35 2006 +0000 changed order of species in Conservation track commit 826e984e0056f85977d214c9faf674c69729bfdf Author: kuhn Date: Tue Apr 4 21:34:48 2006 +0000 Added 'liftOver' tag so easier to find commit b7d4b74c883b04ce2234e1e8c5be3fa5c996764a Author: ann Date: Tue Apr 4 21:24:41 2006 +0000 corrected visibility of Conservation track commit 18e3647450d458a32bd639b675a9bcb55424ee3d Author: ann Date: Tue Apr 4 21:13:11 2006 +0000 added back the blocks for conservation and most conserved commit a2f14af2f04c1b826fae09eabc79da7efdabe494 Author: ann Date: Tue Apr 4 20:57:10 2006 +0000 minor clean-up commit 13227ad0d9f5a95ae8b4755a770d49dbbfa89cb2 Author: ann Date: Tue Apr 4 20:55:15 2006 +0000 added block for assembly track commit 1749faf4a566bbbb709f89ae6471d5778607d714 Author: kate Date: Tue Apr 4 20:47:13 2006 +0000 Make it work with makeLoChain-split, which splits to /iscratch/i/ commit 13343f570aeab2628a9ee8dd89fdd498aa0d1430 Author: kate Date: Tue Apr 4 20:45:40 2006 +0000 Make it work with makeLoChain-split, which splits to /iscratch/i/ commit 41245d94fbc4da4bc6ae20ddec92bf7c8a928647 Author: kate Date: Tue Apr 4 20:44:43 2006 +0000 Make it work with makeLoChain-split, which splits to /iscratch/i/ commit 2d5137ffa8657f59e0f1467e3edcf65987a7b1cc Author: markd Date: Tue Apr 4 19:45:00 2006 +0000 enable panTro2 commit 6c9a93132f4708c764535b64f6f6acf862e4fee6 Author: hiram Date: Tue Apr 4 19:25:02 2006 +0000 Well, at least have a usage message yourself ... commit d6ac071c790ff6884a5f0cf1e632d569ad732617 Author: hiram Date: Tue Apr 4 19:19:52 2006 +0000 Create usage message index from currently built binaries commit 9d1d7959643c3027a34300a5fd4964bbe784dedd Author: hiram Date: Tue Apr 4 19:06:23 2006 +0000 swap of hg17 alignments commit f1b93e99ffd6ab21235eaf564d99e4fed30ef131 Author: heather Date: Tue Apr 4 18:47:21 2006 +0000 show reverse comp of ref allele for negative strand, show both alleles if different, only show DNA link if end > start commit fd769bd9dc5884a60a15cc7f1daf47a792b1d643 Author: heather Date: Tue Apr 4 18:05:41 2006 +0000 fix URL for GeneCards commit efde7301e6c4b15234daee803f04d8170c781a5c Author: kate Date: Tue Apr 4 17:50:53 2006 +0000 Remove mention of pk as a host for this step, as it can't access /iscratch/i, where data is split by the makeLoChain-split script commit 306c80c46a6c3c74a2ada390bca2a717ccf5321a Author: markd Date: Tue Apr 4 17:34:06 2006 +0000 enabled hg18 updates commit 248fbbc3e328862ff7be955b93fe44c32857cf25 Author: kuhn Date: Tue Apr 4 16:48:27 2006 +0000 changed a link to Gene Cards per contributors commit cf452051c97945d93f67cdeeaefbb9279f3ea687 Author: angie Date: Tue Apr 4 16:47:33 2006 +0000 Resolved -Wall warnings: too few args to errAbort, need to cast size_t to int for %d on x86_64, suggested parens around && within ||, unused variable. commit bf90a3c189fe8111b3fedcd5ae952c1322428054 Author: kate Date: Tue Apr 4 16:19:04 2006 +0000 Moved to panTro1 and panTro2 commit c3741ea9417009a2dded397c31044bfea2b93b8e Author: galt Date: Tue Apr 4 15:00:04 2006 +0000 "Encode release log update" commit b6f6687aec96b18c027cadb87d818ac36061f22b Author: galt Date: Tue Apr 4 15:00:01 2006 +0000 "Release log update" commit 61b79366454d1c76fced0c3b668389fcd6273772 Author: fanhsu Date: Tue Apr 4 14:07:17 2006 +0000 Updated GeneCard URL. commit 05674c4ecdccb0d5dd77e80009923fc6ba512e25 Author: kent Date: Tue Apr 4 09:43:29 2006 +0000 Implementing cast double to all numeric types. commit a2d1c970ba74616fa977e470c5f1aa52c3a5f4a1 Author: kent Date: Tue Apr 4 09:39:28 2006 +0000 Implementing cast float to long, double. commit c8b7a23e00722963e22c283fde7a9d057dcf9dbd Author: kent Date: Tue Apr 4 09:19:44 2006 +0000 Implementing cast float to byte, short, int. commit 78da51821400cebdb3df105464a590751bffacfe Author: kent Date: Tue Apr 4 09:06:41 2006 +0000 Implementing cast float to bit. commit 3cc4f6f6adbf1cae2c12386691a7cc2ec47630e5 Author: kent Date: Tue Apr 4 08:05:32 2006 +0000 A baby step towards casting from float to others. commit b5132f92d15261a1d4c31e838cb13aad5fa636f6 Author: kent Date: Tue Apr 4 07:58:17 2006 +0000 Implementing cast long to float. commit 71b599774d080a4e3f0393906d4e9a4c7b9b23ab Author: kent Date: Tue Apr 4 07:48:17 2006 +0000 Implementing cast long to double. commit d2c40044fd9498475d685d18a676647f77e5aca0 Author: kent Date: Tue Apr 4 05:50:29 2006 +0000 Implementing cast long to byte, short, and int. commit 5a8b2e686692a15c0cdd83ded53896ca8d8c5b3b Author: kent Date: Tue Apr 4 05:30:36 2006 +0000 Implementing cast long to bit. commit 2b874a3ad4c274e1a5ca789e072512b976b79be3 Author: kent Date: Tue Apr 4 04:59:11 2006 +0000 Adding casts from bit and byte to other numeric forms. commit a8d3197626ec71b20478987484e2f493a7f11831 Author: kent Date: Tue Apr 4 04:42:56 2006 +0000 Implementing casts of short to bit, long, float, double. commit 886ecf9bab9c3cf2ac32441c8cc3936cb3b6eab2 Author: kent Date: Tue Apr 4 04:15:41 2006 +0000 Adding printBit. commit 18d23d3b2eae6fc1df17bf85f6c149acc862dbd3 Author: kent Date: Tue Apr 4 04:15:12 2006 +0000 Implementing casts of short to int and byte. commit 0936c492e933ae2f932c9087043c3724d5052ea0 Author: kent Date: Tue Apr 4 03:27:52 2006 +0000 Doing casts of int to long, int to float, int to double commit 18ff23fa21580fe2bf629e35517a73a6c69ec82e Author: kent Date: Tue Apr 4 02:07:23 2006 +0000 Starting pentium castathon. commit 6f5b5058f3050bc6df3357c162480aad8dec7a44 Author: kate Date: Tue Apr 4 00:11:01 2006 +0000 Add Angie's script commit 4a60379c06283ad803b9ab5f69a15b8630245816 Author: angie Date: Tue Apr 4 00:01:26 2006 +0000 9-way Conservation. commit f95b6c5bdbd48bf0647c3a7581bb3f841c1bb219 Author: kent Date: Mon Apr 3 23:28:56 2006 +0000 Handling constant bits inside if commit b1a17344fde642e6f98b12fb19ad88edb4bf8b10 Author: kent Date: Mon Apr 3 23:13:16 2006 +0000 Handling string comparisons. commit 05f589f7bec2c55a3e760c5d54df44620dca60f1 Author: fanhsu Date: Mon Apr 3 23:07:30 2006 +0000 Updated to just include one entry for each kgXref entry. commit e27b7488923c39ded83b9608066c9b9e81b9e15c Author: galt Date: Mon Apr 3 22:35:06 2006 +0000 added target=_blank commit 4bc7ac79b416cdd6cac344fafc4d0486c1407849 Author: galt Date: Mon Apr 3 22:27:21 2006 +0000 fixed date in .ra acknowledgements commit 1fbbc913c2a48dbf649659e6bf97dee06e8d0b8b Author: kent Date: Mon Apr 3 22:24:57 2006 +0000 Adding string implicit test for truth. commit d60f043d9ee5c5619409f348a95e10aee3c0cc81 Author: galt Date: Mon Apr 3 22:24:15 2006 +0000 fixed date commit 44ecb6061e2cb3163d3a7b20f9c3b1d57bb87bc6 Author: galt Date: Mon Apr 3 22:13:08 2006 +0000 changes to support jax 20060328 update, using kkr3u00 with mysql5 commit 2d22d4a7ab8a7468f5aef3518073b4f6e9501798 Author: galt Date: Mon Apr 3 22:04:27 2006 +0000 added jax update 20060328 commit 7b11c367cf527f805e47143e2609b2ff128ed86d Author: galt Date: Mon Apr 3 21:59:04 2006 +0000 updated for JAX update 20060328 commit 23cb5c4627e4c183f38e5d71458ac27ef4db24c1 Author: galt Date: Mon Apr 3 21:34:12 2006 +0000 updated to work with new jax update process (has nulls), fixCopyright no longer needed, added check for non-null pub. commit 39a9be6680e1fb9930b1055d64c4443696b1923f Author: kuhn Date: Mon Apr 3 20:37:18 2006 +0000 added /cluster/bin and /cluster/data, which are actually the same machine commit b8b4ec432fad5bc449d86272d92d3e38cf8ad4cb Author: kent Date: Mon Apr 3 19:51:52 2006 +0000 Starting to do string constants. commit 7c7e7c6a1021fe0567d8f6ba6ad0fe3d38490baf Author: kent Date: Mon Apr 3 19:38:14 2006 +0000 Experimenting with assembler syntax. commit 33daf923253ad3a01c87a287a7ec76974b6a41a1 Author: kent Date: Mon Apr 3 18:21:49 2006 +0000 Adding more debugging type-specific simple printers. commit 4105e17a42901682e129241068883d5be677adc7 Author: kent Date: Mon Apr 3 18:21:28 2006 +0000 Rearranging string & array object for more common fields commit dcfc727202397be1934ab3a5f5af1181808f616d Author: kent Date: Mon Apr 3 17:26:39 2006 +0000 Separating out pentConst module from isxToPentium. commit 1bf002ba9b2dd67398c3a5bf06761c0fa4b0c5a6 Author: angie Date: Mon Apr 3 17:22:50 2006 +0000 Swapped rn4 chains. commit b2c9ef51950afdc7643b8372506228ce8c1a2471 Author: angie Date: Mon Apr 3 17:19:25 2006 +0000 Added bin and fixed indexes so it would match what's loaded by hgLoadMafSummary. commit 679a07eb808ddf11f871c254442a8348d5d31bf8 Author: angie Date: Mon Apr 3 16:27:16 2006 +0000 Resolved -Wall warning: unused variable. commit 0a6e099e1a2202c7456a8586584556595de1f168 Author: galt Date: Mon Apr 3 15:00:09 2006 +0000 "Encode release log update" commit ce6eb3bd9dc93b3e2a9b09c837643ddc5f97650d Author: galt Date: Mon Apr 3 15:00:08 2006 +0000 "Release log update" commit f03cb94fe9d7cd161edb1b90f6671c727168fee4 Author: kent Date: Mon Apr 3 10:25:02 2006 +0000 Getting long variables to work as conditionals without comparatives. commit 012818fbabaaeb7592ab6ff8be32b5462eeed547 Author: kent Date: Mon Apr 3 10:13:27 2006 +0000 Getting float/double variables to work as conditionals without comparatives. commit 8e58695db98fcf708416b3b8b373875e5c30fe10 Author: kent Date: Mon Apr 3 09:22:18 2006 +0000 Starting to work on variables as conditionals without comparatives. commit d0cd3d133abf57cb8097bc65518c79483c8c0951 Author: kent Date: Mon Apr 3 08:40:33 2006 +0000 Fixing overlap between spilled register temp space and function parameter space. Getting long comparisons to work. commit 800a4cb506b8d8d794ab5e5e0b3189da68904820 Author: kent Date: Mon Apr 3 07:48:06 2006 +0000 Some work on long comparisons. commit 1489dee117ca885726aca1a3f6872fb66af83059 Author: kent Date: Mon Apr 3 05:19:05 2006 +0000 Fixed problem where some logical ops would get turned into subtraction. Simplifying register return conventions. Returning up to three ints in registers. commit 7b47bcc50c61a94a4114126ae2ddb517d8ef1d81 Author: kent Date: Mon Apr 3 05:00:41 2006 +0000 Simplifying a few things and implementing unary minus for float/double. commit 4db161254a2c3de7f0fcd5144bbb0cdf847531f2 Author: kent Date: Mon Apr 3 03:40:12 2006 +0000 Implementing integer and long not and unary minus. commit 4f24646aaeea79c98435b4c7a58f12ecdf3025e0 Author: kent Date: Mon Apr 3 01:31:34 2006 +0000 Adding support, via subroutine calls, for pentium code generation of multiplies, divides, mods, and right shifts of long longs. Still to go: negs and nots. commit 96538f17aeaf08cea7dc15d47e5dc099ce892442 Author: angie Date: Sun Apr 2 21:45:29 2006 +0000 Resolved -Wall warning: unused variable. commit b3d2f691f9338df557a15e89428570fc7f7295ab Author: kent Date: Sun Apr 2 21:40:58 2006 +0000 Fixed bug in floating point comparison in pentium code. Starting to generate code for longs. commit 705fde482afbb4c879a0045982d998c9c1b4c160 Author: galt Date: Sun Apr 2 20:10:46 2006 +0000 utility for taking freebcp output and making it suitable as a mysql .tab file commit 6787910275b7a0b4727dc6d47b464abf7f8d565e Author: galt Date: Sun Apr 2 15:00:04 2006 +0000 "Encode release log update" commit 43abfcd42cf04a4bd701b92e5c48d91f9c6f5698 Author: galt Date: Sun Apr 2 15:00:02 2006 +0000 "Release log update" commit 72837d3e41fedec3ccdae886df14370f2cf97055 Author: hartera Date: Sun Apr 2 12:15:04 2006 +0000 Corrections made and addition of text to GIS methods. commit c405f5c93c635f9496007f9538f3dc2ee4272b58 Author: kent Date: Sun Apr 2 10:40:42 2006 +0000 I think that multiple returns of many values are working now. commit 6539461d48ff7ad25983a1ffc53cfa28db7a1977 Author: kent Date: Sun Apr 2 10:05:10 2006 +0000 Starting to work on case where more return values than registers we can use for them. commit 04ef5a3674e1a1a376eecfaf887ce39529a53a2e Author: kent Date: Sun Apr 2 09:06:16 2006 +0000 Fixed bug in floating point division. commit 0901ff2e2ff8a14754669fdc5cd0a55cf68ef933 Author: kent Date: Sun Apr 2 08:29:42 2006 +0000 Handing multiple return values. commit c87bc678bab33158b527c3af5452ec883dfd3b63 Author: kent Date: Sun Apr 2 07:47:18 2006 +0000 Dealing with floating point returns. commit 5ca4986cc798cca4fca484d814ea7f849ae036b5 Author: kent Date: Sun Apr 2 05:32:02 2006 +0000 Fixing alignment problem. commit 7b54f72e67efb583fc4d5fd6e82ec489b2aef503 Author: kent Date: Sun Apr 2 04:36:59 2006 +0000 More progress on code generator for floating point. commit 42a2010df7f1b1e6e6a94069c01dd94e8cb2466d Author: baertsch Date: Sun Apr 2 01:14:06 2006 +0000 fix scoring bug commit 03c82a218aa9d5e90e4cdcd903b7216ee5f429b9 Author: baertsch Date: Sat Apr 1 23:36:44 2006 +0000 remove extra fclose commit 03cbb44b735ca42fc33f6b5535a910b687cca140 Author: baertsch Date: Sat Apr 1 20:34:49 2006 +0000 add -passthru commit 49a130b4731faf83d186757cddc19572f2501e85 Author: baertsch Date: Sat Apr 1 20:28:15 2006 +0000 add est usage, fix compile error commit 12a9a57382a8a92c390a5b3428b98ed9fb88673a Author: kent Date: Sat Apr 1 18:53:36 2006 +0000 Making it so that initializations of global and static vars with constants does not produce code, just relies instead of initialization segment. commit 6f43fb13454eb5d2661eae9af9087d9cb8d94112 Author: kent Date: Sat Apr 1 16:23:54 2006 +0000 Implementing function return values. Starting to work on floating point (using xmm registers). commit b7f2ba35c0d2f537735979d9e751fcedd42f93b3 Author: galt Date: Sat Apr 1 16:00:02 2006 +0000 "Encode release log update" commit 3a64d4fd7b37c4e269a581262dcc306627ac7759 Author: galt Date: Sat Apr 1 16:00:01 2006 +0000 "Release log update" commit a7fe2e828a1246bdbf69a7a792e5c1894406bc1a Author: baertsch Date: Sat Apr 1 09:07:23 2006 +0000 add -filter option commit f8de140214f071f9fa8d933d87c233de278fbddf Author: kate Date: Fri Mar 31 01:00:01 2006 +0000 Finish blastz's. Do reciprocal best with human commit 63ac01acffb232cac7f70f588f150d92dd70282b Author: donnak Date: Fri Mar 31 00:47:57 2006 +0000 Added pub by Peter & Mark. commit 258e944eb6322656632cc6bfff1ef9c3ae08691c Author: hiram Date: Fri Mar 31 00:21:34 2006 +0000 Continuing to work on self chain commit c3fd6d3682a4984e43cc070e916d0ee921fb1207 Author: hiram Date: Fri Mar 31 00:21:17 2006 +0000 Running mm8 swap commit afdc63bf70aba2bf11290cfcd9b95725d916437f Author: heather Date: Thu Mar 30 23:56:15 2006 +0000 more feedback from Daryl and Brooke commit 955a1d9b16a43f5e41546a1604e8e01c19ad5caa Author: hartera Date: Thu Mar 30 23:10:03 2006 +0000 Added Pseudogenes track. commit f3e8a9534ca0aa5776a15475870c455ff735794f Author: kayla Date: Thu Mar 30 22:43:29 2006 +0000 changed the netHg18 block to say "$o_Organism" instead of "Net Hg18" commit b5d174ec2962077c7bb9e1596094adf3c10d2c76 Author: heather Date: Thu Mar 30 22:39:11 2006 +0000 typo commit 161bb70469f92017886afa98e9f2d63d1bf95d04 Author: heather Date: Thu Mar 30 22:18:24 2006 +0000 v130 commit fca805645e3cc83bb645b256e744ff1877f2d9ac Author: hartera Date: Thu Mar 30 21:33:23 2006 +0000 Added GIS subtrack description. Added another person to the credits section. commit 1e03ef970bc84aaf5b03042b78f195de3bea6c1c Author: donnak Date: Thu Mar 30 21:01:07 2006 +0000 Updated some of the links. commit 6150efd591e85d80fd4f65097a32b74ac49855c5 Author: donnak Date: Thu Mar 30 20:37:50 2006 +0000 Updated one of RECOMB pubs. commit 7b73bafe0153499eb3f3ccb18b3d73101c3f5b52 Author: hartera Date: Thu Mar 30 20:37:34 2006 +0000 Update pslReps parameeters to those used in assemblies from hg17 onwards. commit 4f51c6da7fbbe04e2a089f6bf328290c543fe57b Author: hartera Date: Thu Mar 30 20:35:27 2006 +0000 Description for hg16 affyU133 track. It has different pslReps parameters than the affyU133 track on subsequent assemblies. commit f7898b62a21589128a6f7ddbd4ddfd01ba5159d1 Author: kent Date: Thu Mar 30 18:27:22 2006 +0000 Further testing of threads. commit faeb5885302ab8da420161276dcabf7b3ef302e8 Author: kent Date: Thu Mar 30 18:27:00 2006 +0000 Testing one more thing. commit 87ddc450d97aeb16a09b1ab06c74ba73b650334c Author: kent Date: Thu Mar 30 18:25:09 2006 +0000 Fixing buglet in error checking. commit 40c3b106b82c759068ad48b8581046a7da70c8f4 Author: kent Date: Thu Mar 30 18:24:30 2006 +0000 Just analysing gcc output on a for with lots of vars. commit 0de4ea50f85db6b07c5ca4ebd828857a4acd387a Author: donnak Date: Thu Mar 30 18:23:19 2006 +0000 Added 2 RECOMB 2006 papers, fixed broken link. commit bf3b9491552a0db23555717e460dff05e2d7db8e Author: kent Date: Thu Mar 30 17:45:06 2006 +0000 Taking the warn-as-error out of makefile. It causes too many problems on other systems. commit df7fd7f836625be87ddf2fdde30165f98639a731 Author: markd Date: Thu Mar 30 17:35:54 2006 +0000 enabled hapRegions handling and xeon est loads in hg18 commit 611c16ec147d3047f890e549d775256760e47953 Author: angie Date: Thu Mar 30 16:54:54 2006 +0000 Swapped rn4 chains. commit 38b34fd0b9b3877fa81319c867674c026ca5d8e5 Author: angie Date: Thu Mar 30 16:53:35 2006 +0000 Resolved -Wall warning: unused variable. commit d0e67a54330ddcc981b39b4d77e5e113312d5907 Author: galt Date: Thu Mar 30 16:00:02 2006 +0000 "Encode release log update" commit c35317c409c1cc55f29745f26bd57b39ad825114 Author: galt Date: Thu Mar 30 16:00:01 2006 +0000 "Release log update" commit 47ab64b5714111f3767b069946cb881674db48a9 Author: kate Date: Thu Mar 30 08:01:14 2006 +0000 chr9 blastz redo commit 6e98510a6fdc94b278570572f41d2e5090d4d470 Author: kent Date: Thu Mar 30 07:19:31 2006 +0000 Some testing and debugging of pentium code generation of functions. commit 55eded866c0fae64b6dc9919c97db6607824138c Author: galt Date: Thu Mar 30 06:41:11 2006 +0000 added support for forced downloading via mime type in response header commit 8c4d5b15c61fd0e3be80b13e9fac5d1c8f2f7ff6 Author: kent Date: Thu Mar 30 06:23:58 2006 +0000 Code generation for functions is starting to work. commit e2e506efc5b9cad6c7bc8cf023cbb416f0b3244a Author: hartera Date: Thu Mar 30 06:14:42 2006 +0000 Removed addHashElUnique function as not needed. Replace its use with hashAdd where needed. commit 847367a02b2614e7e3c91945bc15e5e7c509a8f2 Author: kent Date: Thu Mar 30 05:22:48 2006 +0000 Some more work towards separate functions in assembly. commit c7c0e1bc337c3d89a7d8648c95dd7669db56fbf8 Author: galt Date: Thu Mar 30 04:58:00 2006 +0000 making a function public (not static) commit d7ff37f78beb36471860d566c59a66bb5d824e06 Author: heather Date: Thu Mar 30 02:38:04 2006 +0000 comments from Daryl commit 27a9f57c619ac0841424134905258c0674a3d5c6 Author: angie Date: Thu Mar 30 01:39:19 2006 +0000 Fixed small problems with our descriptions of gaps, brought to our attention by a user question. commit 373fa3e9d197c6c266d70991ad21afc941055c01 Author: hartera Date: Thu Mar 30 01:14:07 2006 +0000 Moved text. Corrected description of class colors and removed irrelevant rows from the table. Changed the format for some of the references. commit c8d4000bb6c1309e8ac3ba83aadcda25028a5f3d Author: hiram Date: Thu Mar 30 00:56:12 2006 +0000 Remove under development message. commit 099cfa24a686d3afef6b2bc00228847a12757a51 Author: hartera Date: Thu Mar 30 00:47:40 2006 +0000 Fixed color. commit d318d968e78f80b450a6d2a7c756d646fba412d2 Author: hartera Date: Thu Mar 30 00:27:01 2006 +0000 Corrected link to Affymetrix sequence download page for HG-U133 Plus 2.0. commit a86be98277f4bae18d50a7e36adb3898ba8c22e3 Author: hiram Date: Wed Mar 29 23:55:08 2006 +0000 Proceeding with human protein mapping, and started panTro2 blastz commit 9db45adcfd2b867fa9c685620e06a7837ff3d527 Author: hiram Date: Wed Mar 29 23:54:27 2006 +0000 Second panTro2 blastz run commit ec260bb613bf486822b65f178b59c3fc76370d2b Author: hiram Date: Wed Mar 29 23:53:15 2006 +0000 measuring the microRNA tracks commit fc7518a614c3a0b5af6c1c886345a997451d641c Author: hiram Date: Wed Mar 29 23:52:59 2006 +0000 Added microRNA tracks commit bbe56a4288919dcc92f03827f15bf32748b986d2 Author: hiram Date: Wed Mar 29 23:28:30 2006 +0000 Correct the name for the picTar html file commit 4f0f81e6c590b8334f4c7f384fdee35f5a004dde Author: hiram Date: Wed Mar 29 23:18:55 2006 +0000 Adding picTar microRNA track commit b201520b7f5865248e0a55ce4dcc14e14d3b68b2 Author: hiram Date: Wed Mar 29 23:17:31 2006 +0000 Correct long labels (until author has better ones) for picTar tracks commit de133b51232136f27c15695eb9e3ca0a5c3bd157 Author: hiram Date: Wed Mar 29 22:54:47 2006 +0000 Adding microRNA tracks from Nikolaus Rajewsky nr at scarbo bio nyu edu commit d7d5a207ef6a91cacb9f24933a93b50c24b1be76 Author: kayla Date: Wed Mar 29 22:35:19 2006 +0000 Added a block for chainHg18. commit fe6732d20106157b5764ba38050c5a37fd810cdc Author: ann Date: Wed Mar 29 22:10:09 2006 +0000 initial document. copied from top level. commit faf60867543acca5f9100f2ae569c104f5acb975 Author: hartera Date: Wed Mar 29 21:42:25 2006 +0000 makeDanRer4 for the Zv6 assembly. Download genomic sequence and agps. Download mitochondrion genome sequence and make agps and lift file for it. commit 48f711fe512080de5832150afa7ad96ba05ef87c Author: kent Date: Wed Mar 29 21:31:22 2006 +0000 A little more work towards function code generation. commit f6f117f9027d5f047ad2748934a2c947c7cde1cc Author: hartera Date: Wed Mar 29 21:22:35 2006 +0000 Loaded sequences for the affyU133Plus2 track. commit ed4fee2893c47ed2031140cd75633785c1485ea8 Author: kent Date: Wed Mar 29 20:34:02 2006 +0000 More refactoring towards separate code generation for each function. commit fd2f9828d37cf459cb0a8e1dd1080a58907ba8d4 Author: heather Date: Wed Mar 29 20:03:46 2006 +0000 initial revision commit 61cd427b1881c23f5b6d7ba00af1648875c76387 Author: kent Date: Wed Mar 29 19:55:51 2006 +0000 Moved much of logic for module-var initialization from gnuMac to isx. commit 32777e4853337ee991d598d0597d698eec8099fe Author: hartera Date: Wed Mar 29 19:41:49 2006 +0000 Ensembl Gene set in progress. Removed mm6 chain and net tables. commit 5ebb75890be19fcd71174fdf096ea42536c21ee9 Author: kent Date: Wed Mar 29 19:03:06 2006 +0000 Fixing missing pf_dyString_dir_from_tuple. commit 91cd2a3848dfc16af2b029c63153c1c6556fc841 Author: kent Date: Wed Mar 29 19:00:08 2006 +0000 Some refactoring in preparation for generating code for each function independently. commit 22416cb0bc035a0ba155b8495bd6f1e865507526 Author: kent Date: Wed Mar 29 18:26:00 2006 +0000 Creating asmCoder module to hold driver for code generation. commit 848a60aaf0d957350359412dca312aedd60a2b90 Author: galt Date: Wed Mar 29 16:00:02 2006 +0000 "Encode release log update" commit 1fc5dfcee8aecae50b4fc585732de1927c2e341f Author: galt Date: Wed Mar 29 16:00:01 2006 +0000 "Release log update" commit a01cc5107f4d38a977b3ea505fb443164a13d0d2 Author: angie Date: Wed Mar 29 15:55:04 2006 +0000 Resolved -Wall warning: unused variable. commit 0ce64e4eca8036221772284f517842df47f9d8bc Author: heather Date: Wed Mar 29 13:56:32 2006 +0000 don't need extFile.h commit 5ddde3804be471dbb4ea107341f88634c0576da3 Author: angie Date: Wed Mar 29 01:46:02 2006 +0000 Removed the ARCH_DBS items from DBS -- make can be invoked with 'DBS=${ARCH_DBS}' on the archaea server where the databases live. commit 97115051d0144d1f838a98af350b0be6a4144b7f Author: donnak Date: Wed Mar 29 01:35:29 2006 +0000 Added Rachel's zfish pub. commit 18dc2c1f47e86607c43c30f0c6ed85be71a41316 Author: hartera Date: Wed Mar 29 01:18:45 2006 +0000 Added an overall track description and a table explaining the color coding for items in the track. commit 65589fc0c239298b7c530e112dd811c80d9ed75c Author: ann Date: Wed Mar 29 00:28:37 2006 +0000 added block for gap track commit d3c6601adce455b88d472d3a790650b7e9037d89 Author: ann Date: Wed Mar 29 00:24:53 2006 +0000 initial document. copied from mm7 commit 9cbcb062dbac2c9daac1952d46919eb0f7d50b14 Author: heather Date: Wed Mar 29 00:18:27 2006 +0000 add comments commit 82e914be1cecbd19b76082a678ec2814d9eac1f9 Author: heather Date: Wed Mar 29 00:15:20 2006 +0000 promote class in-del to deletion for loc_type 2 commit 9d3e12a71af2a1d94520d6c1c423768dea4d146a Author: heather Date: Wed Mar 29 00:07:18 2006 +0000 fix DeletionClassWrongObserved commit 2d14a01ee849e1a54e07a55f022de5e523af6adf Author: kate Date: Wed Mar 29 00:02:42 2006 +0000 Adjust RefSeq track labels and descriptions for panTro2 commit 8c7fcd5fad0faaec1ef1dae9f375be33d99ca3f7 Author: kate Date: Tue Mar 28 23:29:26 2006 +0000 Use genePredReader so that optional bin field is handled commit 32cf4d146ca7d39e0d26913f6eb6fe68c9d1e8c2 Author: donnak Date: Tue Mar 28 23:19:20 2006 +0000 Fixed date on Wolfsberg pub. commit b447ab16c5ea0e7f50dcd10e061750405f123c2a Author: donnak Date: Tue Mar 28 22:27:43 2006 +0000 More updates to chicken genome credits, per LaDeana. commit b44a329139df67af708739eb4e38cccada56b5a1 Author: hartera Date: Tue Mar 28 21:42:16 2006 +0000 Moved some sections and changed size of headings. Added subtrack descriptions for Yale Pseudogenes, UCSC Retrogenes, and UCSC Pseudogenes. Added contact information for the ENCODE Pseudogene annotation group. commit 1ff7a7446cf40c84ad251afc86cb4093165088ea Author: angie Date: Tue Mar 28 21:37:58 2006 +0000 Swapped rn4 chains. commit a47dbbf3ee0eae451ed486355a8d57902eb76ae0 Author: donnak Date: Tue Mar 28 21:37:57 2006 +0000 Updated chicken credits, per LaDeana's request. commit 35182841bfd5a9666074257f54e54a0fbc648674 Author: donnak Date: Tue Mar 28 20:23:45 2006 +0000 Made a few minor edits. commit 2e30676a4ae9d9a13fd234e649e9a7a13610e046 Author: heather Date: Tue Mar 28 19:01:08 2006 +0000 add kayla and brooke commit 89daee9322b7b7d3ed8a2eefbe1ca7d3526df1f2 Author: angie Date: Tue Mar 28 18:18:17 2006 +0000 Use hFindSplitTable instead of safef'ing with chromName which may be NULL -- hFindSplitTable does the same thing but defaults the chrom if necessary. commit 3a919310f73c5ed707f067eed93a93733417f6f7 Author: heather Date: Tue Mar 28 18:13:47 2006 +0000 remove gbExtFile; this now has the usual .as, .c, .sql and ../inc/.h files commit 3e735d4f0b9ec4b742d751d893ce2cc36b5a6f74 Author: heather Date: Tue Mar 28 18:08:40 2006 +0000 add gbExtFile commit f3e7923615ff3b506f885042191114c151d5e6fa Author: kate Date: Tue Mar 28 18:05:35 2006 +0000 Redo phastCons for 17way commit 29c346f73446e423817cc684594fe7b8ecae0e92 Author: heather Date: Tue Mar 28 18:03:14 2006 +0000 for use by kent/src/hg/qa commit af17265fca072807351ef099f1d3cd6816b702ab Author: aamp Date: Tue Mar 28 17:57:07 2006 +0000 A function like slIxFromElement but for slNames. I'm not sure if this is properly named: slNameFindIx. commit 7cf36baa69e2d9d4a575724d6e539979fe300985 Author: kent Date: Tue Mar 28 17:34:05 2006 +0000 Adding frames table to wigMafs. commit 985dcc6264c891ba3a5ef80b196bf7bdd5680784 Author: fanhsu Date: Tue Mar 28 16:47:15 2006 +0000 Temporarily removed conservation track until rebuild is done. commit 8e11f07433880cc744c2f45ad9be01bcc4062ffe Author: hiram Date: Tue Mar 28 16:40:53 2006 +0000 Correct comment on multiz 17-way section commit 220d68a510b23dfa56215306011dc74aa8e8375b Author: angie Date: Tue Mar 28 16:24:02 2006 +0000 Removed methHung1 (database does not exist). commit bb7181fbf99262e264883d9028cfa419194aab3f Author: galt Date: Tue Mar 28 16:00:03 2006 +0000 "Encode release log update" commit e93e5fad59e413abdbeccac05cf5d911a76130d4 Author: galt Date: Tue Mar 28 16:00:01 2006 +0000 "Release log update" commit f614c73d4a6878b125d0e103a39a50d522a0f38c Author: angie Date: Tue Mar 28 15:30:09 2006 +0000 Resolved -Wall warning: unused variable. commit 4d1e014063a2d67c86bcc2b7b55d14fcd60b9712 Author: kent Date: Tue Mar 28 05:26:13 2006 +0000 Avoiding generating separate isx instructions for realVar=tempVar. Making stomp logic allow use of ax/cx/dx right on up to subroutine call. commit 9576493ee6cab5c9f18ce9c7a4bb3aae61c03ac9 Author: aamp Date: Tue Mar 28 04:40:51 2006 +0000 Added more stuff for the affy all exon. In particular, another expression-averaging function like msBedGroupByIndex in hgTracks/expRatioTracks.c. Yeah... it should be shared code... but for now, that's what it is. commit 6304a864f9f31a9123daaa4ae687974f8ead9c68 Author: kent Date: Tue Mar 28 04:05:33 2006 +0000 Testing and debugging if statement assembly code generation. commit 69374e59b36a67af882ce31ade9b7b91b86736ff Author: markd Date: Tue Mar 28 03:06:33 2006 +0000 added nscan to hg18 commit ff5c3fd7d0049c83e3f4feda80fe8870773f2eaf Author: angie Date: Tue Mar 28 02:30:10 2006 +0000 Don't generate nets for self alignments. commit 46eabefa9df3a144b3e952eeb7617f926bb87a94 Author: markd Date: Tue Mar 28 01:59:04 2006 +0000 added -bin option commit 7b54f9b66b7c2650733e032c25402188a7d2265c Author: markd Date: Tue Mar 28 01:50:40 2006 +0000 added bin to nscanGene commit 19684db53f2c5d4d4ecbca8a9a122969a5efa38d Author: heather Date: Tue Mar 28 01:25:04 2006 +0000 "New version number v130" commit a6bc98cff36034de7a1b0b368e5dc2d61996f0dc Author: markd Date: Tue Mar 28 01:18:46 2006 +0000 added canFam1 NSCAN commit 9bfc47728e4d4b4b96d296bdc7f7c35511302ff4 Author: angie Date: Tue Mar 28 00:55:59 2006 +0000 monDom4 and bosTau2 pairwise alignments for Conservation track. Also rheMac2, panTro2 and self for ancestor reconstruction. commit ae84bd5d0bb1e02e4b17fa7baaa6564ae7efde91 Author: heather Date: Tue Mar 28 00:52:48 2006 +0000 remove debug lines committed by mistake commit 0695fc0ea7169df519b945502d696b4b28c5a53f Author: heather Date: Tue Mar 28 00:51:43 2006 +0000 add snp125ExceptionDesc commit db35bb8e356f44ac6f5de2b99d068a2b5a4ee9bb Author: angie Date: Tue Mar 28 00:37:03 2006 +0000 Uncommented out STRIP line. commit d66bca05c38145e469ab3bee425409f4d067f7ee Author: markd Date: Tue Mar 28 00:25:12 2006 +0000 added option to suffix ids commit c4c9c5768838af49a256fe36bdc2b37f3e57bb39 Author: heather Date: Tue Mar 28 00:24:08 2006 +0000 add NewLocTypeWrongSize commit 505d5352c176be494bae9a61f87dcfec0897dec3 Author: kent Date: Tue Mar 28 00:19:16 2006 +0000 Fixing bug in mem-mem comparision. Forgetting register contents at a label. Getting for5.pf test case to go. commit d149630db3fa7cbc844a96a6fa2212725cd08f31 Author: angie Date: Tue Mar 28 00:06:39 2006 +0000 Added recognition of linkedFeatures fields to hFindBed12FieldsAndBinDb, so that hGetBedRangeDb will correctly query linkedFeatures tables and parse out their block structure. commit 571ed8dc169564be1bade4762247355c135de394 Author: kent Date: Mon Mar 27 23:46:57 2006 +0000 Getting rid of some unnecessary instructions at start of loop. commit c16d94f8eb4e727d5198a1b340bbee795ec56f7e Author: kent Date: Mon Mar 27 23:25:36 2006 +0000 Some more loop tinkering commit f54931cf2fa6f8b0d98b6188521f99b109dab106 Author: heather Date: Mon Mar 27 23:15:42 2006 +0000 fix typo commit cdf824ae52020b9b01f790e477acd8ef755732d7 Author: heather Date: Mon Mar 27 22:49:48 2006 +0000 tweak snp125 commit 3874b05325b585ce344351f0ace9982ea3a5bc2c Author: heather Date: Mon Mar 27 22:19:36 2006 +0000 small changes for snp125 commit 81bc68e90b71178b0aeeb1b69448d291e1481ffc Author: angie Date: Mon Mar 27 22:13:49 2006 +0000 Ran DateRepeats (-query human). Swapped rn4 chains. commit a68292e010b97189ed81296870d440e3bffd0edc Author: build Date: Mon Mar 27 22:10:46 2006 +0000 added build build scripts commit 2a06a0123d1006689a6bbdbe1e03ecc7ba884e8a Author: hartera Date: Mon Mar 27 22:08:20 2006 +0000 Minor editing and addition of another external link. commit 7901f99ab21a88055366d1c9839c5241bfe48162 Author: kent Date: Mon Mar 27 21:22:47 2006 +0000 A little more progress on assembly generation for loops. commit 29274573601143e886ef3ba7630640b560e1c2d6 Author: heather Date: Mon Mar 27 21:13:32 2006 +0000 get column order right commit 5d192c0f124d70ce3deddc48d09fcc3572b53baa Author: kent Date: Mon Mar 27 20:38:05 2006 +0000 More work on loops in code generator. commit 5022b0d5cdd8e7bdb038b0601842901ed9a82790 Author: heather Date: Mon Mar 27 20:21:10 2006 +0000 add exception name commit 1a725fc2b0d6381b2e86ac03e93aaa67dd68b93c Author: hiram Date: Mon Mar 27 19:58:34 2006 +0000 missing a closing paren commit 4978230f79ff1dc4401f74439b97b7ddce52934e Author: hiram Date: Mon Mar 27 19:55:33 2006 +0000 Remove the false comment about no blank lines commit 76e4dae818a5d03f64158e13c25b7e5df0e49910 Author: hiram Date: Mon Mar 27 19:49:39 2006 +0000 Remove the comment about the "no blank lines" commit 007bc10e48dfca753a75f1a77861f20b3c87f334 Author: hartera Date: Mon Mar 27 19:36:15 2006 +0000 Added danRer3-specific track entry for Ensembl Genes set with hgGene set to on. commit b7a0b9cdd98f35e4d28be68d119cee083fd82b7b Author: heather Date: Mon Mar 27 19:25:20 2006 +0000 add comment commit 5ed3f2e0e9e059dd3bba909076d79b6ed183b4be Author: kent Date: Mon Mar 27 19:20:26 2006 +0000 Creating a higher order structure for intermediate code list. commit 5a638670606744c4d0f1d58e82f2057ee2126b80 Author: heather Date: Mon Mar 27 19:13:08 2006 +0000 add comment commit 6f29926514446dc20819d1926923bca0d53f73aa Author: heather Date: Mon Mar 27 19:10:24 2006 +0000 fix typo commit a6b1ec823d193ed385441fd50eb7cefcdfdbfd71 Author: kent Date: Mon Mar 27 18:54:05 2006 +0000 Starting to set up tests for code generator. commit 82394b9fd50061b746ace97965011933ba0ad4ef Author: kent Date: Mon Mar 27 18:47:39 2006 +0000 Fixing a register stomping bug during division and shift. commit abb1f933b11ad196ecfeb64b55921fbc375b1b40 Author: angie Date: Mon Mar 27 18:44:07 2006 +0000 Resolved -Wall warning: unused variable. commit 5055edded9ed572c8e3e10419a792491c04ff234 Author: kuhn Date: Mon Mar 27 18:42:21 2006 +0000 fixed typo commit cda6c12eb05e51a7b77cbe477118c48a9deb3d5a Author: kent Date: Mon Mar 27 17:56:34 2006 +0000 A little more work on code generator. commit 6dcd4f9a039eb0141e97346566497bac7c246a41 Author: hartera Date: Mon Mar 27 17:21:25 2006 +0000 Minor edits and added links to external sites. commit 4dce79001d874c6ed6a9a78d01f8badcc62196d6 Author: hartera Date: Mon Mar 27 16:46:18 2006 +0000 Changed name for XRef table for Zebrafish Ensembl Genes set. commit 515545ad6dd30ab5c284ad76f6bc92d2bc2b45ee Author: hartera Date: Mon Mar 27 16:28:45 2006 +0000 Added link to table schema. commit e65531f8415d28a52ca2f8a0e1921a45e492a047 Author: galt Date: Mon Mar 27 16:00:02 2006 +0000 "Encode release log update" commit 231343433cf9b6624cf99030a174f51dba36eca6 Author: galt Date: Mon Mar 27 16:00:01 2006 +0000 "Release log update" commit 1f96799f3dc443cad0f2ece1e0e1d4fe730ee066 Author: heather Date: Mon Mar 27 13:40:08 2006 +0000 remove dropTable commit 6bdf4462e1a7e306bc0a38f8a4897a3a27a7819a Author: hartera Date: Mon Mar 27 06:45:37 2006 +0000 Finished Radiation Hybrid Map track - changed sequence names so unique and re-ran Blat alignments and reloaded all tables. Updated Ensembl Genes XRef information and changed XRef table name and reloaded it. commit 6c55f8223daf1b992ccde9a8d9283524cdd0490f Author: hartera Date: Mon Mar 27 06:40:01 2006 +0000 Changed XRef table name to new name. commit c3a68bdffaa6bcf72bfb68d4f89b9e97af8b0fc5 Author: hartera Date: Mon Mar 27 06:34:19 2006 +0000 Updated the Ensembl Genes link for Ensembl 37. commit a24fed902c3c5ad298c57b0c123d1151f62205f4 Author: hartera Date: Mon Mar 27 06:14:38 2006 +0000 Added rule for RH map tables for zebrafish - rhMapName. Added rules that rhMap is only ignored in danRer1 and danRer2. commit 5cde9c53055cfa9c48af8f3604ea641680ca0bf4 Author: hartera Date: Mon Mar 27 05:32:35 2006 +0000 Additional information and changes were added that were suggested by the RH map sequence provider. commit d6b8fc6cc3e3a30a0541bd4c6143317a2438582d Author: kate Date: Mon Mar 27 03:09:01 2006 +0000 Remove CVS conflict commit 27ba50457fed1e04b8fed176b0116fea0a284da2 Author: kate Date: Mon Mar 27 03:08:51 2006 +0000 Remove CVS conflict commit 6d43a01d5bb122b055f5c9fd5c75c0018100c89d Author: kent Date: Mon Mar 27 02:37:26 2006 +0000 Making hotLive lists for loops. commit 1786750f6b19f7e0686afd59fa6dc423e9b23c4d Author: kent Date: Sun Mar 26 20:02:00 2006 +0000 Adding child and next pointers to isxLoopInfo commit 132f0578c7d9a0a2a7c68dca8e6395a2bf5ea6f1 Author: markd Date: Sun Mar 26 19:18:16 2006 +0000 added support for haplotype chrom filtering commit 49e07230109c5c946f9fae95e6348545c126af5c Author: markd Date: Sun Mar 26 18:32:10 2006 +0000 disabled hg18 updates commit 5c8265fd01a7369401aaba24ddab01c2b2cfdbae Author: galt Date: Sun Mar 26 16:00:02 2006 +0000 "Encode release log update" commit 61c0a828d316712317a046cdd5ce619f7197bfaf Author: galt Date: Sun Mar 26 16:00:01 2006 +0000 "Release log update" commit fd0047597357997cbae2ac5ec256e668b2664629 Author: kent Date: Sun Mar 26 06:51:11 2006 +0000 Little example - moving to an intel machine. commit 0c00d14c431c51cb33c8f7bb067ad73d2cc349e4 Author: kent Date: Sun Mar 26 06:16:36 2006 +0000 Evicting lightweights from stable registers when need be. commit 128a93f1a836ffa0a27f0c69067405faa4334175 Author: kent Date: Sun Mar 26 05:40:01 2006 +0000 Adding weight to isxAddress. commit 7ee51cde5310864427eebd0c007d0122ddc48c4c Author: kuhn Date: Sun Mar 26 05:05:17 2006 +0000 adding a bunch of cgis to the Google exclude list commit 50425b8190361f4f9e09aa2d5117cff6b8574ad6 Author: kent Date: Sun Mar 26 03:53:18 2006 +0000 Setting up isxLoopInfo as the 'left' address of a poLoop instruction' commit e913097f5a20662fc9d3b4623215520859f1fac9 Author: markd Date: Sun Mar 26 00:39:02 2006 +0000 updated usage message to make inFile and selectFile distinction clearer commit 377ea5d9a63eb38d78c47e031ea6e468429d9072 Author: markd Date: Sat Mar 25 21:52:14 2006 +0000 finished genbank load commit ed7b8203a432454aae1b633102fbeaaccc3ed1f2 Author: markd Date: Sat Mar 25 21:17:37 2006 +0000 fixed bug checking for genePred bin column commit 18933e833ad607a846a976787a6a53edef76560d Author: donnak Date: Sat Mar 25 19:43:15 2006 +0000 Fixed typo. commit 8f7ffea9321ac9de67e6ab4dd9b2e2d31f0be2cc Author: donnak Date: Sat Mar 25 19:39:12 2006 +0000 Added pub on human chr11. commit 89d592ede77e3ea831834dfcbde38fbd67a9cf92 Author: galt Date: Sat Mar 25 16:00:02 2006 +0000 "Encode release log update" commit 87368ad142b405fcfc2771e5ebf74da0509a6bd2 Author: galt Date: Sat Mar 25 16:00:01 2006 +0000 "Release log update" commit ddea3b5b4e06075f00ecbdcbd852bebb4c5d7968 Author: kent Date: Sat Mar 25 04:59:56 2006 +0000 Generating isx code for +=, -=, *=, /= commit e1068138f2e1bd0f61e9a15ea5f5a18814c19631 Author: kent Date: Sat Mar 25 04:59:28 2006 +0000 Handling division by constants. commit 42e6244f9dc2b0967cc5e2b7de6d3e282cda9409 Author: kent Date: Sat Mar 25 03:51:08 2006 +0000 Keeping track of where registers will be stomped, and preferentially assigning registers to dodge stomping. commit 516224b3853ec3e7d206f0259dc6808923e7eea3 Author: lowe Date: Sat Mar 25 02:47:24 2006 +0000 Fixed errors in makefile commit 3d4c5c254bd9734c00f411fcd47b16f33365b024 Author: lowe Date: Sat Mar 25 01:24:38 2006 +0000 Deleting duplicate copy of directory in deprecated /archae directory. commit 5f68876fec3d3a76a9e4d5e7eb24ae33071ca25f Author: kate Date: Sat Mar 25 00:54:59 2006 +0000 Fix chr9. Start genscan. commit f0a9f34a2953038d4312bac82fa7c4b860a33e61 Author: heather Date: Sat Mar 25 00:46:24 2006 +0000 only log err500 if -store option specified commit cf2483122f71604c66ce0cfecfe39fdeabcc7504 Author: fanhsu Date: Sat Mar 25 00:31:44 2006 +0000 Hide conservation track until rebuilt. commit 4b0dc29a6f452256c2aeb5063e658278d2ed6431 Author: heather Date: Sat Mar 25 00:21:20 2006 +0000 add qa to UTILS_DIR commit 97d1c9689ab1773f537af05d0b1012fb9a94020f Author: heather Date: Sat Mar 25 00:13:14 2006 +0000 update to current contents commit a13f6469a15be71880eab2a511697d1f4842636b Author: kate Date: Sat Mar 25 00:03:41 2006 +0000 Switch lift files for panTro2. This is a dummy file that can't actually lift the reverse strand contigs, so it renames them. commit d845ab999b3319b8af7ec56cee546e2fac71c64d Author: heather Date: Fri Mar 24 23:51:48 2006 +0000 write to status500 table commit c640fe2bf9c2d6ca814dfe22bc6d1bc627ad80dd Author: kate Date: Fri Mar 24 23:18:21 2006 +0000 Add script to CVS commit dc316d35bdbffc944ee742947afc373ffac5fcae Author: kate Date: Fri Mar 24 23:18:09 2006 +0000 Simple script to generate lift file from an AGP commit 6e873f51807f931639e444cbed723365b5fa9c02 Author: heather Date: Fri Mar 24 22:03:05 2006 +0000 count by machine and status-code commit c5b435beb6790b0c3d2e8a6ccb813ddc8f1e767e Author: hiram Date: Fri Mar 24 21:57:39 2006 +0000 First pass at Opossum blastz, to be redone upon rebuild of panTro2 commit 9215a6b6e1db1cd4144b3a13df331bd7b96b968d Author: hiram Date: Fri Mar 24 21:56:44 2006 +0000 Completed galGal2 and danRer3 chain and net tracks, starting Human proteins tblastn commit 7a312a67b81e8baa9174c4ce0e3892c22b63e5e2 Author: hiram Date: Fri Mar 24 21:43:06 2006 +0000 Remove some cruft from that process commit 9edd5c71c86c5737d557a8ad81a4e852c5f29060 Author: hiram Date: Fri Mar 24 21:38:38 2006 +0000 Blat knownGene proteins to determine exons procedure completed commit 5d53989eebaf4559e355bcb2e5187c93b01f40c8 Author: kent Date: Fri Mar 24 21:27:32 2006 +0000 Starting to develop a regInfo structure with stomping info. commit a405e7770dc3068e4bf29ffa34b1eeedaafc1923 Author: kent Date: Fri Mar 24 20:23:47 2006 +0000 Separating live variable analysis into a separate module. commit 1b2054da14264031444151059ea9992c1cf4971d Author: kent Date: Fri Mar 24 19:32:58 2006 +0000 Adding use count and next use info to live list. commit 172f1fa8394b4ddd65c591a694817fc443df6c03 Author: heather Date: Fri Mar 24 19:32:38 2006 +0000 bare bones, replaces ApacheMonitor.java commit 03c4691fd5d860b20b77ec6a3dd48098f6be5478 Author: hiram Date: Fri Mar 24 19:28:27 2006 +0000 Correct relative reference to libraries, add clean target commit 7326dcd1e8047522a3f8380f2264615807d2380d Author: hiram Date: Fri Mar 24 19:25:42 2006 +0000 Fixup compile warnings for 64 bits commit f7072c97e8397b42f4aabd72d97ef0042cf9f32f Author: kuhn Date: Fri Mar 24 19:09:50 2006 +0000 added protection for cases of new assembly not found on beta commit f9c53e630562014c00711d7e6bb1e5876ceacef3 Author: markd Date: Fri Mar 24 18:45:54 2006 +0000 fixed bug with hap region checking on ref chrom commit 3f73ee5d6332abf7edb02d1e388f2cd3bc7b4c62 Author: kent Date: Fri Mar 24 18:32:15 2006 +0000 Making live lists (but not register allocation) know about loops and conditionals. commit be066abcb88d55ad0ea07a80bfe2ac933ce4820d Author: galt Date: Fri Mar 24 16:00:21 2006 +0000 "Encode release log update" commit 0425042c493360ca9ae1bc80031565447d5bc23f Author: galt Date: Fri Mar 24 16:00:20 2006 +0000 "Release log update" commit 8deaa8be327e2ae0e38ccdc5b3c7d87baa5dcef2 Author: angie Date: Fri Mar 24 15:40:47 2006 +0000 Resolved -Wall warning: unused variable. commit eaa4989067b80dfac8847eb1ab5ecda0cb466f39 Author: baertsch Date: Fri Mar 24 11:20:56 2006 +0000 small fixes , output file fix commit 96c36e6585387d4ba201cc7c9622187b2afc266d Author: markd Date: Fri Mar 24 07:12:59 2006 +0000 added -strand tests for -selectRange commit e030823ac8c1ab571ff79bd64af9b0b5908bf8eb Author: braney Date: Fri Mar 24 02:19:50 2006 +0000 no more Common Ancestor stuff commit 08dee8a3a768c984074d0958d7695c0c21906a7b Author: rhead Date: Fri Mar 24 02:10:15 2006 +0000 added wgRna to tables ignored commit 29d86e5fcbe2aa0e5c6328976a92a1d3b0f14dc7 Author: braney Date: Fri Mar 24 02:00:50 2006 +0000 changing from dog/human nomenclature commit b1cca37ac14011c1c24d90df3f9a9e435380377f Author: braney Date: Fri Mar 24 01:59:30 2006 +0000 we're changing to use boreoeutherian rather than dog/human commit 2d5dc384a92401a9274767d8dffb823e65d61340 Author: braney Date: Fri Mar 24 01:58:03 2006 +0000 add chain and net self commit 67e0212838ab1879ec50b5b0edcac80952d5ad9d Author: hiram Date: Fri Mar 24 01:13:12 2006 +0000 Beginning the blat proteins business commit e47c4aa8880b4904aae3f780a1342ff0ea7488c5 Author: fanhsu Date: Fri Mar 24 00:50:42 2006 +0000 Try again. commit b836b4d6652e30810d61fa2993953647499fec08 Author: fanhsu Date: Fri Mar 24 00:31:41 2006 +0000 Another update on spMrna. commit 4f3c4676da65f2966f46e12c11a07aa86e43ed5d Author: fanhsu Date: Fri Mar 24 00:17:13 2006 +0000 Added a line, "hg18.spMrna.mrnaID minCheck=0.20" commit b1b28e0150830858da6abcb66366677b5741e89d Author: galt Date: Fri Mar 24 00:15:54 2006 +0000 moved sqlSaveQuery to jksql.c at Kates encouragement commit b2115b236ad8cafbc8e502fe76f7bc2956d14807 Author: rhead Date: Fri Mar 24 00:13:55 2006 +0000 Changed Laboratoire de Biologie Moleculair Eucaryote links so that they point to the English language version of the website. commit 194c523973182452e24f98088178c916aba22752 Author: hiram Date: Fri Mar 24 00:10:28 2006 +0000 Added self chains and nets commit 15f290fd2c991a34c9428b71931fdb5d2ff9ba10 Author: kayla Date: Thu Mar 23 23:52:38 2006 +0000 Added hg18 commit 0d6c389f61e806e776343588dfbf6cf06e234989 Author: aamp Date: Thu Mar 23 20:26:14 2006 +0000 Fixing case on include dystring.h commit 2748c95846c8972050ffa563503b7d659ea81622 Author: kent Date: Thu Mar 23 18:54:12 2006 +0000 Making the cvs option work for other people than me I hope. You do need to have the directory in ~/kent/src. commit 70a394d96d94fdda02837e3d13b9f0f0bdd4ea2d Author: rhead Date: Thu Mar 23 18:19:00 2006 +0000 Moved file up a directory commit ca3dbe01aecc032e7b707508ab883e476915a909 Author: rhead Date: Thu Mar 23 18:17:21 2006 +0000 moved file up a directory commit 0e78a7ed7b91e826e226f262019b5e3e54150872 Author: rhead Date: Thu Mar 23 18:16:27 2006 +0000 Moved the file up a directory and added the word snoRNAs commit cdd7bee8dee6bb26ef49698b2b6168c245bdb732 Author: angie Date: Thu Mar 23 16:35:12 2006 +0000 Surprised it took -Wall to catch this. usage was declared with a typeless parameter, which was passed to errAbort. However, usage was then called with no parameter. This resulted in garbage printed out at the beginning of the usage message -- could have been a segv, and again I'm surprised the default compile was quiet about it. commit 05b1da6e0b8ca41e6df681a9bfb0ccd41cb3e77e Author: kent Date: Thu Mar 23 16:18:15 2006 +0000 Fixing a couple of bugs in code generatation of comparisons. commit 9d08e331f506b05dee4269a62dcb88496078b7a6 Author: galt Date: Thu Mar 23 16:00:03 2006 +0000 "Encode release log update" commit d17f64c22056eb094a9a449f76a2bdfa0a436db8 Author: galt Date: Thu Mar 23 16:00:02 2006 +0000 "Release log update" commit 388c8b8fc6528e0fdfe7fcdc311c3c4b329e6da6 Author: kent Date: Thu Mar 23 06:34:30 2006 +0000 Adding intermediate code generation of C-style fors and ifs. Doing branch optimization of isx code. commit bfd69376d04be0344829311f9d7b923d37edc85d Author: galt Date: Thu Mar 23 06:30:45 2006 +0000 fixed file size type commit 1e283d7e2bf5e4f8dbed796cb7610006eadd7def Author: galt Date: Thu Mar 23 06:27:54 2006 +0000 fixed file size overflow commit 7ffefc4972b72c02f770ef79b3559367b2974a74 Author: hartera Date: Thu Mar 23 05:33:45 2006 +0000 Documented creating swapping chains and nets for hg17 over to rheMac2 and creating axtNet, mafNet, liftOver and alignment downloads. commit d00415138097349c6726ab92b4c650ea9a2e9a94 Author: hartera Date: Thu Mar 23 05:30:20 2006 +0000 Did a swap for hg17/rheMac2 chain alignments and created net, axtNet, mafNet, liftOver and also alignment downloads. commit 43dd10524147ecfc419daa4f83f8845d0e4fb399 Author: angie Date: Thu Mar 23 00:53:40 2006 +0000 Bumped up the dispatch order of doMainPage and doSchema, so that links in will do the right thing even if some hgta_do* variables got stuck in the cart during previous errors about conflicting settings, e.g. all fields & intersection. commit 513befdde20957493110522d844db02194912779 Author: angie Date: Thu Mar 23 00:51:58 2006 +0000 Added hgta_doMainPage to hgTables hotlinks, to force a main page display in case the wrong cart vars got stuck in the cart (this could happen when the user tries to get all fields from an intersection, and then keeps navigating using a link or pasted in URL instead of using the back button). commit 7cfb6a2805f64e6dcd8c65c9874a678f0b15d19f Author: kent Date: Wed Mar 22 23:51:57 2006 +0000 Generating assembly code to an in memory structure before actually writing it to a file. commit 5a1da92fc842b99ab03086dbd05accf519904d39 Author: angie Date: Wed Mar 22 23:46:37 2006 +0000 Added a call to cartSaveSession so that the original hgsid's session is changed. Previously, it was creating a new session/hgsid with defaults from hguid, and changing that instead of the original session. commit cef7c9cd949edd1ced8ea935cd278b5ec316111a Author: markd Date: Wed Mar 22 23:35:05 2006 +0000 added handling of haplotypes pseudochromosomes commit e119cc3c0e5325cbbadad51b340922bc0e3725e1 Author: galt Date: Wed Mar 22 23:11:22 2006 +0000 fixed so default makefile points to normal visiGene db commit ab2da209d06db4bc294ea602524a8cd766f0ac1d Author: kate Date: Wed Mar 22 22:42:42 2006 +0000 Update phastCons entries commit c0a87249d2ce3769d2000319019dbb23c514e12f Author: galt Date: Wed Mar 22 22:29:44 2006 +0000 updated to show new usage commit 72a0ec6b8d4521e69bc9b037c093bead911b45fa Author: galt Date: Wed Mar 22 22:27:41 2006 +0000 fixed quoting problem on row insert by changing quotechar commit 7c5e62769d33533f3ef3e98cecf990222e6b1e97 Author: kuhn Date: Wed Mar 22 22:25:38 2006 +0000 format tweak commit 4177bc7b657d90d635912300c1d2f30b9c783b09 Author: hiram Date: Wed Mar 22 19:53:40 2006 +0000 blastzSelf completed commit 3b9f69d0a9ebcfcebbe145e7d9d4697d8e7a1e72 Author: kuhn Date: Wed Mar 22 19:10:28 2006 +0000 relaxed constraints on clonePos. Since Terry no longer does assembly, the lists have begun to drift and not all clones are found in clonePos. commit d31d071c5a9640ecf84de9e0ebeb9ee05b05e966 Author: galt Date: Wed Mar 22 19:02:21 2006 +0000 added back fixCopyright, but fixed it - freez was screwing up mem because it had become a dyString, so I changed the routine to use dyString commit 2234495e15480bde1cad1b3784087d404e6d7537 Author: kuhn Date: Wed Mar 22 18:31:57 2006 +0000 added warning if not run from dev commit a54afb3643ef06a63ee980d5d84081a13e484d35 Author: kuhn Date: Wed Mar 22 18:23:48 2006 +0000 added checking to identify by name all users with a delay commit 3eb38b7c5a59c3a86e3cb434458abaca3afeda97 Author: hiram Date: Wed Mar 22 18:17:59 2006 +0000 Changed default position, and ran self blastz commit 8d4ed5f41c2610477a0cd610a0f8219c47d4c9be Author: hiram Date: Wed Mar 22 18:07:43 2006 +0000 finished with the mm7 to mm5 liftOver commit 1b1a6b38552db086247a8b9a9a419b0c46b906a1 Author: angie Date: Wed Mar 22 16:57:32 2006 +0000 Set HG_WARN to HG_WARN_ERR when descending into subdirectories, to enforce strict checks. commit 6e5fad9768caa68b766c092cf2606f55f5069c53 Author: angie Date: Wed Mar 22 16:52:23 2006 +0000 Resolved -Wall warnings: unused variables. commit 8a0dc09c2225884d212deaa66a1bcd3c198d4442 Author: galt Date: Wed Mar 22 16:00:03 2006 +0000 "Encode release log update" commit c87627483ab763c561f43b60ad4d6ec268a6ff14 Author: galt Date: Wed Mar 22 16:00:02 2006 +0000 "Release log update" commit 9675a0b7006338f52f0486de520e215080b7bb93 Author: genbank Date: Wed Mar 22 15:34:15 2006 +0000 added script to sumerize gbSanity reports commit cbc93c53b40ccf2bc7d461d2073a1e52f5b1f4fd Author: lowe Date: Wed Mar 22 14:10:39 2006 +0000 added new archaeal genome commit 16261f51fd7c72efaa464c95195ca5c5148503fb Author: galt Date: Wed Mar 22 08:18:15 2006 +0000 fixed for new jackson20060125 update commit e825f8217e379ae7ee1b1981f1ea114b40ad72a3 Author: kent Date: Wed Mar 22 07:21:06 2006 +0000 Figuring out that Mac stack wants to be on 16 byte boundary.... commit 1ccb15c82b8225105c834d115cfc51ed795469bb Author: lowe Date: Wed Mar 22 07:17:52 2006 +0000 Fixed typo bug in onClick details page for CodeBlast info. Previously, sent user to unknown genome "pyrAer2" -- fixed to "pyrAer1" so will work correctly. commit 9f5cb64c90dcda90e2e4813341fda855a29557ad Author: kent Date: Wed Mar 22 05:18:04 2006 +0000 Commenting out UCLA sort. commit 25f3b1399b9f022063601c6ed26cdd0d4325c875 Author: heather Date: Wed Mar 22 04:58:33 2006 +0000 based on reviewIndexes commit 5e0de323f9c3be402c166113b2be0a40b72916b4 Author: galt Date: Wed Mar 22 02:58:36 2006 +0000 added flag to control name for visiGene database used by cgi commit f60e59a3329b290738bbeb34f2a0bd5eb2fe4255 Author: galt Date: Wed Mar 22 02:00:47 2006 +0000 added important note about needing to run ANALYZE TABLE commit bb729aeae810fcf216713b22a9d4d3c07d9f7153 Author: donnak Date: Tue Mar 21 22:55:57 2006 +0000 Fixed problem w/multiple tracks named Chimp Chain & Chimp Net. commit e59097782808dfd91cdb787f40b56b3bd999ecda Author: hartera Date: Tue Mar 21 22:55:13 2006 +0000 Added affyU95 search without prefix. Removed shortCircuit from affy searches as chips may share probe IDs so now results from all chips will be returned when searching for an ID. commit c8f32cb03a699311a55d6128abd7ac55158a8c89 Author: donnak Date: Tue Mar 21 22:40:14 2006 +0000 Fixed the order of some of the chain/net tracks for orgs w/more than one pair of alignments. commit 02785dafbfac37c21fd73e6e5169559b9b7806af Author: galt Date: Tue Mar 21 21:55:55 2006 +0000 updated mm5.knownToVisiGene commit f1e8191a13abccdf3535bca2a110d63cb8b7b0f8 Author: kent Date: Tue Mar 21 21:54:44 2006 +0000 Adding -lpthread to link. commit e41e5feca417e89d65fd176a8a40c27c5fdacfb5 Author: angie Date: Tue Mar 21 18:39:41 2006 +0000 Added .gz to path default since that is preferred now. Explicitly state which central database was changed. commit a1c885dbf80d7274d53b44aeab430c268c5cbe13 Author: daryl Date: Tue Mar 21 18:12:00 2006 +0000 added Perlegen data reference commit 08a51d75c2f31cd13453ffe717b090645fd3f486 Author: angie Date: Tue Mar 21 17:32:58 2006 +0000 Offer the select for limit on #items returned for bedGraph as well as wiggle. commit 3df9fbffe43efdf8649c44e454a7e545aa614e36 Author: angie Date: Tue Mar 21 17:08:32 2006 +0000 Ignore NULL or empty values. (previously NULL could cause segv) commit b267907c13513ccddb7d052eeb85b645dfa95eb7 Author: kuhn Date: Tue Mar 21 16:53:47 2006 +0000 changed apachelog lookup from genome-centdb to genome-log commit ae24cacd2285c161c2c6c16366b238fed09c01f3 Author: angie Date: Tue Mar 21 16:45:47 2006 +0000 Resolved -Wall warning: unused variable. commit b06198f6abdba3ddb90f1a786d12ad603301611b Author: galt Date: Tue Mar 21 16:00:03 2006 +0000 "Encode release log update" commit f6584e5514e561100c4957291a37f6f0cf05fe37 Author: galt Date: Tue Mar 21 16:00:01 2006 +0000 "Release log update" commit d0c742f71ff0c5053546788fa58bdb600cd5dec1 Author: fanhsu Date: Tue Mar 21 13:21:21 2006 +0000 Added hg18 to hg17 liftover. commit 4c50f1157905bcf94b73dec16b32e2b8faa2fd01 Author: kent Date: Tue Mar 21 07:33:21 2006 +0000 Fixing missing %% in front of ebp. commit 2e2696c24fa5a7faa693556e5eb3b2d7a799583e Author: kuhn Date: Tue Mar 21 06:50:50 2006 +0000 changed script to use genome-log instead of genome-centdb for apachelog commit b5f7c87651178a56f1ab77581c2da44955567cb4 Author: kent Date: Tue Mar 21 06:50:38 2006 +0000 Getting rid of jkhgap dependency in makefile commit 8ee42e7ce3c7a2f31c6b65dfca56f566be4ed7e2 Author: heather Date: Tue Mar 21 06:06:06 2006 +0000 change machine commit 46bde6d644ae77b0af63bfb3780e96b753c14223 Author: heather Date: Tue Mar 21 05:54:36 2006 +0000 add notes for dbSNP build 125 commit 5ff5f6da7eaea223d8ddbd46eb39bebd8217a851 Author: heather Date: Tue Mar 21 05:33:18 2006 +0000 fix typo commit 8dd1e8742adeec178d7267da3460ed50dd4a54cd Author: galt Date: Tue Mar 21 02:36:02 2006 +0000 added support for db option commit cd32670999ae9504c3dd97ba9e3acad8c1ad66ee Author: markd Date: Tue Mar 21 01:31:05 2006 +0000 fixed typo commit 64790a7e7d86452e7e695d693e3c81ae49586a23 Author: hartera Date: Tue Mar 21 01:30:37 2006 +0000 Added functions to get a Gene Symbol and RefSeq ID from a cross-reference table. For Zebrafish, added the Gene Symbol and RefSeq accession to the description section. commit 67117b773a3a2b2abb1827f6eda798b0faa649ec Author: angie Date: Tue Mar 21 01:29:27 2006 +0000 Re-RepeatMasked with open-3-1-4 which has a fix for rodents, remasked sequence. Getting back to pairwise alignments. commit 748895f0c241409a2ad48d96d39420cb7bc57207 Author: hartera Date: Tue Mar 21 01:24:12 2006 +0000 Changed priority of a link. Removed some lines that were not needed. commit f241ec2b7849bcde91f5ca385760adca87025c26 Author: hartera Date: Tue Mar 21 01:22:19 2006 +0000 Added query to obtain RefSeq Summary. commit 5295340273a96623269519b35218977b52f7ec82 Author: rhead Date: Mon Mar 20 23:47:53 2006 +0000 Fixed typos: changed "and well as" to "as well as," and put a space in "1 Mb." commit fbb27c855de83471b20461a31e7521db33cf4072 Author: angie Date: Mon Mar 20 23:36:12 2006 +0000 Added more sanheads to @fileServerNoLogin. commit 0f6d11f7f07fa62271dfe82123e0f693641da275 Author: heather Date: Mon Mar 20 23:28:44 2006 +0000 add comment commit b4b13752fb9821d5ae28a0d5ebe0fe265be95958 Author: heather Date: Mon Mar 20 23:17:30 2006 +0000 add comment commit 2baf3a0de84bd1af8d499818d698f78294b72c7e Author: markd Date: Mon Mar 20 23:13:11 2006 +0000 disabled panTro2 xeno ESTs commit cec3015374df44ade6c838409c79040dccab7590 Author: fanhsu Date: Mon Mar 20 23:10:11 2006 +0000 Changed mm8 back to mm7. commit e0bf8c9ed2e3a922ff0ef42105bdafa264ccf49d Author: markd Date: Mon Mar 20 23:00:26 2006 +0000 for panTro2, treat human as native commit 9cbff090f70e235ca5fd34bd61ed24b3475a4470 Author: hartera Date: Mon Mar 20 22:58:19 2006 +0000 Added a function to process click through to details for the encodePseudogene track. commit 11b2518f3021a0b751f45627326554dd3f18b62a Author: hartera Date: Mon Mar 20 22:56:31 2006 +0000 Added urls and new trackDb settings for encodePseudogene subtracks. commit 04470f2e2a9133d114b4213288f1ced2bbc0e51c Author: donnak Date: Mon Mar 20 22:49:14 2006 +0000 Updated date for hg18. commit e7d727a0b55a0ea8537389539326f83336eaefbc Author: donnak Date: Mon Mar 20 22:46:54 2006 +0000 Changed date for hg18. commit 6fbaf523328e9254fe4998623ff4fca275e19fb3 Author: fanhsu Date: Mon Mar 20 22:28:28 2006 +0000 Changed mm7 to mm8. commit 616bd11e0d5db180f593bc6ac4d7c873350a73cd Author: kent Date: Mon Mar 20 20:58:48 2006 +0000 Starting on a run time library for calling from assembly-code-generated paraFLow. commit dab9306444c871ab69f05166c68a5cc8998bf2ff Author: fanhsu Date: Mon Mar 20 18:59:27 2006 +0000 Added Summary Statistics and changed description of hg18 to "Mar. 2006". commit 08e3fc4ecf392c11960e090838a56584c3b1191a Author: hiram Date: Mon Mar 20 18:56:36 2006 +0000 Must run xdir.sh in runDir, it doesn't have a cd in it commit c55f0b30cc994bdc5295c4d5ab117ae98bc8c87f Author: fanhsu Date: Mon Mar 20 18:56:34 2006 +0000 Changed "Feb. 2006" to "Mar. 2006" for hg18. commit 64fc5a7c5964d640acc7f6dc052e47baf1a0c12a Author: kent Date: Mon Mar 20 18:13:21 2006 +0000 Handling pentium code generation for functions returning up to three integers. The isx code generation still only handles completely a single return. commit bb5b969be1778e89c204a17f2a2a0f491a2bba97 Author: fanhsu Date: Mon Mar 20 17:45:14 2006 +0000 Set curProtId to UniProt accession if not already set. commit d5abf50734c05c191724b704edb5260f24b431f7 Author: markd Date: Mon Mar 20 17:44:53 2006 +0000 added option to get aggregate stats on all sequences commit 37d2d4f963370d4a825e956c93ddcd3f87019fa5 Author: angie Date: Mon Mar 20 16:49:12 2006 +0000 Add database to error messages (for running in a loop on databases). commit 7f0e568b1a68e4a51936307215642c237bfabacf Author: fanhsu Date: Mon Mar 20 16:21:20 2006 +0000 Moved hg18 chrM line to the end. commit e216ce46f228594fef7cd6d07991430afe6f2147 Author: galt Date: Mon Mar 20 16:00:02 2006 +0000 "Encode release log update" commit 5fb2541916c5673fe309afb4befc730d23990798 Author: galt Date: Mon Mar 20 16:00:01 2006 +0000 "Release log update" commit d7daec3e801121ed5d29c1a74f2748b7b6309e96 Author: kent Date: Mon Mar 20 11:44:18 2006 +0000 Experimenting with xadd. commit 6dc644f9370d604b45b31be84684f0fe56aafe9f Author: kent Date: Mon Mar 20 10:24:06 2006 +0000 Implementing pf__printInt for cross validation of assembler vs. c-code generator. commit 35a194580d4df897ece369b0406e80956b296512 Author: kent Date: Mon Mar 20 10:23:33 2006 +0000 Marking ax,cx,dx as trashed during function call. Making poInput avoid mov mem,mem, loading source into a register if need be. commit 705be453f5bef97f72ee555ffe825dd1f3ee58b3 Author: kent Date: Mon Mar 20 09:49:47 2006 +0000 Tweaking driver so that -isx flag will call assembler on generated machine code and execute it, bypassing the c coder. commit 7d29478ba730b93cdef4d7a5a2bdb3154a6f1c2e Author: kent Date: Mon Mar 20 09:28:51 2006 +0000 Splitting out gnuMac module from rest of pentium code generator. commit eac6a9a6c10edcbf6ab9e41e2479434fc5eba145 Author: daryl Date: Mon Mar 20 08:35:13 2006 +0000 added options winSize, diffQualMin, winQualMin, winMaxDiff and set defaults to previously hardcoded values commit f08858b449c9d6440155619c6ef785ef74bcc175 Author: kent Date: Mon Mar 20 07:58:17 2006 +0000 Getting isxToPentium to make something gnu as will assemble. Generating calls and module/global level data declarations (bss and constant) commit b233bb2d065e02121bc7d6e779c83f13bf967b4d Author: kate Date: Mon Mar 20 04:22:41 2006 +0000 Add new chimp alignments commit 56e9fddfb901e2ddb7583cc6d999a687f658c526 Author: kate Date: Mon Mar 20 03:33:59 2006 +0000 Add comparatives commit aef0a0d8101a77e9d201bd4979706e60b920495d Author: kate Date: Mon Mar 20 03:25:17 2006 +0000 Finish canFam2, galGal2, hg18 comparatives. Start Genscan commit 012cceb96f6a9f362c2f37e1bf33da0c5d969090 Author: kent Date: Sun Mar 19 23:16:28 2006 +0000 Fixed problem with isxToPentium.c using si and di for byte operands. commit ea4378e8995fe0e484f0b49c71cb49d8d762eacf Author: daryl Date: Sun Mar 19 22:32:06 2006 +0000 removed rerty label; generalized the map box commit 21f0f211a32c9eb2c5dac1822485aae71c290498 Author: daryl Date: Sun Mar 19 22:31:02 2006 +0000 cleaned up the html and referenceds a bit commit 5bb626d26ab4a89b3dc50ee8436f938caffa316a Author: kent Date: Sun Mar 19 22:26:40 2006 +0000 Changing isx to something closer to regular 3-address-code commit 07a03b6992964476a3844b1fb24662ac23b04949 Author: daryl Date: Sun Mar 19 22:09:06 2006 +0000 fix typo commit d0f5030408d539e8e53c0ea084b0c3b1a24d7471 Author: kent Date: Sun Mar 19 21:48:21 2006 +0000 rearranging some debugging info commit 24d084361aa060234358613c098602e521748b12 Author: kent Date: Sun Mar 19 21:41:42 2006 +0000 Fixing shifts. commit 2e3d4f06cd3fd369abbe5f5824f2d2e415674036 Author: markd Date: Sun Mar 19 18:18:24 2006 +0000 read list of sequences needing updated into memory to prevent timeouts commit 6b5efb74d246787e6bf9fa807b8206a2b3b64177 Author: markd Date: Sun Mar 19 18:17:06 2006 +0000 removed extFile update from dbload commit f24ce05a509dbf1359922954d0b9dad20f860455 Author: markd Date: Sun Mar 19 18:14:33 2006 +0000 don't leave conf file open commit 0a6747965b917279890f064b5de100b6827608b4 Author: markd Date: Sun Mar 19 17:16:56 2006 +0000 increase timeouts commit 536a0c1e1ce007afaf72b1f4bca80e4d11c53efc Author: galt Date: Sun Mar 19 16:00:03 2006 +0000 "Encode release log update" commit 1107061768b684f1d89849f888470cbeb544f8d0 Author: galt Date: Sun Mar 19 16:00:01 2006 +0000 "Release log update" commit ad8828803bc2acc1db16a5951f6ab943154067c3 Author: kent Date: Sun Mar 19 11:38:34 2006 +0000 Put todo on shift. commit e04ef68ed309353f9db9d00323e755e756211392 Author: kent Date: Sun Mar 19 11:28:16 2006 +0000 Adding pentium code generation for bitwise and/or/xor and shifts. Improving division code a micron. commit fc0d776f1cff896480871b98f204ac2d552839fa Author: kent Date: Sun Mar 19 10:46:52 2006 +0000 Theoretically at least generating code for byte and short in addition to int types. commit df482db1ffcbcc4c10dd713a25c7b44cb1b17ae3 Author: kent Date: Sun Mar 19 08:13:27 2006 +0000 Putting in test case for code generator. commit ebb8fc1e45aeacff7d30944f5b038eaa0212a818 Author: kent Date: Sun Mar 19 08:06:57 2006 +0000 Doing integer division and mod. commit 4b8c3d902e3f25ec09a070533510435a8af601bf Author: kent Date: Sun Mar 19 06:28:58 2006 +0000 Generating integer subtraction. Fixing clogged register bug. Improving register selection. commit a391f0e4287a3ae28c4adbfd37e3e3feefcdabf3 Author: kent Date: Sun Mar 19 03:29:58 2006 +0000 Starting to assign registers and generate pentium code. Just working in a small way for integers. commit f81221b74010ecddc2921a38c9f41d725c2c7090 Author: kate Date: Sun Mar 19 02:22:34 2006 +0000 Add missing path commit 7c6660e134517f446ddd68357dae7b8c1e4eac55 Author: kent Date: Sun Mar 19 00:42:05 2006 +0000 Adding slRefNew commit 63400a9f37fd06b08d7aeac26ae4c27771fe7ff8 Author: kent Date: Sun Mar 19 00:39:25 2006 +0000 Starting to define structures for pentium registers. commit 8ee506e58f61ed5b4f6a25ffd71a13d8dfcd4aff Author: kent Date: Sat Mar 18 20:08:05 2006 +0000 Some more intermediate code experiments commit 36928cd685fff9864c3818b822014c17f74b8582 Author: fanhsu Date: Sat Mar 18 18:20:14 2006 +0000 Created makefile. commit 19f0ace3468c6af98c27790087391ccec830343a Author: fanhsu Date: Sat Mar 18 18:18:45 2006 +0000 Added ID line. commit 44cd6a660f431f1cbe3bd771bbe75eb07f45051d Author: fanhsu Date: Sat Mar 18 18:14:33 2006 +0000 Created hgCalStat.c. commit 021e09604b938d2f71e953f3357ae572619055e4 Author: fanhsu Date: Sat Mar 18 18:11:47 2006 +0000 Try another ID line. commit e0024802d26100fe4735add6e38999e8d1da4bf2 Author: fanhsu Date: Sat Mar 18 18:08:02 2006 +0000 Added # $Id: stats.pl commit ec3cc4f090ccf80a1becfed8ab2f45a63c237a9c Author: fanhsu Date: Sat Mar 18 18:06:18 2006 +0000 Created stats.pl. This was a direct copy from Hiram dated November, 2003. commit d1356afb1f22d4b3485d30f9bb373d660b086c79 Author: fanhsu Date: Sat Mar 18 18:04:17 2006 +0000 Minor format adjustment of 1 line. commit 8640f90bdbd4b83181bfcd4d85d869dc6684cbee Author: fanhsu Date: Sat Mar 18 18:01:14 2006 +0000 Updated with correct hg18 numbers. commit 42b433a18039dbe921e998001faf013dc398cb78 Author: genbank Date: Sat Mar 18 17:32:27 2006 +0000 disabled strPur1 commit 2aa919fcd9b7482db4d35633d1f078d4057d0514 Author: galt Date: Sat Mar 18 16:00:05 2006 +0000 "Encode release log update" commit e5581d04a7740f62949fb404094a4f552bfdb872 Author: galt Date: Sat Mar 18 16:00:04 2006 +0000 "Release log update" commit f20d20d294520498d6f1fc8914a1bee4a7869c6e Author: markd Date: Sat Mar 18 09:01:10 2006 +0000 enabled strPur1 commit 37feee74b899da4b742fdce4ddaa9b1b45423588 Author: aamp Date: Sat Mar 18 08:48:29 2006 +0000 Changes to add a UI option to the new affy human exons track. commit 9c21716b705cd1a9ea5d13d47da981356aa6b4e2 Author: kent Date: Sat Mar 18 07:54:02 2006 +0000 Adding start of an experimental intermediate code generator 'isix' commit 22ecd91d27d1f4499429e4836a09749c027c6ba2 Author: kent Date: Sat Mar 18 06:02:12 2006 +0000 Got rid of some unused parse node types. commit 679882cd27bcdb30021017348d2145190b340e22 Author: kent Date: Sat Mar 18 05:04:55 2006 +0000 Detecting constant initialization loops. commit eedcfcd2a0f5655e98ed75ff32208ac7394129ae Author: kent Date: Sat Mar 18 03:47:45 2006 +0000 Fixed long/int mixup in constFold's unary op. commit 7dd8e33d62cef0664950ba50605f0a25c94eed98 Author: angie Date: Sat Mar 18 02:34:37 2006 +0000 x86_64 -Wall format warning: sizeof returns something larger than int, so cast. commit 8820b08f15ee25c875811e8f2efcd9f0aec4e225 Author: angie Date: Sat Mar 18 02:26:22 2006 +0000 Resolving -Wall warnings - removed unused variables. commit f985ef405821e794c1b0f813cc912da78b47d35c Author: angie Date: Sat Mar 18 02:22:37 2006 +0000 Resolving -Wall warnings - removed unused variables, /* in comment. commit 30f88053c02950ab36026c80dcfb118bf0bea362 Author: angie Date: Sat Mar 18 02:14:00 2006 +0000 Resolving -Wall warnings - removed unused variables, format type, char as array index. commit 9a215dedcaa3f7c5b7665b71211e67e9d43ea85f Author: angie Date: Sat Mar 18 02:11:21 2006 +0000 Resolving -Wall warnings - removed unused variables. commit b40aec504a6b2410eabc1ff586189b74e1abd840 Author: angie Date: Sat Mar 18 02:01:56 2006 +0000 Resolving -Wall warnings - char used as array index. commit bac492bb83fc9f2294f554a5bcc211fe9cf936b1 Author: angie Date: Sat Mar 18 02:00:40 2006 +0000 Resolving -Wall warnings - removed unused variables. commit 91ef411c967d5282dd1be75f7273111ce0cc923d Author: angie Date: Sat Mar 18 01:58:35 2006 +0000 Removed unused variable which also was a duplicate opening of the input file. commit 8a1b9167bc276ead9733403848798e4e3b632cac Author: angie Date: Sat Mar 18 01:51:36 2006 +0000 Resolving -Wall warnings - char used as array index. commit 6e4908ffaef17793f474509b82c34bc22238be63 Author: angie Date: Sat Mar 18 01:47:07 2006 +0000 Resolving -Wall warnings: unused variables and chars used as array indexes. commit ab1b0289e5699a87cb8c6b58a1f3b63cacb68d4d Author: angie Date: Sat Mar 18 01:38:44 2006 +0000 Typo fix. commit cc00998262836f915469cc6ad8fd759de8eb9f85 Author: angie Date: Sat Mar 18 01:37:22 2006 +0000 Removed a couple unused fields. commit 94b1422a36cd5fd607715efc1d39578c43efc1c5 Author: kent Date: Sat Mar 18 01:24:08 2006 +0000 Folding expressions with named constants. commit 642ba9296d23bd231cbccd44ab7a8d4cb7058de2 Author: kent Date: Sat Mar 18 00:45:29 2006 +0000 Making it so that const can be applied along with global. Folding constants. commit 3a974b9152260505acdfd36c434f4d0bf5b5dd00 Author: hartera Date: Sat Mar 18 00:34:27 2006 +0000 Added rules to link the ENCODE Pseudogene subtracks tables to the Class table for this track. commit 59a5190ab869de776b47b2f33b3fbc276806289c Author: fanhsu Date: Sat Mar 18 00:33:43 2006 +0000 Removed a line. (/var/lib/mysql/uniProt -> sp060115) commit aeee1d8c36d857aeece372fad15af29eb7558b44 Author: hiram Date: Sat Mar 18 00:32:48 2006 +0000 Adding PicTar microRNA tracks commit 99ed5d7a9736ccbdc9aad12d0910cc10b4b69245 Author: hiram Date: Sat Mar 18 00:30:58 2006 +0000 Initial contents, to be expanded by the contributor commit 7c31e9fee631b33cae38b175e31fe4ee0f15ea00 Author: hiram Date: Sat Mar 18 00:24:54 2006 +0000 Add picTar microRNA tracks commit ce3dde4202fdaf86e6c70b1b4321eb23d664cb04 Author: donnak Date: Sat Mar 18 00:24:18 2006 +0000 Added some more info to the human genome acknowledgements section. commit 380832e86663d96a79f3eb238eb7351abfe01542 Author: angie Date: Sat Mar 18 00:22:29 2006 +0000 Updated to match what has been loaded. commit 205a0e7390764e082599925387a24e1369a44a0e Author: angie Date: Fri Mar 17 23:57:15 2006 +0000 Adding for tableDescriptions/documentation. commit efa31106d09430044785a369880046c3b85e0c91 Author: angie Date: Fri Mar 17 23:55:46 2006 +0000 Updated to include more current genbank tables. commit b4c01da4fc8b558a667baa432bf96a4a6d08e7ef Author: angie Date: Fri Mar 17 23:55:06 2006 +0000 Updated to reflect the imageClone table that GenBank creates nowadays. commit 73463f6214d86c600aee7c87670f0573cd83fcb8 Author: ann Date: Fri Mar 17 23:49:26 2006 +0000 added block for HInv track commit 98afc9071691b45a57e35f65c18a78f116a40629 Author: fanhsu Date: Fri Mar 17 23:46:22 2006 +0000 Added hg18 stats. commit 794d2070ab2e1555b114d57d1f45cda9ed923b80 Author: ann Date: Fri Mar 17 23:45:53 2006 +0000 edited page to reflect most recent counts at HInv commit 191e6e223bec77c6277989ec2d2ae2c29e94df96 Author: angie Date: Fri Mar 17 23:23:13 2006 +0000 Typo fix. commit 21ab2eab42f73c1500ac46919e45d49113fe94c9 Author: donnak Date: Fri Mar 17 23:11:55 2006 +0000 Minor rewording of score calculation text. commit c62b46d3029e4cebfb3f54202eef844bc1097f70 Author: donnak Date: Fri Mar 17 23:11:24 2006 +0000 Added info abt score calculation. commit 0d3fed9baaa089ceb61951b670a3a0aaff0d21a2 Author: fanhsu Date: Fri Mar 17 22:14:01 2006 +0000 Updated sections regarding proteins and uniProt DBs. commit d73423857280cba4ecdd26b35512703b05d865a1 Author: kent Date: Fri Mar 17 22:05:03 2006 +0000 Making this generate switches on char constants. commit 2f21ccba3d22f6bb4476d5ed07d9b8343e4cc102 Author: donnak Date: Fri Mar 17 21:53:59 2006 +0000 Added commented-out hg18 entry. commit c971a18df6fb19651bb04973770b536126917f23 Author: angie Date: Fri Mar 17 21:27:00 2006 +0000 Moved some copied-around subroutines into HgAutomate package. commit 770ed14fff00d94686d084fe8acb86e60f64d609 Author: angie Date: Fri Mar 17 21:26:20 2006 +0000 Moved some copied-around subroutines into HgAutomate package. Run xdir.sh on $fileServer as suggested by Hiram. commit 96d7394c0d57d7a463e204ccbb4f4fb18d08a5e4 Author: angie Date: Fri Mar 17 21:24:15 2006 +0000 Adding HgAutomate.pm, a perl package (library) with subroutines that help automate trackbuilding in our environment. commit c6b575f18d725daffdb7c99c5f80b2c36e030d26 Author: ann Date: Fri Mar 17 21:22:00 2006 +0000 initial file. copied from /human. commit 9476baf9a0bda7140905fa09745336e97fe331fe Author: ann Date: Fri Mar 17 19:45:14 2006 +0000 added gold track commit 2087b99e2192366730b1de288bdd3bd4fb38113c Author: ann Date: Fri Mar 17 19:42:56 2006 +0000 removed two types that are no longer in the assembly commit 278ce37125fabc36f5183fb391491f3322c7c1ef Author: ann Date: Fri Mar 17 19:33:04 2006 +0000 added three missing gap type descriptions commit 6bba537e4ddd12148a6643e2c0a170a4fd09f567 Author: ann Date: Fri Mar 17 19:24:36 2006 +0000 initial file. copied from /human commit 81e796bbe1708c221c40655087a17a0b947b346b Author: ann Date: Fri Mar 17 17:16:04 2006 +0000 fixed typo with Archana's link commit 1d4241e866e5dbbbf90ec74e9ddbc1b189472996 Author: ann Date: Fri Mar 17 17:14:02 2006 +0000 added link to Brooke's and Archana's CBSE pages commit 4c00711432e4cfe7f79478ee704b2d59d1e87501 Author: donnak Date: Fri Mar 17 17:08:50 2006 +0000 Fixed problem w/Archana's email address. commit f679f3483b0a3100251e0c1d45681f9783369b21 Author: ann Date: Fri Mar 17 16:57:15 2006 +0000 added QA note for mytouch commit 99bc5810d73c79e540a573600a678cc69880f5dc Author: angie Date: Fri Mar 17 16:24:48 2006 +0000 Use optionSpecs/optionInit() instead of optionHash(), so that misspelled options cause error messages instead of confusing results. commit 5fbf23fedcb42e3746fae3b7c8ba7b7ba03d9134 Author: angie Date: Fri Mar 17 16:09:36 2006 +0000 Updated location of chain file (it has been compressed). commit 48f5c70bfb0faacf0d1d6b9d8281daee2ce21451 Author: galt Date: Fri Mar 17 16:00:03 2006 +0000 "Encode release log update" commit 213c2230e2bb3e5b5023b23135b71f5e502031cd Author: galt Date: Fri Mar 17 16:00:02 2006 +0000 "Release log update" commit 98c8b091c2882e031d5454c34925b1466a5b971e Author: genbank Date: Fri Mar 17 07:33:31 2006 +0000 handle lost refpre commit 8b36f2eddc0c53b493e80c7c944b2a272de5b574 Author: donnak Date: Fri Mar 17 03:08:24 2006 +0000 Fixed formatting problem with code snippet. commit 85baefa90283a9e75900847ff87e8a8eaed6e981 Author: kate Date: Fri Mar 17 01:24:49 2006 +0000 Fix dog paths. Continue chaining on human. Load swapped rhesus commit fa4d470f37ae62cab1868307518bb4390028f42d Author: kate Date: Fri Mar 17 00:53:34 2006 +0000 Add update from Sanger commit 79fc3eaa0b9691ee07012cb93b1291f71e02a6ae Author: kate Date: Fri Mar 17 00:45:11 2006 +0000 Add New Sanger chip/chip data commit 4d56aa22bea21787edeb1b9187e00302b83b6f4b Author: kate Date: Fri Mar 17 00:31:26 2006 +0000 Add more Sanger chip/chip -- 5 histones in new cell type (HFL-1) commit 622deffaf80945abcc4a4fef21b1b15ac6121fd8 Author: donnak Date: Fri Mar 17 00:05:20 2006 +0000 Added info about new genome-mirror mailing list. commit 5c0adbb40caa6fad03227eb0236530d950c3fd95 Author: donnak Date: Fri Mar 17 00:04:48 2006 +0000 Added Archana. commit c0842a7c362d71bd58bc695cd267a439d25aa8c5 Author: hartera Date: Thu Mar 16 23:59:17 2006 +0000 Changed names of the encodePseudogene subtracks so that the names all have encode as a prefix. commit 95cfdca45c63f2d8fc265af94d672e0999b8197c Author: heather Date: Thu Mar 16 22:49:47 2006 +0000 had it right the first time commit 19229e6282d9294200195f88fa2262980a2821bb Author: markd Date: Thu Mar 16 21:36:46 2006 +0000 fixed bug causing extFileUpdate to skip entries commit 7854d9e0a5be38d9a34437fa73dc2032a8115293 Author: donnak Date: Thu Mar 16 21:30:14 2006 +0000 Expanded item on % ID and added an item on "I'm feeling lucky". commit c20ff3922f16696e18d30c57aab421e263bd5436 Author: donnak Date: Thu Mar 16 19:52:22 2006 +0000 Added pub on chr12. commit d8651cfd549e6bfec4d12a0a3d6493e39c56a4b8 Author: galt Date: Thu Mar 16 19:34:35 2006 +0000 added steps for running vgProbeTrack and knownToVisiGene commit 4744ec90830bf42fe52bf84143551263cff5d213 Author: hiram Date: Thu Mar 16 19:15:39 2006 +0000 Eliminate -Werror on Solaris compiles commit 374d06546ca1d9b6ec435be0c5eea38a255d656f Author: galt Date: Thu Mar 16 18:51:41 2006 +0000 added support for external re-map (e.g. NIBB frog blatz alignments commit 861a4555af8ca849a161d092bb0329eaaa12fd60 Author: aamp Date: Thu Mar 16 18:28:58 2006 +0000 Only make one thing in the extras column in the Exps table instead of 3, with by default 2 of them being n/a. commit 1387e15c6850ddd99ebd88c95b45726eca616b2a Author: galt Date: Thu Mar 16 16:00:04 2006 +0000 "Encode release log update" commit 0e6620fb4df3b37e293527c58d9e9e6c5d022c26 Author: galt Date: Thu Mar 16 16:00:03 2006 +0000 "Release log update" commit 851f3d11fe6b5881f72ff423eea8d1c3357df083 Author: kent Date: Thu Mar 16 15:27:00 2006 +0000 Adding test case that tends to reveal race conditions on activation records. commit b3ab780f0ef7a819594bca14813e4b026c256b85 Author: kent Date: Thu Mar 16 15:19:31 2006 +0000 Disabling parallelism with if defined(PARALLEL) to have a stable, serial version for reference. commit 8a4091119f91458d13e972686fb195ea9e19786b Author: angie Date: Thu Mar 16 15:18:24 2006 +0000 Another cast to int, for a -Wall warning on x86_64. commit a974980d02148281bcd00361b5d9adea072abef6 Author: heather Date: Thu Mar 16 10:04:55 2006 +0000 fix between off-by-one commit 2f8a32fe7ea83f9f61ef4b6ed54c11b43c980629 Author: markd Date: Thu Mar 16 08:22:22 2006 +0000 added ignore entry commit 78bcf5e12db3c8b637c7b0e1741691ee9771b4b0 Author: aamp Date: Thu Mar 16 06:32:59 2006 +0000 Utility to merge probeset beds from an assembly database with expData tables in hgFixed, creating a bed 15 which can then be loaded into the assembly DB as a microarray track. commit 49455415e0edf03c338506af81bc9156ed08a927 Author: heather Date: Thu Mar 16 02:34:16 2006 +0000 add snpMultiple, snpCompareLoctype, snpMissing commit e612d90221ebf3b208bc30646a4b2d84fc5be49f Author: heather Date: Thu Mar 16 02:32:48 2006 +0000 generate counts for old/new locTypes; report coord/chrom changes commit 8d06a51b29cebfcc023076efd7a55489f778b620 Author: ann Date: Thu Mar 16 01:43:27 2006 +0000 edited order of chain/net tracks in track controls commit 67667d328ccd1cdbbd7fb94107383f1339fcd2dc Author: heather Date: Thu Mar 16 00:47:50 2006 +0000 change hTableExistsDb to sqlTableExists commit 5faae6470966c255027475de95ca5edc40e0ba37 Author: hiram Date: Thu Mar 16 00:18:53 2006 +0000 mm8 is correct and neater commit 5e4d37231cb64145ab4f0defd41666d5dd26f16a Author: kuhn Date: Wed Mar 15 23:49:49 2006 +0000 added a line to explain 'N' in formula - thanks brooke commit 3ce813f6905ab135bc0ea6d5807bbd0e1c0d9ba3 Author: kate Date: Wed Mar 15 23:38:28 2006 +0000 blastz dog commit 0344dbe73e6fba4d554fb3d5411f6bc175579b45 Author: sol Date: Wed Mar 15 23:38:16 2006 +0000 Initial release of description page. commit f9bac47ac6a60f7215bacaa42828ea0c829dcb60 Author: daryl Date: Wed Mar 15 23:01:03 2006 +0000 still needs correction for theta with variable sample sizes commit 3919f3b79936a651e4f2adf4513db15c52509f5d Author: kuhn Date: Wed Mar 15 22:51:18 2006 +0000 fixed typo in 'tandem' commit c9625315cc9477692eab210005b8592c5a4619fb Author: aamp Date: Wed Mar 15 22:47:45 2006 +0000 This was a weird bug. Thankfully errors are now shown when invalid options appear. commit cd8b19477fd20b396dad51d7810e62f95b3d22b3 Author: ann Date: Wed Mar 15 21:31:12 2006 +0000 edited encode_tba23EvoFold track to point to multiz17way (from multiz8way) commit 8ca9ea0d3e5c754a568e44bffe9a66a289d485e4 Author: ann Date: Wed Mar 15 21:30:02 2006 +0000 edited evoFold and RfamSeedFolds tracks to point to multiz17way (from multiz8way) commit c92de5a8cfe1441ea02675dc0ced135ae93f77d9 Author: fanhsu Date: Wed Mar 15 21:10:39 2006 +0000 Added CPG island track build. commit 1dc0ef5a897669ba52cd3763f27cb3b9fc446d6d Author: hiram Date: Wed Mar 15 20:44:01 2006 +0000 wigAsciiToBinary is obsolete, no longer needed in the build commit 94548222d9500c8ca166e5e1129467cd290791ab Author: galt Date: Wed Mar 15 20:04:58 2006 +0000 steps for making nibb frog probe alignments on hg18 commit 69cc2dcd9997061bcc5807773c8b80ab94d8fe86 Author: angie Date: Wed Mar 15 19:37:29 2006 +0000 Added makeTableDescriptions target. commit fe474e4cae2bce0042d9aab01aa0e53351401598 Author: daryl Date: Wed Mar 15 18:56:39 2006 +0000 added -lm commit af81cdda19e22b56695c0ff9a988c9cbbe46f872 Author: kayla Date: Wed Mar 15 18:55:09 2006 +0000 Giving panTro1 its own copy of quality.html. commit ff3c317098eb2a8bf22d3bbfa71bb7ea55ec2138 Author: kayla Date: Wed Mar 15 18:53:12 2006 +0000 Edited the quality block so that it would look like the other assemblies. commit 78902d9e9c61fb1df802e291122d5f7b1c8ca8a5 Author: angie Date: Wed Mar 15 18:37:17 2006 +0000 Set HG_WARN to HG_WARN_ERR (-DJK_WARN -Wall -Werror). commit 26cf821313aea1610d7bf884efb7aa08ba2f7ded Author: angie Date: Wed Mar 15 18:36:16 2006 +0000 Resolving -Wall warnings: unused variables and chars used as array indexes. commit 0f3997e4ca4b442dd3401a97e8665607030402ab Author: ann Date: Wed Mar 15 18:18:51 2006 +0000 updated with correct list of multiz alignment species commit da850ff199b5b303b944f2fe998658c114f5a4d7 Author: fanhsu Date: Wed Mar 15 16:46:51 2006 +0000 Updated logic to avoid printing duplicated pathway links. commit 7fd96870ccb40236d8f5a64834266d5297fcd604 Author: galt Date: Wed Mar 15 16:00:03 2006 +0000 "Encode release log update" commit d83dd24bbe8af70b6949d2370bc94a43710db1f4 Author: galt Date: Wed Mar 15 16:00:02 2006 +0000 "Release log update" commit b8cdd4480d26276129b346860bf5b6ac7eb5e7b2 Author: kent Date: Wed Mar 15 15:32:05 2006 +0000 Another timing measure commit 73674caccefecc7d21bcc2c2460b493618788775 Author: kate Date: Wed Mar 15 02:42:10 2006 +0000 Start pairwise alignments: human and monkey commit 2551c43357ce9406b88748b440a6ef8e9dd65284 Author: kayla Date: Wed Mar 15 01:16:22 2006 +0000 Giving rheMac2 its own quality.html file. commit ab4df8bf9aac71c0d59b443a7ff750a10d0fac46 Author: kayla Date: Wed Mar 15 01:09:26 2006 +0000 Added a quality block so that I could make the quality track go from 0-60. commit 0202a4e4fc700483ae1c20dacfdb6b51856dbd5a Author: ann Date: Wed Mar 15 00:53:33 2006 +0000 initial file. copied from hg17. commit c4fecce1d93e91b075698d61f51d169381e313d8 Author: heather Date: Tue Mar 14 22:38:10 2006 +0000 name change commit 9767382a71924855ca17de587ae67d2fd621df3e Author: galt Date: Tue Mar 14 21:43:25 2006 +0000 adding makedoc for mm6,mm7,hg17 knownToVisiGene table update commit b4f519e306456e6c692b973ffbeaca90202e2208 Author: galt Date: Tue Mar 14 21:37:07 2006 +0000 turning visiGene column on by default commit b2fdff225e50010003c096860cb8fb95f024db44 Author: angie Date: Tue Mar 14 19:02:31 2006 +0000 Resolving -Wall warnings: unused variables and chars used as array indexes. commit 596c63143b83c976ad2f9f19a9dc4a77988384ee Author: fanhsu Date: Tue Mar 14 18:26:05 2006 +0000 Added mrnaRefseq table, KG serach index files, KG gene list pages for Google, microarray tables, and GS tables. commit 9179f6e2f643eb46c4e9a33e1c906b3f36c3e970 Author: ann Date: Tue Mar 14 18:01:59 2006 +0000 changed short label for old Most Conserved track commit 646be144ed01697f2dfb3cabbc19fd333740e186 Author: ann Date: Tue Mar 14 17:52:51 2006 +0000 changed default visibility in new Conservation track commit e84ac29f27a129cdb665b5e323797656914a7314 Author: galt Date: Tue Mar 14 16:00:03 2006 +0000 "Encode release log update" commit a6323f6ee4e68df8e483e849ce9e3cf1a1d31218 Author: galt Date: Tue Mar 14 16:00:02 2006 +0000 "Release log update" commit ef1d7585acdbe1fcbeb462c97976d23c9703464e Author: kent Date: Tue Mar 14 15:55:59 2006 +0000 Fixed race condition on local para vars. commit d6aa969e55a24786d498678283d83eb444dbd386 Author: galt Date: Tue Mar 14 12:30:55 2006 +0000 taking out unneeded intermediary table commit a881cadf7556b9eb327ca5982e2c1b5bbcf92a66 Author: fanhsu Date: Tue Mar 14 05:46:06 2006 +0000 Created otherOrgs.ra. commit 21dd5e4f7f25bc730ea1531b2f7d2cd5092923dc Author: galt Date: Tue Mar 14 04:38:58 2006 +0000 "New version number v129" commit e85a4107fcf12e48c64b91c5edcb76e9813e0022 Author: galt Date: Tue Mar 14 04:22:47 2006 +0000 changed to new structure using vgPrb* tables commit 9708b2c8b31bcbab5de497d5876cf09da1bcc37a Author: galt Date: Tue Mar 14 04:05:31 2006 +0000 removing the last references to old probeExt which became new vgPrb* commit a4c271f1416673f1cddfebb688fbce76205531b3 Author: galt Date: Tue Mar 14 03:27:34 2006 +0000 made probe to vgPrb relationship many to many, reworked the new structure, added support to automatically update the vgProbes track for each assembly and maintain the seq/extFile, added support for using pslmap and chains to make the vgAllProbes track which includes all probes (currently only on hg17), need to still add support for self, external re-map (e.g. NIBB) etc commit cd622454091e22a716bf4746f5507bf2c2f167b5 Author: kent Date: Tue Mar 14 02:49:44 2006 +0000 Some preliminary work towards other para types. commit 68e4c3f3e027114a1abc3fb0dfbd0554a875b9e2 Author: aamp Date: Tue Mar 14 01:36:07 2006 +0000 Affy human all-exon track v0.1. autoSql module for the probes needs comments for many of the fields. Track needs an html description and references/links. Track may also benefit from additional UI controls. Currently the track resides on hg18. commit e692778c3a00b1892f2abc46d88de76893da8e01 Author: fanhsu Date: Tue Mar 14 00:49:00 2006 +0000 Changed primary key to key. commit 37117b38150f468c5c3a8328743d9088a4e69f23 Author: angie Date: Mon Mar 13 23:52:02 2006 +0000 Made a test case for the slight decrease in RepeatMasker coverage from rn3 to rn4, sent to Robert Hubley. Fan caught a typo in loading knownGenePep -- now there are warnings about duplicate entries for the same name, need to resolve those w/Fan. commit 7fa753d87ab56dd277da30565961870cf4e24500 Author: braney Date: Mon Mar 13 23:22:26 2006 +0000 fix bug where "not displayed" message wasn' t being displayed commit 76ac8e82fc91421abb643a35e682bf0beb4e538b Author: kent Date: Mon Mar 13 22:43:37 2006 +0000 Making para...do operate in parallel. commit becfc19606913ea8e1dcbe8154471bee6c93326c Author: ann Date: Mon Mar 13 21:43:04 2006 +0000 Changed short label for Conservation and Most Conserved tracks commit 928aefb8fa19bef5145166ebd48f90cd95fb1566 Author: galt Date: Mon Mar 13 20:44:40 2006 +0000 just a trivial table rename commit 4dcdcd5e0c6a879618e32df37cade7cd74578ae3 Author: galt Date: Mon Mar 13 20:35:32 2006 +0000 added pslRecalcMatch to std utils build commit f1caa3c462ad42deeb6044108a3ff8e04a79dc9a Author: kent Date: Mon Mar 13 20:27:20 2006 +0000 Reworking how dirs are handled in paraRun to make it easier to write back dir contents. Fixing little bug in para's on range. commit d6562667ae4d0b38d66d3c66f65c0195a445bd8e Author: fanhsu Date: Mon Mar 13 19:15:44 2006 +0000 Did some preparation to create /cluster/data/rn4/bed/blastp/known.faa. commit bbf090676106905ef9f526039d7bdc24739f8f09 Author: donnak Date: Mon Mar 13 19:00:10 2006 +0000 Edited description page, changed capitalization for some of the track labels. commit f2201266df4dadb7c3c8ca019a5313fc5eef18a2 Author: kent Date: Mon Mar 13 18:40:08 2006 +0000 Fixed bug in getDirJobs that caused same item to be reused. commit fb1fbab7ca84417c72f2c5dcbdbbb8076f7206b9 Author: kent Date: Mon Mar 13 18:19:52 2006 +0000 Fixed a bad bug - slAddTail that should be dlAddTail - in paraRun.c commit 709fd518dfae04195f0291a83ca95874cd007c41 Author: donnak Date: Mon Mar 13 18:02:08 2006 +0000 Updated reading frame refs in description to match text in UI. commit 96301cc51b8db9f0122efb6d5e1938e956db9c2d Author: donnak Date: Mon Mar 13 18:01:22 2006 +0000 Expanded syntax example for ";" range searches -- mentioned that it can be used for ESTs, mRNAs, etc. commit 95fb4622fabaa5fbca3c11ead38c40f8d42fa688 Author: kuhn Date: Mon Mar 13 17:48:39 2006 +0000 had to replace spaces with a tab commit 9c1c70c1c4905b131c83e5e5a249ec5dea375708 Author: kent Date: Mon Mar 13 17:37:56 2006 +0000 FIxing linux-only bug on isSpace commit 88e9a899eba1087b1b2c49575710d79e0de1bb59 Author: kent Date: Mon Mar 13 17:13:58 2006 +0000 Fixing manger/manager typo commit de49d36ca0865296b158726327970d3145f4ac84 Author: galt Date: Mon Mar 13 16:00:03 2006 +0000 "Encode release log update" commit 495467b9fe4ca581eb99e8c807a468544e4fda44 Author: galt Date: Mon Mar 13 16:00:02 2006 +0000 "Release log update" commit 1d740e6cadafe656e6e12f63944417af8c710399 Author: kent Date: Mon Mar 13 05:23:00 2006 +0000 ifdefing out call to _pf_paraRunInit, which seems to only work on Mac at the moment. commit 5d040e53841274c22354cdf2e97e24d60aee4393 Author: kent Date: Mon Mar 13 04:47:33 2006 +0000 Fixed bug I introduced into msort in non-int-size case. commit 73eda46493bfedc71a860d2b258d4ead05907995 Author: kent Date: Mon Mar 13 04:27:09 2006 +0000 Moving around order of tests a little. commit 6b5ddbb150010ab8b0e3aa3854376aa4dad94479 Author: kent Date: Mon Mar 13 04:23:14 2006 +0000 Adding include to avoid warning. commit d3dcf97555781e5035d708cf6e3476552d777ade Author: kent Date: Mon Mar 13 04:22:43 2006 +0000 Adding stack parameter to thread process function. commit c60b44d711a134dd2661d5008caf2af2881dd01e Author: kent Date: Mon Mar 13 02:32:32 2006 +0000 Adding call to paraRunInit at paraFlow program startup. Add -lpthread to link. commit c3222311af035bf8e3a5d8e7153145fbfc06be95 Author: kent Date: Mon Mar 13 02:28:41 2006 +0000 Adding _pf prefix, and making _pf_paraRunInit responsible for figuring out how many CPUs we have. commit e8b113c04a2d3f781c1f6bc57180ae3ace58dca1 Author: kent Date: Mon Mar 13 02:20:33 2006 +0000 Separating out codeParaDo into a new module in preparation for having it generate parallel code. commit 167946663ef7e1ac9cbb07585501c101c93476cd Author: kent Date: Sun Mar 12 21:47:25 2006 +0000 Fixing array/msort to handle case where user is supplying a paraFlow function. commit 5b858ad9f87674f2967b0cac3e81803c42852ba8 Author: braney Date: Sun Mar 12 20:21:26 2006 +0000 set up cart so detail page will print correct species order. Get rid of GASPACEPORN commit 60b82d5d45e4ea87b6b2c54f0aa122a9f191e416 Author: braney Date: Sun Mar 12 20:20:12 2006 +0000 put species out in correct order in detail page commit 49f184788ff44f0526372b4c74a21ee0576cec24 Author: braney Date: Sun Mar 12 20:12:36 2006 +0000 a liitle edit suggested by b0b commit 46bf89a54e0e7050f9a9127c709539905a4fddd4 Author: galt Date: Sun Mar 12 16:00:03 2006 +0000 "Encode release log update" commit 0b82f688de46390f32e2d54e144aecd8ba0a02b6 Author: galt Date: Sun Mar 12 16:00:02 2006 +0000 "Release log update" commit 3f49e91b120711ec98b13a0315b9a3bb8d968c1b Author: kate Date: Sun Mar 12 08:23:10 2006 +0000 Use new chimp sequence commit 81d40cca3b1d40825bf9fde86a73205f1c324227 Author: kent Date: Sun Mar 12 03:25:29 2006 +0000 Adding -lpthread for linux. commit ba84a933a6e26e0743da1e33f65aff8e67fc3153 Author: mieg Date: Sat Mar 11 23:45:14 2006 +0000 added our own quick-sort and quick-sort-r commit 88897004b1b7346be0a7023c82299298da447bdd Author: kent Date: Sat Mar 11 23:10:06 2006 +0000 Forgot the .c file too. commit e7b2deae0cf7699469b43e6c3f7f18f66f03ca13 Author: kent Date: Sat Mar 11 23:09:22 2006 +0000 Oops forgot to add the .h file. commit d05173df92f92808c87de8989db1151c812ff98b Author: kent Date: Sat Mar 11 23:07:02 2006 +0000 Fixing bug in synQueueGrab. commit 42434591e78bd34629b96c249f11f70294f4f9ca Author: kent Date: Sat Mar 11 23:05:36 2006 +0000 Adding locks around refCounts in 386 assembler. commit af34b494755ef441f7dd542b0d7fb141003d9300 Author: kent Date: Sat Mar 11 21:01:14 2006 +0000 SOme debugging of paraRun. commit afaad3709770deb7cc6229be682a54d895d743c5 Author: kent Date: Sat Mar 11 20:45:30 2006 +0000 SOme debugging of paraRun. commit d8f5e8fc6f6f43e7c7619e17aef2a5732532444e Author: fanhsu Date: Sat Mar 11 19:18:42 2006 +0000 Added Allen Brain. commit f43780ec3c923d15dfcbb4a7f409736ee654bf08 Author: braney Date: Sat Mar 11 16:40:25 2006 +0000 works better commit c5da6293c76c719a00350fe13676ee55993a61b1 Author: kent Date: Sat Mar 11 16:38:29 2006 +0000 Oops , forgot to add these. commit 2e9154bf32a2c0f943801a33ba7bb821ef7afece Author: galt Date: Sat Mar 11 16:00:03 2006 +0000 "Encode release log update" commit b49880b3fa9af23b0a7cae3c466b79eddc94a236 Author: galt Date: Sat Mar 11 16:00:02 2006 +0000 "Release log update" commit 951c7a99b4ad85a629609365de0fa8a61b813b58 Author: braney Date: Sat Mar 11 15:51:26 2006 +0000 fix seed bug. commit 3c5363c4c53859d7ebb54fe0ae85c8d4247af477 Author: braney Date: Sat Mar 11 15:47:43 2006 +0000 read more elements (should bypass word[] routines). Do some error checking. commit ef1057f1343e60ffb3260e0a5434da7606c22847 Author: kent Date: Sat Mar 11 15:20:22 2006 +0000 Adding synQueueGrab commit d5052df20714da970131d32d8cb4e22e5426f8b9 Author: kent Date: Sat Mar 11 15:19:19 2006 +0000 Starting on test framework for parallelism commit 82391ed21f66ef06a5fa75be6bb675736411d667 Author: markd Date: Sat Mar 11 05:51:46 2006 +0000 set gbdb dir on updated extFile entries commit d9b626805cc80187a9cf635b39e1fcb12c8e5e87 Author: kent Date: Sat Mar 11 05:34:41 2006 +0000 Looks plausible, but not tested yet. commit b5823226ad75e7ad59d4d4e0503219e2ccf50465 Author: heather Date: Sat Mar 11 04:11:33 2006 +0000 fix format commit fde702ee1453f39083683b0db2d0f19ea5086c13 Author: heather Date: Sat Mar 11 04:09:14 2006 +0000 remove comments commit 6c93b61e555d0fc238e52442d486cb284a9701c3 Author: heather Date: Sat Mar 11 04:08:07 2006 +0000 add comment commit 725dec536b40b803d775be1bedd40bae0a464433 Author: heather Date: Sat Mar 11 03:59:44 2006 +0000 ack! change = to == commit 0478e5cfc8440f02a48a0e4a25ab0a0bef7074b9 Author: heather Date: Sat Mar 11 03:58:35 2006 +0000 add comment commit 2181214cf00be1ff04001141598444c7331b0ef6 Author: heather Date: Sat Mar 11 03:57:47 2006 +0000 tweaks commit 20be8af8ed890e04c1d53e335a9a5d9047232555 Author: heather Date: Sat Mar 11 03:53:53 2006 +0000 extend SingleClassRangeLocType to 4/5/6 commit 27a073d65db9e49b7786f361f3dde68dc5ac260f Author: heather Date: Sat Mar 11 03:53:21 2006 +0000 change handling of in-del commit 4bac92caf2790f9f5abe491de7cbc123358f23f5 Author: heather Date: Sat Mar 11 03:49:58 2006 +0000 tweak output commit e097be9a4d1b4d60fcff60ea659bab468e9f973d Author: genbank Date: Sat Mar 11 03:37:45 2006 +0000 fixed bu handling partition with no fasta commit ac1db6e91fa5d5c335c0d0f214028cf80168569a Author: heather Date: Sat Mar 11 03:35:42 2006 +0000 adjust coords for between! commit 597426917c846247f453f99c9cba8e4567d55ec4 Author: heather Date: Sat Mar 11 03:03:59 2006 +0000 check for missing SNPs commit f658725d65bbef2f3e0d287cae5088d369113cd4 Author: heather Date: Sat Mar 11 03:03:44 2006 +0000 compare coords commit 3b2e5a7a23f6dd2158f859a740720aae381434a1 Author: kate Date: Sat Mar 11 01:28:58 2006 +0000 Make details page message friendlier: show organism, not db name for components not displayed, by request of A. Zweig commit d1067d911522139349bbbfe76ad138fef7ed469b Author: kate Date: Sat Mar 11 01:11:10 2006 +0000 Phastcons downloads commit db8301fab56d7d5d504780eb79def9b50a474c8f Author: ann Date: Sat Mar 11 00:51:28 2006 +0000 added check for liftOverChain table commit 7c80e00b4486278aff05bdcadad7dd2c0e80ff58 Author: markd Date: Sat Mar 11 00:25:15 2006 +0000 added program to do extFileUpdate commit 07164bdf6fd48398177e40f1c4a3132b01b03bf3 Author: genbank Date: Sat Mar 11 00:23:04 2006 +0000 added program to pull SQL times out of log commit b0a16b35d0a03c6dd02dae9d9b0accee6cfeb8be Author: markd Date: Sat Mar 11 00:07:59 2006 +0000 added program to do extFileUpdate commit bb0341bc8488a9618b30ed0d974e2c19f38ba2b1 Author: kayla Date: Sat Mar 11 00:05:23 2006 +0000 Removed 2 bosTau2 blocks with "release alpha" at the bottom of them. Also removed 2 lines that said "release beta". commit 332d6bd55f324762c54fc2c0773e71dbcf7f66d1 Author: fanhsu Date: Fri Mar 10 23:51:09 2006 +0000 Added PB and corrected a typo. commit ab0f671924f9aafe1971a2fe9efeef9d68393479 Author: kayla Date: Fri Mar 10 23:46:06 2006 +0000 Changed net/chain shortlabels so that bosTau2 gets o_Organism and bosTau1 gets o_db commit e8acc3c5045587d685bdab109971757a4210be85 Author: fanhsu Date: Fri Mar 10 23:44:20 2006 +0000 Corrected a typo. commit 5e9b762927eb5b4cfd32101c4f4e1ac5f88be47c Author: fanhsu Date: Fri Mar 10 23:22:53 2006 +0000 Added logic to get rid of extra quote characters. commit 30befc9e8ff25a5526821445914cfc35e88ba439 Author: angie Date: Fri Mar 10 23:13:20 2006 +0000 Changed some regex-diagnostic printf's to verbose(1's so that they can be turned off for a more concise search test. commit 07bf64130b77e0e0f04677878a17247bae9462ae Author: kuhn Date: Fri Mar 10 23:13:08 2006 +0000 added knownGene.csh, which checks a bunch of stuff for Known Genes commit 846dbb82f636c89e20ec39850e53942c39f90031 Author: angie Date: Fri Mar 10 23:05:16 2006 +0000 Removed ensGene searches which are now covered by top-level trackDb.ra. commit 95c5f9174d1e8c48d3ab4ed604f2e7d8e675721d Author: angie Date: Fri Mar 10 22:57:33 2006 +0000 Adding a couple rn4-specific ensGtp searches: ensGene has versioned accs but ensGtp does not, so do a prefix query on ensGene with the xrefQuery result. commit d3299114d853fe90da839c951d942f3f736a544c Author: angie Date: Fri Mar 10 22:56:22 2006 +0000 Removed ensGene searches which are covered by top-level trackDb.ra now. commit ffb5fc45b7fd9d0f66b65fc7a2bb4991e837398d Author: fanhsu Date: Fri Mar 10 22:56:04 2006 +0000 Updated mrnaRefseq table build to include hg18 mRNAs only. commit 89edbc4c7055a82f7a2b4b2f4e5f6ca6ec613f3f Author: angie Date: Fri Mar 10 22:45:48 2006 +0000 Removed several ensGene searches which are now covered by the top-level trackDb.ra. commit be00c0c9b7e98fa4442387de1f59e86d658ee15b Author: kayla Date: Fri Mar 10 22:44:58 2006 +0000 Changed net/chain shortlabels so that danRer3 gets o_Organism and danRer2 gets o_db commit ef3a4a6b9284ba198c1653f29d4d6a3833c86b2a Author: hiram Date: Fri Mar 10 22:41:40 2006 +0000 Rat can be labelled instead of Rn4 here, there are no overlaps with anything else commit 7c9bd5006b8ac6fd2e538cc8aaf88ca5ee93290c Author: hiram Date: Fri Mar 10 22:32:28 2006 +0000 Mouse can be Mouse here, Mm8 not needed commit 43baa10fd8f8c6fbb83c35d28f16554da129a8a5 Author: hiram Date: Fri Mar 10 22:24:29 2006 +0000 Adding chainHg18.html for the details pages commit d9bea0e3ad250b59beae5a176a9aea36d15e3fe9 Author: angie Date: Fri Mar 10 22:15:32 2006 +0000 One more termRegex tweak for ensGtp search. commit e20eb243d5753e8c045c8e473e734d6a2cee8cea Author: angie Date: Fri Mar 10 22:15:01 2006 +0000 Removing ensGene searches -- covered by top-level trackDb.ra now. commit 8b2cf7382240ee4b2b0ca8c764f914bd069eafba Author: angie Date: Fri Mar 10 22:11:39 2006 +0000 Removed one more ensGene search now covered by top-level trackDb.ra. commit acfcfa55cea402478f85d44e84b6d5b94e5525a0 Author: angie Date: Fri Mar 10 22:09:45 2006 +0000 Removed duplicate ensGene search -- covered by top-level trackDb.ra now. commit c9716f3bae6e271f28dc5ce524615d40419c92c3 Author: angie Date: Fri Mar 10 22:08:03 2006 +0000 Fixes to ensGtp searches: for galGal2, ensGtp does not have versioned accs but ensGene does, so do a prefix query with the result of the xrefQuery. commit ca0691674445df73a50500c6567e76e56ceb7a29 Author: hiram Date: Fri Mar 10 22:04:12 2006 +0000 Can have actual Mouse label here since there aren't any other mouse chains/nets commit a2733d91299fa6d3e22d5bad2ef730c82afe0fdf Author: fanhsu Date: Fri Mar 10 21:53:48 2006 +0000 Added liftover of hg15 to hg17. commit 19cc5139bcda433f389ad936447f2fdfc4ad2797 Author: hiram Date: Fri Mar 10 21:41:24 2006 +0000 Place chain and net Mm8 in the correct order commit c259eb500907d69bea524d76e9ed9cc0d5cf08e5 Author: kent Date: Fri Mar 10 21:37:06 2006 +0000 Checking for arrays with both dimensions and initializations and reporting error. commit 6a1d84940349ac1a2524b0ce36d2cc2d60c938e9 Author: kent Date: Fri Mar 10 19:54:30 2006 +0000 Making qsort_r restriction more specific. (It is on the pentium based Macs. commit 6c02e40b38436578d81cc0588b12eb157c631f95 Author: kent Date: Fri Mar 10 19:51:30 2006 +0000 making output dir in makefile commit ee10dec0dc80c7fcc02daf62de1d3e7e0d40590d Author: hiram Date: Fri Mar 10 19:32:38 2006 +0000 Adding Mm8 so it is in the correct position commit 63cb3aff54f539e208930b4fdecdde88332cb024 Author: angie Date: Fri Mar 10 19:29:37 2006 +0000 Small refinements to ensGene xref search termRegexes. commit 799223e817ddcde10e9269161ecd1c7e6461a804 Author: angie Date: Fri Mar 10 19:26:36 2006 +0000 Added a warning about aliases that map to multiple trueNames. Downgraded lack of alias from warning to info. commit b0a7f9f6a7d270630dcc06fc5bed8be313385586 Author: angie Date: Fri Mar 10 19:25:18 2006 +0000 Make the index on alias non-unique because some aliases do map to multiple trueNames (added a warnings to the hg/stsMarkers/createStsAlias script to highlight these). commit aec6cbaa4bd99cf83f6ca9fd4be9c54c9f5a8376 Author: kent Date: Fri Mar 10 19:23:16 2006 +0000 Fixed signed/unsigned problem. commit 556266955c205cd47e8faffbdfafdc2321d64b28 Author: heather Date: Fri Mar 10 18:37:13 2006 +0000 perf changes: larger hash, don't convert floats commit b0b2e9bf745a094be879c3ac5df048759180acf8 Author: ann Date: Fri Mar 10 17:45:06 2006 +0000 changed the order of zebrafish - Tetraodon - fugu commit 7b21e7e04c2760197b43d192980fb26909ea9334 Author: angie Date: Fri Mar 10 17:43:37 2006 +0000 Replaces sprintf with safef. commit d413bff078ebf71ef00a9d187c617beb4ca59531 Author: heather Date: Fri Mar 10 17:43:04 2006 +0000 name change commit 8df76724b85783eda49bc0c955e8820dfe217d12 Author: ann Date: Fri Mar 10 17:41:32 2006 +0000 switched order of mouse and rat in Description section commit 66d89d4636b61dbe139166e61aeb277a1cd30867 Author: heather Date: Fri Mar 10 17:40:26 2006 +0000 tweaks commit 3c1697cc4f6f87aa7cd68d145e03b4664cea841b Author: ann Date: Fri Mar 10 17:27:03 2006 +0000 added explanation for bases which are shown in lower-case commit 3685acbdec160a88731fd771e1bd2508368e7961 Author: angie Date: Fri Mar 10 17:18:27 2006 +0000 When loading split chain tables, if a $chr.chain is missing because $chr has no alignments, call hgLoadChain on /dev/null to make empty chain and Link tables so the split table set is complete. commit b8e6fbaf8924c0ecf9f83aa8a68b8cca9dc8154b Author: galt Date: Fri Mar 10 16:00:03 2006 +0000 "Encode release log update" commit a737e59f23776b903a32affb381ef04a9a8d5b90 Author: galt Date: Fri Mar 10 16:00:02 2006 +0000 "Release log update" commit 28a049ed36ac537cf91fba37e5ddbb8928d6b4d2 Author: genbank Date: Fri Mar 10 08:16:23 2006 +0000 fixed path commit af6acd722b229e17dfde90dc61c1efc0c34ff7f6 Author: hartera Date: Fri Mar 10 05:07:40 2006 +0000 First draft of description for ENCODE Pseudogene track. commit 6a2a7989d136fabb7eedf71b0bbacb21b69d0c60 Author: fanhsu Date: Fri Mar 10 00:51:12 2006 +0000 Created links.ra. commit b944b3583c3a3e678bea8e607bc951b5e8813867 Author: heather Date: Fri Mar 10 00:28:48 2006 +0000 tweak commit b21e3bb0335d9c2231047472740d7d6e524d4b15 Author: baertsch Date: Fri Mar 10 00:26:02 2006 +0000 added qual for chrUr commit 86b927bc5259743e5874d81697d7a6f84f06889c Author: heather Date: Thu Mar 9 22:51:04 2006 +0000 remove extra column for simple exceptions commit 8d39466c0157daf4128b3c9a79e1a46d5ceb91be Author: heather Date: Thu Mar 9 22:36:57 2006 +0000 another format tweak commit 91753951b563ea5960f0da0dab4ac6fdd91bce21 Author: heather Date: Thu Mar 9 22:26:37 2006 +0000 format changes commit 6fc148049961d2002a5734994ac163cb31f17f19 Author: galt Date: Thu Mar 9 22:21:15 2006 +0000 added check in bac read for state new commit 225b31967be078211d727990007198c504dca4e4 Author: heather Date: Thu Mar 9 22:03:26 2006 +0000 add cloneString commit 1482052aedd9ad542ba28e59161bc4e67a240caf Author: angie Date: Thu Mar 9 21:20:01 2006 +0000 Removing old unused file (it will still be in the CVS attic). commit 3e79e524a7f5d65374c8e55bf9b8a6a9c4569176 Author: angie Date: Thu Mar 9 21:19:08 2006 +0000 Corrected size passed to safef. commit d01e74945adc694b4c4aa676ab64e70ec580907a Author: angie Date: Thu Mar 9 21:11:21 2006 +0000 Corrected size passed to safef. commit ba1435bb97233df8649bad5be479285272bd69e2 Author: angie Date: Thu Mar 9 21:06:55 2006 +0000 Correction to size of parameter variable passed to safef. commit 5ce367da7016b6693490e501beca0823e82e2ca2 Author: angie Date: Thu Mar 9 20:29:09 2006 +0000 Use appropriate size in calls to safef. commit 3e8e6ace8e0f7639a338a44d5d30d0651c323edc Author: heather Date: Thu Mar 9 20:16:55 2006 +0000 fix format commit 1aaa695a553c8d58adf5ee649c11aa507bdf6901 Author: heather Date: Thu Mar 9 20:00:22 2006 +0000 change exceptionTables commit 5f4d382608b987891c2b9d848b472209bc6a3781 Author: hartera Date: Thu Mar 9 19:52:17 2006 +0000 Removed hashAddReplace as not needed. Just use hashAdd when adding element to hash. Modified some comments. Changed a conditional statement in the getGeneSymbol function whose name also changed to getGeneSymbolAndId - statement should check that geneId is not NULL. commit 1811ebcf283acf68a3a2dc2afa1dd0a7322ca8d1 Author: fanhsu Date: Thu Mar 9 19:14:15 2006 +0000 Added maf annotaion for multiz-17way. commit 0ffc73bdb1054419cf4ecfc0195240ff737139c3 Author: angie Date: Thu Mar 9 18:26:58 2006 +0000 Replaced sprintf with safef. commit 06eded0680d48c30ec0c55f12b2ad2de99dcd879 Author: heather Date: Thu Mar 9 18:01:28 2006 +0000 forgot hashAdd commit 3e8068f28e49a72074e00903cfb489de04ca5667 Author: angie Date: Thu Mar 9 17:44:32 2006 +0000 Tell CVS to ignore bin/ and output/ which are both generated and cleaned up by makefile. commit 227236bd7d962bf389500958560acf4d866232b1 Author: angie Date: Thu Mar 9 17:36:45 2006 +0000 Added "%s" format to safef calls where a string was being used as format and no other values were given. This is safer in case the string unexpectedly contains a "%" which would then be interpreted as a format, leading to a segv. commit 489c7c999e0617068ec360b4e59d6163f4b6dd97 Author: angie Date: Thu Mar 9 17:33:31 2006 +0000 Oops, make that bin unsigned. commit 4d6e9e3f1bdf460065102e67324728c684fbbdbe Author: angie Date: Thu Mar 9 17:23:03 2006 +0000 Added bin field. commit bbe405e11f91381122d612ad2e86254e81d5d18a Author: heather Date: Thu Mar 9 17:15:12 2006 +0000 restore load commit da9b407b0578a7b15a0754cef4e07a27defb98a8 Author: heather Date: Thu Mar 9 16:29:53 2006 +0000 add hTableExists commit c4a4d648a26660154001a366144ebdaf945ccd4b Author: galt Date: Thu Mar 9 16:00:03 2006 +0000 "Encode release log update" commit 40ec0cb4182206e846a0ea88322035769927f3b4 Author: galt Date: Thu Mar 9 16:00:02 2006 +0000 "Release log update" commit 51738fd7bf1a685fb9b91cd7f3acc976451e820b Author: galt Date: Thu Mar 9 15:49:37 2006 +0000 fixed minor case-sensitive problem in managing geneSynonym commit 7c82b7c720493b0663eeae7f3550520c5e925c2b Author: kent Date: Thu Mar 9 15:40:34 2006 +0000 Adding library test case. commit f4d20a1cfe10673671af2cc67c6225e9465386ca Author: kent Date: Thu Mar 9 14:40:30 2006 +0000 Changing polymorphic to morph, to in for and para loops to til. Flagging misplaced readables and locals better. commit c3fe3a6ad82f2c23a2d72c4515ed88527ba215bf Author: daryl Date: Thu Mar 9 09:07:16 2006 +0000 generalized the LD cart variables and removed unnecessary code; HapMap LD and Haploview LD track function separately now commit a8e090a39f2a97d9fd3cc2c2a07dbd01c2a47b7a Author: kent Date: Thu Mar 9 06:40:29 2006 +0000 More experimental flexibility commit 271c36a66e458bd3c4a41bd47e2888a4f10e1713 Author: kent Date: Thu Mar 9 06:24:17 2006 +0000 Some thread experiments. commit 6d9ffa528a8fb2b793c73f885efc8dbe0a9c2e5a Author: heather Date: Thu Mar 9 06:05:06 2006 +0000 small tweak commit b736816772cba448756e737ffc6315e4f8e60711 Author: heather Date: Thu Mar 9 05:25:17 2006 +0000 add simple checks (previously in snpLoadFasta) commit 346be0f980e8283d344c0dc1a424150a89901c5b Author: genbank Date: Thu Mar 9 05:24:04 2006 +0000 fixed typo commit c2837b7d482bb8e3a69656f7a0c5d3539ef384e0 Author: heather Date: Thu Mar 9 04:17:12 2006 +0000 add error logging commit af028a92aa8d427976e83a4b7c8d3db23b5961d6 Author: heather Date: Thu Mar 9 04:15:36 2006 +0000 change lengthTooLong to unknown commit f13e9f86a075a843f3b9407ce82b7c2c760356a0 Author: heather Date: Thu Mar 9 03:17:44 2006 +0000 rewrite to use hash commit 5fd6713f9d71c93e9bb42b651bb1c837e6bcb578 Author: kate Date: Thu Mar 9 02:59:19 2006 +0000 CPG Islands. Starting BAC ends commit 944fabf6076ecb954fd040a1af5efc0019001795 Author: kent Date: Thu Mar 9 02:22:19 2006 +0000 Changed error source from lib to library commit 256b04f41ae23e5f1e4d71a202e224fefd5e71c1 Author: angie Date: Thu Mar 9 02:01:48 2006 +0000 Another STS tweak: leave the clone sequence values in the stsInfoRat file so that luConvertPrimerToFa can use them, but strip them out before loading into the stsInfoRat table. commit cf9e9ba007e8eece0853b383e04e74421d056da6 Author: angie Date: Thu Mar 9 02:00:28 2006 +0000 Don't discard the sequence just yet -- it is needed in order for luConvertPrimerToFa to make the clone sequence file. We'll have to strip out the 25th column values before loading into the stsInfoRat table. commit 1efdacb7ad7c4c4a8e4eb5f5ae95be7a8ab84225 Author: angie Date: Thu Mar 9 01:22:05 2006 +0000 Bugfix: added missing \t. commit a3a2469d2c689b08ab20b553a1af09b9e6b6fcf3 Author: angie Date: Thu Mar 9 01:21:40 2006 +0000 Added strict, removed unused code, added tests for 0 instead of "" in numeric columns now that createStsInfoRat defaults them properly. commit 7409f71508faa2685f656917100cd0980e4b8ebf Author: angie Date: Thu Mar 9 01:19:52 2006 +0000 Put 0 or 0.0 instead of empty string for numeric columns in order to avoid tons of warnings from mysql when loading. Don't output the clone sequence value -- it is not used and is often truncated to 255 chars causing more warnings from mysql. commit f5d389cf19a70c6ac8113f71247f79c6f8cabce9 Author: angie Date: Thu Mar 9 01:17:25 2006 +0000 Re-ran STS markers process with some tweaks: resolve missing names in NCBI's UniSTS_rat.sts file using info from UniSTS.sts, and align clone sequences to the genome as done for human (but not for mouse where I picked up the template). Also added full-text index files for knownGene search. commit 03eeab7d08346d2a548922fc78b0621e40b41694 Author: donnak Date: Thu Mar 9 00:55:50 2006 +0000 Updated the RepeatMasker items. commit 2badd8f4f72737ac28587d7914a0f5ef4b13c9ee Author: hiram Date: Thu Mar 9 00:31:45 2006 +0000 Missing a space between danRer3,2 tracks commit 2c016792ea595821e06dc226c3a93dfe819d7a75 Author: hiram Date: Thu Mar 9 00:22:40 2006 +0000 Placing Mm8 chain and net in their proper location commit 8fea398981db2aa63d8b107e7ff0a7560f3e165c Author: hiram Date: Thu Mar 9 00:22:21 2006 +0000 Adding Mm8 chain and net track in the proper location commit 62f5770a91591bb7614b52dc132646c32f15d5b8 Author: hiram Date: Thu Mar 9 00:11:01 2006 +0000 Placing Mm8 chain and net in proper location commit 8cc444d1e29aea6840c2ad947343615f64640a4a Author: hiram Date: Wed Mar 8 23:38:56 2006 +0000 Adding mm8 to the mix commit 666edf4be7eef5ce6955bb5d15ca86ad26b5e9be Author: hartera Date: Wed Mar 8 23:11:47 2006 +0000 Removed duplicated emptyForNull function. commit be8afcd770a8728e8e9719857a8af80008b2f992 Author: hartera Date: Wed Mar 8 23:09:23 2006 +0000 Back out addition of hashAddReplace function as it is not needed. Use of hashRemove within the function could cause memory leaks. commit 7946e370290fb8cb2371f7a0f8064a886a02ba6b Author: hartera Date: Wed Mar 8 23:08:26 2006 +0000 Back out addition of hashAddReplace function as it is not needed. commit 9d80d353c82d6191c3ee18a70f45c6f42197fbaf Author: kent Date: Wed Mar 8 23:03:54 2006 +0000 Avoiding an infinite loop on certain type mismatches. Implementing throw, throwMore and puntMore. commit efc3730dea6ff4743b4b4caa606ac7b7fb14b4c3 Author: heather Date: Wed Mar 8 22:57:12 2006 +0000 change function name commit bad6f4e7bb10fa594f0231d20f341c5d2180c872 Author: heather Date: Wed Mar 8 22:54:37 2006 +0000 remove include commit 2b32794125eb99a8a56e2a44205adcdb3750ad98 Author: heather Date: Wed Mar 8 22:45:43 2006 +0000 add another comment commit 82f31e729f1f8a7c3939b98b3720e2cc94ffbea7 Author: heather Date: Wed Mar 8 22:43:16 2006 +0000 add comment commit 0f1235c2fefa63195056220928ddf4aea7955606 Author: braney Date: Wed Mar 8 22:39:45 2006 +0000 add trace option to keep version numbers over ancestry, add seed option to specify srand seed commit 94d96b5664f05fbff13205b1078d8daa7484075f Author: heather Date: Wed Mar 8 22:32:29 2006 +0000 use hAllChromNamesDb commit b77c82b4f8912c3b4a28a1344dbf5d56eeba8bb0 Author: heather Date: Wed Mar 8 22:20:21 2006 +0000 change chromHash to chromList commit d4df4b78003e224aa1261165b22d05623f27229e Author: heather Date: Wed Mar 8 22:14:53 2006 +0000 use hAllChromNamesDb commit e34c9ed604f9a3b1394ada6479b4c8af24213e21 Author: heather Date: Wed Mar 8 22:07:00 2006 +0000 change chromHash to chromList commit e2ba5b37abb45aac38f1d30e14b5a615931fbe0e Author: heather Date: Wed Mar 8 22:01:49 2006 +0000 change chromHash to chromList commit beef0067c9a8ee917e3b7a00a7cf5dd47aaac3a7 Author: heather Date: Wed Mar 8 21:44:40 2006 +0000 use hAllChromNamesDb commit 04c4b7a2fc09bef2779f4b8ce2cd9120c81f8a29 Author: heather Date: Wed Mar 8 21:17:28 2006 +0000 use hAllChromNamesDb (and therefore handle randoms) commit 09f05c03ec2688de1800f2628550e1802551afd1 Author: heather Date: Wed Mar 8 21:13:05 2006 +0000 use hAllChromNamesDb commit 27286cf9ece93ea2b456961798507dac80f7c72f Author: heather Date: Wed Mar 8 20:59:10 2006 +0000 more cleanup commit 6f5966157e0a41ee7f68d9afb63e7358abca1492 Author: heather Date: Wed Mar 8 20:57:19 2006 +0000 use hAllChromNamesDb commit b219159cabc0c4ed1d33fda139e0d86c2addb535 Author: donnak Date: Wed Mar 8 20:30:27 2006 +0000 Fixed minor formatting issue. commit d5f1fece9866b4ae6a861acec4a0c4edd76e275d Author: heather Date: Wed Mar 8 20:27:59 2006 +0000 handle randoms commit 20f1b141581dc7628afb82a041acaecb3aca97a0 Author: hartera Date: Wed Mar 8 20:16:43 2006 +0000 First draft of RH map description page for danRer3. commit ca98406f1d78f183d3f17eefef6d6c6c9ff48acf Author: hiram Date: Wed Mar 8 20:02:48 2006 +0000 Expanded usage message commit d8e49e35e7e8a9376e9f0973a62a7b8f02f4066b Author: fanhsu Date: Wed Mar 8 19:44:13 2006 +0000 Added RNA structure, KEGG, and BioCarta pathways. commit 111e5df55b5aeaffe59f41e58549c8f4883730de Author: kent Date: Wed Mar 8 19:43:02 2006 +0000 Putting in code to clean up exception variable. commit 282c897b0bb3a1ec2c8343a737998b63f4fdbaf1 Author: kent Date: Wed Mar 8 18:50:54 2006 +0000 Reworking exception handling in preparation for doing exception chaining. commit 691d49fdb74814be88be389d287a8b0006c9cdf4 Author: giardine Date: Wed Mar 8 17:49:22 2006 +0000 Adding landmark track. This track is regulatory regions and other landmarks that are not in other tracks. It is data compiled from various locus experts. commit 7b48aea4e36f072aedd6d77d420c999bc56ee056 Author: kent Date: Wed Mar 8 17:28:40 2006 +0000 Removed mac dependency commit e2b381c4ba785bcf0b63d538e8ee1fc92e4a5a11 Author: donnak Date: Wed Mar 8 17:08:15 2006 +0000 Added Jakob's pub. commit 2977ccc293567bf26d5437324386a09d7a33d3de Author: galt Date: Wed Mar 8 16:00:03 2006 +0000 "Encode release log update" commit e20e05da0ab2683438d5081f4a4b77752583708a Author: galt Date: Wed Mar 8 16:00:02 2006 +0000 "Release log update" commit fdc8f015900ede8d212a698eda2481bcf8df9ed6 Author: mieg Date: Wed Mar 8 10:06:05 2006 +0000 acedb dictionary library commit ef39feadaa75242d22e0060bb7ce148e566429e2 Author: mieg Date: Wed Mar 8 09:58:58 2006 +0000 cosmetics commit c140a4d6ef9bc2ed7f956e95c86e7d42ca06ba0f Author: mieg Date: Wed Mar 8 09:57:23 2006 +0000 changed from malloc to using needLargeZeroedMem commit 0a3c23c1a8709f5c795f005173527c74674e7424 Author: mieg Date: Wed Mar 8 09:30:13 2006 +0000 the funcyion msort has the same prototype as qsort it is exported from acedb commit a64b1cd3ad09e1a91c22846097944468fb0d4e3e Author: heather Date: Wed Mar 8 05:59:53 2006 +0000 fixup previous commit commit aaa5c9e908c6a352cf16c07302f024c8b75872a8 Author: heather Date: Wed Mar 8 05:27:09 2006 +0000 read snpFasta data into hash; handle random commit 6c0e979e2f896d5ac26755c3d2589ea86cb97bb2 Author: kent Date: Wed Mar 8 01:46:20 2006 +0000 Adding functions to read binary byte/short/int/long/float/double. Reworking dummy windows code. commit b18e6a1eb247d14857d9c4350ac72e0ab757d00b Author: galt Date: Wed Mar 8 00:47:47 2006 +0000 updated knownToVisiGene commit 04b9ac0cab7e1315c18243c88feb483414d605ac Author: heather Date: Wed Mar 8 00:40:55 2006 +0000 remove exception handling commit ffa190fed82cc526f7f89ce2803295d0f81ec356 Author: fanhsu Date: Wed Mar 8 00:32:19 2006 +0000 Added maf annotation for multiz-17way. commit c78e083996d2697bc5336ed525ea05fc6c7760b5 Author: angie Date: Wed Mar 8 00:03:32 2006 +0000 Made doStsMapRat() capable of handling tables with bin field. commit a083373459ad47424725291940837396f73f93c5 Author: braney Date: Tue Mar 7 22:26:15 2006 +0000 fix up usage message commit c03992b7a3de5ef99ec1855f95d907bd900bc008 Author: braney Date: Tue Mar 7 22:14:05 2006 +0000 a makefile to make various utilities commit c10c985b11a26067655a04719a39896969e8246e Author: braney Date: Tue Mar 7 22:04:17 2006 +0000 clean up. a little work on delete element commit 7acfc5137723734085fdf44e1ef8a11c348c2650 Author: markd Date: Tue Mar 7 22:03:39 2006 +0000 switched several genomes to 2bit commit 09f196bcbfd28be2bb6f77801783b94a551dc881 Author: braney Date: Tue Mar 7 22:03:28 2006 +0000 getting rid of a bunch of stuff not important in infinite sites model commit 6611943ffa67645d2327c4396a825624a3fb7194 Author: braney Date: Tue Mar 7 22:02:25 2006 +0000 add an option to sort elements before comparing them (for testing the element tree builder) commit ad1c6583d93bc4f5bdbd67a5e287e8566eaa4639 Author: ann Date: Tue Mar 7 21:46:49 2006 +0000 moved up to human level commit 32669bbfcddb0fbb43d57558dbab27398e405258 Author: ann Date: Tue Mar 7 21:46:19 2006 +0000 moved up from hg17, hg18 commit cc14789fb1e550ac388a039cc9e25b3c3a2847c7 Author: fanhsu Date: Tue Mar 7 17:11:18 2006 +0000 Removed a duplicated function. commit 6d1f954c26ba021f2d19971e1540f140a31fc115 Author: kent Date: Tue Mar 7 17:07:05 2006 +0000 Adding a test case commit 11ec87a621f1fc8a94edef45038f6ac003fb329a Author: galt Date: Tue Mar 7 16:00:03 2006 +0000 "Encode release log update" commit d97ee0e7150f3af596aa2c6e60567a0ca29779b2 Author: galt Date: Tue Mar 7 16:00:02 2006 +0000 "Release log update" commit 1ed5b330376986497eea9acc0391a45e05f92206 Author: kent Date: Tue Mar 7 01:51:39 2006 +0000 Oops, forgot to add this commit 06e32a69eb2063cb3d22f2b5d2f9283c2f007772 Author: kent Date: Tue Mar 7 01:50:55 2006 +0000 Oops forgot to add this. commit fe45c4382898cd1e5939c7753987675e17de6bb4 Author: kent Date: Tue Mar 7 01:49:39 2006 +0000 Updating with new readable only default class access. commit 745e8063b87b0f2f1dc72ebe0202e288f294d66e Author: kent Date: Tue Mar 7 01:43:55 2006 +0000 Fixing problem revealed with paraTwoD.pf in Linux commit 2114c966badfc1301c29deecc55eac8f5420bdf4 Author: hartera Date: Tue Mar 7 01:37:17 2006 +0000 Aligned RH map sequences for RH map track and experimented with different parameters for Blat alignment and pslReps filtering. Loaded alignments into database. Add sequences to database but they failed to load completely so had to be dropped. rhMapInfo table created for markers information for RH map. For Ensembl Gene set, updated the *.ra files to add new links and new information to the details pages. commit 500bd727b695710684aabe02ebe469c728dfcf33 Author: ann Date: Tue Mar 7 01:06:54 2006 +0000 edited verbage for easier understanding commit 825a5556bb385329c2ab1dfb59242a3f77c4e5aa Author: kent Date: Tue Mar 7 00:59:24 2006 +0000 Adding -lm to link. commit 6d310854b6ebd83e7f8c1c9d5c2a090e7cd782cb Author: kent Date: Tue Mar 7 00:53:08 2006 +0000 Twiddling the default accessibilities of class members one more time. (Now it's readable/callable by default.) commit f0a418d8938758ca893e9b9b2d0cae9cf502b12e Author: hiram Date: Tue Mar 7 00:08:31 2006 +0000 multiz17way done commit 6188cb05f8da8e1d779e2a7f887947f6a0ded0c4 Author: heather Date: Mon Mar 6 23:46:23 2006 +0000 change name of function commit 857e1fe104f5ec0dc516e305467abf2561fed466 Author: donnak Date: Mon Mar 6 23:29:18 2006 +0000 Minor edits prior to strPur1 release. commit 00977138ddbcb8e316a9be106cd5a6cb542ead5b Author: donnak Date: Mon Mar 6 23:28:49 2006 +0000 Uncommented strPur1 info. commit 377e02b0011df2f0525249a6b97fbb28b73925f5 Author: kent Date: Mon Mar 6 23:14:55 2006 +0000 Some changes to help cVerify go. commit 350c4fe2ec794ba387dbf8d57841ef5c70c03a3f Author: angie Date: Mon Mar 6 23:13:45 2006 +0000 Using a template that has $matrix and $Organism not $organism. commit 8df126edace82385354c098409feb787b73e38cd Author: angie Date: Mon Mar 6 23:12:10 2006 +0000 Added $matrix to this template (no effect unless trackDb.ra contains the info). commit a0428a3c6d4c104ebb208c7d3c6cf3ea9598606f Author: angie Date: Mon Mar 6 23:07:20 2006 +0000 Removed methods section which points to a specific file for the rn3 assembly. commit 8ae16a85e0cfdd1601f1942a8e037b42ea53d575 Author: angie Date: Mon Mar 6 22:50:25 2006 +0000 Removed strip and chmod from compile (handled elsewhere in cgi_build_rules.mk) and made mgsc target more standard (like hgTracks). commit b4f9727fc9b066d7576a2d624a46edf9c3b91696 Author: kent Date: Mon Mar 6 22:44:12 2006 +0000 Works on ParaFlow compiler (but not runtime). Limits on enums, typedefs, and casts to typedef'd things. commit 59726dd7f12c9c314f56d092772b2f0e8bdd8cac Author: heather Date: Mon Mar 6 20:44:57 2006 +0000 handle randoms; small tweaks commit 0a8b7a61e6c199b861a8113438a5d3ed8dac3376 Author: angie Date: Mon Mar 6 20:38:36 2006 +0000 Added hgKgGetText target. commit b5d82cb87fb40e1aa743ea5ec7d453d537aca211 Author: angie Date: Mon Mar 6 20:30:32 2006 +0000 Use ${HG_WARN_ERR} instead of hardcoding HG_WARN. commit 6c12886cacc5b2d8b52a6fb721b64063285aeb26 Author: heather Date: Mon Mar 6 20:19:11 2006 +0000 handle randoms commit 05edd94811a282c90cb1a6b4e4595256af151287 Author: angie Date: Mon Mar 6 20:16:49 2006 +0000 Added a very stringent HG_WARN=-DJK_WARN -Wall -Werror for CGIs. commit 6d19fc7a992dd066149bfddd222914a694dd9dc5 Author: kate Date: Mon Mar 6 20:12:45 2006 +0000 Add note about a typo commit 84bdacae6e0d38a8d7ef654080d255055f3353d9 Author: angie Date: Mon Mar 6 20:02:30 2006 +0000 Removed unused variables caught by -Wall. commit 8c45bd555064d781ea6d2fe350de24b75784d31f Author: heather Date: Mon Mar 6 19:49:51 2006 +0000 handle randoms commit 238b79ec5c6790f9ee2eda1cac9900fceaada294 Author: hartera Date: Mon Mar 6 19:42:59 2006 +0000 Code generated by autoSql for rhMapInfo which contains Radiation Hybrid map marker information. commit a61ff576485ca48efd71ec0c861fa341c0859b3e Author: heather Date: Mon Mar 6 19:42:06 2006 +0000 add comment commit f975b627ce7de2224df3e85f8b399b7945155acc Author: hartera Date: Mon Mar 6 19:42:02 2006 +0000 Table definition for rhMapInfo which contains Radiation Hybrid map marker information. commit e8917327b450dff7acc45d3bc48e13a188944c2a Author: hartera Date: Mon Mar 6 19:40:59 2006 +0000 Definition for rhMapInfo which has marker information for the Radiation Hybrid map. commit 0f4483ba019f6bf5a5724a73b4ab474c9a0b004a Author: heather Date: Mon Mar 6 19:31:02 2006 +0000 add a sqlFreeResult commit af79e8031cb0e30e95c8541641a07ce4b12571c5 Author: angie Date: Mon Mar 6 18:59:00 2006 +0000 Removed unused variables caught by -Wall. commit ea1f3979af1e9698c474dac4824d2d39c3b02d31 Author: hiram Date: Mon Mar 6 18:53:40 2006 +0000 The mRNA and EST tracks were being duplicated here. They are defined in the top level. commit c608aaac2a4a0928152f2e94ee64789b50e1796c Author: angie Date: Mon Mar 6 18:42:33 2006 +0000 Removing unused variables caught by -Wall, unused code. commit 3a8ec279a2cfcae3245413f807d13276d1b96c7a Author: hartera Date: Mon Mar 6 18:40:57 2006 +0000 Code generated by autoSql for ensXRefZfish which links an Ensembl Transcript ID to other database IDs and description. commit 0cc35d0fff570e1c917871e311cd1342ed465dd0 Author: hartera Date: Mon Mar 6 18:39:44 2006 +0000 Table definition for ensXRefZfish linking an Ensembl Transcript ID to other database IDs and description. commit 1e6d20ac7adbe3490d5d60082369e181d4e655ef Author: hartera Date: Mon Mar 6 18:38:19 2006 +0000 Definition for ensXRefZfish to link an Ensembl Transcript ID to other database IDs and description. commit 0a2a600f731cbb14ec70530ba71a59f990f1176a Author: angie Date: Mon Mar 6 18:36:28 2006 +0000 Added extra-level-down lib target, ${STRIP}. commit b5ddd8ff76a3d1ac2749dc93f9b51748c773b85a Author: angie Date: Mon Mar 6 18:32:05 2006 +0000 Resolving unused variable warnings caught by -Wall. commit 79ef645f58681c164baa59c9e47bd1f2e34925f5 Author: angie Date: Mon Mar 6 18:31:29 2006 +0000 Use cgi_build_rules.mk instead of defining targets locally. commit 115e561f0d0967556980f563079915609d586935 Author: angie Date: Mon Mar 6 18:13:18 2006 +0000 Resolving unused variable warnings from -Wall. The second form does not appear to be used and probably could also be removed. commit b07710516123050a692caa0cb7f1d7b116c60069 Author: angie Date: Mon Mar 6 18:09:42 2006 +0000 Resolving warnings caught by -Wall (mostly unused variables). commit 339e72c107433ef191157f3a5128bc598322b689 Author: angie Date: Mon Mar 6 18:02:33 2006 +0000 Resolved -Wall warnings: unused vars & code. commit 26ef3f9636b7ff150a44785347afa19c95af56af Author: angie Date: Mon Mar 6 18:02:09 2006 +0000 Resolved -Wall warnings. commit de891dd3454ba5053b139b414e68042f837bfba0 Author: angie Date: Mon Mar 6 17:58:05 2006 +0000 Fixed errAbort format bug caught by -Wall. commit 14429d9d2c0a2a1fd816b009775de34cfa8c8190 Author: angie Date: Mon Mar 6 17:56:52 2006 +0000 Fixed errAbort format bugs caught by -Wall. commit b45893058482a36530ca2e5de4dc8ff442f6d835 Author: angie Date: Mon Mar 6 17:52:47 2006 +0000 Fixed printf bug caught by -Wall. commit 5586e3d5fb62a4198ebebab3898ce1d659112ee6 Author: angie Date: Mon Mar 6 17:50:03 2006 +0000 Resolving zero-length format string warning from -Wall. commit 7715497adad8ed6ecbfee3ff117627fa4a828b75 Author: angie Date: Mon Mar 6 17:46:35 2006 +0000 Resolving warnings caught by -Wall (mostly removing unused variables). commit f04c6ed06d8882c3eaabd987444b666c5141321b Author: braney Date: Mon Mar 6 17:38:10 2006 +0000 works great with infinite sites and inversions, still probelms with dups commit ca9ff4a499079e66eeb270493b6ba8504915bf99 Author: braney Date: Mon Mar 6 17:37:25 2006 +0000 add infinite sites and make dup and invert work correctly commit f52151de0623439c8df0c05d03c11bcda4b98ff6 Author: braney Date: Mon Mar 6 17:36:42 2006 +0000 fix up printf commit 8bb422023ef84cd30492d393c694e2de83fa876c Author: braney Date: Mon Mar 6 17:36:14 2006 +0000 some utility functions commit 287f535d8378ad5cc81b55ce909bcf44d45fb71e Author: braney Date: Mon Mar 6 17:35:32 2006 +0000 add a few functions commit b7002f6b3f223c0385ff0a5257005e4b3bd94043 Author: angie Date: Mon Mar 6 17:35:15 2006 +0000 Removed unused variable. commit 6e30471b6458727269a6c84352a0bb79b22c61e3 Author: angie Date: Mon Mar 6 17:34:25 2006 +0000 Fix minor problem caught by -Wall: printing a NULL dnaSeq when we meant to print the name of the sequence we couldn't fetch. commit 12d2d8a8179332d0db1221b4be6d25f9d77c9223 Author: angie Date: Mon Mar 6 17:21:44 2006 +0000 Broadened the genbankExclude list a bit. commit 46515e287005bbcd349ed1e3063c2aaee517ecfb Author: angie Date: Mon Mar 6 17:16:47 2006 +0000 BAC ends; several blastz/chain/net; STS markers but found some inconsistencies in files, waiting to hear back from NCBI, will redo; Known Genes. commit d12d72e09b251c2a3b95037f7099423e61233666 Author: angie Date: Mon Mar 6 17:07:18 2006 +0000 Use ptToInt() from obscure.h to avoid compile warnings on x86_64 about casting pointer to int (different size) when retrieving value from int hash. commit b569434b10b6ac30b3740f21f573816306c8eb58 Author: kent Date: Mon Mar 6 17:02:48 2006 +0000 Seems to work commit 384ff55b43ae7a0cc6dbc62667ee0b468dbf79d1 Author: hartera Date: Mon Mar 6 16:21:57 2006 +0000 Adds zebrafish-specific sections. Methods section for Ensembl genes added. commit 61a4ac04f5d035d9fd0160d7b05d6f2e54221e93 Author: hartera Date: Mon Mar 6 16:20:24 2006 +0000 Links for external database IDs for the other organisms section: Blastp best homologs for hg18, mm7, rn3, dm1, ce2 and sacCer1. commit 27fd024ed76dff4d637530c8d251b35e066e8ac2 Author: hartera Date: Mon Mar 6 16:18:09 2006 +0000 Added RefSeq peptide link and changed URL for the Entrez Gene ID link. commit 52895cd1607c538a4544d7c04afb71e528500f10 Author: hartera Date: Mon Mar 6 16:12:03 2006 +0000 Removed function for adding and replacing hash elements and added this to hash.c and hash.h and renamed it as hashAddReplace. Changed table name and structure names to ensXRefZfish as there were other tables with names very similar to ensGeneXRef. Used dyStringCannibalize to prevent memory leaks. commit b4da2b16b7b33b03f3871f66e6d5ebb19b24b750 Author: hartera Date: Mon Mar 6 16:02:01 2006 +0000 Added function, emptyForNull, to return an empty string if a string is NULL. commit 78c42ddea88c2d7396f8c2005f43a7a06a158996 Author: galt Date: Mon Mar 6 16:00:03 2006 +0000 "Encode release log update" commit e408f29584db65f1385d1be93cf84d51f00583df Author: galt Date: Mon Mar 6 16:00:01 2006 +0000 "Release log update" commit 34036cb2fcb8bb00a9cc6b1f959fb1c253e19695 Author: markd Date: Mon Mar 6 07:54:46 2006 +0000 fixed type, added sanity check commit c7de24bc06aa4d0d91b58840cb8911c8ca6350d3 Author: hiram Date: Mon Mar 6 06:14:03 2006 +0000 A single 64 bit compile warning fixed in a printf commit 7e78fe76790e42791921aad7dbcf671cff4aa6e3 Author: hiram Date: Mon Mar 6 05:49:33 2006 +0000 Add upstreamOnly and downstreamOnly options, to be verified they function correctly commit 2b362b8ee9089664bb51f31aa4c76c50021d700a Author: kent Date: Mon Mar 6 05:21:00 2006 +0000 Adding math module with pi. commit 47fff765c71259b49f532f99a39eb26bc7309c68 Author: kent Date: Mon Mar 6 05:20:28 2006 +0000 Updating to use math.pi commit 48a7d0abef26c704a1c50c42e8c224c512220edf Author: markd Date: Mon Mar 6 05:10:23 2006 +0000 move EST loads to friday/sat commit 374a790b262669dc739d60511564a59bb5da918a Author: kent Date: Mon Mar 6 05:07:00 2006 +0000 Adding const and writable type. Makeing 'global' just mean readable. commit b52af56fdd71d099f02a51bfc4901abe04c89a9f Author: kent Date: Sun Mar 5 17:50:08 2006 +0000 Adding missing break that caused bug. commit 57858961431b35cc87264ab6b0ebe0172aef5334 Author: markd Date: Sun Mar 5 16:51:02 2006 +0000 switched to iservers commit ea6610f5b4dd0b36cd079c48cb8023b0f60bf493 Author: galt Date: Sun Mar 5 16:00:02 2006 +0000 "Encode release log update" commit 61ab33f285c25dff987fa5e168054d6fc8992c5f Author: galt Date: Sun Mar 5 16:00:01 2006 +0000 "Release log update" commit 8b25d2a4ab1d396ad514ad9b68f009f8ba83eefe Author: kent Date: Sun Mar 5 07:41:24 2006 +0000 Fixing runType error on pfh where local function types not declared messed things up. commit 2b90d55443736434e489451904f9e36a8d5897e1 Author: markd Date: Sun Mar 5 06:50:21 2006 +0000 fixed error in make target commit 3d3b6c63baf6d807c7c1c8b537a91ef7526b2f7c Author: kate Date: Sun Mar 5 06:40:40 2006 +0000 Add lift file for panTro2 commit 9cb1c33902e09d8a242edfeb0aa022017500de91 Author: daryl Date: Sun Mar 5 06:21:51 2006 +0000 added hgTrackUi support for rerty LD track commit 4b25c46654d017da770451735c196fdbfe59eb8a Author: kent Date: Sun Mar 5 06:09:54 2006 +0000 Fixing a couple of bugs in para ... do where the element is modified. Making it create the .c .pfh and .o files in the directory where the .pf file resides when including and importing. commit 52d724a9a5ddfc7ad00f2889433448cd158bc2e3 Author: kate Date: Sun Mar 5 01:53:13 2006 +0000 Fix bug causing premature end to processing when region end matched maf end commit 767a95fd28d4b636a57c72ac5d373341959db1a7 Author: kate Date: Sun Mar 5 00:13:00 2006 +0000 Remove panTro2 lift file commit 8e80a14d71bd6cbc580ac01ce42fb1193b141325 Author: kent Date: Sat Mar 4 20:23:35 2006 +0000 Using toDo in compiler dir instead. commit 232c166f43895615ec9fdd664fee1444395d28c2 Author: kent Date: Sat Mar 4 18:51:04 2006 +0000 Put back to para since bug is fixed. commit 553e1894349290b7fc8fd5560224748a1d0ff79d Author: kent Date: Sat Mar 4 18:49:45 2006 +0000 Fixing a couple of bugs that came up in 3-D lib example. commit 268f0b17e5d71182c7d7826ada508fb69d5c4a3f Author: kent Date: Sat Mar 4 18:46:07 2006 +0000 Making some of the system vars read-only. commit 61d5feb891d262c9ed458e5a4e62b17a2b618fc6 Author: markd Date: Sat Mar 4 17:44:13 2006 +0000 reenabled hg18 commit 1c9edd3d847b6e68be06e98d31b57eda4f847600 Author: markd Date: Sat Mar 4 16:30:06 2006 +0000 disabled hg18 commit 04af2b1afd92629e59c7226def8f1f9a1b1bb55a Author: galt Date: Sat Mar 4 16:00:03 2006 +0000 "Encode release log update" commit 95bbd449570402fde179ad614f47f9978488bc56 Author: galt Date: Sat Mar 4 16:00:01 2006 +0000 "Release log update" commit fa8e05e58e9d141169edba1f97162016a63ab787 Author: kent Date: Sat Mar 4 12:19:36 2006 +0000 Fixing bogus freaking out by type checker about using a local variable name in a method that is the same as a member variable defined in an ancestor class. commit c170194ebf78a4389f84f0a4cba0703b67bf5422 Author: kent Date: Sat Mar 4 11:41:43 2006 +0000 Adding test case. commit 306be05b81c289b083466dadccb1e0b09d61daf5 Author: kent Date: Sat Mar 4 11:41:18 2006 +0000 Fixing bug where methods couldn't access things in parent class. commit 500c35a1f25b75a176af0570937d7a5e2b63d398 Author: kent Date: Sat Mar 4 11:08:20 2006 +0000 Adding sin and cos commit f9e353d5361ec206039045fe7c4f3e8bfec06582 Author: kent Date: Sat Mar 4 11:07:56 2006 +0000 Fixing bug with nil default initialization of parameter in a separate module. commit 9dd09730f0ff3f39dff28719eaaab647246f8b37 Author: daryl Date: Sat Mar 4 11:05:16 2006 +0000 added support for rerty LD track commit 08b90043c4befd566aa50c68767a53d10bb80236 Author: baertsch Date: Sat Mar 4 04:37:38 2006 +0000 added qual score track commit eb714a6966ed6634eccf7e4f956227ab4da5f597 Author: kate Date: Sat Mar 4 02:37:39 2006 +0000 Chimp genome 2 commit 1ed14d7a13f519dc07c09a0e0201e7c09b57573b Author: donnak Date: Sat Mar 4 02:29:02 2006 +0000 Added entry for assembly-specific gold track. commit a603d3552432282b481f69ff2b55749b474acca5 Author: donnak Date: Sat Mar 4 02:27:51 2006 +0000 Created an assembly-specific version of this file. commit bd5fd84b3fd77ddb7a3dc1d4e7e3e233ecd6323f Author: kate Date: Sat Mar 4 02:25:13 2006 +0000 Masking done, ready to start Genbank commit 07b6a2d941ec191f087b1bd9ce85935f87492cc8 Author: kate Date: Sat Mar 4 02:00:27 2006 +0000 Add new chimp commit 0a239c56b936132091ea5883e4128de87a06cc79 Author: donnak Date: Sat Mar 4 01:47:18 2006 +0000 Added an entry for the gold track - need an assembly-specific version for bosTau2. commit 1db82f3bc42a54de51cbc533adca88f96b280eb0 Author: donnak Date: Sat Mar 4 01:46:36 2006 +0000 Created an assembly-specific version of this file for bosTau2, which is made up of both chromosomes and scaffolds. commit 0ecc5b2a940ea8289afd3f650a0e3df7654e379a Author: heather Date: Sat Mar 4 01:10:50 2006 +0000 handle randoms commit adbb0f2029952234d5c26aad9160aba89b970589 Author: fanhsu Date: Sat Mar 4 00:46:05 2006 +0000 Added GENOSCOPE TETRAODON track. commit 8d5507421279264ce123fa575416c3f46348a202 Author: hiram Date: Sat Mar 4 00:25:57 2006 +0000 Indicate the blastz swap status in the query organism from Mm8 target commit c4d6e3f4c39db053eba3d986768e2b84e7f36cc5 Author: hiram Date: Sat Mar 4 00:06:56 2006 +0000 Adding the blastz swap operations from Mm8 back to the other target organism commit 6b76fe7a2ca91ba39a6d8f728aae8306b7dff6a2 Author: ann Date: Sat Mar 4 00:05:26 2006 +0000 added special hg18 rules for identifier=humanBacAccession commit e38996aac779494bcb8c45e47587f7c8dfb7c200 Author: ann Date: Fri Mar 3 23:27:13 2006 +0000 initial document. copied from phastConsElements10way.html commit ca31c717bf1bc2b903cb2782fce6af7edde7b23c Author: hiram Date: Fri Mar 3 22:27:10 2006 +0000 Add the careful mem handler limit commit 40f5265afebe710b98b094f33fc0ab48d0f45601 Author: kate Date: Fri Mar 3 22:24:34 2006 +0000 Fix compiler warnings commit be87e36f195327f9d0b4fa0c8c02256bf3a9b74c Author: hiram Date: Fri Mar 3 22:23:07 2006 +0000 Add hgHistoryComment() business to record loading activity commit 980723e0e2bdcebc80bdd72de0ddbd40ae5cade1 Author: kate Date: Fri Mar 3 22:18:39 2006 +0000 Utility to extract mafs in a target region directly from a file commit 2003ea3e10873a5f08252087ecec77f8789b52e5 Author: fanhsu Date: Fri Mar 3 22:00:35 2006 +0000 Pruned records from stsMap where chromEnd-chromStart > 5000. commit 6257e1366eb4ab4df8145196a1191009ca1e4d04 Author: braney Date: Fri Mar 3 21:43:27 2006 +0000 I don't even think this works, but I'm checking it in anyway commit 804ab1c50d03d9d9454a7242ff2ef3d3b31edbce Author: braney Date: Fri Mar 3 21:42:25 2006 +0000 warn about orderings not ending in END. commit d310a70a7b5efac1a36ccc24c0c72641385e624e Author: braney Date: Fri Mar 3 21:37:10 2006 +0000 collapse inversion nodes commit 6873a92db75f1ee5559454faf83eefac985a8797 Author: braney Date: Fri Mar 3 21:35:11 2006 +0000 START and END, as well as collasping I nodes commit b01a452360948e1eb9d7a299ef346227c77d51e9 Author: braney Date: Fri Mar 3 21:34:03 2006 +0000 START and END elements, collapsing inversion nodes commit fed9784e5c1b7c0b94b1305e91b88ce11856ac47 Author: braney Date: Fri Mar 3 21:26:26 2006 +0000 collapse inversion nodes commit 40e672063e7997ee49c51426a1d30d5511085beb Author: braney Date: Fri Mar 3 21:25:03 2006 +0000 some fixes so special names are used is a way consistent with the synthesizer commit 7f70798b4ecb477eb65cc9a1df8ecf896ed3a3f4 Author: braney Date: Fri Mar 3 21:22:37 2006 +0000 a utility to compare elTree's commit 1ab607fc4329d53c26f8e0543ca6d93e9b1c2220 Author: braney Date: Fri Mar 3 21:21:07 2006 +0000 a utility to remove an outgroup from a tree, also collapses insert nodes commit 82bb679fb96998920130b87d1bb4689f08be8c86 Author: hiram Date: Fri Mar 3 20:09:16 2006 +0000 Add the procedure to create the chain pile up tracks commit e9ccd72cac687c16564121e55332f283e52bc6f9 Author: angie Date: Fri Mar 3 19:56:18 2006 +0000 Adding scripts used in the rat STS process which were previously kept in /cluster/store locations. The scripts that don't have Rat in the name may be applicable to builds for other organism's STS but will need testing. commit 39e283ac702b2fb36e87618fc452601f36589562 Author: kent Date: Fri Mar 3 19:11:18 2006 +0000 Starting to get library path to work. commit 7bb220e3e24c6a05d20a0625aea35f065933c82b Author: kent Date: Fri Mar 3 17:42:30 2006 +0000 Making it so that paths to the runtime library and required header files are not hard-coded. Adding in a library path. commit be6669bd35ec86a1211cd0046b9974f9ed295f5f Author: galt Date: Fri Mar 3 16:00:02 2006 +0000 "Encode release log update" commit 9b52539033e81b3bfa91318a27e4cc14a76d4ad3 Author: galt Date: Fri Mar 3 16:00:01 2006 +0000 "Release log update" commit d1a6671e38585cf9dbecd8c91c2f8dec91d1f9a9 Author: fanhsu Date: Fri Mar 3 15:38:32 2006 +0000 Added a comment about sequence of HInv tables loading. commit d7d6810be84a84b5cf5400357a28640771fce8e4 Author: donnak Date: Fri Mar 3 06:49:29 2006 +0000 Added announcement for strPur1. commit 68391738fb64fbd1510abe2843421137b227282b Author: donnak Date: Fri Mar 3 06:49:00 2006 +0000 Archived a news item. commit afc9a44e9abdcc4a03e0ea52eb90d9df053b0144 Author: kent Date: Fri Mar 3 05:30:44 2006 +0000 Finishing conversion of ':' to '@' in runtime and expected test outputs. commit 87560fefe70a6e4f9d1d7060b630c1cb77a56508 Author: donnak Date: Fri Mar 3 04:54:49 2006 +0000 Added Chester, moved Adam & Katie. commit cf6247762b7f654d78c2eb3f92881ee56a87fe08 Author: donnak Date: Fri Mar 3 04:47:36 2006 +0000 Added Brooke. commit a3a297d4d6bd051dbdfd0bc5bd010c860b012e5a Author: donnak Date: Fri Mar 3 04:26:25 2006 +0000 Fixed typo in sea urchin section. commit 89c73afb9fc7f62ccfbbfd936d0492b594c7da0e Author: markd Date: Fri Mar 3 03:52:56 2006 +0000 backed out accidental commit of private stuff commit f56811fc458f199653ae321846722b9bb6063171 Author: markd Date: Fri Mar 3 03:50:45 2006 +0000 up maximum chrom size commit 154a55e865438d94b398d2699b4bc546e3989c2d Author: kent Date: Fri Mar 3 01:20:04 2006 +0000 Changing ':' to indicate a named field/parameter to '@'. Using ':' in the new case statement. commit ea28ae2d80e269b9760b8d2718d74e0d0e1555e5 Author: kent Date: Fri Mar 3 01:15:52 2006 +0000 Adding a test case for the case statement. commit 36047cf0c5d2fe6265d1659615feb22fe732eb77 Author: hiram Date: Fri Mar 3 00:37:51 2006 +0000 Adding 17-way conservation track commit 415890b7241d411e8151b92a3eedcbf280b53920 Author: kayla Date: Fri Mar 3 00:36:00 2006 +0000 added strPur1 commit 4b18c411f6cb270badd57ce84181d3efeb15715a Author: kate Date: Thu Mar 2 23:40:56 2006 +0000 Second chimp genome commit ec8e6e21ee375bb4480775cf1236e5f97d9d9bbd Author: angie Date: Thu Mar 2 23:27:12 2006 +0000 Added support for searching ensGene tracks with other species' names and version suffixes. commit bed0de70af14ea188ec545fb945c4a19b5a8a802 Author: kuhn Date: Thu Mar 2 23:15:43 2006 +0000 added hgFixed and changed output formatting a bit commit ca025d0e2fba2e7b2a246ef02a644bcebe5aab15 Author: fanhsu Date: Thu Mar 2 23:11:58 2006 +0000 Added logic to search mrnaRefseq table for related RefSeq. commit f317ad0bb72f07afdb295b2e4fe4868a80edd82b Author: hiram Date: Thu Mar 2 21:31:07 2006 +0000 Fill in the blastz entries commit 8ace526c17526eb8200a88bae10c479fc1b1f275 Author: angie Date: Thu Mar 2 19:02:02 2006 +0000 When reading from userDb or sessionDb, test for file corruption by checking the format of the firstUse field as suggested by Heather. If corrupted, act as though we couldn't find the row (create a new session). commit d76cb4539607a72a80a07127f714367ca5d48952 Author: galt Date: Thu Mar 2 16:00:02 2006 +0000 "Encode release log update" commit 631dda373079dd659f26c5318784e078ebd98e51 Author: galt Date: Thu Mar 2 16:00:01 2006 +0000 "Release log update" commit c51648e8878df2656f75244e5c8aa988b1146d1b Author: kent Date: Thu Mar 2 08:22:59 2006 +0000 Taking out internalErr that was preventing some nice things in for loops. commit 11008e0a2ebabeeb3c4db93f6fbd24b6b12d8a01 Author: aamp Date: Thu Mar 2 08:03:52 2006 +0000 Fixed an EVIL bug where enzymes were getting lost. commit 5a63952b8428ee84f8dc8f0d805faf2de2c2365e Author: kent Date: Thu Mar 2 07:40:10 2006 +0000 Added a test case commit 95732467a2477d066a3c2d80d469d8dc71c95526 Author: kent Date: Thu Mar 2 07:25:06 2006 +0000 Adding a crucial local and getting the whole thing to flow. commit e067400ae6bbe5211aecd37603835238a94bec8c Author: kent Date: Thu Mar 2 07:23:42 2006 +0000 Adding local input parameters to encourage more flowing. commit 63d70c143532d55e97f5c8e1b1897fdea56e4ddc Author: kent Date: Thu Mar 2 05:57:54 2006 +0000 Introducing pptClassAllocFromTuple to be a bit more specific to code generator when a tuple is to be used to initialize a class. In this process fixed a bug where passing a tuple to a function as a parameter of class type used to crash. This had some ripples throughout system, but I think they're worked out and the result is more robust than it used to be. commit 605cbe71caa1dc1de0de24eaa18178e90307c0a9 Author: kent Date: Thu Mar 2 05:51:52 2006 +0000 Reworking things a little so that you can no longer initialize a class with multiple fields from a function returning multiple values directly. It's just too hard to get it right, and arguably confusing to the user as well. commit a807193b7a266b6f529d007a7a69b4d1ef4a00a5 Author: kent Date: Thu Mar 2 05:48:44 2006 +0000 Didn't mean to remove this. commit 3db01ec8218d1d880879b768973390c542999566 Author: kent Date: Thu Mar 2 05:48:06 2006 +0000 Oops, I'm going to have to add this right back. commit 889377c2dbe10bd362e884c09734292197684a9a Author: kent Date: Thu Mar 2 03:21:14 2006 +0000 Reworking things so that variable attributes (global/local/readable/static) apply to individual variables rather than the defining tuple, though if they are not specified in a tuple, the most recently specified attribute is used. commit 89af94a42146d64f991c402ea37a88726ed07249 Author: kent Date: Thu Mar 2 01:03:01 2006 +0000 Cleaning up a few things in parser. commit 822b290ef41615e7ab766b2de6963525ffd0dfc7 Author: kent Date: Thu Mar 2 00:35:09 2006 +0000 Removing global varDecAndAssignToVarInit pass. Making it called from parseTuple instead. commit eaa1e9c1d1bf7d9cfd5f2ecd19bd15093a0714cb Author: kent Date: Thu Mar 2 00:31:10 2006 +0000 Removing global varDecAndAssignToVarInit pass. Making it called from parseTuple instead. commit 87e68e7ffbdba00f3cc6f647056d4e10de72e167 Author: aamp Date: Thu Mar 2 00:08:11 2006 +0000 Forgot this. commit 6137025f359c21d6ceb57b68cae24be2a3aa78e4 Author: aamp Date: Wed Mar 1 23:49:45 2006 +0000 Slight difference to sap track description for strPur1. commit 0668a0fd5918f067f69828468dda306b09e41bc6 Author: kent Date: Wed Mar 1 23:39:37 2006 +0000 Catching more syntax errors in variable declaration lists. commit 8900b31a40df93b1d33edf245b4d8bab6c5bcc7d Author: hiram Date: Wed Mar 1 23:32:35 2006 +0000 Raise the careful mem handler limit to 2Gb on 32 bit machines, and 8 Gb on 64 bit machines commit 0c79b94eda330423a17504e90c680ade71f9b4e8 Author: fanhsu Date: Wed Mar 1 23:27:19 2006 +0000 Added kgXref2 and kgPepMrna. commit e8fe6f49a1fa37499dcd37e60fe1517a1fdab941 Author: hiram Date: Wed Mar 1 23:26:39 2006 +0000 Change default size and autoScale display of the hg17,hg18 pile up tracks commit e0353ed380610d3cec1aaaab5e662350e3f39100 Author: heather Date: Wed Mar 1 23:15:58 2006 +0000 adjust start for chrN_random with loc_type between commit b5601664e8bb41bb150038a2e1526e1964d0f5c2 Author: hiram Date: Wed Mar 1 23:14:59 2006 +0000 Reset display default for the monDom4 pile ups commit 0ade8988571ab490bb0968355e725266066fd9ee Author: hiram Date: Wed Mar 1 23:05:03 2006 +0000 Make the Hg17 chains and nets indicate that they are hg17 commit 0b935b2d61210568af4446a766915e0c68380aed Author: fanhsu Date: Wed Mar 1 22:59:25 2006 +0000 Changed primary key to key. commit 470ec58ff312fc87a579afef3d8e52f497206164 Author: fanhsu Date: Wed Mar 1 22:56:59 2006 +0000 Created makefile. commit 447b139173dd8250d70a106b283710711bb581b3 Author: kent Date: Wed Mar 1 22:56:51 2006 +0000 Implementing new operator. Separating out parseDump.c from pfParse.c Making it so that "int a += 2 ;" is flagged as an error. commit 10b73e02f760c6dfe202da9e36048ad2f704b87c Author: fanhsu Date: Wed Mar 1 22:56:45 2006 +0000 Created kgPepMrna.c. commit fd034098d9f6f8df8d3c0ed0e10bf2b15af9e348 Author: heather Date: Wed Mar 1 21:59:06 2006 +0000 make hash smaller commit 2b25a8b267aa2eb2a37a3761a3ccddc0858ae08b Author: ann Date: Wed Mar 1 21:42:32 2006 +0000 added entry for stsMap track commit 2fed220e8e04d4633c840335f241da6e73e7c953 Author: ann Date: Wed Mar 1 20:51:05 2006 +0000 added QA comments about renaming *Mm6u1* tables to *Mm6* for galGal2 and rn3 chains and nets commit 220334c0afa8362acbb0ba17aba4cad03e229934 Author: ann Date: Wed Mar 1 20:44:52 2006 +0000 removed tracks for chain/net to Mm6u1 commit c2f672cf9d0a3571fb3eafda41cb8e023a277418 Author: ann Date: Wed Mar 1 20:42:28 2006 +0000 the associated tables were renamed from *Mm6u1* to *Mm6* commit 75f9c8aa668455687a5a61c1c613f6a33e9813af Author: ann Date: Wed Mar 1 20:40:26 2006 +0000 removed track entries for chain/net to Mm6u1 commit a9f17b7c6fd473a30fdd13c3ef63268e2ee45d13 Author: ann Date: Wed Mar 1 20:38:56 2006 +0000 the assocaited files were renamed from *Mm6u1* to *Mm6* commit ad1470aea3610093616a6b0879ed3f25d66e4aa8 Author: ann Date: Wed Mar 1 20:37:24 2006 +0000 the assocaited tables were renamed from *Mm6u1* to *Mm6* commit 918915ef966a702d07291c95efc41b88f202cece Author: ann Date: Wed Mar 1 20:32:51 2006 +0000 removed entries for chain/net to Mm6u1 commit fe952ad214bfb259ad971d5371cf6e513251d11a Author: angie Date: Wed Mar 1 19:30:25 2006 +0000 Use environment variable BLAST_DIR (w/default if unset) instead of hardcoding blast path. Also make sure that $BLAST_DIR/formatdb exists. commit a243de70614b459fe5c7e87cfda18365332ad923 Author: ann Date: Wed Mar 1 19:03:15 2006 +0000 switched chains/nets from rheMac1 to rheMac2 commit 78b8f32d5dcb3e50766c28be438f4f3beb437eb0 Author: kent Date: Wed Mar 1 16:23:45 2006 +0000 Refactoring code for addition of new operator, and starting to parse new operator. Removing some old tokens from year 2005 module experiments. commit eab39d2412ffdf725f010068ba48f0489f6cf74e Author: galt Date: Wed Mar 1 16:00:03 2006 +0000 "Encode release log update" commit e2d8b8d911de82d279f82c42ffb832e27ab7a695 Author: galt Date: Wed Mar 1 16:00:02 2006 +0000 "Release log update" commit a118fab792ca18d53d40a20fdeea6be2c894bd0d Author: donnak Date: Wed Mar 1 05:16:58 2006 +0000 Added info about ABA images. commit ba39c46963f7ff3a8f944478c96ede0fe0fd0a00 Author: braney Date: Wed Mar 1 04:10:12 2006 +0000 fix up mouseovers for gap lines commit 22d35b667bb64f9db0401ebd5d95c0f6cdc017af Author: braney Date: Wed Mar 1 04:01:01 2006 +0000 a new details page commit a6e13c9b997b61e9bf2cee84e5957b22b66c7bf4 Author: hartera Date: Wed Mar 1 03:11:16 2006 +0000 Added hashAddReplace function. commit b46bb07deb7e097ca8230180792dafd20aaf647c Author: hartera Date: Wed Mar 1 03:10:01 2006 +0000 Added a new function, hashAddReplace, that adds an element to a hash table but if an element is stored for the same key, it replaces that element with the new one. commit b83bc5f14af1998b2773df36b5e36090781164b0 Author: angie Date: Wed Mar 1 01:29:30 2006 +0000 i386 --> $(MACHTYPE) commit 250a3d2b36b1ac3f63f18eb683f6d24397e32e8b Author: fanhsu Date: Wed Mar 1 01:16:53 2006 +0000 Added alignId. commit cca3f56bf0bc8b86cab60aa0984bee910dd8c8b8 Author: hiram Date: Wed Mar 1 00:22:09 2006 +0000 Starting on the 17-Way commit 712ce3b2e791c4b90adc24a5b0c43857997bbf43 Author: kuhn Date: Wed Mar 1 00:07:42 2006 +0000 turned on default for netMm7 to dense commit 2d8dc62b36e5e086cc7cbdd25fc8fbcc5b6d8e8f Author: angie Date: Wed Mar 1 00:00:48 2006 +0000 Reciprocal best dm2-droSim1 net (special request for user). commit 354f60ac459eaf44fb54b4c04f1831868427e827 Author: kuhn Date: Wed Mar 1 00:00:05 2006 +0000 turned off a bunch of old mouse net tracks for default commit 3db399fe5b8741fef87120793cb1c99bdf7d10e3 Author: kuhn Date: Tue Feb 28 23:49:48 2006 +0000 turned genscan and geneid off by default commit 33a91b8c0a99999a6756c0ab75ab6a1995a729af Author: kuhn Date: Tue Feb 28 23:47:00 2006 +0000 dropped
    tag commit 7fc75cd11db7414753840bf813beb530591bb879 Author: ann Date: Tue Feb 28 23:30:21 2006 +0000 added RheMac2 to chain list commit c1609c2c9ffc17796e7213736f465bb4333a2035 Author: ann Date: Tue Feb 28 23:28:51 2006 +0000 small tweak for hg18 and for flyBase2004Id identifier commit 98132f15296ba4e1d5e7c8ebb9de01426c55cd3e Author: galt Date: Tue Feb 28 23:25:42 2006 +0000 supporting new location of vg text and index in cgi-bin/visiGeneData/ commit de1e3e4c64b70d9b4b36875fe08e7966b5bf6761 Author: fanhsu Date: Tue Feb 28 23:00:40 2006 +0000 Added kgPutBack. commit 209223b201deec78fb7cd564a43bba3266f476a8 Author: kuhn Date: Tue Feb 28 22:48:32 2006 +0000 added leprecaun photo for rat Lepre1 gene, leprecan commit 839f6063d2e1eb56d4bb0f063f73e8d070902c63 Author: fanhsu Date: Tue Feb 28 22:27:37 2006 +0000 Created kgPutBack.c. commit 40d0271f699af595557707cf803207a749b08236 Author: hartera Date: Tue Feb 28 22:20:59 2006 +0000 Skipping links with empty data. commit 5bca3977f2709d52b4efbb4dd72d7c6db67fe558 Author: heather Date: Tue Feb 28 22:13:35 2006 +0000 remove verbose message commit 99e96e41d82153515af1f5f7edc29b02cd628d1b Author: braney Date: Tue Feb 28 22:11:50 2006 +0000 don't set hgSeq.revComp in cart. This shouldn't be a default. commit 27e5c4a7dc97dba505a0b789afef6ff91533c9a5 Author: galt Date: Tue Feb 28 22:09:57 2006 +0000 changing path of visiGene text index commit d58461626eae0348c1dca89ae85612ed8acc9db4 Author: fanhsu Date: Tue Feb 28 22:05:06 2006 +0000 Created makefile. commit d266a23b2eff5235c9c2db1d55d894a0898db496 Author: heather Date: Tue Feb 28 21:43:43 2006 +0000 handle randoms commit 95995d090a6f04726e56459faa19c7339c996f70 Author: kuhn Date: Tue Feb 28 21:39:01 2006 +0000 turned netHg17 default to dense commit 6a864f216f8a7bb7339f7e542201d31703e055ba Author: markd Date: Tue Feb 28 21:07:10 2006 +0000 respond to change in pslSwap api commit 6a035f4d0a07ef0cdc53bfd2a69f17df1d36a47c Author: markd Date: Tue Feb 28 21:05:25 2006 +0000 moved all swap functionality to psl.c function commit 3a1a9a6c3b5c602027939be449cfe6a78f24d46f Author: markd Date: Tue Feb 28 21:04:51 2006 +0000 handle more cases in pslSwap function commit 33f569f1ea24703b1d13e8222dffe30f53a05842 Author: markd Date: Tue Feb 28 21:03:52 2006 +0000 added reverseStrings commit 261538f43f3ddd5f02b47a6b3bc38122c0285759 Author: heather Date: Tue Feb 28 20:57:35 2006 +0000 handle randoms; still unsure about end coord when loc_type != 2 commit 70008a7865d888b3113b88a849e0308145de38f1 Author: angie Date: Tue Feb 28 20:47:18 2006 +0000 Added kgPick target. commit af3cf3a8a867465911e7e94f019925201fd77a8b Author: galt Date: Tue Feb 28 20:42:39 2006 +0000 enabled new location of visiGeneData (just vg text and indexes for now) commit a187a33cea37c68ac232bd1dab48960b68465829 Author: angie Date: Tue Feb 28 20:41:55 2006 +0000 Added kgGetCds target. commit 99f25ba0e39c0c04f889e1d0044e2448b1ba3bb7 Author: galt Date: Tue Feb 28 20:28:56 2006 +0000 added ixIxx to standard utils make commit 64654560bdbf2a5853641c979a20038a1360c65b Author: angie Date: Tue Feb 28 20:19:39 2006 +0000 Fixed hardcoded database. commit ea94f24680d5674154862534d633fe1349c230d3 Author: angie Date: Tue Feb 28 19:56:02 2006 +0000 Added kgCheck target. commit 0c56febb1e65f7ee2bd79c2960906d170450a4d3 Author: hiram Date: Tue Feb 28 19:45:10 2006 +0000 STS markers done. commit e44654c4dbf6f8909b7dff269c88090412e127f8 Author: kent Date: Tue Feb 28 19:43:35 2006 +0000 Enforcing a init method when you have readable or local members. commit 62d3e4ca64511fdd436211b424e67f6b83a5d37f Author: galt Date: Tue Feb 28 19:35:05 2006 +0000 added Allen Brain steps commit 938063ccef10a647330c2352cf26002ed3938c99 Author: hiram Date: Tue Feb 28 19:25:22 2006 +0000 Adding monDom4 chains and nets commit 1244e9db196825954e76f89e7f94aaa39805a621 Author: kate Date: Tue Feb 28 19:20:06 2006 +0000 Add 17way conservation tables commit 3c7462f438cf87eb0775da900d316637a229576f Author: galt Date: Tue Feb 28 19:06:14 2006 +0000 added levels 5,6 commit ffb2dfb2ee39a7eaf044e475443e49ac1dd663db Author: angie Date: Tue Feb 28 19:02:38 2006 +0000 Hooked in protein/. commit c2a5920491e95cd6caebf419d0cb1be0be5fded9 Author: angie Date: Tue Feb 28 19:01:39 2006 +0000 Adding some targets necessary for KG*.sh scripts. commit 65f4e515ccfd6b2310b739d162caba92fd4d7bc2 Author: kent Date: Tue Feb 28 19:01:23 2006 +0000 Implementing readable attribute for members. commit 8ce845ca5ae7fc37ad2126e6c32a7b000301976b Author: galt Date: Tue Feb 28 19:00:54 2006 +0000 added changes at Susan Sunkin request and fixed a minor bug and updated path in makefile now that san was back up commit 9b70e5de17034041533e679ea1e076d448f2650d Author: angie Date: Tue Feb 28 18:55:40 2006 +0000 Added new genome db ($RO_DB) argument to kgPrepBestRef2. commit a6d58361d96ea323dbca89b7cd7b32b220837bde Author: angie Date: Tue Feb 28 18:54:23 2006 +0000 Added genome db argument for hSetDb. commit 1aab9dd1c84574b289ec8d68ed9f683ca8d7f23a Author: fanhsu Date: Tue Feb 28 18:44:08 2006 +0000 Added KGRef3.sh. commit 0f4c3cc9cd9581c2589e5dd42a4842d1f8a83cec Author: kent Date: Tue Feb 28 18:36:28 2006 +0000 Putting in check to prevent you from using local fields of a class outside of the defining module. commit f43b92d5128e995bcbff96e3f141efd9e72a4744 Author: heather Date: Tue Feb 28 18:28:23 2006 +0000 switch to hg18 commit 99299dfd7ef62eee2dc2b7dc0206cc05e323c1b4 Author: fanhsu Date: Tue Feb 28 18:25:08 2006 +0000 Updated. commit 6ae84622e013a7304dcf43b5604c3f1fcdec5d87 Author: fanhsu Date: Tue Feb 28 18:23:50 2006 +0000 Moved to kgBestMrna2. commit 9f9c79769f75a6695245ecb52d4a106a677e41f7 Author: fanhsu Date: Tue Feb 28 18:21:15 2006 +0000 Created. commit d63412f9fb09bcca99b437c8ccabe722ec05923b Author: fanhsu Date: Tue Feb 28 18:21:00 2006 +0000 Created kgResultBestMrna2.c. commit 8992bf6b618362a503fd43b60db835227d83c67e Author: fanhsu Date: Tue Feb 28 18:20:33 2006 +0000 Added makefile. commit 7d19f676a65df05429c3eb7dedebfcd1ccfe30ff Author: angie Date: Tue Feb 28 17:56:04 2006 +0000 oops, check for NULL before trying to traverse hash elements in accessControlFree. commit 863fd03a4d0f0f80e19a4ea01b4efa54d389a1e9 Author: ann Date: Tue Feb 28 17:33:16 2006 +0000 initial file addition (copied from hg17) commit 1b95b1f830cb12b7070de38a3a48f244f285e998 Author: ann Date: Tue Feb 28 17:24:36 2006 +0000 added close paragraph

    to clean up html commit 481895ded9ffda6f0a32cb40d998fbb91582602a Author: fanhsu Date: Tue Feb 28 17:09:06 2006 +0000 Added KG alias tables. commit b71a8f3ece6734bc8603c87cc22d4cc49399a982 Author: fanhsu Date: Tue Feb 28 17:07:19 2006 +0000 Added kgProtMap. commit 9aa074c99042ed252a10b720f7b81c76de61adb2 Author: kuhn Date: Tue Feb 28 16:59:19 2006 +0000 dropped unneeded hyphen commit bb95dad22c5166a26e2df616a20a23bd0e6802ed Author: braney Date: Tue Feb 28 16:58:30 2006 +0000 a few fix-ups commit 694285acbe5d22c4d9ad62af8e16848fbb5e2703 Author: braney Date: Tue Feb 28 16:57:56 2006 +0000 an intermediate check-in (START,END elements) commit 9b05cec53ea002e42c673aaac5cfcb2cd31d1e7f Author: giardine Date: Tue Feb 28 16:56:38 2006 +0000 Added landmark track, it provides landmarks not in other tracks for use with the Human Mutation track. Examples are HSS sites, promoters, enhancers. commit 1e094f04c23cf773eba09cbc255365256cfc8095 Author: heather Date: Tue Feb 28 16:54:16 2006 +0000 remove dangling close anchor commit 8b4ddad3f9786d92bf88378480b3ce2e795b91a2 Author: braney Date: Tue Feb 28 16:36:20 2006 +0000 add a pointer to the chrom breaks commit efcfa2b267eb64660d2cd95d482e3aecee4046f7 Author: braney Date: Tue Feb 28 16:27:12 2006 +0000 an intermediate check-in commit a6452d89577a8b45896ddb9a1147d486659d2b96 Author: galt Date: Tue Feb 28 16:00:03 2006 +0000 "Encode release log update" commit a6b30bf56555cf378fb0e022105caa73780e5854 Author: galt Date: Tue Feb 28 16:00:01 2006 +0000 "Release log update" commit 785cc088389622824cc13276db44762a35e1953f Author: markd Date: Tue Feb 28 15:43:17 2006 +0000 removed C99 construct commit 885c921f78622da9b3ecc14385dc97991819a277 Author: kent Date: Tue Feb 28 15:39:59 2006 +0000 Checking that all fields of a global class are of global types. commit c8fb462dcc82293e4fb4291cc7b8350d09efff5b Author: kent Date: Tue Feb 28 15:27:58 2006 +0000 Adding NULL initialization to avoid compiler warning. commit 29b1a3a0008d6cfe95721d6c49d2a4cea47a4926 Author: kent Date: Tue Feb 28 15:26:43 2006 +0000 Adding pf_module prefix to class names in generated code (since it turns out we can't keep classes truly local because the dynamic typing system needs to know even about the private ones. commit 9293d6d0e6a97251efda82053098082710c1583a Author: kent Date: Tue Feb 28 14:31:14 2006 +0000 More progress in implementing global in front of class. commit 6fde51841aa11a4bfe536c4a5805541649aed113 Author: kent Date: Tue Feb 28 13:35:18 2006 +0000 Starting on making classes global or not commit 96ece9271f45f45f0b11cb0f71f559fe65b88bc9 Author: kent Date: Tue Feb 28 07:19:52 2006 +0000 Blocking writes to merely readable vars from other modules. commit cd3104c1ef4941257ac59fb01997b84042b271f5 Author: kent Date: Tue Feb 28 05:52:39 2006 +0000 Making it so that imported modules respect global/readable on first compile. commit 6b64767b5e31c23ae4325c24aaac2d6f4e7ee6d7 Author: markd Date: Tue Feb 28 05:40:46 2006 +0000 added resize function commit 6a390f94e2194426d514387a13183d48160eb9b6 Author: kent Date: Tue Feb 28 05:31:37 2006 +0000 Teaching code generator about global/readable somewhat. commit 3a9f07bd4653a3c299c07ba8b2accf4fb0734b3f Author: aamp Date: Tue Feb 28 05:04:56 2006 +0000 Fix for 64-bit. commit de442e9a069ce1656f78c39555ebd281881f08d0 Author: kent Date: Tue Feb 28 04:31:51 2006 +0000 Making only globals and readables get flipped into new symbol table on include. commit 570c2287af603244c1c0d2daf9690e3d9656d92e Author: heather Date: Tue Feb 28 01:47:38 2006 +0000 "New version number v128" commit 546f0dc93d63dff0e183fee0188d647c9f78bcf3 Author: hartera Date: Tue Feb 28 01:35:51 2006 +0000 Added entry for Radiation Hybrid map track. Also added search spec for this track. commit 62532c5223c97d2320742d5c991f732440a95540 Author: aamp Date: Tue Feb 28 01:34:19 2006 +0000 Little utility to get random regions in genome. It's a rough draft. commit 59f998e24c74b9231e04075f2eb9f5b2c7a9cc85 Author: aamp Date: Tue Feb 28 01:33:09 2006 +0000 A new function that just sums hashInts. Pretty straight-forward. Maybe long long is silly. It sounds silly anyway. commit cb1b47a2ebb204883cc302b71dec3cb9fc61809f Author: kent Date: Tue Feb 28 01:24:49 2006 +0000 Made it so that global/local/readable can be prepended to symbols outside of a function. Only globals and readables will be written the the .pfh file. This makes it so that if a file is already compiled the non-globals used in another file will cause error. Need to work to make it the way the first time somethings compiled as well. commit 33dcda5275097d4f9d09b4fb469966f45c46beb4 Author: markd Date: Tue Feb 28 01:07:59 2006 +0000 open mgcGenes by default and hide gap track on hg17 commit 39b5f2721666a7086f4d02b02b89d13a0aa07f76 Author: hartera Date: Tue Feb 28 01:02:42 2006 +0000 Made change in jsValidateKeys function so that program the does not crash when no database is specified as it was comparing a NULL value to a string. commit 611ea8c605a10261f280460ea4a07f134188210b Author: angie Date: Tue Feb 28 00:57:59 2006 +0000 Resolve compile warning. commit 9381de22434d667bbfe050e76e95f9679f8da81f Author: kent Date: Tue Feb 28 00:53:33 2006 +0000 Taking another step towards implementing global/readable/local commit 36937a83c4ac1ba165204dadcf459672792b3de2 Author: hartera Date: Tue Feb 28 00:52:34 2006 +0000 Radiation Hybrid map in progress. commit 532423c6bde336326e58246d279a4a42a90b83bd Author: fanhsu Date: Tue Feb 28 00:45:44 2006 +0000 Updated to avoid a compiler error. commit cd33d507fb07808c0e2dcc9d7c683e33b18a928d Author: fanhsu Date: Tue Feb 28 00:43:23 2006 +0000 Updated to avoid a warning commit 592f872e20658c47e6ad9763057261fc4d069613 Author: fanhsu Date: Tue Feb 28 00:41:11 2006 +0000 Added return(0) for main.c. commit 71880bac085d7003ef4c78dd5b94e961fac0ef57 Author: fanhsu Date: Tue Feb 28 00:38:34 2006 +0000 Created kgPrepBestMrna2.c. commit 7d43d37492169f7086acd0c9ee959d5d13a5405d Author: fanhsu Date: Tue Feb 28 00:28:40 2006 +0000 Created kgPrepBestRef2.c. commit 606398f39b8ba11d6098854649b5950908df8acb Author: fanhsu Date: Tue Feb 28 00:26:11 2006 +0000 Added Part I of KG build. commit 9bddaaa3fa4849cfa2db665d5ec97762fb387ed9 Author: kent Date: Mon Feb 27 23:34:52 2006 +0000 Converting bool isStatic to enum pfAccessType in preparation for adding global/readable/local/static. commit 843d5604a8a62332b1d89fe50312b7ee6d0ea47e Author: heather Date: Mon Feb 27 23:05:16 2006 +0000 assert numeric order of snp_id commit f613f7986e72bb313f2d56e15563bad17a018d8d Author: fanhsu Date: Mon Feb 27 22:59:13 2006 +0000 Changed primary key into key. commit 759d383e29606206f0e84215ae6f489ba92c5414 Author: hiram Date: Mon Feb 27 22:52:40 2006 +0000 Add noLoad option to leave files instead of loading them for testing commit 0a27af616c60ae758d918ff1a373e615cf7ce12a Author: kent Date: Mon Feb 27 22:30:16 2006 +0000 taking scope ID out of methods names commit f3c1610e5f0c541e3b136837f042c78cb3a106b5 Author: donnak Date: Mon Feb 27 22:29:39 2006 +0000 Fixed an incorrect date in OH training announcement. commit 74a2e11d6e3d77cbb5d5b0916674c817df0f9229 Author: fanhsu Date: Mon Feb 27 22:28:17 2006 +0000 Created kgCandidateZ.sql. commit d720324e4e43a246029d5c4f2673d6339a491cfd Author: heather Date: Mon Feb 27 22:21:33 2006 +0000 use cloneString commit 7e50e335e6099ba7727db95f6e79c50288235cd7 Author: heather Date: Mon Feb 27 21:28:49 2006 +0000 handle random contigs commit 32aa8b4356e810a3bde3cd9c51cb8e4ea93b2255 Author: donnak Date: Mon Feb 27 21:27:54 2006 +0000 Some minor edits. commit 9e3b8abaae3daaa85b0bc9a0027a925127e1b010 Author: donnak Date: Mon Feb 27 21:25:36 2006 +0000 Added Graph Configuration Help link. commit 5e8e678051edff5f62d0ca1fd2e913a621e76a05 Author: heather Date: Mon Feb 27 21:25:13 2006 +0000 don't miss the last one commit 8f8e29573ef6b583405901824621857ccbc80d8e Author: donnak Date: Mon Feb 27 21:25:00 2006 +0000 Made a few minor edits to Kate's reorg of the Display Conventions section. commit e4ef13969357c7042fd413b35707f95d2c692089 Author: ann Date: Mon Feb 27 21:22:49 2006 +0000 Initial version. commit 77cef03026765349af2b75b8c63127fbfc5593f0 Author: angie Date: Mon Feb 27 21:22:33 2006 +0000 Added {chain,net}Rn4 with descriptions that assume lineage-specific repeat snipping. commit f89046e76a632a64a2a2f02d582bb2015d97b569 Author: heather Date: Mon Feb 27 21:19:41 2006 +0000 handle random contigs commit 0e703f53f0d84e6e57bdf285b29c9a025fcc012d Author: fanhsu Date: Mon Feb 27 21:16:55 2006 +0000 Created kgProtMap2.sh. commit 434b49db0bae80890dccf826a9b65a9eee931a54 Author: donnak Date: Mon Feb 27 21:13:05 2006 +0000 Minor edit to previous addition. commit a6f52194bbbc2c194a01f96b2710914e1f5cd9dd Author: kent Date: Mon Feb 27 21:02:50 2006 +0000 Taking some steps towards making this work with modules in different directories. Still have to deal with using something better than the scope ID to generate mangled names for classes, since the scope ID will be different if compiled as part of 10 files than if compiled as part of one file. commit cad16ccb511e059cd34cb51effc9ad691fbcd1cd Author: donnak Date: Mon Feb 27 20:41:40 2006 +0000 Added seminar announcement from OpenHelix. commit eeca8760188cc4049a3707e449b5cc1eeaea60ba Author: markd Date: Mon Feb 27 20:12:28 2006 +0000 added to-do items commit a85fd0f37e7749298b4acb00bd2ac46fe118e9b1 Author: angie Date: Mon Feb 27 20:11:58 2006 +0000 Re-ran dm2-hg18 pairwise protein blast with 4.2 genes. commit 6145641ee6636c03ae1c39330ed50aff3e1b8c5b Author: angie Date: Mon Feb 27 20:11:11 2006 +0000 Added native RefSeq, rn4 chains/nets. commit 9cc46b002c2d559f508e4c58453864b831072da7 Author: angie Date: Mon Feb 27 19:58:10 2006 +0000 Added size limits to indexes. Changed protein id index from unique to non-unique because sometimes the protein field is empty for multiple rows. commit 311c58d11f953afcf93ce5d949837461adcf0318 Author: kent Date: Mon Feb 27 19:38:56 2006 +0000 Requiring single quotes around module names in import and includes. commit 38d5bf65a8c5299cfeb4f3dc0f3e490d3874c341 Author: fanhsu Date: Mon Feb 27 19:37:26 2006 +0000 Created kgPutBack2.sql to be used during KG build. commit 35230425142a5cbf4174d7f8a02b06d8454c0b82 Author: angie Date: Mon Feb 27 18:50:15 2006 +0000 Added hgLoadSqlTab target. commit 5f800098a880d8485bf7eabfcb7c9daa3533a2f2 Author: fanhsu Date: Mon Feb 27 18:47:47 2006 +0000 Created kgCandidateY.sql. commit 13b1704960707b50278e1a12d911f7481930f05e Author: kuhn Date: Mon Feb 27 18:26:18 2006 +0000 moved some output lines commit 358aee8ad4228ee22b920f33adc92eaaa85d09e8 Author: kent Date: Mon Feb 27 18:14:36 2006 +0000 Implementing the 'as xxx' in 'import module as xxx' commit e50e3731a0c24161f922235b0c8ecc907c3f8d83 Author: fanhsu Date: Mon Feb 27 17:05:35 2006 +0000 Updated to handle the situation that a protein accession number became a secondary accession in a newer UniProt DB release. commit 7b654735bc5247dc290bc0f487d8910a56ae25c4 Author: braney Date: Mon Feb 27 16:54:37 2006 +0000 a few options to print just the leaves, and to leave out the version strings commit 6316655655c8c765e0fa71fde1d50ef0c9af5ba4 Author: daryl Date: Mon Feb 27 16:46:06 2006 +0000 adjusted doHapmapSnps to use new table format commit 4fdc39bbfe432eba0b1b4b608526ca5b8e39e2cb Author: angie Date: Mon Feb 27 16:00:53 2006 +0000 blastz/chain/net rn4. commit b33049206b38cdd3ba1a6fd38885539dbdc6f995 Author: galt Date: Mon Feb 27 16:00:03 2006 +0000 "Encode release log update" commit d1a1d24399a31fc14e770ed4eb66b96af4c9c012 Author: galt Date: Mon Feb 27 16:00:02 2006 +0000 "Release log update" commit 0ab03320cd70685a53d1c9d6ab914233675572df Author: fanhsu Date: Mon Feb 27 15:47:57 2006 +0000 Created KGRef2.sh. commit 0a1cf0e55406f0299238da9335dde9e594a4abaa Author: giardine Date: Mon Feb 27 14:45:28 2006 +0000 Updated credits for track. commit 15f105db4dd8ff793438ea37dc9e6e4943d7cbe3 Author: daryl Date: Mon Feb 27 08:34:08 2006 +0000 hapmap ld: draw track background in dense mode for empty track; map empty track; speed enhancement commit 4e028439c07c8ce599ee9151fb1d9372b8a49fa6 Author: daryl Date: Mon Feb 27 07:56:19 2006 +0000 New format for storing allele counts commit 1e7983948795a2a1d095f0ffe9641d3f47b7e74d Author: hiram Date: Mon Feb 27 07:48:09 2006 +0000 Place the MonDom4 chains and nets in their correct locations commit 94878ca5d33cc99687033d275142f5bd5a2109e9 Author: daryl Date: Mon Feb 27 07:23:51 2006 +0000 calculate Tajima's D commit f1507b5dd4c8ccb2c75d34619e8e8686e30233ee Author: daryl Date: Mon Feb 27 07:21:11 2006 +0000 added support for strand, as alleles are reported on the sense strand but strand info is not in prettybase file and requires supplemental input commit 9c3bbb8a8c1895824f0602a3d355db25301248c0 Author: daryl Date: Mon Feb 27 07:18:19 2006 +0000 HapMap LD: more speed enhancements for untrimmed drawing commit e640985adc86cac41081d8b24c7e10a06ad39339 Author: daryl Date: Mon Feb 27 07:16:56 2006 +0000 HapMap LD: shortening long labels to fit default window commit 00f4eca1bf8fcb2bbfa04678a8cba193d2e1d4fd Author: daryl Date: Mon Feb 27 06:49:15 2006 +0000 HapMap LD: use official names for populations commit 24a9d0a8b64268a5cdaf5402c33c198d53de8238 Author: markd Date: Mon Feb 27 06:47:01 2006 +0000 create pslSwap function commit 0006bdf698455f12eb720936d6f27a112fe75f34 Author: fanhsu Date: Mon Feb 27 05:07:20 2006 +0000 Created KG2.sh. commit c1fb745ef01a2609288a68190396d000d9f5f581 Author: daryl Date: Mon Feb 27 05:03:53 2006 +0000 hapmapLd: updated names to match official descriptions; clarified usage of trios by removing children from analysis commit a76d98f516a3a9ff1546473ab5a2770488f11970 Author: kent Date: Mon Feb 27 03:56:38 2006 +0000 Updating expected output with single instead of double quotes. commit c193456322c4da57ef46f3270dbafe67dca02f57 Author: kent Date: Mon Feb 27 03:56:13 2006 +0000 Updating to use single quotes in scan like it does in print. commit 2766e5196ee2aea5823daf7b7d4ded832c145e12 Author: kent Date: Mon Feb 27 03:41:53 2006 +0000 Updating test case with single-quote output. commit fca56734d381cd46cbb83e86350f4196850cc72b Author: kent Date: Mon Feb 27 03:39:02 2006 +0000 Adding netHttpConnect.net.c commit 0a40f24d9530aab3e1212fb14cd4dd73af7a93e0 Author: kent Date: Mon Feb 27 03:38:54 2006 +0000 Adding netHttpConnect. commit 5e7a24123ffbf61cd2ea67a256d342e2ab0a0ba2 Author: kent Date: Mon Feb 27 03:36:47 2006 +0000 Fixing Mac case insensitive file name stupidity I hope. commit df7e50f57e26a1e527222fa78ea4d33f327fc9c3 Author: kent Date: Mon Feb 27 03:31:17 2006 +0000 Beefing up a test program commit c488ad774b32a9d8f22b6be15f2d383bef4d8143 Author: kent Date: Mon Feb 27 03:30:59 2006 +0000 Changing print to make single rather than double quotes. commit 7e0351bd428352313fc35eb0beea4c3991ee4f95 Author: hiram Date: Mon Feb 27 00:46:38 2006 +0000 chain and net for MonDom4 moved up one level commit 256603398f6bef7cd2cf6e65c6f09ad0f975604b Author: hiram Date: Mon Feb 27 00:46:11 2006 +0000 Adding chain and net MonDom4 to human browsers commit 4dc756efa7745a7ee9083a973b6479044602a2ab Author: hiram Date: Mon Feb 27 00:23:24 2006 +0000 Adding monDom4 pile up track commit 106bbf51bd00f34b9e0e9e211eabd4a953443752 Author: hiram Date: Mon Feb 27 00:22:26 2006 +0000 Remove incorrectly named file commit e97eed1b0028783f6a47d3a3b449418a8462544b Author: hiram Date: Mon Feb 27 00:22:04 2006 +0000 Adding hg18 and hg17 pile up tracks commit 534262b6efeea0880b2a7e678eea5a2b31595af3 Author: kent Date: Sun Feb 26 23:16:41 2006 +0000 Adding array.pop commit ce3c6627a4aaa03ccfc9c2d385b5783b9ea5a455 Author: markd Date: Sun Feb 26 20:06:10 2006 +0000 split algorithm portion of pslMap into a library module commit 735d4b6aec34e372e06a46dfb73e2f0cea87cda8 Author: kent Date: Sun Feb 26 19:26:25 2006 +0000 Generating code for doing += on dirs of numbers. commit 4b2667b83cc89ad6b748bf748115f885cdbdf80b Author: kent Date: Sun Feb 26 18:48:28 2006 +0000 Made fileReadAll work on http's. commit 0649f3a72535c0f1a96a4ded96b7f4e184232d14 Author: kate Date: Sun Feb 26 16:32:46 2006 +0000 Fix compiler warnings commit 0973b93c1de202a50470b9b59e9d8707af0b4838 Author: kate Date: Sun Feb 26 16:29:03 2006 +0000 First cut. Needs further testing commit 32beb917f40c4f00502913d081b399353f5317b3 Author: galt Date: Sun Feb 26 16:00:04 2006 +0000 "Encode release log update" commit a3e5a2d30a4ecb711d84ec2d934db9bbbfd0da9c Author: galt Date: Sun Feb 26 16:00:03 2006 +0000 "Release log update" commit c4ad6f879bda8ed8ccf3e7cda4eafeeac71f4f01 Author: kuhn Date: Sun Feb 26 15:06:09 2006 +0000 if-statement that checked file on the storeUnit was checking wrong filename, causing long run of 'du' more than once a day commit e6f5292508906a40e208335a4040c2e098758137 Author: kent Date: Sun Feb 26 03:17:30 2006 +0000 Expanding import test case. commit a91278033c4e98c4645d5ff7f8276b8e7ac8a7f6 Author: kent Date: Sun Feb 26 03:08:20 2006 +0000 Expanding import test case. commit c15af2617e66c493b1c49154b2cb674c42980e99 Author: kent Date: Sun Feb 26 03:04:01 2006 +0000 Cleaning up import module code a little and expanding test case. commit 1e01970732145cfa4f3b146f12d6d258a9769979 Author: kent Date: Sun Feb 26 02:36:21 2006 +0000 Getting imports of classes to work. (Still need to deal with things out of directory). commit 9717f52c2a6cb92d160f60df15807d1b75a7aeb4 Author: kent Date: Sat Feb 25 22:47:40 2006 +0000 Starting to get import and module.var usage of imported stuff to work. The simple test case in modules/import works. Still needs more testing. Doesn't handle modules in different directories. May be flaky about agreeing on names of member functions when things aren't compiled in the same order. commit ddb97810ce32b85a5a50c6e8407478cc4bf9e7f6 Author: kent Date: Sat Feb 25 18:28:50 2006 +0000 Giving each module a separate scope, and importing names into the scope on include. This is in preparation for the 'import' statement. commit 0925c1392707dde4674e45a9616160728632d25a Author: kent Date: Sat Feb 25 16:22:25 2006 +0000 Renaming strType and dyStrType to stringType and dyStringType, now that the splitting off of dyString from string is finished. commit 86f8706179ef3ea9e3eb7dfccd0938021bb113d6 Author: galt Date: Sat Feb 25 16:00:32 2006 +0000 "Encode release log update" commit e4b0415d35637038c06f3e83576a0cbf43fae2bb Author: galt Date: Sat Feb 25 16:00:31 2006 +0000 "Release log update" commit 4b513d106008e43bf12960fec65924e28c15d731 Author: fanhsu Date: Sat Feb 25 15:53:48 2006 +0000 Added liftOver for hg16 and hg17. commit 49495bf354ba1873346b9db2343e58bdd4271aac Author: kent Date: Sat Feb 25 12:06:11 2006 +0000 Some work towards a better module system. Fixed bug where strings declared outside of the main module would crash. commit c3ff1e549cb78c88eaf2df984506ac983d746fe6 Author: hiram Date: Sat Feb 25 06:37:13 2006 +0000 Do not use the align.unPlaced business with monDom4 commit cb9c8a2e8e64d9086091a9bce1d433dd5bf24651 Author: kate Date: Sat Feb 25 04:52:21 2006 +0000 Add maf gap annotation commit 31c1e1010cad139decd48f9f598a5527b9fb8539 Author: kent Date: Sat Feb 25 03:02:18 2006 +0000 Updating to use dyString where needed. commit 5dfd59169c6be48610c445a6e8843666b71145ce Author: kent Date: Sat Feb 25 02:58:17 2006 +0000 Made string objects immutable. Created a new type, dyString, that is mutable. You can now only do += on dyStrings, and use [] on the left hand of an assignment on dyStrings. commit a710ea42cc80ef08c702eeabb5a7d319f43ab1f4 Author: hiram Date: Sat Feb 25 00:50:24 2006 +0000 Had the monDom4 entry incorrect commit 36a7e10c2e8c61aed2e922c56b2ef4368f548acd Author: fanhsu Date: Sat Feb 25 00:45:21 2006 +0000 Fixed a bug. commit e9b2ca7615abca00be525b6f6ec40fbb65bd47ff Author: heather Date: Sat Feb 25 00:27:51 2006 +0000 use a hash for names, too commit bf494c55f52cf93986eda9c697646df1707482da Author: hiram Date: Sat Feb 25 00:19:56 2006 +0000 Slight change in the PileUp long label commit 20599feb1edb927bf04353e55e81091f7d7cfa6d Author: hiram Date: Sat Feb 25 00:18:38 2006 +0000 Adding a generic monDom4 pile up track commit 314f75ff642f608d03ea2a7988e34e557a536cda Author: hiram Date: Sat Feb 25 00:16:23 2006 +0000 Add a generic hg18 pile up track commit 70b781a28ba1bf0cf2d82977e231e06199ab5985 Author: hiram Date: Sat Feb 25 00:05:53 2006 +0000 Starting monDom4 commit 36a90b90a3f685264e0842472b5f3f6677459b43 Author: ann Date: Fri Feb 24 23:56:15 2006 +0000 moved dmBlastTab check into flyBase2004Id identifier commit 17c1bcb3ac12fda04d129e29bc04a7d698924324 Author: kent Date: Fri Feb 24 23:38:59 2006 +0000 Adding true and false synonyms for 1 and 0. Added ugly as synonym for print for debuggin. Renamed string.start/string.end to string.first/string.last since these are always nouns, not sometimes verbs. Added string.findLast. Made html module read files with no http headers. commit 5632ff2b372f30564ca0c617a06672babe2cf69c Author: hiram Date: Fri Feb 24 23:36:01 2006 +0000 Adding in the extra repeat masking commit 4f1f94b5846f3f1dbdaeebc85a00837903c6583c Author: hiram Date: Fri Feb 24 23:35:22 2006 +0000 A blank line at the end commit 241cfb940685ca2cef7dc73fa0667ab20762130b Author: hiram Date: Fri Feb 24 23:33:53 2006 +0000 STS markers done, all blastz runs done commit 5890e9cee2111d4b61fb4c6ba16c5c1431010be9 Author: hiram Date: Fri Feb 24 23:32:32 2006 +0000 Finishing off MonDom4 chain and net commit b5b04a8d766cf81c625628e346b30d23b5c7cad1 Author: hiram Date: Fri Feb 24 23:21:36 2006 +0000 Added lift over from Mm7 to Mm5 commit 6d6c2a97f9198f559c3b9e148d12997ff5789251 Author: kate Date: Fri Feb 24 22:25:21 2006 +0000 Slight corrections commit e612538faa2ae381ac0695c7a61a9ec9a5fbdfa7 Author: hiram Date: Fri Feb 24 22:05:40 2006 +0000 Was failing when a split table did not exist on all chroms, and cleaned up old constructs that could be dangerous commit fe926e6769b112d60cd36c91e1e2d9a2f64d524a Author: ann Date: Fri Feb 24 21:44:45 2006 +0000 Added first entries for hg18 commit ba54833615102ba69e0572cb624f987d53dcad7a Author: donnak Date: Fri Feb 24 21:21:34 2006 +0000 Added FAQ abt batch extraction of sequence. commit 93a8259af1773e0b48d49545e08719ed3c92641a Author: heather Date: Fri Feb 24 21:15:31 2006 +0000 100x faster to use a hash rather than select count(*) commit bf0d261ce3e2736abcb39318402f3b9409d8c783 Author: kate Date: Fri Feb 24 20:10:26 2006 +0000 Add conservation track description commit 212e2036833c6fc3fab19d8878f1a8aa9650fd6a Author: donnak Date: Fri Feb 24 20:06:04 2006 +0000 Added Fan's Known Genes pub. commit c147d5890949f3babaea8ed4d313731a972393b4 Author: hiram Date: Fri Feb 24 20:05:20 2006 +0000 Remember to do the last bits counted when available commit aea4ea5f1404206b6b41e0dc4901e77627b67407 Author: donnak Date: Fri Feb 24 19:49:12 2006 +0000 Added .2bit & .nib formats. commit 9a63a78a1852aeb91f76d7a0bf82a49f88fa832e Author: galt Date: Fri Feb 24 18:58:45 2006 +0000 increased max zoomout from 4 to 6 commit ac77a8cacdb62530a147fc32e911331d9427d15d Author: kate Date: Fri Feb 24 18:30:52 2006 +0000 Add frames to multiz. Remove older track commit 8279bfb408c3bf4fbcf4a6538cdb517a12d3bd0e Author: kent Date: Fri Feb 24 17:53:47 2006 +0000 Looks like the google and links examples work now. commit 2c2f6df02a524869ef51ef9c59f37e0f7e703d5b Author: angie Date: Fri Feb 24 17:51:27 2006 +0000 Added -noSelf option. commit 057dd4dae892bf838e714a565e67ba56563b398f Author: angie Date: Fri Feb 24 17:48:45 2006 +0000 Added dm2 hgNear/hgGene tables. commit 8a11ae6dcf495d0c922903edb00a021499464b70 Author: kate Date: Fri Feb 24 16:59:28 2006 +0000 Update 17way, add 2X nets commit 5a92663cf4b0667175aef57ede8c052864beb3d0 Author: kuhn Date: Fri Feb 24 16:38:33 2006 +0000 oops. forgot to set depth of du back to 4 after testing commit efbdf69a4498c4ed98690b6133fbac22dfc5ca08 Author: galt Date: Fri Feb 24 16:00:05 2006 +0000 "Encode release log update" commit 77d7ca6781bbe46f38538081a12859de8bfc9d66 Author: galt Date: Fri Feb 24 16:00:04 2006 +0000 "Release log update" commit 6744be0a0a1b4fe63ca66d8149b728c264bf9c21 Author: kent Date: Fri Feb 24 09:04:51 2006 +0000 Fixed a bug where selected member not being set commit 1c044194e6ceab36128b73ec7104771883cde9c3 Author: kent Date: Fri Feb 24 07:44:00 2006 +0000 Adding string.cgiEncode and string.cgiDecode. More work on html library. commit 706bc6845e16834de8eb0ee588dccca54d852b6b Author: kent Date: Fri Feb 24 06:13:33 2006 +0000 Implementing string.between and string.nextBetween. Fixing bug with var substitutions in literal strings when var is nil. commit 5d7685a8f0410bc6230b9bbc742b8e894d1f4e9a Author: kent Date: Fri Feb 24 05:07:31 2006 +0000 Put back in file.readAll. Corrected argument order in netHttpConnect call. commit 2dc49331cd075270b20ea78fb1e203ff7e997a36 Author: kent Date: Fri Feb 24 04:47:01 2006 +0000 Adding library functions file.flush, file.writeNow. Moving file.readAll to be fileReadAll and take a string. Added httpConnect function. commit 3b5c6146294e97aa15c4fb254012e636d977974a Author: galt Date: Fri Feb 24 03:35:22 2006 +0000 added note for next time commit 337a155c77a7ba9ab4972d28064fff4cf89be214 Author: kate Date: Fri Feb 24 01:20:45 2006 +0000 Darken wigMaf track green and blue bars when zoomed out farther than 200K, to reduce visual overload commit 6ce71be6d1a3664b7ef53a608a03e100d44a7fcb Author: fanhsu Date: Fri Feb 24 00:24:57 2006 +0000 Created KG.sh. commit 198a5beaf9ca89a17ea4b9683bc9d22ae09bff28 Author: kuhn Date: Fri Feb 24 00:02:48 2006 +0000 added filtering to remove upper directories if the immediate next biggest directory is a subdir of it. Also stopped the processing at files of 100 Mbytes to speed it up~/CVSqa commit fe0e62bbb01af534cbeb441b199d836f9acc6295 Author: fanhsu Date: Thu Feb 23 23:30:10 2006 +0000 Added Reactome tables. commit e42ca27592c1d7be010ce8bf2e533b220a57604f Author: angie Date: Thu Feb 23 20:50:36 2006 +0000 Updated 4.1 --> 4.2. commit b61139c1dd95dc16f8c0799cd60882004a2f7ce6 Author: fanhsu Date: Thu Feb 23 20:18:25 2006 +0000 Reset default GB position. commit c5749e179e758bf6347139c427ed1e2323faff98 Author: heather Date: Thu Feb 23 19:41:37 2006 +0000 increase size of hash commit 8cd4c31a0e286784e2fdda6c6220d60e0de566ae Author: fanhsu Date: Thu Feb 23 19:10:49 2006 +0000 Updated. commit 3194b9e04e1714c2a40b91095fe326400c4d5239 Author: fanhsu Date: Thu Feb 23 18:49:31 2006 +0000 Added ensGene track (with Build 37 label). commit 21b0d3ea21bb121975927029dec6a4d21c3a71a6 Author: angie Date: Thu Feb 23 18:48:50 2006 +0000 Added rn4, fixed typo ($strPur1 --> $strPur). commit 5ef252a6ef33dea197258329361ef6be3ab34d7d Author: fanhsu Date: Thu Feb 23 18:23:48 2006 +0000 Added protBlat track (default hide). commit f67a859fa3d35fa68bfcaae2e38503c2b4b18b58 Author: giardine Date: Thu Feb 23 17:50:16 2006 +0000 Added PAHdb as a variant source. This database has contributed 488 mutations to the track. commit 6c8ac861c4ff0f7ba71058e4c3561be18aa11418 Author: angie Date: Thu Feb 23 17:22:54 2006 +0000 Program to load a table given a .sql and tab-separated text file (to replace the usual sequence of hgsql commands, and also to add a comment to the history table). commit a93240666424ad9758196c9fb34231bea15a7493 Author: angie Date: Thu Feb 23 16:48:32 2006 +0000 Added rn4 to daily updates on hgwdev. commit 51b367bf83089b013806212b008c4a6952ee317e Author: kent Date: Thu Feb 23 16:47:34 2006 +0000 Adding library functions fileExists, fileRename, fileRemove, and test case for them. commit 7e256a4a5e84cf2da69098414289171352686087 Author: galt Date: Thu Feb 23 16:00:03 2006 +0000 "Encode release log update" commit b67109c5e6b7aa887401a6c9b8331e01c24aefdb Author: galt Date: Thu Feb 23 16:00:02 2006 +0000 "Release log update" commit cbf275617f6c5c5b4a2d6b7274bc92f5d449b912 Author: kent Date: Thu Feb 23 15:31:44 2006 +0000 Updating expected. commit 4267aa61372191a28bc830fed9a5f986503d03f3 Author: heather Date: Thu Feb 23 07:10:29 2006 +0000 save counts to log file commit 1531ce91080b4d69d01fe8f80195652ea3567719 Author: heather Date: Thu Feb 23 07:07:06 2006 +0000 remove some logging commit f4a239d870e81b342a5dd22972fad502eaf0e3d8 Author: heather Date: Thu Feb 23 07:03:10 2006 +0000 continue if count is 1! commit d349326544bcf6d29c56f7f574307e84eb9e1fd3 Author: heather Date: Thu Feb 23 07:00:44 2006 +0000 start the hash fairly large; need quotes in query commit 5e210ee225ef8a3e9ce8f7481b503efb50133be9 Author: heather Date: Thu Feb 23 06:43:11 2006 +0000 use a hash rather than select distinct commit 061036ecd831d8ad8d08660ff72d44af04943a49 Author: heather Date: Thu Feb 23 06:24:30 2006 +0000 eleventh step in dbSNP processing; check for multiple alignments commit 7492c455e12cad9e094027f6e1c585aa319837db Author: heather Date: Thu Feb 23 05:58:26 2006 +0000 add rs to writeToExceptionFile commit 12db9ed542751635e0141238f0b5cbfc02e8d102 Author: markd Date: Thu Feb 23 05:34:59 2006 +0000 added MGC fullLengthSynthetic description commit 117ec4235ed695f7630cfc92481364eeed33a46d Author: heather Date: Thu Feb 23 05:31:01 2006 +0000 use unknown string commit 84c010f808268cc2c01cef6e746a7c23b12b4adf Author: markd Date: Thu Feb 23 05:22:05 2006 +0000 added synthetic status type commit 49fc0bcff62854b86ecf25fbcb4f51aae33ad132 Author: fanhsu Date: Thu Feb 23 04:57:56 2006 +0000 Added 17-way multiz. commit 0321a3ed99c1459e7cc44d1f2f24f1a745fa2834 Author: heather Date: Thu Feb 23 04:51:26 2006 +0000 tweaks for snp125: remove source, add refUCSC commit 17d034d2347abf97f8236a7d9690fa40e49402ec Author: heather Date: Thu Feb 23 04:09:31 2006 +0000 add comment commit 604c34998384d27d19dab553b5aaf6ac3a0aa4e7 Author: heather Date: Thu Feb 23 02:39:34 2006 +0000 don't use enum (for now); limit other columns to match snp125 commit 1519afebbfac55aa32fb84d5127f01567b308503 Author: heather Date: Thu Feb 23 02:37:45 2006 +0000 prepend chr for exception file commit a729e9cbf0f130e1643674cc9eb5bf72b5cd24c4 Author: kent Date: Thu Feb 23 02:29:31 2006 +0000 Improved an error message that used to come across as internalErr. commit 720d2e1171aff3e53f803e26bdbfab62250b829d Author: heather Date: Thu Feb 23 02:29:15 2006 +0000 add exceptions commit 8d8f23518ea28e9e1d780ca62cee5b8e2dda0946 Author: kent Date: Thu Feb 23 02:27:18 2006 +0000 Polishing and testing. It actually looks like this will parse web pages well now. commit c58b174d0ddb76640ffdf6e8c8b25b4a03c9f6f7 Author: heather Date: Thu Feb 23 02:20:15 2006 +0000 add snpFinalTable commit 8ba9c1fc3587a1c30b53b5d1a3fa2573953b2d9c Author: kent Date: Thu Feb 23 02:01:54 2006 +0000 Making fileOpen handle URLs commit 94bec3104aa51a4c696451f4e0159ddb746ffb96 Author: angie Date: Thu Feb 23 01:50:57 2006 +0000 RefSeq includes dog now, so enable native refseq for canFam1 & canFam2. commit f5896b29e7b76364edd927a3cc153dde284d3891 Author: angie Date: Thu Feb 23 01:46:38 2006 +0000 Loaded Ensembl genes. commit 8e132d4406e21f12fd5a4ca113b5786622898d43 Author: baertsch Date: Thu Feb 23 01:41:31 2006 +0000 remove force index if we have the chainId - speed up mysql commit 021a07efc8ea964c2837e4984770717b046029c8 Author: heather Date: Thu Feb 23 01:30:06 2006 +0000 add locTypeStrings. Edit comments. commit 958f827cd4c682fd66e8fec54eb8cef18a6df635 Author: heather Date: Thu Feb 23 01:10:00 2006 +0000 transform chrN_snpTmp to chrN_snp125 commit d80e67b9731ba2f5bc92379f9318cdefc3b4f8af Author: kent Date: Thu Feb 23 01:05:22 2006 +0000 Added string.same library function. commit 2a74b9edcc1aac5780e2e6497cd4fa703dadbeff Author: heather Date: Thu Feb 23 01:05:01 2006 +0000 print string instead of num commit 2a6e3a9a7fb1932b01272d11589ed0adc6ffdc86 Author: kent Date: Thu Feb 23 01:02:18 2006 +0000 Fixing error reporting for unclosed quotes. commit 4493f99e2386c2a4cc14374395c482c5824f47d7 Author: heather Date: Thu Feb 23 00:50:42 2006 +0000 get rid of extra spaces commit 69eaa4b6b3c8775c620e0e2f6f742f398d1185a9 Author: kent Date: Thu Feb 23 00:49:38 2006 +0000 It seems to be parsing the html page, but needs more testing to be sure. commit c0b9d79ffa32d753994e34825b3a0572998adef8 Author: hiram Date: Thu Feb 23 00:44:28 2006 +0000 BACENDs done, and many pair-wise alignments commit 073c25895984ae09ef8dddb5846887b8fd115d22 Author: fanhsu Date: Thu Feb 23 00:18:52 2006 +0000 Updated fly section. commit a69844d3256d4f1573a7cd3bc4f8652e37acdcc1 Author: kuhn Date: Wed Feb 22 23:51:06 2006 +0000 added strPur1 commit 0ab88d47e6e1bc5f72c469a71e7b410704eed152 Author: heather Date: Wed Feb 22 23:37:42 2006 +0000 use enum for strand. drop source. commit faf27c3485cd293ef4a9147c1ee7d1a4adbb5763 Author: heather Date: Wed Feb 22 23:35:26 2006 +0000 drop source. use enum for strand. adjust table create custom function commit dc17f6285bf3218aea87ba659bd23dd0258b3551 Author: heather Date: Wed Feb 22 23:26:41 2006 +0000 observed is simple string, don't need source commit 86d044cabb892b6175fd4652887840c4d0e1b0f6 Author: heather Date: Wed Feb 22 23:24:39 2006 +0000 tweaks commit fb88fe144cba66beb9d096e168a8635c3e9fd919 Author: hartera Date: Wed Feb 22 23:15:04 2006 +0000 Added multiz 5-way maf file downloadables. commit 94ed863039ee839af28f32c05c60d6caa7df96d0 Author: hiram Date: Wed Feb 22 23:06:01 2006 +0000 Adding rheMac2 commit e2952536a74f92151b9f79eb1e254551385abe96 Author: aamp Date: Wed Feb 22 22:51:14 2006 +0000 Fixed bug on hg17 proteins track. Made assembly-level trackDb entry to fix. commit 81963ca60bb316b1e06d08fd2b667351269bcf45 Author: angie Date: Wed Feb 22 22:48:42 2006 +0000 Updated gene annotations to 4.2. commit 8c00fe149d62c34f705b0689540c6df2014f92a4 Author: kent Date: Wed Feb 22 22:45:04 2006 +0000 Looks like it's parsing out tags fine now. commit e1e3f8b2187d6845291d8f46c7b0532eaaf7091f Author: hartera Date: Wed Feb 22 22:31:43 2006 +0000 Removed duplicate copy of Conservation track entry. Added speciesCodonDefault to remaining Conservation track entry. commit 1292ee3c0fe946c7c5fa1ca5c938fe768f3458e1 Author: kent Date: Wed Feb 22 22:31:19 2006 +0000 Adding a couple more string library functions: leadingSpaces and betweenQuotes commit 1083ea02f65df370e83069b13608707d71788d6b Author: jen Date: Wed Feb 22 20:53:59 2006 +0000 Changed DanRer3_5way.jpg to danRer3_5way.jpg. commit f6fa0f35db6a746968680acaefc74d4253378027 Author: kent Date: Wed Feb 22 20:04:21 2006 +0000 Did a better fix than the last one to cCoder.c. The html.pf is working as far as it is implemented now. commit d8218da4615f5df40d780f9405a0c7411db14b54 Author: jen Date: Wed Feb 22 20:03:18 2006 +0000 Removed 5-way from Conservation short/long label. commit e5dd63be22cfd2f0061c198b12e797a16e2e2369 Author: kent Date: Wed Feb 22 19:20:41 2006 +0000 Adding warn and isSpace built in functions. Fixing a bug in cCoder that manifested when there were empty dirs assigned to a member variable. Tinkering more on html library written in ParaFlow. commit 4626b0908c77a1d733711abcfa4f381228bc115e Author: fanhsu Date: Wed Feb 22 18:19:27 2006 +0000 Added mm7 chain and net and renamed short labels for mm8 chain and net. commit fa412a713fcabf273008b7af0e3e90b47b99eb4d Author: kate Date: Wed Feb 22 17:57:45 2006 +0000 17-way downloads commit 224f05bc0daecc0872e67d893fde2edfb828ea20 Author: braney Date: Wed Feb 22 16:42:59 2006 +0000 a too short description of what this directory is doing here commit aef7f131d3e21b9416b09d42640901685dd74c99 Author: fanhsu Date: Wed Feb 22 16:08:35 2006 +0000 Added a bunch of tracks. commit 5ba7e02b0c12d55a5482892b06404f4930978846 Author: galt Date: Wed Feb 22 16:00:05 2006 +0000 "Encode release log update" commit a6f3786a9a80722bd33d91da6ea448ce84fca4cd Author: galt Date: Wed Feb 22 16:00:03 2006 +0000 "Release log update" commit b0f646fbb124fbfde147022a2d0e4e1ed8cdd7d5 Author: fanhsu Date: Wed Feb 22 15:51:37 2006 +0000 Added wgRna track. commit 9141d847abb1f2d8c16167f65a4bc2829046f829 Author: fanhsu Date: Wed Feb 22 15:44:56 2006 +0000 Created wgRna.html for hg18. commit d7e6267f41c33521592c9b2f96d5248fd04aabd4 Author: donnak Date: Wed Feb 22 08:32:00 2006 +0000 Added several bits of info to this page & corrected a few typos. Some of the data in the Assembly details seciton was ripped off verbatim from the Baylor web page -- may want to rewrite. commit 991d1226ba8c68be001220d049f23536e4b4ef2d Author: kent Date: Wed Feb 22 08:03:11 2006 +0000 A little more work on string libraries and on html parser. commit ac0d8d4055893f3ab4d4b19292f39bf78d5f3ecf Author: donnak Date: Wed Feb 22 07:54:04 2006 +0000 Added strPur1 credits. commit 084fdd7a7541e2abab530c7b14b2a8a80f7b05c4 Author: donnak Date: Wed Feb 22 07:33:09 2006 +0000 Added strPur1 to release table. commit 6c1109d07cb9c2e4e6c6abd88e5eb83ba29e70fd Author: kent Date: Wed Feb 22 05:46:24 2006 +0000 Starting a html parser in ParaFlow. Adding some stuff to built-in string library. commit cc36ca66ecebf02565b4bfc7bc72cebf341559e2 Author: kent Date: Wed Feb 22 04:11:36 2006 +0000 Adding a few more string library functions and test cases. commit ca89e8105e40a2616ab6b2ecb3933608215a7b70 Author: kent Date: Wed Feb 22 03:55:46 2006 +0000 Adding a couple of string methods. commit 4f246eb74fc8b9311ddd9085de911f591b25d3be Author: kent Date: Wed Feb 22 03:54:31 2006 +0000 adding stringTest commit a5c119b7ebb4109191442ee336f8ff137e1a123b Author: heather Date: Wed Feb 22 03:43:52 2006 +0000 enable load commit 410cb941cb67c4460c1b55318fd997f07a43a68c Author: kent Date: Wed Feb 22 03:29:06 2006 +0000 Adding some file library functions. commit 17aae56d0502d83eef0cc5aa3c41e88161a4e5dd Author: heather Date: Wed Feb 22 03:28:09 2006 +0000 full pipeline commit 7bee862fb92144a017d945924198a7de86a91c56 Author: kent Date: Wed Feb 22 01:22:31 2006 +0000 Adding more to printFile test case. commit c49359485a6f34603007b997dce8c551a7393794 Author: hartera Date: Wed Feb 22 00:30:34 2006 +0000 Removed duplicate HGNEAR sections. commit 2026d893bb6757a999bc5e2eb055157b824ec216 Author: angie Date: Tue Feb 21 23:19:06 2006 +0000 Minimal table access control for hgTables' "All Tables" listing. commit 907a0a1f25427efe386df920fa44a31c723dd592 Author: angie Date: Tue Feb 21 23:18:16 2006 +0000 Added support for minimal table access control. When the group is "All Tables", if there is a table named tableAccessControl then its contents are used to determine whether each table is restricted, and if it is restricted then whether it is allowed on the current virtual host. This applies only for "All Tables" -- trackDb must be properly constructed in order to take care of the usual group/track/table case. commit c40fbdbfa7d15a5621242372df33530e03f8a52d Author: angie Date: Tue Feb 21 23:03:00 2006 +0000 Added a missing sqlFreeResult (no bug observed -- just for tidiness). commit 1869b796b85051046ecf0b89c574c75e2c0de69a Author: angie Date: Tue Feb 21 22:41:28 2006 +0000 Improved detection of empty input value in cgiOptionalInt -- skip leading spaces before checking. Also added spoof of SERVER_NAME variable to cgiFromCommandLine. commit 95f720d43cb09a7c8df924b771392cefb088e2ca Author: hiram Date: Tue Feb 21 22:09:01 2006 +0000 Show memory size error with commas in the numbers so we can see what it is commit dc828fa65e827a1d6a0c02ce7e73b88d91a354f5 Author: donnak Date: Tue Feb 21 21:41:45 2006 +0000 Added link to Graph Configuration Help reference. commit ab4b28fdd42835632e7b682c42513c58e036c587 Author: donnak Date: Tue Feb 21 21:27:44 2006 +0000 Added link to Graph Configuration Help reference. commit 8fde767d7f58c450902b1b04975a7d1380861a69 Author: jen Date: Tue Feb 21 19:14:59 2006 +0000 Updated danRer net/chains. commit a4087f5bfc0a2f8cd4328adff32b0c512f763dfb Author: jen Date: Tue Feb 21 18:45:29 2006 +0000 Updated danRer net/chains. commit af7c579b6d2421a270d8ea9dc52b6d908f1c321f Author: galt Date: Tue Feb 21 16:00:02 2006 +0000 "Encode release log update" commit 2c4816c10ffa87ece95feb5e2411f42231ddbf41 Author: galt Date: Tue Feb 21 16:00:01 2006 +0000 "Release log update" commit 8d4e78f1ac75b16dad6b88a7f7d877de4ed164d8 Author: kent Date: Tue Feb 21 11:37:34 2006 +0000 Little changes to get it to work on hgwdev. I had to conditionally take out part of the sort (the one where you pass a function pointer) because qsort_r is missing. I commented the test case for the sort out of the makefile. I also commented out the para2d test, which is hanging on hgwdev, though it's fine on the mac. commit 86b89a8fef07f912737ac79398bb99b981c1a811 Author: kent Date: Tue Feb 21 11:01:05 2006 +0000 Fixed chars. commit 8c5a8156cab42ffd31c16bf09955237df3ee05ce Author: kent Date: Tue Feb 21 10:56:36 2006 +0000 Adding expected output for a few test cases. commit 6e74bc5d301634753cc1df58fb3984048fd0908c Author: kent Date: Tue Feb 21 10:54:50 2006 +0000 Adding a quick general test case. commit e8ef6329d78546542bf9b50e89d1ffde049b5c4d Author: kent Date: Tue Feb 21 10:46:33 2006 +0000 Adding a quick general test case. commit 5eb18288f22a79836262e2acf797248bc7f9b379 Author: kent Date: Tue Feb 21 10:45:06 2006 +0000 Fixed case problem that's ok on the Mac. commit c82a6039fa7377f4bb0c44f080b70797b724fb9e Author: kent Date: Tue Feb 21 10:41:55 2006 +0000 Oops forgot to add this when I put in print.c commit 6f4fd104c3fa6cac765578fa176cbfc7b9fa98f3 Author: kent Date: Tue Feb 21 10:39:38 2006 +0000 Creating a char type as distinct from the byte type. Indexing a string yields a char. You can initialize a char (effiently) with a single character constant string. commit 8a9efb0185fbcac3b47b749fd909cbb09a54b14b Author: kent Date: Tue Feb 21 06:51:08 2006 +0000 Making para (el on x to y) filter work. commit 5146240f797e353440e327c0b0a4a1e8781ed8e7 Author: kent Date: Tue Feb 21 06:50:40 2006 +0000 Expanding test case for paraOnRange. commit cba89e50a2b955fd94fba43b0a7f8172f99266ec Author: heather Date: Tue Feb 21 05:52:17 2006 +0000 tenth step in dbSNP processing: get validation status and heterozygosity from SNP table commit f006c2f7827bfb75715cd65f94c7fbba84ff13b5 Author: hiram Date: Tue Feb 21 05:28:58 2006 +0000 Command line too long in doCat run as it constructs the pslParts files, change to find and xargs cat commit 396ed4aa794f4b8bb7ad71e3fc634355528c4e45 Author: kent Date: Tue Feb 21 05:09:47 2006 +0000 Makeing para (i in 1 to 10) get i*i work commit 4316ff6e7d91da504b0a0dd6637f443a86ef6e31 Author: kent Date: Tue Feb 21 04:03:25 2006 +0000 Implementing keys() method for directory collection. commit 5a61149f69ae9181333735dd82b873b7a6991749 Author: kent Date: Tue Feb 21 03:26:16 2006 +0000 Coding for(key:val in collection) varients. Seem to work for dir, array, and string commit 89698bc4951f69697b98fc57ace457f72505d555 Author: heather Date: Tue Feb 21 02:51:48 2006 +0000 ninth step in dbSNP processing; lookup function commit feb65c6b4041ff86064016a62e4f2c96c9be1636 Author: kent Date: Tue Feb 21 02:12:28 2006 +0000 Getting for (key:val in collection) past parser and type checker. Still dies on cCoder. commit 350ff1cff4a6e6ffd935d2e81ac3ccbc434dfbd4 Author: kent Date: Mon Feb 20 23:59:19 2006 +0000 Implimenting a bunch of missing _pf_xxx_dir_from_tuples. commit 86fac342a18a7d7363b63f06583631501492b7bf Author: hiram Date: Mon Feb 20 23:37:40 2006 +0000 Adding chains and nets for Mm8 and Hg18 commit 27bc17ae7141ae26744a0ade9ddd5cb171e6f301 Author: hiram Date: Mon Feb 20 23:37:10 2006 +0000 adding net mm8 commit d66da8e1ab784f637a2fff4c6296146a8a949a8d Author: hiram Date: Mon Feb 20 23:36:39 2006 +0000 html for net Hg18 and chain Mm8 commit 400d591e3480ba9f3f737ba988f67e1faccf74f0 Author: hiram Date: Mon Feb 20 23:35:35 2006 +0000 Adding chain and net Mm8, and net Hg18 commit 2482041a337a31c9d8fd50b41ef759732c83b23a Author: hiram Date: Mon Feb 20 23:31:05 2006 +0000 Adding chain and net tracks for Hg18, Mm8, Hg17 commit 849d7d3527e42e46d08f383efbbdb5101219d711 Author: kent Date: Mon Feb 20 22:27:02 2006 +0000 Adding support for 0b notation for binary numerical constants. commit 4d766d43dc3b94b8685234213e36fd302f13245f Author: heather Date: Mon Feb 20 22:24:56 2006 +0000 remove unused var commit 3062f25b2bde2165b7b055be8c01147d86c3309f Author: heather Date: Mon Feb 20 19:53:18 2006 +0000 handle duplicates commit 250e9ab72ff0de2bb688a41b34d01a120d004159 Author: kent Date: Mon Feb 20 19:40:54 2006 +0000 Adding test case for substituted strings. commit 3ae1a2f77ee9035f4a8b2b389fd32c1a5eef0ced Author: kent Date: Mon Feb 20 16:10:08 2006 +0000 Changed randNum to random to conform to docs. commit 9f9b37c94bf54b5df69e8c6f64bef355a5ecc855 Author: galt Date: Mon Feb 20 16:00:03 2006 +0000 "Encode release log update" commit fe5b6c2fb7c8c39d35bbd709afb6a3a6f7dd10f5 Author: galt Date: Mon Feb 20 16:00:01 2006 +0000 "Release log update" commit 85e0405be47890d581e720afb30c7468851bacab Author: kent Date: Mon Feb 20 15:52:09 2006 +0000 Adding examples, or at least a lot of the examples, from the book. commit 94107149e48640578dc916194197093e6947a4b5 Author: galt Date: Sun Feb 19 16:00:03 2006 +0000 "Encode release log update" commit 075d0be786c5868d57f8782583ddfc51a3f0268c Author: galt Date: Sun Feb 19 16:00:01 2006 +0000 "Release log update" commit 253449eded9c2f1600346f3da7411318c9c95588 Author: kate Date: Sun Feb 19 05:35:29 2006 +0000 mafSplitPos commit 3f5e2a5e00149298599114078f677d4363183ae3 Author: kent Date: Sun Feb 19 03:47:48 2006 +0000 Putting parent member into derived classes, mostly for the benifit of init, which must call parent's init if it exists. commit 4f80da3970a12e52daef2aa7bb0cb75c5f0d0306 Author: kent Date: Sun Feb 19 01:00:24 2006 +0000 Updating docs. commit 974c6649d162c5aaf7b045e92d5f09bb33be7ccd Author: kent Date: Sun Feb 19 00:59:10 2006 +0000 Avoiding cleaning up self when punting from member functions. commit 02a7e3403cb982bfd61b40130330d5fd427e67ba Author: kent Date: Sun Feb 19 00:39:35 2006 +0000 Fixed crash on unterminated quotes. commit 54286fd5d76e8becb3580a517b4fb6a9f27cb88b Author: kent Date: Sun Feb 19 00:31:15 2006 +0000 Making foreach just a varient of for. commit 04e66ebd892d32f2c36cd323016c7e9e4533899b Author: kent Date: Sun Feb 19 00:01:16 2006 +0000 Allowing catches with fewer parameters. commit cef82b6ff3080951ae79aee474fe4c98418979ad Author: kent Date: Sat Feb 18 23:23:17 2006 +0000 Fixing a bug or two in the try/punt/catch system. commit 2d85492c7856c3c08d0d926115ef2df3c56025c2 Author: galt Date: Sat Feb 18 23:07:30 2006 +0000 screenDir no longer needed commit 148622678348e25e9d4c7112b80516a386a1ebe7 Author: galt Date: Sat Feb 18 22:57:49 2006 +0000 san working, so get sizes on .jpg ok, restored commit bb91eb7429369f4827957b402b6438dcedeaddb0 Author: kent Date: Sat Feb 18 21:34:14 2006 +0000 Run time side of try/catch mechanism seems to be working, at least on a simple test case. commit be1a16531cb7509a0021d0c4768738c7a59a6666 Author: braney Date: Sat Feb 18 17:31:32 2006 +0000 another intermediate safety check-in commit ca8142d59a66ecb28cc948fe5969831116877ed0 Author: hiram Date: Sat Feb 18 17:29:40 2006 +0000 Bring the chain and net definitions up to this top level commit 2c9a8957ecd9c08829b9c08dab93c3802c2d867d Author: kate Date: Sat Feb 18 16:29:27 2006 +0000 Cleanup 17-way conservation section commit 9b9f0b4cc336547f67fb66ece233742cf7fe521d Author: fanhsu Date: Sat Feb 18 16:19:25 2006 +0000 Added hg18/rn4 pairwise. commit 51b186ef3dc31f2f70ca36dcc5557603f2285a36 Author: galt Date: Sat Feb 18 16:00:03 2006 +0000 "Encode release log update" commit fbddb96733e6b967fb181be93c33f4688d658cdc Author: galt Date: Sat Feb 18 16:00:02 2006 +0000 "Release log update" commit e49482842c758fbf75181c3a85724eba3655bf16 Author: hiram Date: Sat Feb 18 07:42:37 2006 +0000 Adding monDom4 and Mm8 commit b8eb731b42785e7829d5613f7c650a3381d4662e Author: kent Date: Sat Feb 18 06:41:28 2006 +0000 Working on try/catch some more. commit 45f708dd5b565882ca9fb4a37b994848033c0403 Author: kent Date: Sat Feb 18 04:53:58 2006 +0000 Parsing try/catch. commit 51a980991c28af47a3647c0fe706e3e9d043630c Author: kent Date: Sat Feb 18 02:02:57 2006 +0000 Another little stack dump improvement. commit 6be5ea58ef4b544386bde49e10ad32e5dbefc257 Author: kent Date: Sat Feb 18 02:00:55 2006 +0000 Fixing print (just broke it to improve stack dump.) commit bfa4d5e551e4cf87fb2cd5b7c0d0c1b9ede112b5 Author: kent Date: Sat Feb 18 01:56:42 2006 +0000 Improving stack dump. commit 85a14dc8490232803b6314f12cab1158f51d065c Author: kent Date: Sat Feb 18 01:40:47 2006 +0000 Improving stack dump commit bb4d6d46e7ac2b79ac9840254536978015b4d3f4 Author: kent Date: Sat Feb 18 01:17:52 2006 +0000 Moving local variables to all use _pf_l structure which is hooked into activation record. commit dc97f6f50084003e6b31e61c46593a5e1ed35d39 Author: heather Date: Sat Feb 18 01:14:11 2006 +0000 condense function; need to remove duplicates commit 75f522010de464044f29be1a318429bc0a045f7b Author: hiram Date: Sat Feb 18 00:41:49 2006 +0000 Hg18, Rn4, rheMac2, BacEnds, all proceeding commit 3902b34ef314826d51631c71db1155cee766f2ea Author: donnak Date: Sat Feb 18 00:32:20 2006 +0000 Added danRer3. commit 02930bd4e6e0488ee8fc505711413abb6600208c Author: galt Date: Sat Feb 18 00:28:15 2006 +0000 added an example of using cmdline parms commit bdd40812f5c5fbf35310db6304b8e76284354fd1 Author: galt Date: Sat Feb 18 00:18:56 2006 +0000 added fileName to error msgs to be more informative commit e293e5d532f0e52f826d2c5a41afac289adde175 Author: hiram Date: Sat Feb 18 00:08:34 2006 +0000 Adding mm8 to the build commit b167fd4bdf3bfca647f27d31fcfba5dbda1e8702 Author: hiram Date: Fri Feb 17 23:35:04 2006 +0000 Adding Hg18 chain and Net for Mm8 commit 0979c9d7e0559f4223143d8604c3f6f7710621da Author: heather Date: Fri Feb 17 23:01:41 2006 +0000 filter ContigLocusId table based on group_term. Can be added to snpContigLocFilter. commit 59e91bb67c0bf06560483c6d617f03a028b4aa6a Author: heather Date: Fri Feb 17 21:58:36 2006 +0000 not using error and exception files commit 59f4c193f71761d703f974bb7a4fcd93d1fa5500 Author: heather Date: Fri Feb 17 21:36:39 2006 +0000 retain ctg_id commit f547a287cb7e652c7ddad1f4eab75b3e886e8ba6 Author: heather Date: Fri Feb 17 21:12:41 2006 +0000 retain ctg_id commit d294735689812820d511de4fb2921a10f56fe448 Author: kent Date: Fri Feb 17 21:06:23 2006 +0000 Fixing crash bug in for call with multiple vars in init statment. commit ca17907b664a84bd7aacf89ca4a166b6a841b354 Author: kent Date: Fri Feb 17 21:04:49 2006 +0000 Adding test case. commit 19a37e627343c28c366efc4a08306addf1c7b500 Author: heather Date: Fri Feb 17 20:54:50 2006 +0000 filter on contig_end != in ContigInfo; change atoi to sqlUnsigned commit 3b986d0972fb07f8e4bcdf7e5954678f451a7c20 Author: heather Date: Fri Feb 17 20:52:38 2006 +0000 cloned from snpSplitSimple.c commit 602c757b8c7e7f1b845d1c859f42d1df79bb53a3 Author: heather Date: Fri Feb 17 20:47:03 2006 +0000 retain ctg_id; change atoi to sqlUnsigned commit d561359aae6ca64ff44f9bd72e551523b1b7195f Author: kent Date: Fri Feb 17 20:30:08 2006 +0000 Adding words() and tokens() to string library. Making word mean space-delimited, token mean punctuation/word delimited. Prohibiting foreach constructs that have a tuple for an element, and then fixing bug in foreach (el in call()) functionality. Renaming activate module to ctar and checking it in. commit 02aec3b10925f628157e61270e438869e35ec2e9 Author: heather Date: Fri Feb 17 20:22:14 2006 +0000 filter on contig_end != in ContigInfo commit 96b3b881370218370c75d674175d8b658768286e Author: hiram Date: Fri Feb 17 20:20:43 2006 +0000 Adding chr22PileUp graph commit 76ca679a83a0e1250495a5ee20d5de225edac1ce Author: hiram Date: Fri Feb 17 19:47:11 2006 +0000 Should probably do the chrom size check properly ... commit ad31e45df5f9c82b282ea2b105e709b93e7978c6 Author: hiram Date: Fri Feb 17 19:30:26 2006 +0000 Handle error where incorrect database gives chrom sizes less than the bed coordinates commit eb5fcecd04e2859263607c9e28dd97aa8d7200bf Author: fanhsu Date: Fri Feb 17 17:55:01 2006 +0000 Updated hgncXref table. commit fe80ed5895f8bc3ab43c05a538172ae4ec96fae6 Author: fanhsu Date: Fri Feb 17 17:40:35 2006 +0000 Updated to pick up RefSeq IDs in refSeqMapped field of HGNC DB. commit 9e1c5c18fff9ed399047d3c14143829d1e46c16e Author: galt Date: Fri Feb 17 16:00:03 2006 +0000 "Encode release log update" commit d7faf90e2d5de4db8d8f4a269ebff6ba206d77a6 Author: galt Date: Fri Feb 17 16:00:01 2006 +0000 "Release log update" commit e2fc44021d97b1b8015887c00329a3372af1f04f Author: giardine Date: Fri Feb 17 15:25:20 2006 +0000 Changed sql for checking to see if OMIM is available for RefSeq Gene labels to a faster method using limit. commit 9f91c19532cc532dc7b78376307c11ef69b61097 Author: giardine Date: Fri Feb 17 15:23:23 2006 +0000 Changed sql for checking to see if OMIM is available to a faster method using limit. commit 6b9c4d080c522450153681429f102f1c8333da07 Author: galt Date: Fri Feb 17 09:08:20 2006 +0000 created visiGene loader for ABA Allen Brain Atlas data commit 269215d5a0bf281840e055d5d959f272047aaab8 Author: kent Date: Fri Feb 17 05:33:40 2006 +0000 Test case with a somewhat interesting stack dump when it hits an error. commit 6be2984220942ea2282fc1c89093b20da8b8c7db Author: kent Date: Fri Feb 17 05:05:31 2006 +0000 Looks like the fixed part of the run-time activation record is in place. commit 0ba06a41dfad4a8bc2aa8bf34680cd240a380382 Author: fanhsu Date: Fri Feb 17 05:03:58 2006 +0000 Added BioCyc tables. commit 2e43dd3c566983e4b8e7800eb679af5ab3d71eb5 Author: hartera Date: Fri Feb 17 03:08:17 2006 +0000 Removed the TIGR Gene Index track as an option in the genePredDropDown function. commit 2ddc31fe5f936fc9498cdb07723e26cadde49d36 Author: kent Date: Fri Feb 17 02:19:41 2006 +0000 Created compile-time activation record (ctar) and starting to use it to create structures for run-time activation records. commit c997e38c503a6917edb6f6be27f8f8299a161731 Author: aamp Date: Fri Feb 17 01:34:24 2006 +0000 Got rid of the repeatScout track for now. commit 93cbc4b9fc51d29e5176e1c791390c5ea7b85881 Author: braney Date: Fri Feb 17 01:15:00 2006 +0000 fiddle with names, do cheesy invers commit eb4bd72260f1321f61b73e1e85264b73d38865da Author: braney Date: Fri Feb 17 01:13:42 2006 +0000 seems to work most of the time now commit ced4e81b8d3e6cc9eca65436d7b4001ae63eff02 Author: braney Date: Fri Feb 17 01:13:10 2006 +0000 a few new functions, bigger arrays commit 00e7c62c401cfc35ed9a5bbb5449c1fe671ac8dc Author: braney Date: Fri Feb 17 01:11:53 2006 +0000 more stuff in elements commit 2831c1c11a2e459babca9e98c043c5fcc9ce0a94 Author: braney Date: Fri Feb 17 01:11:29 2006 +0000 reverse those flipped elements commit 47bc7c457893ec32e6acdc22dd43cafa8e0f9389 Author: braney Date: Fri Feb 17 01:10:58 2006 +0000 use arbitrary element namtes commit 0dfd67575252d5981f37a255c16e78816137f966 Author: fanhsu Date: Fri Feb 17 00:52:52 2006 +0000 Created bioCycGenes.sql for genes table used during BioCyc build. commit 59d1c5076787184cffe2124be83a366422d917f0 Author: fanhsu Date: Fri Feb 17 00:52:18 2006 +0000 Created pathways table for BioCyc build. commit f192f94e0bd38043c9d97d27a39c88baec29b418 Author: heather Date: Fri Feb 17 00:48:21 2006 +0000 retain ctg_id; filter on contig_end != 0 in ContigInfo commit 0c6d5acef7ee29fa7dea50bb18b66282b33f9781 Author: heather Date: Fri Feb 17 00:40:02 2006 +0000 add comment commit 3342e714eccee0961b61f5fe170cbca37e98c487 Author: fanhsu Date: Fri Feb 17 00:36:54 2006 +0000 Created kgBioCyc0.c to process raw data file downloaded from BioCyc. commit d51f53231c1d25540c4b953788fb0ddc5ee2cd3b Author: fanhsu Date: Fri Feb 17 00:36:16 2006 +0000 Created makefile. commit a0d2c1629b76148040fab2ab59c54396c9e77394 Author: heather Date: Fri Feb 17 00:34:42 2006 +0000 filter on contig_end != 0; drop ngbr; add ctg_id; chromName is col 3 commit e55bb7451cb2b324f9095a7b2752c89dbda3e164 Author: heather Date: Fri Feb 17 00:24:44 2006 +0000 put chromName in column 3 commit a773334ed25e481edd6aeebc409ac8b0f97a9808 Author: hiram Date: Fri Feb 17 00:02:40 2006 +0000 Done with CPG Islands commit 56d3917b049f63f11f9a321e7bdcf6eae67bc5ce Author: heather Date: Thu Feb 16 23:58:18 2006 +0000 check contig_end, use sqlUnsigned, change verbose to errAbort, drop ngbr commit b0f8466f9e6edb10d623029848defd18a8687449 Author: braney Date: Thu Feb 16 23:43:45 2006 +0000 more intermediat thrashin commit 2194bb7bd9bbc5c2c72c70178c00109a6df0f7e1 Author: aamp Date: Thu Feb 16 23:36:21 2006 +0000 Wrapping things up. commit ffad1d4a1a9f94d5c6cdfb187839457dfe2d66b5 Author: heather Date: Thu Feb 16 23:34:31 2006 +0000 fix comment commit 37c28b97d9577fabc721004f15c08814cdd36f2e Author: heather Date: Thu Feb 16 23:32:28 2006 +0000 add SingleClassRangeLocType, SingleClassWrongObserved(Positive,Negative)Strand commit a56f4061a589db6ab53dc0ca676c9fc327c6edc6 Author: donnak Date: Thu Feb 16 23:31:19 2006 +0000 Minor edit. commit 2598e13ca39df87a0e52f8970e6d137da7fc846c Author: donnak Date: Thu Feb 16 23:26:46 2006 +0000 Extensively edited Display Configuration section. commit 6cb8a6bfcb11589b2833606629285775448b9e5c Author: kent Date: Thu Feb 16 23:02:10 2006 +0000 Making last ; before } optional. commit 46c4bf1b04125af3a17ae9711fe2ea026f511869 Author: kent Date: Thu Feb 16 22:19:32 2006 +0000 Switching errAborts to _pf_run_err in runtime system. commit cb71fe102d4b09a55442c003e3a8a6de71918be2 Author: kent Date: Thu Feb 16 22:15:59 2006 +0000 Saving embryonic activation records with functions. Doing basic stack dump on run-time-error. commit 8b063633b7394be7dd478be369fbcef740218bfd Author: kent Date: Thu Feb 16 21:33:09 2006 +0000 Defining activation record data structures and cleaning out some old ifdefed out code. commit 6ca99c41d2b77a5d08e8e1dbe2f7fdda3c0098a7 Author: kent Date: Thu Feb 16 20:25:00 2006 +0000 Fixed a little bug when you have a method parameter that is the same name as a field in a parent class. commit 22064549eee1b9624f08d75b8017d43f62b9a992 Author: kent Date: Thu Feb 16 19:59:48 2006 +0000 Making named values work in class initializations. Basically there, but will try a little refactoring shortly to reduce code size. commit d7acafc37dadd6e6dfed79158da10d5eceda638f Author: kuhn Date: Thu Feb 16 19:53:39 2006 +0000 added ctgPos to tableIgnored for all dbs commit 47cf2a353f0887d3211e19dc82c264ae2139a195 Author: baertsch Date: Thu Feb 16 19:24:10 2006 +0000 updated DONE and dates commit 4328cbfc1816bfe584371d827c5656c00eb18d09 Author: kent Date: Thu Feb 16 19:03:07 2006 +0000 Enabling named fields in inits of classes with init methods. Fixing bug where type mismatch in default parameters wasn't caught. commit f48f533f39db26d3ded5a69d42a30eba6635ff4f Author: angie Date: Thu Feb 16 18:26:25 2006 +0000 addKnownGeneItems was not filling in pos->browserName, resulting in empty/"(null)" items in hgFind.matches CGI var. commit 06e468f650f2286707f3d06aa4d52f8d17c522af Author: donnak Date: Thu Feb 16 18:11:22 2006 +0000 Fixed broken link. commit e275acdfcca1c4ea1ba6db2d5446373f42275be9 Author: fanhsu Date: Thu Feb 16 17:49:35 2006 +0000 Added KG search indice. commit 19607978120d5d2df1476a8f6a7fb2c292a5dce8 Author: donnak Date: Thu Feb 16 17:36:52 2006 +0000 Added more names to danRer3 credits. commit f6e4592e3167644f302143c864102f091928bcd8 Author: angie Date: Thu Feb 16 16:38:53 2006 +0000 Cover a corner case: search term ends in ; which we use as a separator for multiple search terms. commit 897681e2ee6728d487b925d8e840ee0dcef9d5f1 Author: galt Date: Thu Feb 16 16:00:02 2006 +0000 "Encode release log update" commit af5ffc05f1cfadb447f12bcbae3430d9b70f9825 Author: galt Date: Thu Feb 16 16:00:01 2006 +0000 "Release log update" commit fa0e7605231cc4cc847cb2dce6f3ddf67e986537 Author: kent Date: Thu Feb 16 14:13:42 2006 +0000 Flagging duplicate named parameters. commit 358acd041b8a82dde607478d26bd111ba331a0a0 Author: kent Date: Thu Feb 16 14:01:42 2006 +0000 Allowing name:val parameters to functions. Most of the code should work for name:val initialization of classes, but it's not hooked into there yet. commit 7c9fd6ac4b1d1b5c41b2fa76a6d3eed986f8fce3 Author: kent Date: Thu Feb 16 11:58:46 2006 +0000 Making it so that the key in a key : val pair does not need to be quoted (but must be a simple name or string) in preparation for allowing named parameters. commit e68023ddaedbe71e368f13338ca9ab0caca4f37d Author: kent Date: Thu Feb 16 10:18:57 2006 +0000 Running defaults before init of classes. commit 0d9a8f55f4ecac3284eb38fccf4641b98dc57923 Author: donnak Date: Thu Feb 16 08:02:26 2006 +0000 Archived news item. commit bde7936909f861812db475f2ed7e2f150b9e0b6a Author: donnak Date: Thu Feb 16 08:01:31 2006 +0000 Added danRer3 announcement. commit 2596c5e7cc471da9d08bfd2403543c7b29253f4b Author: kent Date: Thu Feb 16 07:36:17 2006 +0000 Starting to make init method act as constructor. It is working pretty well, but the class is totally zero when it hits init, while I'm thinking it should arrive in init with the default fields if any initialized. commit 4c06029bb470a52fac0c92c98782b44353320405 Author: donnak Date: Thu Feb 16 07:34:02 2006 +0000 Edited danRer3 credits. commit a772988ae01caf3048c685585ffb1952c1d88bdc Author: braney Date: Thu Feb 16 02:17:03 2006 +0000 add a little error message rather than just crashin (what a concept) commit 1e94a9f2eda19e3339509750ea94e72137d26edf Author: kate Date: Thu Feb 16 01:42:30 2006 +0000 Successful multiz run with autoMZ commit d09c4bb2d751a0f7a07062fcce325b3001680296 Author: hiram Date: Thu Feb 16 01:12:09 2006 +0000 Completed second pass at extra Repeat Masking, also completed Hg18 chains and nets commit 1ef83852f052c13498a0f1a17131a8b150d5abb9 Author: kuhn Date: Thu Feb 16 01:12:01 2006 +0000 for some reason, it was giving 'exit 1' even when it was working fine commit 13a88b5dc32bfef7437afa1a8fff735a5815c65f Author: kate Date: Thu Feb 16 00:40:24 2006 +0000 Add V11 multiz cons track commit 98e569fa10029cfeb104adc63f4573b655ca3bed Author: kent Date: Wed Feb 15 23:44:28 2006 +0000 Adding shortcut to quick test. commit 247e466c06dcb9d13f033d5af7910b206f7fb368 Author: kent Date: Wed Feb 15 23:43:00 2006 +0000 Adding quick test. commit 611a90bb116247b7df266d9069b93c16975234a1 Author: fanhsu Date: Wed Feb 15 23:31:45 2006 +0000 Added otherOrgs.ra. commit 897004da127e9007d25abf52f045b00f19e0ca1b Author: hiram Date: Wed Feb 15 23:27:07 2006 +0000 Turn on hg18 net track to show something of interest commit c6820bfceaa436fd18a62c13d22263f829d3ee56 Author: hartera Date: Wed Feb 15 23:20:11 2006 +0000 Removed genomic codon coloring option for TIGR gene index tracks. commit 357351ef1035630a720ec31cc486d039cfd238ee Author: fanhsu Date: Wed Feb 15 22:56:43 2006 +0000 Added 1 line. commit b6ecd9a9c0806111276456214b81cdcf1cc5d73e Author: hartera Date: Wed Feb 15 22:07:09 2006 +0000 Changed test for other database in genericChainClick and genericNetClick to just check for database being set to active in dbDb. commit 7d7e038d4c5324c1ca83cec7479cd325ddd1a9e7 Author: baertsch Date: Wed Feb 15 22:03:18 2006 +0000 fix primary key in ctgPos table and reload data update docs for agp names commit 66181cb5e529fb96ee2b4edb05791dc38875e29e Author: angie Date: Wed Feb 15 21:53:43 2006 +0000 In getChromInfo, don't pass an input string to safef as its format argument -- use format "%s" because the input string could have % in it (those crazy users)!. There may be other places where this applies... commit c98b4cc83f5a2b1badcf03e3e48bbf8a75bdba5b Author: daryl Date: Wed Feb 15 21:38:50 2006 +0000 making hapmapLd track more robust commit 2d981f12fe2b6e84f29b510941c935036f4e93b6 Author: heather Date: Wed Feb 15 21:37:26 2006 +0000 rename SingleClass exception; skip deletion observed strings with multiple forward slash commit ead74898b9212d67b94322a3c280664a9020e086 Author: daryl Date: Wed Feb 15 21:36:02 2006 +0000 update population descriptions for hapmapLd tracks commit 6d7809ef5056fa7d812a3c954171af5de65beaf3 Author: kate Date: Wed Feb 15 21:35:16 2006 +0000 Rename first version of 17way track in preparation for replacing it commit 3855d1d5012049ec1c64aaaef41764e5770c3cd8 Author: heather Date: Wed Feb 15 21:23:31 2006 +0000 check that observed string for in-del doesn't have multiple forward slash commit 3e218280e0b6a0fdd4d4a3c32ae86ba2ec3471aa Author: heather Date: Wed Feb 15 21:17:27 2006 +0000 extend comment commit 40378882eb6d21fb692480d5ffe3497401030d99 Author: kent Date: Wed Feb 15 21:16:13 2006 +0000 Renaming runtime/string.h to pfString.h to avoid conflict with standard string.h in Xcode (Mac IDE) commit fcd479867669dbec70e34d8bff503f081eb6fb2c Author: heather Date: Wed Feb 15 21:05:30 2006 +0000 cleanup based on code review commit 5b281bed1366290556083f531c57c881adfbceba Author: hiram Date: Wed Feb 15 20:22:18 2006 +0000 Adding Hg18 chain and net commit 2e56749eb4e358a366c94e2d36a66e8564f4ff24 Author: kuhn Date: Wed Feb 15 20:07:11 2006 +0000 cleaned up output in case where a database does not exist yet on RR commit bb0526227ecf052602c9b0416669354d648d5092 Author: hartera Date: Wed Feb 15 20:05:55 2006 +0000 Minor edits. Added method for TIGR Genes track. Radiation Hybrid map track in progress using updated data. Obtained protein sequences for hgNear blastp tables and created these blastp tables of homologs for other species for the Ensembl Genes (Known Genes) track details page. Ensembl Known Genes track in progress - added otherOrgs.ra for zebrafish. commit f0000e538c676e814a52db02a9c90f6255d6eca5 Author: kuhn Date: Wed Feb 15 19:51:43 2006 +0000 format tweak commit 04ea63c1534fe1ce0f24e8f9f9edd12dbcebb4f6 Author: fanhsu Date: Wed Feb 15 18:37:08 2006 +0000 Added recombRate tracke. commit 8b1d45b54a3e1273183517833b25150087f4c076 Author: fanhsu Date: Wed Feb 15 17:42:43 2006 +0000 Added the hg18 GS build process. commit 81d5309faf6cf3cb2dd28c3ae515ccb10a7670ae Author: fanhsu Date: Wed Feb 15 16:46:00 2006 +0000 Created description.html. commit 7d5a13dbc971174b975769299030e1e317f98d73 Author: galt Date: Wed Feb 15 16:00:02 2006 +0000 "Encode release log update" commit e093c1a8ec19e58f7f9a0b951f2d138d3c94cd2f Author: galt Date: Wed Feb 15 16:00:01 2006 +0000 "Release log update" commit 4e4752b391322600aba69f938a0c76f2a68d2962 Author: fanhsu Date: Wed Feb 15 13:45:25 2006 +0000 Updated wgRNA track data. commit 85df7fe1f2133151b3a324addae2e0dbea7cc5a1 Author: kent Date: Wed Feb 15 11:18:26 2006 +0000 Fixing several bugs with nested classes. There is still one left with the test case fixes/nestedMethod.pf commit c7f52eb44f822a56c2ffd0988188abf16429d619 Author: kent Date: Wed Feb 15 11:11:33 2006 +0000 Adding a test case for classes declared in other classes and classes declared in functions. commit cabab7ab6d6261816394154a12d4ebced5f7a430 Author: kent Date: Wed Feb 15 08:41:52 2006 +0000 Simplifying code generator, and slightly complicating an aspect of type-checker to deal with change in parse tree that pptDot always has just two children. commit 7417d399ae51b269b8f9915cebd5e583cb708122 Author: kent Date: Wed Feb 15 07:58:38 2006 +0000 Combining [] () and . into same function to fix precedence problem for array[ix].field constructs. commit 1a7b830d1d9a7fa049f76b749a6daba40fc4d6ad Author: kent Date: Wed Feb 15 07:54:54 2006 +0000 Updating docs on operations commit d3c385d340bee036a2db984bec21040c41bbcca7 Author: kent Date: Wed Feb 15 07:53:51 2006 +0000 Putting arrayDot test case into auto-tests now that it's fixed. commit 502da67c05eb8776d939918b25bb4d6d53a2c583 Author: galt Date: Wed Feb 15 07:11:33 2006 +0000 using new version of vgPrepImage to make Allen Brain tiles and thumbs and full-for-download commit 7745ce21c0d5144d979471a70e28a49b746042fd Author: kent Date: Wed Feb 15 03:53:24 2006 +0000 Simplifying parser a bit. Still need to rework precedence of () [] and . to fix test case in fixes/arrayDot.pf commit ab68aed795c12eaf79fc98b5f2c8aaf95471c383 Author: kate Date: Wed Feb 15 01:58:36 2006 +0000 Fix to rheMac2 entries commit cc71f2c06cde18565a5d72f546d9d28c24497ead Author: kate Date: Wed Feb 15 01:49:34 2006 +0000 Add new monnkey chains/nets commit e1c94b4e9ef5bf14558819171c8364fe3c034d44 Author: kuhn Date: Wed Feb 15 00:35:39 2006 +0000 dropped output line that repeats names of files commit 27f7d07e1331118eac78f96d68607d8bf026de90 Author: daryl Date: Wed Feb 15 00:33:04 2006 +0000 removed number of populations as it is different between the assemblies commit 2f552630f904d8c8ab519b3045fb798fd93de229 Author: hiram Date: Wed Feb 15 00:26:01 2006 +0000 Simple Repeats done, RM run underway commit 139dd56c69f57a7397dacda2b6330bc874829e21 Author: hartera Date: Tue Feb 14 23:45:33 2006 +0000 Added irows and frames for 5-Way Conservation track. commit 650ef101bdef9da37cbf1637ab77a49d9a76804f Author: daryl Date: Tue Feb 14 22:41:48 2006 +0000 adding assembly-specific support for hapmapLd track: different data versions and different populations for the assemblies commit 2905b543a9cdfb3c48239db7dad896664467af16 Author: daryl Date: Tue Feb 14 22:37:38 2006 +0000 adding table checks for the hapmap ld track -- different tables are present on different assemblies commit e795f1bc9e8d5759233febd937edd3d55ef2f0e7 Author: daryl Date: Tue Feb 14 22:22:59 2006 +0000 moved to assemly specific directory commit 8f1d09fee3e5aec315b03c77604696dfb86f7d07 Author: hiram Date: Tue Feb 14 21:56:45 2006 +0000 Adding mm8 to the build commit a6c5286e86f7ef8605c9154fd3505db6253a9234 Author: hiram Date: Tue Feb 14 21:56:00 2006 +0000 Initial contents commit fd2b90f6e0c43d7e8f9408904ec2cf4daed5489b Author: kent Date: Tue Feb 14 21:54:23 2006 +0000 Fixing maxIntron bug commit 68132a8c637af55edcc19e5eeefe99f1bfbb271e Author: kuhn Date: Tue Feb 14 21:54:20 2006 +0000 added specific gap details for this assembly commit 12860457f340177db913b35f3938e8e6c3774a38 Author: kent Date: Tue Feb 14 21:52:07 2006 +0000 Documenting recent fix. commit 9f10d3f85859d133bda0d40c92adeb16ac42be81 Author: kent Date: Tue Feb 14 21:51:45 2006 +0000 Adding test case for maxIntron commit 9b9e8c30c7e7ad1c2820092bfff690aa1d5a0d98 Author: hartera Date: Tue Feb 14 21:45:18 2006 +0000 Added rcsid. commit 96fa38e52ef610b52a76dcccb009c0ccfc064f2a Author: hartera Date: Tue Feb 14 21:32:31 2006 +0000 Edited comments. Changed name of program and functions. Added rcsid. commit 9dc82177afd0afba2de93022d7e50605c9a2c357 Author: heather Date: Tue Feb 14 20:50:27 2006 +0000 add comment commit f7c2d12d26474f5059921b6bdfd9740eb7525a7e Author: heather Date: Tue Feb 14 20:42:02 2006 +0000 only check deletions with loc_type 1 (range) and 2 (exact) commit 9749bb2f0809f842cd7f34e3e3755a370469806a Author: heather Date: Tue Feb 14 20:36:06 2006 +0000 don't check contents of observed if size is wrong (deletions) commit 7a72b8893d8c2ce07a1084770fa3b15d0d2d4d72 Author: heather Date: Tue Feb 14 20:20:47 2006 +0000 add DeletionClassWrongObserved commit c1bfce5358891132beadfa92d7da9c8895503e45 Author: heather Date: Tue Feb 14 20:17:58 2006 +0000 tweaks commit 47a11be77a56df249b9d296ad47b28ec7f615988 Author: heather Date: Tue Feb 14 19:48:27 2006 +0000 exceptions for snpReadFasta commit b31f42acdc0c57ea7d8bfe0ef6e9ea723e400caa Author: hiram Date: Tue Feb 14 19:30:00 2006 +0000 Beginning build of Mm8 commit 93d8f756557be539093e1be65dfd1e4cb951de17 Author: kent Date: Tue Feb 14 19:25:34 2006 +0000 Finishing implementation of array.sort(). commit f56c872aeddf4d6f4334d4db1e0088a854d36116 Author: heather Date: Tue Feb 14 19:21:31 2006 +0000 suppress verbose commit 046cadc3231521c6fc672f2b0c935cfb00960d4a Author: ann Date: Tue Feb 14 19:20:34 2006 +0000 Added details about renaming hg17 -> mm6 chain/net tables. commit 4db30a1ea8707023560a880b14a57b4dd7ae182a Author: heather Date: Tue Feb 14 19:05:19 2006 +0000 eighth step in SNP processing. Get molType, class, observed from chrN_snpFasta. commit 5a812c68aace5d09ba71532b55b8c477f8e35eb6 Author: kayla Date: Tue Feb 14 18:59:51 2006 +0000 Fixed two broken links. commit 77a76cfdc2f9f70137b9014489c7b4a3079f693e Author: kent Date: Tue Feb 14 18:38:13 2006 +0000 Starting to implement sort method on arrays. Works on arrays of primative types without a cmp function, and on arrays of ints with a cmp function. commit 5579e18fb9e3d276959665aaf805c062ddd85de7 Author: braney Date: Tue Feb 14 18:09:08 2006 +0000 david and my own edits to explain gap annotation. Donna's going to go over these again commit 1c461a2c986bf3915983dafa39ab899287776148 Author: kent Date: Tue Feb 14 17:53:21 2006 +0000 Splitting array.c out of initVar.c commit ed351b729da45ef5a3ef0bb0bd76499ef505ac85 Author: hartera Date: Tue Feb 14 17:26:20 2006 +0000 Edited program description for usage output. commit c37f9994a063947b30ed43a1c6acd9db07209e60 Author: hartera Date: Tue Feb 14 17:21:24 2006 +0000 Edited to change references to program name. commit c8dd5a44ea21650ac02a3625b62b869a7b23c449 Author: galt Date: Tue Feb 14 16:00:02 2006 +0000 "Encode release log update" commit af5c2161e5e7a4b674f0ce3223270f05b1c395c3 Author: galt Date: Tue Feb 14 16:00:01 2006 +0000 "Release log update" commit 4cfd3d0124418ac496bc2ef362df6c53b00f60df Author: fanhsu Date: Tue Feb 14 14:56:12 2006 +0000 Updated, for spDbTest to use uniProt instead of swissProt. commit 618aa41de7e2e73a65a1f79e64949034f85ee387 Author: fanhsu Date: Tue Feb 14 14:55:33 2006 +0000 Updated expected output of spDbTest. commit 5777c7e7dd51b183d798c4d2e04ad57bfe4834bf Author: fanhsu Date: Tue Feb 14 13:55:22 2006 +0000 Added build process of hg18 KG. commit 30d877304dc3dd8aaf4f494558bdeeae929cbc39 Author: galt Date: Tue Feb 14 09:52:05 2006 +0000 added genePredToFakePsl (and fixed alphabetical order locally) commit 6759921f6435802106cc4fa6103524d2eacf1960 Author: kent Date: Tue Feb 14 09:39:34 2006 +0000 Implementing a generic element type. So far just applying it to array.push, which is basically a synonym for the operator-implemented array.append. (It may be worth keeping a.append, because it is a bit faster since it doesn't have to do any type-lookup during runtime, while array.push does a bit.) commit 969404a885d0dcafc3e5f3134f012fc774447e9a Author: heather Date: Tue Feb 14 05:07:46 2006 +0000 add checking for named and microsat commit 7e58ce556ff9e88986d5e3223a4848e18efa6d09 Author: heather Date: Tue Feb 14 04:45:35 2006 +0000 fix formatting; add checkMixedObserved commit 21e8a9e739f2010eba31acbd0286ef88039e7639 Author: heather Date: Tue Feb 14 04:30:40 2006 +0000 check for exceptions in single and in-del classes commit 4b262f0d40800fad51cd02b3580fba4b65170a97 Author: heather Date: Tue Feb 14 04:02:46 2006 +0000 tweaks commit 9ba5b506a23ce07ae26010fc26c6d7565c7cb737 Author: heather Date: Tue Feb 14 03:57:30 2006 +0000 Create split tables. Don't use lib/snpFasta.c. Don't store in memory. commit fb75fe8ca1cfdec75a70c34b1c7de4b9970473b6 Author: kent Date: Tue Feb 14 03:56:31 2006 +0000 I think I'm handling pptIndirectCalls everywhere I'm handling pptCalls now, which should improve functionPointers. commit b8a4d42550a082ec5ccd63f8ba0f8007a7b78db6 Author: kent Date: Tue Feb 14 03:50:09 2006 +0000 Updating some test cases. commit 9737d3bc49b60f0f8ea29708157aaac5f9c92953 Author: kent Date: Tue Feb 14 03:49:30 2006 +0000 Function pointers now can return tuples. commit 76b5e5c6c1e20269925e808cdb32b373f296a884 Author: kent Date: Tue Feb 14 03:39:05 2006 +0000 Improving type mismatch error messages. commit fd0050559fa070939cb1a8ca3a4941449835c506 Author: kent Date: Tue Feb 14 03:24:05 2006 +0000 Removing some duplicate effort in makefile commit 458f94602934a73aefa610a2573901c4db185593 Author: kent Date: Tue Feb 14 03:22:22 2006 +0000 Fixing run-time so that it seems to work with functionPointers embedded in classes. commit 49a782b3de821b9d3b2d545a335cb49bd6ce3964 Author: heather Date: Tue Feb 14 02:55:33 2006 +0000 "New version number v127" commit a4b2d74b707c22310f2ca5eb7fc727bac6389155 Author: kent Date: Tue Feb 14 01:53:25 2006 +0000 Fixing bug where multiple function pointers declared of same type in comma separated list. I'm noticing there's still a problem instantiating classes containing function pointers, likely in the run-time types. commit a9b68d791ab570a4b65bfae62906ebee7b14dbe1 Author: kent Date: Tue Feb 14 01:48:40 2006 +0000 Adding test case for function pointers. commit 2a9340597ce86aaa9ed4bc4734848d8b24b40777 Author: daryl Date: Tue Feb 14 01:09:37 2006 +0000 add support for RECON libraries commit 60c2719208bd5b8dd0939f4367fced2b0c44773c Author: daryl Date: Tue Feb 14 01:01:26 2006 +0000 ignore header line commit 7e1f813fc022d478661c3d561c4244231ced4bbd Author: kent Date: Tue Feb 14 00:58:34 2006 +0000 Generating code to call function pointers. Seems to work. I noticed there's a bug when you declare more than one function pointer in a line - looks to be in the type-checker. commit 096d67e4168859e60a60a107f733c556c746545f Author: fanhsu Date: Tue Feb 14 00:24:45 2006 +0000 Created makeProteins060115.doc. commit 8a8db341d63dfce8e593ff5b235c47b71cab7a91 Author: daryl Date: Tue Feb 14 00:24:35 2006 +0000 new libraries commit c79c566d95bfe223c9b939fd592c3c69c5b086d5 Author: angie Date: Tue Feb 14 00:17:10 2006 +0000 Added axtChain -linearGap arg (now required). commit 7daccee1847fa6a1ec21512330f15e9de159bca9 Author: daryl Date: Tue Feb 14 00:16:53 2006 +0000 convert prettybase format to bed with allele counts commit 31ecfb4d6c9ef6ff078cd5b246147952c9edcb5d Author: angie Date: Tue Feb 14 00:16:17 2006 +0000 Re-swapped hg17 alignments after re-re-running there. commit eb3096486813f736d9ae9e8aa08b13c34cb1a3ad Author: kent Date: Tue Feb 14 00:10:30 2006 +0000 Making it so that you can assign a function to a function pointer. You still can't call a function pointer. commit 783819b14eb78f6763caa7c4e62ebe7a824dee2a Author: angie Date: Tue Feb 14 00:06:35 2006 +0000 Set up tables for Gene Sorter (& hgGene). commit e86f7494aefc6ffdd39676322eb292c7fad152b9 Author: angie Date: Tue Feb 14 00:04:03 2006 +0000 Re-re-ran (doh!) canFam2 blastz after Kate found that linSpecRep had not been snipped after all. Ran rn4 blastz. commit e0aa3eb72cf71a9647dd930dc2ea02f1713eafd2 Author: daryl Date: Tue Feb 14 00:01:05 2006 +0000 added combined Chinese and Japanese population to HapMap LD track commit 6219ba6c3fb46ef1ffa1fa1c35891563bce9139c Author: angie Date: Tue Feb 14 00:01:03 2006 +0000 Continuing basic tracks: genbank, genscan, alignments, CpGs, ... commit 2fb8f486d13a96b173f8239196f377525ce52d5b Author: angie Date: Mon Feb 13 23:58:20 2006 +0000 Oops, forgot -path for hgAddLiftOverChain. The default should probably be switched to expect .gz (and to check for existence of the file/link). commit 6611cc169cfb0b24ffa3c32cddf4df4701c0aa55 Author: kent Date: Mon Feb 13 23:43:20 2006 +0000 Improving type dump of function pointers. commit 1d998bee153328881fd8c6345f1ae5a342e13d46 Author: kent Date: Mon Feb 13 23:28:12 2006 +0000 Generating code for function pointer declarations. commit 141c22558e5d6ada9cb316bceeb6ab38574a75d9 Author: kent Date: Mon Feb 13 22:31:41 2006 +0000 Getting function pointers past binding names pass. commit d372c6f00d3bf53ba4d647fb50b9616c3ba5342c Author: kent Date: Mon Feb 13 22:11:21 2006 +0000 Got function-pointer declarations through parser. (They are dying at the name-binding stage though.) commit cb264763333c7c04563f4cdcf7536fa341ff999c Author: hartera Date: Mon Feb 13 22:08:24 2006 +0000 Added gnfAtlas2 to the specificUi function so that the affyUi is selected for this track. commit 12b175abbd75aea3a52ae1f9bea92f6fefff2a6a Author: hartera Date: Mon Feb 13 22:07:02 2006 +0000 Added track handler for the GNF Atlas2 track. commit 589f3f9c258a4173b1c961a1e3571d429399ba06 Author: kate Date: Mon Feb 13 22:05:20 2006 +0000 Add custom track button commit fe8fcee53aff203387df4308477568bac230ab12 Author: fanhsu Date: Mon Feb 13 21:12:57 2006 +0000 Changed hugo to hgncXref. commit f3156d290fc83f7fa85b768b283d97afb152bce2 Author: braney Date: Mon Feb 13 20:29:16 2006 +0000 another intermediate, probably I should re-write this pile commit 040304fc19dedb52a718782dba25c62ebfc9b700 Author: angie Date: Mon Feb 13 20:16:33 2006 +0000 Translate assembly.links file (output of Arachne assembler) into AGP for hgGoldGapGl. commit 65a1fe923b69d94f93d6ed9134515755e9cb1c92 Author: angie Date: Mon Feb 13 20:14:49 2006 +0000 Adding /cluster/bin/penn back to $defaultPath, after /cluster/bin/penn/$machType. commit 6f3681d8a4239884d23807e538bdcebe24f10f1e Author: angie Date: Mon Feb 13 20:12:08 2006 +0000 Added -protAccQuery. commit 6a26e63336c8472a7270742f3dadd525ba0f324a Author: hartera Date: Mon Feb 13 19:39:24 2006 +0000 makefile for hgEnsGeneXRef.c commit f538af4df9b24580cb0f892a4a0c154c33ff6743 Author: hartera Date: Mon Feb 13 19:36:49 2006 +0000 Program to parse Ensembl and Genbank data files to create a cross-reference table of Ensembl IDs to other database IDs and a gene description. commit f6667c2b9f341f1a3db266895e3a2487cd847e4f Author: fanhsu Date: Mon Feb 13 17:43:07 2006 +0000 Created links.ra commit 2cb293b18d471a22e2f1f09ad16cbf444689f3b2 Author: galt Date: Mon Feb 13 16:00:02 2006 +0000 "Encode release log update" commit 80571a721215529a0ff23311ac0d1731006d32bf Author: galt Date: Mon Feb 13 16:00:01 2006 +0000 "Release log update" commit 61e8f06e798b7cb66b711a089ecd0108d1639d56 Author: galt Date: Mon Feb 13 08:11:11 2006 +0000 detecting end of thumbnail better commit 5ffadb862c59eb10bc447b204015080a3d1f9111 Author: kent Date: Mon Feb 13 07:44:34 2006 +0000 Catching a syntax error rather than crashing in code 'int x.y;' commit 20440ae3df22d88835d850ddc9f236577c2e10e2 Author: kent Date: Mon Feb 13 06:59:11 2006 +0000 Test case for interfaces across modules. commit 248a3572c4345de80a4c4a02f1c84dc4ecf26f6f Author: galt Date: Mon Feb 13 06:57:05 2006 +0000 integrate jp2ToJpgTIles into vgPrepImage using libjpeg and ERMapper jp2 lib commit 613e1fa83e2d94505ce3198d8effec88c47078c8 Author: kent Date: Mon Feb 13 06:35:37 2006 +0000 Fixing missing polymorphic functions in .pfh files. commit c0a556b844ce32a71f36b0f36ac373776c139ec3 Author: kent Date: Mon Feb 13 06:25:23 2006 +0000 Finishing interfaces I think. Fixing memberDotInClass bug. commit 6065bcfd3b4bba46e04a2d4c032fd562b1bf109d Author: kent Date: Mon Feb 13 06:23:52 2006 +0000 Adding test case for classes with members that are class instances. Used to have problem from not adding 'self' implicitly in these cases. commit 547999770185b7ff4133691eaeaf2739f564ac1f Author: kuhn Date: Mon Feb 13 05:53:19 2006 +0000 fixed the part that adds a name to the files. it was scrambling the order and misreporting the file/name relationship commit 0efe1ef8d35384e96585c3e6820e7e38518e4cd3 Author: daryl Date: Mon Feb 13 04:36:42 2006 +0000 obsolete commit 065283b1953e0bb0ccb99ad2a400c4d84eee9ea6 Author: kent Date: Sun Feb 12 23:13:05 2006 +0000 Generating code for casts of classes to interface. commit ebdc4fffb6b3a624808e883ff17ed27b12cd579d Author: kent Date: Sun Feb 12 21:05:48 2006 +0000 Adding type-checking and generating cast when using a class as an interface. commit 189bab07ae94693ad45448309ea5199355bee441 Author: kent Date: Sun Feb 12 19:51:59 2006 +0000 Starting to add interfaces. You can declare them, but not use them at the moment. commit 871f9f7d1b41ce1680bcd4f4b7d434bb885c5c5d Author: markd Date: Sun Feb 12 16:33:45 2006 +0000 added ignore entry commit 202f1b5b2ef499dbf2e033a51608112b95c80410 Author: galt Date: Sun Feb 12 16:00:02 2006 +0000 "Encode release log update" commit 3ee6c8dac1b7063d59416dedb9ddb32708faf3c3 Author: galt Date: Sun Feb 12 16:00:01 2006 +0000 "Release log update" commit 69b0cab20cb5358494e64b47fe1ffeafb524f615 Author: fanhsu Date: Sun Feb 12 15:35:35 2006 +0000 Added geneNetwork section. commit ee29e52c3acb69621dfdfd290215668fa90685b9 Author: markd Date: Sun Feb 12 07:08:38 2006 +0000 fixed corner cases related split maf blocks commit c8fed8a1b512147b05bd50753a66f2c0cb26e6fa Author: kent Date: Sat Feb 11 17:44:36 2006 +0000 Changing para (...) add to para(...)+ . Similary using *, &&, || instead of multiply, and, or. commit 589d30687f795777d8d3e8ce4204aaa462fc3889 Author: kent Date: Sat Feb 11 16:27:25 2006 +0000 Updating to reflect new uniProt database. commit 3be4f7114a4289107d1be3c96be6b63bed4d2b6d Author: galt Date: Sat Feb 11 16:00:02 2006 +0000 "Encode release log update" commit 10cb0248a5ef19942d158bda4436acc03c03efff Author: galt Date: Sat Feb 11 16:00:01 2006 +0000 "Release log update" commit 272565c4ba1da43bac1f2f071017a4392cb6bc9b Author: daryl Date: Sat Feb 11 10:09:31 2006 +0000 hapmapLd: start from the genotypes files, run Haploview, reformat, and load database commit da1aa7458b66d58a03a6ca725778b168eaf9d171 Author: kent Date: Sat Feb 11 02:03:25 2006 +0000 Made it so that 'flow' is used to declare functions without side effects, and 'para' is just used for the para (el in collection) action constructs. commit 1ac383298e94e4ebad4048494bcbc21d12327330 Author: donnak Date: Sat Feb 11 01:21:39 2006 +0000 Fixed broken link. commit 656b112d508e1a7b46dd56a584a183f4cd9cb3ee Author: aamp Date: Sat Feb 11 01:15:11 2006 +0000 Added a couple tracks. commit 07760ff5f07bb0797a4fff8f429b0ba4c2f39f28 Author: kent Date: Sat Feb 11 01:04:08 2006 +0000 Implemented para actions argmax and argmin. commit 3a1dde9da925837c0eb7e0f260048f953561a1fd Author: hiram Date: Sat Feb 11 00:58:28 2006 +0000 Attempting a blastz with mm7 commit 210f32f2b9619b3bd6c0eb418da46c7810d2d3b6 Author: hiram Date: Sat Feb 11 00:57:39 2006 +0000 Experimental monDom2 blastz commit 6f2c60a98d60946c2e11cc798fd4f81754024643 Author: hiram Date: Sat Feb 11 00:56:45 2006 +0000 Experimental monDom2 alignment failed commit a11102c12f5d37f747cc4122e051682aec22c741 Author: hiram Date: Sat Feb 11 00:55:33 2006 +0000 Starting blastz hg18 commit 01179c31210ded3bd9d8593dd8385e468f2e0933 Author: hiram Date: Sat Feb 11 00:55:09 2006 +0000 Starting blastz monDom4 commit 9ee7e45f2543999a7517cb7ca10e3b6297e19fa3 Author: ann Date: Sat Feb 11 00:15:08 2006 +0000 Added identifier=knownToRefSeqId for mm7 (geneNetworkId table). commit 4400902dd196fc139ab627bd2a0899e596cdfaf4 Author: hiram Date: Sat Feb 11 00:11:39 2006 +0000 Done with repeat masking, ready to start some alignments commit e59d65dd61adf79f04da28234dc41d9aeda3c7bb Author: heather Date: Fri Feb 10 22:08:00 2006 +0000 minor cleanup commit 95fe19847a2d943a5cecca7ec507083f78ba4517 Author: kayla Date: Fri Feb 10 21:33:03 2006 +0000 Added danRer3 commit 44978f5f72d5a5ff974d53338c0fee00e528f890 Author: hiram Date: Fri Feb 10 20:59:16 2006 +0000 No longer any limits in binKeeper - it uses the whole new bin scheme commit 52a771bd8254acf0e2b357be7534a8746c98abd4 Author: donnak Date: Fri Feb 10 20:07:52 2006 +0000 Fixed a typo. commit 3eb8784c67b4adf03a2b789e43f57740b19653ae Author: hiram Date: Fri Feb 10 19:38:35 2006 +0000 Add binTest to the lists of tests to do commit e0738daf6072bd2cc867e082cc1543efa70ce81a Author: heather Date: Fri Feb 10 19:32:12 2006 +0000 exceptions for snpRefUCSC commit e05564ac7789527fbe3e9f4eb6c3b9bb911f55fc Author: hiram Date: Fri Feb 10 19:32:08 2006 +0000 Now checking silently both old and new scheme, both binRange and SQL statements commit 449863d83175d1029717720aefb401a367f86a1e Author: heather Date: Fri Feb 10 19:31:22 2006 +0000 minor bug fixes commit 59fd3c2b707e180741d432ff619a62396fed478b Author: hiram Date: Fri Feb 10 19:27:21 2006 +0000 Now with checks on the SQL statements commit f2409e41291785a5c33bf848441c382148a898cc Author: markd Date: Fri Feb 10 18:44:44 2006 +0000 fixed misspelled keyword commit 2b53d0b9916e0d362c2eb69e402d4b5a11a65292 Author: markd Date: Fri Feb 10 18:32:33 2006 +0000 get rheMac2 ooc from cluster nodes commit fc84ce945d381f373fc4d1193495ee6107c245e0 Author: hiram Date: Fri Feb 10 18:15:05 2006 +0000 Now doing both old and new schemes, plus single location is possible commit 5ee944d1ae015b131de394233c97123477a1adef Author: baertsch Date: Fri Feb 10 18:12:01 2006 +0000 update rheMac2 to point to local scratch drives commit 933b27dd64aca2f4d331191f5a271bed78ac3ca0 Author: hiram Date: Fri Feb 10 18:08:04 2006 +0000 Should be correct now commit b83eb8b0d3b0f78c91dc4bd6ec4d2f31f98159e8 Author: hiram Date: Fri Feb 10 18:07:36 2006 +0000 Properly test end<=MAXEND commit 20e5ba3fb24103ee9b3f5784a849129b6ae9ab66 Author: hiram Date: Fri Feb 10 18:06:44 2006 +0000 MAXEND should be correct and then use the 'end <=' to test commit 8e63386f3224e07b394ac5cc6d72e8626bdd533f Author: hiram Date: Fri Feb 10 17:54:00 2006 +0000 Needed the _binOffsetOldToExtended define in hg/lib/hdb.c moved it to the .h commit 2017fca014e2edab6e7c79d9ca06e35e9846de61 Author: hiram Date: Fri Feb 10 17:53:33 2006 +0000 Needed the _binOffsetOldToExtended define in hg/lib/hdb.c commit 768182115a57f1aa94265c553e8821eb7381f438 Author: kuhn Date: Fri Feb 10 17:19:12 2006 +0000 put in spaces around dashes commit 7199e30bfc46e051724373ff4e4cae4be338fc46 Author: kuhn Date: Fri Feb 10 16:57:32 2006 +0000 decapitalized species part of Latin name commit f346d22ecfbf1a797a5c0a1ef4a3aae73689c391 Author: donnak Date: Fri Feb 10 16:50:48 2006 +0000 Fixed a few typos & made a few other minor format changes. commit d20193f23e126bc88c85b682f6263c1cee0d099a Author: braney Date: Fri Feb 10 16:18:32 2006 +0000 don't show bases in squish or dense mode consistent with non-base mode where pairwise alignments are not shown commit 1518f275016ee2ed869bdbbd9d15a6f7c18b02db Author: galt Date: Fri Feb 10 16:00:02 2006 +0000 "Encode release log update" commit 861787ab07ffebb1fac74dac62ca8465d4412517 Author: galt Date: Fri Feb 10 16:00:01 2006 +0000 "Release log update" commit 7333d73084a249220fad908c1d9d12111d9598fc Author: braney Date: Fri Feb 10 15:57:15 2006 +0000 another intermediate. calcs mix probabilities commit f94b1ba27944c078a9947df9a91498dde631a68a Author: kent Date: Fri Feb 10 10:08:17 2006 +0000 Making it so that you can have multiply-dimensioned arrays initialized with array[N] of array[M] type declarations. commit 84de7d314ad4023ed5a576cce44edcd68bf6d468 Author: kent Date: Fri Feb 10 06:16:19 2006 +0000 Changing dir initialization so that it uses : rather than to. Making foreach (i in 1 to 10) work. commit 38c5657e0643565f7f70801cdd73374f52b4141e Author: kuhn Date: Fri Feb 10 05:01:08 2006 +0000 added link to photo credit commit d695a3878b01e011b70119013be2cd6b4253d963 Author: daryl Date: Fri Feb 10 04:12:22 2006 +0000 adding hapmapSnps table commit 3a7614ff2af18150d7bf24fc2243d02179cd8d47 Author: braney Date: Fri Feb 10 03:57:33 2006 +0000 fix to match doc commit 958986e284ddf703e61f77b6b82b84b33ab3a22b Author: aamp Date: Fri Feb 10 03:25:01 2006 +0000 Yeah /panasas didn't work either. commit 67e666ee1dd788f2cd408608cdaf0335f9c76bfe Author: aamp Date: Fri Feb 10 03:09:52 2006 +0000 Ooops. commit 6ae208b877283d3236b06ceca97922ccedb534b0 Author: aamp Date: Fri Feb 10 02:27:23 2006 +0000 Changed locations. commit e729f4d4669a11c3eab186446dde5d281acb1fcb Author: hiram Date: Fri Feb 10 00:58:27 2006 +0000 Adding extended binRange operations for SQL statements commit ea9cbdd1a17b5717517b6748e2292b4db5a7270b Author: hiram Date: Fri Feb 10 00:56:45 2006 +0000 Adding extended binRange operations commit d138d6eceb84e49f9f817d77ea569d5b551452ae Author: hiram Date: Fri Feb 10 00:56:29 2006 +0000 Adding extended binRange operators commit 7ad94d1389909204e845cfbb6ba5db9d687c6dda Author: hiram Date: Fri Feb 10 00:55:03 2006 +0000 Adding extended binRange operations commit 7a84213e5952190eda1b6587410164fb50118939 Author: fanhsu Date: Fri Feb 10 00:42:49 2006 +0000 Moved GeneNetwork link to .. . commit af6e1add0d171364559bd2d5a4a9c516fa274731 Author: fanhsu Date: Fri Feb 10 00:42:06 2006 +0000 Added link to GeneNetwork. commit 65c3a67806a1ae4e13fdf85a1417c665a7e861cb Author: fanhsu Date: Fri Feb 10 00:40:55 2006 +0000 Moved GeneNetwork to .. . commit cb6f92764c7155e5a7ca40bffb51e0d485484ea9 Author: fanhsu Date: Fri Feb 10 00:39:51 2006 +0000 Added link to GeneNetowrk. commit 5339d5098ad94d203a3a2d4874941eb172f33e1b Author: baertsch Date: Fri Feb 10 00:16:38 2006 +0000 fix gap and ctgPos tables to use half open start fix off by one error in ctgPos.size field caused by error in agp commit 1a50882ddd8d406669a9918eb1b22d4ef06b31b2 Author: hartera Date: Fri Feb 10 00:08:16 2006 +0000 Modified genericChainClick and genericNetClick so that links to other genome in chains and nets details is not active unless the other genome database is present and it is active in dbDb. The score for chains within the browser window are calculated only if the other geneme database is present. commit 39ad15de37822137d582a1dfb6edadf34d94dc3f Author: heather Date: Thu Feb 9 23:57:24 2006 +0000 increment coords for loc_type = 1; atoi --> sqlUnsigned commit 1f4978b716b85c7ae9ca20500ba56b1d7ed8dd40 Author: kuhn Date: Thu Feb 9 23:30:31 2006 +0000 added link to Baylor commit 9596de34ca903f946d3cadf17a998b5b268f33d1 Author: heather Date: Thu Feb 9 23:24:21 2006 +0000 change verbosity commit ac69600934e6099a5db2878cc487994df5a46eb4 Author: heather Date: Thu Feb 9 22:51:29 2006 +0000 sixth step in SNP processing: nib lookup for chr:start-end commit dd599ed18c4e1ee4d3ea286aba35613852030187 Author: angie Date: Thu Feb 9 22:34:34 2006 +0000 rn3-rn4 liftOver as well as a bunch of much older items. commit 849acbfda90dc78c152c97756f3668230a4ac51f Author: hiram Date: Thu Feb 9 22:28:38 2006 +0000 Extended bin range up to 2Gb-1 for end coordinate now commit f398f5ab7a1ab52543f7397e077ef05319d3b124 Author: hiram Date: Thu Feb 9 22:22:18 2006 +0000 Does the old style correctly, both bin numbers and SQL statements, and does the new style bin numbers. commit ad9a06a2945eabc6d109c206c472af49b69434ba Author: fanhsu Date: Thu Feb 9 21:20:46 2006 +0000 Updated to use hgnc table instead of the old hugo table from proteinsYYMMDD DB. commit 55af28827b8a397e905f8c5484732419e55365ac Author: baertsch Date: Thu Feb 9 18:50:32 2006 +0000 fix gap track commit ad57f54f0e8769d6ec1b2c9da3b0556f21ecf1d4 Author: kuhn Date: Thu Feb 9 18:40:31 2006 +0000 dropped reference to gap. reverting to top-level commit 3fcd02023c64b4581dc3da4affb6f52deabfaaba Author: kuhn Date: Thu Feb 9 18:39:44 2006 +0000 gap table was rebuilt. reverting totop-level file which describes the correct types. commit 5702449ea850eea7e27433dffaeb59f74f7e7824 Author: hiram Date: Thu Feb 9 18:29:10 2006 +0000 Initial empty test commit e895f772a5b0814a29df051864af584405b9af6e Author: hiram Date: Thu Feb 9 18:28:41 2006 +0000 Add binTest to the tests commit 79b796caa0cc9f320ef7300ecd301ffe5881ccc0 Author: hiram Date: Thu Feb 9 18:28:06 2006 +0000 Initial source commit e15e53e6294e14371f1bd931c597a8a453deb465 Author: donnak Date: Thu Feb 9 18:21:13 2006 +0000 Modified rheMac2 credits. commit 6deb6ed3feecde1211eb14a5b3d7b4ecf0529d11 Author: donnak Date: Thu Feb 9 18:16:47 2006 +0000 Fixed typo. commit 2cdc7e38345b7bb1d994b58d70098646701aaf6f Author: donnak Date: Thu Feb 9 16:51:03 2006 +0000 Made a few mods to the assembly details text. commit 01dffe731a29fc9070be928c3b9337b33bcaccca Author: donnak Date: Thu Feb 9 16:36:59 2006 +0000 Archived 1 item. commit e1cff6b311a02112ded52e0c08e2bd2262e8ae8b Author: donnak Date: Thu Feb 9 16:36:47 2006 +0000 Added rheMac2 news announcement. commit ac6f4290e4595c3ed87893d3d797a6f2829012c0 Author: galt Date: Thu Feb 9 16:00:02 2006 +0000 "Encode release log update" commit f28042eb6402798c1320da730f0e594b5114e0ec Author: galt Date: Thu Feb 9 16:00:01 2006 +0000 "Release log update" commit cc97d0a45058e48bc35afe7edb6ca88c39227e11 Author: kuhn Date: Thu Feb 9 14:21:25 2006 +0000 set xenoTefGene to pack to make default position more interesting commit 8ef3602c447afe09776129a7cc5d6507f6bb5a1a Author: baertsch Date: Thu Feb 9 13:47:21 2006 +0000 added gold description commit 24b751383896bf61c6a494725baa029857ed89d4 Author: baertsch Date: Thu Feb 9 13:41:50 2006 +0000 add description for gold and ctgPos tracks, remove ctgPos2 add ctgPos commit 922cab1d6bd8735e4fd37c272e4cc8a9daf0c0b9 Author: heather Date: Thu Feb 9 01:02:24 2006 +0000 fifth step in SNP processing: sort by chromStart commit 4aee346d08935c5807e14069522948ac8c974714 Author: angie Date: Thu Feb 9 00:45:17 2006 +0000 Use 2bit instead of nib for rn4 (getting error...). commit 9d31595e9a57bad876762f3a7dad7f2a2d2d9b67 Author: angie Date: Thu Feb 9 00:06:14 2006 +0000 Added rn4. commit 19491224fb34f73368a485c478901a616a939537 Author: kate Date: Wed Feb 8 23:58:28 2006 +0000 More tweaks on GERP display commit eed71a615c1f6236d0ca8ea4f3d04d0b27515cce Author: heather Date: Wed Feb 8 23:54:12 2006 +0000 use carefulClose commit f396690350c8cf45b257fa5896390d2cd864302c Author: heather Date: Wed Feb 8 23:49:16 2006 +0000 use safef commit e0f5e6d192016dbc353da482d776f9ee1931e92a Author: kate Date: Wed Feb 8 23:34:34 2006 +0000 Adjust view limits for GERP conservation commit 526421e90f10136d2b58359ca175f5eff87d1f97 Author: heather Date: Wed Feb 8 22:49:34 2006 +0000 64 chars for fileName commit 418a78046c2a53b28b6cdacbbdfc69bdfcd5f4a3 Author: heather Date: Wed Feb 8 22:47:35 2006 +0000 consolidate fprintf commit c1982b5ad9d16f51e30f426065cc4ca4e1ed299f Author: hiram Date: Wed Feb 8 22:43:19 2006 +0000 Add monDom4 to the make commit 1ac9d61d130949a3c62250fcc6ea477c0f6c0d8e Author: hiram Date: Wed Feb 8 22:42:52 2006 +0000 Initial contents commit 712c979a56dd5434e9fd5334f4fe5b4da2ca6940 Author: kuhn Date: Wed Feb 8 22:32:49 2006 +0000 added link to photo provider commit b7f1250f8c490bb710f8410d5a41fdc24cac0500 Author: kate Date: Wed Feb 8 22:31:04 2006 +0000 Remove split for liftOver -- needs to be broken up more commit 51122f2217da899cfecf62c975859a9329d0006d Author: kate Date: Wed Feb 8 22:29:22 2006 +0000 Prep for liftOver from monDom1 commit bc1af186fea0502e3b622b0c63599346b6e393f9 Author: kate Date: Wed Feb 8 22:28:06 2006 +0000 Start liftOver to monDom2 commit cf888a69bafc85ba6ed349f401d015a9029c74b1 Author: kuhn Date: Wed Feb 8 22:26:43 2006 +0000 fixed a bug that tried to use three machine, even though only two were specified commit 633fbd54feac6c7d7a54676077f5a09214d0ca9e Author: jen Date: Wed Feb 8 22:02:19 2006 +0000 Add comment for seq file repush. commit d4bb9f223aca1bf974147f59e245a5b3dd839d21 Author: heather Date: Wed Feb 8 21:23:11 2006 +0000 add needed cloneString! commit 12a9018cc201899fe0921412f182ec5f4f0cf3fd Author: heather Date: Wed Feb 8 21:21:52 2006 +0000 return non-zero for error commit 98062de3fda25a34cb427e62a1ffabcddb0a2a7d Author: heather Date: Wed Feb 8 21:21:29 2006 +0000 cleanup commit dd4589b73f6e56652d2cfcfeebb5f7bdc06912d3 Author: heather Date: Wed Feb 8 21:19:06 2006 +0000 make all globals static commit 28d3ac0d16643c89f68fec5c0e410decf4f767b5 Author: heather Date: Wed Feb 8 21:13:08 2006 +0000 change verbose to errAbort commit c08cf75ed3ffbdfe4be6b861d4a7e48e81b9dd61 Author: heather Date: Wed Feb 8 20:40:58 2006 +0000 make all globals static commit 25d02c1853dad14badf0512fb4d215afb11b1f07 Author: braney Date: Wed Feb 8 20:34:31 2006 +0000 an intermediate versoin that doesn't even work very well commit f877dcce43bc330b92a3f21ff4247bd92d71d57d Author: jen Date: Wed Feb 8 19:56:58 2006 +0000 Added comment for seq/extFile repush for AffyU133 alignments. commit 5f439796f3c2d41019390f03183ced09268b3fda Author: kuhn Date: Wed Feb 8 19:56:40 2006 +0000 added gap track commit 1b594506b1ee3c099c2641bfec313ad51fa98bc3 Author: jen Date: Wed Feb 8 19:53:11 2006 +0000 Noted push/repush of hgFixed tables cghNci60Exps and rosChr22Dat. commit 186c82d603c167960bca47dafb9a8b8bcdc2d25b Author: kuhn Date: Wed Feb 8 19:52:05 2006 +0000 added gap reference commit d975eeed51f06133ed0512ec1c54e4a243de741e Author: kuhn Date: Wed Feb 8 19:51:34 2006 +0000 changed reference to fragmanet gaps to clone gaps to match the table commit e240a6d828dae91a0ef50a6f5db1e578ea9a4afe Author: baertsch Date: Wed Feb 8 19:32:18 2006 +0000 reload gold with original contig references commit 06d650bc88c19cec124d628068db6bb53aea9fe2 Author: kent Date: Wed Feb 8 17:44:46 2006 +0000 Adding post-decrement/increment. commit a6680f84410a9472b2c55d40db7400fda820faf6 Author: ann Date: Wed Feb 8 16:44:33 2006 +0000 Added contig track commit ffde8278c5842ad2b2a16ec82568d52592446c67 Author: kent Date: Wed Feb 8 16:28:39 2006 +0000 Adding preIncrement/Decrement. Checking for nested assignments. commit e657679b32d97a39305a4bb25b9431618e8561f6 Author: kent Date: Wed Feb 8 16:23:11 2006 +0000 Misc updates to test programs involving mostly removing type declarations inside of (el in collection) constructs. commit 0000b080204d9804316c39c4437ce79b20d7fd70 Author: galt Date: Wed Feb 8 16:00:02 2006 +0000 "Encode release log update" commit f2076b42f2ef671057b0cf35e3bd1e87716987ee Author: galt Date: Wed Feb 8 16:00:01 2006 +0000 "Release log update" commit c92503b8a930bb84f24e1a51d2bddeea917a74f1 Author: kent Date: Wed Feb 8 15:44:31 2006 +0000 Oops, shouldn't have checked in this file, it's not source, but is automatically generated from typeMismatch1.pf by paraFlow. commit 60fbca715733ba4dfaca454ddb63d21faf66046c Author: kent Date: Wed Feb 8 15:43:08 2006 +0000 Oops, forgot to put this autoSql-generated file into CVS. commit 843b8a850dedda61fb34111a2e9788dc349153b0 Author: kent Date: Wed Feb 8 08:00:05 2006 +0000 Adding preincrement test case commit 167c21da5991b05378b6b92df290e2d3d44f57d7 Author: kent Date: Wed Feb 8 07:03:14 2006 +0000 Making it so para do and foreach write back the element they're working on to the collection. commit 2c69d50009a2d704d21108a4a544ec5b3030ae21 Author: kent Date: Wed Feb 8 06:41:31 2006 +0000 Test case for modifying things inside of a para do or foreach. commit 21db15cf05440c30cd7788651118ffe530c69cbb Author: heather Date: Wed Feb 8 05:27:52 2006 +0000 quick and dirty; uses uncommitted gbExtFile.h commit e297b8b936c6fc78dbdd76c7d2c4c711e812b529 Author: markd Date: Wed Feb 8 05:25:47 2006 +0000 added test for translated blat alignments commit ac92d0911291af216695ee341f5192830cb8812d Author: kuhn Date: Wed Feb 8 04:58:24 2006 +0000 modified image tags to change size and set table width to allow a border around image commit 098659be72d049de0253e783a6562244e9eb5c52 Author: jen Date: Wed Feb 8 03:43:31 2006 +0000 Fixed typo (removed extra dot). commit 06de86893141bbf066f98a577371838afddf47f9 Author: baertsch Date: Wed Feb 8 01:58:57 2006 +0000 fix bug in mergeBlocks commit d15930a5ba7e4254c2a8a4d8645218878f76b27f Author: jen Date: Wed Feb 8 01:44:57 2006 +0000 Fixed two errors from revision 1.257 (rheMac2 addition) and revision 1.256 (ratSts rule changes) commit 8d065fc0ba35964530958726354e8efc84723893 Author: kuhn Date: Wed Feb 8 01:02:55 2006 +0000 changed table size to allow border around monkey image and changed image size values to match the actual image commit cb912f6890f8a36c8ef7236ac748dfddb347f0d6 Author: kayla Date: Wed Feb 8 01:01:36 2006 +0000 Moving blocks up from rheMac1 to rheMac (Rhesus ESTs and Rhesus mRNAs). commit b97c717c2212602aa51ec104df750f9312a2c175 Author: kuhn Date: Wed Feb 8 00:49:07 2006 +0000 made it bigger to matdch danRer2 commit 562538df3a36bca678fa46acc14d0ba51e5535c7 Author: hartera Date: Wed Feb 8 00:42:55 2006 +0000 Added tree image for 5-way multiz and conservation track description page. commit b567f590b369537b4df8a7bec5eb4e300d4b5864 Author: hartera Date: Wed Feb 8 00:35:44 2006 +0000 Changed default visibility of Conservation track to pack. commit 23d9d0c85e32b0c32812937ebbee09183339f150 Author: heather Date: Wed Feb 8 00:31:40 2006 +0000 check size for locType 1, calculate end for locTypes 4,5,6 commit 20615c940b36acd150b68ce0eef21415eeb12db2 Author: kuhn Date: Wed Feb 8 00:28:55 2006 +0000 added image for 5way tree commit edb5e5bfdf67de2d4c052a6ba38000457034bc1e Author: kuhn Date: Wed Feb 8 00:19:56 2006 +0000 new 5way image commit ec1ded49c63a8ceac8b8dce1b004d34ea65842e9 Author: heather Date: Tue Feb 7 23:59:58 2006 +0000 only check range size if allele doesn't need to be expanded commit 441fcc9b6cd9b14884ab623be48a1e86485766d1 Author: heather Date: Tue Feb 7 23:44:43 2006 +0000 clean up chromEnd calc for locType 4 and 6; write exceptions commit 8f3a95e080ead2ec8e615bd8da0be44e5e2ff558 Author: kayla Date: Tue Feb 7 23:37:21 2006 +0000 added rheMac2 commit 7e5d6f45956f80267f289a0923180d57d94ddf8d Author: kuhn Date: Tue Feb 7 23:32:04 2006 +0000 changed name to conform to standards and shrunkimage to match size on browser page commit 072f78a34a0e2cb4ca6c33ecffda7507f3387152 Author: fanhsu Date: Tue Feb 7 23:21:12 2006 +0000 Deleted two junk lines in FUGU BLAT section. commit 2ba5f7623fed5c300264bf373f8a1b4e5f1ab0c2 Author: kent Date: Tue Feb 7 23:20:29 2006 +0000 Implementing array append operator. commit 086e23bc29a220b884fbfcc2357bbf4e8c9896e1 Author: fanhsu Date: Tue Feb 7 23:18:08 2006 +0000 Changed CDNA to cDNA. commit e15702100c9eb4120d394a10bbe9e50331be2c92 Author: kent Date: Tue Feb 7 23:14:04 2006 +0000 Adding array append test case. commit 2316c80d9847841c0eb9a4198cc03ac872db732e Author: angie Date: Tue Feb 7 23:13:08 2006 +0000 kkr1u00's $HOST includes the complete domain name so catch that here. commit eedf18bd03412dc70913882965987d765aa84ce6 Author: markd Date: Tue Feb 7 22:07:56 2006 +0000 fixed typo in crontab commit de3359dd03c7577219ed05fd10ddb35ccd79754b Author: markd Date: Tue Feb 7 22:02:29 2006 +0000 poll more frequenly to try to get loads done sooner commit 0e5821da4027fd09a671205f4e3d5956d5c7c84d Author: braney Date: Tue Feb 7 21:59:56 2006 +0000 fix a copy paste error commit bcad198e02fef0659a8bb5a8ee5c057f6373c2ad Author: hiram Date: Tue Feb 7 21:56:51 2006 +0000 Initial contents during the download of the sequence commit 73a2af58d077b353ebc129ff712224c9dcf4ac1a Author: markd Date: Tue Feb 7 21:54:37 2006 +0000 poll more frequenly to try to get loads done sooner commit a0eb1d1973310c8baaa04264f0aa73a95830dd2f Author: angie Date: Tue Feb 7 21:20:10 2006 +0000 Moved .ra files and some .html files down into dm1 and dm2 subdirs (very different db tables). commit 0c0934fe08e9a94168a5b417254e9502c321c6fb Author: angie Date: Tue Feb 7 21:19:13 2006 +0000 Minor polishing. commit 9a5e3fce09c055476ddec0cedbaff3e690108b07 Author: ann Date: Tue Feb 7 20:48:54 2006 +0000 Added rheMac2 to list of assemblies commit acba99ed2b00697b708d040f5a2e8588ea9250d6 Author: angie Date: Tue Feb 7 20:38:12 2006 +0000 One more "table"-existence oops -- it might be a custom track so check for that too. commit da5f16f2eedf7edb14cceb65852be022fc14e409 Author: hiram Date: Tue Feb 7 20:21:42 2006 +0000 fishClones and ideogram done commit f8209c89abcfc0c39aa47aa94aae27f09fd6a477 Author: hiram Date: Tue Feb 7 20:06:07 2006 +0000 currently functioning bander binary 34882 Apr 12 2003 /cluster/bin/i386/bander saved here in CVS since the binary can no longer be built from source commit cc21bbd49c9db1b54d6cc714cbe1bba719807c06 Author: braney Date: Tue Feb 7 19:55:09 2006 +0000 add instructions to build gap annotation for multiz17way commit 5b28cad07b25d559703e6ae7d151eeed5313dc15 Author: hiram Date: Tue Feb 7 19:51:29 2006 +0000 Initial source, works OK today commit f4a3be5ca19fdcd021d2f899dc5348cad9290fbc Author: angie Date: Tue Feb 7 19:06:21 2006 +0000 Oops, check for split table existence too in anyIntersection(). commit 07cbfc59af4f2b656525fc51ff0d7ce41f8a6c56 Author: angie Date: Tue Feb 7 18:34:20 2006 +0000 Added "hgGene on" to release alpha of flyBaseGene. Keeping it out of the release beta until the next CGI release (hgGene changes). commit 4901bd2cd5c9a213a12bbc909e60fec8b5fc7eda Author: angie Date: Tue Feb 7 18:29:01 2006 +0000 Updated to work with dm2.flyBaseGene (and to extract UniProt IDs) in addition to dm1.bdgpGene which is still the default. commit 9bf725d3cbe1e13c87fed680e695d1492b99429c Author: angie Date: Tue Feb 7 18:15:37 2006 +0000 Moving D. mel. files into separate dm1 and dm2 subdirs (very different db tables). commit ae71b9d5684c99bcdc11fda7013e1379e19f399a Author: angie Date: Tue Feb 7 18:14:34 2006 +0000 Added support for dm2 (flyBase2004Xref) in addition to dm1 (bdgpGeneInfo). commit e73c52f8cc10fc720826f8dcdba15322db54ee3c Author: angie Date: Tue Feb 7 18:00:34 2006 +0000 Correction from Carol Bult: it's "The Jackson Laboratory" not "Jackson Laboratories". commit 51f836caa02a14d2c6a1b66bb23804f7e26c29d1 Author: hartera Date: Tue Feb 7 17:53:06 2006 +0000 Created phastCons Scores downloads. commit 3b0f441ae884c710b7563da6f71301ab02cc649d Author: fanhsu Date: Tue Feb 7 17:50:10 2006 +0000 Updated browser default positioin of hg18. commit 0beddad46f767346f4c8ce40bf19d4403bc0072b Author: hiram Date: Tue Feb 7 17:46:37 2006 +0000 allow rsync to preserve times commit 6b970f23ab11a543b675eda7a0d369834e1e2893 Author: hiram Date: Tue Feb 7 17:35:22 2006 +0000 Update note about i386 vs. x86_64 binaries commit 2b9d4fffd3a17fa9759297c88ea0da5b16d52104 Author: kent Date: Tue Feb 7 17:33:06 2006 +0000 Eliminating need for declaring type of element in (el in collection) constructs. Adding check for no global var access in flow functions. commit e343780ce0f14bd6234b47a2ad0935eb11f7ad50 Author: hartera Date: Tue Feb 7 17:17:28 2006 +0000 Cleaned up danRer1 blastz files. commit 2f36a7dab3b21955c2303e55dc82d8c5f90a43a1 Author: kent Date: Tue Feb 7 17:15:17 2006 +0000 Adding some more run-time-error test cases. commit 6dbe35779475115bdf7a4e4fa3813de2231e32ca Author: galt Date: Tue Feb 7 16:00:03 2006 +0000 "Encode release log update" commit a55075291a5f11ff682e09b16826b1c249d5a795 Author: galt Date: Tue Feb 7 16:00:02 2006 +0000 "Release log update" commit 8a1096f5ce41277c4f62c91426737edaf5f2d335 Author: angie Date: Tue Feb 7 07:12:17 2006 +0000 Oops, gotta use double-quotes when there's a variable in there. commit 1c575efa8f5efd278ba4c88b03c8272952cfbf02 Author: donnak Date: Tue Feb 7 05:23:08 2006 +0000 Made a few minor edits. commit f7a9f80f6bcd8c684e6b569c4efc64c703888829 Author: kent Date: Tue Feb 7 03:27:32 2006 +0000 Reverting back so that member writes are not para safe. commit 7c357174a127347016420ed9fb7b527aa839b14a Author: hartera Date: Tue Feb 7 03:26:32 2006 +0000 Description for 5-way alignment conservation track. commit d16a1f517772662a9ec78097ed64f3bbd465aaa5 Author: kent Date: Tue Feb 7 03:26:19 2006 +0000 Not allowing member writes within a para action. commit c05a15f42efe31c9d91f7ad254a2ae66cfdfdebf Author: hartera Date: Tue Feb 7 03:20:25 2006 +0000 Re-made multiz alignment as a 5-way alignment dropping monDom2. Moved the maf annotation section so it is in the multiz alignment section. Created a conservation track using phastCons. Known Genes track in progress. commit 5bb6e4a8212d68fb5b92ee14ff1eaf052698e714 Author: kent Date: Tue Feb 7 03:15:22 2006 +0000 Allowing writes to member variables inside of para blocks. commit 44c7609733f3abf856b7afe9301c5c82d1c895e0 Author: hartera Date: Tue Feb 7 02:57:17 2006 +0000 Added 5-way conservation track: danRer3, tetNig1, fr1, hg18 and mm7. commit dff133ef444a55fdc5245729c88467670d2441ea Author: angie Date: Tue Feb 7 02:56:18 2006 +0000 Several blastz execs have been moved into $MACHTYPE subdirs of /cluster/bin/penn/, so update $defaultPath accordingly. commit 22edabc778511d2dc7fa887844e31f143c117e9a Author: kent Date: Tue Feb 7 02:32:18 2006 +0000 Getting rid or unneeded addition of self var to function scope. This has for a while been done in pfBindVars instead. commit 0599ef18a8fe2b674e451105505bf1b7d28e9cbe Author: kent Date: Tue Feb 7 02:01:08 2006 +0000 Splitting pfCheck.h into checkPara.h and checkPoly.h commit c4aa8f1d0be97210e507513ca345565c130c0328 Author: kate Date: Tue Feb 7 01:29:39 2006 +0000 Add GERP Conservation wiggles commit 3330acbab41bbf24c31371ec9ef2397373770ad8 Author: aamp Date: Tue Feb 7 01:28:28 2006 +0000 Almost works. Not worth much scrutiny at this point besides algorithmically. This utility is pretty specific. commit 9b81f8b51c34926cb551de882e56069d2115fddd Author: angie Date: Tue Feb 7 01:19:11 2006 +0000 When the user clicks on an ID (idVarName), update the search term in the cart (searchVarName) because that is what will be passed forward by orgForm in subsequent clicks. commit 349b4cda25da34f468cee13547516c86e497283c Author: kent Date: Tue Feb 7 01:15:31 2006 +0000 Splitting pfCheck into two modules. commit 5cb4de87b823c74c8b9efc0ec42624ebdbe5c26b Author: daryl Date: Tue Feb 7 00:49:42 2006 +0000 rough methods for hapmap SNPs track commit f662a9174274a2de7b9ebb71ac96416ff019a2d5 Author: kent Date: Tue Feb 7 00:43:58 2006 +0000 Adding some test cases for run time errors. commit c2cde7e310c94c4af71709f5806305fcde66faf5 Author: hiram Date: Tue Feb 7 00:27:37 2006 +0000 Work around a couple of output lines due to some bad clone information in hg18 commit 3f15bf4c98854db8a28d92bf810ba348321db2f0 Author: kent Date: Mon Feb 6 23:32:24 2006 +0000 Adding some more test cases. commit 737af0d86fba0ad8f78ecb4a04431b264c3f39d8 Author: angie Date: Mon Feb 6 23:32:12 2006 +0000 Make sure that we check existence of BLASTZ_ABRIDGE_REPEATS if the _SMSK vars are set, not just vice versa (big oops in hg17-canFam2). commit 5b64d04ee6c4ba45aceea3df8f4cb3e3d985cc74 Author: kent Date: Mon Feb 6 23:31:46 2006 +0000 Making a to do list. commit f2c950f1a40f35e7f91eb7346329fc7780fe38f6 Author: kent Date: Mon Feb 6 23:23:58 2006 +0000 Simplifying slightly commit f2c6c5a66567f7b3f7ec697302edec69317a17aa Author: kayla Date: Mon Feb 6 23:14:30 2006 +0000 changed visibilith of mm6 net to hide commit 1a19fc2944528e1b683f815fb51e99e65d28653c Author: kent Date: Mon Feb 6 22:37:25 2006 +0000 Adding tickTackToe game commit ad72d1ee97a1896f5ed80a5b4f0beebee0ad6cb3 Author: braney Date: Mon Feb 6 22:34:47 2006 +0000 add instructions for maf annotation and frames building commit 23aacee5ebcfab0429b32aee7d2189bb2a2104fa Author: hiram Date: Mon Feb 6 22:32:58 2006 +0000 STS markers done commit 337ec8a1812837767dc78bdb4533670f3c3ede0b Author: braney Date: Mon Feb 6 22:18:22 2006 +0000 add multiz5way commit 86be8e9037591b3d02fe49c0487b222e0080b878 Author: heather Date: Mon Feb 6 22:05:11 2006 +0000 easy cases: exact and between commit 345daed81ac03368dcac380862ad7df12b202145 Author: heather Date: Mon Feb 6 21:54:35 2006 +0000 removing unused function commit d8fc25cc1585548c1ddd38f3cee11ed8c8d517f5 Author: heather Date: Mon Feb 6 21:42:10 2006 +0000 another comment tweak commit ea413c9170b8ad776f5f88df16c0dcaa5c342591 Author: fanhsu Date: Mon Feb 6 21:25:55 2006 +0000 Updated kgPick.c to be independent of spXref3. Use the displayId table of spYYMMDD DB instead. commit 80f88ae1ba0e454c8b25ef68d4985d1c72d80e9c Author: fanhsu Date: Mon Feb 6 21:16:39 2006 +0000 Updated kgGetCds.c to use uniProt info table, instead of the spXref3 table of proteome DB. commit 8a9f5a85824d5ff3d709b99572baf1406cd0f9d7 Author: kent Date: Mon Feb 6 21:04:28 2006 +0000 Expanding test case a bit. commit 76a90cb2ed216c2c5afb6b50f187d4295b518e5e Author: kent Date: Mon Feb 6 20:59:10 2006 +0000 Removing a blank line in generated C code that didn't really help readability. commit fd364cffd383d258163d8f7ce807547d5c975ea4 Author: heather Date: Mon Feb 6 20:42:50 2006 +0000 format and comment tweaks commit 8dcb9ad159feb79422bd191d414142ef99b772f9 Author: kent Date: Mon Feb 6 20:31:58 2006 +0000 Making (el in collection) constructs handle case where collection is element of a larger collection. commit f7c74387de486cf4398d0455ba850cdc930cb751 Author: kent Date: Mon Feb 6 20:30:06 2006 +0000 Making a function static. commit ce71d9310dd2703940e0331ca06c5b93203cc3a8 Author: kent Date: Mon Feb 6 20:29:36 2006 +0000 Adding type handling for para actions and & or. commit 5cf3c7972536fdf56d358cf7a15644d4e5a43903 Author: kent Date: Mon Feb 6 20:28:49 2006 +0000 Adding test case for nexted para statements on 2-D array. commit f946350a66a2920465205d6163f3281a44143283 Author: kate Date: Mon Feb 6 20:20:52 2006 +0000 Better logging commit 831e2ad64eb3fb7af4f64388e1f9dfd04364af18 Author: braney Date: Mon Feb 6 20:17:20 2006 +0000 make mafAddIRows commit 2ce749ed4595784b595504cccf76b0072b4f2d6c Author: kayla Date: Mon Feb 6 20:15:53 2006 +0000 changed mouse net to dense commit c1eff5861bfa4bf383c737cd703323c7c0825838 Author: heather Date: Mon Feb 6 19:56:51 2006 +0000 polish and complete: error handling and database reload commit 0dbde8b9bec85059fc9c0bcd97694ecbe8264aad Author: kent Date: Mon Feb 6 19:48:40 2006 +0000 Fixing case problem in gene description searches. commit 7876f40f7b9a3ef5fdd3cefac5370518b2f1568b Author: braney Date: Mon Feb 6 18:45:36 2006 +0000 use green instead of orange for brackets. Also make anno's 1 bit higher. commit 27444b21d3d730bed8fe0694cff2765c19dfae6f Author: braney Date: Mon Feb 6 18:27:23 2006 +0000 use green for brackets on bridges chains commit 3b0571101e87a8b73b4bb9940c792f592a0ad6b3 Author: heather Date: Mon Feb 6 18:12:34 2006 +0000 edit comment commit bba95c60e478a2f06da4977e5358c9c338129f88 Author: donnak Date: Mon Feb 6 17:59:15 2006 +0000 Replaced refs to contigs with scaffolds in BED & GFF format sections. commit e7b802bd1e4cff7b7a759939ab99f84a92cccb63 Author: donnak Date: Mon Feb 6 17:50:25 2006 +0000 Removed refs to contigs in BED & GFF format (replaced by scaffolds). commit b82ffae76e1b20dca877b28e3763443618195f15 Author: build Date: Mon Feb 6 17:16:07 2006 +0000 build utils before hg, so stringify is available commit d30e7e78f880d7677eb4d0374e4139a4f6c278af Author: donnak Date: Mon Feb 6 16:07:15 2006 +0000 Added the vgPrb_N probe search example to the gateway page. commit 2e62ce8025b5aa2256386a3af0e8b5a9cb6d2bf1 Author: galt Date: Mon Feb 6 16:00:03 2006 +0000 "Encode release log update" commit 336204b49535dd923ad2bd05a148b0bd15ad386b Author: galt Date: Mon Feb 6 16:00:02 2006 +0000 "Release log update" commit a6b7b8496fdf034c2fccad78b8427fff7c8c946d Author: kent Date: Mon Feb 6 15:32:33 2006 +0000 Adding test case for all paras. commit 42ebe3165f6154e5b4718ed45c1b42c3bf526b81 Author: hiram Date: Mon Feb 6 06:37:54 2006 +0000 Continuing with STS markers commit 390056dbb0229495365aadc814fcf7739f369a56 Author: kent Date: Mon Feb 6 01:30:54 2006 +0000 Checking for global writes inside para actions. commit 6819fa5373a01cf0244674bcb4741942776d09ce Author: kent Date: Mon Feb 6 00:15:23 2006 +0000 Generating code for para filter on dirs. commit 3d3a2e0fac44f0739baf63daff1b22e78dad488f Author: kent Date: Sun Feb 5 23:28:50 2006 +0000 Generating code for para filter on arrays. commit 690699ab2d3db6c6f5395f2589e81e8514c03823 Author: kent Date: Sun Feb 5 23:27:38 2006 +0000 Coercing para filter expression to bit. commit d4af386bc3a5cb1fa5cc3a25c14eb7c42993701f Author: kent Date: Sun Feb 5 23:26:55 2006 +0000 Adding _pf_need_mem/_pf_free_mem to runtime. commit 0141ad08f54d589d0d048464a96071314c6da78c Author: kent Date: Sun Feb 5 23:25:07 2006 +0000 Adding test case for para filter on arrays. commit 8f8150d587589d3bd14f9a866bce842d2e16c70b Author: kent Date: Sun Feb 5 22:18:57 2006 +0000 Adding para filter action to type checking pass. commit 8a96c07a52e9cbd6be554f90b330e47e89dcb31b Author: kent Date: Sun Feb 5 22:11:57 2006 +0000 Generating code for para action get where the collection is a directory. commit 2f5f75c049dd22f4049f53192985afa6e8cee532 Author: kent Date: Sun Feb 5 22:11:02 2006 +0000 Added test case for para get on dirs. commit 390958facf999501715002242d9ae4b3b337cd6e Author: kent Date: Sun Feb 5 20:52:18 2006 +0000 Switching pf_dir_new to use elTypeId instead of _pf_type. commit b6f92dd0a30b782246a1d97920dd4e613b832748 Author: kent Date: Sun Feb 5 20:16:47 2006 +0000 Code generator for para gets returning arrays of other things seems to work. commit 7eb659f8db4f329283aa0beb379ce3f97d9fdfeb Author: kent Date: Sun Feb 5 20:16:06 2006 +0000 Adding test cases for para action get on arrays. commit 818aa8195cc848dc4968f7a2acc8f8eacd5ebda0 Author: kent Date: Sun Feb 5 20:01:54 2006 +0000 Code generator for para gets returning arrays of ints seems to work. commit 4f12e700047098bbeee8929ebeaa639956b722a3 Author: kent Date: Sun Feb 5 19:39:59 2006 +0000 Trimming out para actions top and sample. Type checking para action get, and starting on code generation. commit 263d0d518af2325b6f0a194a8418bfb6f804e130 Author: galt Date: Sun Feb 5 16:00:03 2006 +0000 "Encode release log update" commit 641f4a6293c3e5e5e20dc42b85abd7872a4b94ba Author: galt Date: Sun Feb 5 16:00:01 2006 +0000 "Release log update" commit 1d00490f699eca812b722af47b815ded40a1f170 Author: kent Date: Sun Feb 5 08:47:45 2006 +0000 Generating code for para actions add,multiply,min,max commit 753e131e418f254978e4f4f9ab1cc0099041637c Author: kent Date: Sun Feb 5 08:46:58 2006 +0000 Adding more para test cases. commit 1f9e9291e8e6d26672cffa9cc8a1525cb68f2b69 Author: kent Date: Sun Feb 5 07:41:45 2006 +0000 Adding some type checking for para add/multiply/min/max. commit ac9c794a5a4531453fb74c44c288ef65633662cd Author: donnak Date: Sun Feb 5 07:27:42 2006 +0000 Added rheMac2 to release table. commit e2fe9239b4c93ae9382f4590c1583ca04b25cd53 Author: kent Date: Sun Feb 5 07:11:03 2006 +0000 Adding test case. commit 8025858c1adf65f047bd9d1b94c94871d8ba4927 Author: kent Date: Sun Feb 5 07:09:26 2006 +0000 Put in some type checking on para actions. Did cheesy code generation for para do. commit ac0b1e945e1307bddea3584e54614820e5fecf33 Author: donnak Date: Sun Feb 5 07:06:54 2006 +0000 Updated rhesus credits. commit 9d3c35dea3b36c3125e1880a2387d85ec74d0658 Author: donnak Date: Sun Feb 5 07:06:15 2006 +0000 Created this file -- text for rheMac2 gateway page. commit 02f6a8bcddf49e4a61633162e7720040aa49d1d5 Author: kent Date: Sun Feb 5 06:43:01 2006 +0000 Adding some new error test cases. commit de0e669f994646fb6334f1f43f20a3ccb0890ccb Author: kent Date: Sun Feb 5 06:11:28 2006 +0000 Adding some more error test cases. commit a48c5edb21631fd69600964c04484a99e93255c3 Author: kent Date: Sun Feb 5 06:10:54 2006 +0000 Letting para (...) min and other paras that return values act as expressions. commit 42be2aa1875699a0f986c464d063d6902e851fd1 Author: kuhn Date: Sun Feb 5 05:44:32 2006 +0000 consolidated some duplicate code commit 6f21eed27b30cd1e9f7ee12a1453baa8b00cb61e Author: kent Date: Sun Feb 5 05:37:17 2006 +0000 Passing pfc parameter down to pfParseExpression commit 04ada037db9ca47456246092b7715c93edb1027b Author: kent Date: Sun Feb 5 05:24:38 2006 +0000 Adding parens around el in collection part of para statement. commit 03f33f1a9ee7ace6427b5199fd5a74e50479b25a Author: kuhn Date: Sun Feb 5 05:21:30 2006 +0000 added support for RR machines commit 93a6dd734edb7d6d65aaea6eb3a4a2dd8b1ebf93 Author: kuhn Date: Sun Feb 5 04:23:50 2006 +0000 expanded to handle up three machines at a time to reduce redundancy in calling programs commit 7f45d3235b0a8420062f68a5222406786a72c87e Author: kent Date: Sun Feb 5 01:39:43 2006 +0000 Starting to put in para invocations. Adding parenthesis around el in collection part of foreach statement. commit f63b0ff2fe76b5fd8058e045008a2c4a054623ab Author: kent Date: Sun Feb 5 01:39:11 2006 +0000 Adding parenthesis around el in collection part of foreach statement. commit 478be16d1f589c62fdb17858260a3bfbacfb7517 Author: kent Date: Sat Feb 4 19:39:06 2006 +0000 Fixing foreach test case now that syntax is settled. commit df53541f74b87046af5d70c07f7390434f8366f4 Author: markd Date: Sat Feb 4 18:35:08 2006 +0000 added missing expected result commit d33864843c2a07cf6dd307c680dbf34a989237b4 Author: kuhn Date: Sat Feb 4 17:34:59 2006 +0000 added machinename check to newly added third machine commit 0c8c0d298fa69e4041b422372bf811adb430f4f3 Author: galt Date: Sat Feb 4 16:00:02 2006 +0000 "Encode release log update" commit ea71c98084d0387261eb3c90f24a58b2399af489 Author: galt Date: Sat Feb 4 16:00:01 2006 +0000 "Release log update" commit 3e1b2e21b876a52f484b40dc6bb2074cce8cb3f1 Author: daryl Date: Sat Feb 4 11:36:38 2006 +0000 added hapmap primate alleles and DAFs commit 1f175f2582f426c42295e89832e116e78a212de8 Author: heather Date: Sat Feb 4 05:41:10 2006 +0000 extend to loc_type 4-6 commit 7721b597d46b0eee8518d8c25f33fb0baae64aea Author: heather Date: Sat Feb 4 05:29:20 2006 +0000 cleanup commit e11e2ef3556006616fcd0b3b216ad1075a5381d8 Author: heather Date: Sat Feb 4 05:24:28 2006 +0000 convert to using dyString commit 1878229015c4bfaae6e07e6bb8de625db76cdc0f Author: kent Date: Sat Feb 4 05:20:17 2006 +0000 Adding multiAssign test case for tuple/tuple assignments. commit 0e956adc914c573a823474f7748247920e95c95b Author: kent Date: Sat Feb 4 05:18:21 2006 +0000 Removing debugging statement. commit 4b71738c855fc3c1dd56ed60160501e56047eb86 Author: kent Date: Sat Feb 4 05:17:37 2006 +0000 Being a bit more thorough about flattening assignments. commit c4df90c5ba9e67f318134b077ed81b0e7eae086a Author: kent Date: Sat Feb 4 05:03:09 2006 +0000 Flattening tuple/tuple assignments into a list of simple assignments. commit 0802488ce84acedc33647f3ba6615eedfff46ca3 Author: kent Date: Sat Feb 4 04:19:48 2006 +0000 Preventing para functions from returning references to globals. commit b55b845c257927854968e793dbe5f1a05437a920 Author: kent Date: Sat Feb 4 04:00:33 2006 +0000 Detecting when program tries to do arithmetic on objects. commit 1b060d6f5043a2e69a3c955bb070f577ea0634ff Author: kuhn Date: Sat Feb 4 02:58:18 2006 +0000 added support for third machine and for doing all hgw machines at once commit 9fc32e2066e9b1ebdba3aa3b1cf802b4bb937618 Author: kent Date: Sat Feb 4 01:50:28 2006 +0000 Preventing writing to a non-local object assigned to a local variable in a para function in many cases. Not yet handling case where non-local returned by a function call. commit 972b1c328ef8135f754fc8ffe33f229d0ee1cf7b Author: kent Date: Sat Feb 4 01:48:07 2006 +0000 Adding some more test cases. commit 874ee85fe561fce869effd373e86edecc2d5d843 Author: baertsch Date: Sat Feb 4 01:30:33 2006 +0000 New version of automatically generated description file commit 27071634459ef1161b9ce3a251cbb99720db49e6 Author: angie Date: Sat Feb 4 01:23:45 2006 +0000 Pass trackDb to wiggleDataVector from above instead of making wiggleDataVector query trackDb -- in the case of a wiggle that belongs to a wigMaf track, the trackDb query will come up empty. The dataVector trackTable code absolutely requires a trackDb (make it errAbort instead of segv in case I've missed any additional cases where it might get a NULL trackDb). commit eef24dd06d1e57ff2397b194b115ba1ab2dcb457 Author: angie Date: Sat Feb 4 01:18:28 2006 +0000 In anyIntersection, check existence of the specified table (if we just switched to a different database, it might not exist). Clear intersection settings if the table doesn't exist. commit 3f0ff24b75f96e14041fad51d8d8b25ca32970e6 Author: baertsch Date: Sat Feb 4 01:17:13 2006 +0000 remove vibCho1 commit 5334bb136ed82a1b5fd6a437616fff395be05734 Author: jen Date: Sat Feb 4 01:09:56 2006 +0000 Adjusted rules for ratStsTrueName. commit 0fa4c522147e08c5677061a8af022c811a25a112 Author: angie Date: Sat Feb 4 00:41:31 2006 +0000 Broaden the cases in which curTrack->html is used to describe curTable -- previously curTable had to be curTrack->tableName, but now it can be a subtrack or the wiggle of a wigMaf track. commit e0f8cd9ad39ef03b1c76f0ae431a004f6980cd74 Author: baertsch Date: Sat Feb 4 00:29:32 2006 +0000 add chains and nets for hg17 and hg18 commit 7a4b44803721fcea36bd40e043f9f78f3d97faeb Author: heather Date: Sat Feb 4 00:27:35 2006 +0000 fourth step in SNP processing: expand alleles (refNCBI) of form ...(ACGT)#(#)... commit f1c44ab7a33be958b8daadd0544b5517c74069fc Author: hiram Date: Sat Feb 4 00:20:47 2006 +0000 Continuing with the STS markers. BAC ends are done commit 4f71075285a35ff4533cccb3a2f54454011c8a01 Author: kent Date: Fri Feb 3 23:44:37 2006 +0000 Adding another few error handling test cases. commit 5b655d147a52d4a9464694933a75340350be6cdf Author: kent Date: Fri Feb 3 23:44:06 2006 +0000 Adding check for polymorphic declarations outside of a class. commit aa353389d38e02fda4c9618c416a6005500538ff Author: kent Date: Fri Feb 3 23:43:00 2006 +0000 Updating 'include' bit. commit e2346d51d8dde1f523760c0003bb445e34e82985 Author: kent Date: Fri Feb 3 23:42:12 2006 +0000 Doing a better job of dumping polymorphic types. commit 75ddf3e97920968cdc008e61ccefca97810d57f5 Author: kent Date: Fri Feb 3 23:41:25 2006 +0000 Moving where typed-tree is dumped to before the para and flow checks. commit ac2a6591054111ec905af049b44a049e8f026245 Author: kent Date: Fri Feb 3 23:40:56 2006 +0000 Adding sqrt function. commit 89a34fd3c5c490cb8d3c7c5b541cdf6c5106add8 Author: kent Date: Fri Feb 3 23:40:36 2006 +0000 Adding a numerical module. commit 6ead218e67c5b898188a8af91162cddf53b2a026 Author: jen Date: Fri Feb 3 23:10:27 2006 +0000 Adjusted minCheck for hg16.pseudoMrna table. Old version of track will never be rebuilt (and corrected). Other hg dbs use default rules, although hg15 is the only other one with the related table mrnaBlastz. commit c4df1a004b28ad981906aa2e0eab6b0afb1d0ac1 Author: jen Date: Fri Feb 3 23:03:53 2006 +0000 Adjusted minCheck for pseudoGeneLink table. Old version of track will never be rebuilt (and corrected). hg17 and higher will still use default rules. commit 7e7a41d1916d444385b95de213ee20464b1dedde Author: jen Date: Fri Feb 3 23:03:04 2006 +0000 Adjusted minCheck for pseudoGeneLink table. Old version of track will never be rebuilt (and corrected). hg17 and higher will still use default rules. commit d1f9a81cadce6a477a770492fd998d7c77eba5c3 Author: hartera Date: Fri Feb 3 22:58:58 2006 +0000 Edited chrom description to make it generic. commit 65aee93e17892cab8a178af7d8768ee46acf491f Author: ann Date: Fri Feb 3 22:58:42 2006 +0000 re-ordered the mail list options commit ba97f64f27a05c3890453ce1e88e2487302b29c2 Author: hiram Date: Fri Feb 3 22:49:47 2006 +0000 Initial source, updated from existing Terry script in /cluster/bin/scripts commit 2222be1258fd6169ed21d6f710e72549638e8d60 Author: donnak Date: Fri Feb 3 22:45:58 2006 +0000 Re-added genome mailing list address. commit eea588bbf77233e6971acadf083a2f3381752757 Author: hartera Date: Fri Feb 3 22:44:12 2006 +0000 Edited chrom description to make it generic. commit 7f847da3f9ee5a46a67ad51736ba0b7bbcccb269 Author: hartera Date: Fri Feb 3 22:39:35 2006 +0000 Edited chrom description so it is generic. commit 7655fedee6500eec8a822452e98c42582757c2ee Author: markd Date: Fri Feb 3 22:29:48 2006 +0000 fixed problem with spliting adjacent mafFrames when they are in different maf blocks commit 4c54beda1dc1a9ca31da37269e76154fb3163924 Author: hartera Date: Fri Feb 3 22:23:02 2006 +0000 Edited chrom description. commit 975a51dd581942653e216b49f61be3154ec9403d Author: angie Date: Fri Feb 3 22:11:32 2006 +0000 Several fixes for the new mm6 jax tracks' identifiers. commit b7842e0d92bc2b96dee953f484b66a6a472cf4a0 Author: hartera Date: Fri Feb 3 22:10:15 2006 +0000 Edited description for chrom. commit 83e750e9f4f440e74b2b789084355c473e9fa851 Author: hartera Date: Fri Feb 3 22:03:48 2006 +0000 Edited chrom description to make it generic. commit 01688a91337236952d5a47713ab58b6ad7415ec2 Author: kuhn Date: Fri Feb 3 21:57:04 2006 +0000 changed 8 spaces to a tab because it wouldn't work commit 9e88e54efdaec1c2e2edb3b527119418ae52d68e Author: kuhn Date: Fri Feb 3 21:55:17 2006 +0000 fixed a typo commit c962ef98c4e88e7cccac0aa8748834aaa792cf41 Author: kuhn Date: Fri Feb 3 21:51:32 2006 +0000 added dbUpdateTimes.csh, a utility to get a list of tables with timestamp out-of-sync between dev and beta for a whlie database commit e0b17fc7835592b58a44b4994e9a36a9982c19c8 Author: kent Date: Fri Feb 3 21:29:12 2006 +0000 Fixed crash on searching for 'protein 1' commit 9f6dadd00dc7e686693d569585723bf2007e7d8b Author: jen Date: Fri Feb 3 20:13:17 2006 +0000 Deleted rule for dm1 data from identifier locusLinkId on Angie's recomindation. commit 86882dd71c66b0bf3bb076169fbeaf33b5bbd985 Author: kent Date: Fri Feb 3 20:06:38 2006 +0000 Adding test case for type mismatch between classes with no fields. commit 5e3e294f8815be0676f6418464f4c4912ac8772b Author: kent Date: Fri Feb 3 20:05:46 2006 +0000 Fixed bug so that errors/testMismatch1.pf fails with a syntax error rather than a run-time error. commit d946c316ad572839bad9b4ff65aee52f15be1054 Author: hartera Date: Fri Feb 3 19:38:18 2006 +0000 Edited chrom description to make it generic. commit ed195f99a12623b3aae16d6e457298b25b50d65e Author: hartera Date: Fri Feb 3 19:31:08 2006 +0000 Edited descriptions and made the chrom description generic. commit e8c4d1ffe7f4ae472f95d9f1cfd765e73ef3a162 Author: hartera Date: Fri Feb 3 19:27:15 2006 +0000 Description edits including editing of the chrom description field. commit 3729c490cf5f28a84803d83c7562f64b5742e143 Author: hartera Date: Fri Feb 3 19:24:03 2006 +0000 Edited chrom and oChrom fields to make them generic. commit 0e7a170e3a8c16aaa0db2e03356b51f19b695172 Author: hartera Date: Fri Feb 3 19:22:42 2006 +0000 Edited chrom description to make it generic. commit 09d8dfac5ae2cf02d2af9bdaa180ff5c2a2a2706 Author: hartera Date: Fri Feb 3 19:08:42 2006 +0000 Edited chrom and otherChrom description to make them generic. commit c203191b8a2ef166a869187e6f52c227b72633db Author: hartera Date: Fri Feb 3 19:06:21 2006 +0000 Edited chrom description to make it generic. commit 7f460b828dae652f788d1cb884d7f329db79d28a Author: kent Date: Fri Feb 3 19:02:45 2006 +0000 Improving opening comment. commit 8d864be998f1854db089ede80d702511f5e78fd3 Author: ann Date: Fri Feb 3 19:01:17 2006 +0000 Fixed typo commit 251ba87dd39537ef1692cc3d946b1a95053c5ba6 Author: ann Date: Fri Feb 3 18:59:27 2006 +0000 Reworded posting message commit 5bdb8d1cc69dd347743c1e27c3f7d51f28a42606 Author: ann Date: Fri Feb 3 18:59:11 2006 +0000 Added google search box. Reworded posting message commit 682f9b1eb3ffddbe81f6ef775d56a0245d6eda23 Author: hartera Date: Fri Feb 3 18:58:52 2006 +0000 Edited chrom and otherChrom descriptions so that they are generic. commit 8945b0557d995b5bdc9d3d6ecce7fa106d7f7d13 Author: hartera Date: Fri Feb 3 18:53:58 2006 +0000 Edited chrom description to make it generic. commit cbacc3067dbc8fea54be5d5c91b88d7a743a1e3d Author: hartera Date: Fri Feb 3 18:41:58 2006 +0000 Edited chrom description to make it generic. commit 73d71cd4a816ae8b3c4b3e80b83f8fe18fc9d686 Author: angie Date: Fri Feb 3 18:32:24 2006 +0000 Fixed off-by-one start coords of jaxRepTranscript. commit cf35f423944f3a05633eed6e5c48268f82c05c09 Author: baertsch Date: Fri Feb 3 18:05:23 2006 +0000 changed chains nets from rheMac1 to rheMac2 commit 4783c77125533503a986edd1986bd7b811683119 Author: kent Date: Fri Feb 3 16:59:31 2006 +0000 Adding description index instructions. commit 1cae4c318f61c02609fb1309bba3c73d7558375a Author: galt Date: Fri Feb 3 16:00:02 2006 +0000 "Encode release log update" commit ea92281ef4be33df81184022bbf11ad00225d1eb Author: galt Date: Fri Feb 3 16:00:01 2006 +0000 "Release log update" commit c0835ec82fb34b86bc65b94fc151a8e987d56448 Author: hiram Date: Fri Feb 3 06:20:09 2006 +0000 bacEnd pairs tracks reloaded, somewhat better coverage than before but still not up to what hg17 had commit a01121269ab170d87227926f5439d64d9041fca2 Author: jen Date: Fri Feb 3 03:02:23 2006 +0000 Adjusted minChecks for altGraphX checks against hg Dbs. commit c11c1d83571a4cf8180841f3eaf390ace610a5cb Author: jen Date: Fri Feb 3 02:40:32 2006 +0000 Add minCheck values for dm1.bdgp table checks. commit e8740d5bf6a4c8c0fe9dd960b007c9c040e130fa Author: jen Date: Fri Feb 3 02:26:38 2006 +0000 Comment out dm1 check in identifier LocusLinkID. Changing mincheck was not enough to cure the false error. commit c8f491a5786bb2f986e90451abc32b243375aeaf Author: jen Date: Fri Feb 3 02:08:03 2006 +0000 Adjusted mincheck percetages in identifier locusLinkId to resolve false errors. commit ca71b096c3c78c31e5cf56008f21df9c95519c61 Author: kent Date: Fri Feb 3 01:08:43 2006 +0000 Adding a little bit of checking for legality of para and flow vars. commit 54d9f1182d86c75d8b36cf9c03a8b6c1764ca1c1 Author: kent Date: Fri Feb 3 01:07:55 2006 +0000 Stripping commented out code. commit 1e435fc0ac74c54a57d483ec7963cfc8d3a081cb Author: kent Date: Fri Feb 3 01:07:21 2006 +0000 Adding some test cases. They don't all work yet. commit 213df7c35ca925519a5a6707e4794844c2fcba41 Author: jen Date: Fri Feb 3 00:38:18 2006 +0000 Lower percent minmatch for mm7.mrnaRefseq.mrna vs refLink.mrnaAcc in identifier refSeqID. commit 3bd2796baab08f9aab9a75511058e3f31c293272 Author: jen Date: Fri Feb 3 00:20:24 2006 +0000 Lower percent minmatch for mm7.spMrna.mrnaID vs refLink.mrnaAcc in identifier refSeqID. commit da621af31d02e3ff2c298c58b9ae87d5ff75e543 Author: jen Date: Fri Feb 3 00:12:38 2006 +0000 Lower percent minmatch for dm1.bdgpToRefSeq.value vs refLink.mrnaAcc in identifier refSeqID. commit 779c313fb066285ed20860a8c5a7b6448a9c45f1 Author: hiram Date: Fri Feb 3 00:07:39 2006 +0000 Adding monDom1 chain and net for comparison with monDom2 commit c5b58bf8133e5f1ea2ef8afc3d9ce9cac1c2e8ab Author: jen Date: Thu Feb 2 23:47:32 2006 +0000 Adjusted rule for mrnaOrientInfo versus refLink. Added ingore DBs for those with xenoRefGene but no refGene. Also ignore hg15 - does not use autoprocess and rule does not apply. commit ab6a609e354da1b092ea09e508d747f9f1bb3300 Author: fanhsu Date: Thu Feb 2 23:41:13 2006 +0000 Added FUGU BLAT track. commit 6277e61cecf23ac0e65bab8dbbb5dc647ffe89a1 Author: hiram Date: Thu Feb 2 23:33:43 2006 +0000 ideoband track done with files from Wonhee Jang commit eae56fa35ce8dd04f93f87856bd30ec4558a31d8 Author: fanhsu Date: Thu Feb 2 23:29:06 2006 +0000 Added HInv track. commit eaf74530590569555e8c8b1c361edcedd5bb3d25 Author: fanhsu Date: Thu Feb 2 23:23:46 2006 +0000 Created HInv.sql. commit 167c1ce7635b7c9c8b87afec99299000dcd0da9e Author: jen Date: Thu Feb 2 22:24:55 2006 +0000 Adjusted rules for mrnaOrientInfo to remove false errors. Almost every database was failing. Check now effectively verifies that the data exists, but does not place any other conditions. commit c1f2da9a77e34f5b7c378a764a076eb8dba0dabf Author: kent Date: Thu Feb 2 20:46:30 2006 +0000 Adding master paraFlow makefile commit 8343f08647883a02b031e9601ed5fa8c47642834 Author: kent Date: Thu Feb 2 20:45:54 2006 +0000 Adding some more words. commit ad72568beaeabed38ead01e5bd8cb26762823720 Author: kent Date: Thu Feb 2 20:42:10 2006 +0000 Making it handle situation where there is a .pfh but not a .o file for a module better. commit 1d06d0b080dd703b5305ea86c5a22bc121041a9a Author: kent Date: Thu Feb 2 20:41:43 2006 +0000 Moving most of test target to makefile in test directory. commit 1fa23b21b033d7ec7bb68f423d1b232f1013ef3f Author: kent Date: Thu Feb 2 20:41:11 2006 +0000 Adding makefile with test and clean targets. commit 713089fa7c50dfa1277bbae4cc38b555ad44d6a8 Author: daryl Date: Thu Feb 2 20:37:12 2006 +0000 added mm7 commit 924f1d480ae846f5caad177138d9a1711c0be67d Author: kent Date: Thu Feb 2 20:37:01 2006 +0000 Reordering expected. commit bc51691b5453ad87eae8595098f364b9ba6f49a7 Author: ann Date: Thu Feb 2 19:54:53 2006 +0000 added commTrio.csh commit 66c7df4a0081d540f81fc857b593fdfa857c616c Author: ann Date: Thu Feb 2 19:52:49 2006 +0000 Initial script addition. Sorts and compares two files. Counts unique and common records. commit ac9400c19dfa19c9f1513b65a23b6a89afaf304a Author: baertsch Date: Thu Feb 2 19:52:30 2006 +0000 add rheMac2 commit 0e075f249735831a9f5b8bf976c68ad7f3d617db Author: kent Date: Thu Feb 2 19:16:48 2006 +0000 Simplifying it a bit more. commit 8aa09fafa72ba1de4bf181db4da429d79de083ea Author: jen Date: Thu Feb 2 19:12:04 2006 +0000 Adjusted percentages for dupSpMrna table for mouse/rat/human builds versus knownGene.name for older KG builds. commit ffe5632e617d146038bc92799cd370f8bb61b411 Author: kent Date: Thu Feb 2 19:12:02 2006 +0000 Simplifying this to just get known gene descriptions. commit 833f3d4b14ecde3c649b7dd89ce45ecd10079dc5 Author: jen Date: Thu Feb 2 19:08:23 2006 +0000 Adjusted percentages for dupSpMrna table for mouse. commit f8adf9959fdabbce0f77b4c2b9ff4a0a90509a39 Author: hiram Date: Thu Feb 2 17:45:48 2006 +0000 update obsolete usages of the cd ...; make construct commit ef075e4648e6e38a0adf0f21c1e21c1ee637da8e Author: markd Date: Thu Feb 2 17:36:12 2006 +0000 don't default ESTs to 5' commit 03e8150e905cfd7bc09e5bb286f4e6c3c8729375 Author: kent Date: Thu Feb 2 17:25:06 2006 +0000 Adding visiGene probe ID to search. commit 78533c6d259952341bbaad21af0cbea273d7989a Author: markd Date: Thu Feb 2 17:16:37 2006 +0000 allow clone_lib and cell_line fields to be multi-line commit 52982765862d4f5e7a87450812ef3d54b4b533df Author: kent Date: Thu Feb 2 17:15:24 2006 +0000 Adding search of description. commit 09ccb7e92afa35088502a9f01ebe7578b0636ff8 Author: kent Date: Thu Feb 2 16:24:48 2006 +0000 Freen checks on join timing. commit 5d0dd536c530a35a8e713e8ac8064ac8fa67dc83 Author: kent Date: Thu Feb 2 16:24:24 2006 +0000 Fixing a bug that typically only manifested when creating very long strings with dyStringPrintf. commit db5a5bed1988c0f553a452a88472f71ae104f6e8 Author: kent Date: Thu Feb 2 16:22:17 2006 +0000 Removing mutant suppression. commit 91f53c18ae7a5791b5bac624b6bfa54e4ddf04ba Author: kent Date: Thu Feb 2 16:20:11 2006 +0000 Ifdefing out bits of code that call config page. commit f8311c872ef319e37e7448c7f585f9cd620f569d Author: kent Date: Thu Feb 2 16:19:08 2006 +0000 Start of config page. commit 524cf906a6f3591c758abbb790e9be84a17d0857 Author: fanhsu Date: Thu Feb 2 16:07:00 2006 +0000 Fixed a bug on building spMrna table. commit a65934c4b66eae7befd0b837576dd873ab8e332a Author: galt Date: Thu Feb 2 16:00:03 2006 +0000 "Encode release log update" commit 6e087a768b8a395d3c05c7214738defc88651c6d Author: galt Date: Thu Feb 2 16:00:02 2006 +0000 "Release log update" commit 9a555677dc6d439f94f39ee9da63195c2880f870 Author: hiram Date: Thu Feb 2 06:02:14 2006 +0000 Continuing with the STS markers creation commit 5383785476851e6f7000541ae3f0def952225330 Author: kuhn Date: Thu Feb 2 05:48:48 2006 +0000 added support for split tables commit 7562dc0148b1e998101aaaf270e0d9761315cb15 Author: kent Date: Thu Feb 2 02:50:30 2006 +0000 Putting a cap of 500 on the number of known gene matches that are returned. commit c4278ee464be2d676e4fb930004af4e864ba9812 Author: hiram Date: Thu Feb 2 01:23:13 2006 +0000 Continuing with STS marker alignments commit a180839227b1f45d82019dbf67f1f269920b9b75 Author: jen Date: Thu Feb 2 00:51:31 2006 +0000 Added mm7 specific checks to some genbank identifiers. commit c63b90e358731145dc5f4462740c9f74e6d46cf1 Author: kuhn Date: Thu Feb 2 00:14:49 2006 +0000 changed so it outputs only the first chromname, not the word 'split' commit d7d191351122822fd14c8e544568802db790dccb Author: fanhsu Date: Wed Feb 1 23:55:26 2006 +0000 Added gnfAtlas2 track. commit c9998da301b75f02a1802f9ee326890be672de24 Author: hiram Date: Wed Feb 1 23:40:43 2006 +0000 Continuing with the clone and sts markers track developments commit 5c2f4e5aef779d3380f6e2e5e8480d95fd0758a4 Author: jen Date: Wed Feb 1 23:28:52 2006 +0000 Lowered percentage for hg17 (only, not hg15 or hg16) in identifier acemblyName. Removes a long-time false error from being reported by -keys. commit 3c6a11ff2daf2f42f2875eddff1326b6a0e82205 Author: fanhsu Date: Wed Feb 1 22:37:16 2006 +0000 Added AFF U95, U133, and GNF Ratio tracks. commit 1e46ac7149f0d801d1ccfd6f57154a9da90f80a2 Author: daryl Date: Wed Feb 1 21:20:00 2006 +0000 added undefinedYellowColor for missing data, initially in LD and MAF displays commit 08bb9277dd79fd806b47edf70a1fdcc3a7697e7c Author: kent Date: Wed Feb 1 19:35:13 2006 +0000 Optimizing weeding of private images. commit 78101eca54c45a8e6fa9ee378a901d1b33f4d8fd Author: jen Date: Wed Feb 1 19:34:29 2006 +0000 Added gladHumESDistance to identifier knownGeneId. Consistent with other gene sorter distance tables. commit 4c02224032b23e1a89bc22e74cb6d017ad9d6729 Author: hiram Date: Wed Feb 1 19:27:02 2006 +0000 Increased limits on arrays used to construct listings of aliases, now using safef in place of sprintf, removed unused variables commit 883ae1cd8e51352a22129d2c2159d0ab48bc2346 Author: donnak Date: Wed Feb 1 19:01:16 2006 +0000 Fixed broken link. commit 164389b620fe81124906ee0404e3422b446c63f8 Author: ann Date: Wed Feb 1 19:00:56 2006 +0000 corrected link to FAQmaillist commit d634985f902efea8478e5c566d35a804ecdbce30 Author: donnak Date: Wed Feb 1 18:44:48 2006 +0000 Switched Jobs link to open the CBSE jobs page. commit f14cd315f12479266cdd5bf5785f3c9c39b75e20 Author: ann Date: Wed Feb 1 18:42:15 2006 +0000 reworded section on mailing list to point to new FAQ commit 1c45be586c8239964f4f6b1a44231f8d7de094f5 Author: ann Date: Wed Feb 1 18:41:37 2006 +0000 reworded section for mailling list to point to new FAQ commit 5ecc7eabcfb86aeddc710460ec82b979817eec6e Author: ann Date: Wed Feb 1 18:39:24 2006 +0000 Added Q&As to the FAQ commit 5c4c5a1860b9061f7d7babec7701ca261f84e0a2 Author: ann Date: Wed Feb 1 18:33:33 2006 +0000 Added link to new maillist FAQ commit 11ab34f2694a3409e1e740a500a88c23bc0d16dc Author: donnak Date: Wed Feb 1 18:29:27 2006 +0000 Made a few minor edits. commit 02d2c335abf6078f45041df34e088d492c756757 Author: donnak Date: Wed Feb 1 18:12:18 2006 +0000 Made a few tiny edits. commit a24e945873acd267ce09929d13ef103594387680 Author: galt Date: Wed Feb 1 16:00:04 2006 +0000 "Encode release log update" commit 8fb0a7a62c1dcfcc949e0313207ea7daf9de0d2e Author: galt Date: Wed Feb 1 16:00:03 2006 +0000 "Release log update" commit 8b041bf7b855c98a4de92a942cdaf4fd6ded72b4 Author: daryl Date: Wed Feb 1 10:50:25 2006 +0000 another minor rearrangement commit c39ffcd662cea6cff7c7e4c975dcff9bcb1ec69a Author: daryl Date: Wed Feb 1 10:48:32 2006 +0000 expanded population descriptions in LD invert block commit db8f1a6232a9a7c914f828759cfb237988690595 Author: daryl Date: Wed Feb 1 10:43:37 2006 +0000 minor tweaks commit 3821e2e5143117372cc1a1e44f350cc7e82a4c58 Author: daryl Date: Wed Feb 1 10:35:04 2006 +0000 expanded first paragraph, emphasized LOD color scheme, and reformatted HTML commit 3f5f97c63ffc69dd0e33c5763f5cb1b2ebafd1ff Author: daryl Date: Wed Feb 1 10:24:47 2006 +0000 LD: add background map, reduce outline visibility commit a00b384a553f2482b8c0f7d2f3f14e4f732968ae Author: heather Date: Wed Feb 1 10:14:07 2006 +0000 fix handling of range coords; cleanup error logging commit 4e377fab46e03deac31a1fa390fef52441030c50 Author: heather Date: Wed Feb 1 09:57:58 2006 +0000 third step in SNP processing: process locType commit 1fce65918a841cee6aace66726fc4885ba4ebc1e Author: heather Date: Wed Feb 1 09:05:54 2006 +0000 sqlDisconnect --> hFreeConn commit 7aa004e75a9fa7b48eb4f73a6d3e6c8a7f1216b8 Author: heather Date: Wed Feb 1 08:21:54 2006 +0000 rearrange main order commit f7a575a6bdcf3cd57ab30583d9b533eb5cd1add8 Author: heather Date: Wed Feb 1 08:21:23 2006 +0000 filter out where phys_pos = 0 commit 55b1a2e7eaa4abc6066872bbe29a851bb9d2b67d Author: baertsch Date: Wed Feb 1 01:10:58 2006 +0000 fixed spliced exon feature commit 432bb112276dcf955e96434c249a5312aa512809 Author: fanhsu Date: Wed Feb 1 01:05:58 2006 +0000 Added haplotypePos track. commit 426c1f51aa709e0dd80e2b6e3a1aefbcaa7ea32b Author: baertsch Date: Wed Feb 1 00:55:16 2006 +0000 added rheMac2 and gap.html commit 84c9c21dc7b6f2b37dbc527b5596d4bafc15d359 Author: heather Date: Wed Feb 1 00:49:39 2006 +0000 a faster split by writing to 25 open files commit 545b7fb1120c4a3fde500d3c0e7c11c8de172bd7 Author: baertsch Date: Wed Feb 1 00:41:03 2006 +0000 added rheMac2 commit 6911edbbc915e6cd640913463873bfe1c1be3727 Author: kent Date: Tue Jan 31 23:56:52 2006 +0000 Getting copyright and caption text from MGI_NoteChunk table rather than old place due to changes in MGI database. commit ac8e875e2869297c4a20e0c657360b6e65ab16f6 Author: jen Date: Tue Jan 31 23:26:40 2006 +0000 Added comments for RETROGENE track (pseudoGeneLink,psuedoMrna). commit 0b679df6370e79a67e9034b9676df677e09f2a5f Author: kayla Date: Tue Jan 31 21:52:39 2006 +0000 Adding makeRheMac2.doc for Robert commit 5aec4685282030054ba1a530e80a990a04861a2c Author: ann Date: Tue Jan 31 21:43:04 2006 +0000 initial doc - how to post a question to the mailling list commit 88244468ea48f124b27b9a057887b16c72df4d6f Author: heather Date: Tue Jan 31 20:51:37 2006 +0000 fix typo in usage message commit 51efcbf6d73f1cfdec203e656366f0cc2caa15b1 Author: heather Date: Tue Jan 31 20:37:14 2006 +0000 include chromName commit 7811f143abd77e01a6517f376cc2b9e1ff6eec96 Author: heather Date: Tue Jan 31 20:16:34 2006 +0000 add a warning for non-zero orientation of contigs commit 79a313ccb8ba0f2aa98d8d6225f086f11f54bbc4 Author: jen Date: Tue Jan 31 19:49:39 2006 +0000 Added note about ensGtp data error fix from 2004-08 not being pushed to rr. Typo fix. commit b7abeb611c67e3b0021faf54039271b9565888b4 Author: heather Date: Tue Jan 31 19:42:32 2006 +0000 add weightHash from SNPMapInfo commit 94021f24d11405e41be2b0588cc4e12cfa6d0a26 Author: jen Date: Tue Jan 31 19:35:52 2006 +0000 Added note about ensGtp data error fix from 2004-08 not being pushed to rr. commit eb61a81c94fe101bf801c7a728578e62a2e1ca5c Author: jen Date: Tue Jan 31 19:12:53 2006 +0000 Added note about vegaPep table drop. Fix typo. commit fbd5c522a33b7a973202e964b02d36b797c18463 Author: heather Date: Tue Jan 31 18:40:02 2006 +0000 starting to add snp125 rules commit 2a7cb938fb74e1c6aa11b263c2302cee0b2ee40e Author: heather Date: Tue Jan 31 18:35:42 2006 +0000 first step in SNP processing: filter ContigLoc using ContigInfo hash commit 70f728503b842769659aa71a8c1d1d1d8d8c64c5 Author: jen Date: Tue Jan 31 18:19:23 2006 +0000 Added note about vegaPep table drop. commit 8f9d3f84a81cbb102a96f4786b1761ec478b12c9 Author: fanhsu Date: Tue Jan 31 17:20:36 2006 +0000 Updated dbDb hg18 entry to "Feb. 2006" and "NCBI Build 36.1" to be consistent with NCBI. commit 63219909127a3ad842d6740daf606276ab274508 Author: galt Date: Tue Jan 31 16:00:03 2006 +0000 "Encode release log update" commit 1833583401084c10ab5419282a15e927f22b494c Author: galt Date: Tue Jan 31 16:00:01 2006 +0000 "Release log update" commit 662dc484b73839a3a2d91769706a1e9b34e74475 Author: braney Date: Tue Jan 31 06:37:26 2006 +0000 pareameterize the options commit c074a8da5d1aef05b8a2a8a0c1d4844c214a646d Author: braney Date: Tue Jan 31 06:36:46 2006 +0000 wowworking better commit 903acfb81c911c2e7451f8fd04439e733965450e Author: braney Date: Tue Jan 31 06:35:47 2006 +0000 this is working better. Without deletions it seems correct commit 599b8c37f244516c595505837eef500d9151587a Author: braney Date: Tue Jan 31 06:35:03 2006 +0000 the beginnings of some ordered elements commit 90393f4321b7e21222de3495d87ebe095ad5f779 Author: braney Date: Tue Jan 31 06:34:31 2006 +0000 use one big buffer commit a67638680577119588ce884087e3050db3e7743e Author: braney Date: Tue Jan 31 06:33:48 2006 +0000 make sure element leaves are on genome leaves commit da0d844b26cc3b92241623095db530c4825d16b9 Author: heather Date: Tue Jan 31 03:18:02 2006 +0000 "New version number v126" commit 817622b259ab1eadbf1079ad39c3a3428c45747a Author: kate Date: Tue Jan 31 02:41:33 2006 +0000 More 17-way conservation work commit e0462810c96b0f9b49a2b735050e672d5be1189d Author: daryl Date: Tue Jan 31 02:40:25 2006 +0000 return when there are no items to draw commit ae46471681a50ec4ef356a6ef48c8d6cf7fbcffe Author: braney Date: Tue Jan 31 01:23:45 2006 +0000 add chain to ancestor canHg12 commit d4f81e0a6e52c712e0bf98b4aa05d24a36d344db Author: angie Date: Tue Jan 31 01:14:47 2006 +0000 Updated dm2 genes from FlyBase 4.1 to 4.2; extracted a mapping of FlyBase CG*-R* transcript IDs (or just CG* gene IDs where those aren't available) to UniProt identifiers. Still todo: redo the *BlastTab's with 4.2 genes, then build the rest of the hgNear tables for dm2, finding some way to use the new FlyBase->UniProt mapping. commit d08869508898673fba89be47ab70323d985b4bd4 Author: angie Date: Tue Jan 31 01:10:00 2006 +0000 Re-downloaded (the randoms seem to have changed since last time) on a disk with lots of room; basic browser build in progress. commit 55a21a97fb18926d2552613bf2b05bfb710a928e Author: fanhsu Date: Tue Jan 31 00:48:33 2006 +0000 Added initial part of STS marker track build process. commit d59990a8953092793c71d0240ac25523f255e9a2 Author: angie Date: Mon Jan 30 23:32:30 2006 +0000 Added rn4. commit 0c0c00a131e5fd2c58d34ad39e1784c9c465f0c6 Author: angie Date: Mon Jan 30 23:31:43 2006 +0000 First-cut description for rn4 (Baylor 3.4, Nov. 2004). commit 8d42cb108ae87bbe8539d2768802e4c051f00aee Author: heather Date: Mon Jan 30 22:37:42 2006 +0000 bug fixes commit 9905f3a3bff832b494ca209556c1e0fc1804fe3c Author: daryl Date: Mon Jan 30 21:56:57 2006 +0000 added urls for TB, downloads, and FAQs commit 45c5907be3c1f2d24b4e70e2853d8cf4145d35c3 Author: galt Date: Mon Jan 30 19:28:01 2006 +0000 jax update 20060125 commit 0f5a2444563fda553421d5cd46a698638397e777 Author: jen Date: Mon Jan 30 18:30:34 2006 +0000 Added hg17 to pbDb3 (# Define databases that support known genes). commit d434dbae08b8b3e8b78e23ad4361589cb5998b8d Author: galt Date: Mon Jan 30 16:00:03 2006 +0000 "Encode release log update" commit bbfb9643932a30191029649f5a5c499ed77c557a Author: galt Date: Mon Jan 30 16:00:01 2006 +0000 "Release log update" commit dbddc4412413fb53ccb1628d408e3d7716d432d3 Author: daryl Date: Sun Jan 29 21:08:31 2006 +0000 hapmapLD: increase cutoff for suppression of outlines; suppress drawing across large gaps commit e1ad3b767af06ad408cae8a2f552ab6144a2129a Author: galt Date: Sun Jan 29 16:00:04 2006 +0000 "Encode release log update" commit 89526ca1352446ed0e3b269c861c7b14684eaa92 Author: galt Date: Sun Jan 29 16:00:02 2006 +0000 "Release log update" commit c4184dbe4f83dd327b4ded2f2f186d919ed82f0c Author: galt Date: Sat Jan 28 16:00:03 2006 +0000 "Encode release log update" commit 3065424bb97774c5ff78786f0ed422d0b1167e72 Author: galt Date: Sat Jan 28 16:00:02 2006 +0000 "Release log update" commit 8d5b260e3e6cf5fb410123ff2a7bc9fda33abeb0 Author: markd Date: Sat Jan 28 04:21:26 2006 +0000 added option to check query and target sizes commit fb673d55dfb00adde29adf6f3d1b6b3dddd0dd57 Author: markd Date: Sat Jan 28 04:21:07 2006 +0000 improved pslCheck error message and check for qtEnd out of bounds commit cf0ecccbf4eaed26d9b95a3d198dca797732f27e Author: heather Date: Fri Jan 27 23:52:03 2006 +0000 add comment commit 3f9b45e9783f4c427010cc1bdcf1d44685bbfadc Author: heather Date: Fri Jan 27 22:51:35 2006 +0000 fill in writeSnp125Exceptions commit 83693fdd17ec1c1f543c4f4280f5a0571b8faf63 Author: heather Date: Fri Jan 27 22:43:08 2006 +0000 use string for enum exception commit cd3ed5dda96458f335bcb24657378373aad67bc6 Author: hartera Date: Fri Jan 27 22:19:55 2006 +0000 Correction and addition of information on hg18 chain tracks. Multiz 6-way alignment in progress. Known Genes track in progress. commit b90faa8461fa3ad82b4ce6b61b9aa428f5ee5a02 Author: daryl Date: Fri Jan 27 22:19:50 2006 +0000 fix typo commit dfce647d0f800e8b271e256111dc89eff21387cf Author: donnak Date: Fri Jan 27 22:11:16 2006 +0000 Made a few minor edits to acronym defs. Also noticed missing word in first paragraph...Daryl will fix. commit 4be6597819783e928175c6438e6e351b99ce6d55 Author: donnak Date: Fri Jan 27 21:30:19 2006 +0000 Added note abt Build 35 problems w/chr5, also more details abt Build 35 assembly process. commit 36b5452c9ced188eb66db5ea1d1128d0217660bb Author: fanhsu Date: Fri Jan 27 21:10:38 2006 +0000 Updated highlightItem() to address special situations arised due to "hgg_prot" piggy backing of KG mapName. commit d51343f8cd1f9cd1dc678d1921d0a3d0c87e2449 Author: heather Date: Fri Jan 27 20:28:27 2006 +0000 change to read from chrN.gnl and include chrom in tab commit 5cbb76db24362194184dfa30bf19197778678960 Author: heather Date: Fri Jan 27 20:27:00 2006 +0000 fix up table create commit 29f7ea254926cd8162aa9fde7bb005b9f8e22699 Author: hiram Date: Fri Jan 27 18:56:38 2006 +0000 Do not need relative references to help pages. commit 7accd49e05e5847c344e55eece6fce2978cb7c2d Author: hiram Date: Fri Jan 27 18:40:59 2006 +0000 add a document root configuration to the finding of the help directory commit 2de795fb7b65bcdde1d5a81cd8be62b8b65401be Author: hiram Date: Fri Jan 27 18:40:27 2006 +0000 Add document root configuration to the finding of the help directory commit bf73a8d0f371356fd1bea93052b6b8087f6aee94 Author: hiram Date: Fri Jan 27 18:39:43 2006 +0000 add hDocumentRoot() option commit 9b8254406591a43435eb57ad051f9398a015dd10 Author: hiram Date: Fri Jan 27 18:38:50 2006 +0000 add document root default and option commit 5cd13dccb8fb2dd562bb9a9fce4696c5f72a0037 Author: galt Date: Fri Jan 27 16:00:02 2006 +0000 "Encode release log update" commit 7ce19a3d6755ff0a356f67d39301279b2301ae6b Author: galt Date: Fri Jan 27 16:00:01 2006 +0000 "Release log update" commit e203341cd895b74e810db25a846b76a6c60b5c2e Author: fanhsu Date: Fri Jan 27 13:29:02 2006 +0000 Added "-extra" option to form overlapping pieces. commit 51c332ea324afbe455d41b2aef65bb07e6c32b19 Author: kent Date: Fri Jan 27 07:13:34 2006 +0000 Speed tweaking known genes search in case where many genes are returned. Removing 'and' from author search. commit f3bae06b77baa494d950febb94e2eb2e40e1526b Author: kent Date: Fri Jan 27 01:00:45 2006 +0000 Handling multiply-mapped known genes a little better. commit 6b4957533b4915952ac8be561fde891889e7eb74 Author: daryl Date: Thu Jan 26 23:12:25 2006 +0000 removed custom limitedVis settings, which removes limited visibility bug commit 5dcfe99db79fc03822e9380661f3ee95a94f3863 Author: galt Date: Thu Jan 26 22:22:16 2006 +0000 adding TODO note commit 34e72bead392dcd102e34206adacc675ecb19132 Author: lowec Date: Thu Jan 26 22:08:36 2006 +0000 I added filter options for the ends of the axt as well as the beginning commit e3c2d3416a06620eb976d1564f421ce1e591b132 Author: markd Date: Thu Jan 26 21:32:44 2006 +0000 added function to return sequences in all lower-case without masking commit f747adcb4bbf8629fb2fbe2a31a5be9f58e6d112 Author: hiram Date: Thu Jan 26 20:22:25 2006 +0000 Finished with monDom2 blastz business commit 002d16674ab0d179daca8a6efc6390d64d764358 Author: kate Date: Thu Jan 26 20:10:00 2006 +0000 Begin autoMZ alignment commit e86f031ebad26af599f6bc7eccbaa2927cbec0be Author: markd Date: Thu Jan 26 19:56:46 2006 +0000 use va_copy to correctly handle reuse of va_list; add defined to deal with compatibility issues commit ea7c0b1c091b9fc47ea19a26e293b09c20fb40e3 Author: heather Date: Thu Jan 26 19:06:03 2006 +0000 add chrom commit bc9273cb0ce3b237ab1ae82ad61a360cf5956e22 Author: daryl Date: Thu Jan 26 18:27:16 2006 +0000 remove debug code commit 0abae7e88d47cfcfe047aa819b875efb87deb45b Author: angie Date: Thu Jan 26 17:51:19 2006 +0000 Added three new tracks from Jackson Labs/MGI: jaxPhenotype, jaxAllele, jaxRepTranscript. commit c8546d9d85934cea6cc7403f3f3a179c3f34cddc Author: angie Date: Thu Jan 26 17:13:06 2006 +0000 Added three new tracks from MGI/Jackson Labs: jaxRepTranscript, jaxPhenotype, jaxAllele. commit 113a248cbfc448dded0372e8901ad0f5db8e39d0 Author: angie Date: Thu Jan 26 17:11:55 2006 +0000 Removed unused variable. commit e772babe20a3c3f0309ea2653d639b019a586008 Author: angie Date: Thu Jan 26 17:06:22 2006 +0000 Added support for new MGI/Jackson Labs tracks: jaxRepTranscript, jaxPhenotype, jaxAllele. commit 58102c0b574f82642bc72155061c4085834033fe Author: angie Date: Thu Jan 26 17:00:41 2006 +0000 Adding bed12Source: bed 12 + "source" column to distinguish among multiple sources for items in the same track. Used for new jaxAllele and jaxPhenotype tracks. commit 65f107f7f217e310c6be54bf67cc3b25ee6a09f2 Author: angie Date: Thu Jan 26 16:59:04 2006 +0000 Extra info for MGI/Jackson Labs Allele track. commit 6de88814903831ba014c3dc35b5d629a5e0b2ad7 Author: angie Date: Thu Jan 26 16:58:31 2006 +0000 Generic 2-column name <-> alias association table. commit 9d6cd1e8a605d45635f5b093758bb1a2f7bc5cac Author: angie Date: Thu Jan 26 16:38:59 2006 +0000 Changes to Jax Phenotype and Allele tracks: instead of composite tracks, do regular tracks with alternate item naming suggested by Jim. commit 035fd04466ba54232abc65aa5655704fa00e62ad Author: galt Date: Thu Jan 26 16:00:02 2006 +0000 "Encode release log update" commit 1a603daf73c71041e7ad1156d1abd580631b79a6 Author: galt Date: Thu Jan 26 16:00:01 2006 +0000 "Release log update" commit a259d7ff26c475c8e842ad8923808fc1cf279adc Author: daryl Date: Thu Jan 26 06:56:33 2006 +0000 updated visibility logic and spacing commit d9183991439ac91ef3d40b87e5b9d570310f9321 Author: daryl Date: Thu Jan 26 06:55:51 2006 +0000 remove double semicolon commit d75f6aadb45b8bf834ba7b0d87992f18198f7d61 Author: daryl Date: Thu Jan 26 06:55:09 2006 +0000 updated visibility to use enum values (tvDense, tvSquish) commit d1fe717d8367e7267ce9bca2135dd440dc664148 Author: daryl Date: Thu Jan 26 06:53:41 2006 +0000 added descriptions, corrections, and clarifications commit c2269a6e83b13f963144b4495fa1996e690b344c Author: kent Date: Thu Jan 26 03:10:27 2006 +0000 Using UniProt accession rather than displayId. Also adding some speed tweaks that together make it maybe 25% faster. commit 6e63211b66aefc14ec06a4ff384d6d81be4b5277 Author: hiram Date: Thu Jan 26 00:43:30 2006 +0000 Loading the huge chr19 chainLink for MonDom2 commit 7ec8880fcbe20a278b6b541bd1ef305b076bab21 Author: genbank Date: Thu Jan 26 00:40:33 2006 +0000 changed debug message to verbose mgc commit 8113a72107ee5b713bcce3548dc45698bacdad60 Author: jen Date: Wed Jan 25 23:46:18 2006 +0000 Updated gap description for new process. commit c1868b6559407bb16987b509d38c6ae310b52bbe Author: heather Date: Wed Jan 25 23:06:44 2006 +0000 add counter commit b3c6ca058fab02f8162cc79f8e2c3168720c06b4 Author: daryl Date: Wed Jan 25 22:57:04 2006 +0000 suppress map drawing for LD track commit 54d211cf4cef2b734ea4e8ce54f66513cf8e8454 Author: kent Date: Wed Jan 25 22:04:04 2006 +0000 Updating expected to reflect database change. commit fb908ac49c706faf93f2793eabaee507f7a92b11 Author: kent Date: Wed Jan 25 22:02:45 2006 +0000 Fixing small problem with first line of .ixx file found by Angie's sharp eyes. commit 9660540b6b241aed0f3e8bad5e6b57e9877e263f Author: heather Date: Wed Jan 25 21:54:36 2006 +0000 adding snp125 commit 6c336cf0f9c88701a8a2dd07bf23d080ef5d90e7 Author: donnak Date: Wed Jan 25 21:37:14 2006 +0000 Updated symlinks for proteome and UniProt. commit 0502ea557353d86c54fe89225d7463d82fa98cc0 Author: fanhsu Date: Wed Jan 25 20:30:22 2006 +0000 Add chain and net to Hg18. commit cc5ae6b35e5cceed5fa62b63525d75e6e2bc983e Author: genbank Date: Wed Jan 25 20:03:57 2006 +0000 improved refseq error checking commit 86a78ece9233eaacacff4cb7d597572c896af309 Author: kent Date: Wed Jan 25 18:59:14 2006 +0000 Rolling back to before free text search. There are still some issues to work out. commit 287ffeb079ed5d305d26a1a933cc124ec19d204a Author: aamp Date: Wed Jan 25 18:38:56 2006 +0000 Remade some distance tables because of knownGene updates. commit aae98892f225d11b8890c2a96be401eadca9727e Author: jen Date: Wed Jan 25 17:47:06 2006 +0000 mytouch changes logged in makedoc. commit dc3340e968f6b2050ce462cdcb6db00510751705 Author: jen Date: Wed Jan 25 17:01:08 2006 +0000 mytouch changes logged in makedoc. commit d9ad296777dfc978a8ca6a8864c0abb37bd7328a Author: galt Date: Wed Jan 25 16:00:03 2006 +0000 "Encode release log update" commit c486ab783d46e288b71d0e2890754925d034a45e Author: galt Date: Wed Jan 25 16:00:02 2006 +0000 "Release log update" commit 1e49008e73e865b2a18b3fc4bfff176d870b1632 Author: markd Date: Wed Jan 25 08:34:57 2006 +0000 fixed bug in computing fasta offsets commit f4aae7920e9cba1155567c84df575a4afe2d4bb7 Author: daryl Date: Wed Jan 25 05:16:10 2006 +0000 change population invert list to match subTrack order commit bc8405649f0ed425f2243fff74dc882f835080cc Author: donnak Date: Wed Jan 25 03:16:22 2006 +0000 Fixed broken link. commit 8e8a95bf4fb113fc88319100ab4b486835f96b06 Author: angie Date: Wed Jan 25 02:08:01 2006 +0000 Added search for geneMapper (RefSeq accessions). commit fc1b13612a88eff7e5ba46dfa6eae5f87f8a6fbb Author: hiram Date: Wed Jan 25 00:03:02 2006 +0000 clonePos is now on all chroms, remove it from here and let the top level trackDb take care of it commit bea3209cfa7f466406715478258a1a7429f55d91 Author: jen Date: Tue Jan 24 23:39:26 2006 +0000 Added (bang)rn2 for a check that is comparing an empty (unused) table to a track that does not exist for this database (to stop false error report). commit 737e07e9d4821341faaae9b34379f9ec47da941c Author: kent Date: Tue Jan 24 22:32:50 2006 +0000 Updating so MGI stuff is more to their liking. commit d167bf13a7c7cb6f1bc81350caaba98aaadeba00 Author: kent Date: Tue Jan 24 22:32:20 2006 +0000 Changing so that it does not get a whole bunch of gene text, just the gene description. commit b53784610e8e34d3747f6f1a69c2e8a027d4bc6d Author: kent Date: Tue Jan 24 22:31:46 2006 +0000 Added expand parameter to trixSearch commit fc6ed634d476dc63f8425a45207e0149c25410a2 Author: kent Date: Tue Jan 24 22:30:57 2006 +0000 Converting VisiGene to using free text search. It will not look for prefixes though. commit 6251b6e8adbfb595bec67f3a43b34987ddfe4f7c Author: hiram Date: Tue Jan 24 22:06:34 2006 +0000 Starting monDom2 blastz commit d4c57d869bedd22ce64cff22d7f1a9a5fa916626 Author: hiram Date: Tue Jan 24 22:05:23 2006 +0000 Running monDom2 blastz commit 7bc369553d274000c4dec34871c58c8daa408ce8 Author: fanhsu Date: Tue Jan 24 21:51:03 2006 +0000 Added a comment by Kate during code review. commit 3845611f5c6f715117ad5738d2d2458d26968a86 Author: donnak Date: Tue Jan 24 21:49:19 2006 +0000 Removed old sysadmin position, added new one. commit 622132e02645d4da64ed144e24dfe40ed3b87c59 Author: heather Date: Tue Jan 24 21:32:28 2006 +0000 need full name for new locType strings commit 5e1ed2f390ce868ba859b1b351667cd7a5f526ba Author: heather Date: Tue Jan 24 21:18:23 2006 +0000 some bug fixes commit 1a33279fe1e10d487349c83ccd91d76d0e775eaa Author: kent Date: Tue Jan 24 21:17:59 2006 +0000 Checking in fullText version under a new file name for reference. This is not compiled in. commit 9537e47ff3567a327e8f7cebb8b11891b1ecc7b2 Author: kent Date: Tue Jan 24 21:17:27 2006 +0000 Rearranging caption a bit to help make MGI folks happy. commit f807c55140bafbd36e81edeb29a16eccc6ad49a6 Author: angie Date: Tue Jan 24 18:24:32 2006 +0000 Moved geneMapper from tablesIgnored to type genePred. commit a2798b663f3c36cd2d1e8522281b7b1451794c2f Author: angie Date: Tue Jan 24 18:07:38 2006 +0000 Reloaded geneMapper without -genePredExt. commit 6cccaf7d2e81e720185b1ff1650c21338d226821 Author: kent Date: Tue Jan 24 18:04:34 2006 +0000 Adding geneSynonym table info. commit dfe5c33010be982a6eb891b3f572dd5c98ff153c Author: braney Date: Tue Jan 24 17:37:35 2006 +0000 squash annotation when squashing maf blocks together commit 8b076396fc737372b33e9450af4f76e66baef0ac Author: galt Date: Tue Jan 24 16:00:02 2006 +0000 "Encode release log update" commit 9303f849261501e455706230c405c935045f6c8f Author: galt Date: Tue Jan 24 16:00:01 2006 +0000 "Release log update" commit 355185dfc21d035bdc746f6518d7e0401c6e87c3 Author: heather Date: Tue Jan 24 08:05:41 2006 +0000 more missing commas commit 1f50b1b4974fc0f91c44f722646a38690408e16b Author: heather Date: Tue Jan 24 07:55:56 2006 +0000 use snp125DrawItemAt commit b1d48f604214b77e9b09f8be47e1bfa26a3695ba Author: heather Date: Tue Jan 24 07:08:16 2006 +0000 add missing commas commit cdc845b2fde430187abb1a4e43931f0cbb9c4e1f Author: markd Date: Tue Jan 24 04:51:43 2006 +0000 added repair of broken seq entries and bogus locations in fasta files commit 87b9c28ace33c78e15e7aa789c0e30513244404b Author: angie Date: Tue Jan 24 02:46:16 2006 +0000 Updated some wording to fit whole-genome shotgun (instead of clone/contig/ golden-path human-style) assembly. commit cbf05bb39c5ad2101d74d8d965d20edbecfc4543 Author: markd Date: Tue Jan 24 02:34:56 2006 +0000 fixed bug on x86_64 where args is passed by reference commit 48bc4bf1160e1a8648b75482771541bb73fc77de Author: angie Date: Tue Jan 24 02:13:12 2006 +0000 Updated gap.html and added more specific gold.html to describe the assembly methods better. commit 7f989c803ac5ce428a9b67ea74ab2ce6f4c8e777 Author: galt Date: Tue Jan 24 01:38:29 2006 +0000 re-making hg17.mmBlastTab and mmBlastNearBest commit 7539f62028a441d58e63c40a03bc31f2f1ca19e1 Author: galt Date: Tue Jan 24 01:25:21 2006 +0000 changing mm6 to mm7 for hg17.mmBlastTab commit eea7dd706637a249ad28d193980f97c655d8140c Author: fanhsu Date: Tue Jan 24 01:15:07 2006 +0000 HGNC reference table. commit d0bbefe17ed0baf384fd2a05bc73dd3ece429776 Author: hiram Date: Tue Jan 24 00:53:00 2006 +0000 finished with remake and reloaded genscan predictions commit 975c68ae0939d7776bf28655b1472a1f5e4f2333 Author: hiram Date: Tue Jan 24 00:45:50 2006 +0000 Making alt-splicing track, and protein browser tables for hgNear, and starting waba to cb2 commit a5fb1bdf2d39abec13df6574f71e41f2e98a115e Author: hiram Date: Tue Jan 24 00:44:45 2006 +0000 Make altGraphX frames based view be generic and available under goldenPath commit 5d324bfd70d03a9e9bb778431ae0a039bc3577ab Author: hiram Date: Tue Jan 24 00:44:18 2006 +0000 Make the altGraphX frames based view be generic and available under goldenPath commit 7d9ece9a5d77a1e1417b5ae73583ddf85971b69d Author: hiram Date: Tue Jan 24 00:43:35 2006 +0000 Measure featureBits for chainSelfLink to compare with hg18 commit 3478d741b4a86788cd291fcf219286c8147d775f Author: hiram Date: Tue Jan 24 00:42:33 2006 +0000 Continue working on clone placement, finish off blastzSelf commit f6ef053144197ce963172232efd0d2cd05897ffa Author: hiram Date: Tue Jan 24 00:39:11 2006 +0000 done with bosTau2 blastz commit fdb615c454123615679e71fe4c25ee40e627a2dd Author: hiram Date: Tue Jan 24 00:37:17 2006 +0000 New repeat masking done, rebuilt 2bit file, started Hg18 blastz, and genscan commit 3d6305285650fbbed36c2df5baf7c9e3cfd47b1e Author: fanhsu Date: Mon Jan 23 23:44:20 2006 +0000 Added hgnc.sql. commit f20b31ff892a3b963dcd8790f9f24137dd2ac78e Author: fanhsu Date: Mon Jan 23 23:44:06 2006 +0000 Added hgnc.as, table defintion for HGNC data. commit 23fd2e62a3c705fac725546bfc571167e2af6757 Author: fanhsu Date: Mon Jan 23 23:30:10 2006 +0000 added getHgnc.pl to download HGNC data. commit 7fa5cdc4b6b603c659d01d58d9bbad854298f9a5 Author: daryl Date: Mon Jan 23 22:01:10 2006 +0000 more end-of-chrom fixes to exclude items when trim flag is set commit 74e854fd1502f7e5e459b1e2829796c01c63fd1e Author: daryl Date: Mon Jan 23 21:15:38 2006 +0000 another end-of-chromosome fix commit f13bf3d05bda2a8ab3c8fbe20a7469ffa9ac151d Author: angie Date: Mon Jan 23 21:10:36 2006 +0000 Added geneMapper to tablesIgnored. commit 3afaed6e8583da15d438e26e030cdf64ae28b221 Author: heather Date: Mon Jan 23 21:05:29 2006 +0000 add delConrad commit ce61407f00417dab3db4119f6124fafdfac3515f Author: braney Date: Mon Jan 23 20:43:10 2006 +0000 fix usage message commit d6b7b525b902581c7f7d0eb3738d5ed286dcebc1 Author: kuhn Date: Mon Jan 23 20:41:34 2006 +0000 added /cluster/home to list of units being checked commit 39d0c2d1534d2fcad14a3e1c4f06410b13289aef Author: daryl Date: Mon Jan 23 20:34:37 2006 +0000 added code to draw last diamond on chromosome commit da6a21ea6b6b6a78767486065575e98726ec1593 Author: angie Date: Mon Jan 23 20:21:55 2006 +0000 doBlastz -swap dm2. commit 25ad45ec4c1b52e33c0852d756fdc7f647ee1d31 Author: angie Date: Mon Jan 23 20:20:41 2006 +0000 Added GeneMapper predictions from Sourav Chatterji and Lior Pachter. commit 9ef96dc36dd6d49795c2b68f362b1bfbc6048ef9 Author: angie Date: Mon Jan 23 20:19:11 2006 +0000 Translated assembly.links file into AGP, loaded gold and (reloaded) gap. commit 32b4e2083d4f9f873eea37b097e5a321030cf3e5 Author: angie Date: Mon Jan 23 20:18:40 2006 +0000 Translated assembly.links file into AGP, loaded gold and (reloaded) gap. Added GeneMapper predictions from Sourav Chatterji and Lior Pachter. commit 38997d7422697a690477cb1d083921cbded34003 Author: heather Date: Mon Jan 23 20:12:05 2006 +0000 output format changes: use tabs, add strand(+), exonCount(1), exonStarts, exonEnds commit e4d9ecb86344cb84aafefc677251970025e841ac Author: kent Date: Mon Jan 23 20:05:30 2006 +0000 Clarifying a comment a bit. commit 88332a11e7d55e0bcbd9a28525f628fd1e4de985 Author: kent Date: Mon Jan 23 20:05:03 2006 +0000 Moving a misplaced line commit 3a52c2f38a4fe3531dc64ca842eba53a8f8e0afb Author: ann Date: Mon Jan 23 20:02:03 2006 +0000 added special rule for handling mm7 all_sts_primer.qName (identifier=mouseStsTrueName) commit 82eb8e542e206aeaf225dc9849bbffd3285d84a4 Author: heather Date: Mon Jan 23 19:29:12 2006 +0000 generate unique id per chrom commit c3e18aec24803a7c06552494b0051a6ab34e0507 Author: heather Date: Mon Jan 23 19:07:08 2006 +0000 assign identifier to Conrad data commit 4af2e3f175322a4873b9229816aa6152d4ae02c6 Author: angie Date: Mon Jan 23 19:01:54 2006 +0000 Fixed link to Mercator. commit 9ca30a379a7dfc4bdbd83684afc9831fc9d5b72f Author: angie Date: Mon Jan 23 18:39:52 2006 +0000 Tweaked table name to make it distinct from chainDb.as. commit afd6db3fbe4f317f50c493b9620b469eccff0460 Author: galt Date: Mon Jan 23 16:00:03 2006 +0000 "Encode release log update" commit c4fb62d6cc025c398f76c6cda0109d55073b41dc Author: galt Date: Mon Jan 23 16:00:02 2006 +0000 "Release log update" commit 470526fd92d34407ee22a76f96e257825f0cb4b5 Author: markd Date: Mon Jan 23 06:41:41 2006 +0000 fixed missing newline commit 6a887c751d71fe332b5c343fee141a91ab70f6c1 Author: markd Date: Mon Jan 23 06:33:01 2006 +0000 don't abort if seq from file list not in gbSeq commit 6555a57234bf2a59a1cd36440c109810aea64340 Author: heather Date: Mon Jan 23 05:29:53 2006 +0000 read function from tmp table; use loadDatabase for each chrom commit d1a796b855face59862d3585625248ba70de19bc Author: heather Date: Mon Jan 23 05:27:19 2006 +0000 don't need index size commit 72d55882dc6f88700fa53ee409c966a4eb842cd1 Author: heather Date: Mon Jan 23 04:31:53 2006 +0000 send tableName to snp125TableCreate commit 8342ffa376b3485e89dd44a6bee69442e700896c Author: braney Date: Mon Jan 23 03:49:06 2006 +0000 a utility to calculate the first order probabilities commit 13ac158f3a225384e54b9d80adb5b91ce077b6ff Author: braney Date: Mon Jan 23 00:12:46 2006 +0000 add adjacency hash and a new library function commit 76909feaa9ae5ee701e102ec4566e580aea1770d Author: kent Date: Sun Jan 22 23:58:18 2006 +0000 Adding known genes text. commit 0c1f8b6b9a42dc0aa6f09841b65c9e4d52504a88 Author: braney Date: Sun Jan 22 22:56:32 2006 +0000 a new routine and check for zero element genomes commit ad57a3ce8c7249125f02783a47ad6de7e36cd86f Author: kent Date: Sun Jan 22 20:22:54 2006 +0000 Taking out testing limits, since the save part is about as fast as the hash part now. commit 17006dc5b7b3c5e1efd2df1ea33526d470e7732d Author: kent Date: Sun Jan 22 20:20:47 2006 +0000 Adding expression. commit abc3a5b8e41f05a1fa283c3791b4c6cef2c1d729 Author: galt Date: Sun Jan 22 20:12:49 2006 +0000 documented creating knownToVisiGene for human commit 3eda83a0cedba92ac95c93cbeeb7c70a0bee535d Author: markd Date: Sun Jan 22 16:39:24 2006 +0000 added function to read lines into a slName list commit ee7f7d0837ab1b146ec55e653e8123f8aac4c6f7 Author: galt Date: Sun Jan 22 16:00:03 2006 +0000 "Encode release log update" commit 7de04706d9a5e2f2a734e4b1fe5c489cc68fcd1b Author: galt Date: Sun Jan 22 16:00:01 2006 +0000 "Release log update" commit 4745bd40836ec688e3cf85ffed774730350ff6b5 Author: kent Date: Sun Jan 22 10:45:19 2006 +0000 Writing out most of information already searched (except for expressed body parts) and a bit more. Still todo gene-associated free text. commit 6c46f643c710e4eefb0a2bed371a7d233ea167c0 Author: markd Date: Sun Jan 22 08:10:46 2006 +0000 added ability to specify list of peptides commit 980e488b40db3fc15f30581ce2331f7d250f3581 Author: markd Date: Sun Jan 22 08:10:00 2006 +0000 added checking of refPep commit f8648f397eac227cd3454291d47aa6720427c117 Author: daryl Date: Sun Jan 22 07:15:45 2006 +0000 Almost done! Made a few changes based on the review by Bob, Donna, and Andy. More to do tomorrow. commit 7e305438558de56a08532f372b1186303dd1bf92 Author: daryl Date: Sun Jan 22 07:14:10 2006 +0000 update for ortho5 / JAN-2006 commit 700ed619178043628ceccc1bce14ae896120edfe Author: heather Date: Sun Jan 22 03:48:28 2006 +0000 add lookupFunction commit 816f6d2be1639be277f761dd0bf784e23f589405 Author: heather Date: Sun Jan 22 03:48:01 2006 +0000 add func and contigName commit cbf32288f643d72a36fd8751562bd1e897163f92 Author: daryl Date: Sun Jan 22 01:21:30 2006 +0000 filtered fr1 sequences at 1 kb commit 21440f87bd726aed190c2eec737fc356c302dc2f Author: kent Date: Sat Jan 21 18:04:32 2006 +0000 Expanding help line to include arrow keys. commit bf14095635d60153d3916c1b2480206fe4933ec5 Author: kent Date: Sat Jan 21 18:03:55 2006 +0000 Fixing ISO mixed violation. commit b1c6809942c74382b8f7eaf23a04edf2a7ef75e7 Author: galt Date: Sat Jan 21 16:00:03 2006 +0000 "Encode release log update" commit f4d06cf28ff8083c17b057b237ac3f78ffd930fc Author: galt Date: Sat Jan 21 16:00:02 2006 +0000 "Release log update" commit 63dea5a6eaca3c771f669aec9c0f7ab34af77232 Author: markd Date: Sat Jan 21 08:14:09 2006 +0000 fixed bug dealing when a protein is in multiple files commit 32210d79426e32fa233a4775da052a9003b41675 Author: markd Date: Sat Jan 21 07:42:50 2006 +0000 fixed bug where faReadMixedNext would corrupt memory if fasta sequence started with a whitespace commit 07d8b0da130a52aed00c1e7324c5e496e532b599 Author: heather Date: Sat Jan 21 06:40:59 2006 +0000 handle multiple functions for same snp commit 0407576d3b45f60654e23ddfbc7e90b144b39036 Author: daryl Date: Sat Jan 21 06:06:05 2006 +0000 Added a comment to describe the score field in the hapmapLd table. commit 6a6e1a4b531fd29bdfe1ae7538620863b3782cf3 Author: heather Date: Sat Jan 21 05:20:20 2006 +0000 fix typo commit 59a2065d5acdcf880f98d60038a16180077f6487 Author: donnak Date: Sat Jan 21 01:11:29 2006 +0000 Edited this file for accuracy, added $organism substitutions. commit 2942fbbc1792450e9d99b610f2226e376d586de8 Author: donnak Date: Sat Jan 21 01:06:17 2006 +0000 Edited reference format. commit c9e3274f8d3165d7fce9e1272ad52f16415aa9e6 Author: aamp Date: Sat Jan 21 01:00:32 2006 +0000 Updated version seems to work. Added radio buttons for each database to update. The form now connects to rtdbServer and triggers that to run an update, rather than the CGI updating things itself... which wasn't secure. commit 465315da5d3729ff02c49ea3d7472ee5a67d2552 Author: aamp Date: Sat Jan 21 00:57:45 2006 +0000 Changed a comment. commit cbaed7bbf94c39da22c73ffa98bf2af98bc5c713 Author: kuhn Date: Sat Jan 21 00:13:42 2006 +0000 set googlebots to block entirely. this version of the file should not be pushed to RR commit 53abf692c66b4ad9642bbcbc6c6e027c2b147dd6 Author: markd Date: Fri Jan 20 23:57:32 2006 +0000 make error message more useful when seq/extFile link to a bogus location commit cdafcd4e0473eb9a7f31640070a9be8f5a7fa009 Author: heather Date: Fri Jan 20 22:56:54 2006 +0000 change func from enum to set commit 5338c0d2f8c4b34a321adffd73f3f315c6563235 Author: donnak Date: Fri Jan 20 22:41:13 2006 +0000 Replaced incorrect human references with $organism. commit 367ac8b05b8fe25e2412fc7fee10dc2451335224 Author: aamp Date: Fri Jan 20 22:41:12 2006 +0000 Finally seems to work. commit 5b0119c2b9d4d0b2acf3d7f5f994a6d3b35a3a2b Author: donnak Date: Fri Jan 20 22:36:41 2006 +0000 Removed italics from $organism...unnecessary. commit 8583386e2c8febec19b64bea082cea1bcccbbbf5 Author: donnak Date: Fri Jan 20 21:14:18 2006 +0000 Edited References section to use style consistent w/other description pgs. commit 6f26702ef8c4bd1e7b31e720f636fe9bf29dac03 Author: kuhn Date: Fri Jan 20 20:55:29 2006 +0000 added getSplit.csh which reports if a table uses split chroms in a db. if so, returns chromtype prefix such as 'chr10' commit 6f3b449b5fc92bd57f6d800b0d10e149c07fb2c6 Author: hiram Date: Fri Jan 20 20:30:29 2006 +0000 To define the normScore column optionally added by hgLoadChain commit 7510050e9fe6d194d27f54f2fb16ab34b7709e62 Author: markd Date: Fri Jan 20 19:25:34 2006 +0000 fixed handling of deleted peptides commit 2813de30af27cb652805f72a8097f55ed26c3e3f Author: galt Date: Fri Jan 20 19:03:26 2006 +0000 removing unnecessary stupidity commit 23e1d045b9e3a53b7bf501281a38bb6df597b54c Author: kuhn Date: Fri Jan 20 17:33:32 2006 +0000 added qa directory to the disallow list for google commit c68ea48c34f46558a51607016a000f886a0bfa60 Author: kent Date: Fri Jan 20 17:32:39 2006 +0000 Adding instructions for making knownGene.ix/.ixx files for full text searching of known genes. commit 3756f6e126e9f958f1c4761c36a411b28dc278ef Author: kent Date: Fri Jan 20 17:30:24 2006 +0000 Replacing a 5 with a defined constant from trix.h commit 2f2102181f25bca8bba51fdd1f7dc57e4245773b Author: kent Date: Fri Jan 20 17:29:44 2006 +0000 Added a field commit e5fc8ceeaa00a60bedc6f379f264386ce10f57b7 Author: galt Date: Fri Jan 20 16:00:04 2006 +0000 "Encode release log update" commit 0f93947aaf97438af4e8326df5697823a6fef0f3 Author: galt Date: Fri Jan 20 16:00:03 2006 +0000 "Release log update" commit 652c00b3745c853505bb8153e24178ebc30890b6 Author: angie Date: Fri Jan 20 07:47:53 2006 +0000 Additions from Sourav Chatterji. commit d9b87079bdc9e399aa1ab613bf81b52ab706978e Author: angie Date: Fri Jan 20 07:47:35 2006 +0000 geneMapper color tweak requested by Jim. commit d3e621dd1f92998de4c481331106680eae21aa10 Author: kent Date: Fri Jan 20 02:45:36 2006 +0000 Reworking known genes search to use full text indexing. commit e75205ae95a53c9f11d877aad60247ca3b6154c9 Author: kent Date: Fri Jan 20 02:20:58 2006 +0000 Making this tolerate no refSeqSummary table. commit 72cdfc717c58bd3c4e0147077a4cb141b3061a01 Author: kent Date: Fri Jan 20 01:24:50 2006 +0000 Adding knownGene.ix instructions commit 695b64448799bfbc45d9962a571e6e5696787472 Author: kent Date: Fri Jan 20 01:22:44 2006 +0000 Handling searches that just match a reasonable prefix of word. commit 116c692f3572a83ca3a22f1a4eff157905ccd782 Author: daryl Date: Fri Jan 20 01:08:12 2006 +0000 New format for hapmapLd data commit fd431da71ceed2af54a496525d96e11ffbb86a25 Author: daryl Date: Thu Jan 19 23:40:43 2006 +0000 1. Fixed totalHeight bug: set minimum to be lineHeight. 2. Removed redundant call to ldDrawLeftLabels. 3. Cleaned up colorLookup list (once again). commit 9f43ff8aaff4ff17040149fdbfe1fcb58c8e61a1 Author: daryl Date: Thu Jan 19 22:53:15 2006 +0000 Added chromosome restrictions to hapmapLd and hapmapLdHotspot tracks; reordered hapmapLdHotspot subtracks commit f0d489f31ff4f223eaf165f66f4761b775f173d5 Author: daryl Date: Thu Jan 19 22:22:46 2006 +0000 removed caret and added superscript for r^2 in the hapmapLd UI. commit 1c4622c0a8f639cd6bd73de384e7147fbd88481f Author: daryl Date: Thu Jan 19 22:15:50 2006 +0000 Reordered subTracks of hapmapLd commit a73c1d2fd85c7b9164fe00d787665ab28aefffa5 Author: daryl Date: Thu Jan 19 22:08:41 2006 +0000 Added identifier hapmapLdSnpId external=dbSNP fuzzy commit a8de5f07a72f64f3b638f68cd0e8da2937b442d3 Author: heather Date: Thu Jan 19 20:30:08 2006 +0000 sort; do start only commit f2ac811a9ce49601153412c2bf78d0fd66c950c4 Author: angie Date: Thu Jan 19 19:18:05 2006 +0000 Adding a bunch of recent chains/nets and geneMapper annotations from Sourav Chatterji and Lior Pachter at UCB. commit 5f66d72d2f2d67d4feb2ca474d7c4c47ac9e8e23 Author: angie Date: Thu Jan 19 19:17:08 2006 +0000 Descriptions for 12way Conservation and elements. commit 62e7281a879b45c8acdeec2411de990200f04afb Author: fanhsu Date: Thu Jan 19 19:01:42 2006 +0000 Added GOLD and GAP, GCBASE5 and Genbank sections. commit 74483b668141ec7e09aa24e6eb3724f89a88bf85 Author: heather Date: Thu Jan 19 17:46:30 2006 +0000 changed path to example script commit 79421bcf47fd3dc1f444a2c3e05b52790e9c818f Author: heather Date: Thu Jan 19 17:15:00 2006 +0000 fix previous commit commit 089a6c6fa008945fdd33ad071695639f0c7b7178 Author: heather Date: Thu Jan 19 17:09:30 2006 +0000 turn off KG as it is giving error 500 commit 058d701d94501d3cbdc513b52c6debee86f2aef5 Author: kent Date: Thu Jan 19 16:32:27 2006 +0000 First cut of utility to extract text associated with known gene into nice searchable file seems to work. commit cfc24a3018e2a45d5c370c47f95dc1ccbf946055 Author: galt Date: Thu Jan 19 16:00:03 2006 +0000 "Encode release log update" commit 2080a58aea6fcc6bd75c051ca23527b727493501 Author: galt Date: Thu Jan 19 16:00:01 2006 +0000 "Release log update" commit 676b2678b225ceb76f919dbb81f225bac00db076 Author: daryl Date: Thu Jan 19 08:04:49 2006 +0000 Updates for clarity. commit 601fb8c807741870d0bb1e61003bbfd92d2e1c5c Author: daryl Date: Thu Jan 19 07:22:26 2006 +0000 1. NOTted (!) ldInvert to make the moutain plot the default. 2. fixed dense drawing bug -- values were being added to start hash only; now they are added to start and end hashes. commit 8a11e1e57f5acce87ee4f22a22ae6b1aec8dabc2 Author: kent Date: Thu Jan 19 06:41:31 2006 +0000 Ifdefing out some unused code. commit 2345214d2ea4807cc75661ae04a0ff1a5f9fc64c Author: kent Date: Thu Jan 19 06:41:09 2006 +0000 Adding wordPos to trixSearchResult. Removing duplicateds from results for single words. commit 9ec4d738f005bfeee5bbfc2cb07c1ae9933cba93 Author: kent Date: Thu Jan 19 01:38:55 2006 +0000 Adding free routines commit 3256fcd103673cd6339404cd32c6cc62163e2fd4 Author: kent Date: Thu Jan 19 01:38:41 2006 +0000 Testing free routines as well. commit 39ef8e19776683d4105fdbad7d1e01cc25c3d3cb Author: hiram Date: Thu Jan 19 01:22:47 2006 +0000 Continuation of Coverage track construction. Beginning to see results on chr22 commit 193e73ad8410d46d8d1b1807a3cc28768b675e52 Author: hiram Date: Thu Jan 19 01:11:44 2006 +0000 Temporary clonePos track entry since data is only on chr22 for now commit 47f308fc030dd61da66ca4167ab90590cbfe0625 Author: braney Date: Thu Jan 19 00:18:30 2006 +0000 sort species names alphabetically commit dd0241f62d0cd3cfecbbd74d7a97e768987a856f Author: braney Date: Thu Jan 19 00:17:37 2006 +0000 some new routines for outputting element trees commit 466651bce539836d3b1b510a9a3fe9f2e485584a Author: braney Date: Thu Jan 19 00:16:24 2006 +0000 sme new routines in the library commit 5924ae09f097c44ad3d17bc469a1273b933e0244 Author: braney Date: Thu Jan 19 00:15:53 2006 +0000 use the correct branch length (oops) commit 413b71839eb83854508f3081720372d919bcc336 Author: braney Date: Thu Jan 19 00:15:14 2006 +0000 moving stuff to element library, playing with using coded names commit 6057b723ec2fb4b72ce107738ed35efbebaef3ff Author: braney Date: Thu Jan 19 00:13:36 2006 +0000 a utility to synthesize element trees (a very basic first pass) commit 2633c99aad434f12159d8c0fa5386de871d1c5fd Author: braney Date: Thu Jan 19 00:12:46 2006 +0000 a utility to convert an element tree to a list of element lists commit b32c716d56f7187ecd13aa73885386cb02957054 Author: galt Date: Thu Jan 19 00:02:16 2006 +0000 cleaning up some minor debugging lines commit 14ed8e833fd1547afe8476bbdc143795c0641868 Author: donnak Date: Wed Jan 18 23:58:19 2006 +0000 Tweaked fly credits, per Kayla. commit 66a692d779e97de50476c0bb1a1b296e84d01866 Author: donnak Date: Wed Jan 18 23:56:25 2006 +0000 Tweaked droSec1 credits. commit bdf6b5a70e2cd451cea784bf61739e1e3037f498 Author: kent Date: Wed Jan 18 23:43:31 2006 +0000 New text index search module. commit 5f8c0ee3abd812cd1f18ea835872ebbd3041bc87 Author: kent Date: Wed Jan 18 23:42:16 2006 +0000 Moving most of stuff to library. commit 130ce85b566e59dcb988682e2db8d19ce7750fba Author: donnak Date: Wed Jan 18 23:21:33 2006 +0000 Fixed typo in droSec section. commit 843e00b1bfe1b29d02b1e825ca10f902ec7ea2f6 Author: donnak Date: Wed Jan 18 23:19:44 2006 +0000 Fixed broken link in droSec1 announcement. commit 31d1f0458e024f9919b0bfad08c7b9edb6685d03 Author: kent Date: Wed Jan 18 23:17:26 2006 +0000 Ripping out docIx. commit 25e42d7c26fdd5d052928e91c0291d6c6fb8abaf Author: kent Date: Wed Jan 18 23:16:19 2006 +0000 Seems to work. commit 9547459258f732886eb39e48636df03f4340a849 Author: fanhsu Date: Wed Jan 18 22:07:14 2006 +0000 Added BAC Ends tracks. commit 09ff715218623f41847072bc383a0117e37225b7 Author: jen Date: Wed Jan 18 21:58:46 2006 +0000 Removed sgpGene<->sgpPep check (sgpPep table dropped). Added to tables ingored. commit 05721c830630999d26805a338f7773eda69ce914 Author: hiram Date: Wed Jan 18 21:33:08 2006 +0000 Indicate minimum chain score commit 1e042e4e02365ce1a1c8544999c6849e4b3deba2 Author: hiram Date: Wed Jan 18 21:31:33 2006 +0000 Add chain and net for BosTau2 commit f453ec176b6180cdc09d9120a03bc67e97b562da Author: hiram Date: Wed Jan 18 21:28:35 2006 +0000 Add matrix variable for chainSelf and html pages for chain and net self commit 4b21e64d5bae63d47f8b6a9c87e1b61580c34d83 Author: kent Date: Wed Jan 18 21:26:30 2006 +0000 Fixing usage commit 5deb5866c62fe68d7c9c51e655d7ac93ae777c0b Author: hiram Date: Wed Jan 18 20:27:30 2006 +0000 Add chain and net self commit c4bd9dc58f078e1fdc221df57ac364270bcd7f5b Author: jen Date: Wed Jan 18 20:13:49 2006 +0000 Added comment for sgpPep table drop. commit 128b561d14473f455bdfb89a28d9df79311da931 Author: hiram Date: Wed Jan 18 20:01:35 2006 +0000 Adding latest SGP genes commit 026121ea6147dea52df915f1a57a24c5b32c0f30 Author: ann Date: Wed Jan 18 18:24:15 2006 +0000 fixed typo commit 2b156d7276b1ffc9af290f8851128ffff596ebcf Author: donnak Date: Wed Jan 18 17:49:37 2006 +0000 Updated expiration date & payment address, removed version-specific references, added UCSC's tax ID. commit c1528a61364c78f2b2cb2d31d22472b98980e7b4 Author: kent Date: Wed Jan 18 17:38:33 2006 +0000 Removing tStart/tEnd indexes commit a853989c493dde0bb8f73135265d59007a062bbf Author: kent Date: Wed Jan 18 17:20:27 2006 +0000 Taking out measureTiming flag. commit 6b2f466ea19e335bf8d655089efcdd72f8ab4730 Author: ann Date: Wed Jan 18 16:43:35 2006 +0000 removed broken link to mouse fingerprint map commit 3edfb07686a9eada5a674021185e6555198cc778 Author: galt Date: Wed Jan 18 16:00:03 2006 +0000 "Encode release log update" commit f77214786e8d4da59246ae5f5f1652d4da1ddf76 Author: galt Date: Wed Jan 18 16:00:01 2006 +0000 "Release log update" commit f961f1540530a1f09d75d73a3d325535ca2aad4c Author: heather Date: Wed Jan 18 06:32:01 2006 +0000 check that bin index exists before dropping start/end commit a49db9fbfa595b02f1fa46453ef3ef985e2eab36 Author: heather Date: Wed Jan 18 05:47:09 2006 +0000 quick-and-dirty to generate script for start/end index drops commit ab9ea99823dbb00fa4b5d882c2f994d74e3fffaf Author: donnak Date: Wed Jan 18 03:17:12 2006 +0000 Added news item for droSec1 release. commit f950849775dae3c389444050c8c1a1fe0cb9e218 Author: donnak Date: Wed Jan 18 03:16:47 2006 +0000 Added D. sechellia credits. commit ba53cc04fb1561f0c39021efb4c076b224536169 Author: donnak Date: Wed Jan 18 03:12:00 2006 +0000 Archived a news item. commit 3c76db1a501a4c7e7689b0348ddd8ac7e55fa431 Author: kent Date: Wed Jan 18 03:02:23 2006 +0000 Dropping chromStart/chromEnd indexes. commit 4a02823c275a208307e62e13e6b7272cab7a84fd Author: donnak Date: Wed Jan 18 02:49:07 2006 +0000 Added droSec1 release info. commit 093077352c17fb6549cd2e60f65154e6b6bccc96 Author: kent Date: Wed Jan 18 02:45:22 2006 +0000 Removing genoStart and genoEnd indexes. commit df02421e7308a53d83cd48c6a1f50f98429911d4 Author: kent Date: Wed Jan 18 02:30:23 2006 +0000 No longer generating tStart & tEnd indices commit a90c622e129999d5165a5daa1b75eae8e98dfd3c Author: kent Date: Wed Jan 18 02:11:27 2006 +0000 Adding instructions for setting privateUser. commit 9904d1ccf3dca3886036baf6682eed51719e74ec Author: kate Date: Wed Jan 18 01:50:16 2006 +0000 Cons track changes commit 7f17a2467b32a6c2630f53a4e828d246b00a4b2d Author: kuhn Date: Wed Jan 18 01:47:32 2006 +0000 added logic to get the owner of the files in any storeUnit that is nearing capacity commit 804b746908e57116d1c3c57186934f53baf5e951 Author: kate Date: Wed Jan 18 01:04:32 2006 +0000 More conservation track work commit 3adfa8582a2202ccea8aec5d5b8b76da1db63bab Author: ann Date: Wed Jan 18 00:52:29 2006 +0000 another broken link fixed. commit 211c9d6301cf65711264eb16a30f348b317981ec Author: kate Date: Wed Jan 18 00:48:19 2006 +0000 Load Regulome CAP data commit 16dafb0b31849ef23cb75e5751001c143d654c81 Author: kate Date: Wed Jan 18 00:43:15 2006 +0000 UW/Regulome CAP data submission commit d59221d25a113237141abb015871565bffdcd8c8 Author: hiram Date: Wed Jan 18 00:42:41 2006 +0000 The psLayout placement of placed clones pk job has started commit 63dc6475272fe4a638eea49a33842a0bd05c6613 Author: ann Date: Wed Jan 18 00:40:23 2006 +0000 edited broken links found by linkChecker tool commit 87054c069b24c6ec6554f2d0de6e02c6ce54c0aa Author: ann Date: Wed Jan 18 00:13:02 2006 +0000 Edited links found by linkChecker tool commit e34f3bd74ed36b102c2c5f58720d0e5bbcb99250 Author: heather Date: Wed Jan 18 00:02:25 2006 +0000 add support for locType commit 3c517d824d46bc6efc573632b20cdb2ac53fd7f5 Author: heather Date: Tue Jan 17 23:47:50 2006 +0000 add support for snp125 locType commit a0e72313255b102f56a8d6363ca96407de4e22fb Author: heather Date: Tue Jan 17 23:46:34 2006 +0000 add locType commit d443ffdd24ec717ef58271fd8d12b0b1b3d72ac2 Author: kayla Date: Tue Jan 17 23:36:51 2006 +0000 added droSec1 commit 8ef07a5b5c1aa3bcff2057bb966902b37ec4e81c Author: heather Date: Tue Jan 17 23:30:56 2006 +0000 add snp125ColorSourceLocType commit ddd4409d1d9d29c1565a316b1f659ca5ff20717d Author: heather Date: Tue Jan 17 23:19:34 2006 +0000 add locType commit bc6751cb50fefbeca807fe06398ef1c98bfcccd5 Author: heather Date: Tue Jan 17 23:16:19 2006 +0000 adjustments to class and function commit a281df6b387a7b6b268ca275af83af6e871b8581 Author: kate Date: Tue Jan 17 23:15:47 2006 +0000 Add setting for wigMafs, to adjust height of pairwise wiggles in full mode commit 20c9ba3fd207c4ab9c8142a16fbe82205e9769c0 Author: kate Date: Tue Jan 17 23:14:35 2006 +0000 Update with new GERP methods commit 3d813ab3c8dc7d766dfdd1f4b6da31c90c6f6cbc Author: heather Date: Tue Jan 17 23:06:10 2006 +0000 remove duplicate mrna-utr commit ea6e407f9729170d62650f2fe4e65af573c826b6 Author: galt Date: Tue Jan 17 22:57:56 2006 +0000 added support from -fromProbePsl to use the probe track commit 446c382124babeb955660bae197a1bc628416068 Author: angie Date: Tue Jan 17 22:49:50 2006 +0000 Updated vsDm2 chains & nets to get new file conventions. commit 809befe0dd66bc435b68abf149b1e1201b0a95af Author: heather Date: Tue Jan 17 22:36:10 2006 +0000 add locType 4,5,6 commit 2d3d3e9a8ad285be001838a202df1d3938c9c67e Author: jen Date: Tue Jan 17 22:03:21 2006 +0000 Updated for dm2 chain and net. Both apiMel1 and apiMel2. commit 72e4a3099770f2475a114c2b6cf80367086fc138 Author: hiram Date: Tue Jan 17 22:03:16 2006 +0000 Starting blastz run on bosTau2 commit ce7755dbc6fb747077ac237dd563471027f5a69f Author: jen Date: Tue Jan 17 22:02:37 2006 +0000 Updated for dm2 chain and net. Removed and moved data up one level. commit 69a44755dc748c5fd7939759a367e630bbe3a3be Author: kent Date: Tue Jan 17 22:01:49 2006 +0000 Fixed timing output to include total. commit 83ffe74f428d55d95a2834d8277f2a17d768f07e Author: jen Date: Tue Jan 17 21:48:48 2006 +0000 Updated for dm2 chain and net. Removed and moved data up one level. commit a4c0b7f97327b5a831f1f3e2e7d070fcf933e0c6 Author: jen Date: Tue Jan 17 21:48:09 2006 +0000 Updated for dm2 chain and net. commit 4b6aad6f9037d2815b8a8692799627864ac5991a Author: jen Date: Tue Jan 17 21:45:19 2006 +0000 Updated for dm2 chain and net. Fix. commit 94a0f0d22c06466ebbcf6adf757635215211ee77 Author: kent Date: Tue Jan 17 21:43:16 2006 +0000 Removing some indexes that just slow things down. commit f620194cb84da70c55e71f46c44130ab3118f85d Author: jen Date: Tue Jan 17 20:55:15 2006 +0000 Updated for dm2 chain and net. commit 545692c0d1330325d078193092c01b43254160bf Author: jen Date: Tue Jan 17 20:46:31 2006 +0000 Updated for dm2 chain and net. commit e6d0047d5c8767b229ade6167cf66dd144c45c5c Author: heather Date: Tue Jan 17 20:36:46 2006 +0000 locus-region --> locus commit ff4a04da07b634b11c562fa7950e90892f6e81e7 Author: ann Date: Tue Jan 17 20:28:29 2006 +0000 Edited links to the newly-redesigned WUSTL website. commit e804c0b8ea168170f7e6d8144e2bf01645e8bc8d Author: jen Date: Tue Jan 17 20:16:38 2006 +0000 Updated for dm2 chain and net. commit 3bea40be6b8ce1cf7b5e36c70cb34a638b124033 Author: ann Date: Tue Jan 17 20:07:26 2006 +0000 edited sanger link to open in new browser window commit 1ae2f4ff326fc727ea04b492e2b1a62dfc34855c Author: jen Date: Tue Jan 17 20:03:02 2006 +0000 Updated for dm2 chain and net. commit 9571e7001152d895cd01346d03f87bb264dc3cbd Author: angie Date: Tue Jan 17 19:53:47 2006 +0000 Added geneid; re-swapped chains/nets from dm2 (redone there with better params). commit 0f73a38fa21ddcc5204ccea85639acc1e3ae716b Author: heather Date: Tue Jan 17 19:33:53 2006 +0000 trim molType commit 91e83aeaf7f9ee70d45d20142634a563b9ea93e0 Author: heather Date: Tue Jan 17 19:25:30 2006 +0000 extend locType commit 38b202476d00189e2e12f0fd3f58d0919f5363cf Author: heather Date: Tue Jan 17 19:03:42 2006 +0000 fix triAllelic commit cf6bcd8a290c1a52ac14ac9dfe9d2a2538b0a126 Author: hiram Date: Tue Jan 17 18:53:43 2006 +0000 Started self alignment, and continuing with the clone business ... commit e74e7260a2b38aca212edb7fd78c8678db50f7cd Author: heather Date: Tue Jan 17 18:52:52 2006 +0000 fix off-by-one commit 28d700d4f81668e7f9fee68167b6955b7d086868 Author: heather Date: Tue Jan 17 18:16:16 2006 +0000 change order commit fc8e5c92cb8d67a562e41e387d4ec495258a9985 Author: heather Date: Tue Jan 17 18:15:34 2006 +0000 add snp125Exceptions commit f18a2f3ac96f619c6d322c03375b934eb2ee8d30 Author: heather Date: Tue Jan 17 18:14:26 2006 +0000 snp125 exceptions definition commit 32ee43fae4a9506041348bad344bf8519a47f4ff Author: galt Date: Tue Jan 17 16:00:02 2006 +0000 "Encode release log update" commit ac3427959ff45e82e5b23c8ce0c12581036b1de2 Author: galt Date: Tue Jan 17 16:00:01 2006 +0000 "Release log update" commit 0e52e2f8eaf2d68c9ecbfea9fbdc5574cd8be825 Author: daryl Date: Tue Jan 17 07:15:51 2006 +0000 removed session IDs; added missing tags commit 6267b06dfeb7b071de63b7225c3db226f950643e Author: heather Date: Tue Jan 17 06:57:24 2006 +0000 add 2 more checks of deletions commit aa925c487e685aa48c7e56aed226955336653b09 Author: heather Date: Tue Jan 17 06:16:24 2006 +0000 fix function commit 001755dd98207e85840ab47bf6659e990f0c1eeb Author: heather Date: Tue Jan 17 06:06:12 2006 +0000 base this on locType commit c3f54f9fece799f4fa0065ebc8d262e2139fb30d Author: heather Date: Tue Jan 17 05:41:11 2006 +0000 add insertion and deletion as distinct classes commit b2456af143ec598925e11eb28964dcf6799533c8 Author: heather Date: Tue Jan 17 04:10:58 2006 +0000 special handling for in-dels commit bafb2df24242ecdc7dc6597cd9ae92a1e5c2696b Author: heather Date: Tue Jan 17 03:33:41 2006 +0000 "New version number v125" commit 43d3ffb6c063556ed5f41f36f360b12393378105 Author: aamp Date: Tue Jan 17 01:17:58 2006 +0000 Took out some old comments that no longer apply. commit 3820c626b9a1d80b92550f0d810dbdf91e41f699 Author: daryl Date: Tue Jan 17 00:57:45 2006 +0000 Fix typos and formatting. commit 0bb1fe2115db465fbbd08de61847da8349853972 Author: daryl Date: Tue Jan 17 00:27:00 2006 +0000 Completed first draft of the HapMap LD description page. commit a06a642efbda60e7deae95370ca6fac13e11ff3e Author: daryl Date: Mon Jan 16 23:48:40 2006 +0000 Removed negative value colors from LD track as negative values are not present in the data. commit e275bff1c15c99e206abbf098486bf14dbe91ef0 Author: kate Date: Mon Jan 16 23:04:55 2006 +0000 Remove obsolete compgeno tracks (mm4) and reorder species commit d32e87cb2035a841f8fb4a9330cb14c832ae47d8 Author: heather Date: Mon Jan 16 23:00:08 2006 +0000 change primary key to index to allow for duplicates commit 950131e7a272bbc084afb17ad9e9c4a023ab12f4 Author: donnak Date: Mon Jan 16 22:44:31 2006 +0000 Fixed broken link for Gil's Nat. Methods pub. commit b8dabf6acf7776c0c00e430fbd184b5b27a4d1e2 Author: donnak Date: Mon Jan 16 21:54:42 2006 +0000 Added NAR 2006 DB pub. commit baf8c59aaf07d0d91801dfa33f2e4039bd5e5685 Author: fanhsu Date: Mon Jan 16 21:38:29 2006 +0000 Changed "like" into "=" in MySQL query in lookupChromInfo() to improve performance. commit dca2c9e8e28cbb0cd6333fc976ccf218861dec41 Author: markd Date: Mon Jan 16 21:37:27 2006 +0000 fixed bug in creating bin column commit eaba45f694c760c0393ce7a2f85f6484787b184d Author: kent Date: Mon Jan 16 17:29:06 2006 +0000 Respecting privateUser. commit 4ea3676f7901c41c2c2dd68451204ac7dfc74066 Author: galt Date: Mon Jan 16 16:00:03 2006 +0000 "Encode release log update" commit e20df49891532740eac1f8098907386bdc8df160 Author: galt Date: Mon Jan 16 16:00:01 2006 +0000 "Release log update" commit 5f02aac6cb2d3f30e0b78884b2c1e3de8925a3e5 Author: kent Date: Mon Jan 16 06:58:48 2006 +0000 Adding a little more timing info when measureTiming flag is set. commit 308daf6688f32d013271be2bd06883c2632b9fe4 Author: kent Date: Mon Jan 16 06:20:30 2006 +0000 Improving startup speed of browser by replacing hFindSplitTable with a call to the cheaper hTableForTrack in hTrackDb commit f0b3de540f49b9306d0f0bd23e8068d9d9c9d5a7 Author: donnak Date: Mon Jan 16 06:14:04 2006 +0000 Fixed a typo. commit b9418e409b5ed0ba710c8720fec297802ba933a8 Author: braney Date: Sun Jan 15 22:26:34 2006 +0000 get rid of some globals commit e8a611737285c30c9ef9c2be2924d378196eae81 Author: braney Date: Sun Jan 15 22:25:36 2006 +0000 a couple of new routines commit 76cbad65b9d9b0b5b4450e4c1d8e7c6c269f9211 Author: braney Date: Sun Jan 15 22:24:31 2006 +0000 update to element library commit 0f82219baa21e899f7264d0ba0ec30d53276d8d1 Author: braney Date: Sun Jan 15 22:23:57 2006 +0000 some clean up, single point element allocation commit c0e22c0a16e33d3fd2f68a4df315a677086dad4a Author: braney Date: Sun Jan 15 22:22:07 2006 +0000 a utility to take an element tree and output distance matrices commit 1b2023ed0c42123cc180135946d7016b3e656530 Author: galt Date: Sun Jan 15 16:00:09 2006 +0000 "Encode release log update" commit 5b0949f4d800630c17d6a9e6d34f219335ca6f13 Author: galt Date: Sun Jan 15 16:00:08 2006 +0000 "Release log update" commit 96244bc36370768b066d023fce7099206458780d Author: heather Date: Sun Jan 15 15:23:13 2006 +0000 add refUCSC for locType exact and locType range commit 0693c167315d500c5c1bfe4cdec35f4d7856bb2b Author: heather Date: Sun Jan 15 15:01:36 2006 +0000 add error checking (coords and allele) commit 562c5221d7215ed175cefa4c3db983934deccc8e Author: heather Date: Sun Jan 15 05:52:44 2006 +0000 adjustments for locType, class and function commit 8f3339a548c3c130c70f6127d7786a4fd93eb0b2 Author: heather Date: Sun Jan 15 05:42:29 2006 +0000 fasta files contain class commit 6359019e15d8965280fba75b32187e794d194489 Author: heather Date: Sun Jan 15 05:22:51 2006 +0000 ContigLoc does in fact contain locType (range, exact, between) commit e3627e0f4abf97dc366b8a53765a65a673dfd5d8 Author: heather Date: Sun Jan 15 05:17:31 2006 +0000 fix typo commit 2d90888e49a1657ceb0c470bac153c16099521b8 Author: heather Date: Sun Jan 15 05:15:42 2006 +0000 make locType enum commit 8cb90894f6762b01db18240c74ea121d31c9a9b0 Author: heather Date: Sun Jan 15 05:15:21 2006 +0000 correction to locType commit 6cc7d080657d88457a0233004fc8a87825cd4ec8 Author: heather Date: Sun Jan 15 05:03:53 2006 +0000 get class right commit 0aa1b7efddf413aa1446542cfbadcb2736e00e4d Author: kuhn Date: Sun Jan 15 04:31:58 2006 +0000 added a check to see if du file has been created today. if so, does not redo the du commit 4a53a5ef0e46cbf018487bf477fb7e186b4db255 Author: heather Date: Sun Jan 15 03:39:46 2006 +0000 change class to locType commit b2a244a18a09f2bc095b94a5c7d3d2896aa2f570 Author: heather Date: Sun Jan 15 03:17:51 2006 +0000 add class commit 70786bd25761f9eb81672d9554ca28ddd6752956 Author: heather Date: Sun Jan 15 03:08:18 2006 +0000 add locType commit a0928463bfd55bc60a46a72fa060841eda9194ac Author: markd Date: Sun Jan 15 01:27:52 2006 +0000 improved documentation commit 1b94d5f262e8531587e04d08ca7a26213c798dfb Author: markd Date: Sun Jan 15 00:47:26 2006 +0000 improve output and portability commit 63d6ed4e6d2770b22c8239d549ca3280d713c2d0 Author: markd Date: Sun Jan 15 00:46:58 2006 +0000 don't run blat tests until other programs are built commit 5d2e95016a9fc487cb9c11f7b971fb144e45ae10 Author: markd Date: Sat Jan 14 20:19:48 2006 +0000 debugging build and filter scripts commit fda14fd4fde0c5cb52aa0a5d882b7b64f85dfad1 Author: kent Date: Sat Jan 14 16:42:45 2006 +0000 Adding privateUser field commit 598cdd91f30b4d58c19b5f174de66eaf23ee82e7 Author: galt Date: Sat Jan 14 16:00:04 2006 +0000 "Encode release log update" commit 4782a25db69cb719c2afd55a6b8073d50f23fe54 Author: galt Date: Sat Jan 14 16:00:02 2006 +0000 "Release log update" commit da7eeb6e8bd13d26a4aad707f52af2d1746123b5 Author: markd Date: Sat Jan 14 07:59:30 2006 +0000 clean out stale YP_ commit 0a2332c222d5910e19c1a19f3b1b134dc894881f Author: markd Date: Sat Jan 14 03:46:18 2006 +0000 allow overriding COPT in the environment commit 9fecce779ebd28568a6912bad9f2e24c7a96cd09 Author: kent Date: Sat Jan 14 02:31:29 2006 +0000 Adding field to keep some images private. commit dc8980dc168e65e7324a662b410770a757f68317 Author: kate Date: Sat Jan 14 00:30:25 2006 +0000 Fix stale ENCODE urls and incorrect database on an alternate frame page commit 6da189c2eadb136c66165db7e2b48271888786e9 Author: kuhn Date: Sat Jan 14 00:16:28 2006 +0000 added hg17_8way.jpg for 'release beta' block commit abd9f26d2821e7978824fbb630d975221277f61c Author: kuhn Date: Sat Jan 14 00:12:26 2006 +0000 added hg17_8way.jpg for Consservation track and changed the name of the 10way.jpg referenced by the new Conservation track to hg17_10way.jpg commit 6f04c582aaf16969ef88d2396262df2db2d42e23 Author: kuhn Date: Fri Jan 13 23:36:15 2006 +0000 added hg17_8way.jpg for Conservation track and renamed 10way.jpg to hg17_10way.jpg to match convention commit 26a51a3c36ef215216162e6638362abf3179f27f Author: hiram Date: Fri Jan 13 20:14:15 2006 +0000 Add waba file lift (but only for query side), clean up code and makefile commit e250d19bdda682e72a60de4c8981940bb1de54e4 Author: jen Date: Fri Jan 13 19:59:42 2006 +0000 Changed to alpha relase for Yale Chip tracks. commit 69583cdccc93f56e6940359545f858a501400668 Author: ann Date: Fri Jan 13 19:45:49 2006 +0000 brought down from the /drosophila level so I could add the $matrix varaible commit a245f4b9f9617b6ea40b09474953125755396f2e Author: ann Date: Fri Jan 13 19:44:04 2006 +0000 added $matrix variable commit b68ee357de08bb87e84c02cd8f77856fe7132e44 Author: ann Date: Fri Jan 13 19:42:03 2006 +0000 Added chain/net tracks for apiMel2 and dp3 commit 160cd565a46f3a43860d780de61243d2201021c5 Author: heather Date: Fri Jan 13 19:13:28 2006 +0000 reverseComplement refUCSC for negative strand; also get refUCSC for deletion commit 5072b9c47b99aa03de4c1ead5eed01fac427a263 Author: hiram Date: Fri Jan 13 18:59:15 2006 +0000 Add chrom name and gap hashes to speed up measurements on scaffold based assemblies commit 1f2e665bc1a8ee571ce5b0ae9b85e4e46f04c159 Author: ann Date: Fri Jan 13 18:15:26 2006 +0000 added ApiMel2 to chainDest list commit ab179dc223da8bc1c6a90339d99acd92d487dd5b Author: braney Date: Fri Jan 13 17:52:11 2006 +0000 fix a bug where orthologs weren't being carried up the tree commit 1d8c395bc949acbab320ae6abd462f3f4411d8b1 Author: hiram Date: Fri Jan 13 17:11:16 2006 +0000 Starting the clone coverage track business commit a4ce85855f937c06fbc00c03bbe3fccbf36896d8 Author: galt Date: Fri Jan 13 16:00:03 2006 +0000 "Encode release log update" commit 7b5a0b00244696d1ba354539f5aa3550f0de953b Author: galt Date: Fri Jan 13 16:00:02 2006 +0000 "Release log update" commit 5b12ea8119698580ab1523ca3e82bcd4e36831cd Author: donnak Date: Fri Jan 13 05:49:26 2006 +0000 Added links to some of the User's Guides. commit c371c9340fcc645478590d95dbf6ef5ff8b6f5fc Author: daryl Date: Fri Jan 13 05:40:50 2006 +0000 Still needs a few additions and a bit of rewording/rearrangement. commit 5c4a9e2b86b44586f4c8f2bdb51fe74d30135a63 Author: heather Date: Fri Jan 13 05:34:54 2006 +0000 rework; add DeletionClassWrongObserved commit a1ee7e4abf0c2cb73148985ccf99ee8c32377ab1 Author: daryl Date: Fri Jan 13 05:24:23 2006 +0000 fixed indenting commit a333d1adb56aa997ce39224164a19abec724b2b2 Author: daryl Date: Fri Jan 13 05:23:32 2006 +0000 Added support for SNPs with no valid LD data in dense mode -- will now be drawn as a blue box, rather than being omitted entirely. commit 02b521db287c51cbb9d0727b1a0b1d4ac7e682e5 Author: daryl Date: Fri Jan 13 03:18:25 2006 +0000 Added HapMap Linkage Disequilibrium documentation commit a2a23e99123a3615327cc49e5779f7a6a8b849b5 Author: daryl Date: Fri Jan 13 01:00:06 2006 +0000 1) hapmapLd: temporary kluge to deal with misformatted data 2) hapmapLd: remove MAP AREA=POLY as this breaks the map on Safari and MacOS/Firebird commit 1269bd2fb62a50cc1efe50a4c9b130d9aae8cd36 Author: braney Date: Thu Jan 12 23:50:14 2006 +0000 a bunch of new code to annotate mafs with gap information and to do codon translation commit b2f7fd04c8ffde384ad8692dbf283fa1795bc99f Author: heather Date: Thu Jan 12 21:37:12 2006 +0000 add hgLoadNamedTabFile commit 09387405a7f9e12d00cae322e7961176069a6bc4 Author: heather Date: Thu Jan 12 20:54:17 2006 +0000 reading SNPs from split tables, write exceptions to one table, start with checking size commit ed6d44e89d638a04f45bdce29748fd10ccd69bbe Author: heather Date: Thu Jan 12 20:35:39 2006 +0000 writing to Apache error log; will remove if too much; suggestions/guidance from MarkD commit c6e9a9352e7ee3a0ae50c0bc18695d99a8d24308 Author: ann Date: Thu Jan 12 20:24:48 2006 +0000 Edited matrix variable to contain correct values commit 061946a2effca0981eae92b27bc19370eea7786a Author: hiram Date: Thu Jan 12 19:33:05 2006 +0000 Add a pointer to the frames based index view of the alt splice sites commit 35ed02d1ec55a039dabec6ab05b0ff0eefb7dc2d Author: hiram Date: Thu Jan 12 19:01:34 2006 +0000 have moved altGraphX track to this worm top level commit 2222a0411e4ab56ac9f12c0ee11b37e71e2bb714 Author: hiram Date: Thu Jan 12 18:57:44 2006 +0000 moving altGraphX track entry up one level commit 2573ee71c2c00d29d2ddc0e32ad202e3941e60cc Author: ann Date: Thu Jan 12 18:39:54 2006 +0000 Added $matrix variable to chain description pages commit ff124e7759c64df5ae7efd9ded3802fcdfe1e083 Author: ann Date: Thu Jan 12 18:38:55 2006 +0000 Edited matrixHeader variable for 4 chain tracks commit 869185ef53a96f4e3d3743ce00ca353e56579835 Author: ann Date: Thu Jan 12 18:30:36 2006 +0000 added entries for chains to four flies with their matrix entries commit a1b2a822a455ab1243a0bdb1651f5b945f836b49 Author: heather Date: Thu Jan 12 17:41:54 2006 +0000 log db extFile errors to Apache error log commit 199e68812808fca1a0a269fbefa7913f3170120d Author: galt Date: Thu Jan 12 16:00:02 2006 +0000 "Encode release log update" commit e1386fae3d878be2f9e425f2243216cd323e8faf Author: galt Date: Thu Jan 12 16:00:01 2006 +0000 "Release log update" commit 6e6439b9df4e8ffd0697961363c161e128283f76 Author: giardine Date: Thu Jan 12 15:54:33 2006 +0000 changed color for complex variants in hgMut commit 260ee5b4881d4d3b82e190f88eafcce13cd3fd3d Author: fanhsu Date: Thu Jan 12 14:53:52 2006 +0000 Added other pairwise chains and nets. commit 0c3ce812394acfda1c07eac926fde7cf4481a3de Author: fanhsu Date: Thu Jan 12 01:19:10 2006 +0000 Added otherOrgs.ra. commit 7d1831f5ed389a36fdbc0b442ab621375805b4c7 Author: hiram Date: Thu Jan 12 00:58:50 2006 +0000 Added sangerLinks to get click through on WormBase genes functioning, started genbank alignments, added Worm Base Genefinder track and twinscan track commit b8f74fe3853b25cf91f86707c7fc2e425895ad5d Author: fanhsu Date: Thu Jan 12 00:53:45 2006 +0000 Added idSql for dm. commit 6dced2c97383941d7d9d79f609d5332f2c568ab7 Author: kayla Date: Thu Jan 12 00:14:13 2006 +0000 removed droYak2 commit a31de0fcb4af27e658f40feaac0af47ce2e59646 Author: hiram Date: Thu Jan 12 00:14:02 2006 +0000 search on sangerGeneOrf moved up one commit ccb9d5c7a067fd3051ac44c3844cdbb4dc086de4 Author: hiram Date: Thu Jan 12 00:13:03 2006 +0000 Adding sangerGenefinder track commit 8a075c43cec4aad89ae213bbe9b5c7656714d653 Author: hiram Date: Thu Jan 12 00:12:27 2006 +0000 Add some sangerGene searches commit 57a507965fed41e97d3a8ce7968c592ea507143e Author: kayla Date: Thu Jan 12 00:11:27 2006 +0000 Added droYak2 commit 29b6ec53d228a3c68ff25e6b36ffbf5334b75cac Author: angie Date: Wed Jan 11 23:55:21 2006 +0000 Updated sgpGene and ensGene with new data. There are also some much older changes in here, including Conservation. commit c248579e9e388a8f7dcac0dc985c081e127a7a70 Author: kuhn Date: Wed Jan 11 23:08:13 2006 +0000 added protection against running on wrong machine (dev only). added protection against giving it a wrong table name. changed to accomodate change in featureBits that now directs usual output to stderr instead of stdout. commit d7085f923234ccc85e956319617201166caa057a Author: markd Date: Wed Jan 11 22:37:26 2006 +0000 added option to output information about mappings commit 77330e0128c30eeb65db566286250fc8d8d0b068 Author: fanhsu Date: Wed Jan 11 22:35:22 2006 +0000 Added hg18/bosTau2 blastz pairwise and created the 11.ooc file. commit 650a0adb694a7cc22ead2a221686dea06c073723 Author: hiram Date: Wed Jan 11 22:21:08 2006 +0000 Change WS120 to WS140 commit 7ff447b7e3b9c8b65b8f5e111b5ead191a4b5d78 Author: kate Date: Wed Jan 11 22:11:04 2006 +0000 Finish phastCons for 17way commit 278b3518e677b9af2a2ab8d31f9c5c7e57fca9e9 Author: angie Date: Wed Jan 11 22:06:02 2006 +0000 Removed "~/kent/src/utils/" from the doHgNearBlastp.pl path -- it's installed in /cluster/bin/scripts now. commit 3773d5ddd5f9e444233fb9bb19ea95948c073b64 Author: donnak Date: Wed Jan 11 21:53:00 2006 +0000 Edited the gateway page text. commit 835453ca5f053b80cb522ba2dbe87b94e5ae3f01 Author: heather Date: Wed Jan 11 21:51:29 2006 +0000 correct format for error msg commit b687fdaca986dd3d65e0f33f4cdc66aee4169fbd Author: angie Date: Wed Jan 11 21:45:53 2006 +0000 Added *BlastTab tables for hgNear -- more hgNear tables to follow. commit 5f88d1d7b919d2049d802eea39f624ec9fbcb524 Author: heather Date: Wed Jan 11 21:43:43 2006 +0000 too verbose commit 665163de5b66ccd2934dad58822a27f47aed619b Author: angie Date: Wed Jan 11 21:39:20 2006 +0000 Added doHgNearBlastp.pl. commit 548a9730558732ec21c282116438e4a3ff02af13 Author: angie Date: Wed Jan 11 21:38:29 2006 +0000 Fixed the -maxPer used for self hgLoadBlastTab. Fixed the database to prefix translation. Parameterized the blast installation path. Made &cleanup more careful. Added completion message. commit d8fee2e296742b09affe6540cf5e951fa0f192d4 Author: heather Date: Wed Jan 11 21:37:15 2006 +0000 check for table existence commit 241989af36a46c0b019e672f129e5519a0e2340b Author: donnak Date: Wed Jan 11 21:33:11 2006 +0000 Added droYak2. commit 6a358ff4066427156556b43687069fb6f3878041 Author: donnak Date: Wed Jan 11 21:29:33 2006 +0000 Added droYak2 credits. commit 1b27d155ede7e22d31ef67bf12336b9eb2a46a58 Author: donnak Date: Wed Jan 11 21:28:59 2006 +0000 Archived an item. commit d355d6629b9fc58343d696dad977ced75ce335be Author: donnak Date: Wed Jan 11 21:28:46 2006 +0000 Added droYak2 announcement. commit b9c3589358f0ced43b57d612ff9b4c2ac8bfda3d Author: heather Date: Wed Jan 11 21:20:04 2006 +0000 only check the unique values (doh) commit 42e5c8743c6efeacccfae0f437b5d771625a5083 Author: heather Date: Wed Jan 11 21:16:48 2006 +0000 quick and dirty; uses uncommitted gbExtFile.h commit d4534f0795ce0045bfde56d735cfdb635555fc1d Author: heather Date: Wed Jan 11 20:40:23 2006 +0000 add comment commit 5bcd0cf24cf8a66107774c5c68b3f0c056e990e4 Author: jen Date: Wed Jan 11 20:13:51 2006 +0000 Fixed typo (droYak2->DroYak2) and changed order for DroPer1 in # Define various non-self chains. commit 2daf24293155fb22dcaf30cb0fa77c2231c31435 Author: heather Date: Wed Jan 11 20:08:02 2006 +0000 fix error in comment commit 10bb5ca80c335ab4f981b1f89b7ae894bf33fef1 Author: hiram Date: Wed Jan 11 19:16:24 2006 +0000 Adding ce3 to the build commit 7cf65922945cb0f578c9e512303dcfb8ee7d4a04 Author: markd Date: Wed Jan 11 18:56:51 2006 +0000 add a to-do commit c5af57117db46ee014d0f03f4dabc35cc5137ea9 Author: hiram Date: Wed Jan 11 18:52:26 2006 +0000 Fixup genbank path names commit 60a46b063d1ed0b820d27d72cd4a284fd71ba698 Author: hiram Date: Wed Jan 11 18:51:56 2006 +0000 Adding ce3 to the genbank alignments commit 715121d2fead965a44e2828da5930f7ca2946465 Author: galt Date: Wed Jan 11 16:00:02 2006 +0000 "Encode release log update" commit ec30cde8402bb3843cfd6379ab922b7678ec7b61 Author: galt Date: Wed Jan 11 16:00:01 2006 +0000 "Release log update" commit a43a0cb82cc17efd4612ef8cf6ff4b6a24495353 Author: angie Date: Wed Jan 11 01:33:36 2006 +0000 Added sgpGene def to override longLabel (requested by Francisco Camara). commit beb12fd65b86587f0ca06ce1e908836af7e28a65 Author: angie Date: Wed Jan 11 01:27:51 2006 +0000 Added local sgpGene def to override the longLabel. commit 931caa514765341e5f326e35e7b8bdcc5152295b Author: aamp Date: Wed Jan 11 00:58:29 2006 +0000 FINALLY got all the main business with networking, forking, piping and stuff done. Still needs update() to run the rtdbUpdate program and not some sleep(20). commit cb3d6e3e8ad77b96327caf8322948a44f1615e8b Author: kate Date: Wed Jan 11 00:39:13 2006 +0000 Fix EGASP track commit e04d6b5c169612ad5001aaf77eca813b02307c5b Author: kate Date: Wed Jan 11 00:34:04 2006 +0000 Yale chip/chip to Q/A commit 4e3b7780a6dd4e275f7caa813cd289d53cb0b858 Author: angie Date: Tue Jan 10 23:10:58 2006 +0000 Fix: $dm --> dm1 for dm1-specific tables. commit 05c23ae4d4421ffe2425e7dbdcc0a92c3cdc5581 Author: heather Date: Tue Jan 10 23:00:54 2006 +0000 add missing fclose commit 387a1d013119e334ff59fadbbea80a039a815b09 Author: kate Date: Tue Jan 10 22:56:40 2006 +0000 Fix contig accession search commit 7e8e9c6612937ec14372222d602a3fa353eb6adb Author: kate Date: Tue Jan 10 21:55:31 2006 +0000 More work on conservation track commit 1598fc1f457d113ace3de920d3e6eb808406655f Author: kayla Date: Tue Jan 10 21:05:08 2006 +0000 giving droSec1 its own net html file. commit 1191d8dcb96b271f345d332feed013d35c6f1164 Author: kayla Date: Tue Jan 10 21:04:28 2006 +0000 Giving droSec1 its own chain html file commit 72ca96006b6b0bbc6b6d32c0558c5ae9f5dabc17 Author: heather Date: Tue Jan 10 21:03:12 2006 +0000 not using dystring commit 0656c3220dbd73fbc90c62901ee1783bcb4a3aa8 Author: hiram Date: Tue Jan 10 20:43:47 2006 +0000 sangerLinks.as and sangerLinks.sql have been moved to hg/lib commit 0b49e154698ba971eaed69732b4163179acb80b1 Author: hiram Date: Tue Jan 10 20:43:20 2006 +0000 A second route to doing the same thing commit d49d909f0638c18bd517e359bec979c29d8d3a21 Author: hiram Date: Tue Jan 10 20:41:30 2006 +0000 folding in better comments from other copy in near/hgWormLinks commit 121a4ec5bbc15a2c515a238f5b8ff0b93d852da3 Author: hiram Date: Tue Jan 10 20:37:14 2006 +0000 fold in better comments from near/hgWormLinks/ version of this file commit 82586ece7663ed67bf363ccdac456619115b8684 Author: heather Date: Tue Jan 10 20:28:56 2006 +0000 typo in usage message commit 28795d163989050a3e2d5234a2a958584051ea8f Author: kayla Date: Tue Jan 10 20:23:10 2006 +0000 Added a blank line commit fa19f26fda648d0661b5130cbe4b019dc2f5590d Author: kate Date: Tue Jan 10 19:51:10 2006 +0000 17-way multiple alignment commit a0bc9c2e431c0ded51725ce6af01a65c17689e81 Author: kate Date: Tue Jan 10 19:49:10 2006 +0000 Fixes to Brent Lab ENCODE gene prediction track labels and description commit 7a176b8ddd1e5d441191efcf0ad203f8fa91f28a Author: ann Date: Tue Jan 10 18:52:05 2006 +0000 moved opossum from vertebrate to mammal group in Conservation track commit 6bc320bc801566523831e9e64e2db3d814fb58d6 Author: ann Date: Tue Jan 10 18:46:41 2006 +0000 moved opossum from vertebrate to mammal group in Conservation track commit 574c77b3432e3b0920997912de1890535f4ef756 Author: kent Date: Tue Jan 10 18:12:17 2006 +0000 Improving genotype display. commit 27db513f6a371bd1298016d958bb8625c178de12 Author: galt Date: Tue Jan 10 16:00:03 2006 +0000 "Encode release log update" commit 73036c2b7913c2205147e969946d4340803c7901 Author: galt Date: Tue Jan 10 16:00:02 2006 +0000 "Release log update" commit e0bbca5737f389d2b4eea02841dbe90ab0c3defd Author: heather Date: Tue Jan 10 04:52:22 2006 +0000 add support for include/exclude filters commit 9bc91618cd1d446e1af6414a06ffbddb7b901ebf Author: heather Date: Tue Jan 10 04:50:40 2006 +0000 add support for include/exclude filter commit b58363566cb4c9ba5ef4a5ed96961e4b2df78350 Author: heather Date: Tue Jan 10 04:49:08 2006 +0000 add support for include/exclude filter (and fix a block of snp-->snp125) commit 7b56ddab8ec17f6df72dab44b1058f9424c91e82 Author: angie Date: Tue Jan 10 00:43:24 2006 +0000 First cut at script that automates the protein blast runs that build *BlastTab tables for hgNear. It works from a simple config.ra file that defines the databases and paths to use for the run. Still needs more testing before it's ready for group consumption (currently testing on dm2). commit 8f3eb36d12b1a7fa781c25987f5996fae157a4c6 Author: kayla Date: Tue Jan 10 00:41:21 2006 +0000 Added two blocks, one for chainDroSec1 and one for netDroSec1 commit 927beea9a6ea842fe71c7b68065389fa13546811 Author: angie Date: Tue Jan 10 00:36:01 2006 +0000 Added droSec1. commit f6e2df39bef657f1efbe0d1897aa41bab1956890 Author: aamp Date: Tue Jan 10 00:10:36 2006 +0000 Another almost-ready commit. commit 10138d614c173bca234700a5ece5b659fd03a3ae Author: ann Date: Mon Jan 9 23:47:07 2006 +0000 edited species list for Conservation track commit 21a52a328ba114dd0d5469aa6a98f2d544832f7c Author: kayla Date: Mon Jan 9 23:07:16 2006 +0000 Giving droSec1 it's own trackDb.ra commit e27e63f016cfa47c6f730438b8034f3a5e4fade4 Author: kate Date: Mon Jan 9 22:29:48 2006 +0000 Conservation for 17way alignment -- first steps commit b9fcc03dc3597784831840ede775353909a52646 Author: heather Date: Mon Jan 9 22:04:20 2006 +0000 fix typo in comment commit 1598dcc9e57c50bb3e1a3855560c43b5c84bf04d Author: hiram Date: Mon Jan 9 21:58:58 2006 +0000 definition of the sangerLinks table used in the C. elegans browsers commit 66123ce56ff493aba0558f331fa534f9d0237d64 Author: kayla Date: Mon Jan 9 21:00:23 2006 +0000 Giving droSec1 it's own gap file commit 5bde7fb256ac315c17b80ba2d8f99f01c0f059c3 Author: kayla Date: Mon Jan 9 19:45:25 2006 +0000 Added droSec1 and droYak2 commit e372705dbc52309d45a1b61907ec37e5ec697763 Author: kayla Date: Mon Jan 9 19:43:58 2006 +0000 added droSec1 and droYak2 commit a4b4a793ee35542bea5b49bb784d3f340e7e7e55 Author: kent Date: Mon Jan 9 19:40:35 2006 +0000 Updating to reflect creation of knownToAllenBrain table. commit f84c084b4be9f1825839f7e69cc50230067944c2 Author: ann Date: Mon Jan 9 19:33:35 2006 +0000 removed entries for Chains/Nets, Cons, Most Cons with the "U1" label commit 837928772dd0879f77910dbd498a0430b9b73ebc Author: braney Date: Mon Jan 9 19:28:07 2006 +0000 re-order libraries commit a0e90f78a3d3610f06f6acb4490c6a08fcd59ebd Author: braney Date: Mon Jan 9 19:27:13 2006 +0000 fix up for new library commit c51d61dde4e76a52cbec5c0182f06b7b6f782bf1 Author: galt Date: Mon Jan 9 18:49:14 2006 +0000 undid it - realized that if users want redirection then keeping results separate on stderr is better commit 80570d15907797c0a3bf66e32db6ab372bc5a5ca Author: galt Date: Mon Jan 9 18:32:59 2006 +0000 fixed basic result to go to stdout instead of stderr commit 8ff8bda188741d6b3c246503200cb7cd7c48387b Author: galt Date: Mon Jan 9 18:26:12 2006 +0000 initial vgProbeTrack creates probe track for visiGene commit 013701875ae34466c4a660ff4c748d3d93daa406 Author: braney Date: Mon Jan 9 18:24:41 2006 +0000 some changes to support neighbor joined trees commit 739311192a8433ea5b9ebadfba642168b73e72c0 Author: braney Date: Mon Jan 9 18:22:19 2006 +0000 some new routines used by the element tree construction commit 0c570c138457bfbe77ae07668166f40ac146a2f1 Author: braney Date: Mon Jan 9 18:17:02 2006 +0000 now builds element trees for toy examples commit 6497fc9adbfa379e5d0dae3f15ed3bbe0a2c6c3f Author: braney Date: Mon Jan 9 18:14:22 2006 +0000 some new procedures, supports building element trees now commit ca75b551769ff7e6c9e0d251c89d90c0d3a02de3 Author: braney Date: Mon Jan 9 18:11:53 2006 +0000 some new structure elements commit aaebaa486a187a681b00b339b04f48b5642edc36 Author: braney Date: Mon Jan 9 18:00:01 2006 +0000 a utility to print out an element tree (now it just prints something out to stdout) commit 4a4d47b6b538493534a2979900ba717404556564 Author: heather Date: Mon Jan 9 17:59:02 2006 +0000 default and cart values should always match commit 33a1ad5e2fc568ecc78d4859e081b9883fefff7f Author: galt Date: Mon Jan 9 16:00:05 2006 +0000 "Encode release log update" commit 9841968014c1b5d6aa3eeb89f47e2e799659079c Author: galt Date: Mon Jan 9 16:00:04 2006 +0000 "Release log update" commit aaaeaad2dcb1ae575f3e19a01dee53bbcfac3afa Author: daryl Date: Mon Jan 9 07:29:51 2006 +0000 Notes for version of sequences that were submitted for accessioning -- canFam2 only. commit f9fd6a2da355b86bdcd7989130b303a2d99ba2a6 Author: galt Date: Sun Jan 8 16:00:05 2006 +0000 "Encode release log update" commit f9ac2d14aa5d1bc46550967d48d8b28fc9dd1fe8 Author: galt Date: Sun Jan 8 16:00:03 2006 +0000 "Release log update" commit 227f34656aef7c201e535aea348a715db58279de Author: fanhsu Date: Sat Jan 7 21:11:47 2006 +0000 Added hg18/xenTro1 pairwise blastz. commit 69810baef4ec5a79602e1c2bb240e8470b0e7386 Author: fanhsu Date: Sat Jan 7 16:47:14 2006 +0000 Added hg18/tetNig1 blastz pairwise. commit 61249957f403c75b92934ec4b0122f9ee297d6f6 Author: galt Date: Sat Jan 7 16:00:03 2006 +0000 "Encode release log update" commit 6b5dc1f4249e06f26ad77317b4dd119c6e908f4c Author: galt Date: Sat Jan 7 16:00:02 2006 +0000 "Release log update" commit 168ec2222226f498cd2516542261e77ceee33dbe Author: heather Date: Sat Jan 7 05:51:01 2006 +0000 use snp125 consistently commit 09b3ae926281695d1c9f8d97960e5cb6d8119f6f Author: heather Date: Sat Jan 7 05:49:55 2006 +0000 using labels for cart values commit 2d760170ecdc2e68bc883e010484affb1c3167f4 Author: heather Date: Sat Jan 7 05:26:37 2006 +0000 round out snp125Methods commit c812e014d86e85128ec2272978e33d800421ec6b Author: heather Date: Sat Jan 7 05:25:19 2006 +0000 tweak display commit e8605ce9b65f47ed6c6fdfc2c42e8b44e2b10eb7 Author: heather Date: Sat Jan 7 05:17:45 2006 +0000 values must match snp125 table definition commit c4dd41712c9f1914f34793227e772e8dc0d8fbb4 Author: markd Date: Sat Jan 7 01:40:09 2006 +0000 added to-do commit 06c5033920041124375c350b43b19aede2eb1bd3 Author: heather Date: Sat Jan 7 01:26:47 2006 +0000 remove exclude commit e93ad21e195bf8e409b3a2f5a195403612b4afb6 Author: heather Date: Sat Jan 7 00:52:17 2006 +0000 use autoSubmit cgiMakeDropListFull for all color selections commit 8681204b393933dd3da17d0f518d1bf3f8fccbc9 Author: ann Date: Fri Jan 6 23:41:35 2006 +0000 removed net and chain entry for canFam2u1 commit d4e9629a1f35f7284d87ccc220c98852045eeabe Author: aamp Date: Fri Jan 6 22:54:23 2006 +0000 Added forking stuff but it isn't quite ready. makefile is done. commit 07aac0281581f9971251a6b14a1a71e5a8610478 Author: jen Date: Fri Jan 6 19:29:34 2006 +0000 Added droYak2. commit 17e1669dcd409cb5a749ef0e0a9e87ae179addba Author: jen Date: Fri Jan 6 19:26:31 2006 +0000 Added droYak2. commit 61802bf296bb0a3bf82f42a077ea75ab9e408e90 Author: hiram Date: Fri Jan 6 18:44:18 2006 +0000 Add photo image to description page commit 8a3fc41bd48820d3777542547811eb4e30536d64 Author: hiram Date: Fri Jan 6 18:38:06 2006 +0000 Add image commit 3d669b93a00939dac233f7a84d67c9eaae4a2561 Author: jen Date: Fri Jan 6 18:30:57 2006 +0000 Moved down dm2 chain and net and changed short label. commit 1e343a30afb1663ae3f108915c1623daa25a205d Author: hiram Date: Fri Jan 6 18:08:44 2006 +0000 Added image from Blaxter lab commit 6c26bd665f1f5958542b406c128e0a8cf0df93a2 Author: galt Date: Fri Jan 6 16:00:04 2006 +0000 "Encode release log update" commit b67ee53e77580e32330c53895b20735de7cac843 Author: galt Date: Fri Jan 6 16:00:02 2006 +0000 "Release log update" commit 2f1d55a0f040dae5b76a84fc9f24e3eb1348f5a3 Author: fanhsu Date: Fri Jan 6 13:21:41 2006 +0000 Added hg18/fr1 blastz. commit 9448fb143ce744f4e8005e2df6af745bba467e3e Author: angie Date: Thu Jan 5 23:48:25 2006 +0000 Removed mentions of .over.chain file from the download README.txt now that it has moved to the liftOver/ download dir. commit f38c771678e203f1233918219f563688a4060f5c Author: fanhsu Date: Thu Jan 5 23:07:04 2006 +0000 Added pairwise run for hg18/rn3. commit e87837b89a2d770a2aad36c7e49d86ce5a67b448 Author: donnak Date: Thu Jan 5 22:41:53 2006 +0000 Updated References section. commit fd83b4ef6a3ae4d2e68e87a49ab9650ce50f2616 Author: donnak Date: Thu Jan 5 22:40:59 2006 +0000 Updated "in press" reference. commit 7afd7b65e949d62d930a17081640f5f8d62e4914 Author: kuhn Date: Thu Jan 5 20:11:07 2006 +0000 small grammar changes commit 42fbc497d1d6aee8568a38e7a5001d4a6b8cf0db Author: kuhn Date: Thu Jan 5 20:01:41 2006 +0000 added restrict list to encodeRecombHotspots track commit 5a086e57cb7c0282676fccc63b25a70ffcf4d7b2 Author: kayla Date: Thu Jan 5 19:19:02 2006 +0000 added droPer1 commit af4ac9fb347ed237ec574b351e96701c62bc8219 Author: heather Date: Thu Jan 5 18:56:22 2006 +0000 display color choices for each SNP type commit 98af6673505f14cd10572d4f607016fa6e75cfa5 Author: heather Date: Thu Jan 5 18:50:30 2006 +0000 finish out the tweak commit f5a61db612b7e37584c703e69cbd799df1ee4166 Author: heather Date: Thu Jan 5 18:48:07 2006 +0000 tweaks commit 473dfa4fee0d324cd0d232e5272dccd5cedb6c27 Author: heather Date: Thu Jan 5 17:23:57 2006 +0000 add loader to loadSnp125 commit 1dceb18d670bc5e6771ea40a3c7cd084ea151f79 Author: braney Date: Thu Jan 5 16:58:58 2006 +0000 a utility to calculate the distance matrix for the species tree given the distance matrix for all the elements commit b550f3326cb2a1809dbf9794cf39800b98806ba3 Author: braney Date: Thu Jan 5 16:58:13 2006 +0000 a library for the manipulation of element lists commit 3138d8db3a1790289e3aeb4546573e9d1d829d66 Author: braney Date: Thu Jan 5 16:57:38 2006 +0000 an include file for the element library commit 76852e50ab6c91297558c95c69bcccebd6c23be6 Author: braney Date: Thu Jan 5 16:57:00 2006 +0000 a utility to build an element tree from a species tree, distance matrices, and element lists commit 1fb9d218ccf387ca5d318c2db6aff391b7bcd7c1 Author: braney Date: Thu Jan 5 16:56:07 2006 +0000 a utility to convert a neighbor joined tree to a rooted binary tree with outgroup commit b07a59e49f81a9dfbaf8048fba8b6fc33639a791 Author: galt Date: Thu Jan 5 16:00:03 2006 +0000 "Encode release log update" commit 9af99af2ea335628c263c84b09cfe2ecb7a837f9 Author: galt Date: Thu Jan 5 16:00:02 2006 +0000 "Release log update" commit c54797cb39c08532a99f7a11c9397be3c31276e4 Author: galt Date: Thu Jan 5 07:23:46 2006 +0000 adding errAbort if input is missing - handling split-tables/files is the hard bit commit 249a8f340ba0cbf5432c1141c30bc2750efccde9 Author: heather Date: Thu Jan 5 03:41:16 2006 +0000 add snp125Ui commit 8a28b131d83524c83d3b29b171fbc4147d7a3bb1 Author: heather Date: Thu Jan 5 03:40:18 2006 +0000 add snp125 commit 199c0aaddb7b3d1af5a28e05ec74c6c4220b8903 Author: heather Date: Thu Jan 5 03:39:22 2006 +0000 registerTrackHandler for snp125 commit 44211f971331730303eda9be585fa726f6604f44 Author: heather Date: Thu Jan 5 03:38:35 2006 +0000 add snp125Color, loadSnp125 commit 2dfb70c372038ea9ae64d8423a6862b260f2d9a6 Author: heather Date: Thu Jan 5 03:34:58 2006 +0000 add snp125Ui commit d233cb2fce5f6aaaedea8bf2b22cd0b40b72f1e9 Author: heather Date: Thu Jan 5 03:34:38 2006 +0000 patterned after snpUi.h commit 2191270b2a015cb46ac675e5180bb3dee50bd4d7 Author: heather Date: Thu Jan 5 03:34:18 2006 +0000 color tweaks commit e7484c28bdf51173686e4285654d202830f0430b Author: heather Date: Thu Jan 5 03:32:29 2006 +0000 patterned after snpUi.c commit 2e54453ef4b9352742b585df053766806918acc6 Author: donnak Date: Thu Jan 5 00:50:40 2006 +0000 Removed zoo tables. commit 3ec33f5012c68148d33ae31d624ce4410a15d7af Author: donnak Date: Thu Jan 5 00:50:24 2006 +0000 Archived some items. commit 2df832766e7443d9fb140779c571db0a319e3b50 Author: donnak Date: Thu Jan 5 00:50:11 2006 +0000 Added droPer1 credits, removed NISC credits. commit 0c53b3b7cf768c90f2b0c938d8b8f71a11b01a93 Author: donnak Date: Thu Jan 5 00:49:13 2006 +0000 Added droPer1 announcement, archived some old news items. commit e61b76ddeef86903c2295670ef70dc2d34595223 Author: braney Date: Thu Jan 5 00:07:38 2006 +0000 enlarge a buffer that got overflowed by vibrFisc_ES114_1 commit 37e70dd617623878dfadb142318d24510f4e161c Author: kate Date: Wed Jan 4 23:03:01 2006 +0000 Added version to contigAcc accessions commit c4a7152bf56c953e530197a5150a5db41dc8c719 Author: kayla Date: Wed Jan 4 22:59:46 2006 +0000 Added 3 blocks to droPer1's trackDb.ra file since right now it's unclear which level of inhibition is driving the shortlabel. The intention is to remove (dm2) from the shortlabel. commit 8199319f906b0efbf639a85a6972b788ba576e19 Author: donnak Date: Wed Jan 4 20:52:40 2006 +0000 Made a few edits. commit f583cd8514e35c476da2bdf202c83081cf20676f Author: kate Date: Wed Jan 4 20:18:29 2006 +0000 Add contigAcc table commit 17019dfa9a0207a496adfe18a776c89bfc4910d2 Author: aamp Date: Wed Jan 4 19:05:59 2006 +0000 *Very unfinished, but it's a compiling beginning. Makefile even needs work. It compiles it but doesn't seem to make a binary. commit 61b6eeddc630621160906306160599b591f380e4 Author: kayla Date: Wed Jan 4 18:28:10 2006 +0000 Changed the description for huntingtin commit 88c55c8e9eeb589ace7d92054b997f934b01b50f Author: heather Date: Wed Jan 4 17:41:52 2006 +0000 add doSnp125 commit d03a8d3824ff07b2509fedc2a76c782bf11fe51f Author: heather Date: Wed Jan 4 17:36:19 2006 +0000 remove empty column for exception commit 59e296eab6d2fece32b0dcd02358af75c6cf90ff Author: galt Date: Wed Jan 4 16:00:02 2006 +0000 "Encode release log update" commit 35713cfda87e88ca2afc9ab299b9a096deab59ca Author: galt Date: Wed Jan 4 16:00:01 2006 +0000 "Release log update" commit bdac03b24cf5f6874ca3392eaaeb58729174f0e2 Author: kate Date: Wed Jan 4 01:37:58 2006 +0000 Fix downlaods link and swap assembly positions in menu commit 8ebb643cd5f8bfa0181202655e8bd96f8b04022c Author: kate Date: Wed Jan 4 01:28:25 2006 +0000 Local link for downloads, allows genome-test version commit 477c52dacfed7337fcbe36b15667af383e69cc6b Author: kate Date: Wed Jan 4 01:25:16 2006 +0000 Released UVa, Uppsala tracks commit f9ff9cb0638579dbd5566b472b688fc64b58cec4 Author: kayla Date: Wed Jan 4 01:24:06 2006 +0000 Took out "zinc finger" because it didn't yield any hits, and changed "huntington" to "huntingtin" commit 20acd83a90747b6c73d86346d563550427eb9228 Author: heather Date: Wed Jan 4 00:47:33 2006 +0000 remove locType and exception commit 3a48b488d9f61922e79bc3509befc245cfd8f451 Author: heather Date: Tue Jan 3 23:54:19 2006 +0000 add snp125 commit aa6b47c3ac1320d161c339deec326122b864c86c Author: heather Date: Tue Jan 3 23:52:45 2006 +0000 dbSnp build 125 commit c62218c672ca5d9ae1905d5c9033efebdc6e9ed0 Author: heather Date: Tue Jan 3 23:50:21 2006 +0000 add snpTmp commit 426f8faa54a78b4a49190c2c72cbd0e4caabc33d Author: heather Date: Tue Jan 3 23:49:54 2006 +0000 internal table for holding snp chrom coords from contigs commit 9edf05b3716d1bfe28d89b4216cdc1f4b37083bd Author: heather Date: Tue Jan 3 23:39:06 2006 +0000 add snpFasta commit cbb231b5e17990d50350638159403a4787d7f166 Author: heather Date: Tue Jan 3 23:38:42 2006 +0000 internal table for contents of SNP fasta files commit cf65e3333bb90018f132b672f59cfd73a777144b Author: kuhn Date: Tue Jan 3 23:14:55 2006 +0000 test floret for dev commit 888efd7a03e3064492388215e19ee763e3b71500 Author: fanhsu Date: Tue Jan 3 23:08:44 2006 +0000 Turned on genbank update for hg18. commit aceee354a7213e342e67f6d23dabc9cb09243c2f Author: fanhsu Date: Tue Jan 3 23:02:33 2006 +0000 Added hg18. commit ef5213e4d7e026fff712cd3a6da08190afacad76 Author: heather Date: Tue Jan 3 22:13:31 2006 +0000 use cloneString rather than strcpy commit 92f34ee37c2562d5df20c18329d9ec6f4819be2c Author: heather Date: Tue Jan 3 22:08:46 2006 +0000 remove some commented out lines commit 8d4a98e646c9892b7c5b39d3b0675a95fc0a0247 Author: daryl Date: Tue Jan 3 20:53:28 2006 +0000 Changed new Recomb Rate/Hotspot names to distinguish from the older Recomb Rate track commit f5d48705956af20250c2fdfcc4625c3ac4ea9b74 Author: galt Date: Tue Jan 3 16:00:04 2006 +0000 "Encode release log update" commit 6d0c9e262416e4ef9d4180c539fc601be0416052 Author: galt Date: Tue Jan 3 16:00:03 2006 +0000 "Release log update" commit ed6d5cd983303b40956484f3d86aeeb3aba12a05 Author: heather Date: Tue Jan 3 02:51:04 2006 +0000 "New version number v124" commit 64d1ec81b1143fafd9d924a76a5344ee230bc8f5 Author: daryl Date: Mon Jan 2 19:32:02 2006 +0000 minor format editing so that it is easier to compare the differences between snpRecombRate.html and snpRecombHotspot.html commit a46a5aef4a2e67578f7d63188492c0a52dc54f89 Author: galt Date: Mon Jan 2 16:00:03 2006 +0000 "Encode release log update" commit 75f912e71d53fd512bd4f5f181cccabdfa26f1a1 Author: galt Date: Mon Jan 2 16:00:02 2006 +0000 "Release log update" commit 792bec6e9e4bb56d1d3d83f2346dc699b0bfbda1 Author: daryl Date: Mon Jan 2 09:07:08 2006 +0000 Fix LD drawing bug in when trim option is off. commit a6c7df032959121c2abc474214b3d1cbd5c0ffda Author: kate Date: Mon Jan 2 06:54:01 2006 +0000 Add new section commit 83b1038345903ba6b63906c9318441bef086458f Author: kuhn Date: Sun Jan 1 20:22:16 2006 +0000 small rewordings commit e4c9b3ac1800054e66676eaa01ab39af27f6f83b Author: kuhn Date: Sun Jan 1 19:27:45 2006 +0000 a couple more minor weaks commit 30867aa483e03d5136d0ca022af77a581fedb933 Author: kuhn Date: Sun Jan 1 17:49:40 2006 +0000 a few minor changes commit 550ef8f53e7713b9043e9fe07f58021b409097b1 Author: galt Date: Sun Jan 1 16:00:02 2006 +0000 "Encode release log update" commit d7eb9675a8e3a9dc2e54b760826509e3cfc3bd21 Author: galt Date: Sun Jan 1 16:00:01 2006 +0000 "Release log update" commit 3b5974b0fa594873a3c697f89ce6ceb2197842b0 Author: kuhn Date: Sun Jan 1 06:55:57 2006 +0000 Dropped distinction between alpha and beta versions of Yale TAR track. Four of the five subtracks were common between the two versions. dropped 10 subtrack blocks and the main driver block for the old version commit 47c25f437f3d311a099da16508563c2fde5931e4 Author: galt Date: Sat Dec 31 16:00:03 2005 +0000 "Encode release log update" commit f4ff4547628467b78fbba00710bbb3ff6ce476d1 Author: galt Date: Sat Dec 31 16:00:02 2005 +0000 "Release log update" commit 5f9b0c4caa63dce338a90f8fbe302ed0e129e4ef Author: daryl Date: Sat Dec 31 08:52:13 2005 +0000 remove ambiguity: place snpRecombHotspot after snpRecombRate commit 207e8ae74760a7e8559613d0db031e059d3f9821 Author: daryl Date: Sat Dec 31 08:24:25 2005 +0000 Reformatted paragraph to fit screen commit e63adf0c6a9b20c2b919d74444dc0c5610acf4ea Author: daryl Date: Sat Dec 31 08:23:56 2005 +0000 Added verbose(4,*) comment to print target and query coordinates of subChain commit ae8a2401562183bcf45f087eba76560ebe2df8ff Author: daryl Date: Sat Dec 31 07:18:51 2005 +0000 Fixed multiple output bug with bedRegionIn/bedRegionOut commit 86ea29da1dab64d295fc17bcd7edd19d65ab9628 Author: galt Date: Fri Dec 30 16:00:02 2005 +0000 "Encode release log update" commit 3a4b32665e6ff74d0ad067add7a9c22862092614 Author: galt Date: Fri Dec 30 16:00:01 2005 +0000 "Release log update" commit 3b81a0d756f18294d777a40796b0469c30c3a796 Author: fanhsu Date: Fri Dec 30 15:24:12 2005 +0000 Added hg18/canFam2 pairwise. commit 3deec7025f8c170436d2dbbcc66da05a8b99e917 Author: fanhsu Date: Fri Dec 30 00:31:34 2005 +0000 Added gentTable=full to GB link. commit cf59d80fd160c9fd32337a7072da735a75823261 Author: kuhn Date: Thu Dec 29 18:38:53 2005 +0000 made some subscripts out of 'TR50' and fixed 60KB to be 60 kb commit 67d5069df0846e1603a35bc7715aad0e90597ac8 Author: kuhn Date: Thu Dec 29 17:42:14 2005 +0000 deconvoluted a sentence about checking boxes and made the '50' of TR50 a subscript. commit 33ce26de78584235c2156cb06b4f820ee85f5c61 Author: galt Date: Thu Dec 29 16:00:03 2005 +0000 "Encode release log update" commit 72dd80651f0d1e930242fb488c279ae81d71e527 Author: galt Date: Thu Dec 29 16:00:02 2005 +0000 "Release log update" commit c0293da48882b174b38174d8d9b1071e4bf427d8 Author: fanhsu Date: Thu Dec 29 05:01:57 2005 +0000 Added hg18/galGal2 pairwise. commit bce4ddeeff08427551a30b1b58a3362a855be43f Author: heather Date: Thu Dec 29 04:47:03 2005 +0000 remove checkForExceptions, checkForSize commit ee70b7366d4eddb437dcb94bc89e63fbc7e112e6 Author: kuhn Date: Wed Dec 28 21:41:39 2005 +0000 added qa docs to disallow group commit 25625d0b19c873c00fa616bdc66d469ce72bf4e1 Author: kuhn Date: Wed Dec 28 19:38:44 2005 +0000 added some cgis to the off-limits list for googlebot commit 8ca471b0e13c09aa46f794029fec9655935af86a Author: kuhn Date: Wed Dec 28 19:37:47 2005 +0000 adding to cvs commit 5b7b87240afe1d601723e126b0973ffd55bc2c36 Author: markd Date: Wed Dec 28 18:47:50 2005 +0000 don't abort when trackDb table in a path doesn't exist in a database commit 11907c7f75f2a0c6c843e23a85e98a1257112415 Author: galt Date: Wed Dec 28 16:00:02 2005 +0000 "Encode release log update" commit 7894fd52ad5c9efa8b54e4577b539aaf37c4d640 Author: galt Date: Wed Dec 28 16:00:01 2005 +0000 "Release log update" commit 8778c25556085ab92348d953d30ff6c119ae0de7 Author: daryl Date: Wed Dec 28 09:25:59 2005 +0000 Added options to invert LD plots in LD track commit 93876be2db7bd88af310c6087a2d1b3c557b36fd Author: kuhn Date: Wed Dec 28 07:25:12 2005 +0000 turned mm6 back on for hgwbeta and RR, since big push of rebuild has completed commit 1d099f03175d33d31b22859e0e0fc74a342162d7 Author: kuhn Date: Wed Dec 28 05:31:25 2005 +0000 changed a capitalizations commit 18336752a10c442b8f021e396aedaff6b0b148cd Author: kent Date: Tue Dec 27 18:04:29 2005 +0000 A little test cgi for some ajax web work. commit 1306ae078fb4d599b939c7eebccfefce6fc4bf38 Author: galt Date: Tue Dec 27 16:00:03 2005 +0000 "Encode release log update" commit eab8372966f0fde16b12ba9a1fb52d04f13c4834 Author: galt Date: Tue Dec 27 16:00:01 2005 +0000 "Release log update" commit 8615358050d110774866a7c8feeda03fb278d460 Author: galt Date: Mon Dec 26 16:00:03 2005 +0000 "Encode release log update" commit 38aa822016ba1378c4c85e8fa3a131d743fc6bf2 Author: galt Date: Mon Dec 26 16:00:02 2005 +0000 "Release log update" commit a2e854c830364be23b5199853ce5d03653cf90ba Author: fanhsu Date: Mon Dec 26 13:32:52 2005 +0000 Added BLASTZ mm7. commit 4149184c79743cf248d451922fe6f1a7b9dc4b86 Author: galt Date: Sun Dec 25 16:00:04 2005 +0000 "Encode release log update" commit c7d0fc40291ea700924e60536c8e78da28f2fd15 Author: galt Date: Sun Dec 25 16:00:02 2005 +0000 "Release log update" commit f618f07f3d9ebc8855a888ee49592ef338c4485c Author: kent Date: Sun Dec 25 04:23:50 2005 +0000 Adding in a hide association table, and a text output to test cases. commit 634f3d94efbcc26b5d49bec1b9a89c1e542bf1e0 Author: kuhn Date: Sun Dec 25 04:19:20 2005 +0000 turned mm6 back off while EST updates take place manually. then will push to RR before turningback on. commit d7594f6eec336877ede0e276bdc0681e55598b30 Author: kent Date: Sun Dec 25 04:19:16 2005 +0000 Fixing an extra blank line output when tables hidden commit b6dab8ca5f9227855fc61cd5ff9223caae51856f Author: kent Date: Sun Dec 25 04:16:29 2005 +0000 Adding hide to imageProbe parts commit 1abaceb3e09c8294eaa42383eb3f3ae29b7c2bf8 Author: kent Date: Sun Dec 25 04:14:13 2005 +0000 Making it so that you can force a field to be output between tags. Moving a few things from database scanning time to spec-tree building time, which should speed it up a bit if it weren't actually bound by database time. commit 61a29a991485aa7bc7a7f9ea66a304d1be1210c3 Author: daryl Date: Sat Dec 24 23:00:36 2005 +0000 Fix left label drawing bug -- dense mode wasn't working because of improper clipping. commit f0db6d753af6ddaa3c7d0b25ff00693ec033fa67 Author: daryl Date: Sat Dec 24 22:17:30 2005 +0000 cast array subscript characters as integers to remove "array subscript has type 'char'" warning commit b94639ab39d1380c3d8de0650335130113c54101 Author: kuhn Date: Sat Dec 24 17:39:40 2005 +0000 turned on mm6 on beta commit aa26ef42d73569db65558502ec0b32505828ef60 Author: galt Date: Sat Dec 24 16:00:02 2005 +0000 "Encode release log update" commit d8aef15ed464bdd3e2a8a081af53b134aab86a41 Author: galt Date: Sat Dec 24 16:00:01 2005 +0000 "Release log update" commit 128db1e0b52bb695a6a15a643b8fb71953a67939 Author: hartera Date: Sat Dec 24 11:25:24 2005 +0000 Created chain and net tracks and axtNet, mafNet and alignment downloads for hg18 on danRer3. Known Genes track is in progress. commit d1f57d4742ae0b5232b1a73e474468ccfe1c44c5 Author: hartera Date: Sat Dec 24 10:48:15 2005 +0000 Corrections made in Methods section. commit 42d139915841ea1ded6d4dd4ff8e50d42b50309c Author: hartera Date: Sat Dec 24 10:47:01 2005 +0000 Corrections in Methods section. commit 320d808ed43386023e3ba4f4cee2cd40492a8847 Author: hartera Date: Sat Dec 24 10:45:53 2005 +0000 Description for hg18 net track on danRer3. commit e6e2c7519122d5358ece87aec8f85889b7f73400 Author: hartera Date: Sat Dec 24 10:43:37 2005 +0000 Description for hg18 chain track on danRer3. commit cc41d5f5a495fa72694db6f002864ec7bae47831 Author: hartera Date: Sat Dec 24 10:40:44 2005 +0000 added entries for hg18 chain and net tracks. commit d0c2007f44dd2e8474e90d50feea580142a4358d Author: hartera Date: Sat Dec 24 09:56:06 2005 +0000 Minor edits to the Methods section. commit 55e3d61e9d248f51b39d8d9a080092a8427b429d Author: hartera Date: Sat Dec 24 09:46:37 2005 +0000 Finished creating chains, net, mafNet, axtNet and alignment downloads for danRer3 on hg18. commit 7440ece7617526a14c775be54fec0e187e7df0a2 Author: daryl Date: Sat Dec 24 09:40:26 2005 +0000 Updated HapMap LD track to phase II and corrected some names. commit b3302f9688bb8ed7946d324f3af560c4e1dd4bcf Author: daryl Date: Sat Dec 24 09:39:22 2005 +0000 Added dense mode drawing; added mapsSelf to suppress generic map items. commit a9b09c4a4a43d62ddb87d4397869cbe09b080595 Author: hartera Date: Sat Dec 24 00:50:58 2005 +0000 Description for danRer3 net track on hg18. commit ac1b8d7ed7016075031fe9acb20e8a3a40a859bf Author: hartera Date: Sat Dec 24 00:50:15 2005 +0000 Description for danRer3 chain track on hg18. commit b80c1dcf4b250125040024a4b5490ad555754a99 Author: hartera Date: Sat Dec 24 00:49:29 2005 +0000 Added trackDb.ra for hg18. commit b0bc0f023321d1709d84ab30ce31710d10a3e48d Author: donnak Date: Fri Dec 23 22:15:43 2005 +0000 Added droPer1. commit 48147f1f809d45280576b09240ae171391dfff14 Author: donnak Date: Fri Dec 23 22:05:20 2005 +0000 Added droPer1 credits. commit ecb67f33de6152d40250af953aca53d6c6ca392a Author: kuhn Date: Fri Dec 23 21:34:45 2005 +0000 added droPer1 to list of chained-to assemblies commit c418f79e3d934fdf5b958e07d9f950e01e8444b1 Author: kuhn Date: Fri Dec 23 21:23:04 2005 +0000 added droPer1 commit 80e3f2324699d91d0e96c6c381e7d2d99cba84ca Author: kuhn Date: Fri Dec 23 19:09:24 2005 +0000 added a an exit statement in the test block that checks for valid databases. no point in running everything after determining that the db is wrong. commit 4768462515116975f6e74118d21711df20f9d6ab Author: kuhn Date: Fri Dec 23 19:02:24 2005 +0000 added a grep to remove slash to filter out, e.g., Dog/Human when checking genomeClade and restored wildcard there so it works for droPer1 and others with species name in genome field. commit de1113c8d5ee08ff43e10afc0ef769c76fb7759f Author: kuhn Date: Fri Dec 23 18:20:54 2005 +0000 added dumpEmpty.csh commit 4f08fcc06732beb28cbc9baacccc8684d3c72049 Author: kuhn Date: Fri Dec 23 18:17:58 2005 +0000 little utility for clearing away zero-size files commit b70a2fa302c0815d26e1362280c9da6c024870eb Author: galt Date: Fri Dec 23 16:00:02 2005 +0000 "Encode release log update" commit 503d252d16abfb698603fc14667e08204704f421 Author: galt Date: Fri Dec 23 16:00:01 2005 +0000 "Release log update" commit 5c0e49b090aac765e61a2a5eebadf10cdd8c50fb Author: daryl Date: Fri Dec 23 12:26:10 2005 +0000 Update data structures for LD track: more encoding commit ecbce1467887c0e68415d1abb8f3d5e6bfbdf912 Author: daryl Date: Fri Dec 23 12:25:01 2005 +0000 Recombination Rate/Hotspot update commit 673ec30e7a1b84f1164a934fc0b7c3df5dc9fd23 Author: daryl Date: Fri Dec 23 12:23:13 2005 +0000 condensed format for LD structures commit c6b73deda5c5e7cfffb123265175b109d0af2cfe Author: kent Date: Fri Dec 23 08:13:43 2005 +0000 Expanding buffers from 64 to 128 bytes for track names. Replacing sprintfs with safefs. commit 52ad6c045b46a3a8923241c99a5600ba8ba0aa01 Author: kate Date: Fri Dec 23 01:38:14 2005 +0000 Load SCONE Conservation commit 2f387d02139678fcf529fec0123749390fc737a5 Author: kate Date: Fri Dec 23 01:37:53 2005 +0000 Chain/net 2X assemblies on hg17 commit f18a4a53886083c7702dc7c40f4a4f3939972294 Author: kate Date: Fri Dec 23 01:25:08 2005 +0000 Wiggle performance commit 787f8aa07e37b1590542ac9b30be703b4795b9f4 Author: fanhsu Date: Fri Dec 23 01:17:02 2005 +0000 Updated hg18 section. commit 1a3d23a3bfa637f5b6145c062e3ddb2cf60403d8 Author: kate Date: Fri Dec 23 00:59:49 2005 +0000 Add TBA SCONE conservation wiggle commit 27d57395226279a03a3fe3af58ac9208fbea863e Author: kayla Date: Fri Dec 23 00:17:23 2005 +0000 added droPer1 commit a109fe803d52cbf9980d395924b85c26779b927b Author: kate Date: Thu Dec 22 21:50:04 2005 +0000 Progressive alignment up tree for multiz commit 6964ddd7b467cb15faf8decbba30d77dc4a03b2b Author: heather Date: Thu Dec 22 21:39:51 2005 +0000 needed https for affy url commit 0cd3b316a21e99d21034b0f178c40722fdd1e570 Author: kate Date: Thu Dec 22 21:02:04 2005 +0000 Add convenient symlink commit e093b443db622c59de23bc119b223d4edf736b70 Author: hiram Date: Thu Dec 22 20:08:10 2005 +0000 nfsNoodge moved up one command between chainSwap and chainSplit where it belongs commit aa69fded4f0d65eb0497450769a02e056640bc0c Author: kent Date: Thu Dec 22 20:06:30 2005 +0000 Fixed bug in quote escaping. commit 2979c925c1b4809a98f62e002583ca8d9e141f6c Author: kent Date: Thu Dec 22 18:18:55 2005 +0000 Adding version info to doc. commit 7800c65dd766f404f46ad2a22ccad62f2a2180ef Author: kuhn Date: Thu Dec 22 17:53:15 2005 +0000 added -w flag to grep, so tName seach doesn't turn up productName field. Also added logic to stop if the acceptable fields (chrom, tName, genoName) are not found commit a25a8bf0bf65554205ca73ebc4ed2a7ed05d1a2e Author: kuhn Date: Thu Dec 22 17:25:52 2005 +0000 enabling mm6 on dev commit ee3eb75b25c0faee854ebe61d96e4e63050867b4 Author: galt Date: Thu Dec 22 16:00:02 2005 +0000 "Encode release log update" commit 71504a5fbeaa5d3d22f29f44ca00efc249ac7006 Author: galt Date: Thu Dec 22 16:00:01 2005 +0000 "Release log update" commit fbc7d9330b7be19179aa6c0e2f629294fec73b3d Author: giardine Date: Thu Dec 22 14:38:57 2005 +0000 Changed sql on check to see if OMIM was available for known genes. Tests directly running the sql shows it to be about 10x faster and caches the query so repeated runs are faster still. commit 71e782e8ecf85fab1bbead67d59d7848b5593da3 Author: daryl Date: Thu Dec 22 04:13:38 2005 +0000 Changed to use ld.as commit 2f810b44bd6c70874ef693511a5d97cbf2fd21d6 Author: jen Date: Thu Dec 22 01:45:58 2005 +0000 Adjusted canFam1/2 lables. commit 950164b7ac1b71076c3591c7fda550b5cd8a78b1 Author: jen Date: Thu Dec 22 01:40:24 2005 +0000 Adjusted mm6/mm7 net/chain. commit c92e52001862a55fab664a03e16c267221864385 Author: jen Date: Thu Dec 22 01:35:53 2005 +0000 Adjusted canFam2 net/chain. commit 58864d46ce7771f2b063d58201921a5a0a40773d Author: jen Date: Thu Dec 22 01:35:13 2005 +0000 Adjusted canFam2 net/chain. commit 66e10c83d2e4847c99cdd36f703e45cc09780d9c Author: jen Date: Thu Dec 22 01:34:04 2005 +0000 Adjusted canFam2 net/chain. commit 7e5bf26f8a6f6092669642f55068688172e4e598 Author: jen Date: Thu Dec 22 01:27:30 2005 +0000 Adjusted canFam2 net/chain. commit ec99040241ce60fd8155f0d8da21f8e867d2ffa0 Author: jen Date: Thu Dec 22 01:19:32 2005 +0000 Fixed priority for canFam2 with respect to hg17 at top level. commit e8576e36240c2ad2da039acfb5d5bc29a2dddefc Author: kuhn Date: Thu Dec 22 00:58:34 2005 +0000 added countPerChrom.csh, which will check for annotations on every chrom for a table in one or two databases, including one on beta, if desired commit 687347bec63a41fa93bed379d9e4cc322ccbb337 Author: jen Date: Thu Dec 22 00:43:42 2005 +0000 Changed mm7 chain from visibility dense to hide. commit bc6b8531877daa0e7ff8310ed8be67b82e2932d5 Author: daryl Date: Thu Dec 22 00:29:30 2005 +0000 change names commit 2e54900a4b6eee3a73189d6bd0dfa28109644d07 Author: kuhn Date: Thu Dec 22 00:25:41 2005 +0000 added "super_" to list of prefixes for chain/net color to accomodate droPer1 commit fb4ed7c61162b46351e031ef1e1ad8e0fd5abaf6 Author: daryl Date: Thu Dec 22 00:22:39 2005 +0000 nitial version of structures for the Linkage Disequilibrium track commit 7c0491ab7863fffd4cc91e155d92d4bc7f8e70ef Author: daryl Date: Thu Dec 22 00:22:37 2005 +0000 Initial version of structures for the Linkage Disequilibrium track commit 232f7d2e75cf957c179e9df6aae2318b90935396 Author: kayla Date: Thu Dec 22 00:05:30 2005 +0000 *** empty log message *** commit efbc83ef234b9d8457a39936fe1c6b227ff3f17e Author: kayla Date: Wed Dec 21 23:37:56 2005 +0000 Added two blocks to trackDb.ra for droPer chain and net. commit 69259ebaf99068ac31ad8ed8796dfcd97d66462a Author: heather Date: Wed Dec 21 23:17:51 2005 +0000 add search spec for affy500K commit 001b7704d9ca42eebcdd9b7bc07fac146bf8d612 Author: heather Date: Wed Dec 21 23:02:22 2005 +0000 indices for Affy 500K commit 726a2adaed299ed947b18bd1f2ae07bf2248141c Author: heather Date: Wed Dec 21 22:49:14 2005 +0000 url for Affy 500k (not working, checking with Venu) commit 4ce544f0dde2e929c1332bf3f35e17a287170d01 Author: hiram Date: Wed Dec 21 22:38:31 2005 +0000 Run a downloads for rn3 canFam2 to create files, they went missing in action ... commit d45d7df525dbb0d80f5797c8df4849a05cbc99f8 Author: heather Date: Wed Dec 21 22:35:30 2005 +0000 add Affy 500K commit 1237e021f9b92307ebb9712b902c6e14ff4d025f Author: kayla Date: Wed Dec 21 22:33:18 2005 +0000 added droPer1 commit f727b9c624bc77ef879fa799e110f1b62bd1fda2 Author: heather Date: Wed Dec 21 22:25:43 2005 +0000 initial revision commit 44af6e1f9a28837f0673bd02af510d1d1e08a02f Author: heather Date: Wed Dec 21 22:24:45 2005 +0000 add Affy 500K commit fc4fe59d1599491ec596c1735cab137cfc4ff80b Author: heather Date: Wed Dec 21 22:14:08 2005 +0000 standalone util to compare affy SNPs to dbSNP commit 69523f3946692baa890f906f2cb3e6fb58448e89 Author: kayla Date: Wed Dec 21 22:08:59 2005 +0000 Gave droPer1 its own trackDb.ra commit 9dd321f3c040cf5fd66b921ce7b8f925136e47e7 Author: kayla Date: Wed Dec 21 21:47:06 2005 +0000 Added a gap.html file for the droPer1 assembly commit 660049025382727e52813bf7a8504239f1dcd631 Author: kent Date: Wed Dec 21 21:44:48 2005 +0000 Making it use less memory in a pathological case (the the the) commit 73d1d90cdabb8466cf9d33e2462670dfcc1aedb2 Author: ann Date: Wed Dec 21 21:37:41 2005 +0000 Edited short label for mm6 and mm7 chains/nets commit c81add90cb51caea3d6767885937a356b88414ff Author: ann Date: Wed Dec 21 21:32:16 2005 +0000 changed short label on mm6 and mm7 chaing/net tracks commit 74a0b1b9971781ef8fc4e2c8eb7fcfec3fe7b890 Author: ann Date: Wed Dec 21 21:28:58 2005 +0000 changed short label on mouse chain/net commit c971fbfa6e0cd6c2f12cb1ef8b009b413131665d Author: kent Date: Wed Dec 21 21:26:37 2005 +0000 Filling in ordered and unordered spans, and sorting results on them. commit b323885e7c130495949a6446de74fb35efb6b346 Author: braney Date: Wed Dec 21 19:57:27 2005 +0000 fix up the demonstation encode tracks to have db names commit 7f210131ad85cf02464087903bd2f93fc2db38c1 Author: braney Date: Wed Dec 21 19:54:35 2005 +0000 add the reference species to codon translation drop down commit 0f81d454a0409ec4974899a5678796a2847d5815 Author: heather Date: Wed Dec 21 19:51:39 2005 +0000 add space between NAME and VALUE commit cb100e660da1441036f5c6324645593c2a97f298 Author: kent Date: Wed Dec 21 19:22:48 2005 +0000 setting verbosity to 0 commit 2a23bc7a28d7664979385de2a1e1e430114eee7f Author: ann Date: Wed Dec 21 19:06:06 2005 +0000 removed 'frames' line for Conservation track entry commit a57d5ca9837d5bf1b005fb50f0d05b9dcf6c60f0 Author: kuhn Date: Wed Dec 21 18:19:34 2005 +0000 changed so it no longer says that this track shows levels, but rather the location of transcription commit f013b33e814b857da236aa5ff6228edcbb2fe0ec Author: kuhn Date: Wed Dec 21 17:58:33 2005 +0000 added syntenyCow by copying block from hg17. priority setting is overridden in hg15 commit cdcbbc98d88d2c59474a5b1b2bc18769cfedf94a Author: kuhn Date: Wed Dec 21 17:45:03 2005 +0000 moved up from hg15 directory and reformatted references. cvs history is in attic at hg15 level commit 2e700f521a13211b2da3ef40d242e78aa9ad9afe Author: kuhn Date: Wed Dec 21 17:44:03 2005 +0000 removed 'release alpha' from two encodeAffyRna tracks commit e3e950fdf79d62daa2ba772bb3b9566ee7fbd381 Author: kuhn Date: Wed Dec 21 17:40:23 2005 +0000 moved up a level commit fa8ff55aeb092d90ff2bbaa02b71893d239d288a Author: kuhn Date: Wed Dec 21 17:33:01 2005 +0000 moved the file up a directory commit f875ea973388863a366fcdb7612eeffb0677658c Author: galt Date: Wed Dec 21 16:00:02 2005 +0000 "Encode release log update" commit 3f40ad80db9a2c93995568efd7ea5b43a2624066 Author: galt Date: Wed Dec 21 16:00:01 2005 +0000 "Release log update" commit b28dd0cde5b704dd7c0646eb8be468c734445a2e Author: heather Date: Wed Dec 21 13:47:21 2005 +0000 removing humanPhenotypeUi.o on behalf of Belinda; avoids duplicate symbols also in hgMutUi.o commit 8d9d761f9875078fcf94d6905b2c110821b35c9b Author: kent Date: Wed Dec 21 06:48:43 2005 +0000 ifdefing out a performance problem in calcuting omimAvail. It will always be non-avail.... commit d0b674d644784ac5e1a59c18fb44abbd12f4e691 Author: kent Date: Wed Dec 21 05:58:28 2005 +0000 Starting to process multiple-word queries sensibly commit e6f5be2b890a8e5145b90ef8d31d7a909819f0cb Author: heather Date: Wed Dec 21 05:26:34 2005 +0000 read strand correctly; add checkForExceptions, checkForSize commit e5a779357a5c894dd2515e07d1ba6c26b99ce635 Author: kent Date: Wed Dec 21 04:38:55 2005 +0000 Some more objectivication commit f1740e6fca45a3c18d92bedbb3d2de555b7385c1 Author: kent Date: Wed Dec 21 04:18:46 2005 +0000 Objectifying things a bit into trix commit 19b2e5ce5bb1322d74495cd3c6bcc6b6e050a5ec Author: kent Date: Wed Dec 21 02:57:40 2005 +0000 Fixing a bug that manifested on 'kinase' in the uniProt set. commit ba4ce928893c5eb9db3caf1d2116f07cdfd3760a Author: daryl Date: Wed Dec 21 02:31:01 2005 +0000 Rename tables for snpRecombHotspot* tables commit 42468e685b7cfabb3420b4c96250aa54e855f3db Author: kent Date: Wed Dec 21 02:28:25 2005 +0000 Starting to hash out a new search framework. commit 2c0068a80348831613713ac0b2b9e9c93045fc3c Author: heather Date: Wed Dec 21 01:00:37 2005 +0000 put objects in alphabetical order; remove 2nd visiGene.o commit 9286baac3edcd7a9696280fad7147c2ea1f73900 Author: fanhsu Date: Wed Dec 21 00:39:48 2005 +0000 Created 2 bit file. commit 19738f2057d1c34de694b8cd49051ce3f4848a8a Author: hiram Date: Wed Dec 21 00:32:06 2005 +0000 Add geneid data From Francisco Camara commit 5e971976a8d2a4c885a1a79c1338b5fc86b325bb Author: galt Date: Tue Dec 20 23:20:49 2005 +0000 trying -Fa too see if it goes faster without breaking cvs-reports commit 6cb846f6dac9ec16fb7c6ef3f69fc26075da9ac6 Author: kate Date: Tue Dec 20 23:04:50 2005 +0000 Pushed files down a level commit 55757a0ebc1d2d700584b4481b45979388d4ee4a Author: kate Date: Tue Dec 20 23:04:00 2005 +0000 Correct HeLa cell strain in Affy tracks commit 51cd242dfe4204704d138653ea05653e6793104e Author: ann Date: Tue Dec 20 22:59:50 2005 +0000 Edited mouse chain/net tracks so that mm7 is default commit 9511ace64a613991c1e35a2a1440da920cac8913 Author: kate Date: Tue Dec 20 22:52:28 2005 +0000 Split Affy RNA track commit 0fc40e5db21c6b609ca63e916680c9452b10a1ba Author: ann Date: Tue Dec 20 22:47:46 2005 +0000 changed track entries for chain/net to mouse commit 887215612998d7c5a8cf93d1560c806b771fd1fd Author: ann Date: Tue Dec 20 22:39:06 2005 +0000 Added track entries for chain/net mm7 commit f9fdf4520c428a1885e23e04298c27fd81682831 Author: kuhn Date: Tue Dec 20 22:35:27 2005 +0000 deleted composite-track version of encodeAffy*HeLa* tracks. New version splits out 6 wiggle from 6 BED subtracks commit bc4d1143b0d963022657960a2338c14d1f83fce9 Author: ann Date: Tue Dec 20 22:35:18 2005 +0000 Edited tracks for mm7 chain/net commit 2c70766667065e8fe2065826fbe731099da3aa36 Author: heather Date: Tue Dec 20 21:59:06 2005 +0000 add References section commit 80fa4182eee0a85d97d3b7f652cb2089f0935bee Author: kuhn Date: Tue Dec 20 21:57:29 2005 +0000 added a clause commit 92d3e653bc094c5519115ebca434de81dcbfd9e6 Author: kuhn Date: Tue Dec 20 21:44:14 2005 +0000 moved up to mouse level commit 4ab7f5bdf4d082cf776d3f76a0788336b285c951 Author: kuhn Date: Tue Dec 20 21:42:53 2005 +0000 brought xenoRefGene up from mm7 level commit 930fb91623365de1f1549d3d5ca471489e569e46 Author: kuhn Date: Tue Dec 20 21:42:01 2005 +0000 moved file up from mm7 level commit d02a5f4c8edb11f127eaafa6e28127490140e611 Author: markd Date: Tue Dec 20 20:50:44 2005 +0000 allow SCRIPTS, CGI_BIN, and STRIP to be overridden in the environment commit ce8af77f16be83ddcc66075544361d5e4a1234eb Author: kayla Date: Tue Dec 20 20:07:46 2005 +0000 added canFam2 commit fc83c9c1e81a783442473e0987ad843f58d8887e Author: heather Date: Tue Dec 20 19:51:45 2005 +0000 syntenyCow format fix commit ac8da42f0ffc2f3e85e44edfcdf1de9558a3a7b0 Author: ann Date: Tue Dec 20 19:00:30 2005 +0000 Added entries for chain/net mm6 tracks. commit cdc69fdcaa26314fa6068a916c831796dacfd7d5 Author: kuhn Date: Tue Dec 20 18:24:56 2005 +0000 added a reminder about auotdumping commit 0e817ee38b47340fcadef8f808beedf20b829d8b Author: kent Date: Tue Dec 20 18:20:28 2005 +0000 Correcting comment in generated dtd. commit 06389e97c84cb209a57f23823380914bca3e3f2f Author: heather Date: Tue Dec 20 18:20:13 2005 +0000 correct e-val commit 361d8da146a1b9d7a17c23dcf687d831d7d0dfc9 Author: heather Date: Tue Dec 20 18:19:02 2005 +0000 correct BAC/EST count and E-val commit ddeac3617bcbf8b8e04393a6fe144d5a9f7d5e48 Author: galt Date: Tue Dec 20 18:17:42 2005 +0000 added warning about empty fa record with no sequence commit 406c8c689f21fcd442c1051f0aa4f30505c88ecf Author: ann Date: Tue Dec 20 17:59:09 2005 +0000 edited entries for mm6 and mm7 to cause mm7 to be the main mouse chain/net commit 95762411ebac746164d9dfab82e6dee9b1318d7a Author: kent Date: Tue Dec 20 17:55:27 2005 +0000 Adding test case commit f2a1ea9be0b9c1d29afd0175d8dde5f807261cb3 Author: kent Date: Tue Dec 20 17:52:26 2005 +0000 Testing xap. commit 775f6b729d62fb1d658173a0d386d3f16dda9dab Author: markd Date: Tue Dec 20 17:37:17 2005 +0000 reenabled mm6 alignments commit 8b5d0637a974d412ea705fdbf5b8e1ecc12427cd Author: markd Date: Tue Dec 20 17:26:53 2005 +0000 reenabled hg17 updates commit 6ff48345a8e34e98e44dc8fea3adbf3e8b730698 Author: kate Date: Tue Dec 20 17:23:19 2005 +0000 Fix date commit 1b3f01030792dc99a2a03cfc8141a293f3656d0e Author: kate Date: Tue Dec 20 17:23:08 2005 +0000 Add lineage-specific repeats for randoms commit a5a1647e3b48e9f39fd5ccaa07c7dcae11b3b353 Author: galt Date: Tue Dec 20 16:00:03 2005 +0000 "Encode release log update" commit b7b71859ade32c0a8d5bda3cf9729816ce827f7a Author: galt Date: Tue Dec 20 16:00:02 2005 +0000 "Release log update" commit 4a7b89f088415c9a4fbb90a4138dfa5349e2463d Author: donnak Date: Tue Dec 20 07:21:27 2005 +0000 Uncommented canFam2. commit 49f8cb07fc6ffe3d26f8652e46de6a998b687555 Author: donnak Date: Tue Dec 20 05:25:21 2005 +0000 Updated some info for the gateway page. commit 806504ea6871e5a3786099ca50e1bf69deb5774b Author: donnak Date: Tue Dec 20 05:24:26 2005 +0000 Commented out canFam2 announcement to try to straighten out mess currently being made w/pushes. commit f2b903645c6300ee3b5e80b0ed104de03c485706 Author: donnak Date: Tue Dec 20 03:00:23 2005 +0000 Added announcement for canFam2. commit be802c128bb43374222088973a6cd144515c167c Author: kate Date: Tue Dec 20 02:08:07 2005 +0000 Tweak ranges on Affy RNA Signal track commit 8b838e792f09f5acb044d599f19380bb2722ac62 Author: heather Date: Tue Dec 20 01:17:17 2005 +0000 more detail from Denis Larkin commit 4230d3217d566e4d5da4f708eb2b8095e62c23ff Author: fanhsu Date: Tue Dec 20 01:01:45 2005 +0000 Created pbHgnc.c to process new HGNC (HUGO) data. commit 03f8c64444a8951000d91244cb6ec284907c7f96 Author: kate Date: Tue Dec 20 01:01:44 2005 +0000 Split Affy RNA track into Signal and Transfrag tracks commit c737f42c856709a3f0b7dbdcb1bcb02c864334e9 Author: fanhsu Date: Tue Dec 20 01:01:09 2005 +0000 Created makefile commit 1b9b35f70e2870ae2554e4402d2ac817a844ff69 Author: kent Date: Tue Dec 20 00:21:52 2005 +0000 Adding test case corresponding to shapes example in Dr. Dobb's article. commit 2e04adf5c940c95278cd310be402e0f770562446 Author: kent Date: Tue Dec 20 00:20:58 2005 +0000 Prettying up dtd file output when not a lot of child elements commit aaf9d16fcfeb9e7ed7c64ed4ff4d801d113e5c6f Author: donnak Date: Mon Dec 19 23:47:26 2005 +0000 Added canFam2. commit 3a6689264c27cd092013b90aa8b30ef3f53bf517 Author: donnak Date: Mon Dec 19 23:40:11 2005 +0000 Added canFam2 to release list. commit 1305d8db7479ab6d14e3e6334dd079261eb92c4f Author: donnak Date: Mon Dec 19 23:30:54 2005 +0000 Fixed mouse assembly size numbers. commit 719306f008a95c5301b2e3a9fb6c30a718c5f61f Author: donnak Date: Mon Dec 19 23:27:34 2005 +0000 Fixed assembly size numbers. commit d6325d1c1517fd586c915696c10f41ee58600077 Author: hiram Date: Mon Dec 19 22:49:31 2005 +0000 Add hgConvert and hgLiftOver, remove hgCoordConv from cgi-bin listing commit 8fa314914437f4e20b0fefc7404c886c6bc3191e Author: ann Date: Mon Dec 19 22:09:50 2005 +0000 added track entries for chain/net to mm6 commit 1fd04245e845d468e14b504521ed98d1702c6b8c Author: ann Date: Mon Dec 19 20:50:26 2005 +0000 changed typo (mm6 -> mm7) commit f7b88ad9e449e3b9e311416d7797d327a51a9a2c Author: kent Date: Mon Dec 19 19:04:13 2005 +0000 Adding loadNext function generation. Moving start/end handler prototypes to .h file commit e73eacef09df56c2a0621cf3e0473721d822f3ac Author: kent Date: Mon Dec 19 17:51:14 2005 +0000 Implementing xpParseNext. Eliminating recursion in xpParse. commit e91a6fc663d4203680b2eda241897fc57594e0d0 Author: hartera Date: Mon Dec 19 11:05:34 2005 +0000 Started blastz alignments anc creation of chains for zebrafish (danRer3). commit 320156e004e4b647bcb7cd0e2bbcf233d5d462e9 Author: markd Date: Mon Dec 19 06:29:03 2005 +0000 added program to filter make output commit d260ca10927711214b55fa03aeeaebb0d6e5e1dd Author: kent Date: Mon Dec 19 05:21:51 2005 +0000 Converting to use xapOpen/xapNext. commit e9936de0a9fdfbc9ae0cc22e27c0dfb67355549c Author: kent Date: Mon Dec 19 05:18:38 2005 +0000 Making xapParseNext happen. commit ff7d51846e7e3c7e4434ee1210fb9cfa43b379b5 Author: kent Date: Mon Dec 19 05:18:26 2005 +0000 Making xapOpen/xapNext happen. commit 2339a28db00fbf8b59354bbdf7d69f7ba6f79707 Author: kent Date: Mon Dec 19 05:10:17 2005 +0000 Testing xpNext. commit 14d14528c2c59fe1301101587b10bead0381051a Author: kent Date: Mon Dec 19 03:18:09 2005 +0000 Breaking up xpParse into a couple of functions in preparation for converting it away from recursion to iteration using a stack. I'm hoping this will make it easier to do partial parses. commit fab0ce3a26e02d774c10bab9cb61f80ba8363934 Author: kate Date: Mon Dec 19 02:41:35 2005 +0000 Zebrafish (danRer3) alignments commit 19aec1e0824b2a404455561db4abf3b44b20db21 Author: kate Date: Sun Dec 18 19:10:01 2005 +0000 Remove CVS conflict commit 4aece6d5780ee4fad01b21ea18796cc5a2fdd92a Author: kate Date: Sun Dec 18 19:09:26 2005 +0000 More MSA conservation commit 4cc04a2ae60e43372535f297a7bf616266f7c9aa Author: galt Date: Sun Dec 18 16:00:03 2005 +0000 "Encode release log update" commit 3d861c9ddd461f3c7d6ebaeeb4c43bc7f22e4e09 Author: galt Date: Sun Dec 18 16:00:01 2005 +0000 "Release log update" commit 54e4c4bb8467b7e4ff57ddd218e9612ac952247d Author: kent Date: Sun Dec 18 01:34:10 2005 +0000 Adding clean target to avoid error message, even though clean doesn't do anything. commit dec3ff92224926dc262745e49b26f72a0011269e Author: kent Date: Sun Dec 18 01:30:44 2005 +0000 Updating copyright message commit 0adfde23bf0c8cb7be27773b6f1ed7c5eb16c9d4 Author: galt Date: Sat Dec 17 16:00:03 2005 +0000 "Encode release log update" commit fb75533fa4115c7ffdd7ac4e7702fc7ef0189e1d Author: galt Date: Sat Dec 17 16:00:02 2005 +0000 "Release log update" commit d1d0a1b3055d156f537c1ea749c2f401d3b14d45 Author: donnak Date: Sat Dec 17 08:52:44 2005 +0000 Fixed refs & some other things. commit 0bdc2b6fc1ce509648dc70529aede0688297d5a2 Author: donnak Date: Sat Dec 17 08:37:23 2005 +0000 *** empty log message *** commit d488328afc349c68040cbb831d30bc395468e69a Author: donnak Date: Sat Dec 17 08:25:36 2005 +0000 Updated references. commit 033449fe98c4fc0ffe002f6f00a72e108c0272ad Author: donnak Date: Sat Dec 17 07:55:37 2005 +0000 Added mm7 announcement, archived some news items. commit 91a899dc18f8e7aa3f343826ad8ce259031b3f95 Author: donnak Date: Sat Dec 17 06:34:41 2005 +0000 Archived a few news items. commit 40176ffd21c14a95d0889682553548ad3017d6ab Author: donnak Date: Sat Dec 17 06:33:07 2005 +0000 Fixed a bug introduced by previous edit. commit 81b18af899ffa4b3a279df7bf8aea201b0205bcf Author: kent Date: Sat Dec 17 06:27:47 2005 +0000 Some little changes fixing signedness and other minor problems to get code past gcc 4.0.1 on the Mac. commit ab3e069b6a54e927c5c1c59e0beabe57fce4e3ae Author: kent Date: Sat Dec 17 06:24:25 2005 +0000 Fixing signed/unsigned conflict. commit e5e020f3c987ce4159ef1ced851c1d773d355a5e Author: kent Date: Sat Dec 17 05:28:19 2005 +0000 Adding missing -lz on link line to get it to go on Mac. commit 165c93bf0e31c1b931f4058a22e63b783504706b Author: markd Date: Sat Dec 17 03:41:36 2005 +0000 cleanup verbose message commit 175faa41adc10d2c0fd18fd5cf2c3013525d74a5 Author: angie Date: Sat Dec 17 02:17:01 2005 +0000 Updated the liftOver chain file naming and placement, and added call to hgAddLiftOverChain, as requested by QA. Also moved md5sum computation from $dbHost to $workhorse. commit a37833da1696c75910943465a40bc257bc3a294e Author: markd Date: Sat Dec 17 01:54:30 2005 +0000 added canFam2 to hgwbeta commit 4444544098c2001bbbf3e785ab1886acaa346ea7 Author: kate Date: Sat Dec 17 01:30:11 2005 +0000 Add ENCODE CGIs commit 0e3464d04f9a527f425692a168dd1a516878887b Author: hartera Date: Sat Dec 17 00:55:24 2005 +0000 Accommodate changes in Ensembll url format and correct start position off by 1 error. commit 80d42f2b3509470db94c35096aed0ae2ac79b888 Author: hartera Date: Sat Dec 17 00:51:57 2005 +0000 Accommodate change of Ensembl ContigView url for scaffold assemblies. commit 26bda571ce0d393d057d051db3564798a1dfd401 Author: ann Date: Sat Dec 17 00:36:23 2005 +0000 removed extra wording from mm7 chain/nets commit 34b3290746eb8f976c704c2505355b2181c750bd Author: heather Date: Sat Dec 17 00:33:10 2005 +0000 remove hgCoordConv from BROWSER_BINS commit 63a96d3e452c4c9835a05eac1b205617ae671047 Author: ann Date: Sat Dec 17 00:31:35 2005 +0000 added track entries for mm6 chains and nets commit 3b8ac5d734d237792fc6d2ee2553d754a90cfd0d Author: ann Date: Sat Dec 17 00:30:10 2005 +0000 changed mouse nets and chains from mm6 to mm7 commit 48b23a0015f7483d679fdafd1977804235a87a41 Author: donnak Date: Sat Dec 17 00:26:45 2005 +0000 Added mm7 credits...this needs additional work. commit 660e533aa628b19129f769998f84df733381be15 Author: kent Date: Sat Dec 17 00:22:38 2005 +0000 Put back in strip commit 974f13acaa2a8fd18c9029714f559d943dc648b7 Author: donnak Date: Sat Dec 17 00:19:58 2005 +0000 Added mm7. commit c3bdde6bb571e0b15838a94dd33888d3d105cd6d Author: kent Date: Fri Dec 16 22:02:58 2005 +0000 Adding 'as' feature so you can if you prefer have tag names that are different from table names. commit 312be30d3bf550b331e1ef2bf0e2094f06c14d13 Author: fanhsu Date: Fri Dec 16 20:45:09 2005 +0000 Rebuilt mmBlastTab from mm7. commit 6dda1351874c856a339c0c3a78a956621b9b7446 Author: fanhsu Date: Fri Dec 16 20:40:58 2005 +0000 Switched mm4 to mm7. commit 452eab5abc0541407cd4dacdc72844cfea21a1f5 Author: markd Date: Fri Dec 16 20:24:49 2005 +0000 redisable hg17/mm6 for a bit commit e2a03fade08046c055773f688bcd225b3822b6ff Author: kent Date: Fri Dec 16 20:24:03 2005 +0000 Adding copyright and free license comment. commit 5322a51cadb7b746439dad43ee800486790b0798 Author: kent Date: Fri Dec 16 20:17:38 2005 +0000 Updating some copyright messages. commit 0fe6c97f5a338bff847663107ea7f98834f72086 Author: galt Date: Fri Dec 16 19:43:53 2005 +0000 fixed quoting problem commit 572a18c7c6c028936a738bcab737a8b7b0a30925 Author: galt Date: Fri Dec 16 19:21:35 2005 +0000 added warning about what machine must be run from, i.e. hgwdev commit a86a1220deab64253cda2434dd969e9d312408fd Author: fanhsu Date: Fri Dec 16 18:53:31 2005 +0000 Added genscan track. commit 39cd6e67fd2cd5ad240e133bb0ea98e822cb5675 Author: kuhn Date: Fri Dec 16 18:38:47 2005 +0000 re-enabling overnights on hg17, now that the revised tables are on RR. commit 48ddf663c6481c7e9c63e9c1274802f8afbed8f1 Author: kuhn Date: Fri Dec 16 18:19:24 2005 +0000 removed errant line in rgdQtl search block commit e63a975889665b4495f96d4951aa7e96dd68a7d2 Author: galt Date: Fri Dec 16 18:16:10 2005 +0000 improved with bash makefile redirection of stderr commit de23e8e78daa5657e1d4f23e890a6886940c779b Author: galt Date: Fri Dec 16 18:15:20 2005 +0000 updated output commit ccfaf57584ffd1093918e6b2d7099d83f9e2976a Author: hiram Date: Fri Dec 16 18:04:55 2005 +0000 Adding Mm7 chain and Net commit e6188e5e48a030a67e5f0737ac26444d008ef31c Author: ann Date: Fri Dec 16 17:52:35 2005 +0000 moved Mouse to top of list of species commit e85e86bf846ca31051a14dd171ec42dc04761bee Author: galt Date: Fri Dec 16 17:51:25 2005 +0000 fixed test for noDna fasta record commit f4f733ef4a6bc3a2a06f3fd13c8b562b87719bca Author: ann Date: Fri Dec 16 17:47:55 2005 +0000 Changed the order of the species listed to reflect their order in the track. commit 7e31c05be07300078537d25f92687b2de2b09504 Author: daryl Date: Fri Dec 16 16:36:50 2005 +0000 Initial template for preparing next sequence freeze. commit f86419cebe789576e6f16b158c740735e2fc6b4f Author: giardine Date: Fri Dec 16 16:27:09 2005 +0000 Removed limit from sql, it wasn't doing what I had hoped. commit 7023de52cd0002e415a70d8da292bdf66996c2d2 Author: kate Date: Fri Dec 16 16:23:09 2005 +0000 Remove CVS conflict lines commit 479ac0c86c91e0eec43639a180eaeb6f8a7ff590 Author: galt Date: Fri Dec 16 16:00:02 2005 +0000 "Encode release log update" commit 544a2c996b9b77c8c54b33a20b3b123a29a568fa Author: galt Date: Fri Dec 16 16:00:01 2005 +0000 "Release log update" commit 68f09d55749e77ad628119a2422601980c337175 Author: kent Date: Fri Dec 16 10:20:46 2005 +0000 Putting Test in title on hgwdev. commit 1d7cb3f3da19b2294282a2361e9c9997d77f01f2 Author: kent Date: Fri Dec 16 10:14:16 2005 +0000 Adding some warning text to test gateway. commit 5420804fd7510fdfc2ccb4b51511c54a9c36b6b9 Author: markd Date: Fri Dec 16 01:15:00 2005 +0000 make background image configurable commit 086e14e55bee2cd105e79f4f9ec7c760cc377bb0 Author: markd Date: Fri Dec 16 00:19:01 2005 +0000 more genbank todos commit ab9b454e7d28e0b67012e6e9a6f3743aa814f57b Author: donnak Date: Fri Dec 16 00:18:05 2005 +0000 Fixed spelling of UCSC. commit d5eff9dd1219f8f74960314c234f18ed3d0aac4a Author: heather Date: Fri Dec 16 00:08:27 2005 +0000 add McCarroll deletions commit cc7aa18b1d3cc1aed12c00dde7778174366b76a2 Author: heather Date: Fri Dec 16 00:05:41 2005 +0000 add delMccarroll; edit CNP/SV fosmid labels commit 33da4f45d1526addb09f3905426120ef4ee94588 Author: hiram Date: Fri Dec 16 00:02:28 2005 +0000 OpenBSD requires an array size of 1024 for the getcwd() call commit 7a25958c9f88b17c2bc6dbe2f634f2dbbaa7b4f2 Author: kate Date: Thu Dec 15 23:22:50 2005 +0000 Add encode CGI script commit a2dd69242b8803b948cc148366c18d5d411873a0 Author: kuhn Date: Thu Dec 15 22:44:29 2005 +0000 turned mm7 back on. push to RR is complete commit eb4d19e059c5b894009080a09e2cdab9261bfe60 Author: kuhn Date: Thu Dec 15 21:40:26 2005 +0000 turning updates off for mm7 -- until pushes to RR are finished. commit 6c3b91847e6564c13cde860f3a869304b7cee9c3 Author: kuhn Date: Thu Dec 15 21:37:00 2005 +0000 re-enabling alignment updates for hg17 and mm6 commit 9283a5390bf4d02ba916f6cd10215fee963faf2b Author: kuhn Date: Thu Dec 15 21:35:07 2005 +0000 turning updates off for mm7 -- until pushes to RR are finished. commit 9dca5453bb4659a3c234bfc764875bececbae113 Author: angie Date: Thu Dec 15 21:28:08 2005 +0000 Added knownGeneAcc to prevent mrnaAcc from preempting knownGene. Also broadened bacEndPairs termRegex a bit. commit 86f27dcb46d7c22f913f16125fe573ee19aa3e1a Author: kuhn Date: Thu Dec 15 21:07:10 2005 +0000 turning updates of for mm6 and hg17 -- after Mark redid the whole thing with new filters commit a6ec5c77f35a7722a97f937c2bf6d8e8fe4146cb Author: hiram Date: Thu Dec 15 20:33:55 2005 +0000 Add the other two font choices commit 686e50ec9db55d5dbff024b66214dd651a2e14f3 Author: hiram Date: Thu Dec 15 20:18:56 2005 +0000 Properly default to medium when no font style exists commit 246fb3edae082c4ee6f1ce8b285a86165da88c02 Author: hiram Date: Thu Dec 15 20:18:30 2005 +0000 Add the other two options commit 91074c34a6157b61ba665e1c2c69706f9cf8af21 Author: galt Date: Thu Dec 15 20:11:08 2005 +0000 reminder about location of loadQuality.c utility I wrote commit 3c88f4f5c780882e3f8f0181bed1a1451ba0c7e3 Author: kate Date: Thu Dec 15 20:00:48 2005 +0000 Checkin mini-CGI used by ENCODE regions page commit c8add35b164fdd425bf949ec7ccb981b9afda56a Author: kayla Date: Thu Dec 15 19:20:25 2005 +0000 added mm7 commit 6548d47d2bd1c8fe7f601f29c0e10cb75b4fab2b Author: kayla Date: Thu Dec 15 19:16:05 2005 +0000 added canFam2 commit 4237d355737ab8309748bec82372f88e783ccd34 Author: jen Date: Thu Dec 15 19:05:05 2005 +0000 Added monDom2 to databases checked. commit 3c6bb888796c1488a4fbc317c4edb7682feb5618 Author: jen Date: Thu Dec 15 19:01:04 2005 +0000 Added canFam to human proteins. commit 47106b8228854464e67ab4dce1a6407857e4d606 Author: kate Date: Thu Dec 15 18:37:49 2005 +0000 MSA track changes commit 48f56c3b91e2c713b762a2d12988743e59893342 Author: heather Date: Thu Dec 15 18:29:25 2005 +0000 name change commit b5c64c2da9350af0660e90f68a7e7cc9797cf8af Author: heather Date: Thu Dec 15 18:10:44 2005 +0000 add an acknowledgement commit cf71c9c87b6e47b744cd6ec502868e80a7f3717e Author: heather Date: Thu Dec 15 18:09:19 2005 +0000 new PNAS data commit d51b457a1189bbfc7dc7fb65e98e5e9bb73b9468 Author: kent Date: Thu Dec 15 16:41:28 2005 +0000 Bumping experimental version number. commit 8cbf448583ad1fe830b1cf1652853fd056462998 Author: kent Date: Thu Dec 15 16:41:08 2005 +0000 Adding closing tag for a table in controls panel. commit cc5fe09040c8c314ecb6d3940b4bb5980e88f110 Author: kent Date: Thu Dec 15 16:40:38 2005 +0000 Flipping minCheck to double to help avoid rounding errors. commit e48b441db497f3bf4d884a8259cb3d3bccffd322 Author: kent Date: Thu Dec 15 16:40:07 2005 +0000 Making it so that it uses entities rather than non-standard extension to express numerical types in DTD. commit 0d4804166ac9344b2f27b980b7b61de7f9802709 Author: kent Date: Thu Dec 15 16:38:23 2005 +0000 Adding maxGap to options table, and alphabetizing that table. commit 1bdc53e58899c931bc76325fef099d3cbb151774 Author: kent Date: Thu Dec 15 16:37:46 2005 +0000 Adding changes to version.doc commit 29b4e7de66e10d3cde7c3bab12f764287fd14d59 Author: galt Date: Thu Dec 15 16:00:02 2005 +0000 "Encode release log update" commit cfe829e32977d4e481d5b1d70f125b2c0b86fee6 Author: galt Date: Thu Dec 15 16:00:01 2005 +0000 "Release log update" commit 65830be5acece590af1ae903ae7fa0f8ef03c14e Author: kent Date: Thu Dec 15 06:01:01 2005 +0000 Updating docs. commit b7edf097f4028874929baa5397dd4bfe9d9aad48 Author: kent Date: Thu Dec 15 05:49:18 2005 +0000 Making it handle output into subdirectories better. Also linking with improved dtdParse library that handles entities. Also adding test cases. commit f61aa28ed8aca3d0e5131849a082fd5d27215e71 Author: kent Date: Thu Dec 15 05:48:52 2005 +0000 Adding entity parsing. Making it so that the predefined entities %INTEGER; %REAL; %INT; and %FLOAT can be used in place of the non-standard #INT #FLOAT INT FLOAT I defined earlier. I'm using Pascal type REAL/INTEGER just to be compatible with NCBI. commit 070d8bfa09033a4819f9b91a3cbc40a6eced009a Author: kent Date: Thu Dec 15 03:50:04 2005 +0000 Adding a little info to the docs. commit 8f1fb9d55ebe3d0f24d73e77a179bcc225dc694f Author: kent Date: Thu Dec 15 03:14:47 2005 +0000 Adding a "." in front of field name in dump spec files to make them a little easier to read. Adding -maxList option to help make test case expected output a reasonable size. Creating a uniProt and visiGene test case that is actually run by make test and compared against expected. commit f6b486f6cd8806e900cef9d9a746f4de5a86c0cc Author: heather Date: Thu Dec 15 02:55:47 2005 +0000 don't use locType, print nothing for exception (for now) commit 32e8b91bda3b1ad83c7abab83682b30e4f8d2d83 Author: galt Date: Thu Dec 15 02:15:37 2005 +0000 added sgpGene gene pred track from GRIB commit d4d7468511d3904a15555cc0c4dd6bfaf59ec4be Author: angie Date: Thu Dec 15 00:58:42 2005 +0000 Reassigned IDs to self chains, reloaded. commit 9f923dd8a7ec839dd6da77d5ae0a25059157443b Author: hiram Date: Thu Dec 15 00:57:05 2005 +0000 Make all three font choices the same and enforce same behavior as is today present commit 68729f4969d59156a1f333597a33734c1810ab11 Author: jen Date: Thu Dec 15 00:40:36 2005 +0000 Adjusted mouse short label. commit fb42362616433c83604308024296db5f540ed0c8 Author: jen Date: Thu Dec 15 00:36:01 2005 +0000 Added human proteins - in group genes, visibility pack. commit 6d8cc695e351015a9b9029197dfbdda30586173d Author: jen Date: Thu Dec 15 00:32:42 2005 +0000 Moved back down .. each Dbs uses different version of human known genes. commit 2eec49315cac3f268ad618cd638cd3947b7a9a49 Author: jen Date: Thu Dec 15 00:29:05 2005 +0000 Moved from canFam1 to top level dog so assemblies can use it. commit 5a6402d4a6099fc374e13882fff4669bd03e3e25 Author: angie Date: Thu Dec 15 00:13:08 2005 +0000 Added multizNwaySummary, N = 4 to 12. commit 5af97f8501a843692b1e1a6b186d8ac3433dc4a0 Author: hiram Date: Thu Dec 15 00:11:22 2005 +0000 Enable the hidden fonts for better PDF/PS output options commit 8c435491c001954e26f25bcdb2192d080ff3bca6 Author: aamp Date: Thu Dec 15 00:05:41 2005 +0000 Added some human proteins tblastn tracks. commit 88b278a0bf1077c2cc1bd48783d8a5351bdae85d Author: hiram Date: Thu Dec 15 00:02:41 2005 +0000 Adding hidden font options for better PDF/PS output commit 80fe72c9ded808fde6219d3bba2d8f85ef3e0764 Author: hiram Date: Thu Dec 15 00:02:13 2005 +0000 Adding hidden font options for better PS/PDF outputs commit 5e4d53b3cf9adb8e4b455482abec40a4a1ad0e52 Author: hiram Date: Wed Dec 14 23:58:16 2005 +0000 Adding hidden font choices for more PS/PDF output choices commit 77dcb26fd81b6a8a44312166f38509afa3c066bd Author: angie Date: Wed Dec 14 23:13:06 2005 +0000 Added some tablesIgnored: canFam2.uncertified and phastCons{,Elements}Nway, where N is 4-12. Also added multizNway.extfile, N = 4-12. commit e3c34873b7f702179b5e0cd1337b6d106272591b Author: heather Date: Wed Dec 14 22:01:48 2005 +0000 filter on contig group commit 8d81007293f6ac24f610631de250bcf97fa5b50a Author: hiram Date: Wed Dec 14 22:01:18 2005 +0000 3-Way multiz and phastCons track done, maf downloads for David Carter commit 6fa4cf3651d8f642f6ef99383240994d37c9f00c Author: kayla Date: Wed Dec 14 22:00:11 2005 +0000 Added a block of text for Other RefSeq commit db728fbd9c3e89c5100675bfa143c292a8e870d2 Author: kuhn Date: Wed Dec 14 21:54:36 2005 +0000 altered line length commit 2707e67f0229e3bde2d7c41b01fd597c5e8d101d Author: hiram Date: Wed Dec 14 21:41:08 2005 +0000 Start some downloads for David Carter commit f26fd0adfdf4c04160ba38acbf2d13a7041fba99 Author: hiram Date: Wed Dec 14 21:40:41 2005 +0000 Add entry to genomeClade and some new downloads for David Carter commit 2ae9f5bcd7f11e04810355853d09752606a02619 Author: kayla Date: Wed Dec 14 21:37:39 2005 +0000 *** empty log message *** commit f7baa52ef15df312334c53f7e1c82556ffbe55e9 Author: jen Date: Wed Dec 14 20:27:04 2005 +0000 Merged u1 version (with matrix) into regular files. commit a136c51246e8990dc86e6af2322e8c5e8e377c56 Author: ann Date: Wed Dec 14 19:52:58 2005 +0000 Changed the google search parameter num=10 (to work properly with google search). commit 9d41127cdddc942048599a293992abd05f25260e Author: ann Date: Wed Dec 14 19:50:24 2005 +0000 Changed google search parameter to num=10 (for proper google handling). commit 86d1640a5db8674b5d5bc1cbcc47e238a922254c Author: angie Date: Wed Dec 14 19:47:28 2005 +0000 Reran canFam2 alignments. commit 531e557622f18fbf6dbbd528fb83e7bc8df50157 Author: kent Date: Wed Dec 14 19:42:12 2005 +0000 Coping with rounding error on 64 bit machines that leads to it complaining about not all hits being there when in fact they are. commit fbe4d8a64a2ddc17be37ff6ce52e5d9e70927335 Author: giardine Date: Wed Dec 14 18:47:09 2005 +0000 removed some commented code that is not needed commit 3786373fabee163b6cb15f3c8ec984bbfc2acf65 Author: giardine Date: Wed Dec 14 18:45:43 2005 +0000 removed some commented out code that is no longer needed commit 912acb497ca6ba821bac5ba260d3a8674ca4eff4 Author: angie Date: Wed Dec 14 17:48:00 2005 +0000 Added contamination track -- 57 contigs on chrU, from LaDeana. commit 996c53bdcd5eb29744b230ef9c79e1b1168fe4dd Author: angie Date: Wed Dec 14 17:47:20 2005 +0000 Added contamination track and searches for gold. commit 71b55aa2703a54d54011c72e6bc06b2e70159982 Author: kate Date: Wed Dec 14 17:27:14 2005 +0000 Split into hg16 and hg17 versions commit 2e2c2267bdbb56832084ef6dfaa2e8f4897c5ab0 Author: hartera Date: Wed Dec 14 17:16:49 2005 +0000 Minor edit. commit b60b8f8681e506bb86849a7cae7105ca29f051d5 Author: galt Date: Wed Dec 14 16:00:04 2005 +0000 "Encode release log update" commit 384ecce365ff56814de2f98bfa77caeadf63d012 Author: galt Date: Wed Dec 14 16:00:03 2005 +0000 "Release log update" commit c1e39bb436f0ddc4e8869c5fec52adec580ff2d2 Author: aamp Date: Wed Dec 14 08:59:05 2005 +0000 Added a tblastn dm2 flybase proteins track. commit 89cf6480d7c2ee4d2255d93c5c628db7dc6a48e5 Author: galt Date: Wed Dec 14 08:52:20 2005 +0000 moving location of bigImage.html and dot_clear.gif, also fixing minor problem in IE with follower square when over-zoomed commit ad457297cccb780b087046a94bc0be597fc843e5 Author: angie Date: Wed Dec 14 02:36:11 2005 +0000 Redo of hg17 and mm6 chains/nets, multiz and phastCons. commit 96fb6a12446e5afbabc3446e9c2ecd338bdb630d Author: fanhsu Date: Wed Dec 14 00:31:48 2005 +0000 Added hg18. commit 6b7598d986013464c6cfdfe7422522cecea4c7ea Author: fanhsu Date: Wed Dec 14 00:18:10 2005 +0000 Added exonPrimer. commit 8fb0bddfdfb428d0aec87f0ed252b05db3acfec6 Author: hiram Date: Tue Dec 13 20:25:13 2005 +0000 Adding the 3-way multiz commit 1a25f8cbd385b8807b3523fbd3a59c9d6b052d6d Author: aamp Date: Tue Dec 13 20:02:06 2005 +0000 Repeat-masking. commit 48352b9a2585a5f948082e695e6305cad5083507 Author: kate Date: Tue Dec 13 19:57:43 2005 +0000 encodeTbaElements.html commit ce75d768a2ec76433eeba269818ab1530c39ed4a Author: kent Date: Tue Dec 13 19:06:16 2005 +0000 Fixed case sensitivity problem commit 11f5810e3fa7aad54f272024e0d0621269f7a89c Author: donnak Date: Tue Dec 13 18:54:22 2005 +0000 Minor edit. commit de4915a92d7326eb26f0efcafa309fcbde45ac04 Author: donnak Date: Tue Dec 13 18:47:48 2005 +0000 Updated the zoom sections in the gateway page text. commit 96b7c23f79a071bd9e34d67bf2c33c28427be744 Author: donnak Date: Tue Dec 13 17:19:09 2005 +0000 Added link to hgFindSpec. commit 5511b7cec96996a9482c6580dad86cc6a61f9a0a Author: ann Date: Tue Dec 13 17:02:11 2005 +0000 Changed link for web server to stats page on genome. commit 3aa7d3bc4c163bb5be894e78d0c41e0a47addb78 Author: kent Date: Tue Dec 13 16:59:48 2005 +0000 Suppressing output of fields that are just keys for children we are printing soon anyway. commit b490a66b83ae4972681f9ef33a1416bb6a587669 Author: galt Date: Tue Dec 13 16:00:02 2005 +0000 "Encode release log update" commit 5e569c86e22e0a95c72b3858d6dbeff516e12ff2 Author: galt Date: Tue Dec 13 16:00:01 2005 +0000 "Release log update" commit ab97f49b82045e577709709860adbfcd08d074b5 Author: galt Date: Tue Dec 13 06:20:47 2005 +0000 fixed getThumb to handle either relative or absolute url-paths in visiGene.fileLocation commit d04865805b11a8a3f74fad870b786cc858429fbb Author: galt Date: Tue Dec 13 06:19:35 2005 +0000 added some notes commit 3fe51abcdf49f3817a85c38be6250995d330840e Author: galt Date: Tue Dec 13 06:08:08 2005 +0000 added comment to remind about debug flag commit 02cd9e0bd9759b8a95a0a8a31d229c3d0adaf430 Author: galt Date: Tue Dec 13 05:45:21 2005 +0000 fixing indentation consistency commit 1a63979cd1273d3f0a94e19e09197ac454cb5d35 Author: daryl Date: Tue Dec 13 05:43:48 2005 +0000 moved encodeRecomb.html to encodeRecombRate.html; moved hapmapRecomb*.html to snpRecomb*.html commit 4c66049c0ff9da479fb62b0dd308b56721cb6af1 Author: daryl Date: Tue Dec 13 05:42:09 2005 +0000 Update/add recombination tracks commit 55aa48a3c85d079eef2e6c9ba6963411e8491d07 Author: daryl Date: Tue Dec 13 05:39:53 2005 +0000 Updated/added recombination tracks: hapmap, perlegen, and encode commit 74c0de8bf0716f1dbb694e1f517d5966710b76be Author: heather Date: Tue Dec 13 04:50:05 2005 +0000 add support for validity commit cbce3834d75bbfbd69a2f5594ef73b0138152aa5 Author: kate Date: Tue Dec 13 02:19:00 2005 +0000 Reorganize ENCODE Conservation commit 78f6772b8d002dcb6409bbae54f3120b8c4fa593 Author: kayla Date: Tue Dec 13 02:17:01 2005 +0000 added canFam2 commit facb62157252d52d59804f31907ef26deac5c30c Author: kate Date: Tue Dec 13 02:04:30 2005 +0000 Update MSA Elements tracks commit 450cb0937b3f9c707b2e83cbeb5b96bc83bb6862 Author: aamp Date: Tue Dec 13 01:33:36 2005 +0000 Added BLAT servers. commit 241f2aa2236161d27c382dc3f9f705d953262133 Author: aamp Date: Tue Dec 13 01:32:38 2005 +0000 Added BLAT server. commit 34910a6051caa0045f2051565c0ca421c344c559 Author: fanhsu Date: Tue Dec 13 01:22:40 2005 +0000 Added shortCircuit to KG. commit 5fafe50935d72cf532c159aaff2ba7a487a41ef3 Author: heather Date: Tue Dec 13 01:07:44 2005 +0000 "New version number v123" commit b1894e7d620253a7cc832ff49b6c49794014461a Author: fanhsu Date: Tue Dec 13 00:38:43 2005 +0000 Created makeHg18.doc. commit fa5083749f4a7f5cebbfcf0baf84f891cdc1e250 Author: aamp Date: Tue Dec 13 00:15:52 2005 +0000 Just a taste for now... the rest will come soon hopefully. commit 3be931bb1bd7991ac405816b543126d9e2e077e4 Author: aamp Date: Mon Dec 12 23:20:20 2005 +0000 Little utility for condensing AGP files like the apiMel3 Baylor one. Seems to work. commit ef8f72660f44c79e3d017bab0aecdf6e1fb060be Author: ann Date: Mon Dec 12 22:34:44 2005 +0000 Changed variable in some chain tracks from $o_db to $o_Organism. commit 51a3aaa1b6edaad61826a3c2534573d264edad04 Author: ann Date: Mon Dec 12 22:23:38 2005 +0000 Added a few chains and nets so that they would appear in the correct order (and with their matrix variable). commit bcca4fc15db32bc4a672c38e415b1079b18d9a06 Author: heather Date: Mon Dec 12 22:02:11 2005 +0000 strip rs from name for lookup; write chrom tab files; slReverse snp list commit 2f09f1aea625d1cdeb6065cb2c57cd746c19c412 Author: donnak Date: Mon Dec 12 22:00:40 2005 +0000 Added Minmei Hou to credits. commit 5673e2a300334a34fa4cb9f272320df5a9b7b4c8 Author: kate Date: Mon Dec 12 21:19:13 2005 +0000 Spelling & cosmetics commit b98995c2d7b0183ef396f993326041403ed621d3 Author: ann Date: Mon Dec 12 19:38:55 2005 +0000 Switching Conservation track from full to pack by default. commit b53ca8892d6d750dcbb95c231c337d68fba0dfbb Author: markd Date: Mon Dec 12 19:15:53 2005 +0000 fixed expected results related to determining if alignment is complete commit 1ec51faf7a9c165b00a0cd2288661945a831d0a6 Author: ann Date: Mon Dec 12 18:57:55 2005 +0000 Changed Conservation track from dense to full. commit 255481e4732a19d90a36aa891fda52612f2732a7 Author: ann Date: Mon Dec 12 18:54:33 2005 +0000 Hide and unhide tracks per Jim. commit b960ae71956a314ddae77fc07d51b8cc50766144 Author: kent Date: Mon Dec 12 18:33:22 2005 +0000 Separating variable declaration from rest of code. commit 5819480b25d431cff8ef64e69e202133e6d11e07 Author: ann Date: Mon Dec 12 18:20:48 2005 +0000 Changed order of species in Conservation track per Jim. Added line for species which do not display by default in Conservation track. commit 9658342336e32371e2ed3948c3bac4bd4b467670 Author: fanhsu Date: Mon Dec 12 18:02:19 2005 +0000 Created fixAgp.c. commit a4cf7eb702e8dd3f304d16f8b2e7ee03e8d73911 Author: fanhsu Date: Mon Dec 12 18:00:23 2005 +0000 Created makefile. commit 25d4b72fb9a6678ccba6684d57fec0f8287c8848 Author: angie Date: Mon Dec 12 17:37:20 2005 +0000 Re-did self chains from filtering step onward -- the first time around, chr14 self chains were accidentally duplicated. commit 840830d1eff44c2a69621fb4b9a4941ad9b4bebf Author: fanhsu Date: Mon Dec 12 17:03:38 2005 +0000 Added hg18. commit 0d3bcce4b8fbb2dbaf9247be97b79aef20f20653 Author: galt Date: Mon Dec 12 16:00:03 2005 +0000 "Encode release log update" commit c38f129372d4434827f5226f492a6cc30a6815dd Author: galt Date: Mon Dec 12 16:00:02 2005 +0000 "Release log update" commit bd260b3930ba4e630eb18c3fe94c41e93b45c157 Author: lexa Date: Mon Dec 12 14:01:10 2005 +0000 Fixed the form of if and for statements (curly bracket position and indentation) commit c2b5a2b83a9f86b50c3cee0fa95f1f7b6657e36a Author: daryl Date: Mon Dec 12 06:43:49 2005 +0000 Adding support for LS-SNP structure and function tables commit 0d1d82884fc5321fb40cd9b3bd617fa83c0fb870 Author: kent Date: Mon Dec 12 04:04:52 2005 +0000 Adding htmlPageForwarded and htmlPageForwardedNoAbort commit 07827a2920af0f4960ea7e85536cc29f023cc40e Author: kent Date: Mon Dec 12 04:03:40 2005 +0000 Making it easier to put complex urls in command line commit 8738bf3e47016ba85a5b1b5d2cf4d0b548d57344 Author: kent Date: Mon Dec 12 04:02:53 2005 +0000 Fixing some signed/unsigned mixups for benefit of gcc 4.0 commit aabc7876ae657ee6012e3363dda8d75fdf957f9a Author: kent Date: Mon Dec 12 02:48:40 2005 +0000 Fixing a bunch of signed/unsigned mismatches for benefit of gcc 4.0 commit 596de1482e35d18fb195ba05f46bf38c321510c7 Author: galt Date: Mon Dec 12 02:28:25 2005 +0000 fixed dystring.h include commit ca25e7efe710286190bae3a7eb8bd39c5bfcbebe Author: kent Date: Mon Dec 12 02:24:47 2005 +0000 Fixing some signed/unsigned problems version 4.0.1 on Mac is turning up commit 1e07d3627210e58d927cbcfba439693489b4141f Author: galt Date: Mon Dec 12 01:57:01 2005 +0000 "Encode release log update" commit 58c98a981ad2016a3ee15ea4166767a76f0b0798 Author: galt Date: Mon Dec 12 01:57:00 2005 +0000 "Release log update" commit a84f59eddb8508e11983d0e94f1913da02c98457 Author: markd Date: Sun Dec 11 04:50:43 2005 +0000 default font to small if textSize is not understood commit 4f0324892811cba14f6e42cccec0a079cd1e01d3 Author: markd Date: Sun Dec 11 04:46:57 2005 +0000 added function to check config variable to allow extra fonts commit 4fadd95dadbe4c1970e43758e8b4a86e4fce2cb8 Author: braney Date: Sun Dec 11 00:39:29 2005 +0000 a human proteins track commit c514dd42e7d402973a588096a7475ffc278bd7d8 Author: kent Date: Sat Dec 10 17:43:19 2005 +0000 Tweaks to test program to help measure timing. commit bc828570f0732764bc31559e31d8c915c816aa6d Author: kent Date: Sat Dec 10 17:42:48 2005 +0000 Fixing Jackson Labs info on gateway page per email from their folks. commit 13189553b09c7200b1b1a4194edfe07f3540ed74 Author: galt Date: Sat Dec 10 16:00:02 2005 +0000 "Encode release log update" commit 5f0d6a6e4ba531fd34e0d23876e0968551a9cbe9 Author: galt Date: Sat Dec 10 16:00:01 2005 +0000 "Release log update" commit 7431e33155375273b96692441dc26c82ce9930f9 Author: galt Date: Sat Dec 10 05:03:37 2005 +0000 added handling for case of a fasta record with no sequence commit 42e09078659ee3ca9b36ff40654219659042dedb Author: galt Date: Sat Dec 10 04:46:14 2005 +0000 added better random boundary with checking for collision with data in the mime msg commit 236bbbdc89a679a34e9f8b84a1a320597dc41615 Author: kent Date: Sat Dec 10 04:41:25 2005 +0000 Getting rid of some uglyf's commit 83183eb95494c8d3304622329f267486641402f2 Author: kent Date: Sat Dec 10 04:40:40 2005 +0000 Fixing a search bottleneck by making SwissProt accession search exact. commit 6a9790c03d6ee8702169f202b0f82be88dcca064 Author: kent Date: Sat Dec 10 04:36:25 2005 +0000 Not doing much on 1 character queries. commit 0192423650b45032fddaa600d219bcf734d658b4 Author: heather Date: Sat Dec 10 03:04:36 2005 +0000 enable lookupObserved commit b92956046a482ae17559385ed16500010f1c1f9b Author: kent Date: Sat Dec 10 01:37:33 2005 +0000 Making fuzzy searches only match word prefixes (but words can be in middle). Avoiding fuzzy searches of very common words in RNA descriptions or product names commit c4039bf7146120251e8afcc10827ac3e15e777ea Author: galt Date: Sat Dec 10 01:26:08 2005 +0000 added better random boundary with checking for collision with data in the mime msg commit dfd77882ff8cad06207c11ace4ce8d49988b7e42 Author: hiram Date: Sat Dec 10 00:42:31 2005 +0000 10-way update done commit f94f5512c6c56c72cef1b134c43ea407f7154140 Author: ann Date: Sat Dec 10 00:36:48 2005 +0000 moved monDom2 down to vertebrate group. changed order of last three organisms in vert group. commit 866929a20a2d33e91c1e425732d25404a873d896 Author: hiram Date: Fri Dec 9 23:51:36 2005 +0000 Updated to indicate 32 and 64 bit binary download instructions. commit b80ca9251c2e9bebcd371d58136f34f6ab55dff7 Author: fanhsu Date: Fri Dec 9 23:39:27 2005 +0000 Updated mrnaRefseq table to include refseq/refseq pairs. commit 09e6f685ae91bda3d9ff03a7ffd77606fcea36f5 Author: hartera Date: Fri Dec 9 23:23:21 2005 +0000 Free memory for lists. commit 05e2289a4b12ccbf9630b92cc1d39216dfe35171 Author: hiram Date: Fri Dec 9 22:39:36 2005 +0000 Eliminate ifdef concering strtof() use strtod() always, no harm done commit a429ffa87782e8cd7a4cefeb159bd04bca722aa2 Author: kent Date: Fri Dec 9 22:25:51 2005 +0000 Adding knownToVisiGene commit 260fec82a0406b71cb994bd0075280dfc9fc24a5 Author: markd Date: Fri Dec 9 22:01:31 2005 +0000 added to-do items commit 61236bf414fbe4d3266f459b57761daa4dff0774 Author: galt Date: Fri Dec 9 21:02:21 2005 +0000 added case of fa rec with no dna commit 6d6da283fef43a8dbf3af10b91f8296ff3a6cd78 Author: hiram Date: Fri Dec 9 20:59:53 2005 +0000 Add details page for multiz10wayU1 commit 8650076255692c7e719a6a673846ef371f60d35d Author: galt Date: Fri Dec 9 20:59:20 2005 +0000 added a fa record with no body commit 9050ac23321bfc6a7390bb0db65105bbede84be6 Author: giardine Date: Fri Dec 9 20:45:58 2005 +0000 Added availability check for OMIM labels in refGene. Also added some automatic cart corrections for bad label parameters. commit fe8e3a35429108d7591c0bb24b37f971eeea77e1 Author: giardine Date: Fri Dec 9 20:43:47 2005 +0000 Added checks for whether OMIM IDs are available for refGene labels. commit f2ec393c5cafb2a44794140fec4e49a0f95505c6 Author: hiram Date: Fri Dec 9 20:30:42 2005 +0000 Typo error, 144 -> 114 commit 7b33feaa4e87a5ca325116bb55970d80d5389403 Author: hiram Date: Fri Dec 9 20:30:07 2005 +0000 Typo error 144 -> 114 commit 4b8ec06d85e2bf9fea97409877071667f074987d Author: hiram Date: Fri Dec 9 20:28:04 2005 +0000 Updated chains and nets for CanFam2, Rn3, GalGal2 commit 3e56d75b402ab02d6a5f28151a2f5954b5cd8ba7 Author: hiram Date: Fri Dec 9 20:12:43 2005 +0000 Use the matrix variable in the html commit cbf69a50862da5c056fde6c8113a070fc28047dc Author: hiram Date: Fri Dec 9 20:11:33 2005 +0000 Adding updated chains and nets for GalGal2 commit 0fb894a298ff9543b2a2b57e871d0f9b62667553 Author: hiram Date: Fri Dec 9 20:01:15 2005 +0000 Updated alignments to Hg17, Rn3, GalGal2 and CanFam2 commit c517a3d430e8f25a78913d3b9367595420e57597 Author: hiram Date: Fri Dec 9 19:42:20 2005 +0000 Adding update chains and nets for Mm6 commit 0f20b26dec28bea9d02e862bf52d3120a56021ff Author: hiram Date: Fri Dec 9 19:29:20 2005 +0000 Add updated chain and net tracks for Mm6 commit 6fb23fb780f6427d593849a90bab37b1a9116328 Author: heather Date: Fri Dec 9 18:25:52 2005 +0000 don't overwrite existing tables commit 60da25fdcc4fa966ff71a5c30a21c60e106a3a70 Author: giardine Date: Fri Dec 9 17:39:12 2005 +0000 Fixed handling of OMIM ID labels for cases where in cart but not available on current build. Improved handling of bad parameters for label as well. commit e63bb50ecf42732217a326e661c67a7cb88f21c5 Author: galt Date: Fri Dec 9 16:00:04 2005 +0000 "Encode release log update" commit e551db6352af08c9de066a54cf9e68046e181c99 Author: galt Date: Fri Dec 9 16:00:03 2005 +0000 "Release log update" commit ef0f59390aa6e2ff93cbb3cc3b7ef501d9084101 Author: heather Date: Fri Dec 9 07:57:05 2005 +0000 load from chrN_tmp tables commit 364248d96787fa1eb04bc9ee20a0ce6d6dca8beb Author: heather Date: Fri Dec 9 06:53:15 2005 +0000 preprocessor to create chrN_snpTmp tables commit 26756710a09a5430d6d23acd59db8b1c056612ad Author: hartera Date: Fri Dec 9 04:21:20 2005 +0000 Further modification of Methods section. commit f09885e93c2abeadee55e8cb229225ddf8adf78a Author: hartera Date: Fri Dec 9 04:10:52 2005 +0000 Minor edit in Methods section. commit b2c51d37a6c2aadbb004c61cb8e21a959c386053 Author: hartera Date: Fri Dec 9 04:00:33 2005 +0000 Added more details to the methods section. commit b7ffdd578a99ca69c78906c47f23cae18e3fd902 Author: donnak Date: Fri Dec 9 01:14:15 2005 +0000 Added Minmei Hou to credits. commit 46a46679d86b4419cb12053e4b5ae901c06aba3f Author: donnak Date: Fri Dec 9 00:40:16 2005 +0000 Added Minmei Hou to credits. commit 208f893330c7edd43333c9ea4f6f4689f433311b Author: hiram Date: Thu Dec 8 23:52:20 2005 +0000 Change some defaults on the new Mm6 chains and Nets commit 6bbec8614c77b992b7b679b0e43f34a0c37124e0 Author: donnak Date: Thu Dec 8 21:42:38 2005 +0000 Updated update date. commit aaaeba2974bad19a45d203a8e8492cd83470b709 Author: donnak Date: Thu Dec 8 21:39:33 2005 +0000 Updated VisiGene section. Updated coordinate conversion section, but commented out details of hgLiftOver parameters until I have more complete information. commit 035121bb24e1614b181eb679f0fdef15f13efa7c Author: donnak Date: Thu Dec 8 21:38:46 2005 +0000 Updated coordinate conversion section. commit 4ba47675f677151291c974a8baacce11e07b2aff Author: hiram Date: Thu Dec 8 20:40:49 2005 +0000 Add the spanList items to the conservation tracks commit 3976a694345f39373de8e822d7260c208e5ef192 Author: hiram Date: Thu Dec 8 20:40:28 2005 +0000 Add new chain and net tracks for Hg17 commit f7a40f0903996f60ccd4d262e6c70412973e76ca Author: hiram Date: Thu Dec 8 20:38:13 2005 +0000 Add updated chain and net tracks for Mm6 commit 31a46a4c306042bdfe1d4cbb1106401c1b53ce9d Author: hiram Date: Thu Dec 8 20:37:11 2005 +0000 Updated chain and net tracks for Mm6 commit c241e7da1f9ff99fac249c784ce7514d8841e5cf Author: kuhn Date: Thu Dec 8 20:05:12 2005 +0000 adding proteins.csh, a utility for checking integrity of newly build proteinsYYMMDD and spYYMMDD databases. Also checks go database. commit 657e9919c5605bade31783d9455c09bbdcd10f6c Author: hiram Date: Thu Dec 8 19:58:23 2005 +0000 Nearing completion of the rework of the 10-way alignment commit 5d35fb6f8dfa70431a2105b7053c0e4da99c0a6f Author: donnak Date: Thu Dec 8 19:51:04 2005 +0000 Updated info in sample query section. commit 4aac62fbf57c5a0283750c6fe9b75bde20e28199 Author: donnak Date: Thu Dec 8 19:49:20 2005 +0000 Removed incorrect use of MSA acronym in a few sentences. commit 74e2b993d2efe2262467dde58e96ac64da8f272f Author: fanhsu Date: Thu Dec 8 19:02:56 2005 +0000 Changed function name of spAccToId2() to spAnyAccToId(). commit 251dc146ecf74d42a0aacb9156638b7fec79f5c7 Author: markd Date: Thu Dec 8 19:02:50 2005 +0000 fixed problem linking mafFrames when contiguous target is split between maf records commit 7306f3dbd5d1c749d108962a867e9befac7ebef6 Author: kuhn Date: Thu Dec 8 19:02:41 2005 +0000 reversed the renaming of tablenames. proteins.csh relies on them. Added warning to not change them without looking around first. commit c0199110940138ea6320f58beff5382915172b1f Author: fanhsu Date: Thu Dec 8 19:01:18 2005 +0000 hanged function name of spAccToId2() to spAnyAccToId(). commit 238b3925cfec8e8a3b96c03016d85694600f0508 Author: fanhsu Date: Thu Dec 8 18:56:28 2005 +0000 Changed function name of spAccToId2() to spAnyAccToId(). commit ab42e5d2a11816956840c993b0dc0e266b714693 Author: angie Date: Thu Dec 8 18:56:20 2005 +0000 Updated defaultPos. commit d00313c90fdef55ecdd697c248f6f7b78446f89b Author: kuhn Date: Thu Dec 8 18:44:46 2005 +0000 added support for reporting which tables were dropped since beta version. Changed some filenames to avoid collisons when run inside proteins.csh as wrapper. Also fixed bug where table list for beta was not actually coming frm beta. commit 324cdb606d8ee129883a845c9af36af46efb9233 Author: galt Date: Thu Dec 8 16:00:02 2005 +0000 "Encode release log update" commit b48256b631c72102afb967edea7fbac15c5d8c0c Author: galt Date: Thu Dec 8 16:00:01 2005 +0000 "Release log update" commit 2f91383eb96864237f99db0d86a6adc7e851d0c7 Author: braney Date: Thu Dec 8 01:26:01 2005 +0000 add a dm2 proteins track commit 29edcd72be859d968b91e18dc92825a87224b024 Author: hiram Date: Thu Dec 8 00:57:23 2005 +0000 Completed monDom2 chainMm7Link measurement commit b00a8482b2cbc236b9f5a3222157cab9e7996763 Author: hiram Date: Thu Dec 8 00:36:38 2005 +0000 Set Hg17 and Self chain and net labels to normal commit 999f7190e2f97698aea27ce1cb5d603e851d88c5 Author: lowe Date: Thu Dec 8 00:33:29 2005 +0000 Change allows alternate location for help files -- can be set in hg.conf with help.html variable commit 9f7770fd89430be383311fe8184403cea8557c93 Author: angie Date: Thu Dec 8 00:25:41 2005 +0000 Improved treatment of auxiliary (non-dbDb-active) databases. commit cd55c7f2c874c12cbae6ede7a5e6ef66498b1b99 Author: donnak Date: Thu Dec 8 00:16:15 2005 +0000 Made a first editing pass at this, but it needs another pass by someone who can fix up the biological content. I will then do a final edit. commit 68dd5a7dde99f29397a74106c993590653194bfe Author: hiram Date: Thu Dec 8 00:03:20 2005 +0000 multiz17way done commit 0e43a793eb8b1340c776af5e2aad47c1ac7c8388 Author: donnak Date: Wed Dec 7 23:43:08 2005 +0000 Minor edits to these files. commit ab64a1ccf49a73841a40b8b7851373a5567ad996 Author: kate Date: Wed Dec 7 23:30:05 2005 +0000 Add NHGRI raw data. Update Yale chip commit c0feee249466f07239a70b24d26b820080898f35 Author: kate Date: Wed Dec 7 23:24:22 2005 +0000 STAGE to q/a, others now in progress commit 99fbc0cddd3f5e219262377033402095677612d8 Author: donnak Date: Wed Dec 7 23:01:14 2005 +0000 Fairly major rewrite of these descriptions to hopefully improve clarity. commit 5cbcd0147211c19aff037917ce7966de729bb5bd Author: giardine Date: Wed Dec 7 22:41:59 2005 +0000 Resolved conflict between labels and protein ID for hgg_prot. Label options reenabled. commit 805d0952e3911c5fdc13dcb8680bd280f4f78608 Author: giardine Date: Wed Dec 7 22:40:35 2005 +0000 Resolved conflict between labels and protein ID. Now both parts enabled. commit 725ad6c0b819c58ecdc4e0d7368484697d522b79 Author: kuhn Date: Wed Dec 7 20:52:57 2005 +0000 added new proeintsYMDD db and fixed a little grammar thing commit 5801c509b36784ab0549e64da072ab4915bb9acd Author: kate Date: Wed Dec 7 20:22:55 2005 +0000 Tweak MSA track commit afad1bc951bb1a419e4c548e2bd2366a00959836 Author: donnak Date: Wed Dec 7 20:07:25 2005 +0000 Edited this file. commit 172cc23bea5e0f72efbffd90056c6b7758741703 Author: donnak Date: Wed Dec 7 20:06:48 2005 +0000 Edited these files. commit 5500a8003eb356e1d3d4de35323919ad093a4886 Author: donnak Date: Wed Dec 7 19:59:59 2005 +0000 Minor edit to remove extraneous commas. commit 5358dfb5909ee888d9f6418f0186f1ff23fb91b6 Author: kent Date: Wed Dec 7 19:46:21 2005 +0000 Adding field type to atree. commit 257adf300cedb5875c8e9a8f9fc6fa4984fbc6b5 Author: heather Date: Wed Dec 7 18:44:44 2005 +0000 get SNPs one chrom at a time. May not be the final solution. commit 87eb38fb6c7e5f27dedf4dd4cccd22799120a9df Author: braney Date: Wed Dec 7 18:12:32 2005 +0000 a dm2 proteins track commit 84367a0fd6f4c1d6b6c030037effd8d505107d14 Author: donnak Date: Wed Dec 7 17:58:20 2005 +0000 Created this gateway text file for cioSav2. commit 29b859d99f160f084a1d63da0eff6ae9eaf018e4 Author: hiram Date: Wed Dec 7 17:39:12 2005 +0000 fixup incorrect directory specification for trackDb work commit e7aae84362cad286cdb6e2b92dc3f7ea55a6518b Author: braney Date: Wed Dec 7 17:34:02 2005 +0000 add drosophila proteins track commit 2ad9330554d6cad7cfd1f93aafa45bdc9c2ffe37 Author: kate Date: Wed Dec 7 17:14:49 2005 +0000 Tweak Crawford track commit f8f5da8b937d39d67861e3abd7e934598e1ef75f Author: kent Date: Wed Dec 7 17:13:02 2005 +0000 Adding check for over 4 gig to two bit files. commit 0a05decf027b327ed14379b50b9482d2c4925c30 Author: kent Date: Wed Dec 7 17:12:18 2005 +0000 Added to clean target commit 51db8d004a0fd1e871eef346fa646f55ff901c27 Author: kent Date: Wed Dec 7 17:11:58 2005 +0000 Freen tests twoBitTotalSize commit fb312cfa87617d1271231c5aae480fa4e7037765 Author: kent Date: Wed Dec 7 17:05:39 2005 +0000 Making this compile again at request of Antonello Romani commit a9e382a57169c625eca0a344fcd594d8b19e7b96 Author: galt Date: Wed Dec 7 16:00:02 2005 +0000 "Encode release log update" commit f7cf0ffe719d9f8a980bcd94085a6059452e76f6 Author: galt Date: Wed Dec 7 16:00:01 2005 +0000 "Release log update" commit b713a3720eac61c0872b1c6aa4f9c1ae6e8ebeba Author: markd Date: Wed Dec 7 07:15:55 2005 +0000 fixed bug setting frame on negative strand and joining blocks commit 76a0219476bdac6c21fd45bb56f2632fded8188d Author: donnak Date: Wed Dec 7 06:04:28 2005 +0000 Updated info about zoom in/out. commit f4a3f263e6d5462ee84840800edc59ef2ffabc37 Author: kate Date: Wed Dec 7 02:14:31 2005 +0000 Change type on Yale Chip tracks commit 1dc78855dd1fada6ff6458e678f977ece25700ab Author: markd Date: Wed Dec 7 01:33:55 2005 +0000 fixed bug setting cdsEndStatus when ends on exon boundry commit 1af70026e863d72d2e251486273bc79f8a03a04f Author: hiram Date: Wed Dec 7 00:42:51 2005 +0000 add chado to the list of tests, turn into a do-loop script commit 5851189932dfeedcf4686858bc29762226883ad4 Author: kuhn Date: Wed Dec 7 00:26:53 2005 +0000 removed redundant RIKEN commit 99f8948ce443da11f8b89ee6ac39983b3ee746e5 Author: kate Date: Wed Dec 7 00:20:37 2005 +0000 Adjust view limits on NHGRI Dnase Raw data commit 6002252523ffa5990d0ac928797ee0811a2677a9 Author: hiram Date: Tue Dec 6 23:53:48 2005 +0000 when PATH has no . must use ./doTest commit 873540f758b451c96cce86335b38c39a6c0c6e5f Author: hiram Date: Tue Dec 6 23:53:25 2005 +0000 initial contents commit b734073011436be6c8b55d4efd06c253a6745f7d Author: kate Date: Tue Dec 6 23:41:23 2005 +0000 Add NHGRI raw DnaseHs data commit 77f4227836926670da325322ae14e6bbe6692028 Author: angie Date: Tue Dec 6 23:38:07 2005 +0000 Don't ignore hgFixed and proteome. commit a57fbeaee599cfa3c10664f14a39461e1d3710de Author: braney Date: Tue Dec 6 23:30:58 2005 +0000 a first pass at cioSav2 commit 24e0b7177c598e2f44657a48c21d9420dfa6ac63 Author: giardine Date: Tue Dec 6 23:27:58 2005 +0000 Removed call to loadKnownGene which has the call to the label changes. commit 492957801715df2431f5f5bd78a9ed1f8ca8e2d7 Author: giardine Date: Tue Dec 6 23:26:23 2005 +0000 Took out label controls, until conflict with lf->extra can be solved. commit 212dc442169f7e17ce7148738372fbf01d35337a Author: kuhn Date: Tue Dec 6 23:06:12 2005 +0000 added wrong-machine protection commit 24ae4e349952edaa153dcd4e03d174313d8a0f72 Author: kuhn Date: Tue Dec 6 23:05:00 2005 +0000 added wrong-machine protection commit c86e4afa038c1c7e92aa548e2bc8020314ccebfc Author: donnak Date: Tue Dec 6 23:03:42 2005 +0000 Encoded email addresses, added display conventions section. commit 13cfb7a2c9f9e5e21040a5c302399681714bfb81 Author: donnak Date: Tue Dec 6 22:37:19 2005 +0000 Created this gateway page text. commit ac5f1d9d6057b1dd4174efc9c9d543bf419d390f Author: angie Date: Tue Dec 6 22:10:23 2005 +0000 Finished Genbank load. commit 2799acbb6e2d64ed8ebd5daf33b8ac994643c00c Author: markd Date: Tue Dec 6 22:02:26 2005 +0000 disabled mm6 and hg17 while updating alignments commit caf568c2bea356e821ce62a1b433000f5086cb27 Author: daryl Date: Tue Dec 6 21:34:28 2005 +0000 add newline to usage statement commit 3febda6a6fc1537b9c0db6d5a8970cb310519c9a Author: donnak Date: Tue Dec 6 20:24:44 2005 +0000 Made a few edits to the references to standardize with other description pages. commit 1a585b4ff18a0dd3fda126c0ffd5599bfee9d287 Author: kate Date: Tue Dec 6 19:28:40 2005 +0000 Lift and reload Uppsala data. Adjust low scores in STAGE track commit a29de1a1b9309d6cf766cf9a2d4890abc248ef37 Author: heather Date: Tue Dec 6 19:10:27 2005 +0000 data update commit 14b0b0b315aa41f4e32d7abda666fa40168a63b3 Author: hiram Date: Tue Dec 6 19:03:58 2005 +0000 Add U1 most Conserved commit d7b90cd33b39db90f33756f3d9ca19d7f53dd0d6 Author: kate Date: Tue Dec 6 19:00:03 2005 +0000 Technical details replaced by P. Flicek commit 3f262a42f4fce8e5076e79180026d78280337270 Author: hiram Date: Tue Dec 6 18:57:58 2005 +0000 Not Obsolete on the old one, but U1 on the new one commit faf0a5f9ce3b19ba09618f184e9ffaf111ea5db3 Author: kent Date: Tue Dec 6 18:44:15 2005 +0000 Making version numbering more consistent. Adding check for 2bit files bigger than 4 gig. commit e3d48b5feec8481ab64f324a774a9d3b8017e2d9 Author: kent Date: Tue Dec 6 18:28:51 2005 +0000 Making version numbering more consistent. Adding check for 2bit files bigger than 4 gig. commit 5e221d0505d886f136bea18619204ec834513a05 Author: kent Date: Tue Dec 6 18:26:07 2005 +0000 Adding twoBitTotalSize commit 4bd4e6b85b7ed665e1155a3da2e76a655078ea26 Author: kent Date: Tue Dec 6 18:25:47 2005 +0000 Bumping blat version number commit fdbadba09acc7ab13200268ecca02cf05e965235 Author: donnak Date: Tue Dec 6 17:37:48 2005 +0000 Added Theiler search example. commit 99839ac2cb8a4b3847300fea4328bad3bc5b0b86 Author: hiram Date: Tue Dec 6 17:35:28 2005 +0000 Adding updates for canFam2, hg17, rn3 and galGal2 and new 10-way track commit f182d489b27d442cfcaea6022768fedc6592e18e Author: angie Date: Tue Dec 6 17:29:59 2005 +0000 D. sechellia from Broad -- basic tracks all there except Genbank is still in progress. commit 8384f3531b1dbdc3fa3aa0eb771054a3c2468d7a Author: kuhn Date: Tue Dec 6 16:45:39 2005 +0000 added support for a list of files =not= to check commit 430dad71841cfde536fda763523ba8dcdf7a1872 Author: galt Date: Tue Dec 6 16:00:04 2005 +0000 "Encode release log update" commit 0c724d4006c441493c233c2a065dc752771733ac Author: galt Date: Tue Dec 6 16:00:03 2005 +0000 "Release log update" commit e0f2a4fca5701595b624536f666525606c3872d1 Author: angie Date: Tue Dec 6 01:47:45 2005 +0000 Reloaded AGP with names fixed to match sequence names. dm2 chain, net. Genbank tracks. commit de82f537564f99b21fc484b620be955e3e538fd0 Author: markd Date: Tue Dec 6 00:40:27 2005 +0000 added several histogram categories commit dbbeb6eaed38d9d13e01ac3a4227c23a4943dc61 Author: angie Date: Tue Dec 6 00:32:01 2005 +0000 Re-did trfBig on chr10_1 after Jen found bogus values -- not reproducible, no idea how they got there originally. Re-did masking with fixed trfMask and regenerated downloadable sequence and simpleRepeat files. commit bef9e00ae516df8e95491bf532cf61b6c6bdbc8b Author: angie Date: Tue Dec 6 00:20:05 2005 +0000 chain/net for 3 new fly assemblies: droYak2, droPer1, droSec1. commit cabb4682c9f6fe3096779e3fe09107be3ed67afd Author: kuhn Date: Mon Dec 5 23:12:08 2005 +0000 added support for a list of files =not= to check commit 7c33565c247e868f5a31dff9156e99335e890857 Author: hartera Date: Mon Dec 5 23:04:03 2005 +0000 Fixed error in Gencode Genes rule. commit 0d46b602bbe31664ea82c73ffca495c7b39890e1 Author: hartera Date: Mon Dec 5 23:01:40 2005 +0000 Added identifiers and rules for the ENCODE Gencode tables. commit acc1d3401d3adac6c167d278e7679f04233546b0 Author: kate Date: Mon Dec 5 23:00:16 2005 +0000 Add site search for Uppsala Chip/chip commit 88c8136c38e23209595d1d543f7b0ffbe2591bcc Author: galt Date: Mon Dec 5 22:37:34 2005 +0000 added ann to the users wanting auto-lock commit 2ee0d05d336726bb8c08414efbee1af00a8272f8 Author: kate Date: Mon Dec 5 22:32:12 2005 +0000 Fix label problem and adjust viewing parameters in Uppsala track commit f9812197c011eb13a1c20ce85cfa7387a96cc758 Author: kent Date: Mon Dec 5 22:22:02 2005 +0000 Removing #warning, which seems to kill gcc on Mac. commit 9bc984cf0d72a17b3c90963f371b8800552d3427 Author: markd Date: Mon Dec 5 22:20:49 2005 +0000 rename genePredStats to genePredHisto commit b953e2075c84e51beb7269f714f807ee368d07af Author: kent Date: Mon Dec 5 22:14:44 2005 +0000 Adding htmlCookieFileRead commit 16437358115c08fee22ddea169c48ae9bf4a3770 Author: kent Date: Mon Dec 5 22:14:11 2005 +0000 Adding writeGulp commit 7d07880b1fbade734b1cc5986a7233a476b8fece Author: kent Date: Mon Dec 5 22:13:39 2005 +0000 Adding some escapes. commit 46f2293db58dd4e6ba69281e04336a10fa618b0e Author: kent Date: Mon Dec 5 22:09:04 2005 +0000 Adding socket library so will link under Solaris. commit e374955ffa168e3cee01a8ebbe2c8b2bfbbfc9b2 Author: kent Date: Mon Dec 5 22:04:42 2005 +0000 Changing hard error to a warning on WORDSIZE commit 28bb28ece9393af8e76341cf6139c630a0e84d94 Author: kate Date: Mon Dec 5 21:30:57 2005 +0000 New submissions commit 67268dd6d6bd7b7b64a5621bf9d577bcee268e38 Author: kent Date: Mon Dec 5 21:22:59 2005 +0000 Adding webBlat to blatSuite make commit 782fd67c932bd46b6c0f92761d0d39701da75bb2 Author: hartera Date: Mon Dec 5 21:16:06 2005 +0000 Added BosTau2 to the list for the chainDest variable. commit 3174e2040eb1d3aea6aaf67b277cff629f7c66e8 Author: kate Date: Mon Dec 5 20:51:59 2005 +0000 *** empty log message *** commit 236f28e952f4b81d038f2df586b7c1f61818ac8f Author: kent Date: Mon Dec 5 20:50:41 2005 +0000 Avoiding a divide by zero. commit a1e215604f305d0f4a3603cbfc72a70b62841bdf Author: braney Date: Mon Dec 5 20:34:28 2005 +0000 add a new routine that provides a link with a mouseover message commit e510dc860d7d9ede912ec919635274c04a0210a6 Author: kent Date: Mon Dec 5 20:25:28 2005 +0000 Fixing problem with no search box on gateway on IE 6. Making it all in one section. commit 1ca16780aa4a16ac9d3fffb863704ef5cf2eae54 Author: ann Date: Mon Dec 5 19:47:56 2005 +0000 added netFr1 track entry commit 9e94f024768f010bb4b982e81715957e3af9d1fa Author: braney Date: Mon Dec 5 19:26:24 2005 +0000 change the default for chaining between alignments commit f36f06270bf94791fb938ab13e2d7b32585c46c4 Author: kate Date: Mon Dec 5 19:14:01 2005 +0000 Expand based on new intput form Paul Flicek commit 86f8907f724262a7c024806eb0413b737cd6b9e8 Author: donnak Date: Mon Dec 5 18:24:52 2005 +0000 Archived some news items. commit d26acb3b4dc9e6ab10044c2110c57dd2889e5ed1 Author: ann Date: Mon Dec 5 18:08:46 2005 +0000 net track description for fr1 on mm7 database commit 8c1f48cdf59b646cc043404e16dbde8c65e812c1 Author: heather Date: Mon Dec 5 18:05:39 2005 +0000 get rid of quotes commit f3bc1d1c43d21227860c2a7fd23bf53eb70c525e Author: hiram Date: Mon Dec 5 17:42:33 2005 +0000 The conservation tracks needed to move up a bit in priority commit c1ac391cd04950adc24344988b3e6c30e1d8ac03 Author: hiram Date: Mon Dec 5 17:34:19 2005 +0000 A copy of netBosTau1 commit 02d9f50f80d2457b0306ad4aff75a09387aafe3a Author: hiram Date: Mon Dec 5 17:31:30 2005 +0000 Initial source with matrix commit 7036a1f91f89e005bb40b4187c287f04e6ad7325 Author: galt Date: Mon Dec 5 16:00:04 2005 +0000 "Encode release log update" commit 2ebfb88b91dec0844acfe12373508cb2275fb977 Author: galt Date: Mon Dec 5 16:00:03 2005 +0000 "Release log update" commit a8269a3a2d9b0476943f677ed151f1b24b9f54f0 Author: markd Date: Mon Dec 5 06:18:37 2005 +0000 fixed memory leak commit 4ef217142cb05da298cf2f69791e4022839d9066 Author: kuhn Date: Mon Dec 5 01:24:20 2005 +0000 changed link commit 5982fcd5f405c04365fa781fd8f35c44baa61561 Author: kent Date: Mon Dec 5 00:09:01 2005 +0000 Tweaking text one more time commit 70c830c82ee2e0fa95085eb911a3cb598fa9a656 Author: galt Date: Sun Dec 4 23:44:24 2005 +0000 added dbSnoop commit dfb5d34510e74a5db323ab0d3f4976b8b9b3081b Author: kent Date: Sun Dec 4 23:27:23 2005 +0000 Making UCSC VisiGene area resemble hot links bar visually. commit e523a06a565f262cb83f33e30f004e0a50ec2494 Author: braney Date: Sun Dec 4 20:56:07 2005 +0000 add cioSav2 commit f65f017ea4edb4ac084a3c32a68a70c1c61d074a Author: braney Date: Sun Dec 4 20:31:21 2005 +0000 a cioSav2 trackDb commit 8e7ae4f9373726452e77154dcac4b153aff631da Author: braney Date: Sun Dec 4 20:26:39 2005 +0000 fix up alignment track commit da5502309edbdb317b8e0dd076d5a0c56ed129a9 Author: kent Date: Sun Dec 4 19:37:53 2005 +0000 Fixing off-by-one error in reporting of developmental stage. commit 381c425cbd084c4820ccdbd31ccf5d3eddf37e7d Author: galt Date: Sun Dec 4 16:00:04 2005 +0000 "Encode release log update" commit 1e721d0062a2cd32a7c4a15c483edc81339592f4 Author: galt Date: Sun Dec 4 16:00:03 2005 +0000 "Release log update" commit ef3f0cbc7a38cb17b9dc73a661587b958c9999fb Author: galt Date: Sun Dec 4 09:49:04 2005 +0000 improved support for 302 errors to show the location it was trying to redirect the user to commit cb7aba8475d98bd8082adc22fe1a19d1b7757e30 Author: galt Date: Sun Dec 4 09:16:04 2005 +0000 fix bug in free commit 936a49241fd626b5ec85354130d7a687d79ba4c7 Author: galt Date: Sun Dec 4 08:16:06 2005 +0000 fix compiler complaint about unused vars commit f06eafb4c048ac86664af2ab18800420fc07e5bf Author: markd Date: Sun Dec 4 07:38:32 2005 +0000 added function to resize string commit 6263ba19715031b7bc87b99aefc26f8ea2ea1dc2 Author: galt Date: Sun Dec 4 06:30:50 2005 +0000 oops, found another occurrence of memmem to replace commit 6cb4cb12332a5483ee2217b0e930db2162d35ff5 Author: lowe Date: Sun Dec 4 01:36:56 2005 +0000 moved to lowelab dir commit cca54cf404c31d873aab6299252038ce0fb13d12 Author: lowe Date: Sat Dec 3 21:17:01 2005 +0000 moved to lowelab dir commit 5572a4ae09f4fd550c3b092635755d2104ce9d19 Author: lowe Date: Sat Dec 3 21:14:03 2005 +0000 moving to lowelab dir name commit c88c300f5537e8b75a656ada28c34f90aec266ca Author: lowe Date: Sat Dec 3 21:11:19 2005 +0000 Removing unsuccessful move of archae to lowelab dir commit a846b742d6675f75cdf8763bab9fc260cb483fb4 Author: lowe Date: Sat Dec 3 21:09:57 2005 +0000 removed files from unsuccessful directory move commit 95945e4b6c4222c5979314bde109171e2bd6c2fa Author: lowe Date: Sat Dec 3 21:05:33 2005 +0000 moved from archae sudir commit 96f1a8d14100583b1053b8c15d6f0e54460e3e01 Author: lowe Date: Sat Dec 3 21:03:27 2005 +0000 Moved from old archae subdir commit eeba6187ca02b4d77ff1db607758a3031bedce0e Author: lowe Date: Sat Dec 3 21:02:22 2005 +0000 Moved from archae dir structure commit 88cb8f415c725d4fadcc16731ea377012774591d Author: kent Date: Sat Dec 3 20:02:09 2005 +0000 Putting a little error checking on cookie file commit 743f7202a920ffd218abf8df0f7bed6ff1ca3741 Author: kent Date: Sat Dec 3 19:27:18 2005 +0000 Adding cookies option commit 5c9b1eee5fee0dc123882e1eb389fe294b1edad1 Author: kent Date: Sat Dec 3 19:26:42 2005 +0000 Adding a few functions to get pages with cookies commit b34583829bd6c94cda85e13eef41c1c43b0d473f Author: lowe Date: Sat Dec 3 18:38:59 2005 +0000 moved archae dir to lowelab commit 6ed367da213b79d649587f14b26276511d1ca37a Author: lowe Date: Sat Dec 3 18:38:35 2005 +0000 *** empty log message *** commit b34e7055d7b0f3c19d6c921ea8a086f9ce768b5a Author: lowe Date: Sat Dec 3 18:05:56 2005 +0000 Not needed commit f149946be5b2449a5b6fbdd9851c197ae45c0e31 Author: lowe Date: Sat Dec 3 17:20:40 2005 +0000 Added new search specs and tRNA and gbRNA tracks commit f1bba00fc0089ad96854f1d0eb9f23222d8a7a1d Author: lowe Date: Sat Dec 3 17:19:50 2005 +0000 auto generated description page commit 40091e8d9534793a1af4b0107d052224d3875d19 Author: lowe Date: Sat Dec 3 17:12:58 2005 +0000 description.html page templates commit 6222196739e6aa8d550aaa716fab5bfa1f410e55 Author: lowe Date: Sat Dec 3 17:10:57 2005 +0000 Description html for tRNAs track commit 36d5130eb12b7ab91edd5364735fcb1d998af411 Author: lowe Date: Sat Dec 3 17:10:23 2005 +0000 archaea browser credits html commit 98be74c6dcd5e3d41baf89c3d8d6b05a9e5ac4b7 Author: lowe Date: Sat Dec 3 16:41:02 2005 +0000 Removing unneeded directory commit ed95f286bfdd9f864cbf0f49e57f3e589ea0b6f6 Author: galt Date: Sat Dec 3 16:00:02 2005 +0000 "Encode release log update" commit 4b14ec5d80e5514b5909aaff73718212e154b0b4 Author: galt Date: Sat Dec 3 16:00:01 2005 +0000 "Release log update" commit 66dacc4f0de339aeb7fcc96b17b1d47ed077053c Author: markd Date: Sat Dec 3 13:53:27 2005 +0000 added missing target commit e67890b6ada4650ed3eb97a8d5266ad50170ecd1 Author: heather Date: Sat Dec 3 13:26:52 2005 +0000 add lookupObserved (need to handle quotes in snpFasta) commit c88c5a61dad0d7379034b5bbaa3ae69233f730bc Author: heather Date: Sat Dec 3 12:13:56 2005 +0000 tweak index commit 63ea40be1976eb7e2239f95f947037effcc8e19c Author: heather Date: Sat Dec 3 12:10:27 2005 +0000 simple preprocessor for rs_fasta files. Flanks still to be done. commit 39256436544a00e6f40be95a821bf9eee774cc0f Author: kent Date: Sat Dec 3 12:00:39 2005 +0000 A little cleanup commit 2f7382763bbcfe2c667961a338d4d44298b68edc Author: kent Date: Sat Dec 3 11:57:03 2005 +0000 Rearranging VisiGene page that comes up with no search term. commit a04eb71f709bd8a3ce2ee608cdef44d0d9389811 Author: galt Date: Sat Dec 3 11:17:22 2005 +0000 change buffer from debug size of 99 to normal size 32k commit 71105219b07384d7d9f794703424ffbb2085918e Author: galt Date: Sat Dec 3 11:16:40 2005 +0000 added one more series test and cleanup for it commit 7c15439fb26209abad0bbb2d33c1b92292820fb7 Author: galt Date: Sat Dec 3 10:52:12 2005 +0000 added code for posting MIME ENCTYPE form, and a tester for exercising it against hgBlat commit 112e8b5ab92784c026aeb8e3bca3149695020beb Author: kent Date: Sat Dec 3 08:01:41 2005 +0000 Adding dyStringAppendEscapeQuotes commit 12e293fb1c0ff22be91dd8f60d4a4bd723373fc7 Author: kent Date: Sat Dec 3 08:00:45 2005 +0000 Handling literal CDATA in bracket type text commit 866d6d614fe624f78b1bfec231ac16a98c2ff866 Author: fanhsu Date: Sat Dec 3 00:45:51 2005 +0000 Added spAccToId2(). commit 6be8ee08421c1b1195bf8e359b6bb278b88a31e1 Author: kate Date: Sat Dec 3 00:17:48 2005 +0000 Alignment assessments from UC Berkeley commit 1caaa30e4e1d766ca2b062e890c2387e4e2a5c2a Author: hiram Date: Sat Dec 3 00:17:11 2005 +0000 Making progress on phastCons 17-way - have initial data, now to tune it commit 4853d71c820eaf3852b6e564065db423d065663f Author: fanhsu Date: Sat Dec 3 00:11:16 2005 +0000 Use the new function spAccToId2() instead. commit 6c909d3944a5fb3b868d43131a70f24f77ccd7c5 Author: kuhn Date: Sat Dec 3 00:09:24 2005 +0000 incorporated some changes requested by ctrack contributor commit a6716507df015d2d7886f3a9346f816f2397b3fc Author: jen Date: Sat Dec 3 00:03:27 2005 +0000 Added comments for simpleRepeat table change. commit ca849538fe63afd402d0e422e053d8efd4e673b2 Author: hiram Date: Sat Dec 3 00:02:35 2005 +0000 Adding phastCons17 to mouse 17-way commit 1f71312cdf6d40f9cb490f4856ba04c9e3153f8a Author: fanhsu Date: Fri Dec 2 23:57:35 2005 +0000 Added spAccToId2() to help dealing with obsolete protein IDs. commit 8f422a6a1bfa89484c4a450e6ed918422b0d8725 Author: fanhsu Date: Fri Dec 2 23:56:48 2005 +0000 Added logic to deal with obsolete UniProt protein ID. commit a7b7a7d6d8af32926c89a9e6d8f774a98580b66a Author: fanhsu Date: Fri Dec 2 23:55:25 2005 +0000 Added special logic for KG non-unique proteins. commit f736c353b22ec9b7158d6bd4f446acbea52cc1a0 Author: kuhn Date: Fri Dec 2 23:40:10 2005 +0000 added support for bluearc commit 45b060dacbac5bb8c93b3e00d79a37b390169129 Author: fanhsu Date: Fri Dec 2 23:13:40 2005 +0000 Fixed a bug of the situation where a protein has become obsolete or a secondary protein ID. commit 8fd2a51528ef2ec290fa29f5b8250124352c01d7 Author: hartera Date: Fri Dec 2 22:40:52 2005 +0000 Documented removal of axtNet and net downloads for Self alignments as only Self chain track is pushed to RR. commit 785489260e632deddb6777957e97e178b00d1ba0 Author: kent Date: Fri Dec 2 22:30:34 2005 +0000 Adding a numerical escape to test case. commit 7a72ca2380c90b6a67eb6f0c6fcca487e283f26a Author: kent Date: Fri Dec 2 22:28:26 2005 +0000 Adding xmlEscape. commit 71921ced3b9e385433df73e00505c577142cf057 Author: ann Date: Fri Dec 2 22:27:43 2005 +0000 Added $matrix variable to display the blastz scoring matrix commit d2e976eb9c63f4ed7ef4dfd146756f6f85f595e4 Author: kent Date: Fri Dec 2 22:21:28 2005 +0000 Adding xmlCat utility. commit d298c519ae5d004fb14324953d630d8007adbd6e Author: ann Date: Fri Dec 2 22:14:58 2005 +0000 added matrix and matrixHeader variables for 8 chain tracks commit 1fe8cd455f0710f828500fac7334697d678eca27 Author: kent Date: Fri Dec 2 22:11:50 2005 +0000 Clarifying a comment. commit 25d046e58b0948f369f4da78ca18261633ec2ae1 Author: kent Date: Fri Dec 2 22:11:31 2005 +0000 Adding xpReadFrom file, an easy read handler commit 24dd7ebb0fcefd44ee7bc0c287052f902bc0c7c3 Author: kent Date: Fri Dec 2 22:10:34 2005 +0000 Adding xmlEscape module and moving a function in xp.c to it. commit df5a15d19994a99266cc20d88f4da9b90fdf14ae Author: kent Date: Fri Dec 2 22:09:57 2005 +0000 Seems to work commit 65033b01ca9618324d92228d7f160cb28eabeaab Author: donnak Date: Fri Dec 2 21:46:28 2005 +0000 Added announcements for ABA track and VisiGene. Added VisiGene to the "About" section as well. commit bb6cb4d285922dc1174b878cdb263ac466dbed05 Author: kate Date: Fri Dec 2 21:40:13 2005 +0000 Fix Sanger track configs commit c10c56719c278f595ac747723a48d346714be506 Author: heather Date: Fri Dec 2 21:37:50 2005 +0000 add cow synteny track commit 4ef66e6e2013dff0c6dd04c4f6608c1c4d72b4d7 Author: heather Date: Fri Dec 2 21:37:00 2005 +0000 initial revision commit 592fccc94c80901c9e2b0b02d299959a8c206f62 Author: heather Date: Fri Dec 2 21:36:38 2005 +0000 cow synteny track commit f8548482c343c86ae0af013c152589d05f952e27 Author: kate Date: Fri Dec 2 20:55:15 2005 +0000 Fix Sanger chip subtrack label commit f34c2c475041b8663a7780c0a2fb9026f8c5925a Author: ann Date: Fri Dec 2 20:35:06 2005 +0000 Added matrixHeader variable for chainGalGal2 commit 120ebbaef2a9fbc2e45ac747de5197ad13230867 Author: ann Date: Fri Dec 2 20:31:22 2005 +0000 Added $matrix variable to display the blastz scoring matrix commit 72000a85e84f04b258260c6011385d6cc6c73e2e Author: ann Date: Fri Dec 2 20:29:35 2005 +0000 Added matrix variable for BosTau2 and GalGal2 chain tracks. commit a975d871e60105f44a3eb905338314c351729f09 Author: hartera Date: Fri Dec 2 20:15:27 2005 +0000 Created chain and net tracks for self alignments and also axtNet, mafNet and downloads. Started Known Genes. commit 9d26bf8061a57f73086167f62897ee8adbae8bdb Author: hiram Date: Fri Dec 2 19:46:35 2005 +0000 Add bits64 mask for carefulAlloc() masking when on 64 bit machines commit d2e1515b3e88854e3b1980acc49c68b5961bad7a Author: lowe Date: Fri Dec 2 19:44:11 2005 +0000 Added tRNA.o and gbRNAs.o to make commit a81e60d43d7c7908353441b6ad8e60713131aaec Author: galt Date: Fri Dec 2 19:35:08 2005 +0000 fixed couple of minor memory leaks and added memMatch which is more portable than memmem to help e.g. mac commit 51860d79e2b706efeaf450aeb0625a5c1a1757c8 Author: galt Date: Fri Dec 2 19:34:22 2005 +0000 added extern declaration of environ to help e.g. mac commit 06c9e3a51f565de11f785f95f835b9302b2061c6 Author: hiram Date: Fri Dec 2 19:26:24 2005 +0000 Adding bits64 type - works OK on 32 bit hgwdev and x86_64 commit e1845fb5fb0624802c8e26d163ef59223f51ebe5 Author: hiram Date: Fri Dec 2 19:21:42 2005 +0000 Rearrange commit ecf00558216711e7423bf0d2313686fcaba56376 Author: hiram Date: Fri Dec 2 19:17:24 2005 +0000 Need to cast the sizeof operator to (int) for 64 bit compile commit caf981572ab33d606393b9519f897b88b60443fa Author: hiram Date: Fri Dec 2 19:13:55 2005 +0000 Add sizeof utility to print out size of various C data types commit f27f84d70f904bec6316966fcdc8c175e7eb79f5 Author: hiram Date: Fri Dec 2 18:59:21 2005 +0000 Do not abuse the wds chrName pointer, use it properly commit 6123b1d7d0c988d2ad51ee475b0447504b56ad2a Author: hartera Date: Fri Dec 2 18:47:54 2005 +0000 Edited Methods to state that chrNA and chrUn were not aligned. commit c54067ac9493bd6e94630db892a91339df13d6a6 Author: braney Date: Fri Dec 2 18:02:18 2005 +0000 oops, fix up names commit df39d6429258f361a41358b2c5a4c2303a76075b Author: braney Date: Fri Dec 2 18:01:01 2005 +0000 add ciona savignyi commit 501f744f732e860fa12b9a8047b936adb2960cbf Author: giardine Date: Fri Dec 2 17:32:16 2005 +0000 removed "none" option from label checkbox choices. If none checked then displays no label. If no boxes checked or otherwise then displays default. commit 8f2a896b2f3b50e74387f722ce6acfcd38bf178a Author: fanhsu Date: Fri Dec 2 16:38:23 2005 +0000 Created makefile. commit 25bfff0e5cdf6331f044e810e602df359aa6c768 Author: fanhsu Date: Fri Dec 2 16:38:08 2005 +0000 Created fixMd.c to fix seq_contig.md problem. commit 880d0d2460e2c027a3294c31996e3b7de102448c Author: galt Date: Fri Dec 2 16:00:02 2005 +0000 "Encode release log update" commit 33258a1fa378205df249f9541a2b7bd1bf1d4e40 Author: galt Date: Fri Dec 2 16:00:01 2005 +0000 "Release log update" commit 2760e87f34692dc97024df58e7a33bd5f337280a Author: markd Date: Fri Dec 2 08:40:37 2005 +0000 added tmp entries for reloading mm6 and hg17 commit e73e2c8deb1822593e25d41d84e8bbc3145c7146 Author: acs Date: Fri Dec 2 08:40:30 2005 +0000 added notes on new exoniphy run commit 3211f12203e8a28e5426d33da94aa806eb449841 Author: acs Date: Fri Dec 2 08:30:27 2005 +0000 rename exoniphy to exoniphyHMR and exoniphyDog to exoniphy commit 62f301a3d01901ef5a7b368b1f21a66c6a177192 Author: acs Date: Fri Dec 2 08:16:50 2005 +0000 rename exoniphy to exoniphyHMR and exoniphyDog to exoniphy commit 378d64ddbb11248eab506bad7a1168e7dcce43ff Author: kent Date: Fri Dec 2 08:04:46 2005 +0000 Oops, removing a get-it-to-compile-on-mac hack commit a02aaada6567ff4728378e73d7f6867b5dd5a817 Author: kent Date: Fri Dec 2 08:03:47 2005 +0000 Putting in conditional for darwin (mac OS) for custom gcc warnings commit 87a35a52c6e4f873c55ca2118a2771be260cca07 Author: markd Date: Fri Dec 2 05:51:55 2005 +0000 added beginnings program to get stats on a genePreds commit 5b48d7b26dfa656c214f23a1c4b27db095712211 Author: acs Date: Fri Dec 2 05:47:24 2005 +0000 tweaked priority for exoniphy, exoniphyDog commit 5f6b82ab37047f99e76a7a9a8b54347f75c7ed11 Author: markd Date: Fri Dec 2 05:47:20 2005 +0000 fixed memory leak commit 07326e622f5ef18e3e29b166b3c550b910b9a57d Author: acs Date: Fri Dec 2 05:43:34 2005 +0000 added exoniphyDog commit ddc1e9a88f1de3d491ed9089c947790487544eae Author: markd Date: Fri Dec 2 04:56:10 2005 +0000 fixed usage message commit 02f9637170fcebd9bc315d3c0ccbf76cf1de6a9b Author: kent Date: Fri Dec 2 03:30:52 2005 +0000 Added new xml utilities commit f6cb8ce570790416d5a83bd7482f04eeeb6ee488 Author: galt Date: Fri Dec 2 03:00:45 2005 +0000 adding tester program for mime.c mime parser commit 350d8c3bc62d9d3e8f6289d2f1aca0dbe5017090 Author: kent Date: Fri Dec 2 02:43:55 2005 +0000 Modularizing a bit and adding test cases commit 90bfdd61c6c9096fb44a2b0e833951b27d12657c Author: kent Date: Fri Dec 2 01:54:48 2005 +0000 Promoting tables containing nothing but a number or a short string in their text field to fields within a parent table. commit 5980fa0a5942f2f2e7e77747b9952446481a5996 Author: kate Date: Fri Dec 2 01:09:33 2005 +0000 Support #include or include commit fde6277f1c5ae24317f23319fef6348769c87edc Author: fanhsu Date: Fri Dec 2 00:21:42 2005 +0000 Updated to add hgg_prot as extra parameter in the URL to hgGene. commit ce4e6161f4ab3238fbb4c2e2c1dd56d172e51b7e Author: fanhsu Date: Thu Dec 1 23:19:17 2005 +0000 Updated to pass protein ID to hgGene. commit 466bf12e7f9db1b053a8a40d0c3da7540709cba5 Author: fanhsu Date: Thu Dec 1 23:10:34 2005 +0000 Updated to perform special processing to handle situations that there are multiple proteins from one single KG ID. commit dc81ac3583f58b4856974df818c10c1bee61e8eb Author: fanhsu Date: Thu Dec 1 23:06:01 2005 +0000 Added extern curProtId to support non-unique protein ID processing. commit b632664a7a590a563f9960204a8959c824da1742 Author: lowe Date: Thu Dec 1 22:59:05 2005 +0000 include file for 'gbRNAs' track commit 8257e386dd8179e12728cc59f958b1fdf5720974 Author: lowe Date: Thu Dec 1 22:58:38 2005 +0000 include file for 'tRNAs' track commit 07e3b99334d1e66a9c11414ff31f8f3d0fe49261 Author: kate Date: Thu Dec 1 22:19:26 2005 +0000 trackDb includes no longer should be commented commit 16b098397c59d9e16b295a88bac890f6cd71ccba Author: kate Date: Thu Dec 1 22:17:37 2005 +0000 Remove ENCODE dev browser trackDb generator, as it is breaking mirror builds. This will be adapted or abandoned soon commit aa975fbb49e6daeb71d36d11653d733bac00a1b2 Author: giardine Date: Thu Dec 1 21:35:13 2005 +0000 Changed label options to use check boxes instead of a radio button. Allows for mix and match of labels. Still need none to differentiate from not having made a selection. This affects human tracks, Known Genes, RefSeq Genes, and Non-human RefSeq genes. I also did the Human Mutation track the same way. Updated description for the Human Mutation track. commit 2f473efb7f720e309dceae510f7cf83a29e36c63 Author: kent Date: Thu Dec 1 20:18:18 2005 +0000 Putting content strings in a stack rather than in fields, to allow recursive data structures. commit 6982be4123090adf3197297a55569ab4f3bfcf9e Author: kate Date: Thu Dec 1 20:05:39 2005 +0000 Submitter changed his mind commit e25a582e9e4b09a1166da89e19df8c58adc42133 Author: kate Date: Thu Dec 1 19:34:02 2005 +0000 New data from BU commit bb4a728ba54b02a501e318f2873f518bbe9e37a5 Author: kent Date: Thu Dec 1 17:47:27 2005 +0000 Fixing coordinates on destination in the reverse strand commit dd455790e80f0d2f69cd4e8b167773ddf7b7496d Author: galt Date: Thu Dec 1 16:00:03 2005 +0000 "Encode release log update" commit 643920152f4a4b46b29f285daf85492dc844135c Author: galt Date: Thu Dec 1 16:00:02 2005 +0000 "Release log update" commit fd4b9b8848879504b097df63828d1f907b77d045 Author: galt Date: Thu Dec 1 06:53:48 2005 +0000 fixed errors in reading a full buffer and in handling eod (end of data) when end of input reached commit f64ec6b2c34af0b85b9ab04ba61adf0f46feb4ce Author: heather Date: Thu Dec 1 06:41:31 2005 +0000 use refNCBI/refUCSC commit ab4f8e123f02916b190af842a420534c319cd762 Author: lowe Date: Thu Dec 1 01:33:11 2005 +0000 Descriptor file for Genbank ncRNAs 'gbRNAs' track commit 1be4db450d89aa3c972244ef264dba1d17e40ed6 Author: lowe Date: Thu Dec 1 01:32:38 2005 +0000 autoSql c code for trnascan-SE 'tRNAs' track commit db3f9c9b87f184c88288620a882e1a23bcd821de Author: lowe Date: Thu Dec 1 01:31:48 2005 +0000 Descriptor file for trnascan-SE 'tRNAs' track commit 03a9cc189f29da78c1af9b59d250e130997c989a Author: lowe Date: Thu Dec 1 01:30:48 2005 +0000 autoSql c code for non-coding Genbank RNAs track commit af3c1400970aa3013106542b89501b879e47a73b Author: lowe Date: Thu Dec 1 01:28:12 2005 +0000 mysql file for Genbank ncRNAs 'gbRNAs' track commit 0467402dc578b72ea9bbaa587a4f58d6f1dc0243 Author: lowe Date: Thu Dec 1 01:25:52 2005 +0000 mysql file for trnascan-SE 'tRNAs' track commit ab85b3c2b4d999136f06d4469f4884e795d34ccf Author: aamp Date: Thu Dec 1 01:24:16 2005 +0000 Added the convert link back. commit fefb0a9bbfa3e02068415638b973ad6ea26d167c Author: lowe Date: Thu Dec 1 01:23:56 2005 +0000 Changed display of TIGR ORFs track; Added display of 'tRNAs' and 'gbRNAs' tracks; changes should only affect lowelab browser tracks commit 1004699cbb14c3a2a08baa36d9b40ce1c732c337 Author: kent Date: Thu Dec 1 01:14:24 2005 +0000 Moving ds test case to snp subdirectory commit a8c4fb1865ba2fffdfdc288be8b7a5fd9dacd28e Author: kent Date: Thu Dec 1 01:02:36 2005 +0000 Adding atree output, and chado test case commit 8df7bc45cd7f19503862acde56783f4ec5d61216 Author: kent Date: Thu Dec 1 00:42:31 2005 +0000 Integrating test case into makefile commit 7e257e3fa90204cbebd106c2a5eef367d1e1e689 Author: kate Date: Thu Dec 1 00:37:00 2005 +0000 Misc updates commit d5f27b0d48e9421b56603cd23bb061f783a0b0fb Author: kate Date: Thu Dec 1 00:32:35 2005 +0000 *** empty log message *** commit 0fbef020302c5082ec6be2415b4ead0dcc120ee8 Author: hiram Date: Thu Dec 1 00:31:35 2005 +0000 Add multiz10way051130 updated track commit a61d20d6f5ef952111a2ab8f0af8c0cc232d65b4 Author: angie Date: Wed Nov 30 23:52:58 2005 +0000 Added droSec. commit 5ccb3c05b2c9cf530fc80fd871f28d6a6e86b693 Author: angie Date: Wed Nov 30 23:51:21 2005 +0000 Added droSec1. commit 3abd3e57808d655c2f0ce309f72085a3bf602cf0 Author: heather Date: Wed Nov 30 23:32:22 2005 +0000 Add a contigGroup argument. Fully handle chrom==ERROR. Short-circuit (temporary). commit 30eba9f9d72bdab121fd243cb5db32a9599069b9 Author: angie Date: Wed Nov 30 23:01:54 2005 +0000 Elementary description.html for droSec1. commit 54b9a3b8c8d1836e1b3877c892621573b333822d Author: angie Date: Wed Nov 30 23:01:53 2005 +0000 Added droSec1. commit e08efe3d76580f7c35d3345e179644e068c9b3ae Author: kent Date: Wed Nov 30 21:56:29 2005 +0000 Adding a test case commit 5fdec3def86e3d0aff8bc8b988c4ee698a9e0f1e Author: jen Date: Wed Nov 30 21:11:42 2005 +0000 Added gap. commit e1cd6e06687831978331f0f9d7ca1f9c4292cc2f Author: kent Date: Wed Nov 30 20:48:14 2005 +0000 Adding more ideas to todo list commit c3b283603442aa1d2a9e1205e6d1ef86979c1e7a Author: kent Date: Wed Nov 30 20:47:49 2005 +0000 Removed testing statement from makefile commit 6a48a87317e780f24cc8dfba8bff3337a75b79b2 Author: kent Date: Wed Nov 30 20:47:11 2005 +0000 Adding note about unimplementeed status commit 66515e3764774185d17b80eb1d12694c73d49d0f Author: jen Date: Wed Nov 30 20:46:33 2005 +0000 Added a line between two tracks - was causing the 2nd (encodeReseqRegions) to not be populated in the trackDb table! commit ab808fcd65072e4b26f18c31ad9ea947a8a70a00 Author: aamp Date: Wed Nov 30 20:08:24 2005 +0000 Reverted this too. commit 3ef492504aaf7b089c28ce538e6707debee363ed Author: jen Date: Wed Nov 30 19:51:15 2005 +0000 Added dog-specific gap.html file (similiar to canFam1 version). commit beaef2b062139aa0232f68e2627df3cefe7d7fc2 Author: fanhsu Date: Wed Nov 30 18:02:03 2005 +0000 Added #define hggProt "hgg_prot" /* Main protein id. */ commit 5fdb7bfc7dfb8f702b3b3ea2cab044274f024bfc Author: kuhn Date: Wed Nov 30 17:46:13 2005 +0000 grammar tweak commit 19702ec5d8f6ca446b9d980157556b6d93322a8c Author: kent Date: Wed Nov 30 16:03:22 2005 +0000 Avoiding infinite recursion in writeTree. commit a4e330ec67e0d3b8d7c79beed714207bb6b14668 Author: kent Date: Wed Nov 30 16:02:48 2005 +0000 Added apostrophy handling commit 2741aa075f4ae4ee8ed5d09c65674830424b5488 Author: galt Date: Wed Nov 30 16:00:05 2005 +0000 "Encode release log update" commit 8dd3f0a2bde3c2a9789500b652e085f3fe6494c7 Author: galt Date: Wed Nov 30 16:00:04 2005 +0000 "Release log update" commit 2b800beb1a35fa57719e208754d3832224020218 Author: kent Date: Wed Nov 30 08:07:08 2005 +0000 Adding field. commit abf06e5e1b767ddd5233f80d8e09ebb0c83083ec Author: kent Date: Wed Nov 30 07:50:45 2005 +0000 Putting in warning on self-referential data structures. It looks like chado has one - it's feature. It'll take a bit of a rework of the code to handle this I think. I'll need to store th field dyString on a stack rather than in the field itself. commit 741d60f7109a91a5e6cdb7e0483a5e6cb3d4de8b Author: kent Date: Wed Nov 30 06:14:46 2005 +0000 Can handle recursive data structures. commit cca7658c4bd360f77a6027c2baac7068aa04ffe4 Author: kate Date: Wed Nov 30 02:42:58 2005 +0000 Expand overflow message to clarify -- this is out-of-range values, not just too big commit ea5502ad02ac14c0d4d3463c3d190b0fa2771ff2 Author: kent Date: Wed Nov 30 01:32:42 2005 +0000 Applying mixed case names to indexes. Adding another reserved word or two. commit c0d09edd44952e7c8e9e9dbacaedaa7a2bb254ca Author: kent Date: Wed Nov 30 01:16:02 2005 +0000 Fixing a couple of bugs that the musicmoz set brought out. commit 563a199515bc785124858d7763ee92e1970b1b27 Author: kate Date: Wed Nov 30 00:13:48 2005 +0000 Typo commit 5798b5a82a2960a3813779d15cfe0b702f478d97 Author: kate Date: Wed Nov 30 00:11:36 2005 +0000 Fix data versions commit 603ef8c08de60cfc63f11fda3a9775c28600c754 Author: kent Date: Wed Nov 30 00:11:14 2005 +0000 Fixing associations that involve string keys. commit f93028e44ddd1e16cb95c4faa24214fd1af8c10d Author: kent Date: Tue Nov 29 23:40:19 2005 +0000 Adding support for bigint, and dodging a couple more sql reserved words. commit d3918ee35b6d39ddc9c69a4bf0903032c7bd077c Author: kate Date: Tue Nov 29 23:28:50 2005 +0000 Expand label commit 49487ca89d1db90a5c4e619f5119c220648e2204 Author: hartera Date: Tue Nov 29 23:26:13 2005 +0000 Edits to methods section including changes suggested by track contributors. commit 0c7a7901e765fbcc4ff004f349f3685ec6fb1ce7 Author: kate Date: Tue Nov 29 23:17:59 2005 +0000 Add data versions to Regulome tracks commit edbe4c7a405b7f2ed65bb5a0deb0187fcbbd25ba Author: kate Date: Tue Nov 29 23:11:01 2005 +0000 Fix Yale Chip/chip commit 00ba86d7a1c8897338e98417d7d228894ad99021 Author: kent Date: Tue Nov 29 23:08:11 2005 +0000 Making xmlToSql more robust about tables and fields that are reserved words in SQL or C, or contain characters not allowed in an identifier in those languages. commit 89fc0b70124093072f3e9fcf17737190bc04225f Author: kent Date: Tue Nov 29 23:06:39 2005 +0000 Adding mixedCaseName to attributes commit 4c06be2e06e8425131b643a377bd51c52b4ae3a3 Author: hartera Date: Tue Nov 29 22:58:50 2005 +0000 Further changes to the methods section suggested by the track contributors. commit 20b3bc51d8ec105edf2facafd9575dff1f9a0016 Author: jen Date: Tue Nov 29 22:57:25 2005 +0000 Moved track encodeNhgriDnaseHsChip from human to hg17. commit f883cb37abf27eba7207c13d862ec16363d2ae59 Author: jen Date: Tue Nov 29 22:55:54 2005 +0000 Moved track encodeNhgriDnaseHsChip from human to hg17 and added dataVersions. commit fe02a58712d5bcffc72dadb2ccfc2bfdd17168da Author: jen Date: Tue Nov 29 22:49:24 2005 +0000 Changed dataVersions. commit 28424de3e37f63e0af00da8ad12662f3e0dfa65b Author: kate Date: Tue Nov 29 22:08:07 2005 +0000 Add CVS keywords commit 587b0a49fc730c697f456876a9ba673118285051 Author: jen Date: Tue Nov 29 22:06:01 2005 +0000 Added dataVersions for many tracks. commit a903faeb2eca83afa62bc04b6a11f934eb8f6127 Author: jen Date: Tue Nov 29 21:52:36 2005 +0000 Added dataVersions for many tracks. commit 48bb5a5922a8e2c5845e7528a2511662371d3eaf Author: jen Date: Tue Nov 29 21:42:26 2005 +0000 Added dataVersions for many tracks. commit 1444117bc5721ec16f0dad52b62b62369c5239cc Author: kent Date: Tue Nov 29 21:41:39 2005 +0000 Treating : as another word separator commit 4074ef37c623a9a1b5357ad49c404a28f7f13c07 Author: jen Date: Tue Nov 29 21:10:41 2005 +0000 Added dataVersions for many tracks. commit f4d7499c06bd15ff484de801bbe8a5df6c22de89 Author: angie Date: Tue Nov 29 20:59:48 2005 +0000 Added droPer1. commit 4f158fe583f3697ecdd81afdc3a770ac57df645d Author: aamp Date: Tue Nov 29 20:53:43 2005 +0000 Reverting back to liftOverChain without minChainT, minChainQ. commit 88215f3a5cc74bfcb316c7a6568033fc1ea3e9ab Author: kent Date: Tue Nov 29 20:52:35 2005 +0000 Adding copy number info to tree. commit b74541932fa546c687165b12fb7c8b953b1524ed Author: angie Date: Tue Nov 29 20:50:57 2005 +0000 Added droPer1. commit 9cb50004fd46b1383e623582cc4ab7f6a7b59082 Author: hartera Date: Tue Nov 29 20:26:29 2005 +0000 Edited and expanded the Methods section. commit 85d737fdba9c369650eefe8180e249a7eb3fc74b Author: galt Date: Tue Nov 29 20:10:44 2005 +0000 make the arrays handle new size and verify automatically as expanded in future commit a163466f6d2a013b6a8cb93aa26246ffdc6ce979 Author: kent Date: Tue Nov 29 19:42:54 2005 +0000 Adding tree output option. commit dd40cbe5678d63d431dd76902fb183a439b7c9aa Author: hiram Date: Tue Nov 29 19:41:40 2005 +0000 File moved up one directory commit ed197c403783634ed65f7ee7c6752c4a2dfbe3e9 Author: hiram Date: Tue Nov 29 19:41:16 2005 +0000 Moving to correct directory commit 1184a5f8dc9ca7448ed0bbff7907c1bee3d10bbe Author: hiram Date: Tue Nov 29 19:34:52 2005 +0000 Initial contents and place holder files to avoid make strict warnings commit 5d3df45ef53f78255d3a154c3bed14c72e378269 Author: giardine Date: Tue Nov 29 19:34:50 2005 +0000 Uncommented the option of OMIM ID for the label on the known genes track. commit e881cd2f546b3b4d7f93946c4a3003e26a54df6d Author: giardine Date: Tue Nov 29 18:19:48 2005 +0000 *** empty log message *** commit 90616d3392267288d0d392c2c4a412ba9687aff6 Author: giardine Date: Tue Nov 29 18:19:29 2005 +0000 Various improvements to the hgMut* tables. Including separating out the source to a separate table to make lists of sources faster (for exclude list) and can enter the actual source for a LSDB. Added nameTable to Alias table so can allow user to use the common name for labels. Renaming of other fields and tables to make things clearer. Feature added is the ability to chose field for label, hgvs name, ID, common name, all, none. Also pass ID now so when item is clicked on, know for sure which one. commit 1e220bedfe14676f2c5cf8b7bd23094133db86a1 Author: heather Date: Tue Nov 29 17:43:48 2005 +0000 buildUtils locally on 32 bit hgwdev after building on 64 bit hgwbeta commit 5a3fd5ea8d45786d78c69cecf05fd917afb296b2 Author: heather Date: Tue Nov 29 17:42:21 2005 +0000 hgwbeta is 64 bit, hgwdev is not commit f2eccc0b27a3053f16d8898f90ec8a035ecc5aa8 Author: kent Date: Tue Nov 29 17:24:21 2005 +0000 Leaving one empty record at end of stack so as to simplify boundary conditions elsewhere. commit 8a2369510587ae279ae55c13cf2235b56bd77a0c Author: kent Date: Tue Nov 29 17:23:42 2005 +0000 Polishing output. commit 0a8d8f02e1bb7d78008dd139d18211751a50c36f Author: donnak Date: Tue Nov 29 17:16:12 2005 +0000 Modified some of the sample searches, per Jim. commit f592c51266a72d41d3d297d48df6914af6adcf62 Author: galt Date: Tue Nov 29 16:00:02 2005 +0000 "Encode release log update" commit 76aa9f818089a9c4466166008028759554cef57b Author: galt Date: Tue Nov 29 16:00:01 2005 +0000 "Release log update" commit 8acda243bb1defcf0a95d365fe0bafbd3920a37c Author: kent Date: Tue Nov 29 10:26:13 2005 +0000 Clarifying usage. commit 75ba3f292496d5d22b742e7ac9d3326d644fdb4d Author: kent Date: Tue Nov 29 10:08:31 2005 +0000 Seem to write out tables creation statements fine. commit 75014aeafb4214889363805ed8bcd5305bb4d58e Author: kent Date: Tue Nov 29 08:25:19 2005 +0000 I think I've worked the kinks out of tab-file generation of elements that can occur under more than one type of tag. commit 88be300eed0bf951846db148f78e776bc6f86bad Author: kent Date: Tue Nov 29 07:44:16 2005 +0000 Starting to make sql table creation files. commit a7845fe81ab6212485a11541ced6fbddeb390019 Author: kent Date: Tue Nov 29 07:06:46 2005 +0000 Starting to allow multiple parent tables. commit c1e89dc6538087fc04a876abaf220f1b0fce31be Author: kent Date: Tue Nov 29 06:03:01 2005 +0000 Seems to work except when tag has multiple possible parents commit 44bc2a2ee30ca1a050b2bad24ee68c7b291475df Author: kent Date: Tue Nov 29 05:04:28 2005 +0000 Starting to make association tables\n commit 8517e3584a16935e826f2cb36c05c02ab3de13a8 Author: heather Date: Tue Nov 29 04:27:31 2005 +0000 adding hnibForChrom2 commit 3b6da7b6357cfead8c6d0ce77080b84b7350c1fe Author: heather Date: Tue Nov 29 04:27:17 2005 +0000 making hNibForChrom2 public commit e822b2daa064cc58e62cfc0c87ed8cdf6e75adb0 Author: kent Date: Tue Nov 29 04:23:11 2005 +0000 Restricting embedding of child id as a field in the parent table to cases where there are no more than a single instance of child under parent commit 10693122452c9faa1364bf95c4c57caa6d4e2c75 Author: kent Date: Tue Nov 29 03:54:41 2005 +0000 Starting to make interesting tab-separated files. Attributes and elements that have a 1-1 relationship to parent are handled nicely. Other elements are strangely represented - as concatinations of primary ID in parent table rather than as an associateion table. commit ce069e25cc618a1073285712d1c26c4d8c40c629 Author: donnak Date: Tue Nov 29 03:49:40 2005 +0000 Added change from Fan for knownGeneLists link. commit a0491cd718d9fe58dfca592c28f5d23b2712b730 Author: fanhsu Date: Tue Nov 29 03:44:31 2005 +0000 Added knownGeneList. commit c01ddc431f5b10492700bfbe5ca3a9caf1cc0253 Author: heather Date: Tue Nov 29 03:22:37 2005 +0000 "New version number v122" commit 5c16c36272d5c885d4680af8a9a5fa814c8cdcdb Author: fanhsu Date: Tue Nov 29 03:09:03 2005 +0000 Created empty knownGeneLink table to make some old code happy. commit a10c63d656a9532da97b5d35e1ca1417de0e448b Author: heather Date: Tue Nov 29 02:58:53 2005 +0000 add lookupRefAllele() and support functions commit c28a4c0314c63ac2a2f6e6d254be151b229a1d4b Author: hiram Date: Tue Nov 29 01:09:48 2005 +0000 Showing the numbers for lineage specific repeat measurements vs. blastz dynamic masking commit 90e6857e92b0e6179adf470bb3dfa1b97c9b6329 Author: kate Date: Tue Nov 29 01:08:23 2005 +0000 Remove duplicated items for bedNFloatScore commit c18398a4bbca9c34a39beac4874267a2777ab432 Author: donnak Date: Tue Nov 29 00:58:32 2005 +0000 Added some sample queries to the gateway page. commit 79285df9929e3f841a8a9ccedb5e6d3749df1783 Author: angie Date: Tue Nov 29 00:58:31 2005 +0000 Made canFam2 the default db for dog. commit 694252c663a6a4f87ce8c83303c476b0e21bbe46 Author: kent Date: Tue Nov 29 00:55:25 2005 +0000 A little more progress. It should handle attributes well now. The child table handling still needs doing. commit 6c1261f096faa66acc227215b0fb3746ce535ab5 Author: angie Date: Tue Nov 29 00:49:57 2005 +0000 Added Genbank, dm2 chains/nets. commit 9cb4a7b0aacd95aceed5b91914dc14eb432a14ce Author: angie Date: Tue Nov 29 00:36:59 2005 +0000 Added bacEndPairs track using Rachel's CHORI/NCBI sequences and process from canFam1. commit 85fc9cd64cadb47bb8408278016a25eda23907e0 Author: angie Date: Tue Nov 29 00:34:39 2005 +0000 D. persimilis from Broad -- basic tracks except for Genbank, dm2 chains/nets, and dm2 proteins. commit 4de6075b6554dba1763bc1b5b1d5dc9c491fc751 Author: hartera Date: Tue Nov 29 00:31:36 2005 +0000 Rewrote part of the methods section. commit 128da18d38e657c9a731bd98cb040d3d8261dbfa Author: angie Date: Tue Nov 29 00:16:12 2005 +0000 Elementary description.html for droPer1. commit 174dd06ac0931e9dfe5f0dce59cf297cca607a3c Author: angie Date: Tue Nov 29 00:16:11 2005 +0000 Added droPer1. commit 2378df4e50e2429e510c834d14655316aaf8084b Author: kent Date: Tue Nov 29 00:06:19 2005 +0000 Starting to stream through XML file. Still a long way to go before it really works.! commit f256e8dd08fa1bead0af2aa33c208d0948f4e69c Author: kate Date: Mon Nov 28 23:46:22 2005 +0000 Fix coords in Yale RNA tracks. Add Regulome commit c73d473eb44f5c5f1aece32f7939b44912e782b0 Author: kate Date: Mon Nov 28 23:45:47 2005 +0000 Add URL to Yale TARs commit 6732fede2a65fc0800ecb5ccf543891f91130798 Author: aamp Date: Mon Nov 28 22:33:58 2005 +0000 Added "ignore" tables to $mm for RIKEN CAGE tracks. commit cfa061fbaf512594563537a8143f66ccf354d36a Author: kent Date: Mon Nov 28 22:17:49 2005 +0000 Starting to build up data structures for following parent/child table relationships. commit 1208e8307f9dd50f301d66df5c332cf0c3036ce0 Author: kent Date: Mon Nov 28 22:03:22 2005 +0000 Adding dtd info into fields and tables. commit 12f9d7d97bb24b4cda2df109a644fa69ba2e0b66 Author: kent Date: Mon Nov 28 21:46:57 2005 +0000 Searching for and if necessary adding primary keys commit 03ea4c39ad15a43db8848e0cc9e78cd625fae530 Author: kent Date: Mon Nov 28 21:05:09 2005 +0000 Moved the stats file parser to a separate module. commit e2dc17ab289ae2a502a4a9e704498575d9bf3910 Author: kate Date: Mon Nov 28 20:35:34 2005 +0000 Add CVS keyword to identify version commit 7a42fc06073d5336bc32f1f54c50cd3ff57cd70b Author: kent Date: Mon Nov 28 20:34:06 2005 +0000 Parsing stats and dtd. Setting up test case. commit abe41c0b20c00e002030ebb54695a92130c06243 Author: kate Date: Mon Nov 28 19:54:00 2005 +0000 Add include file processing to hgFindSpec commit 2f6e3eccb9e541fd70b47a71f6a50d455036c66a Author: kate Date: Mon Nov 28 19:15:53 2005 +0000 Fix coordinate instructions commit ab4fa129d31203129af65f7352fae39a3c04bb78 Author: kent Date: Mon Nov 28 17:54:49 2005 +0000 Adding statistics output. commit 464eaa3959b4097627d9a2b5a272a88a41bdbfa0 Author: kent Date: Mon Nov 28 16:43:02 2005 +0000 Changing name of xapParse to xapParseFile. commit ebd499308e68ef90d79fd81487f8ac34dd3aa637 Author: kent Date: Mon Nov 28 16:41:33 2005 +0000 Adding dtdParse. commit 42e9a25362a0f6b2c0f5a37307925e759d03a05b Author: galt Date: Mon Nov 28 16:00:02 2005 +0000 "Encode release log update" commit 85cb2d214ee2acb2c71cb9bad16f691c39b5aad5 Author: galt Date: Mon Nov 28 16:00:01 2005 +0000 "Release log update" commit 5ab4eacccff75426984e27c9f0e0e7d34618d5ff Author: kent Date: Mon Nov 28 07:31:37 2005 +0000 Fixed a few typos commit 6d8f9205cf1b00bea3d573734a1a486dfc7246b0 Author: kent Date: Mon Nov 28 07:31:26 2005 +0000 Adding another test case commit 0d5708f902cbd6300e20e67b2110038a2949cb6d Author: donnak Date: Mon Nov 28 07:25:43 2005 +0000 Added more info to VisiGene section. commit 30e1c8a254ccac439e88a485440b02cf754f45ed Author: donnak Date: Mon Nov 28 07:06:45 2005 +0000 Added GENSAT images, updated zoom in/out keyboard shortcuts, added explanation of download link. commit 7ba2b1156a8ba2806226b0a1dbdd404cb0a74ccc Author: kent Date: Mon Nov 28 07:02:48 2005 +0000 Dinking with printing of key fields. commit 6a09b10d0015a4bb0ad73b753c3f4a5733edca05 Author: kent Date: Mon Nov 28 06:51:40 2005 +0000 Handling string keys. commit 8d964d92db7266e7ca29b4e38a8248e0ace5a47b Author: donnak Date: Mon Nov 28 06:37:05 2005 +0000 Added clarification for wildcard searches. commit 64ff55695c1009307aa43b75779bc0115ea2f67e Author: kent Date: Mon Nov 28 05:15:43 2005 +0000 Starting to build test case. commit 527111a6a57969bf201f3c3a3243fc13f6c8bf0f Author: kent Date: Mon Nov 28 05:15:30 2005 +0000 Describing comments commit 79482f04896df202038504e82e69860af3258df6 Author: kent Date: Mon Nov 28 05:14:43 2005 +0000 Simplifying command line. commit 697581f2f3c8f2a5ec34b087549e1225c3ca1a6c Author: kent Date: Mon Nov 28 05:14:16 2005 +0000 No longer using .as files commit 8a5e35fb2f88a90214db57769bd6bfd7072b8f45 Author: jen Date: Mon Nov 28 04:59:03 2005 +0000 Added dataVersions to several tracks. commit 4156077b288168a7dc2e3e1946e63bf0891b38c1 Author: kent Date: Mon Nov 28 04:42:10 2005 +0000 Simplifying command line. First draft of doc file. commit e088354c14eb18b1685f1fea0fa8b666f2368280 Author: jen Date: Mon Nov 28 04:37:05 2005 +0000 Added dataVersions to several tracks. commit ca7d45a495d2f319775df316de6c99c9c0021606 Author: jen Date: Mon Nov 28 04:31:26 2005 +0000 Added dataVersions to several tracks. commit 431d63903a077e744321e99e25e70fb9532843e9 Author: kent Date: Mon Nov 28 02:43:19 2005 +0000 Moving dtd parsing routines to library. commit 28e49d1a8c640b2ac0435cea46e819d9cab02304 Author: kent Date: Mon Nov 28 02:09:14 2005 +0000 Putting dtd prefix in front of data structures in preparation for moving them to library. commit ffe07503dddc13216da2f832c632a4585a1ec6ec Author: kent Date: Sun Nov 27 17:05:55 2005 +0000 Making escCopy public. commit accea877e3e80df823cad0b156ca76fe813d8c34 Author: kent Date: Sun Nov 27 17:05:22 2005 +0000 Added dyStringBumpBufSize. commit 918158823e644fea1069f7b851b2ef1c897ff23e Author: kent Date: Sun Nov 27 17:04:45 2005 +0000 Added captionId. Alphabetized commit 6c5e3d1b973ad0e974686671b03b2d3a0b99abce Author: kent Date: Sun Nov 27 17:04:08 2005 +0000 Added missing expressionPattern field commit 1ea2beaf9f30ee7d9cc86c9e2c49b23becd118cc Author: galt Date: Sun Nov 27 16:00:03 2005 +0000 "Encode release log update" commit 04e31b80fb8c7511e95bb6f24a3145700c23f105 Author: galt Date: Sun Nov 27 16:00:02 2005 +0000 "Release log update" commit 2fb94357078d7d4ee5c4b0dba09b331280913f10 Author: kent Date: Sun Nov 27 11:47:39 2005 +0000 Seems to work. 15 minutes to dump visiGene into 155 meg xml file. commit 45fba5b80f6e33e29fabc1007a618538fe65f328 Author: kent Date: Sun Nov 27 09:44:46 2005 +0000 First draft. commit 40390812355d38bcea81d75e82d6bbbc05c05923 Author: markd Date: Sun Nov 27 06:22:02 2005 +0000 added test case commit 36b6188633634fbdf322697854fb4eee71707ea2 Author: markd Date: Sun Nov 27 06:21:04 2005 +0000 added comment commit 67ce936a8bf7f57b8c2aabb362764961f27be50b Author: kent Date: Sun Nov 27 04:57:28 2005 +0000 Seems to work. commit ae309def7225508550cab80025d477db8f83a77f Author: galt Date: Sat Nov 26 22:35:41 2005 +0000 added featureBits column to pushq commit d12b7aa51b7966ed809ef1c8739c23dd91a7e02a Author: kent Date: Sat Nov 26 22:07:21 2005 +0000 Adding pubUrl. commit 37b46385d86275919ee6b8207de2e4fb7f5dcf90 Author: kent Date: Sat Nov 26 22:01:35 2005 +0000 Patching missing captions. commit f3868aee3a262b1173048a56b1a2052b71a366f3 Author: lowe Date: Sat Nov 26 21:48:59 2005 +0000 New version of automatically generated description file commit 6b5d578b6ead525306f66020e87a3bcd10daf3bd Author: galt Date: Sat Nov 26 21:39:53 2005 +0000 moved featureBits column to end of record for easier data conversion commit 8834b38cb58fa110840d76d0095dd04829eebdf6 Author: galt Date: Sat Nov 26 21:30:43 2005 +0000 added featureBits column to pushq commit 9bd6e708f418804db543c442d77be80bdc87ebd8 Author: kent Date: Sat Nov 26 21:23:11 2005 +0000 Fixing missing captionId. Upper casing GENSAT. commit 188a873e3f030d444c933f29abaad30235882a1f Author: kent Date: Sat Nov 26 21:11:31 2005 +0000 Changing double to single quote to avoid error in searches for names with apostrophes. commit f6e33bcb2ab3648bfdf2815f4a62a9ae5a4c0f9b Author: braney Date: Sat Nov 26 18:57:54 2005 +0000 add some gap annotated alignments commit 5752ff76d92b710cf1e39e6595cebf901439d63c Author: lowe Date: Sat Nov 26 18:51:20 2005 +0000 New version of automatically generated description file commit 1d824b3b482b5a27fb6c46dc0d696e7e0b9f923f Author: markd Date: Sat Nov 26 18:32:21 2005 +0000 used stringify instead of naive awk commit cbe6e7c46c98b9f2698b130de91291a6ad43a0f0 Author: kent Date: Sat Nov 26 18:21:29 2005 +0000 Adding hDbForTaxon commit 39ba60e706893b09c4106c258b2a78fed25cec81 Author: kent Date: Sat Nov 26 18:21:08 2005 +0000 Adding hyperlink to genome browser on bac name commit 0dc7406b273f2c9a9c9e0ce3a4ddbab368c86209 Author: markd Date: Sat Nov 26 17:51:27 2005 +0000 renamed generated message file to avoid cvsup confusion commit 48796930e2a6012077d8a0c71ed8cd60022f504c Author: kent Date: Sat Nov 26 17:50:22 2005 +0000 fixed typo commit 848e101bc2aa0a629689a35ce37fbeecca7bfd44 Author: kent Date: Sat Nov 26 17:30:23 2005 +0000 Adding caption text to doc. commit 4e81a1663013b9177282f23e56109c18e2b5d9c6 Author: kent Date: Sat Nov 26 17:30:07 2005 +0000 Removing expression levels associated with submission too. commit 36bf4dbd8040855416513856cb8f2aa4ddb424e0 Author: kent Date: Sat Nov 26 17:27:30 2005 +0000 Adding in caption/comment. Improving bodyPart and probeColor. commit 8e7257817d1a6b85c7508a038466cfed33d04d80 Author: kent Date: Sat Nov 26 17:26:24 2005 +0000 Removing .full from file names for benefit of image magick convert in tile mode commit 97cf64c86f3797aad799694992f018c65b820982 Author: kent Date: Sat Nov 26 17:25:21 2005 +0000 Freen snoops around for lifOverChain finding hgCentralBack problem. commit 344ca3f755f5562e664a61f628b7d9891689752b Author: kent Date: Sat Nov 26 17:21:50 2005 +0000 Changed fixer to do missing symbolic links. commit d702572fe8a776ff409d7649eaac4e53e379b2c6 Author: kent Date: Sat Nov 26 17:05:49 2005 +0000 A little rough, but it's a one shot thing. Seems to have worked. commit c981f1dae74bfd1d069dad1fdabd3e6c9325a830 Author: kent Date: Sat Nov 26 17:03:50 2005 +0000 Added hyperlink to genbank. commit 2399a952b515eaa4664ba107ea5138088f8024e9 Author: markd Date: Sat Nov 26 16:41:23 2005 +0000 removed 128 character restriction on hg.conf lines commit 3e6ec7bd42d0e944c9bf27b7cd38ebf15b834fdb Author: galt Date: Sat Nov 26 16:00:03 2005 +0000 "Encode release log update" commit 8c513f20b2c2500c8856bde9e2b09ce4417b180d Author: galt Date: Sat Nov 26 16:00:02 2005 +0000 "Release log update" commit 7cc33ad78698088e3053bd062912c1bf62aaebce Author: braney Date: Sat Nov 26 15:47:46 2005 +0000 add an annotated conservation track commit 460cf21f126495ba4f5548590cc7e3dd81efd014 Author: lowe Date: Sat Nov 26 14:57:53 2005 +0000 New version of automatically generated description file commit be17649bfa8add9dc58a0cd7e733337308f1cda7 Author: kent Date: Sat Nov 26 04:52:19 2005 +0000 Adding expressionPattern commit 4b35a15c54b6b91b4444189dc2a8633a9d88fb5c Author: kent Date: Sat Nov 26 04:51:22 2005 +0000 Adding expressionPattern and fixing bug in cellSubtype commit 09a9faac14238e9a576d792303795a95d65e3e2a Author: kent Date: Fri Nov 25 16:37:39 2005 +0000 Adding visiGene.bac table. commit 171479c6582d9c92c0733ae35eb478fd4edec8da Author: kent Date: Fri Nov 25 16:35:31 2005 +0000 Got rid of unused var that was breaking build. commit 518d1569440e47044deaf47148c3bea4c81eaa1d Author: kent Date: Fri Nov 25 16:34:23 2005 +0000 Seems to work commit 9ae9a1ca4bf58727bd481f14aaf954e0c5beaa7c Author: galt Date: Fri Nov 25 16:00:03 2005 +0000 "Encode release log update" commit 7149154eafca92c9873a8e49f180e152fa36eb69 Author: galt Date: Fri Nov 25 16:00:01 2005 +0000 "Release log update" commit 0018108665993917098bd5adf9cc2715af0e2c57 Author: heather Date: Fri Nov 25 11:52:24 2005 +0000 enable second database commit d8bb70df0d5815399d3c3d26ce58af272f49f4d4 Author: heather Date: Fri Nov 25 10:45:22 2005 +0000 add bin (set chromEnd to chromStart for insertions) commit 71bdeadd17c9b019ee7e9291b3488e158faf9fe9 Author: kent Date: Fri Nov 25 06:47:16 2005 +0000 Corrected estimated time commit 2f1447c25f4a0a832bc61846104a1985af4a7ff1 Author: kent Date: Fri Nov 25 06:44:32 2005 +0000 Adding bac table and bac field in probe. commit 9543eeae5cd00f8aa026d2d92dba374a3023b5de Author: kent Date: Fri Nov 25 06:42:26 2005 +0000 A few more small changes to get visiGeneLoad to swallow it. commit c7db7b6b3142531c12c1e35dc3e31339ac8a0076 Author: kent Date: Fri Nov 25 06:41:11 2005 +0000 Adding bac type probes. commit 326372ab086174d58b5823b0bc60e0ac43fc1b63 Author: kent Date: Fri Nov 25 06:40:39 2005 +0000 Some new test sets commit 10ac533783e46bc99a6e8c27fce96328d8377cc7 Author: kent Date: Fri Nov 25 05:44:50 2005 +0000 Adding in .ra file output. Cleaning up a few things in tab file. commit dee2cd8c0ee965fe4f3cdd27885c1df88717c2e3 Author: markd Date: Thu Nov 24 20:37:50 2005 +0000 added more options to control merging of gaps when creating genePreds from psls commit ca5196c15445edb8a4d352dff88e15e5cee7fde8 Author: markd Date: Thu Nov 24 20:36:43 2005 +0000 added more options to control merging of gaps commit e921da5a78ba6373da9c598a7f4e850447bc8c46 Author: markd Date: Thu Nov 24 20:27:57 2005 +0000 added more options to control merging of gaps commit 8a95ecca8df06f1b49ccc8b24cc5fe9d779ac393 Author: kent Date: Thu Nov 24 17:14:46 2005 +0000 Adding cellType and cellSubtype. Caching simple tables. commit 675f140148a9b53f71b6abba0f6f79278520eb66 Author: kent Date: Thu Nov 24 17:14:06 2005 +0000 Suppressing non-dna in primer fields commit 5dda8980e5857c4d4ce1ca621deda18a03098b36 Author: braney Date: Thu Nov 24 17:13:55 2005 +0000 srcSize needs to have the correct value in it for empty rows commit 2315947514dee00b65dc91ac2349327a72a56947 Author: kent Date: Thu Nov 24 17:13:46 2005 +0000 Fixing some shifted fields in cloning.tab commit 5f0e9f285e60ad637fa7844e15dd288f4d3e16f5 Author: kent Date: Thu Nov 24 17:13:16 2005 +0000 Fixing some broken copyright statements. commit f1daab251d6b2ab7f6e129e2f37ea4bf74c4bb95 Author: kent Date: Thu Nov 24 17:12:53 2005 +0000 Adding cellType and cellSubtype tables commit 9601da4691b39cbf2b3d81bdcf1c1e151b5c516b Author: kent Date: Thu Nov 24 17:09:48 2005 +0000 Documenting the gensat work so far. commit 9dda53b1333794bbdeee483498375865f2aa277a Author: galt Date: Thu Nov 24 16:00:04 2005 +0000 "Encode release log update" commit 4a65bcffa85b51943b923239f62878e09795f1ab Author: galt Date: Thu Nov 24 16:00:03 2005 +0000 "Release log update" commit 848ec5afdeaa39f035bc5d4a535c67efaaff73ca Author: kent Date: Thu Nov 24 03:34:50 2005 +0000 Adding noLink option commit e8d9d07eae820062539088c188a537b2a9984731 Author: kent Date: Thu Nov 24 03:19:09 2005 +0000 Fixing crash on probe page for antibodies with no animal source specified. commit 16686c4a775b67c3037660419ea29875ea7981bf Author: kent Date: Thu Nov 24 03:18:35 2005 +0000 Adding a little space after help link commit 0c220a1fe18c8899e95be8ab26ffd9bc2f62e4f6 Author: hartera Date: Thu Nov 24 01:28:44 2005 +0000 Removed Ensembl gene track searches as moved to a higher level trackDb.ra. commit c875e81b270ceed8730f7cc6821ca7c65c268938 Author: hartera Date: Thu Nov 24 01:26:54 2005 +0000 Added Ensembl genes track searches. commit 963b16c0a50672fc1c4f4251b0571a5652f92c95 Author: braney Date: Thu Nov 24 00:58:07 2005 +0000 restructure to include missing data commit 9ce904a6d5ea6466f2a936c616a55ef2f72647e2 Author: heather Date: Thu Nov 24 00:48:55 2005 +0000 add lookupHet() commit 9bd2dd3aa80637e25cbd93cbbf69ee92aab962c0 Author: hartera Date: Wed Nov 23 23:54:02 2005 +0000 Added a rule to the refSeqIod identifier specifically for mm7 mranOrientInfo. commit 3d324fbef3236c01d79200ba75d95b2061e99c7a Author: kate Date: Wed Nov 23 23:38:56 2005 +0000 Extra whitespace for readability commit 771fb32ccc93f8a2fdaac4a97996b989775559b4 Author: kate Date: Wed Nov 23 23:31:24 2005 +0000 Add new CGI commit 36b4dfb12282d304621d2b391168b4ae456ca4f1 Author: kate Date: Wed Nov 23 23:30:40 2005 +0000 CGI to display track version info commit 39f273cfa1bbfd80b628a8ef5b3108983d1cf43f Author: kent Date: Wed Nov 23 23:25:54 2005 +0000 Avoiding using a synonym when have another gene of same name commit dba8a83a7a64f8626a016f6a76cb93038077c7dc Author: kate Date: Wed Nov 23 23:25:41 2005 +0000 Add hook for new ENCODE page commit 494f82dd042db8716ce9a9f16423385df396f580 Author: kate Date: Wed Nov 23 23:25:17 2005 +0000 Add Track Versions CGI commit 3f40dd1c486f83de415b1113e5816a8fd711213d Author: angie Date: Wed Nov 23 22:42:10 2005 +0000 Added droYak2. commit 47bf2871fa7d330d7f0fc49516e30f7b1390f0dd Author: angie Date: Wed Nov 23 22:06:01 2005 +0000 uglyf --> verbose so that output doesn't become invalid .chain . commit 7f253c6462414f7bc219f95d5940238c875331df Author: fanhsu Date: Wed Nov 23 21:31:47 2005 +0000 Added a command line to build the tableDescriptions table. commit f3daff245ddabf0f03a01f4450b6dd14f25f0dd5 Author: galt Date: Wed Nov 23 20:17:57 2005 +0000 removed old code for radio-buttons and zoomMode and multiple cursors commit 2847bda96b113198db5daf60e7604cedbc522f4c Author: kent Date: Wed Nov 23 18:18:14 2005 +0000 Seems to work commit 8870a55811f758f0ce4d4ecfe101b300ea367688 Author: braney Date: Wed Nov 23 17:21:38 2005 +0000 add new row type 'e' for empty row. Also, don't strip trailing '-'s from alignment commit 7e85897dcb71c384d07dc84cb2bd09343448a9c1 Author: braney Date: Wed Nov 23 17:20:50 2005 +0000 don't count empty rows in score commit bbc52a789d7ecac6dd24ce7eabc405fdf138fd6d Author: kent Date: Wed Nov 23 17:14:18 2005 +0000 Putting control bar in table commit 5b17310b331b25df7f22083135c478379f65123d Author: galt Date: Wed Nov 23 16:00:05 2005 +0000 "Encode release log update" commit 18ca13a745521d3ac5b0a8b1a0531538bc4c747b Author: galt Date: Wed Nov 23 16:00:04 2005 +0000 "Release log update" commit a36d3d3dd0876b8516657cd370280a9a9bef33da Author: aamp Date: Wed Nov 23 10:30:47 2005 +0000 Hopefully a bugfix to the reverse-strand coloring problem of enzymes at base-level zoom. commit 4d48bdef764c30e0753d7406c3de2a8a0c66c357 Author: donnak Date: Wed Nov 23 07:52:32 2005 +0000 Added a few words abt wildcards to the text under the search box. commit 3d67356b1a563a9b2ca7ea464f3a4d1255d4a486 Author: donnak Date: Wed Nov 23 07:44:08 2005 +0000 Swapped around a few links in left sidebar. commit 09dc68f373d97bfa2b3ab45f11a7e606c8de82e9 Author: donnak Date: Wed Nov 23 07:31:57 2005 +0000 Changed wording of author line, per Jim. commit b971f16f496f2945645ac24870be10694653810d Author: kuhn Date: Wed Nov 23 04:09:24 2005 +0000 dropped mention of mm5 and liftOver since andy added it to trackDb commit 4b26a23e62e29c3885bee1d3d27d076c2d95b59b Author: kent Date: Wed Nov 23 04:07:51 2005 +0000 Fixing single char search crash. commit ff8ab55443e2bda5dc159cfbd4ab8492ab04ef51 Author: kuhn Date: Wed Nov 23 04:04:27 2005 +0000 dropped periods around PNAS, per donna commit e4043114e1a67554157c96dec279fcfbc7b47eb7 Author: kent Date: Wed Nov 23 03:21:18 2005 +0000 Adding tableDescriptions commit 13cddd9295dce0f39a92571aa9bf754360ab03ae Author: kuhn Date: Wed Nov 23 02:08:22 2005 +0000 reversed an error in previous commit and updated methods and credits to match rikenCageTc.html commit 974d16523bf4bc117dd15e43116de115333d25ce Author: kent Date: Wed Nov 23 01:28:42 2005 +0000 Adding visiGene commit 37ff519a5c0fcb99eb0a5d6096bd01eb885d739a Author: kate Date: Wed Nov 23 01:24:39 2005 +0000 Remove zoo dbs default commit 8995287d580f5b958d07bc06e52926a2d8491bab Author: aamp Date: Wed Nov 23 00:38:05 2005 +0000 Added the origAssembly for the rikenCageTc track too. commit a9c20a7aaaa522ade980379f73c225d92f4c3629 Author: heather Date: Wed Nov 23 00:19:15 2005 +0000 add lookupFunction() commit 79a6373e43763b842cb9063513536fd7d21e4294 Author: fanhsu Date: Wed Nov 23 00:16:19 2005 +0000 Added link to GB with knownGene=pack. commit b4aece41e45af7000ce9bcd569092e5173dac02d Author: kent Date: Tue Nov 22 23:45:29 2005 +0000 Seems to work. commit a55509a6e75241760129c763038f1e9662a8d658 Author: angie Date: Tue Nov 22 23:40:07 2005 +0000 Added local bacEndPairs.html with info about CHORI and the NCBI Trace Archive. commit bc02197cc2074f54adf030a5afb5175703bf5681 Author: kuhn Date: Tue Nov 22 23:37:40 2005 +0000 changed methods, etc, to match other riken track commit 50bf7cfaa4dd0c8bf8551c9d211e49e1afa906ae Author: genbank Date: Tue Nov 22 23:36:30 2005 +0000 added mouse transmap genes commit f7e4613fa9defdaecf02d9b890cb4913f26bfb58 Author: kuhn Date: Tue Nov 22 23:36:25 2005 +0000 changed reference slightly commit 58badc4739e65285ca3a86fcf57de97169deef6d Author: fanhsu Date: Tue Nov 22 23:11:53 2005 +0000 Added a flag, IAmPbTracks. commit 24250308f2186139c780e5503ba53b87a935f1dc Author: fanhsu Date: Tue Nov 22 23:08:22 2005 +0000 Updated doTracks() to perform a logic only if it is called by pbTracks. commit 88876612bf8d1f45db073f9a2321534de1c5833d Author: fanhsu Date: Tue Nov 22 23:02:50 2005 +0000 Added a flag, IAmPbTracks. commit d24d8982764a7e90997d514ee3cfdb38aeb20f42 Author: fanhsu Date: Tue Nov 22 22:53:34 2005 +0000 do it again. commit e3931abc4ab9e6616da0517c5250a7e493792875 Author: fanhsu Date: Tue Nov 22 22:53:01 2005 +0000 updated rcsid. commit 1dfa48344a9949caf0e1010f71f393be66c8e83e Author: fanhsu Date: Tue Nov 22 22:50:45 2005 +0000 Testing added a blank line. commit 7faa342a784433cf503ae93c6519cd8edde3d8d3 Author: aamp Date: Tue Nov 22 22:50:16 2005 +0000 Moved RIKEN tracks to RNA group. commit 77b4f469ac8e48c6199ce649b4b1701874e4ad6a Author: fanhsu Date: Tue Nov 22 22:49:24 2005 +0000 Added rcsid. commit b0183e0936fc4dd2f1814f7479029e36aa2b32fb Author: kuhn Date: Tue Nov 22 22:42:46 2005 +0000 droped a redundant sentence commit a3339b4f6961a0bf7d3a3941cf21afdccee273b1 Author: kuhn Date: Tue Nov 22 22:40:58 2005 +0000 expanded some text based on the reference and tidied up the Methods description a bit commit 8067f20f55a731917632c5b6d622bccad4d3d0dd Author: kate Date: Tue Nov 22 22:26:58 2005 +0000 Change AFFY RNA labels, as per Phil Kapranov commit 2c3c788f8d43deceff184c7b7d04ce527775271b Author: kate Date: Tue Nov 22 21:59:59 2005 +0000 Yet more Regulome tweaks commit 402bb2110a48437b666482e509e91e254c89c24c Author: fanhsu Date: Tue Nov 22 21:43:42 2005 +0000 Updated to reflect the fact that protein-mRNA alignment was done using tblastn now instead of BLAT. commit 7d2fd2e3a5676e81c9af09e5654d9d05fbdffedd Author: kate Date: Tue Nov 22 21:42:51 2005 +0000 More fixes to ENCODE Regulome -- restore wiggle Base track till new data is reviewed commit a0adf8d18883ac759728cdc8cc95539f88625983 Author: fanhsu Date: Tue Nov 22 21:39:21 2005 +0000 Created knownGene.html for mm7 (a copy of mm6 knownGene.html). commit c176f73ed77a8c0f5d506c5bd96f288d73db445f Author: galt Date: Tue Nov 22 21:01:20 2005 +0000 added check for invalid imageId, if not found gives warning instead of err500 commit dada491f47f3d39c70bd70a9b7fbe56f30b25a4e Author: galt Date: Tue Nov 22 20:13:33 2005 +0000 changed to using offsetWidth,offsetHeight instead because it includes the width of the border around the img box commit 595df1c91354ee2b5603235eff7d189b9129ff56 Author: galt Date: Tue Nov 22 20:12:05 2005 +0000 added style to box border to control color and width of border around img commit eabc3202605c8fdad9062f3becb9322a8c4d8973 Author: kate Date: Tue Nov 22 20:11:12 2005 +0000 Interim Regulome track config commit 910231931e8905f64c7d2dc36ecf28d64186ccdd Author: giardine Date: Tue Nov 22 20:08:28 2005 +0000 *** empty log message *** commit a30d55c2acd9e9620c897d15a09352f9dc81f27c Author: giardine Date: Tue Nov 22 20:08:17 2005 +0000 Added OMIM ID as a label option for refGene and Known Genes. Known Genes is commented out, until I am sure it is wanted. commit 58d08add8498c92a4abb8e0b2eb1a70316f83069 Author: donnak Date: Tue Nov 22 19:43:30 2005 +0000 Updated MySql website link. Updated info about Convert link on GB track page (releasing this a bit prematurely...software will be on public site next week). commit 2c308745309bcf458d6823fc1d75d54a232b65e2 Author: kate Date: Tue Nov 22 19:36:25 2005 +0000 Tweak built-in track label commit fc3869086bae3bc7cbda39461e396f1aed2ef1a1 Author: markd Date: Tue Nov 22 19:26:34 2005 +0000 speedup by avoiding opening genome files for each exon commit 880066d3b9a4e8ed3fa655c4fced1458600e9c65 Author: genbank Date: Tue Nov 22 19:14:17 2005 +0000 checked track to genePred format commit ccd57c5fe9a4edc5a411307330a72b51fb474982 Author: hartera Date: Tue Nov 22 19:03:15 2005 +0000 Added encodeUncFaire* tables to list of tables to be ignored for human. commit f0a5ee1ae33ca84dfe98bb2244e37a44c52c865c Author: jen Date: Tue Nov 22 18:38:03 2005 +0000 Fixed maxHeight for Sanger ChIP with Kate. commit 1cb2a54eced9e14f11134d10bfd3ed7a30bdfb20 Author: jen Date: Tue Nov 22 18:24:23 2005 +0000 Changes for ENCODE Sanger ChIP/Hits release. commit 423c25840b729ddcd19f48939aab10ed1c76cd2f Author: ann Date: Tue Nov 22 17:59:17 2005 +0000 changed tense of "build" commit 894be08f287a4991aec711201dfcb2bfb9fc98df Author: kent Date: Tue Nov 22 17:47:41 2005 +0000 Coping with parenthesis in file names. commit 34a26c95a1f9d2207ad48bb57df32910b6978d7e Author: kent Date: Tue Nov 22 17:47:13 2005 +0000 Updating change doc. commit b5f32e77ae514a43e0591f07ad90988800be35ea Author: hiram Date: Tue Nov 22 16:51:31 2005 +0000 Measuring TARs and TransFrags commit 1b18543a02abd2a9b99044d8475f046c4ae5fc24 Author: galt Date: Tue Nov 22 16:00:03 2005 +0000 "Encode release log update" commit dfeec6c78c3eafd886c707017463e633ecdea586 Author: galt Date: Tue Nov 22 16:00:02 2005 +0000 "Release log update" commit 36de2528e601ff55ecd36b033ba169b11cbaef91 Author: kate Date: Tue Nov 22 07:08:48 2005 +0000 Replace position adjustment with fix in hgTracks Convert link commit b8f89f0ce0202512f806077ef7dd340055099577 Author: kate Date: Tue Nov 22 07:08:19 2005 +0000 Fix Convert link commit 779900451badd9208c2b653ec2b9e10b26c1dec9 Author: hiram Date: Tue Nov 22 05:32:16 2005 +0000 Two different self blastz runs commit 34efeb55b13c239eb17f9c7c5d88b0196c60f050 Author: angie Date: Tue Nov 22 01:18:57 2005 +0000 Added some download files that Jen identified as missing. commit 75de0b407739834e83bf8c357fe9bad50fefdb80 Author: angie Date: Tue Nov 22 01:17:17 2005 +0000 Most basic tracks -- still needs Genbank tracks and alignments to dm2. commit 1a6c52be7544d294eb9f14a33a153efa6f685b19 Author: galt Date: Tue Nov 22 01:09:28 2005 +0000 added download link for fullsize image commit c3e3f2e2e28a699f0c27e9ee2169ad179ce0d013 Author: kate Date: Tue Nov 22 01:00:21 2005 +0000 Positional vs. half-open start coordinate conversions needed commit 55f24fc5ada815a8867ff8c27e5a048d2f017f28 Author: galt Date: Tue Nov 22 00:44:12 2005 +0000 added thumbnail follower; reduced margin in thumbnail commit 73fa2c7537814f60e1fe9a254c971ba750e24811 Author: galt Date: Tue Nov 22 00:43:51 2005 +0000 support for alternate bigImg html for testing commit 38dee97a5f5a5d5e4c20be6aea5066d3f146447f Author: galt Date: Tue Nov 22 00:40:39 2005 +0000 added thumbnail follower commit 74b9db1c4af192796f28da1fdee4e40ef3172dcf Author: heather Date: Tue Nov 22 00:31:14 2005 +0000 tweaks to writeSnpTable; now loads without errors or warnings commit ad730d154b2dd47937b5e1852c41db943b98e84b Author: kent Date: Tue Nov 22 00:25:10 2005 +0000 Changed title to Probe Information commit c96a1c5f91542d7695eca9b9b0a7626e31f0890e Author: kent Date: Tue Nov 22 00:16:27 2005 +0000 Making link from gene name to known gene where possible commit 25b2083607697f5d141e49aefc79970b29f0dc60 Author: kent Date: Mon Nov 21 23:09:26 2005 +0000 Rearranging frames so that control bar is full screen. Moving home hyperlink to UCSC. commit bc19e9b0c70374fc3684a7656f3ef0a59e488319 Author: kent Date: Mon Nov 21 23:06:49 2005 +0000 Adding probe to caption. Probe/gene details still needs rework. commit 778779226ceafac0c8503a9b24d5f5af433a69db Author: hiram Date: Mon Nov 21 22:57:46 2005 +0000 Adding Mm7 chain and net commit 7ecfca4844801d12adeac2e80028af33c4474de8 Author: hiram Date: Mon Nov 21 21:11:06 2005 +0000 Done with galGal2, xenTro1, tetNig1, danRer3, fr1 commit 1cad358a279dd9e83ca57796a08811ae91091fb2 Author: kate Date: Mon Nov 21 20:45:21 2005 +0000 Extract ENCODE tracks into include files commit 18b2259f50f336a06c3a18d3d613195d408c0de6 Author: hiram Date: Mon Nov 21 20:11:26 2005 +0000 Hg17 chain and nets done commit 7137764220a30ce3010933c25c90ed9c6af7213d Author: hiram Date: Mon Nov 21 19:56:08 2005 +0000 Place the linear gap option information into the README.txt downloads file commit e2de4c7eb3fb877b989650b629d1cc1d2d1a3428 Author: kent Date: Mon Nov 21 19:45:48 2005 +0000 Seems to work. commit ddf19dac36fe64d1efe1d696cecd9bc6a3ed568d Author: hiram Date: Mon Nov 21 18:47:55 2005 +0000 Add linear gap information to usage message commit 4585e50e04ecd7d72ecb0b16b5fc66338ff81364 Author: hiram Date: Mon Nov 21 17:59:37 2005 +0000 Bringing up to date with more blastz runs ... It is endless ... commit 41a290626e424e14bbbf22bc6f7ea1d488d18170 Author: kent Date: Mon Nov 21 17:38:46 2005 +0000 Updating for new gensat.dtd commit 995909fc4a70bfa9cc5d915153136dde785d7e71 Author: kent Date: Mon Nov 21 17:38:27 2005 +0000 Updating gs.c/gs.h via autoXml from new gensat.dtd. Moving to lib directory so can share it. commit 03b43047c67eda458ead7eb53963f729db3a580e Author: fanhsu Date: Mon Nov 21 17:14:06 2005 +0000 Added KG track. commit 5c6e5b53639a2e782f345e2998edae80464946ba Author: kent Date: Mon Nov 21 16:57:51 2005 +0000 corrected visiGene commit 86a851efe5835d58893b4ed0f91e237112fa83c1 Author: galt Date: Mon Nov 21 16:00:02 2005 +0000 "Encode release log update" commit 9391868a347fefa7a0e8b0b49b8f4e91467d6867 Author: galt Date: Mon Nov 21 16:00:01 2005 +0000 "Release log update" commit 722f42e268286a22fd1fa158a668a228df69c109 Author: aamp Date: Mon Nov 21 11:05:39 2005 +0000 Added instructions for RIKEN CAGE tracks. commit ef0e0b22353aa4167b13355a435d86fef5da7981 Author: aamp Date: Mon Nov 21 09:22:11 2005 +0000 Needed to add two columns to reflect current table in hgcentraltest (and hgcentral?). This affected the hgAddLiftOverChain utility. commit 486a01cb376c20853dc42be45900de6dc301c2c3 Author: aamp Date: Mon Nov 21 09:21:26 2005 +0000 Needed to add two columns to reflect current table in hgcentraltest (and hgcentral?) ... NEEDS description. commit 9877b3afaebac30d6b1bdc72a71e2002ba5af1c8 Author: aamp Date: Mon Nov 21 08:59:06 2005 +0000 Build instructions for mm3/mm4/mm5/mm6->mm7 liftOver chains. commit 2496b63414bd965fcd64ad5ba37066f2d7b457b2 Author: kent Date: Mon Nov 21 03:57:35 2005 +0000 Making it deal with dtd tags that span more than one line commit eca20afb4a44c94028a34c55299c1a62fc9b3e69 Author: kent Date: Mon Nov 21 02:26:49 2005 +0000 Very slightly tweaked dtd from NCBI (Michael DiCuccio) commit 7afeab53fceba9c7cbf7a989a7b4b9f1a7413d4f Author: kent Date: Mon Nov 21 01:35:16 2005 +0000 Creating free functions for objects. commit 57a29c1268faba652c788de43476add9b4847b16 Author: fanhsu Date: Mon Nov 21 01:19:14 2005 +0000 Added genomic position and size display. commit 5bd6a9eb36abadfd9462474af93c271afea36022 Author: markd Date: Sun Nov 20 22:40:41 2005 +0000 don't lost -type argument commit a0d37278ca103dafc1a320b0edc5583d331e2d44 Author: kent Date: Sun Nov 20 22:20:48 2005 +0000 Fixed double parenthesis bug. Improving handling of tag labels that are mixed case. commit 916863ed9c8ee98a32201fe9e955dfc8d153ccf4 Author: markd Date: Sun Nov 20 21:24:01 2005 +0000 Fixed bug were pslFromAlign computed the required number of blocks incorrectly. Fixed bugs were the query and target insert counts were reversed. Remove code that added empty block in an attempt to preserve intermixed inserts. Without this, alignments will be different but equvilant. Simplified code. commit 04df5353f7efb0971a6770b7dae9867487c8217c Author: kent Date: Sun Nov 20 19:24:57 2005 +0000 Improving slideIntron. commit 356c57c113b45cbd2f939bea50e3cb28ed27457f Author: kent Date: Sun Nov 20 19:24:42 2005 +0000 Refining some debugging code that is ifdefed out commit e2a0ab35c84ccc50c94988f93511a8542e82af93 Author: kent Date: Sun Nov 20 19:21:20 2005 +0000 Adding a test case Mark found commit 62a860b1382f15f6619af364fda47da58217431a Author: fanhsu Date: Sun Nov 20 16:21:37 2005 +0000 Increased array size to accomodate more proteins in UniProt. commit 9295d99bcfd47c3d83f5fedcca8105f0279c119a Author: galt Date: Sun Nov 20 16:00:04 2005 +0000 "Encode release log update" commit 90ce955dd91e65856347fc7d970cfd889d1eb5ac Author: galt Date: Sun Nov 20 16:00:03 2005 +0000 "Release log update" commit 7479442c61e79ba085f3ef25582ba9d3638d3ab6 Author: braney Date: Sat Nov 19 22:37:33 2005 +0000 add canHg12 commit 1d034024f8b3b5a04e3e67620c55255e9f9e8332 Author: braney Date: Sat Nov 19 22:35:22 2005 +0000 add something for canHg12 commit 553068009939b788c31fdf4c60d05f23000bfc72 Author: kent Date: Sat Nov 19 17:43:44 2005 +0000 Replaced hgLiftOver with hgConvert in convert link on top bar commit b45e252e29a75499634eeea34457b08e30ba5cdf Author: kent Date: Sat Nov 19 17:43:00 2005 +0000 Added hgVisiGene and hgConvert to cgi target commit 16c2a25035966c3f395b5293e31c3a1623f5c008 Author: galt Date: Sat Nov 19 16:00:02 2005 +0000 "Encode release log update" commit 6fa535dbfa92dd2590c1f65703eda352e2b7c68c Author: galt Date: Sat Nov 19 16:00:01 2005 +0000 "Release log update" commit a38cd4cf6c85cc49822e61f81e28ff82baf641ce Author: markd Date: Sat Nov 19 08:45:20 2005 +0000 added ignore entry commit 7440875206a21065d19eb7b6d68349d1b970f5e1 Author: markd Date: Sat Nov 19 04:52:29 2005 +0000 fixed bug with combining -flatBed and -cds commit edb7154897fc21db307b986109b912db2070aa96 Author: kent Date: Sat Nov 19 03:28:51 2005 +0000 Allowing some varient spelling of tiff and jpeg suffixes commit a4697355ee113f639d7473079f079c7f0a541a9f Author: kent Date: Sat Nov 19 03:25:03 2005 +0000 Improving expression output. commit 4cd2a2cafb9906f222e8d47756f1a661024d2925 Author: fanhsu Date: Sat Nov 19 02:41:59 2005 +0000 Enlarge the array size to accomodate growing number of proteins. commit 570c1bd69ada04e4f386aaf77bd8320575d0cd25 Author: kent Date: Sat Nov 19 02:35:26 2005 +0000 Hopefully making expired search results file fail more gracefully commit 742c680c9c7dd16100b8f227a869c21f5b42b7e3 Author: kent Date: Sat Nov 19 02:29:14 2005 +0000 Finding expression data in XML gmish commit 47bb8b12de4db3b474b911a783890fbabb7c5a6c Author: galt Date: Sat Nov 19 02:17:28 2005 +0000 oops dblClick problem fixed commit a2a341308b7419f870d27e07d90078470870124a Author: kent Date: Sat Nov 19 02:09:18 2005 +0000 Adding xapListOpen and xapListNext, which help you scan through xml files a record at a time rather than loading all in memory commit 932d94b46933381eaf5d61a0c70b0d01ca6e36a9 Author: kent Date: Sat Nov 19 02:08:30 2005 +0000 Treating unexpected end tags as EOF for benefit of partial file readers. commit eb549f59d25049900b45fb853f3f45515f719bc6 Author: galt Date: Sat Nov 19 02:02:29 2005 +0000 fix mouse handline outside IFRAME, and limits of the picture commit 80c6e1491defc91301e1f74aedebac834f222946 Author: kent Date: Sat Nov 19 02:02:28 2005 +0000 Filtering out duplicates and some unwanted file types. Saving all extensions to help see which ones want to keep. commit 62aa28f24f0c8302d0df19b0afe38e3a34970f19 Author: kent Date: Sat Nov 19 02:01:25 2005 +0000 Handling spaces in file names better in a few places. commit 2da43626b6ee86db7c40783357931c107d5ac873 Author: fanhsu Date: Sat Nov 19 01:18:41 2005 +0000 Moved the loading of dupSpMrna table so that joinerCheck does not complain. commit 720c3498d3c1d923af6d728bea12ce713e80a0eb Author: kate Date: Sat Nov 19 01:09:23 2005 +0000 Split MSA alignment assessment tracks commit 15c194a0174d587da4805ef859e220044fe041e5 Author: kate Date: Sat Nov 19 00:29:22 2005 +0000 *** empty log message *** commit 2153a1e71a8b62802d01fae01195ae1cdab79832 Author: fanhsu Date: Fri Nov 18 23:06:54 2005 +0000 Removed two lines creating redudant index. commit 0ef69c09741d5991213537c4bb63f833f01b1f93 Author: jen Date: Fri Nov 18 22:52:02 2005 +0000 Altered outside links to spawn new browser windows. commit f001a480b3344c0e2c77fdb46938799440bfe847 Author: kate Date: Fri Nov 18 22:38:41 2005 +0000 Update ENCODE Sanger Chip commit f56e96b2f4140248e9ab7bfaa2bb4e9d4cd6f76f Author: jen Date: Fri Nov 18 21:18:04 2005 +0000 Removed beta release for encodeUCDavisE2F1Median in preparation for release. commit dd244de66b5e051537021c1ad59552b46e17f4be Author: jen Date: Fri Nov 18 21:09:55 2005 +0000 Removed beta release for encodeUCDavisE2F1Median in preparation for release. commit 97673de7f8e4eea680c1fc0b1e5f127f8ac65e18 Author: jen Date: Fri Nov 18 21:05:52 2005 +0000 Adjusted track labels to be consistent with prior releases. commit fc495b8a92f55c5df8f37416ad980bf4e5494b2e Author: markd Date: Fri Nov 18 20:56:07 2005 +0000 change column name to better match out common terminology commit b24e7dc1d7289eee31ef6edae721059286a22c9b Author: kate Date: Fri Nov 18 20:41:20 2005 +0000 Updated ENCODE Regulome tracks commit cfeb79d64be8990c4aa4c0ec7bf3d1ffb43ab240 Author: kate Date: Fri Nov 18 20:26:18 2005 +0000 Back out bad checkin (1.244), and add Jenns changes from 1.246 commit b516360d09d22b00ae65b0881de663a65f26a1d3 Author: donnak Date: Fri Nov 18 20:07:01 2005 +0000 Corrected link name. commit 578e4706104dcec970ccfd7d42e07e43d01192e4 Author: donnak Date: Fri Nov 18 19:12:41 2005 +0000 Slight rewording of Action section. commit 594d740ee84d4bae4bf76be4e9c9d857c3ef279f Author: donnak Date: Fri Nov 18 19:05:25 2005 +0000 Changed capitalization of several long labels to be consistent with our style, fiddled with visigene column. commit 043c7565d4a513a856d1806d7d33ddad4d0e2dfd Author: donnak Date: Fri Nov 18 19:04:42 2005 +0000 Created this file to provide description text for the VisiGene column. commit a27b3e114c8b6f311c8988ef2c6d495f44760c8b Author: donnak Date: Fri Nov 18 19:04:07 2005 +0000 Minor editing. commit 6f3204a11ca7452fc0b4e38eca3e3143f1b0fba7 Author: donnak Date: Fri Nov 18 19:03:40 2005 +0000 Did some minor editing, fixed ref to be consistent with our format. commit ae4eeed052819835227ab21514137435188c06a9 Author: jen Date: Fri Nov 18 18:56:07 2005 +0000 Adjusted track labels to be consistent with prior releases. commit 6b2b97797b7574a76549f22be6e14c2ada74a706 Author: donnak Date: Fri Nov 18 18:41:28 2005 +0000 Fixed capitalization in several long labels to be consistent with other labels in app. commit 042ba2a9ec9985b173dc75a218ab7f955b596e19 Author: jen Date: Fri Nov 18 18:30:14 2005 +0000 Adjusted track labels to be consistent with prior releases. commit 8cd52d32554c40d033cbd0f00dcf3faa971c97b9 Author: jen Date: Fri Nov 18 18:19:54 2005 +0000 Adjusted track labels to be consistent with prior releases. commit 44c7873a5f678374d0080827956d0e03455ccd3b Author: donnak Date: Fri Nov 18 18:18:56 2005 +0000 Removed spurious hyphen from "in situ" in Allen Brain long label. commit c589d61069099663af9c359f1c9a8602406c00a8 Author: donnak Date: Fri Nov 18 18:17:12 2005 +0000 Fixed capitalization of VisiGene to be consistent w/other column labels. commit a6d11804fe22e0c126c6c30633555ea137fff6e8 Author: hiram Date: Fri Nov 18 18:06:14 2005 +0000 In the middle of rescoring all the alignments commit 074b5b49e060d5002652116157a02dc2be1920d8 Author: kent Date: Fri Nov 18 17:57:35 2005 +0000 Adding some more indexes that should speed build. commit 6327e43128ffdcd0c319e78f1c674a0618d96bdd Author: kent Date: Fri Nov 18 16:37:09 2005 +0000 Polishing usage statement. commit 73d04f71dc5b6d85428b79f7347a35f2ffd5f7cf Author: kent Date: Fri Nov 18 16:36:23 2005 +0000 Seems to work. commit b5ca44d5ce68c7c3702581bcf66ec36d742e1861 Author: galt Date: Fri Nov 18 16:00:03 2005 +0000 "Encode release log update" commit 87f6bf9a6a5ddca7beec6209ddf01d3ddaaf6f48 Author: galt Date: Fri Nov 18 16:00:01 2005 +0000 "Release log update" commit 7c6e7dbbfe03ba996220dea8fffeebe8a7364b59 Author: kent Date: Fri Nov 18 10:39:39 2005 +0000 Made xml parser for gensat via autoXml. Starting to extract data for tab file. commit 9bfbd2b564e18a44443779f640c5bd5a2df579ec Author: donnak Date: Fri Nov 18 08:50:40 2005 +0000 Changed links to custom tracks doc to point to internal section rather than external document. commit d2534bcda827a51c8162b0c1e4a8bc809da332a8 Author: donnak Date: Fri Nov 18 08:42:05 2005 +0000 Yanked the body of this file into the new file customTrackText.html, which is accessed via SSI by both this file and hgTracksHelp.html. commit b2f08df8540a78b627eed7891c38f0228c27eb16 Author: donnak Date: Fri Nov 18 08:34:27 2005 +0000 Created this file, which consists of text that was previously located in customTrack.html. This file is included by both hgTracksHelp.html and customTrack.html. (the latter is kept around for historical reasons only, since all of its information is now included in hgTracksHelp.html). commit 00fa2a80dfc630ef9f4da97e37fe0b911f4e8cef Author: donnak Date: Fri Nov 18 08:29:49 2005 +0000 Added VisiGene section. Yanked annotation track descriptions to a separate file -- trackDescriptions.html -- because they are no longer maintained. commit b1242a549a7b87b8ba6b25f1ee28432f2f718798 Author: donnak Date: Fri Nov 18 08:29:04 2005 +0000 Created this file. The text was previously located at the end of hgTracksHelp.html, but I've yanked it to a separate location because it is no longer maintained. This file is referenced by hgTracksHelp.html. commit 844668896e95307464a5516b5ea501146ae10660 Author: kent Date: Fri Nov 18 06:47:35 2005 +0000 Seems to work commit 58caa1654ff79ee4e53fa560b665449aa7dded50 Author: donnak Date: Fri Nov 18 06:16:35 2005 +0000 Updated gateway text to reflect latest changes to navigation buttons. commit b836db90c3e823f296152854f5eb1a7a0a3d34fb Author: kent Date: Fri Nov 18 04:22:21 2005 +0000 Wrapping some long lines commit b83623ff4150b2c5aade14d71f2e382969a09035 Author: kent Date: Fri Nov 18 04:21:28 2005 +0000 Clarifying a comment commit e53727cfe3ffd87a4d3dd234bc7715332ed0bf32 Author: kent Date: Fri Nov 18 04:20:47 2005 +0000 Seems to work commit 8e63e8df695f50c196d58e707a6daf44744c3932 Author: kent Date: Fri Nov 18 04:20:00 2005 +0000 Starting to work, no MD5 check yet though. commit 90a824958c4b52a601e222ad90d8bdf55347cb0e Author: markd Date: Fri Nov 18 02:14:15 2005 +0000 added program to convert gtfs to genePreds and extract other info commit f130c7b9e090794b2bb8ee78a84b18ad3bc4b97a Author: kate Date: Fri Nov 18 02:05:15 2005 +0000 ENCODE Regulome track update commit 605fb1d6dd2fee68a0784f91ffc9a424aa5a395b Author: donnak Date: Fri Nov 18 00:24:43 2005 +0000 Changed some URLs from genome-test -> genome. commit c54f7f98b3456dad20bd0df9472ba21d40b2ddf6 Author: donnak Date: Fri Nov 18 00:11:55 2005 +0000 Reworked several of the examples, added caveat about itemRgb use (only w/BED9 or less). commit 4a71fd7b355ee2b7e546accddf455a931d0e550d Author: donnak Date: Fri Nov 18 00:11:22 2005 +0000 Modified this text to match revised example in customTrack.html. commit 1dd71fcba433aa8c93cb16b91ea7fdb8ed2dbbaa Author: hartera Date: Fri Nov 18 00:08:03 2005 +0000 Tetraodon net, all.chain and over.chain files had been deleted so these were recreated. Moved tetNig1 and monDom2 blastz alignment output from the san to /cluster/data and recreated download links. Fugu fr1 blastz alignment downloads had been deleted so these were recreated. Self Blastz, chain and net is in progress. commit b5d2d9787482d95c8805351e369b05086215e859 Author: hartera Date: Fri Nov 18 00:01:49 2005 +0000 Documented recreation of downloads for fugu vs danRer3 chain and net alignments as these had been deleted. commit 4ef79a059fbc0bcfc3219f6d95117b4d821680dd Author: fanhsu Date: Thu Nov 17 23:52:56 2005 +0000 Created otherOrgs.ra. commit 41620069b0d7bb087c72550f3a6c56ed3b982f67 Author: fanhsu Date: Thu Nov 17 23:52:25 2005 +0000 Created links.ra. commit 07ec07f30c62671de000eb95fdbdc4b885b66b34 Author: fanhsu Date: Thu Nov 17 23:32:52 2005 +0000 Added mm7 KG/GS/PB build. commit 4e7ffa94c0236911651138e70fa6d92239926257 Author: galt Date: Thu Nov 17 23:17:53 2005 +0000 Adding index to imageFile that speeds up data load by 2.5x commit 3744266ca76a90b6ce0c91102a55ce618a67e6ca Author: kate Date: Thu Nov 17 23:07:35 2005 +0000 Fix MSA track commit 5ca208a9f5dc94ec955429da1baf6d75ecf29261 Author: kate Date: Thu Nov 17 23:06:03 2005 +0000 More tweaks to ENCODE MSA track commit 1f243c6d0ccc22ccd02980486e2df872f3704ff5 Author: kate Date: Thu Nov 17 23:00:19 2005 +0000 Tweak ENCODE MSA track commit b116a450961d9ab2d164843ea5cd5f9384f5fe0b Author: kate Date: Thu Nov 17 22:55:54 2005 +0000 Ariel Schwartz ENCODE MSA alignment agreement commit 38f1ee7ed7156b07bbe7cb93aa630a7394247bb2 Author: kuhn Date: Thu Nov 17 22:54:45 2005 +0000 dropped debugging line left in by mistake commit 97f542ba12af2b601e19ab40800830b85fe3ab20 Author: giardine Date: Thu Nov 17 20:18:17 2005 +0000 *** empty log message *** commit cf5f44b2048fc083cce42ada4d569ae048dd5740 Author: giardine Date: Thu Nov 17 20:17:59 2005 +0000 Changed Human Phenotype track to Human Mutation track. New table prefix is hgMut for all related tables. Changed ethnic table to a general attributes tables. Switched back from composite to single track, but added in filtering on source. Only have hg17 data for now. Removed shading because it made the lighter variants look less reliable rather than less data or links. commit f7543af5b95629133ad187ea467a302bdac40b4f Author: kate Date: Thu Nov 17 19:37:52 2005 +0000 *** empty log message *** commit fedb16c4f41ddd40637a3f860c79988d32e792aa Author: hiram Date: Thu Nov 17 19:32:37 2005 +0000 Add chainLinearGap option commit 3c904a418305f57b2003ac1058d3d341770d1c98 Author: kate Date: Thu Nov 17 19:05:26 2005 +0000 MSA and UTexas commit 48d75d02e359ec273aa079bfdd6bddc0f5e278a1 Author: kate Date: Thu Nov 17 19:05:15 2005 +0000 Update ENCODE Univ Texas STAGE commit 52be6f60ff403d18393721d17c71513b9c6192c9 Author: galt Date: Thu Nov 17 18:52:48 2005 +0000 tiny fix to fit code to handle overzoom better commit 13026978a9141c80c0e3325ff6cc7471afeefe2f Author: fanhsu Date: Thu Nov 17 18:39:02 2005 +0000 RefSeq ra records. Used for KG putback list build. commit 7723ca14d80fec6aad74ed3ddaad1584f7592d21 Author: kent Date: Thu Nov 17 18:27:47 2005 +0000 Tweaking format of results title. Fixing a bug that made dm1 not work. commit 0211d201603292a0ddc5d2ddd3431828f0e91f28 Author: hiram Date: Thu Nov 17 18:01:01 2005 +0000 Adding chain and net for Mm7 commit e452644129191ee3e405d9fc2a08f6a18820b72c Author: hiram Date: Thu Nov 17 17:43:01 2005 +0000 Bringing up to date. Working on 17-way conservation. commit d931b5bffef4c4d027dfe2b5d1b611d384fca19c Author: kent Date: Thu Nov 17 16:55:31 2005 +0000 CHanged UCSC Home to just Home commit 4bbdaac0c843d29a2dd60fcd2aa775fd4a639063 Author: kent Date: Thu Nov 17 16:51:55 2005 +0000 Freen helps fix a mistake in a cluster run. commit 486f70f5389abe7b04d868be89f7a483d820694f Author: kent Date: Thu Nov 17 16:51:15 2005 +0000 Adding index option commit f74d9e44a081a3e5b3eba0d6d6cf4210726d85ee Author: kent Date: Thu Nov 17 16:50:46 2005 +0000 Seems to work. commit 37b630ce5d3133b53d76434d0fdd6ded4097258b Author: galt Date: Thu Nov 17 16:00:04 2005 +0000 "Encode release log update" commit e1b463cd6026aeb32430c52c858d0d58645f539f Author: galt Date: Thu Nov 17 16:00:03 2005 +0000 "Release log update" commit 6e094cef7e899c69b79dad99ce5a6f0fc2d8d02e Author: kent Date: Thu Nov 17 06:32:43 2005 +0000 Putting in UCSC home button commit 4e89d5554367156a3f9dc8d69d8b883d4bec2928 Author: kent Date: Thu Nov 17 06:20:00 2005 +0000 Making it so that image pane is blank after a search that misses. Capitalizing some titles. commit b1b0cee2013937c48667b0073053b30f18275d30 Author: heather Date: Thu Nov 17 06:17:33 2005 +0000 write and load tab file (problem with strand) commit 6a193c63d7f35ad1ba75761edb3827e6c52dc138 Author: kent Date: Thu Nov 17 05:46:18 2005 +0000 Removing some debugging and doing standard pointer null comparison commit 26d6b9b9822737bd35dbbb6fa4e72cc9f4955292 Author: kent Date: Thu Nov 17 05:26:34 2005 +0000 Splitting chainRead into chainReadChainLine and chainReadBlocks commit a53fb1cb7326c6db4a7c4e2a480039e9e901fca2 Author: kent Date: Thu Nov 17 05:25:54 2005 +0000 Adding liftOverChainForDb commit aefed17475085c456c55d2c34979f0fc0f28a56d Author: kent Date: Thu Nov 17 05:25:13 2005 +0000 Working a bit better, still got a bug or two. commit cec9c7422ecc37d8ea7f2053e639d8d21c70048f Author: kent Date: Thu Nov 17 02:58:06 2005 +0000 Putting in hyperlink to genome browser in new assembly. commit 08a82dd4abe965c357099f1f83ae5d543b2255d7 Author: kate Date: Thu Nov 17 01:11:05 2005 +0000 1. UCD chip/chip 2. MSA elements commit afcd87da2b228cfa44fcdeeda46bc5c44f9df961 Author: kent Date: Thu Nov 17 01:00:43 2005 +0000 Still rough but starting to work. commit 682dbb4a230a149e9dc35b95df425aa448623dfc Author: hiram Date: Thu Nov 17 00:35:44 2005 +0000 Comment on where Repeat Masking was done commit 6765dedfddbba088402fd21e8fcc2ce772c2c1cc Author: galt Date: Thu Nov 17 00:13:55 2005 +0000 control panel: changed radio buttons to regular buttons: out in full fit commit 6feddc4ee1a6694bc631dc1a897d94ab5281f3f8 Author: kent Date: Wed Nov 16 23:39:31 2005 +0000 Getting rid of a bunch more unused stuff from hgLiftOver. Working on interface a bit. commit f0b9d5c3942fe102a6f5412fc179c21acc98f6d8 Author: aamp Date: Wed Nov 16 23:21:06 2005 +0000 Build instructions for RIKEN CAGE tracks. commit cedfdf2d376b52ec19d97a515f696c1907cec2a2 Author: fanhsu Date: Wed Nov 16 23:14:09 2005 +0000 Added back the logic to exclude candidates that having noStart and noStop error conditions. Minor updates to reflect suggestions after code review with Rachel. commit 6d18d492d23fcf971f5c0fb6dd8239494779f0fc Author: aamp Date: Wed Nov 16 23:04:23 2005 +0000 Added trackDb entries for rikenCageTc and rikenCageCtss tracks. commit b46d0ba3ad49f6011f3cca19c3d0790b407901c7 Author: aamp Date: Wed Nov 16 22:55:41 2005 +0000 Help pages for RIKEN CAGE mouse tracks. (Bold parts need revising). commit 908b50ab4647d4d777ac3154e3b90abea0c87122 Author: galt Date: Wed Nov 16 22:32:36 2005 +0000 adding utility to create a fake mrna psl from a genePred table or file commit 85745e40f01700fd68f0e7cd7f6add219b924418 Author: heather Date: Wed Nov 16 22:26:34 2005 +0000 handle setCoords errors. Don't bother reversing. Check for ContigInfo. commit deec887f3d8453958b0de65cd800967817f53a6c Author: kate Date: Wed Nov 16 21:25:44 2005 +0000 MSA elements, cont. commit dd41106e451201e6918b10c6d3b4b9961a2bd317 Author: hiram Date: Wed Nov 16 19:52:43 2005 +0000 Now with CORRECT lineage specific repeat track from Mm7 commit 0136d0632e7d2a634d3f3c185ea31930b0a88c9e Author: kent Date: Wed Nov 16 17:55:46 2005 +0000 bumped maxChainsToExplore to 2000 by default commit 16b642acff7b9dbac74339f4f40bbd890d446cf2 Author: markd Date: Wed Nov 16 17:45:25 2005 +0000 make conflict detection optional rather than default commit abae3d347c0ca2c5950af606dd21be3789e9c284 Author: markd Date: Wed Nov 16 17:41:21 2005 +0000 add strand to bed output commit 5f01f181343ada6255a89049da28c19b600c77e4 Author: galt Date: Wed Nov 16 16:00:03 2005 +0000 "Encode release log update" commit b737469d59131d20a482ea326de41c0e28bd2a23 Author: galt Date: Wed Nov 16 16:00:02 2005 +0000 "Release log update" commit d24d7a58f23a069881b36c57b3d84245d5665820 Author: daryl Date: Wed Nov 16 09:59:58 2005 +0000 Added :utr5, :utr3 to usage statement commit 2eedd97e093efc6e6acb281bd569d11c92705212 Author: markd Date: Wed Nov 16 09:41:36 2005 +0000 fixed reading files with psl headers commit f727195450e8ef58555b9c12461e61d4edbf04a6 Author: kent Date: Wed Nov 16 07:00:27 2005 +0000 Removed unnecessary jkhgap.a from link commit 1c509a93128c14ceedec3d5b42cd732ebdba8635 Author: braney Date: Wed Nov 16 00:41:02 2005 +0000 a bunch of changes to calculate N fields commit 4b2babd0e1e30a70f87aca6e21bf090b847fc8ca Author: heather Date: Tue Nov 15 23:20:08 2005 +0000 fix CNP track (data was not displaying) commit b9df0d1e559627b78150f75ce572074531e1305f Author: angie Date: Tue Nov 15 21:32:40 2005 +0000 Updated link to WUSTL D. yakuba page.wq commit 7ede30d5ccf5467890a51885fa3c9c2d951c9370 Author: hartera Date: Tue Nov 15 21:32:13 2005 +0000 Added function to create trace archive links. For dog, added links to the trace archive for BAC clones and BAC ends. commit 38ff7950296181a9eaebdbf708d021672b296c39 Author: angie Date: Tue Nov 15 21:16:12 2005 +0000 Added droYak2. commit 9866f3214894fd1022049227d0bcd84075b26b63 Author: angie Date: Tue Nov 15 21:15:05 2005 +0000 First-cut description (mostly from LaDeana) and trackDb.ra for droYak2. commit 45dc3f95a64537210f01e4bad61ffba9d46433bb Author: hartera Date: Tue Nov 15 20:56:01 2005 +0000 Added entries for bacEndPairs and bacEndPairsBad tracks and searches for these tracks. commit ca279467e9758a0a832afd469a1cb7abb890d2f9 Author: kate Date: Tue Nov 15 20:48:43 2005 +0000 ENCODE MSA Conserved elements commit c1aa45eb01493968ec439acbaa63ed800dcc7a27 Author: hartera Date: Tue Nov 15 20:05:22 2005 +0000 Created BAC end pairs track. commit b8c2b4294005fff1462c0dad88d1cf04fc6ea74e Author: hartera Date: Tue Nov 15 20:03:28 2005 +0000 Description for dog BAC end pairs. commit 23e4692be86790df3117dac70933c8479ed37f71 Author: kent Date: Tue Nov 15 16:59:23 2005 +0000 Linking in original file as well as creating thumbnails and pyramid. commit 8544e230c13eafb0e34760f3c36aee4a80dbbfd8 Author: braney Date: Tue Nov 15 16:38:08 2005 +0000 require that gap costs be specified. commit 60b37dea19dae062173e0ecce7233a46d4d74484 Author: braney Date: Tue Nov 15 16:37:06 2005 +0000 add the ability to specify "loose" or "medium" to specify gap costs commit 15c7e06594272fcc12e40c31c09b891910adc6ab Author: galt Date: Tue Nov 15 16:00:02 2005 +0000 "Encode release log update" commit f003355132d57e8fcb57dd3909d2ddb1250a9973 Author: galt Date: Tue Nov 15 16:00:01 2005 +0000 "Release log update" commit f17e204f15f9d57e5ae70352bd9140de45e7d03a Author: genbank Date: Tue Nov 15 04:07:52 2005 +0000 moved tmpdir for new hgwbeta commit 3e10ada4e3073fa0333c10020d1499f99d3e243a Author: kent Date: Tue Nov 15 04:03:48 2005 +0000 Added column method of splitting commit c53e6761c5b7c31ebfb5a9981ce21b3ab66a02d9 Author: heather Date: Tue Nov 15 02:36:28 2005 +0000 "New version number v121" commit 8747e226034db9bf703612e0917b41743570d63e Author: donnak Date: Tue Nov 15 02:15:12 2005 +0000 Changed label for VisiGene link in left sidebar. commit 4cca2897b7d484ff5b92e22ca4f80c778b7298a5 Author: angie Date: Tue Nov 15 00:59:41 2005 +0000 Added Conservation and "uncertified" assembly regions from Broad. commit 5c797f9c1aafc7de1f87b61990cb0408069da527 Author: angie Date: Tue Nov 15 00:58:36 2005 +0000 Old item from August -- added unmasked cpgIslandGgfAndy for Laura Elnitski. commit 2d7cc5e53f7e3cec7deb6bbb19633402fb3834ff Author: angie Date: Tue Nov 15 00:54:03 2005 +0000 Make the clean target's table-dropping *really* quiet. Using "-" at the beginning of the command was not sufficient -- make would still report that it was ignoring an error. Adding "; /bin/true" made make happy. commit ac9534c9e1981caede5bcaa10750908905d42954 Author: hiram Date: Tue Nov 15 00:36:36 2005 +0000 No need to malloc a string area, OK to have it right on the stack and disappear commit 45788106bd63079f07649ec84b0c408469abea68 Author: hartera Date: Tue Nov 15 00:21:59 2005 +0000 Removed reference to use of lineage-specific repeats. commit 181bb79da06bb13318ec939dd347cb38310f316e Author: hartera Date: Tue Nov 15 00:19:14 2005 +0000 Description for self net track. commit 5c223eecf439042704141e8128b3cc8b9a6239a0 Author: hartera Date: Tue Nov 15 00:18:34 2005 +0000 Description for self chain track. commit 6f0cb71d262059e98b645dd92dc4f72082d4cf5c Author: angie Date: Tue Nov 15 00:14:12 2005 +0000 Added user id to error message about cart stuffing bot. commit a058040a226a7a9f85461ac7da208ccd7786eab9 Author: hartera Date: Tue Nov 15 00:12:58 2005 +0000 Minor edits. commit e4b9efdeb807e430aba6c982c338d741c3a813f1 Author: hartera Date: Tue Nov 15 00:11:19 2005 +0000 Added self chain and net tracks. commit fbc0f650abbfa0dfdbbfc93e16788874b483613f Author: angie Date: Tue Nov 15 00:10:36 2005 +0000 Added comment about deleted experiment. commit afd4717458653950f6299277984321adf35e464d Author: hiram Date: Mon Nov 14 23:51:19 2005 +0000 Make click anywhere in ruler area be the 3X zoom - title line, or window position line, or base position line, any of them. commit 4b002b48e4f49299283c1e5676b03543b9ffa813 Author: kate Date: Mon Nov 14 23:32:59 2005 +0000 ENCODE UC Davis Chip/chip commit 66b2e38c4445f9f176c5d25348fc44c3bdacb0d7 Author: kate Date: Mon Nov 14 23:11:22 2005 +0000 Updates commit 77ca8a288cd8cd55acd9e13f8de3cc35ebf0f656 Author: donnak Date: Mon Nov 14 23:03:16 2005 +0000 Added VisiGene link. commit cd492ad59d7c43ac5cd37e4d341df1d20e911321 Author: donnak Date: Mon Nov 14 23:03:06 2005 +0000 Added VisiGene link to left sidebar. commit 3f5e038cbee3bbf5581088533fa3b62ccba5d5be Author: hartera Date: Mon Nov 14 23:00:07 2005 +0000 Added entries for the mm7 chain and net tracks. commit 33534f3d04d0cc9790540776080544c30efdd6fa Author: hartera Date: Mon Nov 14 22:59:19 2005 +0000 Added entries for the danRer3 chain and net tracks. commit b08572a6b1c6bbeaeab3dd33afc0f270015395c0 Author: donnak Date: Mon Nov 14 22:58:44 2005 +0000 Added credits section to About VisiGene text. commit 223bf9e061b0dcce5f3ac4bf172cd2f0b6a74c9a Author: kate Date: Mon Nov 14 22:34:37 2005 +0000 MSA alignments commit dee0f148999245942f60493715b5ede56076cee6 Author: hartera Date: Mon Nov 14 21:08:00 2005 +0000 Description for danRer3 net track. commit f2feac17a8863f107a0d0dec81080786bc58655f Author: hartera Date: Mon Nov 14 21:07:38 2005 +0000 Description for danRer3 chain track. commit 28439c521dbe1be669fcfee7e39c0d953628d820 Author: hartera Date: Mon Nov 14 20:58:21 2005 +0000 Description of mm7 chain track for danRer3. commit c2602270ce0d908973703cb1d8aea1c4e8775e68 Author: hartera Date: Mon Nov 14 20:57:51 2005 +0000 Description for mm7 net track for danRer3. commit 149ee77b85ed14b8b85ef900535150c5d2942f65 Author: kent Date: Mon Nov 14 20:40:39 2005 +0000 Removing stray line commit 41619d34736ac5cac54e067fb2f9ead0b40b885d Author: donnak Date: Mon Nov 14 19:57:59 2005 +0000 Changed max images from 50 to 25 in About text. commit d1a2f10cc65a27c48feac36fda3f1e498be7151a Author: hiram Date: Mon Nov 14 18:58:08 2005 +0000 Fixup processing of lineage specific repeats commit 6ed4602a2e3c2cb8d60c239da292c86c71f165fc Author: kent Date: Mon Nov 14 18:29:55 2005 +0000 Made first image in thumbnail list displayed on main pane by default. Only have 25 thumbnails. commit f5144e3b32d07ca3856e9dae06b9f0a32a012250 Author: donnak Date: Mon Nov 14 17:51:11 2005 +0000 Added doHelp(), which prints an About VisiGene help section on the hgVisiGene gateway page. Also modified the text printed under the search box on that page. commit 0a28ebbb7631e3e7051332b7219f2d2612775e45 Author: galt Date: Mon Nov 14 16:00:02 2005 +0000 "Encode release log update" commit 3272773e9dfdd91643239911eec7987b07c13bc5 Author: galt Date: Mon Nov 14 16:00:01 2005 +0000 "Release log update" commit e1fe0085ce58042b0e3ccac3536a76c836ef0e68 Author: fanhsu Date: Mon Nov 14 14:48:44 2005 +0000 Added varAcc table in sp051015. commit f06f2df116ce257d0345f0f87b2c9b3c2e70646b Author: markd Date: Mon Nov 14 08:28:19 2005 +0000 create multiz17wayFrames track commit 174b04ed91be6ddecbd3da285e026451cf602d9a Author: kate Date: Mon Nov 14 07:21:57 2005 +0000 More ENCODE alignments commit 2c6de48dda725ae4b820da24c8d7069c553b922b Author: markd Date: Mon Nov 14 06:00:25 2005 +0000 increased make chrom size and hash size commit 617e6177e36171e89d4423e0794078596c7d88a2 Author: kuhn Date: Mon Nov 14 05:10:27 2005 +0000 added automatic du for any store unit at 98% or more commit 00ad1f0407465400cb6497dd8dc420639fd2f1a2 Author: kate Date: Mon Nov 14 04:28:44 2005 +0000 TBA alignments for ENCODE Oct freeze commit f2b2482fdc638381aa7bcd6ffa4c3a71fc631034 Author: kent Date: Sun Nov 13 21:07:02 2005 +0000 Creating index in two passes rather than one. This saves a lot of memory (~2 gig when chromosome 1 is target) commit 45e71b496c22d461a02922f4fcbbc40deb6fd828 Author: kent Date: Sun Nov 13 18:53:03 2005 +0000 Making this behave better on memEater test case. Put in maxChainsToExplore parameter, which helps some, and replace boxClump with boxLump, which helps a lot. commit ff7b635fdc5dac6f8606ebaff3a7acb2eb4f59bd Author: kent Date: Sun Nov 13 18:50:06 2005 +0000 Adding boxLump module - faster but slightly less precise version of boxClump. commit e7407c7acb1504828639489e634a729326a58e0d Author: donnak Date: Sun Nov 13 18:15:11 2005 +0000 Removed reference to old Table Browser. Added link to TB User's Guide. commit 3d52acb8bb4fd0790fa323fa37174ee015781427 Author: galt Date: Sun Nov 13 16:00:02 2005 +0000 "Encode release log update" commit 4485d2cf1737a16b483b27f0b5a3a26414fe0ff0 Author: galt Date: Sun Nov 13 16:00:01 2005 +0000 "Release log update" commit ced23eb82647f354cb854c4c52fce6ebe33e988f Author: kent Date: Sat Nov 12 16:57:57 2005 +0000 Adding another test case. commit ea14922a95c33a6e47a38d6459efa08c4914e404 Author: galt Date: Sat Nov 12 16:00:02 2005 +0000 "Encode release log update" commit c7482970786e940842250284a34eb8fd57e0f7fb Author: galt Date: Sat Nov 12 16:00:01 2005 +0000 "Release log update" commit fe02a6fb0f3cc7518040fbc4f2ce8ec772b881d0 Author: fanhsu Date: Sat Nov 12 14:40:45 2005 +0000 Created kgCheck2.c. This contains new logic of selecting qualified KG candidates based on geneCheck results. commit ba37427e266d6938dd4b16d26f16af46a88f747a Author: fanhsu Date: Sat Nov 12 14:39:31 2005 +0000 Created makefile. commit 7195bb7fe524be3b34d7c6e335d4e49d91c4b0fb Author: kent Date: Sat Nov 12 04:32:43 2005 +0000 little fix changing hg17 to nov 2004 commit defa943bd6f556ab53fbf693ce81f834275a5b25 Author: kent Date: Sat Nov 12 02:52:58 2005 +0000 Adding lock option. commit 6dc89a553bb2761b0ee2770704c39236fbd8b597 Author: kent Date: Sat Nov 12 02:43:24 2005 +0000 Added note to usage commit bd1fb966664b50e3a89397886489ccf1ff5481d2 Author: kent Date: Sat Nov 12 02:42:53 2005 +0000 Shortened NIBB description. commit fa0b9cc6cd8ee5543f17dbdf159ad654100b06b9 Author: kent Date: Sat Nov 12 02:42:21 2005 +0000 Expanded size of search box a little commit 325c03352fb96aaa5d68c69f502c638dcf7db726 Author: kent Date: Sat Nov 12 02:41:55 2005 +0000 Added nibbImageProbes column commit 8021035e6df54855d0035f36071b47725efadd70 Author: kent Date: Sat Nov 12 02:40:47 2005 +0000 Added section for NIBB images commit 522262fa1db788d0c78b1310f8f201ac3175ffb4 Author: kent Date: Sat Nov 12 02:40:21 2005 +0000 Added hard locking/unlocking functions commit 334fd9539eb5e2b0d928a3fb2b620d25d99e91a2 Author: kent Date: Sat Nov 12 01:52:55 2005 +0000 Changed a name in contributor list commit a04e7e9d39a353cf3dd23098073cf645c76d6701 Author: galt Date: Sat Nov 12 01:16:44 2005 +0000 change initial size to fit height as well as width in visible window if possible commit 6657fbdbb6e703ae312b036009c1d6371ecf4488 Author: kent Date: Sat Nov 12 00:27:13 2005 +0000 Adding search of common organism names commit a176bc8a1c55803f0a612d31f0574dd1678c7fd4 Author: kent Date: Sat Nov 12 00:18:27 2005 +0000 Adding search of scientific name of organism commit 771b6defc1ca1e9e9ae5879a0950b47bcd9d2c01 Author: kent Date: Fri Nov 11 19:58:34 2005 +0000 Seems to work. Scary though! commit 1af430fddd5e282a27572035a63d883b40a00966 Author: kent Date: Fri Nov 11 19:57:36 2005 +0000 Fixing a few small problems in .ra file commit 981b25ca1ff13a85ffbc5b40b16f0882df3490c4 Author: kent Date: Fri Nov 11 19:57:02 2005 +0000 Fixed usage commit 5709134acf5267f01930db7482dec63bced8e013 Author: kent Date: Fri Nov 11 19:56:44 2005 +0000 Restoring larger test commit ff60ca647a22f659974867151558c50fc16b6801 Author: angie Date: Fri Nov 11 19:51:40 2005 +0000 Added genePredToBed to scripts target. commit e26a51a24e68665ff144fa08dc771afe79c1cab7 Author: markd Date: Fri Nov 11 18:28:29 2005 +0000 fixed bug expanding genePred commit 04c9fcb515ed9dead7e96070afb22f6631912120 Author: kent Date: Fri Nov 11 17:09:01 2005 +0000 Refining treatment of floating point age value to avoid duplicate specimens commit d75b31adc02b0d060b25cd1383da4e3ea5271cbc Author: kent Date: Fri Nov 11 16:51:05 2005 +0000 Updated contributor commit 0123557bf37587fb9c7e965ea14db185304a6fba Author: kent Date: Fri Nov 11 16:38:58 2005 +0000 Seems to work commit 47045557c4b01c1a19601fd10c5e2f916cebe908 Author: kent Date: Fri Nov 11 16:18:41 2005 +0000 Adding search on submitId commit a78084635d840510828947f8fb096124a568512c Author: galt Date: Fri Nov 11 16:00:04 2005 +0000 "Encode release log update" commit 34bcc125e9d17f0017983b9356d6770a04b6094c Author: galt Date: Fri Nov 11 16:00:02 2005 +0000 "Release log update" commit c07243a77aa32819988694334a09cea3791d265d Author: kent Date: Fri Nov 11 15:39:10 2005 +0000 Putting in n/a for empty reference. commit 2db64b0726cf6fa648819003b84ec9e3467c5017 Author: markd Date: Fri Nov 11 07:47:35 2005 +0000 added functions for building genePreds commit 90f88c8465dbf3839fe0ba71de660fcbde829e10 Author: kent Date: Fri Nov 11 06:14:19 2005 +0000 Improved stage name commit 4a3a55b3f41a50d7694b79f08ac698e12e890aff Author: kent Date: Fri Nov 11 06:13:59 2005 +0000 Added sqlQuickDouble commit 6730c7fe37feadbe29c0782f08d39cf77cd98f4c Author: kent Date: Fri Nov 11 05:58:29 2005 +0000 Adjusting image priorities commit 37fc1448801daf88e73d05f92d5c4b8dda47b413 Author: kent Date: Fri Nov 11 05:58:21 2005 +0000 Sorting thumbnail list better commit 6190932f1224724d8ff080237ba392c7c8ae3168 Author: kent Date: Fri Nov 11 05:57:49 2005 +0000 Adding some frog life stages commit 0aedbbc3b07c30341291eb3f5aece7bd3c8ecc63 Author: kent Date: Fri Nov 11 04:19:55 2005 +0000 Rearranging dyStringPrintf that put in sequence to dyStringAppends to avoid overflowing dyStringPrintf's buffer commit ffa680e21260a28dec78fa8132e63fd08c8084a4 Author: markd Date: Fri Nov 11 03:31:39 2005 +0000 grow psl memory more slowly commit 32b3cda18bd126e849cd125602e3c4d216001cdd Author: kate Date: Fri Nov 11 01:47:31 2005 +0000 Add outside linke for ENCODE Yale chip commit daea50b3baf82da74d2623edd1806d36e7aa9331 Author: kent Date: Fri Nov 11 01:32:48 2005 +0000 Added handy testing file. commit 717dc3412e5ab583c7ef77c7347d4aeb8aaaf523 Author: kent Date: Fri Nov 11 01:32:34 2005 +0000 Seems to work commit e2b36a7076b2bb848870a0e3bfc5fe6bf9bed0e1 Author: kate Date: Fri Nov 11 01:32:17 2005 +0000 ENCODE Yale Chip tracks commit 64c044f751ffa88308e0058ab55371fa64146355 Author: kate Date: Fri Nov 11 01:31:51 2005 +0000 encodeYaleChipPval.html commit a13860c73654b32954284bc05438a83b51d9a991 Author: hiram Date: Fri Nov 11 00:30:40 2005 +0000 Instead of "Base Position" the ruler label now reads chrom name commit f4c292e8c59fb212e218dcf921d6c2b6e72ead52 Author: heather Date: Thu Nov 10 23:59:03 2005 +0000 remove broken link commit 63abbb9af3ab71fa9da7412580f18d2c71e4a77c Author: kent Date: Thu Nov 10 21:29:45 2005 +0000 Corrected outdated name in usage statement. commit 760666c130ca166675ed92329893e28e337b8472 Author: kent Date: Thu Nov 10 20:19:07 2005 +0000 Adding stages commit e9eb7e2fbdb24fb06c332e06e31e7206e092f3bc Author: kent Date: Thu Nov 10 20:05:05 2005 +0000 Starting to work, still needs some more fields. commit 1aee95988a79f298777431bc02695b9afda806db Author: galt Date: Thu Nov 10 16:00:03 2005 +0000 "Encode release log update" commit 56b7e58881bc7c8d5d35c15cde3976804163d301 Author: galt Date: Thu Nov 10 16:00:02 2005 +0000 "Release log update" commit f5292be98b8329b73d831ced0122f9ef8fe85644 Author: kent Date: Thu Nov 10 15:28:00 2005 +0000 Jiggling around xenopus NIBB tracks a little commit 128ededee7109f57d09f618f60ed8f71047a7729 Author: kent Date: Thu Nov 10 15:26:33 2005 +0000 Removing unneeded include commit 82354dd5e8853a33fd86729d6649e2656bfe6ffa Author: aamp Date: Thu Nov 10 11:37:24 2005 +0000 Increased the brightness. commit 6fb3b8252dbf07cdc9a9a6fa8d97546b687c4e7b Author: kent Date: Thu Nov 10 06:16:46 2005 +0000 Starting to hack out a much simpler hgConvert out of hgLiftOver. commit 215bfac7841ea75c39034e02709b81f78d5d6aab Author: kent Date: Thu Nov 10 03:41:11 2005 +0000 Making blat's guess more intelligent about handling U's in RNA sequence. commit 513826417f618bbd26bf461f5d920aa65fec7c44 Author: kent Date: Thu Nov 10 03:40:34 2005 +0000 Moving some logic of seqIsDna to isDna. commit 5af3c50de492bf42cac23f8da80ac8b238be980b Author: kent Date: Thu Nov 10 03:39:48 2005 +0000 Adding raw versions of faNextSeqFromMemText and faSeqListFromMemText commit c74c9c05d772dca66d44398bf9989e42046b0c23 Author: kent Date: Thu Nov 10 03:38:56 2005 +0000 Adding isDna function. commit 62db987f85ae738b0b0b009a305fb2dd4a7ffdd5 Author: kent Date: Thu Nov 10 01:25:26 2005 +0000 Seems to work commit 060c45d0b2d4ae627182480ade126ed90b3b1471 Author: kent Date: Thu Nov 10 01:24:27 2005 +0000 Seems to work. Going to test on kolossus. commit eaaae0c1af789e3b166c9fbd76ea3c9d3cd5ac50 Author: aamp Date: Thu Nov 10 01:17:17 2005 +0000 Changed expScale to brightness in column struct. commit 1e4d90eea17812decede6c83c907057c271fa721 Author: donnak Date: Thu Nov 10 00:56:48 2005 +0000 Added clarification to liftOver link label. commit 8873c8a7de864ad174b8a4caf23dfb37e06e831a Author: heather Date: Thu Nov 10 00:50:39 2005 +0000 add strand commit fbcc20d7883289df64e59023da56c38c597e72ca Author: lowe Date: Thu Nov 10 00:28:55 2005 +0000 New version of automatically generated description file commit 19a8574720634ca559942e923a4b4829b5ca1695 Author: lowe Date: Thu Nov 10 00:26:32 2005 +0000 New version of automatically generated description file commit e1261acef139cf0398111014e70e5e22a2c651d3 Author: angie Date: Thu Nov 10 00:18:54 2005 +0000 Added uncertified track (assembly caveats from Broad). commit fef556133421e5f2f1813f1ebc45c778f05a2f40 Author: lowe Date: Thu Nov 10 00:12:23 2005 +0000 Removed old Genbank track commit c7e30a4bac4b59bcb7837fc120e8b1d7f3f360bb Author: kent Date: Thu Nov 10 00:11:07 2005 +0000 Seems to work. Wow, what a lot of ways there are to misspell posterior! commit 262ee0530e85ac14c9f950ee8b1348dd227dbc66 Author: lowe Date: Wed Nov 9 23:52:13 2005 +0000 New version of automatically generated description file commit 1a4f31d75a5c9b84bdea74fa38dd61af874f22c2 Author: lowe Date: Wed Nov 9 23:51:25 2005 +0000 New version of automatically generated description file commit be5a00624e0c9b5facc2ffaf47d6fad47d29a4da Author: angie Date: Wed Nov 9 23:35:07 2005 +0000 Added multiz4way and phastConsElements4way. commit f61db3bc31c7dcf9a9636a7d0b788b1f50e16291 Author: lowe Date: Wed Nov 9 23:34:53 2005 +0000 New version of automatically generated description file commit ef0463cd748ed741771b68860c8dd0d5241ba4f0 Author: lowe Date: Wed Nov 9 23:26:59 2005 +0000 New version of automatically generated description file commit 8468ee85c613d643e5722c0d359603e94448246a Author: lowe Date: Wed Nov 9 23:16:42 2005 +0000 New version of automatically generated description file commit 0ae7ea3e29bfa62c7fa89a528882c26f90ac0fea Author: lowe Date: Wed Nov 9 23:04:04 2005 +0000 New version of automatically generated description file commit 5bbecd536f25182436275ae5feb0d53779100439 Author: lowe Date: Wed Nov 9 22:56:13 2005 +0000 New version of automatically generated description file commit 6d56810257c3861b542b349b56c023aeacdd026f Author: lowe Date: Wed Nov 9 22:15:13 2005 +0000 New version of automatically generated description file commit 23173fe6f939f5da40a10a2dbfdf9d7bfd3ded55 Author: markd Date: Wed Nov 9 21:56:24 2005 +0000 updated RTCPR tracks commit 077439b751507107ba1a3fac5f5d46b4a7c5d2d4 Author: ann Date: Wed Nov 9 20:21:20 2005 +0000 added genbankRun.csh script commit c214d3652e1b449bed06e7202d791e4bde724d7a Author: ann Date: Wed Nov 9 20:17:39 2005 +0000 utility to check to see if genbank is running on an assembly on the RR commit 5b592924018272d2898fbb140e9c3d135f8a9f9b Author: jen Date: Wed Nov 9 19:49:49 2005 +0000 Corrected netTetNig1 - removed dev comments. commit 76e8d27eb815f7745c02524389c17e90370849d2 Author: galt Date: Wed Nov 9 18:34:02 2005 +0000 fixing compiler complaint about sizeof which is not unsigned int on 64-bit commit 81a0f79be8319b59aa155b593c9f469cd5bf9d8a Author: lowe Date: Wed Nov 9 18:02:12 2005 +0000 New version of automatically generated description file commit d53dfc4405c87615b664a1c54e4a10af9a351181 Author: lowe Date: Wed Nov 9 17:35:44 2005 +0000 New version of automatically generated description file commit 71f746ec76360667bd4cbda425df4cd2d3582d2e Author: lowe Date: Wed Nov 9 17:23:01 2005 +0000 New version of automatically generated description file commit 7a5da2603fe8ef4f890ffe3d1dfd3194470b1ddc Author: lowe Date: Wed Nov 9 17:11:09 2005 +0000 New version of automatically generated description file commit 7502aae7f2940a1136a4ae7e5529a30f410adc0b Author: lowe Date: Wed Nov 9 17:07:40 2005 +0000 New version of automatically generated description file commit d62fcc2e8be9974d9c3370ec87ae80710fcb9804 Author: lowe Date: Wed Nov 9 17:06:08 2005 +0000 New version of automatically generated description file commit 3c7b79d78fb212e0859491f843f1ccb4d190db7d Author: lowe Date: Wed Nov 9 16:57:34 2005 +0000 New version of automatically generated description file commit 91144525e5d5dd5745cb0510b2c4ba0f0b083373 Author: lowe Date: Wed Nov 9 16:57:01 2005 +0000 New version of automatically generated description file commit 76b7cedd5073fe621557864c0feba0a0e8193b77 Author: lowe Date: Wed Nov 9 16:41:49 2005 +0000 New version of automatically generated description file commit 03bd8b56b6d2286fe14558e7caae06f69b67253f Author: lowe Date: Wed Nov 9 16:35:31 2005 +0000 New version of automatically generated description file commit 2e8fc9274f14bfe4af77f1a36532ab2370f6c00a Author: lowe Date: Wed Nov 9 16:14:15 2005 +0000 New version of automatically generated description file commit 069ef2b18e7fa7e5bc420fc614da6ced38c73aed Author: giardine Date: Wed Nov 9 16:13:33 2005 +0000 *** empty log message *** commit c520a59389828abe36345886d1f430ed76364802 Author: giardine Date: Wed Nov 9 16:13:12 2005 +0000 Added color coding by baseChangeType to human phenotype tracks. Added shading based on linkDbs having a link to clinical data. This is hardcoded as GenPhen, it would be better if there was a more general way of determining if the link is source or clinical. Possible separate fields in table? commit 123e6437dc3ecc2ae63aeb9702c6bf4c3763dfd1 Author: giardine Date: Wed Nov 9 16:02:36 2005 +0000 *** empty log message *** commit 104fb79a3210c34805e70581019015b6a382e813 Author: galt Date: Wed Nov 9 16:00:04 2005 +0000 "Encode release log update" commit 0097fab18578bd48fe1e3960bd8ad8b761358eae Author: galt Date: Wed Nov 9 16:00:03 2005 +0000 "Release log update" commit b1a371e276b8453a7fd600db2c93538f2dde4926 Author: lowe Date: Wed Nov 9 15:45:08 2005 +0000 New version of automatically generated description file commit 3715ed627b0befaee4b1472128e59cd13b445424 Author: galt Date: Wed Nov 9 05:11:15 2005 +0000 added mostRecentDead method to help distinguish between new files, resurrected files, and old still dead ones commit e0a1222c6be97e8c5b0c1c6b0edb7ab2ec4e79cf Author: aamp Date: Wed Nov 9 01:53:45 2005 +0000 Added stuff for putting the rtdbUpdate command in a hg.conf file instead of a #define. commit ecd96676894b5452e4f9ac43a27ab53c97b98e2f Author: kate Date: Wed Nov 9 01:22:01 2005 +0000 Updates to ENCODE affy pages commit 98eaea9c8e3af5f0db868876e27e99205f801694 Author: kate Date: Wed Nov 9 01:21:20 2005 +0000 *** empty log message *** commit b28d1c82f6b38c0fa36e0dad03d57579b0bca65f Author: aamp Date: Wed Nov 9 00:58:48 2005 +0000 Another dumb mistake in the aftermath of v1.29 commit 8e8ef23a18177c216f091728da37522b6c36865c Author: kent Date: Wed Nov 9 00:30:04 2005 +0000 Adding section to just make NIBB image probes commit 52e02ca4928e83c56e7bf64dc67da57acabb3584 Author: kent Date: Wed Nov 9 00:29:36 2005 +0000 Updating and correcting allenBrainAli table commit ed84e8ff8a6e68ebd575f3ddf86252fe4b754368 Author: kent Date: Wed Nov 9 00:28:53 2005 +0000 Adding nibbImageProbes track commit ed67cd94b909137ede0013b69b3cc476b2f060ad Author: kate Date: Wed Nov 9 00:12:11 2005 +0000 ENCODE Yale RNA Transmap tweak commit 7798d94de6f1a5733342a83c4c1c95c5d8ab1f6d Author: heather Date: Tue Nov 8 22:13:21 2005 +0000 remove bad comment commit 494f52fcdf6154e6b8a37039691ad73418b54b82 Author: heather Date: Tue Nov 8 22:12:30 2005 +0000 contig assignment commit dcf964461251eb119bf857286cbea1fd5415d649 Author: kent Date: Tue Nov 8 19:26:36 2005 +0000 Seems to work still in new directory commit 4f280ef2df251f7fd8e0bedd01c828fa6b71613f Author: kate Date: Tue Nov 8 19:26:07 2005 +0000 Update commit 32c392393d4874a71be24b25b020baac3bb1f1da Author: kent Date: Tue Nov 8 18:55:47 2005 +0000 Moving to subdirectory commit 48664e54773cfceba838155f49b70da3d89ffec5 Author: ann Date: Tue Nov 8 17:44:40 2005 +0000 Edited per Susan Sunkin's suggestion commit c7162161720a732afc06991b6db4a0d084dff431 Author: aamp Date: Tue Nov 8 17:41:55 2005 +0000 Oops I checked in code that prevented compilation. commit e529322747178dfd67d895c468b78ed98e749bc6 Author: kent Date: Tue Nov 8 16:20:57 2005 +0000 Seems to work commit 61cec6c761563880dbe0d35db7db5b81e74d63fb Author: donnak Date: Tue Nov 8 16:20:06 2005 +0000 Made a few minor edits. commit 2c0c7111e0728ba3cf74138392028ccf0953be1b Author: giardine Date: Tue Nov 8 16:14:35 2005 +0000 Added not available under headings, if there is no data for that section. commit 86d2632512c386cd503dd15a936581115139a156 Author: giardine Date: Tue Nov 8 16:12:01 2005 +0000 Added explaination about subtracks checkboxes. commit 45e97735c34e11880685abd6d683cc11b030cc93 Author: galt Date: Tue Nov 8 16:00:03 2005 +0000 "Encode release log update" commit d0ce3c32cb0ab43b0ca2a13c310d0b4f1ca93692 Author: galt Date: Tue Nov 8 16:00:02 2005 +0000 "Release log update" commit 7ea8b50c28600e8d5cfe5d8afb48c3ec7a9f40c0 Author: kate Date: Tue Nov 8 01:55:11 2005 +0000 Tweak commit e5785e6043626c471af8c23855f26b84f9c20387 Author: kate Date: Tue Nov 8 01:52:33 2005 +0000 Yale and Uppsala data commit d0637e60f2a987f0798877dff9a3d8a7001e5eb8 Author: kate Date: Tue Nov 8 01:50:38 2005 +0000 ENCODE Chip/chip from Sweden commit 6cc8bb43889a57d66e90d0cc942094735dbb98eb Author: aamp Date: Tue Nov 8 01:37:10 2005 +0000 CGI for updating MGC RTDB database. Still a rough cut. Needs hg.conf configurability. commit 64de80e1811ea9695b9ec7f4a0aaeaf9fb0a5299 Author: aamp Date: Tue Nov 8 01:34:57 2005 +0000 Changed makeDir stuff to allow optional parameter for directory permissions. commit 8eaabedf7cc289bfe1e92f24ac98df5a779b9e0e Author: fanhsu Date: Tue Nov 8 01:16:06 2005 +0000 Created kgResultBestMrna2.c, used for KG build. commit 0b04c1813fdd4869b0ec19ba6e76facb31ad670b Author: fanhsu Date: Tue Nov 8 01:14:49 2005 +0000 Updated makefile. commit 97063c1367b3742f834c4a31f5c5bf01eddadb14 Author: fanhsu Date: Tue Nov 8 01:13:16 2005 +0000 Created kgResultBestRef2.c, used for KG build. commit 65228a9ffe42eda7663cf35b748fcb8a764ac867 Author: fanhsu Date: Tue Nov 8 01:12:44 2005 +0000 Created makefile. commit 21e04aad44cfc8da1c01de1dcf8593ff53ffebe3 Author: fanhsu Date: Tue Nov 8 01:05:58 2005 +0000 Added the initial part of KG build. commit a2ed6f68846b482a547b559365bce1de6b07494f Author: galt Date: Tue Nov 8 00:25:31 2005 +0000 closing stdout before exit is needed, otherwise this error occurs and the cgi aborts with error 2 [gzip: stdin: decompression OK, trailing garbage ignored] commit 8e49afe81c4ef57599ea992a57cf269e19a5945a Author: galt Date: Tue Nov 8 00:01:34 2005 +0000 changing it to use Marks new openMem1 pipeline interface commit f273358c299155a6c13c87e2de2bf92bedfca0ce Author: galt Date: Mon Nov 7 23:59:47 2005 +0000 changing ptr conversion method for sparc c-compiler compatibility commit e64a34e4047cbbe0379a5a40d20849b08570ed4e Author: galt Date: Mon Nov 7 23:26:44 2005 +0000 adding support to use mime.c to parse multipart forms/file-uploads commit a9b14d57c6ddd263df1cc6e8679d008f53245e49 Author: kate Date: Mon Nov 7 22:56:31 2005 +0000 Split ENCODE Yale Transmap by release commit e80c0137e371d6149ae051f06d62b02fc4cc5244 Author: galt Date: Mon Nov 7 22:54:10 2005 +0000 (temporarily) increasing threshold so that temp files will not be used commit f4fe6f44272561141d8348a41d25ce060e737cd9 Author: galt Date: Mon Nov 7 22:44:32 2005 +0000 test the file header (not just the filename) when deciding if it will go thru the decompression pipeline commit 394601ef8c43b14cdf7a5e96e9d4966fe6558220 Author: galt Date: Mon Nov 7 22:40:56 2005 +0000 adding support to use mime.c to parse multipart forms/file-uploads commit 4d3eaa74eba58f45fb2b2e4270ecd736fd5646a9 Author: kate Date: Mon Nov 7 20:39:40 2005 +0000 Split Yale TARs into alpha/beta versions commit afaa9829657783d8b17252728f13af3954d6f0a1 Author: kent Date: Mon Nov 7 17:11:00 2005 +0000 Updating xenopus laevis RNA and NIBB EST alignments. commit 5f315f3e53750209d1a50b1da6525f85e8a92a89 Author: galt Date: Mon Nov 7 16:00:08 2005 +0000 "Encode release log update" commit 00be9083fa52193a7c386401762e35d28d5b1c25 Author: galt Date: Mon Nov 7 16:00:05 2005 +0000 "Release log update" commit 673f4075245fee90d9bd12e327e3d969afa5d9e2 Author: lowe Date: Mon Nov 7 07:14:18 2005 +0000 New version of automatically generated description file commit 31092180923fa92b8597749d3133db5bddbfd5f0 Author: lowe Date: Mon Nov 7 06:58:47 2005 +0000 New version of automatically generated description file commit 72b8a062311b12fe53014254b98dc1204ffe95e4 Author: lowe Date: Mon Nov 7 06:46:25 2005 +0000 New version of automatically generated description file commit cf7a5b1663cfc86106a17a5ade920a529ada30a9 Author: lowe Date: Mon Nov 7 05:01:41 2005 +0000 New version of automatically generated description file commit 67d07f38ffa35e7391df7f041ee2c55f72408c72 Author: markd Date: Mon Nov 7 03:53:11 2005 +0000 work on extFile check optimizations commit e7740f91d8543b0a802a2ec11c6e7847bd28895d Author: markd Date: Mon Nov 7 03:36:55 2005 +0000 disable extFileUpdate until performance fix completed commit 432c1c46196b16c7bede3636419c1168915a0617 Author: fanhsu Date: Mon Nov 7 03:25:55 2005 +0000 Updated blastOut.c to print out the target sequence name and length in the detail result section only once. commit 52184a432ae548a0afe4d5ac60039a90450b8c4a Author: kent Date: Mon Nov 7 00:54:00 2005 +0000 Fixed bug in findBestGapPos. Not stripping symbols in makefile. Removing rescoring test. commit 9ec558f5599abfc783cd4d332941adad64216790 Author: kent Date: Mon Nov 7 00:48:01 2005 +0000 Putting in check for score consistency. Making default output omit dynaDrops info. commit 0a75f192b14c6790a1eaad85fd0a250bd1a4e2b0 Author: hiram Date: Sun Nov 6 23:13:10 2005 +0000 Add quartile calculations and tabluar output option commit 258787d5146d939027010ec0f225543f35e90296 Author: markd Date: Sun Nov 6 22:57:43 2005 +0000 reset optimication commit c8792e2ef5d04d1d091fb1f7d5f6b791a2821d50 Author: markd Date: Sun Nov 6 22:56:26 2005 +0000 increased the size of several hash tables commit 41c7a0fd492bbe417d8a24269fd2a5e23eee34da Author: lowe Date: Sun Nov 6 21:21:47 2005 +0000 New version of automatically generated description file commit dc46185189f316f09bf007f87c8214f8d0ebba03 Author: lowe Date: Sun Nov 6 20:07:04 2005 +0000 New version of automatically generated description file commit 3bbf1cccd6c26ea18f06afeec0eece4af2395a6d Author: lowe Date: Sun Nov 6 20:04:21 2005 +0000 New version of automatically generated description file commit 79f53130695be0fb990a33f078c998111e25b2ee Author: markd Date: Sun Nov 6 19:39:00 2005 +0000 speed up extFile updates by tracking of releases that have already been updated commit 9cbb54f21e24d114f0e5a894a66595b0679a3d66 Author: lowe Date: Sun Nov 6 17:37:57 2005 +0000 New version of automatically generated description file commit 3fbec1051e01eaa1987c73bb040f5ab2b0ca8060 Author: lowe Date: Sun Nov 6 17:27:38 2005 +0000 New version of automatically generated description file commit 35ab9b62d83ecadfc7455a3a097c233dec47eaf2 Author: kate Date: Sun Nov 6 17:17:54 2005 +0000 Update ENCODE Yale TAR (and partial update of Yale RNA track) commit d92d7dd2f35524a40ccd15f4add8d55fc193ef19 Author: galt Date: Sun Nov 6 16:00:06 2005 +0000 "Encode release log update" commit c362cf3c689723794eb86fe06240debb47bdd3c8 Author: galt Date: Sun Nov 6 16:00:04 2005 +0000 "Release log update" commit 641815c2a8a404ec249350d61f249e80363d6c16 Author: lowe Date: Sun Nov 6 08:50:10 2005 +0000 New version of automatically generated description file commit 60cd2733b06f1c1f26d472ff218063aa1eeaeff1 Author: hiram Date: Sat Nov 5 23:57:05 2005 +0000 Add Gencode Exonic and Other ESTs to the unannotated TARs and TFs commit 81aa0828ee23d90f803eaabc61fd15c52ce8f09f Author: kent Date: Sat Nov 5 16:44:08 2005 +0000 Updated comment commit 5ea53671725bce9db5ce96a9e48a6f7681bd1582 Author: kent Date: Sat Nov 5 16:43:27 2005 +0000 Updated explanations of search. commit 0e6415bb7cb7222f6a3cb41c9ae328bc0d34d431 Author: kent Date: Sat Nov 5 16:42:53 2005 +0000 Changing several fields to long long commit e889f7354d10e15bce38186cf83ef470c61a5040 Author: galt Date: Sat Nov 5 16:00:05 2005 +0000 "Encode release log update" commit b1a4750e4a08e23ff76651267d77c217142451d6 Author: galt Date: Sat Nov 5 16:00:04 2005 +0000 "Release log update" commit dc58a7a6e8f779e2204c617d7c8f249937063bde Author: kent Date: Sat Nov 5 07:14:54 2005 +0000 Adding table update summary. commit 3641a4cbfd7ae34ed95dabce5b4f8eec0398e24d Author: heather Date: Sat Nov 5 01:06:37 2005 +0000 basic makefile commit 82ff9e673fc1d44bd78b589680d5f3656fb1114d Author: heather Date: Sat Nov 5 01:05:41 2005 +0000 initial revision; gets coords, class and observed commit 5ad6a65e65d0d22f0568e56bd374b99f64640bfb Author: kate Date: Sat Nov 5 00:39:35 2005 +0000 Correct removal of score box from Gencode Introns settings commit 1e6744c05fc6146cee98fe72ce33da16cb48be87 Author: kent Date: Fri Nov 4 23:40:59 2005 +0000 Suppressing inaccurate cardinality printing in split table case. commit aa18b6b1c2331e2288d85397b519982a0f260119 Author: kent Date: Fri Nov 4 23:28:34 2005 +0000 Adding more info to index output. commit 4b6ef4d32fc66c166c8ea739df2bf0acbc1a395f Author: markd Date: Fri Nov 4 22:41:01 2005 +0000 increased dbload logging level commit e84cb4aef31220dbccc6165f0646e6d899e52960 Author: markd Date: Fri Nov 4 22:40:13 2005 +0000 make verbose logging more consistent at each level commit c421672de7744ae58787854238cbe0dd2b38caab Author: kent Date: Fri Nov 4 21:02:05 2005 +0000 Adding info on indexes commit 676aa0dd09a5a760e64273d55c5730fdf722d93b Author: galt Date: Fri Nov 4 20:05:13 2005 +0000 changed order, now shows file prevrev --> newrev commit a6f6d7f560e8509d8143e19b1f08663471bba834 Author: kent Date: Fri Nov 4 19:58:36 2005 +0000 Swapping table size and table fields sections commit 83118718a8c3d5275813d1db55971f5d6cbe4a20 Author: kent Date: Fri Nov 4 19:46:42 2005 +0000 Adding overall database summary, table size section, and unsplit option commit f03eb9251609021a67bb727258c95263b28c54ef Author: kent Date: Fri Nov 4 19:38:13 2005 +0000 Might work. commit ea2c067ab29fbb61870eb09fdd518fd685a35893 Author: galt Date: Fri Nov 4 19:36:30 2005 +0000 added support for logging previous revision. used to display file newrev. Now displays file newrev oldrev commit fc9203cc7a9d6a2208a5fc8ee430b73e6a216f76 Author: fanhsu Date: Fri Nov 4 18:57:16 2005 +0000 Added protMrnaBlast table, used for new KG II build. commit 46a53048f3fde3928d550bafdf91f01691f6e7cf Author: daryl Date: Fri Nov 4 18:42:04 2005 +0000 Updated LS-SNP Functional link commit 00562478a58c800c3d7484e2b1fa3cf80b5b3a8c Author: angie Date: Fri Nov 4 18:09:39 2005 +0000 When doing a subtrack merge of beds, apply the filter only to the primary table. commit afc9740808590b0cbfbe85b51b2ae46dcfecd44d Author: kent Date: Fri Nov 4 17:29:52 2005 +0000 Adding tableStatus, which contains results of mysql show table status command commit ac60e099727454302de1074fe0d56ea739fb10f1 Author: donnak Date: Fri Nov 4 17:12:52 2005 +0000 Created this redirect page. commit 7801292dd2010e660fbfb536da376974dec8d7f3 Author: kent Date: Fri Nov 4 16:34:45 2005 +0000 Added a warning about missing data that catches an error Ann Z. found during QA. commit fad1119588f8c446d8084da027a9c81e097351bf Author: giardine Date: Fri Nov 4 16:07:02 2005 +0000 *** empty log message *** commit e50716855aa95e141e99cc938cdb0a24d4fa3337 Author: giardine Date: Fri Nov 4 16:06:42 2005 +0000 Changed human phenotype track to composite track, added table for ethnic background. Also started with new data dump from HbVar, at least 1 new entry already! commit ec67f419e0ba3544cd946ed4019aaa155cff6446 Author: galt Date: Fri Nov 4 16:00:08 2005 +0000 "Encode release log update" commit 09987fce1bea3e8bb1ab174104c0686ccef7211b Author: galt Date: Fri Nov 4 16:00:07 2005 +0000 "Release log update" commit 2531a247a4c49d5d63089f8e0f99d5256c98d6fd Author: markd Date: Fri Nov 4 08:14:33 2005 +0000 minor change to setting verbose lvel commit d912dbc7b8ae881df54b096b2056001eb0420797 Author: markd Date: Fri Nov 4 08:11:02 2005 +0000 increased verbose level commit 234803f1ca32304980b965c2543ceff85275ef7e Author: markd Date: Fri Nov 4 08:07:38 2005 +0000 changed time loggin to get more info commit 642f288877002a7f21aaa0a2d7ce162cf7d4aeec Author: daryl Date: Fri Nov 4 03:44:24 2005 +0000 Added LS-SNP tables commit 76b108e88b50342b0ef82a741db795c5ff7429e9 Author: daryl Date: Fri Nov 4 03:39:01 2005 +0000 Update to LS-SNP links for Structure and Function (hg16 and hg17 only) commit 7eeabf964b16c0f2664523de101032147471f671 Author: kate Date: Fri Nov 4 01:32:04 2005 +0000 Shorten Affy labels commit 744498902691ae9273c7b7f64a3dc70ec2969d79 Author: kate Date: Fri Nov 4 01:28:19 2005 +0000 ENCODE Oct. freeze Affy Chip tracks commit 6701290923b1ef1e4b24785d7c4054cd8f7ff40e Author: kate Date: Fri Nov 4 01:26:58 2005 +0000 ENCODE Oct freeze Affy Chip tracks (soon to move into include file) commit 12b8224d79f19d82c4de7535a35b3262c1c0e9d0 Author: kate Date: Fri Nov 4 01:26:06 2005 +0000 Add include file processing to trackDb.ra commit c6b324ceec172f19b504098fc936a7bf27bfd8e8 Author: kate Date: Fri Nov 4 01:11:30 2005 +0000 1. Fix score filtering for subtracks 2. Make sure changed subtrack settings are remembered commit 3b6a30fbb7aed4970cad6c741934ace29ff64bbc Author: hiram Date: Fri Nov 4 00:28:05 2005 +0000 Add -shoulderBed and -distOut options commit 8ac55f546d0fd6b0f3b27797e762d4ed4fff04f3 Author: ann Date: Fri Nov 4 00:00:44 2005 +0000 Added Methods section. commit 8de4cf167529be18e33c67679e958948f30f730b Author: kate Date: Thu Nov 3 20:41:15 2005 +0000 Back out map box mods from 1.1023 that are causing problems in full mode. This is Chuck Sugnet's change, so need to verify that his recent track is still OK commit 71fad8ba4442a3e36b14d32e888061a4270de5c6 Author: donnak Date: Thu Nov 3 20:27:39 2005 +0000 Added a link, changed the section headings to correct font. commit 4997859c2390e8dca083c1fec2bf46644c9d5e5a Author: ann Date: Thu Nov 3 19:45:35 2005 +0000 Augmented link to Allen Brain Atlas to target=_blank commit 5f6260ac63dba869b2e15ccd2516623287a01ebd Author: kent Date: Thu Nov 3 18:01:26 2005 +0000 Fixing bug found by Jean-Mark Aury commit 093422811407d6a9600fd61174065353d4b28948 Author: kent Date: Thu Nov 3 17:53:57 2005 +0000 Adding naForEmpty (similar to naForNull) commit 1cbb164a4a13bc0ad89d9409197a19721db4d738 Author: braney Date: Thu Nov 3 16:37:08 2005 +0000 check for matches in toupper() case in mafs, don't do anything with spaces commit 1dfa4e72527b66900a62e8ba4e9d1d907b25df90 Author: galt Date: Thu Nov 3 16:00:03 2005 +0000 "Encode release log update" commit 5c884ab755ed27fe979ab17d6b4730edebbf8d55 Author: galt Date: Thu Nov 3 16:00:02 2005 +0000 "Release log update" commit f7924213745a3e0df7418187f07fa0255c6d1dae Author: kent Date: Thu Nov 3 06:49:22 2005 +0000 Adding another test set. commit 6348bd19eb1955b99757385acfc8ba7a6aca2a05 Author: kent Date: Thu Nov 3 06:49:04 2005 +0000 Creating new probe on same gene when primers aren't the same. commit 2da68fd78421b97174737b25b54561d892008e16 Author: galt Date: Thu Nov 3 01:22:01 2005 +0000 fixed typo in usage() commit d55584f589f011f650d7d29ab68cf09913cf263c Author: angie Date: Thu Nov 3 01:07:47 2005 +0000 Added target for checkAgpAndFa. commit 4471f1460527a323d0d9a035abad987537353e3a Author: donnak Date: Thu Nov 3 00:31:28 2005 +0000 Updated references. commit aedbba4e58475187220f0ae5028e23b7f8171c1f Author: angie Date: Wed Nov 2 23:47:06 2005 +0000 Added highlightItem to doLeftLabels which contains the default code for drawing left labels when in full mode (when in pack mode, left labels are drawn in genericDrawItems). commit 2b8ded5e54b1aed31a808dd93be598e28015203a Author: kent Date: Wed Nov 2 23:33:34 2005 +0000 Adding probe page. commit 154e06b7f9b1b10e41461a1700e100caf37b49b9 Author: hartera Date: Wed Nov 2 21:35:54 2005 +0000 Removed freeze data from long label of Gencode Genes subtracks. Updated table name for Gencode Gene track searches. commit 7a6849080c3e50d247c09f87fe2bf1f8924c8b4d Author: kent Date: Wed Nov 2 21:23:11 2005 +0000 Putting hyperlink around gene name in caption. This will eventually open up a gene & probe info page. commit 90a5e8d0f0b24a8fb1a67ee81a20b49589d34a42 Author: donnak Date: Wed Nov 2 20:43:09 2005 +0000 Made some minor edits to these files. commit 16effba9f9d178d4ce3dfe7d650b0fa23243665b Author: donnak Date: Wed Nov 2 20:37:47 2005 +0000 Corrected spelling of NimbleGen. commit debc194d2560d0c967e7a8795ce5f9885f38b212 Author: donnak Date: Wed Nov 2 20:36:08 2005 +0000 Corrected spelling of NimbleGen, fleshed out Display section. commit 11a99848c6d8924c3a9c539790365b475ee64d68 Author: kuhn Date: Wed Nov 2 20:23:02 2005 +0000 dropped redundant entry for gladHumES track commit d2f464268918dfc81d3b44589a8ca198bc0656b9 Author: jen Date: Wed Nov 2 19:53:04 2005 +0000 Added comment for removed lines from all_sts_primers (bad qName causing joinerCheck error). commit f2bf3e3cf7c83530d877e40a50842dd02f4e4308 Author: giardine Date: Wed Nov 2 18:09:31 2005 +0000 Moved this up to the human directory also. commit ffbd3710cf872fd43c1d35da9e13a5463d9b6f8d Author: giardine Date: Wed Nov 2 18:08:42 2005 +0000 Moved this file up to the human level. commit e5fc614a8b01329f9f2181411e8a6c1d6507a94c Author: galt Date: Wed Nov 2 16:00:03 2005 +0000 "Encode release log update" commit 6a7661e4461a9df684fc7825d7f23cc142f5c04c Author: galt Date: Wed Nov 2 16:00:02 2005 +0000 "Release log update" commit c81bce59a9a216810dfa1da98e86eb1b34234052 Author: kent Date: Wed Nov 2 05:23:10 2005 +0000 Sorting tables by number of rows they have. Adding table type section commit da2dccd83e36e71aa2c2c60c8d2776e97487cff7 Author: kent Date: Wed Nov 2 04:09:03 2005 +0000 Added full path commit 8f1c6ce5c2d06d71908a8923bbddbbffd441e6bb Author: kent Date: Wed Nov 2 03:44:13 2005 +0000 Seems to work commit c6d11e11478ceea4c48be2630a04b08e8032a39d Author: kent Date: Wed Nov 2 01:01:12 2005 +0000 Just some notes Heather and I are sharing on SNP build 125. commit 2a8812d58b51214bd07fa62c74e4e422a7c60ad3 Author: angie Date: Wed Nov 2 00:50:28 2005 +0000 In doGrepQuery, use lineFileChop instead of lineFileRow so that we don't require two fields per line (we only use the first field). commit 8980b7ece1a96ae2d180ffcc391f6f82447c78ca Author: kate Date: Wed Nov 2 00:19:25 2005 +0000 Add freeze for ENCODE Affy RNA commit 43f3dca6ed1d3014740b556df2c1b03067e7d65b Author: markd Date: Wed Nov 2 00:04:21 2005 +0000 disabled variable length dystring buffer x86_64 problem is debugged commit c8d6c5a460f92b5609aeac5db755a0d71be3ca66 Author: jen Date: Tue Nov 1 23:51:52 2005 +0000 Added dataVersion for track encodeGisRnaPet. commit f05cd8ef95440e25d1c4c14ec29c20f06a53e6f9 Author: hartera Date: Tue Nov 1 23:27:42 2005 +0000 Description for Gencode Introns track Oct 2005 freeze. Renamed from encodeGencodeIntronOct.html. commit 39a850f1951dcd1402eb7f12e3e33b7b23f99d83 Author: hartera Date: Tue Nov 1 23:27:12 2005 +0000 Description for Gencode Genes track Oct 2005 freeze. Renamed from encodeGencodeGeneOct.html. commit f73cce7f24da8ac236ea4e4f09b47012308c0d95 Author: kent Date: Tue Nov 1 23:04:03 2005 +0000 Explicitly initializing stack structure to all zeroes to make things more reproducible and to fix the 4-characters between | bug specific to opterons. commit 43f4faf7b0dd6942c2edd083ee6e16836df0a599 Author: jen Date: Tue Nov 1 22:56:55 2005 +0000 Added dataVersion setting. commit b7ff2a344873c31a594d460caf655b32bcab671b Author: kent Date: Tue Nov 1 22:43:19 2005 +0000 Trying to reproduce opteron specific pslShowAlignment problem in a simple case commit 163335dc221cca0c2aaed00adaa6a6d3476545eb Author: kuhn Date: Tue Nov 1 22:37:30 2005 +0000 changed 'replants' to 'replicates' in 8 files commit f2ff5ab7b2fad22faf0f092e395df844f9681dfd Author: jen Date: Tue Nov 1 22:14:22 2005 +0000 Moved Jun 05 version into hg17 (renamed with Jun05) and hg16 (no renaming). Human level is now Oct version. commit 5fd0a954b8106d9e0a27bcb750c71b2c7e5e2726 Author: jen Date: Tue Nov 1 22:13:05 2005 +0000 Moved Gencode from human to hg16. Humal level is now Oct version. commit 3c0fc8533f841089ff380b0f19a0794ba50ad87b Author: hartera Date: Tue Nov 1 22:10:59 2005 +0000 Renamed tracks for updated Gencode Genes and Gencode Introns. commit 157f13cba886983506fa7dcd698c5596b908f2f0 Author: jen Date: Tue Nov 1 22:08:44 2005 +0000 Moved to hg16. Replaced with Oct at human level. commit b8b18fc82a6e5eedd19dab9607583bfd211c4de7 Author: jen Date: Tue Nov 1 22:06:28 2005 +0000 Create trackDb info for GencodeGene/Intron Jun 05 commit 0f9c01f526a9345b39c86943acaa13bffd457940 Author: daryl Date: Tue Nov 1 21:38:43 2005 +0000 Fixed tag -> commit b1436f259b58d36f022d7a716c93bcd58ef70f46 Author: kate Date: Tue Nov 1 21:34:43 2005 +0000 Add dataVersion setting commit 2ebec231577d57e34e860c6377bac319346490d8 Author: kate Date: Tue Nov 1 21:34:29 2005 +0000 trackDb.ra commit b40c524347d1fe1f48f78cfa276136d413f63be2 Author: kate Date: Tue Nov 1 21:31:48 2005 +0000 Add support for dataVersion trackDb setting commit 061e141b1b391ef16450c6be31cda3bf3faa2d5d Author: aamp Date: Tue Nov 1 19:52:00 2005 +0000 Just an extra routine to check an md5 sum. commit 6044b407e2da33509760d817de5f92bb3c7b7692 Author: kent Date: Tue Nov 1 17:05:09 2005 +0000 Fixing dyStringPrintf format string problem commit 68ed1085822e4496d0b0048a6131dfb100b719c5 Author: galt Date: Tue Nov 1 16:00:03 2005 +0000 "Encode release log update" commit 9a07ba4e9f8dbd48fcc2a6135837a5620735b47b Author: galt Date: Tue Nov 1 16:00:02 2005 +0000 "Release log update" commit 1bc6047ec6bc76e87197861935de4c80e191f9a4 Author: lexa Date: Tue Nov 1 12:20:30 2005 +0000 Replaced calloc and free calls by AllocArray, freez and freeMem. Added dynamic masking also to the parts of gapless.c, when multiHits was not true. Changed the command-line option name of dynaBedFile to dynaBedFileQ. Moved a few lines so that we avoid a "mixed code/declarations" warning message. commit 5acd478953b8b2b8fd47a2f2608d12b9d3b63e2c Author: galt Date: Tue Nov 1 03:19:07 2005 +0000 "New version number v120" commit 54104a66dc3e60da066783b5c5975c3819f8b9a8 Author: hartera Date: Tue Nov 1 00:50:56 2005 +0000 Changed name for Oct Gencode Intron and Genes tracks and added track handler for the renamed June 2005 freeze for Gencode Genes and Introns tracks. commit aec1ecdf870a905ad2626e994e35f91d151be28f Author: angie Date: Tue Nov 1 00:44:29 2005 +0000 Regenerated canFam2 axt & maf using latest netToAxt. commit b017619f545cd2e92eb26f8c097082dd8534d532 Author: angie Date: Tue Nov 1 00:43:37 2005 +0000 Regenerated canFam2 axt & maf with latest netToAxt; loaded three new tracks from Jackson Labs / MGI. commit f29ccb0fce36b7beb1b33791c59532fea262b2c2 Author: kate Date: Tue Nov 1 00:38:25 2005 +0000 Affy RNA from ENCODE Oct. freeze ready for Q/A commit 2c8542dc19d19540e528856c28b1d4111d43704f Author: aamp Date: Tue Nov 1 00:32:13 2005 +0000 Changed "replicas" to "replicates". commit 554dd105c53c10936565f80f025b630d04bb3d3a Author: kent Date: Tue Nov 1 00:30:48 2005 +0000 Adding sort to allenBrainAli. Updating match/mismatch scores in hg17 version. commit ba6002e42648609c0290a52154d8ae20037e0850 Author: kent Date: Tue Nov 1 00:29:39 2005 +0000 Adding dnaSeqHash commit afd89a367dcb25e67125247c8e7f6c2fe0928343 Author: fanhsu Date: Tue Nov 1 00:04:27 2005 +0000 Created sp051015 and proteins051015 DBs. commit 2459dbdaee2fab94e3fb29cb35810b47a2dacaf8 Author: kuhn Date: Mon Oct 31 23:46:42 2005 +0000 slight grammar changes commit 3e1270392f86bc377be0ca68f078eea20976528e Author: kuhn Date: Mon Oct 31 23:45:42 2005 +0000 slight format changes commit f8d0e0adf43ea852fdd29e37c6394931a39b47b6 Author: kuhn Date: Mon Oct 31 23:40:26 2005 +0000 slight grammer changes commit d25e862d3561ce99e87da28ecf5bbfa825b86e68 Author: aamp Date: Mon Oct 31 23:15:30 2005 +0000 Added the gladstone. Wow this slipped through the cracks. commit 4bd1f2b4007628a05f85f1e2a16959010b5ad30a Author: kate Date: Mon Oct 31 23:11:48 2005 +0000 Reorder in-progress tracks by submission date commit d264574e6f2cb9088b7db897edfab7194f883cf3 Author: kate Date: Mon Oct 31 23:06:58 2005 +0000 Date commit c3511e4322ecd4c1ccf474b6fde0f211c6f1faf1 Author: daryl Date: Mon Oct 31 23:01:41 2005 +0000 Updated LS-SNP Reference commit ccfa6e3449fc45d118f27089bd922d6d183ddc01 Author: daryl Date: Mon Oct 31 23:01:13 2005 +0000 Updated LS-SNP URL commit fb66ba9a72661c2997ed497c46889348d63a504f Author: daryl Date: Mon Oct 31 23:00:47 2005 +0000 Backing out incomplete changes from the last review. commit 51380107281686b471295efca9b864a317ce4d65 Author: kate Date: Mon Oct 31 22:45:45 2005 +0000 Add references commit bdb14a01f66b20535deeee1dd9baf87e2e3745df Author: kate Date: Mon Oct 31 22:38:49 2005 +0000 Update UTexas Chip entries commit 32b8b4955953ce13d4e2c3b6b8c56c62ff00672b Author: kate Date: Mon Oct 31 22:35:26 2005 +0000 Various commit 8a73b4b3c2737c60fd1605343123991ad5e4ad38 Author: kate Date: Mon Oct 31 22:29:53 2005 +0000 updates commit 2cf1b323c3b2a0ae156f2bf93ce216916c76506e Author: kent Date: Mon Oct 31 22:29:42 2005 +0000 Adding search to Allen Brain track commit a59bba34e50002b8830648b7dbc188c1258e63eb Author: kate Date: Mon Oct 31 22:28:12 2005 +0000 ENCODE UT Austin Chip ready for Q/A commit f4b9595cb78f5ba710544dd4da555ff8c87a26aa Author: kayla Date: Mon Oct 31 22:18:32 2005 +0000 rat needed it's own gnfAtlas2.html because the generic wasn't specific enough. commit 8068fe43465ef837325a18095e0bc6d18fd3892c Author: kayla Date: Mon Oct 31 22:17:38 2005 +0000 mouse needed it's own gnfAtlas2.html because the generic wasn't specific enough. commit 02d32b92f4c390b0b15ef114046b214bee274648 Author: kayla Date: Mon Oct 31 22:16:13 2005 +0000 human needed it's own gnfAtlas2.html because the generic wasn't specific enough. commit 2e1297b340d11836cf9ce96c41cde385d14dc6d5 Author: kate Date: Mon Oct 31 22:15:19 2005 +0000 ENCODE Oct. NHGRI DnaseHS data ready for Q/A commit 0d1bc1baba43758c2e63f3d756426e6ae508b76a Author: donnak Date: Mon Oct 31 21:47:25 2005 +0000 Substituted < for <. commit a83a4924f1135ed1b015fa48e0cf0710c8d6e503 Author: kate Date: Mon Oct 31 21:37:54 2005 +0000 Update for hg17 commit e913344db4fb851efb5ca0a862c113c9867fe121 Author: kent Date: Mon Oct 31 20:34:58 2005 +0000 Seems to work commit ac29c54dcaaaa1ca41514caf75c3177a5b102132 Author: kate Date: Mon Oct 31 18:45:37 2005 +0000 Expand description a bit commit a5d1b735506b7b66470e15840fbb47caeb5fb862 Author: galt Date: Mon Oct 31 16:00:05 2005 +0000 "Encode release log update" commit 4707eb473d325dbc47afc9e23dd04194cbd55eac Author: galt Date: Mon Oct 31 16:00:04 2005 +0000 "Release log update" commit 3ed98db5004ee606122211383134a306b93aa3f0 Author: lowe Date: Mon Oct 31 05:51:04 2005 +0000 COG sql script for loading archaeal COG info commit 8836a7e1a8f4f2927f06c8680ff11047cf0b48a1 Author: kate Date: Sun Oct 30 16:07:26 2005 +0000 UC Davis Oct. ENCODE data commit a7776bb3fc06f9242d2af707522d941d10fc01e9 Author: galt Date: Sun Oct 30 16:00:06 2005 +0000 "Encode release log update" commit a2894666a7bb00f593695aed2d8978268a7dd21d Author: galt Date: Sun Oct 30 16:00:04 2005 +0000 "Release log update" commit b6c2ff708c84e0e4a8dc68dad5c07b6f6515b8ed Author: kate Date: Sun Oct 30 15:27:03 2005 +0000 More tracks in progress commit d726f81ad7f0daf7391546b67402fc753ef92017 Author: kate Date: Sun Oct 30 15:12:58 2005 +0000 Regulome Oct. data commit d46c953e25a3a897be3ef66601354d96e4a8abd2 Author: kent Date: Sun Oct 30 05:31:31 2005 +0000 Adding Allen Brain track commit f4a69ede7eca4be95c072b1e60259374240163a0 Author: hiram Date: Sun Oct 30 02:29:51 2005 +0000 Add OtherESTs and Exonic tracks to G&T ENCODE group Analysis track, regions commit cae9dd7ef2f0442310e6bc29eb6c871849781556 Author: hiram Date: Sun Oct 30 01:43:56 2005 +0000 Add the LSR track for debuggin commit 75f7d06ee7e3b1720f37905c4a7478bef02b0ec0 Author: kate Date: Sun Oct 30 00:47:13 2005 +0000 Add ENCODE Oct. freeze Regulome tracks commit f1d4c9a293981f00e91885551a2c13a027831172 Author: kent Date: Sat Oct 29 17:30:15 2005 +0000 Freen goes to test some print format strings. commit de746f4e55d0b308955ea1111eccc6c24dfb5a7f Author: kent Date: Sat Oct 29 17:29:22 2005 +0000 Added a few comments commit 958b5e3b55bb3e568bf0da1bd5c5ecb4ebe8d35e Author: markd Date: Sat Oct 29 16:49:52 2005 +0000 speed up genomic mappings by not rescanning map psl for each block mapped commit f19296f38cd1f6e7a023ea547f7b3a69e70419ae Author: giardine Date: Sat Oct 29 15:36:31 2005 +0000 *** empty log message *** commit 20d2b9efd854bc2737a30ff0e960a6b49f1509b9 Author: giardine Date: Sat Oct 29 15:35:55 2005 +0000 Added search by hgvs name and aliases. Also altered dbId to be a separate ID for each db link. Moved .html file up to human, need to remove lower level files yet under hg16 and hg17. commit c6bd0d3147f85b6af205b8d364460e65584fd063 Author: galt Date: Sat Oct 29 15:00:04 2005 +0000 "Encode release log update" commit 3f49fd04f017a2a0b0bdd9869d827f6252b4c1a0 Author: galt Date: Sat Oct 29 15:00:03 2005 +0000 "Release log update" commit b8364e3c5038db90babf1c5bccdf379e0601f787 Author: markd Date: Sat Oct 29 07:27:08 2005 +0000 fixed typo commit 0cb209357528754711fa9da8f5a4d45375cdfc94 Author: markd Date: Sat Oct 29 07:26:25 2005 +0000 allow using chains directly for mapping instead of converting them to psls commit a94392f92e427cdd46b0bf53b6ce512caa790971 Author: markd Date: Sat Oct 29 07:23:44 2005 +0000 added functions for build psl commit 89810d2ebbf80c641f334b14059c417b9fe0c866 Author: markd Date: Sat Oct 29 02:54:59 2005 +0000 changed terminology to make code clearer commit 1044b3734927ae080e5f63dfa1627964e18b94ab Author: fanhsu Date: Fri Oct 28 23:17:28 2005 +0000 Added descritption lines to the result of KG fuzzy search on description. commit 594a5d92003a92d81729a8ee5fbf128df8330a36 Author: kate Date: Fri Oct 28 23:10:30 2005 +0000 Adjust priorities in encodeChrom group commit 37b6b0cb018391efa023f5dfb9ad8e16eb395ce0 Author: kate Date: Fri Oct 28 22:54:53 2005 +0000 Add ENCODE U Virginia TR50 track commit ec5aa5b4fdbea49d6046bc3df57b5ab3e7b62de1 Author: angie Date: Fri Oct 28 21:44:39 2005 +0000 In hgPositionsHtml, encode pos->name and pos->description for CGI and HTML before printing out since they can contain characters like ">". commit a7bd74fa1a89dc259365fa7d517f6f53771c2597 Author: fanhsu Date: Fri Oct 28 21:24:14 2005 +0000 Added spToProteinsVar. commit cfc351a18ae52c6ea096f92027bb5638ba75b959 Author: markd Date: Fri Oct 28 19:22:12 2005 +0000 removed string size restriction on dyStringPrintf commit 57def13c492d55a25b4cfd2ae1337150601b0e16 Author: kent Date: Fri Oct 28 19:15:53 2005 +0000 More work on allen brain track - putting it on mm7 commit 9e9decffcaa3cc918bfb38d10a9fe1ee6229f160 Author: kent Date: Fri Oct 28 19:15:08 2005 +0000 More work on allen brain track - putting it on mm7 commit d4104e8d5baa980dbe298298f1653f04196a9aa0 Author: kent Date: Fri Oct 28 18:37:38 2005 +0000 Starting to work on allenBrain for mm7 commit b3e20b873e57813143e7b499ae1605f3f827c037 Author: markd Date: Fri Oct 28 17:49:46 2005 +0000 move sql program exec code to common module commit e7fb8fe4dd6d3ece06e95fcb119fd5120f6c69fc Author: hiram Date: Fri Oct 28 17:31:36 2005 +0000 Clean short and long labels on the conservation track commit d0e64ed77502f54bf4b82a59375f1a2c2ddf6281 Author: hiram Date: Fri Oct 28 17:29:54 2005 +0000 Loading mafSummary commit e42a284c96ba201e1ab11ab49e6e300e18789722 Author: kent Date: Fri Oct 28 17:18:09 2005 +0000 Polishing Allen Brain column. commit 1f2df7997001cb4675821735242599b948d8a4c7 Author: kent Date: Fri Oct 28 17:16:47 2005 +0000 Changing order of creation of allenBrain tables to satisfy joinerCheck -times commit 0b63e21526c38bc90690b148ef6449fe86bd952e Author: kent Date: Fri Oct 28 17:15:58 2005 +0000 Increasing index size on allenBrainUrl since now have longer identifiers commit fcad3c539eba9520a9f5761445d9fd9649bb6747 Author: kent Date: Fri Oct 28 17:15:13 2005 +0000 Tweaking priority of allenBrain link commit f8f5409a0388a837bf2db9dcb5721d766783c724 Author: kent Date: Fri Oct 28 17:02:41 2005 +0000 Fixing and working around some warnings in dyStringPrintf commit f51fde1468fb38c23935acfb3873a283a9bb8d5c Author: kent Date: Fri Oct 28 16:38:54 2005 +0000 Clearing up warnings from dyStringPrintf. commit 3aa3a13e0c0458651f518ccff4045714bf72747b Author: galt Date: Fri Oct 28 15:00:04 2005 +0000 "Encode release log update" commit 3bde6bf5903046136c26af5a6b6515ff55a88e7d Author: galt Date: Fri Oct 28 15:00:03 2005 +0000 "Release log update" commit 07321eb6fe01daa0c0a6f0093d96ecf007825a99 Author: kent Date: Fri Oct 28 06:40:31 2005 +0000 Added allenBrainProbe identifier commit 1ddc01f75261ea2946389100f988e0f956518896 Author: kent Date: Fri Oct 28 06:30:56 2005 +0000 Adding Allen Brain Atlas track. commit 604fec2d9e04f421dafafed7567627e0b6ce183a Author: kent Date: Fri Oct 28 06:27:16 2005 +0000 Polishing text commit 84c939cd616d9d116f417a17dc46637a9b191bf2 Author: kent Date: Fri Oct 28 06:24:39 2005 +0000 Adding Allen Brain Atlas details page. commit bda85b5b9e1031f1324ed27bf8b83b3bb2330eae Author: galt Date: Fri Oct 28 06:20:54 2005 +0000 added routines to convert between pointer and size_t commit a4776720b6a65ffddbb6aa722ba768009a770a31 Author: kent Date: Fri Oct 28 06:17:31 2005 +0000 Adding rpToUrl.tab output commit c19a5b11c6696b11dd58c9ae5c0e329aba58a8a0 Author: kent Date: Fri Oct 28 05:44:52 2005 +0000 Adding database load info to allenBrainAli table commit 7b1f7191031ae2f4611625abc7970c122a2c7936 Author: hiram Date: Fri Oct 28 05:16:11 2005 +0000 Add in dasNov1 to the multiz17way commit 6a82bf100490cc2194adbfac423ba552b295e907 Author: galt Date: Fri Oct 28 03:35:29 2005 +0000 added call to new sqlUnsignedLong commit 3f3b0ccad2a035d76325f461fff0a41ea55970fe Author: galt Date: Fri Oct 28 03:34:47 2005 +0000 added call to new sqlUnsignedLong and improved the text parser as it looks for cr/lf commit 8992d7059b886c6caded7cfa843e75e4d9a011c4 Author: galt Date: Fri Oct 28 02:34:49 2005 +0000 added sqlUnsignedLong routine commit 4f074f5d7fc79e56e6debdaf50d8ff5243c3e22d Author: kent Date: Fri Oct 28 01:43:00 2005 +0000 Redoing allenBrainAli table commit 7ecad6743c4eed20eec6661cd68dd45a6198a5b2 Author: kent Date: Fri Oct 28 01:25:14 2005 +0000 Adding a couple of extra sequences. commit 8214eaf6610a2368ec3dac51e6978a427917f14a Author: kent Date: Fri Oct 28 00:46:02 2005 +0000 Mostly working. Waiting on a little data from Susan Sunkin to complete. commit 2615f09b80ee51efff2f5778269f102cefdda41f Author: kent Date: Fri Oct 28 00:45:40 2005 +0000 Added a few more extra seqs. commit f658ff4f54f83ca4ea698784219920ab211cce63 Author: kent Date: Fri Oct 28 00:16:29 2005 +0000 Adding in these sequences that are added by hand to the collection commit 914ff876748b1e76bb131ba852fd758a88f8faa2 Author: hiram Date: Fri Oct 28 00:06:06 2005 +0000 Rabbit swap loaded, corrected 17-way procedure to include all, missed dasNov1 before commit bcf789c1a7c4e5f162bfc3555057373affc5ca99 Author: hiram Date: Thu Oct 27 23:53:24 2005 +0000 First pass at the 17-way alignment commit f6ed6b4473d5dbf67961ce3177f6f39f7d19480e Author: markd Date: Thu Oct 27 23:36:52 2005 +0000 fixed quoting problems with hgsql and friends; removed duplicated code, added hgsqlimport commit dc1632ad50a445407d44284d1aa9e6a446f5f75b Author: fanhsu Date: Thu Oct 27 23:19:00 2005 +0000 Rebuilt gnfAtlas2Distance table. commit 7609f8bc411ac371d2c5af25a69650a6a227bae4 Author: hiram Date: Thu Oct 27 23:11:06 2005 +0000 Bring up to date with GENSCAN track and alignment experiments commit 985e977796027460e930e9d994730e7bafb42785 Author: hiram Date: Thu Oct 27 23:08:18 2005 +0000 Bring up to date with Mm7 alignment experiments commit bcb09e6f29803320c7ad88902ac022c6e9db1ff5 Author: hiram Date: Thu Oct 27 23:07:02 2005 +0000 Bring up to date with Cb2 alignments and Aceview track added commit fa1faa56705f5539ec88b38b3ffb1da24c1893cc Author: hiram Date: Thu Oct 27 23:06:21 2005 +0000 Bring up to date with remanei alignments commit 59f42cf141e0608f24734fbf9ffd4ca557addb6f Author: galt Date: Thu Oct 27 23:03:10 2005 +0000 fixed error converting string to pointer commit 375a601d6ff8c41037c63ab420dc12679d5978e1 Author: galt Date: Thu Oct 27 22:57:16 2005 +0000 fixed error converting string to pointer commit 031ca0167551891ec190d4e91b0a15fc3087a2d1 Author: hiram Date: Thu Oct 27 22:55:30 2005 +0000 Beginning the 17-way alignment commit bb3c876abbd39fd560ce01dd8b807f67c5280601 Author: kent Date: Thu Oct 27 22:01:23 2005 +0000 Bumping up number of | separated words allowed commit 570e23a9d434ddb0334e2b6b21f10e87945feb41 Author: hiram Date: Thu Oct 27 20:04:57 2005 +0000 Add fixStepToBedGraph to install target commit c56798e734b9ae6b02535d2c2074c6ba01abb070 Author: hiram Date: Thu Oct 27 20:03:53 2005 +0000 Initial source commit 88a1038045c1261600e490dcff40724ed4d269b2 Author: kent Date: Thu Oct 27 17:44:23 2005 +0000 Adding year commit 77e57572b98ee13ed9fb1c8cd5346e5f872d81c9 Author: kent Date: Thu Oct 27 17:23:06 2005 +0000 Simplifying some code now that search is simpler. commit 67820d0e789388b4693ba987fe5828da4319e4ac Author: kent Date: Thu Oct 27 17:12:22 2005 +0000 Making it so that only images matching all search words are returned. commit c025517a67f1a0f05abb4ed1b0b3354f7ede5dd0 Author: kent Date: Thu Oct 27 17:02:03 2005 +0000 Adding format checking to dyStringPrintf commit 896a26195824efdd706e3617f651c3acefe24515 Author: kent Date: Thu Oct 27 15:33:20 2005 +0000 Adding wordBits field to visiMatch structure. This is a step in route to a more traditional search. commit d40b754781523f62f502847e3580687434177fd4 Author: galt Date: Thu Oct 27 15:00:05 2005 +0000 "Encode release log update" commit 8588fc780926416980cb64a72797ea9fd543658b Author: galt Date: Thu Oct 27 15:00:02 2005 +0000 "Release log update" commit 3422b7d85c14b7ef72fb98921cf6071dbe7f2cd1 Author: lowe Date: Thu Oct 27 14:21:20 2005 +0000 Update track for RNA gene files commit 192e5fcb8ec3906f5c7db6041484f2c3fe97a263 Author: lowe Date: Thu Oct 27 14:20:42 2005 +0000 New description page commit 172380e2130debeb6e4cd2235e8206791ac354ce Author: lowe Date: Thu Oct 27 08:47:01 2005 +0000 Added individual tracks for tRNAs or Genbank-annotated RNAs commit 42dbb5bfd30bfa6273ae9fdb15b266e8d060af6d Author: lowe Date: Thu Oct 27 08:46:26 2005 +0000 Added tRNA genes and Genbank RNA genes tracks commit 50f9be2fc0b85d7b1ea12105621d6e34994bd70e Author: galt Date: Thu Oct 27 08:46:20 2005 +0000 fixed performance problem finding Mac line-endings in getNextFlatLine commit bbbfb17c54ed389624e822de109320636e03c0c9 Author: lowe Date: Thu Oct 27 08:45:14 2005 +0000 Added specific table defs for different types of RNAs commit df7e4442032e458219f899aa8fa8df271e18372f Author: baertsch Date: Thu Oct 27 07:19:14 2005 +0000 archaea minor fix commit ecb861ad46900be1d56ce574768afb986517614e Author: baertsch Date: Thu Oct 27 07:02:28 2005 +0000 archaea - allow gi: or not for ncbi reference commit 17530c8a180511866512949b731145a82b1d0bf4 Author: kate Date: Thu Oct 27 06:02:49 2005 +0000 Sanger tracks commit e0b9921419b740ac860eabe6de807ffb2b24e8e6 Author: kate Date: Thu Oct 27 06:00:40 2005 +0000 ENCODE Oct. freeze Sanger Chip/chip commit 97e9975fbb63561b275d9fea317a6c4e1f9a304e Author: kate Date: Thu Oct 27 04:00:20 2005 +0000 ENCODE Oct. freeze NHGRI DNaseI HS commit ef1714890537c0a51aa0fec428f1ee5f769f9ccd Author: baertsch Date: Thu Oct 27 03:56:15 2005 +0000 read refSeq table for archaea species commit 06ebe1848ec54ade8ae1811804cc20125d83f183 Author: kent Date: Thu Oct 27 03:53:24 2005 +0000 Cleaned up code a little per Andy's review. commit 4d42ff211897a83bb582641af2d93d7b5d878109 Author: kate Date: Thu Oct 27 03:47:18 2005 +0000 ENCODE U North Carolina FAIRE data commit 3afbcd3acaf597e29559662541aa38e05bf5d991 Author: baertsch Date: Thu Oct 27 03:43:13 2005 +0000 update for archaea commit 8d80780964f936cb3eaa3a67f7539abd498560cb Author: hartera Date: Thu Oct 27 03:34:22 2005 +0000 Changed joiner pair list sort to a sort based on both elements on the pair and not just one. commit 52534c6ab2c540c1d1391a9967044de82ffb5ab7 Author: lowe Date: Thu Oct 27 02:16:50 2005 +0000 Changes made before auto genome-building script written -- just now checking in to clear diffs commit bf62da703f90fdc89e4f2dfe0b95fb0127399c43 Author: lowe Date: Thu Oct 27 02:09:42 2005 +0000 Removed unneeded tRNA track -- will fold tRNAs in with rnaGenes track instead commit 7a1f6fe2e6e3c047c6d726a004f93b85087c3857 Author: lowe Date: Thu Oct 27 02:09:01 2005 +0000 Removed un-needed tRNA track -- will fold in with rest of rnaGenes track commit 76f851e8bae40d4dda06dfd1dcf3c2d82ee28388 Author: baertsch Date: Wed Oct 26 23:49:14 2005 +0000 *** empty log message *** commit 46c4dd9997771a2d73909da5617c5b098688e965 Author: kate Date: Wed Oct 26 22:22:35 2005 +0000 update commit 969fde6180d31b103e181c3255a6dddb4ba72b53 Author: hiram Date: Wed Oct 26 21:37:10 2005 +0000 Moved danRer3 up one level commit 0cfa60cb06d619768a7566736e367945e3a34391 Author: hiram Date: Wed Oct 26 21:36:39 2005 +0000 Moved up one level commit 086d037b31f8b6ae7d80c217c63fd91ef7509f42 Author: hiram Date: Wed Oct 26 21:36:03 2005 +0000 DanRer3 can be at this level commit e4f7f162f17692435eb57a31554aad82812bb6b4 Author: kent Date: Wed Oct 26 20:38:41 2005 +0000 Adding sex to caption and search commit 977b301a8ce4543aea0b9b1083ce9fc35a88ed6e Author: kent Date: Wed Oct 26 20:26:25 2005 +0000 Adding visiGeneSex. commit ea2fa12a0eaee540e6dd296812b5f34f020a7beb Author: kent Date: Wed Oct 26 20:15:51 2005 +0000 Freen tests some visiGene stuff. commit 3ac903ecd262ccb488e2dd8c87b4bd5d3d81800e Author: kent Date: Wed Oct 26 20:15:11 2005 +0000 Updating instructions, mostly to include /gbdb/visiGene parameter commit 75cf02796318d64142792576acb903635d252ed4 Author: kent Date: Wed Oct 26 20:14:20 2005 +0000 Putting in instructions for allen brain atlas tables, which still are preliminary commit 4f6f9875942708620912147273fa2f4ba90a4d55 Author: kent Date: Wed Oct 26 20:12:18 2005 +0000 Adding Allen Brain Atlas link commit b9767638f2821d8a380e1a39eabbbf851be9a480 Author: kent Date: Wed Oct 26 20:11:46 2005 +0000 Adding a fairly minimal test target commit ea9b32a8ce001e51d6395c055d3d2937d8a0bd10 Author: kent Date: Wed Oct 26 19:53:02 2005 +0000 Changing handling of body parts a little so that an image that matches more than one body part in a search will score higher than one that just matches one. commit c052e8e3fc537c2a0b6572a36d17bc151ee3619d Author: kent Date: Wed Oct 26 19:51:07 2005 +0000 Adding comma to search results commit 047ab90960f20de4e6a349c26891a82322199453 Author: kent Date: Wed Oct 26 19:50:27 2005 +0000 Including sex in specimen table commit 6c7595175bcb4f07f1504764a73f85b5023d38fd Author: kent Date: Wed Oct 26 19:49:36 2005 +0000 Listing digoxygenin as a color since we don't know whether it will be red or purple - depends on how it is developed. Avoiding loading the Paul Gray images from JAX since we have them already separately. commit 30d96de322fe7579a16e71d0d925aff1c26a926f Author: donnak Date: Wed Oct 26 19:06:27 2005 +0000 Changed author search description to conform to that of other assemblies. commit eaa44d18c0e1afa7e87638248062f20cd96e2b20 Author: donnak Date: Wed Oct 26 19:05:16 2005 +0000 Changed double dash to —. commit 1e089475a4c0eb2f30dec8202428f3d06c154e8f Author: donnak Date: Wed Oct 26 19:00:38 2005 +0000 Edited author search description to conform to other assemblies. commit 08663f5bf17480dd031ff6a7dac9269466748814 Author: donnak Date: Wed Oct 26 18:55:34 2005 +0000 Made a tiny edit. commit 5ebbe8e74fd3abbb66f600080f46b03d98b6e6d9 Author: donnak Date: Wed Oct 26 18:53:25 2005 +0000 Made tiny edit. commit d89ef6ae97662ecf14e263761eb6ea6fd4ede0f9 Author: donnak Date: Wed Oct 26 18:50:40 2005 +0000 Edited the author format description to conform to other assemblies. commit d4e212a9ea566ea234371d379ad83fa820c5e3bc Author: donnak Date: Wed Oct 26 18:15:20 2005 +0000 Edited this file, changed reference to use our standard format. commit a43252374dd87fea9acbe968f17cd7ae1b17a4f9 Author: donnak Date: Wed Oct 26 18:07:50 2005 +0000 Changed double dash to —. commit 976ab0fce215a58e90f7fb066e52dbbb36bc7d78 Author: donnak Date: Wed Oct 26 18:06:59 2005 +0000 Fixed incorrect page numbers in citation. Change double dash to —. commit 61b87d29d1227c4e7204c2a0917f940ec47d87c2 Author: fanhsu Date: Wed Oct 26 17:56:27 2005 +0000 Corrected hardwired commentType for DISEASE. commit c6895595d8da593ffc0e7ed5ef6aaf06a9b8bacc Author: angie Date: Wed Oct 26 17:35:01 2005 +0000 Error message enhancement and bugfix in axtSubsetOnT() from Michael Pheasant. commit 57bf907f30f2d99dc7910361ecdc55de2e3510f6 Author: kent Date: Wed Oct 26 17:00:19 2005 +0000 Slight polish. commit c492f87034187c842f5020dc409416b8b2e71fa9 Author: baertsch Date: Wed Oct 26 15:55:54 2005 +0000 copied from fan's tree - seems to work commit 7a15ecada893d4081beaed02b41e637902dfb2bb Author: galt Date: Wed Oct 26 15:00:04 2005 +0000 "Encode release log update" commit c8d25a834ef2df36c232272d3eeb2a1f00791f15 Author: galt Date: Wed Oct 26 15:00:03 2005 +0000 "Release log update" commit 168cfe68c2432b4c054936aae60783cbcf5ccb9d Author: kent Date: Wed Oct 26 14:53:10 2005 +0000 Moved around code a little to get rid of warnings about mixed declarations and code commit 2785fabf3baaee03eb4ee1fba10a13c221ec0fc2 Author: kent Date: Wed Oct 26 00:32:29 2005 +0000 Put in hgBotDelay call in maf details page. commit 9b150ec4b939d7d75c05fb6d0d69cd8ac91dea18 Author: markd Date: Tue Oct 25 23:46:06 2005 +0000 fixed 64bit problem in printf format commit 9a1967bf8e4961485c39b2187cbb4d0c7841d69a Author: kate Date: Tue Oct 25 22:03:35 2005 +0000 Mods to ENCODE UT-Austin Chip/chip commit c6afca3b8e7081ea761ae90cbbf37bfe30a4bb72 Author: hiram Date: Tue Oct 25 22:00:39 2005 +0000 span is only winSize-overlap, not just winSize commit c17b5e574472fec8381427afbf16d69ba4c84bc6 Author: jen Date: Tue Oct 25 21:32:30 2005 +0000 Documented changes to hapmapRecombRate table. commit c8b7fe2b0a3ad4507e73c3af0d649645b2835ec6 Author: ann Date: Tue Oct 25 21:03:08 2005 +0000 Capitalized Blastz Dynamic Masking commit a88015708d7471615691e8709811bddab58417fc Author: hiram Date: Tue Oct 25 19:26:31 2005 +0000 Proper ordering of all the chain and net alignments commit cb15a09ca146d0e8bac7956435519e3898409509 Author: fanhsu Date: Tue Oct 25 16:41:29 2005 +0000 Added kgBestMrna2, kgBestRef2, and pfamXref. commit 9943f3c117853e7067d2e78f555cc80e52aa6a6a Author: kent Date: Tue Oct 25 16:26:24 2005 +0000 Fixed bug where you got zeros at divider positions in text output of expression. commit 83e6bad012a3306d2dc2c5bb0fdbdcc3a6321c8c Author: fanhsu Date: Tue Oct 25 16:25:28 2005 +0000 Added hgKgMrna. commit 4c2783cdaf7f37742bbacb8b6e2e8a56eb2d9202 Author: fanhsu Date: Tue Oct 25 16:22:08 2005 +0000 Updated target directory for binary. commit 0c544f403d2daa22bb7694c14967973aad50add4 Author: galt Date: Tue Oct 25 15:00:03 2005 +0000 "Encode release log update" commit 66c3696f2856e5ca764ac6be3ab73de4722363e8 Author: galt Date: Tue Oct 25 15:00:01 2005 +0000 "Release log update" commit 317331a8e903e7b06e4838390cd7aeb95ee06ac1 Author: genbank Date: Tue Oct 25 07:56:48 2005 +0000 added new groups for mgc, and bcgsc commit 20f964d07a499a1f96ae588fc0220852e8515675 Author: markd Date: Tue Oct 25 05:35:51 2005 +0000 fixed coredump with drop on genePreds commit cd70aa1f32787efd173fc84eb321b66ce41e7278 Author: baertsch Date: Tue Oct 25 02:04:48 2005 +0000 various fixes for kegg and swiss prot details for archaea browser commit 571b240e4264eb0c8b45447543cf9153ef1a912b Author: baertsch Date: Tue Oct 25 01:50:31 2005 +0000 fix sql table check in uniProtFindPrimAccFromGene() commit 224d9349a3de002f5b36256935332679fbdfd86a Author: aamp Date: Tue Oct 25 00:31:04 2005 +0000 Red Flour Beetle update. Needs a few more tracks but alignments are FINALLY UP. commit 12bea003e6373751c888ae74235c0c2662dc4ae9 Author: kent Date: Tue Oct 25 00:14:05 2005 +0000 Adding allenBrainUrl table commit 5273432b117726a1d605d04b8efb176829623c9d Author: baertsch Date: Mon Oct 24 23:57:35 2005 +0000 check for table exists in uniProtFindPrimAccFromGene() commit ac7e884da90a3fbbbabd52d80706720f55cd48c5 Author: baertsch Date: Mon Oct 24 23:43:00 2005 +0000 add hPdbFromGdb() to uniProtFindPrimAccFromGene() to get prot db name commit ee38b569292e4289be9fc07fd7ff621a175f5b16 Author: kate Date: Mon Oct 24 23:25:49 2005 +0000 New NHGRI DNAseI HS commit 0b8d3124206272670b096edfe36cc97d92108c14 Author: kate Date: Mon Oct 24 22:34:28 2005 +0000 FAIRE track commit 4157cdfc2d67254377ffbc24868834297813b6bd Author: kent Date: Mon Oct 24 22:16:29 2005 +0000 Changing lineFileOpen to pslFileOpen so that program can handle psls with headers. commit 3070af2e40b2c12f8dbe4eb4bcb5fe919105ac5f Author: galt Date: Mon Oct 24 21:56:19 2005 +0000 new mime processing code, e.g. handling multipart mime-encoded form posts commit 1df46b7637253dd6d167f069b03e3f318c18613f Author: kate Date: Mon Oct 24 21:52:05 2005 +0000 Sanger chip/chip commit a3839485d11afe4482d95a746d3b80bb4b3d577c Author: kate Date: Mon Oct 24 21:06:16 2005 +0000 Affy tracks for Oct. freeze commit ed5af6c623fe79bdae24db8779f31ab0efbfec7a Author: kate Date: Mon Oct 24 21:05:11 2005 +0000 Misc commit 3651b8f8091a0d0f014ee76efa7d7f3e68660260 Author: kate Date: Mon Oct 24 21:02:04 2005 +0000 Start Sanger and Affy tracks commit 118776adf06e9c9059054ccc4535170401a7c50b Author: ann Date: Mon Oct 24 20:57:10 2005 +0000 Changed spelling (added hyphen) to Lineage-Specific Repeats in 4 places. commit c91d4dde5172348c4993897daae458914420aadf Author: kate Date: Mon Oct 24 20:30:50 2005 +0000 Fix typo commit 7a83c74501e244f67d0c4d68e855adae46209f4d Author: kate Date: Mon Oct 24 20:04:16 2005 +0000 tweak priorities on ENCODE Affy RNA tracks commit e5e5e9b6d36886567dd52bb2151a7c50db27603a Author: kate Date: Mon Oct 24 20:00:32 2005 +0000 ENCODE Affy RNA tracks commit 9508bbd18e963e14d3a76cf80b2baa26097a1c78 Author: jen Date: Mon Oct 24 19:51:05 2005 +0000 Set all human, xenTro and rat net tracks to hide. commit 9ac8fcb439fcb83a1a7f6a1a552570d50e26cc61 Author: braney Date: Mon Oct 24 19:34:50 2005 +0000 add canHg11 commit d5192760a043ce5105802d9fbd060869037d303a Author: braney Date: Mon Oct 24 19:28:10 2005 +0000 oops, take out cvs inserted lines commit 330817909b5b4966217e76a44e0956a7f77ebe82 Author: donnak Date: Mon Oct 24 19:26:43 2005 +0000 Capitalized Tetraodon. commit 64ff83e16cc91a7d8be3818d552a044fb9be7bea Author: donnak Date: Mon Oct 24 19:24:03 2005 +0000 Reworded 1 sentence in Methods section. commit c8247d84b1b0456e4a830a23664da141b8d7cb4c Author: galt Date: Mon Oct 24 18:41:10 2005 +0000 fixed range problem on cmpare function (double does not fit into int ) , now compare returns 1,0,-1 which is fine for the sorting algorithm commit 4a85bbac5b329fb10f4dcad9b9d25ddcab248923 Author: fanhsu Date: Mon Oct 24 18:07:46 2005 +0000 Added spDisease.displayID. commit 7b7f63098f7401a9f952516fadbd638f93dd7784 Author: fanhsu Date: Mon Oct 24 17:00:25 2005 +0000 Updated to reflect changes made to construct sp051015 DB. commit e1ee0473a10ab4f23166e62f2bfb2d5108faf683 Author: fanhsu Date: Mon Oct 24 16:59:28 2005 +0000 Updated to reflect changes made in constructing proteins051015 DB. commit 0dddd64c134b8bc152dd1f9139ffc1b72ffb658b Author: galt Date: Mon Oct 24 15:00:04 2005 +0000 "Encode release log update" commit 491d9384f7d3a742452c04237ada6a32af655dc3 Author: galt Date: Mon Oct 24 15:00:03 2005 +0000 "Release log update" commit 3fe2cfee16e73b8846cb402aab772370a85d4c12 Author: daryl Date: Mon Oct 24 07:49:04 2005 +0000 Updated LS-SNP links to reflect new snp-human release for hg17 commit 4661a5f9dfd51103e22f04c3331ad3ce9b31eca2 Author: lowe Date: Mon Oct 24 05:34:23 2005 +0000 Updated trackDb.ra in /bacteria to be same as in /archae commit 65564758ba257b75432e1ee8c3e38946502e6245 Author: lowe Date: Sun Oct 23 23:19:09 2005 +0000 Copied track files from archae to bacteria -- Todd commit 4178f47de82b9a7d9d2f5626d72054ad64e2a418 Author: hiram Date: Sun Oct 23 22:35:53 2005 +0000 Beginning to arrange chains and nets in order of evolutionary tree commit 38716f45b4ed4d13a5d3a3e54eb22c31c985d2bd Author: braney Date: Sun Oct 23 18:33:02 2005 +0000 a new ancestor commit 8dcb8a61cb2be90da67633e30a9072137fff1097 Author: kate Date: Sun Oct 23 16:52:30 2005 +0000 ENCODE Affy RNA track for hg17 commit 3bcd65f5adf0c1e634ccab748236c5b99135f4ef Author: hiram Date: Sun Oct 23 16:25:40 2005 +0000 Adding dasNov commit a5d6d2894e0b1284e64f025705ab68490aef676f Author: hiram Date: Sun Oct 23 16:23:24 2005 +0000 Adding rheMac, oryCun, loxAfr, echTel, dasNov commit bd6dca00c4651bf75ce58c816e5f4ba52c654a16 Author: hiram Date: Sun Oct 23 16:22:21 2005 +0000 Adding oryCun, rheMac, loxAfr, echTel commit 7bf0dadaf9637e9f14c2e1b43c41ca0064cf9a92 Author: kate Date: Sun Oct 23 15:41:07 2005 +0000 Replace whacked file commit 0e30ae0d54c63915ebbfbcc2a2b13b3a5b4910fd Author: kate Date: Sun Oct 23 15:39:11 2005 +0000 Cleanup commit 20622cee5db4e53df93414e65e89c0f037d19ea0 Author: galt Date: Sun Oct 23 15:00:07 2005 +0000 "Encode release log update" commit 3c04947999dd569042d6d22849a6e8125e8a2ed3 Author: galt Date: Sun Oct 23 15:00:05 2005 +0000 "Release log update" commit 07ced6b032ba192274eb2c2982d08034d6176ad0 Author: daryl Date: Sun Oct 23 07:56:21 2005 +0000 chr X data update for hapmapRecombHotspot commit d821414aa4c2b78daee8dd8f1f5beb155ac888d1 Author: daryl Date: Sun Oct 23 07:55:17 2005 +0000 Added hapmapSnps commit 9cbda83dd464b2775344c826bde490376aa84d7e Author: daryl Date: Sun Oct 23 07:54:41 2005 +0000 Significant update of hapmapRecombHotspots.html, minor correction of hapmapRecombRates.html commit cfafbb618be208c7a89b152202b18b27cae27cc1 Author: daryl Date: Sun Oct 23 07:51:49 2005 +0000 1. Restricted area map for hapmapLd track to (<200) items and (> 5x5) pixels. 2. Removed sum of squares calculations for hapmapLd dense mode. commit 44682a111e9ff343de354209f452d9097112b2f0 Author: daryl Date: Sun Oct 23 07:44:46 2005 +0000 override doMapItems for hapmapLd track commit 172599abb2608e5b701bdc9c7b2541d4190ab38b Author: daryl Date: Sun Oct 23 07:41:54 2005 +0000 1. Updated LS-SNP URL and links to LS-SNP. 2. Updated dbSnp links so that only rsIds will have such links. 3. Modularized cnpSharp details. 4. Changed some // comments to /* */ commit 86a42ca3ad359de1507577c40432e918c9c69881 Author: aamp Date: Sun Oct 23 04:16:23 2005 +0000 Empty initial trackDb.ra and description.html for triCas2 commit 8d158147a645c98271f185f7e41afdab7a67751d Author: aamp Date: Sun Oct 23 04:16:22 2005 +0000 Added triCas2 (red flour beetle). commit 0ee765eb0e758a73055c69e91c0a132bcf6ebf20 Author: kate Date: Sat Oct 22 15:49:48 2005 +0000 Tweak ENCODE UCSD Ng track config commit 0304879bd08d6f53bee21a4e3dc60e1f019022f6 Author: kate Date: Sat Oct 22 15:46:44 2005 +0000 Adjust ENCODE UCSD nimblegen chipchip track settings and update description commit 967e0eb6ce76a1c50b295c1a6942d3725e36b4ca Author: kent Date: Sat Oct 22 15:26:33 2005 +0000 Added report of number of things bigger than last bin commit 7c913f5d4c5d7013674574f1e025f9bb6a416055 Author: galt Date: Sat Oct 22 15:00:05 2005 +0000 "Encode release log update" commit 7b63d85fe3fdfca718153560ea225551ff3fac8f Author: galt Date: Sat Oct 22 15:00:04 2005 +0000 "Release log update" commit 294b4c22345d1cc61c3cf2686bfb6018992ecd62 Author: hartera Date: Sat Oct 22 03:20:18 2005 +0000 Unique list of joinable fields before printing out with the schema to a html page. commit 79083c8722041c68dcdb0a8246b00b167c791542 Author: heather Date: Sat Oct 22 02:32:05 2005 +0000 more output tweaks commit c59b1301835be0637b94f4f34ec8845abc397d56 Author: heather Date: Sat Oct 22 02:18:03 2005 +0000 change output commit c6fad4409d7f72eadcb08a3e9ac96a7c5036378e Author: heather Date: Sat Oct 22 01:04:40 2005 +0000 hard code hgTracks commit c8d229d9c34972f3bb1d7f96c79cbdaa1371351d Author: heather Date: Sat Oct 22 00:54:06 2005 +0000 print date and time commit 9101b32e15e054546a8707af75bfd3c2e68f48c0 Author: heather Date: Sat Oct 22 00:38:37 2005 +0000 read in list of machines to use commit 69d59f4df45bbfd6b50e0158f3be03bc1f94c77c Author: kate Date: Fri Oct 21 23:19:28 2005 +0000 ENCODE GIS PET RNA and Affy RNA tracks commit 2f3d74a57ae85ac6fe2eb4620a3007d2f6faddce Author: kate Date: Fri Oct 21 23:19:04 2005 +0000 ENCODE GIS PET RNA track commit 5de6adb42b95893a115060aa336a91f9d30cb3ac Author: kate Date: Fri Oct 21 23:18:44 2005 +0000 ENCODE GIS PET RNA commit a530b7b91bb25271540994802a9f494fc2f07f50 Author: kate Date: Fri Oct 21 19:31:24 2005 +0000 Fix date commit 22d3efe05b25e23bd14439eef834f09707f4f0f8 Author: kate Date: Fri Oct 21 19:30:11 2005 +0000 Passed Gencode and GIS RNA to Q/A commit 6f67a99bcf4377c943f5b46d05aed54d12eff9e5 Author: markd Date: Fri Oct 21 18:46:06 2005 +0000 added interface to get pipeline input from a memory buffer commit aca65d0beaab74dd1529f82e80c6359bf7a2754c Author: baertsch Date: Fri Oct 21 18:18:05 2005 +0000 simplified genbank load commit a4ccbc6f01f9b04c4b26d33d22dab03279af8120 Author: kate Date: Fri Oct 21 17:52:13 2005 +0000 1. Add searches for Gencode 2. Add 'smart' setting to Chuck's track for compatibility with new code commit d71ad1a8b6338915468e07fd00ae3198bfb23dbc Author: kate Date: Fri Oct 21 17:50:54 2005 +0000 Implement subtrack cart handling and track handler for October Gencode data commit 54012be94d1afcba3e3ddd474ee59b1d43c801ca Author: galt Date: Fri Oct 21 17:45:25 2005 +0000 added quickHeap commit 5cae183f015508a854f8cccbae4bc5386b0fccc0 Author: ytlu Date: Fri Oct 21 17:21:10 2005 +0000 add chrs that are recently anontaed by vega commit 4d8a13fa6805d18e75b8a94ab1e1e622c0186077 Author: galt Date: Fri Oct 21 15:00:05 2005 +0000 "Encode release log update" commit 9c446b7af72c419d9c2575d00c9069cf248378cb Author: galt Date: Fri Oct 21 15:00:04 2005 +0000 "Release log update" commit c61cd644c6301d92971aaee1a887d6c922d41953 Author: kate Date: Fri Oct 21 05:45:47 2005 +0000 Affy Transfrags and RNA signal commit cd3d6fc4745b663b60848b412e8c3e84e60380a5 Author: galt Date: Fri Oct 21 05:38:13 2005 +0000 changed over to using new general-purpose quickHeap library routines, which are based on the previous version of cMS commit 01269e94db596a0bdf023f502da4ca842f99ffeb Author: galt Date: Fri Oct 21 05:36:08 2005 +0000 adding quickHeap array-heap general purpose routines to library commit c25c065fe88fc1fd277a6b964211e13b0fdabf6c Author: markd Date: Fri Oct 21 03:54:47 2005 +0000 fixed bug with reverse source strand maf block containing multiple exons commit d40173a02696858ee7933c6164f99b008f4c24e1 Author: baertsch Date: Fri Oct 21 03:49:04 2005 +0000 add genbank refseq and cog commit f86b7e1ea3d6e0fa6a98f3e4315bb09fb8e423c7 Author: kent Date: Fri Oct 21 02:09:35 2005 +0000 Adding genotype to caption. commit 24b5691ba39328c77ff99f08b956876a81c3d873 Author: kent Date: Fri Oct 21 02:09:13 2005 +0000 Adding visiGeneGenotype commit f91d28da644f29fd2cd1df4dbfb6b44aed58c504 Author: kent Date: Fri Oct 21 02:08:50 2005 +0000 Adding sqlQuickNonemptyString commit 19731144f989e0a3fb3ac017fda330546c5825a7 Author: kent Date: Fri Oct 21 01:42:29 2005 +0000 Adding strain info to caption. commit edbb0f0717a37aef3942df0139a81e68843839db Author: kent Date: Fri Oct 21 01:42:19 2005 +0000 Adding visiGeneStrain commit 29b90c6b5a530b056f90999e51eeba79c3c3b830 Author: hiram Date: Thu Oct 20 23:54:05 2005 +0000 Needed by rosChr22Dat.c commit 9f81f58c05dd86944b43c5e1d0c1d574f0dbcb31 Author: hiram Date: Thu Oct 20 23:53:18 2005 +0000 An initial makefile commit fcc3f9e4c7887159db5d885e224068a643c2f463 Author: hiram Date: Thu Oct 20 23:52:24 2005 +0000 Initial source from Chuck's home directory, cleaned up to avoid warnings commit 17e4cc867ea279d5d8d00c08357e7edcdda689ab Author: kpollard Date: Thu Oct 20 23:22:02 2005 +0000 fixed punctuation commit 176252c455e035e86e6923fbbf8681e3f2ce27fa Author: kpollard Date: Thu Oct 20 23:06:48 2005 +0000 made description page commit e99f90d164e7f76159a9cd4a7a7c65bcf9fd799f Author: kpollard Date: Thu Oct 20 23:02:58 2005 +0000 description page commit cc94b5249c725476d2484587e1c4506d9ff9c30c Author: kate Date: Thu Oct 20 23:01:18 2005 +0000 Misc updates commit d75105d1d86fe21c6c71eb6e807e9831378169d1 Author: hiram Date: Thu Oct 20 22:41:01 2005 +0000 Added filter to STS markers processing commit 06403a7a2f85c9084962dd16328b416004cfaef9 Author: hartera Date: Thu Oct 20 22:36:12 2005 +0000 Added code for pslxFileOpenWithMeta so that if file contains only meta data, it does not abort. commit 65e780809fce55d7c9f6068f6b89a6af3aa4e8ef Author: kent Date: Thu Oct 20 22:32:31 2005 +0000 Suppressing double-hit on search when have expression data on multiple genes where more than one gene hits a tissue/organ commit e42db484532e2275489590ef2efb3e0ce1652470 Author: kent Date: Thu Oct 20 22:26:21 2005 +0000 Moving captioning stuff to new module - printCaption commit 8f80377c7331ea8cba742ec858e0936d1aacff32 Author: kent Date: Thu Oct 20 21:42:16 2005 +0000 Moving some stuff to library, removing unused code, and making several routines static with shorter names. commit f4b8f5f6f63b4fd2b82d3b74b30990e6b9282d6d Author: kent Date: Thu Oct 20 21:39:50 2005 +0000 Adding vgGeneNameFromId to library, and refactoring visiGeneGeneName to use it commit 1355fd9d2ec51223f2752a1bd663698918ac4842 Author: kent Date: Thu Oct 20 21:39:21 2005 +0000 Adding sqlQuickNumList to library commit a77db5ca40478a6b7af11c5ffc736159fbcfeb35 Author: galt Date: Thu Oct 20 21:29:42 2005 +0000 now expanded to handle even enormous numbers of files, plus new heapsort for keeping it quick commit 393a339611f6918439e06236a79f55418ee10b06 Author: kate Date: Thu Oct 20 21:25:19 2005 +0000 Postpone subtrack visibility processing. Reduces clutter in cart commit 2880dabef5571c91d525c5acaae8a299c45b24c3 Author: markd Date: Thu Oct 20 21:09:12 2005 +0000 added support to use in converting maf alignments commit f9b16aec077841ee020ae0e0f5a4d093c20ba7aa Author: kpollard Date: Thu Oct 20 21:07:00 2005 +0000 description file commit 98e024c2bceac6be1d9f7fcb5096a6f19d0459d4 Author: markd Date: Thu Oct 20 21:05:44 2005 +0000 fixed program commit 32b2cf5955c81c0f73bd3f03b629c7a20c6b427a Author: kent Date: Thu Oct 20 19:58:33 2005 +0000 Moving a function level comment to the right place commit 9d53bca0ba7cf43983c5a4e1a595c10d704c41cb Author: kent Date: Thu Oct 20 19:51:18 2005 +0000 Finishing up making expression work on panels with multiple probes. Removing a stray comma in case where had a whole list of unknown genbanks. commit 81c6d8bec71361291b70a88493d9daf8ef245af3 Author: hartera Date: Thu Oct 20 19:47:08 2005 +0000 Made 2bit files for Blastz alignments. Created danRer3 chain and net tracks and associated downloads. commit 0985531ed83e8715ca8ff935ec1365c9dc7e291d Author: hartera Date: Thu Oct 20 19:43:37 2005 +0000 Description for danRer3 net track. commit 3e341db380d7468e9222a9b636f242afa5ece2f7 Author: hartera Date: Thu Oct 20 19:43:15 2005 +0000 Description for danRer3 chains track. commit a4e15b8725125a512b2f04ac4c693b6c6616c488 Author: hartera Date: Thu Oct 20 19:42:37 2005 +0000 Added chain and net tracks for danRer3. commit f26ae07889d9c50d1ec6acbb58c75ff4b6501ad6 Author: kent Date: Thu Oct 20 19:25:21 2005 +0000 Improving caption when have info on expression of multiple genes in the same pane. It's not perfect yet though. commit eb0026402a459e202d64c8d577adb435bf9a807b Author: hartera Date: Thu Oct 20 19:21:32 2005 +0000 Finished chain and net tracks and associated dowloads for tetraodon (tetNig1). commit 5b2a7aa88f2952762da7c82b591cc63e062dca07 Author: kuhn Date: Thu Oct 20 19:17:22 2005 +0000 extended monitoring to parse apachelogs.access_log, too commit 18685e440fcb8d94ba69a630b183e461b12d1a98 Author: kate Date: Thu Oct 20 19:08:06 2005 +0000 Change gene class to enum commit 66b27e7e4883688affd372c860bb5ebad616f130 Author: kate Date: Thu Oct 20 19:00:53 2005 +0000 Reloaded Gencode Genes as per France D. commit 783f6750ad7198743a2073276d211806f70a45a7 Author: fanhsu Date: Thu Oct 20 18:50:16 2005 +0000 Updated wgRna track per updated data from Michel Weber. commit 4a3d00a7997622ad0aeebf82a44de9f9410cc068 Author: baertsch Date: Thu Oct 20 18:34:43 2005 +0000 check if table kegg exists commit 213d39bf86bd023db5b2ca12a4a33baa6e409436 Author: hartera Date: Thu Oct 20 18:30:38 2005 +0000 Description for tetraodon (tetNig1) net track on danRer3. commit ea2a17171f86ae595028b54772892ba1fae11239 Author: hartera Date: Thu Oct 20 18:27:59 2005 +0000 Description for tetraodon (tetNig1) chain track. commit 737d0bb3db574612473f3aabf3d00472bcc344e3 Author: fanhsu Date: Thu Oct 20 18:23:38 2005 +0000 Updated miRNA section with 1 line modification of data, per Weber's request on 10/18/05. commit 988ddfee5a283238d828ebf6a6e5e4caf72bff3c Author: hartera Date: Thu Oct 20 18:22:35 2005 +0000 Added chain and net tracks for tetraodon (tetNig1). commit 2ac6fa700f37a103c664b2ce325488b2ca289fc5 Author: kate Date: Thu Oct 20 18:01:32 2005 +0000 Update for liftover chains commit 605e4a13fe0e0cc5259a67522a979188f0a1a8d2 Author: angie Date: Thu Oct 20 17:45:22 2005 +0000 Added description of sequence masking (the difference between cpgIslandGgfAndy and cpgIslandGgfAndyMasked). commit 5801b6f75157ec8ab7c0354e7047a6687efd473e Author: markd Date: Thu Oct 20 17:17:20 2005 +0000 removed dead code; switched to terminology matching maf.h commit 94ce445bbf511bca29393ca72096a7bf4222186a Author: kate Date: Thu Oct 20 17:12:45 2005 +0000 liftover chains to mm6 commit 9cda4a3f00c8cf4aafc71e1bfba0e94d249ace21 Author: galt Date: Thu Oct 20 15:00:04 2005 +0000 "Encode release log update" commit 4012726d79d6a3cd5e9e470de453f75e02dc3c43 Author: galt Date: Thu Oct 20 15:00:03 2005 +0000 "Release log update" commit 3277359e2ab733710937b656442e899f3c9f299f Author: baertsch Date: Thu Oct 20 14:44:14 2005 +0000 add other genes in kegg pathway link commit 3077f28c8d9c90812fd049ae8088f84ea3aa6246 Author: baertsch Date: Thu Oct 20 13:31:46 2005 +0000 add kegg commit 7b1cd405cac541c087d5a247ba3c3819b0bedfe2 Author: baertsch Date: Thu Oct 20 13:24:11 2005 +0000 add kegg links for archaea commit 302aa2446f0e484c23e45c4f16b5148163f47e4f Author: lexa Date: Thu Oct 20 13:12:39 2005 +0000 Cleaned-up version of dynamic masking with bed file output and a second type of masking available. 1) Position-based masking is invoke by setting -dynaLimitQ and/or -dynaLimitT to a value <999999 bed file output is invoked by specifying -dynaBedFile=filename 2) Word-based masking is invoked by setting -dynaWordCoverage to a value >0 It is possible to combine the two methods. commit 632cd38bb79b525c1d416bdbfed96e1fda8843ec Author: markd Date: Thu Oct 20 09:03:12 2005 +0000 fixed bug with reading maf records multiple times commit 143cb4a08ecabdb8ee10fce8fed22c7be50892bb Author: markd Date: Thu Oct 20 07:56:39 2005 +0000 added mafFetch command commit ca9ea6624d9df65d6d307773aaa3ba30cb67639e Author: daryl Date: Thu Oct 20 06:32:22 2005 +0000 1. Updated map area to use 'hapmapLd' in stead of 'ld' 2. Fixed bug in selecting shade from negShades and posShades 3. Used tg->mapName in stead of explictly stating shortLabel commit 75990b48e5a148015cee7f442766f59900336a72 Author: markd Date: Thu Oct 20 03:19:11 2005 +0000 support great than 4gb files commit 83b26c44f9fee74323e768c0b632d94e4554adbb Author: sugnet Date: Thu Oct 20 01:15:32 2005 +0000 Fixing issues on affyTxnPhase2 track. Trying to make it so gif click map is laid out the same as the drawing phase. commit c7af387de302466112934f26105ca8284a9543e3 Author: galt Date: Wed Oct 19 23:42:05 2005 +0000 made geneid track for cow2 commit 96bcf79929078edac20189a79c6410b34e397b9e Author: markd Date: Wed Oct 19 23:40:21 2005 +0000 handle genes that map to multiple locations commit b4689386e7a7f216b4f74564fb1f8ec4dd3d30df Author: kate Date: Wed Oct 19 23:38:47 2005 +0000 Update GIS PET RNA commit d2cd0f4ee0ef0b4901363c58cfafdd571c7f319b Author: kate Date: Wed Oct 19 23:37:52 2005 +0000 GIS PET RNA commit 07ea263326eec478349b308ed9a10c3b8a8f20e6 Author: hartera Date: Wed Oct 19 22:10:24 2005 +0000 Removed the bacEndPairsBad ttable chack from danRerBacExtName. commit 0c16dae90dee7a1598d8dcd6b26aa420c8d95205 Author: galt Date: Wed Oct 19 22:09:10 2005 +0000 fixed div by zero problem commit 0778b9f0a14c6702853ece3f3bd1038deaeda266 Author: kate Date: Wed Oct 19 22:07:22 2005 +0000 Add subtrack to ENCODE GIS RNA track commit 4003f839d22a982e737eaa38a93c328ebee8c260 Author: markd Date: Wed Oct 19 22:06:58 2005 +0000 handle genes that map to multiple locations commit 1de3ff105892c8fc41aee74ef27578ec9ea5b04e Author: fanhsu Date: Wed Oct 19 21:48:53 2005 +0000 Added fuzzy search on KG description. commit 18988f0b6952a2c6e92d9b04a68fcab906194f95 Author: markd Date: Wed Oct 19 19:30:41 2005 +0000 added buildMafFrames commit dcd7ae42ae172130e7d9702d6ee087753efc95fd Author: kent Date: Wed Oct 19 19:29:34 2005 +0000 Adding verbosity to aid debugging. Adding 'distinct' to the monster select statement to prevent duplicate rows. commit d8899607e882569a53200b3e9a72ddbd0b1e35a2 Author: hartera Date: Wed Oct 19 19:19:37 2005 +0000 Started Tetraodon Blastz, chaining and netting again with larger overlap for target sequence chunks for Blastz. Finished monDom2 chain and net tracks. Radiation Hybrid map track and STS markers track in progress. commit fcb75fb508c0308109531754d2e8380862c6ec1f Author: hartera Date: Wed Oct 19 18:56:49 2005 +0000 Documented swap for danRer3 vs monDom2 chain and net tracks to make danRer3 chain and net tracks on monDom2. commit 4d4c26253b006923395007fb9aa77a9477aa11cb Author: hartera Date: Wed Oct 19 18:53:33 2005 +0000 Description for danRer3 net track. commit b53d63ecbc846f797031ac57c3a2c7fc63af1cb6 Author: hartera Date: Wed Oct 19 18:52:45 2005 +0000 Description for danRer3 chains track. commit 9d1e5e5aa5cec050802ef7f1a63efb1cf51a08e4 Author: hartera Date: Wed Oct 19 18:51:44 2005 +0000 Added danRer3 chain and net tracks. commit 3cc8e959ebf4c88f43da47658ad78e65754674bf Author: galt Date: Wed Oct 19 18:39:53 2005 +0000 changing ZM cgi var go hgp_zm and removing center from zoom-modes commit 5fa7054a0443ddf710d6ad7fb6fec3fb5ef501a9 Author: baertsch Date: Wed Oct 19 18:38:03 2005 +0000 lowelab genbank track - change null to none commit f8068f35da9f628a7c53058802e07fc0901cee80 Author: ann Date: Wed Oct 19 18:33:35 2005 +0000 Added files at the assebly level because they are all slightly different. Edited files to more accurately reflect the fact that SAGE data is not avaliable for all clusters. commit f079df897b5c0e121bf6eb5cd7def1b09e79205e Author: fanhsu Date: Wed Oct 19 18:31:17 2005 +0000 Corrected one line. commit d58ea5b170f12c7d64e4c699cc50d52c57c6f65f Author: fanhsu Date: Wed Oct 19 18:24:52 2005 +0000 Added featureId table and added featureId field in the feature table. commit ee8d43210078b89eae63dc3a3f1397e67799728a Author: kent Date: Wed Oct 19 18:24:03 2005 +0000 Making this work with an empty cart again. Oops, forgot to null check before the strcmp! commit 014fc0b221f16aa1f22d1bf5a66a055dd4b6e0ee Author: kent Date: Wed Oct 19 18:23:23 2005 +0000 Adding differentStringNullOk commit 4705f193dab8fafbe1035abbcc42c2decadf2e33 Author: ann Date: Wed Oct 19 18:05:30 2005 +0000 Moved this file back down to hg16 as there is one diff between the hg16 and hg15 files. commit c25bf26ca989f346fbec07de46442fc384adfeca Author: ann Date: Wed Oct 19 18:00:38 2005 +0000 Added html file at this level (moved up from human/hg15 and human/hg16) commit 3f5bee9a696688557950880b283d5ece54b1b07f Author: kent Date: Wed Oct 19 17:38:34 2005 +0000 Making it so on IE the first image is selected on a new search even if you hit the enter key instead of the search box. commit 9760057e8dbc6f15a200a84c9b8d0a13cc14a4da Author: ann Date: Wed Oct 19 17:31:06 2005 +0000 Moved this file down to the human/ directory commit 8b0e4799dac2b128514d06d1084c00982aff861a Author: ann Date: Wed Oct 19 17:29:07 2005 +0000 Removed from human/hg15 becuase it was moved up to human/ commit 4a3f4c910a4c575bbd8416498d10b816b6fb44ef Author: kent Date: Wed Oct 19 17:28:38 2005 +0000 Fixing problem where first in list not selected on a new search in IE commit 691a7faefe231492007a927382d0df6c5f361a52 Author: kate Date: Wed Oct 19 16:49:11 2005 +0000 1. Fix Gencode Genes 2. Crawford lab data submitted commit 354e83dd50a157dc771aa57806ca1732c62da1ff Author: ann Date: Wed Oct 19 16:21:07 2005 +0000 Changed highlighted description to reflect what actually happens on page commit dbb9ae3ecc51a23ee02182f6f55e5101be3a2eb3 Author: ann Date: Wed Oct 19 16:17:09 2005 +0000 Added at this level because it is unique to mm7 commit ec5613f117c5cbe18851b58ba2b951fa8ef98889 Author: ann Date: Wed Oct 19 16:16:24 2005 +0000 Added 'release alpha' to cpgIslandGgfAndyMasked track entry commit 4f872976a7187a7e08d5f18254ed888845ff1fad Author: kate Date: Wed Oct 19 16:01:52 2005 +0000 Fix formatting error commit ea550044f20a8b16b26936f957bf345375aad50b Author: galt Date: Wed Oct 19 15:00:06 2005 +0000 "Encode release log update" commit 596542eef7b0fc8f8982f2cf2ccf3ea8bde8016a Author: galt Date: Wed Oct 19 15:00:04 2005 +0000 "Release log update" commit b9f5a9d730d0369b4ed5f7f99f13deae2951bbaa Author: hartera Date: Wed Oct 19 03:56:54 2005 +0000 Description for opossum (monDom2) chain track. commit 9a8866a33a3e213f98537a876e7c51c91c085d59 Author: hartera Date: Wed Oct 19 03:56:19 2005 +0000 Description for opossum (monDom2) net track. commit 4fbf123e8339201064902c50adf70a78b340c615 Author: hartera Date: Wed Oct 19 03:45:49 2005 +0000 Added chain and net tracks for monDom2. commit b40835abedb26764582d0d431ab0bc43885f8966 Author: baertsch Date: Wed Oct 19 01:10:17 2005 +0000 *** empty log message *** commit dd3dd86afa9975a78872fe7c2d43a44fbd2ba307 Author: baertsch Date: Wed Oct 19 01:10:13 2005 +0000 add entrez gene id commit 94d75585fa0cb1bede80ac92f982a658a40ff405 Author: jen Date: Wed Oct 19 00:28:04 2005 +0000 Updated minCheck value for ensPep w/ Fan. commit 3dcb9adb72f6241446dcc7698cab05caf04cecb2 Author: kate Date: Wed Oct 19 00:00:24 2005 +0000 Update to News item for hg17 browser commit 8c3eaf7a11ffec49dd74253ec68ea6315d8732ef Author: galt Date: Tue Oct 18 23:07:20 2005 +0000 fixed 64-bit atoi should be atol for storing pointer in either 32 and 64-bit commit 05f4927aa7c55ab7e38931d0e13828cd349338d0 Author: donnak Date: Tue Oct 18 21:51:21 2005 +0000 Archived some moldy news items. commit 5b0586c0a2614a1cfd8aa70c85158474305562b8 Author: donnak Date: Tue Oct 18 21:51:07 2005 +0000 Added news announcement re: hg17 encode browser. commit ab155f5333cdec07d7b2b01d332dbb6870082a3d Author: giardine Date: Tue Oct 18 21:08:49 2005 +0000 Added .as and .sql files for Human Phenotype track commit 37c4085181bc3f3b5ffca93a3273b203cd8b8105 Author: donnak Date: Tue Oct 18 20:07:41 2005 +0000 Added OH ASHG announcement. commit 0a5cefbb8d5f4151079d54eac31570a79bb2b83c Author: kate Date: Tue Oct 18 20:01:35 2005 +0000 More expected datasets. Status changes commit cd79ea11a1a485169d4a7d8d9217419a5d593190 Author: baertsch Date: Tue Oct 18 19:55:04 2005 +0000 loaded genbank and cog commit 099153a4d00b3ae4089eac49dfcabfa02b6fa760 Author: lowec Date: Tue Oct 18 19:24:58 2005 +0000 An option, -noNs, was added that will output the lengths as before, but does not count Ns commit 12fa026cebd7322aeace9996d5cd2b5b991a9c92 Author: lowec Date: Tue Oct 18 19:23:03 2005 +0000 A function to return the length of the sequence, minus the number of N's was added commit 554b7f968c6efb380a7db286ae56cb2baa52b9a4 Author: lowec Date: Tue Oct 18 19:21:04 2005 +0000 A funtion to return the length of a sequence, minus the number of N's was added commit c1d8574d376f319bc5d59681c995dc9785c65a47 Author: hartera Date: Tue Oct 18 18:16:02 2005 +0000 Commented out kimExpDistance checks for ce2 for the wormBaseId identifier. The Sanger gene set used for the Kim microarray data is a different version to the set used for C. elegans databases. Changed rule for estOrMrnaAccession for ce2. commit 89b428593209a95473f4608b325fe64bbe90746c Author: galt Date: Tue Oct 18 17:15:55 2005 +0000 fix 64-bit bug commit fd6942fbeb46deddd9c87996185eafeb7022f5ac Author: kent Date: Tue Oct 18 17:04:25 2005 +0000 Seems to work commit 621b6632abade83d509c61b6afaf199fbf62e0fe Author: galt Date: Tue Oct 18 15:00:05 2005 +0000 "Encode release log update" commit 6e1f7ea696531d72eccdda2cb4aecedf8d3188b0 Author: galt Date: Tue Oct 18 15:00:04 2005 +0000 "Release log update" commit a2fb68a0a7bfa92e2968bd2f2ed97c23ba1641c8 Author: heather Date: Tue Oct 18 12:33:00 2005 +0000 add note about negative strand to header line commit 0d076de11c2d3d068bd745bcba992541e8a64ca7 Author: kent Date: Tue Oct 18 05:48:34 2005 +0000 Seems to work commit 2e2465d039e3f4bf5fe04dac1e0d01336725fbbd Author: heather Date: Tue Oct 18 02:49:10 2005 +0000 "New version number v119" commit 98f25598f05d0ef6390bd465b5270c1730e5bf3a Author: fanhsu Date: Mon Oct 17 23:53:40 2005 +0000 Updated miRNA track info per Michel Weber's request. commit 6de5625543619d4c7b03efd855601fd79ca584f9 Author: fanhsu Date: Mon Oct 17 23:51:44 2005 +0000 Updated miRNA.html per Michel Weber's request. commit c2d513f946452027021b052db8d92c6dae5cb738 Author: fanhsu Date: Mon Oct 17 23:41:17 2005 +0000 Updated miRNA per Michel Weber's request. commit b986badc9273d593e6c25ff0a92f52a1287c32bb Author: aamp Date: Mon Oct 17 23:30:36 2005 +0000 Description of vars changes suggested by Bob. commit 796714d19c5f509b664e6ac9811839a93a41ba9c Author: fanhsu Date: Mon Oct 17 22:13:15 2005 +0000 Updated spToDb.c to accomodate new "FT /FTId=xxxx" lines. commit 8d2f0df47f59d140d3dd45c2d76d9521226adb7c Author: ann Date: Mon Oct 17 22:09:32 2005 +0000 Added 'release alpha' for affyTxnPhase2 track. commit 88b49b096807e89ad234f9415d4e100cf0f49774 Author: heather Date: Mon Oct 17 22:08:25 2005 +0000 get chrom size from chromInfo commit 54b158c0ec01b6870203be79e7707b847a7a1c96 Author: kate Date: Mon Oct 17 20:35:01 2005 +0000 Update alignments commit 295d20805219ae4563b028af541489790ef5f747 Author: kate Date: Mon Oct 17 19:13:51 2005 +0000 Rearrange left menu commit 444287a623c2afee599674cd1ff7d9ae6c53f9ca Author: kate Date: Mon Oct 17 19:10:04 2005 +0000 Oct. freeze final submissions commit 69efa6a73d5a3a449f5c293dbb6aee940fb31ab4 Author: kent Date: Mon Oct 17 18:41:28 2005 +0000 Making it so variable declarations don't follow statements to be ISO C compatible commit 18f2ab18cb0d87a6fbf8058ef5030935127f3f46 Author: kent Date: Mon Oct 17 18:25:35 2005 +0000 Fixing warning message commit 5ef30895283adecf380508e8ca47110ff3b14e77 Author: kate Date: Mon Oct 17 17:26:32 2005 +0000 Split COnservation track into alpha and beta versions commit 1d9c9b9870f383a533e709920c79b93c9e45504d Author: kate Date: Mon Oct 17 17:19:51 2005 +0000 Back out maf summary table for cons track (for now) commit f172430e753436b1815b3bca521185f6ee3fb1b7 Author: giardine Date: Mon Oct 17 17:02:50 2005 +0000 *** empty log message *** commit f22ec613a3bae82e8560a660899e805955fa85da Author: giardine Date: Mon Oct 17 17:02:29 2005 +0000 Fixed wording and credits. commit ebdf877478b2499e502f5d0e6fcedd744d733f5a Author: fanhsu Date: Mon Oct 17 16:53:10 2005 +0000 Rebuilt NIAGene track according to new data provided by NIA per Daewood. commit b7806413248429a9edd8f2fddc69c42432da6439 Author: hartera Date: Mon Oct 17 16:38:42 2005 +0000 Formats a FASTA DNA sequence file by removing numbering at beginning of lines and concatenating all sequence into one line for each sequence record. commit 500d6047e35c07cc4086b569aee8a86a412a47b9 Author: hartera Date: Mon Oct 17 16:35:56 2005 +0000 makefile for formatFastaSeq.c. commit e897765741c1e718c22bac197fe2c70fcfe2182f Author: heather Date: Mon Oct 17 15:55:39 2005 +0000 tweaks commit 6bcf216b541c52a0db2a537cc9da1c77d32c7ac7 Author: markd Date: Mon Oct 17 15:46:41 2005 +0000 added function to get log file handle commit b55269ddefb8496079c1d471c1c8749f3ade0ace Author: galt Date: Mon Oct 17 15:00:11 2005 +0000 "Encode release log update" commit 16329592e9a63854df14dc454d011dff9ee930e8 Author: galt Date: Mon Oct 17 15:00:10 2005 +0000 "Release log update" commit 165c4a7af71caba56f8a33a00b1a3bb140fc075c Author: baertsch Date: Mon Oct 17 00:14:42 2005 +0000 add ec codes to archaea genbank detail page commit d02312282afa50238f148564dcc61b20cff9b4db Author: baertsch Date: Mon Oct 17 00:13:20 2005 +0000 add ec.o ecCode.o ecAttribute.o commit 274a3840fbef591756b342f33b3f4812661cdcad Author: baertsch Date: Mon Oct 17 00:12:12 2005 +0000 *** empty log message *** commit c0b94dc581bbcad316f91b51a3db21f427a9dfd5 Author: baertsch Date: Mon Oct 17 00:12:09 2005 +0000 void getEcHtml(char *ecNumber) /* fetch ec codes and descriptions and output html */ tables for storing ec codes and attributes commit fed5efc94be8a61f21c248863b2727955e3b6403 Author: baertsch Date: Sun Oct 16 23:35:16 2005 +0000 add ; commit 7b01fe50eed1c07c6a555f76a1ec8cca499b7b3d Author: baertsch Date: Sun Oct 16 23:33:52 2005 +0000 fix comment commit a1905c8167be7c5689d3a6cd84ca313787daf485 Author: baertsch Date: Sun Oct 16 23:31:41 2005 +0000 /* fetch ec codes and descriptions and output html */ commit dd2499847fe3dbd2b6d90eb9b8caa9ec02a8118a Author: markd Date: Sun Oct 16 16:33:08 2005 +0000 added tests for gene that maps to multiple locations commit d327ec3b24db3af38cd760c7e27ae48207c22e55 Author: galt Date: Sun Oct 16 15:00:03 2005 +0000 "Encode release log update" commit b3bfee434d35dae3898760828711dc5b7001fd49 Author: galt Date: Sun Oct 16 15:00:02 2005 +0000 "Release log update" commit 7f4a36fc99f9d389d7de84d9bbfef9fd51a69200 Author: fanhsu Date: Sun Oct 16 14:06:34 2005 +0000 Updated again to fix a line to make "make HG_WARN=-pedantic " work. commit cf88a5ab674a1e55eced57c00092504f1a7dc1c7 Author: markd Date: Sun Oct 16 06:09:37 2005 +0000 change algorithm for linking mafFrames to only link if codon is split commit b1c7dd07aa57405b818d8f11fdd7be0c3c3b001a Author: heather Date: Sat Oct 15 22:00:53 2005 +0000 reverse complement reference allele commit 2e9c5a58bc005a1b85c4643226f8f9687778edcc Author: kpollard Date: Sat Oct 15 15:00:28 2005 +0000 finished multiz track commit c274c048ee6754bf09730de748e07174945bab6c Author: galt Date: Sat Oct 15 15:00:03 2005 +0000 "Encode release log update" commit ed7af381be5dedd33f5699e3a85ae8bf00d6b0af Author: galt Date: Sat Oct 15 15:00:02 2005 +0000 "Release log update" commit 5652c3f1d06b51b57421582d59d22d42cdec1d0c Author: fanhsu Date: Sat Oct 15 14:02:20 2005 +0000 Updated to avoid compiler warning of: "blastOut.c:535: warning: ISO C89 forbids mixed declarations and code" commit 81d74f3dcb55db2c48911ecaa4076526fb85d200 Author: galt Date: Sat Oct 15 09:01:38 2005 +0000 changing from genePix to visiGene commit bd1cbf0d92a7568c5c83ee45ad02424ee351ba0b Author: kent Date: Sat Oct 15 07:26:57 2005 +0000 Listing full and partial match counts commit c02815be5e4bb742b2c580eaa70cbfec0e81da2f Author: kent Date: Sat Oct 15 06:51:46 2005 +0000 Getting rid of zoom center commit 137ab8eeec844e718629dd648194bb09f663a699 Author: kent Date: Sat Oct 15 06:47:42 2005 +0000 Making it so that when you search something, the first image in the returned list appears in the big image pane commit 4c36f4a04249d58508278e724723e1f6e58f3ecb Author: galt Date: Sat Oct 15 06:43:49 2005 +0000 suppressing dot_clear.gif error_log message commit 00e1fd96358fbdee7d51d5676c584246f110e703 Author: kent Date: Sat Oct 15 06:34:41 2005 +0000 Moving search from thumbnail frame to outer page. Outer page stores it in a temp file and passes temp file name to thumbnail frame. commit 2cfc7b67894cfc7681418165f2fde400f5078fc3 Author: heather Date: Sat Oct 15 06:21:11 2005 +0000 S and W stay the same when complemented commit 2b80e78e1c663898371a34ab262c36901a90c4e1 Author: baertsch Date: Sat Oct 15 04:11:45 2005 +0000 updated for new genbank laoded procedure commit adeb46bdec9f02614e513e6165f60bad1847f34f Author: kpollard Date: Sat Oct 15 04:11:27 2005 +0000 finished multiz track commit 40d6cc813d3e031b6dce8fc769f9b8ee6457b3e4 Author: baertsch Date: Sat Oct 15 03:23:15 2005 +0000 add ec number to genbank update commit 718262853f675815b6dc6c1d48793efd343b0a33 Author: baertsch Date: Sat Oct 15 03:21:36 2005 +0000 add EC number and Brenda link commit b0179136294de37c15351525bfd5f5efd8c0aa2e Author: kpollard Date: Sat Oct 15 03:16:49 2005 +0000 fixed multiz track name commit 44e607a31ab78ddce6fea23a65bbd9b1a3a0016e Author: galt Date: Sat Oct 15 03:07:43 2005 +0000 change from genePix to visiGene commit a068759ee0f519e96d83f3a2711573ca216b4b65 Author: baertsch Date: Sat Oct 15 02:51:26 2005 +0000 add EC number commit 7bf50f14365f0fc801150cc6ed68fd3ced04c3f0 Author: baertsch Date: Sat Oct 15 02:33:01 2005 +0000 *** empty log message *** commit c302316387910cd12b329fd653c6315a99f06c72 Author: baertsch Date: Sat Oct 15 02:32:58 2005 +0000 add gene name commit 715fad88e67b1b40078d56ce3ccd3bd3e7ca4b58 Author: baertsch Date: Sat Oct 15 02:21:07 2005 +0000 *** empty log message *** commit d168930b078ab990a6eef2a47744ffe5f22eb80e Author: baertsch Date: Sat Oct 15 02:21:04 2005 +0000 add ec number commit 59fce26da225de8fecba5c7cb2e8e8dd8557c85c Author: baertsch Date: Sat Oct 15 02:07:54 2005 +0000 update instructions for loading genbank commit 4adab31d38dcc74b6589f5e2cd9a880b685e4442 Author: kpollard Date: Sat Oct 15 02:05:34 2005 +0000 fixed species commit 6888949144c21aaa4788517976897392c3160d67 Author: kpollard Date: Sat Oct 15 02:04:57 2005 +0000 Details page for multiz track commit 8021179a846f4aaef73ff8cec64ce8eaccd71fec Author: kpollard Date: Sat Oct 15 01:33:33 2005 +0000 Details page for multiz track commit d8dc3ed6a7edf5b4590f9fab2a26275e05c5c8e5 Author: baertsch Date: Sat Oct 15 01:30:39 2005 +0000 export loadGenePred() commit bc2bf3595a3922131708ce70289c382cc5cae716 Author: baertsch Date: Sat Oct 15 01:28:38 2005 +0000 archaeaGeneMethods commit a59f276b6b2c12b99786e549ef66efdb776b5304 Author: kpollard Date: Sat Oct 15 01:26:24 2005 +0000 New multiz track commit 9599052dbb71a2caf0faef8dda2438bb241f5338 Author: baertsch Date: Sat Oct 15 01:25:26 2005 +0000 add go pfam interpro modbase to archaea gene details page commit 81787163f442a502b1735628c0a42da94524bd06 Author: baertsch Date: Sat Oct 15 01:23:02 2005 +0000 char *uniProtFindPrimAccFromGene(char *gene) /* Return primary accession given gene name. * NULL if not found. */ commit 093f3f0ffc9288f2a0d5e4e7ca9646e6a704e283 Author: markd Date: Sat Oct 15 00:35:06 2005 +0000 changed prev/next frame info to be in the direction of transcription commit c9cac61beb4046dfcdc5da1872e0bae9b69b5cfb Author: kpollard Date: Sat Oct 15 00:00:58 2005 +0000 finished blastz and chains commit ef1553b4d188a30b877279b92873f6fc6a6ad1b0 Author: aamp Date: Sat Oct 15 00:00:18 2005 +0000 Sort fix for hTrackDb(). commit 6a95a4e33a94c0ef0ab6140b4ab0f5a8e3451bf0 Author: kpollard Date: Fri Oct 14 23:57:01 2005 +0000 fixed Blastz to be blastz commit 55b1b086616731deae8e50815e868a98780759cd Author: kpollard Date: Fri Oct 14 23:50:02 2005 +0000 added halMar1 blastz commit 1ecffda36721424d41a8866ac6386f6be983294f Author: kpollard Date: Fri Oct 14 23:47:12 2005 +0000 added haloHalo1 blastz commit 76cad0fde9a86e127d098f66b8f424d169e33d94 Author: kpollard Date: Fri Oct 14 23:41:46 2005 +0000 added haloHalo1 chains commit b4273bdddf9eecce33badb2561735b1fd9ffe439 Author: kpollard Date: Fri Oct 14 23:15:27 2005 +0000 haloHalo1 chains and blastz commit aca80698be810c10965bdff0c3a890c102e07339 Author: baertsch Date: Fri Oct 14 22:57:32 2005 +0000 add color grey for cog code - commit 11f784a6fb6071a7dc96d67e7171d1b1e08d2a2c Author: ann Date: Fri Oct 14 22:37:53 2005 +0000 Edited Reference - corrected several errors. commit 78a1b13f2a8f7705d01a9b967b03385b653ed008 Author: ann Date: Fri Oct 14 22:25:46 2005 +0000 Spelled newly added author's name correctly. commit e48eb79612f0d04bd7ec03fda178c9451e8a6ecf Author: ann Date: Fri Oct 14 22:22:23 2005 +0000 Added full names of authors. commit 63bf645dee5fa134ecc5fee47a1619abe0da5bc4 Author: ann Date: Fri Oct 14 22:12:46 2005 +0000 Edited shortLabel for cpgIslandGgfAndyMasked commit 21c99160b5bff37eee6cb8ccad6511ea5eb58f33 Author: ann Date: Fri Oct 14 21:34:37 2005 +0000 Added a group (encodeChip) to the encodeYaleChIPSTAT1Sites composite track. commit 68b020c8366bcdf325f01fc965ef396056603e39 Author: hartera Date: Fri Oct 14 20:57:48 2005 +0000 For blastHg17KGPep01Id, relaxed minCheck for knownGene names since known Genes changed a lot with the KGII process. commit d474c6d47c31f05a10223d1a8d9e6551de113ab0 Author: kent Date: Fri Oct 14 19:38:55 2005 +0000 Putting in mark where weaker matches begin commit 8297498c8d6bacb1b39c30a0b428a13a817c7a4f Author: galt Date: Fri Oct 14 17:47:22 2005 +0000 added fix so that it will not panic if the parent.parent.controls does not exist commit ecf128a7f82c4f6121d3ba773c41e7b070c53d88 Author: ann Date: Fri Oct 14 16:13:07 2005 +0000 Added entry for gap track. commit 22da0c734a94c71967222311f2b8243b672a2ce9 Author: hartera Date: Fri Oct 14 15:57:20 2005 +0000 Made changes to exclude some databases for the identifiers blastHg17KGPep01Id and blastHg17KGPep02Id. commit 62dec676feca2d849eb43f0325d5da64e3ed3b1d Author: ann Date: Fri Oct 14 15:51:33 2005 +0000 *** empty log message *** commit 7e729d7d394619303ec69bebefab46d2f644f2dd Author: galt Date: Fri Oct 14 15:00:11 2005 +0000 "Encode release log update" commit fd541fd7ef099fa3cf99ca83eef55d58e1c91e57 Author: galt Date: Fri Oct 14 15:00:09 2005 +0000 "Release log update" commit 6b938c0a81530da1acf39b53dec194c11482cd4e Author: baertsch Date: Fri Oct 14 13:17:27 2005 +0000 add cog colors for refseq genbank tracks commit 766bf45c222c3a0c078d7b63c9b5e48c5cdee203 Author: baertsch Date: Fri Oct 14 13:15:30 2005 +0000 paint barbs in contrasting color instead of always white, add archaea track handler commit de3db24329269a86984e5afb55605fea37ed9e95 Author: galt Date: Fri Oct 14 07:44:29 2005 +0000 fixed bug: needed cart vars reset for compr local custtrk file commit b8b0fbce76ef051f3390e9dcb9d8beec217c5060 Author: kent Date: Fri Oct 14 06:03:19 2005 +0000 Removing hyperlink from current page. commit efc6a5e2b50b7dd160793c9c0c9c509d48c9dfad Author: heather Date: Fri Oct 14 04:20:00 2005 +0000 random position, fixed chrom commit db855d725cf1570f5474bf57b2ec89d6fa5abcd9 Author: donnak Date: Fri Oct 14 04:13:20 2005 +0000 Modified the "Add your own custom tracks" page to have a separate section w/info on how to load tracks. Also moved the Reset button to the bottom of the large text box, at Bob's request. commit 8333efd4ea76d6bf4d12987623f3219e7d82cc4d Author: heather Date: Fri Oct 14 04:02:20 2005 +0000 add hgTracksRandom commit 82a7ad809fca024b1df02d302fd2104e22df773d Author: heather Date: Fri Oct 14 04:01:46 2005 +0000 basic structure, not random yet commit 6978bd9c67c44b98f1ee35e3f0cd6422afc74c53 Author: kent Date: Fri Oct 14 03:59:49 2005 +0000 Adding interesting test case - a 10 kb sequence that when aligned to itself makes blatz run out of memory after about 10 minutes of chewing. commit efc6de8c8381a300dd36b5ab52650c5f4bf72e77 Author: kpollard Date: Fri Oct 14 03:24:24 2005 +0000 finished chain track commit 068bcda2ff911527c7a81c0540d9fdfe42273b55 Author: ann Date: Fri Oct 14 01:01:04 2005 +0000 Moved this file down from mouse because mm7 has different types of gaps. commit ffb906153b9c29a51e273fd35bd76d39e6a441ad Author: ann Date: Fri Oct 14 01:00:19 2005 +0000 Moved this file down from mouse because mm6 has different types of gaps. commit 21bedb30490f15879657c25ba1123ae8a013ea5b Author: aamp Date: Thu Oct 13 23:15:51 2005 +0000 Start of a bugfix caused by trackDb changes. commit eec2b3f7ae7f4c30a10cf57cf1a8e28534cb44dc Author: hiram Date: Thu Oct 13 22:46:37 2005 +0000 And html pages to go with chain and net MonDom2 commit fea1cd94e6b8b12faba2e44ed8f14b11474c0784 Author: hiram Date: Thu Oct 13 22:44:23 2005 +0000 Add chain and net for MonDom2 commit 7900189fc89cf842e4b553f56046dd0060c61540 Author: donnak Date: Thu Oct 13 22:20:30 2005 +0000 Added "format" tag. commit a637a2cbae48c6eb7a54434b2dc0327adf40c54e Author: kpollard Date: Thu Oct 13 21:59:28 2005 +0000 working on blastz track commit 8cfc0519eb7fb3d8f7ec96173b5cf9ccf4e2bc4a Author: kpollard Date: Thu Oct 13 21:57:57 2005 +0000 GC percent and multiz tracks done. commit 46817196928c1f04e094d7db6f541aa0aa3e543f Author: kpollard Date: Thu Oct 13 21:47:52 2005 +0000 Details page for multiz track commit 580b10ed9a66b66b2fcaa226c0ddf45f34c2d0e3 Author: kpollard Date: Thu Oct 13 21:45:10 2005 +0000 Added multiz track commit 4fa07cfdb4b8437758d82014cdbb3d81a6ac611b Author: giardine Date: Thu Oct 13 20:47:17 2005 +0000 fixed type in track.ra file commit 647f8fa1ca45d61f5b3a75e7d8b99d20f5b0f879 Author: kpollard Date: Thu Oct 13 20:34:51 2005 +0000 halMar1 blastz commit 664370a8737f5ede6eaa2edb5493f7e612290942 Author: kpollard Date: Thu Oct 13 20:29:48 2005 +0000 finished multiz commit 1ce347acaea892971390ac0dd84693a12ddd8f00 Author: giardine Date: Thu Oct 13 20:21:37 2005 +0000 *** empty log message *** commit 58603f40b122d4c0d903bcd338e43b291244b074 Author: giardine Date: Thu Oct 13 20:21:08 2005 +0000 I have added the Human Phenotype track. This track is to consolidate variants from locus specific databases. It provides links to source databases, aliases, and filters on mutation type and location. commit 6aae23dd8f43efe54ff65506612c594d850c32f0 Author: donnak Date: Thu Oct 13 20:09:12 2005 +0000 Made some minor HTML mods, added link for Bioinformatics Inst. commit 9e2db6a23bfe7844b3e420062979746f8c371322 Author: donnak Date: Thu Oct 13 19:58:07 2005 +0000 Fixed a typo, added a Display section, made a few other edits. commit 8c6e3f0ef68b2e37983478fdcffd929ade7599a7 Author: hiram Date: Thu Oct 13 18:53:29 2005 +0000 Added build 35 statistics commit e8282d9ccd1715c09a63aac420e36bc6264e21ea Author: hiram Date: Thu Oct 13 18:28:19 2005 +0000 Begin to add Mm7, mm7 commit 4cf16a6c1c02812336289dbe6de02b8cc8ee7624 Author: donnak Date: Thu Oct 13 17:39:24 2005 +0000 Added Brian to dp3 credits. commit 294092ff18e5870091b394ef61fe12d294c1e965 Author: donnak Date: Thu Oct 13 16:59:02 2005 +0000 Added dp3 credits. commit f8be0da362f0954d85dfb439227e6a32ddba00ad Author: lexa Date: Thu Oct 13 16:55:56 2005 +0000 Fixed a bad bug that caused a segmentation fault if dynamic masking was not used. commit 3461d6d87249be20a0470c98bd9c5b2a7b987e35 Author: kpollard Date: Thu Oct 13 16:47:59 2005 +0000 started chainHalMar1 track commit b90119103a52a17cf205ae67ac9279870b3d7e3a Author: lexa Date: Thu Oct 13 16:47:20 2005 +0000 Added dynamic masking that can be activated by command line parameters -dynaLimitT and -dynaLimitQ (typical values between 10 and 1000) The query mask is printed out into a bed file called dynamask.bed Needs more work. LX commit 50c80bf1243d43d1b55dbbb9cab112a383cb2f2b Author: kpollard Date: Thu Oct 13 16:40:17 2005 +0000 fixed priority of chimp/mouse/rat conserved commit ee8996a17a371b27557d8acd014533fb00e91b7b Author: kpollard Date: Thu Oct 13 16:38:24 2005 +0000 >100bp, >96% ID in chimp/mouse/rat elements html page commit 5e796ebb1fe90cdb9ff8d3c4cf1b724111e491d6 Author: kpollard Date: Thu Oct 13 16:37:39 2005 +0000 recent human elements html page commit 3fd127ce23eaa8973e8f5c02d30044f60f77aedd Author: kpollard Date: Thu Oct 13 16:34:57 2005 +0000 fixed track name for rh elements allb100i96 track commit 5e625af8104ad008029ab28bf92e9a052b6745f4 Author: donnak Date: Thu Oct 13 15:39:05 2005 +0000 Fixed typo. commit b338d7374ea2f461f05dd4a64d5e132310b71a90 Author: galt Date: Thu Oct 13 15:00:03 2005 +0000 "Encode release log update" commit 7c1a3e0e5989f0db19a340dde50b5088e826aff7 Author: galt Date: Thu Oct 13 15:00:02 2005 +0000 "Release log update" commit ac6691f860aa78ba31138eee8c4c47fe2e5b4147 Author: markd Date: Thu Oct 13 07:42:34 2005 +0000 added nscan peptide tracks commit f0869a4d976e7b5306595b26dba5f683c7e3774c Author: baertsch Date: Thu Oct 13 06:06:36 2005 +0000 add archae gene prediction track commit 4f47b537f8d380a151834a9b04436ddfa64725ef Author: baertsch Date: Thu Oct 13 06:02:49 2005 +0000 add gene details for archaea browser commit 1b7ba3ce1459d18507357d3f2f32b27080b50164 Author: kpollard Date: Thu Oct 13 05:54:21 2005 +0000 worked on multiz track - almost done. commit 46149681606f9348cda29e623bdaee10a0ac563a Author: kpollard Date: Thu Oct 13 05:50:59 2005 +0000 Details page for multiz track commit 45f43092be81a3fe8dc3e1360f54117cc3d9ebf7 Author: kpollard Date: Thu Oct 13 05:49:04 2005 +0000 New multiz track commit bd87f0a611eb10566937718c9004d7398c686aa0 Author: kpollard Date: Thu Oct 13 05:29:36 2005 +0000 finished multiz track commit 43d02e5b14347a6fff5c73e8878a80a532297216 Author: baertsch Date: Thu Oct 13 03:36:08 2005 +0000 sql for cogs table (attributes of refSeq gene) commit 55790d5042ce4d1f775a4aa8aaa02f81114315ec Author: baertsch Date: Thu Oct 13 03:35:30 2005 +0000 *** empty log message *** commit d6697ec82ec5875cb844d22aded94523a3d46b17 Author: baertsch Date: Thu Oct 13 03:35:25 2005 +0000 add protein and gi fields commit 0058814128ddaafadbe993560c124e40d8f2eaac Author: baertsch Date: Thu Oct 13 03:19:28 2005 +0000 load genbank details commit 7389cb994f571acb0d246e9de3d11872e5b98fbb Author: baertsch Date: Thu Oct 13 03:16:25 2005 +0000 add cog codes and new gene pred format commit 7b6b5dca2a191c26528fb5ad11828ed04811f85e Author: lowe Date: Thu Oct 13 03:01:06 2005 +0000 Basic tracks for G/C and tandem repeats added by Todd. Ready for Katie to add multiZ commit ed93b6fffea2e82d6833807c95548663511aa9df Author: kpollard Date: Thu Oct 13 01:39:22 2005 +0000 Details page for multiz track commit 3e146cf03fa7c4ac49e4443117c51cb83a21dc3e Author: kpollard Date: Thu Oct 13 01:37:31 2005 +0000 New multiz track commit e9c7e48d386969a0b61ed7d82b9fb0c522debf7b Author: hiram Date: Wed Oct 12 23:49:37 2005 +0000 Can have full Organism name on DanRer3 chain and net commit f7d74e615c9893bfc6d0e60c0ea18a3083f03501 Author: hiram Date: Wed Oct 12 23:47:59 2005 +0000 Add chain and netDanRer3 for Mm7 commit 7a25bca240e2dc69469dcee41afb4ec21f4682e7 Author: hartera Date: Wed Oct 12 23:28:34 2005 +0000 Added BAC end tracks. Testing for bacCloneXRef and bacCloneAlias tables. Tetraodon, blastz, chains and net created. Opossum blastz in progress. commit cf2d98d7d647ff247e46f2236635fb865495f95c Author: hiram Date: Wed Oct 12 21:32:13 2005 +0000 Adding chain and net Mm7 commit 37b6b08c4795cd2f2938083a9f5bdeaea6221977 Author: heather Date: Wed Oct 12 20:43:34 2005 +0000 need to call dnaUtilOpen() for ntCompTable commit b089495f3d5c2f33ae2512dfe16cbe4a7edcb8da Author: kate Date: Wed Oct 12 20:16:07 2005 +0000 UC Davis submitted data commit d412aac37eb3bfb5d2dc516cc78ae3bfa2c17dff Author: hiram Date: Wed Oct 12 19:50:58 2005 +0000 Adding html for net Mm7 commit d18b0517efd5faf8f9cef833e30106e99c133984 Author: hiram Date: Wed Oct 12 19:38:59 2005 +0000 Adding html for chain Mm7 commit e6d2139b1af1c5b0cb4f063d0199314eabed7dec Author: kpollard Date: Wed Oct 12 19:23:24 2005 +0000 fixed sequence names in blastz to match chromInfo table commit 114e67049baa232ca2a8bbca189d49fcfc9d95c0 Author: hiram Date: Wed Oct 12 18:19:14 2005 +0000 bigZips should reside under /cluster/data/mm7/bigZips with symlinks on hgwdev to pick those up into goldenPath commit 36118ccb17f6b3011cc5f95da10fd7e1d4bdba03 Author: galt Date: Wed Oct 12 15:00:03 2005 +0000 "Encode release log update" commit 60bad596b713d0ba0b9f1e75ca7812e68949b7ca Author: galt Date: Wed Oct 12 15:00:02 2005 +0000 "Release log update" commit c64d0698ba2faa84e8e6a0322f744ee139f7ff60 Author: kpollard Date: Wed Oct 12 05:46:29 2005 +0000 added blastz chainHalMar1 track commit 35a8bd4bd229be228a6d1bc202e91879aef1d4ec Author: kpollard Date: Wed Oct 12 05:21:30 2005 +0000 added malMar1 chains commit f324816d9442f88d87d3896b0412534a3106c1a5 Author: kpollard Date: Wed Oct 12 05:12:25 2005 +0000 fixed halMar1 chains commit 44a7dc86619219879e3338699cceb0594c90b248 Author: kpollard Date: Wed Oct 12 05:10:01 2005 +0000 halMar1 chains commit b0127a1b9e070e5630e53ea43292f11049882f46 Author: kpollard Date: Wed Oct 12 04:04:20 2005 +0000 added multiz track commit 398f15dd494bfe296ffa9e6779f316b6c47c9578 Author: kpollard Date: Wed Oct 12 03:52:24 2005 +0000 Details page for multiz track commit bba7a755c8cb0a6e4e0496664a7e96e7eb77df9f Author: kpollard Date: Wed Oct 12 03:50:41 2005 +0000 New multiz track commit e9ae6b42f5676ca7a1d2bab7b09350fe72175b35 Author: kpollard Date: Wed Oct 12 02:46:50 2005 +0000 added multiz track commit 3684a79106a4c5f0d04f08c65673ffba79ed2e90 Author: kpollard Date: Wed Oct 12 00:31:53 2005 +0000 started multiz track commit dc516822493909954725df8c625b5ed0e6f5eadc Author: kuhn Date: Tue Oct 11 23:45:34 2005 +0000 added checkStoreUnits.csh for quick monitoring of space on /cluster/store* commit 0e570864c1cb34e5c6d3104b5017f6ccea71833e Author: kate Date: Tue Oct 11 23:27:00 2005 +0000 Update for Gencode October freeze commit 2db5a6c54d7551164c36795d34376759a3b66bd7 Author: kate Date: Tue Oct 11 23:20:04 2005 +0000 Received DNAseI data from NHGRI commit dfe34d48d108963fbb8263f5fa5e84ad24ea3f3d Author: kate Date: Tue Oct 11 23:01:30 2005 +0000 Revise Gencode Oct subtrack label commit abced99f5091a5126836b62f7e741bbf82f37fdd Author: kate Date: Tue Oct 11 23:01:08 2005 +0000 Add new validation status for Oct freeze commit ca34e54fe298d3a39f0e66075a7baca9468f72ab Author: kuhn Date: Tue Oct 11 22:55:04 2005 +0000 some small tweaks, one rewording and trimmed the lines to 80 char or less commit d2a9200b6b5ede99720396e95797c5fd9e0b7b3f Author: kate Date: Tue Oct 11 22:42:22 2005 +0000 Add status for Oct. Gencode commit 9c8f476cd618559ce8887cbba98b23da2004923f Author: fanhsu Date: Tue Oct 11 22:18:45 2005 +0000 Removed redudant statements discovered by Hiram. commit 432010f2d7d0216a042e86e4aab07f8bb942db57 Author: galt Date: Tue Oct 11 21:36:34 2005 +0000 changed genePix column to visiGene commit dcf9b3f23bb4136fd12fcf939f41ae762f2ffb0e Author: hiram Date: Tue Oct 11 21:33:10 2005 +0000 For Mm7 track commit cfe2e689656d33a642019eb1c47747d75eccd5be Author: kayla Date: Tue Oct 11 21:29:45 2005 +0000 added droGri1 commit aab9912189f0791f8441ba74cfb93982e1448fc6 Author: hiram Date: Tue Oct 11 21:16:29 2005 +0000 Done with tetNig1 commit 8276ee2c083a8afb8d67f67b3932ffc9489177ad Author: hiram Date: Tue Oct 11 20:44:36 2005 +0000 Adding chain and net tracks for Mm7 commit d18223365f666a73863db10d33dfdeefe0531e5f Author: aamp Date: Tue Oct 11 20:17:50 2005 +0000 More trackDb changing around and simplifying. commit 424e94663a8e09af61569ff9e908b37824c71008 Author: hiram Date: Tue Oct 11 17:48:08 2005 +0000 html pages for Mm7 chain and net commit c88c1ce8637bed71a688a90ec358e01bf94c46af Author: hiram Date: Tue Oct 11 17:39:04 2005 +0000 Add Mm7 chain and net commit b4851ce51f17119a83abcd952237caac00059efd Author: galt Date: Tue Oct 11 15:00:03 2005 +0000 "Encode release log update" commit 501e6d387344daf99a27691a6779c49b61bbfef1 Author: galt Date: Tue Oct 11 15:00:02 2005 +0000 "Release log update" commit f75b335a9d8f390038568a752c10d50141bb365d Author: genbank Date: Tue Oct 11 06:25:49 2005 +0000 added transmap track commit f73b7341bba58b8a6bb8f359e551c346e6e304f5 Author: heather Date: Tue Oct 11 04:31:40 2005 +0000 fix off-by-one in assert commit 1fc7b4aa97264768023ad58e228d1531627ce872 Author: kate Date: Tue Oct 11 03:27:00 2005 +0000 Gencode genes commit 93c825f6314d4b9d96522f6ed234d3798fdad811 Author: kate Date: Tue Oct 11 03:12:58 2005 +0000 Add Oct. Gencode intron handling commit 5ffd0df7d54138b9873ed30d7ac2eb1296500f81 Author: kate Date: Tue Oct 11 03:08:11 2005 +0000 Gencode October freeze commit c530eb869ad456cf12e25dd95b87df55f41b993b Author: kate Date: Tue Oct 11 02:44:00 2005 +0000 Update status commit 0ba438c1fe617ba56871e0819906ad97ea3bb474 Author: kate Date: Tue Oct 11 02:15:50 2005 +0000 October freeze added new status commit 05584ddec7b73bded00d77a99f79013ddd22195a Author: kate Date: Tue Oct 11 01:04:05 2005 +0000 Worked on UCSD tracks, UNC, UTexas commit 8c2e9e42d9df5e38e6dfc98e28bccc02ff6e5f19 Author: kate Date: Tue Oct 11 01:02:11 2005 +0000 Update commit ea45d1768c22f85fffdc83cb28f15a40c5f5bf48 Author: kate Date: Tue Oct 11 00:33:58 2005 +0000 Add Univ Texas Chip/chip for ENCODE commit 8dc6a11a1aa58238b31a173d2f2085287bd6d286 Author: kpollard Date: Tue Oct 11 00:19:28 2005 +0000 added multiz track commit 5126147f605dde6afb4b695c37dbd8cb94da09f5 Author: kpollard Date: Tue Oct 11 00:17:45 2005 +0000 Details page for multiz track commit 37887b9a298175b4bde1191d0647add6cc831660 Author: kpollard Date: Tue Oct 11 00:15:49 2005 +0000 New multiz track commit 385eff501c29c56f10306559e0b6d811e5148bb7 Author: galt Date: Mon Oct 10 23:51:51 2005 +0000 document new knownToVisiGene which replace knownToGenePix commit 4e5bde6cd2ea4c3be09162ad3ab7209ad9c22900 Author: galt Date: Mon Oct 10 23:40:58 2005 +0000 trivial cleanup commit fc3a26cf657c86f7cc6cee48671c94f6374de3ff Author: galt Date: Mon Oct 10 23:37:52 2005 +0000 converted from knownToGenePix commit b451a75568c10a29c8ada535b5e4c0693410d98e Author: kate Date: Mon Oct 10 23:23:32 2005 +0000 New submission from UNC. Moved UCSD along. commit d22170fac00199cd9932a48c0d8b180ed294298f Author: kayla Date: Mon Oct 10 23:07:15 2005 +0000 wasn't supposed to add droGri1 yet commit 75307839a14c5623b3bb3bd34d11bfd932b9cf77 Author: kayla Date: Mon Oct 10 23:04:58 2005 +0000 added droGri1 to the list of assemblies that get updated. commit 530078f697f2db043a4b1ed4d55237c0e2f292bd Author: heather Date: Mon Oct 10 22:56:53 2005 +0000 tweaks commit e6e6c6632871bfe2904eab9c51da2faef6941d0d Author: kate Date: Mon Oct 10 22:38:33 2005 +0000 Minor edits commit 33a6eab42fe1fbb4a7bafabf3d638649ad3ca673 Author: kate Date: Mon Oct 10 22:18:46 2005 +0000 Add 12 new UCSD chip/chip datasets to LI Ng track commit 1f85c65ee209c015fe3c360b4b2d94619165bc2e Author: heather Date: Mon Oct 10 22:03:41 2005 +0000 reverse complement genes on negative strand commit 0b05793dc45a68fc1f7f9af669deba8048009a1c Author: kayla Date: Mon Oct 10 21:39:59 2005 +0000 removed now extraneous line of text from the gap description page commit 5583431abf4a0c3be6907eba3a740c450d0179a7 Author: heather Date: Mon Oct 10 21:36:16 2005 +0000 allow flank to extend into adjoining exons commit 0d6b956af83978a6f75a8473874fde1b4f6f11db Author: aamp Date: Mon Oct 10 20:54:50 2005 +0000 Simplified some code and hopefully fixed a bug. commit 6a1d1436e3e5164d15bac3637a8cc9cc38045d52 Author: kpollard Date: Mon Oct 10 20:48:14 2005 +0000 added multiz track commit f0076a99076527d2cc3cf7d205daeb05c7221097 Author: kpollard Date: Mon Oct 10 20:46:49 2005 +0000 Details page for multiz track commit db2fc404b023a8b001ca92bef1ac2d279bbe2f0a Author: kpollard Date: Mon Oct 10 20:44:51 2005 +0000 New multiz track commit 4b62752386f4964f78b3766e08c77bc2933bb5a9 Author: kate Date: Mon Oct 10 20:42:37 2005 +0000 Remove dollar matrix tag from the html if theres no matrix trackDb setting to facilitate reuse of the description commit b9d5c3f53bc648d1244d8c349ed6f1419e659307 Author: ann Date: Mon Oct 10 20:19:18 2005 +0000 Changed "Hela" to "HeLa" commit 1c2b7508699533569d289c933ff637d92939266b Author: kpollard Date: Mon Oct 10 20:18:41 2005 +0000 added multiz track commit d22435c71e6d4b23732971c95561dd7cae704226 Author: galt Date: Mon Oct 10 20:18:36 2005 +0000 updates for compressed cust trks commit dfe9d7d0e388a39a8ea7737608b58694420b3416 Author: ann Date: Mon Oct 10 20:18:35 2005 +0000 Changed concensus to "American" spelling commit d6039931deb375000a40ae8b31f19907a0e0e2fb Author: kpollard Date: Mon Oct 10 20:17:34 2005 +0000 fixed typo commit 17f589f870a0665227ac5722567ffdeb2d49750c Author: kpollard Date: Mon Oct 10 20:07:37 2005 +0000 Details page for multiz track commit 261de8892801ebe2a84bd219c02128476c2961c5 Author: kpollard Date: Mon Oct 10 20:00:15 2005 +0000 New multiz track commit 98ca4c12ea749dfbb046765aca5850b46d9f2eae Author: kent Date: Mon Oct 10 19:59:55 2005 +0000 Putting back hgpDoId command commit 0ba5b6b038d6a10d215032582e3220568dbd62ab Author: kent Date: Mon Oct 10 19:22:31 2005 +0000 putting in code that presents images in pages if results are larger than 50 commit d2ef7b614dfbe1a9a5595e8df598f0d26f673858 Author: galt Date: Mon Oct 10 18:59:53 2005 +0000 added support for determining size of file uploaded in MIME/multipart form commit c6d6d10f2c6d5fdea9336ab56650e9703bca4249 Author: galt Date: Mon Oct 10 18:58:52 2005 +0000 mods to support compressed custom tracks streams from url or local file upload commit afa4c7dd658f300e7cd0cc72a65f1ab5cb195e4e Author: galt Date: Mon Oct 10 18:57:23 2005 +0000 added virtual program /dev/memwriter to support streaming from a memory block commit 2992e8c887f17628addd3a8a233c999c0ecc557a Author: galt Date: Mon Oct 10 18:56:26 2005 +0000 Added support for binary streams containing 0 passed in compressed customTrack commit 2d291bb666390e75a89d5c40334c908de4938763 Author: donnak Date: Mon Oct 10 18:28:02 2005 +0000 Added droGri1 release announcement. commit ed8ed86be7b3f96332afcf732335aebf4475b02c Author: donnak Date: Mon Oct 10 18:27:45 2005 +0000 Uncommented droGri1 info. commit 386f2cb54e75513b9a1f2ae0bb46254e768237b3 Author: donnak Date: Mon Oct 10 18:27:17 2005 +0000 Added D. grimshawi credits. commit ab53f0f14d8a8a2400c44c92748ed05f69e0ee0b Author: donnak Date: Mon Oct 10 18:27:01 2005 +0000 Archived some articles. commit ff3c584db34aa964fd6757fb48ba802838c4eec7 Author: kent Date: Mon Oct 10 18:14:28 2005 +0000 Adding a little bit to timing stats commit c71b3f85eb9b53656f5f12dfcb36b88172dd37f7 Author: donnak Date: Mon Oct 10 18:00:08 2005 +0000 Updated the sample queries in this file. commit 2f06ddf920da35c63616ee5a0210514aaffd7cc3 Author: kent Date: Mon Oct 10 17:35:04 2005 +0000 Switching to new search logic commit f87fa3bc4f5fd322d60ea3405b9dd9ca0d648207 Author: kent Date: Mon Oct 10 16:41:27 2005 +0000 Separating logic that handles names from other multiple word logic to avoid 'sm' in 'smith sm' from matching 'small intesting' commit 31eb203ce4cf0a5c572988cae437fc90e39688a1 Author: donnak Date: Mon Oct 10 15:44:03 2005 +0000 Added droAna2 announcement. commit 294bc88a84e0305f4be67507e4f064bd9e0c0fc2 Author: kent Date: Mon Oct 10 15:24:09 2005 +0000 Modularizing a bit commit 984573c974cd9f8994e997fee88b25e5a1140323 Author: galt Date: Mon Oct 10 15:00:04 2005 +0000 "Encode release log update" commit d0682385c5feaa92de097987266d8eebfcc467f1 Author: galt Date: Mon Oct 10 15:00:03 2005 +0000 "Release log update" commit d3a0d69249071ee0626fc7f3ab95b12fde1d6096 Author: kpollard Date: Mon Oct 10 06:26:22 2005 +0000 started multiz track commit f9147d8ab407ae84962d43ec35d7934662b915da Author: kpollard Date: Mon Oct 10 06:25:45 2005 +0000 added multiz track commit 35fb9152e9e95d9224943d6239f7aa05757b6363 Author: kpollard Date: Mon Oct 10 05:28:00 2005 +0000 fixed speciesOrder names commit 628e271caf3c6076409adeb112b62ab5ce3428ce Author: kpollard Date: Mon Oct 10 04:46:51 2005 +0000 Details page for multiz track commit 2252aa8875ca4ada38e84fb02aeadb60f333b1dc Author: kpollard Date: Mon Oct 10 04:43:33 2005 +0000 New multiz track commit 541e442f27bbc7a9c62c6156a64c57ad85b3aee6 Author: fanhsu Date: Sun Oct 9 23:13:03 2005 +0000 Removed dvBed track. This is a prototype. Not ready for prime time yet. commit 75f40a15f9f1461c2ac1b92224e2ef06fe4c5a0a Author: kpollard Date: Sun Oct 9 23:02:07 2005 +0000 finished 4way multiz track commit 69978f23c71ba2da19c23416dc94cdaf8750541a Author: kpollard Date: Sun Oct 9 22:08:52 2005 +0000 Details page for multiz track commit 76c5e549f53379163fe883483594c16ed1cb5d17 Author: kpollard Date: Sun Oct 9 22:00:20 2005 +0000 New multiz track commit d077d26217f6b264d8048e279d2cc10de10095fa Author: kpollard Date: Sun Oct 9 21:41:14 2005 +0000 merged file from /cluster/data with the file here commit 08fc6a68b4022622ebe31064f49e99d205daff31 Author: kpollard Date: Sun Oct 9 21:29:30 2005 +0000 multiz track for therKoda1 commit fcb82970076ca21719d41bd4aba340a52c372e10 Author: kpollard Date: Sun Oct 9 21:27:07 2005 +0000 Details page for multiz track commit d1621105229d119a99b0683727c327240dbf102a Author: kpollard Date: Sun Oct 9 21:24:01 2005 +0000 New multiz track commit 8c4c06e41810260755c9df4c0c1917cd15d1f3aa Author: hartera Date: Sun Oct 9 15:17:12 2005 +0000 Reloaded cgapAlias table. commit 35f06deab02f9cc028d3b06a1b7db4afa9e52ec0 Author: galt Date: Sun Oct 9 15:00:06 2005 +0000 "Encode release log update" commit b899b0556935953e203cd6b54381d54fa832465b Author: galt Date: Sun Oct 9 15:00:04 2005 +0000 "Release log update" commit 55df84cbbaf1e21eb325ee09af50fadc2736215a Author: markd Date: Sun Oct 9 07:01:37 2005 +0000 reenabled bosTau2 commit f500426cc150b45aae8eacf972c532afea287725 Author: kent Date: Sun Oct 9 04:41:26 2005 +0000 Hiding a bunch of tracks by default commit 42b3ebc19ddcdd077cc8a9afceea5fa625bccbe4 Author: kpollard Date: Sun Oct 9 03:04:12 2005 +0000 multiz track for pyrHor1 commit 2ee3f902942732774621523a85098279a66066d3 Author: kpollard Date: Sun Oct 9 02:54:22 2005 +0000 Details page for multiz track commit c2d4544b4e278a6f9a09e1015f7a683c35e9be43 Author: kpollard Date: Sun Oct 9 02:52:10 2005 +0000 New multiz track commit 9a7e6b932bfb0e9ae9a494346b21fba67ef1e62e Author: kpollard Date: Sun Oct 9 02:19:49 2005 +0000 fixed tree figure commit dbd7e9f06821135038436bc8aa83401f5b5f3cbc Author: kpollard Date: Sun Oct 9 02:19:20 2005 +0000 added tree figure commit 934991b7843214e8cacbf46d6600891399c3e890 Author: kpollard Date: Sun Oct 9 02:07:57 2005 +0000 multiz track for pyrAby1 commit a4ac1431a3384681adbfda0bca67a748bcc3fbd5 Author: kpollard Date: Sun Oct 9 02:03:47 2005 +0000 Details page for multiz track commit f9777990a50ebd4ec23c46e08e691728be27c627 Author: kpollard Date: Sun Oct 9 01:59:41 2005 +0000 New multiz track commit e9c64773572a11cc83af56ed7c6d8f29e410585e Author: kpollard Date: Sun Oct 9 00:46:25 2005 +0000 added DONE to multiz commit 0ac032c06647801f0170b46b3fd9d88ef568d9be Author: kpollard Date: Sun Oct 9 00:42:24 2005 +0000 made new multiz track commit 71c00b022637f778fc80f219837a31f299009e81 Author: kpollard Date: Sun Oct 9 00:40:17 2005 +0000 eliminarted ld multiz html file commit db5b1dff9adbbf55bbcdf795d62ffe4ec2270b4b Author: kpollard Date: Sun Oct 9 00:38:43 2005 +0000 Details page for multiz track commit 411f8c583ed8a520156ea986fa38822fe7b0b935 Author: kpollard Date: Sun Oct 9 00:37:00 2005 +0000 New multiz track commit 2c2a53167f22d21f212e909184c8c175882ca486 Author: markd Date: Sat Oct 8 21:19:41 2005 +0000 addded prev/next links to mafFrames rows to handle codon split across maf blocks commit 348acb71b69ce0d03c9b5540f261a6c13d404a3a Author: kpollard Date: Sat Oct 8 20:22:14 2005 +0000 finished multiz commit 6c74ae0234027219c7fcd53a58b804dd16a10b7a Author: kpollard Date: Sat Oct 8 20:07:47 2005 +0000 fixed multiz entry commit 735e1d26c2b9052eb3ef1cb90942d0617c98817a Author: markd Date: Sat Oct 8 20:05:25 2005 +0000 don't create empty binKeeper objects when chrom not in table commit 7b6a299d8e4a00603c3ace52c1e35b7c151e0a5b Author: kpollard Date: Sat Oct 8 20:04:27 2005 +0000 fixed multiz entry commit 2616de9a4370afe81042e8d6db4c0fa369bfa67c Author: baertsch Date: Sat Oct 8 19:57:07 2005 +0000 remove extra pseudogene subtrack type - possible browser hang? commit 4887f646f3be584d6adfd21ccd056abffa760be2 Author: braney Date: Sat Oct 8 18:12:31 2005 +0000 add self track commit f0a0d4a10247a8e9f6d057ceb9a9ce5b4839cf1a Author: kent Date: Sat Oct 8 16:13:29 2005 +0000 SHowing year commit c10008cec166a3a21390d391a9d3fa021f9c006b Author: kent Date: Sat Oct 8 16:12:25 2005 +0000 Searching on year commit dc9778e9b7c739ee3f4b9cea172228902824d2a6 Author: kent Date: Sat Oct 8 15:58:59 2005 +0000 Adding visiGeneYear commit c3ee1c2d631ebcfdd7ab9511b012f7534f0311a9 Author: kent Date: Sat Oct 8 15:58:34 2005 +0000 Patching in year commit 1c740e5da8662d2b858e753dc0bfdad54a65f0df Author: kent Date: Sat Oct 8 15:40:14 2005 +0000 Adding year to submissionSet commit f956ef5d08da56268e74fac7cfaf20d3498cf1c2 Author: kent Date: Sat Oct 8 15:27:49 2005 +0000 Stripping trailing # from body part. Adding year field commit b1d56c2e24fdd6cee0041cd03ffb49d9c0e80495 Author: galt Date: Sat Oct 8 15:00:05 2005 +0000 "Encode release log update" commit fcbf3ae4dce581a2bdc92b77fe31cd1e642a9ff8 Author: galt Date: Sat Oct 8 15:00:04 2005 +0000 "Release log update" commit a301edc97b1b5f99931aac4f2a585f0a494884ff Author: kent Date: Sat Oct 8 07:27:30 2005 +0000 Adding expression to caption commit 021066b11653e9fa3fe1c632f847260c138a80df Author: kpollard Date: Sat Oct 8 04:53:18 2005 +0000 added multiz track commit 0a97fe5254fda140a6281034f5b744565b425074 Author: kpollard Date: Sat Oct 8 04:44:25 2005 +0000 Details page for multiz track commit 3e69f678171cded61c6f01725154829216fd7ffd Author: kpollard Date: Sat Oct 8 04:41:17 2005 +0000 Added multiz track commit cb14e6d5f8fa61e537a284cc29588eb0a03d72b0 Author: markd Date: Sat Oct 8 04:22:45 2005 +0000 added MGC tracks to hard code list of mrna to do base rendering commit 3821bf42dd5b9127ebd80a37dc4de524fef5479e Author: braney Date: Sat Oct 8 02:40:47 2005 +0000 add mgcIncompleteMrna to mrna track display commit e436451ce710d664d7352fe8070d2f48a14496d5 Author: kent Date: Sat Oct 8 00:01:16 2005 +0000 You can search on Theiller stages commit e8e8eebfbca2a0ac7994cc4521bef6f7e23e3dfe Author: hiram Date: Fri Oct 7 22:57:52 2005 +0000 STS markers done commit 14993226fb40ae7d9be93ab099ebc155c96a68a5 Author: hartera Date: Fri Oct 7 22:57:13 2005 +0000 Added code so that when opening and reading a psl file with meta data, it does not get stuck in a loop in if file is empty after the comment lines. commit 86c1ca085e4649a82d66cecd2c13b853585fe5bb Author: braney Date: Fri Oct 7 22:26:25 2005 +0000 add speciesCodonDefault to describe default species to translate codon commit 796c1501eef7309286ea3078803091b03f967e49 Author: kate Date: Fri Oct 7 21:25:42 2005 +0000 Static pages for hg17 ENCODE browser commit f144500be4f8124b4844f9099b793dbf3f823ece Author: baertsch Date: Fri Oct 7 21:15:07 2005 +0000 reorder pseudogene subtracks commit cdbf2ff3d5726edf26f79518cfc0815bf1b8892f Author: kate Date: Fri Oct 7 21:11:29 2005 +0000 Fix punctuation commit 78c6099493c5a4c4e6fcce7f294829b3c0ab504a Author: kate Date: Fri Oct 7 21:11:03 2005 +0000 NHGRI DNAseI track. Work on 8-way multiple alignment to remove overlaps commit d4fdc115f5a5483847d09b12b0a75a201c49e1e5 Author: kate Date: Fri Oct 7 21:09:58 2005 +0000 Update to NHGRI track commit 75a50cba8a53c7eef263cde372df6f38f6e7363a Author: kpollard Date: Fri Oct 7 20:56:50 2005 +0000 Details page for multiz track commit 7064a9828fc4d06e63c99d1c9f61b6d49cccc867 Author: kpollard Date: Fri Oct 7 20:51:32 2005 +0000 Added multiz track commit 627449e278eda6b607464ba9d62ce8f8980d1761 Author: kent Date: Fri Oct 7 20:40:56 2005 +0000 Adding body parts from specimen table as well as expression tables to search commit 2f9915e94db7649c23c824c7f2c69ca1c4a5562c Author: kent Date: Fri Oct 7 20:32:29 2005 +0000 Making search work on refSeq, genbank, locus link, and uniprot accessions. Also on body parts if expressed there. commit 5094817c0fa98723e9960bde6d640ca2f2fc7c0e Author: markd Date: Fri Oct 7 20:29:13 2005 +0000 added functions that take file descriptors commit bdc032a31dc86971de15743ad94549b8b5b40eb5 Author: kent Date: Fri Oct 7 20:07:15 2005 +0000 Patching database for another Jackson quirk - to remove # from end of bodyPart commit 971f1d768efb16a4326157a1a31123d580904d64 Author: hiram Date: Fri Oct 7 20:00:04 2005 +0000 Rework the usage of the _LIMIT variable commit 76ebc58237ce5a25fcc7290049d2569ff9a5c143 Author: heather Date: Fri Oct 7 19:36:30 2005 +0000 delete Ensembl link for bosTau1 commit faeaf466fef508c97f8cf222b6db851653a46743 Author: braney Date: Fri Oct 7 18:33:10 2005 +0000 a little more sophisticated handling of codon frame translation commit 0983b73191c0d69238c5a923d709283481bc168c Author: heather Date: Fri Oct 7 18:23:23 2005 +0000 add NCBI MapView link for danRer2 and galGal2 commit 01128043b4e5effde3ec8b011926af144efe2908 Author: braney Date: Fri Oct 7 18:12:43 2005 +0000 add a striing used in codon translation commit 315c76ca69950e565c1389d9bcd8d1c4fdf90da2 Author: heather Date: Fri Oct 7 17:56:56 2005 +0000 adding new Ensembl links and removing fr1 commit 6e0e73d60193f848c83f52f97ea6d0073f225536 Author: kpollard Date: Fri Oct 7 17:42:08 2005 +0000 fixed link and typo commit fc3633fe62e15af0da674c9eb877e6755f2526f6 Author: kate Date: Fri Oct 7 15:58:27 2005 +0000 Gencode and Sanger data submissions commit a6f995720c349e5d346dd153b6cd7119d88d354d Author: galt Date: Fri Oct 7 15:00:04 2005 +0000 "Encode release log update" commit 4a28e5d562fc9a048461a1bea5ef40717550766e Author: galt Date: Fri Oct 7 15:00:03 2005 +0000 "Release log update" commit cb677ed41b99828f26f5a31a121a92967ee959ee Author: aamp Date: Fri Oct 7 07:51:00 2005 +0000 Silly bug which pretty much killed the partitioning step for 2bits where SEQ_LIMIT is unspecified. Well. Now it's ok to be unspecified. commit e81abe800bf88a69e90386a47f02a5dfaf88d57f Author: kent Date: Fri Oct 7 05:50:59 2005 +0000 Adding search on gene name as well as contributor commit 5831d47917e45583f0e2814cc1de491e30648b2d Author: markd Date: Fri Oct 7 05:21:19 2005 +0000 added hgLoadMafFrames commit b511965a5bbd7ce075ded333760534c26b870ab6 Author: markd Date: Fri Oct 7 05:18:23 2005 +0000 added genePredCdsSize function commit ee4a1b1f172d6460b8b5486ef70be5b3e9cf231b Author: markd Date: Fri Oct 7 05:17:17 2005 +0000 added mafFrames related programes commit e9c5a170b3d8e7e1c68cfc58d465ebc05d146c91 Author: markd Date: Fri Oct 7 05:14:26 2005 +0000 added program to generate single coverage genePred file for use with genePredToMafFrames commit 17334e9880ff49c1806acede9852c013e562c39b Author: markd Date: Fri Oct 7 05:12:00 2005 +0000 added program to generate mafFrames from genePreds commit 939e99ea74b88a483ff34e64a70636b2a922ab54 Author: kent Date: Fri Oct 7 02:25:47 2005 +0000 A little further along in googlish search commit b39fa29d1e50567f4150bc552084f3bba46d0609 Author: kayla Date: Thu Oct 6 23:54:59 2005 +0000 added droAna2 commit 65cd3d476b24dac95c5dca6a186ee7c32ea3c33b Author: sugnet Date: Thu Oct 6 23:50:52 2005 +0000 Human Exon Array probe set track from affymetrix splicing sensitive microarray commit 8bb3bc569e09a32a984ebd70ab4109e3ca124acb Author: kent Date: Thu Oct 6 21:58:40 2005 +0000 Fixed typo in usage. commit 4397113372150e7d3fd3a0b01a53edbce4ed4652 Author: kuhn Date: Thu Oct 6 21:41:49 2005 +0000 removed bacEndPairs kruft from mark's previous commit commit 1a8e7264bcf9509e359a357a30361ef491703ca5 Author: kuhn Date: Thu Oct 6 21:36:23 2005 +0000 resolved collision from previous commit commit ecd1401515b93f605d8dcb0d5828ebcb6e15268e Author: kuhn Date: Thu Oct 6 21:34:42 2005 +0000 resolved collision from previous commit commit 49c12d2b96cd92d2e3ec963936950fd0ca65d256 Author: kate Date: Thu Oct 6 21:29:52 2005 +0000 Corrections to NHGRI Dnase track commit e8f8300010d36d6d3d2e1f9b1d4e0e06f841fb86 Author: kate Date: Thu Oct 6 21:20:50 2005 +0000 Update NHGRI Dnase track entry commit 4aee48f64bd971fc49802f0b8d3d44fff32fde09 Author: kate Date: Thu Oct 6 21:14:28 2005 +0000 Misc commit c564070bf01493aed2f624d1528bfb4120452bbc Author: kent Date: Thu Oct 6 21:10:07 2005 +0000 Starting to put in structure for googlish searches commit 2b6f907d8aea7bce216ea8453c6ef59602319ee3 Author: kate Date: Thu Oct 6 21:03:07 2005 +0000 Reformatting and an update commit 0ae77e7e0a0b6cd42effd006c7c9f2fd58196948 Author: kate Date: Thu Oct 6 20:41:53 2005 +0000 Clarification commit 6399946aada05b7d014df77df9666b1267b0160f Author: kate Date: Thu Oct 6 19:06:55 2005 +0000 Fix memory problem parsing matrix setting commit 605fcc37e1d939b521af9c4c1c7d8c7497adabbc Author: kate Date: Thu Oct 6 18:51:49 2005 +0000 Add matrix header commit e0b4b7b366da6986f05ffbe780c663969870a9c9 Author: kate Date: Thu Oct 6 16:06:28 2005 +0000 Correct the methods description commit 6c8844ab1922477cb862fc0511c820aba635f5c5 Author: donnak Date: Thu Oct 6 15:33:33 2005 +0000 Added droAna2 announcement. commit 37fd906251ff1773be55ae442c791374ae176fa6 Author: galt Date: Thu Oct 6 15:00:06 2005 +0000 "Encode release log update" commit 83e33656a5edf599758a645db975ea062d347a7a Author: galt Date: Thu Oct 6 15:00:05 2005 +0000 "Release log update" commit b37fbf44c5081a89dd25faad967ff3734a4dae45 Author: markd Date: Thu Oct 6 06:32:09 2005 +0000 disable bosTau2 updated until problem with refseq tables can be resolved commit 452f55fd77802f474b0a3ccf52060284c6eb8b5d Author: kayla Date: Thu Oct 6 01:18:29 2005 +0000 removed Scaffold from type of gap since there aren't any commit 9af7dbf94accc6896db3a627927479a155b7a068 Author: kate Date: Thu Oct 6 00:54:50 2005 +0000 Affy data submitted commit 153e4e7aaa7a6aad6bb3bcef59158e3d507e72b3 Author: kate Date: Thu Oct 6 00:49:02 2005 +0000 STAT1 Chip-PET data in ENCODE regions, from Singapore commit e502e4dd791e8fa35d066808d940d2bfc2a0c5e8 Author: kate Date: Thu Oct 6 00:18:08 2005 +0000 Bold the matrix column headers for tables in description page commit 40cde126fa6e3340f1ccb941e8b1155bb6a43083 Author: aamp Date: Wed Oct 5 23:30:05 2005 +0000 I forgot to take my path partitionSequence.pl out of there. Also I added some stuff to the help. commit 02ce4eac076f9578c7482964a1f4fd9ea28f8218 Author: kate Date: Wed Oct 5 23:25:54 2005 +0000 Add NHGRI DNAseI HS genome-wide data from Greg Crawford (Collins lab) commit 63fcb00aa275fe766e7389e21ea56a3843be90f6 Author: kate Date: Wed Oct 5 23:24:37 2005 +0000 Add NHGRI DNaseI hypersensitive data (genome-wide). commit cb5b75c9091e2ec5ad7a24a64a04a317e51ac195 Author: heather Date: Wed Oct 5 22:25:39 2005 +0000 Ensembl moved from mm5 to mm6 commit 111035c6e45d9fc484452984a62abc4a8c0e03c3 Author: donnak Date: Wed Oct 5 21:59:17 2005 +0000 Edited droAna credits. commit a2aadd36d07af79191853a0558a896be856ec23e Author: donnak Date: Wed Oct 5 21:59:01 2005 +0000 Uncommented droAna2 from release table. commit efed8d44054bf87ac92848032ef84b6709f921f6 Author: aamp Date: Wed Oct 5 21:41:18 2005 +0000 Added extra step: partition. And extra DEF vars SEQ_LIMIT. commit 62a5b98ab2b184656b92563828e23ff9dd76053b Author: heather Date: Wed Oct 5 21:05:13 2005 +0000 fix for RT #1269. Ensembl apparently changed things. Removed support for wider view. Reported by OpenHelix commit 79b01603893911897842a6fabe91068e2854e77b Author: donnak Date: Wed Oct 5 20:45:30 2005 +0000 Modified the help text for the Flip Reverse Primer option, per Bob. commit b5ff60f9726298044701f9ca78718bec7e84013c Author: kuhn Date: Wed Oct 5 19:51:22 2005 +0000 added reference to Pruitt paper commit 11c32b312b87a0bdd7d6cfd0d0177a7d935407e9 Author: kuhn Date: Wed Oct 5 19:38:51 2005 +0000 added reference to Pruitt paper commit 98b39a96b2d1a684d781616b7a367acfb69833fb Author: kent Date: Wed Oct 5 19:07:43 2005 +0000 Clarifying coloring of mismatching amino acids commit 84d0b2e146ac42d8272eceffe61c500df86540d6 Author: jen Date: Wed Oct 5 19:07:37 2005 +0000 Adjusted otherRefGene -> squish and blastDm2FB -> pack. commit c58e9e284be8abae0c74f229c999ab57217b853f Author: hiram Date: Wed Oct 5 18:23:34 2005 +0000 For chain and net canFam2 commit e6d55518b21ec5e17018faecff045b2f3fad3e40 Author: fanhsu Date: Wed Oct 5 18:02:48 2005 +0000 Added minIdentity to parameters of gfOutputBlast() and gfOutputAny(). commit adb548b211105eeeb5416237a636db150ca18baa Author: kate Date: Wed Oct 5 17:51:09 2005 +0000 Add matrix variable commit c334df6378747965fe48574327fbbee3d362ae5b Author: galt Date: Wed Oct 5 15:00:03 2005 +0000 "Encode release log update" commit ba65d7625da871ba33382cb6dcad2b2318bc3cbb Author: galt Date: Wed Oct 5 15:00:02 2005 +0000 "Release log update" commit c3b5157e1d494f5fcee9a4d288b4ea166fa80d38 Author: aamp Date: Wed Oct 5 12:04:29 2005 +0000 Added support for multiple grps defined in db.grp in hg.conf. commit f936fe5bd512902e15531b7cec4064353662c6ba Author: fanhsu Date: Wed Oct 5 10:35:50 2005 +0000 Added a default 0.0 value for the minIdentity parameter of axtBlastOut(). commit 7b013b88a6df66b0ee7be6a86d3557e2582d4e31 Author: fanhsu Date: Wed Oct 5 10:13:28 2005 +0000 Added minIdentity to gfOutputAny() parameters. commit 68765fa4ff499191130bc108c79845b675f7a5dc Author: fanhsu Date: Wed Oct 5 10:10:31 2005 +0000 Added minIdentity to gfOutputBlast() and gfOutputAny() parameters. commit a2621cc75ea636d31e191a7670773e9568ba7c02 Author: fanhsu Date: Wed Oct 5 10:08:35 2005 +0000 Added minIdentity to axtBlastOut() parameters. commit 815a572d67dd0f3a28a806e377e00536a276b98d Author: fanhsu Date: Wed Oct 5 10:06:52 2005 +0000 Added minIdentity to the function parameters. commit 1d645b7117cb9dd2489e87a7a7d5d16ec85717d0 Author: markd Date: Wed Oct 5 04:57:40 2005 +0000 removed confusingly named function added by some misguided programmer commit 83c389db39a480392fe44c907a8b0cfb099f515e Author: markd Date: Wed Oct 5 04:55:43 2005 +0000 fixed bug with added frames when both start and stop are not defined commit 9fa257399a6730b1686d48331614f92fa7db6cad Author: donnak Date: Wed Oct 5 00:17:50 2005 +0000 Added markd to bosTau2 credits. commit 6dc0b1ee24f68c5235dc0932bbda123d6a341aa4 Author: hiram Date: Wed Oct 5 00:02:56 2005 +0000 Cleaning up loose ends. commit a41bb32b685940a4c8c9d9729e43dac472eae7fb Author: kate Date: Tue Oct 4 23:58:10 2005 +0000 Change Sanger entry at the request of Ian Dunham commit 9857ea008fb60cfbabb72d95e9bff6998d2f7b95 Author: donnak Date: Tue Oct 4 23:22:05 2005 +0000 Fixed typos. commit 7db700991c43bea182d6c0e423560e24d87ced00 Author: donnak Date: Tue Oct 4 23:05:15 2005 +0000 Changed HUGO to HUGO Gene Nomenclature Committee or HGNC, per request from HUGO. commit ac7cb7a9a1b77b235e4de9369d5c5c9dde5e1c8f Author: donnak Date: Tue Oct 4 23:01:32 2005 +0000 Changed HUGO to HUGO Gene Nomenclature Committee or HGNC, per request from HUGO. Also fixed up a few grammar/formatting items while I was in this file, because it may be viewable by the public via the TB. commit a5b6d9175f9d8b226eff14a3281277b01ec3675f Author: donnak Date: Tue Oct 4 22:59:31 2005 +0000 Changed HUGO to HUGO Gene Nomenclature Committee or HGNC, per request from HUGO. commit 33800ae9cabccd8db063f279a18c916acd71c952 Author: donnak Date: Tue Oct 4 22:57:15 2005 +0000 Changed HUGO to HUGO Gene Nomenclature Committee or HGNC, per request from HUGO. Also fixed up a few grammar/formatting items while I was in this file, because it may be viewable by the public via the TB. commit 701d26ce6b078529f26006c146706089e0e2b07c Author: donnak Date: Tue Oct 4 22:53:05 2005 +0000 Changed HUGO to HUGO Gene Nomenclature Committee or HGNC, per request from HUGO. Also fixed up a few grammar/formatting items, because this file may be visible to the public via the TB. commit 3df0e1eb1ddb0f93460a76d720feb32c5f66cc00 Author: donnak Date: Tue Oct 4 22:46:40 2005 +0000 Changed HUGO to HUGO Gene Nomenclature Committee or HGNC, per request from HUGO. Also fixed up a few grammar things while I was in the file, in case these strings are visible to the public via TB. commit 6556746bce4a6e7269e6b0a5ce96667b26a118f1 Author: donnak Date: Tue Oct 4 22:40:48 2005 +0000 Changed HUGO to HUGO Gene Nomenclature Committee or HGNC, per request from HUGO. commit 5353d32ebda5e0a636ac68eb70c66087b25a9932 Author: donnak Date: Tue Oct 4 22:39:20 2005 +0000 Changed HUGO to HUGO Gene Nomenclature Committee or HGNC, per request from HUGO. Also fixed up grammar & typos while I was in the file. commit abad3583160e283a47f7a4dd245707c376fdf21b Author: donnak Date: Tue Oct 4 22:32:23 2005 +0000 Changed HUGO to HGNC, at HUGO's request. commit 7e50c5da684ef46eaedb0b2074463f2354107876 Author: donnak Date: Tue Oct 4 22:29:38 2005 +0000 Changed HUGO to HGNC in printf string, in case it is ever accessible to public. commit 599c2543d9626f1e8d6a9df7b16c1900f7f85a87 Author: donnak Date: Tue Oct 4 22:27:07 2005 +0000 Changed HUGO to HGNC at HUGO folks' request. Also made a few minor grammar edits while in this file, because this text may be accessible to the public via TB. commit e13d25d2eca90e9a17d3baf1b58517870b32a23f Author: hiram Date: Tue Oct 4 22:22:02 2005 +0000 Adding Mm7 chain and nets commit 61fc61383da179643bf6d3e1bb942dc17eba39b2 Author: donnak Date: Tue Oct 4 22:18:31 2005 +0000 Changed HGNC to HUGO Gene Nomenclature Committee. commit 01120d4ad3788fba7bb3a738da6cc8ca6a726add Author: donnak Date: Tue Oct 4 22:16:12 2005 +0000 Changed HUGO to HUGO Gene Nomenclature Committee, per request from HUGO folks. commit 869218e308691021fd879de5515a222256ffed5d Author: donnak Date: Tue Oct 4 22:08:34 2005 +0000 Changed HUGO to HGNC, per Fan. commit 0c6c90c5439c3bcfad7ef90a6ec7ba2c5973b04a Author: donnak Date: Tue Oct 4 22:02:10 2005 +0000 Changed HUGO to HUGO Gene Nomenclature Committee, per request from Fan. commit 99615a50b55635bb0834eb16d8c335b3055f1aa3 Author: donnak Date: Tue Oct 4 21:59:27 2005 +0000 Changed HUGO refs to HUGO Gene Nomenclature Committee, per Fan. commit df594771b70a212671737bcd499a5ca9abc072af Author: kpollard Date: Tue Oct 4 21:53:28 2005 +0000 fixed grammar commit 4325fe4c1687995aa82d8661954cc0e65c1d29d1 Author: kpollard Date: Tue Oct 4 21:47:44 2005 +0000 fixed example commit 248498406f7eb842781a7ef638cfc9c04a047c76 Author: kpollard Date: Tue Oct 4 21:37:03 2005 +0000 finished description page commit 2734393508609b63aee54fa53db50f48d65535d8 Author: kpollard Date: Tue Oct 4 21:25:46 2005 +0000 finished description page commit e6c1c20d9d42d1d10e0c938aa52d78149a926990 Author: markd Date: Tue Oct 4 21:13:30 2005 +0000 enabled bosTau2 commit 4741ce37e761e0072e5f32efad7e77f5e69051bb Author: kpollard Date: Tue Oct 4 21:03:26 2005 +0000 added info from NCBI commit 587ec99ca254ba89ef7b4e422bd9d0023359f36a Author: hiram Date: Tue Oct 4 20:23:07 2005 +0000 Finished with Fr1 commit 5e7d9abead0d22a949fad07c0073a83e988767b5 Author: donnak Date: Tue Oct 4 19:48:36 2005 +0000 Archived a few articles. commit c523d437ed09a95d014144dcf5d6a89dab04f608 Author: donnak Date: Tue Oct 4 19:48:21 2005 +0000 Added announcement for bosTau2 release, archived some articles. commit 894b9cd576d40947c2d1c58700b5747570e56fc7 Author: donnak Date: Tue Oct 4 19:21:52 2005 +0000 Updated information for several people. commit ba8d3fe62b1e6c1b4766da2767fbd9c36d693929 Author: donnak Date: Tue Oct 4 19:01:39 2005 +0000 Minor formatting change. commit 5eaf367772e5714ec1e3c447fc5ecc51ec815aa8 Author: donnak Date: Tue Oct 4 19:00:33 2005 +0000 More updates to blockCount descriptions, per Jim. commit 9950ec80caa386c018e0e64ae2e8616dd1eb929a Author: donnak Date: Tue Oct 4 18:57:57 2005 +0000 Added PslInfo clarification, per Jim. commit 40ff331d8fcbde71a86e3071b21265756f82b6d2 Author: donnak Date: Tue Oct 4 18:56:40 2005 +0000 Added another PSL format clarification, per Jim. commit 508d62e35302b8124424264d4e0669a6deaf06a5 Author: donnak Date: Tue Oct 4 18:28:06 2005 +0000 Fixed typo. commit 39107aee29a17a96169d237929756326da5287ea Author: donnak Date: Tue Oct 4 15:40:24 2005 +0000 Updated PslInfo description, per Jim. commit bb6ccef104904ec9ce02fec68c562249addecf56 Author: donnak Date: Tue Oct 4 15:36:37 2005 +0000 Updated info, per Jim. commit e7a872992e34e53958950dd524030971faec1781 Author: donnak Date: Tue Oct 4 15:27:00 2005 +0000 Added more text to this page, although it is still incomplete. commit ab42101abaeb539245904c3d528030c8d6cdc156 Author: donnak Date: Tue Oct 4 15:24:09 2005 +0000 Added bosTau2. commit adc63f4fc839f6e841f9edb581cf4760e28832a8 Author: donnak Date: Tue Oct 4 15:23:56 2005 +0000 Added bosTau2 credits. commit b5a534949ed9f4b6855bf200147395b42e670e72 Author: galt Date: Tue Oct 4 15:00:06 2005 +0000 "Encode release log update" commit 5951f41ffc9a38da5c4f803aaba26dd87a5cab29 Author: galt Date: Tue Oct 4 15:00:05 2005 +0000 "Release log update" commit 82ab93b6036200b4dbd55e2bd24f613a19ef65ea Author: galt Date: Tue Oct 4 02:07:15 2005 +0000 "New version number v118" commit d41ed6842c7569d7ba9a0f089ec2d010e6562d4a Author: kpollard Date: Tue Oct 4 01:09:58 2005 +0000 worked on description page commit fa6f1af576ad70aedc7d31e8cba304a1f61a0611 Author: kpollard Date: Tue Oct 4 01:09:02 2005 +0000 first draft of description page commit bdd6d10ce1ff1812f9646a6fd808f9937bfb1d92 Author: kpollard Date: Tue Oct 4 00:02:24 2005 +0000 fixed search example commit 501d77c51e4b6e64dcfb71dda23a28e66b30c82d Author: kpollard Date: Tue Oct 4 00:02:10 2005 +0000 description file for therVolc1 commit a84e9d13f401b46b9b328466f04acc2308b45b9e Author: kuhn Date: Mon Oct 3 23:51:53 2005 +0000 small tweaks commit e626eb13cedfd01b047f8b7e6bdaf040e14697f3 Author: kpollard Date: Mon Oct 3 23:30:14 2005 +0000 new description file commit a9511953fc37b1477d887f330d2885d52c53cb80 Author: ann Date: Mon Oct 3 22:25:24 2005 +0000 Hyphenization change (Pan-S) to (PanS). commit b4e04655f21f29ab35ad7cb128c3c134e79d5e06 Author: donnak Date: Mon Oct 3 22:09:02 2005 +0000 Fixed some of the examples & edited bits of the narrative. commit 6af2f83b664f52b77ba4387e3344a9d0de2e5e67 Author: donnak Date: Mon Oct 3 22:07:57 2005 +0000 Added organism-specific entry for xenoRefGene to pick up italicized format for organism names. commit ca039b10310c4bcfe38ab73d42b9e1503b53c401 Author: kate Date: Mon Oct 3 21:40:43 2005 +0000 Update commit 4c0b382c0966d9e0ae2bf02d70d56113d0b35d41 Author: heather Date: Mon Oct 3 21:35:32 2005 +0000 oops commit 6a48e1e6ee2af86d52ff5e29aafe6ef29aa3c881 Author: heather Date: Mon Oct 3 21:34:57 2005 +0000 wrapper for mysqladmin commit 5e07a54a57030e491d480e3f9a06f00abea92ce6 Author: fanhsu Date: Mon Oct 3 21:15:14 2005 +0000 Updated ncbiBlastOut() to implement -minIdentity logic. commit 307fd1dfb0a9b79f41b26d038b865f203a527846 Author: kpollard Date: Mon Oct 3 20:53:58 2005 +0000 finished TIGR and description.html commit 6b182c53a14e0df0e014315beb16063b4a82ae8c Author: kpollard Date: Mon Oct 3 20:51:48 2005 +0000 fixed link to gene in example searches commit 1fd6e53cc5582bc249d248d8ae99c8d7ecff6f4a Author: kpollard Date: Mon Oct 3 20:46:35 2005 +0000 fixed typo and link commit 7624323999984d7cf6bdf35d07d38ed19084dbaa Author: kpollard Date: Mon Oct 3 20:14:35 2005 +0000 finished TIGR ORFs commit d14c7d5bee39703a86bfa9a54f7e85ab18d64e5f Author: kent Date: Mon Oct 3 20:13:02 2005 +0000 Name searching about half way done commit 8443d680e2365b5d4944302a8865609618d00b68 Author: kate Date: Mon Oct 3 18:44:40 2005 +0000 Fix misspelled name commit b2ea606f0f722361eb5376022def5c80115d6a2e Author: kate Date: Mon Oct 3 18:33:38 2005 +0000 Tweak display of matrix on description page commit 8212f00b2529519843c3b4a27f5fe7e7cd8daf96 Author: kpollard Date: Mon Oct 3 18:26:43 2005 +0000 added Todd's make doc for ferrAcid1 commit 1318a7e53e8434d4518b5efdff39e8cd91414425 Author: kpollard Date: Mon Oct 3 18:26:16 2005 +0000 added Todd's make doc for therVolc1 commit 891fb2e7f42a4672076a8539b18f71922e3ca80d Author: kpollard Date: Mon Oct 3 18:25:55 2005 +0000 added Todd's make doc for therAcid1 commit 92d76b44ff6ff31bbbc847f982960a831a7abf7c Author: kuhn Date: Mon Oct 3 18:22:21 2005 +0000 some small wording and hyphenation changes commit e5713a196259e9fc7eaef93662872ad882c5900c Author: braney Date: Mon Oct 3 15:01:10 2005 +0000 took out some old annotation stuff commit 2a3fc18f9a381b67f348278591d366ef3ae92413 Author: galt Date: Mon Oct 3 15:00:04 2005 +0000 "Encode release log update" commit 5c87ae1d5740839b59d69ef3963baf96d70e92e1 Author: galt Date: Mon Oct 3 15:00:03 2005 +0000 "Release log update" commit c32bc31bca862b3e708592698081c912085086a0 Author: markd Date: Sun Oct 2 20:10:28 2005 +0000 added testsed for start and stop not being defined commit 90df4b8deb3c038d0bf93f52616a9f9be0fca04a Author: markd Date: Sun Oct 2 20:09:51 2005 +0000 added function to default exonFrames; added reverse-complement function, fixed bug with added frames when both start and stop are not defined commit 45e6d09c5d30116fc42232d6a8b5ae726e382b8c Author: markd Date: Sun Oct 2 20:08:27 2005 +0000 added missing external defintion for free function commit 8a9968b79aaba191bad5d3ffcf402ad528a55a7b Author: braney Date: Sun Oct 2 19:07:20 2005 +0000 add frames defintion for codon translation commit c18d547b0f63823b8a4dba06049a165cebf19db6 Author: braney Date: Sun Oct 2 19:05:55 2005 +0000 take out some stuff that once was used but isn't anymore commit 23647464a679250479e7e60c188833ffe45b4fb8 Author: braney Date: Sun Oct 2 18:59:22 2005 +0000 take out some stuff that was interfering with codon translation that isn't used anyway commit ddbb10e5ab356d2de1b299e8591c9d5594c9a185 Author: braney Date: Sun Oct 2 18:48:09 2005 +0000 the complement of a gap is the same gap commit 31040594a550098804e403dda4cd79a5c24a7fa1 Author: braney Date: Sun Oct 2 18:47:19 2005 +0000 add a button for maf translation of codons commit c14bb85439407ee4f46c6c3481addf02eff73863 Author: lowe Date: Sun Oct 2 16:59:02 2005 +0000 Added all new archaeal species -- 25 total 25 now commit 9b14be103e7d52afc1258f0dca1a23647d26f9b7 Author: galt Date: Sun Oct 2 15:00:04 2005 +0000 "Encode release log update" commit 8b43ded2b8bc149e1ac1b52aab15877c93c0d2a8 Author: galt Date: Sun Oct 2 15:00:03 2005 +0000 "Release log update" commit 184acd75e582d7714b586ab1700cd026315b7c7b Author: baertsch Date: Sat Oct 1 18:49:44 2005 +0000 test commit 7195250625cfcd4c7ac9a460a67df7b1ed0e2b74 Author: galt Date: Sat Oct 1 15:00:02 2005 +0000 "Encode release log update" commit 3c00b1417c83aac946635df9644735497b1771da Author: galt Date: Sat Oct 1 15:00:01 2005 +0000 "Release log update" commit 6090f1722fdc234db1b8caa297805013a87fd3ed Author: angie Date: Sat Oct 1 00:58:06 2005 +0000 Add position to "view table schema" URL so that it's part of the newly created session. (As Ann found, userDb might have been updated with a different db's position so taking it from the cart can cause problems.) commit 9b5a3e4a592adb549ece0e5d322b42b344674ce9 Author: galt Date: Sat Oct 1 00:25:45 2005 +0000 fixed capitalization commit a3c856d1d1c1ef8c95bd5bb57346ba336bc86cbf Author: galt Date: Sat Oct 1 00:21:24 2005 +0000 added text to the Add Your Own Custom Track dialog which explains the new upload options/features commit 59e597767b182e70390f1ce4222a2360eb9ebbbd Author: kate Date: Fri Sep 30 23:50:28 2005 +0000 RT 1266. Support matrix variable in track description commit 6d3547030ad54dfcdbe8a0729e103b094458989c Author: kuhn Date: Fri Sep 30 23:42:52 2005 +0000 shortened shortLabel for TargetScanS track commit 7f62d50c394ddfcd2216efc32edd064e77962825 Author: kuhn Date: Fri Sep 30 23:41:36 2005 +0000 shortened short label for ENCODE Reseq Regions track commit 5907671ba54666cbe6add12d1b4c6dd5183c2ecb Author: kuhn Date: Fri Sep 30 23:40:11 2005 +0000 changed some wording a little commit d36fc7ed2e212cb25d1ef0949f1a309337f05be8 Author: galt Date: Fri Sep 30 20:59:20 2005 +0000 adding automatic decompression support to net-linefile, i.e. urls ending in .gz etc commit bc63ad7ac29a670605b8eb72ab19f47e0003eaf7 Author: donnak Date: Fri Sep 30 20:29:12 2005 +0000 Updated link for Gil's latest pub. commit 69a7e34767e356621b2a2f6fef03b70abf289e5f Author: donnak Date: Fri Sep 30 20:24:48 2005 +0000 Moved Fan's pub from 2004 to 2005 section. commit c667919dc59d8b0ff0f0b48532cc1ec29ac7e28f Author: donnak Date: Fri Sep 30 20:18:01 2005 +0000 Updated page, per David. commit ae87f0abcfc10f87457dc5a31159b28832b2710f Author: donnak Date: Fri Sep 30 20:02:14 2005 +0000 Added chr18 pub. commit 06d8f9a3908b065af3cf90e4e7636f8c8974c136 Author: heather Date: Fri Sep 30 19:44:23 2005 +0000 include alternate name and full band name commit 0e1e18dec862dc0dafe056f2ab4baebf6004ae86 Author: donnak Date: Fri Sep 30 19:40:59 2005 +0000 Fixed some typos found by Katy. commit 0bb117b785db9f4cc192d84d6372d285d533197e Author: kate Date: Fri Sep 30 18:28:58 2005 +0000 FGenesh update to EGASP, new GIS data commit 3fe4d3034e914f2478c21accfa4c36353caf2e1c Author: kate Date: Fri Sep 30 18:21:11 2005 +0000 New ENCODE tracks commit 8d2773f567bb54d4b8339e22a1477c5bbe6fb937 Author: kate Date: Fri Sep 30 18:17:11 2005 +0000 Add Fgenesh info commit 000b2d86dfc8e67365fcf30ff6ad5c5a4c87fdda Author: kpollard Date: Fri Sep 30 18:04:13 2005 +0000 initial make doc for picrTorr1 commit 5e1964ccb5105b08a3cd29ef20e6101fb8dea0dd Author: donnak Date: Fri Sep 30 18:03:27 2005 +0000 Fixed typo. commit 120d1cf3ffbdb92ac837be3f2646c9ca95560bfb Author: kpollard Date: Fri Sep 30 17:54:18 2005 +0000 fixed errors in description file and ordering commit 91e9b05dc6ecd9745ff2d74884402330573a7fcb Author: kate Date: Fri Sep 30 17:48:35 2005 +0000 New ENCODE data commit 37e9f5d87a78f7633bc1cbc65d882c12c935cde9 Author: kpollard Date: Fri Sep 30 17:45:45 2005 +0000 draft description file for P. torridus commit e8f451ae75554f28aa9568b7b364c243ebcc7b55 Author: kpollard Date: Fri Sep 30 17:44:08 2005 +0000 fixed typos commit 9900c9295c931955cedc114b50c5273e46a743d0 Author: kuhn Date: Fri Sep 30 17:22:28 2005 +0000 added targetScanS to tablesIgnored for hg commit ebaf9161ad79a377f7004c8f54e5de5b2bf525d9 Author: kate Date: Fri Sep 30 16:16:07 2005 +0000 UCSD data submitted commit f32b784a7777784da9e0c8c052b40d7b6ec191e9 Author: kent Date: Fri Sep 30 15:36:37 2005 +0000 Adding test case (not in make test, takes too long) for bug reported in blast output. Still can't reproduce bug after trying on Pentium and Opteron linux. NOw to test on Solaris. commit e4f8cb44837a502646ea7bfc6985616e12bdd651 Author: galt Date: Fri Sep 30 15:00:03 2005 +0000 "Encode release log update" commit 6bfb0c269e6a94b4c8960cbfc41143b5b5bc9bfc Author: galt Date: Fri Sep 30 15:00:02 2005 +0000 "Release log update" commit 26f9ecf5073e7d197ad730b2490eb664b538d278 Author: markd Date: Fri Sep 30 05:33:37 2005 +0000 added nscan track commit 0ff488016d1addde3eed696fb90c0f28c2c460a7 Author: kpollard Date: Fri Sep 30 02:22:22 2005 +0000 edits to description.html section commit 74cb6438cd1d0b0f24ff2153a1cd2efcf981234d Author: kpollard Date: Fri Sep 30 02:06:43 2005 +0000 make doc for archeoglobus commit 524ea3304819e70ab90ada352f7a67a0c873957e Author: kpollard Date: Fri Sep 30 02:05:27 2005 +0000 details about archFulg1 genome commit 8871ace208c359feeaabb247ec65cf2f2d4b8572 Author: kpollard Date: Fri Sep 30 00:41:58 2005 +0000 :q q:quu commit 62bbb25ac5082b81b6be1a3e010dedd058f44f04 Author: ann Date: Fri Sep 30 00:25:50 2005 +0000 Changed shortLabel for all_mrna to conform to 16-char limit. commit 0baff85cf630474aac42b7820c788a3e37a10ce1 Author: kpollard Date: Fri Sep 30 00:16:54 2005 +0000 Fixed multiz phastCons track smoothing commit 2d67bdff924697833f328778af62d95007baba96 Author: hartera Date: Thu Sep 29 23:50:09 2005 +0000 Added internal name prefix for another library. commit 9a0854321b640072abad12729f8044e1deef5a85 Author: hiram Date: Thu Sep 29 23:47:16 2005 +0000 Correct an error in definitions commit 9524394b31bce7a1e05965a4b624ebae027df743 Author: kpollard Date: Thu Sep 29 23:37:21 2005 +0000 Fixing phylogenetic tree in details page commit 9a2858b3ccf67bba13fa8ae866cce4ace1445234 Author: kpollard Date: Thu Sep 29 23:29:49 2005 +0000 Added phylogenetic tree to details page commit b11565900bf69129a97952b7fcecc1be1a83f847 Author: markd Date: Thu Sep 29 23:16:51 2005 +0000 added genbank build description commit 6142a5fd8d062b1d2a7bcfb1626300a4c2580380 Author: markd Date: Thu Sep 29 23:10:42 2005 +0000 reenabled load of xeno mrnas until various issues have been fixed commit 7caf581b7edc7aa34e445393a935aac98623648a Author: markd Date: Thu Sep 29 23:06:30 2005 +0000 enabled auto-alignment of mm7 commit d98cd3c1b91ee3302dda88babd6234e516e8c78b Author: hiram Date: Thu Sep 29 22:50:58 2005 +0000 Working on bacends and STSmarkers processing commit 2adaeb9fbd0dbd566dfdacee8fa108fc65cf9780 Author: hartera Date: Thu Sep 29 22:20:04 2005 +0000 Description for BAC end singles. commit c56fcf456e3522b07b256c7dd3b781ca602b1966 Author: hartera Date: Thu Sep 29 22:19:43 2005 +0000 Description for BAC end pairs. commit f1a6c612cb2a8444a4dc86355a673b0cf61f8809 Author: hartera Date: Thu Sep 29 22:18:33 2005 +0000 Added BAC end pairs, singles and bad pairs tracks. Added searches for BAC end tracks. commit 0e0f8cddbe0b297eb1f59778fd7c88f469f8bfb4 Author: ann Date: Thu Sep 29 22:14:28 2005 +0000 Edited two typos in Altschul reference. commit 8f90d1165fbbb1b47c4e6e89785da5bc821a66cf Author: heather Date: Thu Sep 29 22:11:36 2005 +0000 new implementation commit 563d459bfd4e1e49ed0b9a6f6e006c07af43e770 Author: kate Date: Thu Sep 29 22:08:45 2005 +0000 Update for BU Orchid and GIS tracks commit 6d5cd1f81e7f4138f3dfc5485edb556252006ef5 Author: heather Date: Thu Sep 29 22:03:10 2005 +0000 new implementation commit 40cc15d8986d11d4f270fd6e434be56dd56f4cf3 Author: baertsch Date: Thu Sep 29 21:52:04 2005 +0000 remove Human reference commit ee2637dbdebc7f9729cc5730156b0fb4d98b7627 Author: ann Date: Thu Sep 29 21:14:43 2005 +0000 Added this file to augment existing trackDb.ra file. commit 997499d0ea879e571878d92b4ab18149cdc19554 Author: galt Date: Thu Sep 29 19:19:08 2005 +0000 spelling fix change attatch to attach commit ccc7b81edab087bddb9e2a781f1b977c855da193 Author: galt Date: Thu Sep 29 19:10:53 2005 +0000 test with full paths commit c9a7008f749f6ef40f0af623844a499995d775c9 Author: galt Date: Thu Sep 29 19:09:15 2005 +0000 enlarged field for extSource commit da612745f8181c266af62573c7bb91d4037584bc Author: galt Date: Thu Sep 29 19:07:26 2005 +0000 added -lump option, useful with scaffolds commit 25d61ddcae34003199ff6ad092cfd165a54f6834 Author: hiram Date: Thu Sep 29 18:23:31 2005 +0000 Add changes to allow separate processing for random contigs commit 64997c43b71a6cfd619f730791e8a11abbe98b10 Author: kate Date: Thu Sep 29 17:52:56 2005 +0000 Update commit 1ba58c5d548badf1f87ec5e7e0414b78e59c8c58 Author: galt Date: Thu Sep 29 15:00:04 2005 +0000 "Encode release log update" commit 606fce648978f63126e5f443d3f08060592f528e Author: galt Date: Thu Sep 29 15:00:03 2005 +0000 "Release log update" commit ad551f970bddacbc752c447c95f12b5ac5d25091 Author: markd Date: Thu Sep 29 07:10:45 2005 +0000 disabled building and load ests commit 612a0a308f58a52190b29852ddb7b423a937f5d5 Author: kate Date: Thu Sep 29 00:10:53 2005 +0000 Need to quote tags in here docs (shell syntax) commit 2eb3e9b4ee63debba5c0b113eb94833b3d261222 Author: kate Date: Wed Sep 28 22:52:13 2005 +0000 Update downloads path commit df64b2aea9c7cf5307f936e930441236863efc82 Author: angie Date: Wed Sep 28 22:10:45 2005 +0000 Since blastz ignores anything in the .q file after the matrix, warn if the given .q file contains anything after the matrix definition -- we used to think that parameters could be given there but they are ignored. commit 28a893bdd9d95a022204ebae4461dda2db15f35e Author: aamp Date: Wed Sep 28 21:38:22 2005 +0000 More instructions to the Wash U. guys. commit 6692b84badb64baef5b54d70f2fe4219a2b33902 Author: ann Date: Wed Sep 28 21:21:59 2005 +0000 Edited two typos in Altschul reference. commit 72fb9ad0e60469fdf10cc6c114bc0b7ba1349725 Author: kent Date: Wed Sep 28 20:20:11 2005 +0000 Making caption parts that are shared and pane-specific work nicely so there's less to read on multiple-pane pictures. commit 62bd2e03aab90ccab2f6e9984d6d7547b3bfa0a6 Author: hartera Date: Wed Sep 28 18:45:58 2005 +0000 Removed some commented out debugging lines and added some in to print with the verbose option. Changed variable names to be more self-explanatory and added some extra comments. commit b7c46638ccc0c70140d8b4539672245abd07becd Author: hartera Date: Wed Sep 28 17:49:29 2005 +0000 Added $ to gensub2 in one instance as it should be a variable. commit a422d5efd6e04b32b1c1a4a776a422a1b1440300 Author: kent Date: Wed Sep 28 17:12:05 2005 +0000 Making structure so that can group together common elements across panes in caption. commit ccb6385b1a30e0fc03d10110e97882d8eb87b898 Author: galt Date: Wed Sep 28 15:00:04 2005 +0000 "Encode release log update" commit ccb952804186b1c11e2f8a6b281743538e6d48b8 Author: galt Date: Wed Sep 28 15:00:02 2005 +0000 "Release log update" commit 76cbb49b0f033c92b02da52b91e0d6ca1c3138d6 Author: markd Date: Wed Sep 28 05:40:40 2005 +0000 added object for store frames for MAFs commit 7cdf04131767fbb3ae0dbe332a97a2dbb5233c28 Author: jen Date: Wed Sep 28 00:16:27 2005 +0000 Added rhesus and human to xenoRefGene organism list. Allows joined tables to show up in table browser. commit f9f6adc5047e59d25b1cc422772f87288d46e2a5 Author: galt Date: Tue Sep 27 23:30:16 2005 +0000 fix minor text commit acdc80316be5005df81d4771a10514b971bdcee5 Author: galt Date: Tue Sep 27 23:11:33 2005 +0000 added more info about the assembly commit 059979f67d066a754a5b1fcb4bb57af58796c445 Author: aamp Date: Tue Sep 27 23:07:22 2005 +0000 Fixed a problem in r1.262 with $Organism appearing in the text in hgTrackUi and perhaps elsewhere. Also removed comments I meant to remove ealier. commit b070ff3e9fca0e954d965138bcd760f75fedc3bb Author: markd Date: Tue Sep 27 21:39:36 2005 +0000 disabled large delete optimization, as it doesnt scale for ests commit 223e6ff302086e48aba79e7b5dd51eade6f32779 Author: ann Date: Tue Sep 27 20:54:35 2005 +0000 Changed visibility to dense at top level for xenoRefGene. Changed shortLabel for xenoRefGene, xenoMrna, and xenoEst to "Other ...". Made necessary changes to trackDb.ra and visiblity.ra files below as a consequence. commit 4d171a7a4115f45c6779b515e0957e6f0b268553 Author: kate Date: Tue Sep 27 20:27:09 2005 +0000 Add spanList to wiggles to improve performance commit f0990b5f1bb93839f56dc247cbe8ec6aab74033d Author: jen Date: Tue Sep 27 18:22:27 2005 +0000 Added bosTau2 to database list. commit 14cbc7b96cfd04546c22b40a15635facf0ff65cc Author: angie Date: Tue Sep 27 17:54:32 2005 +0000 Fixed one more spot in pcrQuery that I missed in 1.49. commit 56b266b6b684e2ff67127c369e84b0de5e7f860b Author: angie Date: Tue Sep 27 17:51:23 2005 +0000 And one more little test case. commit 5d99aedfffa80b4720f4c67f45c9e7f48f195ceb Author: angie Date: Tue Sep 27 17:38:22 2005 +0000 Added another pcrDirect test: - strand of second sequence. commit a036b86662a34a2db37a7c0ce5df22d8c194f6a6 Author: aamp Date: Tue Sep 27 16:48:53 2005 +0000 Utility to do short-match on the command-line. Yeah it's not quite findMotif. commit 592e05b4ac9b72bec7e31717920ce6d8a6473084 Author: galt Date: Tue Sep 27 15:00:03 2005 +0000 "Encode release log update" commit 5037d6d35bf148f1f65e76eadf107408585db9df Author: galt Date: Tue Sep 27 15:00:02 2005 +0000 "Release log update" commit 9245a81da3b430f93474ab045f76129184dcbb9f Author: galt Date: Mon Sep 26 23:56:00 2005 +0000 added chromosomes downloads steps commit 4ce1fd2799871636d6a670d70901638d915c00bc Author: angie Date: Mon Sep 26 22:57:30 2005 +0000 In hGetIndexedDbsMaybeClade(), if central db has clade for this db, then do a relational query on dbDb and genomeClade instead of separately querying the genome and clade of each active db which was way less efficient. commit bc612e4d30d2c8c2edb0efe32d008f7875763103 Author: hartera Date: Mon Sep 26 22:43:00 2005 +0000 Removes overlapping records from a linked feature series file. commit e7b4aea7633215835786e9f91835e3170e8f05e9 Author: hartera Date: Mon Sep 26 22:41:52 2005 +0000 makefile for lfsOverlap commit 866c0e7582a7a1d20f248b884c46f70038e97382 Author: galt Date: Mon Sep 26 22:41:42 2005 +0000 added option -v to invert selection commit ecb65fcf3c89d6d31e3a171f18bd677a234a0b2b Author: galt Date: Mon Sep 26 22:23:46 2005 +0000 fixed $organism, rather than write a trackUi handler, because this track is probably unique to bosTau2 commit cdbbec3edfe6ed399f71a9d26dbe6de474780b02 Author: angie Date: Mon Sep 26 20:50:38 2005 +0000 Finished 12way phastCons, added bacEndPairs (sources suggested by Roger Hoskins, BDGP). commit ce8398b0dce5918832aba1d74114438ff61c9202 Author: angie Date: Mon Sep 26 20:47:04 2005 +0000 Added multiz12way and phastConsElements12way. Added search for bacEndPairs. commit 98de0b9489343bc4ad091436320dd28d72a1fc65 Author: hiram Date: Mon Sep 26 19:08:59 2005 +0000 With the chainSelf experiments commit 9059d2271782680c8d519cab24c69737804ca9d2 Author: hiram Date: Mon Sep 26 19:08:30 2005 +0000 With the chain Hg17 experiments commit 14d586ccbf6ff8bcd28c0a28584b3a53b8ed94de Author: hiram Date: Mon Sep 26 19:07:55 2005 +0000 With the chainMm7 experiments commit dd341c6ba88ceaf6a795f7e42e1b661d79fcf9a4 Author: kate Date: Mon Sep 26 18:33:50 2005 +0000 Add downloads commit ab8f2ebc6da29c7c5203f83dd4f9d8d81542bbe0 Author: aamp Date: Mon Sep 26 18:31:10 2005 +0000 Some repeat-related things. commit 42cd31e9c4ac2b3475c90873b1cac6e3b318f940 Author: ann Date: Mon Sep 26 18:01:40 2005 +0000 Changed shortLabel for xenoRefGene to "Other RefSeq". commit 153b697b4d044fb3303a22749e1031d592872f4c Author: ann Date: Mon Sep 26 18:00:17 2005 +0000 Removed section on xenoRefGene (will inherit from parent drosophila). Changed shortLabel of xenoMrna to "Other mRNAs". commit e401c9035ede3bf891f350c4f3862ae27a978211 Author: ann Date: Mon Sep 26 17:49:32 2005 +0000 Changed shortLabels for xenoRefGene and xenoMrna to "Other..." and changed visibility of xenoRefGene to dense (from hide). commit 8af0ee80d8befafb144a39a87ea28eac8aec72fa Author: ann Date: Mon Sep 26 17:18:16 2005 +0000 Changed shortLabel for xenoMrna to "Other mRNAs" commit dae493a3ec0cc2fc911888957cdec18b62bfb5bc Author: braney Date: Mon Sep 26 16:53:56 2005 +0000 add support for 2bit commit 614b48ce4a4011a7a4d79078a7a633d5268ac31c Author: kate Date: Mon Sep 26 16:33:45 2005 +0000 Changes to improve inheritance of composite config by subtracks commit 3c145276dce8d8eea2863e52f40433d88e4ab61f Author: galt Date: Mon Sep 26 15:00:03 2005 +0000 "Encode release log update" commit ea311c1f96b20a5d84d1917ad1d384796344bdab Author: galt Date: Mon Sep 26 15:00:02 2005 +0000 "Release log update" commit 9adb0127263a93d228af3bbde70664bbefa59f59 Author: braney Date: Sun Sep 25 23:14:58 2005 +0000 another misnamed track commit 43e3d4bb17464d462d3c2391a9ff102fabe3aa24 Author: braney Date: Sun Sep 25 21:57:17 2005 +0000 a weird track that should be called something else commit 0a1a84fdc311d5f647b1feb79ba8aa9a4681653f Author: markd Date: Sun Sep 25 20:57:56 2005 +0000 added database advisory lock just in case high-level lock is removed commit 804dca114298a9b4d109934e3849d7c86c61ed89 Author: galt Date: Sun Sep 25 15:00:04 2005 +0000 "Encode release log update" commit 0d36648236967a3d190bb3e4c64544820883e8b0 Author: galt Date: Sun Sep 25 15:00:03 2005 +0000 "Release log update" commit bfce8c2ae00e6ca07fe585a700f3c8c79a487f69 Author: markd Date: Sat Sep 24 20:31:35 2005 +0000 skip trackDbs in path if there don't exist commit 1d629407ec122f265715b0aa8fa146ca2f8986f3 Author: braney Date: Sat Sep 24 18:26:35 2005 +0000 add new id for new protein track commit 018d8c4e9138d0d8a2fb5642a63a310d9d8a9616 Author: galt Date: Sat Sep 24 15:00:04 2005 +0000 "Encode release log update" commit 3646435e590ac25835c289bc025e218022b99e0d Author: galt Date: Sat Sep 24 15:00:03 2005 +0000 "Release log update" commit 069f8769317cb7852d865939a78318a4fa0d8388 Author: aamp Date: Sat Sep 24 00:38:36 2005 +0000 OK this one deserves some attention: I generalized the trackDbLocal concept with the the normal trackDb concept so that the db.trackDb setting in hg.conf allows multiple trackDb tables (comma-delimited). Basically the rows of all the trackDb tables listed are combined (union). Rows that are common to several tables have priority in a left-to-right manner, and the first table listed overrides all subsequent tables. commit 16be16b4f9a166dedc2653a40748e1a98d88d941 Author: heather Date: Fri Sep 23 23:28:29 2005 +0000 include reference allele in name for fa output commit 52ca19f6b80a599b73cb7f3b64ed81f8fb753495 Author: markd Date: Fri Sep 23 23:08:17 2005 +0000 fixed description of gbSanity commit ba3b38fbe24d7d48cc2768172995e8e6f0e9d591 Author: galt Date: Fri Sep 23 22:31:38 2005 +0000 added cow1->2 liftover commit 53b30f0ecfeb91a3a77a3c6fa63bb1273f433896 Author: galt Date: Fri Sep 23 21:50:36 2005 +0000 Code needs loChain structure zeroed out, otherwise the Y/N strings have no terminating 0 (multiple and fudgeThick) commit 40bb3a5a1e1c7df1416540a35c3a6958a457cb41 Author: sugnet Date: Fri Sep 23 21:00:03 2005 +0000 lib files for mouse chip cgi visualization commit 2ebb0e4247274bfd91e578b18d7e1a0538f6af4a Author: sugnet Date: Fri Sep 23 20:56:23 2005 +0000 cgi programs for visualizing splicing commit 22a7d35ce0a0e4adca042ed9c5c37ddd54195bfe Author: sugnet Date: Fri Sep 23 20:52:43 2005 +0000 program for matching up orf predictions. commit 70b3d958092b9369e43d30b30738b1e6c9a7b878 Author: sugnet Date: Fri Sep 23 20:51:18 2005 +0000 Removed exonMatch from makefile. commit 9dbed6ad12d5e770b257d4ba32de7b640afc09db Author: sugnet Date: Fri Sep 23 20:49:42 2005 +0000 program for breaking up beds into pieces. commit 8b70d8c2df356a442b0df56ea51a2275d4425c54 Author: sugnet Date: Fri Sep 23 20:40:38 2005 +0000 Catching up on some overdue commits for alt-splice research commit 386b4e288e68b9082d88f467469ea0fa76439eb3 Author: sugnet Date: Fri Sep 23 20:37:25 2005 +0000 Lots of stuff... commit 55f417f6fb572e423a6e9510276ce04a2891d08f Author: kate Date: Fri Sep 23 18:39:16 2005 +0000 Updates commit e373a6308ae4b0620a7bf8fd2368a28ac791d529 Author: heather Date: Fri Sep 23 17:20:06 2005 +0000 another flavor commit 3359813124197f92c1cfad5b82cf8a4490b879dd Author: markd Date: Fri Sep 23 16:43:38 2005 +0000 fixed problems with gbGetSeqs retriving psls commit 9c5d86ec95472f53c8e774cf15a4532656480497 Author: galt Date: Fri Sep 23 06:19:27 2005 +0000 looked like options array not being used commit 8e7131373ac09bf07083c4e9e05a291428223322 Author: markd Date: Fri Sep 23 04:21:04 2005 +0000 added mm7 xeno refseq commit 40b250ae8c8762ef890004f960188e913d2674fd Author: angie Date: Fri Sep 23 01:28:50 2005 +0000 Fix for bug that has affected PCR results since genoFind.c r1.18, 12/9/04: In genoPcrDirect(), add clump->target->start to clump->tStart and tEnd before calling gfClumpDump. In pcrQuery(), do not subtract clump->target->start before returning tStart and tEnd. These changes are necessary because PCR clumps, unlike regular blat query clumps, have already had clump->target->start subtracted out (inside gfPcrClumps). isPcr expected this but gfServer did not, so the change to genoFind fixed isPcr but broke gfServer. commit 74ba4304eee8ae227a70deccde0849fe9a5121ab Author: angie Date: Fri Sep 23 01:23:17 2005 +0000 Added a few notes about the different coords used for clump->tStart and tEnd in PCR clumps as opposed to regular blat query clumps. commit cf9c53173cf11d924b55518d7eb2079259576f37 Author: angie Date: Fri Sep 23 00:31:23 2005 +0000 Added gfServer test to top-level test target. commit 5ef401f285d0fe8159b51dc5317a542ec9d10a55 Author: ann Date: Fri Sep 23 00:27:52 2005 +0000 Fixed typos in reference paper's title and journal number. commit 70afb4e50478bcb2086b19edbf0304c86a42347d Author: ann Date: Fri Sep 23 00:12:13 2005 +0000 Removed entry for genscan track, because it is inherited from top of hierarchy. commit 48e80bccbfa46e3d5b646f0b49d2ea1be1f46ef7 Author: ann Date: Fri Sep 23 00:10:58 2005 +0000 Removed entry for genscan (as it is already specified in trackDb.ra) commit b422af43788097bc76ab1c1005b2490401ce011b Author: ann Date: Fri Sep 23 00:09:42 2005 +0000 Changed xenoRefGene visibility to pack. commit e10c80f93e1f31a5ff3560f2797867444ee04133 Author: galt Date: Fri Sep 23 00:01:19 2005 +0000 fixes/workarounds for safari and FFmac commit 4ac1f3a1432a35a8964742876760ea04031ab416 Author: markd Date: Thu Sep 22 22:52:05 2005 +0000 don't print messages to stdout so it can be used in a pipe commit 120f6e03a5b5863bfd331dc813b4d4384846c2dd Author: kuhn Date: Thu Sep 22 22:48:04 2005 +0000 added some text to describe the methods commit b4dda018b2a0ae3b8af542e184e692a6c4a08f65 Author: kuhn Date: Thu Sep 22 22:01:09 2005 +0000 moved reference to separate section commit b7102c644a43e4337dad0af81bd65fa88d17326a Author: ann Date: Thu Sep 22 21:24:39 2005 +0000 Removed because it was redunant with the top-level genscan.html file. commit e8c941d77b63444baf5fc12f83d0096a4ca85771 Author: ann Date: Thu Sep 22 21:12:56 2005 +0000 Changed publication year on second pub to 1997 (correct year). commit 4bea5b0fdab36c4ba83407b4877eea1d4b8bd96f Author: baertsch Date: Thu Sep 22 20:25:23 2005 +0000 add url for yale pseudogene commit 1a7b714ed455b556b7422d7f0a801717bbf2149d Author: kuhn Date: Thu Sep 22 20:04:09 2005 +0000 added a comment in usage statement about a gotcha concerning realTime mode commit 497fc5fcf285e45ea2a0730a1e5202f9563af36a Author: daryl Date: Thu Sep 22 19:38:41 2005 +0000 Truncated long label for regPotential5X so that it draws completely commit 905b95a2c4eeb274535bc4fa5cebf5583a5cc81f Author: kate Date: Thu Sep 22 17:57:58 2005 +0000 Fix typos in Uva track commit bcee9e1a837f4edd280ce30c6be614fe1de1598c Author: angie Date: Thu Sep 22 17:25:18 2005 +0000 testPcr was not actually making an output file and didn't have an expected file; fixed that. commit db0c3e519233da3ea41c7adb63b01b355218d3c4 Author: baertsch Date: Thu Sep 22 02:27:43 2005 +0000 description for yale pseudogene commit faff32c27553565eb6ee983f05834d797975f9b7 Author: galt Date: Wed Sep 21 23:08:14 2005 +0000 need symbolic debugging info for gdb commit 526621435201f224f19ddb2c3911139d7176cf90 Author: ann Date: Wed Sep 21 22:32:38 2005 +0000 Changed publication year on second pub to 1997 (correct year). commit 57360f703efc32d7511578f220ef615b11d79b48 Author: heather Date: Wed Sep 21 22:04:23 2005 +0000 memory handling commit f433e1e516e3caa7e8e9163128d6115494e4ac81 Author: heather Date: Wed Sep 21 22:00:50 2005 +0000 minor cleanup commit 751d9e57dbffe2603f5acda47387769241d0b759 Author: kate Date: Wed Sep 21 21:28:28 2005 +0000 Minor update from Yale commit cf1aeda3d801b691e0694af0906fb0add4101f9f Author: baertsch Date: Wed Sep 21 20:53:33 2005 +0000 add encode consensus pseudogenes commit 2f1fb2966db188edc221595a60cdbdab25685c34 Author: jen Date: Wed Sep 21 20:44:12 2005 +0000 Removed hg16-specific comments in Methods section to made description more generic. commit 54aa20aec3966dfc71297783f5aee6c1a2b11cff Author: kuhn Date: Wed Sep 21 19:27:40 2005 +0000 added job number for QA job commit 4239120faf05cbdb9b68e5501128cd3fd483b4fe Author: braney Date: Wed Sep 21 17:43:27 2005 +0000 a human proteins track commit a4d6fba177e8112052cfa8fb07dc23b19f0e5178 Author: angie Date: Wed Sep 21 17:05:29 2005 +0000 Additional info from Roger Hoskins and Pieter deJong. commit 1a9efe919cd18c342cb052b15daaa5b4a05a3ea2 Author: ann Date: Wed Sep 21 16:37:51 2005 +0000 Adding xenoRefGene back in (to set visiblity to dense) commit 74b0262a0e19dd7dc3d86ce81f5f030a1103ce2f Author: galt Date: Wed Sep 21 15:00:03 2005 +0000 "Encode release log update" commit 4dcbb9c71a1ac61db7fd242a1fb116cd69362fbb Author: galt Date: Wed Sep 21 15:00:02 2005 +0000 "Release log update" commit 93714df4dba41954618711494ad9aaaddb78fb9b Author: aamp Date: Wed Sep 21 14:55:53 2005 +0000 Added a program to download RTDB from a web server and load it. Also added and modified the README explaining the whole RTDB situation. commit c3ad6ab23fdb6d67067244ed6b9341451ca815b2 Author: daryl Date: Wed Sep 21 02:03:13 2005 +0000 Changed view defaults for encode recombination rate track and Tajima's D track;
    Removed wiggle credit from Taj D details pages. commit 13314f901d2f25796d7618a110f02b9a6870f58a Author: angie Date: Wed Sep 21 00:26:16 2005 +0000 Incorporating some edits from Todd Lowe. commit 478ab4464e4d8886acb4192abad4786e385b2cf3 Author: angie Date: Wed Sep 21 00:06:13 2005 +0000 Added description of bacEndPairs with new notNCBI setting (also here to pick up ./bacEndPairs.html description). commit d2686914231b0583e3b4fa6be6f1e4a55424dfe5 Author: angie Date: Wed Sep 21 00:05:03 2005 +0000 First-cut description for D. mel. BAC ends (not from NCBI). commit 4756cba797735b3232d97d6aa9143101ad1a8469 Author: angie Date: Wed Sep 21 00:03:56 2005 +0000 Added support for new trackDb setting notNCBI -- inhibits links back to NCBI in doLinkedFeaturesSeries (for non-NCBI bacEndPairs in dm2). commit d5e4f1b10596b42562cb72dc255551438804595b Author: baertsch Date: Tue Sep 20 23:59:50 2005 +0000 temp fix for pseudogene tracks commit cf7c8f94b44b578dd6326f041fe951fd5e375825 Author: jen Date: Tue Sep 20 23:43:33 2005 +0000 Updated 'release notes' link - was broken due to a change at FlyBase web site. commit 38a00999fc19d501c8949e3f0aebe3d098f9532d Author: hiram Date: Tue Sep 20 23:40:09 2005 +0000 Correct usage message for -seqList style of name in the file, the : should not be there if there is no start-end commit ebcb905091b9c072a92655fea5e925f027361812 Author: markd Date: Tue Sep 20 22:51:20 2005 +0000 fixed incorret computation of download directory commit b901ef9d16e71dea7d8b9653ecc1fe7d0ab12b7b Author: baertsch Date: Tue Sep 20 22:17:37 2005 +0000 *** empty log message *** commit bf74f591bb8615cad2bd0d8c2c965cfc05e21c04 Author: baertsch Date: Tue Sep 20 22:17:33 2005 +0000 add new types for pseudogenes to genCodeGeneClass commit 702c0b5c7d1bd5c3db2a7db267fd8cb0113d455d Author: jen Date: Tue Sep 20 22:15:59 2005 +0000 Fixed two errors: italicized D. ana and added dp3. commit 09100e1b737b84ba372ca79db0ea88fb5b19a9a4 Author: kuhn Date: Tue Sep 20 22:03:22 2005 +0000 fixed misnamed assembly in droMoj1 commit e4052fa13f242bd769bcf3788a80a821e74c4a50 Author: markd Date: Tue Sep 20 21:50:26 2005 +0000 enabled some missing genomes on hgwdev commit a482f20619dfc36e342ee32b47668875974a6a2c Author: markd Date: Tue Sep 20 21:50:05 2005 +0000 enabled droEre 1 on rr commit 2dd7a45bbd5ee2e822b400c13a8183a4cbce0646 Author: daryl Date: Tue Sep 20 21:46:04 2005 +0000 Updated descriptions for Tajima's D tracks commit 8d171aae637f957fd90d41d4aa4131ea053c598c Author: daryl Date: Tue Sep 20 21:43:06 2005 +0000 Finished Tajima's D tracks commit 888537e541ab99a42ce470381e341806356aa67e Author: kate Date: Tue Sep 20 21:33:34 2005 +0000 *** empty log message *** commit ce8c622b3a17cf88f161165a26363dc1fd723677 Author: kate Date: Tue Sep 20 21:32:40 2005 +0000 Add two new ENCODE tracks (additional DNA Replication data from U Virginia) commit 2bbb7f5ca75b964989e03ad49a477ddd600f2fab Author: jen Date: Tue Sep 20 21:21:10 2005 +0000 Activated changes from Donna for droEre1, droMjo2, and DroVir2 releases. commit ae5e91ca63f603f04eae91a6dd778311eaaa7632 Author: hartera Date: Tue Sep 20 21:19:23 2005 +0000 Added a print statement to print the size of gap between blocks that causes them to be merged for ffShAliPart function. commit 8aefcc93b5b662119dd5ef537963b54abf03d7ef Author: baertsch Date: Tue Sep 20 20:52:47 2005 +0000 update name for havana pseudogene subtrack commit 3463587588fa49dcd2ea304799aca5cf8fe02834 Author: baertsch Date: Tue Sep 20 20:50:50 2005 +0000 added GIS pseuodgene sub track commit 53daa8aa90071b4f9f5ea7ead4e7b1e348777d33 Author: baertsch Date: Tue Sep 20 20:50:12 2005 +0000 added search for pseudogene tracks commit 377c3cec02de562d8e3e767642e72d87843e21ab Author: ann Date: Tue Sep 20 20:31:39 2005 +0000 Changed three references from "D. vir." to "D. gri." commit 4d5db6f23a6829bd566c4e4b942ae74a4672ed3f Author: markd Date: Tue Sep 20 19:52:25 2005 +0000 fixed incorrect file locations commit 4795b65dbbaff76e46ca15c8a0eab7a2d1a80173 Author: daryl Date: Tue Sep 20 19:10:44 2005 +0000 format changes for readability commit 92441bb906b4e7e1408c17522e6cf54accabe837 Author: jen Date: Tue Sep 20 19:02:13 2005 +0000 Changed moj to ere for several labels. commit d3081edf354e6e8178e028321bf22522b427767a Author: hiram Date: Tue Sep 20 18:45:52 2005 +0000 Correct slight errors in that lift file creation commit 1d5d349f5992ae4fc2b3a8bf3583553f4a619c59 Author: hiram Date: Tue Sep 20 18:24:32 2005 +0000 danRer3 blastz underway, starting tetNig1 commit 1d43fbc3c98d43b5e3ceab78bd4e84929ea708f4 Author: hiram Date: Tue Sep 20 18:23:57 2005 +0000 Add the create of the lift file for the contig scaffolds commit 7cf136759cbd08d4e42f3badb758aa632c0e3877 Author: angie Date: Tue Sep 20 18:08:17 2005 +0000 Checking in to get the geneid description in there for QA... a couple items in progress: 12-way phastCons and BAC ends. commit 19ecea17c221300837ae3f779994faafc4de3d9e Author: ann Date: Tue Sep 20 16:32:29 2005 +0000 Removed double "cell" word, and added "mapped on whole genome". commit 852318af68c66280b1566663e0619b4cccee3e6f Author: ann Date: Tue Sep 20 16:18:14 2005 +0000 Added the words "genome-wide". commit 92330c774bc91a0dc46de9a50f7717132e419d49 Author: galt Date: Tue Sep 20 15:00:06 2005 +0000 "Encode release log update" commit 0a2089394abd867cc6e6e23e7104736557742fb6 Author: galt Date: Tue Sep 20 15:00:05 2005 +0000 "Release log update" commit e337016d3a52202da0d95b0da308fe2dfdf512c8 Author: daryl Date: Tue Sep 20 05:56:12 2005 +0000 Added hapmapRecombRate and hapmapRecombHotspot tracks commit aaaceb47bd12a751d35383ea8b588c32a2c86330 Author: daryl Date: Tue Sep 20 05:24:06 2005 +0000 Added hapmapRecombRate and hapmapRecombHotspot tracks commit bd4cb6901ad9edd738edb5d89e20a31d6b41c13e Author: heather Date: Tue Sep 20 03:07:20 2005 +0000 "New version number v117" commit 1a7e28c832a78945e23123294bb260a50b64200e Author: genbank Date: Tue Sep 20 02:19:41 2005 +0000 reenabled anoGam1 commit 2329d0d5c787bc55500109abc48d254367c0d41d Author: angie Date: Mon Sep 19 23:51:25 2005 +0000 taking xenoRefGene back out -- it's in the top level already, redundant here. commit fa947415d88f8f0811fa08a35a72cda2a03af686 Author: angie Date: Mon Sep 19 23:40:13 2005 +0000 Added xenoRefGene (thanks to Ann for noting its omission). commit 812f6fb87cedc27cf502484d870d6c116432d24f Author: ann Date: Mon Sep 19 23:08:47 2005 +0000 Edited two search items because the previous scaffold did not have 50,000 bases. commit 0ed97c8825d32c3970696cd8cfb0b96fa299010c Author: kate Date: Mon Sep 19 23:02:12 2005 +0000 1. BU Orchid data from submitter. 2. New UVa tracks commit 18c960ebb2a23d600474c1af73bdf0351e07c20f Author: kate Date: Mon Sep 19 23:01:10 2005 +0000 Cosmetic changes to failure screens, for clarification commit 7cef744d917b2283cdbb3600a19ef9a0b40e3d01 Author: daryl Date: Mon Sep 19 22:43:45 2005 +0000 Added regPotential5X track and description commit 8432018c899280c8e089a2cfb3dfba0028a553ea Author: daryl Date: Mon Sep 19 22:37:10 2005 +0000 Added regPotential5X track commit aec1ec2b623af2b827d7da4d04dd3567baa3bfed Author: kate Date: Mon Sep 19 21:57:55 2005 +0000 Add cell lines for new tracks. Other updates. commit 676fa97365ff93440afe7d29714d95184dcd9eb6 Author: ytlu Date: Mon Sep 19 21:45:04 2005 +0000 add detail for pseudoUcsc2 track commit 8b4164ae8b68a03e061135aff4e8c1bbd3e58cfb Author: ytlu Date: Mon Sep 19 21:43:57 2005 +0000 add a encode pseudogene track by yontao Lu's methods commit da7b4c3896385ea54d6724269da4fd29f1067bd9 Author: sugnet Date: Mon Sep 19 20:35:51 2005 +0000 Added documentation for affy transcriptome phase 2 track. commit 930201addfbfe902d3e6b58ba0526e0e7c22a858 Author: sugnet Date: Mon Sep 19 19:27:20 2005 +0000 Added exonWalk docs commit 7f80401192a7bea8540d96c5f3c24979c6d14928 Author: sugnet Date: Mon Sep 19 19:05:32 2005 +0000 Added docs for altGraphX track. commit 587f24916413ffd32c5fa17ef1372828f3f16690 Author: sugnet Date: Mon Sep 19 18:52:17 2005 +0000 Adding bin field commit 09aa5d8d5eeef624fb7a187d5a629af857e571a4 Author: kent Date: Mon Sep 19 16:07:30 2005 +0000 Adding index on image.imageFile commit edd59147c5ddeb1eb0bce346f02b1aa3adf4dc67 Author: kent Date: Mon Sep 19 16:06:55 2005 +0000 Adding visiGenePaneLabel commit 701c292bb8df7a551ddb2d2309d6f4142cbdd3a8 Author: galt Date: Mon Sep 19 15:00:06 2005 +0000 "Encode release log update" commit bf4cf59715384252cd46679d3e2453ddf28fd0a4 Author: galt Date: Mon Sep 19 15:00:05 2005 +0000 "Release log update" commit ff3e3df616379ce67358f5f3e3ecc1bb28a09449 Author: braney Date: Sun Sep 18 18:04:10 2005 +0000 fix bug where missing CDS caused errAbort commit f0f42e0baddf837375efcbeee27aba98e6296901 Author: galt Date: Sun Sep 18 15:00:04 2005 +0000 "Encode release log update" commit f9a7100c9f0d5f3fa779805a049e38cbc8166999 Author: galt Date: Sun Sep 18 15:00:03 2005 +0000 "Release log update" commit bd24076a61c97609872bef3bbd5e7d9eee318c97 Author: markd Date: Sun Sep 18 07:37:12 2005 +0000 handle unplaced chromsomes even if no gap betwen contings commit 8f4392a12f0d3da7516fa84ec4d4d8fb1abae31d Author: genbank Date: Sat Sep 17 18:50:28 2005 +0000 disable anoGam1 on hgwbeta due to corruption commit 6de47b44c6b193c776ff7698b36ff7bc49b97b07 Author: genbank Date: Sat Sep 17 18:50:04 2005 +0000 enabled rr updates of some flys and ci2 commit 63e49b377fa23dd8ecbc2bb123aa81206ab304a2 Author: galt Date: Sat Sep 17 15:00:02 2005 +0000 "Encode release log update" commit c13a23ff5347832e6bf4171037794216aa83ed69 Author: galt Date: Sat Sep 17 15:00:01 2005 +0000 "Release log update" commit 7513cbdbe97920c877139feb028318ece677b50e Author: hiram Date: Sat Sep 17 13:23:39 2005 +0000 Add a chainCanFam2 commit cf5df8edf6f9058d62e2f005862ce3eb2b29f4cf Author: hiram Date: Sat Sep 17 05:54:25 2005 +0000 Add self blastz chain net commit d54a052df09f050b25fd7adb0e013184433a8b5c Author: baertsch Date: Sat Sep 17 00:12:45 2005 +0000 slightly darker gray for blastz mrna alignments commit c1392d5ff4b166d4e2db45007a93744522b2f8ad Author: hiram Date: Fri Sep 16 23:51:55 2005 +0000 Several alignments in progress commit 1d5cada29d6922d4870bfabc50b495f584112453 Author: kuhn Date: Fri Sep 16 23:37:28 2005 +0000 added in new QA job commit 0eb4ed73758eb2c47f0f80be8f76ad282d7b13f1 Author: heather Date: Fri Sep 16 21:47:30 2005 +0000 generate upstream files commit b801647dff48deb0208a50c808f2b5da33788adc Author: markd Date: Fri Sep 16 21:21:56 2005 +0000 disabled oryCun1 commit 8698f826057feea9c9b7a835d4e3e47e49b22774 Author: angie Date: Fri Sep 16 20:46:59 2005 +0000 Added -hgConf option (support for running on hgwbeta). commit f2e7a893dba0a441a4bce7eea883cd3872b0c795 Author: angie Date: Fri Sep 16 20:25:16 2005 +0000 Added db to warning message about both split and nonsplit forms of table. commit 14adb0a38160179d9731652675bb2fdd884b5560 Author: fanhsu Date: Fri Sep 16 17:45:25 2005 +0000 Removed makeMm6Kg2.doc. It is obsolete. commit abaa75267467b6db21a212dcc38a5193370d1445 Author: galt Date: Fri Sep 16 15:00:03 2005 +0000 "Encode release log update" commit 398c58a8fa149ba36320c0e71128cf103cdb3e2e Author: galt Date: Fri Sep 16 15:00:01 2005 +0000 "Release log update" commit ef8748aeb2254aa7449e6eaa5e9a8f5863b79bae Author: markd Date: Fri Sep 16 05:36:07 2005 +0000 fixed invalid html commit a8af4c82256943eb1eb5be19a20b8a21739b63c9 Author: heather Date: Thu Sep 15 23:50:48 2005 +0000 remove data check that no longer applies commit 84cd19bb70dd934fd56f10fa3555b7f9b1e4ee54 Author: heather Date: Thu Sep 15 23:46:04 2005 +0000 DIPs commit 9b4bf8c3bb7f11efede237323693cbdd83111d58 Author: ann Date: Thu Sep 15 22:50:38 2005 +0000 Added subscript to log10 commit e650b044eb9702ef94c71be4d39c05aed4da18c0 Author: ann Date: Thu Sep 15 21:00:02 2005 +0000 fixed typo in References section commit 29d3024f1dbbc0109b9c2424389ca261ee524efe Author: kate Date: Thu Sep 15 20:27:04 2005 +0000 Splitting encode_tba23Evofold docs between assemblies, as they reference different alignments commit 2049f8c76d82f1aa54a077a9777a6895b1a8f649 Author: ann Date: Thu Sep 15 19:20:59 2005 +0000 inserted missing space commit 8c2bd9b08e5d589b6074a082c2b743ebeff3a736 Author: galt Date: Thu Sep 15 19:08:32 2005 +0000 updating - nearly done with basic - don't have chains yet - human proteins done commit cd15034f4e92dacb3b1beb1e265dc5599782ec60 Author: kate Date: Thu Sep 15 18:38:29 2005 +0000 Fix Jigsaw track. Update Stanford promoters commit 21828e3a301064f5d030797f9b6cc76f41730e88 Author: kate Date: Thu Sep 15 18:36:19 2005 +0000 Add Stanford Promoters download commit 1b5d149b9bb49366ec5b897d241c06146134c46b Author: kate Date: Thu Sep 15 17:43:15 2005 +0000 Update commit 737aad152d113f641de0f63c91f2873598c78e3f Author: jen Date: Thu Sep 15 17:38:56 2005 +0000 Added unknown category (type=dash) commit 3ff1f3e2fa0344e8ddffab989b1b4728e30e9782 Author: galt Date: Thu Sep 15 15:00:04 2005 +0000 "Encode release log update" commit cf2c13e565a8c15c473e63223cd5da4c5df873e2 Author: galt Date: Thu Sep 15 15:00:03 2005 +0000 "Release log update" commit eda0367873a126f031d34dd9765e999f4f047196 Author: baertsch Date: Thu Sep 15 07:55:53 2005 +0000 add 3 pseudogene tracks commit a668eaac58c7a72c23df6d03f68b86b1ecf9592f Author: markd Date: Thu Sep 15 06:15:53 2005 +0000 added option to get cds from upper case commit 4e010b3909e049448fa245cdf4529045b0f8511a Author: genbank Date: Thu Sep 15 00:29:37 2005 +0000 fixed typo commit 94fc8638ff4bf7b02b33eb6f5ba7f8d08db9eeb7 Author: hiram Date: Wed Sep 14 22:49:54 2005 +0000 Adding blastzMm7 commit 3efa40fd705b945d0555d24693663baa2cebdeec Author: fanhsu Date: Wed Sep 14 22:48:58 2005 +0000 Added a new ID, knownToRefSeqId for geneNetowrkId. commit c88adf6ad44b25670f4fed02aad5b7312c793911 Author: hiram Date: Wed Sep 14 22:48:08 2005 +0000 Add Mm7 chain and net commit ad7700a14be8abfd0c509bbe362e668b9bdf5b27 Author: hiram Date: Wed Sep 14 22:46:22 2005 +0000 Adding Ce3 chain and net commit 26414d5657f28d7582151be0657374336f9fec15 Author: hiram Date: Wed Sep 14 22:45:30 2005 +0000 Adding CaeRem1 chain and net commit e9f755a35e9e9fd14b72788cfc931f8e05fd7bc4 Author: fanhsu Date: Wed Sep 14 22:29:53 2005 +0000 Added Gene Network. commit c1775d6f7c5eded8aa02251454654af72f5c6b6d Author: markd Date: Wed Sep 14 21:10:04 2005 +0000 pass through tracing from gbAlignGet commit 30f06fba0b996fbdc6bbc93f766091cfa2dc0452 Author: hiram Date: Wed Sep 14 20:47:38 2005 +0000 Reworked the sequence with the fixed bit in chrI commit c203cf1f0ae0d88b862611f2258b5b54d0c2d76c Author: hiram Date: Wed Sep 14 20:46:54 2005 +0000 Added blat server commit 57624ecee3da065805eaa7b82dd38c39e6106135 Author: hiram Date: Wed Sep 14 20:46:29 2005 +0000 Initial contents of makeMm7.doc commit 3c35576b679b4bbf82c3d2bcf3e8e4d0821f3e78 Author: hiram Date: Wed Sep 14 20:45:25 2005 +0000 Working on blastz Mm7 commit f869d5885bb4d55d2d4b637bb7f05c278109096a Author: ann Date: Wed Sep 14 19:13:12 2005 +0000 Changed the '2' in log2 to subscript` commit cdfad0017d4f4612a5a895cf93c779c3037bb3b9 Author: heather Date: Wed Sep 14 15:49:38 2005 +0000 not needed commit d9f95da0bbe2b039414470a2f8a5ec42e054f105 Author: galt Date: Wed Sep 14 15:00:02 2005 +0000 "Encode release log update" commit a0d5be4c7cfc90b8b8115cf98300965f1ee6140a Author: galt Date: Wed Sep 14 15:00:01 2005 +0000 "Release log update" commit f5e303eaf994ef2821a2ee56edc617ed2e21e2f2 Author: kate Date: Wed Sep 14 00:15:51 2005 +0000 Remove duplicate entry for tba23_EvoFold commit 617f37a3e1ae7b16a01c5ccf903a2d8a9c84395d Author: sugnet Date: Tue Sep 13 23:56:51 2005 +0000 Added affyTxnPhase2 documents to hg17. commit 159a106351546e0a8200cf029768d9d87604481f Author: kate Date: Tue Sep 13 21:41:34 2005 +0000 Revert from corrupted version commit 2e172119a31c7218a20ccaad891eaed6d628f589 Author: ann Date: Tue Sep 13 21:08:28 2005 +0000 Changed link to GIS site (they changed their website) commit e5e1e5fef95b99471c00e1ef9a223cfb4f51d51a Author: ann Date: Tue Sep 13 21:04:02 2005 +0000 Edited the two links to GIS (they changed their website) commit 0f88eeee28f4af1e6b202f152b5ee856a781f32a Author: heather Date: Tue Sep 13 20:46:52 2005 +0000 add comment commit 0ed377097e539c12f96d6d5f9c04dcb24111822e Author: braney Date: Tue Sep 13 19:58:38 2005 +0000 an improved(?) trackDb.ra for canHG10 commit 31b80499e9e3274419c1fd5a3000b1f3cbc23f57 Author: braney Date: Tue Sep 13 19:48:34 2005 +0000 add human proteins track (KGII) commit 1511df73831386f453e9b1ae802cab870e26b4cd Author: braney Date: Tue Sep 13 19:41:58 2005 +0000 a human proteins track commit 9aded9fde826300e60b37bf5a0f82cc32d7b0537 Author: hiram Date: Tue Sep 13 19:39:23 2005 +0000 Add the zeroBed option to print out the elements with zero distance commit b4737266c6d0792da1d52113cb3463df0f5f9104 Author: braney Date: Tue Sep 13 19:37:08 2005 +0000 free up the maf's as we read them. commit 324f41dc2a5c33102d7915fbcb9708b09880cb53 Author: donnak Date: Tue Sep 13 18:17:36 2005 +0000 Fixed minor grammar issue. commit 0beceaf6e6c43f96b306e783b1928508745edcb7 Author: heather Date: Tue Sep 13 18:13:09 2005 +0000 don't do trackDb or table description on kolossus commit 22017dfbc433fe9df3840a0e1241f5d0feeeb854 Author: braney Date: Tue Sep 13 17:50:09 2005 +0000 add an option to output a bed file with N locations commit 6bfce9f1052c0a67a62dfd76b7cd839ec63b1339 Author: braney Date: Tue Sep 13 17:38:29 2005 +0000 add a routine to output a bed file with N locations commit 9d2b612eeaed1f3f4b6f1f419f435530d4d08180 Author: braney Date: Tue Sep 13 17:31:00 2005 +0000 allow zero length sequence lines in maf (e.g. lines with all '-'s commit 5129852d96ac3b5936ada470aa312e161e0aa5a4 Author: acs Date: Tue Sep 13 16:55:47 2005 +0000 fixed minor indentation problem in dless stuff commit e2f3583692960d8714fac705712cd895e4b6460f Author: acs Date: Tue Sep 13 16:54:09 2005 +0000 renamed variable, at suggestion of Heather commit 14dd4a001fffa6286ec1f82211d0107fee0f776f Author: galt Date: Tue Sep 13 15:00:05 2005 +0000 "Encode release log update" commit 92c666f69d33c45ebc62e4d353d4bcf9cb71fbc2 Author: galt Date: Tue Sep 13 15:00:02 2005 +0000 "Release log update" commit e89006931f3e7598a20f30694ae5e0fff35a39fa Author: braney Date: Tue Sep 13 02:26:16 2005 +0000 add self chain/net, the beginnings of tBLASTn track commit fb32f9ab5ab1a6690bee4622f6259d64812bfff6 Author: braney Date: Tue Sep 13 02:24:26 2005 +0000 add the net self track commit 86bf5ab638657ef93a387dd8df244950c84a9cee Author: fanhsu Date: Tue Sep 13 00:19:49 2005 +0000 deleted one row from acemblyClass where class != 'main' and class != 'putative' commit 40e2db947f0ada2d870a2634a7865dbd049803c6 Author: acs Date: Mon Sep 12 23:58:12 2005 +0000 added dlessMD commit 8321052c233d88faa6beba3c6b19deff8ea8db97 Author: acs Date: Mon Sep 12 23:56:55 2005 +0000 added dlessMD track handler commit aa874d5c3ed24fb0557c9b46c84a4888d0318fd1 Author: acs Date: Mon Sep 12 23:56:11 2005 +0000 allow tracks to start with "dless" rather than having to match exactly commit d9acaf285ac3068c19bccb466006f47ef19b94fd Author: donnak Date: Mon Sep 12 23:38:07 2005 +0000 Fixed incorrect link. commit 25b4d62fa2169d37e39bb688905fdc491b4052d0 Author: baertsch Date: Mon Sep 12 22:40:21 2005 +0000 add meta data support commit b56d204bea762bb461bb8966685090f7b0fd009d Author: aamp Date: Mon Sep 12 22:07:40 2005 +0000 This is for the MGC task. A new perl library for downloading files though the web in the same careful way the gbFtp.pm library does. Several functions in this one are absent, most notably ones like ftpOpen(), ftpClose() and the remote directory listing. commit 8833f426d31c85cf874f9118189fd8391645c522 Author: kate Date: Mon Sep 12 21:58:16 2005 +0000 1. Adding missing 'end' statement. Turn off verbose output from chainer (too much when using scaffolds). Perhaps should change axtChain to verbose=3 commit 3e308c3001016104dcc91fbc8a7d89f0ab3e5ad0 Author: markd Date: Mon Sep 12 21:57:15 2005 +0000 removed reconstructed orgs from auto update commit b59efce11190807d368e2f73d0a4e3700b67732a Author: donnak Date: Mon Sep 12 20:55:28 2005 +0000 Added announcement for 3 flies, commented out until assemblies are released. commit 36c9e1e8f49414a6c575d36a6747b125cfa31d73 Author: donnak Date: Mon Sep 12 20:19:32 2005 +0000 Archived 1 item. commit 4d870ea6a24d0e2e5b93ce0bfebb6ee1babe3b4e Author: donnak Date: Mon Sep 12 20:19:18 2005 +0000 Added news announcement for ci2 release. commit a9a96e76e8154f8f8520cc5cd705ea8c73363d6f Author: donnak Date: Mon Sep 12 20:17:59 2005 +0000 Updated reference to use standard format. commit f4c84ca7f8083a7f75d8139f812088ffd276e087 Author: braney Date: Mon Sep 12 20:08:56 2005 +0000 need trackDb.ra for db specific chainSelf entry commit a1eb6b474529f3dea1707eb8f0822c902815a475 Author: donnak Date: Mon Sep 12 19:24:16 2005 +0000 Removed 2 extraneous periods. commit 90758b677a72e64522715ee9a5cb9183fb376ced Author: donnak Date: Mon Sep 12 19:20:28 2005 +0000 Recommented flies...won't be released for a while. commit fdfd1f0aba63fd55b6b63a22b109d6da49002218 Author: donnak Date: Mon Sep 12 19:12:50 2005 +0000 Some final updates to ci2, droEre1, droVir2, droMoj2 credits. commit 486d651f1198767007f2be485a1c006c66aa70bc Author: kate Date: Mon Sep 12 18:35:15 2005 +0000 Split TBA23 Evofold entries so that we can reference a different alignment table commit 6c791766378ea55f60710dd10ef2782f14f305c5 Author: kayla Date: Mon Sep 12 18:23:16 2005 +0000 fixed broken link commit 648986ed15f0390d8ee147cb4e70cb6de0ea53e6 Author: kate Date: Mon Sep 12 18:11:56 2005 +0000 Minor update commit 9e50ca2fa1f984a06903ca9fcd3d367d2c58da28 Author: angie Date: Mon Sep 12 17:27:02 2005 +0000 Label change: "chosen fields..." --> "selected fields...". commit 059a1453ddafefdf9be1cc78be843b0991cad7a4 Author: ann Date: Mon Sep 12 16:52:36 2005 +0000 Changed link to GIS website commit bdf251b5ede5083005676ed69e00fb4e06517a01 Author: braney Date: Mon Sep 12 16:52:08 2005 +0000 add search methods commit c007f9a9f950a8af9a1e94b2286988f3ea478e55 Author: fanhsu Date: Mon Sep 12 16:43:56 2005 +0000 Updated acembly track from NCBI. commit 494963290ad1260ba67b8d9502a768956c5d37dd Author: braney Date: Mon Sep 12 16:42:46 2005 +0000 add canHg10 commit 3e44f5f8311214dc917088705d9aaab71945d33f Author: galt Date: Mon Sep 12 15:00:02 2005 +0000 "Encode release log update" commit b8ffc127148eff6ad65505a76c19a348ae7022d9 Author: galt Date: Mon Sep 12 15:00:01 2005 +0000 "Release log update" commit 372440da46924e4a7d1df0cabd2c08e8d66bb99c Author: markd Date: Mon Sep 12 14:42:53 2005 +0000 added file listing string tables commit ad1804f92b1b8208c98d8782c4b63646995f0833 Author: markd Date: Mon Sep 12 04:59:04 2005 +0000 added mm7 commit 90b5708ed743e262b616ed0b6cea73b5731f6e4d Author: markd Date: Mon Sep 12 04:17:35 2005 +0000 use -bestOverlap commit 9244e487763afc07da0f0a25aea6e620488474bb Author: markd Date: Mon Sep 12 04:14:42 2005 +0000 optionally use poly-T head for ESTs commit f1ab720cf2591b91153a67b40967baeac835ee02 Author: galt Date: Sun Sep 11 15:00:02 2005 +0000 "Encode release log update" commit bf1f1654c43ee512dbb00e705fe47bf8ea9147d6 Author: galt Date: Sun Sep 11 15:00:00 2005 +0000 "Release log update" commit 1d6a60cece6825765989c54cae86ea63041462e6 Author: braney Date: Sat Sep 10 23:42:51 2005 +0000 a new ancestor commit ad8983d2e7ce3784337cf19c0d76ca3c3657700c Author: braney Date: Sat Sep 10 19:44:53 2005 +0000 a new ancestor reconstruction commit 443aefca7254fd0a824735c802b698c50cde93bd Author: acs Date: Sat Sep 10 15:39:56 2005 +0000 added dless commit f6b905ecb70b77c591c26ab27eeb1c3f7826d1ef Author: galt Date: Sat Sep 10 15:00:02 2005 +0000 "Encode release log update" commit 02853bd413ca9fbc0ae3be430c9416355ed2d916 Author: galt Date: Sat Sep 10 15:00:01 2005 +0000 "Release log update" commit df10379d092b60d3de69dabaed056ebf0c2c440d Author: acs Date: Sat Sep 10 07:43:25 2005 +0000 changed to single dless track, now supported commit 4c2e8d3f91dde0e48849fe0a72e0770f547273de Author: acs Date: Sat Sep 10 07:42:12 2005 +0000 added support for dless track commit 3974180532dfe4ac612a4b4a694cae2b7c5e95aa Author: heather Date: Sat Sep 10 03:56:24 2005 +0000 tweak verbose commit 1c4cc7085ba72a98ad8ad0e8cd9fb6670c6b0a49 Author: heather Date: Sat Sep 10 03:46:02 2005 +0000 initial revision commit 8fe23fe208c972c875df97f998ef55235ad28621 Author: heather Date: Sat Sep 10 01:36:52 2005 +0000 initial revision commit 78aa5ab64df4670fa27c0ea29f94d93c86e24ccf Author: kent Date: Fri Sep 9 22:51:04 2005 +0000 Making captions under thumbnails list all gene names (and omit colors) commit ef365ade3e39f8c76b43b4f6227ea62520a4320e Author: kent Date: Fri Sep 9 22:50:21 2005 +0000 Added visiGeneImageFile and visiGeneImagesForFile commit 021eee14d12c27f77bf900cd79fc23e06350b051 Author: hiram Date: Fri Sep 9 22:11:55 2005 +0000 Adding track blastSangerGene commit 98f528b31e3f80ebe96799c3a6a60b2d5befb667 Author: heather Date: Fri Sep 9 20:59:03 2005 +0000 add ann to email notification commit 2392f269e54928c4b6acc76e6e28ec7882de9e80 Author: braney Date: Fri Sep 9 18:29:13 2005 +0000 add search rules for Human Proteins track commit 7c03c284b5b12ab5fb8d397095f90867e5295424 Author: jen Date: Fri Sep 9 18:29:10 2005 +0000 Added tracks to file commit 4e171657ff7572819af7a9d49bf523135e09f2c2 Author: kate Date: Fri Sep 9 18:01:15 2005 +0000 Update after Sept. lift commit 6ca31369569c915fb5f9f09f768f1045b59be35d Author: fanhsu Date: Fri Sep 9 16:36:03 2005 +0000 Changed Acembly Genes to AceView Genes. commit b876ebe4ec9266782d87e5e642797956dcfaebfe Author: galt Date: Fri Sep 9 15:13:18 2005 +0000 "Encode release log update" commit d76987818cd5956e0335172675856ef7ded71037 Author: galt Date: Fri Sep 9 15:12:45 2005 +0000 "Release log update" commit 1f194293872d3b30d91fbfa7aac338aca80edce7 Author: markd Date: Fri Sep 9 05:21:16 2005 +0000 allow glob patterns in unplacedChroms spec commit cd2cd1d0dd2e33078a838062be961769768e700e Author: donnak Date: Fri Sep 9 00:32:30 2005 +0000 Updated sample position queries. commit ac47809ce7ce94e2fc3e2bb6d674ea50547504dd Author: angie Date: Fri Sep 9 00:30:05 2005 +0000 Watch out for case-insensitive duplicate names (e.g. luTest5 vs. lutest5) -- although mysql allows those tables to be created separately, it barfs when we try to load a table indexed on those names (index is case-insensitive). So ignore subsequent tables that have the same names (case-insensitive) as tables previously encountered. commit c1b4ed347ab180e9a586a45f2ca8e3a77c51885d Author: ann Date: Fri Sep 9 00:23:51 2005 +0000 Updated file with information from Angie. commit dacb0ac6f103552130c2ae8ba578bb8840f5136c Author: jen Date: Fri Sep 9 00:19:13 2005 +0000 Created trackDb.ra commit 3b0fc6b49998965d9f0785f314923e12c0fd22e3 Author: jen Date: Fri Sep 9 00:14:17 2005 +0000 Updated description. commit 119a97c3100f54b18dea185990031a4643c49333 Author: fanhsu Date: Fri Sep 9 00:10:12 2005 +0000 Changed Acembly Genes to AceView Genes. commit 15efd1297d0827945b588586c2b76be37f3cfb95 Author: jen Date: Fri Sep 9 00:07:18 2005 +0000 Updated description. commit 8cf2e8af2d2fd28e2289081f4724ce8668896147 Author: galt Date: Thu Sep 8 23:16:12 2005 +0000 added contig-Orientation track black=known ori, gray=unknown ori commit 376c46bcae98684651b38a95aae1e95814b0bb4a Author: galt Date: Thu Sep 8 23:15:31 2005 +0000 added new tracks commit 284e0794794ae0b927076adb7c894bc468bbc8a5 Author: aamp Date: Thu Sep 8 23:13:57 2005 +0000 Fixed date thing. commit 486403d53a5c9d047c9e3d07ca43d513f4de3040 Author: hiram Date: Thu Sep 8 22:41:19 2005 +0000 Use the DEF variable TMPDIR commit 9ed4dbfd317f5f6189605ed54e025be5d8af94c6 Author: donnak Date: Thu Sep 8 22:25:32 2005 +0000 Fixed broken link. commit d287c693b334a25d8453df1a414b12a0368dbe7c Author: donnak Date: Thu Sep 8 22:17:40 2005 +0000 Added this example file that is cited in the customTrack.html description of the itemRgb attribute. commit dc035746012d6a350a1839384bc204fff9d9aa68 Author: donnak Date: Thu Sep 8 22:16:43 2005 +0000 Added documentation for itemRgb attribute. commit 820a266542ab4890ae7d9bc0fe079eed63a96996 Author: baertsch Date: Thu Sep 8 22:12:44 2005 +0000 remove debug statement commit 8c26a9fd66f89531ac50293a4d5d689e77b54d71 Author: galt Date: Thu Sep 8 22:05:48 2005 +0000 safari-related fixes (not final version) commit e9015dac77aff14eac0fc64e04593323232df8e6 Author: markd Date: Thu Sep 8 20:30:43 2005 +0000 don't include mismatches when calculating minimum not repeat size commit 165cb294398ead7679fbe107acbdba956d700bf1 Author: donnak Date: Thu Sep 8 18:42:59 2005 +0000 Updated some of the search examples. commit a593a8f1965c2c6aa1a2bb5bb4b9aa8f6604c8f1 Author: donnak Date: Thu Sep 8 18:17:16 2005 +0000 Added new paper by David. commit 8804e26e965891ced4ad962df1683983569f995c Author: kate Date: Thu Sep 8 17:48:48 2005 +0000 Make hg17 ENCODE tracks. Most are lifted from hg16 versions commit d6f7ee3eae2733af2887d0458b02c4111ea061e6 Author: kent Date: Thu Sep 8 17:26:14 2005 +0000 Added visiGeneAcknowledgement, visiGeneSubmissionSource, and fixed visiGeneXxxUrl commit acaa00669a051276098da83bc38944786ebaa342 Author: markd Date: Thu Sep 8 15:27:31 2005 +0000 enabled alignment of all current databases commit 4b7249a430d9647866a258ce6c05e188e6162dec Author: markd Date: Thu Sep 8 15:27:15 2005 +0000 removed uses of panasas commit 066ac3e4b6120b00c3bbfdd257674e35123d5dcf Author: galt Date: Thu Sep 8 15:00:03 2005 +0000 "Encode release log update" commit 3d17a615c2bcc1894cc48a2793a05a3f05c000ea Author: galt Date: Thu Sep 8 15:00:02 2005 +0000 "Release log update" commit 3514ebf5c87f4291b5be3257ab6ccc985a5b2a73 Author: kent Date: Thu Sep 8 08:28:17 2005 +0000 Adding a line of instructions. commit 14b984d517b3313d2612b3fa770cdedb2725e982 Author: kent Date: Thu Sep 8 08:22:32 2005 +0000 Suppressing duplicate images in thumbnail list. Rearranging caption. commit ff5d934da25dad13971336635682fa6f32a99491 Author: kent Date: Thu Sep 8 05:23:07 2005 +0000 Adding submissionSource and acknowledgement tags to system commit bc997708a0917cd85097b8420368813d4e119cda Author: markd Date: Thu Sep 8 03:01:36 2005 +0000 added triCas commit b7339386b95a1fada27e16c4fba0265b4047e192 Author: kent Date: Wed Sep 7 23:44:14 2005 +0000 Seems to do the job commit 1fb2354bbaebe72b91ed4996a87a996b426dbd1a Author: angie Date: Wed Sep 7 23:38:28 2005 +0000 Added all_mrna entry (needed for scaffold-based). commit 082b29f00d86df374af65b6f5c37391dfc5c5f65 Author: hartera Date: Wed Sep 7 23:23:58 2005 +0000 Added droAna2 database to be excluded from the refSeqId rule to check mrnaOrientInfo.name. commit 6aaf357407c36f3dfc1ecdf9a68de355bb1aa5af Author: kent Date: Wed Sep 7 22:45:56 2005 +0000 Adding caption table and imageFile.caption field commit e8bfcbb65c677b6102f89bd4931f3a5664fe3c67 Author: hartera Date: Wed Sep 7 22:04:19 2005 +0000 Added Drosophila databases to be excluded from the rule to check mrnaOrientInfo.name for the refSeqId identifier. commit 09ce46d7dc5fb6a02868dae048866c332b4fcbed Author: kate Date: Wed Sep 7 21:36:20 2005 +0000 Change link to liftOver help commit 40cb6399a54401d1ef59324fc52bc3ab3b509052 Author: kuhn Date: Wed Sep 7 21:28:10 2005 +0000 some minor grammar tweaks and reformatting of file to shorten lines commit d074bad672392533dbff5884e475731d1ffd98f9 Author: kate Date: Wed Sep 7 21:25:23 2005 +0000 Add named section for liftOver commit c3cd64efdf82a501cb8a795b690b8bb61f5a6f50 Author: kate Date: Wed Sep 7 21:06:46 2005 +0000 Add function to get a table name for a track. Use it to get table update time for split tables commit 636c288b13b66ff2fc21e388ea8e114607f2d4fd Author: kent Date: Wed Sep 7 20:47:40 2005 +0000 Fixing a possible bug. Adding verbose status info. commit 099d7209d1e3630c052efc49cc92638ab7f535eb Author: hiram Date: Wed Sep 7 19:28:36 2005 +0000 Backout Roberts changes, and implement clear outputs to allow easier graphing commit 3061aad0ed1562e10c30a640cd20b3a7e760bbff Author: jen Date: Wed Sep 7 19:04:24 2005 +0000 Created trackDb for species. commit c4b404141c3eeab06c9e5492a5bc0bb783e682f1 Author: jen Date: Wed Sep 7 18:59:50 2005 +0000 Adjusted which default tracks are on. commit d06f4bf6cf9a3ded6c431741672f085d6c9d421b Author: kuhn Date: Wed Sep 7 18:57:12 2005 +0000 changed some wording a little commit 2c5f656ac5c541830209acd32eafd0793e19a4ad Author: kate Date: Wed Sep 7 17:23:41 2005 +0000 Prune time from table update date display commit 20fec488d7dbb8a94457385870dde716ec46daf4 Author: jen Date: Wed Sep 7 17:15:02 2005 +0000 Removed duplicated track entry for netDm2 commit a23fb834a31ea9a6d891bad1e68fbef0d784926c Author: markd Date: Wed Sep 7 16:14:56 2005 +0000 use mm6 files in iscratch rather than panasus commit 574bc9a6d2ae74ed9773aa05cd359c1675ef5207 Author: galt Date: Wed Sep 7 15:00:03 2005 +0000 "Encode release log update" commit 198d5d5cfd5e60863722c3653c5eb081bab2ac3a Author: galt Date: Wed Sep 7 15:00:02 2005 +0000 "Release log update" commit 3f70c24b73382503158be9fb9856612b3d817de1 Author: aamp Date: Wed Sep 7 00:01:57 2005 +0000 Changed some stuff according to Mark's suggestions. commit 3158a1e09d6b634153a8d560296ad22ccac09639 Author: donnak Date: Tue Sep 6 23:51:17 2005 +0000 Updated Allen reference. commit e52d396b0fe50c2969f3807c91cf0828011fdcbb Author: genbank Date: Tue Sep 6 23:51:01 2005 +0000 removed relatively useless rsync stats commit a38398c0c00633efaf729c7e8108ecdbff89fee9 Author: heather Date: Tue Sep 6 22:46:09 2005 +0000 include 64 bit utils build commit 2855d9a745f8d24d1c8bba33fd1aa4c6c96380ff Author: acs Date: Tue Sep 6 21:45:03 2005 +0000 added dless tracks commit 368ec801beb772a27d4190236b135ae42858fd21 Author: fanhsu Date: Tue Sep 6 21:23:49 2005 +0000 Added GeneNetwork link. commit 4dfb87ff0f7e2852b50fb514ffde7ce99a7dfe60 Author: fanhsu Date: Tue Sep 6 21:19:47 2005 +0000 Created geneNetworkId table for link to GeneNetwork. commit e438c8f1f9e245e08daa39499fb6f63a0d9b0d4b Author: fanhsu Date: Tue Sep 6 21:15:30 2005 +0000 Added GeneNetwork link. commit cecfe7e0e03e32592cf083d7710259fe4312422d Author: fanhsu Date: Tue Sep 6 21:14:21 2005 +0000 Added link to GeneNetwork. commit 0a646c419c035d47fd0887759b68b05dbd72edab Author: fanhsu Date: Tue Sep 6 21:12:16 2005 +0000 Changed "Jackson Labs" to "Jackson Lab". commit 28659e5c3774e52dddf778a09d27750bd3b1c9d0 Author: fanhsu Date: Tue Sep 6 21:07:09 2005 +0000 Changed Jackson Labs to Jackson Lab. commit 945107b1d538715c919f674705c33a4b3039637d Author: kate Date: Tue Sep 6 20:12:42 2005 +0000 Update reference commit d13c5288ad50b88aa9cfb57e2797c0f8ca373b24 Author: donnak Date: Tue Sep 6 19:48:43 2005 +0000 Updated some refs to new format. commit 9be08bc40acadff1dd7bc4bef7210bb1a516927b Author: jen Date: Tue Sep 6 18:54:11 2005 +0000 Added file for new db (came from droVir1). commit 80f32d0580346329bc023f8fee28d573c9bcb311 Author: hiram Date: Tue Sep 6 17:49:54 2005 +0000 Use the specified blastz binary from the DEF file, was only using simply 'blastz' commit 4f358a159207fe350e88ef25fef870c37cb74713 Author: braney Date: Tue Sep 6 15:46:33 2005 +0000 fix mRNA bases display commit 4dfa2c2acd9ee50e6c9fae22c266ed995a6d6d7f Author: braney Date: Tue Sep 6 15:42:47 2005 +0000 add support for ruler complementing, fix for showing bases on mRNA commit 14dad788ae59a8ac74664fea9130092a9e7bbc96 Author: braney Date: Tue Sep 6 15:40:42 2005 +0000 when complementing DNA, change a space into a space commit 0dfd4d1e6991b362f8c9a53049718ead69c3ee15 Author: galt Date: Tue Sep 6 15:00:03 2005 +0000 "Encode release log update" commit 6215faad657a88a4be49b7bce1438c61c5f731d9 Author: galt Date: Tue Sep 6 15:00:02 2005 +0000 "Release log update" commit 10c26d89624b799c49c7abdaa2533ed4304698d9 Author: markd Date: Tue Sep 6 04:14:03 2005 +0000 added missing ooc commit e2ed0eb75c59e9cfec9ab192bec9c3fcad1920e7 Author: heather Date: Tue Sep 6 02:25:15 2005 +0000 "New version number v116" commit d0183b6b2129614daf3152f57ff863481ee2813a Author: markd Date: Mon Sep 5 17:53:39 2005 +0000 documentation update commit c2edb33f3ffe9a5e80963cf5055b3c09905a8043 Author: markd Date: Mon Sep 5 17:29:29 2005 +0000 trim leading/trailing spaces from conf values commit 9f216b3bc848ec5582f33225ab7186fdc450a7bc Author: galt Date: Mon Sep 5 15:00:05 2005 +0000 "Encode release log update" commit 29e9b5398a5665bb6aa0a11557859ea87652fc7a Author: galt Date: Mon Sep 5 15:00:03 2005 +0000 "Release log update" commit 8e0dd010cf22e37ffeb717164d1b7037d7fbf750 Author: markd Date: Mon Sep 5 06:47:14 2005 +0000 disable genomes with missing ooc and in progress genomes commit d71ebe9c647cd6ab95bae386daa45ea92ff5a6f9 Author: markd Date: Mon Sep 5 06:45:08 2005 +0000 found several genomes with missing ooc files commit 614bcc7bed18a5bbb3541f25579c427f2747d6f4 Author: markd Date: Sun Sep 4 22:31:36 2005 +0000 ensure tree is rebuild before install commit e00c04c3fd3d0ed6db27190190830e762bed5b70 Author: markd Date: Sun Sep 4 22:30:48 2005 +0000 fixed bug in passing in para priority commit 45678ea451d9a63419ee6cdb7332e5eb138efca6 Author: markd Date: Sun Sep 4 16:59:21 2005 +0000 added option to disable prefiltering commit 6bbc64ea552d5cc6cf4aad293cc644511f7303b9 Author: markd Date: Sun Sep 4 16:21:51 2005 +0000 doc updates commit 51e47eea7df299344f4d3b62b04958a7dcadbd03 Author: markd Date: Sun Sep 4 16:21:47 2005 +0000 added option to disable prefiltering commit 8b0158c2eac33cbaa6f98c067cf8ca78d17833bc Author: markd Date: Sun Sep 4 15:10:48 2005 +0000 fixed bug in computing localNearBest with gaps; removed multAlnSeqs verbose output, since it was hard to compute correctly commit 0b096097b3717c96059da275850a23b20b8a4c3f Author: galt Date: Sun Sep 4 15:00:03 2005 +0000 "Encode release log update" commit c6b8c124cbe09423ebd62e2a7012670776bad403 Author: galt Date: Sun Sep 4 15:00:01 2005 +0000 "Release log update" commit 085623f5b3c704284875ee787071bc491f6fb5a6 Author: markd Date: Sun Sep 4 14:44:10 2005 +0000 fixed bug in documentation commit 3aa0bc7f9c1156c98f238739835e33c3535c2c3b Author: kate Date: Sat Sep 3 21:08:34 2005 +0000 Add utility commit ae1c7937a6ce804a1063e69612f535d11c0aec56 Author: galt Date: Sat Sep 3 15:00:03 2005 +0000 "Encode release log update" commit b3c1ba1fd03a6f4e46ba767e910f6a5e95c77772 Author: galt Date: Sat Sep 3 15:00:02 2005 +0000 "Release log update" commit 2458f5516c0f6ff74138477857d7ddbe2c6fe71e Author: kent Date: Sat Sep 3 02:08:36 2005 +0000 Added new apacheLog module. commit 9a51c1b21248ff15bb3488eb29a39baf5696fe02 Author: kent Date: Sat Sep 3 02:08:18 2005 +0000 Moved some stuff to new apacheLog library module commit 7a18492b6760b962f1e933dc3eed1eb3f93d2bc3 Author: kent Date: Sat Sep 3 02:07:42 2005 +0000 Moving some stuff to new library module from hgAccessCrawl. commit c7276b74a08d8ca96461c70a0fc3fb01be5e6cb8 Author: kent Date: Sat Sep 3 01:58:05 2005 +0000 Added detection for a few more bots commit d56c9a9e0660a15852a95a2f16b659ca3f89ed07 Author: kate Date: Sat Sep 3 00:08:47 2005 +0000 Add indicators of original assembly for ENCODE tracks commit 1af1f7312b44c8dc848c9a1ad57fb10b69f2098f Author: kate Date: Sat Sep 3 00:01:15 2005 +0000 Change to subtrack UI. Now includes clear/add buttons for all subtracks, if there are 'many' (currently 8 or more) subtracks commit 4c4a8158e556077ff422668a40d344c13447f540 Author: kate Date: Sat Sep 3 00:00:03 2005 +0000 Add support for 'origAssembly' trackDb setting, to generate a comment on details page indicating data has been lifted commit 29ddbc888f8f888ae30442ac10dfd48a1f04f989 Author: kate Date: Fri Sep 2 23:59:04 2005 +0000 Add utility function commit 505a6b3b4a07bf67799f1115aa845d5985b1cd05 Author: braney Date: Fri Sep 2 20:33:55 2005 +0000 take out printf commit 855d6335e7479c8d31d6d0db6f27b2ea66c55279 Author: heather Date: Fri Sep 2 20:27:48 2005 +0000 add a cast commit fa7d50a5f2e42f910c7deaa4cd0d804aea25c56c Author: heather Date: Fri Sep 2 19:28:38 2005 +0000 preserve alphabetical order commit 407dfad098ce97f8c7d3e093da1898c61301e8e8 Author: fanhsu Date: Fri Sep 2 18:55:19 2005 +0000 Added pseudoGene.o. commit a09292800b0ff826ede3aefeadf09be9588850bf Author: fanhsu Date: Fri Sep 2 18:35:30 2005 +0000 Added pseudo gene section. commit 9342936017a4e2c3b07f1780cba249fcb722a3b9 Author: kuhn Date: Fri Sep 2 17:51:59 2005 +0000 removed wildcard from genomeClade query commit 78d6ee3c740a495227f051e3bf09cc48a2921ba8 Author: donnak Date: Fri Sep 2 17:36:40 2005 +0000 Fixed typo introduced by Mark in rev 1.62. commit 859cde4313586d6b5175ee9f1e5c32f3db3947ee Author: fanhsu Date: Fri Sep 2 17:36:29 2005 +0000 Added pseudo gene section. commit a20ff22c2c614d0605de90452229fe95bfdc65cc Author: fanhsu Date: Fri Sep 2 17:35:42 2005 +0000 Created pseudoGene.c. commit 14079a8e6f22fcfb4a569d8dadfce3b431e7a566 Author: fanhsu Date: Fri Sep 2 17:35:11 2005 +0000 Updated to add the pseudo gene section. commit 9131b9aacdb02dd95c35f5714307b78def59c1d9 Author: markd Date: Fri Sep 2 16:59:03 2005 +0000 added droAna2 ooc commit b7c7e1237fae90dcad8a989cd122633d976ac11c Author: donnak Date: Fri Sep 2 16:10:23 2005 +0000 Added link for Nature chimp article. commit f2c20cc5d616a887f1e815172adf002681387d68 Author: galt Date: Fri Sep 2 15:00:03 2005 +0000 "Encode release log update" commit 64ff81a2d5ecab52be61322339fd9759348aab05 Author: galt Date: Fri Sep 2 15:00:02 2005 +0000 "Release log update" commit 357da93a5a38b484ac399f7e788f7cd865245543 Author: markd Date: Fri Sep 2 07:10:52 2005 +0000 fixed usage msg commit 8c5d293c3afa9e8d4a718cf69dd5285777f7c1f4 Author: markd Date: Fri Sep 2 07:02:30 2005 +0000 fixed typo commit 295e433b101b71f34c0075ff618b80123df37e6b Author: markd Date: Fri Sep 2 06:38:51 2005 +0000 added unplaced chromosome info commit 9d1b22e5fd5ae966c90a8ceb16ec4b73feb26477 Author: markd Date: Fri Sep 2 04:50:04 2005 +0000 added -ignoreNs filter option commit 268161f5acfac21a6f6f6fd716285f7eaefae297 Author: markd Date: Fri Sep 2 04:38:28 2005 +0000 added -ignoreNs option commit 9d0596731912d7055960ee94c3ce9e9e45b5aca2 Author: kate Date: Fri Sep 2 01:05:06 2005 +0000 Add last update time for table to details page commit f8b1e3af52be1a19972d75bc1014eb3112352a56 Author: heather Date: Fri Sep 2 00:51:46 2005 +0000 notes for snpMask files commit eddf6535574311db0c250de06c8ea2e09dd3fab5 Author: heather Date: Fri Sep 2 00:43:45 2005 +0000 add snp/snpMask commit eccf6c417fc692c0ecaba861716d223a1a5cedd1 Author: braney Date: Thu Sep 1 23:37:39 2005 +0000 tblastn of D. mel. Proteins commit 7eeb42348f1711dcd572c12c74deacad0255945e Author: heather Date: Thu Sep 1 23:24:44 2005 +0000 set strict to TRUE by default commit 8c906fc07d5ebe5c71226c4f5deb1b774b4631dc Author: markd Date: Thu Sep 1 21:49:04 2005 +0000 added droGri1 ooc commit 09807e5b328feffad585a41298a881e97c7a2b20 Author: heather Date: Thu Sep 1 20:32:43 2005 +0000 ntChars (dnaUtil) includes N commit f540e0f0d6f01c58c9705bb4c33e53a49598a281 Author: kent Date: Thu Sep 1 17:43:06 2005 +0000 Adding some test cases. They also need chr19, which is too big to commit commit c0e18f5433708199af6487497eb5381be795c2d3 Author: kent Date: Thu Sep 1 17:37:56 2005 +0000 Adding logic to construct a PubMed link for the publicationUrl commit e1fe6093ac347e99a03af0c14e55b0d93eada250 Author: kent Date: Thu Sep 1 17:37:14 2005 +0000 This is working for patching in the pubUrl commit ae4a482b27ed8c0c163d0a262a295fd2b03f9904 Author: markd Date: Thu Sep 1 16:26:22 2005 +0000 daily enable alignments for several genomes that are not enabled commit 950a78e9785ddeaabc9f209aacf7e2996efc4e08 Author: markd Date: Thu Sep 1 15:50:06 2005 +0000 fixed incorrect check for cds being available and deleted stray debugging print commit 1c522fc81d6db4f0061638e27aad3ef30a4087f1 Author: galt Date: Thu Sep 1 15:00:03 2005 +0000 "Encode release log update" commit 64a81c273caa6a29e018829675a9818b69078120 Author: galt Date: Thu Sep 1 15:00:02 2005 +0000 "Release log update" commit 2dbb90e939730fd77163d5f06d01c4266be90ef1 Author: heather Date: Thu Sep 1 04:12:54 2005 +0000 use ntCompTable, use errAbort in main, use lower case IUPAC if repeat commit 8be61bc90c9209d4dcd2f1fb459dfe7d89d7c653 Author: markd Date: Thu Sep 1 04:06:48 2005 +0000 disabled align of genomes that are still in progress commit 68b1c426f27eb66489f6322627955ad435b893bc Author: markd Date: Thu Sep 1 04:01:01 2005 +0000 redid danRer3 genbank commit eeed3d21e767fbff4532bb020f2032fd6d32e4dc Author: heather Date: Thu Sep 1 03:52:52 2005 +0000 make snpMaskChrom for now commit 852bde189e228a4f37641e6eed2b795e57e5e137 Author: heather Date: Thu Sep 1 03:52:37 2005 +0000 initial revision commit afb2b40171c2a27f7bfbed7d3587083e509e7dc9 Author: markd Date: Thu Sep 1 03:47:52 2005 +0000 build missing download files daily commit 26d6b8eaab5a3ee6d206c58561a80b3ced70859b Author: markd Date: Thu Sep 1 00:05:45 2005 +0000 added ability to create download only if it doesn't exists commit 74a23eb3bfe201c7833d23ccd14422cfa43778c5 Author: markd Date: Wed Aug 31 23:52:23 2005 +0000 added redo of genbank commit 6817604a5512d04e19e46e5b525375018272ba67 Author: kate Date: Wed Aug 31 23:44:10 2005 +0000 Prune Sangamo track label commit 356322af7ee909331b8d2be86d1b844227c4b082 Author: markd Date: Wed Aug 31 23:40:10 2005 +0000 removed no longer relevant, comment out lines commit f2911bec659c78e57b5c4dbd6f3d4310bcb06119 Author: markd Date: Wed Aug 31 23:22:04 2005 +0000 up window overlap and max gap size commit b325e66511fa1a7e52d3f3b86c4a3820c8d7a2e1 Author: markd Date: Wed Aug 31 22:41:11 2005 +0000 don't print Longest running job if no jobs are running commit a3805497a1c8d1ef4e0a4c17b91e5310a22e7134 Author: kate Date: Wed Aug 31 22:20:08 2005 +0000 Fix db in this page commit 314c6d3c5fa15833c28c09c2b41329d754da1fb7 Author: kuhn Date: Wed Aug 31 21:12:19 2005 +0000 added filenames to record of Googlebot KG lists to make them easier to find by grep commit 3a0f31e24722656e1374c1930ee62cbc163856c6 Author: markd Date: Wed Aug 31 20:26:35 2005 +0000 simplify interface, always do eta calculation commit bf5af054f8780e7d349af6ed8795dd4f91ea4c88 Author: markd Date: Wed Aug 31 18:29:31 2005 +0000 fixed paramters name and incorrect kk locations commit 1f9dbac76a87fc4494fcf87e5ed81407a37ac257 Author: donnak Date: Wed Aug 31 18:19:41 2005 +0000 Updated fly entries to add several genome browser credits, commented out until assemblies are released on RR. commit 7acc77ef1bc1b85e5b99aee3fe0b26e3e54ae06f Author: donnak Date: Wed Aug 31 18:14:57 2005 +0000 Added several new fly releases, commmented out until they're out on the RR. commit 97f0942978159ab75fa1686ad724989f24ef0236 Author: donnak Date: Wed Aug 31 17:59:51 2005 +0000 Added D. erecta credits, updated some of the other fly credits. commit 703bd03cc66892dd7a850a613bd3fc065b94ff4e Author: donnak Date: Wed Aug 31 17:42:30 2005 +0000 Added full company name for Agencourt. commit c47c7320c9a5f0867e2cff94303e76031ffe7217 Author: donnak Date: Wed Aug 31 17:37:19 2005 +0000 Updated some of the sample queries, made a few other minor edits. commit b61b4ba71ca94bf7a04711188c246ee74a6be83d Author: hiram Date: Wed Aug 31 16:46:59 2005 +0000 Add blastz-normalizeLav source, and to makefile install business commit e6aa005ea6fe69f1f1d8fc1f4f6bfd36200c055b Author: hiram Date: Wed Aug 31 16:45:17 2005 +0000 Copy of script as it now exists in bin scripts commit 741afe51bca6eb2fae8a6abac22aec6be67859e9 Author: hiram Date: Wed Aug 31 16:41:45 2005 +0000 Use the bin env trick to invoke perl commit e95de2c364584c06fa1de1847f43625e7da76660 Author: galt Date: Wed Aug 31 15:00:02 2005 +0000 "Encode release log update" commit d38306fd93c63ff2e9fdc4230d0a1869e7aa7812 Author: galt Date: Wed Aug 31 15:00:01 2005 +0000 "Release log update" commit 8666b85868144fa76766209d2bccc11b2a4c731f Author: markd Date: Wed Aug 31 14:41:05 2005 +0000 fixed 64 bit portability problems commit c16a31348452536cc58e8e6c9615e9107c668a3c Author: baertsch Date: Wed Aug 31 08:00:07 2005 +0000 fix spelling mistake commit 1dab131d093bdb9026d69e42e4f4ff14ea270e9e Author: baertsch Date: Wed Aug 31 07:36:27 2005 +0000 fix shift lines in blastp track (codeBlast) [horrible code should be fixed] commit 9bd87e78d31becf223bcf6fdc053b4e6ec1e3d9b Author: baertsch Date: Wed Aug 31 07:35:42 2005 +0000 remove debug statement commit 5929a22de833612a6e1e544e88f66b8166b7c05c Author: baertsch Date: Wed Aug 31 07:29:52 2005 +0000 remove hardcoded link to hgwdev-kschnied.cse.ucsc.edu in codeBlastp cross browser links commit 19e23235f52bc4d12e62a6530568714de7b8442e Author: baertsch Date: Wed Aug 31 07:27:07 2005 +0000 fixed codeBlastp track display for off by 2 errors. horrible hack to horrible code. commit 257c3ac966836de5dafd780215fcbfbe2793985c Author: markd Date: Wed Aug 31 06:17:39 2005 +0000 added assembly categories commit 50642eece0911f2005658df8fdbf618eef76487d Author: markd Date: Wed Aug 31 05:09:57 2005 +0000 added -minAlnSize option commit 8e39d7842fd68c7804de4d8f879d85a3ac3305b7 Author: markd Date: Wed Aug 31 00:28:18 2005 +0000 added notes on filtering parameters commit 4cf07dbf647831f913b4aa0d15c4c69500ecc6e7 Author: kate Date: Tue Aug 30 23:59:02 2005 +0000 Change from code review commit 068af2d9232dd05c1c3e781f42463de7b912331c Author: kate Date: Tue Aug 30 23:50:12 2005 +0000 Changes from code review commit 6e0545be8e89916c17460b229550db2df4924da6 Author: heather Date: Tue Aug 30 23:49:15 2005 +0000 undo CVS testing commit 40ab3907fb23c026cb19cec7cce91e0bddd92cf0 Author: heather Date: Tue Aug 30 23:19:14 2005 +0000 more CVS testing commit f25ec874cda1eb474dd370c8a3fb44655ec86def Author: kayla Date: Tue Aug 30 23:08:30 2005 +0000 undid cvs test commit 3370056cb0b44ea2c2daf701eaf55356afa3902f Author: heather Date: Tue Aug 30 23:04:34 2005 +0000 testing CVS commit 7e13af24fdd2ee405b1a21832e1023a68db4d892 Author: donnak Date: Tue Aug 30 23:02:04 2005 +0000 Created this file to add an assembly-specific gap track description. commit d31f69269464cb5ef402d13b0a4bd0e60733ab84 Author: donnak Date: Tue Aug 30 22:39:53 2005 +0000 Replaced existing erroneous description with this generic one. Angie may want to add more detail. commit e3968aff6b3f168d29063c8038b04105b52df52a Author: donnak Date: Tue Aug 30 22:37:41 2005 +0000 Created this file as a preliminary description until Angie can fill in more information. We need to distinguish the difference between contig & scaffold gaps. commit c5028a496086ee5e7de3181a37a6513e8a5a172f Author: hiram Date: Tue Aug 30 20:39:11 2005 +0000 Fixup long label for Yale neutrophil TARs commit fcb31eeb99295aadb3d7b636facc0d95b30e8602 Author: kuhn Date: Tue Aug 30 17:53:08 2005 +0000 added sangamoDnaseHs to tablesIgnored commit 9b078fd19d21b4a9aa7982eded74e6f3fb288b22 Author: heather Date: Tue Aug 30 17:49:03 2005 +0000 add DV commit 350deedb43ec640e709b9781cfe6f6e2831b867c Author: galt Date: Tue Aug 30 15:00:02 2005 +0000 "Encode release log update" commit b4d7f5e11dc5d9230f8f5ba18079caa0b49cf820 Author: galt Date: Tue Aug 30 15:00:01 2005 +0000 "Release log update" commit 70c30d6fd65d4003618026b32c3f8492506a15cc Author: aamp Date: Tue Aug 30 05:42:50 2005 +0000 Beginning of the MGC RTDB auto-update project. commit 17d4fd6888ecfd514b039140d80aff12ef05a738 Author: daryl Date: Tue Aug 30 05:23:46 2005 +0000 Removed old LD track commit cf71633c49bd2fe19b3c8952d18bff97a51d3626 Author: daryl Date: Tue Aug 30 05:22:00 2005 +0000 Added hapmapLdHotspot; indented tajdSnp and tajdAD; commented out ld commit 7bd1fadc6dcbe5cbe5906a504916bf99fd09e0c6 Author: daryl Date: Tue Aug 30 05:17:08 2005 +0000 chimpFixedDiff commit a30671f06b98e22237f0c960a9cd40de2b32d586 Author: daryl Date: Tue Aug 30 01:31:16 2005 +0000 Added encodeRecombHotspot; modified evoFold commit d39831438f7355722a6ceef0feef1672b86eb749 Author: kuhn Date: Tue Aug 30 00:41:38 2005 +0000 added some spaces around a hyphen commit dfa103ccc776130c4b9920986dc0e1d71aa123de Author: markd Date: Mon Aug 29 23:43:40 2005 +0000 changes to support alignment categories commit 325df5ca929bafb984853fd456a834af3bae4ad6 Author: hiram Date: Mon Aug 29 23:06:09 2005 +0000 Improve the byname usage message to make it clear how it works. commit 004fc474d9ea631893d1f25012b6afad7dda069c Author: galt Date: Mon Aug 29 22:55:49 2005 +0000 cleanup and bug-fix in ruler-related stuff - labels looked off by one commit b55404f871fbe6d6d9295e8c410e78ecbfbae4c7 Author: kuhn Date: Mon Aug 29 22:54:44 2005 +0000 changed spelling of leukophoresis and commented out a reference link that was not functioning commit eb01cf20039a4892ead19c3511148a5a6eaf7996 Author: donnak Date: Mon Aug 29 22:54:39 2005 +0000 Added commented-out entry for droEre1. commit d5d1b568c05e0d9eaf13c9ec48af8a8db9ddf900 Author: donnak Date: Mon Aug 29 22:53:22 2005 +0000 Fixed broken WUSTL links...they've rearranged their site (again). commit 8fd2db140a27469d496fce0203f5cb5ea619ed51 Author: donnak Date: Mon Aug 29 22:40:14 2005 +0000 Added link to Codon Coloring Help reference. commit 7424ecdd58fb21f315c0c9c85aa68009efece554 Author: donnak Date: Mon Aug 29 22:38:38 2005 +0000 Fixed WUSTL URL -- they've changed their website structure (again). commit 67f16a1c63c8a362aa89ed3292efc8a388bc298f Author: galt Date: Mon Aug 29 22:13:40 2005 +0000 fixed dyStringPrintf 4000 limit for updating one record with big sql string commit 4ba822c95825e84fa312466d0a81e920d342b27e Author: donnak Date: Mon Aug 29 21:55:15 2005 +0000 Made small mod in C. intestinalis section. commit cd9298a6b6a2806947f1271dc4cd7cf29c926f54 Author: donnak Date: Mon Aug 29 21:53:57 2005 +0000 Fixed ci2 entry in release table. commit 23e2682c1493f36f37a4c89c6f0bac507b2d04de Author: donnak Date: Mon Aug 29 21:29:01 2005 +0000 Modified the description text displayed on the correlation page. commit c2d893f11845bad2dfe9d6939cb6334b8f8e07ff Author: kate Date: Mon Aug 29 21:05:58 2005 +0000 Change some labels on subtrack selection UI to clarify commit b0ebadcf8aee853ad58279838dd1ca29f2f161b6 Author: kent Date: Mon Aug 29 20:59:45 2005 +0000 Ripping out debugging. 64 bit bug seems fixed. Had to do with subtracting two pointers from different allocations in ffMergeClose commit 22c9e0a66bbf75c418586304c6e5780aedf9234d Author: kent Date: Mon Aug 29 20:51:33 2005 +0000 Adding some debugging - committing to cross test 32 & 64 bit versions commit 65b8f68abb7cd93ff2f50c599207d68e0f981daa Author: kent Date: Mon Aug 29 20:48:22 2005 +0000 Fixing 64-bit specific problem where ffMergeClose not working commit 58d7b978869392213d053b639f4febae0beaa716 Author: kent Date: Mon Aug 29 20:28:12 2005 +0000 Adding some debugging - committing to cross test 32 & 64 bit versions commit 8b3dfd04234955284e89e9220dabc60e04190e30 Author: kent Date: Mon Aug 29 20:22:23 2005 +0000 Adding some debugging - committing to cross test 32 & 64 bit versions commit 701939bee16947903efc77f9db7813ec8ae7843e Author: kent Date: Mon Aug 29 20:09:16 2005 +0000 Adding some debugging - committing to cross test 32 & 64 bit versions commit 8cf751b823618342695599b1b95d887890f91f3a Author: kent Date: Mon Aug 29 20:07:11 2005 +0000 Adding some debugging - committing to cross test 32 & 64 bit versions commit f5867b971929fff8d0a12fea8fadd6c78b2aba03 Author: kent Date: Mon Aug 29 20:02:19 2005 +0000 Adding some debugging - committing to cross test 32 & 64 bit versions commit a1df2967c2d9b90ab5700c2255e8936373f08136 Author: kuhn Date: Mon Aug 29 19:35:00 2005 +0000 added showProcessList.csh commit 3bc04a777890712cd38a4c303e868c85bde8d45d Author: kuhn Date: Mon Aug 29 19:33:10 2005 +0000 quick utility to query hgcentral for which RR nodes are getting hits commit caad9d0746eab3409abdfc2cdc153f977eb218bc Author: baertsch Date: Mon Aug 29 19:32:46 2005 +0000 rollback premature change commit 9e8166b295e000ae02ce8c702b9fa4be62842a14 Author: kate Date: Mon Aug 29 18:32:26 2005 +0000 Fix typos in ENCODE Unann Transfrags subtrack config commit cac6a5672f835127383a3f15c873d0f427a493d9 Author: kent Date: Mon Aug 29 18:13:27 2005 +0000 Adding some debugging - committing to cross test 32 & 64 bit versions commit bc976280d7017c390b841dfb72450c43d68fa1af Author: kent Date: Mon Aug 29 18:12:43 2005 +0000 Adding some debugging - committing to cross test 32 & 64 bit versions commit 01478bc375a0d4bd593bd90d049dfabc7735888c Author: kent Date: Mon Aug 29 18:07:27 2005 +0000 Adding some debugging - committing to cross test 32 & 64 bit versions commit 4abe6dce5e0ee11d982c54f4c1e4cc69cadfa689 Author: kent Date: Mon Aug 29 18:00:37 2005 +0000 Adding some debugging commit 1d4a45e21cb964bf7cb0780221e1d5ae37eee492 Author: kent Date: Mon Aug 29 17:54:26 2005 +0000 Adding some debugging commit 11f12d13c62114993a786124b6293517dbf95bcd Author: kate Date: Mon Aug 29 17:52:34 2005 +0000 Fix typo in new option commit ff5409adb53c83aa7e91e36a298c7ae8b8c11948 Author: kent Date: Mon Aug 29 17:45:34 2005 +0000 Adding some debugging commit ac297abd55684234611357aa40dbe65aec19aa26 Author: kate Date: Mon Aug 29 17:43:55 2005 +0000 Add error check for missing gene name commit 62a79d0446a328966d9cfe9b80096129e74ab2d3 Author: donnak Date: Mon Aug 29 17:14:13 2005 +0000 Minor edit to references. commit 40cac28abc6b198ff06b617423e3010a045d2506 Author: donnak Date: Mon Aug 29 15:31:41 2005 +0000 Added missing ref, reformatted some of the refs, changed a few HTML things. commit fe3e30e812e8a78e740b3d27d01f1dc81de37c75 Author: galt Date: Mon Aug 29 15:00:05 2005 +0000 "Encode release log update" commit effb5f5acd792924d07d80fb7b2669bc916e1925 Author: galt Date: Mon Aug 29 15:00:04 2005 +0000 "Release log update" commit 958ed56c9aa4b313ce05bc272fad556